Array 1 340-6 **** Predicted by CRISPRDetect 2.4 *** >NZ_PQNA01000033.1 Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain STM032/04 STM032_04_contig33, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 339 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 278 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 217 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 156 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 95 29 100.0 32 ............................. CCGGACCTAAACCTGAAAAAACCGACGCCCAA 34 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 6 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGAGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GGGTTA # Questionable array : NO Score: 6.26 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.01, 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 : GTGTTCCCCGCGCCAGCGGGGATAAACCG # 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 [4,5] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG 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 [5.0-70.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.51 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 2-1677 **** Predicted by CRISPRDetect 2.4 *** >NZ_PQNA01000046.1 Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain STM032/04 STM032_04_contig46, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 2 29 100.0 32 ............................. GGTCAGTGAATAGCTATGTAACCGCCGGACTC 63 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 124 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 185 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 246 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 307 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 368 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 429 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 490 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 551 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 612 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 673 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 734 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 795 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 856 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 917 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 978 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 1039 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 1100 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 1162 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 1223 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 1284 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 1345 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 1406 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 1467 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 1528 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 1589 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 1650 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 28 29 98.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AG # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.18 # Score Detail : 1:0, 2:3, 3:0, 4:0.92, 5:0, 6:0.25, 7:0.01, 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 : GTGTTCCCCGCGCCAGCGGGGATAAACCG # 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: F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.50,-12.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-10] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [1.7-63.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 17810-19225 **** Predicted by CRISPRDetect 2.4 *** >NZ_PQNA01000046.1 Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain STM032/04 STM032_04_contig46, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 17810 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 17871 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 17932 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 17994 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 18055 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 18116 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 18177 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 18238 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 18299 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 18360 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 18421 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 18482 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 18543 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 18604 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 18665 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 18727 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 18830 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 18891 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 18952 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 19013 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 19074 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 19135 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 19196 29 96.6 0 A............................ | A [19222] ========== ====== ====== ====== ============================= ========================================================================== ================== 23 29 99.6 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.12 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 5:0, 6:0.25, 7:-0.11, 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 : GTGTTCCCCGCGCCAGCGGGGATAAACCG # 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: F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.50,-12.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [71.7-48.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.92,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //