Array 1 3107408-3105748 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP040686.1 Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain USDA15WA-1 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 3107407 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 3107346 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 3107285 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 3107224 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 3107163 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 3107102 29 100.0 32 ............................. CCATTATTCAACCCTCCAGGCTCGCGCCGGCT 3107041 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 3106979 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 3106918 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 3106857 29 100.0 32 ............................. CCGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 3106796 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 3106735 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 3106674 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 3106613 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 3106552 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 3106491 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 3106429 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 3106326 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 3106265 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 3106204 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 3106143 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 3106082 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 3106021 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 3105960 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 3105899 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 3105838 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 3105777 29 96.6 0 A............................ | A [3105750] ========== ====== ====== ====== ============================= ========================================================================== ================== 27 29 99.6 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.14 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 5:0, 6:0.25, 7:-0.09, 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 3125032-3123539 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP040686.1 Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain USDA15WA-1 chromosome, complete genome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 3125031 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 3124970 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 3124909 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 3124848 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 3124787 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 3124726 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 3124665 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 3124604 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 3124543 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 3124482 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 3124421 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 3124360 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 3124299 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 3124238 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 3124177 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 3124116 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 3124054 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 3123993 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 3123932 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 3123871 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 3123810 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 3123749 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 3123688 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 3123627 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 3123566 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 25 29 98.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.17 # Score Detail : 1:0, 2:3, 3:0, 4:0.91, 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 [9-1] 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], //