Array 1 1030259-1031872 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014975.1 Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2009K-1640 isolate USDA-ARS-USMARC-1906 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1030259 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 1030320 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 1030381 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 1030442 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 1030503 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 1030564 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 1030625 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 1030686 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 1030747 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 1030808 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 1030869 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 1030930 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 1030991 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 1031052 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 1031113 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 1031174 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 1031235 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 1031296 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 1031357 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 1031418 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 1031479 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 1031540 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 1031601 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 1031662 29 96.6 32 ........A.................... CAGGTTATGCGCAAAAATTAATTCATATTATA 1031723 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 1031784 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 1031845 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 27 29 98.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.20 # Score Detail : 1:0, 2:3, 3:0, 4:0.94, 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 [0-9] 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 2 1048005-1048644 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014975.1 Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2009K-1640 isolate USDA-ARS-USMARC-1906 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1048005 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 1048066 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 1048127 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 1048188 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 1048249 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 1048310 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1048371 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1048432 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1048493 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1048554 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1048615 29 96.6 0 A............................ | A [1048641] ========== ====== ====== ====== ============================= ================================ ================== 11 29 99.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.23 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 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 [0-3] 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], //