Array 1 41-984 **** Predicted by CRISPRDetect 2.4 *** >NZ_MXBX01000007.1 Salmonella enterica subsp. enterica serovar Copenhagen strain SAL3328 NODE_7_length_125068_cov_0.145932, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 41 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 102 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 163 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 224 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 285 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 346 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 407 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 469 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 530 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 591 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 652 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 713 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 774 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 835 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 896 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 957 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 16 29 97.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : ATAAACCGGTCGTTCATCAGGCACTACCGGCACTTTCTGGG # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.13 # Score Detail : 1:0, 2:3, 3:0, 4:0.87, 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 [2-8] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [31.7-63.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 17117-18898 **** Predicted by CRISPRDetect 2.4 *** >NZ_MXBX01000007.1 Salmonella enterica subsp. enterica serovar Copenhagen strain SAL3328 NODE_7_length_125068_cov_0.145932, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 17117 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 17178 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 17239 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 17300 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 17361 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 17423 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 17484 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 17545 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 17606 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 17667 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 17728 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 17789 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 17850 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 17911 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 17972 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 18033 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 18094 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 18155 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 18217 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 18320 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 18381 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 18442 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 18503 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 18564 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 18625 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 18686 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 18747 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 18808 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 18869 29 96.6 0 A............................ | A [18895] ========== ====== ====== ====== ============================= ========================================================================== ================== 29 29 99.6 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATNCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # 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: 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], // Array 1 590-12 **** Predicted by CRISPRDetect 2.4 *** >NZ_MXBX01000024.1 Salmonella enterica subsp. enterica serovar Copenhagen strain SAL3328 NODE_24_length_71961_cov_0.121205, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 589 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 528 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 467 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 406 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 345 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 284 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 223 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 162 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 101 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 40 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 10 29 99.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GAATTATTTCTG # 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 [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [15.0-70.0]%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], //