Array 1 191337-191063 **** Predicted by CRISPRDetect 2.4 *** >NZ_CATY01000002.1 Salmonella enterica subsp. enterica serovar Agona str. 16.H.08, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 191336 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 191275 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 191214 29 100.0 32 ............................. GCAGAAACAGAAACCGGATATGAGCCATCCAT 191153 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGGCAAGGGCTGAAAA 191092 29 93.1 0 A...........T................ | A [191065] ========== ====== ====== ====== ============================= ================================ ================== 5 29 97.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AGATACCACGTGTTCCCCGCGCCAGCGGGGATAAACCGGATCATCACCCAGGCATTTTCTGGAATATGAAGTGTTCCCCGCGCCAGCGGGGATAAACCGAATCCCGATGATCATGAATATTTCTGGCGCCAGTGTTCCCCGCGCCAGCGGGGATAAACCGGCTAAAACGGCGCTTGAGAACAGTATCAATATGTGTTCCCAGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTCCCCACTATTTCGCGTGTTCCCCGCGCCAGCGGGGATAAACCGGCTAAAACGGCGCTTGAGAACAGTATCAATATGTGTTCCCCGCGCCAGCGGGGATAAACCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTCCCCACTATTTCGC # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACACGTTGCTGGTATCCGTCTTTTTTACCCAGGTTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCAGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # Questionable array : NO Score: 5.96 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 5:0, 6:0.25, 7:0.01, 8:0.8, 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 [3-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [50.0-15.0]%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 2 192499-191677 **** Predicted by CRISPRDetect 2.4 *** >NZ_CATY01000002.1 Salmonella enterica subsp. enterica serovar Agona str. 16.H.08, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 192498 29 100.0 32 ............................. GAGGCGCTGGCCGCGCTGGCCGCAGAAAAATT 192437 29 100.0 32 ............................. GTAGCCTTCAGACACTTTAGCCAGGTTCCCTA 192376 29 100.0 32 ............................. AGCGAAAATAAAGACGACGAACTCGTCACAAC 192315 29 100.0 32 ............................. CGCACCTGCCGGGACATGACCCTGCCGGAGCT 192254 29 100.0 32 ............................. GTCATTTTCTTGTTAATGGCGCTTGCATTAAC 192193 29 100.0 32 ............................. CTGTGTGGTCTGTGCATAACGGTGTAACAGAG 192132 29 100.0 32 ............................. CTGGGAAGATTGGGCGCTTTCAATATCTTCCA 192071 29 100.0 32 ............................. AAAAATAGTCCTGAACGATAGCCCGCGCGGTC 192010 29 100.0 32 ............................. CAGGAGTGGTTGGAGACTGTCGTCAAGCCTGA 191949 29 100.0 32 ............................. TTTTATAACGACACTAAAACCCGCCAGTTATA 191888 29 100.0 32 ............................. ATTTTAACGGCAAGGTCGACAGGAGATACCAC 191827 29 100.0 32 ............................. GATCATCACCCAGGCATTTTCTGGAATATGAA 191766 29 100.0 32 ............................. AATCCCGATGATCATGAATATTTCTGGCGCCA 191705 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 14 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTGAACCCCCTCAGCCTGCGTCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCTTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTAGGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GCTAAAACGGCGCTTGAGAACAGTATCAATATGTGTTCCCAGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTCCCCACTATTTCGCGTGTTCCCCGCGCCAGCGGGGATAAACCGGCTAAAACGGCGCTTGAGAACAGTATCAATATGTGTTCCCCGCGCCAGCGGGGATAAACCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTCCCCACTATTTCGCGTGTTCCCCGCGCCAGCGGGGATAAACCGTGACGAGGTGCGAGCGATGGTATCAAGGCCTAGTGTTTCCCGCGCCAGCGGGGATAAACCGGGTTAACCAGGGGTTTTTCCCCACTATTTCGCGTGTTCCCCGCGCCAGCGGGGATAAACCGGCAGAAACA # 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: 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 [40.0-70.0]%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], // Array 3 209639-208627 **** Predicted by CRISPRDetect 2.4 *** >NZ_CATY01000002.1 Salmonella enterica subsp. enterica serovar Agona str. 16.H.08, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ============================================================================================================================================================================================= ================== 209638 29 100.0 0 ............................. - Deletion [209610] 209609 25 69.0 32 ----G.GA.TT.................. GCATCCCGGACAACAGGATCATCCCATTTATT 209552 29 100.0 32 ............................. GCGACTGGCTGGTCAGCACGCCGTTAGTCGCC 209491 29 100.0 32 ............................. AAATTGTTTGATAGATTGGCAAAAGCGATGGA 209430 29 100.0 32 ............................. GCATCCCGGACAACAGGATCATCCCATTTATT 209369 29 100.0 32 ............................. CCAACTGGCCTAAAGCAAATCCCGGCTTAGGC 209308 29 100.0 86 ............................. GNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 209193 29 55.2 32 NNNNNNNNNNNNT................ GCGACTGGCTGGTCAGCACGCCGTTAGTAGCC 209132 29 100.0 32 ............................. GTTAAGGGGGAGTGAGATGCAGATAAAAACGA 209071 29 100.0 31 ............................. TTCCAAAAATCACGTCACCCGTTGTGATCTG 209010 29 93.1 0 ...........................TC - Deletion [208982] 208983 17 55.2 32 ------------T................ GCGACTGGCTGGTCAGCACGCCGTTAGTAGCC 208934 29 100.0 32 ............................. AAGGTTAGCGTTGTCATTGATCTGGTCGGCAA 208873 29 96.6 189 ............T................ AGCGGCTAAACCTGCCGGTTATCGCTGAGCAGGTGTTCCCCGCGCCAACAAGGATAGCCGTTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAA 208655 29 55.2 0 A.CA.AAGG.A..TG.A.C.......T.. | ========== ====== ====== ====== ============================= ============================================================================================================================================================================================= ================== 15 29 88.3 42 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATGATATACGTTTAGT # Right flank : TTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGCGAAAACTTTATCTGGTCAGGGGAAATACCAGTGGTCGCGCCTGAAGCCTACGGCATTTTTGGCGGCCACGATGCGGAGCCGGACTCTATTTTGGATGAGGGCGTACTGATTTACCAATCGACAAAAGGATTAGTCATCATTACGGGATGCGGGCATCG # Questionable array : NO Score: 3.88 # Score Detail : 1:0, 2:3, 3:0, 4:0.41, 5:0, 6:0.25, 7:-1.78, 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 [-8.90,-10.50] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [17-6] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [46.7-68.3]%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], //