Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010806.1 Corchorus olitorius cultivar O-4 contig10838, 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: 25637
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Found at i:3934 original size:41 final size:40
Alignment explanation
Indices: 3639--4519 Score: 720
Period size: 40 Copynumber: 21.9 Consensus size: 40
3629 AGGGAATAAG
*
3639 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT-TT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
* * * *
3678 AGACAACACCTTCCGGTGGGGAAGGGAAAACTGGGAAT-TT
1 A-ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
* * * * *
3718 AAACAACACCTTCCGGTGGGGAAGGGCGAACTAGGAATTG-A
1 -AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-TGCT
* * * *
3759 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTAT-TT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
* * * * *
3798 AAACAACACCTTCCGGTGGGGAAGGGTAAATTGGGAAT-TT
1 -AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
*
3838 AAACAACACCTTCCGATGAGGAAGGGCAAACT-GG-ACGC-
1 -AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
*
3876 AACAACACC-TCCTGATGAGGAAGGGCAAATTGGGAAATGCT
1 AACAACACCTTCC-GATGAGGAAGGGCAAACTGGG-AATGCT
* * *
3917 GACAACACCTTCCGATGAGGAAGGGCAAATTGGGAATACT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
* * * * *
3957 GACAACACCTTCCAATAAGGAAGGGCAAACTGGACAAAGGC-
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG--GAATGCT
* * *
3998 AACAACACCTCCCGATGAGGAAGGGCAAATTGGGAAT-AT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
* * * * * *
4037 GACAACACTTTCCGATGAGGACGAGCAAACTGGACAAAGGC-
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG--GAATGCT
* * * *
4078 AACAACACCTCCCGATGAGGAAGGGTAAATTGGGAAT-TT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
* *
4117 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-
1 -AACAACACCTTCCGATGAGGAAGGGCAAACTGG--GAATGCT
* *
4159 AACAACACCTCCCGATGAGGAAGGGCAAATTGGGAAATGCT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGG-AATGCT
* * * * *
4200 GACAACACCTTCCAATGAGGAAGGGTAAACTGGACAAAGGC-
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG--GAATGCT
* * * *
4241 AACAACACCTCCCGATGAGGAAGGGTAAATTGGGAAT-TT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
* * *
4280 AAACAACACCTTCCGATGAGGAAGGGTAAATTAGGAATGCT
1 -AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
* *
4321 GACAACACCTTCCGATGAGGAAGGGCAAACTGGAGAAAGAC-
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG-GAATG-CT
** * *
4362 AACAACACCTTCCGATGAGGAAGAACAAATTGGTAAATGCT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG-GAATGCT
* * * * *
4403 GACAACACCTTCCGATGAAGATGGGCAAATTGGCAAATGCT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG-GAATGCT
* * ** * *
4444 GACAACACCTTCCGATGAGGAATGGCAAGTTAGGAAT-TT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
* * *
4483 AAACAACACCTTCCG-TGGGGAAGGGCGAACTAGGAAT
1 -AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT
4520 TATCGAAGGA
Statistics
Matches: 692, Mismatches: 115, Indels: 70
0.79 0.13 0.08
Matches are distributed among these distances:
36 3 0.00
37 26 0.04
38 3 0.00
39 55 0.08
40 317 0.46
41 275 0.40
42 13 0.02
ACGTcount: A:0.36, C:0.21, G:0.27, T:0.16
Consensus pattern (40 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
Found at i:4596 original size:43 final size:43
Alignment explanation
Indices: 4537--4648 Score: 179
Period size: 43 Copynumber: 2.6 Consensus size: 43
4527 GGAAAACTGA
* *
4537 ACCTTCCGACCGGGAAGGGGCATTTTGGGAAATGAAAACAAGG
1 ACCTTCCAACCAGGAAGGGGCATTTTGGGAAATGAAAACAAGG
* *
4580 ACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAGGG
1 ACCTTCCAACCAGGAAGGGGCATTTTGGGAAATGAAAACAAGG
*
4623 ACCTTCCAAACAGGAAGGGGCATTTT
1 ACCTTCCAACCAGGAAGGGGCATTTT
4649 TTGGAAAGAG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.19
Consensus pattern (43 bp):
ACCTTCCAACCAGGAAGGGGCATTTTGGGAAATGAAAACAAGG
Found at i:5288 original size:50 final size:51
Alignment explanation
Indices: 5230--5470 Score: 226
Period size: 50 Copynumber: 4.8 Consensus size: 51
5220 ATCGTAAGCC
* *
5230 AATCAAAAATTTC-ATCTTCATTTACAAATTAATTAAAAGGTT-AATCTTTT
1 AATCAAAAA-TTCAATCTTTATTTACAAATTACTTAAAAGGTTCAATCTTTT
* * * * * *
5280 AATAAAAAAAATCCAATCTTTATTCACGAATTACTTAAAAGCTTCAAT-TTTC
1 AAT--CAAAAATTCAATCTTTATTTACAAATTACTTAAAAGGTTCAATCTTTT
* * * * *
5332 ACTTAAAAATTCAATCTTTATTCATAAATTACTTAAAAGTTTC-ATCTTTT
1 AATCAAAAATTCAATCTTTATTTACAAATTACTTAAAAGGTTCAATCTTTT
*
5382 AATCAAAAATCCAATCTTTATTTACAAATTGA-TTAAAA-GTTCAATCTTTT
1 AATCAAAAATTCAATCTTTATTTACAAATT-ACTTAAAAGGTTCAATCTTTT
* ** *
5432 ACTCAAAGCCTTC-ATTTTTATTTACAAATTACTTAAAAG
1 AATCAAA-AATTCAATCTTTATTTACAAATTACTTAAAAG
5471 ACTTCATCTT
Statistics
Matches: 155, Mismatches: 26, Indels: 19
0.77 0.13 0.09
Matches are distributed among these distances:
49 6 0.04
50 107 0.69
51 5 0.03
52 34 0.22
53 3 0.02
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.40
Consensus pattern (51 bp):
AATCAAAAATTCAATCTTTATTTACAAATTACTTAAAAGGTTCAATCTTTT
Found at i:5452 original size:100 final size:101
Alignment explanation
Indices: 5232--5481 Score: 267
Period size: 100 Copynumber: 2.5 Consensus size: 101
5222 CGTAAGCCAA
* * * * *
5232 TCAAAAATTTC-ATCTTCATTTACAAATTAATTAAAAGGTTAATCTTTTAATAAAAAAAATCCAA
1 TCAAAAA-TTCAATCTTTATTCACAAATTACTTAAAAGCTTCATCTTTTAAT-AAAAAAATCCAA
*
5296 TCTTTATTCACGAATTACTTAAAAGCTTCAATTTTCAC
64 TCTTTATTCACAAATTACTTAAAAGCTTCAATTTTCAC
* * * *
5334 TTAAAAATTCAATCTTTATTCATAAATTACTTAAAAGTTTCATCTTTTAAT-CAAAAATCCAATC
1 TCAAAAATTCAATCTTTATTCACAAATTACTTAAAAGCTTCATCTTTTAATAAAAAAATCCAATC
* *
5398 TTTATTTACAAATTGA-TTAAAAG-TTCAATCTTTTAC
66 TTTATTCACAAATT-ACTTAAAAGCTTCAAT-TTTCAC
** * *
5434 TCAAAGCCTTC-ATTTTTATTTACAAATTACTTAAAAGACTTCATCTTT
1 TCAAA-AATTCAATCTTTATTCACAAATTACTTAAAAG-CTTCATCTTT
5482 ATTTACGAAT
Statistics
Matches: 125, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
99 6 0.05
100 63 0.50
101 16 0.13
102 40 0.32
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.41
Consensus pattern (101 bp):
TCAAAAATTCAATCTTTATTCACAAATTACTTAAAAGCTTCATCTTTTAATAAAAAAATCCAATC
TTTATTCACAAATTACTTAAAAGCTTCAATTTTCAC
Found at i:11271 original size:30 final size:30
Alignment explanation
Indices: 11235--11295 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
11225 TCAACAGTAG
11235 TCTTCATAGCTTGTAGCCCCCCTGATTTCA
1 TCTTCATAGCTTGTAGCCCCCCTGATTTCA
11265 TCTTCATAGCTTGTAGCCCCCCTGATTTCA
1 TCTTCATAGCTTGTAGCCCCCCTGATTTCA
11295 T
1 T
11296 TCAGCATGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.33, G:0.13, T:0.38
Consensus pattern (30 bp):
TCTTCATAGCTTGTAGCCCCCCTGATTTCA
Found at i:15679 original size:66 final size:66
Alignment explanation
Indices: 15603--15730 Score: 186
Period size: 66 Copynumber: 1.9 Consensus size: 66
15593 AGGCAATCGA
* * *
15603 ACCAAGAGAAATCCAACGAAAAGAAAATAT-AGAGAGGACGAAAAAAGAACACAAAAGGGGAATT
1 ACCAAGAGAAACCCAACGAAAACAAAATATGA-AGAGGAAGAAAAAAGAACACAAAAGGGGAATT
15667 GG
65 GG
* * *
15669 ACCAAGAGAAACCCAACGAAAACAAAATATGAAGAGGAAGAACAAAGAATACAGAAGGGGAA
1 ACCAAGAGAAACCCAACGAAAACAAAATATGAAGAGGAAGAAAAAAGAACACAAAAGGGGAA
15731 ACATTAAGAG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 54 0.98
67 1 0.02
ACGTcount: A:0.57, C:0.13, G:0.23, T:0.06
Consensus pattern (66 bp):
ACCAAGAGAAACCCAACGAAAACAAAATATGAAGAGGAAGAAAAAAGAACACAAAAGGGGAATTG
G
Found at i:16488 original size:39 final size:39
Alignment explanation
Indices: 16434--16512 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
16424 TCCATAAAAG
*
16434 TGAGTTTGAATCACAGTGAACATTGCATTCCAAGAATGT
1 TGAGTTTGAATCACAGTGAACATTGCATCCCAAGAATGT
*
16473 TGAGTTTGGATCACAGTGAACATTGCATCCCAAGAATGT
1 TGAGTTTGAATCACAGTGAACATTGCATCCCAAGAATGT
16512 T
1 T
16513 TTTTTCTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (39 bp):
TGAGTTTGAATCACAGTGAACATTGCATCCCAAGAATGT
Done.