Array 1 272126-272930 **** Predicted by CRISPRDetect 2.4 *** >NZ_CARD01000001.1 Salmonella enterica subsp. enterica serovar Agona str. 71.E.05, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 272126 29 100.0 32 ............................. AAATTGTCTGATAGATTGGCAAAAGCGATGGA 272187 29 72.4 16 ................ACT..C.GGT.A. CACGCCGTTAGTCGCC Deletion [272232] 272232 29 100.0 32 ............................. AAATTGTCTGATAGATTGGCAAAAGCGATGGA 272293 29 100.0 32 ............................. GCATCCCGGACAACAGGATCATCCCATTTATT 272354 29 100.0 32 ............................. CCAACTGGCCTAAAGCAAATCCCGGCTTAGGC 272415 29 100.0 32 ............................. GTTAAGGGGGAGTGAGATGCAGATAAAAACGA 272476 29 100.0 32 ............................. CGGGCGCAATTGTTACCGCCTGCCCGACGCTT 272537 29 100.0 32 ............................. TTATTGTCTGATAGATTGGCAAAAGCGATGGA 272598 29 100.0 32 ............................. GCATCCCGGACAACAGGATCATCCCATTTATT 272659 29 100.0 32 ............................. CCAACTGGCCTAAAGCAAATCCCGGCTTAGGC 272720 29 100.0 32 ............................. TTTCCAAAAATCACGTCACCCGTTGTGATCTG 272781 29 100.0 32 ............................. AAGGTTAGCGTTGTCATTGATCTGGTCGGCAA 272842 29 96.6 32 ............T................ AGCGGCTAAACCTGCCGGTTATCGCTGAGCAG 272903 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 14 29 96.6 31 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATGATATACGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 5.99 # Score Detail : 1:0, 2:3, 3:0, 4:0.83, 5:0, 6:0.25, 7:-0.09, 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: F [5,4] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.50,-12.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [8-6] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [70.0-63.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0.41 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 289216-289609 **** Predicted by CRISPRDetect 2.4 *** >NZ_CARD01000001.1 Salmonella enterica subsp. enterica serovar Agona str. 71.E.05, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 289216 29 100.0 32 ............................. GAGGCGCTGGCCGCGCTGGCCGCAGAAAAATT 289277 29 100.0 32 ............................. GTAGCCTTCAGACACTTTAGCCAGGTTCCCTA 289338 29 100.0 32 ............................. AGCGAAAAAAAAGACGACGAACTCGTCACAAC 289399 29 100.0 32 ............................. CGCACCTGCCGGGACATGACCCTGCCGGAGCT 289460 29 100.0 31 ............................. GTTGTGGTCTGTGCATAACGGTGTAACAGAG 289520 29 100.0 32 ............................. CTGGGAAGATTGGGCGCTTTCAATAACTTCCA 289581 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 7 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTGAACCCCCTCAGCCTGCGTCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTCGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCTTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTAGGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GGCTAAAACGGCGCTTGAGAACAGTATCAATATGTGTTCCCCGCGCCAGANNNNNNCTGGAGGGTAGAAACCGCGTGATTGCTTGGAGCCTTCCACAAAGCCGGATTGTTCCCCGCGCCAGCGGGGATAAACCGATTTTAACGGCAAGGTCGACAGGAGATACCACGTGTTCCCCGCGCCAGCGGGGATAAACCGAAAAATAGTCCTGAACGATAGCCCGCGCGGTCGTGTTCCCCGCGCCAGCGGGGATAAACCGCAGGAGTGGCTGGAGACTGTCGTCAAGCCTGAGTGTTCCCCGCGCCAGCGGGGATAAACCGTTTTATAACGACACTAAAACCCGCCAGTTATAGTGTTCCCCGCGCCAGCGGGGATAAACCGATTTTAACGGCAAGGTCGACAGGAGATACCACGTGTTCCCCGCGCCAGCGGGGATAAACCGGATCATCACCCAGGCATTTTCTGGAATATGAAGTGTTCCCCGCGCCAGCGGGGATAAACCG # 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: F [5,4] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.50,-12.