Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008262.1 Corchorus capsularis cultivar CVL-1 contig08283, whole genome shotgun sequence
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: 112410
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:4955 original size:23 final size:23
Alignment explanation
Indices: 4929--4975 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4919 ATGCGTTCAT
4929 CAGGAAATGATATTGCCAATACA
1 CAGGAAATGATATTGCCAATACA
4952 CAGGAAATGATATTGCCAATACA
1 CAGGAAATGATATTGCCAATACA
4975 C
1 C
4976 GACCTGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (23 bp):
CAGGAAATGATATTGCCAATACA
Found at i:7586 original size:102 final size:102
Alignment explanation
Indices: 7410--7613 Score: 399
Period size: 102 Copynumber: 2.0 Consensus size: 102
7400 CTCCGTGACC
7410 TTCTTTTTCAGCTGAATAATATGTGCTAACCATTTTCTCATGCGCCAAGGAACTGACTCCGGCTT
1 TTCTTTTTCAGCTGAATAATATGTGCTAACCATTTTCTCATGCGCCAAGGAACTGACTCCGGCTT
7475 CTCTGTTAGAAATTTTCTGAAATTAGAGAGAAAACAA
66 CTCTGTTAGAAATTTTCTGAAATTAGAGAGAAAACAA
*
7512 TTCTTTTTCAGCTGAATAATATGTGCTAACCATTTTCTCATGCGCTAAGGAACTGACTCCGGCTT
1 TTCTTTTTCAGCTGAATAATATGTGCTAACCATTTTCTCATGCGCCAAGGAACTGACTCCGGCTT
7577 CTCTGTTAGAAATTTTCTGAAATTAGAGAGAAAACAA
66 CTCTGTTAGAAATTTTCTGAAATTAGAGAGAAAACAA
7614 GACTTAGAGG
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (102 bp):
TTCTTTTTCAGCTGAATAATATGTGCTAACCATTTTCTCATGCGCCAAGGAACTGACTCCGGCTT
CTCTGTTAGAAATTTTCTGAAATTAGAGAGAAAACAA
Found at i:14327 original size:14 final size:14
Alignment explanation
Indices: 14310--14408 Score: 53
Period size: 14 Copynumber: 7.2 Consensus size: 14
14300 TTTATTTTAT
*
14310 AAATTTTTTTAAGA
1 AAATTCTTTTAAGA
**
14324 AAATTCAGTTAAG-
1 AAATTCTTTTAAGA
* * *
14337 AAATTTTATTTTA-T
1 AAATTCT-TTTAAGA
14351 AAATTCTTTTAAGA
1 AAATTCTTTTAAGA
**
14365 AAATTCAATTAAG-
1 AAATTCTTTTAAGA
* * *
14378 AAATTTTATTTTA-T
1 AAATTCT-TTTAAGA
14392 AAATTCTTTTAAGA
1 AAATTCTTTTAAGA
14406 AAA
1 AAA
14409 ATTCAGTTCA
Statistics
Matches: 60, Mismatches: 19, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
13 18 0.30
14 42 0.70
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (14 bp):
AAATTCTTTTAAGA
Found at i:14344 original size:41 final size:41
Alignment explanation
Indices: 14299--14423 Score: 214
Period size: 41 Copynumber: 3.0 Consensus size: 41
14289 CGTGCGGCTG
*
14299 TTTTATTTTATAAATTTTTTTAAGAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
*
14340 TTTTATTTTATAAATTCTTTTAAGAAAATTCAATTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
*
14381 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTCAGAAA
1 TTTTATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAGAAA
14423 T
1 T
14424 GAAATTTTGT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
41 63 0.80
42 16 0.20
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (41 bp):
TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
Found at i:14755 original size:11 final size:11
Alignment explanation
Indices: 14741--14778 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
14731 ATTCATAACA
14741 AATTTATAATT
1 AATTTATAATT
14752 AATTTATAATT
1 AATTTATAATT
14763 -ATTTGATAATT
1 AATTT-ATAATT
*
14774 TATTT
1 AATTT
14779 TATATAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:15026 original size:103 final size:103
Alignment explanation
Indices: 14835--15044 Score: 273
Period size: 103 Copynumber: 2.0 Consensus size: 103
14825 AATAAAAATA
* * * * *
14835 TAATAAATAAAACATTAGAAAATTAACTATTGACACTTGTTAAAGAAACTAAATGTCAAGTGGCA
1 TAATAAACAAAACATTAGAAAATTAAATATTGACACTTGTCAAAAAAACTAAATGCCAAGTGGCA
***
14900 CTCAATGAGGGTCTTGTACATAAAATTAATAGTAGGTT
66 CTCAATGAAACTCTTGTACATAAAATTAATAGTAGGTT
* *
14938 TAATAAACAAAATATTAGAAAATTAAATATTGACACTTGTCAAAAAAACCT-AATGCCATGTGGC
1 TAATAAACAAAACATTAGAAAATTAAATATTGACACTTGTCAAAAAAA-CTAAATGCCAAGTGGC
*
15002 ACTCAATGAAAACT-TTGCT-TATAAAATTAATAGTAGGTT
65 ACTCAATG-AAACTCTTG-TACATAAAATTAATAGTAGGTT
15041 TAAT
1 TAAT
15045 TTCACTCTTT
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
103 88 0.95
104 5 0.05
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (103 bp):
TAATAAACAAAACATTAGAAAATTAAATATTGACACTTGTCAAAAAAACTAAATGCCAAGTGGCA
CTCAATGAAACTCTTGTACATAAAATTAATAGTAGGTT
Found at i:18382 original size:2 final size:2
Alignment explanation
Indices: 18375--18399 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18365 TTCTGCAAAG
18375 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
18400 ATTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21475 original size:73 final size:73
Alignment explanation
Indices: 21388--21534 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
21378 TTGCCTATAC
*
21388 ACTCTTTGTTTACCTTCCCACATTTACTTTCCTACAAGCTTACCTGTCATCAAGACATTCCTTTG
1 ACTCTTTGTTTACCTTCCCACACTTACTTTCCTACAAGCTTACCTGTCATCAAGACATTCCTTTG
21453 CTAGCTTA
66 CTAGCTTA
21461 ACTCTTTGTTTACCTTCCCACACTTACTTTCCTACAAGCTTACCTGTCATCAAGACATTCCTTTG
1 ACTCTTTGTTTACCTTCCCACACTTACTTTCCTACAAGCTTACCTGTCATCAAGACATTCCTTTG
21526 CTAGCTTA
66 CTAGCTTA
21534 A
1 A
21535 GCCCTAGCAA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.22, C:0.31, G:0.08, T:0.39
Consensus pattern (73 bp):
ACTCTTTGTTTACCTTCCCACACTTACTTTCCTACAAGCTTACCTGTCATCAAGACATTCCTTTG
CTAGCTTA
Found at i:28532 original size:31 final size:29
Alignment explanation
Indices: 28490--28551 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
28480 AATTCACCGT
* *
28490 AACAGAGGGTGCAATGTGGAACAAAAATAA
1 AACAGAGGGTGCAAAGT-GAACAAAAAAAA
*
28520 AACATGAGGGTGCAAAGTGATCAAAAAAAA
1 AACA-GAGGGTGCAAAGTGAACAAAAAAAA
28550 AA
1 AA
28552 TTGGATGCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.53, C:0.10, G:0.24, T:0.13
Consensus pattern (29 bp):
AACAGAGGGTGCAAAGTGAACAAAAAAAA
Found at i:30460 original size:31 final size:31
Alignment explanation
Indices: 30406--30504 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 31
30396 AAAATGACAC
* * * **
30406 GTGGCATGCCACGTGCCATTTTTTGAAACAT
1 GTGGCATGCCATGTGTCACTTTTTGGTACAT
* *
30437 GTGGCATGCCATATGTCACTTTTTGGTACAC
1 GTGGCATGCCATGTGTCACTTTTTGGTACAT
* *
30468 GTGGCGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATGCCATGTGTCACTTTTTGGTACAT
30499 GTGGCA
1 GTGGCA
30505 CGACTTTTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.34
Consensus pattern (31 bp):
GTGGCATGCCATGTGTCACTTTTTGGTACAT
Found at i:30519 original size:53 final size:53
Alignment explanation
Indices: 30454--30556 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
30444 GCCATATGTC
** *
30454 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
* * *
30507 ACTTTTTTGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
30557 GTGCCACGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:34639 original size:172 final size:172
Alignment explanation
Indices: 34348--34694 Score: 685
Period size: 172 Copynumber: 2.0 Consensus size: 172
34338 TCAATGATAT
*
34348 TGAAGATGATGCGTGTTCATGTTAGTTATACTTGAGTAGGTCGTTTATTACGGTCATGTTACTGA
1 TGAACATGATGCGTGTTCATGTTAGTTATACTTGAGTAGGTCGTTTATTACGGTCATGTTACTGA
34413 ATTGAACATAATTTCATTCTTTTAGTCCTTTTTCCGAAGTGCATACAGAATGGTATTCTTCAACG
66 ATTGAACATAATTTCATTCTTTTAGTCCTTTTTCCGAAGTGCATACAGAATGGTATTCTTCAACG
34478 TATCAAATTTTATTAGCAATAAATGTGATTGTTAGGTTTATA
131 TATCAAATTTTATTAGCAATAAATGTGATTGTTAGGTTTATA
34520 TGAACATGATGCGTGTTCATGTTAGTTATACTTGAGTAGGTCGTTTATTACGGTCATGTTACTGA
1 TGAACATGATGCGTGTTCATGTTAGTTATACTTGAGTAGGTCGTTTATTACGGTCATGTTACTGA
34585 ATTGAACATAATTTCATTCTTTTAGTCCTTTTTCCGAAGTGCATACAGAATGGTATTCTTCAACG
66 ATTGAACATAATTTCATTCTTTTAGTCCTTTTTCCGAAGTGCATACAGAATGGTATTCTTCAACG
34650 TATCAAATTTTATTAGCAATAAATGTGATTGTTAGGTTTATA
131 TATCAAATTTTATTAGCAATAAATGTGATTGTTAGGTTTATA
34692 TGA
1 TGA
34695 GAGAGATTCT
Statistics
Matches: 174, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 174 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.41
Consensus pattern (172 bp):
TGAACATGATGCGTGTTCATGTTAGTTATACTTGAGTAGGTCGTTTATTACGGTCATGTTACTGA
ATTGAACATAATTTCATTCTTTTAGTCCTTTTTCCGAAGTGCATACAGAATGGTATTCTTCAACG
TATCAAATTTTATTAGCAATAAATGTGATTGTTAGGTTTATA
Found at i:42236 original size:45 final size:45
Alignment explanation
Indices: 42185--42270 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
42175 TAATAGAGTA
42185 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
*
42230 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAG
42271 TTGGAGAAGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
Found at i:43003 original size:166 final size:165
Alignment explanation
Indices: 42723--43205 Score: 646
Period size: 166 Copynumber: 2.9 Consensus size: 165
42713 TAAACATATT
* * * * * *
42723 GAATTACTAAAAGATCTCCATCC-CGGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGTCTTT
1 GAATTAATAAAAGATCCCCA-CCAAGGATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTTT
* * **
42787 TCTCACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTTTTGAGGGGATTAACTAACTAGCCT
65 TCT-ACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACT
* *
42852 TTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTG
129 TTTTGGTCATTTCTCAATTGACTTGAATAGAATAGTG
* * * * ** * * *
42889 GAATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGAGAACT-TTTTTTTTTGTCTTT
1 GAATTAATAAAAGATCCCCACCAAGGATTGATGAT-GAGCTAGAGAACTAATTTTTTTCGTCTTT
* * *
42953 TCGTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTCAGGGGATTAAATAAGTAATCT
65 TC-TACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACT
* *
43018 TTTTGGTCATTTCTGAATGGACTTGAATAGAATAGTG
129 TTTTGGTCATTTCTCAATTGACTTGAATAGAATAGTG
* *
43055 GAATTAATAAAAGATCCCCATCAAGGATTGATGATGAGCTAGAGAACTAATCTTTTTCGTCTTTA
1 GAATTAATAAAAGATCCCCACCAAGGATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTTT-
*
43120 TCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAATTT
65 TCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTT
43185 TTTGGTCATTTCTCAATTGAC
130 TTTGGTCATTTCTCAATTGAC
43206 AAATGACTCA
Statistics
Matches: 272, Mismatches: 40, Indels: 10
0.84 0.12 0.03
Matches are distributed among these distances:
165 14 0.05
166 244 0.90
167 14 0.05
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.39
Consensus pattern (165 bp):
GAATTAATAAAAGATCCCCACCAAGGATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTTTT
CTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTT
TTGGTCATTTCTCAATTGACTTGAATAGAATAGTG
Found at i:44328 original size:83 final size:84
Alignment explanation
Indices: 44206--44363 Score: 255
Period size: 83 Copynumber: 1.9 Consensus size: 84
44196 AAAAATATAT
*
44206 TTAAAAAAATATAATATATCTAAGTTTTGCAATTAAAATAGTAAAATGGTAAAAATAAAATAGTT
1 TTAAAAAAATATAATATATATAAGTTTTGCAATTAAAATAGTAAAATGGTAAAAATAAAATAGTT
44271 ATAAAGAGGTTAGATTTAA
66 ATAAAGAGGTTAGATTTAA
* * * * *
44290 TTAAAAAACTCTAATGTATATAAGTTTT-TAATTAAAATAGTAAAATGGTAAAACTAAAATAGTT
1 TTAAAAAAATATAATATATATAAGTTTTGCAATTAAAATAGTAAAATGGTAAAAATAAAATAGTT
44354 ATAAAGAGGT
66 ATAAAGAGGT
44364 AGAAAAGTGT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
83 44 0.65
84 24 0.35
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.34
Consensus pattern (84 bp):
TTAAAAAAATATAATATATATAAGTTTTGCAATTAAAATAGTAAAATGGTAAAAATAAAATAGTT
ATAAAGAGGTTAGATTTAA
Found at i:44393 original size:117 final size:114
Alignment explanation
Indices: 44261--44474 Score: 322
Period size: 115 Copynumber: 1.8 Consensus size: 114
44251 ATGGTAAAAA
* *
44261 TAAAATAGTTATAAAGAGGTTAGATTTAATTAAAAAACTCTAATGTATATAAG-TTTTTAATTAA
1 TAAAATAATTATAAAGAGATTAGATTTAATTAAAAAACTCT-A---ATATAAGTTTTTTAATTAA
* * *
44325 AATAGTAAAATGGTAAAACTAAAATAGTTATAAAGAGGTAGAAAAGTGTCAGT
62 AATAGAAAAACGGTAAAAATAAAATAGTTATAAAGAGGTAGAAAAGTGTCAGT
*
44378 TAAAATAATTATAAAGAGATTAGATTTAATTAAAAAATTCTAATATAAGTTTTTTTAATTAAAAT
1 TAAAATAATTATAAAGAGATTAGATTTAATTAAAAAACTCTAATATAAG-TTTTTTAATTAAAAT
44443 AGAAAAACGGTAAAAATAAAATAGTTATAAAG
65 AGAAAAACGGTAAAAATAAAATAGTTATAAAG
44475 GGCTAAATGT
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
113 7 0.08
115 43 0.48
116 1 0.01
117 38 0.43
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (114 bp):
TAAAATAATTATAAAGAGATTAGATTTAATTAAAAAACTCTAATATAAGTTTTTTAATTAAAATA
GAAAAACGGTAAAAATAAAATAGTTATAAAGAGGTAGAAAAGTGTCAGT
Found at i:44877 original size:30 final size:29
Alignment explanation
Indices: 44843--44901 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
44833 CATAGCAGAA
*
44843 GGGTTTATCTGGCCAAAATTGATAGTTCAG
1 GGGTTTATCTGGCAAAAATTGA-AGTTCAG
*
44873 GGGTTTATTTGGCAAAAATTGAAGTTCAG
1 GGGTTTATCTGGCAAAAATTGAAGTTCAG
44902 AGGCTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (29 bp):
