Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020733.1 Corchorus olitorius cultivar O-4 contig20766, 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: 56860
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1325 original size:3 final size:3
Alignment explanation
Indices: 1317--1342 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1307 TTTGTTTTAT
1317 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1343 TAAAATACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3573 original size:33 final size:33
Alignment explanation
Indices: 3529--3594 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3519 ATTCTGCACG
3529 TCAGGTAGTTCTTCATCCTTAAGACTTTCATCT
1 TCAGGTAGTTCTTCATCCTTAAGACTTTCATCT
* * * *
3562 TCAGGTGGTTCTTCGTTCTTAAGATTTTCATCT
1 TCAGGTAGTTCTTCATCCTTAAGACTTTCATCT
3595 GTGTCATCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.45
Consensus pattern (33 bp):
TCAGGTAGTTCTTCATCCTTAAGACTTTCATCT
Found at i:5215 original size:26 final size:25
Alignment explanation
Indices: 5180--5256 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 25
5170 CTTTAATTCA
5180 ATAC-AAACATCATTTCCATATCCT
1 ATACAAAACATCATTTCCATATCCT
*
5204 ATCCATAAACATCATTT-CAGTATCCT
1 ATACA-AAACATCATTTCCA-TATCCT
*
5230 -TACAATAACATCACTTCTCATATCCT
1 ATACAA-AACATCATTTC-CATATCCT
5256 A
1 A
5257 ATAACACACT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
24 4 0.09
25 14 0.33
26 23 0.53
27 2 0.05
ACGTcount: A:0.36, C:0.29, G:0.01, T:0.34
Consensus pattern (25 bp):
ATACAAAACATCATTTCCATATCCT
Found at i:5504 original size:21 final size:21
Alignment explanation
Indices: 5478--5597 Score: 167
Period size: 21 Copynumber: 5.9 Consensus size: 21
5468 GCTTGATCAA
5478 CACCAGAGGCTTCGACAGTAG
1 CACCAGAGGCTTCGACAGTAG
*
5499 CACCAGAGGCTTCGACAATAG
1 CACCAGAGGCTTCGACAGTAG
*
5520 CACCAGAGGCTTTGAC-GATAG
1 CACCAGAGGCTTCGACAG-TAG
* *
5541 CACCAGAGGCTTCAAAAGTAG
1 CACCAGAGGCTTCGACAGTAG
5562 CACCAGAGGCTTCGACAGTAG
1 CACCAGAGGCTTCGACAGTAG
5583 ---CAGAGGCTTCGACAG
1 CACCAGAGGCTTCGACAG
5598 GACCTCCAAC
Statistics
Matches: 89, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
18 15 0.17
21 73 0.82
22 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.28, T:0.15
Consensus pattern (21 bp):
CACCAGAGGCTTCGACAGTAG
Found at i:5928 original size:21 final size:21
Alignment explanation
Indices: 5883--5981 Score: 59
Period size: 21 Copynumber: 5.0 Consensus size: 21
5873 AAGCAGTAGT
*
5883 AGAGGCTTCAACAGAAGCACT
1 AGAGGCTTCAACAGAAGCACC
* * *
5904 AGAGGCTTCGATAGTAGCACC
1 AGAGGCTTCAACAGAAGCACC
* *
5925 AGA-G--TCAGC--AAG-AGC
1 AGAGGCTTCAACAGAAGCACC
*
5940 AGAGGCTTCAACAGGAGCACC
1 AGAGGCTTCAACAGAAGCACC
* *
5961 AGCA-GCTTCAAGAGGAGCACC
1 AG-AGGCTTCAACAGAAGCACC
5982 TTGCACACAG
Statistics
Matches: 58, Mismatches: 13, Indels: 14
0.68 0.15 0.16
Matches are distributed among these distances:
15 5 0.09
16 3 0.05
18 6 0.10
20 3 0.05
21 40 0.69
22 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.28, T:0.12
Consensus pattern (21 bp):
AGAGGCTTCAACAGAAGCACC
Found at i:6088 original size:24 final size:24
Alignment explanation
Indices: 6056--6108 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
6046 ACACGTGCGA
6056 CTTTTCTTTTTCTTTTTGCATTAT
1 CTTTTCTTTTTCTTTTTGCATTAT
*
6080 CTTTTCTTTTTCTTTTTGCATTCT
1 CTTTTCTTTTTCTTTTTGCATTAT
6104 CTTTT
1 CTTTT
6109 GTTTGTTGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.72
Consensus pattern (24 bp):
CTTTTCTTTTTCTTTTTGCATTAT
Found at i:6487 original size:10 final size:10
Alignment explanation
Indices: 6472--6525 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
6462 ATATATGAGC
6472 TGAAATAAAT
1 TGAAATAAAT
6482 TGAAATAAAT
1 TGAAATAAAT
* *
6492 TAAAACAAAT
1 TGAAATAAAT
6502 TAGATAAATAAAT
1 T-G--AAATAAAT
*
6515 TGAAACAAAT
1 TGAAATAAAT
6525 T
1 T
6526 AGCTAAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
10 27 0.75
12 1 0.03
13 8 0.22
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (10 bp):
TGAAATAAAT
Found at i:6511 original size:23 final size:23
Alignment explanation
Indices: 6484--6535 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
6474 AAATAAATTG
6484 AAATAAATTAAAACAAATTAGAT
1 AAATAAATTAAAACAAATTAGAT
* *
6507 AAATAAATTGAAACAAATTAGCT
1 AAATAAATTAAAACAAATTAGAT
6530 AAATAA
1 AAATAA
6536 CACAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (23 bp):
AAATAAATTAAAACAAATTAGAT
Found at i:7373 original size:30 final size:30
Alignment explanation
Indices: 7337--7442 Score: 212
Period size: 30 Copynumber: 3.5 Consensus size: 30
7327 TTCCCTTTTA
7337 GATTCACCATTTCCATCAACATCAATAGGT
1 GATTCACCATTTCCATCAACATCAATAGGT
7367 GATTCACCATTTCCATCAACATCAATAGGT
1 GATTCACCATTTCCATCAACATCAATAGGT
7397 GATTCACCATTTCCATCAACATCAATAGGT
1 GATTCACCATTTCCATCAACATCAATAGGT
7427 GATTCACCATTTCCAT
1 GATTCACCATTTCCAT
7443 ACATTTTTAG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.31
Consensus pattern (30 bp):
GATTCACCATTTCCATCAACATCAATAGGT
Found at i:8327 original size:33 final size:33
Alignment explanation
Indices: 8285--8349 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
8275 ATTCTGCACG
8285 TCAGGTAGTTCTTCATCCTTAAGACTTTCATCT
1 TCAGGTAGTTCTTCATCCTTAAGACTTTCATCT
* * *
8318 TCAGGTAGTTCTTCGTTCTTAAGATTTTCATC
1 TCAGGTAGTTCTTCATCCTTAAGACTTTCATC
8350 CGTGTCATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.45
Consensus pattern (33 bp):
TCAGGTAGTTCTTCATCCTTAAGACTTTCATCT
Found at i:10563 original size:33 final size:32
Alignment explanation
Indices: 10500--10563 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
10490 AATATCATAA
*
10500 AATCAACCTTTAAGAAAAAATCACATGAAAAG
1 AATCAACCTTTAACAAAAAATCACATGAAAAG
*
10532 AATCAACCTTTCATACAAAGAA-CACATGAAAA
1 AATCAACCTTT-A-ACAAAAAATCACATGAAAA
10564 AAAAAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 11 0.39
33 11 0.39
34 6 0.21
ACGTcount: A:0.55, C:0.19, G:0.08, T:0.19
Consensus pattern (32 bp):
AATCAACCTTTAACAAAAAATCACATGAAAAG
Found at i:28773 original size:15 final size:15
Alignment explanation
Indices: 28753--28784 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28743 CAATAAACAT
28753 CACTATTCTGAAAAG
1 CACTATTCTGAAAAG
28768 CACTATTCTGAAAAG
1 CACTATTCTGAAAAG
28783 CA
1 CA
28785 AATCTAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (15 bp):
CACTATTCTGAAAAG
Found at i:34033 original size:20 final size:21
Alignment explanation
Indices: 33991--34042 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
33981 GTTGTTGTTT
*
33991 TTTATTTTTACTAAATCGTTA
1 TTTATTTTTATTAAATCGTTA
* *
34012 TTTATTTTTATTTAATTG-TA
1 TTTATTTTTATTAAATCGTTA
*
34032 TTTGTTTTTAT
1 TTTATTTTTAT
34043 AATTAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67
Consensus pattern (21 bp):
TTTATTTTTATTAAATCGTTA
Found at i:34525 original size:22 final size:22
Alignment explanation
Indices: 34500--34548 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
34490 TTAGTTCTTA
**
34500 ATTTTACTTGTTCACCTTACAC
1 ATTTTACCCGTTCACCTTACAC
*
34522 ATTTTGCCCGTTCACCTTACAC
1 ATTTTACCCGTTCACCTTACAC
34544 ATTTT
1 ATTTT
34549 GCTATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.06, T:0.45
Consensus pattern (22 bp):
ATTTTACCCGTTCACCTTACAC
Found at i:34549 original size:22 final size:22
Alignment explanation
Indices: 34509--34550 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
34499 AATTTTACTT
34509 GTTCACCTTACACATTTTGCCC
1 GTTCACCTTACACATTTTGCCC
34531 GTTCACCTTACACATTTTGC
1 GTTCACCTTACACATTTTGC
34551 TATTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.33, G:0.10, T:0.38
Consensus pattern (22 bp):
GTTCACCTTACACATTTTGCCC
Found at i:46894 original size:22 final size:22
Alignment explanation
Indices: 46840--46883 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
46830 TTCTTCTCGT
46840 ACTTCTTCTCTCTAAAAAATTC
1 ACTTCTTCTCTCTAAAAAATTC
* *
46862 ACTTCTTCTCTTTAAAAGATTC
1 ACTTCTTCTCTCTAAAAAATTC
46884 TCTGTTTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.02, T:0.43
Consensus pattern (22 bp):
ACTTCTTCTCTCTAAAAAATTC
Found at i:49142 original size:17 final size:18
Alignment explanation
Indices: 49106--49146 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
49096 ATAATTAACA
*
49106 AAAAAAGTTGAATCATCT
1 AAAAAAGTTAAATCATCT
*
49124 AAAAAAGTTAAATGA-CT
1 AAAAAAGTTAAATCATCT
49141 AAAAAA
1 AAAAAA
49147 ATAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22
Consensus pattern (18 bp):
AAAAAAGTTAAATCATCT
Done.