Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g01296.P1
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: 11961
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Found at i:1128 original size:14 final size:13
Alignment explanation
Indices: 1103--1157 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
1093 TGTAGGTGTC
1103 TGAAAAAA-AAAA
1 TGAAAAAATAAAA
1115 TGAAAAAATCAAAA
1 TGAAAAAAT-AAAA
1129 T-AAATCAAATAAAA
1 TGAAA--AAATAAAA
*
1143 TTAAAAAATTAAAA
1 TGAAAAAA-TAAAA
1157 T
1 T
1158 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:5291 original size:37 final size:37
Alignment explanation
Indices: 5241--5331 Score: 164
Period size: 37 Copynumber: 2.4 Consensus size: 37
5231 TTATTACGAA
5241 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
5278 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
5315 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
5332 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:5429 original size:48 final size:48
Alignment explanation
Indices: 5371--5570 Score: 373
Period size: 48 Copynumber: 4.2 Consensus size: 48
5361 TGTTACAACA
*
5371 TTCACATTAGCCATTCGGCTTTACCACACATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
5419 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
5467 TTCACATTAGCCCTTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
5515 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATGT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
5563 TTCACATT
1 TTCACATT
5571 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:5662 original size:96 final size:97
Alignment explanation
Indices: 5562--5801 Score: 383
Period size: 96 Copynumber: 2.5 Consensus size: 97
5552 CACACATATG
* *
5562 TTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
*
5627 TCGGCCATTAGGCCTTATCAC-ATATATACTC
66 TCGGCCATTAGGCCTTATCACAATATATACAC
* *
5658 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATGTATATACACTTTCACATTCATCACA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
*
5723 TTGGCCATTAGGCCTTATCACATATATATATACAC
66 TCGGCCATTAGGCCTTATCAC--A-ATATATACAC
*
5758 TTTCACATTCATCACATTGGCCATTAGGCCGTATCACATATATA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
5802 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:5774 original size:51 final size:49
Alignment explanation
Indices: 5562--5801 Score: 385
Period size: 49 Copynumber: 4.9 Consensus size: 49
5552 CACACATATG
* *
5562 TTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
* * *
5611 CTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACTC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
*
5658 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATGTATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
5707 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATATATACAC
*
5758 TTTCACATTCATCACATTGGCCATTAGGCCGTATCACATATATA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
5802 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:9337 original size:22 final size:23
Alignment explanation
Indices: 9310--9355 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
9300 TTAGATTAGT
*
9310 GAAATTAAAA-TAAAATTAAAAA
1 GAAATTAAAAGAAAAATTAAAAA
9332 GAAATTAAAAGGAAAAATTAAAAA
1 GAAATTAAAA-GAAAAATTAAAAA
9356 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.