Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g03617.F6
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: 4151
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Found at i:957 original size:24 final size:24
Alignment explanation
Indices: 924--1109 Score: 219
Period size: 24 Copynumber: 7.8 Consensus size: 24
914 TTTTGGTTCC
* * *
924 AGTACTCCTGCCTTCGGTGCCACG
1 AGTACCCCTGCCTTTGGTGCCACA
* *
948 AGCACCCCTGCTTTTGGTGCCACA
1 AGTACCCCTGCCTTTGGTGCCACA
*
972 AGTACCCCTGCCTTTGGTGCCACG
1 AGTACCCCTGCCTTTGGTGCCACA
* *
996 AGTGCCCCTGCTTTTGGTGCCACA
1 AGTACCCCTGCCTTTGGTGCCACA
* * *
1020 AGTGCCCCTGCTTTTGGTGGCACA
1 AGTACCCCTGCCTTTGGTGCCACA
* **
1044 AGTACCCCTGCCTTTGGTTCCATG
1 AGTACCCCTGCCTTTGGTGCCACA
* *
1068 AGTACTCCAGCCTTTGGTGCCACA
1 AGTACCCCTGCCTTTGGTGCCACA
*
1092 AGCACCCCTGCCTTTGGT
1 AGTACCCCTGCCTTTGGT
1110 TCAACTGGAA
Statistics
Matches: 136, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 136 1.00
ACGTcount: A:0.14, C:0.35, G:0.24, T:0.27
Consensus pattern (24 bp):
AGTACCCCTGCCTTTGGTGCCACA
Found at i:1028 original size:72 final size:72
Alignment explanation
Indices: 924--1109 Score: 246
Period size: 72 Copynumber: 2.6 Consensus size: 72
914 TTTTGGTTCC
* * * *
924 AGTACTCCTGCCTTCGGTGCCACGAGCACCCCTGCTTTTGGTGCCACAAGTACCCCTGCCTTTGG
1 AGTACCCCAGCCTTTGGTGCCACAAGCACCCCTGCTTTTGGTGCCACAAGTACCCCTGCCTTTGG
989 TGCCACG
66 TGCCACG
* * * ** *
996 AGTGCCCCTGCTTTTGGTGCCACAAGTGCCCCTGCTTTTGGTGGCACAAGTACCCCTGCCTTTGG
1 AGTACCCCAGCCTTTGGTGCCACAAGCACCCCTGCTTTTGGTGCCACAAGTACCCCTGCCTTTGG
* *
1061 TTCCATG
66 TGCCACG
* *
1068 AGTACTCCAGCCTTTGGTGCCACAAGCACCCCTGCCTTTGGT
1 AGTACCCCAGCCTTTGGTGCCACAAGCACCCCTGCTTTTGGT
1110 TCAACTGGAA
Statistics
Matches: 97, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 97 1.00
ACGTcount: A:0.14, C:0.35, G:0.24, T:0.27
Consensus pattern (72 bp):
AGTACCCCAGCCTTTGGTGCCACAAGCACCCCTGCTTTTGGTGCCACAAGTACCCCTGCCTTTGG
TGCCACG
Found at i:1125 original size:48 final size:48
Alignment explanation
Indices: 1032--1132 Score: 132
Period size: 48 Copynumber: 2.1 Consensus size: 48
1022 TGCCCCTGCT
* * * * *
1032 TTTGGTGGCACAAGTACCCCTGCCTTTGGTTCCATGAGTACTCCAGCC
1 TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAATGAGAACTCCAGCA
*
1080 TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAACTG-GAAGTCCAGCA
1 TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAA-TGAGAACTCCAGCA
1128 TTTGG
1 TTTGG
1133 GAGCACTGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 44 0.96
49 2 0.04
ACGTcount: A:0.18, C:0.30, G:0.24, T:0.29
Consensus pattern (48 bp):
TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAATGAGAACTCCAGCA
Found at i:1230 original size:24 final size:24
Alignment explanation
Indices: 1203--1267 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
1193 TGGAGCATCA
*
1203 AGCACACCTGCTTTTGGCACTTCC
1 AGCACTCCTGCTTTTGGCACTTCC
* *** *
1227 AGCACTCCTGCATTTGGGGGTTCG
1 AGCACTCCTGCTTTTGGCACTTCC
1251 AGCACTCCTGCTTTTGG
1 AGCACTCCTGCTTTTGG
1268 AGCATCTTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.14, C:0.31, G:0.25, T:0.31
Consensus pattern (24 bp):
AGCACTCCTGCTTTTGGCACTTCC
Found at i:1372 original size:24 final size:24
Alignment explanation
Indices: 1334--1438 Score: 147
Period size: 24 Copynumber: 4.4 Consensus size: 24
1324 CATTTGGTAG
* *
1334 CTTTGGTGCCTCAAGCACTCCTGC
1 CTTTGGTTCCACAAGCACTCCTGC
1358 CTTTGGTTCCACAAGCACTCCTGC
1 CTTTGGTTCCACAAGCACTCCTGC
*
1382 CTTTGGTTCCACAAGCACCCCTGC
1 CTTTGGTTCCACAAGCACTCCTGC
* * * *
1406 CTTTGGTGCTACCAGCACTCCGGC
1 CTTTGGTTCCACAAGCACTCCTGC
1430 CTTTGGTTC
1 CTTTGGTTC
1439 AACTGGAAGT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.13, C:0.37, G:0.20, T:0.30
Consensus pattern (24 bp):
CTTTGGTTCCACAAGCACTCCTGC
Found at i:1521 original size:327 final size:327
Alignment explanation
Indices: 1008--1627 Score: 889
Period size: 327 Copynumber: 1.9 Consensus size: 327
998 TGCCCCTGCT
** * * * ** *
1008 TTTGGTGCCACAAGTGCCCCTGCTTTTGGTGGCACAAGTACCCCTGCCTTTGGTTCCATGAGTAC
1 TTTGGTGCCACAAGCACCCCTGCCTTTGGTGCCACAAGCACCCCTGCCTTTGGTTCCACAAGCAC
* * *
1073 TCCAGCCTTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAACTGGAAGTCCAGCATTTGGGAGCA
66 CCCAGCCTTTGGTGCCACAAGCACCCCGGCCTTTGGTTCAACTGGAAGTCCAGCATTCGGGAGCA
** *
1138 CTGGAACTGCATTTGGTGTGTCCAATGCCCCAGTCTTTGGAACAGGTGGCACATTTGGAGCATCA
131 CTGGAACTGCATTTGGCATGTCCAATGCCCCAGTCTTTGGAACAGGAGGCACATTTGGAGCATCA
* * * *** *
1203 AGCACACCTGCTTTTGGCACTTCCAGCACTCCTGCATTTGGGGGTTCGAGCACTCCTGCTTTTGG
196 AGCACACCTGCTTTTGGCACATCAAGCACACCTGCATTTGGCACTTCAAGCACTCCTGCTTTTGG
*
1268 AGCATCTTCAAGTCCATCATTCAGCTTTGGGTCAGCATTTGGGCAGTCAACACCCGCATTTGGTA
261 AGCATCTTCAACTCCATCATTCAGCTTTGGGTCAGCATTTGGGCAGTCAACACCCGCATTTGGTA
1333 GC
326 GC
* * * *
1335 TTTGGTGCCTCAAGCACTCCTGCCTTTGGTTCCACAAGCACTCCTGCCTTTGGTTCCACAAGCAC
1 TTTGGTGCCACAAGCACCCCTGCCTTTGGTGCCACAAGCACCCCTGCCTTTGGTTCCACAAGCAC
* * * *
1400 CCCTGCCTTTGGTGCTACCAGCACTCCGGCCTTTGGTTCAACTGGAAGTCCAGCATTCGGGAGCA
66 CCCAGCCTTTGGTGCCACAAGCACCCCGGCCTTTGGTTCAACTGGAAGTCCAGCATTCGGGAGCA
* * * *
1465 GTGGAACTGCATTTGGCATGTCTAATGCCTCAGTCTTTGGCACAGGAGGCACATTTGGAGCATCA
131 CTGGAACTGCATTTGGCATGTCCAATGCCCCAGTCTTTGGAACAGGAGGCACATTTGGAGCATCA
* *
1530 AGCACACCTGCTTTTGGCACATCAAGCACACCTGCTTTTGGCACTTCAAGCAGTCCTGCTTTTGG
196 AGCACACCTGCTTTTGGCACATCAAGCACACCTGCATTTGGCACTTCAAGCACTCCTGCTTTTGG
* * *
1595 AGCATCTTCTACTCCTTCCTTCAGCTTTGGGTC
261 AGCATCTTCAACTCCATCATTCAGCTTTGGGTC
1628 TAGCCCAACT
Statistics
Matches: 254, Mismatches: 39, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
327 254 1.00
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.29
Consensus pattern (327 bp):
TTTGGTGCCACAAGCACCCCTGCCTTTGGTGCCACAAGCACCCCTGCCTTTGGTTCCACAAGCAC
CCCAGCCTTTGGTGCCACAAGCACCCCGGCCTTTGGTTCAACTGGAAGTCCAGCATTCGGGAGCA
CTGGAACTGCATTTGGCATGTCCAATGCCCCAGTCTTTGGAACAGGAGGCACATTTGGAGCATCA
AGCACACCTGCTTTTGGCACATCAAGCACACCTGCATTTGGCACTTCAAGCACTCCTGCTTTTGG
AGCATCTTCAACTCCATCATTCAGCTTTGGGTCAGCATTTGGGCAGTCAACACCCGCATTTGGTA
GC
Found at i:1546 original size:24 final size:24
Alignment explanation
Indices: 1525--1594 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
1515 ACATTTGGAG
1525 CATCAAGCACACCTGCTTTTGGCA
1 CATCAAGCACACCTGCTTTTGGCA
1549 CATCAAGCACACCTGCTTTTGGCA
1 CATCAAGCACACCTGCTTTTGGCA
* **
1573 CTTCAAGCAGTCCTGCTTTTGG
1 CATCAAGCACACCTGCTTTTGG
1595 AGCATCTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (24 bp):
CATCAAGCACACCTGCTTTTGGCA
Done.