Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3498
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: 51648
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Found at i:11344 original size:14 final size:14
Alignment explanation
Indices: 11325--11352 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11315 TATATTAGTA
11325 TTTTCTATTCTATT
1 TTTTCTATTCTATT
11339 TTTTCTATTCTATT
1 TTTTCTATTCTATT
11353 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:11360 original size:6 final size:6
Alignment explanation
Indices: 11349--11422 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
11339 TTTTCTATTC
*
11349 TATTAG TATTAGAG TATTAG -ATTAG TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATT--AG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
11396 TATTAG --TTAG -ATTAG -ATTAG TATTAG T
1 TATTAG TATTAG TATTAG TATTAG TATTAG T
11423 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:11375 original size:11 final size:11
Alignment explanation
Indices: 11350--11426 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
11340 TTTCTATTCT
11350 ATTAGTATTAG
1 ATTAGTATTAG
11361 ---AGTATTAG
1 ATTAGTATTAG
**
11369 ATTAGTATTCT
1 ATTAGTATTAG
11380 ATTAGTATTAG
1 ATTAGTATTAG
11391 ATTAGTATTAG
1 ATTAGTATTAG
11402 -TTAG-ATTAG
1 ATTAGTATTAG
11411 ATTAGTATTAG
1 ATTAGTATTAG
11422 -TTAGT
1 ATTAGT
11427 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:11380 original size:30 final size:30
Alignment explanation
Indices: 11344--11422 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
11334 CTATTTTTTC
11344 TATTCTATTAGTATTAG-AGTATTAGATTAG
1 TATTCTATTAGTATTAGTAGTATTAG-TTAG
11374 TATTCTATTAGTATTAGATTAGTATTAGTTAG
1 TATTCTATTAGTATTAG--TAGTATTAGTTAG
**
11406 -ATTAGATTAGTATTAGT
1 TATTCTATTAGTATTAGT
11423 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:11394 original size:5 final size:5
Alignment explanation
Indices: 11364--11425 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
11354 GTATTAGAGT
**
11364 ATTAG ATTAG TATTCT ATTAG TATTAG ATTAG TATTAG -TTAG ATTAG
1 ATTAG ATTAG -ATTAG ATTAG -ATTAG ATTAG -ATTAG ATTAG ATTAG
11411 ATTAG TATTAG -TTAG
1 ATTAG -ATTAG ATTAG
11426 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:11411 original size:20 final size:21
Alignment explanation
Indices: 11350--11426 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
11340 TTTCTATTCT
11350 ATTAGTATTAG--AGTATTAG
1 ATTAGTATTAGTTAGTATTAG
11369 ATTAGTATTCTA-TTAGTATTAG
1 ATTAGTA-T-TAGTTAGTATTAG
11391 ATTAGTATTAGTTAG-ATTAG
1 ATTAGTATTAGTTAGTATTAG
11411 ATTAGTATTAGTTAGT
1 ATTAGTATTAGTTAGT
11427 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:19636 original size:32 final size:32
Alignment explanation
Indices: 19595--19656 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
19585 CATCTATTTT
19595 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
19627 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
19657 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:23800 original size:22 final size:22
Alignment explanation
Indices: 23774--23817 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
23764 TTATCTCTTT
23774 TGATTGAAAAGGAGCAATAAAA
1 TGATTGAAAAGGAGCAATAAAA
23796 TGATTGAAAAGGAGCAATAAAA
1 TGATTGAAAAGGAGCAATAAAA
23818 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:26066 original size:21 final size:21
Alignment explanation
Indices: 26042--26085 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
26032 ACGACCTAAT
*
26042 TAAATAGAAAGGATA-ATTAAA
1 TAAATA-AAAGGATACAATAAA
*
26063 TAAATAAAATGATACAATAAA
1 TAAATAAAAGGATACAATAAA
26084 TA
1 TA
26086 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:36017 original size:13 final size:13
Alignment explanation
Indices: 35999--36026 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35989 AATATAGGGG
35999 AAAATGTACCATT
1 AAAATGTACCATT
36012 AAAATGTACCATT
1 AAAATGTACCATT
36025 AA
1 AA
36027 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:43338 original size:32 final size:32
Alignment explanation
Indices: 43302--43363 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
43292 AGCTTTTGGT
43302 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
43334 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
43364 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:51544 original size:6 final size:6
Alignment explanation
Indices: 51533--51606 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
51523 GGGATCACTA
51533 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
*
51576 A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A
51607 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:51550 original size:5 final size:5
Alignment explanation
Indices: 51530--51591 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
51520 GCCGGGATCA
51530 CTAA- CTAAT ACTAAT CTAAT CTAA- CTAAT ACTAAT CTAAT ACTAAT
1 CTAAT CTAAT -CTAAT CTAAT CTAAT CTAAT -CTAAT CTAAT -CTAAT
**
51576 AGAAT ACTAAT CTAAT
1 CTAAT -CTAAT CTAAT
51592 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:51568 original size:11 final size:11
Alignment explanation
Indices: 51529--51605 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
51519 AGCCGGGATC
51529 ACTAA-CTAAT
1 ACTAATCTAAT
51539 ACTAATCTAAT
1 ACTAATCTAAT
51550 -CTAA-CTAAT
1 ACTAATCTAAT
51559 ACTAATCTAAT
1 ACTAATCTAAT
**
51570 ACTAATAGAAT
1 ACTAATCTAAT
51581 ACTAATCTAAT
1 ACTAATCTAAT
51592 AC---TCTAAT
1 ACTAATCTAAT
51600 ACTAAT
1 ACTAAT
51606 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:51584 original size:22 final size:21
Alignment explanation
Indices: 51529--51605 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
51519 AGCCGGGATC
51529 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
51550 -CTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
51570 ACTAA-TAGAATACTAATCTAAT
1 ACTAACT--AATACTAATCTAAT
51592 ACT--CTAATACTAAT
1 ACTAACTAATACTAAT
51606 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:51623 original size:15 final size:15
Alignment explanation
Indices: 51603--51631 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
51593 CTCTAATACT
51603 AATAGAATAGAAAAA
1 AATAGAATAGAAAAA
51618 AATAGAATAGAAAA
1 AATAGAATAGAAAA
51632 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
AATAGAATAGAAAAA
Done.