Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold627
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: 42204
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:10050 original size:13 final size:13
Alignment explanation
Indices: 10032--10079 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
10022 ATATCAAGTT
10032 AAAAAAAAAATTG
1 AAAAAAAAAATTG
*
10045 -AAAAAAAATTCTG
1 AAAAAAAAAAT-TG
*
10058 AACAAAAAAATTG
1 AAAAAAAAAATTG
10071 AAAAAAAAA
1 AAAAAAAAA
10080 GAGAGCTAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 9 0.31
13 12 0.41
14 8 0.28
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (13 bp):
AAAAAAAAAATTG
Found at i:15294 original size:11 final size:10
Alignment explanation
Indices: 15278--15317 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
15268 TAGTTTCTCG
15278 AAAAAAAACTC
1 AAAAAAAA-TC
*
15289 AAAAAAAATT
1 AAAAAAAATC
15299 AAAAAAAATTC
1 AAAAAAAA-TC
15310 AAAAAAAA
1 AAAAAAAA
15318 ACTAGTTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:15304 original size:21 final size:21
Alignment explanation
Indices: 15278--15317 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
15268 TAGTTTCTCG
15278 AAAAAAAACTCAAAAAAAATT
1 AAAAAAAACTCAAAAAAAATT
*
15299 AAAAAAAATTCAAAAAAAA
1 AAAAAAAACTCAAAAAAAA
15318 ACTAGTTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAAAAAACTCAAAAAAAATT
Found at i:15380 original size:14 final size:13
Alignment explanation
Indices: 15361--15406 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
15351 TCAAGTTGTG
15361 AAAAAAAATTTGA
1 AAAAAAAATTTGA
15374 AAAAAAAATTGTGA
1 AAAAAAAATT-TGA
15388 AAAAAAAA-TTGA
1 AAAAAAAATTTGA
15400 AAAAAAA
1 AAAAAAA
15407 GAGAGCTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.31
13 11 0.34
14 11 0.34
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTTGA
Found at i:15385 original size:26 final size:26
Alignment explanation
Indices: 15356--15406 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
15346 GGATATCAAG
*
15356 TTGTGAAAAAAAATTTGAAAAAAAAA
1 TTGTGAAAAAAAAATTGAAAAAAAAA
15382 TTGTGAAAAAAAAATTGAAAAAAAA
1 TTGTGAAAAAAAAATTGAAAAAAAA
15407 GAGAGCTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.22
Consensus pattern (26 bp):
TTGTGAAAAAAAAATTGAAAAAAAAA
Found at i:19242 original size:34 final size:34
Alignment explanation
Indices: 19204--19295 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 34
19194 TAAAGTCATG
19204 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
1 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
* *
19238 CATTA---AA--TT-AAGTCAAGTT-AGTTT--A-
1 CATTATGTAACTTTCATGT-TAGTTAAGTTTGCAT
19263 -ATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
1 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
19296 TTGAAAACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 23
0.61 0.06 0.33
Matches are distributed among these distances:
24 4 0.09
26 1 0.02
27 2 0.05
28 8 0.19
29 12 0.28
30 8 0.19
31 2 0.05
32 1 0.02
34 5 0.12
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (34 bp):
CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
Found at i:20614 original size:12 final size:11
Alignment explanation
Indices: 20584--20613 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
20574 TAGTTTCTTG
20584 AAAAAAAACTC
1 AAAAAAAACTC
*
20595 AAAAAAAATTC
1 AAAAAAAACTC
20606 AAAAAAAA
1 AAAAAAAA
20614 AAAATAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAAAAACTC
Found at i:20676 original size:14 final size:14
Alignment explanation
Indices: 20657--20690 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
20647 TATCAAGTTG
20657 AAAAAAAATT-TGA
1 AAAAAAAATTGTGA
20670 AAAAAAAATTGTGA
1 AAAAAAAATTGTGA
20684 AAAAAAA
1 AAAAAAA
20691 GAGAGCTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (14 bp):
AAAAAAAATTGTGA
Found at i:24889 original size:24 final size:23
Alignment explanation
Indices: 24835--24912 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 23
24825 GAATAAACAA
*
24835 GAAATGGTATTTGGTTTAGGTAC
1 GAAATGGTATTTGGATTAGGTAC
**
24858 GATTTGGTATTTAGGAATT-GGTAC
