Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3023
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: 31358
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:5494 original size:17 final size:19
Alignment explanation
Indices: 5472--5511 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
5462 TTAAATCAAG
*
5472 TAAATAAT-ATAA-ATAAA
1 TAAATAATAATAATAAAAA
5489 TAAATAATAATAATAAAAA
1 TAAATAATAATAATAAAAA
5508 TAAA
1 TAAA
5512 ACTTTACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 4 0.20
19 8 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAATAATAATAATAAAAA
Found at i:8015 original size:12 final size:13
Alignment explanation
Indices: 7996--8027 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
7986 GAATGTGAAC
7996 AGAAAGAAATTGA
1 AGAAAGAAATTGA
8009 A-AAAG-AATTGA
1 AGAAAGAAATTGA
8020 AGAAAGAA
1 AGAAAGAA
8028 GAGAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.41
12 8 0.47
13 2 0.12
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (13 bp):
AGAAAGAAATTGA
Found at i:8039 original size:23 final size:23
Alignment explanation
Indices: 8007--8050 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
7997 GAAAGAAATT
8007 GAAAAAGAATT-GAAGAAAGAAGA
1 GAAAAAGAATTAGAA-AAAGAAGA
*
8030 GAAAATGAATTAGAAAAAGAA
1 GAAAAAGAATTAGAAAAAGAA
8051 ACAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (23 bp):
GAAAAAGAATTAGAAAAAGAAGA
Found at i:17636 original size:22 final size:23
Alignment explanation
Indices: 17604--17647 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
17594 GATTCATTAA
*
17604 TTTTTAGTTATTT-TAGTTTGTG
1 TTTTTAATTATTTATAGTTTGTG
17626 TTTTTAATTATTTCATAGTTTG
1 TTTTTAATTATTT-ATAGTTTG
17648 CACATCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.18, C:0.02, G:0.14, T:0.66
Consensus pattern (23 bp):
TTTTTAATTATTTATAGTTTGTG
Found at i:19094 original size:14 final size:13
Alignment explanation
Indices: 19071--19119 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
19061 ATAGTAGTTT
19071 CTCGAAAAAAAAA
1 CTCGAAAAAAAAA
19084 CTCGAAAAAAAAA
1 CTCGAAAAAAAAA
*
19097 TTC--AAAAAAAA
1 CTCGAAAAAAAAA
*
19108 TTCGAAAAAAAA
1 CTCGAAAAAAAA
19120 CTAGTTTCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
11 11 0.33
13 22 0.67
ACGTcount: A:0.69, C:0.12, G:0.06, T:0.12
Consensus pattern (13 bp):
CTCGAAAAAAAAA
Found at i:19181 original size:14 final size:14
Alignment explanation
Indices: 19157--19209 Score: 99
Period size: 14 Copynumber: 3.9 Consensus size: 14
19147 GGATATCAAG
19157 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
19171 TT-TGAAAAAAAAA
1 TTGTGAAAAAAAAA
19184 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
19198 TTGTGAAAAAAA
1 TTGTGAAAAAAA
19210 GAAGAAGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.34
14 25 0.66
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:19187 original size:27 final size:28
Alignment explanation
Indices: 19157--19209 Score: 99
Period size: 27 Copynumber: 1.9 Consensus size: 28
19147 GGATATCAAG
19157 TTGTGAAAAAAAAATT-TGAAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAAA
19184 TTGTGAAAAAAAAATTGTGAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAA
19210 GAAGAAGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (28 bp):
TTGTGAAAAAAAAATTGTGAAAAAAAAA
Found at i:20396 original size:21 final size:21
Alignment explanation
Indices: 20372--20415 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
20362 TTGGTATTTG
*
20372 GGAATTAGTTCGAAATAGTAT
1 GGAATTAGTACGAAATAGTAT
* *
20393 GGAATTGGTACGAAATGGTAT
1 GGAATTAGTACGAAATAGTAT
20414 GG
1 GG
20416 TATTTGGTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.32, T:0.30
Consensus pattern (21 bp):
GGAATTAGTACGAAATAGTAT
Found at i:20425 original size:22 final size:22
Alignment explanation
Indices: 20382--20439 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
20372 GGAATTAGTT
*
20382 CGAAATAGTATGG-AATTGGTA
1 CGAAATGGTATGGTAATTGGTA
*
20403 CGAAATGGTATGGTATTTGGTA
1 CGAAATGGTATGGTAATTGGTA
*
20425 CGAATTGGTAATGGT
1 CGAAATGGT-ATGGT
20440 TGAAAAGGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 12 0.38
22 15 0.47
23 5 0.16
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (22 bp):
CGAAATGGTATGGTAATTGGTA
Found at i:25972 original size:17 final size:17
Alignment explanation
Indices: 25947--26000 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
25937 TCTCTTTTCA
*
25947 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
25964 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
25981 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
25998 TTC
1 TTC
26001 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:28442 original size:22 final size:22
Alignment explanation
Indices: 28391--28442 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
28381 TCCACGTCTT
*
28391 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
28413 -TTCATTTTCTTTCTTTCTTC-AA
1 TTTC-TTTTCTTTCTTT-TTCTAA
28435 TTTCTTTT
1 TTTCTTTT
28443 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.12
22 17 0.65
23 6 0.23
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Done.