Array 1 88333-89948 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHFL01000027.1 Salmonella enterica subsp. enterica serovar Infantis strain CVM N44705 N44705_contig_28, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 88333 29 100.0 33 ............................. TCGTACACCAGCGCTTTACCGGAGTGTCCGTGC 88395 29 100.0 32 ............................. ATCAAATATCAGATAACCCCCGTCGGCAAACC 88456 29 100.0 32 ............................. ATCACATTCCTGAAAAATGACTCCCTTAGCGA 88517 29 100.0 32 ............................. GAAGATATTGAAAGCGCCCAATCTTCCCAGCT 88578 29 100.0 32 ............................. TCCAGCATTGACGCGAACCCTGCGCCGCTGGC 88639 29 100.0 32 ............................. GCTGAAATATTGCTATTTCCGAAGGGGCTGAT 88700 29 100.0 32 ............................. TCCCGCCTGAACAAAATCGACCACGTTATTAA 88761 29 96.6 32 ...........A................. GCTCCCGCGGGCGCTCCTGTTGGCCAGCATCA 88822 29 100.0 32 ............................. CGTCCAATACGAGCTGAGTGCGCACGCCCTTA 88883 29 100.0 32 ............................. CAGATCGACCGCCTGGAGGTTGAGGTGGTTGG 88944 29 100.0 32 ............................. GCGTGGATTGATTCTGATCGCCGTGGGCGGGC 89005 29 100.0 32 ............................. GAAACAGAGATCGCGTCCGATAATGCCGACAT 89066 29 100.0 32 ............................. AGAATATTCAACTCCAGCGGGAAAAAGACGCA 89127 29 100.0 32 ............................. AACTTTCATCAAACTGGATCGAAGGGCCACTT 89188 29 100.0 32 ............................. CCGGTTTTAGCTCGCTGGAAACCTCGCTTTTG 89249 29 100.0 32 ............................. ACGCCGAGGGTGAATATTTAGACCGGGACGCA 89310 29 100.0 32 ............................. GGATCATCAATGTGGGAAGTTATCACAACGGA 89371 29 100.0 33 ............................. CGAAATTCAGCGTCTGGAATGCAAGGATTTTGT 89433 29 100.0 32 ............................. GCTATATCCCCGAATCGTGCGCTACGTGAAAA 89494 29 100.0 32 ............................. ACGAGGTCATTTTCAGCACTCGTCAGGCGCTG 89555 29 100.0 32 ............................. ATGCCCTGTTCGGCAAAATCCCGCCACGCTGG 89616 29 100.0 32 ............................. TAAAACCGGTGCTGGATTTTGATGAAGACGAA 89677 29 100.0 32 ............................. CCATTCAACATCGCACTTAAGAACTTGTGCCA 89738 29 100.0 32 ............................. CGATATTTATCCAGACTGTCGGACAGGGTGGT 89799 29 100.0 32 ............................. CCTCATCGGGAGCCAACGCCGCGAGAATACGC 89860 29 96.6 32 ............................C AGCACAATCATTATTAGATGAACTTTCATCAA 89921 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 27 29 99.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCGCGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAACAGTTTATAAACAACAATATACGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGACCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGTCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATATGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCATGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGATATTACCCGCAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # 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 [1-6] 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 1 1067-1889 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHFL01000034.1 Salmonella enterica subsp. enterica serovar Infantis strain CVM N44705 N44705_contig_35, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1067 29 100.0 32 ............................. GCGGAATACCACTATATAAAGCCCCTCAACCC 1128 29 100.0 32 ............................. ATTTTTACAAAAACTGGCCCCCTGAATTCATC 1189 29 100.0 32 ............................. TTGATTTTAATGGCGGGCGAATTGTATTTAAC 1250 29 100.0 33 ............................. TTTCCTGTAACATTCCGATATATAATTCTCCGC 1312 29 100.0 32 ............................. GCCCAATTGCCGGCGACGGTTTCCATGTCAGC 1373 29 100.0 32 ............................. TGGCGAAACAGGCCAGAGAACGCGAATTGCAG 1434 29 100.0 32 ............................. CGTGTTCGATGTAGGTTTCTTCCTGAAGGCGA 1495 29 100.0 32 ............................. CTACCAGGCCCGTTTGTCTCAACCATGACCAA 1556 29 100.0 32 ............................. TTGGCATGGCTGGCGACGTAGCGAACAAAATC 1617 29 100.0 32 ............................. CATAAATTACTCGATGCGTACCTGTGAAATCT 1678 29 100.0 32 ............................. ATACAGTAGCAAAATAAAAAGGCCGCGTGAGC 1739 29 100.0 32 ............................. CAATGCCGTTTTGCCCGAGTTTTCACCGCCGT 1800 29 100.0 32 ............................. CTCTATTGCCGGGGGTCGAGATGGCCGCCTGC 1861 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 14 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTAAACCACCTCAGCCTGCGCCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GTGATCCGCGCCTATGACGCAATGGTAACGACGTGTTCCCCGCGCCAGCGGGGAT # Questionable array : NO Score: 6.26 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 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 [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: F [71.7-33.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.51,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 48-968 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHFL01000013.1 Salmonella enterica subsp. enterica serovar Infantis strain CVM N44705 N44705_contig_14, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 48 29 96.6 32 .............C............... GGCGTTTTATTCGACCTGAAAAAATGGATCGT 109 29 100.0 32 ............................. ACATCTCGCGGACAATAGCGATTTCCACCGTC 170 29 100.0 32 ............................. CGTTTCGTTCATTTATTTAGTTTCCTGTTTCG 231 29 96.6 29 ............................C CTTGTTAAATACAGGCGGCGGCGGGGTTG 289 29 100.0 32 ............................. AACGGCGACGGGATCGTTTTTTGTGGCGAAAA 350 29 100.0 32 ............................. CAGGATTGGATTAATGAAGACGGGTACGAAAT 411 29 100.0 32 ............................. AGATTGCAGAATTATATTTCACGCTGGCAGCA 472 29 100.0 32 ............................. CTGTTGTTATGCGTTGGATCGTAATAGTTAAC 533 29 100.0 32 ............................. CTTGGCAGGGCTGCGCCGCAATGGCAGCAACA 594 29 100.0 32 ............................. GTCTTATAAATTGGGCTGATAGTGCCGCTGAT 655 29 96.6 32 .............C............... TACCTGCCGGGACTGGAGTGCAGGTAACCCCA 716 29 96.6 9 .............C............... CGGCCAGCC Deletion [754] 754 29 79.3 32 A.T.AAA.A.................... ACAGGGTATATGAGCTTATACGTCATGAACCA GC [768] 817 29 96.6 32 .............C............... TCGTTGGTGGCGTTCGTCACCTGGCTGTCGGT 878 29 96.6 32 .............C............... AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 939 29 89.7 0 A...........TC............... | A [965] ========== ====== ====== ====== ============================= ================================ ================== 16 29 96.8 30 GTGTTCCCCGCGCTAGCGGGGATAAACCG # Left flank : AGCGGGGATAAACCGCAGGAGACGGCCAGCCGCACCGGTGGCGGTGCG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACATCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCTCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGTAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 5.79 # Score Detail : 1:0, 2:3, 3:0, 4:0.84, 5:0, 6:0.25, 7:-0.13, 8:1, 9:0.83, # 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 : GTGTTCCCCGCGCTAGCGGGGATAAACCG # Alternate repeat : GTGTTCCCCGCGCCAGCGGGGATAAACCG # 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 GTGTTCCCCGCGCTAGCGGGGATAAACCG 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 [2-13] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [21.7-48.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.28,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //