Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2822
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: 63700
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1458 original size:11 final size:11
Alignment explanation
Indices: 1442--1488 Score: 85
Period size: 11 Copynumber: 4.2 Consensus size: 11
1432 TAGTAGTTTC
1442 TTCAAAAAAAA
1 TTCAAAAAAAA
1453 TTCAAAAAAAA
1 TTCAAAAAAAA
1464 TTCAAAAAAAAA
1 TTC-AAAAAAAA
1476 TTCAAAAAAAA
1 TTCAAAAAAAA
1487 TT
1 TT
1489 TGGTTTCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
11 24 0.69
12 11 0.31
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:1462 original size:12 final size:12
Alignment explanation
Indices: 1445--1486 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
1435 TAGTTTCTTC
1445 AAAAAAAATTC-
1 AAAAAAAATTCA
1456 AAAAAAAATTCA
1 AAAAAAAATTCA
1468 AAAAAAAATTCA
1 AAAAAAAATTCA
1480 AAAAAAA
1 AAAAAAA
1487 TTTGGTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:1475 original size:23 final size:23
Alignment explanation
Indices: 1445--1488 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1435 TAGTTTCTTC
1445 AAAAAAAATTCAAAAAAAATTCA
1 AAAAAAAATTCAAAAAAAATTCA
1468 AAAAAAAATTCAAAAAAAATT
1 AAAAAAAATTCAAAAAAAATT
1489 TGGTTTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (23 bp):
AAAAAAAATTCAAAAAAAATTCA
Found at i:1549 original size:16 final size:16
Alignment explanation
Indices: 1528--1566 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
1518 TATCAAGTTG
1528 AAAAAAAATTCGTGAA
1 AAAAAAAATTCGTGAA
1544 AAAAAAAATTCGTGAA
1 AAAAAAAATTCGTGAA
1560 AAAAAAA
1 AAAAAAA
1567 GAAGCTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (16 bp):
AAAAAAAATTCGTGAA
Found at i:4355 original size:20 final size:20
Alignment explanation
Indices: 4332--4378 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
4322 GGGTTAAAAT
*
4332 TGAGCTGAATTAAGCTTGAG
1 TGAGCTGAATTAAGCTCGAG
* * *
4352 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTAAGCTCGAG
4372 TGAGCTG
1 TGAGCTG
4379 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTAAGCTCGAG
Found at i:8509 original size:23 final size:22
Alignment explanation
Indices: 8457--8509 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
8447 TCCACGTCTT
*
8457 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
8479 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
8502 TTTCTTTT
1 TTTCTTTT
8510 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:17287 original size:10 final size:10
Alignment explanation
Indices: 17261--17287 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
17251 AAAATTCGAA
17261 AAAAAAATTC
1 AAAAAAATTC
17271 AAAAAAATTC
1 AAAAAAATTC
17281 AAAAAAA
1 AAAAAAA
17288 AAGTTTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:17289 original size:12 final size:13
Alignment explanation
Indices: 17233--17289 Score: 75
Period size: 13 Copynumber: 4.6 Consensus size: 13
17223 TCGGTATTGT
*
17233 AAAAAAAATTTCA
1 AAAAAAAAATTCA
*
17246 AAAAAAAAATTCG
1 AAAAAAAAATTCA
17259 AAAAAAAAATTC-
1 AAAAAAAAATTCA
17271 --AAAAAAATTCA
1 AAAAAAAAATTCA
17282 AAAAAAAA
1 AAAAAAAA
17290 GTTTGTATTC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 10 0.26
13 29 0.74
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:17377 original size:28 final size:28
Alignment explanation
Indices: 17333--17401 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
17323 TAGTATTGAA
* *
17333 GAAAAAAAAGAAGAAAAAAATTCGGAATT
1 GAAAAAAAA-AAGAAAAAAAATCGAAATT
17362 -AAAAAAAAAAGAAAAAAAATCGAAATT
1 GAAAAAAAAAAGAAAAAAAATCGAAATT
17389 GAAAAAAAAAAGA
1 GAAAAAAAAAAGA
17402 GTGATTGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 17 0.46
28 20 0.54
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (28 bp):
GAAAAAAAAAAGAAAAAAAATCGAAATT
Found at i:19325 original size:17 final size:15
Alignment explanation
Indices: 19305--19343 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
19295 GTGAGCGAGA
19305 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
19322 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
19337 AAGATGA
1 AA-ATGA
19344 GTGGGACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:25202 original size:23 final size:22
Alignment explanation
Indices: 25150--25202 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
25140 TCCACGTCTT
*
25150 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
25172 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
25195 TTTCTTTT
1 TTTCTTTT
25203 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:35526 original size:15 final size:15
Alignment explanation
Indices: 35501--35556 Score: 96
Period size: 15 Copynumber: 3.7 Consensus size: 15
35491 GGATATCAAG
35501 TTGTGAAAAAAAAAT
1 TTGTGAAAAAAAAAT
35516 TT-TGAAAAAAAAAT
1 TTGTGAAAAAAAAAT
35530 TTGTGAAAAAAAAAT
1 TTGTGAAAAAAAAAT
35545 TTCGTGAAAAAA
1 TT-GTGAAAAAA
35557 GAAGAAGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.36
15 16 0.41
16 9 0.23
ACGTcount: A:0.59, C:0.02, G:0.12, T:0.27
Consensus pattern (15 bp):
TTGTGAAAAAAAAAT
Found at i:36494 original size:17 final size:18
Alignment explanation
Indices: 36472--36517 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
36462 AAGAGTGACG
36472 AGAGAAAAAGAAACGAAA
1 AGAGAAAAAGAAACGAAA
**
36490 A-AGAACAAA-AATTGAAA
1 AGAGAA-AAAGAAACGAAA
36507 AGAGAAAAAGA
1 AGAGAAAAAGA
36518 TTGGAGAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.72, C:0.04, G:0.20, T:0.04
Consensus pattern (18 bp):
AGAGAAAAAGAAACGAAA
Found at i:44872 original size:4 final size:4
Alignment explanation
Indices: 44863--44890 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
44853 TTAAACTAAG
44863 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
44891 AATAAACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:46254 original size:23 final size:22
Alignment explanation
Indices: 46202--46254 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
46192 TCCACGTCTT
*
46202 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
46224 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
46247 TTTCTTTT
1 TTTCTTTT
46255 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:48606 original size:4 final size:4
Alignment explanation
Indices: 48597--48629 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
48587 TTAAACTAAG
48597 TAAA TAAA TAAA TAAA TAAA TAAA TAAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA T-AAA TAAA
48630 ACTTTACAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:49974 original size:16 final size:15
Alignment explanation
Indices: 49945--49985 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
49935 TCGAAAAAAA
*
49945 GAAAAAAAAGAAATC
1 GAAAAAAAAAAAATC
*
49960 GAAAAGAAAAAAAATT
1 GAAAA-AAAAAAAATC
49976 GAAAAAAAAA
1 GAAAAAAAAA
49986 TTGTATACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.78, C:0.02, G:0.12, T:0.07
Consensus pattern (15 bp):
GAAAAAAAAAAAATC
Found at i:51833 original size:30 final size:30
Alignment explanation
Indices: 51797--51854 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
51787 TGAAGGTAAC
51797 AAAACAAGTGCTCATTTCCTTCACAATCAG
1 AAAACAAGTGCTCATTTCCTTCACAATCAG
51827 AAAACAAGTGCTCATTTCCTTCACAATC
1 AAAACAAGTGCTCATTTCCTTCACAATC
51855 GCTTTAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.28, G:0.09, T:0.28
Consensus pattern (30 bp):
AAAACAAGTGCTCATTTCCTTCACAATCAG
Found at i:53170 original size:21 final size:21
Alignment explanation
Indices: 53125--53187 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
53115 TTTGAACCAT
* *
53125 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
53147 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
53168 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
53188 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:54328 original size:15 final size:15
Alignment explanation
Indices: 54296--54329 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
54286 GTTCAACGAA
*
54296 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
54311 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
54326 GAGG
1 GAGG
54330 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:59630 original size:27 final size:27
Alignment explanation
Indices: 59593--59797 Score: 223
Period size: 27 Copynumber: 7.6 Consensus size: 27
59583 TAAATTGTAC
*
59593 AGCACTAAGTGTGCGATTTGGCTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
59620 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** **
59647 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
59673 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
59701 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
59728 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
59756 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
59783 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
59798 GACTTAATAT
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
27 128 0.84
28 24 0.16
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:59654 original size:54 final size:54
Alignment explanation
Indices: 59594--59797 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
59584 AAATTGTACA
* * *
59594 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
** ** * *
59648 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTG
**
59702 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTG
* * *
59757 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
59798 GACTTAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
Done.