GGGTTTATCTGGCAAAAATTGAAGTTCAG
Found at i:44888 original size:29 final size:30
Alignment explanation
Indices: 44843--44912 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
44833 CATAGCAGAA
*
44843 GGGTTTATCTGGCC-AAAATTGATAGTTCAG
1 GGGTTTATTTGGCCAAAAATTGA-AGTTCAG
44873 GGGTTTATTTGG-CAAAAATTGAAGTTCAG
1 GGGTTTATTTGGCCAAAAATTGAAGTTCAG
* *
44902 AGGCTTATTTG
1 GGGTTTATTTG
44913 ACCGTTGGCG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.36
Consensus pattern (30 bp):
GGGTTTATTTGGCCAAAAATTGAAGTTCAG
Found at i:50484 original size:19 final size:19
Alignment explanation
Indices: 50462--50515 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
50452 TTAAATTTTC
50462 TATTTTAAAATTAAAACTT
1 TATTTTAAAATTAAAACTT
***
50481 TATTTTAAAATTAATGTTT
1 TATTTTAAAATTAAAACTT
*
50500 TATTTTAAAAATAAAA
1 TATTTTAAAATTAAAA
50516 TATGTGTGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
TATTTTAAAATTAAAACTT
Found at i:53072 original size:19 final size:20
Alignment explanation
Indices: 53023--53072 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
53013 AACATTTTGC
53023 TAAAAACTATTTAAAATATTT
1 TAAAAA-TATTTAAAATATTT
** *
53044 TTTAAA-ATTTAAATTA-TT
1 TAAAAATATTTAAAATATTT
53062 TAAAAATATTT
1 TAAAAATATTT
53073 TTATATTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
18 6 0.26
19 13 0.57
21 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAAAATATTTAAAATATTT
Found at i:53310 original size:19 final size:20
Alignment explanation
Indices: 53270--53333 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
53260 TTGACACTGT
*
53270 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAAATGAGA
*
53291 TTA-CACTGTACAAATTAGA
1 TTAGCACTGTACAAATGAGA
* *
53310 TCAGGTACTGTACAAATGAGA
1 TTA-GCACTGTACAAATGAGA
53331 TTA
1 TTA
53334 TTAGAACAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 15 0.43
20 1 0.03
21 19 0.54
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (20 bp):
TTAGCACTGTACAAATGAGA
Found at i:60390 original size:15 final size:14
Alignment explanation
Indices: 60370--60404 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
60360 TGGGTTTTGG
60370 TTTTCTTTTTCTTTC
1 TTTTCTTTTT-TTTC
*
60385 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTC
60399 TTTTCT
1 TTTTCT
60405 CTTTAACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTCTTTTTTTTC
Found at i:64901 original size:1 final size:1
Alignment explanation
Indices: 64895--64932 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
64885 CAATAATGCT
64895 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
64933 CCCTCAACTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:66309 original size:16 final size:15
Alignment explanation
Indices: 66288--66321 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
66278 TATATTGTTT
66288 AAAAAATTAAAATATA
1 AAAAAATT-AAATATA
*
66304 AAAAAATTATATATA
1 AAAAAATTAAATATA
66319 AAA
1 AAA
66322 GTTAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAAATTAAATATA
Found at i:71618 original size:6 final size:6
Alignment explanation
Indices: 71600--71650 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
71590 TGTCTTGCTG
* *
71600 TTCTCC TTTTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTTC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC
71648 TTC
1 TTC
71651 GTGGATGAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (6 bp):
TTCTCC
Found at i:72728 original size:17 final size:18
Alignment explanation
Indices: 72706--72747 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
72696 AGGATACATG
72706 CCACGTGTCA-TTTTTGT
1 CCACGTGTCATTTTTTGT
72723 CCACGTGTCATTTTTTGT
1 CCACGTGTCATTTTTTGT
72741 CCACGTG
1 CCACGTG
72748 GCATGCCACG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.43
Consensus pattern (18 bp):
CCACGTGTCATTTTTTGT
Found at i:78065 original size:23 final size:23
Alignment explanation
Indices: 78039--78090 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
78029 TTTTCTCTAC
78039 TTTTCTTTGGGCTGCTACTGGTT
1 TTTTCTTTGGGCTGCTACTGGTT
* **
78062 TTTTATTTTTGCTGCTACTGGTT
1 TTTTCTTTGGGCTGCTACTGGTT
78085 TTTTCT
1 TTTTCT
78091 ACTTCAGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.06, C:0.15, G:0.19, T:0.60
Consensus pattern (23 bp):
TTTTCTTTGGGCTGCTACTGGTT
Found at i:87705 original size:27 final size:28
Alignment explanation
Indices: 87675--87728 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
87665 TCATAACTCC
87675 CCTCTGTT-TTCTCC-TTCACATCTCTTT
1 CCTCT-TTCTTCTCCTTTCACATCTCTTT
*
87702 CCTCTTTCTTCTCCTTTCTCATCTCTT
1 CCTCTTTCTTCTCCTTTCACATCTCTT
87729 CACCATGGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 2 0.08
27 11 0.46
28 11 0.46
ACGTcount: A:0.06, C:0.39, G:0.02, T:0.54
Consensus pattern (28 bp):
CCTCTTTCTTCTCCTTTCACATCTCTTT
Found at i:88907 original size:37 final size:37
Alignment explanation
Indices: 88812--88907 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 37
88802 AATTTGCCTT
88812 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
** ** * *
88849 TTTGTTTTGAATCGTTGTATTTAATTTTTCTTTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCCTTTTGTC
*
88887 TTTGTCTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
88908 GGGCTTAAAT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
37 17 0.36
38 30 0.64
ACGTcount: A:0.14, C:0.18, G:0.11, T:0.57
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
Found at i:89991 original size:121 final size:119
Alignment explanation
Indices: 89741--89975 Score: 323
Period size: 122 Copynumber: 2.0 Consensus size: 119
89731 CGAATAATGG
* *
89741 AAAACTTTATATTTTCCGATTGTACCATTTTTCCAATTATATTTCTAAATTGACATTATTAAAAT
1 AAAATTTTATATTTTCCGATTGTACCATTTTTCCAAATATATTTCTAAATTGACATTATT--AAT
* *
89806 TTATTACTTAAAAATTAATTATAAAATTTCAATTTAGATCGAATTATAAGTTATGG
64 TTATTACTTAAAAATTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTATGC
* * * **
89862 GAAATTTTATGTTTTCCGATTGTACCCTTTTTTCCAAATATATTTCTAAATTTCCATTATT-ATT
1 AAAATTTTATATTTTCCGATTGTA-CCATTTTTCCAAATATATTTCTAAATTGACATTATTAATT
*
89926 TATTA-TGTAAAAATTAATTA-AAATTTTCAATTTAGACCGAATTATAAGTT
65 TATTACT-TAAAAATTAATTATAAAATTTCAATTTAGACCGAATTATAAGTT
89976 TGTCAAATTG
Statistics
Matches: 103, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
118 29 0.28
119 21 0.20
121 21 0.20
122 32 0.31
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (119 bp):
AAAATTTTATATTTTCCGATTGTACCATTTTTCCAAATATATTTCTAAATTGACATTATTAATTT
ATTACTTAAAAATTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTATGC
Found at i:90272 original size:22 final size:21
Alignment explanation
Indices: 90238--90346 Score: 83
Period size: 22 Copynumber: 5.0 Consensus size: 21
90228 TTTATAAGAT
* * *
90238 GGTTATTATAATTTTATGAGGA
1 GGTTATCAAAATTTCAT-AGGA
* *
90260 GGTTATCAAAATTGCATAGTA
1 GGTTATCAAAATTTCATAGGA
* *
90281 TGGTTACCAAAATTTCATATGA
1 -GGTTATCAAAATTTCATAGGA
*
90303 AGTTATCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* *
90327 GGTTATTAAAATTTCTTAGG
1 GGTTATCAAAATTTCATAGG
90347 TTGGTTATTG
Statistics
Matches: 68, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
21 20 0.29
22 30 0.44
24 18 0.26
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:90312 original size:21 final size:22
Alignment explanation
Indices: 90261--90341 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 22
90251 TTATGAGGAG
* *
90261 GTTATCAAAATTGCATAGTATG
1 GTTATCAAAATTTCATAGTATA
*
90283 GTTACCAAAATTTCATA-TGA-A
1 GTTATCAAAATTTCATAGT-ATA
*
90304 GTTATCAAAATTTCATAGGATCA
1 GTTATCAAAATTTCATAGTAT-A
*
90327 GGTTATTAAAATTTC
1 -GTTATCAAAATTTC
90342 TTAGGTTGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
21 18 0.38
22 16 0.33
23 1 0.02
24 13 0.27
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTATA
Found at i:90355 original size:22 final size:24
Alignment explanation
Indices: 90259--90368 Score: 72
Period size: 22 Copynumber: 4.9 Consensus size: 24
90249 TTTTATGAGG
* * *
90259 AGGTTATCAAAATTGCATAGTAT-
1 AGGTTATTAAAATTTCATAGGATC
** *
90282 -GGTTACCAAAATTTCATATGA--
1 AGGTTATTAAAATTTCATAGGATC
*
90303 A-GTTATCAAAATTTCATAGGATC
1 AGGTTATTAAAATTTCATAGGATC
*
90326 AGGTTATTAAAATTTCTTAGG-T-
1 AGGTTATTAAAATTTCATAGGATC
* * *
90348 TGGTTATTGAAACTTCATAGG
1 AGGTTATTAAAATTTCATAGG
90369 GTAGTTAATT
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
21 18 0.25
22 34 0.48
23 2 0.03
24 17 0.24
