Array 1 485798-486679 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAAIFV010000002.1 Salmonella enterica subsp. salamae serovar II 1,4,12,27:e,n,x:e,n,x strain HZ259 NODE_2_length_745881_cov_64.880579, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 485798 29 100.0 32 ............................. CAATGGCTACCGCTGTTGACTCGCTTTTAACT 485859 29 100.0 32 ............................. ACATAAAAAACGAGAGGGCAACAATAACACAG 485920 29 100.0 32 ............................. GCCTCTAACACGGAGCAGAAATGATAAGTGAC 485981 29 100.0 32 ............................. AACACGTATTACACAATATTGCAGACTAGAAT 486042 29 100.0 32 ............................. CGAATACGGCGTCCGGCGTGTCTCCGGTGGTG 486103 29 100.0 32 ............................. CCAACTCCTCCCCTCGCTGCTGCGTGATTTTC 486164 29 100.0 32 ............................. CATCCGGCAATCTGGGAGCTATTCCAGATAAA 486225 29 96.6 32 ............T................ CGATCACCAGCTCGTTTGTCCCTGGCTGGCAG 486286 29 96.6 32 ............................T TGATACGTAGTTTGGCTGAATCTTCCAGAAAA 486347 29 100.0 32 ............................. GTTTAATCTGATATCCCCAGTACTAAAGGAGT 486408 29 100.0 32 ............................. TGAATGATAATTTCATATTAGTTCCTTAATCA 486469 29 100.0 32 ............................. CTATTATTTCCAAAATCGCCACGCTACAGCAC 486530 29 100.0 32 ............................. AAAGGACACCTATTAAGCGCTGAACTATCTAA 486591 29 96.6 32 ......A...................... GTGTGGTTCCAGGTCGTGCTCCGGGAAGGCCA 486652 28 86.2 0 .............C..T......-.G... | ========== ====== ====== ====== ============================= ================================ ================== 15 29 98.4 32 GTGTTCCCCGCGCTAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGTCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACTTGCATTGCGCGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTACATATCGCCTGATGCATTATCAATCTTACGGACGGCCTGTCGTTGCCGTCTGTGACTCATCTATTACCTTGCATTGTTTATTTTCTCTATACGAATTTCGATGAGTGTATAAAAGCACTGATAAATTTTCCCATAGCGAGGCATGGATCACGCTATTTTGGTAAATTAAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGTAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTACGTTGGTAGAATGTAGTGCTGATAAAAAGTAGTTTATAAACAACGATATACATTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCCGGTACAAACCTGTAAAGTAAAAAGGCCGCATTTTCTCAGGGAGGATTTTATACAGGAGAAAGCCATGGCGTTAACGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCATTAAGGGTCAGACCAGGATTAAGCCTGTTGGTCCAGGATGAGTCTACGTCGATCTTGTTCGACACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACTTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCAGATATTGCGCGCGAACGCTATGCGGCAATGACTTTTCTCGGTATTACCCGAAGAATAAAAAAATTGTCGCGTGAGATAGACTATTCACGCTACCGAATGGTGTACACGCGTGACCCTCTGCCGATTAG # Questionable array : NO Score: 6.18 # Score Detail : 1:0, 2:3, 3:0, 4:0.92, 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 : GTGTTCCCCGCGCTAGCGGGGATAAACCG # 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: NA [5,5] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCGCTAGCGGGGATAAACCG 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 [0-5] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [71.7-61.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.55,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 503252-504074 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAAIFV010000002.1 Salmonella enterica subsp. salamae serovar II 1,4,12,27:e,n,x:e,n,x strain HZ259 NODE_2_length_745881_cov_64.880579, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 503252 29 100.0 32 ............................. GCTAGCAAATACAGTGGTGATTTAAAACTTAC 503313 29 100.0 33 ............................. AAACCATTTGGCGAGTATTTCTCTCGCGAGGGC 503375 29 100.0 32 ............................. GCGAATGATCTTGGTATCTTGACAGGTGGCAG 503436 29 100.0 32 ............................. GGAGTTAGCTAGCTTTATTTCACTGATTCGCA 503497 29 100.0 32 ............................. TCCATTATCCCGTGTGTACGCCTGTAATTTGA 503558 29 100.0 32 ............................. CAAATCAATCGCAAAAACTTTGAGAAATATGG 503619 29 100.0 32 ............................. GCGATGAGCGCAATACCACAAAATTTTTCATA 503680 29 100.0 32 ............................. TCGATTTGCAATATTTTTTACCCAATTGGATC 503741 29 100.0 32 ............................. ATAGACACGAAGTGATTTCAACGTTTCCCCGT 503802 29 100.0 32 ............................. GACGCTATCGATGACATGCTGATTAACGATGC 503863 29 100.0 32 ............................. CGCGTTTAGATCTGTGGGCCCGCTGGATTGCT 503924 29 100.0 32 ............................. ATCGGGCGGGATATGTGCTGGATTCGTATTAG 503985 29 93.1 32 ...........A.T............... TTTTTCTGTCGCTGGTGGGCACTGACACGGCG 