Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 121 of 141
Found at i:38483045 original size:20 final size:20
Alignment explanation
Indices: 38483002--38483050 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
38482992 CTTGTATAAT
* ** *
38483002 TTTTATTTATTTTTATTTCG
1 TTTTATTTATTTTCATGCCA
38483022 TTTTATTTATTTTCATGCCA
1 TTTTATTTATTTTCATGCCA
*
38483042 TTTTTTTTA
1 TTTTATTTA
38483051 CACATTCCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.71
Consensus pattern (20 bp):
TTTTATTTATTTTCATGCCA
Found at i:38484452 original size:19 final size:19
Alignment explanation
Indices: 38484425--38484464 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
38484415 AAATCCTTCC
38484425 TTTGATTTTGAAAAAT-ATT
1 TTTGATTTT-AAAAATAATT
*
38484444 TTTGTTTTTAAAAATAATT
1 TTTGATTTTAAAAATAATT
38484463 TT
1 TT
38484465 CATTTTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
TTTGATTTTAAAAATAATT
Found at i:38484456 original size:18 final size:20
Alignment explanation
Indices: 38484425--38484464 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
38484415 AAATCCTTCC
38484425 TTTGATTTTGAAAAAT-ATT
1 TTTGATTTTGAAAAATAATT
*
38484444 TTTG-TTTTTAAAAATAATT
1 TTTGATTTTGAAAAATAATT
38484463 TT
1 TT
38484465 CATTTTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTGATTTTGAAAAATAATT
Found at i:38484470 original size:19 final size:18
Alignment explanation
Indices: 38484429--38484477 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
38484419 CCTTCCTTTG
* *
38484429 ATTTTGAAAAATATTTTT
1 ATTTTTAAAAATATTTTC
*
38484447 GTTTTTAAAAATAATTTTC
1 ATTTTTAAAAAT-ATTTTC
38484466 ATTTTCTAAAAA
1 ATTTT-TAAAAA
38484478 GTTGTAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.40
19 9 0.36
20 6 0.24
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (18 bp):
ATTTTTAAAAATATTTTC
Found at i:38485318 original size:23 final size:23
Alignment explanation
Indices: 38485292--38485344 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
38485282 TTTATACGGG
38485292 TCAACCCCCAACATTACTAACGA
1 TCAACCCCCAACATTACTAACGA
38485315 TCAACCCCCAACATTACTAACGA
1 TCAACCCCCAACATTACTAACGA
*
38485338 TAAACCC
1 TCAACCC
38485345 AAATGTGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.40, G:0.04, T:0.17
Consensus pattern (23 bp):
TCAACCCCCAACATTACTAACGA
Found at i:38498861 original size:17 final size:17
Alignment explanation
Indices: 38498839--38498874 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
38498829 GAAATTAAGG
* *
38498839 AAAAAATATCCCATAAT
1 AAAAAAAATCCCAAAAT
38498856 AAAAAAAATCCCAAAAT
1 AAAAAAAATCCCAAAAT
38498873 AA
1 AA
38498875 TCTCCCACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAAAAATCCCAAAAT
Found at i:38500522 original size:51 final size:50
Alignment explanation
Indices: 38500446--38500616 Score: 270
Period size: 51 Copynumber: 3.4 Consensus size: 50
38500436 TTTGAGTACT
* *
38500446 TCTGATCAGTGACAAGTGATAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTT-AGCTACACTTA
* *
38500497 TCTGATCAGTGACAAGTTACAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
38500548 TCTGATCAGTGACAAGTGGCAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
38500598 TCTGATCAGGGACAAGTGA
1 TCTGATCAGTGACAAGTGA
38500617 TAAATGATCA
Statistics
Matches: 110, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
50 30 0.27
51 78 0.71
52 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (50 bp):
TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:38516671 original size:21 final size:20
Alignment explanation
Indices: 38516647--38516693 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
38516637 GTCTAACAAT
*
38516647 AAAAAAAATTTGAAAAAGTC
1 AAAAAAAAATTGAAAAAGTC
* *
38516667 AAAAAAAAATTGAAAATGTG
1 AAAAAAAAATTGAAAAAGTC
38516687 AAAAAAA
1 AAAAAAA
38516694 GCTACTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.17
Consensus pattern (20 bp):
AAAAAAAAATTGAAAAAGTC
Found at i:38534976 original size:3 final size:3
Alignment explanation
Indices: 38534968--38535005 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
38534958 ACGAAGGTGG
* *
38534968 CAA CAA CAA CAA CAA CAA CAA CAA AAA TAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
38535006 GCGGTAGCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.29, G:0.00, T:0.03
Consensus pattern (3 bp):
CAA
Found at i:38538395 original size:27 final size:26
Alignment explanation
Indices: 38538348--38538398 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
38538338 TATTTTTTAG
* *
38538348 AATTTTTTTAAAAATATAAAATTTGA
1 AATTTTTATAAAAATAGAAAATTTGA
*
38538374 AATTTTTATAAATATTAGAAAATTT
1 AATTTTTATAAA-AATAGAAAATTT
38538399 TTCATTTCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (26 bp):
AATTTTTATAAAAATAGAAAATTTGA
Found at i:38539544 original size:20 final size:20
Alignment explanation
Indices: 38539519--38539562 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
38539509 CATACAAATT
38539519 AGAAAGAAAGGAAA-AGAGAA
1 AGAAAGAAA-GAAAGAGAGAA
*
38539539 AGAAAGAAAGAAAGGGAGAA
1 AGAAAGAAAGAAAGAGAGAA
38539559 AGAA
1 AGAA
38539563 GAGACGCACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (20 bp):
AGAAAGAAAGAAAGAGAGAA
Found at i:38544076 original size:14 final size:14
Alignment explanation
Indices: 38544057--38544083 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38544047 GATATTTTAC
38544057 CTTTCGAAGAACAA
1 CTTTCGAAGAACAA
38544071 CTTTCGAAGAACA
1 CTTTCGAAGAACA
38544084 CCATACGGAT
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:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
CTTTCGAAGAACAA
Found at i:38567775 original size:18 final size:19
Alignment explanation
Indices: 38567743--38567778 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
38567733 TAATATATCA
*
38567743 TTTAATATATGAATTTAAT
1 TTTAATATATCAATTTAAT
38567762 TTTAATAT-TCAATTTAA
1 TTTAATATATCAATTTAA
38567779 AGCTCAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTAATATATCAATTTAAT
Found at i:38569007 original size:27 final size:27
Alignment explanation
Indices: 38568975--38569038 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
38568965 CCTTATAATT
*
38568975 TAATTATTTTAAAAATTGTAAAATTTTA
1 TAATTAATTTAAAAATT-TAAAATTTTA
**
38569003 -AATTAATTTAACCATTTAAAATTTTA
1 TAATTAATTTAAAAATTTAAAATTTTA
38569029 TAATTTAATT
1 TAA-TTAATT
38569039 ATAATATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 10 0.32
27 15 0.48
28 6 0.19
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (27 bp):
TAATTAATTTAAAAATTTAAAATTTTA
Found at i:38571230 original size:19 final size:18
Alignment explanation
Indices: 38571185--38571232 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
38571175 CATTTTTAGT
*
38571185 TTTTATTTATATATTTATA
1 TTTTATTTA-ATATTTTTA
**
38571204 TAATATTTAATATTTTTA
1 TTTTATTTAATATTTTTA
38571222 TTTTGATTTAA
1 TTTT-ATTTAA
38571233 CTTTCATATC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTATTTAATATTTTTA
Found at i:38572901 original size:4 final size:4
Alignment explanation
Indices: 38572894--38572931 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
38572884 ATACACATGT
*
38572894 ATGG ATGG ATGG ACGG ATGG ATGG ATGG ATGG ATGG AT
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG AT
38572932 ATAGATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.03, G:0.47, T:0.24
Consensus pattern (4 bp):
ATGG
Found at i:38577387 original size:26 final size:24
Alignment explanation
Indices: 38577357--38577403 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
38577347 ATGTTATAAT
38577357 TTTTTTTATTTACCAAAATATATA
1 TTTTTTTATTTACCAAAATATATA
*
38577381 TTTTTTTATTTATCAAAATATAT
1 TTTTTTTATTTACCAAAATATAT
38577404 CAAAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTTTTATTTACCAAAATATATA
Found at i:38577490 original size:27 final size:27
Alignment explanation
Indices: 38577452--38577536 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
38577442 GCCTGATCAA
* *
38577452 GCCAATTAAATTGGCGGCACCAAAGGT
1 GCCAAATAAATTGGCGGCACCAATGGT
*
38577479 GCCAAATAAATTGGTGGCACCAATGGT
1 GCCAAATAAATTGGCGGCACCAATGGT
*
38577506 GCCAAAGT-CATTGGC-GCACC-ATGGT
1 GCCAAA-TAAATTGGCGGCACCAATGGT
38577531 GCCAAA
1 GCCAAA
38577537 GGAAAAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
25 11 0.21
26 5 0.10
27 35 0.67
28 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.19
Consensus pattern (27 bp):
GCCAAATAAATTGGCGGCACCAATGGT
Found at i:38577623 original size:18 final size:19
Alignment explanation
Indices: 38577586--38577652 Score: 91
Period size: 19 Copynumber: 3.6 Consensus size: 19
38577576 TATTTATTAT
*
38577586 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
38577605 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
38577623 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
38577642 TTTTAATTTAA
1 TTTTAATTTAA
38577653 CAAAATATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
18 15 0.38
19 25 0.62
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:38577632 original size:37 final size:37
Alignment explanation
Indices: 38577591--38577661 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
38577581 ATTATTTTTT
* *
38577591 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAACAAAATATTCTC
38577628 ATTTAATAACTCTATTTTAATTTAACAAAATATT
1 ATTTAATAACTCTATTTTAATTTAACAAAATATT
38577662 AAGTAATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAACAAAATATTCTC
Found at i:38581202 original size:125 final size:123
Alignment explanation
Indices: 38580980--38581231 Score: 414
Period size: 125 Copynumber: 2.0 Consensus size: 123
38580970 ACCAGGTCCT
* *
38580980 AGTTTGATGGTTTCATTCTCATCATACTAATTCCTAACAATGTTGTCTATGAGAGCATGGATATG
1 AGTTTGATGATTTCATTCTCATCATACTAATTCCTAACAATGTTGTCTATGAAAGCATGGATATG
* *
38581045 ATTTAATAAATTCGAAGCTAAAACCATGATCAGATAGTTGAAAACAGTTGTCTATGAACG
66 AATTAATAAATACGAAGCTAAAACCATGATCAGATAGTTGAAAACAGTTG--TATGAACG
* *
38581105 AGTTTGATGATTTCATTCTCATCATATTAATTCCTAACAATGTTGTCTATGAAAGCATGGCTATG
1 AGTTTGATGATTTCATTCTCATCATACTAATTCCTAACAATGTTGTCTATGAAAGCATGGATATG
* *
38581170 AATTGATAAATACGAAGTTAAAACCATGATCAGATAGTTGAAAACAGTTGTATGAACG
66 AATTAATAAATACGAAGCTAAAACCATGATCAGATAGTTGAAAACAGTTGTATGAACG
38581228 AGTT
1 AGTT
38581232 ACAAGGATTT
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
123 12 0.10
125 107 0.90
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (123 bp):
AGTTTGATGATTTCATTCTCATCATACTAATTCCTAACAATGTTGTCTATGAAAGCATGGATATG
AATTAATAAATACGAAGCTAAAACCATGATCAGATAGTTGAAAACAGTTGTATGAACG
Found at i:38587711 original size:13 final size:13
Alignment explanation
Indices: 38587693--38587718 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38587683 TATAAAATCA
38587693 TTTGACTTTTGAC
1 TTTGACTTTTGAC
38587706 TTTGACTTTTGAC
1 TTTGACTTTTGAC
38587719 CACCCATTTT
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:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
TTTGACTTTTGAC
Found at i:38589164 original size:2 final size:2
Alignment explanation
Indices: 38589152--38589183 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
38589142 GCATATTGAC
*
38589152 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38589184 GAATGTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:38598965 original size:2 final size:2
Alignment explanation
Indices: 38598958--38598987 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
38598948 ATTAGAATAG
38598958 AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
38598988 CTTATGATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38605372 original size:201 final size:202
Alignment explanation
Indices: 38605027--38605430 Score: 801
Period size: 201 Copynumber: 2.0 Consensus size: 202
38605017 ATAATTTACG
38605027 ATTTCGAAAATATAATCACCAAATATAAATTTAAATATGTAATGAAAAAAAATCCTAAATTAAAC
1 ATTTCGAAAATATAATCACCAAATATAAATTTAAATATGTAATGAAAAAAAATCCTAAATTAAAC
38605092 ATATTATAAAGATGACAATTATAAATTTAAATATAATGTTTATTCAATTTTAACTGATGAAGAAA
66 ATATTATAAAGATGACAATTATAAATTTAAATATAATGTTTATTCAATTTTAACTGATGAAGAAA
38605157 GTTGTTGAAACACAAAGTTTAGTTTTAAATTAATTGTGTATAGTAATTAAAATATATTATA-TAA
131 GTTGTTGAAACACAAAGTTTAGTTTTAAATTAATTGTGTATAGTAATTAAAATATATTATATTAA
38605221 ATTATTA
196 ATTATTA
38605228 ATTTCGAAAATATAATCACCAAATATAAATTTAAATATGTAATGAAAAAAAATCCTAAATTAAAC
1 ATTTCGAAAATATAATCACCAAATATAAATTTAAATATGTAATGAAAAAAAATCCTAAATTAAAC
38605293 ATATTATAAAGATGACAATTATAAATTTAAATATAATGTTTATTCAATTTTAACTGATGAAGAAA
66 ATATTATAAAGATGACAATTATAAATTTAAATATAATGTTTATTCAATTTTAACTGATGAAGAAA
38605358 GTTGTTGAAACACAAAGTTTAGTTTTAAATTAATTGTGTATAGTAATTAAAATATATTATATTAA
131 GTTGTTGAAACACAAAGTTTAGTTTTAAATTAATTGTGTATAGTAATTAAAATATATTATATTAA
38605423 ATTATTA
196 ATTATTA
38605430 A
1 A
38605431 AAATTGATAA
Statistics
Matches: 202, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
201 191 0.95
202 11 0.05
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.37
Consensus pattern (202 bp):
ATTTCGAAAATATAATCACCAAATATAAATTTAAATATGTAATGAAAAAAAATCCTAAATTAAAC
ATATTATAAAGATGACAATTATAAATTTAAATATAATGTTTATTCAATTTTAACTGATGAAGAAA
GTTGTTGAAACACAAAGTTTAGTTTTAAATTAATTGTGTATAGTAATTAAAATATATTATATTAA
ATTATTA
Found at i:38606188 original size:18 final size:20
Alignment explanation
Indices: 38606162--38606209 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
38606152 TTTTTTAAAA
38606162 TTATAAAAAAATTA-TAA-AT
1 TTAT-AAAAAATTATTAATAT
* *
38606181 TTGTAAAATATTATTAATAT
1 TTATAAAAAATTATTAATAT
38606201 TTATAAAAA
1 TTATAAAAA
38606210 TGTTAATGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 8 0.35
19 6 0.26
20 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TTATAAAAAATTATTAATAT
Found at i:38606737 original size:18 final size:19
Alignment explanation
Indices: 38606706--38606743 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
38606696 TTATTATATT
*
38606706 TTTAGTAATATTTTATAAA
1 TTTAGTAATATTTTAAAAA
*
38606725 TTTA-TAATTTTTTAAAAA
1 TTTAGTAATATTTTAAAAA
38606743 T
1 T
38606744 AAATTGCGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTAGTAATATTTTAAAAA
Found at i:38608696 original size:30 final size:30
Alignment explanation
Indices: 38608660--38608728 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
38608650 AAAATAAAAA
38608660 ATATGGGTATCAAATAATAGAAAGTCAAAG
1 ATATGGGTATCAAATAATAGAAAGTCAAAG
* *
38608690 ATATGGGTATCAAATATTGGAAAGTCAAAG
1 ATATGGGTATCAAATAATAGAAAGTCAAAG
38608720 ATATGGGTA
1 ATATGGGTA
38608729 ACGAGATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (30 bp):
ATATGGGTATCAAATAATAGAAAGTCAAAG
Found at i:38608702 original size:15 final size:16
Alignment explanation
Indices: 38608682--38608728 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
38608672 AATAATAGAA
38608682 AGTCAAAGATATGGGT
1 AGTCAAAGATATGGGT
* **
38608698 A-TCAAATAT-TGGAA
1 AGTCAAAGATATGGGT
38608712 AGTCAAAGATATGGGT
1 AGTCAAAGATATGGGT
38608728 A
1 A
38608729 ACGAGATATT
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 14 0.61
16 5 0.22
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
AGTCAAAGATATGGGT
Found at i:38612864 original size:20 final size:19
Alignment explanation
Indices: 38612839--38612877 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
38612829 TAAGGGTCAA
38612839 AATATTATTTATGAGATAAT
1 AATATTATTTATGA-ATAAT
* *
38612859 AATATTTTTTTTGAATAAT
1 AATATTATTTATGAATAAT
38612878 CTCATTACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (19 bp):
AATATTATTTATGAATAAT
Found at i:38620412 original size:15 final size:16
Alignment explanation
Indices: 38620375--38620414 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
38620365 CACCAAAATT
*
38620375 GTTAATTAAATTTAGC
1 GTTAATTAAACTTAGC
*
38620391 TTTAATTAAACTTAG-
1 GTTAATTAAACTTAGC
38620406 GTTAATTAA
1 GTTAATTAA
38620415 GTTAATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (16 bp):
GTTAATTAAACTTAGC
Found at i:38621569 original size:26 final size:26
Alignment explanation
Indices: 38621502--38621571 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 26
38621492 TTGCGGATAC
*
38621502 TCTGAAGCTTGTGTGAGCAGCACTGA
1 TCTGAAGCTTGTGTGAGCAACACTGA
* * * *
38621528 ACT-AAGATTGTATGAGCAAC-CTTGG
1 TCTGAAGCTTGTGTGAGCAACAC-TGA
38621553 TCTGAAGCTTGTGTGAGCA
1 TCTGAAGCTTGTGTGAGCA
38621572 TCCCGAATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
24 1 0.03
25 18 0.53
26 15 0.44
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (26 bp):
TCTGAAGCTTGTGTGAGCAACACTGA
Found at i:38623496 original size:17 final size:16
Alignment explanation
Indices: 38623473--38623532 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
38623463 AGTGATTATC
38623473 TTAATATTAAATTTAA
1 TTAATATTAAATTTAA
*
38623489 TCTAATATT-TATCTTAA
1 T-TAATATTAAAT-TTAA
* * *
38623506 TAAATATTATATTTAT
1 TTAATATTAAATTTAA
38623522 TTAATATTAAA
1 TTAATATTAAA
38623533 GTGATTAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
16 21 0.58
17 15 0.42
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATATTAAATTTAA
Found at i:38624801 original size:5 final size:5
Alignment explanation
Indices: 38624793--38624818 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38624783 GAGATGGAAT
38624793 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
38624819 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:38627682 original size:19 final size:20
Alignment explanation
Indices: 38627658--38627695 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
38627648 AGTACATTTT
38627658 ATGCAGTACAA-AATAAAAA
1 ATGCAGTACAAGAATAAAAA
38627677 ATGCAGTACAAGAATAAAA
1 ATGCAGTACAAGAATAAAA
38627696 TTGTAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.61, C:0.11, G:0.13, T:0.16
Consensus pattern (20 bp):
ATGCAGTACAAGAATAAAAA
Found at i:38629322 original size:29 final size:29
Alignment explanation
Indices: 38629290--38629348 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
38629280 TAATTTTTAA
*
38629290 ATGTAGTGTTTTTTAAAAATAAAAAATAT
1 ATGTAGTGTATTTTAAAAATAAAAAATAT
*
38629319 ATGTGGTGTATTTTAAAAATAAAAAATAT
1 ATGTAGTGTATTTTAAAAATAAAAAATAT
38629348 A
1 A
38629349 GTTTATATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (29 bp):
ATGTAGTGTATTTTAAAAATAAAAAATAT
Found at i:38631277 original size:29 final size:29
Alignment explanation
Indices: 38631245--38631303 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
38631235 TAATTTTTAA
*
38631245 ATGTAGTGTTTTTTAAAAATAAAAAATAT
1 ATGTAGTGTATTTTAAAAATAAAAAATAT
*
38631274 ATGTGGTGTATTTTAAAAATAAAAAATAT
1 ATGTAGTGTATTTTAAAAATAAAAAATAT
38631303 A
1 A
38631304 GTTTATATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (29 bp):
ATGTAGTGTATTTTAAAAATAAAAAATAT
Found at i:38631404 original size:9 final size:9
Alignment explanation
Indices: 38631390--38631422 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
38631380 TCGAATTGAT
38631390 TCGATTAAC
1 TCGATTAAC
38631399 TCGATTAAC
1 TCGATTAAC
*
38631408 TTGATTAAC
1 TCGATTAAC
38631417 TCGATT
1 TCGATT
38631423 CGAATAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (9 bp):
TCGATTAAC
Found at i:38633346 original size:11 final size:11
Alignment explanation
Indices: 38633330--38633355 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38633320 TTTTTTAAAA
38633330 TTTTAAAATAC
1 TTTTAAAATAC
38633341 TTTTAAAATAC
1 TTTTAAAATAC
38633352 TTTT
1 TTTT
38633356 TTTAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:38634559 original size:544 final size:544
Alignment explanation
Indices: 38633531--38634622 Score: 2058
Period size: 544 Copynumber: 2.0 Consensus size: 544
38633521 GTACCTCTAG
*
38633531 TTCAAGCCCACACTGTAGTACCCCTAACCCGAATCCATCTCTAGAACAGGGTTACGAAGCATTAC
1 TTCAAGCCCACACTGTAATACCCCTAACCCGAATCCATCTCTAGAACAGGGTTACGAAGCATTAC
38633596 CAGAGTTTACAAATTAAACATACAGAAAATGCAAACATTTCATATCATATAGCATTCATGTCAAA
66 CAGAGTTTACAAATTAAACATACAGAAAATGCAAACATTTCATATCATATAGCATTCATGTCAAA
* *
38633661 AACTGATTAAAATAATACATATTGTCTCTTGTAAGAGCCCTCGAAGCCCAAAATACACATTAGAA
