Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2791
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: 74783
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Found at i:1295 original size:14 final size:14
Alignment explanation
Indices: 1276--1304 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1266 ACAGATGGAT
1276 TCGTATAATTCTTA
1 TCGTATAATTCTTA
1290 TCGTATAATTCTTA
1 TCGTATAATTCTTA
1304 T
1 T
1305 ATATATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TCGTATAATTCTTA
Found at i:5527 original size:20 final size:21
Alignment explanation
Indices: 5461--5529 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
5451 TCACTTCGTT
5461 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
5482 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
* * *
5503 TCTTTTTGTCTAACTCACTTC
1 TCTTTTTGTCCAAGTTACTTC
5524 -CTTTTT
1 TCTTTTT
5530 TCTTTGTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.12, C:0.25, G:0.09, T:0.55
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:7922 original size:18 final size:18
Alignment explanation
Indices: 7889--7982 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
7879 AAGGTTTTCT
7889 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
7904 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
*
7922 TATTGATGCTAGTGACGA
1 TATTGATGATAGTGACGA
* *
7940 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
*
7958 TATTGATGATAGTGACGC
1 TATTGATGATAGTGACGA
7976 TATTGAT
1 TATTGAT
7983 CGTGACCTTG
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:16256 original size:14 final size:14
Alignment explanation
Indices: 16237--16264 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16227 TATATTAGTA
16237 TTTTCTATTCTATT
1 TTTTCTATTCTATT
16251 TTTTCTATTCTATT
1 TTTTCTATTCTATT
16265 AGTATTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:16272 original size:6 final size:6
Alignment explanation
Indices: 16261--16334 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
16251 TTTTCTATTC
*
16261 TATTAG TATTAGAG TATTAG -ATTAG TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATT--AG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
16308 TATTAG --TTAG -ATTAG -ATTAG TATTAG T
1 TATTAG TATTAG TATTAG TATTAG TATTAG T
16335 TAGTGATCCC
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
4 4 0.07
5 23 0.39
6 26 0.44
8 6 0.10
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (6 bp):
TATTAG
Found at i:16287 original size:11 final size:11
Alignment explanation
Indices: 16262--16338 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
16252 TTTCTATTCT
16262 ATTAGTATTAG
1 ATTAGTATTAG
16273 ---AGTATTAG
1 ATTAGTATTAG
**
16281 ATTAGTATTCT
1 ATTAGTATTAG
16292 ATTAGTATTAG
1 ATTAGTATTAG
16303 ATTAGTATTAG
1 ATTAGTATTAG
16314 -TTAG-ATTAG
1 ATTAGTATTAG
16323 ATTAGTATTAG
1 ATTAGTATTAG
16334 -TTAGT
1 ATTAGT
16339 GATCCCGGCT
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 8 0.14
9 5 0.09
10 13 0.23
11 31 0.54
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:16292 original size:30 final size:30
Alignment explanation
Indices: 16256--16334 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
16246 CTATTTTTTC
16256 TATTCTATTAGTATTAG-AGTATTAGATTAG
1 TATTCTATTAGTATTAGTAGTATTAG-TTAG
16286 TATTCTATTAGTATTAGATTAGTATTAGTTAG
1 TATTCTATTAGTATTAG--TAGTATTAGTTAG
**
16318 -ATTAGATTAGTATTAGT
1 TATTCTATTAGTATTAGT
16335 TAGTGATCCC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 1 0.02
30 17 0.39
31 14 0.32
32 4 0.09
33 8 0.18
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (30 bp):
TATTCTATTAGTATTAGTAGTATTAGTTAG
Found at i:16306 original size:5 final size:5
Alignment explanation
Indices: 16276--16337 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
16266 GTATTAGAGT
**
16276 ATTAG ATTAG TATTCT ATTAG TATTAG ATTAG TATTAG -TTAG ATTAG
1 ATTAG ATTAG -ATTAG ATTAG -ATTAG ATTAG -ATTAG ATTAG ATTAG
16323 ATTAG TATTAG -TTAG
1 ATTAG -ATTAG ATTAG
16338 TGATCCCGGC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 8 0.17
5 22 0.46
6 18 0.38
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.47
Consensus pattern (5 bp):
ATTAG
Found at i:16323 original size:20 final size:21
Alignment explanation
Indices: 16262--16338 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
16252 TTTCTATTCT
16262 ATTAGTATTAG--AGTATTAG
1 ATTAGTATTAGTTAGTATTAG
16281 ATTAGTATTCTA-TTAGTATTAG
1 ATTAGTA-T-TAGTTAGTATTAG
16303 ATTAGTATTAGTTAG-ATTAG
1 ATTAGTATTAGTTAGTATTAG
16323 ATTAGTATTAGTTAGT
1 ATTAGTATTAGTTAGT
16339 GATCCCGGCT
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.13
20 23 0.44
21 7 0.13
22 15 0.29
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (21 bp):
ATTAGTATTAGTTAGTATTAG
Found at i:24547 original size:32 final size:32
Alignment explanation
Indices: 24506--24567 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
24496 CATCTATTTT
24506 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
24538 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
24568 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:28712 original size:22 final size:22
Alignment explanation
Indices: 28686--28729 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28676 TTATCTCTTT
28686 TGATTGAAAAGGAGCAATAAAA
1 TGATTGAAAAGGAGCAATAAAA
28708 TGATTGAAAAGGAGCAATAAAA
1 TGATTGAAAAGGAGCAATAAAA
28730 AAATCGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.18
Consensus pattern (22 bp):
TGATTGAAAAGGAGCAATAAAA
Found at i:30978 original size:21 final size:21
Alignment explanation
Indices: 30954--30997 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
30944 ACGACCTAAT
*
30954 TAAATAGAAAGGATA-ATTAAA
1 TAAATA-AAAGGATACAATAAA
*
30975 TAAATAAAATGATACAATAAA
1 TAAATAAAAGGATACAATAAA
30996 TA
1 TA
30998 CTAAAGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (21 bp):
TAAATAAAAGGATACAATAAA
Found at i:40929 original size:13 final size:13
Alignment explanation
Indices: 40911--40938 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40901 AATATAGGGG
40911 AAAATGTACCATT
1 AAAATGTACCATT
40924 AAAATGTACCATT
1 AAAATGTACCATT
40937 AA
1 AA
40939 CGAATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (13 bp):
AAAATGTACCATT
Found at i:48252 original size:32 final size:32
Alignment explanation
Indices: 48216--48277 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
48206 AGCTTTTGGT
48216 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
48248 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
48278 AAAATAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:56443 original size:6 final size:6
Alignment explanation
Indices: 56432--56505 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
56422 GGGATCACTA
56432 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
*
56475 A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A
56506 GAATAGAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
4 3 0.05
5 22 0.38
6 27 0.47
8 6 0.10
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (6 bp):
ACTAAT
Found at i:56449 original size:5 final size:5
Alignment explanation
Indices: 56429--56490 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
56419 GCCGGGATCA
56429 CTAA- CTAAT ACTAAT CTAAT CTAA- CTAAT ACTAAT CTAAT ACTAAT
1 CTAAT CTAAT -CTAAT CTAAT CTAAT CTAAT -CTAAT CTAAT -CTAAT
**
56475 AGAAT ACTAAT CTAAT
1 CTAAT -CTAAT CTAAT
56491 ACTCTAATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 8 0.17
5 22 0.46
6 18 0.38
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.34
Consensus pattern (5 bp):
CTAAT
Found at i:56467 original size:11 final size:11
Alignment explanation
Indices: 56428--56504 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
56418 AGCCGGGATC
56428 ACTAA-CTAAT
1 ACTAATCTAAT
56438 ACTAATCTAAT
1 ACTAATCTAAT
56449 -CTAA-CTAAT
1 ACTAATCTAAT
56458 ACTAATCTAAT
1 ACTAATCTAAT
**
56469 ACTAATAGAAT
1 ACTAATCTAAT
56480 ACTAATCTAAT
1 ACTAATCTAAT
56491 AC---TCTAAT
1 ACTAATCTAAT
56499 ACTAAT
1 ACTAAT
56505 AGAATAGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 8 0.14
9 5 0.09
10 13 0.23
11 31 0.54
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (11 bp):
ACTAATCTAAT
Found at i:56483 original size:22 final size:21
Alignment explanation
Indices: 56428--56504 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
56418 AGCCGGGATC
56428 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
56449 -CTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
56469 ACTAA-TAGAATACTAATCTAAT
1 ACTAACT--AATACTAATCTAAT
56491 ACT--CTAATACTAAT
1 ACTAACTAATACTAAT
56505 AGAATAGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.17
20 21 0.40
21 5 0.10
22 17 0.33
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (21 bp):
ACTAACTAATACTAATCTAAT
Found at i:56536 original size:13 final size:13
Alignment explanation
Indices: 56502--56528 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56492 CTCTAATACT
56502 AATAGAATAGAAA
1 AATAGAATAGAAA
56515 AATAGAATAGAAA
1 AATAGAATAGAAA
56528 A
1 A
56529 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AATAGAATAGAAA
Found at i:56536 original size:18 final size:18
Alignment explanation
Indices: 56496--56545 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
56486 CTAATACTCT
56496 AATACTAATAGAATAG--
1 AATACTAATAGAATAGAA
56512 AA-A--AATAGAATAGAA
1 AATACTAATAGAATAGAA
*
56527 AATACTAATATAATAGAA
1 AATACTAATAGAATAGAA
56545 A
1 A
56546 GAAAAGAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
13 10 0.36
15 3 0.11
16 3 0.11
18 12 0.43
ACGTcount: A:0.64, C:0.04, G:0.10, T:0.22
Consensus pattern (18 bp):
AATACTAATAGAATAGAA
Done.