Array 1 6-1360 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHFW01000020.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N44716 N44716_contig_20, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 6 29 86.2 32 T..A...GT.................... CCGCTGACGCACTGGATCAACCTGACGCAACG A [12] 68 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 129 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 190 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 251 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 312 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 373 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 434 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 495 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 556 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 617 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 679 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 782 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 843 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 904 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 965 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 1026 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1087 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1148 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1209 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1270 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1331 29 96.6 0 A............................ | A [1357] ========== ====== ====== ====== ============================= ========================================================================== ================== 22 29 98.9 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TCAGGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.08 # Score Detail : 1:0, 2:3, 3:0, 4:0.95, 5:0, 6:0.25, 7:-0.12, 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: R [6-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [3.3-48.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0.68 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 395-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHFW01000049.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N44716 N44716_contig_49, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 394 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 333 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 272 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 211 29 100.0 33 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTGC 149 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 88 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 7 29 99.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : C # Questionable array : NO Score: 6.21 # Score Detail : 1:0, 2:3, 3:0, 4:0.95, 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: NA [0.0-0.0]%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], // Array 2 17959-16527 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHFW01000049.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N44716 N44716_contig_49, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 17958 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 17897 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 17836 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 17775 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 17714 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 17653 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 17592 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 17531 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 17470 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 17409 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 17348 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 17287 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 17226 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 17165 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 17104 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 17042 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 16981 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 16920 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 16859 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 16798 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 16737 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 16676 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 16615 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 16554 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 24 29 98.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.16 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 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], //