Array 1 174-22 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAHWWQ010000010.1 Salmonella enterica subsp. enterica serovar Javiana strain SVJ878 JVAK878_contig_10, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 173 29 100.0 33 ............................. CTCATAGCTCGGATCACCGCGATATACCGGATC 111 29 100.0 32 ............................. GGAGGACGCTACTATCGGATTCGCTCCGGGGG 50 29 96.6 0 .G........................... | ========== ====== ====== ====== ============================= ================================= ================== 3 29 98.9 33 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : ACACCAAAAATCGTTGCGCCAGTAGAAATGGTATGGCGGTTTATCCCCGCTGACGCGGGGAACACTGTTGAGTTGTACGCGGTGGCAACTGTAGGGGCGGTTTATCCCCGCTGGCGCGGGGAACACCCGCTCCCTCCCAATAACCCCATATTTGACCCCGGTTTATCCCCGCTGGCGCGGGGAACACTTCCCTGGTGCTGAGTGATGGATATTGCCGCCCGGTTTATCCCCGCTGGCGCGGGGAACACTCCCCGGAGCGAATCCGATAGTAGCGTCCTCCCGGTTTATCCCCGCTGGCGCGGGGAACACGATCCGGTATATCGCGGTGATCCGAGCTATGAGCGGTTTATCCCCGCTGGCGCGGGGAACACTAGCGGCCAATGGACCGCCACACGAGAAAATACGGTTTATCCCCGCTGGCGCGGGGAACACGGCCGCCGCCTCACCCGCGCTACCGATACTAAACCGTATTTTCTCGTGTGGCGGTCCATTGGCCGCTA # Right flank : GGGCGGCAATATCCATCACTCA # Questionable array : NO Score: 5.31 # Score Detail : 1:0, 2:3, 3:0, 4:0.95, 5:0, 6:0.25, 7:0.02, 8:0.4, 9:0.69, # 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 [3,5] 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 [-5.60,-7.20] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: R [16.7-45.0]%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 2 242-697 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAHWWQ010000010.1 Salmonella enterica subsp. enterica serovar Javiana strain SVJ878 JVAK878_contig_10, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================= ================== 242 29 100.0 32 ............................. TATTTTCTCGTGTGGCGGTCCATTGGCCGCTA 303 29 100.0 33 ............................. CTCATAGCTCGGATCACCGCGATATACCGGATC 365 29 100.0 32 ............................. GGAGGACGCTACTATCGGATTCGCTCCGGGGA 426 29 100.0 32 ............................. GGCGGCAATATCCATCACTCAGCACCAGGGAA 487 29 100.0 32 ............................. GGGTCAAATATGGGGTTATTGGGAGGGAGCGG 548 29 100.0 32 ............................. CCCCTACAGTTGCCACCGCGTACAACTCAACA 609 29 96.6 32 ............T................ CCATACCATTTCTACTGGCGCAACGATTTTTG 670 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================= ================== 8 29 97.4 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : TGAGTGATGGATATTGCCGCCCGGTTTATCCCCGCTGGCGCGGGGAACCCCCCCCGGAGCGAATCCGATAGTAGCGTCCTCCCGGTTTATCCCCGCTGGCGCGGGGAACACGATCCGGTATATCGCGGTGATCCGAGCTATGAGCGGTTTATCCCCGCTGGCGCGGGGAACACTAGCGGCCAATGGACCGCCACACGAGAAAATACGGTTTAGTATCGGTAGCGCGGGTGAGGCGGCGGCCG # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCTGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTTCCGGGGAGGCTTTTATACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTAATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGCATCATCTGCCATCCCGATATTGCGCGTGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGGAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGACCCCCTGCCGATTGG # Questionable array : NO Score: 6.13 # Score Detail : 1:0, 2:3, 3:0, 4:0.87, 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 [0-6] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [40.0-63.3]%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 3 10228-10806 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAHWWQ010000010.1 