Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1681
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: 16734
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:5499 original size:52 final size:52
Alignment explanation
Indices: 5421--5549 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
5411 CGAAATATGA
*
5421 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
*
5473 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
5525 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
5550 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
Found at i:5560 original size:52 final size:51
Alignment explanation
Indices: 5421--5569 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 51
5411 CGAAATATGA
*
5421 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGC
*
5473 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGC
*
5525 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
5570 ATGTATCGAT
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 89 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTAGGC
Found at i:5576 original size:13 final size:13
Alignment explanation
Indices: 5558--5582 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5548 CAAAGATCAG
5558 TGTATCGATACAA
1 TGTATCGATACAA
5571 TGTATCGATACA
1 TGTATCGATACA
5583 TTTGGGTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5649 original size:19 final size:18
Alignment explanation
Indices: 5625--5722 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
5615 TAGCTTACAT
5625 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
5644 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
5657 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
5676 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
5689 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
5709 TGTATCGATACAAA
1 TGTATCGATACAAA
5723 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:5661 original size:32 final size:32
Alignment explanation
Indices: 5620--5720 Score: 184
Period size: 32 Copynumber: 3.1 Consensus size: 32
5610 GACAGTAGCT
*
5620 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
5652 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
5684 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
5717 TACA
1 TACA
5721 AATCGTTGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 52 0.78
33 15 0.22
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:5662 original size:13 final size:13
Alignment explanation
Indices: 5644--5700 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
5634 ACAAAACTTA
5644 TGTATCGATACAT
1 TGTATCGATACAT
5657 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
5675 ATGTATCGATACAT
1 -TGTATCGATACAT
5689 TGTATCGATACA
1 TGTATCGATACA
5701 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:8163 original size:21 final size:21
Alignment explanation
Indices: 8139--8191 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
8129 TTCAACAATT
*
8139 TGTATTGATACAATAAG-GCAA
1 TGTATCGATACAATAAGTG-AA
8160 TGTATCGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
8180 TGTATCGATACA
1 TGTATCGATACA
8192 TGCCTGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:8181 original size:20 final size:21
Alignment explanation
Indices: 8139--8212 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
8129 TTCAACAATT
* *
8139 TGTATTGATACAATAAG-GCAA
1 TGTATCGATAC-ATAAGTGAAA
8160 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAAGTGAAA
***
8180 TGTATCGATACATGCCTGAAA
1 TGTATCGATACATAAGTGAAA
8201 TGTATCGATACA
1 TGTATCGATACA
8213 GGACCATATG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.47
21 25 0.53
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATAAGTGAAA
Found at i:8204 original size:21 final size:20
Alignment explanation
Indices: 8158--8212 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
8148 ACAATAAGGC
*
8158 AATGTATCGATACATAAGTG
1 AATGTATCGATACATAACTG
**
8178 AATGTATCGATACATGCCTG
1 AATGTATCGATACATAACTG
8198 AAATGTATCGATACA
1 -AATGTATCGATACA
8213 GGACCATATG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACATAACTG
Found at i:8267 original size:20 final size:20
Alignment explanation
Indices: 8242--8313 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
8232 AAGGAAATTC
8242 TATCGATACATTTTTCAATG
1 TATCGATACATTTTTCAATG
* ****
8262 TATCGAAACA-TAAGAAATTG
1 TATCGATACATTTTTCAA-TG
* *
8282 TATCAATACATTTTTCATTG
1 TATCGATACATTTTTCAATG
8302 TATCGATACATT
1 TATCGATACATT
8314 CTAGGTTTTG
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
19 3 0.08
20 32 0.86
21 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTTTCAATG
Found at i:8291 original size:40 final size:40
Alignment explanation
Indices: 8235--8312 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
8225 ATTCTGGAAG
*
8235 GAAATTCTATCGATACATTTTTCAATGTATCGAAACATAA
1 GAAATTCTATCAATACATTTTTCAATGTATCGAAACATAA
* * *
8275 GAAATTGTATCAATACATTTTTCATTGTATCGATACAT
1 GAAATTCTATCAATACATTTTTCAATGTATCGAAACAT
8313 TCTAGGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (40 bp):
GAAATTCTATCAATACATTTTTCAATGTATCGAAACATAA
Found at i:16656 original size:15 final size:17
Alignment explanation
Indices: 16631--16665 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
16621 AAGGTTAGAA
16631 TCAATTTTATTATT-TT
1 TCAATTTTATTATTATT
16647 TCAA-TTTATTATTATT
1 TCAATTTTATTATTATT
16663 TCA
1 TCA
16666 TGCACTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (17 bp):
TCAATTTTATTATTATT
Done.