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: F [70.0-43.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.51,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 3 289714-290917 **** Predicted by CRISPRDetect 2.4 *** >NZ_CARD01000001.1 Salmonella enterica subsp. enterica serovar Agona str. 71.E.05, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================================ ================== 289714 29 96.6 32 T............................ ATTTTAACGGCAAGGTCGACAGGAGATACCAC 289775 29 100.0 32 ............................. AAAAATAGTCCTGAACGATAGCCCGCGCGGTC 289836 29 100.0 32 ............................. CAGGAGTGGCTGGAGACTGTCGTCAAGCCTGA 289897 29 100.0 32 ............................. TTTTATAACGACACTAAAACCCGCCAGTTATA 289958 29 100.0 32 ............................. ATTTTAACGGCAAGGTCGACAGGAGATACCAC 290019 29 100.0 32 ............................. GATCATCACCCAGGCATTTTCTGGAATATGAA 290080 29 100.0 48 ............................. AGCGAAAAAAAAGACGACGAACTCGTCACAACGTGTTCCCCGCGCCAG 290157 29 93.1 32 CA........................... ATTTTAACGGCAAGGTCGACAGGAGATACCAC 290218 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 290279 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 290340 29 100.0 32 ............................. AATCCCGATGATCATGAATATTTCTGGCGCCA 290401 29 100.0 32 ............................. AAGGTTAGCGTTGTCATTGATCTGGTCGGCAA 290462 29 89.7 46 ............T............T..A GCGGGGATAAACCGGGTTAACCAGGGGTTTTTCCCCACTATTTCGC 290537 29 100.0 32 ............................. GCTAAAACGGCGCTTGAGAACAGTATCAATAT 290598 29 100.0 32 ............................. TGACGAGGTGCGAGCGATGGTATCAAGGCCTA 290659 29 96.6 32 .....T....................... GGTTAACCAGGGGTTTTTCCCCACTATTTCGC 290720 29 100.0 32 ............................. ATTTTAACGGCAAGGTCGACAGGAGATACCAC 290781 29 86.2 16 ..................AAC.G...... GATATGAGCCATCCAT A [290799] Deletion [290826] 290827 29 100.0 32 ............................. AGGGGCGTTCCGCAGTCGGCAAGGGCTGAAAA 290888 29 93.1 0 A...........T................ | A [290914] ========== ====== ====== ====== ============================= ================================================ ================== 20 29 97.6 33 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGTGTTCCCCGCGCCAGCGGGGATAAACCGGAGGCGCTGGCCGCGCTGGCCGCAGAAAAATTGTGTTCCCCGCGCCAGCGGGGATAAACCGGTAGCCTTCAGACACTTTAGCCAGGTTCCCTAGTGTTCCCCGCGCCAGCGGGGATAAACCGAGCGAAAAAAAAGACGACGAACTCGTCACAACGTGTTCCCCGCGCCAGCGGGGATAAACCGCGCACCTGCCGGGACATGACCCTGCCGGAGCTGTGTTCCCCGCGCCAGCGGGGATAAACCGGTTGTGGTCTGTGCATAACGGTGTAACAGAGGTGTTCCCCGCGCCAGCGGGGATAAACCGCTGGGAAGATTGGGCGCTTTCAATAACTTCCAGTGTTCCCCGCGCCAGCGGGGATAAACCGGCTAAAACGGCGCTTGAGAACAGTATCAATATGTGTTCCCCGCGCCAGANNNNNNCTGGAGGGTAGAAACCGCGTGATTGCTTGGAGCCTTCCACAAAGCCGGA # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACACGTTGCTGGTATCCGTCTTTTTTACCCAGGTTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.07 # Score Detail : 1:0, 2:3, 3:0, 4:0.88, 5:0, 6:0.25, 7:-0.06, 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: F [5,4] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-13.50,-12.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [1-21] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [38.3-48.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0.27 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //