Array 1 1-395 **** Predicted by CRISPRDetect 2.4 *** >NZ_MWVC01000211.1 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 KO STM2896::STM0928 BCW_7514_1__paired__contig_212, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 62 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 123 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 184 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 245 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 306 29 100.0 32 ............................. ATCGGAAAAGCGTCGACTTGGGAAAGCCAGTA 367 29 72.4 0 .AT.............G.A.C.....AAA | ========== ====== ====== ====== ============================= ================================ ================== 7 29 94.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : AAAAAAAGAGAAGAGTTCTGATAAGGAGAGTAGTTCTCCCTGCTCC # Questionable array : NO Score: 5.99 # Score Detail : 1:0, 2:3, 3:0, 4:0.73, 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 [6,4] 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 [-14.90,-14.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [4-9] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [0.0-45.0]%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 3-276 **** Predicted by CRISPRDetect 2.4 *** >NZ_MWVC01000043.1 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 KO STM2896::STM0928 BCW_7514_1__paired__contig_43, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 3 29 100.0 32 ............................. TCTGGTTATAACATCGCAGCAAAATCAAAAGA 64 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 125 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 186 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 247 29 96.6 0 A............................ | A [273] ========== ====== ====== ====== ============================= ================================ ================== 5 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GCG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTACCGTTCGGGAAGGAGGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACAGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATGCCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # 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: 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 [0.0-48.3]%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 35603-36424 **** Predicted by CRISPRDetect 2.4 *** >NZ_MWVC01000044.1 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 KO STM2896::STM0928 BCW_7514_1__paired__contig_44, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 35603 29 100.0 32 ............................. GGCTTTGGTGAAGATTTCTGATTTGGTCATTT 35664 29 100.0 32 ............................. GATCGGGTGGTGCCGGTGGGCCATGTGGCGCT 35725 29 100.0 32 ............................. GCAGCGGTTGAGTAACTCCTCGTCCACGTCGA 35786 29 100.0 32 ............................. CTCCAGCGCTCGAATTTATTTGAGGCCACCAC 35847 29 100.0 32 ............................. GCGAGGTCAATAAAAAATGGTGTGGCTTTACC 35908 29 100.0 32 ............................. CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 35969 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 36030 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGCTGTTTAGTTCCT 36091 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 36152 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 36213 29 100.0 32 ............................. TTGACGGTGACGTCAGTGCCGAAGGCGAAATA 36274 29 100.0 32 ............................. CCAGCTTACGCTATTTACGACGTTATTGAGCA 36335 29 93.1 32 .................A........T.. AAACGAAAGAGGCTATGCGGTTGTTTATCGGT 36396 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 14 29 99.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGTGTGTTCCCCGCGCCAGCGGGGATAAACCGTGCAGAGTTGTATCTTACCCTGTTTACGTTTCGTGTTCCCCGCGCCAGCGGGGATAAACCGTTATCCCAATATATTTCGCTATCAGTTACATCGTGTTCCCCGCGCCAGNNCCAGCGGGGATAAACCGGAATTACTGGCTAACGACGAACTGACAGTTGAGTGTTCCCCGCGCCAGCGGGGATAAACCGCCGGACCTAAACCTGAAAAAACCGACGCCCAAGTGTTCCCCGCGCCAGCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAGCGGGGATAAACCGTTCCAGAACCGTTTGACTTACTGTGGCCATTA # Right flank : CCCCGATAGCGACGCTTCTGTAGTCACTGGCAGTGTTCCCCGCGCCA # 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 [0-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [40.0-28.3]%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], // Array 1 213-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_MWVC01000083.1 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 KO STM2896::STM0928 BCW_7514_1__paired__contig_83, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 212 29 55.2 32 NNNNNNNNNNNNN................ TTACGTGTTTATTCATCTGTTGCATTAGATTC 151 29 96.6 32 ............................T GAGGCGTACAGGCTGTTAGATGAGAAATTACC 90 29 100.0 32 ............................. TGGATTATCTGTATTTTACGGAAGTGGGCGCG 29 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 4 29 88.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGTGTGTTCCCCGCGCCAGCGGGGATAAACCGTGAGCAACGACAGTAAATAATTTTTCGTGCTGGTGTTCCCCGCGCCAGCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCAGCGGGGATAAACCGCAACCAGGCTGGATCGTAACTCCTATCCCCTCGTGTTCCCCGCGCCAGCGGGGATAAACCGCCAGTGGGCGTAGCCAGCTCATCGCTATTTTGCGTGTTCCCCGCGCCAGCGGGGATAAACCGCGTTGCGGATTATCGTTAAGACTGAAGGAAGTGTGTTCCCCGCGCCAGCGGGGATAAACCGCGTCACTACCGAGACCGAGACCGAGACCGAGAGTGTTCCCCGCGCCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN # Right flank : G # Questionable array : NO Score: 5.26 # Score Detail : 1:0, 2:3, 3:0, 4:0.40, 5:0, 6:0.25, 7:0.01, 8:0.6, 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 [0-13] 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 2 487-335 **** Predicted by CRISPRDetect 2.4 *** >NZ_MWVC01000083.1 Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 KO STM2896::STM0928 BCW_7514_1__paired__contig_83, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 486 29 100.0 33 ............................. CCAGTGGGCGTAGCCAGCTCATCGCTATTTTGC 424 29 100.0 32 ............................. CGTTGCGGATTATCGTTAAGACTGAAGGAAGT 363 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 3 29 100.0 33 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGTGTGTTCCCCGCGCCAGCGGGGATAAACCGTGAGCAACGACAGTAAATAATTTTTCGTGCTGGTGTTCCCCGCGCCAGCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCAGCGGGGATAAACCGCAACCAGGCTGGATCGTAACTCCTATCCCCTC # Right flank : GCGTCACTACCGAGACCGAGACCGAGACCGAGAGTGTTCCCCGCGCCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAGCGGGGATAAACCGTTACGTGTTTATTCATCTGTTGCATTAGATTCGTGTTCCCCGCGCCAGCGGGGATAAACCTGAGGCGTACAGGCTGTTAGATGAGAAATTACCGTGTTCCCCGCGCCAGCGGGGATAAACCGTGGATTATCTGTATTTTACGGAAGTGGGCGCGGTGTTCCCCGCGCCAGCGGGGATAAACCG # Questionable array : NO Score: 5.67 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.02, 8:0.4, 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 [26.7-33.3]%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], //