Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold676
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: 9792
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Found at i:6622 original size:52 final size:51
Alignment explanation
Indices: 6562--6762 Score: 186
Period size: 53 Copynumber: 3.8 Consensus size: 51
6552 TGAAATAACA
* * * * *
6562 GGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTTGGAAATAAAACCG
* * * * * * *
6613 GAGTTGGAGTATCCTCGATTAAAGGAAAATTGGTGTTTTCGAAAATAAAACCGG
1 G-GTTGGAGTATCCCCGATT-ATGAAAAATTAGTATTTTTGGAAATAAAACC-G
* * * *
6667 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTTAGCAATAAAACCG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTATTTTTGGAAATAAAACCG
* * *
6719 GGATTGGAATATCCCCGATTATGAAAAATCAATATTTTTGGAAA
1 GG-TTGGAGTATCCCCGATTATGAAAAATTAGTATTTTTGGAAA
6763 GTCGGGGTTG
Statistics
Matches: 121, Mismatches: 24, Indels: 9
0.79 0.16 0.06
Matches are distributed among these distances:
51 1 0.01
52 37 0.31
53 81 0.67
54 2 0.02
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTTGGAAATAAAACCG
Found at i:6829 original size:27 final size:26
Alignment explanation
Indices: 6765--6841 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 26
6755 TTTGGAAAGT
6765 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
6793 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
6820 CGGGGTTGGAGTAATCCCCGAT
1 CGGGGTTGGAGT-ATCCCCGAT
6842 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 17 0.38
28 23 0.51
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:9373 original size:19 final size:18
Alignment explanation
Indices: 9349--9416 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
9339 CAGTAGCTAA
9349 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
9368 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
9383 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
9400 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
9417 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:9389 original size:13 final size:13
Alignment explanation
Indices: 9371--9395 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9361 ACAATACTTA
9371 TGTATCGATACAT
1 TGTATCGATACAT
9384 TGTATCGATACA
1 TGTATCGATACA
9396 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:9393 original size:32 final size:32
Alignment explanation
Indices: 9352--9414 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
9342 TAGCTAATTA
*
9352 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
9384 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
9415 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:9479 original size:21 final size:21
Alignment explanation
Indices: 9453--9528 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
9443 TGGGACCCTA
9453 TATCGATACATTTGTAGAATG
1 TATCGATACATTTGTAGAATG
9474 TATCGATACATTTGT-GAATG
1 TATCGATACATTTGTAGAATG
* *
9494 TATCGATACA-TTCTACAAATG
1 TATCGATACATTTGTA-GAATG
9515 TATCGATACATTTG
1 TATCGATACATTTG
9529 GAATTTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.06
20 15 0.31
21 29 0.59
22 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (21 bp):
TATCGATACATTTGTAGAATG
Found at i:9515 original size:41 final size:40
Alignment explanation
Indices: 9453--9532 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
9443 TGGGACCCTA
* *
9453 TATCGATACATTTGTAGAATGTATCGATACATTTGTGAATG
1 TATCGATACATTTCTAAAATGTATCGATACATTTG-GAATG
9494 TATCGATACA-TTCTACAAATGTATCGATACATTTGGAAT
1 TATCGATACATTTCTA-AAATGTATCGATACATTTGGAAT
9533 TTTTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.22
41 28 0.78
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (40 bp):
TATCGATACATTTCTAAAATGTATCGATACATTTGGAATG
Done.