Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1034
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: 11194
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:54 original size:22 final size:22
Alignment explanation
Indices: 16--66 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
6 TCAAAAATTT
*
16 AAATAT-AATTTATTAATTATA
1 AAATATAAATATATTAATTATA
*
37 AAATATAAATATATTAATTTTA
1 AAATATAAATATATTAATTATA
*
59 GAATATAA
1 AAATATAA
67 TATTTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATATAAATATATTAATTATA
Found at i:65 original size:16 final size:15
Alignment explanation
Indices: 13--79 Score: 52
Period size: 16 Copynumber: 4.6 Consensus size: 15
3 GAGTCAAAAA
13 TTTAAATATAAT--T
1 TTTAAATATAATAAT
*
26 TATTAATTATAA-AA-
1 T-TTAAATATAATAAT
* *
40 TATAAATATATTAAT
1 TTTAAATATAATAAT
*
55 TTTAGAATATAATATT
1 TTTA-AATATAATAAT
71 TTTAAATAT
1 TTTAAATAT
80 CATTTTATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
13 8 0.20
14 12 0.29
15 8 0.20
16 13 0.32
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (15 bp):
TTTAAATATAATAAT
Found at i:75 original size:22 final size:21
Alignment explanation
Indices: 13--75 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
3 GAGTCAAAAA
13 TTTAAATATAAT-TTATTAAT
1 TTTAAATATAATATTATTAAT
*
33 TATAAAATATAA-ATATATTAAT
1 T-TTAAATATAATAT-TATTAAT
*
55 TTTAGAATATAATATTTTTAA
1 TTTA-AATATAATATTATTAA
76 ATATCATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
20 1 0.03
21 12 0.34
22 20 0.57
23 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTAAATATAATATTATTAAT
Found at i:200 original size:48 final size:49
Alignment explanation
Indices: 106--232 Score: 163
Period size: 48 Copynumber: 2.6 Consensus size: 49
96 TAAAACAAAG
*
106 TTAATATTTTATATATTAAAATTATTATAATATTACGTTTATAATTAAA
1 TTAATATTTTATATATTAAAATTATTATAATATTACGTTTAGAATTAAA
* * *
155 TTAATATATTTA-ATTTTAAAA-TGTTATAATATTACTTTTAGAATTAAA
1 TTAATAT-TTTATATATTAAAATTATTATAATATTACGTTTAGAATTAAA
*
203 TTAAAATTTTTATATATT-AAATTATT-TAAT
1 TTAATA-TTTTATATATTAAAATTATTATAAT
233 TTAATTTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
48 40 0.60
49 23 0.34
50 4 0.06
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (49 bp):
TTAATATTTTATATATTAAAATTATTATAATATTACGTTTAGAATTAAA
Found at i:912 original size:18 final size:18
Alignment explanation
Indices: 884--919 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
874 TTAAGTTAAT
884 AAATATTTAAAAAATAAAA
1 AAATATTTAAAAAA-AAAA
903 AAAT-TTTAAAAAAAAAA
1 AAATATTTAAAAAAAAAA
920 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AAATATTTAAAAAAAAAA
Found at i:917 original size:13 final size:13
Alignment explanation
Indices: 899--937 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
889 TTTAAAAAAT
*
899 AAAAAAATTTTAA
1 AAAAAAAATTTAA
912 AAAAAAAA-TTAA
1 AAAAAAAATTTAA
924 AAATAAAAATTTAA
1 AAA-AAAAATTTAA
938 CTTAGAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 7 0.30
13 12 0.52
14 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAAAATTTAA
Found at i:918 original size:14 final size:14
Alignment explanation
Indices: 899--935 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
889 TTTAAAAAAT
899 AAAAAAATTTTAAA
1 AAAAAAATTTTAAA
913 AAAAAAA--TTAAA
1 AAAAAAATTTTAAA
925 AATAAAAATTT
1 AA-AAAAATTT
936 AACTTAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 7 0.35
13 5 0.25
14 7 0.35
15 1 0.05
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAAAATTTTAAA
Found at i:1619 original size:19 final size:18
Alignment explanation
Indices: 1590--1637 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
1580 AATATAATTT
*
1590 TTAAA-AATTTTAAAATA
1 TTAAATAATTTTAAAAAA
1607 TATAAATAATTTTAAAAAA
1 T-TAAATAATTTTAAAAAA
1626 TTAAAT-ATTTTA
1 TTAAATAATTTTA
1638 TGTCAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 7 0.25
18 9 0.32
19 12 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATAATTTTAAAAAA
Found at i:4834 original size:97 final size:97
Alignment explanation
Indices: 4668--4852 Score: 273
Period size: 97 Copynumber: 1.9 Consensus size: 97
4658 AGATATTGGA
*
4668 TCATTGCAATATCCAACCCAAAATCCCCATTAACGGCCCAATCTCTCTTCGACAGGCCTTGACTG
1 TCATTGCAATATCCAACCCAAAATCCCCATTAACGGCCCAATCTCTCTTCGACAGGCCTTGACTC
**
4733 AGAAGCTTCTGGAGACCCACTTTTGGGTCAGG
66 AGAAGCTTCTACAGACCCACTTTTGGGTCAGG
* * * ***
4765 TCATTGCCATGTCCAACCCAAAATCCCCTTTCGTGGCCCAAAT-TCTCTTCGACAGGCCTTGACT
1 TCATTGCAATATCCAACCCAAAATCCCCATTAACGGCCC-AATCTCTCTTCGACAGGCCTTGACT
4829 CAGAAGCTTCTACAGACCCACTTT
65 CAGAAGCTTCTACAGACCCACTTT
4853 CGGATTAAGT
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
97 75 0.96
98 3 0.04
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (97 bp):
TCATTGCAATATCCAACCCAAAATCCCCATTAACGGCCCAATCTCTCTTCGACAGGCCTTGACTC
AGAAGCTTCTACAGACCCACTTTTGGGTCAGG
Found at i:4966 original size:16 final size:16
Alignment explanation
Indices: 4941--4971 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4931 TTCGTGTCAT
4941 TTTTAGGTTCAGATCG
1 TTTTAGGTTCAGATCG
*
4957 TTTTATGTTCAGATC
1 TTTTAGGTTCAGATC
4972 ATTTCGGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTAGGTTCAGATCG
Found at i:5484 original size:169 final size:169
Alignment explanation
Indices: 5277--5617 Score: 538
Period size: 169 Copynumber: 2.0 Consensus size: 169
5267 GCCACGATTG
** ** *
5277 AATTTTGAAATTTCATTTAATCACGACTTGAATTTTTTTTGATTCCATTGTTATGTTCTAGCTAA
1 AATTTTGAAATTTCATTTAATCACGACTCAAATTTTTTTCAATTCCATCGTTATGTTCTAGCTAA
* * *
5342 AGAAATAAAAACATATTCGATAATTGATAATAATAATTACAAATATATCTTTTTATGATACTCAA
66 AGAAATAAAAACATATTCGATAATTGACAATAATAATTACAAATATATCTTTTTATCATACCCAA
*
5407 GTAAGAAGTAATTTCATATTAAAAAATTAAAAATAAAAC
131 GTAAGAAGCAATTTCATATTAAAAAATTAAAAATAAAAC
* *
5446 AATTTTGAAATTTTATTTGATCACGACTCAAATTTTTTTCAATTCCATCGTTATGTTCTAGCTAA
1 AATTTTGAAATTTCATTTAATCACGACTCAAATTTTTTTCAATTCCATCGTTATGTTCTAGCTAA
* *
5511 AGAAATAAAAGCATATTCGATAATTGACAATGATAATTACAAATATATCTTTTTATCATACCCAA
66 AGAAATAAAAACATATTCGATAATTGACAATAATAATTACAAATATATCTTTTTATCATACCCAA
* * *
5576 GTGAGAAGCAATTTCATATTAAAAAATTTAAAATAGAAC
131 GTAAGAAGCAATTTCATATTAAAAAATTAAAAATAAAAC
5615 AAT
1 AAT
5618 AATAGTTATT
Statistics
Matches: 156, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
169 156 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (169 bp):
AATTTTGAAATTTCATTTAATCACGACTCAAATTTTTTTCAATTCCATCGTTATGTTCTAGCTAA
AGAAATAAAAACATATTCGATAATTGACAATAATAATTACAAATATATCTTTTTATCATACCCAA
GTAAGAAGCAATTTCATATTAAAAAATTAAAAATAAAAC
Found at i:5986 original size:23 final size:22
Alignment explanation
Indices: 5960--6017 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
5950 TAATACTTAA
*
5960 GTTCAGGTCATTTCGAGTTAATT
1 GTTCAAGTCATTTCGAGTT-ATT
* *
5983 GTTCAAGTCATTTGGGGTTATT
1 GTTCAAGTCATTTCGAGTTATT
*
6005 GTTGAAGTCATTT
1 GTTCAAGTCATTT
6018 TGGGTTTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (22 bp):
GTTCAAGTCATTTCGAGTTATT
Found at i:6012 original size:22 final size:23
Alignment explanation
Indices: 5960--6023 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
5950 TAATACTTAA
* *
5960 GTTCAGGTCATTTCGAGTTAATT
1 GTTCAAGTCATTTCGGGTTAATT
*
5983 GTTCAAGTCATTTGGGGTT-ATT
1 GTTCAAGTCATTTCGGGTTAATT
* *
6005 GTTGAAGTCATTTTGGGTT
1 GTTCAAGTCATTTCGGGTT
6024 TAGATCATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.19, C:0.09, G:0.27, T:0.45
Consensus pattern (23 bp):
GTTCAAGTCATTTCGGGTTAATT
Found at i:6033 original size:16 final size:16
Alignment explanation
Indices: 6010--6088 Score: 76
Period size: 15 Copynumber: 5.0 Consensus size: 16
6000 TTATTGTTGA
6010 AGTCATTTTGGGTTT-
1 AGTCATTTTGGGTTTG
* *
6025 AGATCATTTCGGATTTG
1 AG-TCATTTTGGGTTTG
*
6042 AGTCA-TTTGGGTTCG
1 AGTCATTTTGGGTTTG
6057 -GATCA-TTTGGGTTTG
1 AG-TCATTTTGGGTTTG
6072 AGTCATTTTCGGGTTTG
1 AGTCATTTT-GGGTTTG
6089 GGTCGATCGA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 1 0.02
15 24 0.46
16 18 0.35
17 9 0.17
ACGTcount: A:0.15, C:0.10, G:0.29, T:0.46
Consensus pattern (16 bp):
AGTCATTTTGGGTTTG
Found at i:6054 original size:31 final size:30
Alignment explanation
Indices: 6010--6079 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
6000 TTATTGTTGA
*
6010 AGTCATTTTGGGTTTAGATCATTTCGGATTTG
1 AGTCA-TTTGGGTTCAGATCATTT-GGATTTG
* *
6042 AGTCATTTGGGTTCGGATCATTTGGGTTTG
1 AGTCATTTGGGTTCAGATCATTTGGATTTG
6072 AGTCATTT
1 AGTCATTT
6080 TCGGGTTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 14 0.40
31 16 0.46
32 5 0.14
ACGTcount: A:0.17, C:0.10, G:0.27, T:0.46
Consensus pattern (30 bp):
AGTCATTTGGGTTCAGATCATTTGGATTTG
Found at i:6913 original size:28 final size:27
Alignment explanation
Indices: 6860--6914 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
6850 TAAGATAAAA
* *
6860 ATTTTATGTTAATTTTTAATTTTTAAT
1 ATTTTATATTAATTTTTAATTGTTAAT
6887 ATTTTATAATTAATTTATT-ATTGTTAAT
1 ATTTTAT-ATTAATTT-TTAATTGTTAAT
6915 TATTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 15 0.62
29 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (27 bp):
ATTTTATATTAATTTTTAATTGTTAAT
Found at i:7371 original size:33 final size:33
Alignment explanation
Indices: 7333--7401 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
7323 ATATTTTTAA
* * *
7333 ATTAAAATA-ATATATATTTATGTAAAAATAATT
1 ATTAAAATATATAAATATTAATAT-AAAATAATT
*
7366 ATTAAAATATATAAATATTAATATAAAATTATT
1 ATTAAAATATATAAATATTAATATAAAATAATT
7399 ATT
1 ATT
7402 TTTAAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 20 0.65
34 11 0.35
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (33 bp):
ATTAAAATATATAAATATTAATATAAAATAATT
Found at i:8009 original size:6 final size:5
Alignment explanation
Indices: 7990--8019 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
7980 AATTTGTGAT
7990 AATAA AATAA AATAAA AATAA AATAA AATA
1 AATAA AATAA AAT-AA AATAA AATAA AATA
8020 GATATAACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:8026 original size:11 final size:10
Alignment explanation
Indices: 7990--8019 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
7980 AATTTGTGAT
7990 AATAAAATAA
1 AATAAAATAA
8000 AATAAAAATAA
1 AAT-AAAATAA
8011 AATAAAATA
1 AATAAAATA
8020 GATATAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AATAAAATAA
Done.