131 AACCGATTAAAATAATACATATTGTCTCTTATAAGAGCCCTCGAAGCCCAAAATACACATTAGAA
38633726 ACAGATCGGGACTAAATAAAAAACTTAGAGAATTTTTCAGAAACACTTAAAATTTTCAACACTAC
196 ACAGATCGGGACTAAATAAAAAACTTAGAGAATTTTTCAGAAACACTTAAAATTTTCAACACTAC
38633791 AGGGGTCACATGGTCGTGTGACTCATACGTGTGACCCAAGTTAGTATACTCACACAGGCTGGGAC
261 AGGGGTCACATGGTCGTGTGACTCATACGTGTGACCCAAGTTAGTATACTCACACAGGCTGGGAC
*
38633856 ATGGCCGTGTGTCCCTATTTCGAATGCTCACACGGCCTAAGACACATTTGACTCGTAAATATTAA
326 ATGGCCGTGTGTCCCTATTTCGAATGCTCACACAGCCTAAGACACATTTGACTCGTAAATATTAA
38633921 ATAATAATATTTACAAACTTACTCGTCGAATTTGGTGGCCCCAAAACCACTGTTTCCGACACCAC
391 ATAATAATATTTACAAACTTACTCGTCGAATTTGGTGGCCCCAAAACCACTGTTTCCGACACCAC
38633986 TGAAAAACGAGCGGTTACAATATATTTTGATTTAAATCTCATATATTATTTTCCAATAAATTCTT
456 TGAAAAACGAGCGGTTACAATATATTTTGATTTAAATCTCATATATTATTTTCCAATAAATTCTT
*
38634051 AACTTCAAGTACCGAAATTTAAGA
521 AACTTCAAGTACCGAAATTCAAGA
*
38634075 TTCAAGCCCACACTGTAATACCCCTAACCCGAATCCATCTCTAGAATAGGGTTACGAAGCATTAC
1 TTCAAGCCCACACTGTAATACCCCTAACCCGAATCCATCTCTAGAACAGGGTTACGAAGCATTAC
38634140 CAGAGTTTACAAATTAAACATACAGAAAATGCAAACATTTCATATCATATAGCATTCATGTCAAA
66 CAGAGTTTACAAATTAAACATACAGAAAATGCAAACATTTCATATCATATAGCATTCATGTCAAA
*
38634205 AACCGATTAAAATAATACATATTGTCTCTTATATGAGCCCTCGAAGCCCAAAATACACATTAGAA
131 AACCGATTAAAATAATACATATTGTCTCTTATAAGAGCCCTCGAAGCCCAAAATACACATTAGAA
* *
38634270 ACAGATCGGGACTAAATCAGAAACTTAGAGAATTTTTCAGAAACACTTAAAATTTTCAACACTAC
196 ACAGATCGGGACTAAATAAAAAACTTAGAGAATTTTTCAGAAACACTTAAAATTTTCAACACTAC
*
38634335 AGGGGTCACATGGTCGTGTGACTCATACGTGTGACCCAAGTTAGTATACTCACACGGGCTGGGAC
261 AGGGGTCACATGGTCGTGTGACTCATACGTGTGACCCAAGTTAGTATACTCACACAGGCTGGGAC
38634400 ATGGCCGTGTGTCCCTATTTCGAATGCTCACACAGCCTAAGACACATTTGACTCGTAAATATTAA
326 ATGGCCGTGTGTCCCTATTTCGAATGCTCACACAGCCTAAGACACATTTGACTCGTAAATATTAA
* * *
38634465 ATAATAATATTTACGACCTTACTCGTCGAATTTGGTGGCCCTAAAACCACTGTTTCCGACACCAC
391 ATAATAATATTTACAAACTTACTCGTCGAATTTGGTGGCCCCAAAACCACTGTTTCCGACACCAC
*
38634530 TGAAAAACGAGCTGTTACAATATATTTTGATTTAAATCTCATATATTATTTTCCAATAAATTCTT
456 TGAAAAACGAGCGGTTACAATATATTTTGATTTAAATCTCATATATTATTTTCCAATAAATTCTT
38634595 AACTTCAAGTACCGAAATTCAAGA
521 AACTTCAAGTACCGAAATTCAAGA
38634619 TTCA
1 TTCA
38634623 CTATACGCAA
Statistics
Matches: 534, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
544 534 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (544 bp):
TTCAAGCCCACACTGTAATACCCCTAACCCGAATCCATCTCTAGAACAGGGTTACGAAGCATTAC
CAGAGTTTACAAATTAAACATACAGAAAATGCAAACATTTCATATCATATAGCATTCATGTCAAA
AACCGATTAAAATAATACATATTGTCTCTTATAAGAGCCCTCGAAGCCCAAAATACACATTAGAA
ACAGATCGGGACTAAATAAAAAACTTAGAGAATTTTTCAGAAACACTTAAAATTTTCAACACTAC
AGGGGTCACATGGTCGTGTGACTCATACGTGTGACCCAAGTTAGTATACTCACACAGGCTGGGAC
ATGGCCGTGTGTCCCTATTTCGAATGCTCACACAGCCTAAGACACATTTGACTCGTAAATATTAA
ATAATAATATTTACAAACTTACTCGTCGAATTTGGTGGCCCCAAAACCACTGTTTCCGACACCAC
TGAAAAACGAGCGGTTACAATATATTTTGATTTAAATCTCATATATTATTTTCCAATAAATTCTT
AACTTCAAGTACCGAAATTCAAGA
Found at i:38637946 original size:29 final size:29
Alignment explanation
Indices: 38637910--38637976 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
38637900 TAAAATAGTT
*
38637910 ACTTATGTTTCAATTGTTATATTTCAGCC
1 ACTTATGTTTCAATTGTTACATTTCAGCC
* *
38637939 ACTTATGTTTGAATTGTTACATTTCAGTC
1 ACTTATGTTTCAATTGTTACATTTCAGCC
38637968 ACTTATGTT
1 ACTTATGTT
38637977 AAAGTGTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (29 bp):
ACTTATGTTTCAATTGTTACATTTCAGCC
Found at i:38640095 original size:17 final size:18
Alignment explanation
Indices: 38640073--38640113 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
38640063 TTTAATAAAA
38640073 TTATAAAAAAA-TGATTT
1 TTATAAAAAAATTGATTT
38640090 TTATAAAAAAAATTGATTT
1 TTAT-AAAAAAATTGATTT
38640109 TTATA
1 TTATA
38640114 TTTTCATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.18
18 8 0.36
19 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (18 bp):
TTATAAAAAAATTGATTT
Found at i:38640845 original size:30 final size:30
Alignment explanation
Indices: 38640785--38640844 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
38640775 TTTAAAAAGA
* **
38640785 ATAATTTTTTATATATTCTTTAGAATTTTT
1 ATAATTTTTTAAATATAATTTAGAATTTTT
*
38640815 ATAATTTTTTAAATATAAATTTTGAATTTT
1 ATAATTTTTTAAATAT-AATTTAGAATTTT
38640845 AAAAATGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (30 bp):
ATAATTTTTTAAATATAATTTAGAATTTTT
Found at i:38644391 original size:9 final size:9
Alignment explanation
Indices: 38644362--38644544 Score: 86
Period size: 9 Copynumber: 19.2 Consensus size: 9
38644352 ATGATAAAAA
*
38644362 ATAAAAATCA
1 ATAAAAAT-T
*
38644372 ATAAAAGTT
1 ATAAAAATT
*
38644381 ATAAACATT
1 ATAAAAATT
**
38644390 ATTAAATTTT
1 A-TAAAAATT
*
38644400 AATAAAAAAT
1 -ATAAAAATT
38644410 AT-AAAATT
1 ATAAAAATT
38644418 ATTAAAAATT
1 A-TAAAAATT
38644428 ATTAAAAAATT
1 A-T-AAAAATT
*
38644439 ATAAAAATC
1 ATAAAAATT
38644448 ATAAACAATT
1 ATAAA-AATT
* *
38644458 ACAAAAATG
1 ATAAAAATT
*
38644467 GTAAAAATT
1 ATAAAAATT
38644476 -TATAAAATT
1 ATA-AAAATT
*
38644485 GTAAGAAAATT
1 AT-A-AAAATT
*
38644496 ATAAAAAAT
1 ATAAAAATT
*
38644505 GTAAAGAA--
1 ATAAA-AATT
38644513 ATAAAAATT
1 ATAAAAATT
*
38644522 CATTAAAAAGAT
1 -A-TAAAAA-TT
38644534 ATAAAAATT
1 ATAAAAATT
38644543 AT
1 AT
38644545 CGTATCAAAA
Statistics
Matches: 134, Mismatches: 24, Indels: 31
0.71 0.13 0.16
Matches are distributed among these distances:
7 2 0.01
8 12 0.09
9 49 0.37
10 46 0.34
11 24 0.18
12 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:38644395 original size:10 final size:10
Alignment explanation
Indices: 38644363--38644446 Score: 59
Period size: 10 Copynumber: 8.7 Consensus size: 10
38644353 TGATAAAAAA
* *
38644363 TAAAAATCAA
1 TAAAAATTAT
*
38644373 TAAAAGTTA-
1 TAAAAATTAT
*
38644382 TAAACATTAT
1 TAAAAATTAT
** *
38644392 TAAATTTTAA
1 TAAAAATTAT
*
38644402 TAAAAAATA-
1 TAAAAATTAT
38644411 T-AAAATTAT
1 TAAAAATTAT
38644420 TAAAAATTAT
1 TAAAAATTAT
38644430 TAAAAAATTA-
1 T-AAAAATTAT
38644440 TAAAAAT
1 TAAAAAT
38644447 CATAAACAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
8 6 0.10
9 15 0.25
10 30 0.51
11 8 0.14
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:38644433 original size:28 final size:29
Alignment explanation
Indices: 38644363--38644444 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
38644353 TGATAAAAAA
* *
38644363 TAAAAATCAAT-AAAAGTTATAAACATTAT
1 TAAAAATTAATAAAAAATTATAAA-ATTAT
**
38644392 TAAATTTTAATAAAAAA-TATAAAATTAT
1 TAAAAATTAATAAAAAATTATAAAATTAT
*
38644420 TAAAAATTATTAAAAAATTATAAAA
1 TAAAAATTAATAAAAAATTATAAAA
38644445 ATCATAAACA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 19 0.43
29 21 0.48
30 4 0.09
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (29 bp):
TAAAAATTAATAAAAAATTATAAAATTAT
Found at i:38644444 original size:19 final size:19
Alignment explanation
Indices: 38644412--38644544 Score: 62
Period size: 19 Copynumber: 6.8 Consensus size: 19
38644402 TAAAAAATAT
38644412 AAAATTATTAAAAATTATTAA
1 AAAATTA-T-AAAATTATTAA
*
38644433 AAAATTATAAAAATCA-TAA
1 AAAATTAT-AAAATTATTAA
* * * **
38644452 ACAATTACAAAAATGGTAA
1 AAAATTATAAAATTATTAA
* *
38644471 AAATTTATAAAATT-GTAA
1 AAAATTATAAAATTATTAA
*
38644489 GAAAATTATAAAA-AATGTAA
1 -AAAATTATAAAATTAT-TAA
38644509 AGAAA-TA-AAAATTCATTAA
1 A-AAATTATAAAATT-ATTAA
38644528 AAAGA-TATAAAAATTAT
1 AAA-ATTAT-AAAATTAT
38644545 CGTATCAAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
18 14 0.16
19 43 0.49
20 18 0.20
21 13 0.15
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAATTATAAAATTATTAA
Found at i:38644452 original size:38 final size:38
Alignment explanation
Indices: 38644361--38644452 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 38
38644351 AATGATAAAA
* **
38644361 AATAAAAATCAATAAAAGTTATAAACATTATTAAATTTT
1 AATAAAAATC-ATAAAAGTTATAAAAATTATTAAAAATT
38644400 AATAAAAAAT-ATAAAA-TTATTAAAAATTATTAAAAAATT
1 AAT-AAAAATCATAAAAGTTA-TAAAAATTATT-AAAAATT
38644439 -ATAAAAATCATAAA
1 AATAAAAATCATAAA
38644453 CAATTACAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
37 9 0.20
38 23 0.50
39 8 0.17
40 6 0.13
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (38 bp):
AATAAAAATCATAAAAGTTATAAAAATTATTAAAAATT
Found at i:38644577 original size:22 final size:22
Alignment explanation
Indices: 38644552--38644595 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
38644542 TATCGTATCA
38644552 AAAGAAGCATTTTATAATTTTT
1 AAAGAAGCATTTTATAATTTTT
38644574 AAAGAAGCATTTTATAATTTTT
1 AAAGAAGCATTTTATAATTTTT
38644596 CTATAACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (22 bp):
AAAGAAGCATTTTATAATTTTT
Found at i:38644763 original size:10 final size:9
Alignment explanation
Indices: 38644749--38644859 Score: 59
Period size: 10 Copynumber: 12.1 Consensus size: 9
38644739 TTTTGATACA
38644749 TTTTATAAT
1 TTTTATAAT
*
38644758 TATTTATTAT
1 T-TTTATAAT
*
38644768 TTTTATAAAA
1 TTTTAT-AAT
*
38644778 TTTTACAAT
1 TTTTATAAT
*
38644787 TTTTAATAAA
1 TTTT-ATAAT
*
38644797 CTTTAT-AT
1 TTTTATAAT
*
38644805 TTTTATTAAA
1 TTTTA-TAAT
*
38644815 ATTTA-ATAT
1 TTTTATA-AT
*
38644824 TTTTATAAC
1 TTTTATAAT
*
38644833 TTTTATTGAT
1 TTTTA-TAAT
38644843 TTTTAT--T
1 TTTTATAAT
38644850 TTTTATAAT
1 TTTTATAAT
38644859 T
1 T
38644860 GTTTTTCCAC
Statistics
Matches: 75, Mismatches: 17, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
7 7 0.09
8 6 0.08
9 29 0.39
10 33 0.44
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:38644780 original size:18 final size:18
Alignment explanation
Indices: 38644749--38644848 Score: 85
Period size: 19 Copynumber: 5.3 Consensus size: 18
38644739 TTTTGATACA
*
38644749 TTTTATAATTATTTATTAT
1 TTTTATAA-AATTTATTAT
**
38644768 TTTTATAAAATTTTACAAT
1 TTTTATAAAA-TTTATTAT
*
38644787 TTTTAATAAACTTTA-TAT
1 TTTT-ATAAAATTTATTAT
*
38644805 TTTTATTAAAATTTAATAT
1 TTTTA-TAAAATTTATTAT
**
38644824 TTTTATAACTTTTATTGAT
1 TTTTATAAAATTTATT-AT
38644843 TTTTAT
1 TTTTAT
38644849 TTTTTATAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
17 1 0.01
18 23 0.34
19 38 0.57
20 5 0.07
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (18 bp):
TTTTATAAAATTTATTAT
Found at i:38645024 original size:2 final size:2
Alignment explanation
Indices: 38645019--38645048 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38645009 AGTGCAAAAA
38645019 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
38645049 CACGGGCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38645211 original size:89 final size:88
Alignment explanation
Indices: 38645055--38645222 Score: 223
Period size: 89 Copynumber: 1.9 Consensus size: 88
38645045 AGAGCACGGG
* ** * *
38645055 CTTAATTGCTTTTTTGAAAAAGTTTGAAGGCATTTTTTTATGTATTTTGAAAGTTCAAGTACCCA
1 CTTAATTGCTTTTTTGAAAAAGTTTGAAGGCATTTTTATACATATTTTGAAAGTTAAAATACCCA
38645120 ATTGAGCGTAAAAAAAAGTAGGGC
66 ATTGAGCG-AAAAAAAAGTAGGGC
* *
38645144 CTTAATTGCTTTTTTTGAAAAAGTTTG-AGAGCCTTTTTATACAT-TTTTGAAAGTTAAAATACT
1 CTTAATTGC-TTTTTTGAAAAAGTTTGAAG-GCATTTTTATACATATTTTGAAAGTTAAAATACC
*
38645207 CAATTGAGTGAAAAAA
64 CAATTGAGCGAAAAAA
38645223 GCATAGACTT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
88 6 0.09
89 36 0.52
90 27 0.39
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.39
Consensus pattern (88 bp):
CTTAATTGCTTTTTTGAAAAAGTTTGAAGGCATTTTTATACATATTTTGAAAGTTAAAATACCCA
ATTGAGCGAAAAAAAAGTAGGGC
Found at i:38647058 original size:111 final size:111
Alignment explanation
Indices: 38646864--38647075 Score: 284
Period size: 111 Copynumber: 1.9 Consensus size: 111
38646854 TCATCAGTGC
* *
38646864 GGTTTGATGAAGGTACCAGCGAGCTTGTATCGAGCAATGGGTTAAATGCAGTCGGTGTAAGCAAT
1 GGTTTGATGAAGGTACCAGCGAGCTAGTATCGAGCAATGGATTAAATGCAGTCGGTGTAAGCAAT
* * *
38646929 GCAAGAAGGCAAAGTTTGAGATCAAGTGAGAGGCTTGCTAGAGAAG
66 GCAAGAAGGCAAAGTTTGAGAGCAAATGAAAGGCTTGCTAGAGAAG
** * *
38646975 GGTTTGATGAAGGTACTGGCGAGCTCAGT-TCGAGCTATGGATTAAATGCAGAT-GGTGTTAGCA
1 GGTTTGATGAAGGTACCAGCGAGCT-AGTATCGAGCAATGGATTAAATGCAG-TCGGTGTAAGCA
* * *
38647038 GTTCAAGCAGGCAAAGTTTGAGAGCAAATGAAAGGCTT
64 ATGCAAGAAGGCAAAGTTTGAGAGCAAATGAAAGGCTT
38647076 CCCGGAGCTG
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
111 84 0.97
112 3 0.03
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.24
Consensus pattern (111 bp):
GGTTTGATGAAGGTACCAGCGAGCTAGTATCGAGCAATGGATTAAATGCAGTCGGTGTAAGCAAT
GCAAGAAGGCAAAGTTTGAGAGCAAATGAAAGGCTTGCTAGAGAAG
Found at i:38650669 original size:15 final size:15
Alignment explanation
Indices: 38650649--38650699 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
38650639 CAATAAATTG
38650649 AAAATAAATTTTTAA
1 AAAATAAATTTTTAA
*
38650664 AAAAT--ATTTATATTA
1 AAAATAAATTT-T-TAA
*
38650679 AAAATAAAATTTTAA
1 AAAATAAATTTTTAA
38650694 AAAATA
1 AAAATA
38650700 TTTATACTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
13 4 0.14
14 1 0.03
15 20 0.69
16 1 0.03
17 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATAAATTTTTAA
Found at i:38650685 original size:30 final size:31
Alignment explanation
Indices: 38650649--38650710 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
38650639 CAATAAATTG
*
38650649 AAAATAAATTTTTAAAAAATATTTATA-TTA
1 AAAATAAAATTTTAAAAAATATTTATACTTA
38650679 AAAATAAAATTTTAAAAAATATTTATACTTA
1 AAAATAAAATTTTAAAAAATATTTATACTTA
38650710 A
1 A
38650711 CTAACACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAATAAAATTTTAAAAAATATTTATACTTA
Found at i:38651801 original size:4 final size:4
Alignment explanation
Indices: 38651757--38651782 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
38651747 TTCCTTTTTC
38651757 TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TG
38651783 AACATGTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:38654775 original size:12 final size:13
Alignment explanation
Indices: 38654758--38654786 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
38654748 TTAATATAAT
38654758 AAAAAGAAAA-AG
1 AAAAAGAAAATAG
38654770 AAAAAGAAAATAG
1 AAAAAGAAAATAG
38654783 AAAA
1 AAAA
38654787 GGAATTACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAAAGAAAATAG
Found at i:38655358 original size:43 final size:43
Alignment explanation
Indices: 38655279--38655502 Score: 290
Period size: 43 Copynumber: 5.2 Consensus size: 43
38655269 TAAAGATAAG
* * * *
38655279 CGCCACTAAATGTCATGTTCTTTATCGCCGCTTTTATAGCAAA
1 CGCCGCTAAATGTCATGTTCTTTAGCGGCGCTTTTATAGAAAA
* * * *
38655322 CGCCGTTAAAGGTCATGTTCTTTAGCGGCGCCTTTATAGCAAA
1 CGCCGCTAAATGTCATGTTCTTTAGCGGCGCTTTTATAGAAAA
*
38655365 CGCCGCTAAATGTCATATTCTTTAGCTGG-GCTTTTATA-AGAAA
1 CGCCGCTAAATGTCATGTTCTTTAGC-GGCGCTTTTATAGA-AAA
*
38655408 CGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGAAAA
1 CGCCGCTAAATGTCATGTTCTTTAGCGGCGCTTTTATAGAAAA
* * *
38655451 CGACGCTAAATGTCATATTCTTTAGCGGCGCTTTTATTGAAAA
1 CGCCGCTAAATGTCATGTTCTTTAGCGGCGCTTTTATAGAAAA
*
38655494 CGCCACTAA
1 CGCCGCTAA
38655503 TTTTGGCAGA
Statistics
Matches: 158, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
42 2 0.01
43 153 0.97
44 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (43 bp):
CGCCGCTAAATGTCATGTTCTTTAGCGGCGCTTTTATAGAAAA
Found at i:38659536 original size:12 final size:12
Alignment explanation
Indices: 38659521--38659546 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38659511 ATCATCCTCT
38659521 TCATCAGATTCA
1 TCATCAGATTCA
38659533 TCATCAGATTCA
1 TCATCAGATTCA
38659545 TC
1 TC
38659547 TCTTAATCTT
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:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCAGATTCA
Found at i:38661280 original size:9 final size:9
Alignment explanation
Indices: 38661266--38661509 Score: 139
Period size: 9 Copynumber: 27.0 Consensus size: 9
38661256 TAAGTATAAT
38661266 TAAGTTATG
1 TAAGTTATG
38661275 TAAGTTATG
1 TAAGTTATG
* * *
38661284 ATATGATATA
1 -TAAGTTATG
*
38661294 T-ATTTATG
1 TAAGTTATG
38661302 T-A-TTATG
1 TAAGTTATG
*
38661309 CAAGTTATG
1 TAAGTTATG
*
38661318 TAAGTTCTG
1 TAAGTTATG
*
38661327 TGAGTTATG
1 TAAGTTATG
38661336 TAAGTTATG
1 TAAGTTATG
* *
38661345 ATATGATATATA
1 -TAAG-T-TATG
38661357 TAAGTTAT-
1 TAAGTTATG
38661365 TAAGTTATG
1 TAAGTTATG
38661374 TAAGTTATG
1 TAAGTTATG
*
38661383 TGAGTTATG
1 TAAGTTATG
*
38661392 TAAATTATG
1 TAAGTTATG
* *
38661401 TTATGATATATA
1 -TAAG-T-TATG
38661413 TAAGTTAT-
1 TAAGTTATG
38661421 TAAG---T-
1 TAAGTTATG
38661426 TAAGTTATG
1 TAAGTTATG
* *
38661435 TGAGTTATTT
1 TAAGTTA-TG
38661445 TAAGTTATGG
1 TAAGTTAT-G
* *
38661455 TATGATATATA
1 TAAG-T-TATG
38661466 TAAGTTAT-
1 TAAGTTATG
*
38661474 TAAGTTAAG
1 TAAGTTATG
38661483 TAAGTTATG
1 TAAGTTATG
* *
38661492 TGAGTTATT
1 TAAGTTATG
38661501 TAAGTTATG
1 TAAGTTATG
38661510 GTATAATATA
Statistics
Matches: 180, Mismatches: 36, Indels: 38
0.71 0.14 0.15
Matches are distributed among these distances:
5 5 0.03
7 5 0.03
8 26 0.14
9 99 0.55
10 24 0.13
11 12 0.07
12 9 0.05
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:38661374 original size:56 final size:56
Alignment explanation
Indices: 38661268--38661520 Score: 325
Period size: 56 Copynumber: 4.5 Consensus size: 56
38661258 AGTATAATTA
* * *
38661268 AGTTATGTAAGTTATGATATGATATATATTTATGTATTATGCAAGTTATGTAAGTTCTGTG
1 AGTTATGTAAGTTATGATATGATATATA--TAAG--TTAT-TAAGTTATGTAAGTTATGTG
38661329 AGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
1 AGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
* *
38661385 AGTTATGTAAATTATGTTATGATATATATAAGTTATTAAG---T-TAAGTTATGTG
1 AGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
* * *
38661437 AGTTATTTTAAGTTATGGTATGATATATATAAGTTATTAAGTTAAGTAAGTTATGTG
1 AGTTA-TGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
* * *
38661494 AGTTATTTAAGTTATGGTATAATATAT
1 AGTTATGTAAGTTATGATATGATATAT
38661521 GTAATAATCC
Statistics
Matches: 177, Mismatches: 10, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
52 16 0.09
53 33 0.19
56 77 0.44
57 20 0.11
59 3 0.02
61 28 0.16
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.46
Consensus pattern (56 bp):
AGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATGTG
Found at i:38661427 original size:24 final size:24
Alignment explanation
Indices: 38661395--38661480 Score: 59
Period size: 24 Copynumber: 3.4 Consensus size: 24
38661385 AGTTATGTAA
*
38661395 ATTATGTTATGATATATATAAGTT
1 ATTAAGTTATGATATATATAAGTT
* * *
38661419 ATTAAGTTAAG-T-TATGTGAGTT
1 ATTAAGTTATGATATATATAAGTT
38661441 ATTTTAAGTTATGGTATGATATATATAAGTT
1 A--TTAAG---T--TATGATATATATAAGTT
38661472 ATTAAGTTA
1 ATTAAGTTA
38661481 AGTAAGTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 18
0.65 0.10 0.25
Matches are distributed among these distances:
22 9 0.20
23 1 0.02
24 16 0.35
26 1 0.02
27 1 0.02
29 8 0.17
30 1 0.02
31 9 0.20
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (24 bp):
ATTAAGTTATGATATATATAAGTT
Found at i:38661473 original size:109 final size:108
Alignment explanation
Indices: 38661318--38661520 Score: 325
Period size: 109 Copynumber: 1.9 Consensus size: 108
38661308 GCAAGTTATG
* *
38661318 TAAGTTCTGTGAGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTATGTAAGTTATG
1 TAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTAAGTAAGTTATG
* *
38661383 TGAGTTATGTAAATTATGTTATGATATATATAAGTTATTAAGT
66 TGAGTTATGTAAATTATGGTATAATATATATAAGTTATTAAGT
* *
38661426 TAAGTTATGTGAGTTATTTTAAGTTATGGTATGATATATATAAGTTATTAAGTTAAGTAAGTTAT
1 TAAGTTATGTGAGTTA-TGTAAGTTATGATATGATATATATAAGTTATTAAGTTAAGTAAGTTAT
* *
38661491 GTGAGTTATTTAAGTTATGGTATAATATAT
65 GTGAGTTATGTAAATTATGGTATAATATAT
38661521 GTAATAATCC
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
108 15 0.17
109 71 0.83
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (108 bp):
TAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATAAGTTATTAAGTTAAGTAAGTTATG
TGAGTTATGTAAATTATGGTATAATATATATAAGTTATTAAGT
Found at i:38662817 original size:20 final size:20
Alignment explanation
Indices: 38662794--38662841 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38662784 AGTTTATCTT
*
38662794 TATTTTTTCTTTTTTATTTC
1 TATTTTTACTTTTTTATTTC
