Array 1 273-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHJF01000111.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46860 N46860_contig_111, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 272 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 211 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 150 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 89 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 5 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : C # Questionable array : NO Score: 5.99 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 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: NA [0-0] 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: R [0,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 1432-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHJF01000101.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46860 N46860_contig_101, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1431 28 93.1 32 -............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 1371 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 1310 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 1249 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 1188 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 1127 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 1066 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 1005 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 943 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 882 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 821 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 760 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 699 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 638 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 577 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 516 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 455 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 394 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 333 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 272 29 100.0 32 ............................. GTCGTTCATCAGGCACTACCGGCACTTTCTGG 211 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 150 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 89 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 24 29 98.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : C # 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: F [2-5] 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 [0.41,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 505-49 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHJF01000034.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46860 N46860_contig_34, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 504 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 443 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 382 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 321 29 100.0 32 ............................. AAAAAACAGAAGAACGGCAAGCGGCACCTCAA 260 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 199 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 138 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 77 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 8 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GGCAACCCATTAATTAACTAAGCAGTAATAAACGTGTTCCCCGCGCCAG # 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 [43.3-70.0]%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 1-212 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHJF01000038.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N46860 N46860_contig_38, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 28 96.6 32 -............................ TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 61 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 122 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 183 29 93.1 0 A........A................... | A [210] ========== ====== ====== ====== ============================= ================================ ================== 4 29 96.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 3.88 # Score Detail : 1:0, 2:3, 3:0, 4:0.83, 5:-1.5, 6:0.25, 7:0.01, 8:0.6, 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 [-10.50,-8.90] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [1-2] 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], //