Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014515.1 Corchorus capsularis cultivar CVL-1 contig14536, 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: 94352
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:652 original size:2 final size:2
Alignment explanation
Indices: 645--679 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
635 GCAATTTCTG
645 AT AT 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 AT AT A
680 AACCCCTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3455 original size:24 final size:24
Alignment explanation
Indices: 3428--3485 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3418 GACCCTGCTT
* *
3428 CCACAACCACCACCACCACATCCC
1 CCACAACCACCACCACCACAGCCA
* * *
3452 CCACATCCGCCAGCACCACAGCCA
1 CCACAACCACCACCACCACAGCCA
3476 CCACAACCAC
1 CCACAACCAC
3486 TGCTGTTCAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.59, G:0.05, T:0.03
Consensus pattern (24 bp):
CCACAACCACCACCACCACAGCCA
Found at i:3507 original size:36 final size:36
Alignment explanation
Indices: 3467--3663 Score: 158
Period size: 36 Copynumber: 5.5 Consensus size: 36
3457 TCCGCCAGCA
3467 CCACAGCCACCACAACCACTGCTGTTCACCATGATT
1 CCACAGCCACCACAACCACTGCTGTTCACCATGATT
* ** * * *
3503 CCACAACCACCACAACCTCCACCAC-ATCCGCCA-GCA--
1 CCACAGCCACCACAA---CCACTGCTGTTCACCATG-ATT
*
3539 CCACAGCCACCACAACCACTGCTGTTAACCATGATT
1 CCACAGCCACCACAACCACTGCTGTTCACCATGATT
** * * *
3575 CCACAGCCACCACAACCTCCACCAC-ATCCTCCA-GCA--
1 CCACAGCCACCACAA---CCACTGCTGTTCACCATG-ATT
3611 CCACAGCCACCACAACCACTGCTGTTCACCATGATT
1 CCACAGCCACCACAACCACTGCTGTTCACCATGATT
3647 CCACAGCCACCACAACC
1 CCACAGCCACCACAACC
3664 TCCACCACAT
Statistics
Matches: 121, Mismatches: 24, Indels: 32
0.68 0.14 0.18
Matches are distributed among these distances:
33 10 0.08
34 11 0.09
35 2 0.02
36 75 0.62
37 2 0.02
38 11 0.09
39 10 0.08
ACGTcount: A:0.30, C:0.48, G:0.09, T:0.13
Consensus pattern (36 bp):
CCACAGCCACCACAACCACTGCTGTTCACCATGATT
Found at i:3538 original size:72 final size:72
Alignment explanation
Indices: 3426--3716 Score: 483
Period size: 72 Copynumber: 4.0 Consensus size: 72
3416 CTGACCCTGC
* *
3426 TTCCACAACCACCACCACCACATCCCCCACATCCGCCAGCACCACAGCCACCACAACCACTGCTG
1 TTCCACAACCACCA-CA--ACCTCCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTG
3491 TTCACCATGA
63 TTCACCATGA
*
3501 TTCCACAACCACCACAACCTCCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTA
1 TTCCACAACCACCACAACCTCCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTC
3566 ACCATGA
66 ACCATGA
* *
3573 TTCCACAGCCACCACAACCTCCACCACATCCTCCAGCACCACAGCCACCACAACCACTGCTGTTC
1 TTCCACAACCACCACAACCTCCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTC
3638 ACCATGA
66 ACCATGA
* *
3645 TTCCACAGCCACCACAACCTCCACCACATCCACCAGCACCACAGCCACCACAACCACTGCTGTTC
1 TTCCACAACCACCACAACCTCCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTC
*
3710 ATCATGA
66 ACCATGA
3717 CATTAGTACT
Statistics
Matches: 208, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
72 192 0.92
74 2 0.01
75 14 0.07
ACGTcount: A:0.30, C:0.48, G:0.08, T:0.13
Consensus pattern (72 bp):
TTCCACAACCACCACAACCTCCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTC
ACCATGA
Found at i:3687 original size:36 final size:36
Alignment explanation
Indices: 3503--3699 Score: 158
Period size: 36 Copynumber: 5.5 Consensus size: 36
3493 CACCATGATT
* *
3503 CCACAACCACCACAACCTCCACCACATCCGCCAGCA
1 CCACAGCCACCACAACCTCCACCACATCCACCAGCA
** * **
3539 CCACAGCCACCACAA---CCACTGCTGTTAACCATG-A
1 CCACAGCCACCACAACCTCCACCAC-ATCCACCA-GCA
*
3573 TTCCACAGCCACCACAACCTCCACCACATCCTCCAGCA
1 --CCACAGCCACCACAACCTCCACCACATCCACCAGCA
** * *
3611 CCACAGCCACCACAA---CCACTGCTGTTCACCATG-A
1 CCACAGCCACCACAACCTCCACCAC-ATCCACCA-GCA
3645 TTCCACAGCCACCACAACCTCCACCACATCCACCAGCA
1 --CCACAGCCACCACAACCTCCACCACATCCACCAGCA
3683 CCACAGCCACCACAACC
1 CCACAGCCACCACAACC
3700 ACTGCTGTTC
Statistics
Matches: 123, Mismatches: 22, Indels: 32
0.69 0.12 0.18
Matches are distributed among these distances:
33 10 0.08
34 11 0.09
35 2 0.02
36 76 0.62
37 2 0.02
38 12 0.10
39 10 0.08
ACGTcount: A:0.31, C:0.50, G:0.08, T:0.11
Consensus pattern (36 bp):
CCACAGCCACCACAACCTCCACCACATCCACCAGCA
Found at i:30641 original size:19 final size:19
Alignment explanation
Indices: 30617--30655 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
30607 TAAATCTTAG
30617 ATGAATGAGACTGTTTTAA
1 ATGAATGAGACTGTTTTAA
30636 ATGAATGAGACTGTTTTAA
1 ATGAATGAGACTGTTTTAA
30655 A
1 A
30656 AGCAACTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (19 bp):
ATGAATGAGACTGTTTTAA
Found at i:32321 original size:6 final size:6
Alignment explanation
Indices: 32305--32356 Score: 97
Period size: 6 Copynumber: 8.8 Consensus size: 6
32295 CTGAAAAGCA
32305 GCTCA- GCTCAT GCTCAT GCTCAT GCTCAT GCTCAT GCTCAT GCTCAT
1 GCTCAT GCTCAT GCTCAT GCTCAT GCTCAT GCTCAT GCTCAT GCTCAT
32352 GCTCA
1 GCTCA
32357 GGCTGTGACT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 41 0.89
ACGTcount: A:0.17, C:0.35, G:0.17, T:0.31
Consensus pattern (6 bp):
GCTCAT
Found at i:49732 original size:2 final size:2
Alignment explanation
Indices: 49725--49750 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49715 ATGAATTAAC
49725 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
49751 CTTGGCATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53560 original size:2 final size:2
Alignment explanation
Indices: 53553--53586 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
53543 TTCTGCTTCC
53553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53587 TATTATCTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54769 original size:3 final size:3
Alignment explanation
Indices: 54761--54813 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
54751 CCCCATCCTT
54761 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54809 TTC TT
1 TTC TT
54814 GTGTTCTAGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:55612 original size:15 final size:13
Alignment explanation
Indices: 55575--55605 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
55565 ATAAAAAAAA
55575 ATATATACTATAT
1 ATATATACTATAT
*
55588 ATATCTACTATAT
1 ATATATACTATAT
55601 ATATA
1 ATATA
55606 ATAACTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATATACTATAT
Found at i:60552 original size:2 final size:2
Alignment explanation
Indices: 60545--60581 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
60535 AAATGCTTGG
60545 AT AT AT 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 AT AT AT A
60582 CAAGATGCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:74827 original size:32 final size:31
Alignment explanation
Indices: 74753--74828 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
74743 TAACTTCAAA
* *
74753 TCAGGACATTTTGCCTCATGAGCTTCCAAATT
1 TCAGGACATTTTGCCTCATAAACTTCCAAA-T
* *
74785 TC-GGATATTTTGCCTCTTAAACTCTCCAAAT
1 TCAGGACATTTTGCCTCATAAACT-TCCAAAT
*
74816 TCAAGACATTTTG
1 TCAGGACATTTTG
74829 ACCCGTGACG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 20 0.56
32 16 0.44
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (31 bp):
TCAGGACATTTTGCCTCATAAACTTCCAAAT
Found at i:82664 original size:34 final size:34
Alignment explanation
Indices: 82603--82741 Score: 212
Period size: 34 Copynumber: 4.2 Consensus size: 34
82593 GTTTCATCGG
* *
82603 CCCTGCCCAGTGGG-T-T-ATAATAACTGGAAGG
1 CCCTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
82634 CCCTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
*
82668 CCATGCCCAGTGGGTTGTGAAAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
* *
82702 CCCTGTCCAGTGGGTTGTGATAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
82736 CCCTGC
1 CCCTGC
82742 TAACGGGTTA
Statistics
Matches: 98, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
31 14 0.14
32 1 0.01
33 1 0.01
34 82 0.84
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (34 bp):
CCCTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
Done.