Array 1 1065-1215 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYVL01000108.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N31411 N31411_contig_108, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1065 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 1126 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 1187 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 3 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : CAACCAGGCTGGATCGTAACTCCTATCCCCTCGTGTTCCCCGCGCCAGCG # Questionable array : NO Score: 5.67 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.02, 8:0.4, 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 [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: F [71.7-30.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.51,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 1-1414 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYVL01000012.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N31411 N31411_contig_12, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1 28 96.6 32 -............................ CGTCACTACCGAGACCGAGACCGAGACCGAGA 61 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 122 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 183 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 244 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 305 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 366 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 427 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 488 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 549 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 610 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 671 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 733 29 100.0 32 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATT 794 29 65.5 13 ..............GA..C.TTCC.G.GC ACGTTACTCGATC Deletion [836] 836 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 897 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 958 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 1019 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 1080 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1141 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1202 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1263 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1324 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1385 29 96.6 0 A............................ | A [1411] ========== ====== ====== ====== ============================= ================================= ================== 24 29 98.0 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.09 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 5:0, 6:0.25, 7:-0.06, 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 [2-3] 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: F [5.65,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 750-50 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYVL01000014.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N31411 N31411_contig_14, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 749 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 688 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 627 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 566 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 505 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 444 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 383 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 322 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 261 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 200 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 139 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 78 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 12 29 99.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTGACGGTGACGTCAGTGCCGAAGGCGAAATAGTGTTCCCCGCGCCAGC # 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 [31.7-70.0]%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], // Array 1 2121-1361 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYVL01000048.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N31411 N31411_contig_48, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 2120 28 96.6 32 -............................ CCAGCTTACGCTATTTACGACGTTATTGAGCA 2060 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 1999 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 1938 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 1876 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 1815 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 1754 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 1693 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 1632 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 1571 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 1510 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 1449 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 1388 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 13 29 96.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 5.86 # Score Detail : 1:0, 2:3, 3:0, 4:0.83, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.77, # 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 [6-5] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [63.3-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //