Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2186
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: 38043
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:4087 original size:40 final size:40
Alignment explanation
Indices: 3989--4251 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
3979 TCCTCGTTCA
* * * * *
3989 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
4028 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
4068 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
4108 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
4148 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
4188 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
4228 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
4252 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:12004 original size:40 final size:40
Alignment explanation
Indices: 11906--12168 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
11896 TCCTCGTTCA
* * * * *
11906 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
11945 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
11985 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
12025 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
12065 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
12105 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
12145 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
12169 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:19124 original size:17 final size:18
Alignment explanation
Indices: 19092--19141 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
19082 TTCCACTTTG
*
19092 TTCTTTTTTAATTTAT-AT
1 TTCTTATTT-ATTTATGAT
19110 TTCTTATTTATTTATGAT
1 TTCTTATTTATTTATGAT
*
19128 TT-TTATTTTTTTAT
1 TTCTTATTTATTTAT
19142 TCTCAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (18 bp):
TTCTTATTTATTTATGAT
Found at i:19173 original size:22 final size:23
Alignment explanation
Indices: 19148--19203 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
19138 TTATTCTCAA
**
19148 ATTTCTTCTTTTATTA-TTTTTT
1 ATTTCTTCTTTTACAATTTTTTT
*
19170 ATTTCTT-TATTACAATTTTTTT
1 ATTTCTTCTTTTACAATTTTTTT
19192 ATTTCTTCTTTT
1 ATTTCTTCTTTT
19204 CAGATCATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 5 0.18
22 20 0.71
23 3 0.11
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (23 bp):
ATTTCTTCTTTTACAATTTTTTT
Found at i:22480 original size:84 final size:84
Alignment explanation
Indices: 22339--22505 Score: 289
Period size: 84 Copynumber: 2.0 Consensus size: 84
22329 CTTCTGTATG
* *
22339 TGCAATTGTATTTAGGGATTGGCAATGGAGTAGGACAGGGATAAATATTATTAAATCCATTATTG
1 TGCAATTGTATTTAGGGATTGGCAATGGAGTAGGACAGGGACAAATATTATTAAATCCATTATCG
22404 TTCTACGGTTGGCACGTCC
66 TTCTACGGTTGGCACGTCC
* *
22423 TGCAATTGTTTTTAGGGATTGGCAATGGAGTAGGACAGGGACAAATATTGTTAAATCCATTATCG
1 TGCAATTGTATTTAGGGATTGGCAATGGAGTAGGACAGGGACAAATATTATTAAATCCATTATCG
*
22488 TTCTATGGTTGGCACGTC
66 TTCTACGGTTGGCACGTC
22506 TTGCCTTACG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.34
Consensus pattern (84 bp):
TGCAATTGTATTTAGGGATTGGCAATGGAGTAGGACAGGGACAAATATTATTAAATCCATTATCG
TTCTACGGTTGGCACGTCC
Found at i:23052 original size:4 final size:5
Alignment explanation
Indices: 23031--23071 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
23021 GCCTAGGAAA
23031 ATTTT ATTTT ATTTT A-TTT ATTTTT ATTTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT A-TTTT A-TTTT ATTTT ATTTT
23072 TGATTTTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 20 0.59
6 10 0.29
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:23058 original size:6 final size:6
Alignment explanation
Indices: 23032--23083 Score: 52
Period size: 6 Copynumber: 8.2 Consensus size: 6
23022 CCTAGGAAAA
*
23032 TTTTAT TTTATTT TATTTAT TTTTAT TTTTA- TTTTAT TTTTGAT TTTATAT
1 TTTTAT TTT-TAT T-TTTAT TTTTAT TTTTAT TTTTAT TTTT-AT TTT-TAT
23083 T
1 T
23084 AAATTAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
5 5 0.13
