Array 1 1433-1 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHHW01000040.1 Salmonella enterica subsp. enterica serovar Liverpool strain CVM N46814 N46814_contig_41, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 1432 29 100.0 32 ............................. CCCCGCGAGAAAACATCCAAATGCATTATCTT 1371 29 100.0 32 ............................. GATCCGCCAGGCGATAGCGCGCGCGGGTCCAT 1310 29 100.0 32 ............................. TACCTACCGAAAACCTCTTCTCCGGCACCGCT 1249 29 100.0 32 ............................. CAATTTTTAACGATCACTCAGATAAAACAGCA 1188 29 100.0 32 ............................. GTGGTAATCATGACGCATCGTCACCACGTCAA 1127 29 100.0 32 ............................. ATAACGACGACGATATCGCCGTTATACTGGGC 1066 29 100.0 32 ............................. TTCATCAATTCGGACAAAGTCGGCCACGATGC 1005 29 100.0 32 ............................. GCGAGGTTCTGCGCCCTGCTTCCAGTTCAAAA 944 29 100.0 32 ............................. ACGCGGTGTATCAGCAAACCTTCGATGCGGAG 883 29 100.0 32 ............................. GACGTTGTAGACCAGCGCCTTACTGGTGATGA 822 29 100.0 32 ............................. CGACCCCCCATTTTTCTGAATCGTAGACGAAC 761 29 96.6 32 ............T................ CAATTTGTTTGTTATCCCTGGTGAGTGCAACA 700 29 100.0 32 ............................. CGTATTCCCGGCACTGTTTATGGCATTGGCCC 639 29 100.0 32 ............................. CCAGCAGTCACTATTGATTCAAATGTTTTATA 578 29 100.0 32 ............................. TACCAGACCATCATTGATTTCAATGTAATTAC 517 29 100.0 32 ............................. CAGGGCAACGTCGTCATCGATGAGGCTGCGTT 456 29 100.0 32 ............................. CGGCCCCGTATAAATCTCGTGGCGCACAAATG 395 29 100.0 32 ............................. AAGAACGCTGCTGGCAGTCTGACCCTATTGAT 334 29 100.0 32 ............................. CGCCGTCACATCCTGATTTATCCAGTGTAGGG 273 29 96.6 32 .G........................... TTTTTAGTGCGTTTTTTAACCTTTGGTGGAAT 212 29 100.0 32 ............................. GGAAAAACACGTATCTGGTGGACAACCGGTGC 151 29 100.0 32 ............................. GCCGTTACTGAGCGCAGCGGGTTAGAGGTAAA 90 29 100.0 32 ............................. GGGCTTTCCCTTAGTGCCTGGACTATTGAGGC 29 29 96.6 0 .............C............... | ========== ====== ====== ====== ============================= ================================ ================== 24 29 99.6 32 GTGTTCCCCGCGCTAGCGGGGATAAACCG # Left flank : | # Right flank : G # 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 : 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: R [matched GTGTTCCCCGCGCTAGCGGGGATAAACCG 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 [2-0] 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 [0,5.28 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], // Array 1 399-4 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHHW01000004.1 Salmonella enterica subsp. enterica serovar Liverpool strain CVM N46814 N46814_contig_4, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 398 29 100.0 32 ............................. ATTGATGATTTTATAGCTACTACTCCATATCA 337 29 100.0 32 ............................. TTTGGTGCACCGCCAATGTCTCGTTATCAGAA 276 29 100.0 32 ............................. ACCCGGCAGGAAGTAGATTCATTTGCTGATGA 215 29 100.0 32 ............................. GCAGCGTTACAACCTGATAGAATGGGGGTATT 154 29 100.0 32 ............................. GGGGTATTCATAAAAGTGTCTGTTGGTGAGGA 93 29 100.0 32 ............................. ATGGAACAGCTATGGACGGCGAACGCCACCGC 32 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 7 29 100.0 32 GCGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTACAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCGCGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACGGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATGATATACGTTTAGT # Right flank : GAGC # 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 : GCGTTCCCCGCGCCAGCGGGGATAAACCG # 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 [3,5] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GCGTTCCCCGCGCCAGCGGGGATAAACCG 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 [1.7-70.0]%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 1 50-445 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHHW01000041.1 Salmonella enterica subsp. enterica serovar Liverpool strain CVM N46814 N46814_contig_43, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 50 29 100.0 32 ............................. CTGGAGTCTCTGTTTGTGGTCTTGGGAACGCA 111 29 100.0 32 ............................. TGGTCACTACACCAGCGGGAGAGGCAACTTTA 172 29 100.0 32 ............................. ACGCTTGCCAGTGGTCCGTTTGGCAAATATGC 233 29 100.0 32 ............................. GTGTCTCGTTGCGCCACCGGCAACTCGTGGCC 294 29 100.0 33 ............................. CACCTCATGAACCGCACCGCAGCGATTCACCGA 356 29 100.0 32 ............................. CTGCTGATTTTCCTGGTGTTAAAAGCGGTGAG 417 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================= ================== 7 29 100.0 32 GCGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCAGCGGGGATAAACCGCACGCAGTAGCCGTTTTTCATCCTCGCTCAGAG # Right flank : | # 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 : GCGTTCCCCGCGCCAGCGGGGATAAACCG # 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 [5,3] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GCGTTCCCCGCGCCAGCGGGGATAAACCG 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: F [35.0-0.0]%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 1-264 **** Predicted by CRISPRDetect 2.4 *** >NZ_LHHW01000042.1 Salmonella enterica subsp. enterica serovar Liverpool strain CVM N46814 N46814_contig_44, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ============================================================================================= ================== 1 27 89.7 93 --...........C............... ACGGCGGAACGCTGGCCGATAAGGTACGTTGCGTGCTCCCCGCGCCAGCGGGGATAAACCGAACCAAAACAGACGCGGGGCCATTCGCTACAC 121 29 100.0 32 ............................. GCGCGAGTAGACGAGGCTAGCTGCAATATCGC 182 29 100.0 32 ............................. AAAACATAGTGAGGTATAATCCTTAACAGGTT 243 22 72.4 0 .............C........------- | Deletion [265] ========== ====== ====== ====== ============================= ============================================================================================= ================== 4 29 90.5 52 GTGTTCCCCGCGCTAGCGGGGATAAACCG # Left flank : | # Right flank : TA # Questionable array : NO Score: 3.14 # Score Detail : 1:0, 2:3, 3:0, 4:0.53, 5:0, 6:0.25, 7:-2.24, 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 : GTGTTCCCCGCGCTAGCGGGGATAAACCG # Alternate repeat : GTTCCCCGCGCCAGCGGGG # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: R [1,3] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTGTTCCCCGCGCTAGCGGGGATAAACCG with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: NA [1-1] Score: 0/0.41 # AT richness analysis in flanks prediction: NA [0.0-5.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.5,0.37 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //