Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_031323
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 658522
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:168163 original size:36 final size:36
Alignment explanation
Indices: 168064--168145 Score: 164
Period size: 36 Copynumber: 2.3 Consensus size: 36
168054 GTACTTTCGA
168064 GCTGATCTGTAACGGATCAAAGCGACCGTTAGTCGG
1 GCTGATCTGTAACGGATCAAAGCGACCGTTAGTCGG
168100 GCTGATCTGTAACGGATCAAAGCGACCGTTAGTCGG
1 GCTGATCTGTAACGGATCAAAGCGACCGTTAGTCGG
168136 GCTGATCTGT
1 GCTGATCTGT
168146 GATTGGTCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.24
Consensus pattern (36 bp):
GCTGATCTGTAACGGATCAAAGCGACCGTTAGTCGG
Left flanking sequence: Indices 167564 -- 168063
TAGAATGAAGATCAATAATGGGCGGAAAGGCTTTACACAAGACCACAGAGCGAGAGAGAGAGCCT
TCGCTTACTTGCTTAACCGTGCCCTCCTATCGTACCTATATCCCCTTTCCTTCAGTTACATCCAG
TCTCAGTGCAGCTTCCAACTACCGATGGGAGAAGGCTTGGACGTATAGCAAGATTAAATAAGAGG
TATGGCATACGGGAATGATGGTATATGAAATGAAAGGCTGGAAACAGAGCTGGAGATGAGCGCTA
GCCAATGGTTAATACTTCAGAAAGCACCTTAGCAATTACCAGTAATGCCCCTATCGACCTCCGTC
TTGTTTTTTGCTAGCTTGAGTGACGAACTTGACTATCTCATTAAACGCCGAATATCCATATATAT
TTCTTTTTTTTATGGAAGATAGTCGGCCCACTTCTAGCCGTTCCTGCGATTATGCCTGTTCTAGC
CCTACCATACACCCCTATCATCATAATATAAAGGGGTACTTTCGA
Right flanking sequence: Indices 168146 -- 168645
GATTGGTCAAGGCGACCGAGAGGACACATACCTCCTCCATATTCCTTAAATAGGAAAGACTCGGA
TACGGCATGCGAGAAGTATAATAGTTTACTGAACAACTACTTAGATCTTGATTGATTTGGATGCA
ATGGAATTTTATCATTACTCCAAAAAAAAGCCATCTCATGAGTATACATGACCCCACTACCTGTA
TAAAGCGTACATCTCTGCTCAGGGAGTAGGTCAAAGCTTTTTATAAGAAAAGTCAAAAGCTGGAA
TCCGAGAAGACAAGACCCCCTAAGAGCTTCTTGTAAACCAATTATTCGATCTGGAGATCCCAGCA
AGGCTGCCGGAGACATCACTAAACCCAGGGGTGTCTCTTGCAAAGAAGAATTCGTAGAGATTTTC
CCAGAACCCCAGTCCAGCCTACCCGACTGATATAATGACGAATTAACTCTCCGTCCTTATTAGTA
GTAGGCGAATAGTGACCCTATTTGTATGCGCATTCACACGACGGG
Found at i:180065 original size:14 final size:14
Alignment explanation
Indices: 180046--180072 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
180036 TTGTTCAGAA
180046 AAGAAACAAGGAAC
1 AAGAAACAAGGAAC
180060 AAGAAACAAGGAA
1 AAGAAACAAGGAA
180073 TGAAAAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.11, G:0.22, T:0.00
Consensus pattern (14 bp):
AAGAAACAAGGAAC
Left flanking sequence: Indices 179546 -- 180045
AAAACCATACCTAGTACATGAACTATTAAAGCCTCAATCGTATATTGACCGAACTCTGAAAGCAA
TTCCATATCATTTCTTTCGGGTACCCTTCCCCTAAGATAATCCTTAGCACTTTCCTTATGTTCTT
TGATTAAGGTTCTTATTATGTTGGGTACTGACTTAAACATAGATTCCTCATCGAACGACATAGTA
AGGTCCTCAATACCACTTTGGATATCAACTAATTCTTTTTCGCTTAATGGTAATCTAGCTTTTGC
ATTATGCAAAATTTCGAAAACTTCTTCCTTATACTTAATATTTTTTGTTTTACCCTTCTGTTCAC
TTATGTTAGTATTTTGCAATAAATGATTGTAAAACCCATTCCAAAATCTTATTAGTTCATTTTTT
TCTTCTTCTTTCCTCGGCAAATCACTCAATGACAGGTTTAACCAGATTTGATTTGGCATGGCGTT
