Array 1 162772-160813 **** Predicted by CRISPRDetect 2.4 *** >NZ_NJAM01000019.1 Salmonella enterica subsp. enterica serovar Infantis strain UZH-SAL-99-15 99_15_contig_19, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 162771 29 100.0 32 ............................. GCGGAATACCACTATATAAAGCCCCTCAACCC 162710 29 100.0 32 ............................. ATTTTTACAAAAACTGGCCCCCTGAATTCATC 162649 29 100.0 32 ............................. TTGATTTTAATGGCGGGCGAATTGTATTTAAC 162588 29 100.0 33 ............................. TTTCCTGTAACATTCCGATATATAATTCTCCGC 162526 29 100.0 32 ............................. GCCCAATTGCCGGCGACGGTTTCCATGTCAGC 162465 29 100.0 32 ............................. TGGCGAAACAGGCCAGAGAACGCGAATTGCAG 162404 29 100.0 32 ............................. CGTGTTCGATGTAGGTTTCTTCCTGAAGGCGA 162343 29 100.0 32 ............................. CTACCAGGCCCGTTTGTCTCAACCATGACCAA 162282 29 100.0 32 ............................. TTGGCATGGCTGGCGACGTAGCGAACAAAATC 162221 29 100.0 32 ............................. CATAAATTACTCGATGCGTACCTGTGAAATCT 162160 29 100.0 32 ............................. ATACAGTAGCAAAATAAAAAGGCCGCGTGAGC 162099 29 100.0 32 ............................. CAATGCCGTTTTGCCCGAGTTTTCACCGCCGT 162038 29 100.0 32 ............................. CTCTATTGCCGGGGGTCGAGATGGCCGCCTGC 161977 29 100.0 32 ............................. GTGATCCGCGCCTATGACGCAATGGTAACGAC 161916 29 96.6 32 ............................T GTAGCGCAGGGACTGGCAACGGTGCCGGGCGT 161855 29 100.0 32 ............................. CAGGAGACGGCCAGCCGCACCGGTGGCGGTGC 161794 29 100.0 32 ............................. GGCGTTTTATTCGACCTGAAAAAATGGATCGT 161733 29 96.6 32 .............T............... ACATCTCGCGGACAATAGCGATTTCCACCGTC 161672 29 96.6 32 .............T............... CGTTTCGTTCATTTATTTAGTTTCCTGTTTCG 161611 29 93.1 29 .............T..............C CTTGTTAAATACAGGCGGCGGCGGGGTTG 161553 29 96.6 32 .............T............... AACGGCGACGGGATCGTTTTTTGTGGCGAAAA 161492 29 96.6 32 .............T............... CAGGATTGGATTAATGAAGACGGGTACGAAAT 161431 29 96.6 32 .............T............... AGATTGCAGAATTATATTTCACGCTGGCAGCA 161370 29 96.6 32 .............T............... CTGTTGTTATGCGTTGGATCGTAATAGTTAAC 161309 29 96.6 32 .............T............... CTTGGCAGGGCTGCGCCGCAATGGCAGCAACA 161248 29 96.6 32 .............T............... GTCTTATAAATTGGGCTGATAGTGCCGCTGAT 161187 29 100.0 32 ............................. TACCTGCCGGGACTGGAGTGCAGGTAACCCCA 161126 29 100.0 11 ............................. CGGCCAGCCAT Deletion [161087] 161086 29 72.4 32 T.AAA.AG...TG................ ACAGGGTATATGAGCTTATACGTCATGAACCA 161025 29 100.0 32 ............................. GGCGATGCGGGCGCATTGTACGCGATGCAGAC 160964 29 100.0 32 ............................. TCGTTGGTGGCGTTCGTCACCTGGCTGTCGGT 160903 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 160842 29 93.1 0 A...........T................ | A [160815] ========== ====== ====== ====== ============================= ================================= ================== 33 29 97.8 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTAAACCACCTCAGCCTGCGCCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACATCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCTCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGTAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.10 # Score Detail : 1:0, 2:3, 3:0, 4:0.89, 5:0, 6:0.25, 7:-0.04, 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: 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 [11-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [50.0-71.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.92 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 179815-179054 **** Predicted by CRISPRDetect 2.4 *** >NZ_NJAM01000019.1 Salmonella enterica subsp. enterica serovar Infantis strain UZH-SAL-99-15 99_15_contig_19, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 179814 29 100.0 33 ............................. TCGTACACCAGCGCTTTACCGGAGTGTCCGTGC 179752 29 100.0 32 ............................. ATCAAATATCAGATAACCCCCGTCGGCAAACC 179691 29 100.0 32 ............................. ATCACATTCCTGAAAAATGACTCCCTTAGCGA 179630 29 100.0 32 ............................. GAAGATATTGAAAGCGCCCAATCTTCCCAGCT 179569 29 100.0 32 ............................. TCCAGCATTGACGCGAACCCTGCGCCGCTGGC 179508 29 100.0 32 ............................. GCTGAAATATTGCTATTTCCGAAGGGGCTGAT 179447 29 100.0 32 ............................. TCCCGCCTGAACAAAATCGACCACGTTATTAA 179386 29 100.0 32 ............................. GCTCCCGCGGGCGCTCCTGTTGGCCAGCATCA 179325 29 100.0 32 ............................. CGTCCAATACGAGCTGAGTGCGCACGCCCTTA 179264 29 100.0 32 ............................. CAGATCGACCGCCTGGAGGTTGAGGTGGTTGG 179203 29 100.0 32 ............................. CCTCATCGGGAGCCAACGCCGCGAGAATACGC 179142 29 96.6 32 ............................C AGCACAATCATTATTAGATGAACTTTCATCAA 179081 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 13 29 98.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCGCGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAACAGTTTATAAACAACAATATACGTTTAGT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGACCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGTCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATATGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCATGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGATATTACCCGCAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.18 # Score Detail : 1:0, 2:3, 3:0, 4:0.92, 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 [6-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [63.3-70.0]%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], //