Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3211
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: 35097
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:1638 original size:30 final size:30
Alignment explanation
Indices: 1543--1639 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
1533 AGCTCACTCC
*
1543 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
* * * * **
1573 TATCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
1603 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
1633 TAGCTCA
1 TAGCTCA
1640 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 3 0.06
30 43 0.88
31 3 0.06
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:3349 original size:11 final size:11
Alignment explanation
Indices: 3333--3375 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 11
3323 AAGAAATTCG
*
3333 AAAAAAAATTA
1 AAAAAAAATAA
3344 AAAAAAAATCGAA
1 AAAAAAAAT--AA
3357 AAAAAAAA-AA
1 AAAAAAAATAA
3367 AAAAAAAAT
1 AAAAAAAAT
3376 CGAAGTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 10 0.36
11 9 0.32
13 9 0.32
ACGTcount: A:0.86, C:0.02, G:0.02, T:0.09
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:3352 original size:23 final size:22
Alignment explanation
Indices: 3312--3379 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
3302 TATTGGATTT
* * * *
3312 AAAAAAAAGAGAAGAAATTCGA
1 AAAAAAAAAAAAAAAAAATCGA
**
3334 AAAAAAATTAAAAAAAAATCGAA
1 AAAAAAAAAAAAAAAAAATCG-A
3357 AAAAAAAAAAAAAAAAAATCGA
1 AAAAAAAAAAAAAAAAAATCGA
3379 A
1 A
3380 GTATAAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 18 0.47
23 20 0.53
ACGTcount: A:0.78, C:0.04, G:0.09, T:0.09
Consensus pattern (22 bp):
AAAAAAAAAAAAAAAAAATCGA
Found at i:3391 original size:23 final size:23
Alignment explanation
Indices: 3333--3379 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
3323 AAGAAATTCG
**
3333 AAAAAAAATTAAAAAAAAATCGA
1 AAAAAAAAAAAAAAAAAAATCGA
3356 AAAAAAAAAAAAAAAAAAATCGA
1 AAAAAAAAAAAAAAAAAAATCGA
3379 A
1 A
3380 GTATAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.83, C:0.04, G:0.04, T:0.09
Consensus pattern (23 bp):
AAAAAAAAAAAAAAAAAAATCGA
Found at i:4322 original size:37 final size:37
Alignment explanation
Indices: 4271--4341 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
4261 CATTCTTGTA
4271 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
4308 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
4342 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:4341 original size:6 final size:6
Alignment explanation
Indices: 4281--4330 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
4271 AAGAGAAAAC
*
4281 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
4330 A
1 A
4331 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:4423 original size:11 final size:12
Alignment explanation
Indices: 4391--4421 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4381 TTGAGAGAAC
4391 TTGAAAAAGCCT
1 TTGAAAAAGCCT
4403 TTGAAAAAGCCT
1 TTGAAAAAGCCT
4415 TTGAAAA
1 TTGAAAA
4422 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:6600 original size:30 final size:30
Alignment explanation
Indices: 6566--6662 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
6556 AGCTCACTCC
6566 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
6596 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
6626 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
6656 TAGCTCA
1 TAGCTCA
6663 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:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:15477 original size:24 final size:25
Alignment explanation
Indices: 15450--15496 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
15440 TATCTCTCAA
15450 TTTC-AACTCATTTTTTCTTTTTGT
