Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2459
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: 21766
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Found at i:1377 original size:27 final size:27
Alignment explanation
Indices: 1347--1524 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
1337 ATATTGAGTC
* * * *
1347 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
1374 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
1401 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
1429 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
1456 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
1483 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
1510 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1525 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:1486 original size:82 final size:81
Alignment explanation
Indices: 1368--1523 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
1358 TGCTATATAA
* *
1368 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
1433 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
1450 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
1514 CACTTAGTGC
65 CACTTAGTGC
1524 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:9527 original size:27 final size:27
Alignment explanation
Indices: 9510--9687 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
9500 ATATTAAGTC
9510 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* ** *
9537 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
9564 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* *** ** *
9592 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
* * **
9619 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTCAGTGCTAT-ATAATCAACT
* * * * *
9646 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
*
9673 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
9688 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:9649 original size:82 final size:81
Alignment explanation
Indices: 9531--9686 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
9521 TGCTATATAA
* *
9531 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
9596 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
9613 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
9677 CACTTAGTGC
65 CACTTAGTGC
9687 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:9670 original size:54 final size:54
Alignment explanation
Indices: 9510--9686 Score: 205
Period size: 54 Copynumber: 3.3 Consensus size: 54
9500 ATATTAAGTC
* * * *
9510 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
9564 CGCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
9619 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
9673 CGCACACTTAGTGC
1 CGCACACTTAGTGC
9687 TGTACAATTT
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
52 1 0.01
54 57 0.55
55 45 0.43
56 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:13469 original size:20 final size:20
Alignment explanation
Indices: 13418--13458 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
13408 AAACATGTAA
*
13418 TAAATTAAGACAAATTTAAT
1 TAAACTAAGACAAATTTAAT
* *
13438 TAAACTAGGACACATTTAAT
1 TAAACTAAGACAAATTTAAT
13458 T
1 T
13459 CGGCTAAGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (20 bp):
TAAACTAAGACAAATTTAAT
Found at i:14867 original size:19 final size:19
Alignment explanation
Indices: 14843--14881 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
14833 AATAAATTAC
14843 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
14862 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
14881 T
1 T
14882 GCTGGAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:18517 original size:48 final size:48
Alignment explanation
Indices: 18462--18567 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
18452 TTGTCTTTTC
*
18462 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
18510 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
18558 TTTCTTTTTC
1 TTTCTTTTTC
18568 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:18564 original size:18 final size:18
Alignment explanation
Indices: 18543--18626 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 18
18533 TTTTCACATC
*
18543 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTCACTTT
* **
18561 CTTTTTCCATGACACTCGTT
1 CTTTTTCAATCTCACT--TT
* * *
18581 CTTTTACACTCTC-GTTT
1 CTTTTTCAATCTCACTTT
*
18598 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCACTTT
18617 CTTTTTCAAT
1 CTTTTTCAAT
18627 TTCTTGTTCC
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
17 6 0.12
18 25 0.52
19 7 0.15
20 10 0.21
ACGTcount: A:0.17, C:0.29, G:0.04, T:0.51
Consensus pattern (18 bp):
CTTTTTCAATCTCACTTT
Found at i:19603 original size:10 final size:9
Alignment explanation
Indices: 19590--19626 Score: 56
Period size: 10 Copynumber: 3.9 Consensus size: 9
19580 CTTTTCACTT
19590 TTTTTTGTTC
1 TTTTTT-TTC
19600 TTTTTTTTAC
1 TTTTTTTT-C
19610 TTTTTTTTC
1 TTTTTTTTC
19619 TTTTTTTT
1 TTTTTTTT
19627 TTTCTTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 11 0.42
10 15 0.58
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:19604 original size:12 final size:12
Alignment explanation
Indices: 19587--19640 Score: 58
Period size: 11 Copynumber: 4.6 Consensus size: 12
19577 AGACTTTTCA
*
19587 CTTTTTTTTGTT
1 CTTTTTTTTCTT
*
19599 C-TTTTTTT-TA
1 CTTTTTTTTCTT
19609 CTTTTTTTTCTT
1 CTTTTTTTTCTT
*
19621 TTTTTTTTTCTT
1 CTTTTTTTTCTT
19633 CATTTTTT
1 C-TTTTTT
19641 GAATTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 2 0.06
11 14 0.40
12 13 0.37
13 6 0.17
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.83
Consensus pattern (12 bp):
CTTTTTTTTCTT
Found at i:19611 original size:22 final size:22
Alignment explanation
Indices: 19581--19629 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
19571 ACTCCAAGAC
* *
19581 TTTTCACTTTTTTTTGTTCTTT
1 TTTTTACTTTTTTTTCTTCTTT
*
19603 TTTTTACTTTTTTTTCTTTTTT
1 TTTTTACTTTTTTTTCTTCTTT
19625 TTTTT
1 TTTTT
19630 CTTCATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.04, C:0.10, G:0.02, T:0.84
Consensus pattern (22 bp):
TTTTTACTTTTTTTTCTTCTTT
Found at i:19639 original size:34 final size:34
Alignment explanation
Indices: 19588--19652 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
19578 GACTTTTCAC
* * * *
19588 TTTTTTTTGTTCTTTTTTTTACTTTTTTTTCTTT
1 TTTTTTTTCTTCATTTTTTGAATTTTTTTTCTTT
19622 TTTTTTTTCTTCATTTTTTGAATTTTTTTTC
1 TTTTTTTTCTTCATTTTTTGAATTTTTTTTC
19653 AATTTCCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.82
Consensus pattern (34 bp):
TTTTTTTTCTTCATTTTTTGAATTTTTTTTCTTT
Done.