Array 1 38-675 **** Predicted by CRISPRDetect 2.4 *** >NZ_CTJO01000078.1 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 strain EWV4 isolate EWV4, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 38 29 100.0 32 ............................. TTTGCCGATCCCCTTCCAGACCACCCTTTACA 99 29 100.0 32 ............................. TGCAGAGTTGTATCTTACCCTGTTTACGTTTC 160 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 221 29 100.0 32 ............................. GACTGTTTATACCGGATTCCATGCGTTTTCAG 282 29 100.0 32 ............................. GAATTACTGGCTAACGACGAACTGACAGTTGA 343 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 404 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 465 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 526 29 100.0 32 ............................. TTTTGATACGTAGTATTCATTACGCCTCCTAG 587 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 648 28 96.6 0 ............................- | ========== ====== ====== ====== ============================= ================================ ================== 11 29 99.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : ACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGTG # Right flank : | # Questionable array : NO Score: 6.25 # Score Detail : 1:0, 2:3, 3:0, 4:0.99, 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 [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [48.3-0.0]%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 1 395-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_CTJO01000087.1 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 strain EWV4 isolate EWV4, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 394 28 96.6 32 -............................ TCTGGTTATAACATCGCAGCAAAATCAAAAGA 334 29 100.0 32 ............................. TGAGCAACGACAGTAAATAATTTTTCGTGCTG 273 29 100.0 32 ............................. AGCCGTTTCCGCTAAATACCCCCGCAGTGATT 212 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 151 29 96.6 32 .....T....................... GCACTATTTCGAATGTCTCGACGCCAGATTTA 90 29 100.0 31 ............................. CAACCCATTAATTAACTAAGCAGTAATAAAC G [62] 29 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 7 29 99.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : G # 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: F [1-1] 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 317160-317432 **** Predicted by CRISPRDetect 2.4 *** >NZ_CTJO01000001.1 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 strain EWV4 isolate EWV4, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 317160 29 100.0 32 ............................. TTATCCCAATATATTTCGCTATCAGTTACATC 317221 29 100.0 32 ............................. TGCTTTGGTGAAGATTTCTGATTTGGTCATTT 317282 29 100.0 32 ............................. TCGAGGTCAATAAAAAATGGTGTGGCTTTACC 317343 29 100.0 32 ............................. TTCCAGAACCGTTTGACTTACTGTGGCCATTA 317404 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 5 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GGGCAGAGTTGTATCTTACCCTGTTTACGTTTCGTGTTCCCCGCGCCAGCGGGGATAAACCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGTGTTCCCCGCGCCAGCGGGGATAAACCGAATTATTTCTGTGGCTGGGGTTTCGATTCGATGTGTTCCCCGCGCCAGCGGGGATAAACCGTAGATCCTCAACGGTCAGGCTGTTTAGTTCCTGTGTTCCCCGCGCCAGCGGGGATAAACCGCAGGTTATGCGCAAAAATTAATTCATATTATAGTG # Questionable array : NO Score: 6.06 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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: NA [5,5] 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 [70.0-45.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.55,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 317746-318261 **** Predicted by CRISPRDetect 2.4 *** >NZ_CTJO01000001.1 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 strain EWV4 isolate EWV4, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 317746 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 317807 29 100.0 32 ............................. TAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 317868 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 317929 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 317990 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 318051 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 318112 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 318173 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 318234 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 9 29 96.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : ACCGTGCTTTGGTGAAGATTTCTGATTTGGTCATTTGTGTTCCCCGCGCCAGCGGGGATAAACCGTCGAGGTCAATAAAAAATGGTGTGGCTTTACCGTGTTCCCCGCGCCAGCGGGGATAAACCGTTCCAGAACCGTTTGACTTACTGTGGCCATTAGTGTTCCCCGCGCCAGCGGGGATAAACCGGGCAGAGTTGTATCTTACCCTGTTTACGTTTCGTGTTCCCCGCGCCAGCGGGGATAAACCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNA # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGTCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAGCAGTCGAATCATCTGCCATCCCGATATTGCACGTGAACGTTATGCAGCAATGACTTTTCTTGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.11 # Score Detail : 1:0, 2:3, 3:0, 4:0.85, 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 [0-7] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [1.7-63.3]%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 3 334393-334727 **** Predicted by CRISPRDetect 2.4 *** >NZ_CTJO01000001.1 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 strain EWV4 isolate EWV4, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 334393 29 100.0 32 ............................. TTCTTGAATATGATTGCGGGTATATGTGGATA 334454 29 100.0 32 ............................. AACGAATTGAGACTATTAGAGATTATTCGCCT 334515 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 334576 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 334637 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 334698 29 96.6 0 A............................ | A [334724] ========== ====== ====== ====== ============================= ================================ ================== 6 29 98.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # 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 [0-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [71.7-48.3]%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], //