1 TTTCTAACTCATTTTTTCTTTTTGT
* *
15474 TTTCTCACTCTTTTTTTCTTTTT
1 TTTCTAACTCATTTTTTCTTTTT
15497 CCATCTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (25 bp):
TTTCTAACTCATTTTTTCTTTTTGT
Found at i:15510 original size:20 final size:20
Alignment explanation
Indices: 15462--15514 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
15452 TCAACTCATT
15462 TTTTCTTTTTGTTTTCTCAC
1 TTTTCTTTTTGTTTTCTCAC
15482 TCTTT-TTTTCT-TTTTC-CATC
1 T-TTTCTTTT-TGTTTTCTCA-C
15502 TTTTCTTTTTGTT
1 TTTTCTTTTTGTT
15515 CCTTTGCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
19 6 0.21
20 18 0.64
21 4 0.14
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.74
Consensus pattern (20 bp):
TTTTCTTTTTGTTTTCTCAC
Found at i:15516 original size:18 final size:19
Alignment explanation
Indices: 15462--15516 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 19
15452 TCAACTCATT
15462 TTTTCTTTTTGTTTTCTCACTC
1 TTTTCTTTTTG--TTC-CACTC
*
15484 TTTT-TTTCTTTTTCCA-TC
1 TTTTCTTT-TTGTTCCACTC
15502 TTTTCTTTTTGTTCC
1 TTTTCTTTTTGTTCC
15517 TTTGCCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 12 0.41
19 5 0.17
20 3 0.10
21 3 0.10
22 6 0.21
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTTCTTTTTGTTCCACTC
Found at i:17743 original size:13 final size:13
Alignment explanation
Indices: 17711--17743 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
17701 TTTCAATTAA
*
17711 TTTTTTCTTTGAT
1 TTTTTTTTTTGAT
17724 TTTTTTTTTTGAT
1 TTTTTTTTTTGAT
17737 TTTTTTT
1 TTTTTTT
17744 CAAAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTTGAT
Found at i:29485 original size:1 final size:1
Alignment explanation
Indices: 29479--29561 Score: 76
Period size: 1 Copynumber: 83.0 Consensus size: 1
29469 CCTCGTTAAA
* * * * * * * * * *
29479 TTTTTTTTGTGTTTGTTTTCTTTTGTTTTCTTTCTTTTTTGTTTTTTTTTTTTGTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29544 TTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTT
29562 GTTCTGATAT
Statistics
Matches: 62, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.01, C:0.04, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:29547 original size:30 final size:30
Alignment explanation
Indices: 29478--29564 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
29468 TCCTCGTTAA
*
29478 ATTTTTTTTGTGTTTGTTTTCTTTTGTTTTCT
1 ATTTTTTTT-TGTTT-TTTTTTTTTGTTTTCT
* *
29510 -TTCTTTTTTGTTTTTTTTTTTTGTTTTTT
1 ATTTTTTTTTGTTTTTTTTTTTTGTTTTCT
*
29539 ATTTTTTTTTTTTTTTTTTTTTTGTT
1 ATTTTTTTTTGTTTTTTTTTTTTGTT
29565 CTGATATGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 14 0.29
30 28 0.57
31 7 0.14
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.86
Consensus pattern (30 bp):
ATTTTTTTTTGTTTTTTTTTTTTGTTTTCT
Found at i:29867 original size:15 final size:15
Alignment explanation
Indices: 29847--29894 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
29837 TTTTTTTTGG
29847 TGTTTTATTTTTATTT
1 TGTTTTATTTTTA-TT
*
29863 TTTTTTATGTTGTTATT
1 TGTTTTAT-TT-TTATT
*
29880 TGTTTTATTGTTATT
1 TGTTTTATTTTTATT
29895 CATTCTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 5 0.19
16 8 0.30
17 11 0.41
18 3 0.11
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.77
Consensus pattern (15 bp):
TGTTTTATTTTTATT
Found at i:29891 original size:18 final size:17
Alignment explanation
Indices: 29847--29894 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
29837 TTTTTTTTGG
*
29847 TGTTTTATTTTTATTTT
1 TGTTTTATTGTTATTTT
*
29864 T-TTTTA-TGTTGTTATT
1 TGTTTTATTGTTATT-TT
29880 TGTTTTATTGTTATT
1 TGTTTTATTGTTATT
29895 CATTCTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 5 0.20
16 8 0.32
17 6 0.24
18 6 0.24
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.77
Consensus pattern (17 bp):
TGTTTTATTGTTATTTT
Done.