Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3459
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: 30160
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Found at i:1307 original size:15 final size:15
Alignment explanation
Indices: 1287--1351 Score: 64
Period size: 15 Copynumber: 4.4 Consensus size: 15
1277 GTATCTTCGG
1287 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
1302 TTTCTTTGTTCTGGG
1 TTTCTTTATTCTGGA
1317 TTT-TTCTA-TCTTGGA
1 TTTCTT-TATTC-TGGA
*
1332 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
1346 TTTCTT
1 TTTCTT
1352 GTTATCTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
14 12 0.29
15 25 0.61
16 4 0.10
ACGTcount: A:0.08, C:0.14, G:0.15, T:0.63
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:3577 original size:49 final size:50
Alignment explanation
Indices: 3458--3643 Score: 220
Period size: 49 Copynumber: 3.8 Consensus size: 50
3448 AATGATCTAT
* * * *
3458 TGTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCGAAAAC
1 TGTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-C-AAGAC
* **
3510 TGTGA--TCACGTGTGTAGTACTAAGTGCAGG-TACTACGTGTATTAGA-
1 TGTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAAGAC
*
3556 TGGTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAC
1 T-GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAAGAC
* *
3607 TGT-TGGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
3644 TGCGTACCAG
Statistics
Matches: 117, Mismatches: 12, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
46 1 0.01
47 6 0.05
49 65 0.56
50 39 0.33
51 1 0.01
52 5 0.04
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.28
Consensus pattern (50 bp):
TGTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAAGAC
Found at i:3643 original size:99 final size:98
Alignment explanation
Indices: 3459--3643 Score: 273
Period size: 99 Copynumber: 1.9 Consensus size: 98
3449 ATGATCTATT
* * *
3459 GTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCGAAAACTGTGATCACGTGTG
1 GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACC-AAAACTGTGATCACATGTG
3524 TAGTACTAAGTGCAGGTACTACGTGTATTAGATG
65 TAGTACTAAGTGCAGGTACTACGTGTATTAGATG
* * * *
3558 GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-AGACTGTTGGTCGCATGTG
1 GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAAAACTG-TGATCACATGTG
3622 TAGTACTAAGTGCAGGCTACTA
65 TAGTACTAAGTGCAGG-TACTA
3644 TGCGTACCAG
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
97 5 0.06
98 25 0.32
99 47 0.61
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.28
Consensus pattern (98 bp):
GTGAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAAAACTGTGATCACATGTGT
AGTACTAAGTGCAGGTACTACGTGTATTAGATG
Found at i:5569 original size:29 final size:29
Alignment explanation
Indices: 5489--5608 Score: 86
Period size: 33 Copynumber: 4.0 Consensus size: 29
5479 TGTTAAAATT
* * *
5489 ATAATAATAA-AGATA-AAGATAAACAAC
1 ATAATAATAATATATATAATATAAATAAC
5516 ATAATAAATAATATATGATAAAATATAAATAA-
1 ATAAT-AATAATATAT-AT--AATATAAATAAC
*
5548 ATAATAGATAATATATATAATAGACAACATAAC
1 ATAATA-ATAATATATATAAT--ATAA-ATAAC
*
5581 ATAATAATATAAATATATAATA-AAATAA
1 ATAATAATA-ATATATATAATATAAATAA
5609 TATACGATAA
Statistics
Matches: 76, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
27 5 0.07
28 5 0.07
29 10 0.13
30 3 0.04
31 7 0.09
32 21 0.28
33 25 0.33
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (29 bp):
ATAATAATAATATATATAATATAAATAAC
Found at i:8582 original size:13 final size:13
Alignment explanation
Indices: 8559--8599 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
8549 TAACACTTTT
*
8559 AAATGACTATATG
1 AAATGGCTATATG
*
8572 AAATGGTTATATG
1 AAATGGCTATATG
8585 AAATGGCTATATG
1 AAATGGCTATATG
8598 AA
1 AA
8600 TCGATTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (13 bp):
AAATGGCTATATG
Found at i:8607 original size:26 final size:26
Alignment explanation
Indices: 8559--8610 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
8549 TAACACTTTT
*
8559 AAATGACTATATGAAATGGTTATATG
1 AAATGACTATATGAAATGATTATATG
*
8585 AAATGGCTATATG-AATCGATTATATG
1 AAATGACTATATGAAAT-GATTATATG
8611 GAGATAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (26 bp):
AAATGACTATATGAAATGATTATATG
Found at i:10730 original size:43 final size:42
Alignment explanation
Indices: 10662--10803 Score: 144
Period size: 43 Copynumber: 3.3 Consensus size: 42
10652 TACATGTAAG
*
10662 TGGGACATTGGCAT-TCTATTGTGATTACGTGTAAGACCTTGTC
1 TGGGACATTGGCATGT-TA-TGTGATTACGTGTAAGACCATGTC
* *
10705 TGGGACATTGGCATCGTTATATGATTTCGTGTAAGACCATGTC
1 TGGGACATTGGCAT-GTTATGTGATTACGTGTAAGACCATGTC
* * * * * *
10748 TGAGACATTTGCATTGATATGTGATAACATGTAAGACCATATC
1 TGGGACATTGGCA-TGTTATGTGATTACGTGTAAGACCATGTC
*
10791 TGGGATA-TGGCAT
1 TGGGACATTGGCAT
10804 TGTACAAGCT
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
41 1 0.01
42 4 0.05
43 73 0.89
44 3 0.04
45 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.35
Consensus pattern (42 bp):
TGGGACATTGGCATGTTATGTGATTACGTGTAAGACCATGTC
Found at i:20815 original size:46 final size:46
Alignment explanation
Indices: 20765--20890 Score: 216
Period size: 46 Copynumber: 2.7 Consensus size: 46
20755 TGGTTGAGCA
*
20765 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
20811 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
20857 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
20891 GGGGCGGGTT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Done.