Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4589
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: 14288
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:549 original size:48 final size:48
Alignment explanation
Indices: 485--632 Score: 215
Period size: 48 Copynumber: 3.1 Consensus size: 48
475 TTGATGTACA
*
485 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTAAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* *
533 AGATATATATATGTGGTAAAGTCGAAAGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
** ** * *
581 AGCCATGCATATGTGGTAAAGCCAAATGGATAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
629 AGAT
1 AGAT
633 GTGTATATAT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 87 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (48 bp):
AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
Found at i:5329 original size:11 final size:11
Alignment explanation
Indices: 5300--5337 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5290 GGTAATAAAG
*
5300 AAATGGAAAACA
1 AAAT-GAAAAAA
5312 AAA-GAAAAAA
1 AAATGAAAAAA
5322 AAATGAAAAAA
1 AAATGAAAAAA
5333 AAATG
1 AAATG
5338 TGTGTGTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 9 0.38
11 12 0.50
12 3 0.12
ACGTcount: A:0.76, C:0.03, G:0.13, T:0.08
Consensus pattern (11 bp):
AAATGAAAAAA
Found at i:6592 original size:80 final size:79
Alignment explanation
Indices: 6496--6665 Score: 207
Period size: 79 Copynumber: 2.1 Consensus size: 79
6486 GGACTAAGAT
* *
6496 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGAGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTCGTGCGAGATATCAAA-TCCGAGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
6560 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
6576 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTCGTGCGAGATATCAAATCCGAGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
6641 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
6655 CCGAAGGCATT
1 CCGAAGGCATT
6666 TGAACGAGGA
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 37 0.48
80 37 0.48
81 3 0.04
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTCGTGCGAGATATCAAATCCGAGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:6647 original size:39 final size:39
Alignment explanation
Indices: 6496--6665 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 39
6486 GGACTAAGAT
* * * *
6496 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGAGTTAAGCC
1 CCGAAGGCA-TTGTGCGAGTTACTAAA-TCCGGGTTATGTC
* * *
6536 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGG-CATTGTGCGAGTTACTAAATCCGGGTTATGTC
*
6576 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATT-GTGCGAGTTACTAAATCCGGGTTATGTC
* * *
6616 CCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTATGTC
6655 CCGAAGGCATT
1 CCGAAGGCATT
6666 TGAACGAGGA
Statistics
Matches: 116, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
39 38 0.33
40 74 0.64
41 4 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTATGTC
Found at i:6685 original size:79 final size:79
Alignment explanation
Indices: 6535--6700 Score: 174
Period size: 79 Copynumber: 2.1 Consensus size: 79
6525 CGAGTTAAGC
* * * ** * *
6535 CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATT
1 CCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACT
**
6600 AAATCCGGGTTATGT
66 AAATCC-GGTTAAAT
* * * *
6615 CCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGC
1 CCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-C
*
6678 TATATCCGGTTAAAT
65 TAAATCCGGTTAAAT
6693 CCCGAAGG
1 CCCGAAGG
6701 TACGTGATTT
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.21
79 48 0.68
80 8 0.11
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACT
AAATCCGGTTAAAT
Found at i:8892 original size:8 final size:8
Alignment explanation
Indices: 8879--8908 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
8869 GCTGGAGATC
*
8879 CTATCAAA
1 CTATCAAG
8887 CTATCAAG
1 CTATCAAG
8895 CTATCAAG
1 CTATCAAG
8903 CTATCA
1 CTATCA
8909 TATTAGGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (8 bp):
CTATCAAG
Found at i:12723 original size:46 final size:46
Alignment explanation
Indices: 12551--12720 Score: 173
Period size: 46 Copynumber: 3.7 Consensus size: 46
12541 TGTAACCCGC
* **
12551 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-AAGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA-CATTCGCAT
* * ** * *
12597 CCATAAGTGAACTCAGACTCAACTCAACAAGCTCGGACGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGAC-ATTCGCAT
* *** *
12643 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
12690 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
12721 TTCAGATGCT
Statistics
Matches: 97, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
46 62 0.64
47 35 0.36
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Done.