Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014086.1 Corchorus capsularis cultivar CVL-1 contig14107, 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: 8209
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Found at i:1274 original size:21 final size:22
Alignment explanation
Indices: 1229--1347 Score: 83
Period size: 21 Copynumber: 5.5 Consensus size: 22
1219 TTTACTGAAT
* *
1229 TACTGATTACAATCATTA-TTT-
1 TACTGATTAC-TTCTTTACTTTG
1250 TACTGATTA-TTCTTTACTTTG
1 TACTGATTACTTCTTTACTTTG
1271 TACTGATTACTAT-TTTACTCTTG
1 TACTGATTACT-TCTTTACT-TTG
*
1294 T--TGATTACCTTC-TTACTTTT
1 TACTGATTA-CTTCTTTACTTTG
* *
1314 TACTGATTACCAT-TTTACTCTTT
1 TACTGATTA-CTTCTTTACT-TTG
1337 TACTGATTACT
1 TACTGATTACT
1348 ATTTTCTGCT
Statistics
Matches: 82, Mismatches: 5, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
19 5 0.06
20 6 0.07
21 30 0.37
22 24 0.29
23 17 0.21
ACGTcount: A:0.23, C:0.18, G:0.07, T:0.53
Consensus pattern (22 bp):
TACTGATTACTTCTTTACTTTG
Found at i:1346 original size:15 final size:15
Alignment explanation
Indices: 1328--1383 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
1318 GATTACCATT
1328 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
1343 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
1356 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
1371 TTACTCTTTTACT
1 TTACTCTTTTACT
1384 TCTTACTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 7 0.22
14 6 0.19
15 19 0.59
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:1459 original size:21 final size:21
Alignment explanation
Indices: 1364--1494 Score: 87
Period size: 21 Copynumber: 6.5 Consensus size: 21
1354 TGCTCCTTTT
*
1364 TTACTGATTACTCTTTTACTTC
1 TTACTGATTACTATTTTAC-TC
*
1386 TTACTGATTACTATTTGACTC
1 TTACTGATTACTATTTTACTC
* * * * *
1407 TTATTAATTACCACTTTGCTC
1 TTACTGATTACTATTTTACTC
* * *
1428 TCACTGGTTACTGTTTTACTC
1 TTACTGATTACTATTTTACTC
*
1449 TTAATGATTAC----TT--TC
1 TTACTGATTACTATTTTACTC
*
1464 -TACTGATTACTATTTTACCTT
1 TTACTGATTACTATTTTA-CTC
1485 TTACTGATTA
1 TTACTGATTA
1495 TCATTACTTT
Statistics
Matches: 80, Mismatches: 21, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
14 9 0.11
15 2 0.03
17 2 0.03
18 2 0.03
21 39 0.49
22 26 0.32
ACGTcount: A:0.22, C:0.20, G:0.08, T:0.50
Consensus pattern (21 bp):
TTACTGATTACTATTTTACTC
Found at i:1600 original size:35 final size:34
Alignment explanation
Indices: 1559--1647 Score: 115
Period size: 35 Copynumber: 2.6 Consensus size: 34
1549 TTACTTTTTG
* *
1559 CTGATTACCCTTTACTCTTTACCGTTCTTCCTTTA
1 CTGATTACTCTTTACT-TTTACCATTCTTCCTTTA
* * *
1594 CTGATTATTCTTTACGTTTTACCATTCTTCTTTTG
1 CTGATTACTCTTTAC-TTTTACCATTCTTCCTTTA
1629 CTGATTACTCTTTACTTTT
1 CTGATTACTCTTTACTTTT
1648 TTATCATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 4 0.09
35 42 0.89
36 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.07, T:0.54
Consensus pattern (34 bp):
CTGATTACTCTTTACTTTTACCATTCTTCCTTTA
Found at i:1675 original size:14 final size:14
Alignment explanation
Indices: 1656--1695 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1646 TTTTATCATT
1656 TTACTCTTTACTAA
1 TTACTCTTTACTAA
* *
1670 TTACTCCTTACTGA
1 TTACTCTTTACTAA
*
1684 TTATTCTTTACT
1 TTACTCTTTACT
1696 CTTTACCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.53
Consensus pattern (14 bp):
TTACTCTTTACTAA
Found at i:2092 original size:47 final size:47
Alignment explanation
Indices: 1931--2182 Score: 427
Period size: 47 Copynumber: 5.4 Consensus size: 47
1921 TTTTACTTGA
* * **
1931 TTACTGATTTACTGATTACTATTA-TCTTGACTTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACT-TTGAC-TCCGATTAATCTCTTT
1979 TTACTGATTTACTGATTACCATCACTTTGACTCCGATTAATCTC-TT
1 TTACTGATTTACTGATTACCATCACTTTGACTCCGATTAATCTCTTT
*
2025 TTACTGATTTACTGATTACCATCACTTTAACTCCGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTCCGATTAATCTCTTT
2072 TTACTGATTTACTGATTACCATCACTTTGACTCCGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTCCGATTAATCTCTTT
2119 TTACTGATTTACTGATTACCATCACTTTGACTCCGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTCCGATTAATCTCTTT
2166 TTACTGATTTACTGATT
1 TTACTGATTTACTGATT
2183 TTCTTTTTAC
Statistics
Matches: 196, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
46 45 0.23
47 123 0.63
48 27 0.14
49 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.47
Consensus pattern (47 bp):
TTACTGATTTACTGATTACCATCACTTTGACTCCGATTAATCTCTTT
Found at i:2972 original size:50 final size:50
Alignment explanation
Indices: 2908--3010 Score: 161
Period size: 50 Copynumber: 2.1 Consensus size: 50
2898 AAGGTGACAT
*
2908 TTTATCTACTAATTACTTAAAAATTCAATCTTTCATTCAAAGGTTAAAGC
1 TTTATCTACCAATTACTTAAAAATTCAATCTTTCATTCAAAGGTTAAAGC
* * * *
2958 TTTATTTACCAATTATTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
1 TTTATCTACCAATTACTTAAAAATTCAATCTTTCATTCAAAGGTTAAAGC
3008 TTT
1 TTT
3011 TAGTCAAATG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.45
Consensus pattern (50 bp):
TTTATCTACCAATTACTTAAAAATTCAATCTTTCATTCAAAGGTTAAAGC
Found at i:3039 original size:20 final size:20
Alignment explanation
Indices: 2984--3039 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2974 TTAAAAATTC
* *
2984 AATCTTTTATTCAAAGGTTA
1 AATCTTTTAGTCAAATGTTA
3004 AATCTTTTAGTCAAATGTTA
1 AATCTTTTAGTCAAATGTTA
* *
3024 CATCTTTTAGCCAAAT
1 AATCTTTTAGTCAAAT
3040 ATCCTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (20 bp):
AATCTTTTAGTCAAATGTTA
Found at i:5715 original size:27 final size:27
Alignment explanation
Indices: 5677--5743 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
5667 TTAAAAAAAT
* *
5677 AAATGACTAAAATGCCCCTGAGTGCCA
1 AAATGACCAAAATGCCCCTGAGTGCAA
*
5704 AAATGACCAAAATGCCCCTGGGTGCAA
1 AAATGACCAAAATGCCCCTGAGTGCAA
5731 AAATGACCAAAAT
1 AAATGACCAAAAT
5744 ACCCTTAGGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAGTGCAA
Done.