Array 1 1-514 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYWU01000074.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N38229 N38229_contig_74, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 28 96.6 32 -............................ TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 61 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 122 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 183 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 244 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 305 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 366 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 427 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 488 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 9 29 98.5 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : | # Questionable array : NO Score: 6.19 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 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: NA [1-1] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [0.0-0.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 263-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYWU01000026.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N38229 N38229_contig_26, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 262 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 201 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 140 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 79 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 18 18 62.1 0 ..................----------- | ========== ====== ====== ====== ============================= ================================ ================== 5 29 92.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : G # Questionable array : NO Score: 5.68 # Score Detail : 1:0, 2:3, 3:0, 4:0.62, 5:0, 6:0.25, 7:0.01, 8:0.8, 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 17888-16395 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYWU01000026.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N38229 N38229_contig_26, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 17887 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 17826 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 17765 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 17704 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 17643 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 17582 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 17521 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 17460 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 17399 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 17338 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 17277 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 17216 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 17155 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 17094 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 17033 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 16972 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 16910 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 16849 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 16788 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 16727 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 16666 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 16605 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 16544 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 16483 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 16422 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], // Array 1 1-620 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYWU01000075.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N38229 N38229_contig_75, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 1 28 96.6 33 -............................ AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 62 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 165 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 226 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 287 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 348 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 409 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 470 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 531 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 592 29 96.6 0 .....T....................... | ========== ====== ====== ====== ============================= ========================================================================== ================== 10 29 99.3 37 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GGTTAACCAGGGGTTTTTCCCCACTATTTCGCGTGTTCCCCGCGCCAGCG # Questionable array : NO Score: 5.89 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 5:0, 6:0.25, 7:-0.32, 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: NA [1-1] Score: 0/0.41 # AT richness analysis in flanks prediction: R [0.0-33.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //