Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011146.1 Corchorus capsularis cultivar CVL-1 contig11167, 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: 40266
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3031 original size:27 final size:28
Alignment explanation
Indices: 2976--3031 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
2966 TTATTTGAAA
* *
2976 ATTTCTCTTTTAATTATCCACGCCTCTT
1 ATTTCTCTTTTAATTATCCACACCACTT
* *
3004 ATTTCT-TTTTAATTGTCCACATCACTT
1 ATTTCTCTTTTAATTATCCACACCACTT
3031 A
1 A
3032 AAATAACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.21, C:0.25, G:0.04, T:0.50
Consensus pattern (28 bp):
ATTTCTCTTTTAATTATCCACACCACTT
Found at i:6887 original size:6 final size:6
Alignment explanation
Indices: 6876--6913 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
6866 TTGTTACCAA
6876 AAAAAC AAAAAC AAAAAC AAAAAC -AAAAC -AAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
6914 CAACATTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:6891 original size:5 final size:5
Alignment explanation
Indices: 6877--6916 Score: 53
Period size: 5 Copynumber: 7.4 Consensus size: 5
6867 TGTTACCAAA
6877 AAAAC AAAAAC AAAAAC AAAAAC AAAAC AAAAC AAAAC AA
1 AAAAC -AAAAC -AAAAC -AAAAC AAAAC AAAAC AAAAC AA
6917 CATTGTACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 17 0.50
6 17 0.50
ACGTcount: A:0.82, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:9181 original size:19 final size:19
Alignment explanation
Indices: 9157--9216 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
9147 ACTGTTTAGG
*
9157 TACTGTACAGATGAAATTA
1 TACTGTACAGATAAAATTA
* *
9176 TACTGTATAGATCAAATTA
1 TACTGTACAGATAAAATTA
9195 GGTACTGTACAGATAAAATTA
1 --TACTGTACAGATAAAATTA
9216 T
1 T
9217 TAGAGCAGCG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 18 0.51
21 17 0.49
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (19 bp):
TACTGTACAGATAAAATTA
Found at i:9202 original size:21 final size:21
Alignment explanation
Indices: 9152--9215 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
9142 TTGACACTGT
*
9152 TTAGGTACTGTACAGATGAAA
1 TTAGGTACTGTACAGATAAAA
* *
9173 TTA--TACTGTATAGATCAAA
1 TTAGGTACTGTACAGATAAAA
9192 TTAGGTACTGTACAGATAAAA
1 TTAGGTACTGTACAGATAAAA
9213 TTA
1 TTA
9216 TTAGAGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
21 20 0.54
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (21 bp):
TTAGGTACTGTACAGATAAAA
Found at i:10529 original size:31 final size:31
Alignment explanation
Indices: 10491--10596 Score: 121
Period size: 31 Copynumber: 3.5 Consensus size: 31
10481 TTTGGCTAGT
10491 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * * **
10522 TGCTCAAATAAGGGTCTGATC-TTT--TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCCAAAA
10551 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
10582 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
10597 TTGTCTCATG
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 2 0.03
29 18 0.31
30 4 0.07
31 33 0.56
32 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:10666 original size:31 final size:31
Alignment explanation
Indices: 10628--10760 Score: 166
Period size: 31 Copynumber: 4.4 Consensus size: 31
10618 CTGACACGGA
10628 GCCCTTATTTGAGCATTTTCGATAACGTTAG
1 GCCCTTATTTGAGCATTTTCGATAACGTTAG
10659 GCCCTTATTTGAGCATTTTCGATAACGTTAG
1 GCCCTTATTTGAGCATTTTCGATAACGTTAG
* ** * **
10690 ACCCTTATTTG-GCCAAATT--A-AAAGATCGG
1 GCCCTTATTTGAG-CATTTTCGATAACG-TTAG
10719 GCCCTTATTTGAGCATTTTCGATAACGTTAG
1 GCCCTTATTTGAGCATTTTCGATAACGTTAG
10750 GCCCTTATTTG
1 GCCCTTATTTG
10761 GCCAAATTAA
Statistics
Matches: 84, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.04
29 17 0.20
30 2 0.02
31 59 0.70
32 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (31 bp):
