Array 1 108564-108141 **** Predicted by CRISPRDetect 2.4 *** >NZ_CASQ01000036.1 Salmonella enterica subsp. enterica serovar Agona str. 27.O.98, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= =========================================================== ================== 108563 29 93.1 32 TG........................... GCTAAAACGGCGCTTGAGAACAGTATCAATAT 108502 29 100.0 59 ............................. GATCATCACCCAGGTGGAACTGGGAACGCAACTGAGCGAACTCAGTACGCTGGATTCAC 108414 29 96.6 32 T............................ TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 108353 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 108292 29 100.0 32 ............................. GCAGAAACAGAAACCGGATATGAGCCATCCAT 108231 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGGCAAGGGCTGAAAA 108170 29 93.1 0 A...........T................ | A [108143] ========== ====== ====== ====== ============================= =========================================================== ================== 7 29 97.1 37 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : ACAGGAGATACCACGTGTTCCCCGCGCCAGCGGGGTGATTTTAATGGCAAGGTCGACAGGAGATACCACGTGTTCCCCGCGCCAGCGGGGATAAACCGGATCATCACCCAGGCATTTTCTGGAATATGAAGTGTTCCCCGCGCCAGCGGGGATAAACCGAATCCCGATGATCATGAATATTTCTGGCGCCAGTGTTCCCCGANNNNNNNNNTGGAACTGGGAACGCAACTGAGCGAACTCAGTACGCTGGATTCACTGGTTCCCCGCGCCAGCGGGGATAAACCGAATCCCGATGATCATGAATATTTCTGGCGCCAGTGTTCCCCGCGCCAGCGGGGATAAACANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGGAACTGGGAACGCAACTGAGCGAACTCAGTACGCTGGATTCAC # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACACGTTGCTGGTATCCGTCTTTTTTACCCAGGTTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCAGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 5.74 # Score Detail : 1:0, 2:3, 3:0, 4:0.85, 5:0, 6:0.25, 7:-0.21, 8:1, 9:0.85, # 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 [-8.90,-10.50] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [2-2] Score: 0/0.41 # AT richness analysis in flanks prediction: F [50.0-36.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 109856-108905 **** Predicted by CRISPRDetect 2.4 *** >NZ_CASQ01000036.1 Salmonella enterica subsp. enterica serovar Agona str. 27.O.98, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ============================================= ================== 109855 29 100.0 32 ............................. GAGGCGCTGGCCGCGCTGGCCGCAGAAAAATT 109794 29 100.0 32 ............................. GTAGCCTTCAGACACTTTAGCCAGGTTCCCTA 109733 29 100.0 45 ............................. AGCGAAAAAAAAGACGACGAACTCGTCACCTTTCAATATCTTCCA 109659 29 100.0 32 ............................. CTGGGAAGATTGGGCGCTTTCAATATCTTCCA 109598 29 100.0 32 ............................. CTGGGAAGATTGGGCGCTTTCAATATCTTCCA 109537 29 100.0 32 ............................. CGCACCTGCCGGGACATGACCCTGCCGGAGCT 109476 29 100.0 32 ............................. GTCATTTTCTTGTTAATGGCGCTTGCATTAAC 109415 29 100.0 32 ............................. CTGTGTTGTCTGTGCATAACGGTGTAACAGAG 109354 29 100.0 32 ............................. CTGGGAAGATTTGGCGCTTTCAATATCTTCCA 109293 29 100.0 32 ............................. AAAAATAGTCCTGAACGATAGCCCGCGCGGTC 109232 29 100.0 32 ............................. CAGGAGTGGCTGGAGACTGTCGTCAAGCCTGA 109171 29 100.0 32 ............................. TTTTATATCGACACTAAAACCCGCCAGTTATA 109110 29 100.0 32 ............................. ATTTTAACGGCAAGGTCGACAGGAGATACCAC 109049 28 79.3 27 .....................