Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01235.F1
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: 4559
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Found at i:878 original size:6 final size:6
Alignment explanation
Indices: 867--897 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
857 TTCTCTCTCA
867 TCTCCG TCTCCG TCTCCG TCTCCG TCTCCG T
1 TCTCCG TCTCCG TCTCCG TCTCCG TCTCCG T
898 ATCCCTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.16, T:0.35
Consensus pattern (6 bp):
TCTCCG
Found at i:950 original size:7 final size:7
Alignment explanation
Indices: 938--973 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
928 TTAAAAAAAA
938 TTAATTT
1 TTAATTT
945 TTAATTT
1 TTAATTT
952 TTAATTT
1 TTAATTT
959 TTAATTT
1 TTAATTT
966 TTAATTT
1 TTAATTT
973 T
1 T
974 CTTTCATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTAATTT
Found at i:1923 original size:231 final size:231
Alignment explanation
Indices: 1541--2014 Score: 630
Period size: 231 Copynumber: 2.1 Consensus size: 231
1531 GATCTCCAAT
* * * *
1541 TTAGTGTAGAACAATGTGAGCAGCAATGTAAGGAGTTTAAGTTGATGGAGGAAGTGGTAAATGAT
1 TTAGTGTAAAACAATGTGAGCAGCAATGTAAGGAGTTTAAGTTGATGGAGGAAATAGTAAAAGAT
* * * * * * *
1606 AAGTTGGGGGAAATTAGGTTAAAAGAGAATGATTTGGAGAATTGCTTGAGTGATTATGTGTTGAG
66 AAGTTGGAGGAAATTAGGGTAAAAGAGAATGATTTGGAGAAGTGCTTGAGCGAGTATGAGTTGAA
* * * ***
1671 AGAACAACAATTTGGGTTGAAAGAGAAGAGTTTTGAGAAGCGGTGTATGGAGTTTGAGTTGGAAG
131 AGAACAACAAATTGAGTTGAAAGAGAAGAGTTTTGAGAAGCGGTATATGGAGTTTGAAAGGGAAG
**
1736 AAAAGGCTTTGGAAGAACGTCGCAGAGATCTTGAAG
196 AAAAGGCTTTCAAAGAACGTCGCAGAGATCTTGAAG
*
1772 TTAGTGTAAAACAATGTGAGCGGCAATGTGAA-GAGTTTAAGTTGATGGA-GAAATCAGTAAAAG
1 TTAGTGTAAAACAATGTGAGCAGCAATGT-AAGGAGTTTAAGTTGATGGAGGAAAT-AGTAAAAG
* * *
1835 ATAAGTTGGAGGAAGTTGGGGTGAAAGAGAAAT-ATTTGGAGAAGTGCTTGAGCGAGTATGAGTT
64 ATAAGTTGGAGGAAATTAGGGTAAAAGAG-AATGATTTGGAGAAGTGCTTGAGCGAGTATGAGTT
* * *
1899 GAAAGAAGAACAAATTGAGTTGAAAGAGAAGAGTTTTGTGAAGCGTTATATGGAGTTTGAAAGGG
128 GAAAGAACAACAAATTGAGTTGAAAGAGAAGAGTTTTGAGAAGCGGTATATGGAGTTTGAAAGGG
* * *
1964 AAGAGAAGGCTTTCAAAGAACGTTGTAGAGATCTTGAAG
193 AAGAAAAGGCTTTCAAAGAACGTCGCAGAGATCTTGAAG
*
2003 TTAATGTAAAAC
1 TTAGTGTAAAAC
2015 TGTATGAGCA
Statistics
Matches: 210, Mismatches: 30, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
230 4 0.02
231 201 0.96
232 5 0.02
ACGTcount: A:0.36, C:0.05, G:0.32, T:0.26
Consensus pattern (231 bp):
TTAGTGTAAAACAATGTGAGCAGCAATGTAAGGAGTTTAAGTTGATGGAGGAAATAGTAAAAGAT
AAGTTGGAGGAAATTAGGGTAAAAGAGAATGATTTGGAGAAGTGCTTGAGCGAGTATGAGTTGAA
AGAACAACAAATTGAGTTGAAAGAGAAGAGTTTTGAGAAGCGGTATATGGAGTTTGAAAGGGAAG
AAAAGGCTTTCAAAGAACGTCGCAGAGATCTTGAAG
Found at i:2094 original size:231 final size:231
Alignment explanation
Indices: 1627--2094 Score: 507
Period size: 231 Copynumber: 2.0 Consensus size: 231
1617 AATTAGGTTA
* * * * * * *
1627 AAAGAGAATGATTTGGAGAATTGCTTGAGTGATTATGTGTTGAGAGAACAACAATTTGGGTTGAA
1 AAAGAGAATGATTTGGAGAAGTGCTTGAGCGAGTATGAGTTGAAAGAACAACAAATTGAGTTGAA
* *** **
1692 AGAGAAGAGTTTTGAGAAGCGGTGTATGGAGTTTGAGTTGGAAGAAAAGGCTTTGGAAGAACGTC
66 AGAGAAGAGTTTTGAGAAGCGGTATATGGAGTTTGAAAGGGAAGAAAAGGCTTTCAAAGAACGTC
* * * * * * **
1757 GCAGAGATCTTGAAGTTAGTGTAAAACAATGTGAGCGGCAATGTGAAGAGTTTAAGTTGATGGAG
131 GCAGAGATCTTGAAGTTAATGTAAAACAATATGAGCAGAAATATGAAGAGTTGAAGTTGACAGAG
* * ***
1822 AAATCAGTAAAAGATAAGTTGGAGGAAGTTGGGGTG
196 AAATCAGTAAAAGATAAGTTGGAAGAAATTAAAGTG
*
1858 AAAGAGAAAT-ATTTGGAGAAGTGCTTGAGCGAGTATGAGTTGAAAGAAGAACAAATTGAGTTGA
1 AAAGAG-AATGATTTGGAGAAGTGCTTGAGCGAGTATGAGTTGAAAGAACAACAAATTGAGTTGA
* * *
1922 AAGAGAAGAGTTTTGTGAAGCGTTATATGGAGTTTGAAAGGGAAGAGAAGGCTTTCAAAGAACGT
65 AAGAGAAGAGTTTTGAGAAGCGGTATATGGAGTTTGAAAGGGAAGAAAAGGCTTTCAAAGAACGT
* * **
1987 TGTAGAGATCTTGAAGTTAATGTAAAACTGTATGAGCAGAAATAT-AAGAGGCTTGAAG-TGACA
130 CGCAGAGATCTTGAAGTTAATGTAAAACAATATGAGCAGAAATATGAAGA-G-TTGAAGTTGACA
** *
2050 GAGAAATGGGTGCAAAA-A-CAGTTGGAAGAAATTAAAAG-G
193 GAGAAATCAGT--AAAAGATAAGTTGGAAGAAATT-AAAGTG
2089 AAAGAG
1 AAAGAG
2095 GAGGAATTTG
Statistics
Matches: 194, Mismatches: 37, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
230 4 0.02
231 176 0.91
232 10 0.05
233 4 0.02
ACGTcount: A:0.38, C:0.06, G:0.31, T:0.25
Consensus pattern (231 bp):
AAAGAGAATGATTTGGAGAAGTGCTTGAGCGAGTATGAGTTGAAAGAACAACAAATTGAGTTGAA
AGAGAAGAGTTTTGAGAAGCGGTATATGGAGTTTGAAAGGGAAGAAAAGGCTTTCAAAGAACGTC
GCAGAGATCTTGAAGTTAATGTAAAACAATATGAGCAGAAATATGAAGAGTTGAAGTTGACAGAG
AAATCAGTAAAAGATAAGTTGGAAGAAATTAAAGTG
Done.