Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3114
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: 39030
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:5020 original size:15 final size:13
Alignment explanation
Indices: 5000--5048 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 13
4990 ACTCTCCTCA
5000 TTCTTTTCTTTCTTT
1 TTCTTTTC--TCTTT
5015 TTCTTTTCACTCTTT
1 TTCTTTT--CTCTTT
5030 TT-TTTTCTCTTT
1 TTCTTTTCTCTTT
5042 TTCTTTT
1 TTCTTTT
5049 TCTCGCTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 8 0.26
13 4 0.13
14 4 0.13
15 14 0.45
17 1 0.03
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTTTTCTCTTT
Found at i:5051 original size:14 final size:14
Alignment explanation
Indices: 5000--5052 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
4990 ACTCTCCTCA
*
5000 TTCTTTTCTTTCTTT
1 TTCTTTT-TCTCTTT
*
5015 TTC-TTTTCACTCTT
1 TTCTTTTTCTCT-TT
5029 TT-TTTTTCTCTTT
1 TTCTTTTTCTCTTT
5042 TTCTTTTTCTC
1 TTCTTTTTCTC
5053 GCTCAATAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 7 0.22
14 22 0.69
15 3 0.09
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (14 bp):
TTCTTTTTCTCTTT
Found at i:9010 original size:301 final size:301
Alignment explanation
Indices: 8468--9025 Score: 1080
Period size: 301 Copynumber: 1.9 Consensus size: 301
8458 CAGATTAAGA
*
8468 CACATTTATTTAATTAAATGATTTGAGCTGATTCTAAACTAACACAACTAATTAAATTTATTGAA
1 CACATTTATTTAATTAAATGATTTGAGATGATTCTAAACTAACACAACTAATTAAATTTATTGAA
8533 AATAAATTTAATCAGCTCCTTGAACTAATTAAGTGCCGAATTGAGCTAAATTGAGCTGACACAAG
66 AATAAATTTAATCAGCTCCTTGAACTAATTAAGTGCCGAATTGAGCTAAATTGAGCTGACACAAG
8598 CTAAAATCAGCTTGTAGGAAATTGCGAATCAAGCTAGTTGAGCTGGGCGTTTTATGGGCAATCAA
131 CTAAAATCAGCTTGTAGGAAATTGCGAATCAAGCTAGTTGAGCTGGGCGTTTTATGGGCAATCAA
8663 CCCATCACTCCACAATCGAGCAATATAGCTTGCTACAGCATCTTGGAACTTCATGGCACGTGCTC
196 CCCATCACTCCACAATCGAGCAATATAGCTTGCTACAGCATCTTGGAACTTCATGGCACGTGCTC
8728 GAGTAATTGGCCCCAAAGGCAACTCCATGGATTCGGCACCT
261 GAGTAATTGGCCCCAAAGGCAACTCCATGGATTCGGCACCT
*
8769 CACATTTTTTTAATTAAATGATTTGAGATGATTCTAAACTAACACAACTAATTAAATTTATTGAA
1 CACATTTATTTAATTAAATGATTTGAGATGATTCTAAACTAACACAACTAATTAAATTTATTGAA
8834 AATAAATTTAATCAGCTCCTTGAACTAATTAAGTGCCGAATTGAGCTAAATTGAGCTGACACAAG
66 AATAAATTTAATCAGCTCCTTGAACTAATTAAGTGCCGAATTGAGCTAAATTGAGCTGACACAAG
8899 CTAAAATCAGCTTGTAGGAAATTGCGAATCAAGCTAGTTGAGCTGGGCGTTTTATGGGCAATCAA
131 CTAAAATCAGCTTGTAGGAAATTGCGAATCAAGCTAGTTGAGCTGGGCGTTTTATGGGCAATCAA
* *
8964 CCCATCACTCCACAATCGAGCAATATAGCTTTCTACAGCATCTTGGAACTTCTTGGCACGTG
196 CCCATCACTCCACAATCGAGCAATATAGCTTGCTACAGCATCTTGGAACTTCATGGCACGTG
9026 ATACGAACTC
Statistics
Matches: 253, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
301 253 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (301 bp):
CACATTTATTTAATTAAATGATTTGAGATGATTCTAAACTAACACAACTAATTAAATTTATTGAA
AATAAATTTAATCAGCTCCTTGAACTAATTAAGTGCCGAATTGAGCTAAATTGAGCTGACACAAG
CTAAAATCAGCTTGTAGGAAATTGCGAATCAAGCTAGTTGAGCTGGGCGTTTTATGGGCAATCAA
CCCATCACTCCACAATCGAGCAATATAGCTTGCTACAGCATCTTGGAACTTCATGGCACGTGCTC
GAGTAATTGGCCCCAAAGGCAACTCCATGGATTCGGCACCT
Found at i:9989 original size:21 final size:23
Alignment explanation
Indices: 9944--9990 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
9934 TCACCTGCAA
* *
9944 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
9967 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
9988 TAA
1 TAA
9991 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:21088 original size:20 final size:20
Alignment explanation
Indices: 21065--21111 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
21055 GGGTTAAGAT
*
21065 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
21085 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
21105 TGAGCTG
1 TGAGCTG
21112 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:22837 original size:48 final size:48
Alignment explanation
Indices: 22782--22887 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
22772 TTGTCTTTTC
*
22782 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
22830 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
22878 TTTCTTTTTC
1 TTTCTTTTTC
22888 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:27082 original size:15 final size:16
Alignment explanation
Indices: 27062--27099 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
27052 TATCAAGTTG
27062 AAAAAAAA-TTCGTGA
1 AAAAAAAATTTCGTGA
27077 AAAAAAAATTTTCGTGA
1 AAAAAAAA-TTTCGTGA
27094 AAAAAA
1 AAAAAA
27100 GAAGCTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.38
17 13 0.62
ACGTcount: A:0.63, C:0.05, G:0.11, T:0.21
Consensus pattern (16 bp):
AAAAAAAATTTCGTGA
Found at i:36126 original size:15 final size:16
Alignment explanation
Indices: 36106--36137 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
36096 AGAAAATGAA
36106 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
36121 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
36137 A
1 A
36138 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:36268 original size:21 final size:18
Alignment explanation
Indices: 36243--36287 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
36233 ACGAGAGTAC
36243 AAAAGAAATGAGTGATGTGA
1 AAAAGAAA-GAG-GATGTGA
*
36263 TAAAAGAAAGAGGATTTGA
1 -AAAAGAAAGAGGATGTGA
36282 AAAAGA
1 AAAAGA
36288 GTTTGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 3 0.13
21 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.27, T:0.18
Consensus pattern (18 bp):
AAAAGAAAGAGGATGTGA
Done.