Array 1 1390-1623 **** Predicted by CRISPRDetect 2.4 *** >NZ_FOQP01000034.1 Megasphaera elsdenii strain YE34, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ================================ ==================================== ================== 1390 32 100.0 35 ................................ ATGGTCGACGCATCCATCAGGGTATCCGTGTCGAA 1457 32 100.0 35 ................................ TGTTCGAATAAAATACTGAATCCCTGCCGGTTCAT 1524 32 100.0 36 ................................ AACGATTTCACCCAGGCGGCGGGAAAAACCGCTAGT 1592 32 100.0 0 ................................ | ========== ====== ====== ====== ================================ ==================================== ================== 4 32 100.0 36 GTCGCACCCTTCACGGGTGCGTGGATTGAAAT # Left flank : TGCAATGACTCCATCCATAGTAACCTGATGTAGAAACGCCCAGTTCTGCCAGCACTCCAGATACCGAAAAATGGCGTTTCTCCTGATGGGCTTTTTCGGCTTCCTGTTTGACGCTATGGTAAATGGCGGGAATTATTTGTCTAGAATGCTGATAGCTTTTTTTAAGACATTGATGGCATCCTTGGCATCTCGTAATTCACGTTTCAAACGAGCGATTTCCTTGGCTTCATCAGATGCATAGTTTCCGGATCCGCGATATGGCATTTCCCCATTATCCCGTAATTGCTTTTGCCATCGGGACAGTGTCTGTTGGGAAATTCCTAAATTATGGGCACACCCAATCAGTCCTAAGTCACGATGATCATGGTAATATTGGACAGCATCCATTTTAAATTGTTTGTTGAACTTCGTCATACTAAGGCCCCCTATATATACTTTTATTGTATCACTTTATGGAAAACCTCAGTTTGACTTGTCCTATTTATATGCTAGCACCAACT # Right flank : | # Questionable array : NO Score: 8.86 # Score Detail : 1:0, 2:3, 3:3, 4:1.00, 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 : GTCGCACCCTTCACGGGTGCGTGGATTGAAAT # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: F Score: 4.5/4.5 # A,T distribution in repeat prediction: R [6,9] Score: 0.37/0.37 # Reference repeat match prediction: F [matched GTCGCACCCTTCGCGGGTGCGTGGATTGAAAT with 97% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [-7.10,-8.60] Score: 0.37/0.37 # Array degeneracy analysis prediction: R [1-0] Score: 0.41/0.41 # AT richness analysis in flanks prediction: F [65.0-0.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [9.27,1.15 Confidence: HIGH] # Array family : I-C [Matched known repeat from this family], // Array 1 9755-10224 **** Predicted by CRISPRDetect 2.4 *** >NZ_FOQP01000020.1 Megasphaera elsdenii strain YE34, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ======================= ===================================================== ================== 9755 23 100.0 53 ....................... GAATCCTTGAACCTCTAACAAGCTCCATATTTGTGTTTGTTGATAAGAACCAC 9831 23 100.0 51 ....................... TCGTGGGGCGTGTATAAAATACATGACTACTATATTCATGATAAGAACCAC 9905 23 100.0 50 ....................... AAAACTACCGTCATAGCCGTTCATGTGCTGGAGCAGGTGATAAGAACCAC 9978 23 100.0 51 ....................... AGGTTACTAAGCTGTTCGTACGGAGTTTCAAACGGCCACGATAAGAACCAC 10052 23 100.0 51 ....................... GCTTCATAACCAGCTAGCGTGCGCCGGGCTATGCCAATGGATAAGAACCAC 10126 23 100.0 52 ....................... TTTCTTTTTAGGGATAAGACCTTTCATAGGTTTCTTAGGCGATAAGAACCAT 10201 23 91.3 0 .............A........A | T [10221] ========== ====== ====== ====== ======================= ===================================================== ================== 7 23 98.8 52 AATCCCCGTAAGGGGACGGAAAC # Left flank : CCCCTGTGAATCGCCAACGCATGGCTTATAAGCGATTGAATCAATGGATTGGAGAATCATTGTTGACAAACCTGTGATTACTGCATTATTATCATGTGCCGTTCGTCATAAATTTCGGCTATGCCTAGAATTCGTGCGGGACGCCCTTTGGGCTAGGCGTCCCCTACGAAATCGCATACAGGCGATGGCAAGGAGCGTAGACCGCGCAGCCCATACTTGTCTAATAGCAGATCTTTACGAATCATGAACTACGGTTTTTGATGGATTTATGCTGTAATATAAATTAATTAGGTAATACCGTATTTATGCGCCCAACTTGCTTTTTGAAAACATAAAAAGAATCATTCCGCCCCGCTGGCTTAAAAATCAGCGATAGGACGATTTTTGAAAATCATTTTCCGCAAAAATGTGAAAAATGAGGAGAAAAGAAAATCCGCCCCGCAAAAGGCATTTTCGATGGCGCTATGAAGCCATTTATAAGGGGTGCGGATAAGAACCAC # Right flank : AAAAAGCAGTCTAATTTTCGTGTTTTCCTTTTTTGTGGAAAACTTTGATAAATTAGTCTGCTTTAGGCAGATAATGTATAAAAAAAAGAAGCTGTCGTATTTGAGCTGCCCCCCAATCGTTAGATGTTAGGTCTAACAATTGGGGGTCACATCAACTTCTGACCGTCAGCCCCCATAAGAACTCACAGGTCATCAATGAAGTCGGCCGGAACATCGAAGACCAATACGGCTACGCTTATTTGCCGACAGATTTCAAGAAAAACAACGGCTTCCTTACATCGACGAAAATGACCGAAGCCTACCACCTCTACCGCCAGCCCTATTGCGGTTGCATCTTCGGTGCCCGCGACCAGGGCCTGGATTTGGAAAAAATCCGCCAAGATGCGGAAGCCTTTTTGGCCCAGCAGGAATCGACCACAGGGAGATAATAGATGGAGGAAGATAAAAAGAACTGACGCAAGCTTAGGTAGAATCCGGCTATTCACACAAAAGGATGTTGT # Questionable array : NO Score: 5.79 # Score Detail : 1:0, 2:3, 3:0, 4:0.94, 5:0, 6:0.25, 7:-0.40, 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 : AATCCCCGTAAGGGGACGGAAAC # 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 [14,3] Score: 0.37/0.37 # Reference repeat match prediction: F [matched AATCCCCGAAAGGGGACGGAAAC with 96% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [-9.10,-9.60] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-4] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [50.0-71.7]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.28,0.64 Confidence: HIGH] # Array family : I-C [Matched known repeat from this family], // Array 1 192852-193843 **** Predicted by CRISPRDetect 2.4 *** >NZ_FOQP01000004.1 Megasphaera elsdenii strain YE34, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================ ================================= ================== 192852 28 100.0 32 ............................ AGAACAACCCGCCGGTCCGGACCGAAAAGATT 192912 28 100.0 32 ............................ GCAAGAAACTGAATAGTAACAGGGCGAAGGAA 192972 28 100.0 33 ............................ AAGTCGCCATTTCACTCACCTCTCAATATGATT 193033 28 100.0 32 ............................ GCAAGAAACTGAATAGTAACAGGGCGAAGGAA 193093 28 100.0 33 ............................ AAGTCGCCATTTCACTCACCTCTCAATATGATT 193154 28 100.0 32 ............................ AAACACGCCGTGACGCCACGTACTAAGCGGCC 193214 28 100.0 32 ............................ CATTGCCGGTCTGCTGGGCGTCGTGGAGCGCT 193274 28 100.0 32 ............................ ATCAAAGACGACGCAGTCCCCGACTTCCAGGT 193334 28 100.0 32 ............................ ATTACGCTCACCGCCTAAGCAAAGCACGTATC 193394 28 100.0 32 ............................ GACTTTTCGGCGACATTCTTTCGGACATTCTT 193454 28 100.0 32 ............................ TTCTGATGGCACCCCTTGCGGTGCAGACGAAC 193514 28 100.0 33 ............................ ATGTAGTACAAAGGAAAACTTAAGAGAAAACAT 193575 28 100.0 32 ............................ AGCCGGTGTCACCACATAGTGGATGCGGCGCC 193635 28 100.0 32 ............................ ATAGGCAAAATCCCAGCCCGGTACATCGACAT 193695 28 100.0 32 ............................ CAGAACTGTATCGGTTGGTTTGTCTGTTAATC 193755 28 100.0 32 ............................ TATACCATGCTGAAAGCGTGGAATACAGGCCA 193815 28 92.9 0 .........................T.T | A [193836] ========== ====== ====== ====== ============================ ================================= ================== 17 28 99.6 32 GGTATCTGCCGAGTAGGCAGTTTAGAAA # Left flank : GGTACGTTGAAGTGGTTCTGGTAACCGGATGTCATGCTGTCGTGGTTGCCGATGCTGCTGGCTTCGGGCAGATTGCGCAGGGCTGCGGCCGAAAGGTAAGCGGCGTACTGGATTTCCTGTTCGTTCAGCTTGGTTGCCGACTGGTCTTCCGCCGGCTGGTTGATTTGGTCGCCAGGAGAGACGAGGAAGTTGATTTCCGGATGCTGCGCGAGGGCGCTATTAAGGGTCTTGTTCCAGTTAGTCTAGGCGCCGTTTGTAAGAAAAAAGAACGAAAAATGTCAAAAAGATGTAAAGAAATTACTGAAAAAGCTGCGGCACAAAATCTGGAATCATGTAATGATTAATAGTCACTGCAACCTGCATAAATTTTACCAAAAAAATAAGATGTTTTTCAGATGCAGGAAACATGCGGCCTTATAAGGCTATTTTGATTTTTGGGGAATTTTGTTTATAAGCGTTGCAGTTAGGTAGCGACGCGGTTCAACGTATGATATAATACT # Right flank : TATATTCCTTTAAAAGATAAATAATATTGAATGGGAATTTCAAATGTGGTATAATGAGAATAATTAATTCGGTATTTAATATAAGGAGGCATTTTCTGTGGGAATATTTATGGATTATGTCGTAGAAAATTCAGCGAAGAAAAAGAAAACACATAATGCTTGGCTGCAAAGTGTGGTTGATCGTATTCCTTCTTGTACCTTGTCGACGCATGTCGGTAAATTTACGAATCCTGAAGTAAAAGTAAATATTCTTGATAGAGGACAGGGAACAAATAGGGAATATGTGAGTACCGATACGGTGACACATGATATTGATATCGTTGTTTCTTCGGCAGCTTATTTAAGTACGGCGAGTTTATTGATGCTGCCTTTAGAAGATAGACAGTTGGTGCTTCTTCATCTCAAGCAGCGTGATTTAGCATTAAAAAAAGATTTCACTTCTCTCGGTATTGATTATGAAAAAGTTTGCACAGATGTTGATGGACTTTTTCAAGCCGCGC # 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 : GGTATCTGCCGAGTAGGCAGTTTAGAAA # 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:53.57%AT] # Reference repeat match prediction: F [matched GTTATCCGCCGAGTAGGCGGTTTAGAAG with 92% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-8.20,-7.70] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-3] Score: 0.41/0.41 # AT richness analysis in flanks prediction: R [63.3-78.3]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.28,0.27 Confidence: HIGH] # Array family : I-F [Matched known repeat from this family], // Array 2 197726-198412 **** Predicted by CRISPRDetect 2.4 *** >NZ_FOQP01000004.1 Megasphaera elsdenii strain YE34, whole genome shotgun sequence Array_Orientation: Forward Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================ ================================ ================== 197726 28 100.0 32 ............................ TTTACGCTGCTGCGCGTTCTGCACCGGGCTTT 197786 28 100.0 32 ............................ GTAACCGGCCGTGAAAGCCAAAGCCGAAGCGA 197846 28 100.0 32 ............................ TTTGGCTCCTGTCCTCTTTCTGATTATATTGT 197906 28 100.0 32 ............................ ACATGGCACGGCTTAAATCATCGGAAAAATAC 197966 28 100.0 32 ............................ ATATGTAGCACACGGAAACGTACTGTTCCACA 198026 28 100.0 32 ............................ TCTTGATACCGATTTACGGCCAGGACGAGCAG 198086 28 100.0 32 ............................ AGAACTTCAAAGCTTGGCTTTCGTTTGCCATT 198146 28 100.0 32 ............................ TGCATGATGAGCATGGACTTCATACCGTAACC 198206 28 100.0 32 ............................ TTCTCAGCTTAGGGAGAAGCAAACGAACCCGA 198266 28 100.0 32 ............................ TGTACCATGACCGGTGTTCCCTTGAAGACGGC 198326 28 100.0 32 ............................ ATTTTGTCCGAATATGTTGTAGACAGCTCTTT 198386 27 92.9 0 ......................G.-... | ========== ====== ====== ====== ============================ ================================ ================== 12 28 99.4 32 GTTATCTGCCGCACAGGCAGTTTAGAAA # Left flank : CTGACATTCCTCAAGCCTTGCGTTTCTTGCAGGATTACATCCATCTTACGGCGATTCGAGAGGTGGCCGCTCCTCGTATCAAGGGCTATGCCGTATATCGCCGCTATCAACCGGACAGCTCCCGCTTTCGAAAAGCCAAACGTTATGCAAAGAGAAATGGTATATCTTATGAAAAAGCCTTTAAATTGATGAAAACAAAAAAGCCTAGACGACTTCCGTACGTGCAGCTGAAAAGCAAAACGACTCAGCAGAAATTCAGCCTTTTCATTGAAAAAATAGAAGCTCCTGCTTGTGAGGGTAATTTTAACGCCTATGGTCTGAGCCAGCAGGCGACAGTACCGGAATTTTGAGGAAAATCATGTTTGATTGCCCCAAAAATTAATAAGTATCTTAAAATCAAGGAAACAAGCGGATCTTTGCCGTCTCAGAAAATTTTTGGTAAAATGAAAAAGAACGCTTGACAGTAAGTGGCTGTGCGAATTTGCGCATGTTGTCCTACA # Right flank : ATTTACTGTTGGATAGAGGTGTTTGTATGAAACAGCAAGTCGAGACCGCAGCTTTGAAAGCTATTTTACATTCTAAGCGGGCGAATATATATTATTTGGATAAATGCCGGGTCATGCAGAAGGATGGACGGGTTGTCTATTTGACGGAAGGAAAAAAGGAAAATCTTTATTGGAATATCCCTATTGCGAATACAACGGTTATTTTGTTGGGAACCGGCACTTCTATTACGCAGGCGGCGATGCGGCTTTTGGCGAGTGCCGGCGTCCTTGTTGGCTTTTGCGGCGGCGGGGGAACTCCTTTATTTGCAGGCACTGAAGTGGAATGGCTTAATCCGCAGAGTGAATATCGGCCGACAAGCTATGTACAGGGCTGGCTTTCATTTTGGTTTGATGAAGCCCGGCGGTTGGCAGTAGCAAAACACTTTCAACAACAGCGCTGTTCATTTTTGCAGCGCACTTGGGAGAAAGACCGGGAACTTTCCGATTACGGTTTTTATTTT # 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 : GTTATCTGCCGCACAGGCAGTTTAGAAA # 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:53.57%AT] # Reference repeat match prediction: F [matched GTTCACTGCCGCACAGGCAGTTTAGAAA with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: F [-8.20,-7.70] Score: 0.37/0.37 # Array degeneracy analysis prediction: F [0-2] Score: 0.41/0.41 # AT richness analysis in flanks prediction: NA [58.3-56.7]%AT Score: 0/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: F [5.28,0 Confidence: HIGH] # Array family : I-F [Matched known repeat from this family], //