Add parsing test to regression

soedinglab · Apr 21, 2021 · c2e680a · c2e680a
1 parent c12da22
commit c2e680a
Show file tree

Hide file tree

Showing 7 changed files with 339 additions and 0 deletions.
diff --git a/examples/crisprdetect_test b/examples/crisprdetect_test
@@ -0,0 +1,133 @@
+Array 1 3140266-3139749 		**** Predicted by CRISPRDetect 2.3 *** 
+>gi|389839000|ref|NC_017933|-Cronobacter sakazakii ES15 chromosome, complete genome.		Array_Orientation: Reverse
+
+  Position	Repeat	   %id	Spacer	Repeat_Sequence              	Spacer_Sequence                 	Insertion/Deletion
+==========	======	======	======	=============================	================================	==================
+   3140266	    29	 100.0	    32	.............................	ACGGTCGCGTTGCGGATCTGGATGTGGTCAAT	
+   3140205	    29	 100.0	    32	.............................	CTTTTGTCGATGAGCGTGTGCAGAAGATTGTC	
+   3140144	    29	 100.0	    32	.............................	AACGTGTAAATCAACTGGAGGCACGGGTCAAA	
+   3140083	    29	  96.6	    32	............T................	AGACCAGACGCCGATACCAGCGAAGAAATGGC	
+   3140022	    29	  96.6	    32	............T................	CCGCCATCAGGCGGCTCACTCGATGCGGATGA	
+   3139961	    29	  96.6	    32	............T................	CGCGACTACGCGTCCTGGAATAAACGCGCCAA	
+   3139900	    29	 100.0	    32	.............................	CGACACGATCCGCCGCCTCGGCTATGAGGCTG	
+   3139839	    29	 100.0	    32	.............................	ATTGCGGGATGACCAGTTCGCGAGCTTTCTGA	
+   3139778	    29	 100.0	     0	.............................	|                               	
+==========	======	======	======	=============================	================================	==================
+         9	    29	  98.9	    32	GTGTTCCCCGCGCGAGCGGGGATAAACCG	                                	       
+
+# Left flank :   ATGAATCCGGTTTCGATTTCCAGACGTTCGGCGTTAACCGTCGTATCCCGGTGGATTTGGACGGCCTGCGCCTTGTCTCGTTTTTACCGCTCGAAAATCAGTAGGTTATTCGCTCTTTAACAATGCGAGATTGTGAACCAAACGTTGGTAGGATGTTGTTGCGCGAAAAAGTGTAATAAATACAAGTATATAGTTTTAGA
+# Right flank :  ACGTAACCGGTTTTCGACACGGTGATCGGGGAGTATTCCCCGCGCGCGAATAACTCCTGACCGCCGGGCTCACCCTGCCTTTAAACTTTACAGGCATTATTGAACATGAATAAAACCATTTGCACCTTACTTATTACTGCCGCGTTGTGTAGTACTACCGCTGTTGCCAGTGATGAAACGCTTGAACAAAAACCGCAGCA
+
+# Questionable array : NO	 Score: 9.10
+# 	Score Detail : 1:1, 2:3, 3:0, 4:0.95, 5:0, 6:1, 7:1.15, 8:1, 9:1,
+# 	Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7:exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats),
+# Primary repeat :     GTGTTCCCCGCGCGAGCGGGGATAAACCG
+# Alternate repeat :   GTGTTCCCCGCGTGAGCGGGGATAAACCG
+
+# Directional analysis summary from each method:
+# 	Motif ATTGAAA(N) match prediction:         NA Score: 0/4.5
+# 	A,T distribution in repeat prediction:     R [4,5] Score: 0.37/0.37
+# 	Reference repeat match prediction:         R [matched GTGTTCCCCGCGCGAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5
+# 	Secondary Structural analysis prediction:  R [-12.00,-13.50] Score: 0.37/0.37
+# 	Array degeneracy analysis prediction:      NA [0-0] Score: 0/0.41
+# 	AT richness analysis in flanks prediction: R [43.3-68.3]%AT Score: 0.27/0.27
+# 	Longer leader analysis prediction:         NA [107,97] Score: 0/0.18
+# 	----------------------------------------------------------------------------
+# 	Final direction:         R [0,5.51   Confidence: HIGH] 
+
+# Identified Cas genes:  Cas1:YP_006344002 [3140655-3141572]; Cas2:YP_006344001 [3140362-3140655]; Cas3':YP_006344008 [3146583-3149216]; Cas4:YP_006341839 [800040-803522]; Cas5:YP_006344004 [3142414-3142953]; Cas6e:YP_006344003 [3141569-3142219]; Cas7:YP_006344005 [3142963-3144036]; Cse1:YP_006344007 [3144654-3146216]; Cse2:YP_006344006 [3144048-3144653]; Helicase Cas3:YP_006344008 [3146583-3149216]; RAMP Cas5:YP_006344004 [3142414-3142953]; RAMP Cas6e:YP_006344003 [3141569-3142219]; 
+# Array family : I-E [Matched known repeat from this family],   
+# Sequence source strain : ES15
+# Taxonomy hierarchy : Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Cronobacter.; Cronobacter sakazakii ES15
+//
+
+
+Array 2 3167632-3166685 		**** Predicted by CRISPRDetect 2.3 *** 
+>gi|389839000|ref|NC_017933|-Cronobacter sakazakii ES15 chromosome, complete genome.		Array_Orientation: Reverse
+
+  Position	Repeat	   %id	Spacer	Repeat_Sequence              	Spacer_Sequence                  	Insertion/Deletion
+==========	======	======	======	=============================	=================================	==================
+   3167632	    29	  96.6	    32	.C...........................	AATATTTGCAGCTTTGTTCAACCCGCAAGCTA 	
+   3167571	    29	 100.0	    32	.............................	TACCGATTGCCGGTTTCGTGGATTTAGATAAG 	
+   3167510	    29	 100.0	    32	.............................	CCTCGTTTTCACCTGAGCAATTGCCACTTACC 	
+   3167449	    29	 100.0	    32	.............................	TTGTTAGCAAAACCCGTCTTACGACGGGCTTT 	
+   3167388	    29	 100.0	    32	.............................	CGCCAGGTCCCTCCCTGAGACCAGGGGATTTG 	
+   3167327	    29	 100.0	    32	.............................	ATGTGGCGCGCACGTTAATGACCGCAGAACGC 	
+   3167266	    29	  96.6	    32	............................T	CGAATTATAACGACTCAAATTGGGAGGTGGAC 	
+   3167205	    29	 100.0	    32	.............................	TTGGCACCGGAATCCAGCCAAACTTTAAATTT 	
+   3167144	    29	 100.0	    32	.............................	GGTGCTATGGAGTGGTGCCGGTGCGGCCCCCA 	C [3167138]
+   3167082	    29	 100.0	    32	.............................	GCTATCACGCCAATCACAGCAGCGCAGGTTAA 	
+   3167021	    29	  96.6	    32	...................A.........	GGCATGATGTGGATGCGATTAACGGGCTTACC 	
