Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g01326.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: 6332
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Found at i:3793 original size:210 final size:210
Alignment explanation
Indices: 3520--4103 Score: 620
Period size: 210 Copynumber: 2.8 Consensus size: 210
3510 GCAATGGAAA
* * * * *
3520 GAAGCAACAAGCTTGCTCAATAGAATGATGAATGAAGGAGTCCATCCTGATGTTGTGACTTTCAA
1 GAAGCAACAACCGTGCTCAATAGAATGATGAATGAAGGAGTACATCCTGATGTAGTAACTTTCAA
* * ** * ** *
3585 TTCTTTAATCAATGCTTTATGCAAGTAAAAGAGGACTTCAGAAGCCTTTACTGTGTTGGAATTAA
66 TTCTTTAATCAATGCCTTATGCAAGGAAAAGAGGACTGAAGAAGCCATTACCATGTTGGAACTAA
*
3650 TGA-TACAGAGAAATGTAAAACCTAACGTTGTCACATACAATTGTTTAATATATGAGTTTTGCAG
131 TGAGT-CAGAGAAATGTAAAACCTAACATTGTCACATACAATTGTTTAATATATGAGTTTTGCAG
3714 TTCGGGCAAATGGACG
195 TTCGGGCAAATGGACG
*
3730 GAAGCAACAACCGTGCTCAATAGAATGATGAATGAAGGAGTACATCTTGATGTAGTAACTTTCAA
1 GAAGCAACAACCGTGCTCAATAGAATGATGAATGAAGGAGTACATCCTGATGTAGTAACTTTCAA
3795 TTCTTTAATCAATGCCTTATGCAAGGAAAAGAGGACTGAAGAAGCCATTACCATGTTGGAACTAA
66 TTCTTTAATCAATGCCTTATGCAAGGAAAAGAGGACTGAAGAAGCCATTACCATGTTGGAACTAA
** * * * ** * *
3860 TGAGTCAGAGAGGTGTAAAACCTGACATTGTGACCTACAATTGTTTAATACGTG-GATTGTGCAA
131 TGAGTCAGAGAAATGTAAAACCTAACATTGTCACATACAATTGTTTAATATATGAG-TTTTGCAG
* ** * *
3924 TTCAGATAAACGTG-CA
195 TTCGGGCAAATG-GACG
* * * * * * * * * * * * * *
3940 GAAGCCACAAGCTTGTTTAGTAGGATGTTGAATGGAGGAGTCCAGCCTGATATGGAAACTTT-AA
1 GAAGCAACAACCGTGCTCAATAGAATGATGAATGAAGGAGTACATCCTGATGTAGTAACTTTCAA
* * * * * * *
4004 GATCTTTAATCAATGCTTTGTACAAGGAAAACAAGTA-TGAAGAAGCCATTAGCATGTTGGAACT
66 -TTCTTTAATCAATGCCTTATGCAAGGAAAA-GAGGACTGAAGAAGCCATTACCATGTTGGAACT
* *
4068 AATGAGTCAGAGAAATGTAATACCTGACATTGTCAC
129 AATGAGTCAGAGAAATGTAAAACCTAACATTGTCAC
4104 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:4165 original size:210 final size:206
Alignment explanation
Indices: 3796--4371 Score: 636
Period size: 210 Copynumber: 2.8 Consensus size: 206
3786 AACTTTCAAT
* * *
3796 TCTTTAATCAATGCCTTATGCAAGGAAAAGAGGACTGAAGAAGCCATTACCATGTTGGAACTAAT
1 TCTTTAATCAATGCTTTGTGCAAGGAAAA-AAGACTGAAGAAGCCATTACCATGTTGGAACTAAT
** *
3861 GAGTCAGAGAGGTGTAAAACCTGACATTGTGACCTACAATTGTTTAATACGTGGATTGTGCAATT
65 GAGTCAGAGAAATGTAAAACCTGACATTGTCACCTACAATTGTTTAATACGTGGATTGTGCAATT
*
3926 CAGATAAACGTGCAGAAGCCACAAGCTTGTTTAGTAGGATGTTGAATGGAGGAGTCCAGCCTGAT
130 CAGATAAACGTGCAGAAGCCACAAGCTTGTATAGTAGGATGTTGAAT---GGAGTCCAGCCTGAT
*
3991 ATGGAAACTTTAAGA
192 ATGGAAACCTTAAGA
* *
4006 TCTTTAATCAATGCTTTGTACAAGGAAAACAAGTA-TGAAGAAGCCATTAGCATGTTGGAACTAA
1 TCTTTAATCAATGCTTTGTGCAAGGAAAA-AAG-ACTGAAGAAGCCATTACCATGTTGGAACTAA
* ** * * *
4070 TGAGTCAGAGAAATGTAATACCTGACATTGTCACCTACTGCTT-TTTAATACTTGGATTGTGGAG
64 TGAGTCAGAGAAATGTAAAACCTGACATTGTCACCTAC-AATTGTTTAATACGTGGATTGTGCAA
* * ** ** * *
4134 TTTAGGTAATTGTGCAGAAGTGACTAGCTTGTATAGTAGGATGTTGAATGGAGTCCAGCCTGATG
128 TTCAGATAAACGTGCAGAAGCCACAAGCTTGTATAGTAGGATGTTGAATGGAGTCCAGCCTGATA
*
4199 TGGAAACCTTAAGC
193 TGGAAACCTTAAGA
* * * *** *
4213 TCTTTAATCAATGCTTTGTGCAAAGAAAAAAAGATTGAAGAAGCCATTACCTTGTACAAATTAAT
1 TCTTTAATCAATGCTTTGTGC-AAGGAAAAAAGACTGAAGAAGCCATTACCATGTTGGAACTAAT
* * * * * * * * * *
4278 GATTCAGAGAGATCTGAAACCAGACATCGTCACCTACAGTTGTTTAATACATGGATTATGCAAAT
65 GAGTCAGAGAAATGTAAAACCTGACATTGTCACCTACAATTGTTTAATACGTGGATTGTGCAATT
* * * *
4343 CAGGA-CAATGTGGAGAAGCAACAAGCTTG
130 CA-GATAAACGTGCAGAAGCCACAAGCTTG
4372 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:4312 original size:207 final size:206
Alignment explanation
Indices: 3796--4371 Score: 638
Period size: 207 Copynumber: 2.8 Consensus size: 206
3786 AACTTTCAAT
* * * * *
3796 TCTTTAATCAATGCCTTATGCAAGGAAAAGAGGACTGAAGAAGCCATTACCATGTTGGAACTAAT
1 TCTTTAATCAATGCTTTGTGCAAGGAAAAAAAGATTGAAGAAGCCATTACCATGTTGGAACTAAT
* * * *
3861 GAGTCAGAGAGGTGTAAAACCTGACATTGTGACCTACAATTGTTTAATACGTGGATTGTGCAATT
66 GAGTCAGAGAGATGT-AAACCTGACATTGTCACCTAC-GTTGTTTAATACATGGATTGTGCAATT
*
3926 CAGATAAACGTGCAGAAGCCACAAGCTTGTTTAGTAGGATGTTGAATGGAGGAGTCCAGCCTGAT
129 CAGATAAACGTGCAGAAGCCACAAGCTTGTATAGTAGGATGTTGAAT-G-GGAGTCCAGCCTGAT
*
3991 ATGGAAACTTTAAGA
192 ATGGAAACCTTAAGA
* * *
4006 TCTTTAATCAATGCTTTGTACAAGGAAAACAAG-TATGAAGAAGCCATTAGCATGTTGGAACTAA
1 TCTTTAATCAATGCTTTGTGCAAGGAAAAAAAGAT-TGAAGAAGCCATTACCATGTTGGAACTAA
* * * *
4070 TGAGTCAGAGAAATGTAATACCTGACATTGTCACCTACTGCTT-TTTAATACTTGGATTGTGGAG
65 TGAGTCAGAGAGATGTAA-ACCTGACATTGTCACCTAC-G-TTGTTTAATACATGGATTGTGCAA
* * ** ** *
4134 TTTAGGTAATTGTGCAGAAGTGACTAGCTTGTATAGTAGGATGTTGAAT-GGAGTCCAGCCTGAT
127 TTCAGATAAACGTGCAGAAGCCACAAGCTTGTATAGTAGGATGTTGAATGGGAGTCCAGCCTGAT
* *
4198 GTGGAAACCTTAAGC
192 ATGGAAACCTTAAGA
* * *** *
4213 TCTTTAATCAATGCTTTGTGCAAAGAAAAAAAGATTGAAGAAGCCATTACCTTGTACAAATTAAT
1 TCTTTAATCAATGCTTTGTGCAAGGAAAAAAAGATTGAAGAAGCCATTACCATGTTGGAACTAAT
* * * * * *
4278 GATTCAGAGAGATCTGAAACCAGACATCGTCACCTACAGTTGTTTAATACATGGATTATGCAAAT
66 GAGTCAGAGAGATGT-AAACCTGACATTGTCACCTAC-GTTGTTTAATACATGGATTGTGCAATT
* * * *
4343 CAGGA-CAATGTGGAGAAGCAACAAGCTTG
129 CA-GATAAACGTGCAGAAGCCACAAGCTTG
4372 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:4552 original size:38 final size:38
Alignment explanation
Indices: 4510--4587 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
4500 CGTGAAGCCG
*
4510 AATGAATTTACTTACAGGATAATGATTGAAGAAGTGTA
1 AATGAATTTACTTACAGGATAATGATCGAAGAAGTGTA
* *
4548 AATGAATTTACTTACAGGGTAATGATCGAAGAGGTGTA
1 AATGAATTTACTTACAGGATAATGATCGAAGAAGTGTA
4586 AA
1 AA
4588 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.