1 GAAATGGTATTT-GG-ATTAGGTAC
*
24882 GAAATGGTA--TGGTATTTGGTAC
1 GAAATGGTATTTGG-ATTAGGTAC
*
24904 GAATTGGTA
1 GAAATGGTA
24913 ATGGTTCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 5 0.11
22 14 0.31
23 10 0.22
24 14 0.31
25 2 0.04
ACGTcount: A:0.27, C:0.04, G:0.31, T:0.38
Consensus pattern (23 bp):
GAAATGGTATTTGGATTAGGTAC
Found at i:24903 original size:22 final size:23
Alignment explanation
Indices: 24875--24917 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
24865 TATTTAGGAA
24875 TTGGTACGAAATGGT-ATGGTAT
1 TTGGTACGAAATGGTAATGGTAT
*
24897 TTGGTACGAATTGGTAATGGT
1 TTGGTACGAAATGGTAATGGT
24918 TCAAAAACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.26, C:0.05, G:0.33, T:0.37
Consensus pattern (23 bp):
TTGGTACGAAATGGTAATGGTAT
Found at i:26105 original size:30 final size:30
Alignment explanation
Indices: 26047--26105 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
26037 TTGAAAAGGT
* *
26047 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
26077 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
26106 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:27964 original size:20 final size:20
Alignment explanation
Indices: 27918--27964 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
27908 AGCTTGTTTC
*
27918 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
27938 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
27958 CAGCTCA
1 CAGCTCA
27965 ATCTTAACCC
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:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:29945 original size:11 final size:11
Alignment explanation
Indices: 29929--29962 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
29919 TAGTAGTTTC
*
29929 TTCAAAAAAAT
1 TTCAAAAAAAA
29940 TTCAAAAAAAAA
1 TTC-AAAAAAAA
29952 TTCAAAAAAAA
1 TTCAAAAAAAA
29963 AAATTGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:29964 original size:13 final size:12
Alignment explanation
Indices: 29932--29963 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29922 TAGTTTCTTC
*
29932 AAAAAAATTTCA
1 AAAAAAAATTCA
29944 AAAAAAAATTCA
1 AAAAAAAATTCA
29956 AAAAAAAA
1 AAAAAAAA
29964 AATTGGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:30025 original size:16 final size:16
Alignment explanation
Indices: 30004--30061 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
29994 GATATCAAGT
30004 TGAAAAAAAAATTTCG
1 TGAAAAAAAAATTTCG
30020 TGAAAAAAAAAATTTCG
1 TG-AAAAAAAAATTTCG
*
30037 TGAAAAAAAAAATTCG
1 TGAAAAAAAAATTTCG
30053 TGAAAAAAA
1 TGAAAAAAA
30062 GAAGAAGCTA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
16 24 0.60
17 16 0.40
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.21
Consensus pattern (16 bp):
TGAAAAAAAAATTTCG
Found at i:30028 original size:17 final size:17
Alignment explanation
Indices: 30006--30061 Score: 105
Period size: 17 Copynumber: 3.4 Consensus size: 17
29996 TATCAAGTTG
30006 AAAAAAAAATTTCGTGA
1 AAAAAAAAATTTCGTGA
30023 AAAAAAAAATTTCGTGA
1 AAAAAAAAATTTCGTGA
30040 AAAAAAAAA-TTCGTGA
1 AAAAAAAAATTTCGTGA
30056 AAAAAA
1 AAAAAA
30062 GAAGAAGCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
16 13 0.33
17 26 0.67
ACGTcount: A:0.64, C:0.05, G:0.11, T:0.20
Consensus pattern (17 bp):
AAAAAAAAATTTCGTGA
Found at i:33983 original size:11 final size:11
Alignment explanation
Indices: 33967--34066 Score: 71
Period size: 12 Copynumber: 8.7 Consensus size: 11
33957 TATTGTATTG
33967 AAAAAAAATCA
1 AAAAAAAATCA
*
33978 AAAAAAATTCGA
1 AAAAAAAATC-A
*
33990 AAAAAAAATTTGA
1 AAAAAAAA--TCA
34003 AAAAAAAATTC-
1 AAAAAAAA-TCA
*
34014 AAAAAAAAT-G
1 AAAAAAAATCA
34024 AAAAAAAATCGA
1 AAAAAAAATC-A
*
34036 AAAAAAAA-AA
1 AAAAAAAATCA
*
34046 AAAAAAGAAGTGA
1 AAAAAA-AA-TCA
34059 AAAAAAAA
1 AAAAAAAA
34067 AAAAAAGTGA
Statistics
Matches: 73, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
10 17 0.23
11 19 0.26
12 20 0.27
13 16 0.22
14 1 0.01
ACGTcount: A:0.78, C:0.04, G:0.07, T:0.11
Consensus pattern (11 bp):
AAAAAAAATCA
Found at i:33993 original size:13 final size:13
Alignment explanation
Indices: 33977--34043 Score: 83
Period size: 13 Copynumber: 5.6 Consensus size: 13
33967 AAAAAAAATC
33977 AAAAAAAATTCGA
1 AAAAAAAATTCGA
*
33990 AAAAAAAATTTGA
1 AAAAAAAATTCGA
34003 AAAAAAAATTC--
1 AAAAAAAATTCGA
34014 AAAAAAAA-T-G-
1 AAAAAAAATTCGA
34024 AAAAAAAA-TCGA
1 AAAAAAAATTCGA
34036 AAAAAAAA
1 AAAAAAAA
34044 AAAAAAAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
10 10 0.20
11 9 0.18
12 8 0.16
13 22 0.45
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.13
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:34061 original size:18 final size:18
Alignment explanation
Indices: 34039--34079 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
34029 AAATCGAAAA
34039 AAAAAAAAAAAAAGAAGTG
1 AAAAAAAAAAAAA-AAGTG
34058 AAAAAAAAAAAAAAAGTG
1 AAAAAAAAAAAAAAAGTG
34076 AAAA
1 AAAA
34080 GTCTTGCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAGTG
Found at i:34079 original size:11 final size:10
Alignment explanation
Indices: 33965--34079 Score: 72
Period size: 10 Copynumber: 10.6 Consensus size: 10
33955 ACTATTGTAT
33965 TGAAAAAAAA
1 TGAAAAAAAA
*
33975 TCAAAAAAAA
1 TGAAAAAAAA
33985 TTCGAAAAAAAAA
1 -T-G-AAAAAAAA
33998 TTTGAAAAAAAAA
1 --TG-AAAAAAAA
*
34011 TTCAAAAAAAA
1 -TGAAAAAAAA
34022 TGAAAAAAAA
1 TGAAAAAAAA
34032 TCGAAAAAAAAA
1 T-G-AAAAAAAA
**
34044 AAAAAAAAGAA
1 TGAAAAAA-AA
34055 GTGAAAAAAAA
1 -TGAAAAAAAA
*
34066 --AAAAAAAG
1 TGAAAAAAAA
34074 TGAAAA
1 TGAAAA
34080 GTCTTGCGAG
Statistics
Matches: 86, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
8 7 0.08
10 29 0.34
11 14 0.16
12 16 0.19
13 18 0.21
14 2 0.02
ACGTcount: A:0.77, C:0.03, G:0.09, T:0.11
Consensus pattern (10 bp):
TGAAAAAAAA
Found at i:34079 original size:12 final size:11
Alignment explanation
Indices: 33967--34066 Score: 87
Period size: 11 Copynumber: 8.7 Consensus size: 11
33957 TATTGTATTG
*
33967 AAAAAAAATCA
1 AAAAAAAATGA
*
33978 AAAAAAATTCGA
1 AAAAAAAAT-GA
33990 AAAAAAAATTTGA
1 AAAAAAAA--TGA
**
34003 AAAAAAAATTC
1 AAAAAAAATGA
34014 AAAAAAAATG-
1 AAAAAAAATGA
34024 AAAAAAAATCGA
1 AAAAAAAAT-GA
*
34036 AAAAAAAA-AA
1 AAAAAAAATGA
34046 AAAAAAGAAGTGA
1 AAAAAA-AA-TGA
34059 AAAAAAAA
1 AAAAAAAA
34067 AAAAAAGTGA
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
10 16 0.22
11 21 0.29
12 18 0.25
13 17 0.23
14 1 0.01
ACGTcount: A:0.78, C:0.04, G:0.07, T:0.11
Consensus pattern (11 bp):
AAAAAAAATGA
Found at i:38510 original size:20 final size:21
Alignment explanation
Indices: 38475--38513 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
38465 CAGCTCGTTG
38475 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
38496 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
38514 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:38921 original size:13 final size:13
Alignment explanation
Indices: 38903--38928 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38893 TGTGTCCTAA
38903 TATGAATTAAATT
1 TATGAATTAAATT
38916 TATGAATTAAATT
1 TATGAATTAAATT
38929 GCTTTCAGGT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:41067 original size:18 final size:18
Alignment explanation
Indices: 41046--41080 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41036 AGTGAAGAAG
41046 AAAAGAAAACAAAAAAGA
1 AAAAGAAAACAAAAAAGA
*
41064 AAAAGAAAACGAAAAAG
1 AAAAGAAAACAAAAAAG
41081 TGAGAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAGAAAACAAAAAAGA
Found at i:41072 original size:12 final size:12
Alignment explanation
Indices: 41028--41123 Score: 54
Period size: 12 Copynumber: 7.9 Consensus size: 12
41018 TAATGAATTC
**
41028 AAAAAGAAAGTG
1 AAAAAGAAAAAG
*
41040 AAGAAG-AAAAG
1 AAAAAGAAAAAG
41051 AAAACA-AAAAAG
1 AAAA-AGAAAAAG
*
41063 AAAAAGAAAACG
1 AAAAAGAAAAAG
** *
41075 AAAAAGTGAGAG
1 AAAAAGAAAAAG
*
41087 AAAAA-AAAATG
1 AAAAAGAAAAAG
*
41098 AAGAAAAGAAAATTG
1 -A-AAAAGAAAA-AG
41113 AAAAAGAAAAA
1 AAAAAGAAAAA
41124 TATGAAAATG
Statistics
Matches: 63, Mismatches: 14, Indels: 14
0.69 0.15 0.15
Matches are distributed among these distances:
11 9 0.14
12 34 0.54
13 13 0.21
14 5 0.08
15 2 0.03
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (12 bp):
AAAAAGAAAAAG
Done.