-.G.TTTT AATGGCAAGGTCGACAGGAGATACCAC 108994 29 100.0 32 ............................. GATCATCACCCAGGCATTTTCTGGAATATGAA 108933 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ============================================= ================== 16 29 98.7 33 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTGAACCCCCTCAGCCTGCGTCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCTTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTAGGTAGTAAAAAAGGGCTTTTTGAACAAATATATAGTTTTAGT # Right flank : AATCCCGATGATCATGAATATTTCTGGCGCCAGTGTTCCCCGANNNNNNNNNTGGAACTGGGAACGCAACTGAGCGAACTCAGTACGCTGGATTCACTGGTTCCCCGCGCCAGCGGGGATAAACCGAATCCCGATGATCATGAATATTTCTGGCGCCAGTGTTCCCCGCGCCAGCGGGGATAAACANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGGAACTGGGAACGCAACTGAGCGAACTCAGTACGCTGGATTCACTGGTTCCCCGCGCCAGCGGGGATAAACCGGCTAAAACGGCGCTTGAGAACAGTATCAATATGTGTTCCCCGCGCCAGCGGGGATAAACCGGATCATCACCCAGGTGGAACTGGGAACGCAACTGAGCGAACTCAGTACGCTGGATTCACTTGTTCCCCG # Questionable array : NO Score: 6.19 # Score Detail : 1:0, 2:3, 3:0, 4:0.94, 5:0, 6:0.25, 7:0.00, 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: R [43.3-70.0]%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 3 126626-126142 **** Predicted by CRISPRDetect 2.4 *** >NZ_CASQ01000036.1 Salmonella enterica subsp. enterica serovar Agona str. 27.O.98, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 126625 29 100.0 32 ............................. GCATCCCGGACAACAGGATCATCCCATTTATT 126564 29 100.0 3 ............................. GCA Deletion [126533] 126531 25 72.4 32 ----....G..AAT............... CCAACTGGCCTAAAGCAAATCCCGGCTTAGGC 126474 29 100.0 32 ............................. CCAACTGGCCTAAAGCAAATCCCGGCTTAGGC 126413 29 100.0 32 ............................. GTTAAGGGGGAGTGAGATGCAGATAAAAACGA 126352 29 100.0 32 ............................. TTTCCAAAAATCACGTCACCCGTTGTGATCTG 126291 29 100.0 32 ............................. AAGGTTAGCGTTGTCATTGATCTGGTCGGCAA 126230 29 96.6 32 ............T................ AGCGGCTAAACCTGCCGGTTATCGCTGAGCAG 126169 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================ ================== 9 29 94.6 28 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATGATATACGTTTAGTGTGTTCCCCGCGCCAGCGGGGATAAACCGGCGACTGGCTGGTCAGCACGCCGTTAGTCGCCGTGTTCCCCGCGCCAGCGGGGATAAACCGAAATTGTCTGATAGATTGGCAAAAGCGATGGAGTGTTCCCCGCGCCAGCGGGGATAAACCGGTTAAGGGGGAGTGAGATGCAGATAAAAACGAGTGTTCCCCGCGCCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAGCGGGGATAAACCGCCAACTGGCCTAAAGCAAATCCCGGCTTAGGC # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 5.63 # Score Detail : 1:0, 2:3, 3:0, 4:0.73, 5:0, 6:0.25, 7:-0.35, 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 [6-5] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [63.3-35.0]%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], // Array 4 126940-126789 **** Predicted by CRISPRDetect 2.4 *** >NZ_CASQ01000036.1 Salmonella enterica subsp. enterica serovar Agona str. 27.O.98, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 126939 29 100.0 32 ............................. GCGACTGGCTGGTCAGCACGCCGTTAGTCGCC 126878 29 100.0 32 ............................. AAATTGTCTGATAGATTGGCAAAAGCGATGGA 126817 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 3 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATGATATACGTTTAGT # Right flank : GTTAAGGGGGAGTGAGATGCAGATAAAAACGAGTGTTCCCCGCGCCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAGCGGGGATAAACCGCCAACTGGCCTAAAGCAAATCCCGGCTTAGGCGTGTTCCCCGCGCCAGCGGGGATAAACCGGCATCCCGGACAACAGGATCATCCCATTTATTGTGTTCCCCGCGCCAGCGGGGATAAACCGGCATCCCGGACAATAGCGGGGATAAACCGCCAACTGGCCTAAAGCAAATCCCGGCTTAGGCGTGTTCCCCGCGCCAGCGGGGATAAACCGCCAACTGGCCTAAAGCAAATCCCGGCTTAGGCGTGTTCCCCGCGCCAGCGGGGATAAACCGGTTAAGGGGGAGTGAGATGCAGATAAAAACGAGTGTTCCCCGCGCCAGCGGGGATAAACCGTTTCCAAAAATCACGTCACCCGTTGTGATCTGGTG # Questionable array : NO Score: 5.67 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.02, 8:0.4, 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: R [38.3-70.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.51 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //