Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g01326.F2
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: 4104
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Found at i:1565 original size:210 final size:210
Alignment explanation
Indices: 1292--1875 Score: 620
Period size: 210 Copynumber: 2.8 Consensus size: 210
1282 GCAATGGAAA
* * * * *
1292 GAAGCAACAAGCTTGCTCAATAGAATGATGAATGAAGGAGTCCATCCTGATGTTGTGACTTTCAA
1 GAAGCAACAACCGTGCTCAATAGAATGATGAATGAAGGAGTACATCCTGATGTAGTAACTTTCAA
* * ** * ** *
1357 TTCTTTAATCAATGCTTTATGCAAGTAAAAGAGGACTTCAGAAGCCTTTACTGTGTTGGAATTAA
66 TTCTTTAATCAATGCCTTATGCAAGGAAAAGAGGACTGAAGAAGCCATTACCATGTTGGAACTAA
*
1422 TGA-TACAGAGAAATGTAAAACCTAACGTTGTCACATACAATTGTTTAATATATGAGTTTTGCAG
131 TGAGT-CAGAGAAATGTAAAACCTAACATTGTCACATACAATTGTTTAATATATGAGTTTTGCAG
1486 TTCGGGCAAATGGACG
195 TTCGGGCAAATGGACG
*
1502 GAAGCAACAACCGTGCTCAATAGAATGATGAATGAAGGAGTACATCTTGATGTAGTAACTTTCAA
1 GAAGCAACAACCGTGCTCAATAGAATGATGAATGAAGGAGTACATCCTGATGTAGTAACTTTCAA
1567 TTCTTTAATCAATGCCTTATGCAAGGAAAAGAGGACTGAAGAAGCCATTACCATGTTGGAACTAA
66 TTCTTTAATCAATGCCTTATGCAAGGAAAAGAGGACTGAAGAAGCCATTACCATGTTGGAACTAA
** * * * ** * *
1632 TGAGTCAGAGAGGTGTAAAACCTGACATTGTGACCTACAATTGTTTAATACGTG-GATTGTGCAA
131 TGAGTCAGAGAAATGTAAAACCTAACATTGTCACATACAATTGTTTAATATATGAG-TTTTGCAG
* ** * *
1696 TTCAGATAAACGTG-CA
195 TTCGGGCAAATG-GACG
* * * * * * * * * * * * * *
1712 GAAGCCACAAGCTTGTTTAGTAGGATGTTGAATGGAGGAGTCCAGCCTGATATGGAAACTTT-AA
1 GAAGCAACAACCGTGCTCAATAGAATGATGAATGAAGGAGTACATCCTGATGTAGTAACTTTCAA
* * * * * * *
1776 GATCTTTAATCAATGCTTTGTACAAGGAAAACAAGTA-TGAAGAAGCCATTAGCATGTTGGAACT
66 -TTCTTTAATCAATGCCTTATGCAAGGAAAA-GAGGACTGAAGAAGCCATTACCATGTTGGAACT
* *
1840 AATGAGTCAGAGAAATGTAATACCTGACATTGTCAC
129 AATGAGTCAGAGAAATGTAAAACCTAACATTGTCAC
1876 CTACTGCTTT
Statistics
Matches: 314, Mismatches: 55, Indels: 10
0.83 0.15 0.03
Matches are distributed among these distances:
209 3 0.01
210 306 0.97
211 5 0.02
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (210 bp):
GAAGCAACAACCGTGCTCAATAGAATGATGAATGAAGGAGTACATCCTGATGTAGTAACTTTCAA
TTCTTTAATCAATGCCTTATGCAAGGAAAAGAGGACTGAAGAAGCCATTACCATGTTGGAACTAA
TGAGTCAGAGAAATGTAAAACCTAACATTGTCACATACAATTGTTTAATATATGAGTTTTGCAGT
TCGGGCAAATGGACG
Found at i:1937 original size:210 final size:206
Alignment explanation
Indices: 1568--2143 Score: 636
Period size: 210 Copynumber: 2.8 Consensus size: 206
1558 AACTTTCAAT
* * *
1568 TCTTTAATCAATGCCTTATGCAAGGAAAAGAGGACTGAAGAAGCCATTACCATGTTGGAACTAAT
1 TCTTTAATCAATGCTTTGTGCAAGGAAAA-AAGACTGAAGAAGCCATTACCATGTTGGAACTAAT
** *
1633 GAGTCAGAGAGGTGTAAAACCTGACATTGTGACCTACAATTGTTTAATACGTGGATTGTGCAATT
65 GAGTCAGAGAAATGTAAAACCTGACATTGTCACCTACAATTGTTTAATACGTGGATTGTGCAATT
*
1698 CAGATAAACGTGCAGAAGCCACAAGCTTGTTTAGTAGGATGTTGAATGGAGGAGTCCAGCCTGAT
130 CAGATAAACGTGCAGAAGCCACAAGCTTGTATAGTAGGATGTTGAAT---GGAGTCCAGCCTGAT
*
1763 ATGGAAACTTTAAGA
192 ATGGAAACCTTAAGA
* *
1778 TCTTTAATCAATGCTTTGTACAAGGAAAACAAGTA-TGAAGAAGCCATTAGCATGTTGGAACTAA
1 TCTTTAATCAATGCTTTGTGCAAGGAAAA-AAG-ACTGAAGAAGCCATTACCATGTTGGAACTAA
* ** * * *
1842 TGAGTCAGAGAAATGTAATACCTGACATTGTCACCTACTGCTT-TTTAATACTTGGATTGTGGAG
64 TGAGTCAGAGAAATGTAAAACCTGACATTGTCACCTAC-AATTGTTTAATACGTGGATTGTGCAA
* * ** ** * *
1906 TTTAGGTAATTGTGCAGAAGTGACTAGCTTGTATAGTAGGATGTTGAATGGAGTCCAGCCTGATG
128 TTCAGATAAACGTGCAGAAGCCACAAGCTTGTATAGTAGGATGTTGAATGGAGTCCAGCCTGATA
*
1971 TGGAAACCTTAAGC
193 TGGAAACCTTAAGA
* * * *** *
1985 TCTTTAATCAATGCTTTGTGCAAAGAAAAAAAGATTGAAGAAGCCATTACCTTGTACAAATTAAT
1 TCTTTAATCAATGCTTTGTGC-AAGGAAAAAAGACTGAAGAAGCCATTACCATGTTGGAACTAAT
* * * * * * * * * *
2050 GATTCAGAGAGATCTGAAACCAGACATCGTCACCTACAGTTGTTTAATACATGGATTATGCAAAT
65 GAGTCAGAGAAATGTAAAACCTGACATTGTCACCTACAATTGTTTAATACGTGGATTGTGCAATT
* * * *
2115 CAGGA-CAATGTGGAGAAGCAACAAGCTTG
130 CA-GATAAACGTGCAGAAGCCACAAGCTTG
2144 CTTAGTAAGA
Statistics
Matches: 304, Mismatches: 56, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
206 3 0.01
207 141 0.46
208 8 0.03
210 149 0.49
211 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (206 bp):
TCTTTAATCAATGCTTTGTGCAAGGAAAAAAGACTGAAGAAGCCATTACCATGTTGGAACTAATG
AGTCAGAGAAATGTAAAACCTGACATTGTCACCTACAATTGTTTAATACGTGGATTGTGCAATTC
AGATAAACGTGCAGAAGCCACAAGCTTGTATAGTAGGATGTTGAATGGAGTCCAGCCTGATATGG
AAACCTTAAGA
Found at i:2084 original size:207 final size:206
Alignment explanation
Indices: 1568--2143 Score: 638
Period size: 207 Copynumber: 2.8 Consensus size: 206
1558 AACTTTCAAT
* * * * *
1568 TCTTTAATCAATGCCTTATGCAAGGAAAAGAGGACTGAAGAAGCCATTACCATGTTGGAACTAAT
1 TCTTTAATCAATGCTTTGTGCAAGGAAAAAAAGATTGAAGAAGCCATTACCATGTTGGAACTAAT
* * * *
1633 GAGTCAGAGAGGTGTAAAACCTGACATTGTGACCTACAATTGTTTAATACGTGGATTGTGCAATT
66 GAGTCAGAGAGATGT-AAACCTGACATTGTCACCTAC-GTTGTTTAATACATGGATTGTGCAATT
*
1698 CAGATAAACGTGCAGAAGCCACAAGCTTGTTTAGTAGGATGTTGAATGGAGGAGTCCAGCCTGAT
129 CAGATAAACGTGCAGAAGCCACAAGCTTGTATAGTAGGATGTTGAAT-G-GGAGTCCAGCCTGAT
*
1763 ATGGAAACTTTAAGA
192 ATGGAAACCTTAAGA
* * *
1778 TCTTTAATCAATGCTTTGTACAAGGAAAACAAG-TATGAAGAAGCCATTAGCATGTTGGAACTAA
1 TCTTTAATCAATGCTTTGTGCAAGGAAAAAAAGAT-TGAAGAAGCCATTACCATGTTGGAACTAA
* * * *
1842 TGAGTCAGAGAAATGTAATACCTGACATTGTCACCTACTGCTT-TTTAATACTTGGATTGTGGAG
65 TGAGTCAGAGAGATGTAA-ACCTGACATTGTCACCTAC-G-TTGTTTAATACATGGATTGTGCAA
* * ** ** *
1906 TTTAGGTAATTGTGCAGAAGTGACTAGCTTGTATAGTAGGATGTTGAAT-GGAGTCCAGCCTGAT
127 TTCAGATAAACGTGCAGAAGCCACAAGCTTGTATAGTAGGATGTTGAATGGGAGTCCAGCCTGAT
* *
1970 GTGGAAACCTTAAGC
192 ATGGAAACCTTAAGA
* * *** *
1985 TCTTTAATCAATGCTTTGTGCAAAGAAAAAAAGATTGAAGAAGCCATTACCTTGTACAAATTAAT
1 TCTTTAATCAATGCTTTGTGCAAGGAAAAAAAGATTGAAGAAGCCATTACCATGTTGGAACTAAT
* * * * * *
2050 GATTCAGAGAGATCTGAAACCAGACATCGTCACCTACAGTTGTTTAATACATGGATTATGCAAAT
66 GAGTCAGAGAGATGT-AAACCTGACATTGTCACCTAC-GTTGTTTAATACATGGATTGTGCAATT
* * * *
2115 CAGGA-CAATGTGGAGAAGCAACAAGCTTG
129 CA-GATAAACGTGCAGAAGCCACAAGCTTG
2144 CTTAGTAAGA
Statistics
Matches: 305, Mismatches: 54, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
206 2 0.01
207 148 0.49
208 4 0.01
209 2 0.01
210 147 0.48
211 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (206 bp):
TCTTTAATCAATGCTTTGTGCAAGGAAAAAAAGATTGAAGAAGCCATTACCATGTTGGAACTAAT
GAGTCAGAGAGATGTAAACCTGACATTGTCACCTACGTTGTTTAATACATGGATTGTGCAATTCA
GATAAACGTGCAGAAGCCACAAGCTTGTATAGTAGGATGTTGAATGGGAGTCCAGCCTGATATGG
AAACCTTAAGA
Found at i:2324 original size:38 final size:38
Alignment explanation
Indices: 2282--2359 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
2272 CGTGAAGCCG
*
2282 AATGAATTTACTTACAGGATAATGATTGAAGAAGTGTA
1 AATGAATTTACTTACAGGATAATGATCGAAGAAGTGTA
* *
2320 AATGAATTTACTTACAGGGTAATGATCGAAGAGGTGTA
1 AATGAATTTACTTACAGGATAATGATCGAAGAAGTGTA
2358 AA
1 AA
2360 GCCATTACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.41, C:0.06, G:0.23, T:0.29
Consensus pattern (38 bp):
AATGAATTTACTTACAGGATAATGATCGAAGAAGTGTA
Done.