Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold575
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: 7521
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Found at i:733 original size:19 final size:17
Alignment explanation
Indices: 709--762 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 17
699 CCATCATGGT
709 TGTATCGATACAAATAG
1 TGTATCGATACAAATAG
*
726 AATGTATCAATACACAAGCTAG
1 --TGTATCGATACA-AA--TAG
748 TGTATCGATACAAAT
1 TGTATCGATACAAAT
763 CCATCAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 1 0.03
19 13 0.43
20 13 0.43
22 3 0.10
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (17 bp):
TGTATCGATACAAATAG
Found at i:906 original size:20 final size:21
Alignment explanation
Indices: 864--908 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
854 CAAGCTACTA
864 TATCAATACAAGCCTTAAAAG
1 TATCAATACAAGCCTTAAAAG
* *
885 TATCAATACATG-CTTCAAAG
1 TATCAATACAAGCCTTAAAAG
905 TATC
1 TATC
909 GATAGAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (21 bp):
TATCAATACAAGCCTTAAAAG
Found at i:5445 original size:50 final size:51
Alignment explanation
Indices: 5283--5445 Score: 197
Period size: 50 Copynumber: 3.2 Consensus size: 51
5273 ATAACAGGGC
* * * * * ***
5283 TGGAGTATCTCCAATTGTGGAAAATCGATGCTTTAGAAATAAGGCCGGGGT
1 TGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAATCGGGGT
* *
5334 TGGAGTAT-CCCGATTGT-GAGAAATTGGTGTTTTGGAAATAAAATCGGAGT
1 TGGAGTATCCCCGATTGTGGA-AAATTGGTGTTTTAGAAATAAAATCGGGGT
*
5384 TGGAGTATCCCCGATTGTGGAAAATTGGTATTTTAG-AATAAAATCGGGGT
1 TGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAATCGGGGT
5434 TGGAGTATCCCC
1 TGGAGTATCCCC
5446 TCGAAAATAA
Statistics
Matches: 96, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
49 2 0.02
50 62 0.65
51 30 0.31
52 2 0.02
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.30
Consensus pattern (51 bp):
TGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAATCGGGGT
Found at i:5464 original size:28 final size:29
Alignment explanation
Indices: 5428--5500 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
5418 AGAATAAAAT
5428 CGGGGTTGGAGTATCCCCTCGA-AAATAA
1 CGGGGTTGGAGTATCCCCTCGAGAAATAA
* *
5456 CGGGATTGGAGTAT--CCTCGATGACATAA
1 CGGGGTTGGAGTATCCCCTCGA-GAAATAA
5484 CGGGGTTGGAGTA-CCCC
1 CGGGGTTGGAGTATCCCC
5501 GATTATGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
26 6 0.16
28 30 0.79
29 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.22
Consensus pattern (29 bp):
CGGGGTTGGAGTATCCCCTCGAGAAATAA
Found at i:5546 original size:106 final size:106
Alignment explanation
Indices: 5382--5620 Score: 313
Period size: 106 Copynumber: 2.3 Consensus size: 106
5372 TAAAATCGGA
* *** * *
5382 GTTGGAGTATCCCCGATTGTGGAAAATTGGTATTTTAGAATAAAATCGGGGTTGGAGTATCCCCT
1 GTTGGAGTATCCCCGATTGTGAAAAATCAATATTTTAGAATAAAACCGGGGTTAGAGTATCCCCT
* * * *
5447 CGAAAATAAC-GGGATTGGAGTATCCTCGATGACATAACGGG
66 CGAAAATAACAGGG-TTAGAGTATCCCCGATGAAATAACGAG
* *
5488 GTTGGAGTA-CCCCGATTATGAAAAATCAATATTTTAGATATAAAGCCGGGGTTAGAGTATCCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATCAATATTTTAGA-ATAAAACCGGGGTTAGAGTATCCCC
*
5552 TCGGAAATAACAGGGTTAGAGTATCCCCGATGAAATAACGAG
65 TCGAAAATAACAGGGTTAGAGTATCCCCGATGAAATAACGAG
5594 GTTGGAGTATCCCC-AGTTGTGAAAAAT
1 GTTGGAGTATCCCCGA-TTGTGAAAAAT
5621 TTAGAAATTT
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
105 24 0.21
106 74 0.64
107 17 0.15
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (106 bp):
GTTGGAGTATCCCCGATTGTGAAAAATCAATATTTTAGAATAAAACCGGGGTTAGAGTATCCCCT
CGAAAATAACAGGGTTAGAGTATCCCCGATGAAATAACGAG
Found at i:5576 original size:28 final size:27
Alignment explanation
Indices: 5536--5607 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
5526 TATAAAGCCG
**
5536 GGGTTAGAGTATCCCCTCGGAAATAAC
1 GGGTTAGAGTATCCCCGAGGAAATAAC
*
5563 AGGGTTAGAGTATCCCCGATGAAATAAC
1 -GGGTTAGAGTATCCCCGAGGAAATAAC
*
5591 GAGGTTGGAGTATCCCC
1 G-GGTTAGAGTATCCCC
5608 AGTTGTGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (27 bp):
GGGTTAGAGTATCCCCGAGGAAATAAC
Found at i:6715 original size:20 final size:20
Alignment explanation
Indices: 6690--6737 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
6680 AAATCTGATT
6690 TTGGCACACAAATAAGCATC
1 TTGGCACACAAATAAGCATC
* *
6710 TTGGCACATAAATAAGCATG
1 TTGGCACACAAATAAGCATC
6730 TTGGCACA
1 TTGGCACA
6738 AACAACATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
TTGGCACACAAATAAGCATC
Done.