Array 1 334-61 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCIK01000394.1 Salmonella enterica subsp. enterica serovar Newport strain SE89 NEWPORT_S4_trimmed_contig_421, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ============================================================================================ ================== 333 29 100.0 32 ............................. ATAAATTATCGGGAAATCATAATCAGCGCCGC 272 29 100.0 32 ............................. TCGAGTTCTGGCACGTCAGACTGACGTATCGC 211 29 75.9 92 ..................CCA.A.CT.A. ACCAATTGCATTTATAATTTGTGCTATCCTTTTCCTGTAAGTTCCCCGCGAGGCGAGCGTGGGGATGAACCGGCTACTTGGTAGCCTCAAAC 90 29 82.8 0 .A..........T............C.TT | C [88] ========== ====== ====== ====== ============================= ============================================================================================ ================== 4 29 89.7 52 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GCAC # Right flank : TGGCTGAACCCAAAAACACCTAGCCAACTTTTCTTATCTCACATTAAAATTGACGTCATTG # Questionable array : NO Score: 3.15 # Score Detail : 1:0, 2:3, 3:0, 4:0.49, 5:0, 6:0.25, 7:-2.19, 8:0.6, 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: NA [4,4] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTGTTCCCCGCGCCAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [-9.60,-9.80] Score: 0/0.37 # Array degeneracy analysis prediction: R [8-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [60.0-1.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,4.91 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 30774-29585 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCIK01000007.1 Salmonella enterica subsp. enterica serovar Newport strain SE89 NEWPORT_S4_trimmed_contig_7, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 30773 29 100.0 32 ............................. TTGATTTACCCGCCACTTATTCCCCATTGCAT 30712 29 96.6 32 ..........................T.. GGACTATCAAACCATCTATGATGCCAATTTTA 30651 29 100.0 32 ............................. CCTGGCGATCGCATTTGGGTGCGGGAAACATT 30590 29 100.0 32 ............................. CCGAATATGGTGATAATGTTGCACCTTCGCTC 30529 29 100.0 32 ............................. GACTCGGCCTGTTTTTTGATTTTGACAATCAG 30468 29 100.0 32 ............................. CCAATAACCGACGAGGGCAAACGCCGTGCGCG 30407 29 100.0 32 ............................. AGGACTGAGGGAATAGGGACCGTAATTGTAAA 30346 29 100.0 32 ............................. ACAATGTTGCGTCTAATTCTCATTAATTAAAA 30285 29 100.0 32 ............................. CAGACGAAAATCAGCCCGCATATTCCGACACA 30224 29 100.0 32 ............................. AACAGTGGTTTTAGGTTGTCGGTGCTGATCCC 30163 29 100.0 32 ............................. ATTAAACAACAGGATTTTGCAATTACTGTTGG 30102 29 100.0 32 ............................. CAGACGGCAGCAGCGTGAAACACGTCAGTATT 30041 29 100.0 32 ............................. TCAGCTGTTCCATACTCACCCCCTGTGCAATC 29980 29 100.0 32 ............................. GCGATGTATGCCGCGACGATCGAGAGCGAACT 29919 29 100.0 32 ............................. CAGCAGATGAAAAATATTTACAGATTGGTAAA 29858 29 100.0 32 ............................. AAAAAATCCCGCTGACAATATTTTGCCACCTC 29797 29 100.0 32 ............................. CCGGAAAACTATCTCTATCGCAGGCTGGATAT 29736 29 100.0 32 ............................. TTCCAAAGGTACTCCCATATCTCCAGCCAACG 29675 29 100.0 32 ............................. TAAGTTACGCCAGTGCGGGCGTGTTGCTCATC 29614 29 100.0 0 ............................. | A [29587] ========== ====== ====== ====== ============================= ================================ ================== 20 29 99.8 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GCCAGCGGGGATAAACCGTGGGCGCCCGGATTGTTTGCGTGCGGCGACG # Right flank : TTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATTCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCTCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCGT # 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: 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 [1-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [50.0-25.0]%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], // Array 1 11628-10444 **** Predicted by CRISPRDetect 2.4 *** >NZ_VCIK01000065.1 Salmonella enterica subsp. enterica serovar Newport strain SE89 NEWPORT_S4_trimmed_contig_70, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 11627 27 93.1 32 --........................... TGCTGGCGGCAAAAGAACTCGCTAAATGGGAA 11568 29 100.0 32 ............................. CAGTGCGGCAGCGCGCAATCGAGACACGCCAT 11507 29 100.0 32 ............................. CACAAAACGCCAGTGGCATGGTACAACCCGTA 11446 29 100.0 32 ............................. GCGTGACCATGTTTAACTCTAAATCAGGCCGT 11385 29 96.6 32 ........A.................... TCATGCTTTCGACTAAATACTACCGCGACAAC 11324 29 100.0 32 ............................. AAAATAACAACATTATCAGTGTGAAAAGTCTC 11263 29 100.0 32 ............................. AGATATGAAAAACGTAAAAATTTACACCGCCA 11202 29 100.0 32 ............................. CAATAGGACAGCCATTCGAGCGCCCAGAGTTT 11141 29 100.0 32 ............................. GTCAGTATGCACTGCTTGATAAAGTCAGGCCA 11080 29 100.0 32 ............................. AACTAACGTCTATAGCTAAATGTAGAGAAAAC 11019 29 100.0 32 ............................. CAGTTTGGAGTCAATGTTATTTCTTCAGGTCA 10958 29 100.0 32 ............................. TCTCGCTGGTTGCTCCAACTCCTGATATGCCG 10897 29 100.0 32 ............................. TAAAAATCTTCTTTCATATAACCGTAAGGGTT 10836 29 100.0 32 ............................. AGGGTTTTGTCACCTCAACGGTCGGGAGTGCA 10775 29 100.0 32 ............................. GTGCAACAGTTTCTTACCGCAAGCAGTTTGAA 10714 29 100.0 32 ............................. ATCATCGGGATTCATTTTGTTGTCCGGGTGGC 10653 29 100.0 32 ............................. CGGTGCTCTATGTCTAAAAATAAAAGCGGTTC 10592 29 93.1 32 ........T...................C AGCACAATCATTATTAGATGAACTTTCATCAA 10531 28 96.6 32 .............-............... GGGATCGCGCTGGCGGTCGCATCCGTTGCCGT 10471 28 82.8 0 ...............A.AA.....G-... | ========== ====== ====== ====== ============================= ================================ ================== 20 29 98.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : | # 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 [8-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [63.3-0.0]%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], //