Array 1 1-1069 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYTR01000019.1 Salmonella enterica subsp. enterica serovar Hadar strain CVM N29317 N29317_contig_19, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 1 29 100.0 32 ............................. GCTGAGATAATTGCCGATCATCTTGAAGACAT 62 29 100.0 32 ............................. AATGATGAGGGGCTGGCAACGTTTAGCGCCAC 123 29 100.0 32 ............................. CTGGCCACTCAACAGGGAAATATCGCGTGCGC 184 29 96.6 32 A............................ CCCATCAAGATAAACATCATAGCGAGCACCTG 245 29 100.0 32 ............................. TTTGAAATCGCTATTCTTATTGCTGTAGCAGT 306 29 100.0 32 ............................. CGTTAACTAAAACGAACAAAACAGGGAAATCA 367 29 100.0 33 ............................. GCCGTGCGTCAGATCACCCCAAACGCTTTCTTT 429 29 100.0 33 ............................. GCATTAGATTGCGTTGACGGTCACGTTCTTATC 491 29 100.0 32 ............................. CGCCTCACTGATATTCTGCGGCGAGCTGAAAA 552 29 100.0 32 ............................. CCGGAAAACTATCTCTATCGCAGGCTGGATAT 613 29 100.0 32 ............................. TAAGTTACGCCAGTGCGGGCGTGTTGCTCATC 674 29 100.0 32 ............................. GAGACGCCAGATGAATTCTGCGGGACAAGAGA 735 29 100.0 32 ............................. AACGCAGGAGAACCAGCCGCCGGTCATCCTGC 796 29 100.0 32 ............................. GTCTGACCAGTGGCGTGGGGGGATTGCAATTT 857 29 100.0 32 ............................. CGTGGCTGGAGCAATGAACAGATTAAAGGGGT 918 29 100.0 32 ............................. AAGCCATTGACGCAACGGAAAACGCCAATGCT 979 29 96.6 32 .................A........... GTATGATTTGGACATAGCTAATGATGTAAAGT 1040 29 100.0 0 ............................. | A [1067] ========== ====== ====== ====== ============================= ================================= ================== 18 29 99.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : GTTTCAACAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCTGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATGACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # 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 : 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 [1-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [0.0-0.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.65,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 66-1374 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYTR01000080.1 Salmonella enterica subsp. enterica serovar Hadar strain CVM N29317 N29317_contig_80, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 66 29 96.6 32 ..T.......................... GCACTATTTCGAATGTCTCGACGCCAGATTTA A [70] 128 29 100.0 32 ............................. AACTTAACTCCAGCATTCTGGCAATTGTTGCG 189 29 100.0 32 ............................. GCGACATCAAAATCTATTTTTCATTCTATCTG 250 29 100.0 32 ............................. CTCCAGCCACATTGCGGCGCGACCGCTTTTAA 311 29 100.0 32 ............................. CAATGTTTCATGCTACGCAAGAGACCAGAACG 372 29 100.0 32 ............................. TGGTGGAGTGCCGAACCGCTACCGTTTCAAAG 433 29 100.0 32 ............................. TCATGGCGTCATTCGGTACTGATATGCCAATG 494 29 100.0 32 ............................. TCGTTTGTAGCCGAAAACCGGCTGGCGCTGAT 555 29 100.0 32 ............................. TAATGAATCGCCTTTCTAAAATGAAAGACGAC 616 29 100.0 32 ............................. GCATCGAACCGCTTATCCGTCTGTACCCACTC 677 29 100.0 32 ............................. CTTTCATTGCGCAGGGTATGCAGTCGGTTTCC 738 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 799 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 860 29 100.0 32 ............................. AATGGGATGTTCTCGATAATGGCGACGACGAA 921 29 100.0 32 ............................. CGGTCATTTTAAAGAATCCCGTTAAACAACAC 982 29 100.0 32 ............................. GACATTTCAGTTTTGAGCATGAACCTGATTCA 1043 29 100.0 32 ............................. CAGATCCTCAACGGTCAGGTTGTTTAGTTCCT 1104 29 100.0 32 ............................. AAAACCGTACAACAGACAAAATATAAATATTG 1165 29 100.0 32 ............................. CGGAGGATGGAATATTTCCGAGGCTGGCGATT 1226 29 96.6 32 .............T............... ATGCCGGAACGCTGATGGCGTTTGACATGAGC 1287 29 100.0 32 ............................. AATTATTTCTGTGGCTGGGGTTTCGATTCGAT 1348 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 22 29 99.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTATAAGAGACAGCGCTGGCGCGGGGAACACTCTTTTGATTTTGCTGCGATGTTATAACCAGACGG # Right flank : | # 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 : 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 [2-2] Score: 0/0.41 # AT richness analysis in flanks prediction: F [48.3-0.0]%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], // Array 1 13-590 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYTR01000059.1 Salmonella enterica subsp. enterica serovar Hadar strain CVM N29317 N29317_contig_59, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 13 29 96.6 32 .C........................... CCAGCTTACGCTATTTACGACGTTATTGAGCA C [16] 75 29 100.0 32 ............................. CCCCGATAGCGACGCTTCTGTAGTCACTGGCA 136 29 96.6 32 .........................G... CGTCACTTTCTGACATTTTATTCAGTTCGTTA 197 29 96.6 32 ..........T.................. TCATTTCTGGACGGGGCTGTGTGACGAATACG 258 29 100.0 32 ............................. TGTCCAATTAACCCAAACTTTGCGCGCTTAAT 319 29 93.1 32 A............T............... GGATATGTGAAGTTCAGGTAGCCCATTACGCA 380 29 100.0 32 ............................. TTGATCGAGAGTGCGAAGAGGCAGAACGGGCA 441 29 100.0 32 ............................. GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 502 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 563 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 10 29 96.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTATAAGAGACAG # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTGATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGATTAAGCCTGTTGGTCGAGGATGAGTCTACGTCGATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGTGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGGAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.01 # Score Detail : 1:0, 2:3, 3:0, 4:0.83, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.92, # 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 [3-7] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [13.3-63.3]%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], // Array 2 17272-17725 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYTR01000059.1 Salmonella enterica subsp. enterica serovar Hadar strain CVM N29317 N29317_contig_59, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 17272 29 100.0 32 ............................. CGACGCTTCCATCGTCTGGCATTCCTGTTCGT 17333 29 100.0 32 ............................. CCCGCGTATTAACAACGACGAGCAGGGCGTGC 17394 29 100.0 32 ............................. GTTGCGCAGCCATTGAGCTGCAAACGGATCAA 17455 29 100.0 32 ............................. CGCCCCCCGCATACAGCGAGAGACGGGCCATG 17516 29 100.0 32 ............................. CGCCGGGCGCGGGAGTCCCGGGCGATCCTCCC 17577 29 100.0 32 ............................. GCCCGAAATCAACTTGCAACATTTCAGTTGGC 17638 29 100.0 32 ............................. CATATGATTGACGACAATGAATTTTTTTTCAA 17699 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 8 29 99.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CTTATTGAAGATGTTCTCGCGGCAGGGGAAATTCAACCGCCGTTACCTCCTGAAGATTCACAACCCATAGCGATCCCTCTTCCTGTTGCGTTGGGAGATTCCGGTCATCGGAGTACCTAACGATGAGTATGCTGGTTGTCGTTACCGAAAATGTTCCTCCTCGTCTGCGGGGGAGGCTGGCCGTCTGGTTACTGGAAATTCGAGCTGGTGTGTATGTTGGTGATGTTTCCACAAAGATCCGCGAGATGATATGGCAACAGGTTTCCGTTCTGGCAGATGAGGGAAATGTTGTTATGGCGTGGGCGACAAATACAGAATCAAGTTTTGAGTTTCAGACTTTTGGTGTAAATCGACGTATTCCGGTAGATCTTGATGGACTGCGATTGGTGTCGTTTCTACCTGTTGAAAATCAATAAGTTATAGATCTTTAAAAATTAGGAAAAGTTGGTGGGTTTTTTGTGCGCTAAAAAAGTATTTAAATTCAATTGGGTAGATTTAGA # Right flank : | # Questionable array : NO Score: 6.21 # Score Detail : 1:0, 2:3, 3:0, 4:0.95, 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 [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [70.0-0.0]%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], //