6 17 0.44
7 14 0.36
8 3 0.08
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:23063 original size:21 final size:20
Alignment explanation
Indices: 23032--23070 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
23022 CCTAGGAAAA
23032 TTTTATTTTATTTTATTTAT
1 TTTTATTTTATTTTATTTAT
23052 TTTTATTTTTATTTTATTT
1 TTTTA-TTTTATTTTATTT
23071 TTGATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTATTTTATTTTATTTAT
Found at i:24081 original size:38 final size:38
Alignment explanation
Indices: 24030--24105 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
24020 AATTTTGCAG
*
24030 GTAAGATTGGAGTCATGGGCACAACTATTGCTACGACC
1 GTAAGATTGGAGTCATGGGCACAACTATTACTACGACC
*
24068 GTAAGATTGGAGTCATGGGCACGACTATTACTACGACC
1 GTAAGATTGGAGTCATGGGCACAACTATTACTACGACC
24106 TTCGGCACGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (38 bp):
GTAAGATTGGAGTCATGGGCACAACTATTACTACGACC
Found at i:27660 original size:16 final size:16
Alignment explanation
Indices: 27639--27709 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
27629 GTTTGGTTCA
27639 CTGTAATGAAATA-AGG
1 CTGTAATGAAATAGA-G
*
27655 CTGTAATTAAATAGAG
1 CTGTAATGAAATAGAG
27671 CTGTAATTG-AATAGAG
1 CTGTAA-TGAAATAGAG
* * *
27687 TTGTAATGGAATAAAG
1 CTGTAATGAAATAGAG
*
27703 CTATAAT
1 CTGTAAT
27710 CAGTAATTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
15 2 0.04
16 42 0.91
17 2 0.04
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (16 bp):
CTGTAATGAAATAGAG
Found at i:28385 original size:2 final size:2
Alignment explanation
Indices: 28378--28958 Score: 264
Period size: 2 Copynumber: 297.5 Consensus size: 2
28368 TCATCTCCTT
* * * *
28378 TC TC TC TC TC TC TC TC TC CC TC TC TC TC CC CC TC TC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
28420 CC TC TC CC TC TC TC TC TT TC CC TC CC TC TC TC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * *
28462 CC TC TC TC TC CC TC CC CC TC TC TC TC TC TC TC TC CC TC CC CC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * * *
28504 TT TC -C CC ATT TC CC CC TC TC TC TC CC CC TC -C T- TC TC CC TC
1 TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
28544 TC TC TC TA TC TC TC TC CC TC CC TC TC TC TC TGC -C TC -C T- TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC TC TC TC TC
* * *
28584 TC CC TC TC TC TC TGC -C TC TC TA TC TC CC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
28626 TC CC TC CC TC AT- TC TC CC TT TC TC T- TC -C TC TC TT TC CC TC
1 TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * * * * * *
28666 TC TC AC TC TC TC TC -C CC TC AC AC AC AC AC AC AC AC TC TT TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
28707 TC TC TC TC TC TC TC TC -C CC AC TC TC TC CC CC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
28748 TC CC TC TC CC TC TC TC TC TC CC AC TC TC CC AC TC -C T- TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
28788 TC CC TC TC TC TC TC TC TC CC TC TC TC TC CC CC TC TC CC AC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
28830 TC TC TC CC CC TC TC CC TC TC CC CC TC TAC -C AC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC TC TC TC TC TC TC
* * * * * *
28872 CC CC TC CC TC TC CC TC TC TC -C TC TC TC -C CC T- TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
28911 -C TC TC CC TC CC CC CC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28952 TC TC TC T
1 TC TC TC T
28959 TTATTTTCAC
Statistics
Matches: 442, Mismatches: 113, Indels: 48
0.73 0.19 0.08
Matches are distributed among these distances:
1 19 0.04
2 419 0.95
3 4 0.01
ACGTcount: A:0.03, C:0.59, G:0.00, T:0.38
Consensus pattern (2 bp):
TC
Found at i:33576 original size:22 final size:22
Alignment explanation
Indices: 33551--33592 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
33541 TTTAATAAAA
33551 AAAATATCTACAAAATATTCTT
1 AAAATATCTACAAAATATTCTT
* *
33573 AAAATATTTACAGAATATTC
1 AAAATATCTACAAAATATTC
33593 CTACACTCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCTT
Done.