Array 1 1032558-1034171 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014967.1 Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2011K-1702 isolate USDA-ARS-USMARC-1910 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1032558 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 1032619 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 1032680 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 1032741 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 1032802 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 1032863 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 1032924 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 1032985 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 1033046 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 1033107 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 1033168 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 1033229 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 1033290 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 1033351 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 1033412 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 1033473 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 1033534 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 1033595 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 1033656 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 1033717 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 1033778 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 1033839 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 1033900 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 1033961 29 96.6 32 ........A.................... CAGGTTATGCGCAAAAATTAATTCATATTATA 1034022 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 1034083 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 1034144 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 1050304-1050943 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP014967.1 Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2011K-1702 isolate USDA-ARS-USMARC-1910 chromosome, complete genome Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1050304 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 1050365 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 1050426 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 1050487 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 1050548 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 1050609 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1050670 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1050731 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1050792 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1050853 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1050914 29 96.6 0 A............................ | A [1050940] ========== ====== ====== ====== ============================= ================================ ================== 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], //