Array 1 1-740 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYVI01000050.1 Salmonella enterica subsp. enterica serovar Senftenberg strain CVM N31402 N31402_contig_50, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1 29 100.0 32 ............................. CGAGTCTGGAAATTGAGGACACCGAAACCGGC 62 29 100.0 32 ............................. TGCTGGTGGGCGGTACGCCGTGCCAGGCGTTC 123 29 96.6 32 ............................T TATCCTTACCCTCAACGGCGCAGGCCGATCTC 184 29 100.0 32 ............................. CGATCTGGTGAGCGCATCGGTTCGGGAGAGTG 245 29 100.0 32 ............................. GATTGTTCAGATTGGGAATTTGACCAACGCCC 306 29 69.0 11 ................TAAT..CGT.T.C GTGAACCAGTT TT [326] Deletion [346] 348 29 100.0 32 ............................. GGGAATATCGTTAAAGTGGTTTACCACAATAT 409 29 100.0 32 ............................. GCGCTCAGGGCCGCCTTGCTGCGGGCACTCAT 470 29 100.0 32 ............................. GACGTGATCAAACAATTTGGCCGCCCGGAACA 531 29 100.0 32 ............................. CGATCAAGCGAATGCGTCGGCTGGAGCATCGC 592 29 100.0 32 ............................. GTTTTCGCGGCCGCGAGATTGTTCTTGCCGAC 653 29 100.0 32 ............................. TACCGTTTTTACTCCCCCGCATTTGGTTACAC 714 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 13 29 96.8 30 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # Right flank : | # Questionable array : NO Score: 5.95 # Score Detail : 1:0, 2:3, 3:0, 4:0.84, 5:0, 6:0.25, 7:-0.14, 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 [1-1] 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 49-871 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYVI01000049.1 Salmonella enterica subsp. enterica serovar Senftenberg strain CVM N31402 N31402_contig_49, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 49 29 100.0 32 ............................. TGCTCGAGCCGACATTGATCCCGCAAAAATAC 110 29 100.0 33 ............................. GACAATTAGTTCCGACAGACGCCGGTATTAAAT 172 29 96.6 32 ............T................ CCCACGCGCGGCCGCACTGGCCTCGCGGATAA 233 29 100.0 32 ............................. TCCGGGCCGCCGCTACCACCACTCAGCGGCGT 294 29 100.0 32 ............................. CCTAATGGTGATGGGGCGTTTAATCTTATCTC 355 29 100.0 32 ............................. TGGTTTAATAGTATCGGGCAGCATTTTACCGA 416 29 100.0 32 ............................. ATCTCAATTAGTCCGTTTCCGGTTGAATCAAT 477 29 96.6 32 ...C......................... GGGTGTACCACGGCATGATGACGGCCAGCCAT 538 29 100.0 32 ............................. ATTGACAACAGTCTGCTTACCCGAGCTGCTCC 599 29 100.0 32 ............................. TCCTGTCGGCGGTACGGTGGACATCCCGCAGG 660 29 96.6 32 .........A................... CCAGTCAGCCACTGTTCTTTGCCGTACCTTTC 721 29 100.0 32 ............................. GGGTTATAACCGGGATACCATCCGCTCCAACC 782 29 100.0 32 ............................. CGCCACGTTTTTTGCATTTTATTGGCATCATC 843 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 14 29 99.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CAGCGGGGATAAACCGCGCAGACGGCGCAATTGGATTCGGTGATCGGGG # Right flank : GGCAACTGGGCGATCATCTGGGCGCTGTTTATGTGTTCCCCGCGCCAGC # Questionable array : NO Score: 6.22 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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 [1-1] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [30.0-30.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 51-567 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYVI01000051.1 Salmonella enterica subsp. enterica serovar Senftenberg strain CVM N31402 N31402_contig_51, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 51 29 100.0 32 ............................. TACCGAACGGCTCAAAGTATGTTCCAATTGAC 112 29 100.0 32 ............................. GTTGAAACCAGCATTCCTTATGCTGTGCTGCC 173 29 100.0 32 ............................. GAGATTTTTCTTGTCCCGCCACACCAGCGGCT 234 29 100.0 32 ............................. TGCATCATCTGATTCGTACGATACGGCAGGGT 295 29 100.0 32 ............................. GGCTGACAAACGAGCAGGTTGAATTTGTCCTG 356 29 100.0 32 ............................. CATGGTCTGTACCGCCTGCATTTCTGCATTGT 417 29 100.0 32 ............................. GGCCGCACCGCTGGCGATCACGATTAATCAGC 478 29 100.0 32 ............................. CGCCTCGCAAAACTGGTCGGGGTTTTTCCCCA 539 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 9 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GCCAGCGGGGATAAACCGGGACCATTGAAACGGCGCTGACATCAGATGTTG # Right flank : TTCGTGTTCTAACAGCAGATCGCTGATACGGCGTGTTCCCCGCGCCAGCG # 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: NA [36.7-33.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.24,0 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 156342-157222 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYVI01000016.1 Salmonella enterica subsp. enterica serovar Senftenberg strain CVM N31402 N31402_contig_16, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 156342 29 100.0 32 ............................. CCGATATCAAAAAAGCGTTTAAACGCCTTGCC 156403 29 96.6 32 ............................T TCCTGCGCTTTGGCCAGTTTGGAACCCGCCGC 156464 29 100.0 32 ............................. GCACAATTTGTGCTTTTGCAATTCACTTTGAA 156525 29 100.0 32 ............................. TGATCACAGAACTGACCGGGTACACCATACCT 156586 29 100.0 32 ............................. TGATCACAGAACTGACCGGGTACACCATACCT 156647 29 100.0 32 ............................. TAACGCCGTTCTGCATACGCTCTACCGCGCGC 156708 29 100.0 32 ............................. GGGAATGTATGGATTTAGAAGAAGAGCTGGCA 156769 29 100.0 32 ............................. GGGTATTACGGCGACACAGCGCTTGTTGTCTA 156830 29 100.0 32 ............................. TTAACAAATGTTTTTAAAACGCTTATAACAAA 156891 29 100.0 32 ............................. TTTAAAAATTTATCTCGATAAATCCAACGATG 156952 29 100.0 32 ............................. AATGATCGTATTTTTCGCTACGTCGCACAAAT 157013 29 100.0 32 ............................. CCCGTTATTTGTAGTTAACGGGCACGTAGTGG 157074 29 100.0 32 ............................. ATCGGGCAGCTCAACGCGGCTATGAAAATCAC 157135 29 100.0 32 ............................. TTGATCGCCGTGGCGGTGAGATTAGAAACGCG 157196 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 15 29 99.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGCTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATGATATACGTTTAGT # Right flank : | # Questionable array : NO Score: 6.22 # Score Detail : 1:0, 2:3, 3:0, 4:0.96, 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 [1-1] 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], // Array 1 638-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYVI01000017.1 Salmonella enterica subsp. enterica serovar Senftenberg strain CVM N31402 N31402_contig_17, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 637 29 100.0 32 ............................. GCAATTTCCGATATGCGACTTGGGACACCAAT 576 29 100.0 32 ............................. ACACCGACTCATCCGTTGTTACTCCTGGTATT 515 29 100.0 32 ............................. CGCTACGCCCTGCCCGGTCTCGGTCTCGGTCT 454 29 100.0 32 ............................. CACATCGGGAGCCTCAATCAACCCGGCACGGA 393 29 100.0 32 ............................. AGTTCGATATCCCTTAACGGTACTGCCGTCCT 332 29 100.0 32 ............................. CCTCACGCAATTGAGCCTCTTTCTCGACACGC 271 29 100.0 32 ............................. GGCCAGTTCAACAAACACCACGACGCGGGAAT 210 29 100.0 32 ............................. TTCATCACCGTCAGCAAGCTGCGATCCGAAAT 149 29 100.0 32 ............................. CCAGCTTGCCGATATCAACGACCTATACCTGT 88 29 100.0 32 ............................. GTTAAAATTTGGGAGGATCGCCCGGGACTCCC 27 27 93.1 0 ...........................-- | ========== ====== ====== ====== ============================= ================================ ================== 11 29 99.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CTTATTGAAGATGTTCTCGCGGCAGGGGAAATTCAACCGCCGTTACCTCCTGAAGATTCACAACCCATAGCGATCCCTCTTCCTGTTGCGTTGGGAGATTCCGGTCATCGGAGTACCTAACGATGAGTATGCTGGTTGTCGTTACCGAAAATGTTCCTCCTCGTCTGCGGGGGAGGCTGGCCGTCTGGTTACTGGAAATTCGAGCTGGTGTGTATGTTGGTGATGTTTCCGCAAAGATCCGCGAGATGATATGGCAACAGGTTTCCGTTCTGGCAGATGAGGGAAATGTTGTTATGGCGTGGGCGACAAATACAGAATCAGGTTTTGAGTTTCAGACTTTTGGTGTAAATCGACGTATTCCGGTAGATCTTGATGGACTGCGATTGGTGTCGTTTCTACCTGTTGAAAATCAATAAGTTAGAGATCTTTAAAAATTAGGAAAAGTTGGTGGGTTTTTTGTGCGCTAAAAAAGTATTTAAATTCAATTGGGTAGATTTAGA # Right flank : C # 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: 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 [1-0] 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: R [0,5.65 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 18309-17183 **** Predicted by CRISPRDetect 2.4 *** >NZ_JYVI01000017.1 Salmonella enterica subsp. enterica serovar Senftenberg strain CVM N31402 N31402_contig_17, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 18308 29 100.0 32 ............................. ACACAATACGTATCAGTAAAGACACAAATTGT 18247 29 100.0 32 ............................. CGCATTACCGGGAAAACCTGGGAAGAGACGAT 18186 29 100.0 32 ............................. TCTTGTTTGTTTCTGATTCTTTTTCTGAATGA 18125 29 100.0 32 ............................. AGTCAGAAGAGGACTCATTAGTATCACTCTCA 18064 29 100.0 32 ............................. AATAAACAGCGTCGTAAATGGATCGAGGAAAT 18003 29 100.0 32 ............................. CATCTCTCTATATGCAGCGCCAGCCAGCGCAA 17942 29 100.0 32 ............................. CTTTCCTTGCGTCAATTTTGAGGGAGATTGAT 17881 29 100.0 32 ............................. ATCCCGCGCTCTATTAAAATCTTTGATTGCGT 17820 29 100.0 32 ............................. GTAATGTGCGCCGCGCCGGTGATATCTACTTT 17759 29 96.6 32 .....T....................... CCATTGCTGACAGGCAGTGATTTCAATGTGTC 17698 29 100.0 32 ............................. GTCATGAATGGCCTCATAAAAACGATGTTGGT 17637 29 100.0 32 ............................. TGTTCGCGCTAAATAATGCAGTAGGCCGCGCT 17576 29 100.0 32 ............................. CCAGAAATTTAAATGGCTATTCCTGGCTGTAG 17515 29 100.0 32 ............................. GCGCAATTGCAGTTTGACGCGGTGCTGTCATT 17454 29 100.0 32 ............................. TCGTTTGTGGCGTCAGTAATACTATTATCGGT 17393 29 96.6 32 .............T............... TTTTTAAATCCGGACAGACCCTGTAACGGATC 17332 29 100.0 32 ............................. ATCCGACTGTATGCCCAGCAGAACGAGGGCGC 17271 29 96.6 32 .............T............... CACGAGTGGCAAATTGATTTCGACGAAAAACC 17210 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================ ================== 19 29 98.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AGCGGGGATAAACCGGCGCACCGCTTTAGAGTGCCAGGCATAGGCA # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGGGCTGGAGCGGATAAATCGTTGAAGGCCAGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGTGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTATCGAATGATGTACACGCGTGACCCCCTGCCGATTGGC # Questionable array : NO Score: 6.19 # Score Detail : 1:0, 2:3, 3:0, 4:0.93, 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: R [7-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [63.3-31.7]%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], //