Array 1 7-1621 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYYC01000003.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N38944 N38944_contig_3, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 7 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 68 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 129 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 190 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 251 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 312 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 373 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 434 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 495 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 556 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 617 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 678 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 739 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 800 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 861 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 922 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 983 29 100.0 32 ............................. CCCCGATAGAGACGCTTCTGTAGTCACTGGCA 1044 29 100.0 33 ............................. GTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGC 1106 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 1167 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 1228 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 1289 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 1350 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 1411 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 1472 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 1533 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 1594 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 27 29 98.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TTTAGTG # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # 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 [-13.50,-12.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-10] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [8.3-63.3]%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 1-454 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYYC01000068.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N38944 N38944_contig_68, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1 28 96.6 33 -............................ CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 62 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 123 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 184 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 245 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 306 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 367 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 428 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================= ================== 8 29 98.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : | # 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 [-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 1-804 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYYC01000018.1 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- strain CVM N38944 N38944_contig_18, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 1 28 96.6 32 -............................ CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 61 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 123 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 226 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 287 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 348 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 409 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 470 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 531 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 592 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 653 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 714 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 775 29 96.6 0 A............................ | A [801] ========== ====== ====== ====== ============================= ========================================================================== ================== 13 29 99.2 36 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 5.98 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 5:0, 6:0.25, 7:-0.23, 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 [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], //