Array 1 3125100-3124295 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP040648.1 Salmonella enterica subsp. enterica serovar Rough O:-:- strain PNCS009880 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 3125099 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 3125038 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 3124977 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 3124916 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 3124855 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 3124793 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 3124690 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 3124629 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 3124568 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 3124507 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 3124446 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 3124385 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 3124324 29 96.6 0 A............................ | A [3124297] ========== ====== ====== ====== ============================= ========================================================================== ================== 13 29 99.5 36 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 5.99 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.23, 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 [3-0] 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 3143519-3141232 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP040648.1 Salmonella enterica subsp. enterica serovar Rough O:-:- strain PNCS009880 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 3143518 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 3143457 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 3143396 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 3143335 29 100.0 32 ............................. GCTCATTAAATAACTATATAACCCCCGGACTC 3143274 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 3143213 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 3143152 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 3143091 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 3143030 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 3142969 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 3142908 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 3142847 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 3142786 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 3142725 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 3142664 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 3142603 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 3142542 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 3142481 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 3142420 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 3142359 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 3142298 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 3142237 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 3142175 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 3142114 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 3142053 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 3141992 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 3141931 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 3141870 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 3141809 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 3141747 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 3141686 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 3141625 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 3141564 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 3141503 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 3141442 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 3141381 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 3141320 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 3141259 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 38 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 [12-0] 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], //