Array 1 45500-48558 **** Predicted by CRISPRDetect 2.4 *** >NZ_JWQY01000008.1 Salmonella enterica subsp. enterica serovar Senftenberg strain CFSAN024724 CFSAN024724_contig0007, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 45500 29 100.0 32 ............................. CACATTTCCTCAGTGTGCTTCAGAGGGTGGTA 45561 29 100.0 32 ............................. CCGATATCAAAAAAGCGTTTAAACGCCTTGCC 45622 29 96.6 32 ............................T TCCTGCGCTTTGGCCAGTTTGGAACCCGCCGC 45683 29 100.0 32 ............................. GCACAATTTGTGCTTTTGCAATTCACTTTGAA 45744 29 100.0 32 ............................. TGATCACAGAACTGACCGGGTACACCATACCT 45805 29 100.0 32 ............................. TGATCACAGAACTGACCGGGTACACCATACCT 45866 29 100.0 32 ............................. TAACGCCGTTCTGCATACGCTCTACCGCGCGC 45927 29 100.0 32 ............................. GGGAATGTATGGATTTAGAAGAAGAGCTGGCA 45988 29 100.0 32 ............................. GGGTATTACGGCGACACAGCGCTTGTTGTCTA 46049 29 100.0 32 ............................. TTAACAAATGTTTTTAAAACGCTTATAACAAA 46110 29 100.0 32 ............................. GGGGCGGCAATGGTGGTCAGGGTGATGGCGGC 46171 29 100.0 32 ............................. TTTAAAAATTTATCTCGATAAATCCAACGATG 46232 29 100.0 32 ............................. AATGATCGTATTTTTCGCTACGTCGCACAAAT 46293 29 100.0 32 ............................. CCCGTTATTTGTAGTTAACGGGCACGTAGTGG 46354 29 100.0 32 ............................. ATCGGGCAGCTCAACGCGGCTATGAAAATCAC 46415 29 100.0 32 ............................. TTGATCGCCGTGGCGGTGAGATTAGAAACGCG 46476 29 100.0 32 ............................. CTGCCAAACTTCTGACAATCCCGGACAGCATC 46537 29 100.0 32 ............................. CGAGTCTGGAAATTGAGGACACCGAAACCGGC 46598 29 100.0 32 ............................. TGCTGGTGGGCGGTACGCCGTGCCAGGCGTTC 46659 29 96.6 32 ............................T TATCCTTACCCTCAACGGCGCAGGCCGATCTC 46720 29 100.0 32 ............................. CGATCTGGTGAGCGCATCGGTTCGGGAGAGTG 46781 29 100.0 32 ............................. GATTGTTCAGATTGGGAATTTGACCAACGCCC 46842 29 69.0 11 ................TAAT..CGT.T.C GTGAACCAGTT TT [46862] Deletion [46882] 46884 29 100.0 32 ............................. GGGAATATCGTTAAAGTGGTTTACCACAATAT 46945 29 100.0 32 ............................. GCGCTCAGGGCCGCCTTGCTGCGGGCACTCAT 47006 29 100.0 32 ............................. GACGTGATCAAACAATTTGGCCGCCCGGAACA 47067 29 100.0 32 ............................. CGATCAAGCGAATGCGTCGGCTGGAGCATCGC 47128 29 100.0 32 ............................. GTTTTCGCGGCCGCGAGATTGTTCTTGCCGAC 47189 29 100.0 32 ............................. TACCGTTTTTACTCCCCCGCATTTGGTTACAC 47250 29 100.0 32 ............................. CAGGAGCAAGCACAAACATAGAGCAAATTAAA 47311 29 100.0 32 ............................. CCAGTGCATTCGAACTCATGGAACGGTGCTAA 47372 29 100.0 32 ............................. GCGCACCGCTTTAGAGTGCCAGGCATAGGCAA 47433 29 100.0 32 ............................. ACACAATACGTATCAGTAAAGACACAAATTGT 47494 29 100.0 32 ............................. CGCATTACCGGGAAAACCTGGGAAGAGACGAT 47555 29 100.0 32 ............................. TCTTGTTTGTTTCTGATTCTTTTTCTGAATGA 47616 29 100.0 32 ............................. AGTCAGAAGAGGACTCATTAGTATCACTCTCA 47677 29 100.0 32 ............................. AATAAACAGCGTCGTAAATGGATCGAGGAAAT 47738 29 100.0 32 ............................. CATCTCTCTATATGCAGCGCCAGCCAGCGCAA 47799 29 100.0 32 ............................. CTTTCCTTGCGTCAATTTTGAGGGAGATTGAT 47860 29 100.0 32 ............................. ATCCCGCGCTCTATTAAAATCTTTGATTGCGT 47921 29 100.0 32 ............................. GTAATGTGCGCCGCGCCGGTGATATCTACTTT 47982 29 96.6 32 .....T....................... CCATTGCTGACAGGCAGTGATTTCAATGTGTC 48043 29 100.0 32 ............................. GTCATGAATGGCCTCATAAAAACGATGTTGGT 48104 29 100.0 32 ............................. TGTTCGCGCTAAATAATGCAGTAGGCCGCGCT 48165 29 100.0 32 ............................. CCAGAAATTTAAATGGCTATTCCTGGCTGTAG 48226 29 100.0 32 ............................. GCGCAATTGCAGTTTGACGCGGTGCTGTCATT 48287 29 100.0 32 ............................. TCGTTTGTGGCGTCAGTAATACTATTATCGGT 48348 29 96.6 32 .............T............... TTTTTAAATCCGGACAGACCCTGTAACGGATC 48409 29 100.0 32 ............................. ATCCGACTGTATGCCCAGCAGAACGAGGGCGC 48470 29 96.6 32 .............T............... CACGAGTGGCAAATTGATTTCGACGAAAAACC 48531 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 51 29 98.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGCTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATGATATACGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGGGCTGGAGCGGATAAATCGTTGAAGGCCAGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGTGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.17 # Score Detail : 1:0, 2:3, 3:0, 4:0.94, 5:0, 6:0.25, 7:-0.02, 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 [1-8] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [70.0-63.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 81689-79584 **** Predicted by CRISPRDetect 2.4 *** >NZ_JWQY01000007.1 Salmonella enterica subsp. enterica serovar Senftenberg strain CFSAN024724 CFSAN024724_contig0006, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 81688 29 100.0 32 ............................. GCAATTTCCGATATGCGACTTGGGACACCAAT 81627 29 100.0 32 ............................. ACACCGACTCATCCGTTGTTACTCCTGGTATT 81566 29 100.0 32 ............................. CACATCGGGAGCCTCAATCAACCCGGCACGGA 81505 29 100.0 32 ............................. AGTTCGATATCCCTTAACGGTACTGCCGTCCT 81444 29 100.0 32 ............................. CCTCACGCAATTGAGCCTCTTTCTCGACACGC 81383 29 100.0 32 ............................. GGCCAGTTCAACAAACACCACGACGCGGGAAT 81322 29 100.0 32 ............................. TTCATCACCGTCAGCAAGCTGCGATCCGAAAT 81261 29 100.0 32 ............................. CCAGCTTGCCGATATCAACGACCTATACCTGT 81200 29 100.0 32 ............................. GTTAAAATTTGGGAGGATCGCCCGGGACTCCC 81139 29 100.0 32 ............................. GGACCATTGAAACGGCGCTGACATCAGATGTT 81078 29 100.0 32 ............................. TACCGAACGGCTCAAAGTATGTTCCAATTGAC 81017 29 100.0 32 ............................. GTTGAAACCAGCATTCCTTATGCTGTGCTGCC 80956 29 100.0 32 ............................. GAGATTTTTCTTGTCCCGCCACACCAGCGGCT 80895 29 100.0 32 ............................. TGCATCATCTGATTCGTACGATACGGCAGGGT 80834 29 100.0 32 ............................. GGCCGCACCGCTGGCGATCACGATTAATCAGC 80773 29 100.0 32 ............................. CGCCTCGCAAAACTGGTCGGGGTTTTTCCCCA 80712 29 100.0 32 ............................. TTCGTGTTCTAACAGCAGATCGCTGATACGGC 80651 29 100.0 32 ............................. CCAGTAATGAAACGCTGGCAACATTGACGAGC 80590 29 100.0 32 ............................. CGCAGACGGCGCAATTGGATTCGGTGATCGGG 80529 29 100.0 32 ............................. TGCTCGAGCCGACATTGATCCCGCAAAAATAC 80468 29 100.0 32 ............................. GGATGCCGATAGCGGTCAGTAATGAAAATGGC 80407 29 100.0 32 ............................. AAGATCCTGTCTCTTTTGTGCGGAGCGCCGAC 80346 29 100.0 32 ............................. TTCGTTTGATCTCCACTCACAACGGTATTGAA 80285 29 100.0 33 ............................. GACAATTAGTTCCGACAGACGCCGGTATTAAAT 80223 29 96.6 32 ............T................ CCCACGCGCGGCCGCACTGGCCTCGCGGATAA 80162 29 100.0 32 ............................. TCCGGGCCGCCGCTACCACCACTCAGCGGCGT 80101 29 100.0 32 ............................. CCTAATGGTGATGGGGCGTTTAATCTTATCTC 80040 29 100.0 32 ............................. ATTGACAACAGTCTGCTTACCCGAGCTGCTCC 79979 29 100.0 32 ............................. TCCTGTCGGCGGTACGGTGGACATCCCGCAGG 79918 29 96.6 32 .........A................... CCAGTCAGCCACTGTTCTTTGCCGTACCTTTC 79857 29 100.0 32 ............................. GGGTTATAACCGGGATACCATCCGCTCCAACC 79796 29 100.0 32 ............................. CGCCACGTTTTTTGCATTTTATTGGCATCATC 79735 29 100.0 32 ............................. GGCAACTGGGCGATCATCTGGGCGCTGTTTAT 79674 29 100.0 32 ............................. GTGCTCCAGTGGGCTGCTAAGGGGCTTGGTGG 79613 29 100.0 0 ............................. | A [79586] ========== ====== ====== ====== ============================= ================================= ================== 35 29 99.8 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CTTATTGAAGATGTTCTCGCGGCAGGGGAAATTCAACCGCCGTTACCTCCTGAAGATTCACAACCCATAGCGATCCCTCTTCCTGTTGCGTTGGGAGATTCCGGTCATCGGAGTACCTAACGATGAGTATGCTGGTTGTCGTTACCGAAAATGTTCCTCCTCGTCTGCGGGGGAGGCTGGCCGTCTGGTTACTGGAAATTCGAGCTGGTGTGTATGTTGGTGATGTTTCCGCAAAGATCCGCGAGATGATATGGCAACAGGTTTCCGTTCTGGCAGATGAGGGAAATGTTGTTATGGCGTGGGCGACAAATACAGAATCAGGTTTTGAGTTTCAGACTTTTGGTGTAAATCGACGTATTCCGGTAGATCTTGATGGACTGCGATTGGTGTCGTTTCTACCTGTTGAAAATCAATAAGTTAGAGATCTTTAAAAATTAGGAAAAGTTGGTGGGTTTTTTGTGCGCTAAAAAAGTATTTAAATTCAATTGGGTAGATTTAGA # Right flank : TTTCCCCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCAGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.25 # Score Detail : 1:0, 2:3, 3:0, 4:0.99, 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 [3-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [48.3-70.0]%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], //