Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012119.1 Corchorus capsularis cultivar CVL-1 contig12140, 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: 18556
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2820 original size:102 final size:102
Alignment explanation
Indices: 2644--2841 Score: 360
Period size: 102 Copynumber: 1.9 Consensus size: 102
2634 ACTATTTATT
*
2644 TTATACTAATAATCAATTATTAATCAAATTATGCATTCGAGCATTTGATTCAATTTAGTGATACT
1 TTATACCAATAATCAATTATTAATCAAATTATGCATTCGAGCATTTGATTCAATTTAGTGATACT
2709 TAATTACTTCTATAACTTATATATATATATATATATA
66 TAATTACTTCTATAACTTATATATATATATATATATA
* *
2746 TTATACCAATAATCAATTATTACTCAAATTATGCATTCGAGCATTTGATTCAATTTAGTGGTACT
1 TTATACCAATAATCAATTATTAATCAAATTATGCATTCGAGCATTTGATTCAATTTAGTGATACT
*
2811 TAATTACTTCTATAACTTATATATATGTATA
66 TAATTACTTCTATAACTTATATATATATATA
2842 GGTTGGCATT
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.43
Consensus pattern (102 bp):
TTATACCAATAATCAATTATTAATCAAATTATGCATTCGAGCATTTGATTCAATTTAGTGATACT
TAATTACTTCTATAACTTATATATATATATATATATA
Found at i:3053 original size:31 final size:31
Alignment explanation
Indices: 3018--3083 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
3008 AACTTTATGT
* *
3018 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCATT-TTCTTTAAAACATA
3049 TTTCCAATTGTACCATTTTCTTTAAAACATA
1 TTTCCAATTGTACCATTTTCTTTAAAACATA
3080 TTTC
1 TTTC
3084 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCATTTTCTTTAAAACATA
Found at i:3858 original size:22 final size:22
Alignment explanation
Indices: 3833--3972 Score: 131
Period size: 22 Copynumber: 6.3 Consensus size: 22
3823 TGTCTCTAAG
*
3833 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
3855 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
3878 -GGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
3899 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
3921 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
3945 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
3967 TGGTTA
1 TGGTTA
3973 ATTATAACTA
Statistics
Matches: 97, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
21 3 0.03
22 74 0.76
23 3 0.03
24 17 0.18
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:3949 original size:46 final size:46
Alignment explanation
Indices: 3877--3965 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
3867 TTTCATGAGG
*
3877 AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATC
1 AGGTTATCAAAATCTCATAGTGTGGTTACCAAAATTTCATAGGATC
* * ***
3923 AGGTTATTAAAATCTCTTAG-GTTGGTTATTGAAATTTCATAGG
1 AGGTTATCAAAATCTCATAGTG-TGGTTACCAAAATTTCATAGG
3966 GTGGTTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
45 1 0.03
46 35 0.97
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (46 bp):
AGGTTATCAAAATCTCATAGTGTGGTTACCAAAATTTCATAGGATC
Found at i:3958 original size:68 final size:66
Alignment explanation
Indices: 3832--3972 Score: 167
Period size: 68 Copynumber: 2.1 Consensus size: 66
3822 TTGTCTCTAA
* * *
3832 GTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAAAATTTCATAG
1 GTGGTTACCAAAATTTCATAAGATGGTTATTAAAATCTCATGAGGAGGTTATCAAAATTTCATAG
*
3897 T
66 G
* * * **
3898 GTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATCTC-TTAGGTTGGTTATTGAAATTTCA
1 GTGGTTACCAAAATTTCATAAGAT--GGTTATTAAAATCTCATGAGG-AGGTTATCAAAATTTCA
3962 TAGG
63 TAGG
3966 GTGGTTA
1 GTGGTTA
3973 ATTATAACTA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
66 22 0.35
67 4 0.06
68 37 0.59
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.39
Consensus pattern (66 bp):
GTGGTTACCAAAATTTCATAAGATGGTTATTAAAATCTCATGAGGAGGTTATCAAAATTTCATAG
G
Found at i:4046 original size:24 final size:22
Alignment explanation
Indices: 4012--4068 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
4002 AAGAGATTAT
*
4012 CAAAATGTCATAGTGAGGTTATA
1 CAAAATTTCATAGTGAGGTTA-A
* *
4035 TAAGAATTTCATAGTGTGGTTAA
1 CAA-AATTTCATAGTGAGGTTAA
4058 CAAAATTTCAT
1 CAAAATTTCAT
4069 TAAATATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 8 0.28
23 5 0.17
24 16 0.55
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:4378 original size:22 final size:22
Alignment explanation
Indices: 4162--4390 Score: 148
Period size: 22 Copynumber: 10.5 Consensus size: 22
4152 TAGGGAGTAC
*
4162 CAAAATTTGATAGAA-A-GTTAT
1 CAAAATTTCATA-AAGAGGTTAT
* * *
4183 C-AAATTTCATAGAGTGATTAT
1 CAAAATTTCATAAAGAGGTTAT
* *
4204 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAAAGA--GG-TTAT
*
4229 CAAAATTT-ATAGAA-AGATTAT
1 CAAAATTTCATA-AAGAGGTTAT
** **
4250 CAAAA-TTCATAGTGTTGTTAT
1 CAAAATTTCATAAAGAGGTTAT
*
4271 CAAAATTTCA-AAGCGAGGTTAT
1 CAAAATTTCATAA-AGAGGTTAT
* * * *
4293 CAAAATTACATAATGTGATTAT
1 CAAAATTTCATAAAGAGGTTAT
* * * * *
4315 CATAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAAAGAGGTTAT
*
4337 CAAAATTTTATAAAGAGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
4359 CAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
*
4381 CAAATTTTCA
1 CAAAATTTCA
4391 AAATTTGATT
Statistics
Matches: 158, Mismatches: 38, Indels: 23
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.01
20 11 0.07
21 28 0.18
22 99 0.63
23 2 0.01
24 5 0.03
25 12 0.08
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAAAGAGGTTAT
Found at i:4520 original size:19 final size:19
Alignment explanation
Indices: 4496--4545 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
4486 TTATGGAGTA
4496 ATCAAATTTCAAGGAGGAT
1 ATCAAATTTCAAGGAGGAT
* * *
4515 ATCAAAATTCAGGGAGGCT
1 ATCAAATTTCAAGGAGGAT
*
4534 GTCAAAATTTCA
1 ATC-AAATTTCA
4546 TATGAAGGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (19 bp):
ATCAAATTTCAAGGAGGAT
Found at i:4710 original size:23 final size:22
Alignment explanation
Indices: 4430--5030 Score: 177
Period size: 22 Copynumber: 27.8 Consensus size: 22
4420 ATTTCTGGGG
*
4430 AGGTTATCAAAATTTCATAGTA
1 AGGTTATCAAAATTTCATAGGA
* *
4452 TGGTTA-CCAAA--T--TAGGA
1 AGGTTATCAAAATTTCATAGGA
* * *
4469 AGGTTATTAAACTTTTATTATGG-
1 AGGTTATCAAAATTTCA-TA-GGA
*
4492 A-GTAATC-AAATTTCA-AGG-
1 AGGTTATCAAAATTTCATAGGA
* *
4510 AGGATATCAAAA-TTC--AGGG
1 AGGTTATCAAAATTTCATAGGA
* * *
4529 AGGCTGTCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATAGGA
*
4551 AGGTTATCAAAATTTCATA-GT
1 AGGTTATCAAAATTTCATAGGA
* * *
4572 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATAGGA
* * *
4595 AGATTAACAAAATTTCATAATG-
1 AGGTTATCAAAATTTCAT-AGGA
* ** *
4617 AGATTATCAAAAAATCATAGGG
1 AGGTTATCAAAATTTCATAGGA
*
4639 AGGTTATCAAAA-TT--T--GT
1 AGGTTATCAAAATTTCATAGGA
* *
4656 A-GTTATCAAGATTTCATAAGA
1 AGGTTATCAAAATTTCATAGGA
*
4677 AGGTTATCAAAATTTTATAGGA
1 AGGTTATCAAAATTTCATAGGA
*
4699 AGATTTATCAAAATTTCATAGCG-
1 AG-GTTATCAAAATTTCATAG-GA
*
4722 AGGTTATCACAATTTCATAGTG-
1 AGGTTATCAAAATTTCATAG-GA
* * *
4744 TGATTATCAAAATTTCAGAGTG-
1 AGGTTATCAAAATTTCATAG-GA
* *
4766 TGATTA-CTAACAATTCATAATCATATGG-
1 AGGTTATC-AA-AA-T--T--TCATA-GGA
* * * * *
4794 AGCTTTTTAAATTTTCATAACG-
1 AGGTTATCAAAATTTCAT-AGGA
* * *
4816 TGGTTATCAATATATCATATGG-
1 AGGTTATCAAAATTTCATA-GGA
* * *
4838 AGGTTATCAACATCTCATAGTGT
1 AGGTTATCAAAATTTCATAG-GA
* * *
4861 TGGTCATCAAAATTTCATTGGGA
1 AGGTTATCAAAATTTCA-TAGGA
*
4884 A-GTTATCAAAATTTCATATTG-
1 AGGTTATCAAAATTTCATA-GGA
* *
4905 AGGTCT-TCAAAATTCCTTAGGA
1 AGGT-TATCAAAATTTCATAGGA
* * * *
4927 AAGTTAACCAAATTTCATAAGA
1 AGGTTATCAAAATTTCATAGGA
* ** **
4949 AGATTAAAAAAATTT-ATAAAA
1 AGGTTATCAAAATTTCATAGGA
* * * *
4970 AGGTTCTCGAAATTCCATAGTA
1 AGGTTATCAAAATTTCATAGGA
** *
4992 TCGTTATTAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
5014 AGGTTATCAAAATTTCA
1 AGGTTATCAAAATTTCA
5031 CAATGGGATC
Statistics
Matches: 425, Mismatches: 109, Indels: 90
0.68 0.17 0.14
Matches are distributed among these distances:
16 9 0.02
17 13 0.03
18 8 0.02
19 21 0.05
20 7 0.02
21 40 0.09
22 262 0.62
23 44 0.10
24 7 0.02
26 2 0.00
27 1 0.00
28 10 0.02
29 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:6473 original size:18 final size:20
Alignment explanation
Indices: 6451--6497 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
6441 TTTAAGAAAA
6451 ATTAGTAAATATT-T-ATTT
1 ATTAGTAAATATTATGATTT
* *
6469 GTTAGTATATATTATGATTT
1 ATTAGTAAATATTATGATTT
6489 ATTAGTAAA
1 ATTAGTAAA
6498 ACATATGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (20 bp):
ATTAGTAAATATTATGATTT
Found at i:10152 original size:45 final size:46
Alignment explanation
Indices: 10054--10179 Score: 236
Period size: 45 Copynumber: 2.8 Consensus size: 46
10044 TTTAATGTTA
10054 TATTCCTAATTTAATCAGTGCAAATTAAACTATATTTTTTAATTGT
1 TATTCCTAATTTAATCAGTGCAAATTAAACTATATTTTTTAATTGT
10100 TATTCCTAATTTAATCAGTGCAAATTAAACTAT-TTTTTTAATTGT
1 TATTCCTAATTTAATCAGTGCAAATTAAACTATATTTTTTAATTGT
*
10145 TATTCCTAATTTAATCCGTGCAAATTAAACTATAT
1 TATTCCTAATTTAATCAGTGCAAATTAAACTATAT
10180 ATATATAGAG
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
45 44 0.56
46 34 0.44
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (46 bp):
TATTCCTAATTTAATCAGTGCAAATTAAACTATATTTTTTAATTGT
Found at i:15472 original size:2 final size:2
Alignment explanation
Indices: 15465--15495 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15455 TTAGACTTGC
15465 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15496 GTAGTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18200 original size:30 final size:30
Alignment explanation
Indices: 18122--18224 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
18112 GGTGTCCGAT
* * * *
18122 GTGGCATGCCACGTGTATCAAAAAGTGATAT
1 GTGGCATGCCACATGTACCAAAAA-TGACAC
* * *
18153 GGGGCACGCCACTTGTACCAAAAATGACAC
1 GTGGCATGCCACATGTACCAAAAATGACAC
18183 GTGGCATGCCACATGTACCAAAAATGACAC
1 GTGGCATGCCACATGTACCAAAAATGACAC
18213 GTGGCATGCCAC
1 GTGGCATGCCAC
18225 GTCGGATGCC
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
30 43 0.68
31 20 0.32
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.18
Consensus pattern (30 bp):
GTGGCATGCCACATGTACCAAAAATGACAC
Done.