Array 1 290034-291649 **** Predicted by CRISPRDetect 2.4 *** >NZ_LMXO01000001.1 Salmonella enterica subsp. enterica serovar Infantis strain 120100 salm120100_contig_1, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 290034 29 100.0 33 ............................. TCGTACACCAGCGCTTTACCGGAGTGTCCGTGC 290096 29 100.0 32 ............................. ATCAAATATCAGATAACCCCCGTCGGCAAACC 290157 29 100.0 32 ............................. ATCACATTCCTGAAAAATGACTCCCTTAGCGA 290218 29 100.0 32 ............................. GAAGATATTGAAAGCGCCCAATCTTCCCAGCT 290279 29 100.0 32 ............................. TCCAGCATTGACGCGAACCCTGCGCCGCTGGC 290340 29 100.0 32 ............................. GCTGAAATATTGCTATTTCCGAAGGGGCTGAT 290401 29 100.0 32 ............................. TCCCGCCTGAACAAAATCGACCACGTTATTAA 290462 29 100.0 32 ............................. GCTCCCGCGGGCGCTCCTGTTGGCCAGCATCA 290523 29 100.0 32 ............................. CGTCCAATACGAGCTGAGTGCGCACGCCCTTA 290584 29 100.0 32 ............................. CAGATCGACCGCCTGGAGGTTGAGGTGGTTGG 290645 29 100.0 32 ............................. GCGTGGATTGATTCTGATCGCCGTGGGCGGGC 290706 29 100.0 32 ............................. GAAACAGAGATCGCGTCCGATAATGCCGACAT 290767 29 100.0 32 ............................. AGAATATTCAACTCCAGCGGGAAAAAGACGCA 290828 29 100.0 32 ............................. AACTTTCATCAAACTGGATCGAAGGGCCACTT 290889 29 100.0 32 ............................. CCGGTTTTAGCTCGCTGGAAACCTCGCTTTTG 290950 29 100.0 32 ............................. ACGCCGAGGGTGAATATTTAGACCGGGACGCA 291011 29 100.0 32 ............................. GGATCATCAATGTGGGAAGTTATCACAACGGA 291072 29 100.0 33 ............................. CGAAATTCAGCGTCTGGAATGCAAGGATTTTGT 291134 29 100.0 32 ............................. GCTATATCCCCGAATCGTGCGCTACGTGAAAA 291195 29 100.0 32 ............................. ACGAGGTCATTTTCAGCACTCGTCAGGCGCTG 291256 29 100.0 32 ............................. ATGCCCTGTTCGGCAAAATCCCGCCACGCTGG 291317 29 100.0 32 ............................. TAAAACCGGTGCTGGATTTTGATGAAGACGAA 291378 29 100.0 32 ............................. CCATTCAACATCGCACTTAAGAACTTGTGCCA 291439 29 100.0 32 ............................. CGATATTTATCCAGACTGTCGGACAGGGTGGT 291500 29 100.0 32 ............................. CCTCATCGGGAGCCAACGCCGCGAGAATACGC 291561 29 96.6 32 ............................C AGCACAATCATTATTAGATGAACTTTCATCAA 291622 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 27 29 99.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCGCGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAACAGTTTATAAACAACAATATACGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGACCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGTCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATATGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCATGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGATATTACCCGCAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # 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 [0-6] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [70.0-63.3]%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 307932-309829 **** Predicted by CRISPRDetect 2.4 *** >NZ_LMXO01000001.1 Salmonella enterica subsp. enterica serovar Infantis strain 120100 salm120100_contig_1, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 307932 29 100.0 32 ............................. GCGGAATACCACTATATAAAGCCCCTCAACCC 307993 29 100.0 32 ............................. ATTTTTACAAAAACTGGCCCCCTGAATTCATC 308054 29 100.0 32 ............................. TTGATTTTAATGGCGGGCGAATTGTATTTAAC 308115 29 100.0 33 ............................. TTTCCTGTAACATTCCGATATATAATTCTCCGC 308177 29 100.0 32 ............................. GCCCAATTGCCGGCGACGGTTTCCATGTCAGC 308238 29 100.0 32 ............................. TGGCGAAACAGGCCAGAGAACGCGAATTGCAG 308299 29 100.0 32 ............................. CGTGTTCGATGTAGGTTTCTTCCTGAAGGCGA 308360 29 100.0 32 ............................. CTACCAGGCCCGTTTGTCTCAACCATGACCAA 308421 29 100.0 32 ............................. TTGGCATGGCTGGCGACGTAGCGAACAAAATC 308482 29 100.0 32 ............................. CATAAATTACTCGATGCGTACCTGTGAAATCT 308543 29 100.0 32 ............................. ATACAGTAGCAAAATAAAAAGGCCGCGTGAGC 308604 29 100.0 32 ............................. CAATGCCGTTTTGCCCGAGTTTTCACCGCCGT 308665 29 100.0 32 ............................. CTCTATTGCCGGGGGTCGAGATGGCCGCCTGC 308726 29 100.0 32 ............................. GTGATCCGCGCCTATGACGCAATGGTAACGAC 308787 29 96.6 32 ............................T GTAGCGCAGGGACTGGCAACGGTGCCGGGCGT 308848 29 100.0 32 ............................. CAGGAGACGGCCAGCCGCACCGGTGGCGGTGC 308909 29 100.0 32 ............................. GGCGTTTTATTCGACCTGAAAAAATGGATCGT 308970 29 96.6 32 .............T............... ACATCTCGCGGACAATAGCGATTTCCACCGTC 309031 29 96.6 32 .............T............... CGTTTCGTTCATTTATTTAGTTTCCTGTTTCG 309092 29 93.1 29 .............T..............C CTTGTTAAATACAGGCGGCGGCGGGGTTG 309150 29 96.6 32 .............T............... AACGGCGACGGGATCGTTTTTTGTGGCGAAAA 309211 29 96.6 32 .............T............... CAGGATTGGATTAATGAAGACGGGTACGAAAT 309272 29 96.6 32 .............T............... AGATTGCAGAATTATATTTCACGCTGGCAGCA 309333 29 96.6 32 .............T............... CTGTTGTTATGCGTTGGATCGTAATAGTTAAC 309394 29 96.6 32 .............T............... CTTGGCAGGGCTGCGCCGCAATGGCAGCAACA 309455 29 96.6 32 .............T............... GTCTTATAAATTGGGCTGATAGTGCCGCTGAT 309516 29 100.0 32 ............................. TACCTGCCGGGACTGGAGTGCAGGTAACCCCA 309577 29 100.0 11 ............................. CGGCCAGCCAT Deletion [309617] 309617 29 72.4 32 T.AAA.AG...TG................ ACAGGGTATATGAGCTTATACGTCATGAACCA 309678 29 100.0 32 ............................. TCGTTGGTGGCGTTCGTCACCTGGCTGTCGGT 309739 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 309800 29 93.1 0 A...........T................ | A [309826] ========== ====== ====== ====== ============================= ================================= ================== 32 29 97.7 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTAAACCACCTCAGCCTGCGCCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACATCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCTCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGTAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.09 # Score Detail : 1:0, 2:3, 3:0, 4:0.89, 5:0, 6:0.25, 7:-0.05, 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 : GTGTTCCCCGCGCTAGCGGGGATAAACCG # 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 [0-11] 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], // Array 1 37-432 **** Predicted by CRISPRDetect 2.4 *** >NZ_LMXO01000317.1 Salmonella enterica subsp. enterica serovar Infantis strain 120100 salm120100_contig_294, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 37 29 100.0 32 ............................. CAGATCGACCGCCTGGAGGTTGAGGTGGTTGG 98 29 100.0 32 ............................. GCGTGGATTGATTCTGATCGCCGTGGGCGGGC 159 29 100.0 33 ............................. GAAACAGAGCTCGCGTCCGATAATGCCGAAATG 221 28 89.7 32 ..-......AG.................. AGAAAATTCAACGCCAGGGGGAAAAAGTCGCA 281 29 96.6 32 ......................G...... AGCTGTCATAAAACTGGATCGAAGGGCCCCTT 342 29 89.7 32 ....C...A.................A.. AGGGGCGATCCGCTGTCGACAAGGGCCGAAAA 403 29 72.4 0 AA..CT......TA......C.....A.. | A [424] ========== ====== ====== ====== ============================= ================================= ================== 7 29 92.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : ACCGCGTCCAATACGAGCTGAGTGCGCACGCCCTTAG # Right flank : TTTCATCAGCATATCAGGACGTTTTTTCCGACTTCGCCAGCTCTTTTACCAATGGCAGAATTACCCGAACTAC # Questionable array : NO Score: 6.06 # Score Detail : 1:0, 2:3, 3:0, 4:0.80, 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 [23.3-43.3]%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 1 434-38 **** Predicted by CRISPRDetect 2.4 *** >NZ_LMXO01000935.1 Salmonella enterica subsp. enterica serovar Infantis strain 120100 salm120100_contig_945, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 433 29 86.2 33 ....C.........G.....A....C... CAAAATTCAGCTTCTGAAAGGAAAGTATTTTGT 371 28 79.3 33 ....C......C..G.....A.-.....C GGCTATACCCCCGAATCGTGCGCTACGTAAAAA 310 29 82.8 32 ..T.C.........G.G........C... ACGAGGTCATTTTCACCACTCGTCGGGCGCTG 249 29 89.7 32 ..T.C...........G............ CCATTCAACATCGCACTTAAGAACTTGTGCCA 188 29 100.0 32 ............................. CGATATTTATCCAGACTGTCGGACAGGGTGGT 127 29 100.0 32 ............................. CCTCATCGGGAGCCAACGCCGCGAGAATACGC 66 29 96.6 0 ............................C | ========== ====== ====== ====== ============================= ================================= ================== 7 29 90.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCACAACGG # Right flank : CAGCACAATCATTATTAGATGAACTTTCATCAAGTGTT # Questionable array : NO Score: 5.36 # Score Detail : 1:0, 2:3, 3:0, 4:0.54, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.56, # 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 [0-17] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [43.3-5.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.68,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //