Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012015.1 Corchorus capsularis cultivar CVL-1 contig12036, 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: 30038
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Found at i:7028 original size:23 final size:26
Alignment explanation
Indices: 6980--7031 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
6970 TCCCCTCTAA
6980 TTCACTTATGAGTTAATTCATGCATGT
1 TTCACTTATGAGTTAA-TCATGCATGT
7007 TTCACTTATGAG-T-A-CATGCATGT
1 TTCACTTATGAGTTAATCATGCATGT
7030 TT
1 TT
7032 GGTTTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 11 0.44
25 1 0.04
26 1 0.04
27 12 0.48
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.44
Consensus pattern (26 bp):
TTCACTTATGAGTTAATCATGCATGT
Found at i:7725 original size:22 final size:21
Alignment explanation
Indices: 7697--7739 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
7687 CCTATTGAAC
7697 TGTTTTGACCACTTTTACCACG
1 TGTTTTGACCACTTTT-CCACG
7719 TGTTTTGACCACTTTTCCACG
1 TGTTTTGACCACTTTTCCACG
7740 CCATCTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.16, C:0.28, G:0.14, T:0.42
Consensus pattern (21 bp):
TGTTTTGACCACTTTTCCACG
Found at i:8805 original size:46 final size:46
Alignment explanation
Indices: 8735--8826 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
8725 TTAACAAGTC
* *
8735 TCAAAATTACAATCCAAAAATTCAAGTACAAGAAAAAATGAGACAT
1 TCAAAATCACAATCCAAAAATTCAAGTACAAGAAAAAAGGAGACAT
* * *
8781 TCAAAATCACAATCCAACAGTTCAAGTACAAGAATAAAGGAGACAT
1 TCAAAATCACAATCCAAAAATTCAAGTACAAGAAAAAAGGAGACAT
8827 GAGAATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.18
Consensus pattern (46 bp):
TCAAAATCACAATCCAAAAATTCAAGTACAAGAAAAAAGGAGACAT
Found at i:9373 original size:36 final size:36
Alignment explanation
Indices: 9326--9419 Score: 179
Period size: 36 Copynumber: 2.6 Consensus size: 36
9316 ATTGGACTCT
9326 TAAAACGTCAATTAAATTGGAACAAGATTTTATCTC
1 TAAAACGTCAATTAAATTGGAACAAGATTTTATCTC
9362 TAAAACGTCAATTAAATTGGAACAAGATTTTATCTC
1 TAAAACGTCAATTAAATTGGAACAAGATTTTATCTC
*
9398 TAAAACGTCAATCAAATTGGAA
1 TAAAACGTCAATTAAATTGGAA
9420 TGGAGGGAGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.31
Consensus pattern (36 bp):
TAAAACGTCAATTAAATTGGAACAAGATTTTATCTC
Found at i:12695 original size:22 final size:22
Alignment explanation
Indices: 12644--12768 Score: 71
Period size: 22 Copynumber: 5.7 Consensus size: 22
12634 TGAATATTTT
*
12644 TATGAAATTTTGATAACTAGCC
1 TATGAAATTTTGATAACTAACC
* *
12666 TGTTAAATTTTGATAA-TAACC
1 TATGAAATTTTGATAACTAACC
* * *
12687 ATATGAAATTTTGACAA-TTACT
1 -TATGAAATTTTGATAACTAACC
* **
12709 TATAAAATGGTGATAAACT--CC
1 TATGAAATTTTGAT-AACTAACC
* *
12730 ATAAGAAACTTTGATAACCTAA-C
1 -TATGAAATTTTGATAA-CTAACC
*
12753 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
12769 ACCTTTCTAT
Statistics
Matches: 75, Mismatches: 21, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
21 17 0.23
22 56 0.75
23 2 0.03
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACTAACC
Found at i:20239 original size:18 final size:18
Alignment explanation
Indices: 20218--20276 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
20208 ACATTTTCTA
20218 TTTCCCTCCTTACTCTTT
1 TTTCCCTCCTTACTCTTT
* * * *
20236 TTTCCACGACATT-TTC-TG
1 TTTCC-C-TCCTTACTCTTT
20254 TTTCCCTCCTTACTCTTT
1 TTTCCCTCCTTACTCTTT
20272 TTTCC
1 TTTCC
20277 ACGACATTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
16 3 0.10
17 3 0.10
18 17 0.59
19 3 0.10
20 3 0.10
ACGTcount: A:0.08, C:0.36, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCCCTCCTTACTCTTT
Found at i:20310 original size:38 final size:36
Alignment explanation
Indices: 20201--20311 Score: 168
Period size: 36 Copynumber: 3.0 Consensus size: 36
20191 TTGAATTTCA
*
20201 TTCCACAACATTTTCTATTTCCCTCCTTACTCTTTT
1 TTCCACGACATTTTCTATTTCCCTCCTTACTCTTTT
*
20237 TTCCACGACATTTTCTGTTTCCCTCCTTACTCTTTT
1 TTCCACGACATTTTCTATTTCCCTCCTTACTCTTTT
* *
20273 TTCCACGACATTTTTTTTATTTCCCTCCTTACGCTTTT
1 TTCCACGACA--TTTTCTATTTCCCTCCTTACTCTTTT
20311 T
1 T
20312 CTCAATGTCT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
36 44 0.65
38 24 0.35
ACGTcount: A:0.14, C:0.32, G:0.04, T:0.51
Consensus pattern (36 bp):
TTCCACGACATTTTCTATTTCCCTCCTTACTCTTTT
Found at i:21425 original size:25 final size:25
Alignment explanation
Indices: 21391--21456 Score: 123
Period size: 25 Copynumber: 2.6 Consensus size: 25
21381 TGGTTTAGTC
21391 AACCATATTAGCGTTTGGCCAAAAA
1 AACCATATTAGCGTTTGGCCAAAAA
21416 AACCATATTAGCGTTTGGCCAAAAA
1 AACCATATTAGCGTTTGGCCAAAAA
*
21441 AACCATATTTGCGTTT
1 AACCATATTAGCGTTT
21457 TATTCTGTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (25 bp):
AACCATATTAGCGTTTGGCCAAAAA
Found at i:23016 original size:16 final size:16
Alignment explanation
Indices: 22995--23029 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
22985 TGAATATACT
22995 CATACTTCCCTTGAAC
1 CATACTTCCCTTGAAC
23011 CATACTTCCCTTGAAC
1 CATACTTCCCTTGAAC
23027 CAT
1 CAT
23030 TCAATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.37, G:0.06, T:0.31
Consensus pattern (16 bp):
CATACTTCCCTTGAAC
Found at i:24414 original size:18 final size:19
Alignment explanation
Indices: 24391--24429 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
24381 TTACCCCTCT
24391 TCTCTCTCC-CCCACTAAG
1 TCTCTCTCCTCCCACTAAG
*
24409 TCTCTCTCCTCCCACTTAG
1 TCTCTCTCCTCCCACTAAG
24428 TC
1 TC
24430 AAGATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.13, C:0.49, G:0.05, T:0.33
Consensus pattern (19 bp):
TCTCTCTCCTCCCACTAAG
Done.