Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga12g00891.N1
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, 983
Length: 1639
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Found at i:1309 original size:22 final size:22
Alignment explanation
Indices: 1281--1328 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
1271 GGTTAGGGTA
*
1281 GGTTAGGGTTTTTATGGTTTAG
1 GGTTAGGGTTTTTAGGGTTTAG
* *
1303 GGTTAGGTTTTTTAGGGTTTAT
1 GGTTAGGGTTTTTAGGGTTTAG
1325 GGTT
1 GGTT
1329 TTTGTAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.52
Consensus pattern (22 bp):
GGTTAGGGTTTTTAGGGTTTAG
Found at i:1340 original size:19 final size:17
Alignment explanation
Indices: 1298--1342 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
1288 GTTTTTATGG
1298 TTTAGGG-TTA-GGTTT
1 TTTAGGGTTTATGGTTT
1313 TTTAGGGTTTATGGTTT
1 TTTAGGGTTTATGGTTT
1330 TTGTAAGGGTTTA
1 TT-T-AGGGTTTA
1343 ATTAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.27
16 3 0.12
17 7 0.27
18 1 0.04
19 8 0.31
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (17 bp):
TTTAGGGTTTATGGTTT
Found at i:1374 original size:4 final size:4
Alignment explanation
Indices: 1365--1432 Score: 52
Period size: 4 Copynumber: 17.2 Consensus size: 4
1355 AGGGTGTAAG
* * *
1365 ATTA ATTA ATTAA ATTA AAT- ATTA ATTA A-AA ATTA ATTAA ATTA AAT-
1 ATTA ATTA ATT-A ATTA ATTA ATTA ATTA ATTA ATTA ATT-A ATTA ATTA
**
1412 ATTA ATTA AAAA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA A
1433 ATTCGGGTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
3 6 0.12
4 35 0.71
5 8 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (4 bp):
ATTA
Found at i:1390 original size:16 final size:16
Alignment explanation
Indices: 1369--1421 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
1359 TGTAAGATTA
1369 ATTAATTAAATTAAAT
1 ATTAATTAAATTAAAT
1385 ATTAATT--A--AAA-
1 ATTAATTAAATTAAAT
1396 ATTAATTAAATTAAAT
1 ATTAATTAAATTAAAT
1412 ATTAATTAAA
1 ATTAATTAAA
1422 AAATTAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
11 7 0.22
12 3 0.09
13 1 0.03
14 1 0.03
15 3 0.09
16 17 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTAATTAAATTAAAT
Found at i:1406 original size:27 final size:28
Alignment explanation
Indices: 1368--1435 Score: 129
Period size: 27 Copynumber: 2.5 Consensus size: 28
1358 GTGTAAGATT
1368 AATTAATTAAATTAAATATTAATT-AAA
1 AATTAATTAAATTAAATATTAATTAAAA
1395 AATTAATTAAATTAAATATTAATTAAAA
1 AATTAATTAAATTAAATATTAATTAAAA
1423 AATTAATTAAATT
1 AATTAATTAAATT
1436 CGGGTTTAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 24 0.60
28 16 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
AATTAATTAAATTAAATATTAATTAAAA
Found at i:1431 original size:16 final size:15
Alignment explanation
Indices: 1365--1432 Score: 63
Period size: 16 Copynumber: 4.6 Consensus size: 15
1355 AGGGTGTAAG
1365 ATTAATTAATTAAATTA
1 ATTAATTAATTAAA--A
*
1382 AAT-ATTAATTAAAA
1 ATTAATTAATTAAAA
*
1396 ATTAATTAAATTAAAT
1 ATTAATT-AATTAAAA
1412 ATTAATT-A--AAAA
1 ATTAATTAATTAAAA
1424 ATTAATTAA
1 ATTAATTAA
1433 ATTCGGGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
12 10 0.23
13 1 0.02
14 4 0.09
15 3 0.07
16 24 0.55
17 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAATTAATTAAAA
Done.