Array 1 58-1289 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHNL01000025.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N51275 N51275_contig_25, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 58 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 119 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 180 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 241 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 302 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 363 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 424 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 485 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 546 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 608 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 711 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 772 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 833 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 894 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 955 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 1016 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 1077 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 1138 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 1199 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 1260 29 96.6 0 A............................ | A [1286] ========== ====== ====== ====== ============================= ========================================================================== ================== 20 29 99.5 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TCCCCGCGCCAGCGGGGATAAACCGTTGCAGGGCGATATTGTTGTTGGTGAATGGGAG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.09 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.13, 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 [1-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [40.0-48.3]%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 90822-92254 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHNL01000013.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N51275 N51275_contig_13, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 90822 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 90883 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 90944 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 91005 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 91066 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 91127 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 91188 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 91249 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 91310 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 91371 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 91432 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 91493 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 91554 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 91615 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 91676 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 91737 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 91799 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 91860 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 91921 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 91982 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 92043 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 92104 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 92165 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 92226 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 24 29 98.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : CGGCACTTTCTGGGTGTTCCCCGCGCC # 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: 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 [0-5] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [70.0-13.3]%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 16209-16348 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHNL01000063.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N51275 N51275_contig_63, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 16209 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 16270 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 16331 18 62.1 0 ..................----------- | ========== ====== ====== ====== ============================= ================================ ================== 3 29 87.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : | # Questionable array : NO Score: 4.73 # Score Detail : 1:0, 2:3, 3:0, 4:0.37, 5:0, 6:0.25, 7:0.02, 8:0.4, 9:0.69, # 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 [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [71.7-0.0]%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 58-270 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHNL01000082.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N51275 N51275_contig_82, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 58 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 120 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 181 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 242 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 4 29 100.0 33 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TCCCCGCGCCAGCGGGGATAAACCGAAAATGCAGGTGGGGTAACGAATGCGAGATTGG # Right flank : CCGCTGACGCACTGGATCAACCTGACGCAACGGTGTTCCCCGCGCCAGC # Questionable array : NO Score: 5.86 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.01, 8:0.6, 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 [40.0-26.7]%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], //