Array 1 318336-318727 **** Predicted by CRISPRDetect 2.4 *** >NZ_AHUC01000002.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 37978 SEEN978_11, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 318336 29 100.0 32 ............................. TGCTGGCGGCAAAAGAACTCGCTAAATGGGAA 318397 29 100.0 32 ............................. CAGTGCGGCAGCGCGCAATCGAGACACGCCAT 318458 29 100.0 32 ............................. CACAAAACGCCAGTGGCATGGTACAACCCGTA 318519 29 100.0 32 ............................. GCGTGACCATGTTTAACTCTAAATCAGGCCGT 318580 29 96.6 32 ........A.................... TCATGCTTTCGACTAAATACTACCGCGACAAC 318641 29 100.0 32 ............................. AAAATAACAACATTATCAGTGTGAAAAGTCTC 318702 26 89.7 0 ..........................--- | ========== ====== ====== ====== ============================= ================================ ================== 7 29 98.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACTTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCTCTATCAATTTTACGGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTAATGCTGATAAAAAGTAGTTTATAAACAATGATATCCGTTTAGT # Right flank : | # Questionable array : NO Score: 6.16 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 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 [0-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [73.3-0.0]%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 35-613 **** Predicted by CRISPRDetect 2.4 *** >NZ_AHUC01000001.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 37978 SEEN978_10, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 35 29 100.0 32 ............................. CAGACGGCAGCAGCGTGAAACACGTCAGTATT 96 29 96.6 32 ............................A CCAATAACCGAAATATCCACGGTGGAAATTTC 157 29 100.0 32 ............................. TCAGCTGTTCCATACTCACCCCCTGTGCAATC 218 29 100.0 32 ............................. GCGATGTATGCCGCGACGATCGAGAGCGAACT 279 29 100.0 32 ............................. CAGCAGATGAAAAATATTTACAGATTGGTAAA 340 29 100.0 32 ............................. AAAAAATCCCGCTGACAATATTTTGCCACCTC 401 29 100.0 32 ............................. CCGGAAAACTATCTCTATCGCAGGCTGGATAT 462 29 100.0 32 ............................. TTCCAAAGGTACTCCCATATCTCCAGCCAACG 523 29 100.0 32 ............................. TAAGTTACGCCAGTGCGGGCGTGTTGCTCATC 584 29 100.0 0 ............................. | A [611] ========== ====== ====== ====== ============================= ================================ ================== 10 29 99.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CGATTAAACAACAGGATTTTGCAATTACTGTTGGG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATTCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCTCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # Questionable array : NO Score: 6.25 # Score Detail : 1:0, 2:3, 3:0, 4:0.99, 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: R [36.7-48.3]%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], // Array 1 562-44 **** Predicted by CRISPRDetect 2.4 *** >NZ_AHUC01000005.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 37978 SEEN978_14, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 561 29 100.0 32 ............................. ATTGTTATTGCGGTAACGGATAATTTATCATT 500 29 100.0 32 ............................. CCTGGCGATCGCATTTGGGTGCGGGAAACATT 439 29 93.1 33 ..........................A.C GCCGAATATGGTGATAATGTTGCACCTTCGCTC 377 29 100.0 32 ............................. GACTCGGCCTGTTTTTTGATTTTGACAATCAG 316 29 100.0 32 ............................. CCAATAACCGACGAGGGCAAACGCCGTGCGCG 255 29 100.0 32 ............................. AGGACTGAGGGAATAGGGACCGTAATTGTAAA 194 29 100.0 32 ............................. ACAATGTTGCGTCTAATTCTCATTAATTAAAA 133 29 100.0 32 ............................. CAGACGAAAATCAGCCCGCATATTCCGACACA 72 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 9 29 99.2 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AAACCGATTATCCCGGAAATCGTGATCAACTACGCAG # Right flank : GAACAGTGGTTTTAGGTTGTCGGTGCTGATCCCGTGTTCCCCGC # 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: 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: F [0-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [31.7-33.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.41,5.24 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 391-57 **** Predicted by CRISPRDetect 2.4 *** >NZ_AHUC01000019.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 37978 SEEN978_33, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 390 29 100.0 32 ............................. CTGGAACGGCAGTATTTAAAAGGGGTTATTGA 329 29 100.0 32 ............................. TGGGCGCCCGGATTGTTTGCGTGCGGCGACGG 268 29 100.0 32 ............................. TTGATTTACCCGCCACTTATTCCCCATTGCAT 207 29 96.6 32 ..........................T.. GGACTATCAAACCATCTATGATGCCAATTTTA 146 29 100.0 32 ............................. CGCGGGGCTGGTATTCGATACAGACCCGGCTA 85 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 6 29 99.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CTTATTGAAGATGTTCTCGCGGCAGGGGAAATTCAACCGCCGTTACCTCCTGAAGATTCACAACCCATAGCGATCCCTCTTCCTGTTGCGTTGGGAGATTCCGGTCATCGGAGTACCTAACGATGAGTATGCTGGTTGTCGTTACCGAAAATGTTCCTCCTCGTCTGCGGGGGAGGCTGGTCGTCTGGTTACTGGAAATTCGAGCTGGTGTGTATGTTGGTGATGTTTCCGCAAAGATCCGCGAGATGATATGGCAACAGGTTTCCGTTCTGGCAGATGAGGGAAATGTTGTTATGGCGTGGGCGACAAATACAGAATCAGGTTTTGAGTTTCAGACTTTTGGTGTAAATCGACGTATTCCGGTAGATCTTGATGGACTGCGATTGGTGTCGTTTCTACCTGTTGAAAATCAATAAGTTATAGATCTTTAAAAATTAGGAAAAGTTGGTGGGTTTTTTGTGCGCTAAAAAAGTATTTAAATTCAATTGGGTAGATTTAGG # Right flank : GGGAATAAAAAATGAATTTGAGTCAACTCTATAAGTGTTCCCCCGCGCCAGCGGGGG # 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: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: R [48.3-68.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.51 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 2 17882-17060 **** Predicted by CRISPRDetect 2.4 *** >NZ_AHUC01000019.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 37978 SEEN978_33, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 17881 29 100.0 32 ............................. GTCAGTATGCACTGCTTGATAAAGTCAGGCCA C [17872] 17819 29 100.0 32 ............................. AACTAACGTCTATAGCTAAATGTAGAGAAAAC 17758 29 100.0 32 ............................. CAGTTTGGAGTCAATGTTATTTCTTCAGGTCA 17697 29 100.0 32 ............................. TCTCGCTGGTTGCTCCAACTCCTGATATGCCG 17636 29 100.0 33 ............................. TAAAAAATCTTCTTTCATATAACCGTAAGGGTT 17574 29 100.0 32 ............................. AGGGTTTTGTCACCTCAACGGTCGGGAGTGCA 17513 29 100.0 32 ............................. GGCGCCCGCGTTTCTCGGCTCGGCGCAATATC 17452 29 100.0 32 ............................. GTAGTGCAACGCCGGTGATTTTACCAGTATCA 17391 29 100.0 32 ............................. GTGCAACAGTTTCTTACCGCAAGCAGTTTGAA 17330 29 100.0 32 ............................. ATCATCGGGATTCATTTTGTTGTCCGGGTGGC 17269 29 100.0 32 ............................. CGGTGCTCTATGTCTAAAAATAAAAGCGGTTC 17208 29 93.1 32 ........T...................C AGCACAATCATTATTAGATGAACTTTCATCAA 17147 28 96.6 32 .............-............... GGGATCGCGCTGGCGGTCGCATCCGTTGCCGT 17087 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================= ================== 14 29 98.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AGTT # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGGCCCCCTGCCGATTGGC # Questionable array : NO Score: 6.16 # Score Detail : 1:0, 2:3, 3:0, 4:0.90, 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 [8-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [63.3-6.7]%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], //