* * *
38662814 TATTTGTAGTTTTTTATTTT
1 TATTTTTACTTTTTTATTTC
38662834 TATTTTTA
1 TATTTTTA
38662842 TTTGAATTCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (20 bp):
TATTTTTACTTTTTTATTTC
Found at i:38663032 original size:23 final size:22
Alignment explanation
Indices: 38663004--38663079 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 22
38662994 TTGACATTAC
38663004 TTTTAAACTTATTATTAGTATAG
1 TTTTAAA-TTATTATTAGTATAG
* *
38663027 TTTTAAAATGTAATA-TACTATTA-
1 TTTT-AAAT-TATTATTAGTA-TAG
38663050 TTTTAAATTATTATT-G-ATATG
1 TTTTAAATTATTATTAGTATA-G
38663071 TTTTAAATT
1 TTTTAAATT
38663080 TATCATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
19 2 0.05
20 1 0.02
21 13 0.30
22 5 0.12
23 13 0.30
24 9 0.21
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.54
Consensus pattern (22 bp):
TTTTAAATTATTATTAGTATAG
Found at i:38664371 original size:9 final size:9
Alignment explanation
Indices: 38664349--38664569 Score: 189
Period size: 9 Copynumber: 24.0 Consensus size: 9
38664339 AATATATATA
38664349 TAAGTTAT-
1 TAAGTTATG
38664357 TAAGTTATG
1 TAAGTTATG
38664366 TAAGTTATG
1 TAAGTTATG
* *
38664375 TGAGTTATT
1 TAAGTTATG
38664384 TAAGTTATGG
1 TAAGTTAT-G
* *
38664394 TATGATATATA
1 TAAG-T-TATG
38664405 TAAGTTAT-
1 TAAGTTATG
*
38664413 TAAGTTAAG
1 TAAGTTATG
38664422 TAAGTTATG
1 TAAGTTATG
* *
38664431 TGAGTTATT
1 TAAGTTATG
38664440 TAAGTTATGG
1 TAAGTTAT-G
* *
38664450 TATGATATATA
1 TAAG-T-TATG
38664461 TAAGTTAT-
1 TAAGTTATG
*
38664469 TAAGTTAAG
1 TAAGTTATG
38664478 TAAGTTATG
1 TAAGTTATG
* *
38664487 TGAGTTATT
1 TAAGTTATG
*
38664496 TAAGCTATGG
1 TAAGTTAT-G
* *
38664506 TATGATATATA
1 TAAG-T-TATG
38664517 TAAGTTAT-
1 TAAGTTATG
38664525 TAAGTTATG
1 TAAGTTATG
38664534 TAAGTTATG
1 TAAGTTATG
38664543 TAAGTTATG
1 TAAGTTATG
*
38664552 TAAATTATG
1 TAAGTTATG
38664561 TAAGTTATG
1 TAAGTTATG
38664570 ATATATATTT
Statistics
Matches: 171, Mismatches: 29, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
8 30 0.18
9 109 0.64
10 12 0.07
11 11 0.06
12 9 0.05
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:38664574 original size:56 final size:56
Alignment explanation
Indices: 38664342--38664560 Score: 384
Period size: 56 Copynumber: 3.9 Consensus size: 56
38664332 TTTCGACAAT
*
38664342 ATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATTTAAGTTATGGTATG
1 ATATATATAAGTTATTAAGTTAAGTAAGTTATGTGAGTTATTTAAGTTATGGTATG
38664398 ATATATATAAGTTATTAAGTTAAGTAAGTTATGTGAGTTATTTAAGTTATGGTATG
1 ATATATATAAGTTATTAAGTTAAGTAAGTTATGTGAGTTATTTAAGTTATGGTATG
*
38664454 ATATATATAAGTTATTAAGTTAAGTAAGTTATGTGAGTTATTTAAGCTATGGTATG
1 ATATATATAAGTTATTAAGTTAAGTAAGTTATGTGAGTTATTTAAGTTATGGTATG
* * * *
38664510 ATATATATAAGTTATTAAGTTATGTAAGTTATGTAAGTTATGTAAATTATG
1 ATATATATAAGTTATTAAGTTAAGTAAGTTATGTGAGTTATTTAAGTTATG
38664561 TAAGTTATGA
Statistics
Matches: 156, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 156 1.00
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (56 bp):
ATATATATAAGTTATTAAGTTAAGTAAGTTATGTGAGTTATTTAAGTTATGGTATG
Found at i:38665025 original size:33 final size:33
Alignment explanation
Indices: 38664983--38665048 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
38664973 TAAAAAAGAG
38664983 TTGTTTTTGCGGCAATTTTAAAATGGAAATTAA
1 TTGTTTTTGCGGCAATTTTAAAATGGAAATTAA
38665016 TTGTTTTTGCGGCAATTTTAAAATGGAAATTAA
1 TTGTTTTTGCGGCAATTTTAAAATGGAAATTAA
38665049 AAAAATTGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.42
Consensus pattern (33 bp):
TTGTTTTTGCGGCAATTTTAAAATGGAAATTAA
Found at i:38665723 original size:13 final size:13
Alignment explanation
Indices: 38665705--38665736 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
38665695 AAAGAACTTG
38665705 CAGCAACATTAAC
1 CAGCAACATTAAC
38665718 CAGCAACATTAAC
1 CAGCAACATTAAC
38665731 CA-CAAC
1 CAGCAAC
38665737 TTGCAGCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.47, C:0.34, G:0.06, T:0.12
Consensus pattern (13 bp):
CAGCAACATTAAC
Found at i:38666591 original size:20 final size:20
Alignment explanation
Indices: 38666562--38666602 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
38666552 ATTTGGAAGA
38666562 GATTTCGAAGGGGAATTAGG
1 GATTTCGAAGGGGAATTAGG
*
38666582 GATTTGGAAGGGGAATTAGG
1 GATTTCGAAGGGGAATTAGG
38666602 G
1 G
38666603 GCCGGGTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.44, T:0.24
Consensus pattern (20 bp):
GATTTCGAAGGGGAATTAGG
Found at i:38667030 original size:40 final size:38
Alignment explanation
Indices: 38666986--38667074 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 38
38666976 CGTTTGGGCA
38666986 AAAAACGCCACTAAAAATCAAGCATTAACGGCGCTTTTAT
1 AAAAACGCCACTAAAAAT-AAGCATTAACGGCG-TTTTAT
*** * *
38667026 AAAAACGTTTTCTAAAAATAAGCATTAGCGGCGTTTTCT
1 AAAAACG-CCACTAAAAATAAGCATTAACGGCGTTTTAT
38667065 AAAAAGCGCC
1 AAAAA-CGCC
38667075 GCAAAAAGCC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
39 10 0.25
40 22 0.55
41 8 0.20
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (38 bp):
AAAAACGCCACTAAAAATAAGCATTAACGGCGTTTTAT
Found at i:38667183 original size:41 final size:41
Alignment explanation
Indices: 38667122--38667453 Score: 533
Period size: 41 Copynumber: 8.1 Consensus size: 41
38667112 TTTTGGGGCA
*
38667122 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTACTGCTCTGGCC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGCC
* *
38667163 TTTAGCGGCATTTTTAAAGAAGCGCCGCTAATGCTCTGGCC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGCC
*
38667204 TTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGCTCTGGCC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGCC
*
38667245 TTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGCTCTGGCC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGCC
* *
38667286 TTTAGCGGCGTTTTTGACGAAGCGCCGCTAATGCTCGGGCC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGCC
* *
38667327 TTTAGCGGCGTTTTTGAAGAAGCACCGCTAATGCTCCGGCC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGCC
*
38667368 TTTAGCGGCGTTTTTGAAGAAGCG--ACTAATGCTCTGGCC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGCC
* * *
38667407 TTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCGGGCC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGCC
38667448 TTTAGC
1 TTTAGC
38667454 ACTAAGCTTA
Statistics
Matches: 272, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
39 35 0.13
41 237 0.87
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGCC
Found at i:38668924 original size:43 final size:43
Alignment explanation
Indices: 38668858--38669186 Score: 380
Period size: 43 Copynumber: 7.7 Consensus size: 43
38668848 TAAATTTTTT
* * ** *
38668858 TAAAGGTTAT-GTTTTTAGCGGCGTTTTTTCGAGAAGCGCCGC
1 TAAAGGTTATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
38668900 TAAAGGTTATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTTATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * * *
38668943 TAAAGATCATGGTCTTTAGTGGCGTTTGTAGGAAAAGCGCCGC
1 TAAAGGTTATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * **
38668986 TAAAGGTCT-TTGTCTTTAGCGGCGTTTGTGGTAAAATTGCCGC
1 TAAAGGT-TATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* *
38669029 TAATGGTCT-TGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGC
1 TAAAGGT-TATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * *
38669072 TAAAGGTCATGGTCTTTAACGGCGTTTGT-GAAAGAAGCGCCGC
1 TAAAGGTTATGGTCTTTAGCGGCGTTTGTGGGAA-AAGCGCCGC
* *
38669115 TAATGGTTTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTTATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * *
38669158 TAAAGGTCT-TGTTCTTTAGTGGCTTTTGT
1 TAAAGGT-TATGGTCTTTAGCGGCGTTTGT
38669187 TTCTAAAAAC
Statistics
Matches: 247, Mismatches: 34, Indels: 11
0.85 0.12 0.04
Matches are distributed among these distances:
42 13 0.05
43 230 0.93
44 4 0.02
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (43 bp):
TAAAGGTTATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
Found at i:38669110 original size:129 final size:129
Alignment explanation
Indices: 38668858--38669186 Score: 432
Period size: 129 Copynumber: 2.6 Consensus size: 129
38668848 TAAATTTTTT
* * * ** *
38668858 TAAAGGTTAT-GTTTTTAGCGGCGTTTTTTCGAGAAGCGCCGCTAAAGGT-TATGGTCTTTAGCG
1 TAAAGGTTTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCT-TGGTCTTTAGCG
** *
38668921 GCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGGTCTTTAGTGGCGTTTGTAGGAAAAGCGCCGC
65 GCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGGTCTTTAACGGCGTTTGTAGAAAAAGCGCCGC
* ** *
38668986 TAAAGGTCTTT-GTCTTTAGCGGCGTTTGTGGTAAAATTGCCGCTAATGGTCTTGGTCTTTAGCG
1 TAAAGGT-TTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCG
* *
38669050 GCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGGTCTTTAACGGCGTTTGT-GAAAGAAGCGCCG
65 GCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGGTCTTTAACGGCGTTTGTAGAAA-AAGCGCCG
38669114 C
129 C
* * *
38669115 TAATGGTTTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTTTAGTGG
1 TAAAGGTTTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGG
*
38669180 CTTTTGT
66 CGTTTGT
38669187 TTCTAAAAAC
Statistics
Matches: 174, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
128 13 0.07
129 160 0.92
130 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (129 bp):
TAAAGGTTTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGG
CGTTTGTGGGAAAAGCGCCGCTAAAGATCATGGTCTTTAACGGCGTTTGTAGAAAAAGCGCCGC
Found at i:38669959 original size:28 final size:28
Alignment explanation
Indices: 38669896--38669960 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
38669886 CTTAAATACT
* * * *
38669896 AAACCCTAAACCTTAAACTCCAAATCAC
1 AAACTCTAAACCATAAACGCAAAATCAC
38669924 AAACTCTAAACCATAAACGCAAAACTCA-
1 AAACTCTAAACCATAAACGCAAAA-TCAC
*
38669952 AAATTCTAA
1 AAACTCTAA
38669961 TCCGAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 28 0.90
29 3 0.10
ACGTcount: A:0.51, C:0.29, G:0.02, T:0.18
Consensus pattern (28 bp):
AAACTCTAAACCATAAACGCAAAATCAC
Found at i:38669998 original size:7 final size:7
Alignment explanation
Indices: 38669972--38670060 Score: 58
Period size: 7 Copynumber: 12.9 Consensus size: 7
38669962 CCGAAAATAA
*
38669972 TAAACAT
1 TAAACCT
* *
38669979 TATACCC
1 TAAACCT
38669986 TAAACCT
1 TAAACCT
*
38669993 TAAACCC
1 TAAACCT
38670000 TAAACCT
1 TAAACCT
*
38670007 TAAATAC-
1 TAAA-CCT
*
38670014 T-AACCC
1 TAAACCT
38670020 TAAACC-
1 TAAACCT
*
38670026 TAAACTT
1 TAAACCT
38670033 TAAACCT
1 TAAACCT
*
38670040 TAAAACCA
1 T-AAACCT
*
38670048 TAAACCC
1 TAAACCT
38670055 TAAACC
1 TAAACC
38670061 AAAAAGTGTA
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
5 1 0.02
6 8 0.12
7 48 0.75
8 7 0.11
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAACCT
Found at i:38670038 original size:20 final size:20
Alignment explanation
Indices: 38669984--38670043 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
38669974 AACATTATAC
*
38669984 CCTAAACCTTAAACCCTAAA
1 CCTAAACTTTAAACCCTAAA
*
38670004 CCTTAAA-TACT-AACCCTAAA
1 CC-TAAACT-TTAAACCCTAAA
*
38670024 CCTAAACTTTAAACCTTAAA
1 CCTAAACTTTAAACCCTAAA
38670044 ACCATAAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 5 0.16
20 22 0.69
21 5 0.16
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (20 bp):
CCTAAACTTTAAACCCTAAA
Found at i:38670061 original size:14 final size:14
Alignment explanation
Indices: 38669972--38670060 Score: 83
Period size: 14 Copynumber: 6.4 Consensus size: 14
38669962 CCGAAAATAA
* *
38669972 TAAACATTATACCC
1 TAAACCTTAAACCC
38669986 TAAACCTTAAACCC
1 TAAACCTTAAACCC
**
38670000 TAAACCTTAAATAC
1 TAAACCTTAAACCC
*
38670014 T-AACCCTAAA-CC
1 TAAACCTTAAACCC
* *
38670026 TAAACTTTAAACCT
1 TAAACCTTAAACCC
*
38670040 TAAAACCATAAACCC
1 T-AAACCTTAAACCC
38670055 TAAACC
1 TAAACC
38670061 AAAAAGTGTA
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
12 2 0.03
13 15 0.25
14 32 0.53
15 11 0.18
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:38670516 original size:40 final size:38
Alignment explanation
Indices: 38670454--38670544 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 38
38670444 TCCCAAGTTT
* *
38670454 TTTGCGGCGTTTTTCTATAAGCGCCCCTAATGCTTGATCA
1 TTTGCGGCGTTTTACTAAAAGCGCCCCTAATGCTT-A-CA
* * *
38670494 TTTGCGGCGTTTTAGTAAAAGCGCCGCTATTGCTTACA
1 TTTGCGGCGTTTTACTAAAAGCGCCCCTAATGCTTACA
38670532 TATTGCGGC-TTTT
1 T-TTGCGGCGTTTT
38670545 GTTAGAATTC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
38 7 0.16
39 8 0.18
40 30 0.67
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (38 bp):
TTTGCGGCGTTTTACTAAAAGCGCCCCTAATGCTTACA
Found at i:38672842 original size:23 final size:24
Alignment explanation
Indices: 38672799--38672843 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
38672789 CCAAAACACC
38672799 CTAGCCCAATTGAAACCCAAAATA
1 CTAGCCCAATTGAAACCCAAAATA
38672823 CTAGCCC-ATT-ACAACCCAAAA
1 CTAGCCCAATTGA-AACCCAAAA
38672844 CCCACTGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 1 0.05
23 12 0.60
24 7 0.35
ACGTcount: A:0.44, C:0.33, G:0.07, T:0.16
Consensus pattern (24 bp):
CTAGCCCAATTGAAACCCAAAATA
Found at i:38673170 original size:32 final size:32
Alignment explanation
Indices: 38673134--38673197 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
38673124 CAATCTCAAG
38673134 GTGATTGTTTGATTTTGGAACAAGATCCATAT
1 GTGATTGTTTGATTTTGGAACAAGATCCATAT
38673166 GTGATTGTTTGATTTTGGAACAAGATCCATAT
1 GTGATTGTTTGATTTTGGAACAAGATCCATAT
38673198 TTTGATAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (32 bp):
GTGATTGTTTGATTTTGGAACAAGATCCATAT
Found at i:38673929 original size:13 final size:13
Alignment explanation
Indices: 38673905--38673930 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38673895 ATATTATTAC
38673905 ATTATTATTTATT
1 ATTATTATTTATT
38673918 ATTATTATTTATT
1 ATTATTATTTATT
38673931 CGGTTACACC
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTATTATTTATT
Found at i:38673981 original size:2 final size:2
Alignment explanation
Indices: 38673969--38674006 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
38673959 AAAATCTTGT
*
38673969 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38674007 AGCATGCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:38680278 original size:204 final size:205
Alignment explanation
Indices: 38679928--38680338 Score: 815
Period size: 204 Copynumber: 2.0 Consensus size: 205
38679918 TAATTGAATC
38679928 AAGTTATTTGATTTTTTCGAGTAAAATTTATAATTCGAGTTTTGAGTTCAAGTCGAGTAGAATTT
1 AAGTTATTTGATTTTTTCGAGTAAAATTTATAATTCGAGTTTTGAGTTCAAGTCGAGTAGAATTT
38679993 TACAATTCGAATAACTCGAACAATTCGAGTAATAGATTGATATAAATACCCTTTTGATCCCAGTC
66 TACAATTCGAATAACTCGAACAATTCGAGTAATAGATTGATATAAATACCCTTTTGATCCCAGTC
38680058 AGTTTTAAAAATGAGCAAATTGGTCTTTTTCAACAAAAATTACAAAAAAAAATCAAAATAA-TTT
131 AGTTTTAAAAATGAGCAAATTGGTCTTTTTCAACAAAAATTACAAAAAAAAATCAAAATAATTTT
38680122 TAAAATTCAA
196 TAAAATTCAA
38680132 AAGTTATTTGATTTTTTCGAGTAAAATTTATAATTCGAGTTTTGAGTTCAAGTCGAGTAGAATTT
1 AAGTTATTTGATTTTTTCGAGTAAAATTTATAATTCGAGTTTTGAGTTCAAGTCGAGTAGAATTT
38680197 TACAATTCGAATAACTCGAACAATTCGAGTAATAGATTGATATAAATACCCTTTTGATCCCAGTC
66 TACAATTCGAATAACTCGAACAATTCGAGTAATAGATTGATATAAATACCCTTTTGATCCCAGTC
38680262 AGTTTTAAAAATGAGCAAATTGGTCTTTTTCAACAAAAATTACAAAAAAAAATCAAAATAATTTT
131 AGTTTTAAAAATGAGCAAATTGGTCTTTTTCAACAAAAATTACAAAAAAAAATCAAAATAATTTT
38680327 TAAAATTCAA
196 TAAAATTCAA
38680337 AA
1 AA
38680339 TATTTATAAA
Statistics
Matches: 206, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
204 191 0.93
205 15 0.07
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (205 bp):
AAGTTATTTGATTTTTTCGAGTAAAATTTATAATTCGAGTTTTGAGTTCAAGTCGAGTAGAATTT
TACAATTCGAATAACTCGAACAATTCGAGTAATAGATTGATATAAATACCCTTTTGATCCCAGTC
AGTTTTAAAAATGAGCAAATTGGTCTTTTTCAACAAAAATTACAAAAAAAAATCAAAATAATTTT
TAAAATTCAA
Found at i:38680343 original size:18 final size:19
Alignment explanation
Indices: 38680309--38680351 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
38680299 AATTACAAAA
*
38680309 AAAAATCAAAATAATTTTT
1 AAAAATCAAAATAATTTAT
*
38680328 AAAATTCAAAAT-ATTTAT
1 AAAAATCAAAATAATTTAT
38680346 AAAAAT
1 AAAAAT
38680352 TCCAAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATCAAAATAATTTAT
Found at i:38680364 original size:18 final size:19
Alignment explanation
Indices: 38680308--38680358 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
38680298 AAATTACAAA
*
38680308 AAAAAATCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
38680327 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
38680346 AAAAATTCCAAAA
1 AAAAATT-CAAAA
38680359 ATTATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 18 0.67
20 5 0.19
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:38688230 original size:15 final size:15
Alignment explanation
Indices: 38688199--38688341 Score: 70
Period size: 15 Copynumber: 9.5 Consensus size: 15
38688189 CGTTAGCTCC
* *
38688199 CCACCACCAGCTTCT
1 CCACCACCGGCTACT
*
38688214 CCTCCACCGGCTACT
1 CCACCACCGGCTACT
* * * *
38688229 CCTCCCCCAGCTACC
1 CCACCACCGGCTACT
* * *
38688244 CCACCTCCCGCAACT
1 CCACCACCGGCTACT
* *
38688259 CCCCCACCGGCTTCT
1 CCACCACCGGCTACT
* * *
38688274 CCACCTCAGGCTACC
1 CCACCACCGGCTACT
* *
38688289 CCACCACCTGCTTCT
1 CCACCACCGGCTACT
* * *
38688304 CCCCCTCCTGCTACT
1 CCACCACCGGCTACT
* * * *
38688319 CCTCCTCCAGCTACC
1 CCACCACCGGCTACT
38688334 CCACCACC
1 CCACCACC
38688342 AGCTCCTTTG
Statistics
Matches: 94, Mismatches: 34, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 94 1.00
ACGTcount: A:0.15, C:0.59, G:0.08, T:0.18
Consensus pattern (15 bp):
CCACCACCGGCTACT
Found at i:38688239 original size:30 final size:30
Alignment explanation
Indices: 38688205--38688330 Score: 101
Period size: 30 Copynumber: 4.2 Consensus size: 30
38688195 CTCCCCACCA
* *
38688205 CCAGCTTCTCCTCCACCGGCTACTCCTCCC
1 CCAGCTTCTCCACCTCCGGCTACTCCTCCC
* * * *
38688235 CCAGCTACCCCACCTCCCGCAACTCC-CCC
1 CCAGCTTCTCCACCTCCGGCTACTCCTCCC
* * * * *
38688264 ACCGGCTTCTCCACCTCAGGCTACCCCACCA
1 -CCAGCTTCTCCACCTCCGGCTACTCCTCCC
* * * *
38688295 CCTGCTTCTCCCCCTCCTGCTACTCCTCCT
1 CCAGCTTCTCCACCTCCGGCTACTCCTCCC
38688325 CCAGCT
1 CCAGCT
38688331 ACCCCACCAC
Statistics
Matches: 72, Mismatches: 22, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
29 3 0.04
30 67 0.93
31 2 0.03
ACGTcount: A:0.13, C:0.57, G:0.10, T:0.21
Consensus pattern (30 bp):
CCAGCTTCTCCACCTCCGGCTACTCCTCCC
Found at i:38688246 original size:45 final size:45
Alignment explanation
Indices: 38688193--38688345 Score: 175
Period size: 45 Copynumber: 3.4 Consensus size: 45
38688183 CCCGCCCGTT
*
38688193 AGCT-CCCCACCACCAGCTTCTCCTCCACCGGCTACTCCTCCCCC
1 AGCTACCCCACCACCAGCTTCTCCCCCACCGGCTACTCCTCCCCC
* * ** * * *
38688237 AGCTACCCCACCTCCCGCAACTCCCCCACCGGCTTCTCC-ACCTC
1 AGCTACCCCACCACCAGCTTCTCCCCCACCGGCTACTCCTCCCCC
* * * *
38688281 AGGCTACCCCACCACCTGCTTCTCCCCCTCCTGCTACTCCTCCTCC
1 A-GCTACCCCACCACCAGCTTCTCCCCCACCGGCTACTCCTCCCCC
38688327 AGCTACCCCACCACCAGCT
1 AGCTACCCCACCACCAGCT
38688346 CCTTTGGCTT
Statistics
Matches: 87, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
44 8 0.09
45 76 0.87
46 3 0.03
ACGTcount: A:0.15, C:0.58, G:0.09, T:0.18
Consensus pattern (45 bp):
AGCTACCCCACCACCAGCTTCTCCCCCACCGGCTACTCCTCCCCC
Found at i:38688523 original size:6 final size:6
Alignment explanation
Indices: 38688512--38688537 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
38688502 ACCGATACGG
38688512 TATGTA TATGTA TATGTA TATGTA TA
1 TATGTA TATGTA TATGTA TATGTA TA
38688538 CGCATATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:38706553 original size:27 final size:24
Alignment explanation
Indices: 38706508--38706567 Score: 59
Period size: 27 Copynumber: 2.4 Consensus size: 24
38706498 ACATATAATC
38706508 TCAATTCAATCACAATTCCTCACATTT
1 TCAATTCAATCACAATT-C-CACA-TT
***
38706535 TCAATTCAATCATTTTTCCACATT
1 TCAATTCAATCACAATTCCACATT
38706559 TCAA-TCAAT
1 TCAATTCAAT
38706568 AATTAATCCG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 5 0.17
24 6 0.20
25 4 0.13
26 1 0.03
27 14 0.47
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (24 bp):
TCAATTCAATCACAATTCCACATT
Found at i:38707039 original size:14 final size:17
Alignment explanation
Indices: 38707020--38707057 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
38707010 ATTTATTTCT
38707020 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
38707034 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
38707051 TAATATA
1 TAATATA
38707058 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:38707065 original size:12 final size:11
Alignment explanation
Indices: 38707037--38707080 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
38707027 ATATTTATAA
38707037 TATAATTAATT
1 TATAATTAATT
*
38707048 TAATAATATACTT
1 T-ATAAT-TAATT
38707061 TATAATTAATT
1 TATAATTAATT
38707072 TATATATTA
1 TATA-ATTA
38707081 TATAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.32
12 14 0.50
13 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TATAATTAATT
Found at i:38707084 original size:20 final size:23
Alignment explanation
Indices: 38707032--38707094 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
38707022 ATATAATATT
38707032 TATA-ATATAATTAATTTAATAA
1 TATATATATAATTAATTTAATAA
* *
38707054 TATACTTTATAATTAATTTATATAT
1 TATA-TATATAATTAATTTA-ATAA
* *
38707079 TATATAAATAAATAAT
1 TATATATATAATTAAT
38707095 ATAAATATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 4 0.12
24 22 0.67
25 7 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATATATAATTAATTTAATAA
Found at i:38707096 original size:20 final size:20
Alignment explanation
Indices: 38707049--38707097 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
38707039 TAATTAATTT
*
38707049 AATAATATACTTTATAATTA
1 AATAATATACTTTATAAATA
* *
38707069 ATTTATATA-TTATATAAATA
1 AATAATATACTT-TATAAATA
38707089 AATAATATA
1 AATAATATA
38707098 AATATCTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATATACTTTATAAATA
Found at i:38712232 original size:16 final size:16
Alignment explanation
Indices: 38712211--38712262 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
38712201 CCAAAACTAA
38712211 AAATAAATTTACCTTT
1 AAATAAATTTACCTTT
***
38712227 AAAT-AA-TTA-CAAA
1 AAATAAATTTACCTTT
38712240 AAATAAATTTACCTTT
1 AAATAAATTTACCTTT
38712256 AAATAAA
1 AAATAAA
38712263 AATTTGGCCG
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 5 0.19
14 5 0.19
15 5 0.19
16 12 0.44
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAAATTTACCTTT
Found at i:38718892 original size:6 final size:6
Alignment explanation
Indices: 38718888--38718940 Score: 63
Period size: 6 Copynumber: 8.5 Consensus size: 6
38718878 AAGCCAAACA
*
38718888 AAAACAG AA-AAG AAAGAAAG AAAAAG AAAAAG AAAAAG AAAAAG AGAAAG
1 AAAA-AG AAAAAG AAA-A-AG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
38718938 AAA
1 AAA
38718941 GACGTAAGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
5 4 0.10
6 28 0.68
7 4 0.10
8 5 0.12
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:38720967 original size:408 final size:408
Alignment explanation
Indices: 38720212--38721029 Score: 1620
Period size: 408 Copynumber: 2.0 Consensus size: 408
38720202 CCATTGTATG
38720212 AATAAATGTGGTCATAAATATTCAAATGTGCTTATAATTAAAATATGCATATTATATTGTCTTGT
1 AATAAATGTGGTCATAAATATTCAAATGTGCTTATAATTAAAATATGCATATTATATTGTCTTGT
38720277 TTTTAAATATTCGGATTATATAAATACCACTGAGTTTTACTCAGCGTACGGTTTTGTTTTCTGTG
66 TTTTAAATATTCGGATTATATAAATACCACTGAGTTTTACTCAGCGTACGGTTTTGTTTTCTGTG
38720342 CGCAGATTAGGTACTTCAATTTTGATCGCCGATTCAGCATCCAACAATGCTCCCGAACTCAAATG
131 CGCAGATTAGGTACTTCAATTTTGATCGCCGATTCAGCATCCAACAATGCTCCCGAACTCAAATG
38720407 TGGTGATGTCTATCTTTTGTGTCGGCATGTACCTAGGGTGTCTAAATAATAGTTATTTTGTGGAT
196 TGGTGATGTCTATCTTTTGTGTCGGCATGTACCTAGGGTGTCTAAATAATAGTTATTTTGTGGAT
38720472 TGATTGTAAATGAGATTATAAGTTTAATATTGGTTGATTTTATACATATAAACATGTATTTGTGT
261 TGATTGTAAATGAGATTATAAGTTTAATATTGGTTGATTTTATACATATAAACATGTATTTGTGT
38720537 TTGAAACCATAGTATGGTATGGTAAATTGAATCAAAGCTTAGTATGTGCATGTGAATTTAAGTTA
326 TTGAAACCATAGTATGGTATGGTAAATTGAATCAAAGCTTAGTATGTGCATGTGAATTTAAGTTA
38720602 ATGTTTTAGGTAGATATA
391 ATGTTTTAGGTAGATATA
38720620 AATAAATGTGGTCATAAATATTCAAATGTGCTTATAATTAAAATATGCATATTATATTGTCTTGT
1 AATAAATGTGGTCATAAATATTCAAATGTGCTTATAATTAAAATATGCATATTATATTGTCTTGT
38720685 TTTTAAATATTCGGATTATATAAATACCACTGAGTTTTACTCAGCGTACGGTTTTGTTTTCTGTG
66 TTTTAAATATTCGGATTATATAAATACCACTGAGTTTTACTCAGCGTACGGTTTTGTTTTCTGTG
38720750 CGCAGATTAGGTACTTCAATTTTGATCGCCGATTCAGCATCCAACAATGCTCCCG-ACTCAAAAT
131 CGCAGATTAGGTACTTCAATTTTGATCGCCGATTCAGCATCCAACAATGCTCCCGAACTC-AAAT
38720814 GTGGTGATGTCTATCTTTTGTGTCGGCATGTACCTAGGGTGTCTAAATAATAGTTATTTTGTGGA
195 GTGGTGATGTCTATCTTTTGTGTCGGCATGTACCTAGGGTGTCTAAATAATAGTTATTTTGTGGA
38720879 TTGATTGTAAATGAGATTATAAGTTTAATATTGGTTGATTTTATACATATAAACATGTATTTGTG
260 TTGATTGTAAATGAGATTATAAGTTTAATATTGGTTGATTTTATACATATAAACATGTATTTGTG
38720944 TTTGAAACCATAGTATGGTATGGTAAATTGAATCAAAGCTTAGTATGTGCATGTGAATTTAAGTT
325 TTTGAAACCATAGTATGGTATGGTAAATTGAATCAAAGCTTAGTATGTGCATGTGAATTTAAGTT
38721009 AATGTTTTAGGTAGATATA
390 AATGTTTTAGGTAGATATA
38721028 AA
1 AA
38721030 CTAGGCCAAA
Statistics
Matches: 409, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
407 4 0.01
408 405 0.99
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.40
Consensus pattern (408 bp):
AATAAATGTGGTCATAAATATTCAAATGTGCTTATAATTAAAATATGCATATTATATTGTCTTGT
TTTTAAATATTCGGATTATATAAATACCACTGAGTTTTACTCAGCGTACGGTTTTGTTTTCTGTG
CGCAGATTAGGTACTTCAATTTTGATCGCCGATTCAGCATCCAACAATGCTCCCGAACTCAAATG
TGGTGATGTCTATCTTTTGTGTCGGCATGTACCTAGGGTGTCTAAATAATAGTTATTTTGTGGAT
TGATTGTAAATGAGATTATAAGTTTAATATTGGTTGATTTTATACATATAAACATGTATTTGTGT
TTGAAACCATAGTATGGTATGGTAAATTGAATCAAAGCTTAGTATGTGCATGTGAATTTAAGTTA
ATGTTTTAGGTAGATATA
Found at i:38722694 original size:14 final size:14
Alignment explanation
Indices: 38722675--38722703 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
38722665 GATAAATTAT
38722675 ACTCAGTTTTGCTA
1 ACTCAGTTTTGCTA
38722689 ACTCAGTTTTGCTA
1 ACTCAGTTTTGCTA
38722703 A
1 A
38722704 GGCAATGAGG
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:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (14 bp):
ACTCAGTTTTGCTA
Found at i:38726829 original size:66 final size:66
Alignment explanation
Indices: 38726738--38726903 Score: 183
Period size: 66 Copynumber: 2.5 Consensus size: 66
38726728 GAAAAATCAA
* * * * * * *
38726738 ATATT-AGATCTTTCCAAGCTTCTGAATGAGATATCAGGCCTTCTTAATCCTAAGCTCC-GAAAT
1 ATATTAAG-TCTTCCCAAGCTCCTGAACGAGATATCAAGCCTTCTTAATCCCAAGATCCTGAAAG
38726801 GC
65 GC
* * * *
38726803 AATATTGAGTCTTCTCAAGCTCCTGAACGAGATATCAAGTCTTCTTAATCCCAAGATCCTGAACG
1 -ATATTAAGTCTTCCCAAGCTCCTGAACGAGATATCAAGCCTTCTTAATCCCAAGATCCTGAAAG
38726868 GC
65 GC
* *
38726870 ATATTAAGTCTTCCCAAGCTCCTAAACAAGATAT
1 ATATTAAGTCTTCCCAAGCTCCTGAACGAGATAT
38726904 TGGGTCTTCT
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
66 77 0.92
67 7 0.08
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (66 bp):
ATATTAAGTCTTCCCAAGCTCCTGAACGAGATATCAAGCCTTCTTAATCCCAAGATCCTGAAAGG
C
Found at i:38729477 original size:18 final size:20
Alignment explanation
Indices: 38729438--38729477 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
38729428 AACATTTACA
38729438 CTTTGATATTATATAATTAAT
1 CTTTGATATTATATAA-TAAT
38729459 CTTT-ATATTATATAA-AAT
1 CTTTGATATTATATAATAAT
38729477 C
1 C
38729478 ATAATTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
20 11 0.58
21 4 0.21
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (20 bp):
CTTTGATATTATATAATAAT
Found at i:38742830 original size:2 final size:2
Alignment explanation
Indices: 38742825--38742862 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
38742815 AACACACACG
38742825 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38742863 GAATATAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38743935 original size:44 final size:45
Alignment explanation
Indices: 38743879--38744054 Score: 221
Period size: 45 Copynumber: 4.0 Consensus size: 45
38743869 AACCGTTACA
* *
38743879 CGGTGG-ATCAGCACATAGC-ACCACCCTTATAATCAATTATATT
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATATT
* ** *
38743922 CGCTGGAATCAGCACATAGCAACCACCTTTATTTTCAATGATCTT
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATATT
* * * **
38743967 CGGTGGAGTCAGCACATAGTAACCACCTTTATAATCAATGGTACC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATATT
* *
38744012 CGGTGGAATCAACACATAGCAACCACTTTTATAATCAATGATA
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATA
38744055 CTCAGTACAC
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
43 5 0.05
44 13 0.12
45 93 0.84
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATATT
Found at i:38744129 original size:51 final size:53
Alignment explanation
Indices: 38744066--38744166 Score: 125
Period size: 55 Copynumber: 1.9 Consensus size: 53
38744056 TCAGTACACG
*
38744066 TAGTAGCCTGCACATAGTAC-T-ACACATGTGACCATTACTATCACTTTCGCA
1 TAGTAGCCTGCACACAGTACGTCACACATGTGACCATTACTATCACTTTCGCA
* * * *
38744117 TAGTGGCCTGCACACAGTCCGTGCCACATATGTGATCATTACTATCACTT
1 TAGTAGCCTGCACACAGTACGT--CACACATGTGACCATTACTATCACTT
38744167 CATTCGTACC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
51 17 0.41
52 1 0.02
55 23 0.56
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (53 bp):
TAGTAGCCTGCACACAGTACGTCACACATGTGACCATTACTATCACTTTCGCA
Found at i:38745170 original size:18 final size:17
Alignment explanation
Indices: 38745144--38745182 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
38745134 ATTTTCCTTC
38745144 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
38745161 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
38745179 CACA
1 CACA
38745183 ATTTATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:38747137 original size:15 final size:15
Alignment explanation
Indices: 38747117--38747151 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