CCGTAGTATTAGTTCGATCCATTAGGTTCTTCGATTTGTTCAGAA
Right flanking sequence: Indices 180073 -- 180572
TGAAAAGAAAGAAGGATAGTCAAATTGAACTAGTTTATATCACCTAAGGAAGTATGGGAAAGGGT
CCCACTGCTTCATTGAGAAAGAGAGCAAGAATGACGCCACCCAACAAGACGGCGATGGTTTTTTT
ATCTGGCAAGGTGCTACGTGAAGCATCCAAATCCGGGATCTCCGCGGGAAGATTTAGTGGATCAT
AAACTCTATTCACTGACTGCCTGCCAAGTCTCAACTTTGTTATACAAGTTGATTAGACTCTCTTG
AAGAGCATTCTCTAGAGTGGTATCACTATCATTCAAATATTATATAGCCTTACTTTTTTGTGAAA
GTATCACTTTTAGTGTATCCATGTTATTAACGTCGAGAGGATTAATATAATTCGCTGCATCAACA
GGGATATAAGCCCACCAAACGGTGGCTATTAAAAGTAAATAAAGCAAAAGAAGTCTGTTATCCAC
CAAATAAGAATGATTCAGAATTTCGGATAAAGTGAAATCCTTTAT
Found at i:182735 original size:21 final size:21
Alignment explanation
Indices: 182710--182752 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
182700 GCTCGAGAAC
*
182710 TCACGAACTGAAGA-GCTCACG
1 TCACGAACTAAAGATGCT-ACG
182731 TCACGAACTAAAGATGCTACG
1 TCACGAACTAAAGATGCTACG
182752 T
1 T
182753 GACGCTTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (21 bp):
TCACGAACTAAAGATGCTACG
Left flanking sequence: Indices 182210 -- 182709
GGACAGTTTCACTCAGCTGAGACCCAGAGCTTCTTCTCTTTCATATGCTACATCGGCCACATCCT
TTGAAGAATCCGAAGTAGCGATTCCCTTCCTCGCTCAGGAAAGTAAGAAGGAAAGGCATAAAGCA
AGTACTGCGAACCCCTTTAAGCACGAGATTAGACAGTTGTGATTGCGCTTTCACCCATGATGGGA
TTCTTTGGGCTAGGATGCTAAAGAGATGGCTATGAGAGGGTCTTAGCCTGTAGTAGCTTGACAGT
AGGAAGAGTCTAAAGGCCTAACCGCAGCTATTGAATCAACTATTCTTATTCAAGCTTTCTTGACG
TCTTTCTACGCGGAAAGCTATAGATTCATAGATCGGTCGTTCCAGATGTGATGTTGCAAGCCGCC
GATCAACGCAACCAATATCTGACGCGAGGCCTTTATACGATTACGATAAAGATCGAGTCGATTAG
TCAGCTTTGCCTTGTTGATAGGCTAAAGCATAGCAGCTCGAGAAC
Right flanking sequence: Indices 182753 -- 183252
GACGCTTCCTTCATATGCGGATACAAGGGCCCAGCCCATTATGACTAGTGAAGGCTCCTTTTTTG
TTTGCTTTACTTCCCCCCCCTTATTTTTTTTTCATAAGTGGTCATATTCATCTAGTTTTCTCGCT
TTAGGAGTCTGAACAAATTGAAGAACCTAATGGATCCAACTTATAGAAGGACCCGAACCCGCGTA
TCGCCTTGGTGGAATCTATAAAAGTTATGTCGAATTGCGATATGATTGAGAGGGCCCCTCTTTTA
ATGATGAGTAGGATCACATCACGACAGGGAACAAGCTCTTTGCGCCCCACGTATGGCTTCTACTG
TGATGTTCGATGAATAGTATGCCGAGGGGGCTGCTTGCTGTTTCGATTTCACTCGTTGAAGAATG
TCTTTCCTTTTCAAAACTTGTACCTGGCGGGTTTCTAAACTATACAATCAAAAGTGATAAGGTAA
TATTCGCCTGAAGCGAATGGAGACCTCTCTTTATCCGCCTTCGGG
Found at i:298181 original size:11 final size:11
Alignment explanation
Indices: 298153--298182 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
298143 TACTCGCCTT
*
298153 TATTATAATTA
1 TATTATTATTA
298164 TATTATTATTA
1 TATTATTATTA
298175 TATTATTA
1 TATTATTA
298183 AATAGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTATTATTA
Left flanking sequence: Indices 297653 -- 298152
CTTGGGGATTGCTTCTGCCCTTACTGTACTGTGCTTCCAACTACCGCCCACTTCATTAGTAAAGT
TTAAAAGCAGCAGCTAGCTTTATTGACTCCACCAGAGGTGCGTAGCGAGGTACGTGCCGATTTCC
TATTAGCTTGTGTAACTCATGTCACCTAACGAATCAATTAGCTGTTCTGATGAGCGAGTTTGCTA
TATTTTGTGTGTCTACATGGTTGATTGGCCGGCATCCCCACTACTTGTATTGATTTCGTCCCCCT
GTATGCTGTGTACCGCGTGCTGGCTTCACTCCACTTGAAGAGAGTCTCTTAGTCACCAGTGTATT
AGAGTTAAGAGAGGGGGCGGGCATATCTTTCTAAAGGACGGGGATTCGTGTACTGATTGCTTGCC
TTAGCTTCCTTCTAATGCTCGAACTACACTCTCCTAGCTTCTTGCTTCCTAGTATCAGGCCTATG
GTCCATCCAAAGGCAGGAGCTTTACGACACTTCCTTACTCGCCTT
Right flanking sequence: Indices 298183 -- 298682
AATAGAAAAGGCATATCTTGAAGACAGAAGTCGCTTAACTGCTTGCTGCGCCTATTACCTCTTTG
CTTTCTTGCATCTCGAAACTGATTCAAGGTATACTATCTCCTATCTTATATGAGATAGCTTTCAC
AGGGATTCTTGCTAAAAAGAAATTAACATAGAGAGCGACTAGAGTTCACTTCAGGAATAGGGGTT
GATAAAAGGAAATCCCTATGCAGCAGTTTATGATTTTCAACCTAACAGGGACAGACAGAGGCATT
GACATATCAAATTTGTCTCGTTTCCCTTTGAGCAGATCAGAGCTGATGACAAGAGAGAGACCAGT
TAATTAGGGTGCCCGGGGCATGCGCTCTAACTTGGATAGTTGCACGAAAAAGGGGAAAGCCCGAC
TCAACTTAACGCAAGGGCTCGTTGCAGACCGGGCGTAAAGCATGGAATTCTGCCTAACTAAGTTT
GATCGGGCCTTAAAGCCTATCCTTTTATGTATGGATACCTCGCTT
Found at i:333976 original size:18 final size:18
Alignment explanation
Indices: 333953--333989 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
333943 CTCTTTCCAT
333953 AGAGGAGAGATAAATAAA
1 AGAGGAGAGATAAATAAA
333971 AGAGGAGAGATAAATAAA
1 AGAGGAGAGATAAATAAA
333989 A
1 A
333990 AGAAAAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.27, T:0.11
Consensus pattern (18 bp):
AGAGGAGAGATAAATAAA
Left flanking sequence: Indices 333453 -- 333952
GGCAGGCTAAGTGAAATAATATACTATAGAATCTTATGAATCACGCACGGCACACTTTCTATATC
TCCTCCGTCTACAAGGTGAACAGCTTAGCTTACAGCACAGCGTGTTCGCCACCACACTGGCTGGC
TGGTGCATTGGCCTTACTGTAATAAGTCCGAAAGGTATGCCTCTTCGATTAGAACGCTCCATATC
TCGTGACACGCTCCGCGTGGCATTTTTTTTTAGAAAGTCCGTATAACATAACTTCAAAAGATTCA
TTCTTTATGAATCAAGTACCAAAAAAAGGGTGCATTGCCTCTTTGAGTGAAGAAGAGAAGGGCTT
TGTATAGACACTCTTGAGCCATGTTTTCGTCGCCCTAGGCTTACCATTATTTCATTTCATTCTAT
TGATTGGTTCGAGCTCCAAAGAACATATACATGGAGCTATGTCGACTTACGTACGTCTCGTTGAC
TAAACGATCAGGTATACCACGCCACGTATCATCCCCTCTTTCCAT
Right flanking sequence: Indices 333990 -- 334489
AGAAAAGATATAGTGATCGTGCCGTAAGACCTTGTTCGTTTCTACTTGACTAAGTAGTATTCCAC
TCGTGCAGTGGGTGTATGGGCCAGCCCATGGTCATGGTGTGGTCAGCTATGATATACTCAACTTC
TTCTTTAGTAGGTTTATCTACAACATCTGGTGGTGCCCTCGTGGGCACGTTCCTCTCTGGCTCGG
TCTGGTCTAATCGAAGTCAACTGACTCACATGGAATAGGGGTGAGTTTTCACCGAGCTGGTCGCT
TGAGTCTATAGGCTACCTCTCCTATCCGCTTTTCTACAAGGTCTACTTTCAGACCGGGCCAAGCC
TTTAGGTTGTTTAAGTAGGTTTGGGCTAGGTCGTTGCGCTCCTGCCACCTCTTGTCAAAGTAGGC
TGATGGGCAAGCCCCCTCCTGTCGCAATGGTGTGGGGCGTCAAAGGCTGTTGCCCCGTGGCCAAC
TCGAAGGGGCTGAAGTTCGACGCAGAGCTTTTTGGTTGTTAAGTT
Found at i:379386 original size:18 final size:18
Alignment explanation
Indices: 379363--379401 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
379353 AAGGTTTTCT
379363 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
*
379381 TATTGATGCTAGTGACGA
1 TATTGATGATAGTGACGA
379399 TAT
1 TAT
379402 CGATCGTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.36
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Left flanking sequence: Indices 378863 -- 379362
AATCCGTTTCCAATTCTGGTTATGGTACGGACAAAGCCCCAGAGGGCCATGACCAAGATCTTCAA
GGACATGTTGCATAAGACGAAAATGCAGTCAAGAGCCGAGACCCACCTCCGAGCGGTCTTCGAAA
GGTTACGACAGCACAACCTGAAGATGAACCCGTTAAAGTCTTTCTTTGGGCTGTCTTCGGACAAG
TTTCTTGGATTCATTGTGCGGAAAGACACAAGTCGATCCTGCACTAAAGCCATCCTCGAGATGAA
GCCACCTCGGAGAGAAAGGACTTCAAGGACGTCAGCCTACCTATAGAAGATTCATTTCCCATCTC
ATGGAAAACCCTTTTCGCTCCGCTTAGCCTTATCCCCCTCTAGGGGGATTTTAGTGATAGGTTCT
ATAGGAACTGGACGATCCTATTTGGTCAAATACCTAGCGACAAACTCCTATGTTCCTTTCATTAC
GGTATTTCTGAACAAGTTCCTGGATAACAAGCCTAAAGGTTTTCT
Right flanking sequence: Indices 379402 -- 379901
CGATCGTGACCTTGATACGGAGCTGGAACTGCTAACTATGATGAATGCGCTAACTATGGATATGA
TGCCGGAAATAGACCGATTTTATATCACCCTTCAATTCGAATTAGCAAAAGCAATGTCTCCTTGC
ATAATATGGATTCCAAACATTCATGATCTGGATGTGAATGAGTCGAATTACTTATCCCTCGGTCT
ATTAGTGAACCATCTCTCTGAAAGATGTTCCACTAGAAATATTCTTGTTATTGCTTCGACTCATA
TTCCCCAAAAAGTGGATCCCGCTCTAATAGCTCCGAATAAATTAAATACGTGCATTAAGATACGA
AGGCTTCTTATTCCACAACAACAAAAGCACTTTTTCACTCTTTCATATACTAGGGGATTTCACTT
GGAAAAGAAAATGTTCCATACTAACGGATTCGGGTCCATAACCATGGGTTCCAATGCACGAGATC
TTGTAGCACTTACCAATGAGGCCCTATCGATTAGTATTAAACAGA
Found at i:405349 original size:2 final size:2
Alignment explanation
Indices: 405342--405383 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
405332 GCCAGCCGCT
*
405342 TA TA TA TA TA T- TA TA -A TA TA TA TA TA -A TA TC TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
405381 TA T
1 TA T
405384 TATTTTCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 404842 -- 405341
GAATCTTTGCTCTTCTCTTTTGCATTTCCGCTGCCTGCGTTCTTCTTCGTGTCCGTCCGTATCGC
AAAGCTGGTCGACGCCAGCTGTAATGGTTGAAAATAGGGGTCCAACCAAAATCAAGCTTTTTTCG
ATAAAGCAAACGATTTGTTCCGACAACTTCGGACCAGATTAACCCCTTTGAATTAGCCGATCTTA
CAAGATCGATCGGGCGGGCTGGTTGGGAAGGGGTGATTAGCGGAGAAAAGAATTGCTGAGAGATA
GATTCTGGTCAGGACGAATGAGTGGCTGTGCAGCATGCTCCGGAGGAGATTGACCCTTCTCCGAG
TCAGTCCAGTCAGAAAGGGGAGGGCCCGCTGTCTAGACTGCATTTCGGGAGTTTGAACACCATCC
CATTTTAACCAAAAATACAACCCTGTCAAAGATATCTAACCTTCCTTCCTTATGAGTGGAAATCC
AATCCCGTTTTGTCTTTTTTTTTGCATAAAAAGCAGCCAGCCGCT
Right flanking sequence: Indices 405384 -- 405883
TATTTTCTATTTTTTTGAAACCCTTCTTCCGACCTTTTTTGAAAAGCGCATACTTTCTCTTCCAA
AAATGACCTCTCCAGTCGGGCCAGTCGGGAAAGGCATGAGATATTTACCTAAGCAAGCTACCTTG
AGCGGATCCCACGTTAGTCCCAAGACGTTGGTCTCTAACTCGAAAAGTAAATGCTTGAGCTTGAG
TGAGAAGGGCCTCCTCGCTTATTGACTTGAACCACTGACCTTTAGAACGAACCTATAGGACAAAA
GGAACTTAACTAAGGGCATCTGACAAAGAGCAAACAGCTTATCTCAACTACTTGACTTGAGTCCC
AGTACTGAAAGACGTAACTTCAGGAGTTTCCCTGAAAGAATAGTAAGGCTGGATGGAATGAAGGG
GAAAGGTTTACAAATAAATCAATCAAAGGAACCAAAACATAAAGAGAAGCCTAAGCTCTAGGTCG
ATGTGGTGTAGACGAGCCCCAGGAGCAAAGCGTTCTTGCTCCTTC
Found at i:407153 original size:19 final size:19
Alignment explanation
Indices: 407129--407168 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
407119 ATATTATGTG
407129 ATTAGTTAGTATTCCAAAT
1 ATTAGTTAGTATTCCAAAT
* *
407148 ATTAGTTGGTATTTCAAAT
1 ATTAGTTAGTATTCCAAAT
407167 AT
1 AT
407169 CCGATTCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (19 bp):
ATTAGTTAGTATTCCAAAT
Left flanking sequence: Indices 406629 -- 407128
TGTTGGTCCACTAGAGAAACGAGACTTCATAAGTTCAGGGACTTGAGAATGGAACAAAAAAGAGG
AAGACTCAACCGTCTTCCGAAAAGAGATGCAGCTATGTTGAAAAGACAATTATCTCGCCCGCAAA
CATATCTGGGCGGGATTAAATATATGACAGGGTTACCCGATATTGTAATCATCGTTGATCAGCAC
GAAGAATATACGGCCCTGCGAGAGTGTATCACTTTGGGAATTCCAACAATTTCTTTAATCGATAC
AAATTGTGACCCCGATCTTGCCAGTCATGAGTTTAAATCGAATGATGACGCTATATCTTCAATCC
GCTTAATTCTTAACAAATTAGTATTCGCAATTTGTGAGGGTCGTTCTAGCTATATAAGAAATCCT
TGATTAATAATAAGATAAATAACTTACTTCGAAAATCCGATAGATTTATGGAATCGGTTATTATT
TCTGAATTTCAAAAAAGAGATAAAAATAACTGGGGATATTATGTG
Right flanking sequence: Indices 407169 -- 407668
CCGATTCAAGTAGGCAAAGAGATGGTTGAATCAAAATAATTTTGTTTAAAGTTCGATTTTTTTTC
AGAGGGCAATATGAATGTGTTATCATGTTCCATCAACACACTAAAAGGGTTATACGATATATCCG
CTGTGGAAGTAGGCCAACATTTCTATTGGCAAATAGGGGGTTTCCAAGTCCATGGCCAAGTACTT
ATTACTTCTTGGGTTGTAATTGCTATCTTATTAGGTTCAGCTACTATAGCTGTTCGGAACCCACA
AACCATTCCGACTGGGGGTCAGAATTTCTTCGAATATGTTCTTGAATTCATTCGAGATGTGAGTA
AAACTCAAATTGGAGAAGAATATGGCCCTTGGGTTCCTTTTATTGGAACTATGTTTCTATTTATT
TTTGTTTCTAATTGGTCAGGAGCTCTTTTACCTTGGAAAATCATACAATTACCTCATGGAGAGTT
AGCCGCACCCACGAATGATATAAATACTACCGTTGCTTTGGCTTT
Found at i:452914 original size:20 final size:20
Alignment explanation
Indices: 452885--452923 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
452875 CCGTTGATGT
* *
452885 ATAGAGATGGGTGCGCTTCA
1 ATAGAAATGGATGCGCTTCA
452905 ATAGAAATGGATGCGCTTC
1 ATAGAAATGGATGCGCTTC
452924 CCACTAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (20 bp):
ATAGAAATGGATGCGCTTCA
Left flanking sequence: Indices 452385 -- 452884
TGGGATGAAATTCCATATGATTAGTGGACCGATAGCCTCACGTTCCTCTTATTGATGGACGAATA
GGAATTTCCCCTTTCTTCTTTTGGTCGTTTCCAAGTCTTGTGACTGTCAGTTACTCGGAAAGGAA
AGTAGGCCCACGGAATCGCTCTTCTTAGGTATTTTCTGATCCATGGGTCGCATTAAAAACGAGAT
CGATGGAGCTTTCTTCTATTATTCCTCTCGCTACGATGACGGTATTGAAATAACAAGAACCCTGG
CGGTACCAAAACGGACGCTAAGACTTTCCGGGATAGTATTAGGATCTCCTTGTCCTCGGTTGTGT
TCCAAGCTGCTTTCACTCCGCTAAGAGATATGGGGGATACTCGTCGCTGAACGCCAACCCAATCT
GGTCTTTCGTTGAAAATCTCTTTGATAAAGTGCGAGTTCGGTGGCACTGAGACAGATGACGATCC
TGGTACTACATAATGAGAGAATCTTTGCACCAAACCCGTTGATGT
Right flanking sequence: Indices 452924 -- 453423
CCACTAATTCTGTCTTGAGCCTTGAATGAACTACATTCGATTCCTTTGCGGAACCTGTGTCCACC
CTTGAAGCCTAAATTCAGTGGTTTTTGAGCGTATTGGTTCCTCTCGGGACTTGGTCTGCAACGAT
TTCCTCTGTTTCGGGGCGTACTTCTACTCTCGACCTTCTCTTCGGCCGTGTTCTAAGCTGCTTCC
ATTCACTAAGAAAGGAGAAGGCCTATTGCGTGATTCGTCCGGTTGAACCTCCTTCTTCAGTCGGG
AGGCAGACCAGAAGAGAAGTATGTCTCAGCAGTCTAAAAAGCGTATCGATGTTTCAAGCACCGGG
TCATTCTTCTTTATATTATATTGTTCCAGTTCCGAGGCAGTCGCATCAAAATGAGGCTGCAACAA
AAAAAAACTATCAGTGATTGGGCCATTCGCTCCTCGAAGGAGGGGGATCTTGTGTGGTTCAAGGT
CTTCTCGCTTCCCTCTCTTTAATTTAAGGTTCTTTCGGATTCCGG
Found at i:479740 original size:15 final size:15
Alignment explanation
Indices: 479717--479747 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
479707 TAGATCCATT
479717 ATTCAGATAACTATA
1 ATTCAGATAACTATA
*
479732 ATTCCGATAACTATA
1 ATTCAGATAACTATA
479747 A
1 A
479748 AAAGAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (15 bp):
ATTCAGATAACTATA
Left flanking sequence: Indices 479217 -- 479716
TAAGGCTCCTCCTCCGAATGAAATCCAATGGGATCCAGAGAGACCATGTCTTCATCCATAGGATG
CCAAGTACCGGGATCGATCGAAAGTTCGATTCTATCTGAACTACTCATTTTCAAATGATATCCAC
ATTGTTCACAAATATTGGTTTTTGATTTCAAAAATTTCTTATAATTTAATCCATAACAATTTTCG
CATTGAACCCACAAATGCCTGTATTTTTGAGTTACATCGAGATCATTAGACCTTTCTCTTAGAGT
TAAATCACTACTCTTCGTGTGGGTTCGTATACCGGACCTCGCGCTTTCACTACTATTTGTATGTT
TACCAAAAATACACCTAGAAATGTAACTGTCACTACTATCACTTACAATGGACGTATCCATATAG
ATTTGAGACTGAAGATAACTGTCAATACAACTATTAATGTGATTATTCCAACTATATTGAGTATC
ATACATGTAACGATTGTAGTAGGGATCTTCACTCGTAGATCCATT
Right flanking sequence: Indices 479748 -- 480247
AAAGAACTTTCTAGTTCACTCAGAAAAGAATGATCATTGTCAATTTCAAAAATCTGATTTTCAAT
ATAAAAATAGATAGCATAACTGTCTCCATTACTATCTCTAACTAAAAAAGTATCATCAGAGATGA
AATTCCGAATGTCTTTGATGCCGAATAAATGATCGACATTACTGTAACTAGAATTGTCACGACCC
CTCCAACTATGAATGTTTTTAGCTTTTCTATTCGTATCTTCACTTTGACTAGTATTTTCAATAGG
ACCAAGATTGTCCATTGATTTATTTATTCCATACCTGCGTTCTAACTCCTTCTTAAACACCATCG
AATTAAACCACCACCTTTCCATAGAGTTTTCTTCCCCTTTTAGCAGCTTGTGACAAGGCTAATAG
AATAGTTGGACAAAGAGCCTATTCTTCTTCACTTAAACAACCTATCTGCTCTTCGAGCACCTGGT
GCTCTCACTTCCTTTTTCTTCTCGGAGAATTTTCCGCTCCTTCTA
Found at i:491311 original size:21 final size:21
Alignment explanation
Indices: 491285--491325 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
491275 AAACGCCTAC
491285 GAAAAGATCGCTTGGATTTAA
1 GAAAAGATCGCTTGGATTTAA
*
491306 GAAAAGGTCGCTTGGATTTA
1 GAAAAGATCGCTTGGATTTA
491326 TCCATGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
GAAAAGATCGCTTGGATTTAA
Left flanking sequence: Indices 490785 -- 491284
ACTAGCTCTGACTTTGGGCGGGGCCCATACTAGTAAGAGAATCGCTTCTTTAATATCTTTAATAG
AAGGCCTTTACCCCTCCTGATCCAAGCTGAGCTAACAAGTCGTGCATTCCTTGCCCAATAGAGGG
CACCTCCCCGGATAGCCCGATCGGGATGATAAAAGGTTTCTTCTTTCTTAATGGCAGGCCAAGCA
GCCAAGTCCCGTGCTTTCTCCATCCTTTCTTTTAGGAATTTCCACGTGCAAGAACTTCTACTCTC
ATTGATTGAGGTGCCCTCGCTAACTCCGAGACAGGCAACCGCGTCTATCCTGCCATTACATCGAG
GTGTGCCCACCAGTTGCTAGTCTGAGTCTCTGTGCATTTTTCTAGTACCAGAATCAGACGATTCT
