Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010060.1 Corchorus capsularis cultivar CVL-1 contig10081, whole genome shotgun sequence
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: 18482
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:64 original size:2 final size:2
Alignment explanation
Indices: 57--85 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47 ATTACTAGTA
57 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
86 AATCCTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1596 original size:18 final size:19
Alignment explanation
Indices: 1566--1611 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
1556 ATATAGCCTC
1566 TGATCAATTGCTA-TAATT
1 TGATCAATTGCTAGTAATT
1584 TGAT-AATTCGCTAGTAA-T
1 TGATCAATT-GCTAGTAATT
*
1602 TGATTAATTG
1 TGATCAATTG
1612 TGGTAGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.16
18 14 0.56
19 7 0.28
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (19 bp):
TGATCAATTGCTAGTAATT
Found at i:2390 original size:6 final size:6
Alignment explanation
Indices: 2381--2447 Score: 79
Period size: 6 Copynumber: 11.7 Consensus size: 6
2371 GAGTGGGAGT
* *
2381 GGGATG GGGATG GGGATG GGGATG GGGACG GGGACG GGGA-G TGGGATG
1 GGGATG GGGATG GGGATG GGGATG GGGATG GGGATG GGGATG -GGGATG
2429 GGGA-- -GGATG GGGATG GGGA
1 GGGATG GGGATG GGGATG GGGA
2448 GGCCGGAGAG
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
3 3 0.05
5 1 0.02
6 50 0.91
7 1 0.02
ACGTcount: A:0.18, C:0.03, G:0.67, T:0.12
Consensus pattern (6 bp):
GGGATG
Found at i:2390 original size:12 final size:13
Alignment explanation
Indices: 2369--2448 Score: 73
Period size: 12 Copynumber: 6.4 Consensus size: 13
2359 GGGGGGGAGT
2369 GGGAGT-GGGA-G
1 GGGAGTGGGGATG
2380 TGGGA-TGGGGATG
1 -GGGAGTGGGGATG
2393 GGGA-TGGGGATG
1 GGGAGTGGGGATG
* *
2405 GGGA-CGGGGACG
1 GGGAGTGGGGATG
2417 GGGAGT-GGGATG
1 GGGAGTGGGGATG
2429 GGGAGGATGGGGATG
1 GGGA-G-TGGGGATG
2444 GGGAG
1 GGGAG
2449 GCCGGAGAGT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
11 1 0.02
12 43 0.74
13 2 0.03
14 2 0.03
15 10 0.17
ACGTcount: A:0.17, C:0.03, G:0.68, T:0.12
Consensus pattern (13 bp):
GGGAGTGGGGATG
Found at i:2390 original size:18 final size:19
Alignment explanation
Indices: 2363--2448 Score: 59
Period size: 18 Copynumber: 4.9 Consensus size: 19
2353 GAGGGTGGGG
2363 GGGAGT-GGGA-GTGGGAGT
1 GGGAGTGGGGATG-GGGAGT
2381 GGGA-TGGGGATGGGGA-T
1 GGGAGTGGGGATGGGGAGT
*
2398 GGG-GATGGGGACGGGGACG-
1 GGGAG-TGGGGATGGGGA-GT
2417 GGGAGT-GGGATGGGGA--
1 GGGAGTGGGGATGGGGAGT
2433 -GGA-TGGGGATGGGGAG
1 GGGAGTGGGGATGGGGAG
2449 GCCGGAGAGT
Statistics
Matches: 57, Mismatches: 2, Indels: 20
0.72 0.03 0.25
Matches are distributed among these distances:
14 1 0.02
15 13 0.23
17 5 0.09
18 32 0.56
19 5 0.09
20 1 0.02
ACGTcount: A:0.17, C:0.02, G:0.67, T:0.13
Consensus pattern (19 bp):
GGGAGTGGGGATGGGGAGT
Found at i:7982 original size:46 final size:46
Alignment explanation
Indices: 7915--8002 Score: 158
Period size: 46 Copynumber: 1.9 Consensus size: 46
7905 GTGTCACTGT
7915 TTTAAGGCATCAATCATGGGATTTATGGTAAGAAAGAAATATCTGA
1 TTTAAGGCATCAATCATGGGATTTATGGTAAGAAAGAAATATCTGA
* *
7961 TTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATAT
1 TTTAAGGCATCAATCATGGGATTTATGGTAAGAAAGAAATAT
8003 TAAGGAAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.31
Consensus pattern (46 bp):
TTTAAGGCATCAATCATGGGATTTATGGTAAGAAAGAAATATCTGA
Done.