Array 1 490266-491453 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAAHTQ010000002.1 Salmonella enterica subsp. salamae serovar II 1,4,12,27:e,n,x:e,n,x strain HAZEL-228 NODE_2_length_701080_cov_26.423098, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 490266 29 96.6 32 ...C......................... GATGCCCGATAATTCTATATATCGGGCATTGA 490327 29 100.0 32 ............................. GAGCACGCCGGTAGCGCTTACAGCAATATCAT 490388 29 100.0 32 ............................. TACAAACTCGAACCCATCCTCGTAAATTTTGC 490449 29 100.0 32 ............................. ATTCATGTCATCAGATGTCGCCATTTCATCAG 490510 29 100.0 32 ............................. GCGACAAATTAACTCAGGACATTGATGTCAAA 490571 29 96.6 32 ............................C TCTGTAATCGCAGTTCCCATACCTGCAACTGC 490632 29 100.0 32 ............................. TATGAGATAAGCAAATCTGACGCTTATGGATT 490693 29 100.0 32 ............................. ATGAAGATAGCTAGAAATCTGGTTTTGGGTGA 490754 29 100.0 31 ............................. ATTCCTACCCGCAGGGGGGGCAGGGCAATGC 490814 29 100.0 32 ............................. GGAAAATCGTTTACCGCTGGAGCAATCAGGGC 490875 29 100.0 33 ............................. TATTGTCATTGTGTTCAGGGAACAGGGCATAGC 490937 29 100.0 32 ............................. CGTGATTTCGAAGCCGGATTGATTACGTTAGA 490998 29 100.0 32 ............................. ACAAACGCACCGAATGTCAGGCTGACGCCTGA 491059 29 96.6 32 ........G.................... AGTACAGCGATCTCTATCTCCTCCGAATCCCC 491120 29 100.0 32 ............................. ACATATATACTCACCCCGTTTGCATTATCAGG 491181 29 100.0 32 ............................. ATACGAGCTTCTGCGCCATGAACCAGAGAGGG 491242 29 100.0 32 ............................. TTAGGGATCGGCGTGTCGGTGTATTTCTGCCC 491303 29 100.0 32 ............................. CTGGCAGATTTTGCCCCATTGATGCCCCATAA 491364 29 100.0 32 ............................. CAGGTTGGGTTTATCTACCGGGTAGATTCTAT 491425 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 20 29 99.5 32 GTGTTCCCCGCGAGAGCGGGGATAAACCG # Left flank : TGCTGTTCCCGTTCTCGCGTCTGGTGCATATCTGGAGCGTGCCGGTTGAGTATCTGACCCGTAAATATCAGCTTGTTCGCGCACGTCACTGATTGTGTGCTGATTATCTCAAGCCGCCGTGGGGCTGAGGCGTATTCAGCACTATAGCGGGAAAATAGCGCGGGCATGGAGATTGACTTCATGCCCGTTTTTTTGCATTTCCTATCGGGCTCATCCCGTATCTCACGACCTGCCGCAGACGCTCCCTTGAACTCTTTGCCGACGATATGCGCAAAATCTTACTCCCCCTTGATGTGATGATGTATTAATCTCCGAGTTTTCCGTCATATGACACTCGGCATAGTATGTTGGTAGATTTTAAGAGAGAATCATGGGTGTGGTTTTTTATTATATGAAATCAATTGGTTATATGCTCTTTAATAATGCGGTATTGTTATTTATGTGTTGGTAAGATGTTGCTGCATGAAAATGTTGTTTATAAACATAGGGATGGCACTAGA # Right flank : GACGGAGTTTGAAGACGAACATCAGGGGCTGGGGTGTTCCCCGCGCGAGCGCTGAGTTTGTGGGGTTAGTTCACTCCGGCAGGTTTTTTATGGCTGTTTGCCGGATGGCGGCATAAATGCCTTATCCGGCACCGATCTTATCTCGGAGTTGCATCGAACCTTCTCATCCTTCCCCGTACGGAGAGATATGAGGCAGTGTGCTTAATGGGGATAATATACGCGACGGAAGTGATGGTGGTGGGGGAAGGATTATTCGTCGCTCCGCTCCTCACCCTTCGGGTCGTTGCCTGCGGCAACGCTTTCTCGCTGCGCTCGAATCGAACCTTAGTCGAAGCTTCTCATCCTTCCCCGTACGGAGAGATATGAGGCAGTGTGCTTAACGGGGATAATATACGCGACGGAAGTGATGGTGGTGGGGGAAGGATTATTCGTCGCTCCGCTCCTCACCCTTCGGGTCGTTGCCTGCGGCAACGCTTTCTCGCTGCGCTCGAATCGAACCT # Questionable array : NO Score: 6.23 # Score Detail : 1:0, 2:3, 3:0, 4:0.97, 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: R [2-1] Score: 0.41/0.41 # 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 [5.51,0.41 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 186485-187366 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAAHTQ010000005.1 Salmonella enterica subsp. salamae serovar II 1,4,12,27:e,n,x:e,n,x strain HAZEL-228 NODE_5_length_441423_cov_31.996925, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 186485 29 100.0 32 ............................. CAATGGCTACCGCTGTTGACTCGCTTTTAACT 186546 29 100.0 32 ............................. ACATAAAAAACGAGAGGGCAACAATAACACAG 186607 29 100.0 32 ............................. GCCTCTAACACGGAGCAGAAATGATAAGTGAC 186668 29 100.0 32 ............................. AACACGTATTACACAATATTGCAGACTAGAAT 186729 29 100.0 32 ............................. CGAATACGGCGTCCGGCGTGTCTCCGGTGGTG 186790 29 100.0 32 ............................. CCAACTCCTCCCCTCGCTGCTGCGTGATTTTC 186851 29 100.0 32 ............................. CATCCGGCAATCTGGGAGCTATTCCAGATAAA 186912 29 96.6 32 ............T................ CGATCACCAGCTCGTTTGTCCCTGGCTGGCAG 186973 29 96.6 32 ............................T TGATACGTAGTTTGGCTGAATCTTCCAGAAAA 187034 29 100.0 32 ............................. GTTTAATCTGATATCCCCAGTACTAAAGGAGT 187095 29 100.0 32 ............................. TGAATGATAATTTCATATTAGTTCCTTAATCA 187156 29 100.0 32 ............................. CTATTATTTCCAAAATCGCCACGCTACAGCAC 187217 29 100.0 32 ............................. AAAGGACACCTATTAAGCGCTGAACTATCTAA 187278 29 96.6 32 ......A...................... GTGTGGTTCCAGGTCGTGCTCCGGGAAGGCCA 187339 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 203939-204578 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAAHTQ010000005.1 Salmonella enterica subsp. salamae serovar II 1,4,12,27:e,n,x:e,n,x strain HAZEL-228 NODE_5_length_441423_cov_31.996925, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 203939 29 100.0 32 ............................. GCTAGCAAATACAGTGGTGATTTAAAACTTAC 204000 29 100.0 33 ............................. AAACCATTTGGCGAGTATTTCTCTCGCGAGGGC 204062 29 100.0 32 ............................. GCGAATGATCTTGGTATCTTGACAGGTGGCAG 204123 29 100.0 32 ............................. GGAGTTAGCTAGCTTTATTTCACTGATTCGCA 204184 29 100.0 32 ............................. TCGATTTGCAATATTTTTTACCCAATTGGATC 204245 29 100.0 32 ............................. ATAGACACGAAGTGATTTCAACGTTTCCCCGT 204306 29 100.0 32 ............................. GACGCTATCGATGACATGCTGATTAACGATGC 204367 29 100.0 32 ............................. CGCGTTTAGATCTGTGGGCCCGCTGGATTGCT 204428 29 100.0 32 ............................. ATCGGGCGGGATATGTGCTGGATTCGTATTAG 204489 29 93.1 32 ...........A.T............... TTTTTCTGTCGCTGGTGGGCACTGACACGGCG 204550 29 89.7 0 ........A..................GC | ========== ====== ====== ====== ============================= ================================= ================== 11 29 98.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGCTCGCTGCCGGTGAAATTGAACCACCTCAGCCTGCGCCGGATATGTTGCCGCCAGCAATACCTGAGCCGGAATCTCTGGGTGACAGCGGACATCGGGGGCATGGTTAATGAGCATGGTGGTGGTGGTGACAGAAAACGTACCGCCGCGCCTGCGAGGGCGGCTTGCCATATGGTTACTGGAGATTCGTGCAGGGGTTTATGTTGGCGATACATCGAAACGCATTCGAGAGATGATCTGGCAACAGATTACACAACTGGGCGGAGTCGGAAACGTAGTAATGGCTTGGGCAACAAATACTGAGTCTGGTTTTGAGTTTCAGACCTGGGGGGAAAACCGCCGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCCCTTGAAAATCAATGAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTAACGTTGGTAGTTTGTTGAGCAGTAAAAAAAATCTTTTAGAACAAATATATAGTTTTAGT # Right flank : CTTTTCACCAGCAGATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGTCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGACTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGACGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCGCTCATTC # 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 : 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], //