38747107 ATCCAAATTC
38747117 TAAATGCAAAT-GAAA
1 TAAATG-AAATAGAAA
38747132 TAAATGAAATAGAAA
1 TAAATGAAATAGAAA
38747147 TAAAT
1 TAAAT
38747152 AAGTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.23
Consensus pattern (15 bp):
TAAATGAAATAGAAA
Found at i:38751372 original size:11 final size:11
Alignment explanation
Indices: 38751335--38751374 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
38751325 TTCAAAAATT
*
38751335 CTCTCAAGTTC
1 CTCTTAAGTTC
38751346 CTCTTAAGTTC
1 CTCTTAAGTTC
*
38751357 CTCTTAAGTTT
1 CTCTTAAGTTC
38751368 CTCTTAA
1 CTCTTAA
38751375 CTCCCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.20, C:0.28, G:0.07, T:0.45
Consensus pattern (11 bp):
CTCTTAAGTTC
Found at i:38753168 original size:125 final size:124
Alignment explanation
Indices: 38753011--38753383 Score: 593
Period size: 124 Copynumber: 3.0 Consensus size: 124
38753001 TAAACATGCT
*
38753011 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTGCACAAATTCTTCTCAAATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTT-CACAAATTCTTCTCAAATAGCATCCTGCT
*
38753076 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAGTATTTCTTCCATTACCG
65 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAGTATTTCTTCCATGACCG
*
38753136 ACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
* * * * *
38753201 GAAGCAATTTTATACTATTTGCTCAGAAACATCAAAAAAAATTATTTCTTCTATGACCT
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAGTATTTCTTCCATGACCG
*
38753260 ACTGTAGTAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
* * ** * *
38753325 GAAGCGATTTTATACTATTTGATCAGAAACGTTAACTCAAAATTATTTCTTCCAAGACC
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAAGTATTTCTTCCATGACC
38753384 TAAAAACCCT
Statistics
Matches: 229, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
124 176 0.77
125 53 0.23
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (124 bp):
ACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAGTATTTCTTCCATGACCG
Found at i:38757242 original size:8 final size:8
Alignment explanation
Indices: 38757219--38757252 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
38757209 TCCACTGATT
38757219 CACGACTC
1 CACGACTC
38757227 CACG--TC
1 CACGACTC
38757233 CACGACTC
1 CACGACTC
38757241 CACGACTC
1 CACGACTC
38757249 CACG
1 CACG
38757253 GTGCTTCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
8 18 0.75
ACGTcount: A:0.24, C:0.50, G:0.15, T:0.12
Consensus pattern (8 bp):
CACGACTC
Found at i:38757252 original size:22 final size:22
Alignment explanation
Indices: 38757201--38757252 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
38757191 ATTGGATCTA
* *
38757201 ACTCCACCTCCACTGATTCACG
1 ACTCCACGTCCACTGATCCACG
38757223 ACTCCACGTCCAC-GACTCCACG
1 ACTCCACGTCCACTGA-TCCACG
38757245 ACTCCACG
1 ACTCCACG
38757253 GTGCTTCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.23, C:0.48, G:0.12, T:0.17
Consensus pattern (22 bp):
ACTCCACGTCCACTGATCCACG
Found at i:38757660 original size:76 final size:76
Alignment explanation
Indices: 38757534--38758520 Score: 1965
Period size: 76 Copynumber: 13.0 Consensus size: 76
38757524 GGTTTGCCAG
*
38757534 AATTGTTTGTAATTACTTGTATATTATAATAATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
38757599 AAATTCAAATT
66 AAATTCAAATT
38757610 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
38757675 AAATTCAAATT
66 AAATTCAAATT
38757686 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
38757751 AAATTCAAATT
66 AAATTCAAATT
38757762 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
38757827 AAATTCAAATT
66 AAATTCAAATT
38757838 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
38757903 AAATTCAAATT
66 AAATTCAAATT
38757914 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
38757979 AAATTCAAATT
66 AAATTCAAATT
38757990 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
38758055 AAATTCAAATT
66 AAATTCAAATT
38758066 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
38758131 AAATTCAAATT
66 AAATTCAAATT
38758142 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
38758207 AAATTCAAATT
66 AAATTCAAATT
38758218 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
38758283 AAATTCAAATT
66 AAATTCAAATT
38758294 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
38758359 AAATTCAAATT
66 AAATTCAAATT
38758370 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
38758435 AAATTCAAATT
66 AAATTCAAATT
38758446 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
38758511 AAATTCAAAT
66 AAATTCAAAT
38758521 AAGTAATCTT
Statistics
Matches: 910, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 910 1.00
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (76 bp):
AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
AAATTCAAATT
Found at i:38771177 original size:20 final size:20
Alignment explanation
Indices: 38771152--38771191 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38771142 CGTAAAATGA
*
38771152 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
38771172 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
38771192 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:38771181 original size:34 final size:35
Alignment explanation
Indices: 38771137--38771203 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
38771127 CAGTAAAATA
*
38771137 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
38771171 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
38771204 CTGGCGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:38771207 original size:14 final size:15
Alignment explanation
Indices: 38771131--38771207 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
38771121 GATTGCCAGT
* *
38771131 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
38771145 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
38771159 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
38771179 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
38771194 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
38771208 CGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:38771921 original size:60 final size:61
Alignment explanation
Indices: 38771807--38771924 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 61
38771797 ATTGGCTTAA
* *
38771807 TAACAAATTTAGCCTTAAATGTTTACAGATTCTACCAGTTTAATTCTAAATCTAAAAGATT
1 TAACAAATTTAGCCTTAAATGTTTACAAAATCTACCAGTTTAATTCTAAATCTAAAAGATT
** * * *
38771868 TAACAAATTTAGCCTT-AATGTTTACAAAATCTGTCATTTTAGTTCTAATTCTAAAAG
1 TAACAAATTTAGCCTTAAATGTTTACAAAATCTACCAGTTTAATTCTAAATCTAAAAG
38771925 TTATAAAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 34 0.68
61 16 0.32
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.39
Consensus pattern (61 bp):
TAACAAATTTAGCCTTAAATGTTTACAAAATCTACCAGTTTAATTCTAAATCTAAAAGATT
Found at i:38771965 original size:6 final size:6
Alignment explanation
Indices: 38771954--38771978 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38771944 ATATTTGAGA
38771954 TATATT TATATT TATATT TATATT T
1 TATATT TATATT TATATT TATATT T
38771979 TAACACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:38775029 original size:21 final size:21
Alignment explanation
Indices: 38774996--38775037 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
38774986 TCCAATAACA
38774996 AGGGAAAAGCTTGTGAT-TTAT
1 AGGGAAAAGCTTG-GATATTAT
38775017 AGGGAGAAA-CTTGGATATTAT
1 AGGGA-AAAGCTTGGATATTAT
38775038 CTCAACTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.16
21 13 0.68
22 3 0.16
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.31
Consensus pattern (21 bp):
AGGGAAAAGCTTGGATATTAT
Found at i:38775463 original size:32 final size:32
Alignment explanation
Indices: 38775427--38775494 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
38775417 TTGTAAACTA
38775427 AATTTGACCCCAA-AACCTTTCAAAACA-AGTCG
1 AATTTGA--CCAACAACCTTTCAAAACAGAGTCG
* *
38775459 AATTTGACCAACAAGCTTTCAAAATAGAGTCG
1 AATTTGACCAACAACCTTTCAAAACAGAGTCG
38775491 AATT
1 AATT
38775495 GTTGCTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 4 0.12
31 12 0.38
32 16 0.50
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (32 bp):
AATTTGACCAACAACCTTTCAAAACAGAGTCG
Found at i:38792112 original size:239 final size:239
Alignment explanation
Indices: 38791693--38792171 Score: 906
Period size: 239 Copynumber: 2.0 Consensus size: 239
38791683 ATAAAGGATG
38791693 AGTCACCAGAAGAAACAACTGCAACACTGGGTGAAGCCACACTAGTCTGTCGAAACGAGTCAAGG
1 AGTCACCAGAAGAAACAACTGCAACACTGGGTGAAGCCACACTAGTCTGTCGAAACGAGTCAAGG
38791758 ATGTAAAGACCACCTTGTGCCTTACCAATCCCCCTCATCTTTCCACTGGAGAGATCTTGTATAAG
66 ATGTAAAGACCACCTTGTGCCTTACCAATCCCCCTCATCTTTCCACTGGAGAGATCTTGTATAAG
* *
38791823 ACAAAATTGGGGGTAAAAAGAAACAACACAATTAAGATCGTTAGTAAGTTTTGAAACAGAAAGAA
131 AAAAAATTAGGGGTAAAAAGAAACAACACAATTAAGATCGTTAGTAAGTTTTGAAACAGAAAGAA
38791888 GATTATAGTGAAAATTGGGAACATAAAGAACTTTGGTTAACTGT
196 GATTATAGTGAAAATTGGGAACATAAAGAACTTTGGTTAACTGT
* *
38791932 AGTCACCAGAAGAAACAACTGCAACACTGGGTGAAGCCACACTAGTCTGTCGAAACGGGTCAATG
1 AGTCACCAGAAGAAACAACTGCAACACTGGGTGAAGCCACACTAGTCTGTCGAAACGAGTCAAGG
38791997 ATGTAAAGACCACCTTGTGCCTTACCAATCCCCCTCATCTTTCCACTGGAGAGAT-TCTGTATAA
66 ATGTAAAGACCACCTTGTGCCTTACCAATCCCCCTCATCTTTCCACTGGAGAGATCT-TGTATAA
38792061 GAAAAAATTAGGGGTAAAAAGAAACAACACAATTAAGATCGTTAGTAAGTTTTGAAACAGAAAGA
130 GAAAAAATTAGGGGTAAAAAGAAACAACACAATTAAGATCGTTAGTAAGTTTTGAAACAGAAAGA
38792126 AGATTATAGTGAAAATTGGGAACATAAAGAACTTTGGTTAACTGT
195 AGATTATAGTGAAAATTGGGAACATAAAGAACTTTGGTTAACTGT
38792171 A
1 A
38792172 AGGTAGGTAA
Statistics
Matches: 235, Mismatches: 4, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
238 1 0.00
239 234 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (239 bp):
AGTCACCAGAAGAAACAACTGCAACACTGGGTGAAGCCACACTAGTCTGTCGAAACGAGTCAAGG
ATGTAAAGACCACCTTGTGCCTTACCAATCCCCCTCATCTTTCCACTGGAGAGATCTTGTATAAG
AAAAAATTAGGGGTAAAAAGAAACAACACAATTAAGATCGTTAGTAAGTTTTGAAACAGAAAGAA
GATTATAGTGAAAATTGGGAACATAAAGAACTTTGGTTAACTGT
Done.