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.37
Consensus pattern (24 bp):
AGGTTATTAAAATTTCATAGGATC
Found at i:90479 original size:22 final size:22
Alignment explanation
Indices: 90454--90535 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 22
90444 TCATAATGTT
90454 GTTAACAAAATTTCATTAGGAG
1 GTTAACAAAATTTCATTAGGAG
* ** *
90476 GTT-ACTAATATTTCATGGGGAA
1 GTTAAC-AAAATTTCATTAGGAG
* * *
90498 GTTATCAAAATTTTA-TAGTGTG
1 GTTAACAAAATTTCATTAG-GAG
*
90520 GTTATCAAAATTTCAT
1 GTTAACAAAATTTCAT
90536 ATGAAGGTTA
Statistics
Matches: 44, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
21 3 0.07
22 40 0.91
23 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (22 bp):
GTTAACAAAATTTCATTAGGAG
Found at i:90544 original size:22 final size:22
Alignment explanation
Indices: 90498--91127 Score: 113
Period size: 22 Copynumber: 28.8 Consensus size: 22
90488 TCATGGGGAA
* *
90498 GTTATCAAAATTTTATAGTG-TG
1 GTTATCAAAATTTCATA-TGAAG
90520 GTTATCAAAATTTCATATGAAG
1 GTTATCAAAATTTCATATGAAG
*
90542 GTTAT-AAAAGTCTCAATTTCAT-AAG
1 GTTATCAAAA-TTTC-A--T-ATGAAG
* * *
90567 GAGTACCAAAATTTGATA-GAAG
1 G-TTATCAAAATTTCATATGAAG
*
90589 GTTATC-AAATCTCATA-G-A-
1 GTTATCAAAATTTCATATGAAG
*
90607 -TTATCGAAATTTCATA-GAGATCG
1 GTTATCAAAATTTCATATGA-A--G
**
90630 GATTATCAAAATTTCATAGTG-TT
1 G-TTATCAAAATTTCATA-TGAAG
* * * *
90653 GTTTTCAAAATTTCAAAGCGAGG
1 GTTATCAAAATTTCATA-TGAAG
* *
90676 GTTATCAAAATTTCATA-GTAT
1 GTTATCAAAATTTCATATGAAG
* * * *
90697 GTAGATCAAATTTTCATAGGGAG
1 GT-TATCAAAATTTCATATGAAG
* *
90720 ATTAACAAAA-TTCATAATG-AG
1 GTTATCAAAATTTCAT-ATGAAG
* *
90741 GTTAGCAAAA--T--T-TGTA-
1 GTTATCAAAATTTCATATGAAG
* * *
90757 GTTATCAAGATTTCATAAGAAA
1 GTTATCAAAATTTCATATGAAG
* * *
90779 GTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATATGAAG
* *
90801 GTTTATCAAAATTTTATAGGAAG
1 G-TTATCAAAATTTCATATGAAG
* *
90824 ATTTATCAAAATTTCATAACG-AG
1 -GTTATCAAAATTTCAT-ATGAAG
* ** *
90847 ATTATCGCAATTTCATAGTG-TG
1 GTTATCAAAATTTCATA-TGAAG
* * *
90869 ATTATCAAAATTTCAGAGTG-TG
1 GTTATCAAAATTTCATA-TGAAG
* *
90891 ATTA-CTAACAA-TTCATATGGAG
1 GTTATC-AA-AATTTCATATGAAG
** *
90913 GTT-TTTAAATTTC-TATAACATG
1 GTTATCAAAATTTCATATGA-A-G
* * * *
90935 GTTGTCAATATATCATATGGAG
1 GTTATCAAAATTTCATATGAAG
* * **
90957 GTTATCAACATCTCATAGTGTTG
1 GTTATCAAAATTTCATA-TGAAG
90980 GTTATCAAAATTTCAT-TGGGAA-
1 GTTATCAAAATTTCATAT--GAAG
91002 GTTATCAAAATTTCATATTG-AG
1 GTTATCAAAATTTCATA-TGAAG
* * *
91024 GTCT-TCAAAA-TTCCTTTGGGAG
1 GT-TATCAAAATTTCATAT-GAAG
*
91046 GTTGA-CAAAATTTCATAAGAAG
1 GTT-ATCAAAATTTCATATGAAG
* ** * * **
91068 ATTAAAAAAAATT-AAAAAAAG
1 GTTATCAAAATTTCATATGAAG
* * * * *
91089 GTTCTCGAAATTTTATAGGGAG
1 GTTATCAAAATTTCATATGAAG
91111 GTTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
91128 ATGGGATCAT
Statistics
Matches: 448, Mismatches: 103, Indels: 114
0.67 0.15 0.17
Matches are distributed among these distances:
16 10 0.02
17 6 0.01
18 12 0.03
19 1 0.00
20 18 0.04
21 60 0.13
22 214 0.48
23 89 0.20
24 6 0.01
25 21 0.05
26 6 0.01
27 5 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATATGAAG
Found at i:90621 original size:18 final size:17
Alignment explanation
Indices: 90590--90624 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
90580 TGATAGAAGG
90590 TTATCAAATCTCATAGA
1 TTATCAAATCTCATAGA
*
90607 TTATCGAAATTTCATAGA
1 TTATC-AAATCTCATAGA
90625 GATCGGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (17 bp):
TTATCAAATCTCATAGA
Found at i:90810 original size:23 final size:23
Alignment explanation
Indices: 90758--90837 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
90748 AAATTTGTAG
* * * *
90758 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* *
90780 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGAT
90803 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
90826 TTATCAAAATTT
1 TTATCAAAATTT
90838 CATAACGAGA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:90852 original size:45 final size:45
Alignment explanation
Indices: 90758--90883 Score: 114
Period size: 45 Copynumber: 2.8 Consensus size: 45
90748 AAATTTGTAG
* * * ** *
90758 TTATCAAGATTTCATAAGAA-AGTTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGAAGA-TTATCAAAATTTCATAACGAGGA
*
90803 TTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAACGA-GA
1 TTATCAAAATTTCATAGGAAGA-TTATCAAAATTTCATAACGAGGA
** *
90848 TTATCGCAATTTCATAGTG-TGATTATCAAAATTTCA
1 TTATCAAAATTTCATAG-GAAGATTATCAAAATTTCA
90884 GAGTGTGATT
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
44 14 0.21
45 34 0.51
46 19 0.28
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (45 bp):
TTATCAAAATTTCATAGGAAGATTATCAAAATTTCATAACGAGGA
Found at i:92485 original size:7 final size:7
Alignment explanation
Indices: 92473--92515 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
92463 GAACACCCAA
92473 TGCATAG
1 TGCATAG
92480 TGCATAG
1 TGCATAG
*
92487 TGCATGG
1 TGCATAG
92494 TGCATAG
1 TGCATAG
92501 TGCATAG
1 TGCATAG
92508 TGCATAG
1 TGCATAG
92515 T
1 T
92516 ACAGGTACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (7 bp):
TGCATAG
Found at i:95572 original size:21 final size:21
Alignment explanation
Indices: 95528--95573 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
95518 TTTTTTATTT
*
95528 TTTTTCAATTTATCAACCTTC
1 TTTTTCAATTTATCAACCTCC
* * *
95549 TTTTTCAATTTTTTAATCTCC
1 TTTTTCAATTTATCAACCTCC
95570 TTTT
1 TTTT
95574 CACGCTCAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTCAATTTATCAACCTCC
Found at i:111032 original size:29 final size:29
Alignment explanation
Indices: 110974--111032 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
110964 CTTTACTCTG
* * **
110974 CTGATTACTTCTTTTATTTTTACTTTTTA
1 CTGATTACCTCTTTTATTTTTAATGATTA
111003 CTGATTACCT-TTTTACTTTTTAATGATTA
1 CTGATTACCTCTTTTA-TTTTTAATGATTA
111032 C
1 C
111033 CATTGCTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.20, C:0.15, G:0.05, T:0.59
Consensus pattern (29 bp):
CTGATTACCTCTTTTATTTTTAATGATTA
Found at i:111073 original size:15 final size:15
Alignment explanation
Indices: 111049--111082 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
111039 TTCTTACTGA
*
111049 TTAC-TATTACTTTT
1 TTACTTATTACTGTT
111063 TTACTTATTACTGTT
1 TTACTTATTACTGTT
111078 TTACT
1 TTACT
111083 CTTACTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.21, C:0.15, G:0.03, T:0.62
Consensus pattern (15 bp):
TTACTTATTACTGTT
Found at i:111125 original size:43 final size:43
Alignment explanation
Indices: 111000--111235 Score: 275
Period size: 43 Copynumber: 5.6 Consensus size: 43
110990 TTTTTACTTT
* * * *
111000 TTACTGATTACCTTTTTACTT-TTTAATGATTAC-C-ATTGCTTC
1 TTACTGATTACC-TTTTACTTCTTTACTAATTACTCTCTTAC-TC
* * * * *
111042 TTACTGATTA-CTATTACTTTTTTACTTATTACTGTTTTACTC
1 TTACTGATTACCTTTTACTTCTTTACTAATTACTCTCTTACTC
*
111084 TTACTGATTACCTTTTTCTTCTTTACTAATTACTCTCTTACTC
1 TTACTGATTACCTTTTACTTCTTTACTAATTACTCTCTTACTC
* * * * * *
111127 TTACTGACTGCCTTTTACTT-TTTACTTATTATTATTTTACTC
1 TTACTGATTACCTTTTACTTCTTTACTAATTACTCTCTTACTC
111169 TTACTGATTACCTTTTACTTCTTTACTAATTACTCTCTTACTC
1 TTACTGATTACCTTTTACTTCTTTACTAATTACTCTCTTACTC
111212 TTACTGATTACCTTTTACTTCTTT
1 TTACTGATTACCTTTTACTTCTTT
111236 TCCTTAATTA
Statistics
Matches: 164, Mismatches: 25, Indels: 9
0.83 0.13 0.05
Matches are distributed among these distances:
40 7 0.04
41 11 0.07
42 58 0.35
43 88 0.54
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.55
Consensus pattern (43 bp):
TTACTGATTACCTTTTACTTCTTTACTAATTACTCTCTTACTC
Found at i:111133 original size:85 final size:85
Alignment explanation
Indices: 110991--111246 Score: 313
Period size: 85 Copynumber: 3.0 Consensus size: 85
110981 CTTCTTTTAT
* * * * *
110991 TTTTACTTTTTACTGATTACCTTTTTACTT-TTTAATGATTAC-C-ATTGCTTCTTACTGATTAC
1 TTTTAC-TCTTACTGATTACCTTTTT-CTTCTTTACTAATTACTCTCTTAC-TCTTACTGATTAC
* *
111053 TATTACTTTTTTACTTATTACTG
63 TTTTACTTTTTTACTTATTACTA
**
111076 TTTTACTCTTACTGATTACCTTTTTCTTCTTTACTAATTACTCTCTTACTCTTACTGACTGCCTT
1 TTTTACTCTTACTGATTACCTTTTTCTTCTTTACTAATTACTCTCTTACTCTTACTGA-TTACTT
*
111141 TTAC-TTTTTACTTATTATTA
65 TTACTTTTTTACTTATTACTA
*
111161 TTTTACTCTTACTGATTACCTTTTACTTCTTTACTAATTACTCTCTTACTCTTACTGATTACCTT
1 TTTTACTCTTACTGATTACCTTTTTCTTCTTTACTAATTACTCTCTTACTCTTACTGATTA-CTT
*
111226 TTACTTCTTTTCCTTAATTAC
65 TTACTT-TTTTACTT-ATTAC
111247 CGATCACTAA
Statistics
Matches: 148, Mismatches: 15, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
83 3 0.02
84 29 0.20
85 94 0.64
86 11 0.07
87 7 0.05
88 4 0.03
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.55
Consensus pattern (85 bp):
TTTTACTCTTACTGATTACCTTTTTCTTCTTTACTAATTACTCTCTTACTCTTACTGATTACTTT
TACTTTTTTACTTATTACTA
Found at i:111390 original size:38 final size:38
Alignment explanation
Indices: 111333--111458 Score: 225
Period size: 38 Copynumber: 3.3 Consensus size: 38
111323 ATTACCATTT
*
111333 TTACCTTGACTCTTAATTATCAATTTTACTGATTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
* *
111371 TTACTTTGACTCTTGATTATCAATTTTACTGGTTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
111409 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
1 TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
111447 TTACTTTGACTC
1 TTACTTTGACTC
111459 CATTTTACTG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 83 1.00
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.49
Consensus pattern (38 bp):
TTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
Found at i:111491 original size:32 final size:32
Alignment explanation
Indices: 111431--111541 Score: 92
Period size: 29 Copynumber: 3.7 Consensus size: 32
111421 TTAATTATCA
* *
111431 ATTTTACTGATTA---CTATTACTTTGACTCC
1 ATTTTACTGATTACTTCTTTTACTTTCACTCC
111460 ATTTTACTGATTACTTCTTTTACTTTCACTCC
1 ATTTTACTGATTACTTCTTTTACTTTCACTCC
* * * * *
111492 ATTCTACTG-TTCACTTC--CT-CTTTTATTTC
1 ATTTTACTGATT-ACTTCTTTTACTTTCACTCC
*
111521 TTTTTACTGATTACTTCTTTT
1 ATTTTACTGATTACTTCTTTT
111542 TTTTATTTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
29 32 0.49
30 3 0.05
31 3 0.05
32 27 0.42
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.55
Consensus pattern (32 bp):
ATTTTACTGATTACTTCTTTTACTTTCACTCC
Found at i:111544 original size:29 final size:29
Alignment explanation
Indices: 111459--111549 Score: 76
Period size: 32 Copynumber: 3.0 Consensus size: 29
111449 ACTTTGACTC
* *
111459 CATTTTACTGATTACTTCTTTTACTTTCACTC
1 CATTTTACTGATTACTTCTTTT--TTT-ATTT
* * *
111491 CATTCTACTG-TTCACTTCCTCTTTTATTT
1 CATTTTACTGATT-ACTTCTTTTTTTATTT
*
111520 CTTTTTACTGATTACTTCTTTTTTTTATTT
1 CATTTTACTGATTACTTC-TTTTTTTATTT
111550 TATCTTTTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
29 15 0.32
30 14 0.30
31 2 0.04
32 16 0.34
ACGTcount: A:0.15, C:0.22, G:0.03, T:0.59
Consensus pattern (29 bp):
CATTTTACTGATTACTTCTTTTTTTATTT
Found at i:111647 original size:32 final size:31
Alignment explanation
Indices: 111611--111683 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 31
111601 AATTATCAAT
*
111611 TTACTGATTAATCCC-TTTACCTTGACTCTTAA
1 TTACTGATT-A-CCCTTTTACCTTGACCCTTAA
*
111643 TTACTGACTTACCCTTTTACTTTGACCCTTAA
1 TTACTGA-TTACCCTTTTACCTTGACCCTTAA
111675 TTACTGATT
1 TTACTGATT
111684 GCTACTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
31 5 0.14
32 30 0.81
33 2 0.05
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (31 bp):
TTACTGATTACCCTTTTACCTTGACCCTTAA
Found at i:111692 original size:32 final size:32
Alignment explanation
Indices: 111626--111696 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
111616 GATTAATCCC
* * *
111626 TTTACCTTGACTCTTAATTACTGACTTACCCT
1 TTTACTTTGACCCTTAATTACTGACTTACACT
*
111658 TTTACTTTGACCCTTAATTACTGA-TTGCTACT
1 TTTACTTTGACCCTTAATTACTGACTTAC-ACT
111690 TTTACTT
1 TTTACTT
111697 CCTCTCTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 3 0.09
32 31 0.91
ACGTcount: A:0.21, C:0.24, G:0.07, T:0.48
Consensus pattern (32 bp):
TTTACTTTGACCCTTAATTACTGACTTACACT
Found at i:111770 original size:38 final size:39
Alignment explanation
Indices: 111673--111770 Score: 110
Period size: 38 Copynumber: 2.5 Consensus size: 39
111663 TTTGACCCTT
* * *
111673 AATTACTGATTGCTACTTTTACTTCCTCTCTTAGTTATC
1 AATTACTGATTACTACTTTTACTTCCTCTCTTAATTACC
* * *
111712 AATTTACTAATTAATCCTTTTACTT-C-CTCTTAATTACC
1 AA-TTACTGATTACTACTTTTACTTCCTCTCTTAATTACC
111750 AATTGACTGATTACTACTTTT
1 AATT-ACTGATTACTACTTTT
111771 TTTTTATCTT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
37 2 0.04
38 25 0.52
39 3 0.06
40 18 0.38
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (39 bp):
AATTACTGATTACTACTTTTACTTCCTCTCTTAATTACC
Done.