504046 29 89.7 0 ........A..................GC | ========== ====== ====== ====== ============================= ================================= ================== 14 29 98.8 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCTGAGCCGGAATCTCTGGGTGACAGCGGACATCGGGGGCATGGTTAATGAGCATGGTGGTGGTGGTGACAGAAAACGTACCGCCGCGCCTGCGAGGGCGGCTTGCCATATGGTTACTGGAGATTCGTGCAGGGGTTTATGTTGGCGATACATCGAAACGCATTCGAGAGATGATCTGGCAACAGATTACACAACTGGGCGGAGTCGGAAACGTAGTAATGGCTTGGGCAACAAATACTGAGTCTGGTTTTGAGTTTCAGACCTGGGGGGAAAACCGCCGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCCCTTGAAAATCAATGAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTAACGTTGGTAGTTTGTTGAGCAGTAAAAAAAATCTTTTAGAACAAATATATAGTTTTAGT # Right flank : CTTTTCACCAGCAGATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGTCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGACTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGACGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCGCTCATTC # Questionable array : NO Score: 6.20 # Score Detail : 1:0, 2:3, 3:0, 4:0.94, 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: F [0-5] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [75.0-48.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.92,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 490261-491265 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAAIFV010000001.1 Salmonella enterica subsp. salamae serovar II 1,4,12,27:e,n,x:e,n,x strain HZ259 NODE_1_length_1618781_cov_56.738788, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 490261 29 100.0 32 ............................. GATGCCCGATAATTCTATATATCGGGCATTGA 490322 29 100.0 32 ............................. GCGACAAATTAACTCAGGACATTGATGTCAAA 490383 29 96.6 32 ............................C TCTGTAATCGCAGTTCCCATACCTGCAACTGC 490444 29 100.0 32 ............................. TATGAGATAAGCAAATCTGACGCTTATGGATT 490505 29 100.0 32 ............................. ATGAAGATAGCTAGAAATCTGGTTTTGGGTGA 490566 29 100.0 31 ............................. ATTCCTACCCGCAGGGGGGGCAGGGCAATGC 490626 29 100.0 32 ............................. GGAAAATCGTTTACCGCTGGAGCAATCAGGGC 490687 29 100.0 33 ............................. TATTGTCATTGTGTTCAGGGAACAGGGCATAGC 490749 29 100.0 32 ............................. CGTGATTTCGAAGCCGGATTGATTACGTTAGA 490810 29 100.0 32 ............................. ACAAACGCACCGAATGTCAGGCTGACGCCTGA 490871 29 96.6 32 ........G.................... AGTACAGCGATCTCTATCTCCTCCGAATCCCC 490932 29 100.0 32 ............................. ACATATATACTCACCCCGTTTGCATTATCAGG 490993 29 100.0 32 ............................. ATACGAGCTTCTGCGCCATGAACCAGAGAGGG 491054 29 100.0 32 ............................. TTAGGGATCGGCGTGTCGGTGTATTTCTGCCC 491115 29 100.0 32 ............................. CTGGCAGATTTTGCCCCATTGATGCCCCATAA 491176 29 100.0 32 ............................. CAGGTTGGGTTTATCTACCGGGTAGATTCTAT 491237 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 17 29 99.6 32 GTGTTCCCCGCGAGAGCGGGGATAAACCG # Left flank : TGCTGTTCCCGTTCTCGCGTCTGGTGCATATCTGGAGCGTGCCGGTTGAGTATCTGACCCGTAAATATCAGCTTGTTCGCGCACGTCACTGATTGTGTGCTGATTATCTCAAGCCGCCGTGGGGCTGAGGCGTATTCAGCACTATAGCGGGAAAATAGCGCGGGCATGGAGATTGACTTCATGCCCGTTTTTTTGCATTTCCTATCGGGCTCATCCCGTATCTCACGACCTGCCGCAGACGCTCCCTTGAACTCTTTGCCGACGATATGCGCAAAATCTTACTCCCCCTTGATGTGATGATGTATTAATCTCCGAGTTTTCCGTCATATGACACTCGGCATAGTATGTTGGTAGATTTTAAGAGAGAATCATGGGTGTGGTTTTTTATTATATGAAATCAATTGGTTATATGCTCTTTAATAATGCGGTATTGTTATTTATGTGTTGGTAAGATGTTGCTGCATGAAAATGTTGTTTATAAACATAGGGATGGCACTAGA # Right flank : GACGGAGTTTGAAGACGAACATCAGGGGCTGGGGTGTTCCCCGCGCGAGCGCTGAGTTTGTGGGGTTAGTTCACTCCGGCAGGTTTTTTATGGCTGTTTGCCGGATGGCGGCATAAATGCCTTATCCGGCACCGATCTTATCTCGGAGTTGCATCGAACCTTCTCATCCTTCCCCGTACGGAGAGATATGAGGCAGTGTGCTTAATGGGGATAATATACGCGACGGAAGTGATGGTGGTGGGGGAAGGATTATTCGTCGCTCCGCTCCTCACCCTTCGGGTCGTTGCCTGCGGCAACGCTTTCTCGCTGCGCTCGAATCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGTACGGAGAGATATGAGGCAGTGTGCTTAACGGGGANNNNTCGTCGCTCCGCTCCTCACCCTTCGGGTCGTTGCCTGCGGCAACGCTTTCTCGCTGCGCTCGAATCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGTACGGAGAGATA # 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 : GTGTTCCCCGCGAGAGCGGGGATAAACCG # 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 [6,4] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCGAGAGCGGGGATAAACCG 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 [1-1] Score: 0/0.41 # AT richness analysis in flanks prediction: F [63.3-40.0]%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], //