Array 1 30004-28161 **** Predicted by CRISPRDetect 2.4 *** >NZ_LVFQ01000002.1 Salmonella enterica subsp. enterica serovar Typhimurium strain CFSAN033901 CFSAN033901_contig0001, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 30003 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 29942 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 29881 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 29820 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 29759 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 29698 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 29637 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 29575 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 29514 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 29453 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 29392 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 29331 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 29270 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 29209 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 29148 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 29087 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 29026 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 28965 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 28904 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 28842 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 28739 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 28678 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 28617 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 28556 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 28495 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 28434 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 28373 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 28312 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 28251 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 28190 29 96.6 0 A............................ | A [28163] ========== ====== ====== ====== ============================= ========================================================================== ================== 30 29 99.5 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.14 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.08, 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: R [3-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [50.0-71.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.92 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 47017-46135 **** Predicted by CRISPRDetect 2.4 *** >NZ_LVFQ01000002.1 Salmonella enterica subsp. enterica serovar Typhimurium strain CFSAN033901 CFSAN033901_contig0001, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 47016 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 46955 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 46894 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 46833 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 46772 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 46711 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 46650 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 46589 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 46528 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 46467 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 46406 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 46345 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 46284 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 46223 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 46162 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================ ================== 15 29 98.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # 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: 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: R [6-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [63.3-70.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //