Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g01296.P2
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: 12747
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Found at i:1914 original size:14 final size:13
Alignment explanation
Indices: 1889--1943 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
1879 TGTAGGTGTC
1889 TGAAAAAA-AAAA
1 TGAAAAAATAAAA
1901 TGAAAAAATCAAAA
1 TGAAAAAAT-AAAA
1915 T-AAATCAAATAAAA
1 TGAAA--AAATAAAA
*
1929 TTAAAAAATTAAAA
1 TGAAAAAA-TAAAA
1943 T
1 T
1944 TTTTCCGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
12 8 0.22
13 6 0.16
14 16 0.43
15 7 0.19
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (13 bp):
TGAAAAAATAAAA
Found at i:6077 original size:37 final size:37
Alignment explanation
Indices: 6027--6117 Score: 164
Period size: 37 Copynumber: 2.4 Consensus size: 37
6017 TTATTACGAA
6027 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
6064 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
6101 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
6118 TTTCCAAGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 47 0.90
38 5 0.10
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:6215 original size:48 final size:48
Alignment explanation
Indices: 6157--6356 Score: 373
Period size: 48 Copynumber: 4.2 Consensus size: 48
6147 TGTTACAACA
*
6157 TTCACATTAGCCATTCGGCTTTACCACACATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
6205 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
6253 TTCACATTAGCCCTTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
6301 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATGT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
6349 TTCACATT
1 TTCACATT
6357 CATCGCATCG
Statistics
Matches: 148, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 148 1.00
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.34
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
Found at i:6448 original size:96 final size:97
Alignment explanation
Indices: 6348--6587 Score: 383
Period size: 96 Copynumber: 2.5 Consensus size: 97
6338 CACACATATG
* *
6348 TTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
*
6413 TCGGCCATTAGGCCTTATCAC-ATATATACTC
66 TCGGCCATTAGGCCTTATCACAATATATACAC
* *
6444 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATGTATATACACTTTCACATTCATCACA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
*
6509 TTGGCCATTAGGCCTTATCACATATATATATACAC
66 TCGGCCATTAGGCCTTATCAC--A-ATATATACAC
*
6544 TTTCACATTCATCACATTGGCCATTAGGCCGTATCACATATATA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
6588 CATCTCATAC
Statistics
Matches: 132, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
96 81 0.61
100 51 0.39
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.34
Consensus pattern (97 bp):
TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
TCGGCCATTAGGCCTTATCACAATATATACAC
Found at i:6560 original size:51 final size:49
Alignment explanation
Indices: 6348--6587 Score: 385
Period size: 49 Copynumber: 4.9 Consensus size: 49
6338 CACACATATG
* *
6348 TTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
* * *
6397 CTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACTC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
*
6444 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATGTATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
6493 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATATATACAC
*
6544 TTTCACATTCATCACATTGGCCATTAGGCCGTATCACATATATA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
6588 CATCTCATAC
Statistics
Matches: 178, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
47 44 0.25
49 87 0.49
51 47 0.26
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.34
Consensus pattern (49 bp):
TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
Found at i:10123 original size:22 final size:23
Alignment explanation
Indices: 10096--10141 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
10086 TTAGATTAGT
*
10096 GAAATTAAAA-TAAAATTAAAAA
1 GAAATTAAAAGAAAAATTAAAAA
10118 GAAATTAAAAGGAAAAATTAAAAA
1 GAAATTAAAA-GAAAAATTAAAAA
10142 TTTTGTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
24 11 0.52
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.20
Consensus pattern (23 bp):
GAAATTAAAAGAAAAATTAAAAA
Done.