Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2508
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: 26453
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:1418 original size:20 final size:20
Alignment explanation
Indices: 1395--1446 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1385 ATATATCAAA
*
1395 GTATCGATACATATGTATTT
1 GTATCGATACATAGGTATTT
1415 GTATCGATACATAGGTATTT
1 GTATCGATACATAGGTATTT
1435 GTATCGATACAT
1 GTATCGATACAT
1447 TAAGGTTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (20 bp):
GTATCGATACATAGGTATTT
Found at i:1544 original size:13 final size:13
Alignment explanation
Indices: 1526--1550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1516 ATATTGCATA
1526 GTATCGATACATC
1 GTATCGATACATC
1539 GTATCGATACAT
1 GTATCGATACAT
1551 GATCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
GTATCGATACATC
Found at i:1564 original size:20 final size:21
Alignment explanation
Indices: 1539--1590 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1529 TCGATACATC
1539 GTATCGATACATGATCA-AAT
1 GTATCGATACATGATCAGAAT
** * *
1559 GTATCGATAGTTGTTGAGAAT
1 GTATCGATACATGATCAGAAT
1580 GTATCGATACA
1 GTATCGATACA
1591 GGTGATTGGT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (21 bp):
GTATCGATACATGATCAGAAT
Found at i:1690 original size:33 final size:32
Alignment explanation
Indices: 1632--1695 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1622 CTTAACTGTT
* *
1632 TGTATCGATACACACAATATGTATCGATACAA
1 TGTATCGAAACACACAAAATGTATCGATACAA
*
1664 TGTATCGAAACATCCCAAAATGTATCGATACA
1 TGTATCGAAACA-CACAAAATGTATCGATACA
1696 TTGGCTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (32 bp):
TGTATCGAAACACACAAAATGTATCGATACAA
Found at i:2756 original size:13 final size:13
Alignment explanation
Indices: 2738--2763 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2728 TACAGCAAGT
2738 ATGTATCGATACA
1 ATGTATCGATACA
2751 ATGTATCGATACA
1 ATGTATCGATACA
2764 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5016 original size:21 final size:21
Alignment explanation
Indices: 4983--5027 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4973 TTGCAAATTG
*
4983 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
5005 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
5025 AAA
1 AAA
5028 ATGAAAACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:6851 original size:15 final size:15
Alignment explanation
Indices: 6831--6861 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6821 TAAAAATGTC
*
6831 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
6846 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
6861 C
1 C
6862 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:8946 original size:20 final size:20
Alignment explanation
Indices: 8867--8946 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
8857 AATGTCCAAA
*
8867 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
8887 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
8912 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
8932 TTGTATCGATACATT
1 ATGTATCGATACATT
8947 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:8950 original size:13 final size:13
Alignment explanation
Indices: 8932--8970 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
8922 ACATTTTTCT
8932 TTGTATCGATACA
1 TTGTATCGATACA
8945 TTGTATCGATACA
1 TTGTATCGATACA
*
8958 CTGTATCGATACA
1 TTGTATCGATACA
8971 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:10820 original size:21 final size:21
Alignment explanation
Indices: 10794--10838 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
10784 ATTTACAGAA
10794 TTACTTGATTAAGGGGGAGAT
1 TTACTTGATTAAGGGGGAGAT
10815 TTACTTGATTAAGGGGGAGAT
1 TTACTTGATTAAGGGGGAGAT
10836 TTA
1 TTA
10839 TTAGAGAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (21 bp):
TTACTTGATTAAGGGGGAGAT
Found at i:10825 original size:29 final size:29
Alignment explanation
Indices: 10762--10818 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
10752 ATTTTGATAT
10762 GAATTACTTGATTAAGGGGGAGATTTACA
1 GAATTACTTGATTAAGGGGGAGATTTACA
10791 GAATTACTTGATTAAGGGGGAGATTTAC
1 GAATTACTTGATTAAGGGGGAGATTTAC
10819 TTGATTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.32
Consensus pattern (29 bp):
GAATTACTTGATTAAGGGGGAGATTTACA
Found at i:11547 original size:13 final size:13
Alignment explanation
Indices: 11529--11554 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11519 TACAGCAAGT
11529 ATGTATCGATACA
1 ATGTATCGATACA
11542 ATGTATCGATACA
1 ATGTATCGATACA
11555 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:13392 original size:20 final size:20
Alignment explanation
Indices: 13367--13441 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
13357 TTTTACCCAG
13367 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
13387 ATGTATCGATAAATGTATGA
1 ATGTATCGATACATTTTTCA
* * * *
13407 ATATTTCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
13427 ATGTATCGATACATT
1 ATGTATCGATACATT
13442 CTGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:24477 original size:31 final size:31
Alignment explanation
Indices: 24439--24499 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
24429 TAGCTAATTA
* *
24439 TGTATCGATACAATACTTATGTATCGATACT
1 TGTATCGATACAACACTTATGGATCGATACT
24470 TGTATCGATACAACACTTATGGATCGATAC
1 TGTATCGATACAACACTTATGGATCGATAC
24500 AAATCGTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (31 bp):
TGTATCGATACAACACTTATGGATCGATACT
Done.