Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01721.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: 4217
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Found at i:1142 original size:18 final size:18
Alignment explanation
Indices: 1121--1172 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1111 TTCTAATTCA
1121 ATTTTAATTTCGA-TTCTG
1 ATTTTAATTTCGATTTC-G
* *
1139 ATTTTGATTTTGATTTCG
1 ATTTTAATTTCGATTTCG
*
1157 ATTTTAATTTCAATTT
1 ATTTTAATTTCGATTT
1173 TAAAACACTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 25 0.89
19 3 0.11
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.60
Consensus pattern (18 bp):
ATTTTAATTTCGATTTCG
Found at i:1160 original size:12 final size:12
Alignment explanation
Indices: 1121--1250 Score: 62
Period size: 12 Copynumber: 10.3 Consensus size: 12
1111 TTCTAATTCA
*
1121 ATTTTAATTTCG
1 ATTTTGATTTCG
* *
1133 ATTCTGATTTTG
1 ATTTTGATTTCG
1145 ATTTTGATTTCG
1 ATTTTGATTTCG
* *
1157 ATTTTAATTTCA
1 ATTTTGATTTCG
* **
1169 ATTTTAAAACACTCACTG
1 ATTTT----GA-TTTC-G
*
1187 ATTTTGATTTTG
1 ATTTTGATTTCG
* *
1199 ATTTTGATTCCA
1 ATTTTGATTTCG
*
1211 ATTTTGATCTCG
1 ATTTTGATTTCG
* *
1223 ATTTAGATTTAG
1 ATTTTGATTTCG
* *
1235 AATTTGATTTTG
1 ATTTTGATTTCG
1247 ATTT
1 ATTT
1251 CGATCTGGAT
Statistics
Matches: 84, Mismatches: 28, Indels: 12
0.68 0.23 0.10
Matches are distributed among these distances:
12 74 0.88
13 1 0.01
14 1 0.01
16 1 0.01
17 2 0.02
18 5 0.06
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.54
Consensus pattern (12 bp):
ATTTTGATTTCG
Found at i:1196 original size:6 final size:6
Alignment explanation
Indices: 1185--1250 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
1175 AAACACTCAC
* ** * * *
1185 TGATTT TGATTT TGATTT TGATTC CAATTT TGATCT CGATTT AGATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
* *
1233 AGAATT TGATTT TGATTT
1 TGATTT TGATTT TGATTT
1251 CGATCTGGAT
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.56
Consensus pattern (6 bp):
TGATTT
Found at i:1408 original size:26 final size:26
Alignment explanation
Indices: 1379--1456 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
1369 TATCTGTCAT
1379 TGTATGAATGCATTATCAAACTGATG
1 TGTATGAATGCATTATCAAACTGATG
* ** *
1405 TGTATTG--TGTA-TATC-TGC-CAT-
1 TGTA-TGAATGCATTATCAAACTGATG
1426 TGTATGAATGCATTATCAAACTGATG
1 TGTATGAATGCATTATCAAACTGATG
1452 TGTAT
1 TGTAT
1457 TATGTATATC
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
20 2 0.05
21 4 0.11
22 5 0.14
23 5 0.14
24 5 0.14
25 5 0.14
26 9 0.24
27 2 0.05
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (26 bp):
TGTATGAATGCATTATCAAACTGATG
Found at i:1411 original size:47 final size:47
Alignment explanation
Indices: 1305--1472 Score: 246
Period size: 47 Copynumber: 3.6 Consensus size: 47
1295 GCCATGTGCA
* * * * *
1305 TGATGTTTATTGTTTGTTTCTGCCATTGTATGAATGCTATTATCAAAT
1 TGATGTGTATTGTGTATATCTGCCATTGTATGAATGC-ATTATCAAAC
* *
1353 TGATGCGTATTGTGTATATCTGTCATTGTATGAATGCATTATCAAAC
1 TGATGTGTATTGTGTATATCTGCCATTGTATGAATGCATTATCAAAC
1400 TGATGTGTATTGTGTATATCTGCCATTGTATGAATGCATTATCAAAC
1 TGATGTGTATTGTGTATATCTGCCATTGTATGAATGCATTATCAAAC
* *
1447 TGATGTGTATTATGTATATCTTCCAT
1 TGATGTGTATTGTGTATATCTGCCAT
1473 GATGTTTATT
Statistics
Matches: 109, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
47 78 0.72
48 31 0.28
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.45
Consensus pattern (47 bp):
TGATGTGTATTGTGTATATCTGCCATTGTATGAATGCATTATCAAAC
Found at i:1493 original size:9 final size:9
Alignment explanation
Indices: 1479--1508 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
1469 CCATGATGTT
1479 TATTGTGTA
1 TATTGTGTA
1488 TATTGTGTA
1 TATTGTGTA
1497 TATTGTGTA
1 TATTGTGTA
1506 TAT
1 TAT
1509 CTAGCATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (9 bp):
TATTGTGTA
Found at i:1806 original size:15 final size:15
Alignment explanation
Indices: 1786--1814 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1776 AAAGAAAACA
1786 TGTCTGGTAGTGATG
1 TGTCTGGTAGTGATG
1801 TGTCTGGTAGTGAT
1 TGTCTGGTAGTGAT
1815 AGTGATGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.38, T:0.41
Consensus pattern (15 bp):
TGTCTGGTAGTGATG
Done.