Array 1 44-378 **** Predicted by CRISPRDetect 2.4 *** >NZ_APHD01000183.1 Salmonella enterica subsp. enterica serovar Newport str. Pond080-2TTA SEEN2TTA_29, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 44 29 100.0 32 ............................. CATTCGCTCAATAGCGGCCCGCGTGGCGGTGA 105 29 100.0 32 ............................. GGGATTATGTCCTCTAAAGACTGGCTAATCAC 166 29 100.0 32 ............................. CGCGCCCTGCGTGATTTTGAAAATCTGGTGGA 227 29 96.6 32 .........................G... TTGAATACGTCGCGATACCAGTCACTCCGGAA 288 29 93.1 32 ..C..........T............... AGGGGCGTTCCGCAGTCGGCAAGGGCTGAAAA 349 29 93.1 0 A...........T................ | A [375] ========== ====== ====== ====== ============================= ================================ ================== 6 29 97.1 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GGGATAAACCGACTAACGAAAGATTAAACCAGCGCATTGAGTTG # Right flank : GTTTCACCAGCATATCAGGACGTTTTTTCCGCCTTCGCCAGCTCTTTTACCAACGGCAGCATTATCCGCACTACATCGCGGCTACGGCGCTCAATCCGCCCTGGCAGCGCCTTGTCAATATGCTGTTGATTATCAAGCCGTACGTCGTGCCAGCTATTGCCGTTCGGGAAGGATGCATTTTTCACGCGTTGCTGGTATCCGTCTTTTTTACCCAGATTCCAGTTCGTCGCCTCAACAGAAAGCACCGATATTCCCGCTTTATCGAAAACCTCCGCATCATTACAGCAACCCGTTCCTTTGGGGTAGGATGGATTGCGTCCCGGATTGGTGTTGGCGGCGATACCATAACGGCGCGCAATCGCTAATGCCCGATCGCGGGTCAGTGTACGCACCGCTTCCGGCGTATTTTTCCCGCTATTAAAATAGAGCTTGTCGCCAACAATCAGGTTATCGAGATTAATCACCAGCAGCGTATTTTTCTTCTCAGCGTCACTCATCCG # Questionable array : NO Score: 6.11 # Score Detail : 1:0, 2:3, 3:0, 4:0.85, 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: NA [41.7-48.3]%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 33-243 **** Predicted by CRISPRDetect 2.4 *** >NZ_APHD01000216.1 Salmonella enterica subsp. enterica serovar Newport str. Pond080-2TTA SEEN2TTA_53, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 33 29 100.0 32 ............................. CAGGTTATGCGCAAAAATTAATTCATATTATA 94 29 96.6 32 .................A........... GACGAGTTCTGGAAATGGTTAGCTGATAAAGA 155 29 100.0 32 ............................. CGTTCATCGGCAGCGTCACGCAATATGAAGAT 216 28 82.8 0 ...............A.AA....-.G... | ========== ====== ====== ====== ============================= ================================ ================== 4 29 94.9 32 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : CGGTCATTTTAAAGAATCCCGTTAAACAACACG # Right flank : GTTGCATAATCATAATCTGTGTACCAGTAATGGCAGCTACAAACCTGTAAAGTAAAAAGGCCGCGTTTTCCCGGGGAGGCTTTTAGACAGGAGAAGGCCATGGCGTTAAGGATCAGGGTATTGCTCGAAAATCATAAGGGAGCTGGAGCGGATAAATCGTTGAAGGCCCGGCCAGGGTTAAGCCTGTTGGTCGAGGATGAGTCTACGTCTATCTTGTTCGATACCGGCCCTGATGGCAGTTTTATGCAAAACGCGTTGGCGATGGGGATCGACCTGTCCGATGTGTCTGCTGTGGTGCTTTCGCATGGTCATTACGATCATTGCGGCGGCGTGCCGTGGCTTCCTGATAACAGTCGAATCATCTGCCATCCCGATATTGCGCGCGAACGTTATGCGGCAATGACTTTTCTCGGTATTACCCGAAAAATAAAAAAATTGTCGTGTGAGGTGGACTATTCACGCTACCGAATGATGTACACGCGTGGCCCCCTGCCGATTGG # Questionable array : NO Score: 5.61 # Score Detail : 1:0, 2:3, 3:0, 4:0.75, 5:0, 6:0.25, 7:0.01, 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: 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 [1-5] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [33.3-63.3]%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 2 16490-16823 **** Predicted by CRISPRDetect 2.4 *** >NZ_APHD01000216.1 Salmonella enterica subsp. enterica serovar Newport str. Pond080-2TTA SEEN2TTA_53, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 16490 29 100.0 32 ............................. CCAGCCTGTAGCGTGGGGGCGTTGGGTAGCCT 16551 29 100.0 32 ............................. CATCTTTTACGCATGTTGATGTGCGTTCAAAT 16612 29 100.0 32 ............................. AAATCGTCAATAAAATTATTGGCGCGCCATCC 16673 29 100.0 32 ............................. ATAATTTGCTGAACTACGTCCGTATTGAGCTG 16734 29 100.0 32 ............................. TGGCCGGAGCCTAAAGACGGGGAGCCGCGTTT 16795 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 6 29 100.0 34 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GTACTCGCTGCCGGTGAAATTAAACCACCTCAGCCTGCGCCGGATATGCTGCCGCCAGCAATACCGGAACCTGAATCACTGGGTGATAGCGGCCATCGGGGGCATGGTTGATGAGTATGGTGGTTGTGGTCACGGAAAACGTACCGCCGCGCCTGCGGGGACGTCTTGCCGTCTGGTTACTTGAGGTTCGTGCAGGTGTTTATGTTGGCGATACCTCGAAGCGTATTCGGGAAATGATTTGGCAACAGATCACACAGCTTGGCGGAGTCGGAAACGTAGTAATGGCCTGGGCAACAAATACTGAGTCTGGTTTTGAGTTCCAGACCTGGGGTGAAAACAGACGTATTCCGGTAGATTTGGATGGACTTAGATTAGTTTCTTTTCTTCCTGTTGAAAATCAATAAGTTGAATGTTCTTTAATAATAAGGAATTGTTATTTTACCGTTGGTAGTTTGTTAGGTAGTAAAAAAGGGCTTTTAGAACAAATATATAGTTTTAGT # Right flank : GGGGGTGATAACCGCCTCGCT # 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 : 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 [70.0-11.7]%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 1 824-33 **** Predicted by CRISPRDetect 2.4 *** >NZ_APHD01000068.1 Salmonella enterica subsp. enterica serovar Newport str. Pond080-2TTA SEEN2TTA_161, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= ================================ ================== 823 29 100.0 32 ............................. TTGCGTATTTCGATTGTCTGGACATTTCGTAC 762 29 100.0 32 ............................. GCAGAATATGATTTATATAGAACCAATGAACT 701 29 100.0 32 ............................. CCGGCGTGTGTTGTTGAGGATCAGTCTGGAGA 640 29 100.0 32 ............................. CGGGCCATGTTCTTTTCCCTCTAAAAAATCCG 579 29 96.6 32 ............................C GTTGCTCAAAAAACTGAACGAGGGTAACTACC 518 29 100.0 32 ............................. ATTGTGTTGTCGCCGCTAGTGGCTTGGGTTAA 457 29 100.0 32 ............................. AATATCCACTTAAACACAACCATTATTCGCTA 396 29 100.0 1 ............................. G Deletion [367] 366 29 86.2 32 T.TC..A...................... CCGGCATCAGCGCCGATCCGTTCATAGTGCCC 305 29 100.0 32 ............................. GTCCGTCAGGTTGGATCGGATGGCATTCCGGT 244 29 100.0 32 ............................. CTTTCATTGCGCAGGGTATGCAGTCGGTTTCC 183 29 100.0 32 ............................. CGTCAGCGCGGTATTGAGGCCGGGGACCGCCC 122 29 100.0 32 ............................. AACAGGAACAGGAAAAAAAAGATTTGTCCGGT 61 29 100.0 0 ............................. | ========== ====== ====== ====== ============================= ================================ ================== 14 29 98.8 30 GTGTTCCCCGCGCCAGCGGGGATAAACCG # Left flank : GAAATCAAGCATCCCGTTGGGCGAGTTCGTGATATTGAGGCGCTGGATGAACTGTTAGCCACGTTGAGCGATGATAAACCGCGTGTGATTGCTTTGCAGCCCATTAGCCAGAAAGAAGACGCGACGCGTCTGTGTATTGAAACGTGTATTGCACGTAACTGGCGGCTGTCTATGCAAACGCATAAATATTTAAATATCGCCTGATGCATTACTAATCTTACAGACGGCCTGCCGATGCCGTCTGTGACTCATCCATTACCTTGCATTGTTTATTTTCTCTATGTGAATTTCGATGAGTGTATAAAAGCGCTGATAAATTTTTCCATAGCGATGCACGGATCACGCTATTTTGGTAAATTTAAAGAAAAAATCATTCTATGAACTTTTTTGCATCAAAATCAGCAAATTAGCTGTTCTTTAATAATTTAAATTGTTGCGATTATGTTGGTAGAATGTGGTGCTGACAAAAAGTAGTTTATAAACAATTATATCCGTTTAGT # Right flank : GACGTTTTAACAGGGTAATATTTACTTAATTAT # Questionable array : NO Score: 5.97 # Score Detail : 1:0, 2:3, 3:0, 4:0.94, 5:0, 6:0.25, 7:-0.22, 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 [0-1] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [41.7-70.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.41,5.51 Confidence: HIGH] # Array family : I-E [Matched known repeat from this family], //