Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011477.1 Corchorus capsularis cultivar CVL-1 contig11498, 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: 16788
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 AT AT AT AT 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 AT AT AT AT A
38 GACACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:465 original size:22 final size:22
Alignment explanation
Indices: 440--481 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
430 TAATTTTATT
*
440 TTAATATTT-ATATAGAAAATTG
1 TTAA-ATTTGATATAAAAAATTG
462 TTAAATTTGATATAAAAAAT
1 TTAAATTTGATATAAAAAAT
482 ATCATTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (22 bp):
TTAAATTTGATATAAAAAATTG
Found at i:2068 original size:1 final size:1
Alignment explanation
Indices: 2062--2090 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
2052 GAGACATGGG
2062 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2091 GAGATGAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2417 original size:84 final size:85
Alignment explanation
Indices: 2270--2428 Score: 243
Period size: 84 Copynumber: 1.9 Consensus size: 85
2260 CTACTGCACG
*
2270 AAGTTAATGGAAGATTTGGGGATTTCATGAAAAATAAAATAAAATAGAAACTAGTAAATGGAAGT
1 AAGTTAATAGAAGATTTGGGGATTTCATGAAAAATAAAAT--AATAGAAACTAGTAAATGGAAGT
2335 ACTTAGTAGTACCTACCCGACA
64 ACTTAGTAGTACCTACCCGACA
2357 AAGTTAATAGAAGATTTGGGGATACTTCATGAAAAATAAAAT-A-A-AAACTAGTAAATGGAAGT
1 AAGTTAATAGAAGATTTGGGGAT--TTCATGAAAAATAAAATAATAGAAACTAGTAAATGGAAGT
*
2419 ATTTAGTAGT
64 ACTTAGTAGT
2429 TCTAATTTCC
Statistics
Matches: 68, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
84 27 0.40
85 1 0.01
86 1 0.01
87 22 0.32
89 17 0.25
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (85 bp):
AAGTTAATAGAAGATTTGGGGATTTCATGAAAAATAAAATAATAGAAACTAGTAAATGGAAGTAC
TTAGTAGTACCTACCCGACA
Found at i:4258 original size:27 final size:26
Alignment explanation
Indices: 4227--4307 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 26
4217 CGTTTACTCT
4227 TTTATTGGTACTTTTACCAACAATTTC
1 TTTATTGGTA-TTTTACCAACAATTTC
* **
4254 TTTATT--T-TTATTA-GAA-AAAAT-
1 TTTATTGGTATT-TTACCAACAATTTC
4275 TTTATTGGTAATTTTACCAACAATTTC
1 TTTATTGGT-ATTTTACCAACAATTTC
4302 TTTATT
1 TTTATT
4308 TTTATTAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 16
0.65 0.10 0.26
Matches are distributed among these distances:
21 6 0.15
22 3 0.08
23 5 0.12
24 6 0.15
25 5 0.12
26 3 0.08
27 12 0.30
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (26 bp):
TTTATTGGTATTTTACCAACAATTTC
Found at i:4279 original size:48 final size:48
Alignment explanation
Indices: 4226--4320 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
4216 TCGTTTACTC
*
4226 TTTTATTGGTACTTTTACCAACAATTTCTTTATTTTTATTAGAAAAAA
1 TTTTATTGGTAATTTTACCAACAATTTCTTTATTTTTATTAGAAAAAA
4274 TTTTATTGGTAATTTTACCAACAATTTCTTTATTTTTATTAGAAAAA
1 TTTTATTGGTAATTTTACCAACAATTTCTTTATTTTTATTAGAAAAA
4321 GTTTATCCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (48 bp):
TTTTATTGGTAATTTTACCAACAATTTCTTTATTTTTATTAGAAAAAA
Found at i:5091 original size:12 final size:12
Alignment explanation
Indices: 5074--5099 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5064 GGGCCTTAAA
5074 TCGTAATTTTAT
1 TCGTAATTTTAT
5086 TCGTAATTTTAT
1 TCGTAATTTTAT
5098 TC
1 TC
5100 CAATGTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.58
Consensus pattern (12 bp):
TCGTAATTTTAT
Found at i:6110 original size:2 final size:2
Alignment explanation
Indices: 6103--6127 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6093 TATAATAGTG
6103 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6128 TAAATTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7620 original size:2 final size:2
Alignment explanation
Indices: 7615--7639 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7605 TGTATATATA
7615 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
7640 TCTTTCCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:8554 original size:13 final size:13
Alignment explanation
Indices: 8536--8561 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8526 TTTCTCTTTA
8536 TTTATAAATAAAT
1 TTTATAAATAAAT
8549 TTTATAAATAAAT
1 TTTATAAATAAAT
8562 AAATGGTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATAAATAAAT
Found at i:10079 original size:15 final size:15
Alignment explanation
Indices: 10059--10087 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10049 TCATGATAAT
10059 AATAATTAATAAATC
1 AATAATTAATAAATC
10074 AATAATTAATAAAT
1 AATAATTAATAAAT
10088 GTGGAAAGGG
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:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAATTAATAAATC
Found at i:16184 original size:16 final size:16
Alignment explanation
Indices: 16163--16212 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 16
16153 AACGTTGAAG
16163 TTATAACCTTATTTTT
1 TTATAACCTTATTTTT
16179 TTATAACCTCTATAGTTTTT
1 TTATAA-C-CT-TA-TTTTT
16199 TTAGTAACCTTATT
1 TTA-TAACCTTATT
16213 AGATGTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
16 6 0.21
17 3 0.10
18 4 0.14
19 4 0.14
20 9 0.31
21 3 0.10
ACGTcount: A:0.26, C:0.14, G:0.04, T:0.56
Consensus pattern (16 bp):
TTATAACCTTATTTTT
Done.