AATCAGACGAAACTATGGATTTTTTCGATGTTCACTAATAAATCGACTAATTAAACTCATGTTTC
TATAATCAATTCGATCCCCCGATTGAATCGGGGGCAAACGCCTAC
Right flanking sequence: Indices 491326 -- 491825
TCCATGGTTTTTTGTGTTTTTTTGTTTAGTTTAGTTTATTTCTTATCCCAAAATCCTATTTTTCT
TTCTTAATTGTAATTCATTTTAACCCCAAATAGGATGCTTTTTATTTTCTATTTAAATATGTTAT
ATATAATGTAATTTTTGACCCTTCCTTGAAAGACTAAGATATACTCTGTTCGATCTATTTCTTTA
TTTCCCCATGAATCATATGTTTGTAACAATAGGGACAGAATTTTCTCAATTCTAATCGATTAGGC
GTATTGTGCCGGTTCTTTTGAGTAATATATCTGGAAATGCCCCTTGATACCTTCTTAACACCATT
TCGGACACAACTGGTACATTCCAAAATCACCGTTACTCGCGCATCTTTCCCCTTAGCCATGAACC
TCCTTTGGATTTTTGATTTACTCAATTCTTTGATTTTCGATTCGAAACGAAGAAAAGGAAGGAAA
AAATAGAAGTTACTAACTTGAAATCCAATTCTAAAAGATCAAAAT
Found at i:541105 original size:16 final size:14
Alignment explanation
Indices: 541075--541103 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
541065 AGCTGTTGAT
541075 ACTAGATATATAAA
1 ACTAGATATATAAA
541089 ACTAGATATATAAA
1 ACTAGATATATAAA
541103 A
1 A
541104 AAGGTAACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (14 bp):
ACTAGATATATAAA
Left flanking sequence: Indices 540575 -- 541074
TTTGTCTTTTTTTAGTAGAGATCTACTCCGATGCTTACTGGAGATAGACTCCTATTTATGCTAAC
TATCTTTGTTTGGTTTTCTTTTTTATGTTTGCATGTATGGGAACCCTAGTTGAAAATGTTTACTA
CTTATGCTTTTAGAATAATAAAGACTTTTTCGTATAAATGTGCTGAAAATCAAGTTCTTTCCTTT
TTTTCTTTCTATAGTGGAGATAGTAGCACGTAATTACAGACATATTATTAAAGTGGTAAGAACGG
GTTTCGTTCTAGTGCCCGAAAAGAATATTCCAAAGCTTTTCCGTTACAGAACCGTACGTGAGATT
TTCATCTCATACGGCTCCTCCCTTATGTGCATAATGAAAAGCAAATAATATATATAATAAATAAT
AAGCTTTCAATATTCTAATTCTCAATTTAGTGGTAGTGGGGCTAGTGTTTTTACAAGAAATCTCT
AGCCTGCGAAAGATCTTTTTCTTTTTTTAGTATCAAGCTGTTGAT
Right flanking sequence: Indices 541104 -- 541603
AAGGTAACTCCAAAAATTTCTTTGTCCCCAACGCCCATGAATTTCAAGGAATTAAGAACTTCAAC
AGTCTTCTATGGGGTATCCAAAGTACGAACGAGATGGATTTTGTTGTACCAACCATTCTTGTTAA
TCCCGATCCCGATAAGGAAAGGGGGTAATTTCTAACAAAGTTTTCGTTTTTTTTAATTCCTAGGC
GTAGTGCTTTTTCCCCTATGCCGCCTATTGGTACTAGTGGAGTAGAGTTGGCCTACAATAAATAA
TCCATAGGTGTAACCTTTCGCTCAATACTAAAATCGACAATTGAAGCATCTAAGGCTGCATTAAT
CGGGAATACACGACAGAAGGAATTGGTTTATTTACAAACCTCATCTCTGCCCTTCAACTGAAACA
AACTATCAACCAGGGCTGAATCCTCAAATAAGGAAGGAAGAAGGATAATTTTGAAAAGAAGGACA
TTAATGCTTTATGAAAGCAATCTGTACGAGGCCTCACTTTCTAAG
Found at i:552413 original size:24 final size:24
Alignment explanation
Indices: 552386--552442 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
552376 AGTAAAGGCG
552386 CGTTAGCGCATCCGTTTTCTTGCT
1 CGTTAGCGCATCCGTTTTCTTGCT
552410 CGTTAGCGCATCCGTTTTCTTGCT
1 CGTTAGCGCATCCGTTTTCTTGCT
552434 CGTTAGCGC
1 CGTTAGCGC
552443 TTTAGTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.09, C:0.30, G:0.23, T:0.39
Consensus pattern (24 bp):
CGTTAGCGCATCCGTTTTCTTGCT
Left flanking sequence: Indices 551886 -- 552385
AAGTGCTAAGTTTCAGATCAGTGAATAACCCGAAACGAAAGAAGAGACATTTCTCGCTCGGCGCC
TAAAGCGCACTATGCTCCGCTTCAACAAATGAGAGTTTTCGGTGGAACCGGTGAACCACGCGAGC
TGGTTAGATGCGTGGGACAGAGGGCTCGTAGTACCTGCTAGCGCAGCTATGCAGTGGAAGGGAAG
GAGCCTAAATCGACCCCCTTCTTTCTTTTTTTTTTTCAAAGAAAAAAAAAGCAGTACAAGGAGAC
TTTTATGTCGGATGAGACTAAGCAGCTACCGACCGTTCCGACGCGCCCTTGACCTATCTTGATTA
AAACCAAAAACCTATCTAAAGTGGAGCCTAGTTTAAGCTGTCAAACAAATGATAGAATGGAAAAA
ATAACCACTAGTAGGGATATGGATGGAGTCTCGCTCAGTAAAGAGAGTTGTAGATTCCTAAGATC
ATGATAGAGTGTCCTTGACTTTAGATTAGAATCTTAGTAAAGGCG
Right flanking sequence: Indices 552443 -- 552942
TTTAGTTTTCAATAAGGACGTTTAGGCTTGACTAATAAGATAGAAAGGGCTTTTTTTTCATCAGG
ATGGGCAGGTTTGGAACCCTATTTATACAATATATAAAAAAGCCCTTTCCTTTCAAATGACAACT
GCCTCTTCCTGCTGCGAGGGCGTTGCACGAAACCAAACCGCCCCCCGCCCGATCAAGTACCAGTT
GCTTCGCTGGTAGGCCCACTTAGGTTAGGGGGGCATTGTCCCTCAGTTCTTACCAACCTCCGGTG
TGTAATCGACATGTTGCTAGCTAGAACTCGGTCGAATAAGAATCATTGATTCCCTCTGCTGTCAA
TTTCTTATTCATTCATGGCGCTCGGCCGGTGCTCCTTTCTCATCTCAAACCAGAACAACTCTGAA
CGTTAGGGAAGATAAGGGAAGACCACCTGAGCGAACCGACCGAAGGGACTTGACTTATCCGAACC
GAACGCTAGCGGCTTAAAGCTAAGCCTATCACGAGAATCAAAATC
Found at i:552450 original size:24 final size:24
Alignment explanation
Indices: 552386--552452 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
552376 AGTAAAGGCG
*
552386 CGTTAGCGCATCCGTTTTCTTGCT
1 CGTTAGCGCATCAGTTTTCTTGCT
*
552410 CGTTAGCGCATCCGTTTTCTTGCT
1 CGTTAGCGCATCAGTTTTCTTGCT
* *
552434 CGTTAGCGCTTTAGTTTTC
1 CGTTAGCGCATCAGTTTTC
552453 AATAAGGACG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.09, C:0.27, G:0.21, T:0.43
Consensus pattern (24 bp):
CGTTAGCGCATCAGTTTTCTTGCT
Left flanking sequence: Indices 551886 -- 552385
AAGTGCTAAGTTTCAGATCAGTGAATAACCCGAAACGAAAGAAGAGACATTTCTCGCTCGGCGCC
TAAAGCGCACTATGCTCCGCTTCAACAAATGAGAGTTTTCGGTGGAACCGGTGAACCACGCGAGC
TGGTTAGATGCGTGGGACAGAGGGCTCGTAGTACCTGCTAGCGCAGCTATGCAGTGGAAGGGAAG
GAGCCTAAATCGACCCCCTTCTTTCTTTTTTTTTTTCAAAGAAAAAAAAAGCAGTACAAGGAGAC
TTTTATGTCGGATGAGACTAAGCAGCTACCGACCGTTCCGACGCGCCCTTGACCTATCTTGATTA
AAACCAAAAACCTATCTAAAGTGGAGCCTAGTTTAAGCTGTCAAACAAATGATAGAATGGAAAAA
ATAACCACTAGTAGGGATATGGATGGAGTCTCGCTCAGTAAAGAGAGTTGTAGATTCCTAAGATC
ATGATAGAGTGTCCTTGACTTTAGATTAGAATCTTAGTAAAGGCG
Right flanking sequence: Indices 552453 -- 552952
AATAAGGACGTTTAGGCTTGACTAATAAGATAGAAAGGGCTTTTTTTTCATCAGGATGGGCAGGT
TTGGAACCCTATTTATACAATATATAAAAAAGCCCTTTCCTTTCAAATGACAACTGCCTCTTCCT
GCTGCGAGGGCGTTGCACGAAACCAAACCGCCCCCCGCCCGATCAAGTACCAGTTGCTTCGCTGG
TAGGCCCACTTAGGTTAGGGGGGCATTGTCCCTCAGTTCTTACCAACCTCCGGTGTGTAATCGAC
ATGTTGCTAGCTAGAACTCGGTCGAATAAGAATCATTGATTCCCTCTGCTGTCAATTTCTTATTC
ATTCATGGCGCTCGGCCGGTGCTCCTTTCTCATCTCAAACCAGAACAACTCTGAACGTTAGGGAA
GATAAGGGAAGACCACCTGAGCGAACCGACCGAAGGGACTTGACTTATCCGAACCGAACGCTAGC
GGCTTAAAGCTAAGCCTATCACGAGAATCAAAATCCTTGATCGAC
Done.