Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_046754
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: 637893
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:99894 original size:20 final size:20
Alignment explanation
Indices: 99858--99896 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
99848 AAGCTACTGG
99858 TTCTGTTCTGTCATACTCTA
1 TTCTGTTCTGTCATACTCTA
*
99878 TTCTAGTTCTTTC-TACTCT
1 TTCT-GTTCTGTCATACTCT
99897 CGAGTTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.13, C:0.26, G:0.08, T:0.54
Consensus pattern (20 bp):
TTCTGTTCTGTCATACTCTA
Left flanking sequence: Indices 99358 -- 99857
CTCCGGGCCAGTCCTAAAAGCCCATCAAATTAAAGTCCGCCTTTCCCTTCCCTCAAGAGCTAAAT
CGACTGCGGATCTTAGCAGCATCGCTTATTCCTCCATCTTCTTAAATAGAAAGAGCATCGGAGTC
GTTCACAAGAACTGACTCTTCTCTTTCTCGCTTTCTAGGTTTCGAAAGAGAAGTGCTTAAATTAA
GCAGAAGTGATCAACGAAGACCTAATATATAAAGCACTGCTGCCATTTCCTTTGCTATCTTTCAG
TCCTAAAGTGAAAGTCAATCAAGAGGGTAAAGTAAACTCGATCTATCTTTCCGCCCGAACTTCTC
ACCTGGTATGTCCTGTATGCCCTACCAGGGGAATCCTGGAGTTACTGAAGGATATTCTGATTCAA
GCTCTGAACAAAAGCTCATTCTTTTCTTGTACCCTCATCGGCATCTCCTTACGCTGATTCAATAG
CAACTGGATTGTGAACAAGAGCACGTGAAAGCTCAAAGCTACTGG
Right flanking sequence: Indices 99897 -- 100396
CGAGTTACCTTTCGAGCAGACTCAGAAAAAGAAGAAGCCCACGAAGCGGTAGCAGCTACTTCTTC
TGCTTCTTCGGTTGTTGCCACCTAATTAGCTACGATCAATGAAAATATCGTAATATAAGAAAGCT
GTGCCACGAACAGCGCTTTGCCCCTTCTATTCTATATAAGCTGCACTACGCCGAATGATAAAGAT
TTCCTGCTCCCATCTATTTGTTGTGGGGCATCCCATGCTTTCTGTTGGTCAACAACCAACAAGCA
AACCTTATCTATTGTTTACTCGTACAGGCTTGACGGAGTTAAGCTGTCTGGAGGGAATCCTTTTT
AAAAAATCAATCATGCCTCAACTGGATAAATTCACTTATTTTACACAATTCTTCTGGTTATGCCT
TTTCTTCTTTACTTTCTATATAAAAATATGCAATGATGGAGATGGAGTACTTGGGATCAGCCGAA
TTCTAAAACTACGGAACCAACTCCTTTCACAACGGGGAAAGAAGA
Found at i:101505 original size:15 final size:15
Alignment explanation
Indices: 101485--101514 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
101475 TTAAATTGAA
101485 TAAGTAAAATAAAAG
1 TAAGTAAAATAAAAG
101500 TAAGTAAAATAAAAG
1 TAAGTAAAATAAAAG
101515 GCTATAACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (15 bp):
TAAGTAAAATAAAAG
Left flanking sequence: Indices 100985 -- 101484
GCACCTTACTCGACTAGAAGAGGACCAATCCGAAGGGGTCCTAACAAGGTCGGGGAGTTCTGTCC
GTCTACTTTCTTAATATGGAACTGGGATTGAGACTTTCACTTTCATGCTAGGAGTTGAAGATGGA
CTAAGCTGTTCCCCCAAGAGCAGTCCAATCTTAACGCTTAACGTCAGTAGCTCCTCGAATTCCCG
AGGCCGACCCGTAACACCTTCTACTTACTATGAACTAGGATCAACTCATAACATAAACTCAAAGA
CGCCAGAAAAGCACATTTAACGCGATTCATCAGGTTGTTCAGAGGCTCAGGCTTTGGATTAAATC
ATAAATGCACCTCAACCGAAGGTACTGCAAAAAAGGAGTCTAGTTTCATCTTCGTGATTCCCTGA
CTGTAAGGCATCCCAAGGAGCGTGAAGGATTTGAAGCTGAGTAGCCCGATAGCACAGGCAAATTG
ATTTGTTCAATTTGGCCCATCCATCTTTTTGCGATTTAAATTGAA
Right flanking sequence: Indices 101515 -- 102014
GCTATAACCTCTTCCTGCTCTTCCCAAGCAGCAAGAACAAGAGGGGATCTTGCCGATTCTGATTA
ACTTGCGAAAAACAGGGAAAACTAAATCACATCTTCCTCTTAATTAAGGGCTCGATAAGCATAAG
CCTTTTAGTCCCACAGCTCCTTACAGAACACTTGCTACCGTGGCCTAAAACGCACCTTCGTAGAG
GAACGTGCTACTTTATAAAAAGAAAAGACCGGGGCAAAGGAGCCAAGACAGTAAGACTGTTGCTA
GCACGACTTATGGCTTTTAAATCTCTTTCTTCATATATGATACCGTCCGCTTTTCTATCCGAAAC
TATAGAACAAAAGAAATATAGATATTTCCATGGTAGGAATAGGACAGTTGCACTAAGGAATAGAG
CTAGGGATTTGATAAAGGTGATAGGACAGGGTTCCCTGCCTTAGTCTCAAATAGGGCGCAAGCTA
AGGATATGTATACCTGGGTGAAACTTTTTTTATTGGGTTTATGAG
Found at i:114642 original size:14 final size:14
Alignment explanation
Indices: 114623--114650 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
114613 CAGTCACCTC
114623 CTTTATCTTTATAG
1 CTTTATCTTTATAG
114637 CTTTATCTTTATAG
1 CTTTATCTTTATAG
114651 TTAGTGGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
CTTTATCTTTATAG
Left flanking sequence: Indices 114123 -- 114622
AAACTTTCCTAATCTTGACCAACGGATACGAGAGCAAGGGATATTCCAACTGGTTGAGCTGATAC
GAGTAGTTAAAAATCCTCGTCTTCATTAAGGAAGGCGGATAAAGAATCTATTTCCTTATTCTGGG
CATCGAGGTATGTCTTTGATTCCGCCGGAAGAATGAAAGTGCTCAATCCGATCCCCTGCCTTAGC
CTTTGCTTTCCTATTCTCCCCTCTTGGGGAAGATTAGATCCTTAGTCCTCCTTCCCGGGTGCTCC
TCTTCCTGCTTCAAGGCAGGTCGGAACCATATTGAATGGGGTTATGGTTCATTGCCCTGGCATCT
GTCTTGTACGTTGGTGTTGGGCACGCTTTATTTATTTGAGTGTCCGTGTCCAAAAAGAGATTTGG
GTGTGAAGCAGGCTCTAGACCCGCTTCTGGTGCCCCTACAAGCCCAGACCAGTGTGACACCGAAG
CTCCTTTCTATGAAAGCCTCGGTCGGAGACCTTTACAGTCACCTC
Right flanking sequence: Indices 114651 -- 115150
TTAGTGGTTCTATCTTAGTTTCTTTCCATTTTCTTTTTCGATTTTTATTTTGTTTTTTCGACAGT
ACTGGATTTCGGGGAAAAGAAATCATCTTCTAAGGTCAATGAAAAACTGACTTGATTTGACCCGT
TAGATTAGACTCTTCTTGAAATCGGTCAACGTTGAGGACAACAAACTCCTCTACAACATTATCTT
ACGCAGCAGGAGCGGTATCTAAGCTGACTGAAGGGCTTTTGCCCAGTCCAGTGACATCTAAGTTG
ACTGGCCGGAATTCACTGCTCGAAAGCAGAGAATAGATTAGACTAGCGGATCGCTTTCCTTAGGT
TGAGTTGACAGCTTCGCTAGAGATTCTTTTTTTAGGGCTGCTAGAATGCGGTTTGTAGTTACACT
AATCAAAGTGTTGAAAAAGATGCCTTTTCAGGTTCCAGTCTTCTTCACTGGATTCAACTTAGGTG
GAGTAGGAGTGGAGCTTTCCCCCTTATGTTATGGAGTTTCTTCCT
Found at i:118018 original size:3 final size:3
Alignment explanation
Indices: 118010--118034 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
118000 AGGTAGAAAG
118010 AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT A
118035 TGACTGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
AGT
Left flanking sequence: Indices 117510 -- 118009
CTAGAACAAGGATGTCATTCTAATAGTTTAGAAAAAATGAGTCCAAAGGTCTCTCTCTATAGAGG
AAAAGAGGTAACTACAAATATAGCACTAAAGATCTAGCACATTCTCTCTTACCACTAGCTCCTAC
TAGTTCCTTGCTCTTTGCATTAGAATGGACAAGCTTATCTTGCTCAGTTAGGTAGATGGATAAGT
GTAATCTAACTCAGAAAGGGGCAATGGAAGTTAACCTTTGATCAGAGAACTTGCTTGGCTAGAAA
AGTATGTGTAACTAGCCTGATTAGCCTATTAAATTAGATAAGACAATCTCTAGGGCTAAGCGTAT
GGATCTGACTGGATAGCCTAGTCTTAGAAAGAAGGATTCTTTAGTAAAAGTTTTACTGCCATCCC
GCTGGTAAAGTACTGGAAGCTATATGAGAAAAAGGGTTGTATCCTTTCATTCTTATCTATCTGAA
TTGTCTCCTTATTATGCTATGGAAGTTCTTGAAAAAGGTAGAAAG
Right flanking sequence: Indices 118035 -- 118534
TGACTGTGAAGCAGCTTTTTGATTGAGTCAAGAGAATAGGAAAGATAACAAGCTTATAGAGAGAT
ATCATTGCTTCTTTTTCTGTGGAATCTCTCACTTACCTAGGAAATGAAACCCTATAGGTGAAGGA
TGCTTGGTAAGAAGAACTCATGTCCTCAACTCCAAGACTTTTTATTTTACCATTATTCCCTTTTA
GATAGAGTGTTAGTAGCTTTCCCTTTTTCTATCTTCTATTGTTTTTCATGTAACTGGGAAGACTA
GCGAGACAGACTCAACAAAGGGGAGAAAGGAAATAGATTCAATAAATACCTTAGCCACTCCCTAA
TAAGAGAGAAGGTGGCAGCTATATAGAGATAAGAGGGCATGTAGTGGATATCTAAGAATCCTTGT
GTCTAAGTGAAAGGTATGCTTCTGTCTCAATAGTATCCAAGCAGAGTGTAGTAAAGAAGAAAGAT
GGTAAAGTAGGGCTGAGAAGTTCATTGAGAGTCGACCCTTTCTAT
Found at i:123296 original size:12 final size:12
Alignment explanation
Indices: 123279--123304 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
123269 ATGAGGAGCC
123279 GCCTTGACAAAA
1 GCCTTGACAAAA
123291 GCCTTGACAAAA
1 GCCTTGACAAAA
123303 GC
1 GC
123305 ATCGATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.15
Consensus pattern (12 bp):
GCCTTGACAAAA
Left flanking sequence: Indices 122779 -- 123278
CATATACTACTGGTGCTGGAATGAAACGCAGCCTCGGAACAGAATTATGCTGCTTGCTGGGCCCT
GATGGTGGAACTGGCATTTTTGAGGGGAAGAAAGCGGCCCCCGGCAGAGTGGGCAGCATCGCTTT
CCCTCGTGTAGCTATGATGCCATTCAGAAACAACCCAAGAAAAAGAAAAAACAGTATTTCGCATA
TTATTGCCATCACTGTAAAAAAGATTGAGCTGTAGGCATCAAGGTAAGGGACCGAGATTCTATAC
TGCTGCAGAAACGGAATCAAAGGGATTGGTTGGAAGATAAAACAAGCATGATTGCCCGAGTGGTT
GGAAAATAAAGAAAGAATGATTAACTGGTTGCAGGTCCCTTGGATCATGGGCCAGAGCTACTTGG
GTAGAGACCGCTGAATTTGGACAGACCGAGGCTAGAATATGGACTTAGGCCTTTTGATGGCTGTC
ATTTTATGGGCTATTTCTATTTTTCAGGATTTCATATGAGGAGCC
Right flanking sequence: Indices 123305 -- 123804
ATCGATTAAAGCCTTGTAGATCGAAGTATGCAAAAGGGTCTAAGGGGTTCGATTACTCATTTTTG
TCCCTACAACTCTTGTCAATGAATAGCAAGGAAGTATTGATAGGGAGGGTTTTACACCAGAAAAG
AAATGGAAAGAAAGAGCTCCAGGAAATTCCTCAACTCTTCTAAAGTATAGAGATCAAAGAGTTTT
TGGGCTTCTTGATAAGACATAAACATATCTATAAAATGAGTCCATAACTTTAATTTCAATTATAT
CATTATATATGATTTGGCCCTTTCTCCTTTATATAGGATATTGAGTGAACCAATCTAGTCCAATC
CCAAACGGTTCTAGATATTCTGGAGGTGGAGCTTGTTGAGGAGGGAGGAGCTTCCCAAGATGATG
TGATGGGTGAGGTCAATTCACGTGGCCTAGCCTAGTCTCTGCAAAGCAGCAAACAAAGCCCACTC
CGCCCAATATCAAGCAAACGTCATGTCCAAGCCGAAAGACCTCTC
Found at i:168557 original size:19 final size:19
Alignment explanation
