Array 1 2978335-2976902 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP040601.1 Salmonella enterica subsp. enterica serovar Infantis strain TR01 Mutant chromosome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================== ================== 2978334 29 100.0 33 ............................. GTCGGAATACCACTATATAAAGCCCCTCAACCC 2978272 29 100.0 32 ............................. GACCAGGAACTCAAAAACTCTCGACTGAATAT 2978211 29 100.0 32 ............................. GTAGTCTTCATATGCAGCGACATCATTGCCGA 2978150 29 100.0 32 ............................. CATCGCATCGTTCGATTTTGTCACTCCTCCTC 2978089 29 100.0 33 ............................. ATACGCTTGTCGCCCAGGAAGGCAGATGCAGAC 2978027 29 100.0 32 ............................. TCGTTGGTGGCGTTCGTCACCTGGCTGTCGGT 2977966 29 100.0 32 ............................. AGGAGTCTGGATGTGGAGGTTTGCTCATCGCG 2977905 29 100.0 32 ............................. CGTGTTCGATGTAGGTTTCTTCCTGAAGGCGA 2977844 29 100.0 34 ............................. NNARCAYYRGTGCCCCGTCCACGGACACCGGATT 2977781 29 100.0 30 ............................. TCCAGCATTGACGCGAACCCTGCGCCCTMA 2977722 29 100.0 30 ............................. GCTCGACRGNCTGGAGGTTGAGGTGGTTGG 2977663 29 100.0 32 ............................. GCGWGATTATGGCAACTCAGAGTATATTACCC 2977602 29 100.0 32 ............................. CCGGGATCCGTCATCGGTCGTGGTTCACTGCA 2977541 29 100.0 32 ............................. AAAAATTTAGCTTTTGCACTCTCCCTTAGCGA 2977480 29 100.0 32 ............................. GAAGATATTGAAAGCGCCCAATCTTCCCAGCT 2977419 29 100.0 32 ............................. TGGAATGGATAGTTGAAAGGAAGCTGGCAGAA 2977358 29 100.0 32 ............................. GCTTGTGCGTGCTGACGTACTTGATCAGGGGG 2977297 29 100.0 32 ............................. TGTGACGGGATCGCGTTTATGTCGTGGCGCGG 2977236 29 100.0 32 ............................. TCTGATTTTTTGCTTTTTCTTTCATTGCATCT 2977175 29 100.0 32 ............................. TACATCACGGCAGCAGAAATGGAGACATATCG 2977114 29 100.0 32 ............................. TGAATTTCTTAATGGCTTTCAATMGTAACGAC 2977053 29 96.6 32 ............................N GTAGCGCAGGGACTGGCAACGGTGCCGGGCGT 2976992 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 2976931 29 93.1 0 A...........T................ | A [2976904] ========== ====== ====== ====== ============================= ================================== ================== 24 29 99.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTAAACCACCTCAGCCTGCGCCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTGCGTTTGGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTATGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACATCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCTCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGTAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 6.24 # Score Detail : 1:0, 2:3, 3:0, 4:0.98, 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 [4-0] 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 2995896-2995070 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP040601.1 Salmonella enterica subsp. enterica serovar Infantis strain TR01 Mutant chromosome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= =================================== ================== 2995895 29 100.0 33 ............................. TCCCGCCTGAACAAAATCCAGCGGCACGGCTCA 2995833 29 100.0 32 ............................. AGGATCGTTTCGTTACAGGTCAGCGCATCAAA 2995772 29 100.0 32 ............................. AAAATTCAGAGAAAGCGGCGCAGACGCTGTTC 2995711 29 100.0 32 ............................. GCGCGACGAAAATGGAATGTCTCCGCCGACAT 2995650 29 100.0 31 ............................. AGAATATTCAACTCCAGCGGGAAAAAGTGGT 2995590 29 100.0 32 ............................. CCTCATCGGGAGCCAACGCCGCGAGAATACGC 2995529 29 96.6 33 ............................C AGCACAATCATTATTGGCGGAATCAATATCGTT 2995467 29 100.0 33 ............................. CTCATAGCTCGGATCACCGCGATATACCGGATC 2995405 29 100.0 32 ............................. GGAGGACGCTACTATCGGATTCGCTCCGGGGA 2995344 29 100.0 35 ............................. GGCGGCAATATCCATCATATTTAGACCGGGACGCA 2995280 29 100.0 32 ............................. GGATCATCAATGTGGGAAGTTATCACAACGGA 2995219 29 100.0 32 ............................. CGAAATTAGTTGCCACCGCGTACAACTCAACA 2995158 29 96.6 32 ............T................ CCATACCATTTTATTAGATGAACTTTCATCAA 2995097 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= =================================== ================== 14 29 98.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CGCGCCAGCGGGGATAAACCGCCGCTTCGCGAAATCGGCCAGGTGGTATTAAGTGTTCCCCGCGCCAGCGGGGATAAACCGGACGTCCGATAATGCCGACGCGTGTTCCCCGCGCCAGCGGGGATAAACCGATTTANTGTATTTAACGTGTTCCCCGCGCCAGCGGGGATAAACCGTTTCCTGTAACATTCCGATATATAATTCTCCGCGTGTTCCCCGCGCCAGCGGGGATAAACCGGCCCAATNNNNNGAATACCACTATATAAAGCCCCTCAACCCGTGTTCCCCGCGCCAGCGGGGATAAACCGATTTTTACAAAAACTGGCCCCCTGAATTCATCGTGTTCCCCGCGCCAGCGGGGATAAACCGNNATTAAGTGTTCCCCGCGCCAGCGGGGATAAACCGGCTCCCGCGGGCGCTCCTGTTGGCCAGCATCAGTGTTCCCCGCGCCAGCGGGGATAAACCGNNGCTGAAATATTGCTATTTCCGAAGGGGCTGAT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGACCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGTCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATATGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCATGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGATATTACCCGCAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.17 # Score Detail : 1:0, 2:3, 3:0, 4:0.91, 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: F [63.3-43.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //