Array 1 2978650-2977217 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP040600.1 Salmonella enterica subsp. enterica serovar Infantis strain TR01 chromosome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================== ================== 2978649 29 100.0 33 ............................. GTCGGAATACCACTATATAAAGCCCCTCAACCC 2978587 29 100.0 32 ............................. GACCAGGAACTCAAAAACTCTCGACTGAATAT 2978526 29 100.0 32 ............................. GTAGTCTTCATATGCAGCGACATCATTGCCGA 2978465 29 100.0 32 ............................. CATCGCATCGTTCGATTTTGTCACTCCTCCTC 2978404 29 100.0 33 ............................. ATACGCTTGTCGCCCAGGAAGGCAGATGCAGAC 2978342 29 100.0 32 ............................. TCGTTGGTGGCGTTCGTCACCTGGCTGTCGGT 2978281 29 100.0 32 ............................. AGGAGTCTGGATGTGGAGGTTTGCTCATCGCG 2978220 29 100.0 32 ............................. CGTGTTCGATGTAGGTTTCTTCCTGAAGGCGA 2978159 29 100.0 34 ............................. NNARCAYYRGTGCCCCGTCCACGGACACCGGATT 2978096 29 100.0 30 ............................. TCCAGCATTGACGCGAACCCTGCGCCCTMA 2978037 29 100.0 30 ............................. GCTCGACRGNCTGGAGGTTGAGGTGGTTGG 2977978 29 100.0 32 ............................. GCGWGATTATGGCAACTCAGAGTATATTACCC 2977917 29 100.0 32 ............................. CCGGGATCCGTCATCGGTCGTGGTTCACTGCA 2977856 29 100.0 32 ............................. AAAAATTTAGCTTTTGCACTCTCCCTTAGCGA 2977795 29 100.0 32 ............................. GAAGATATTGAAAGCGCCCAATCTTCCCAGCT 2977734 29 100.0 32 ............................. TGGAATGGATAGTTGAAAGGAAGCTGGCAGAA 2977673 29 100.0 32 ............................. GCTTGTGCGTGCTGACGTACTTGATCAGGGGG 2977612 29 100.0 32 ............................. TGTGACGGGATCGCGTTTATGTCGTGGCGCGG 2977551 29 100.0 32 ............................. TCTGATTTTTTGCTTTTTCTTTCATTGCATCT 2977490 29 100.0 32 ............................. TACATCACGGCAGCAGAAATGGAGACATATCG 2977429 29 100.0 32 ............................. TGAATTTCTTAATGGCTTTCAATMGTAACGAC 2977368 29 96.6 32 ............................N GTAGCGCAGGGACTGGCAACGGTGCCGGGCGT 2977307 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGACAAGGGCTGAAAA 2977246 29 93.1 0 A...........T................ | A [2977219] ========== ====== ====== ====== ============================= ================================== ================== 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 2996211-2995385 **** Predicted by CRISPRDetect 2.4 *** >NZ_CP040600.1 Salmonella enterica subsp. enterica serovar Infantis strain TR01 chromosome Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= =================================== ================== 2996210 29 100.0 33 ............................. TCCCGCCTGAACAAAATCCAGCGGCACGGCTCA 2996148 29 100.0 32 ............................. AGGATCGTTTCGTTACAGGTCAGCGCATCAAA 2996087 29 100.0 32 ............................. AAAATTCAGAGAAAGCGGCGCAGACGCTGTTC 2996026 29 100.0 32 ............................. GCGCGACGAAAATGGAATGTCTCCGCCGACAT 2995965 29 100.0 31 ............................. AGAATATTCAACTCCAGCGGGAAAAAGTGGT 2995905 29 100.0 32 ............................. CCTCATCGGGAGCCAACGCCGCGAGAATACGC 2995844 29 96.6 33 ............................C AGCACAATCATTATTGGCGGAATCAATATCGTT 2995782 29 100.0 33 ............................. CTCATAGCTCGGATCACCGCGATATACCGGATC 2995720 29 100.0 32 ............................. GGAGGACGCTACTATCGGATTCGCTCCGGGGA 2995659 29 100.0 35 ............................. GGCGGCAATATCCATCATATTTAGACCGGGACGCA 2995595 29 100.0 32 ............................. GGATCATCAATGTGGGAAGTTATCACAACGGA 2995534 29 100.0 32 ............................. CGAAATTAGTTGCCACCGCGTACAACTCAACA 2995473 29 96.6 32 ............T................ CCATACCATTTTATTAGATGAACTTTCATCAA 2995412 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], //