Indices: 168522--168560 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
168512 GAGCAAGCCC
*
168522 AAACAGAAGCAACAAGAAA
1 AAACAGAAGCAAAAAGAAA
168541 AAACA-AAGCAAGAAAGAAA
1 AAACAGAAGCAA-AAAGAAA
168560 A
1 A
168561 CAGCTCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.72, C:0.13, G:0.15, T:0.00
Consensus pattern (19 bp):
AAACAGAAGCAAAAAGAAA
Left flanking sequence: Indices 168022 -- 168521
TGATCTTCACTGGTCGGAGGCTAAGAGCTTTCTTTGACTCTGAGTCATATGGGATGGGTCCCTAC
TCTCACTATGACATAGTGGCCCAACGGTTCCTATGAAAGTCATAGCCGGACCTACTCTCCTCTCG
CCGATGGTTTGAGAGTTGCGTTGGCGTGACGCTAATCTACTGATATTCGAGTGCTTGAGTTTCAC
TCATGTAGAGATAACGAAGGGAAAGGGCATTTGAGGGAGAGCCCAACCCAAGGGAAGGGGCAAAG
AAAGGACCTGAGCACATTGACATCGAAGAAAAGGCCAATGAAAATAGGGAAAGTCCTATTCAAGC
CGCTTTACCGACGAGGTTAAAGAGCGGTAGCCCCTCCTTCGAGCAAGCAAGCGGCACTAAAAGCA
GGATGAAAGCAAGCAAGGAGTGTAAGCCACTTGCCCGATAGGGTAAGGAGCGGAGACCCTTCCTT
CATTCATTAAGTTTAGGGAGTCAGGGATAACAGAGGAGCAAGCCC
Right flanking sequence: Indices 168561 -- 169060
CAGCTCTTTGTCTTACTGTGCCCGAGGAAGGGAAGAAAGAAGATGACAGACAAAGCACAACGGAG
GAATGAACTTCAAGCATGGAGGGGGAAAGTAACGGCACTCAAAGCTGTCTTCCATCAACCAAGCA
TGAAACAGAAGCCATGGACTAAGATGACTGGACAGGAGCGATAAGCAGCTATCAGCCACTCGAAC
CAAGTTAGAGGTTTTTTTCATGAGAGTCTTTCTAACATTCTTCACCTGAACCCGGGAACAGCTTT
GACTTAGATACTCTATTGTCAGATAGTTGAATGGCACCGGGAATGGATTAGGGAGCAAAGGAGAT
TAGGGAAAGTCGAAAGCCCTTTTTCCAACTGAGAGGGGCAGGAGAAGGATAGAAAGGTAGTTTCC
TCCAGCAAGAGGGATGACTTCTTCCTTTCCGCAAATAACAAGCGCTTTTCTTCGCCACATCGCGT
ATAACGGGAATCGAACCCCCCTGCTGCTGGCGGGCGGATGGAGAA
Found at i:191373 original size:15 final size:16
Alignment explanation
Indices: 191353--191385 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
191343 TATATAATAT
*
191353 ATAATATAAT-CTATA
1 ATAATAGAATCCTATA
191368 ATAATAGAATCCTATA
1 ATAATAGAATCCTATA
191384 AT
1 AT
191386 TAGAATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (16 bp):
ATAATAGAATCCTATA
Left flanking sequence: Indices 190853 -- 191352
AGCGGTCCTGGAAAAAATACATTAGATATAGCAGGACTTTCTTTTCTCGGGGGATATAGAAAAAA
GTATAAGCCCATTAGAAATAGAAAGAATTGAATTAGCTAAGTCAGAATGAAGGGGGCCCAGGAAA
AGGCACAAGACGTTCTTAGATTGGACATTACCGGTCAAAGCATGGATTCTAAGCCTTTCCTCGAT
CGGTAGGAGACAATCCTGTTAAGGGTAAGGAGAAAGTAAGTAGTCGGCCTAACCTTCGGTTCCCG
TAACCAAGTTTTTTTTTTCTTACTGAATTAATCCATACTTTTTTAGAAGTGTGGGGCAAAGAGCG
ACTTCTACTTCTAACTAAAGGCGAACAGCCGGCAGTGCAAGCAAATAGAGAGCCTCCGCCCGTTT
GAGTCGTTGCGAGCCGGAAAGCGTACCGGCAGTTTGAGTCGCAAAAGGGCCGCTTGCTTAATTAT
ATTATTCATTCTAATAATAGATATAGAATATTATATATATAATAT
Right flanking sequence: Indices 191386 -- 191885
TAGAATAGAATCCATTTTTTTTTATCTAATTCTTCATTCCTGAGAAGAGGAAGAAGCAGATAGAG
CAAAGGCCTCCCCGTCGCCTTCCGTCCGCTCTTCCCGAAGTGAGCGAATTGCATGTAGAGATCTG
TAGGGGCTTATAGTTTAATTGGTTGAAACGTACCGCTCATAACGGTTAGATTGTAGGTTCGAGCC
CTACTAAGCCTACCACATCATGATTGGATAACCACGCACAGAAGATGATTTCGGGGGAACGGGAG
TGCCTTCTTTTATCGTCTTTATGGTTGGTGATAGTCATTCTTTCTCCTCATAGCATTCAGTATTC
AAGTGCGTCTTTCTAGTTGTCGAGTATCTCGTTCAATCGCTTGAATAGGTCCAACCGGGAATCGT
CGAATCTCTAACGATCGCATCTTTCTGTCTGATCGGAGGTGGCTAAGGTGGGTTCATCATGGAAG
TCTACGGTTTCTGCGGTCAGCTCGCCCTGAAAAGACTGAACTTGC
Found at i:204385 original size:22 final size:22
Alignment explanation
Indices: 204357--204406 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
204347 CCAGCATTTG
204357 CATAGCCAGAGAATCCCTCCAC
1 CATAGCCAGAGAATCCCTCCAC
* *
204379 CATAGCCAGAGATTCCCTCCAG
1 CATAGCCAGAGAATCCCTCCAC
204401 CATAGC
1 CATAGC
204407 ATTGCCAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.30, C:0.38, G:0.16, T:0.16
Consensus pattern (22 bp):
CATAGCCAGAGAATCCCTCCAC
Left flanking sequence: Indices 203857 -- 204356
CGAGTTAGCCTCCTTATGCTATCACGAGGGGAACCCTCCCTCACCCCCGCACTTTTCCTCCCCAA
ACCAAATAGAAAGATGGTCAATTAGTAAGAACTTACTTGACAGGATCATGAGATACCAAAGGAAA
CAGATGGATCTCCTTTTCGGGTCTCACCCCAGGCTGCTTTAGCCCTCATGAATCCCCTTCATACC
AAGCGACCATTGCCAATAAGATTTCAGGTGTCGCTACCCTGGACCATCAGTCTCAGTCTGATTTA
GACTTAACACCTGCTATGAGAGGTTTTCGGACACTATGTCCTTAATTTTATGTAAGAGAATAAAA
AGAAAAACATACAGCAGGAGACCGGCATTTAATAGAGCTTTGTTCCTTTTAAGGTCTCTATCCGT
GGATTGAATAGAGCTTTGTTCCTTTTAAGGTCATTCTCTATCTAGGGATTTCCTAAGTGTATTAA
GCTTAGTGCCATTACCCAAAGACTTCATAATCCCTCCAGCATTTG
Right flanking sequence: Indices 204407 -- 204906
ATTGCCAGAGAACGACATTAGTTTTACTCTAAAGGTGATCATAATGGTATAGGTACTTTGGCACA
CAAGCTGTGAGAGTGAAGGCAAGCTATCTCCATAAGGTGTTGTTAATCTTCGTGCTAACCAAACG
GGCTTCATCTTAGGCTTGCCACCTAAGGAATTGGTTTTAGTGAAACAAGCAGAAAGTTTGTTATC
GGCGGATGACGACTCCTAAGGCTTCGATCAATGGTAGAGATCCGATCCTTCTAGTGAGGAGATGG
CCTCTGGTCGTGCGGGTAGGTTGCAAGAGGCTAATGCCGAGTCCATAATGTCCGTGATAGAAGAG
TGGCTGCTGGGTGCAGATCTCGTACTTCGGTTGAAGTTTTGCAAGGAGCTCTCGCGATCGGCGCT
CAGCAACATCAAGATCTGGGTGGCGCGATTGTTGATGCTGTTGATTCCGACACTCATGGTACTGA
AGATGCAAATCCTCAAGAGCTGGGTGCTACGGTTACTGCTGTGAC
Found at i:213604 original size:17 final size:17
Alignment explanation
Indices: 213582--213615 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
213572 TGGTCCCTTA
213582 TGAAATGACTTTTCTCG
1 TGAAATGACTTTTCTCG
213599 TGAAATGACTTTTCTCG
1 TGAAATGACTTTTCTCG
213616 ATCAAAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (17 bp):
TGAAATGACTTTTCTCG
Left flanking sequence: Indices 213082 -- 213581
AGCTCGCTTGTTTCCTTCTTTCGTAAGGTTTCCGTCTTAGTAGGAACTCCCCTAGTAGCTTCTAT
TCCCCCTACCCAGTAAGTCTTCCTTTACTGTTAGCTCCTTATCTAAGGGGTAAGCCCCTGTAACT
ACTAACAAGAGAAGGTCGCTGCTGATGTCCCCCACCCACCCATTAATGAAGAAGTGGGCTACTTC
TGACCAACATCCATTCTCAAAGATGGAAGTGTTGAAAGTCCTATTAGGACCTCCAATAGCCGAAG
AGTTGAGTTCCTTCTATACAGATGCAGTTTCGTTTCCTGCTGCTTTAGTTAGGTCGTCTGTAACT
CCCGACTGAGTTCATTATGTACGCTGTCCCTTATCAGTACCACCCCATCGATAACATGCCTTGAT
TGTTCCCTTTCGTTCCCAGGCACACGCGCTGGATGCGGACATTGAATGTCCTCACCGATCAACCG
CTCATGAATGAACACCAAACAACCAAGCTTTTGACTGGTCCCTTA
Right flanking sequence: Indices 213616 -- 214115
ATCAAAATGGCAGGAATTGGGTCCTGACATGTGCCTACTGAAATACCTAGAAAGCATTCCTTCAC
TTTCCTTATAAGGGGCGCTGCCTGATTTGCATGAATGCCGAACCCCAATAAATGAGTATTGGTTC
ACGTCTTAATCATCCCATTGTTTTCAAATAGACATGCCATATTGGCTTTCTCCGAGGCCATAAGA
AGGTAGTTGCTTAGGGACCATACAAGTAGCGAATAAGGGAGTTGCTGTTGCCGCTCATACAGGAG
GGCGGATGTAACTAATGAATAGAGAAGGGGGTATCCCTGTGTCCCCCAACTGTTAGCAAAGATGG
ACCCGTACCAACTTCAATAGTCTCGGATATGCCCCCTAAGCTGTAACCACTGCGTGAAGGCCTTT
TTCAAGTAAACAGTCAACAAGTAAGTCGGCTGTTTCCGGCCGAAAGCTACATCGCAGTAATGAAT
ACAACCAATTAAGTCGGTAGCACCTAGAGCGTCGAAGCCTTTAAG
Found at i:224629 original size:13 final size:13
Alignment explanation
Indices: 224607--224641 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
224597 ATCAGACAAT
224607 AATAAGAATAATA
1 AATAAGAATAATA
*
224620 AATAATAATAATA
1 AATAAGAATAATA
224633 AA-AAGAATA
1 AATAAGAATA
224642 TTCATGAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (13 bp):
AATAAGAATAATA
Left flanking sequence: Indices 224107 -- 224606
ATCACAGATTCAGACAATGAGTAAATACTAAACCCGCAAAAGGAAGCCTGCCCTATGATTACCAA
CCTCCGTAGTCTTTGTTGGGAACGTCAAGATAGGAATAAGGAAGCACCAAAAGGACCCCAGGTTG
CTCTGTTCACCCAAGCAATACGTCATCAAGGTGTAAATAGAGTCAGCTCACTTTCAAGCAAATCA
ACAAAATAACTTATAGTAAAAGGAAACCAGATAAACATGACAATAGTCTTTCGACGCAAAATTCA
CATAGATAAGAGCAAGAGAACAAGATTCACAATATTTCAAGAGAACCCACACAAAAAAGGGAACG
GGATACCGTTATATTGGGTCAAGGTTTGCACACTCCAACTCCCACTCTCAATGCCTTTATTTAGG
TCAAGCTCCAACAGGTAGATTACACTAAAAGAAATCCACTCAGACTAACAACCTTTTTCACTTAT
TTCTTTTGAGAAAGACATTTTCATATACTGGTTCAATCAGACAAT
Right flanking sequence: Indices 224642 -- 225141
TTCATGAGGATGTTGAAGATTTATTCACATCTTTATTAGAGCAAGGGTTGATCGAGCTTCCCGAA
CCTAAGAGACCGGATGAGGTGGGACGAGTAGGAGATCCCAAATACTGTAATTCCATCGGGTTATT
TGTCATCCGATAGATTATTGTTGAGTTCTTAAAGTGAAAAAAGTTTGAAAATGATGGTGTCATTG
AAATAGACCCTCCTAAGCAACCTGTGGTCACTTCAAATGCTTGTAATAGTTGGAGATATTCTTTG
CCCGATAGCTGAGATCTCGCCAAGCATAGCCTATATCTAGATCTAGTTCTAGCACCGGAAGAGCA
ATTTCAGAGGATCTCACAAAATATGATGAAAGATATATTCAAGGAGAATGGAGCACTCGTGTTAG
CCAAAGGAGTAGGGAAGTCTGGTTTGGGCAACTCCTTATACTGAGACTTGCAAGAGCCGGTGGAA
AAAAATCCTTATGATCCGGTAGAAGCTGGAGCTGTGGAAAATCAA
Found at i:262437 original size:15 final size:15
Alignment explanation
Indices: 262417--262447 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
262407 ATAAAAAATA
262417 TAAAAAAGAAAAAGGC
1 TAAAAAA-AAAAAGGC
262433 TAAAAAAAAAAAGGC
1 TAAAAAAAAAAAGGC
262448 ACTCATCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.71, C:0.06, G:0.16, T:0.06
Consensus pattern (15 bp):
TAAAAAAAAAAAGGC
Left flanking sequence: Indices 261917 -- 262416
AGGCTGGGCTGCGTACTTTTCGGCGCCCACCTTTTCTTTAGGTGTTGGGGCAAGCCCCAGGAAAG
TCTAGGTTGGCTCCCAGCTCCATCTCGGTCGGCATCCTGCTCTCGAGGGAATGGAGTCCTGGAGC
GAACTACTCATTGCTGTCTTGCCCAAGGAAGGGCATTTGGAACATTCTTTTTAGGGAGGGAAAAC
GTGGTTGACAAGCCACTTCGAGGAGGCGACTGGAGTGCTTTCATCAAATAATGCATGTGGGCTGA
GCCATTCCCATCCCGACGTGGTGGCCCGATTCGGCCTGGCCTGGTCGGGAAGAGATTCACATAGA
GACAGACTACTGTTATCTGGGAATATCTTTCTATGTTAGCTAGCGGGGGCGGGCTTTGCTTTCCT
ATGGTAGTCCCGCGGCGGCCTCTGACCGTCCGTCCCGTCTCATCTTGATTTGGCTATACTTGTAT
GTAGCCAGCCATGTTAGCTTCACATGAGAGCCTTTATAAAAAATA
Right flanking sequence: Indices 262448 -- 262947
ACTCATCAGTCGGCCCCTTTCCTATTCAGCCTTGCCACCTCTCCAGTTAAGAGAATAGGTCCCGC
GGCCGCCCGCCTGAATCTATACTAGCTGCCACGCACGACCCGAACGATTTCAGCGCCCCTCTCCA
GATAAGAAGCAAAGCGTGCCATCACCTACAGCCCTTTCCTCTGCCGGGGACTTCCATGAAATGAA
AACGGGCGGCATCGTCGTATGCTCGACATTTGTTGCCCTGGTTTATACCCCGGAGTACTCCTATG
GCCGATCTGTCACCCAACCTCCTTAAACAACCTAAAGGCTTGGCCCCGTTCCGTTTGGAGTTGGA
GAATGGGCCTTATGGCACGGCTTAGTCAGTTATTCTCGCAGATAAGATTCGGACCGCCACTTCTC
TGAAAGCATGGTTTTTGCCTCCCTCCTTGGAGTTCGTCCATTCGTTGGGCGATCCCTTGCTCTCA
CGTTCGAGTGTTTGCTCGTCGTTTAGGCCGGTGAGTGAGATTTCT
Found at i:329013 original size:28 final size:28
Alignment explanation
Indices: 328973--329030 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
328963 AACTTTTCAA
328973 TATAAAGAAAGACCTTGTACATCTGTCC
1 TATAAAGAAAGACCTTGTACATCTGTCC
329001 TATAAAGAAAGACCTTGTACATCTGTCC
1 TATAAAGAAAGACCTTGTACATCTGTCC
329029 TA
1 TA
329031 ACTTTGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (28 bp):
TATAAAGAAAGACCTTGTACATCTGTCC
Left flanking sequence: Indices 328473 -- 328972
AGTGGGATAGCTGAAAGCTTTTGATATGGATCTTAAGTAAGCACAAACCTGTGATAAAGGTAGTT
TCCCCCTCTTGGCATTGTAGGAGTCATTCCAGTAGTTTCATTCCAAGCATAAAAAGTACCCGCAT
TGAATTCGCCTTCGTGGCAGTCTCTTAGGCGTCAGATTTTAGGCAAGCAGAAGGATCAGATAAGA
CATAGATTTATTTTAGTGGGAGTTATCCATCTAGGTCAAGCGCTAATATATACATTGATTTCCTT
TAGAGTTGAGAGTAAAATAGCTAGAAGAAGGCTAGGAAGGTGGAAGAGAAATTACCTATAATAAG
AAAGAGAATCCAATTTTATAATATGAATTTGAATGGATTCTCCACTAACTGGAAAACCTGCCAAT
CCACTCTTCCTTTTTGGTCTGCCACTACTGTCTTACTGAAGCTGGCTTGCCTTGCGTAGATCAAA
AACTTTTCAAACTCTTTTGGTCGGCTTACTAATAGAACTTTTCAA
Right flanking sequence: Indices 329031 -- 329530
ACTTTGATAACACTGGAATACATACTTTACTTCCGCGGGTATTGGCTTTCGGGCTTGATGAGCTC
CACCTTAAAGAGAAAAAAAATGGGCCTACTGCATGGGTTAATGTTGATAGGATCTGGGAGATTGG
AAAAGACATCCCGGTAAATGTATTTCTTTTAATAAAGGAAAGCTTCCACGTCACATCCGATAGTC
TGATTGGACTTCTGCTGGAACTGGCTGGTCACACTCGGTAAGACTTTTTTTATCCTGTAAGACTG
GCTTTTAATAGAACCCCTAACATCTCTAAGAAAGCATCGACCCTCGCTGATGCTCGTACATACTT
TGATTTCCGACTAAATAAAAGAGGCTTTCTTTGCAGCATCCGTCTTGCAAGCAACCTATCCCCCT
ATATTAGATTAATCGGGTTACAAAAACTCTAACGGATATAGAGCCAACGGACGCTATGGATTTGT
TGTACCATTTTACGTGCTTGAACTCAGAACACACGCCATCCGATC
Found at i:379509 original size:25 final size:25
Alignment explanation
Indices: 379464--379511 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
379454 GAAGCGAGAC
*
379464 TCGACTGTTAAGGACCCAGAGGGGA
1 TCGACTGTTAAGGACACAGAGGGGA
* *
379489 TCGACTGTTAAGGAGAGAGAGGG
1 TCGACTGTTAAGGACACAGAGGG
379512 AAGCACAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.40, T:0.17
Consensus pattern (25 bp):
TCGACTGTTAAGGACACAGAGGGGA
Left flanking sequence: Indices 378964 -- 379463
CGCATTCGCTGCATCTGAAGGGACGATTTCAGATAGGTAGGTTGGGTTGCTCGTTGTGGTTGCCC
GGACCTCGATCTAGATCCAAGATAAACCAAAAGCATGGGTCGTGGTCGGCAGATATATATGATTC
TGCCGGGGCTTGGGCTTGACTTCTTTCTTCATGAATGATTTTGGAGAAGCCTGCCTCGAGAGAGA
CATATGGCATATCTGACTGCCTGATTGGCGAGCAGCTGTCCTCATTCATAAGTCCAAAGAACTAG
CAACCAAACTGGTCGCAAGCAGGAGAGTGACCAGGCCTGATACTGATTGAAACGTTTATTTAATT
GGAAGCCGTTCAGATAGCCCTAATTAGTTTTAATTAGTTTAGTCAATGTTGAGCTGTCATATCTA
GCTGCCATATATGTAAACATGCCCTAAAAGTAAAGGGATCATATTTCCTTTAGTAACCACTTTTA
CCCATCCGCTCTTCTCCTGACCGATTGGAGGAAGAGAAGCGAGAC
Right flanking sequence: Indices 379512 -- 380011
AAGCACAAGGTTGGTGACCCGGGGGAAAGCGAATGCAGATCTCACGCAAAGTGAAATCTCAAGAT
TCAGATTGGGTTTGTGTTCGGTGTGGAGTAGATAGGGCTATTCCTTAGCAAGGCTATTCAGTAAA
GGCGAGAAGGGATCTATAGCAAGGGCAGCCCGGGTCTACCCGCAGAGTTGAGGAAGATAGATCAA
ACAGCCTTAGCGCTTTAGCTTGAACTGTAACCTTACCCTCGCTACTGACCTGTCGCTTGGCCCGA
AAGACTGGAACTAGAAGTCAACTGTGCCTAGACCTCAATCAATACGCTTACTGAGAGTACCGGTA
CCAGAACAAGAACAAGGATTTCTCTTTGGTCAAAGCCGCCGCACTTGAACCGTAACCAGCTAATG
CATCGCCTTCTATCTGCATTTCTAAGACCAGTCCCTTATTCTGCTAACCAATTAGGTTGGTTCAT
CAGGTGCCAAGGCATCTCTTTCTCCCAGGTCCCATCTCGAACATT
Found at i:381373 original size:22 final size:22
Alignment explanation
Indices: 381347--381391 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
381337 TAGTGGAGCC
381347 TTCGTGTACCAATTTCAGTGGT
1 TTCGTGTACCAATTTCAGTGGT
381369 TTCGTGTACCAATTTCAGTGGT
1 TTCGTGTACCAATTTCAGTGGT
381391 T
1 T
381392 GAGTTTCGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (22 bp):
TTCGTGTACCAATTTCAGTGGT
Left flanking sequence: Indices 380847 -- 381346
AATCACTCCGTTGGGACGGGAACATGTATCCCTCCCAACCAAAAATCTTTTTGTCTAAATCAGCT
TTCGGCCTATCGATTTAACCGGGAGCTGCTGTTGAGCACTCTCACCGGATTCCCTATGCGCTGAT
TGATGCTTCCTCTCCGACTCGATGAGACCACACTACTGAGTGAGCTTCTTTCTGGCGCTCTTCCT
AGGATTCCTAATGCCTCTTGCTTCAACACAGAATAAGGTCTTTTCTCGGCCACTTTGTCATGAAA
TGAAAGCACAGTGAGTGAGTCTTCTTTCCGAGTCGAGTACTAGGCAGTCAATGTAGAGTTCACTT
CATTTGTCAGACTCCCGGTACCGAAGCAAAGTACTCATCCGAAAAGACGGTTTGATCATGCCCTT
TGTCCTCAACCCATGGTTCTCCTATATCTCCTAACTTTCGCTTTGCTTTCTCTTGAGCCCGCATT
TCGTGTTTTTTAAGATATTAAGAGGTGAACCCGCATAGTGGAGCC
Right flanking sequence: Indices 381392 -- 381891
GAGTTTCGCACTCCCGTCATCTTCCTCTTCTTTTTGGAAAATCCCAAATAGTCATCAGAAACAAG
CTAGCCGAGCATTGATTTGGGTGTGGGTGGGGTATGGTGCCCCAACGGATGGATCTCCATCAACA
TGGGATTTTTCCGAGGGGATCAATGTCTGGTCGAACCAAGCTTCCTTCTCTCTCTCTTGCTTCCC
CACCTGTGACTGAAGCTTCCACATGAACTTGACTTTCCTATCTGAGTAGACCGAAAGTTCTACTT
TTTGGGAGGGACATTAAAAAGGTAGCTTTCTCCCTGGTCGATCAGTCGTTCAATCCTTTCCTCTT
GATCAAATGCATTTCTAAAAGATTCTCACAACACAATGGACTCCAATACTGAACTGAGACGGACC
CAGACCCCCTACCGAAAGGGCTCTGTACCTATATGTTCTTTATCTCAAGCGATAGCTTTCAAGTG
CCCGACCCTCTTCCCTTGATCAATGAGTGAGAAAGCAATAGCCAG
Found at i:413268 original size:14 final size:14
Alignment explanation
Indices: 413249--413277 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
413239 GGCTTACTGT
413249 TTAGGTAGGATAGA
1 TTAGGTAGGATAGA
413263 TTAGGTAGGATAGA
1 TTAGGTAGGATAGA
413277 T
1 T
413278 GGATGTAGTC
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:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (14 bp):
TTAGGTAGGATAGA
Left flanking sequence: Indices 412749 -- 413248
GCAAGGACCCGCAACTCTCGAAGGGGCCACCCACCGCCCGATGTAGCGATGTAGCAAATCCTCCC
TTTACTCAATGTACCGCGCTTAGCCTCTTTCAATCAAGGGAAAAAAAAAGAGTGACGAACCCGGT
CATAGGTTGGTCCAAAGAACGAGAGTCGGCTTCCTTAAGGGAGTTCTTCCTCAGTAGCTCAGTGG
TAGAGCGGTCGGCTGTTAACTGACTGGTCGTAGGTTCAAATCCTACTTGGGGAGAATTTTGAGTT
ATCGCTTTTCTGACGCCTGTTTTTCTCTTTAGTTTCTAAACTAGCAGAATCGTGGGACATCAAAA
GTGGGAAGTTGATTGTAGGGTTTTATTCTTCACTCTCGTATAGGTGAACTTGGTTCGTTCAATTC
TTAGGGAAAAGGAAGGATCCACTGTGAATGAATGGGAAGACTGGAGTAGTATCTTCATTAGCCGG
AAGGACTCCACTAGCTCGAAGAACGAACAAGAAAAGGCTTACTGT
Right flanking sequence: Indices 413278 -- 413777
GGATGTAGTCCAATGGCTAAAGCTCTGCCAGCTTCTTGTAGACTGAACTCTCTTCTCTTTAGGTT
CCGAGTTGCTTTTTTTGGGGTAAGATTTTTCTTCGCCACTAGTACCAACGAAGTTCTTGGTTATT
TGAAAGGAGGAAGGAAGATCTCCACTCATTTCATTCATTCAGTGCCTACGGCGAGGCGCGACCCA
CAACAAACAAAGGCAACTTCGTTGCTTGCTGTAGCCCTCTTTTAGTAGACTAGGCTGAGTAAGCG
TAAGCTATTTAAGTAGGCAGGGTAGGCTCGCAGCTTCGCCAGAAGCGACTAGTCGCCTCCTTTCC
TCCGCCGAAAGATGCTTAGCCAGAAGCGACGAAGGGGGGGCGTCGGGAAGGCCGACGACTACATG
ACATGAGGGAGAAGCTGTCGTAGAAGCTTTGCCCCTTGCTTTACAGAGATTGTTATGAACTGACT
AAATGACTAGATTCTCCCGGCTAAGCTAATAAATAGTATTTGTTC
Found at i:425450 original size:7 final size:7
Alignment explanation
