Array 1 61007-60275 **** Predicted by CRISPRDetect 2.4 *** >NZ_FXUT01000023.1 Listeria costaricensis isolate CLIP201600682, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== =========================== ====================================== ================== 61006 27 100.0 35 ........................... AGGAGAAGACCGGGCAATATCTTTCTCCTGATCGG 60944 27 100.0 38 ........................... AAAGTTATCTGTACGCGTAATTTAAAGCGGCGTCCTAC 60879 27 100.0 37 ........................... AAAGACATTTCCGACGGATTTTATAAAATTCTCTTTT 60815 27 100.0 37 ........................... ATAGCTAACAAGTGAATTTTCTGGATTACTTTCATTC 60751 27 100.0 38 ........................... ATGTCGAGAAATTCCAGAATTTATCACAGAAATGACCG 60686 27 100.0 38 ........................... AGAGGGTAAAACAATCTGGGATTTCCTTGAAAGTCTGC 60621 27 100.0 37 ........................... AATGCTCAGCCAGCCTCGAAGCGAATACGCGGAAATT A [60609] 60556 27 100.0 37 ........................... TTCCGGAAACAATTAGAAGGTAGCGATGACCCAAGAG A [60544] 60491 27 100.0 37 ........................... TCCTAAAAATTCAAGTTATTCAAGAAGTCCAGTGCTT A [60479] 60426 27 100.0 35 ........................... TACAGTAGTTGTAATAGCATCAGTTTTTTCGCCCA 60364 27 96.3 36 ...............G........... TCTGTTATGGTATCCACTGTTCCAGTCTCCGGTATT 60301 27 77.8 0 ......A........A.....ACC..C | ========== ====== ====== ====== =========================== ====================================== ================== 12 27 97.8 37 GTTTAAGTAGTCATTTTGAAATGTAAA # Left flank : CTCAAATCATTGCAGCTTGCCCTCGTTTGCAAGGAAATTCGTTGAGACCCTATATAAAAGTGAAGACAGTATTAAGCGATGGAAAGGATGTTCTTATTTGTGGAAAACGGAAACCACGACTTTCTTCAGAAAAGGACAAAGCGAAGATTAAGAAATATGAGCAGGAATTTGAGCGATTATTGGCAGTTTACAAAGGCAAACAATTGTGAAATAAGATTTACGTGAGATTGAACCATTTAGATACTTGTGTCGTTGAAAAGATATAAGTTGTTTTTGGAGACTAAAATATTTTTTTATAAAGTTTAAGAGAAATCTGTCGACCTGAGATAATGTAATTTTCCCGGGAGGTCGACAGAAAACGAAAAGCATTGATAGAACAGGGATTTGGGATTGGAGATGAATTTTTTTGAAAATATTTTGGGTCGAAAAATCCAAAGTTAACCGAGATCGACGGAAAATAAGTTCTGAGGTATTATGGGAGTAAGCGTTTGAAGCAGCGA # Right flank : GCTATTCATTTTACACCTCAATCATTCACCATAAACCCCATTATCCAACTAATTCCACATTCAACCCTAAACTTTCCCCGCCCAAACACTCCTTTCATTTGACCTCGCACCCTCGCCATTCTAAAATAAGCTATACCACTCGAAAGGAGGCAAACAAGATGAAGCAAAAAGAAGTTTATACTTTTTTAACTTTTCCGGGTACGGCTGAAGAGGCGGTCGCGTTTTATGTGTCGCTTTTTGATGATGCGGAAATTCTTGATATGACGCGGATTACGGAACGAGATCGGGGCGAGGTTGGGAAGATTTTGAACCTGACGTTTACGCTTGCGGGGCAGAATTTTATGGCGCTCGATATGGAGGAGCAGTATTTTGTTCCTTTTAGCTGGACGACGTCGATTCTGATTGATTGTCCGAGTGAGGCCGAGTTTGATCGCTTGTTTGAGGCTTTTTCGAAAGAGGGTCAGGTGATGATGGGGCCGGAGGAAATTGGGCCGCTCAAA # Questionable array : NO Score: 3.25 # Score Detail : 1:0, 2:0, 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 : GTTTAAGTAGTCATTTTGAAATGTAAA # 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 [Repeat is AT rich:77.78%AT] # Reference repeat match prediction: NA # Secondary Structural analysis prediction: NA [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: R [3-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [63.3-55.0]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,0.41 Confidence: MEDIUM] # Array family : NA // Array 1 29152-29498 **** Predicted by CRISPRDetect 2.4 *** >NZ_FXUT01000011.1 Listeria costaricensis isolate CLIP201600682, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================ ====================================== ================== 29152 28 100.0 36 ............................ AGCTTAGTCTATCAACATTCGCATCACATGAATAAA 29216 28 100.0 35 ............................ AATTCGTTAATTAATTCATTTAAACCGTCGCTATT 29279 28 100.0 38 ............................ ACTTCTTGCCCACTTTCACGTTCCTCAATGGTTTGTGT 29345 28 100.0 34 ............................ TTTGCTAGTAAGTTAAGGCTTGCGCAGCCATCAT 29407 28 96.4 35 ........................G... TTTAGTCAAGCCGGGAAGCGACACGGCGCGAAAGA 29470 28 82.1 0 A............ACA......A..... | G [29495] ========== ====== ====== ====== ============================ ====================================== ================== 6 28 96.4 36 GTTTAAATAGTCATTGTGAAATGTAAAT # Left flank : CTGCAACAGGTCGTCCAGTCTTGCTGGGTATCACGAAAGCATCGCTTGAAACTGACAGCTTCTTGTCAGCCGCTTCCTTCCAAGAAACAACACGTGTCTTGACGGATGCAGCGATTAAAGGAAAACGTGATGAACTTCTAGGTCTGAAAGAAAACGTAATCCTTGGTAAACTGGTTCCAGCTGGTACAGGTATCAACCGTTACCGCAATCTGAAACCACAAGTCGTTTTGGATGACACAGAGGTATCCGAAGAAACAACGAATGCTTAATTAAATGATAAACAGATCCGCTTTCGGGCGGGTCTGTTTTTTTCTGTCGACCGGAGATAATGTAAATTTGGCGGGGGATCGACAGAAATGCGAAATTGCTTGGGAGAGAAAGGGAGTGGAGGATTAGATAGAGAGTGAGGAGAGTTTGGAAGAGGAGGAAACTAGGATTTTTTGGAGGTCGACAGAAAATAGGTTTTGAGGTAAGATGGGTGTGTGGGTTTGAGACGACGG # Right flank : TTCATAGTCGTTAGTTGGCTGAAAGATTCTACGCATTCCGTTACAAGGCAATCGAATTTTCTAAAATAACAAGATGTAATCGTTCTCTTTCAGAGCTGTTACATCTTGCTAATTTAAATCTATCATCTGCTTTAACATCTAAGGAGGAGAAAAAGTGAGACAAAATGTATTATGGATTGTTGCTGATCAGTTGCGAGCACAAGCTTTGAGTTTGAATCATGATCAGAATGTTGTGACGCCTAATATTGATCGCTTAGCTCGGACAGGAATGAGTTTTTCTGATGCTGTGTCAGGATATCCAGTGTGCTGTCCATTCCGGGGGTCTATGTTGACAAGTATTTATCCGCATAAATGTGTTCCTGCGCATGAAAAACAGCTTGATCCTAGGCAGCCAACGATTGCGAATGTTTTTAATGACAATGGCTATGAGACTTTTTATCTTGGGAAATGGCATTTGGATGGCTACCAAGAGCGCTTTGGACGTGCGGCTGATCACATTA # Questionable array : NO Score: 3.08 # Score Detail : 1:0, 2:0, 3:0, 4:0.82, 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 : GTTTAAATAGTCATTGTGAAATGTAAAT # 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 [Repeat is AT rich:78.57%AT] # Reference repeat match prediction: NA # Secondary Structural analysis prediction: NA [-0.50,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-7] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [51.7-61.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [0.41,0.27 Confidence: LOW] # Array family : NA // Array 2 57562-57329 **** Predicted by CRISPRDetect 2.4 *** >NZ_FXUT01000011.1 Listeria costaricensis isolate CLIP201600682, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ============================== ================== 57561 36 100.0 30 .................................... TGTTGATTCTGCGTATAAGTCTATGCGCTT 57495 36 100.0 29 .................................... CGAAGAAAAACACTGTCCAGATTGTGGAG 57430 36 100.0 30 .................................... AAATTTGATCATTTCAGTGATGAAGATTTG 57364 36 88.9 0 ..........................T....AC.C. | ========== ====== ====== ====== ==================================== ============================== ================== 4 36 97.2 30 GTTTTAGTCCTCTTTCATTTAGAGGTAGTCTTTCAC # Left flank : CTCTTTCATTTAGAGGTAGTCTTTCACATATATTTAACAACAACCAACAAATTTAA # Right flank : ATTATACCATCGCACTGGCTCAATGCAACAGCTCGCAAAATAAATCAACGACCCTTGTCCTTGCCAGATCAATATCACTCTATCAATCATTCTTCAATAAACATCCACCCATTGAGGCTCACTACATGGGGCATTCCACAGGTGGATGTCTACTGGGTTACCTTTTATTTTTTAAAGTAGCGGCTGTACCTAGCAATAAAAAACCTAGAAGTATACCCACGCCTGTCGTATCGCCTGTATTCGGTAGCTTGCTAGTTTGCTTGCTTAAACTTGGCGGTTCGCTTATGGTCATCGTCGTCATTTGACTTGGATGGTTCTTCTGCCTAGCTGCCTCTGTATCATTTACTGGCTTGATCATATTCGGTTTTGACGAATCCTTGCCACCTGCGCTACCTTTCAAACCGCCAGAAGAATCTTCTCTTGTCACAACAATAACCGTACGCTCAAAGGTTGCCGTTTCCCCGTCAGAATCCATTACTTCATAGGTCACATGATAGGTG # Questionable array : NO Score: 2.72 # Score Detail : 1:0, 2:0, 3:0, 4:0.86, 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 : GTTTTAGTCCTCTTTCATTTAGAGGTAGTCTTTCAC # 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 [Repeat is AT rich:63.89%AT] # Reference repeat match prediction: NA # Secondary Structural analysis prediction: NA [-5.50,-5.50] Score: 0/0.37 # Array degeneracy analysis prediction: R [4-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [55.0-70.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,0.68 Confidence: HIGH] # Array family : NA // Array 1 35-316 **** Predicted by CRISPRDetect 2.4 *** >NZ_FXUT01000015.1 Listeria costaricensis isolate CLIP201600682, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================= =================================== ================== 35 29 100.0 34 ............................. GGCTTTATATAGATGTGATTACTTACTATAATCG 98 29 96.6 34 C............................ TTAATATAGAAGTTAATGCCCAGGTTAGCCAATA 161 29 96.6 35 A............................ ACGGTCGTTTACTATGTTCAAACGTGGGAAGAATG 225 29 100.0 34 ............................. TCCTCTACTTCTTCTAATTTTGTCGCATATTTCA 288 29 86.2 0 T...........C...A.......C.... | ========== ====== ====== ====== ============================= =================================== ================== 5 29 95.9 34 GGTTTAAATACTTATTGTGAAATGTAAAT # Left flank : TTGTTTCAGGAAGAAAGTGCACATAACCGACACGG # Right flank : TAATTGTGTGTTAAACTCACTGATTGCCTCGCTAGCGTTTAAATATTCATCATGAAAATTTTTCGTAATCTAATCACCAAACTTCTAAACGATCTCCCTCACTTAACCCCATACCAGTTCCCTATTCTCCCTCAATCCCCATCACACAACCCCCGTACTTTCCAAGGCCTCAAATCACCGCCCCACCCGCACAACCAAAACCACTTCCCTTGAAAAAAAATTCATCCACTCCAAAACATCTGAAAGTAAAACCAAAAATCGCGAAAACGATTTCAAATAAGAACGCTTTCTGCTAAACTGTCCATGATATAAATTATTTATGGATGGTGATAAAATGACAAAGAAAATCGTTGCTGTTACTGCATGTGCAGCGGGTATCGCCCATACTTACATGGCGGCTGAGTCAATCGAGAAAGCAGCTAAGAAACTGGGCTACGAGGCGAAAGTCGAGACGAATGGGGCCATTGGTGCCGAAAACGTTTTGACTCCTGAGGACATCG # Questionable array : NO Score: 5.78 # Score Detail : 1:0, 2:3, 3:0, 4:0.80, 5:0, 6:0.25, 7:0.01, 8:0.8, 9:0.92, # 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 : GGTTTAAATACTTATTGTGAAATGTAAAT # 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 [Repeat is AT rich:82.14%AT] # Reference repeat match prediction: F [matched GTTTTAACTACTTATTATGAAATGTAAAT with 93% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: NA [0.00,0.00] Score: 0/0.37 # Array degeneracy analysis prediction: F [0-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [31.7-68.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [4.91,0.27 Confidence: HIGH] # Array family : II-A [Matched known repeat from this family], // Array 1 3749-3516 **** Predicted by CRISPRDetect 2.4 *** >NZ_FXUT01000037.1 Listeria costaricensis isolate CLIP201600682, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ==================================== ============================== ================== 3748 36 100.0 30 .................................... AGAATGGCGATGACAAATATCGTTTTCTCG 3682 36 100.0 29 .................................... CTTTTAAATGTCTCTCTGCTGTAATGTGA 3617 36 100.0 29 .................................... ATTAGTGAGCATCAGCCAACAGTTGACTA 3552 36 86.1 0 ..........................CA....AAT. | A [3519] ========== ====== ====== ====== ==================================== ============================== ================== 4 36 96.5 30 GTTTTAGTCCTCTTTCATTTAGAGGTAGTGTTTTAC # Left flank : | # Right flank : CTCATTTAAGCTTCAAAAGCCTTTCCACAAGCTGACAATATTCATCTGAAACTTGTTTTTCAGTAACACCTCTATTTCCTAAGTGCCGTATCTCTTTCGGCTTGCAACTTTTAATTTCAAAATCATGACGACTAGCTTCAGTTAAAGACTTATTCTTCAAAGTTAATACTATTCCATGACCTTCCAATAAGTCAATCAATGACTTTGTAACAGCATTCTTTAATTTTCTGTCGTAAGATACTAATTCTCTAACCGAATTATACAATTCTAATATTGATTGACTACCGCCGCCCCTTAGTTTATCCCAGTGATCAATCTCATTTCTTACTGATTTTGCTCCATTATATTGACCATTAATACAAAAAGCTTGAATTTCTTCTAACTTTCCTATCAAATAGCTTGTTTCTTCTAGCTGATTACTAAGCTCCACCTCTCCGTTTATATAATCGACTTCATACGATTTAAATTTAACACGCCTTGATAAATCTACCCATGATTTA # Questionable array : NO Score: 2.68 # Score Detail : 1:0, 2:0, 3:0, 4:0.82, 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 : GTTTTAGTCCTCTTTCATTTAGAGGTAGTGTTTTAC # 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 [Repeat is AT rich:66.67%AT] # Reference repeat match prediction: NA # Secondary Structural analysis prediction: NA [-5.50,-5.50] Score: 0/0.37 # Array degeneracy analysis prediction: R [6-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [66.7-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0.27,0.41 Confidence: LOW] # Array family : NA // Array 1 332618-332314 **** Predicted by CRISPRDetect 2.4 *** >NZ_FXUT01000010.1 Listeria costaricensis isolate CLIP201600682, whole genome shotgun sequence Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ===================================== ============================= ================== 332617 37 100.0 29 ..................................... TGTTTGACATTTATTTAAAACAAGTATTC 332551 37 100.0 29 ..................................... AACGCCAGAACATGAGTCAGAGGAGGTCG 332485 37 97.3 29 ....................................G GAGTGATCGGACGAAAGGGTTTCGTATCA 332419 37 100.0 27 ..................................... TATAAGGGCGCGGCCATATGGCGAGGT 332355 37 83.8 0 ................A...C.......C..CC..A. | CTC,TT [332326,332330] ========== ====== ====== ====== ===================================== ============================= ================== 5 37 96.2 29 ATTTTGGTACTCTGCTGATTTATGGTATTAAGGAATA # Left flank : TTTATGGTATTAAGGAATCAAGTCTATTTTATGAGTGCAGACGACTT # Right flank : ACAGGACGCTGCCCGCGTCCTGTCAATTCACTGCCTCATTCCTCCTCACAAAATCTCAAATCCACCGGTGACACGCCTCGAAACTCACTTCGGCCTTCCATTTTTTCGATAATCGCCTCTAGCACTTCTTCGGTTGGGCTGTAGCCATTAATTACCGTCATTACATCGGCAAAGTCATACCCATGATAGGGGCTCGCCACCGAAATCAATGCGGTCGGGACCTCGTGAATGAACCACGGTGCGTCAAAGCCAGCAAGGGATTTGAATTCCGCGCGAAGTGAAGTCTGGTTCGACATCGTATCCTTTTTGACAAAGTAAAGGATTACATCATATTTAGCTCGAAATGCCGCAATGCTTTCCTTTGCACTTTCCATCATCACCCGAATATCACTATGATCAATAAAAATGACTTCATAGCCGCGTTCGCTTAACTTTTTGCCGAAAATTTCGTGGGCTTTTGGTTTTCGTTTCTGCATTTTTAGAAGAAGTTTTGTCATTCC # Questionable array : NO Score: 2.82 # Score Detail : 1:0, 2:0, 3:0, 4:0.96, 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 : ATTTTGGTACTCTGCTGATTTATGGTATTAAGGAATA # 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 [Repeat is AT rich:70.27%AT] # Reference repeat match prediction: NA # Secondary Structural analysis prediction: R [0.00,-1.70] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [55.0-53.3]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,0.78 Confidence: HIGH] # Array family : NA //