Array 1 472175-473484 **** Predicted by CRISPRDetect 2.4 *** >NZ_LSLR01000001.1 Salmonella enterica subsp. enterica strain ADRDL-LA-5-2013 NODE1, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 472175 29 100.0 32 ............................. CCTTCGTTATTTACGACATTAACATTAACCGT 472236 29 100.0 32 ............................. CTTAATGCTTTTTCGTCCGCCCATAGAAATAA 472297 29 96.6 33 ...................A......... GTATCAAAGGTCATCAGGTGTTCGCCTTTCAGC 472359 29 96.6 32 ............................A GCAGATTGGTATCTGGTACGACGACTGCCGCC 472420 29 100.0 32 ............................. ACTGTTAAAATGCTTCAGGACGGTGAAGTAAA 472481 29 100.0 32 ............................. TCCACTGTACCGCCGACAGGACTTTTTAACGT 472542 29 100.0 32 ............................. CGCAGGCGCTGGACGCGCTGCACAGACAGTCC 472603 29 100.0 32 ............................. GTGCGGTCGAGGTGGCGAGGTTGATAGCAGTA 472664 29 100.0 32 ............................. CGAATATGTTGATCGGGATTCTGGCCGCACTG 472725 29 100.0 32 ............................. CGTTTATCGCTCTGAGAGTGGCGCTCGTTACT 472786 29 100.0 32 ............................. GCGCTGACCATGATTGCAGTCAGGGTCGGCAT 472847 29 100.0 32 ............................. GGGGAATGATGAAACGAATTAGTAAAAACAAA 472908 29 100.0 32 ............................. AAATGGCATAGCCACCCCAGACAGTGGCTTCT 472969 29 100.0 32 ............................. GACCGATCCGGGAACAACCGGAACAACGCGGG 473030 29 100.0 32 ............................. CCAGTAACGCTGGCGTGATAATTTTGGTCGCC 473091 29 100.0 32 ............................. CAATACGACTGGACTGGATTTGATTCATTAAC 473152 29 100.0 32 ............................. CAGAGCCTGGAGCTCTCGACTCCTGATTTTGG 473213 29 100.0 32 ............................. GGGTAACGTCCTTTGCTGGTGTTTTTGTGTCT 473274 29 100.0 32 ............................. AAACACCAACATTACGGCACGCAAGAGGTTAT 473335 29 96.6 32 ........T.................... GTTGGAGGGCGGTTCTGATGGCGAAACTTATC 473396 29 100.0 32 ............................. TACCAACAATTCAGCGTTACGCCAACGGTAAC 473457 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 22 29 98.8 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGCGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACTTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATTGCCTGATGCTCTATCAATTTTACGGACGGCCTGCCGATGCCGTCTGTGACTTATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCGGATAAATTTTTCCATAGCGATGCATGGATCACACTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTGGTGCTGATAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGAGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGGAAAATAAAAAAATTGTCGCGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.20 # Score Detail : 1:0, 2:3, 3:0, 4:0.94, 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 [2-6] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [70.0-63.3]%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 2 483248-483948 **** Predicted by CRISPRDetect 2.4 *** >NZ_LSLR01000001.1 Salmonella enterica subsp. enterica strain ADRDL-LA-5-2013 NODE1, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 483248 29 100.0 32 ............................. CGGGTGATTTTAATGATGTGCTGACTACCGGC 483309 29 100.0 32 ............................. GCGTTCTACAGTAAGGTTTACAGCCTGAGCAA 483370 29 100.0 32 ............................. GTACGGAAATTTGTGTCAGATATTGCCGGGAA 483431 29 100.0 32 ............................. TGCCCACAGTTCGTCGTGAATTGCGCAGGATA 483492 29 100.0 32 ............................. GTTCTCAATAAATTTTCCCGGCTGCCGGATCT 483553 29 100.0 32 ............................. ATTGGGACCATTCCAATGGTCAGTTTCACGGA 483614 29 100.0 32 ............................. AAACCAGAATTGCTGAAGTAAATTGCAAAAGA 483675 29 100.0 32 ............................. ATATCGAACGGGTTACGGCTGTCGGTGTAACT 483736 29 96.6 32 ............T................ ATATTTTGGCAACTCGTCGTACATTATCGCCA 483797 29 100.0 32 ............................. TCGCACAACGCCTGGATATCCGCCCATCGGCC 483858 29 100.0 32 ............................. TCTTTGTGGTAAATATGGAATCGATTAACCCC 483919 29 100.0 0 ............................. | A [483946] ========== ====== ====== ====== ============================= ================================ ================== 12 29 99.7 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CTGATTTCTCAGCGGGTTGATACACGCAAAGAGGTTGAGCGCAGCGTAGATATTGGCTGGCTACATAGTGAAGAGGCGTGTCTTGAACATATAGGTGAAGCAGTGGAAAAAGGAAACTGTATCGCCTGGATACGTAACTCCGTTGATGATGCGATTCGTATCTATCGCCAGCTTCAACTGAGTAAGGTCGTCGCCACGGAAAACCTTTTACTCTTCCATAGTCGCTTTGCTTTTCACGATCGTCAGCGGATTGAGTCGCAGACGCTGAATCTCTTTGGCAAACAGAGCGGCGCGCAACGTGCCGGTAAGGTCATTATCGCCACGCAGGTCATCGAACAAAGTCTGGATATTGACTGCGATGAGATGATCTCTGATTTAGCGCCGGTGGATTTATTAATTCAGCGGGCCGGTCGACTACAGCGTCATATTCGCGATCGTAACGGTCTGGTGAAAAAGAGTGGGCAGGATGAGCGAGAGACGCTAGTGCTGCGCATTCTTGC # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCAGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATTCG # 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 [0-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [43.3-48.3]%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 1 252-402 **** Predicted by CRISPRDetect 2.4 *** >NZ_LSLR01000257.1 Salmonella enterica subsp. enterica strain ADRDL-LA-5-2013 NODE348, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 252 29 100.0 32 ............................. CCGGTCAGCACACCGGGTGTGCTGGTTTACGA 313 29 100.0 32 ............................. CGTTTAAAGACGGCCTGGCAAACAGCAATTTC 374 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 3 29 100.0 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATCTTACCGTTGGTAGTTTGTTAGGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGTG # Right flank : CCCCACAAATCACTGGTCGATTTCGT # Questionable array : NO Score: 5.67 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:0.25, 7:0.02, 8:0.4, 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: F [70.0-21.7]%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 34-305 **** Predicted by CRISPRDetect 2.4 *** >NZ_LSLR01000366.1 Salmonella enterica subsp. enterica strain ADRDL-LA-5-2013 NODE452, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 34 29 100.0 32 ............................. ATTAAACGCCCCATCACCATTAGGCTTGGGGT 95 29 100.0 32 ............................. GTAAACCGTGTGCTGACAGGTCATAAACTCAC 156 29 100.0 32 ............................. GTTACGCAGCCATTGAGGTGCAAACGGATCAA 217 29 100.0 32 ............................. ATTTTAGAATTACGCATTGAGCCGATGATGTA 278 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 5 29 96.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTGTCGGTGTAAGTTGCTAAATACTCAGGTAAAG # Right flank : TTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAAACTGTAAAGTAAAAAGGCCGCGGTTTCCCGGGGAGGCTTTTAGACA # Questionable array : NO Score: 5.89 # Score Detail : 1:0, 2:3, 3:0, 4:0.83, 5:0, 6:0.25, 7:0.01, 8:0.8, 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 [0-5] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [33.3-65.0]%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 18-352 **** Predicted by CRISPRDetect 2.4 *** >NZ_LSLR01000389.1 Salmonella enterica subsp. enterica strain ADRDL-LA-5-2013 NODE473, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 18 29 100.0 32 ............................. GCATTGCTGCAATCACCTCAACCGGCGATCCA 79 29 100.0 32 ............................. GTACTGGCCTATTCCACATACAGTGGCACGCG 140 29 100.0 32 ............................. CGGGCAAATGCCCGCTTTCTTGTTTCTATCAG 201 29 100.0 32 ............................. CCAAAACTGAAATGACCAGTTACGTTGATCAT 262 29 100.0 32 ............................. TGATATTTTTGGTTATTTGCGATTTAGTTTTT 323 29 96.6 0 ........T.................... | A [350] ========== ====== ====== ====== ============================= ================================ ================== 6 29 99.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CCGTATTCTCATAGCAGG # Right flank : TTTCCCCAGCATATCAGGACGTTTTTTCCGCCTTCGC # 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: F [0-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [15.0-30.0]%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 1 571-54 **** Predicted by CRISPRDetect 2.4 *** >NZ_LSLR01000075.1 Salmonella enterica subsp. enterica strain ADRDL-LA-5-2013 NODE168, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 570 28 93.1 32 ........-...........A........ GCGGGCCGCGCGGGGGATCTATCAGTTCGACC C [557] 509 29 96.6 32 ...........................G. GTAAACCGTGTGCTGACAGGTCATAACCTCAC 448 29 93.1 32 ................G........C... TCAGCTACTTGAGCAGGCAAGTGAACGAGTTA 387 29 100.0 32 ............................. CCACTGCAAACGGACCCGTATATGAGGGCGGT 326 29 100.0 32 ............................. ATACCGCCTCTTACATTGGCGCCGTATCAAAA 265 29 100.0 32 ............................. CCGGGTGCACGCTTTTATTTTTTATGGTCGCC 204 29 100.0 32 ............................. GGAACAGGCCGTGCTGTATCCGCCGGTCGACA 143 29 93.1 32 .........C............C...... GAATTGCTCGCGCATGTCCGGCAAAACTCCAG 82 29 93.1 0 ...C....................C.... | ========== ====== ====== ====== ============================= ================================ ================== 9 29 96.6 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : ATCGCGCAGGTCAGGCAAAAACCCA # Right flank : GGCGGGCCAGGCTGGGGCTCGATCCGGCCGACCGTGAGCCCTGAGCCTGCGAGG # Questionable array : NO Score: 5.90 # Score Detail : 1:0, 2:3, 3:0, 4:0.83, 5:0, 6:0.25, 7:0.01, 8:1, 9:0.81, # 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 [4-6] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [20.0-18.3]%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], //