+   3166960	    29	  96.6	    32	.C...........................	AAGCAGACAAACTGGAAAGTTGTTATCTGGAA 	
+   3166899	    29	  93.1	    32	.C..........T................	TCGCCGCGCATGAGCTGTGTCAGTTCGGATGT 	
+   3166838	    29	 100.0	    33	.............................	AACGCTCGCAGCAGGTACGCTGCAGCAACCAGC	
+   3166776	    29	  93.1	    32	.C......T....................	TACCTTGAGAAAACCGCGCAATCTGTGCTGGT 	
+   3166715	    29	  79.3	     0	.C...........C...A..A....C..T	|                                	T [3166687]
+==========	======	======	======	=============================	=================================	==================
+        16	    29	  97.0	    32	CTGTTCCCCGCGCGAGCGGGGATAAACCG	                                 	       
+
+# Left flank :   GGCGCTTGTGCTGGCAATCATGGATTTATCACCGCACAGGGTGAACAATCCGGTAGATGTTAACAGCCCACAAGCGTCGCGAAAAAACGCCTTCAAAATCAATAGGGCAGCCGTTCTTTAACAAGATGGGTTGTTGTAAAAATGTTGGTAGGATGTGGAAGGCGAAAAAATGCCATTCAGTACAGAGGGTTACCGTTAGT
+# Right flank :  TCCGCGTTCTTCGCGCCTGTCACTCGCCGCCCTCATTCCCGCCACAATCTTCAGCAACGTTTATACTTCAAAGCCCTTGTTAAATTTTGAACACTGCGCAACGAAGGAGAGGCTATGCGAGTACACCATCTCAACTGCGGTTGTATGTGTCCTTTGGGCGGCGCGCTGTACGATGGCTTCAGTAAAGGGCTGCACGCGCA
+
+# Questionable array : NO	 Score: 8.87
+# 	Score Detail : 1:1, 2:3, 3:0, 4:0.85, 5:0, 6:1, 7:1.04, 8:1, 9:0.98,
+# 	Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7:exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats),
+# Primary repeat :     CTGTTCCCCGCGCGAGCGGGGATAAACCG
+# Alternate repeat :   NA
+
+# Directional analysis summary from each method:
+# 	Motif ATTGAAA(N) match prediction:         NA Score: 0/4.5
+# 	A,T distribution in repeat prediction:     R [3,5] Score: 0.37/0.37
+# 	Reference repeat match prediction:         R [matched GTGTTCCCCGCGCGAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5
+# 	Secondary Structural analysis prediction:  R [-5.60,-7.20] Score: 0.37/0.37
+# 	Array degeneracy analysis prediction:      R [8-1] Score: 0.41/0.41
+# 	AT richness analysis in flanks prediction: R [38.3-53.3]%AT Score: 0.27/0.27
+# 	Longer leader analysis prediction:         NA [155,216] Score: 0/0.18
+# 	----------------------------------------------------------------------------
+# 	Final direction:         R [0,5.92   Confidence: HIGH] 
+
+# Identified Cas genes:  Cas1:YP_006344002 [3140655-3141572]; Cas2:YP_006344001 [3140362-3140655]; Cas3':YP_006344008 [3146583-3149216]; Cas4:YP_006341839 [800040-803522]; Cas5:YP_006344004 [3142414-3142953]; Cas6e:YP_006344003 [3141569-3142219]; Cas7:YP_006344005 [3142963-3144036]; Cse1:YP_006344007 [3144654-3146216]; Cse2:YP_006344006 [3144048-3144653]; Helicase Cas3:YP_006344008 [3146583-3149216]; RAMP Cas5:YP_006344004 [3142414-3142953]; RAMP Cas6e:YP_006344003 [3141569-3142219]; 
+# Array family : I-E [Matched known repeat from this family],   
+# Sequence source strain : ES15
+# Taxonomy hierarchy : Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Cronobacter.; Cronobacter sakazakii ES15
+//
+
+
+Array 3 3450969-3450821 		**** Predicted by CRISPRDetect 2.3 *** 
+>gi|389839000|ref|NC_017933|-Cronobacter sakazakii ES15 chromosome, complete genome.		Array_Orientation: Reverse
+
+  Position	Repeat	   %id	Spacer	Repeat_Sequence             	Spacer_Sequence                 	Insertion/Deletion
+==========	======	======	======	============================	================================	==================
+   3450969	    28	 100.0	    32	............................	ACGATGCCTGCCGCTTTCCTCCGCTGATACTC	
+   3450909	    28	 100.0	    32	............................	CGAGTGATGTAGATCATTACAGCGCCGGGCTC	
+   3450849	    28	  78.6	     0	....................TC.CAT.T	|                               	
+==========	======	======	======	============================	================================	==================
+         3	    28	  92.9	    32	GTTCACTGCCGTACAGGCAGCTTAGAAA	                                	       
+
+# Left flank :   CGCACCGAAGAGCAAACCACTGAACGAATGAAACGATAAAAGTGATGGGCGTTGCGCCTGGGCGTCTAAACCCTTTTTTATGCTCCGCTTGTAAAGCATTGATTTTTTAATGCGTGCAGTTGTGGTGATAAAAAAGGGTTTCAGGCGTTAAAAAGCAAAAATTTGTTTTTAATTCAGGCATTCCGGTAATATTCGCTCTT
+# Right flank :  CCAATTCCCTCGCCGTCATACTTGACCTTCCCGCAAGGGGAGGGTTTAAGCTCAACGGGTGCACGTTGACGATAAGGACGGGAAGATGCAACGCCGAGAGTTTATCAAGTACACCGCCGCGCTGGGGGCGCTCAGCGCGCTGCCGACATGGAGCCGGGCCGCATTTGCCGCAGAGCAACCCGCGCTGCCCATCCCCGCGC
+
+# Questionable array : NO	 Score: 8.76
+# 	Score Detail : 1:1, 2:3, 3:0, 4:0.65, 5:0, 6:1, 7:2.02, 8:0.4, 9:0.69,
+# 	Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7:exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats),
+# Primary repeat :     GTTCACTGCCGTACAGGCAGCTTAGAAA
+# Alternate repeat :   NA
+
+# Directional analysis summary from each method:
+# 	Motif ATTGAAA(N) match prediction:         NA Score: 0/4.5
+# 	A,T distribution in repeat prediction:     F [5,4] Score: 0.37/0.37
+# 	Reference repeat match prediction:         R [matched GTTCACTGCCGTACAGGCAGCTTAGAAG with 100% identity] Score: 4.5/4.5
+# 	Secondary Structural analysis prediction:  NA [-0.20,0.00] Score: 0/0.37
+# 	Array degeneracy analysis prediction:      F [0-1] Score: 0.41/0.41
+# 	AT richness analysis in flanks prediction: R [48.3-66.7]%AT Score: 0.27/0.27
+# 	Longer leader analysis prediction:         R [95,398] Score: 0.18/0.18
+# 	----------------------------------------------------------------------------
+# 	Final direction:         R [0.78,4.95   Confidence: HIGH] 
+
+# Identified Cas genes:  Cas1:YP_006344002 [3140655-3141572]; Cas2:YP_006344001 [3140362-3140655]; Cas3':YP_006344008 [3146583-3149216]; Cas4:YP_006341839 [800040-803522]; Cas5:YP_006344004 [3142414-3142953]; Cas6e:YP_006344003 [3141569-3142219]; Cas7:YP_006344005 [3142963-3144036]; Cse1:YP_006344007 [3144654-3146216]; Cse2:YP_006344006 [3144048-3144653]; Helicase Cas3:YP_006344008 [3146583-3149216]; RAMP Cas5:YP_006344004 [3142414-3142953]; RAMP Cas6e:YP_006344003 [3141569-3142219]; 
+# Array family : I-F [Matched known repeat from this family],   
+# Sequence source strain : ES15
+# Taxonomy hierarchy : Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Cronobacter.; Cronobacter sakazakii ES15
+//
+
+
diff --git a/examples/crt_test b/examples/crt_test
@@ -0,0 +1,64 @@
+ORGANISM:  NC_004547.2 Erwinia carotovora subsp. atroseptica SCRI1043, complete genome
+Bases: 5064019
+
+
+CRISPR 1   Range: 4124152 - 4125860
+POSITION	REPEAT				SPACER
+--------	----------------------------	--------------------------------
+4124152		TGAATAGGCTGCCTGTACGGCAGTGAAC	GGGTTGCCTCGGCCTGAACAGCGATCTCGCGTG	[ 28, 33 ]
+4124213		TTTCTAAGCTACCTGTACGGCAGTGAAC	TTGAAATTAGTGACGTGAGCAGAATCGTAAAC	[ 28, 32 ]
+4124273		TTTCTAAGCTGCCTGTACGGCAGTGAAC	CGATACTCGGATACGCTCCCAGACCTTATCGA	[ 28, 32 ]
+4124333		TTTCTAAGCTGCCTGTGCGGCAGTGAAC	AACACGCCGCGCGATTTTGTCCACAATGCGCA	[ 28, 32 ]
+4124393		TTTCTAAGCTGCCTGTGCGGCAGTGAAC	TGTCGAGCGCTGATTCGTCGGTCACTGGATAC	[ 28, 32 ]
+4124453		TTTCTAAGCTGCCTGTGCGGCAGTGAAC	TCCATAGTCCTCGGAAGGGACGACGATGTGAC	[ 28, 32 ]
+4124513		TTTCTAAGCTGCCTGTACGGCAGTGAAC	CATTAATTGACGTCTCTCTATCAATTATCTGT	[ 28, 32 ]
+4124573		TTTCTAAGCTGCCTGTACGGCAGTGAAC	CCGAGCCTGTATTACAGGTGGTTATGGCGACA	[ 28, 32 ]
+4124633		TTTCTAAGCTGCCTGTACGGCAGTGAAC	ACGCTTGATATTGCTTATGGCGTGTTAGTTCA	[ 28, 32 ]
+4124693		TTTCTAAGCTGCCTGTACGGCAGTGAAC	GATCGGCAAAGATAATCAGGCACTCATCACCG	[ 28, 32 ]
+4124753		TTTCTAAGCTGCCTGTACGGCAGTGAAC	TGAATGAGCCGGCCAATCTATATCACTACACT	[ 28, 32 ]
+4124813		TTTCTAAGCTGCCTGTACTGCAGTGAAC	GGCGCGTCAGTGAAGTGGATGTATCCGTGCCA	[ 28, 32 ]
+4124873		TTTCTAAGCTGCCTGTGTGGCAGTGAAC	GCGGGGGCTAATGTGTCTGAGGCTGGTAGATC	[ 28, 32 ]
+4124933		TTTCTAAGCTGCCTGTGCGGCAGTGAAC	CCAGACCGCAGCAACTACCAGTTAGCTCAACA	[ 28, 32 ]
+4124993		TTTCTAAGCTGCCTGTACGGCAGTGAAC	GAGCAATTCGCGCATGAGTTCGCGTCTACGCT	[ 28, 32 ]
+4125053		TTTCTAAGCTGCCTGTACGGCAGTGAAC	GCGTTAGGCTCGTCGGTGTAGATCAACTTTCC	[ 28, 32 ]
+4125113		TTTCTAAGCTGCCTGTACGGCAGTGAAC	TCTTTGTAATCACCTGTACGGCTGGCCCACAC	[ 28, 32 ]
+4125173		TTTCTAAGCTGCCTGTACGGCAGTGAAC	TTACGGACGCAATCTATGTGCCGTGTAACGAT	[ 28, 32 ]
+4125233		TTTCTAAGCTGCCTGTACGGCAGTGAAC	ACGCTGCGTAAGCTGGCAACCGGTGAGGTGCA	[ 28, 32 ]
+4125293		TTTCTAAGCTGCCTGTACGGCAGTGAAC	TTTGTCCTTGAGCCTGACCGCTTCCGCCATCG	[ 28, 32 ]
+4125353		TTTCTAAGCTGCCTGTACGGCAGTGAAC	CTGTCGCAGTATTTGACCCACGACGTGATGCT	[ 28, 32 ]
+4125413		TTTCTAAGCTGCCTGTACGGCAGTGAAC	AGCTTGCGTTGCTCGTCTGTCAAATTGCGGGT	[ 28, 32 ]
+4125473		TTTCTAAGCTGCCTGTACGGCAGTGAAC	AGGCGATGGTGTCGTGGTCTGACCCTGCAAAC	[ 28, 32 ]
+4125533		TTTCTAAGCTGCCTGTACGGCAGTGAAC	AACCGTCGCTCGCTGGCCACTGTACGATTCGC	[ 28, 32 ]
+4125593		TTTCTAAGCTGCCTGTACGGCAGTGAAC	ACTCTGTTATTCCCCAACTGGCGTATGCCGAG	[ 28, 32 ]
+4125653		TTTCTAAGCTGCCTGTACGGCAGTGAAC	CCTGACGGCAACGCCGACGCCGATCCGACACA	[ 28, 32 ]
+4125713		TTTCTAAGCTGCCTGTACGGCAGTGAAC	AATCAATGGCTCAGGGGATTCTACAACCCTAA	[ 28, 32 ]
+4125773		TTTCTAAGCTGCCTGTACGGCAGTGAAC	GCATCCGTCCAGACCGTATCGATAGTCTCTGC	[ 28, 32 ]
+4125833		TTTCTAAGCTGCCTGTACGGCAGTGAAC	
+--------	----------------------------	--------------------------------
+Repeats: 29	Average Length: 28		Average Length: 32
+
+
+
+CRISPR 2   Range: 4135961 - 4136589
+POSITION	REPEAT				SPACER
+--------	----------------------------	--------------------------------
+4135961		GTTCACTGCCGTACAGGCAGCTTAGAAA	AGCCTGAACCCGTCCGATTATCAAGATGGGAA	[ 28, 32 ]
+4136021		GTTCACTGCCGTACAGGCAGCTTAGAAA	AGCTCCGACCGACATGCGCTTAAAGGCGGCGA	[ 28, 32 ]
+4136081		GTTCACTGCCGTACAGGCAGCTTAGAAA	ATGCAGATATTGTAACTAAGCATCATATTGCAT	[ 28, 33 ]
+4136142		GTTCACTGCCGTACAGGCAGCTTAGAAA	TGTAGGCCATATAACAAATACTCAAAGATAAC	[ 28, 32 ]
+4136202		GTTCACTGCCGTATAGGCAGTTTAGAAA	TTGCGATTGGCACCGTTAACCGCTCAGTGACC	[ 28, 32 ]
+4136262		ATTCACTGCCGTATAGGCAGCTTAGAAA	TCCAGTACTCAGGATCGTGTTGGTACGATAAA	[ 28, 32 ]
+4136322		GTTCACTGCCGTATAGGCAGCTTAGAAA	AGTTCTGACACTCGTTAAACGTCATAACGCGC	[ 28, 32 ]
+4136382		GTTCACTGCCGTACAGGCAGCTTAGAAA	GAAATATCCACCTGGACACTGTCCATAAAGAA	[ 28, 32 ]
+4136442		GTTCACTGCCGTATAGGCAGCTTAGAAA	ACGACGGATAGTCTCTGTCTGACGAACGCAAC	[ 28, 32 ]
+4136502		GTTCACTGCCGTATAGGCAGCTTAGAAA	GCCCTGAAAAAAATGGGTTGTGATGACCATGC	[ 28, 32 ]
+4136562		GTTCACTGCCGTGCAGGCAGTTCAGTGT	
+--------	----------------------------	--------------------------------
+Repeats: 11	Average Length: 28		Average Length: 32
+
+
+
+Time to find repeats: 858 ms
+
+
+
diff --git a/examples/empty_test b/examples/empty_test
diff --git a/examples/fasta_test b/examples/fasta_test
@@ -0,0 +1,30 @@
+>CP003088.1_1473010_1473988_1_spacer_1473037_34
+GGGCAGTCTCAGTCGCCCATTCTGAACGGCAAAG
+>CP003088.1_1473010_1473988_2_spacer_1473098_34
+TTGCAGCGCGTGAGCCGTTCGTCGATCTCGGTGG
+>CP003088.1_1473010_1473988_3_spacer_1473159_34
+CTGGAGGTGATGACGATGGAAGAGCTACACAAGG
+>CP003088.1_1473010_1473988_4_spacer_1473220_34
+GGCACAAAAGTCGCCGCGCCGGCCATCATCGGAG
+>CP003088.1_1473010_1473988_5_spacer_1473281_34
+CGCCGCTGCCGCCGCTTTTGTCGAGGCCCTGCGG
+>CP003088.1_1473010_1473988_6_spacer_1473342_71
+CATGCGGTCGTGTTCGTCCAGCAACTTCCTCACGGTCTTGCGCAAAGCACGCGCATAGTCATATGCGCCGG
+>CP003088.1_1473010_1473988_7_spacer_1473440_34
+TAGACGGCTCCGTGTAACGCCCTCTGTCTTGGGA
+>CP003088.1_1473010_1473988_8_spacer_1473501_34
+TCGCAGTACTGGCCGATGGCGTAAAGCCCCCACG
+>CP003088.1_1473010_1473988_9_spacer_1473562_34
+CGGCCTTGTGGATCATGATACGTCCCCGTGACGG
+>CP003088.1_1473010_1473988_10_spacer_1473623_34
+TCGTCGATCCGATCCAGTTTCACGCAGTAGTATG
+>CP003088.1_1473010_1473988_11_spacer_1473684_34
+ACAGATTTCGGCCCTTACACGCTGCGCCTCGACG
+>CP003088.1_1473010_1473988_12_spacer_1473745_34
+CGCCGGGCGTCGTTCAGTACGAGGAGGGTCCGGG
+>CP003088.1_1473010_1473988_13_spacer_1473806_34
+TGAAACGATTGGTGCAATTGACGATGGATATCGG
+>CP003088.1_1473010_1473988_14_spacer_1473867_34
+GAGCGCGCTGTAGCCCATGCCCTGCGCGATGCGG
+>CP003088.1_1473010_1473988_15_spacer_1473928_34
+CCCACCCCTGACGACAGAGGGCGACTCGCTCCCG
diff --git a/examples/minced_test b/examples/minced_test
@@ -0,0 +1,37 @@
+Sequence 'NC_000913.3' (4641652 bp)
+
+CRISPR 1   Range: 2877701 - 2878463
+POSITION	REPEAT				SPACER
+--------	-----------------------------	--------------------------------
+2877701		CGGTTTATCCCCGCTGATGCGGGGAACAC	CAGCGTCAGGCGTGAAATCTCACCGTCGTTGC	[ 29, 32 ]
+2877762		CGGTTTATCCCTGCTGGCGCGGGGAACTC	TCGGTTCAGGCGTTGCAAACCTGGCTACCGGG	[ 29, 32 ]
+2877823		CGGTTTATCCCCGCTAACGCGGGGAACTC	GTAGTCCATCATTCCACCTATGTCTGAACTCC	[ 29, 32 ]
+2877884		CGGTTTATCCCCGCTGGCGCGGGGAACTC	CCGGGGGATAATGTTTACGGTCATGCGCCCCC	[ 29, 32 ]
+2877945		CGGTTTATCCCCGCTGGCGCGGGGAACTC	TGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAG	[ 29, 32 ]
+2878006		CGGTTTATCCCCGCTGGCGCGGGGAACTC	AAGCTGGCTGGCAATCTCTTTCGGGGTGAGTC	[ 29, 32 ]
+2878067		CGGTTTATCCCCGCTGGCGCGGGGAACTC	TAGTTTCCGTATCTCCGGATTTATAAAGCTGA	[ 29, 32 ]
+2878128		CGGTTTATCCCCGCTGGCGCGGGGAACTC	GCAGGCGGCGACGCGCAGGGTATGCGCGATTCG	[ 29, 33 ]
+2878190		CGGTTTATCCCCGCTGGCGCGGGGAACTC	GCGACCGCTCAGAAATTCCAGACCCGATCCAAA	[ 29, 33 ]
+2878252		CGGTTTATCCCCGCTGGCGCGGGGAACTC	TCAACATTATCAATTACAACCGACAGGGAGCC	[ 29, 32 ]
+2878313		CGGTTTATCCCCGCTGGCGCGGGGAACTC	AGCGTGTTCGGCATCACCTTTGGCTTCGGCTG	[ 29, 32 ]
+2878374		CGGTTTATCCCCGCTGGCGCGGGGAACTC	TGCGTGAGCGTATCGCCGCGCGTCTGCGAAAG	[ 29, 32 ]
+2878435		CGGTTTATCCCCGCTGGCGCGGGGAACTC	
+--------	-----------------------------	--------------------------------
+Repeats: 13	Average Length: 29		Average Length: 32
+
+CRISPR 2   Range: 2904014 - 2904407
+POSITION	REPEAT				SPACER
+--------	----------------------------	---------------------------------
+2904014		GGTTTATCCCCGCTGGCGCGGGGAACTC	GACAGAACGGCCTCAGTAGTCTCGTCAGGCTCC	[ 28, 33 ]
+2904075		GGTTTATCCCCGCTGGCGCGGGGAACAC	CTGTTTTCGCAAATCTATGGACTATTGCTATTC	[ 28, 33 ]
+2904136		GGTTTATCCCCGCTGGCGCGGGGAACAC	GGGCGCACGGAATACAAAGCCGTGTATCTGCTC	[ 28, 33 ]
+2904197		GGTTTATCCCCGCTGGCGCGGGGAACAC	TGGCTCTGCAACAGCAGCACCCATGACCACGTC	[ 28, 33 ]
+2904258		GGTTTATCCCCGCTGGCGCGGGGAACAC	GAAATGCTGGTGAGCGTTAATGCCGCAAACACA	[ 28, 33 ]
+2904319		GGTTTATCCCCGCTGGCGCGGGGAACAC	ATTACGCCTTTTTGCGATTGCCCGGTTTTTGCC	[ 28, 33 ]
+2904380		GGTTTATCCCCGCTGGCGCGGGGAACAC	
+--------	----------------------------	---------------------------------
+Repeats: 7	Average Length: 28		Average Length: 33
+
+Time to find repeats: 426 ms
+
+