Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023426.1 Corchorus olitorius cultivar O-4 contig23459, 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: 19075
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:1433 original size:23 final size:23
Alignment explanation
Indices: 1387--1433 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1377 AACTATCTAC
* * *
1387 TGATTACTTTTTCTTTAGTTTTT
1 TGATTACTCTTTCTTTACTCTTT
1410 TGATTACTCTTTCTTTACTCTTT
1 TGATTACTCTTTCTTTACTCTTT
1433 T
1 T
1434 TAGTTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.15, G:0.06, T:0.66
Consensus pattern (23 bp):
TGATTACTCTTTCTTTACTCTTT
Found at i:1442 original size:78 final size:79
Alignment explanation
Indices: 1333--1482 Score: 223
Period size: 78 Copynumber: 1.9 Consensus size: 79
1323 AGTCAATTAC
* *
1333 TGATTACTATTTTTAACTCTTTTTAGCTTAATTATTC-TGAATTAAACT-ATCTACTGATTACTT
1 TGATTACTATTTTTAACTCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTACTGATTACTA
1396 TTTCTTTAGTTTTT
66 TTTCTTTAGTTTTT
* * * *
1410 TGATTACTCTTTCTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTACTGCTTACT
1 TGATTACTATTT-TTAACTCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTACTGATTACT
1475 ATTTCTTT
65 ATTTCTTT
1483 TACTTCTTAG
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
77 11 0.17
78 22 0.34
79 11 0.17
80 20 0.31
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.55
Consensus pattern (79 bp):
TGATTACTATTTTTAACTCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTACTGATTACTA
TTTCTTTAGTTTTT
Found at i:1482 original size:57 final size:57
Alignment explanation
Indices: 1412--1779 Score: 336
Period size: 57 Copynumber: 6.5 Consensus size: 57
1402 TAGTTTTTTG
* *
1412 ATTACTCTTTCTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTACTG
1 ATTACTCTTTCTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTA
* * * *
1469 CTTACTATTTCTTT--TACTTCTTAGCTTAATTACTCTTGAATTAAACTAATCTTCT-
1 ATTACTCTTTCTTTACT-CTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTA
*
1524 A--A--------TTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTATTCTTCTA
1 ATTACTCTTTCTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTA
* *
1571 ATTACTCTTTCTTTCACTCTTTTTAGTTTAATTATTC-TGAATTAAACTATTCTTCTA
1 ATTACTCTTTCTTT-ACTCTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTA
* * ** **
1628 ATTACTCTTTCACTTACTCTTTTTAGTTTAATTACTTCTACT-ACTTACTCTTTCTTTCCCTTCT
1 ATTACTCTTTC-TTTACTCTTTTTAGTTTAATTAC-TCT--TGAATTAAAC--T-AAT--CTTCT
1692 A
57 A
* *
1693 ATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACT-TCTAAATTAAACTAATCTTCTG
1 ATTACTCTTTC-TTTACTCTTTTTAGTTTAATTACTCT-TGAATTAAACTAATCTTCTA
*
1751 ATTGCTCTTTCTTTTACTCTTTTTAGTTT
1 ATTACTCTTTC-TTTACTCTTTTTAGTTT
1780 TATCACTTCT
Statistics
Matches: 260, Mismatches: 25, Indels: 51
0.77 0.07 0.15
Matches are distributed among these distances:
45 2 0.01
46 36 0.14
47 2 0.01
49 1 0.00
53 1 0.00
55 1 0.00
56 36 0.14
57 64 0.25
58 58 0.22
60 6 0.02
61 2 0.01
62 3 0.01
63 8 0.03
64 1 0.00
65 39 0.15
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.54
Consensus pattern (57 bp):
ATTACTCTTTCTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTA
Found at i:1544 original size:46 final size:46
Alignment explanation
Indices: 1489--1580 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
1479 CTTTTACTTC
1489 TTAGCTTAATTACTCTTGAATTAAACTAATCTTCTAATTACTCTTT
1 TTAGCTTAATTACTCTTGAATTAAACTAATCTTCTAATTACTCTTT
* *
1535 TTAGTTTAATTACTCTTGAATTAAACTATTCTTCTAATTACTCTTT
1 TTAGCTTAATTACTCTTGAATTAAACTAATCTTCTAATTACTCTTT
1581 CTTTCACTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.50
Consensus pattern (46 bp):
TTAGCTTAATTACTCTTGAATTAAACTAATCTTCTAATTACTCTTT
Found at i:1788 original size:58 final size:58
Alignment explanation
Indices: 1526--1790 Score: 318
Period size: 58 Copynumber: 4.5 Consensus size: 58
1516 AATCTTCTAA
*
1526 TTACTCTTTTTAGTTTAATTAC-TCTTGAATTAAACTATTCTTCTAATTACTCTTTCTT
1 TTACTCTTTTTAGTTTAATTACTTC-TAAATTAAACTATTCTTCTAATTACTCTTTCTT
* * **
1584 TCACTCTTTTTAGTTTAATTA-TTCTGAATTAAACTATTCTTCTAATTACTCTTTCAC
1 TTACTCTTTTTAGTTTAATTACTTCTAAATTAAACTATTCTTCTAATTACTCTTTCTT
* ** *
1641 TTACTCTTTTTAGTTTAATTACTTCTACTACTTACTCTTTCTTTCCCTTCTAATTACTCTTTCTT
1 TTACTCTTTTTAGTTTAATTACTTCTA--AATTAAAC--T-ATT--CTTCTAATTACTCTTTCTT
* * *
1706 TTACTCTTTTTAGTTTAATTACTTCTAAATTAAACTAATCTTCTGATTGCTCTTTCTT
1 TTACTCTTTTTAGTTTAATTACTTCTAAATTAAACTATTCTTCTAATTACTCTTTCTT
* *
1764 TTACTCTTTTTAGTTTTATCACTTCTA
1 TTACTCTTTTTAGTTTAATTACTTCTA
1791 CTGCTTACTT
Statistics
Matches: 178, Mismatches: 20, Indels: 18
0.82 0.09 0.08
Matches are distributed among these distances:
57 51 0.29
58 68 0.38
60 6 0.03
61 1 0.01
62 1 0.01
63 7 0.04
65 44 0.25
ACGTcount: A:0.22, C:0.20, G:0.03, T:0.55
Consensus pattern (58 bp):
TTACTCTTTTTAGTTTAATTACTTCTAAATTAAACTATTCTTCTAATTACTCTTTCTT
Found at i:1788 original size:123 final size:122
Alignment explanation
Indices: 1565--1807 Score: 378
Period size: 123 Copynumber: 2.0 Consensus size: 122
1555 TTAAACTATT
* *
1565 CTTCTAATTACTCTTTCTTTCACTCTTTTTAGTTTAATTATTCTGAATTAAACTATTCTTCTAAT
1 CTTCTAATTACTCTTTCTTTCACTCTTTTTAGTTTAATTATTCTAAATTAAACTAATCTTCTAAT
*
1630 TACTCTTTCACTTACTCTTTTTAGTTTAATTACTTCTACTACTTACTCTTTCTTTCC
66 TACTCTTTCACTTACTCTTTTTAGTTTAATCACTTCTACTACTTACTCTTTCTTTCC
* *
1687 CTTCTAATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTTCTAAATTAAACTAATCTTCTGA
1 CTTCTAATTACTCTTTCTTTCACTCTTTTTAGTTTAATTA-TTCTAAATTAAACTAATCTTCTAA
* ** * * *
1752 TTGCTCTTTCTTTTACTCTTTTTAGTTTTATCACTTCTACTGCTTACTTTTTCTTT
65 TTACTCTTTCACTTACTCTTTTTAGTTTAATCACTTCTACTACTTACTCTTTCTTT
1808 TACTTGTTAG
Statistics
Matches: 109, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
122 39 0.36
123 70 0.64
ACGTcount: A:0.20, C:0.21, G:0.03, T:0.56
Consensus pattern (122 bp):
CTTCTAATTACTCTTTCTTTCACTCTTTTTAGTTTAATTATTCTAAATTAAACTAATCTTCTAAT
TACTCTTTCACTTACTCTTTTTAGTTTAATCACTTCTACTACTTACTCTTTCTTTCC
Found at i:4032 original size:2 final size:2
Alignment explanation
Indices: 4025--4059 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4015 ATACATACAT
*
4025 AC AC AC AC AC AC AC AC AC TC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
4060 GATATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.49, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:8074 original size:14 final size:15
Alignment explanation
Indices: 8055--8091 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
8045 ATTAACAATC
8055 TTTTCTCTACATCT-
1 TTTTCTCTACATCTA
*
8069 TTTTCTCTTCATCTA
1 TTTTCTCTACATCTA
8084 TTTT-TCTA
1 TTTTCTCTA
8092 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTCTCTACATCTA
Found at i:9173 original size:5 final size:6
Alignment explanation
Indices: 9158--9182 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9148 TATTTTCCGT
9158 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
9183 CTAAGAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Done.