Array 1 410-14 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHKC01000058.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N48679 N48679_contig_58, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 409 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 348 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 287 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 226 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 165 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 103 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 42 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 7 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GCGTCGCGGAAAAT # Questionable array : NO Score: 6.26 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: R [10.0-71.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.51 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 1-394 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHKC01000075.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N48679 N48679_contig_75, 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 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 366 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 7 29 99.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : CGTCGCGGAAAAT # 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: R [1-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [0.0-10.0]%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 50-810 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHKC01000076.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N48679 N48679_contig_76, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 50 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 111 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 172 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 233 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 294 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 355 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 416 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 477 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 538 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 599 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 660 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 721 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 782 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 13 29 99.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCAGCGGGGATAAACCGCCGGCATCAGCGCCGATCCGTTCATAGTGCCCG # Right flank : GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGCGTGTTCCCCGCGCCAGCGGGGATA # Questionable array : NO Score: 6.22 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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 [0-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [28.3-41.7]%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 1 1-333 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHKC01000094.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N48679 N48679_contig_94, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 28 96.6 32 -............................ TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 61 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 122 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 183 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 244 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 305 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 6 29 98.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : CGTCGCGGAAAAT # 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: 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 [-10.50,-8.90] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [0.0-10.0]%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 161854-160866 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHKC01000017.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N48679 N48679_contig_17, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 161853 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 161792 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 161731 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 161670 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 161609 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 161547 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 161444 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 161383 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 161322 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 161261 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 161200 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 161139 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 161078 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 161017 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 160956 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 160895 29 96.6 0 A............................ | A [160868] ========== ====== ====== ====== ============================= ========================================================================== ================== 16 29 99.6 35 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CGCCAGCGGGGATAAACCGACGCCCCGAATGTGTTTGCCTCGCCCGCTGC # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.05 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 5:0, 6:0.25, 7:-0.18, 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 [3-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [50.0-26.7]%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], //