Indices: 425438--425472 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
425428 AATGAGGACA
425438 CTTATAT
1 CTTATAT
425445 CTTATAT
1 CTTATAT
425452 CTTATAT
1 CTTATAT
425459 CTTATAT
1 CTTATAT
425466 CTTATAT
1 CTTATAT
425473 ATAGGATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (7 bp):
CTTATAT
Left flanking sequence: Indices 424938 -- 425437
CGTCGGTGAATGCTTTCTTGCCAACATGCCCTCCTTTTAGACATAGATCTATCATTACCGACTAA
GGAAGGGCAAACGTGGAAGATTTCCAATCATTTTGACAATGTCGTACCTTCCTTCTCGTTTGATC
CCTGGTACTTTCTATTTACTATTCCTCTTGAAAGCACTGTGGAATTAGACAAAGTCTTTCACCAA
GCTGACTGAATGTCGTACCCTTTGCTACTTAGATTTTCCTGCGAGTTCGATTTCTTCTTACTTAG
TAGAATGGCAACCCTTGGAGTTCGATCCAAACAAAAGCAGAATGCCGGAAAGCAAATCCAATTCA
ATCTTGACTTCCTTTTAACTTCTAGGCTTTTACCCGAGTTGCAGAGAAGAAAGAGATGAGATTGA
CCAAATCGGAATGCGCACCTTCTCTCATGCCCCTCCAATGCCTCAGTTTAGGCTATGACTGATTG
ATGAGCCTTCTATCTCCTTCGGTCAAGCAAGGCTGAATGAGGACA
Right flanking sequence: Indices 425473 -- 425972
ATAGGATATAGGCTTTCTGCCTTCGCTAACAGAAGAGAAGAAGAAAGGTTTTAGCATAGAATGAG
AGAAGGAAAAATAGCATTACTTACTTTTCTCCCATGCTTTGACAAGTGAGTGTGGGATGAGGGTG
CTCACTAATAATATAAAAGAAGAAAACGAAAGGGCAAGTTTCAATTACGAGAACGAACATTAATG
GATTACTTTGTCTCCATTGCTGGGAATTTCAATTGAATCTCCTTCCATACTTCACAAGCAGCCGC
TAGAAAAGGACTCTATTTGCTAGCCTCACATCCCTCATTACGAGCTTCTGGAGCTACTCGATTAG
CGACGGAACCGGGTGCCCTAAACTTCCTCCACCGAATTCTAGTACGGAAGAATCTCGGTCAGAGC
GGGCATATGCCAAAGGTGAATACCCCTGAAGCTACGGGTAGAGAGAGCCAATCTTGAGTGAAATA
CCGCGGCTCCTGCTTTCTCAGGTTGAGGAGTGAGTCGGAATGCTG
Found at i:430848 original size:18 final size:18
Alignment explanation
Indices: 430825--430861 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
430815 ATTTAACAAC
430825 AACATTATAAGAAAAGAT
1 AACATTATAAGAAAAGAT
430843 AACATTATAAGAAAAGAT
1 AACATTATAAGAAAAGAT
430861 A
1 A
430862 TTAATAGATA
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:0.05, G:0.11, T:0.22
Consensus pattern (18 bp):
AACATTATAAGAAAAGAT
Left flanking sequence: Indices 430325 -- 430824
TAACGCAATTCCGGGAGGAGTCGGTAATTGGGCACTGGATCCCTTCGGACCTGGAAAACGTGTAA
CGCTGGGTCGGGGTTTGGTGAACCAACTGGTCGCTCTTCTAGTTGAAGTATCGGGCCCCTTTTTC
GTTGTCTAGGTTACACCTTCGGAATACCCCAGAAAGGGAATTCTTCTCTACTTCCCGTGATCTTC
ACTTTACGCCACACCGACTCCCTTTTCGAAACGTCATAAGGCGTGGAATTAGACCAAGGGGAATC
TCCATAGGAACTAGTCCCTCAGATTTCGCACGTAGGAGATCGAGACACAGCCCCAGGGCTATGGG
GAAAGATGTAGATCGATCGCCCTAGATAGACAACTACATAGAGGGTCTCTACAAGTCTATATATT
CTTAGATTTCGTTCCCCCCGTGACGATCAATATCACAACCAATGAGGTCTGCAAGTTTCACATCT
AAGTAATACCCGATCCGGTAGTTTACGATATAGATATTTAACAAC
Right flanking sequence: Indices 430862 -- 431361
TTAATAGATATCGGTAGTTGTCCGGTCGTACCCAAACAATAAGATTCCAGAGGGAAATGCACCTA
AGATCAAATATTTCGAGCCGGCTTCCGTGGAAAATTCAGACTTTCTTTTTGATGCTGCGATCACA
TAAAAACATAAACTTTGAGGCTCAATAGCTAAATACATGGCAATTGAATCATGAGCCGAGATCAT
AAAGAGCATACTGCGAGTAGGAAGTAGAATTAATACAATGAATTCAAAAGCATCAAACCTCTCTT
GTTCGGAAGAATCGAAACACATCGAAATGGTACCAGCCGTACTTAATAATAGAAGGATTTGGCAG
AAATATGTAAAATTGTCCCTCCTAAAAAAATTATTCCAGAATAAATGGGCAATAGTTAGGAGAGG
TGCGCCAGCGGCGAGCAGAAGCAAGGTTATTAGATACCTCAGGAAAGCCCGGCCAGAACCACACG
TGCAAGTTTCCCTGCATGTGGCTCGTCCGTGATAACTTCTTCGGA
Found at i:560449 original size:13 final size:13
Alignment explanation
Indices: 560431--560456 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
560421 TTGCTGCATT
560431 ATTCATAAACTAA
1 ATTCATAAACTAA
560444 ATTCATAAACTAA
1 ATTCATAAACTAA
560457 GCTCGCAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
ATTCATAAACTAA
Left flanking sequence: Indices 559931 -- 560430
ATAGGCTGCCCCTTGAGGGCGCATTAATGAGTCGATGCTGTTACGGCTTTACGAGGTGGAGATAT
AACGGATTGAATTCCTTTGGATTGATGTAGCTTTCATTCTGAGGTAGCTCTTTCGAGAGCTTACT
TGGCAGCTTGTGTGTAATCGAATTCGAGGGTCTGATCTTACTATTTCCTTGCGTTAAGGACTACC
GGAACGGAAGTTTCGCAAACTCCATTGCTTGAGCGAACCACTATGCTTGGCTGCTTATGGCGCTT
AAAAAGTAGAATAATGGAGGCAGTTGGAATGGCCAGAAAGCTTGAACCGCTCCTTATCAGTCGCT
CCTTGTTGTCTTTGTTCGTTCTTCGGGCTAGAAAAAATCCCAGTTTCGAATCGCACTAAGCCCAA
GTAGAGCTAACGAGAGTCGCCTTGGTCCATGAAGGAAAAGCTCAAGCTCTATCTCCTTGCTCTGG
TAGCTCAAAGCCCACCGGTACTGTCGACCCTACGATTGCTGCATT
Right flanking sequence: Indices 560457 -- 560956
GCTCGCAGGATCTAAAGTGGAGTCTCGCTACATGATATGGAAATATCAATGGAAAAAGTCTCGCT
CGCTTAGACAGGAGCGATATAGGCAGGTGTTGTCTTGTTATCTTTTCACCTATCTAACTCCGGTT
CGATGGGTTCGGGTGGCCTAACGAGATTAGCATTGCAGGTCTTTTTCATATGAACGGGAAAGAAG
AGAACCTCGATCGGGCCTGAGAAAATGGTAGCCCCGATGGGAAGCCCCATATGGAATGCTCTCTG
TACTCTCTTTTCCATCATTCCAAGTGGTCCAGCGGTCGCAAGCAGGGGAATGGCTTTCCGGCTAG
TCTTTTTATCCTCAAAGCCCTATTCAAAAGCTCCGGTCTAGTCTGATAGTGGTAAAGTGGAAAAT
TACGTGAATTACGTGAAGTAGTATACCACTATGTGGTCATCTTAGTCGGCTAAGAGCCATTGCTT
TCATAAACGTGATTTCAATCGTACGTCTCGTCTCCGTCTATTCTT
Found at i:591318 original size:24 final size:24
Alignment explanation
Indices: 591285--591332 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
591275 CCCTCCCCTT
*
591285 AAGATTCCTCACCGCCTGGGTATG
1 AAGATACCTCACCGCCTGGGTATG
* *
591309 AAGATACCTCACTGCCTGGTTATG
1 AAGATACCTCACCGCCTGGGTATG
591333 TTTGCAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (24 bp):
AAGATACCTCACCGCCTGGGTATG
Left flanking sequence: Indices 590785 -- 591284
AGACAAGAACTACATTGCTATACCTGAATCAGTTTGACTCAATGCTTGCACTTAGACCTTTCCCC
CAAGCTTCCTTCTATGCTGCCAGAAGCGGAGAGGAGGGTTTTCACAACACTTAAACCGAAAGAAG
AAATGCCCTAGCTCAGCTTCCTAGCATGACACATCAGCTACGCCATCAGAGACTGAATTAGAGCC
TGGAATGATCCTCCACTTGCTAGTCATGAAATATCACCGCTCCGTCTTTCGTTGCTCTCTTAAGC
TGCTTTACGAGTGCAACCAAGTTCAAGAAACTGCTAATTAAGATACGATGCTGGTATCTATCTAA
AAGTCAATATCTGTGAGAAGCTTCTTTCTCATAAACATCCGAAGCAACGAGAGATGCCCAAAATC
CTATTTCCTCTTTCCTCCATAACCTTACCAATACTCCCTCGCCTGGAATTCTCCCAGTAAGCTGA
TCAGACACAGCCCTGGACTTCCCTTCACTACCAACCCCTCCCCTT
Right flanking sequence: Indices 591333 -- 591832
TTTGCAAGTTGCAGAAAGCATTGTATGGTCTTAAACAGGCATCACGCGCTTGGTATGATAAGTTT
TATAGCTTTTTAATCAGTAAAGGCTTTCTTATGAGCCGTAGTGATTCCTCGTTATTTATTCAAAC
TAACAGTTTGCGAACTACAATTCTTGCGGTTTATGTGGATGATATTATTATAACTGGCAGTGATA
CCTCTTATATCTCCACTCTAATCACTGAATTAAGTGCTCCGCTATAAAGAACCTCGGGAACTTGA
ACTATTTTCTTGGCATTGAGGTACTCAAGACAAGAATGATCGTGGACTTTTTTTAACACAGCAAA
AATATGCGTTGGATCTCCTCCAGAGAGCTGCTATGCTGAATTGTAAGCCCTGCTCTTCTCCAATT
AACTTTAAAATCAGTCCTCTGCTGCAGTCTCTTCTACTCCATTTCATAATCCATCTCTGTACAGA
AGCATCGTTGGAGCCCTGCAGTATATTACAAGACCTGATTTGGCC
Found at i:605661 original size:19 final size:19
Alignment explanation
Indices: 605610--605662 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
605600 CATGGATGCG
605610 AACTTTAACAAAGAAC-TT
1 AACTTTAACAAAGAACTTT
* *
605628 -A-GTTAATTAAA-AACTTT
1 AACTTTAA-CAAAGAACTTT
605645 AACTTTAACAAAGAACTT
1 AACTTTAACAAAGAACTT
605663 AGTTAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 9
0.67 0.10 0.23
Matches are distributed among these distances:
16 7 0.27
17 6 0.23
18 4 0.15
19 9 0.35
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (19 bp):
AACTTTAACAAAGAACTTT
Left flanking sequence: Indices 605110 -- 605609
ATCCTTCTCGTTCGATCCGTGCTTTTAACGAATTACCACTTATTCTGTGGCCTCTAGCCTTCTAC
CCCTCTCCTGACGTCGAGCCGCTTCGCCCCTTAGTCCAGAGCAGGAGCAGCGGATTCGCCTACTT
CAAAGTCTAAAGTCAATAATCCGGATTTCCCCTCTTTCCTTCAAGCAAGGCTGACTTCATTAGCT
ATAGGTAGACTTCACACAAATCCAATCGTACAAGCAAGTAGATCAACATCAACGTTGAATAGTTT
CATTCCATCTAGGGTTCCCTGCAAACTTCTTATATCTACCGGGGCAACAACCTCTTCCTTGAAGA
CCCTGTATTGCTTGTCTTTCTTCTCCTAGTTACTTCTTGGATTCGCCGCAAACAGATGACTAAAA
GCGCTTACTAAGCATAGTCCCGGAAATTCCAATGCAATTAGCAGCGAATCTTGCACTTGAGGAGC
AGATCTCTATCTGTAAGAGCAGATTAGGCGCATGCCATGGATGCG
Right flanking sequence: Indices 605663 -- 606162
AGTTAATTAAAAGGCTCTGCGCAGCAATTTTCCTCGTAGGCAGAGGTTGGACAGAGACTCAAACA
TATAAGGCAAAGGTGTGCAGGAAAGGCACCCGGACTTATTTCCAATCGCATATAGAGTGAGCGAA
GCACGGGTAGATCCCATTACAGATTGAGTAGGGGGAACCCCAACTAAAGTAGCAAAGAGAAAGTC
AGCAGCAATTGCTAATCTCTTGATCTATGCACTTTCAATAGCACGCAGAGGTGAGGATCGACTAA
GCATTTCCAGTAGGAGAACTCGCCCAAAGGGAACATTTAGAGTTGTTCCAGAAAGGTCCGCAGGT
GAAAGAAAAGAGACTGGCTCTCTCTATCTATTATACTTATACGCAATATCTTGAAAGGCGAAGAG
TGACTACTTCTTTCTGCTTGTATTGTACTTCCTGTTCCTGTAGTGATACAGGACTCGTGCAAGAG
CGCTTACGGCAGGAGATGAGGCTTAGAATCCAGATCAGATTCCAT
Done.