GCCCTTATTTGAGCATTTTCGATAACGTTAG
Found at i:10727 original size:60 final size:60
Alignment explanation
Indices: 10658--10797 Score: 253
Period size: 60 Copynumber: 2.3 Consensus size: 60
10648 GATAACGTTA
10658 GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
*
10718 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
* *
10778 GACCCTTATTTGAACATTTT
1 GGCCCTTATTTGAGCATTTT
10798 GACAAACATT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 77 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
Found at i:10729 original size:29 final size:29
Alignment explanation
Indices: 10691--10789 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
10681 TAACGTTAGA
10691 CCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGGCCAAATTAAAAGATCGGG
** * **
10720 CCCTTATTTGAG-CATTTTCGATAACG-TTAGG
1 CCCTTATTTG-GCCAAATT--A-AAAGATCGGG
*
10751 CCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGGCCAAATTAAAAGATCGGG
10780 CCCTTATTTG
1 CCCTTATTTG
10790 AACATTTTGA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 3 0.06
29 27 0.51
30 2 0.04
31 18 0.34
32 3 0.06
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGATCGGG
Found at i:10817 original size:60 final size:60
Alignment explanation
Indices: 10660--10820 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 60
10650 TAACGTTAGG
* * * * *
10660 CCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAACATTTTCGAAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
* * *
10720 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGAACATTTTCGAAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
**
10780 CCCTTATTTGAACATTTT-GACAAACATTAGGTTCTTATTTG
1 CCCTTATTTGAACATTTTCGA-AAACATTAGGCCCTTATTTG
10821 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
59 2 0.02
60 91 0.98
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (60 bp):
CCCTTATTTGAACATTTTCGAAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
Found at i:14504 original size:39 final size:39
Alignment explanation
Indices: 14450--14528 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
14440 TAAACGCTAC
14450 ACTAGGAACATCATCATCTGGCTTTAAACAGTATCCAAG
1 ACTAGGAACATCATCATCTGGCTTTAAACAGTATCCAAG
* *
14489 ACTAGGAATATCATCATCTGGCTTTGAACAGTATCCAAG
1 ACTAGGAACATCATCATCTGGCTTTAAACAGTATCCAAG
14528 A
1 A
14529 AATTAAAAAT
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:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (39 bp):
ACTAGGAACATCATCATCTGGCTTTAAACAGTATCCAAG
Found at i:34452 original size:30 final size:29
Alignment explanation
Indices: 34389--34458 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
34379 ACCTAACCGT
*****
34389 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAAGC
34418 CAAATAAGCCCCTGAACTATTAAAAAAAGC
1 CAAATAAGCCCCTGAACTATT-AAAAAAGC
34448 CAAATAAGCCC
1 CAAATAAGCCC
34459 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAAGC
Found at i:36938 original size:16 final size:17
Alignment explanation
Indices: 36914--36947 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
36904 TCTAGGTTGG
*
36914 AAGATAGAAAA-AAAAA
1 AAGAAAGAAAAGAAAAA
36930 AAGAAAGAAAAGAAAAA
1 AAGAAAGAAAAGAAAAA
36947 A
1 A
36948 TTAATGGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAAAGAAAAA
Found at i:37807 original size:33 final size:33
Alignment explanation
Indices: 37762--37836 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
37752 ATGCATCTTT
* * *
37762 CCCTTCTTTTGCCTTCTCCTCC-GCATATTCTGC
1 CCCTTCTCTTGCCTTCTCC-CCTGCATATGCCGC
*
37795 CCCTTCTCTTGCCTTCTCCCCTGTATATGCCGC
1 CCCTTCTCTTGCCTTCTCCCCTGCATATGCCGC
37828 CCCTTCTCT
1 CCCTTCTCT
37837 CGTCATGGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.05, C:0.45, G:0.09, T:0.40
Consensus pattern (33 bp):
CCCTTCTCTTGCCTTCTCCCCTGCATATGCCGC
Done.