Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2684
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: 37636
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:4485 original size:44 final size:45
Alignment explanation
Indices: 4422--4538 Score: 166
Period size: 44 Copynumber: 2.6 Consensus size: 45
4412 AACCATTGAG
*
4422 TGGTTTATCCACACTGTATTAGCAACTTTTATTTGCAATAATGAA
1 TGGTTTATCCACACTGTATTAGCAACTTTTATTTGCAACAATGAA
*
4467 TGGTTTA-CCACACTGTATTAGCAGA-TTTTATTTGCAACAATGAG
1 TGGTTTATCCACACTGTATTAGCA-ACTTTTATTTGCAACAATGAA
* * *
4511 TGGTCTATCCACACCGTACTAGCAACTT
1 TGGTTTATCCACACTGTATTAGCAACTT
4539 GTCTATAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
44 40 0.62
45 24 0.38
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (45 bp):
TGGTTTATCCACACTGTATTAGCAACTTTTATTTGCAACAATGAA
Found at i:4643 original size:21 final size:21
Alignment explanation
Indices: 4613--4652 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4603 TGGTTTATCC
*
4613 ACAATGAGTGGTTCATCCACA
1 ACAATAAGTGGTTCATCCACA
*
4634 ACAATAAGTGGTTTATCCA
1 ACAATAAGTGGTTCATCCA
4653 TGACGTGGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
ACAATAAGTGGTTCATCCACA
Found at i:8150 original size:29 final size:29
Alignment explanation
Indices: 8118--8180 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
8108 TTTAAAAAAA
8118 TTATATTA-TTTTTTTA-ATATTTAATAATT
1 TTATATTACTTTTTTTATATA-TTAA-AATT
*
8147 TTATA-TACTTTTTTTATTTATTAAAATT
1 TTATATTACTTTTTTTATATATTAAAATT
8175 TTATAT
1 TTATAT
8181 ATATAGGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
28 11 0.37
29 17 0.57
30 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (29 bp):
TTATATTACTTTTTTTATATATTAAAATT
Found at i:8174 original size:28 final size:27
Alignment explanation
Indices: 8114--8182 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
8104 TTCTTTTAAA
*
8114 AAAATTATAT-TATTTTTTTAATATTT
1 AAAATTTTATATATTTTTTTAATATTT
*
8140 AATAATTTTATATACTTTTTTT-ATTTATT
1 AA-AATTTTATATA-TTTTTTTAATAT-TT
8169 AAAATTTTATATAT
1 AAAATTTTATATAT
8183 ATAGGCATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
26 2 0.05
27 8 0.22
28 16 0.43
29 11 0.30
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (27 bp):
AAAATTTTATATATTTTTTTAATATTT
Found at i:11163 original size:41 final size:41
Alignment explanation
Indices: 11118--11220 Score: 170
Period size: 41 Copynumber: 2.5 Consensus size: 41
11108 TTTTCGAATC
11118 AATGAAAAGGTTGAAAAGGATGTTATCTGAAAACAATAACA
1 AATGAAAAGGTTGAAAAGGATGTTATCTGAAAACAATAACA
** *
11159 AATGAAAAGGTTGAAAAGGATGTTATCTGAAAATGATATCA
1 AATGAAAAGGTTGAAAAGGATGTTATCTGAAAACAATAACA
*
11200 AATGAAAAGGTCGAAAAGGAT
1 AATGAAAAGGTTGAAAAGGAT
11221 ATCAATGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (41 bp):
AATGAAAAGGTTGAAAAGGATGTTATCTGAAAACAATAACA
Found at i:11232 original size:24 final size:24
Alignment explanation
Indices: 11187--11258 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
11177 GATGTTATCT
*
11187 GAAAATGATATCAAATGAAAAGGTC
1 GAAAAGGATATC-AATGAAAAGGTC
11212 GAAAAGGATATCAATGAAAAGGTC
1 GAAAAGGATATCAATGAAAAGGTC
* *
11236 GAAAAGAATAGCAATGAAAAGGT
1 GAAAAGGATATCAATGAAAAGGT
11259 TGGTATCTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
24 33 0.75
25 11 0.25
ACGTcount: A:0.53, C:0.07, G:0.24, T:0.17
Consensus pattern (24 bp):
GAAAAGGATATCAATGAAAAGGTC
Found at i:15912 original size:55 final size:55
Alignment explanation
Indices: 15862--16028 Score: 235
Period size: 55 Copynumber: 3.0 Consensus size: 55
15852 CACACAGTTT
* * *
15862 GACAGACGACCTATGACGCGGTAGTGTGGCCCTATTTCGAATACTCACACAAGTG
1 GACACACGACCTATGACACGGTAGTGTAGCCCTATTTCGAATACTCACACAAGTG
* * * * *
15917 GACACACGACTTACGACACAGTAGTGTAGCTCTATTTCGAATACTCACACGAGTG
1 GACACACGACCTATGACACGGTAGTGTAGCCCTATTTCGAATACTCACACAAGTG
** *
15972 GACACACGACCTATGACACGGCCGTGTAGCCCTATTTTGAATACTCACACAAGTG
1 GACACACGACCTATGACACGGTAGTGTAGCCCTATTTCGAATACTCACACAAGTG
16027 GA
1 GA
16029 TACATGGGCT
Statistics
Matches: 96, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 96 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (55 bp):
GACACACGACCTATGACACGGTAGTGTAGCCCTATTTCGAATACTCACACAAGTG
Found at i:17604 original size:46 final size:46
Alignment explanation
Indices: 17537--17698 Score: 258
Period size: 46 Copynumber: 3.6 Consensus size: 46
17527 TTTGAGTACT
*
17537 TCTGATCAAGAGACAAAGTGATAAGTGTTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
17583 TCTGATCAAGAGGCAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
17629 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTGGCTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
17674 TCTGATC-AGGGACAAA-TGATAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTG
17699 ATCATACATA
Statistics
Matches: 110, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
43 9 0.08
44 8 0.07
45 19 0.17
46 74 0.67
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:19498 original size:48 final size:48
Alignment explanation
Indices: 19439--19681 Score: 315
Period size: 48 Copynumber: 5.1 Consensus size: 48
19429 AAGCTGCTAG
* * * * *
19439 TACGTTGTGGATGAACCATTGGTCGTGCAGATAAATTGTCGACTAAGA
1 TACGTTTTGGATGAACCACTGGTCGTGCAGATAAACTATCGACTAAAA
* * * *
19487 TACGTTTTGGATGAACCACTAGTTGTGTAGATAAACTATCGACTAAGA
1 TACGTTTTGGATGAACCACTGGTCGTGCAGATAAACTATCGACTAAAA
*
19535 TACGTTTTGGATGAACCACTGGTCGTGCAGATAAACTACCGACTAAAA
1 TACGTTTTGGATGAACCACTGGTCGTGCAGATAAACTATCGACTAAAA
* * ** * *
19583 TACGTTTTGGATGAACCATTAGTCAAGTAGATAAACTACCGACTAAAA
1 TACGTTTTGGATGAACCACTGGTCGTGCAGATAAACTATCGACTAAAA
** *
19631 TACGTTTTGGATGAACCACTGGTCAAGCAGATAAACTGTCGACTAAAA
1 TACGTTTTGGATGAACCACTGGTCGTGCAGATAAACTATCGACTAAAA
19679 TAC
1 TAC
19682 ATTGCGGATA
Statistics
Matches: 173, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 173 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (48 bp):
TACGTTTTGGATGAACCACTGGTCGTGCAGATAAACTATCGACTAAAA
Found at i:19540 original size:96 final size:96
Alignment explanation
Indices: 19439--19681 Score: 360
Period size: 96 Copynumber: 2.5 Consensus size: 96
19429 AAGCTGCTAG
* * * *
19439 TACGTTGTGGATGAACCATTGGTCGTGCAGATAAATTGTCGACTAAGATACGTTTTGGATGAACC
1 TACGTTTTGGATGAACCACTGGTCGTGCAGATAAACTGTCGACTAAAATACGTTTTGGATGAACC
*** * *
19504 ACTAGTTGTGTAGATAAACTATCGACTAAGA
66 ACTAGTCAAGTAGATAAACTACCGACTAAAA
**
19535 TACGTTTTGGATGAACCACTGGTCGTGCAGATAAACTACCGACTAAAATACGTTTTGGATGAACC
1 TACGTTTTGGATGAACCACTGGTCGTGCAGATAAACTGTCGACTAAAATACGTTTTGGATGAACC
*
19600 ATTAGTCAAGTAGATAAACTACCGACTAAAA
66 ACTAGTCAAGTAGATAAACTACCGACTAAAA
**
19631 TACGTTTTGGATGAACCACTGGTCAAGCAGATAAACTGTCGACTAAAATAC
1 TACGTTTTGGATGAACCACTGGTCGTGCAGATAAACTGTCGACTAAAATAC
19682 ATTGCGGATA
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 131 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (96 bp):
TACGTTTTGGATGAACCACTGGTCGTGCAGATAAACTGTCGACTAAAATACGTTTTGGATGAACC
ACTAGTCAAGTAGATAAACTACCGACTAAAA
Found at i:23808 original size:3 final size:3
Alignment explanation
Indices: 23802--23827 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
23792 CACCTCCCCA
23802 TCG TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TC
23828 ATTTGCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
TCG
Found at i:25543 original size:16 final size:17
Alignment explanation
Indices: 25522--25555 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
25512 CCATTTTGAA
25522 ATATTA-ATTAATTTTT
1 ATATTATATTAATTTTT
25538 ATATTATATTAATTTTT
1 ATATTATATTAATTTTT
25555 A
1 A
25556 CAAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTATATTAATTTTT
Found at i:26482 original size:22 final size:22
Alignment explanation
Indices: 26448--26495 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
26438 AATTTGAAAT
* *
26448 AAAAAATTTAATTAAAAATAAA
1 AAAAAACTAAATTAAAAATAAA
* *
26470 AAAAAACTAAATTACAAATATA
1 AAAAAACTAAATTAAAAATAAA
26492 AAAA
1 AAAA
26496 GCATATTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAAACTAAATTAAAAATAAA
Done.