Salmonella enterica subsp. enterica serovar Javiana strain SVJ878 JVAK878_contig_10, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 10228 29 100.0 32 ............................. GCCTTTTGAGTGCCGTTTTTGCGTGTTTTGAG 10289 29 100.0 32 ............................. CCTCTAATTTCATAAAATCACCTGCAAATAAT 10350 29 100.0 32 ............................. GCCACGCCATTTACGCCTGTATAATTTACCAA 10411 29 100.0 32 ............................. AGAGCAGGAGATCGGCACCAGTTTTTCCAGCA 10472 29 100.0 32 ............................. GGGTGAGTGTAACCTATTAATATTTAATTAAA 10533 29 100.0 32 ............................. ATGTACTGAATAAAACTATCGCTAAACCCTTC 10594 29 100.0 32 ............................. ATGTACTGAATAAAACTATCGCTAAACCCTTC 10655 29 100.0 32 ............................. TTCAAACTCGATCACGGCGAAACCGTTCACGA 10716 29 100.0 32 ............................. GAAGTGGAGAGTCGCTGGAAAATGCTCATAAA 10777 29 93.1 0 A...........T................ | A [10803] ========== ====== ====== ====== ============================= ================================ ================== 10 29 99.3 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : AGATAAGCTGGTGGCGGCATTTTCCCGTGGGGTGAGGCGTAGTGTGCAGGCGCCGTTGCTAGGCCATGACGATTATCCCTGGCTGACTCAGGTCACACAAACAGAGTTGATTTCTCAGCGGGTTGATACACGCAAAGAGGTTGAACGTAGCGTAGATATTGGCTGGCTACATAGTGAAGAGGCGTGTCTTGAACGTATAGGTGAAGCAGTGGAAAAAGGAAACTGTATCGCCTGGATACGTAACTCCGTTGATGATGCGATTCGTATCTATCGCCAGCTTCAACTGAGTAAGGTCGTCGCCACGGAAAACCTTTTACTCTTCCATAGTCGCTTTGCTTTTCACGATCGTCAGCGGATTGAGTCGCAGACGCTGAATCTCTTTGGCAAACAGAGCGGCGCGCAACGTGCCGGTAAGGTCATTATCGCCACGCAGGTAATCGAACAAAGTCTGGATATTGACTGCGATGAGATGATCTCTGATTTAGCGCCGGTGGATTTAT # Right flank : GTTTCACCAGCTTATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATTCGCCCAGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCTAGATTAATGACCAGCAGCGTATTGTTCTTCTCAGCGTCACTCATTCG # 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 [0-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [58.3-48.3]%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 1 232-20 **** Predicted by CRISPRDetect 2.4 *** >NZ_JAHWWQ010000006.1 Salmonella enterica subsp. enterica serovar Javiana strain SVJ878 JVAK878_contig_6, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 231 29 93.1 32 .T........................G.. CGGTGCCCCATAGCGGCTATATGCGGACGCAA 170 29 100.0 32 ............................. CCAGTATCGGTAGCGCGGGTGAGGCGGCGACC 109 29 93.1 32 ........................G..G. CACTTTGGCGTGGGGAGGGCGCGTGGACGCGC 48 29 75.9 0 T...G....CG...C.G.....A...... | ========== ====== ====== ====== ============================= ================================ ================== 4 29 90.5 32 GGGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGCTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATAAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTGGAATGTAGTGCTGATAAAAAGTAGTTTATGAACAATGATATCCGTTTAGT # Right flank : GCAAGTTGTCGGGTAAGCCG # Questionable array : NO Score: 3.58 # Score Detail : 1:0, 2:3, 3:0, 4:0.53, 5:-1.5, 6:0.25, 7:0.01, 8:0.6, 9:0.69, # 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 : GGGTTCCCCGCGCCAGCGGGGATAAACCG # 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 [3,3] 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 [-6.30,-6.50] Score: 0/0.37 # Array degeneracy analysis prediction: R [7-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [16.7-68.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.18 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //