Array 1 629-51 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYTD01000097.1 Salmonella enterica strain CVM 43838 43838_contig_98, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 628 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 567 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 506 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 445 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 384 29 100.0 32 ............................. TGACGCTGGTCTATACCGGCAACGAACGCGAC 323 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 262 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 201 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 140 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 79 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 10 29 99.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCAGCGGGGATAAACCGAACAGGAACAGGAAAAAAAAGATTTGTCCGG # Right flank : GGTGAGTTCGGTTTTAATTTCGTCGCTAAGCTGCGTGTTCCCCGCGCCAGC # 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: 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 [2-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [36.7-43.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 34-420 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYTD01000115.1 Salmonella enterica strain CVM 43838 43838_contig_116, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 34 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 95 29 100.0 24 ............................. CCGGCATCAGCGCCGATCCGTTCC Deletion [148] 148 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 209 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 270 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 331 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 392 29 96.6 0 .................A........... | ========== ====== ====== ====== ============================= ================================ ================== 7 29 98.5 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTTTTGATACGTAGTATTCATTACGCCTCCTAGG # Right flank : GACGAGTTCTGGAAATGGTTAGCTGATAAAGAGTGTTCCCCGCG # Questionable array : NO Score: 6.11 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 5:0, 6:0.25, 7:-0.07, 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 [0-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [33.3-36.7]%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 52-917 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYTD01000019.1 Salmonella enterica strain CVM 43838 43838_contig_19, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ========================================================================== ================== 52 29 100.0 32 ............................. ATATTCGCCGCTTTCCATTTACCGAACGTAAC 113 29 100.0 32 ............................. CCACGTTCGGCGATGTTGGCCCCATCGGTCCA 174 29 100.0 33 ............................. AAACGGTAGTGTTTTAAAACCGTTTCGAGGTGC 236 29 100.0 74 ............................. AATAAGGCGCGGTGCCACCCTCGGCTTTAATTGTGTTCCCCGCGCCGACGCGTTCCAGCGCACGTTACTCGATC 339 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 400 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 461 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 522 29 100.0 32 ............................. GCACTATTTCGAATGTCTCGACGCCAGATTTA 583 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 644 29 100.0 32 ............................. GCAACCCATTAATTAACTAAGCAGTAATAAAC 705 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 766 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 827 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 888 29 96.6 0 A............................ | A [914] ========== ====== ====== ====== ============================= ========================================================================== ================== 14 29 99.5 35 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CGCCAGCGGGGATAAACCGACGCCCCGAATGTGTTTGCCTCGCCCGCTGCCG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.01 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 5:0, 6:0.25, 7:-0.21, 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 [0-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [26.7-48.3]%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 34-726 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYTD01000063.1 Salmonella enterica strain CVM 43838 43838_contig_63, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 34 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 95 29 100.0 24 ............................. CCGGCATCAGCGCCGATCCGTTCT Deletion [148] 148 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 210 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 271 29 100.0 32 ............................. CGTCACTACCGAGACCGAGACCGAGACCGAGA 332 29 100.0 32 ............................. CCGCTGACGCACTGGATCAACCTGACGCAACG 393 29 100.0 32 ............................. TTGCAGGGCGATATTGTTGTTGGTGAATGGGA 454 29 100.0 32 ............................. CGTCGCGGAAAATTTCGCATTGACGATAAAGA 515 29 100.0 32 ............................. TTACGTGTTTATTCATCTGTTGCATTAGATTC 576 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 637 29 100.0 32 ............................. ACGCCCCGAATGTGTTTGCCTCGCCCGCTGCC 698 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 12 29 99.7 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTTTTGATACGTAGTATTCATTACGCCTCCTAGG # Right flank : | # Questionable array : NO Score: 6.21 # Score Detail : 1:0, 2:3, 3:0, 4:0.99, 5:0, 6:0.25, 7:-0.03, 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 [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [33.3-0.0]%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 1-266 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYTD01000064.1 Salmonella enterica strain CVM 43838 43838_contig_64, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 23 79.3 32 ------....................... TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 56 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 117 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 178 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 239 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 5 29 91.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 5.57 # Score Detail : 1:0, 2:3, 3:0, 4:0.59, 5:0, 6:0.25, 7:0.01, 8:0.8, 9:0.92, # 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 [1-5] 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: F [5.65,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 16398-16731 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYTD01000064.1 Salmonella enterica strain CVM 43838 43838_contig_64, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 16398 29 96.6 32 ............................T CCCACCGCGCTGATTAACGACGGACTGTTACA 16459 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 16520 29 100.0 32 ............................. AACCGCTGGCGGGCTGATTGGTCTGCAACCAC 16581 29 100.0 32 ............................. CAACCAGGCTGGATCGTAACTCCTATCCCCTC 16642 29 100.0 32 ............................. AAAATGCAGGTGGGGTAACGAATGCGAGATTG 16703 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 6 29 99.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : | # Questionable array : NO Score: 6.23 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 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 [1-0] 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 [5.51,0.41 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //