Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold722
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: 20999
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:715 original size:14 final size:14
Alignment explanation
Indices: 669--708 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
659 GGAAAATTCG
669 AAAAAAAAAAAA--
1 AAAAAAAAAAAATT
681 AAAAAAAAAAAATT
1 AAAAAAAAAAAATT
695 AAAAAAAAAAAATT
1 AAAAAAAAAAAATT
709 TTGAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.46
14 14 0.54
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAAAAAAAAATT
Found at i:725 original size:1 final size:1
Alignment explanation
Indices: 669--706 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
659 GGAAAATTCG
**
669 AAAAAAAAAAAAAAAAAAAAAAAATTAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
707 TTTTGAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.95, C:0.00, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:730 original size:17 final size:17
Alignment explanation
Indices: 668--733 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 17
658 AGGAAAATTC
668 GAAAAAAAAAA--AAAA
1 GAAAAAAAAAATGAAAA
*
683 -AAAAAAAAAATTAAAA
1 GAAAAAAAAAATGAAAA
**
699 -AAAAAAAATTTTGAAAA
1 GAAAAAAAA-AATGAAAA
*
716 GAAAAAAAAAGTGAAAA
1 GAAAAAAAAAATGAAAA
733 G
1 G
734 TCTTTGTGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
14 10 0.24
16 12 0.29
17 12 0.29
18 8 0.19
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (17 bp):
GAAAAAAAAAATGAAAA
Found at i:1661 original size:37 final size:37
Alignment explanation
Indices: 1610--1680 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
1600 CATTCTTGTA
1610 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
1647 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
1681 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:1680 original size:6 final size:6
Alignment explanation
Indices: 1620--1669 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
1610 AAGAGAAAAC
*
1620 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
1669 A
1 A
1670 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:1762 original size:11 final size:12
Alignment explanation
Indices: 1730--1760 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1720 TTGAGAGAAC
1730 TTGAAAAAGCCT
1 TTGAAAAAGCCT
1742 TTGAAAAAGCCT
1 TTGAAAAAGCCT
1754 TTGAAAA
1 TTGAAAA
1761 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:3966 original size:30 final size:30
Alignment explanation
Indices: 3932--4028 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
3922 AGCTCACTCC
3932 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
3962 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
3992 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
4022 TAGCTCA
1 TAGCTCA
4029 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:7392 original size:40 final size:40
Alignment explanation
Indices: 7337--7594 Score: 360
Period size: 40 Copynumber: 6.5 Consensus size: 40
7327 TGGATGATAA
* * *
7337 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
7377 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
7417 CCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
7457 CCGGGCTAAGTCCCGAAGGCATTTGTTCGAGTTGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
7497 CCGGGCTAAGCCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
7537 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
7577 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
7595 TACTTGGCTT
Statistics
Matches: 198, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 16 0.08
40 182 0.92
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:10814 original size:23 final size:22
Alignment explanation
Indices: 10762--10814 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
10752 TCCACGTCTT
*
10762 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
10784 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
10807 TTTCTTTT
1 TTTCTTTT
10815 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:13191 original size:12 final size:13
Alignment explanation
Indices: 13174--13202 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
13164 TTAAACTAAG
13174 TAAATAAAT-AAA
1 TAAATAAATAAAA
13186 TAAATAAATAAAA
1 TAAATAAATAAAA
13199 TAAA
1 TAAA
13203 ACTTTACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:14485 original size:30 final size:30
Alignment explanation
Indices: 14451--14547 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
14441 TAAACTAAAA
*
14451 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGTTAAAGT
** * * * * *
14481 TGAGCTGTGGC-TAAACTCCTAAGTTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGTTAAAGT
*
14511 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGTT-AAAGT
14541 TGAGCTA
1 TGAGCTA
14548 GGAGTGAGTT
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 1 0.02
30 42 0.88
31 5 0.10
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGTTAAAGT
Found at i:14486 original size:19 final size:19
Alignment explanation
Indices: 14451--14495 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
14441 TAAACTAAAA
*
14451 TGAGCT-AAGCTTTAGCTCG
1 TGAGCTAAAGCTTGAGCT-G
14470 TGAGCTAAAG-TTGAGCTG
1 TGAGCTAAAGCTTGAGCTG
14488 TG-GCTAAA
1 TGAGCTAAA
14496 CTCCTAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.25
18 3 0.12
19 12 0.50
20 3 0.12
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (19 bp):
TGAGCTAAAGCTTGAGCTG
Found at i:17529 original size:79 final size:80
Alignment explanation
Indices: 17372--17596 Score: 246
Period size: 79 Copynumber: 2.8 Consensus size: 80
17362 TTGAATGATG
* * * * * * *
17372 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAA-TTACTATAACCGGGCTAAG-TCCCGAAGGCAT
17435 TTGTGCGAGATACTAAA
64 TTGTGCGAGATACTAAA
*
17452 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGA-TACTA-ATTCCGGGCTAAG-CCCGAAGGCA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGA-ATTACTATA-ACCGGGCTAAGTCCCGAAGGCA
*
17513 TTTGTGCGAGTTACTAAA
63 TTTGTGCGAGATACTAAA
** * *
17531 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACTGGGCTATGTCCCGAAGGCATTT
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
17596 G
66 G
17597 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
78 2 0.02
79 67 0.54
80 45 0.36
81 9 0.07
82 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:17560 original size:40 final size:40
Alignment explanation
Indices: 17372--17596 Score: 253
Period size: 40 Copynumber: 5.7 Consensus size: 40
17362 TTGAATGATG
* * * * *
17372 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
17412 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
17452 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
17492 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
17531 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
17572 -CTGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
17597 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
39 35 0.21
40 119 0.73
41 10 0.06
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:17615 original size:119 final size:120
Alignment explanation
Indices: 17372--17602 Score: 267
Period size: 119 Copynumber: 1.9 Consensus size: 120
17362 TTGAATGATG
*
17372 TCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
**
17437 GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
66 GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGATACTAAT
* * * * **
17492 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * *
17554 TTGTGCGA-ATTACTATAA-CTGGGCTATG-TCCCGAAGGCATTTGAACGAG
64 TTGTGCGAGA-TACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAG
17603 GAGCTATATC
Statistics
Matches: 94, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
118 3 0.03
119 71 0.76
120 20 0.21
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGATACTAAT
Found at i:17618 original size:79 final size:79
Alignment explanation
Indices: 17425--17629 Score: 197
Period size: 79 Copynumber: 2.6 Consensus size: 79
17415 GGACTAAGAT
** **
17425 CCGAAGGCATTTGTGCGAGAT-ACTAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAA-ATCCCGAAGGCATTTGTGCGAGATAC
*
17488 TAATTCCGGGCTAAGC
64 TAATACCGGGCTAAGC
** * *
17504 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGTGCGAGA-TACT
* *
17568 -ATAACTGGGCTATGTC
65 AAT-ACCGGGCTAAG-C
* *
17584 CCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
17630 TACGTGATTT
Statistics
Matches: 108, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
78 5 0.05
79 78 0.72
80 25 0.23
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGTGCGAGATACTA
ATACCGGGCTAAGC
Done.