Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009664.1 Corchorus capsularis cultivar CVL-1 contig09685, 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: 18108
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:88 original size:18 final size:18
Alignment explanation
Indices: 62--98 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
52 CGCGACCCAC
62 TGTTCTTCTTCTTTTTTT
1 TGTTCTTCTTCTTTTTTT
*
80 TGTTTTTCTTCTTTTTTT
1 TGTTCTTCTTCTTTTTTT
98 T
1 T
99 TCTTCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (18 bp):
TGTTCTTCTTCTTTTTTT
Found at i:100 original size:13 final size:14
Alignment explanation
Indices: 77--106 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
67 TTCTTCTTTT
77 TTTTGTTTTTCTTC
1 TTTTGTTTTTCTTC
91 TTTT-TTTTTCTTC
1 TTTTGTTTTTCTTC
104 TTT
1 TTT
107 AAAGGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTGTTTTTCTTC
Found at i:1652 original size:12 final size:10
Alignment explanation
Indices: 1627--1739 Score: 50
Period size: 11 Copynumber: 12.1 Consensus size: 10
1617 GTTGGTTCTC
1627 TAAATATATT
1 TAAATATATT
1637 TAAACTATATT
1 TAAA-TATATT
*
1648 TTAA-AT-TT
1 TAAATATATT
*
1656 T-ATTA-ATT
1 TAAATATATT
* *
1664 TATATATAAT
1 TAAATATATT
* * *
1674 AAAACATATA
1 TAAATATATT
1684 T-AATATATTT
1 TAAATATA-TT
1694 TAAATATATT
1 TAAATATATT
1704 T--ATATA--
1 TAAATATATT
1710 -AAATATATT
1 TAAATATATT
*
1719 TATAATATATA
1 TA-AATATATT
1730 T-AATATATT
1 TAAATATATT
1739 T
1 T
1740 TAAAATTTAT
Statistics
Matches: 75, Mismatches: 15, Indels: 27
0.64 0.13 0.23
Matches are distributed among these distances:
7 6 0.08
8 12 0.16
9 17 0.23
10 17 0.23
11 23 0.31
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.50
Consensus pattern (10 bp):
TAAATATATT
Found at i:1684 original size:2 final size:2
Alignment explanation
Indices: 1679--1819 Score: 54
Period size: 2 Copynumber: 76.5 Consensus size: 2
1669 ATAATAAAAC
* * * *
1679 AT AT AT A- AT AT AT -T TT AA AT AT AT TT AT AT A- AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
1718 TT AT A- AT AT AT AT A- AT AT AT -T TT A- AA AT TT AT TT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1756 AT AT AT AT AA AA AC AT AT AT A- AT AT A- AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1795 TT TT AA AT AT AT A- AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1820 AAAATATCTA
Statistics
Matches: 104, Mismatches: 23, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
1 12 0.12
2 92 0.88
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1698 original size:45 final size:44
Alignment explanation
Indices: 1642--1781 Score: 165
Period size: 45 Copynumber: 3.1 Consensus size: 44
1632 ATATTTAAAC
*
1642 TATATTTTAAATTTTATTAATTTATATATAATAAAACATATATAA
1 TATATTTTAAA-TTTATTTATTTATATATAATAAAACATATATAA
* * * * * *
1687 TATATTTTAAATATATTTATATAAAATATATTTATAATATATATAA
1 TATATTTTAAATTTATTTAT-TTATATATA-ATAAAACATATATAA
1733 TATATTTTAAAATTTATTTATTTATATAT-ATAAAAACATATATAA
1 TATATTTT-AAATTTATTTATTTATATATAAT-AAAACATATATAA
1778 TATA
1 TATA
1782 ATATATATAA
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
44 8 0.10
45 33 0.42
46 26 0.33
47 11 0.14
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (44 bp):
TATATTTTAAATTTATTTATTTATATATAATAAAACATATATAA
Found at i:1716 original size:9 final size:9
Alignment explanation
Indices: 1679--1817 Score: 69
Period size: 9 Copynumber: 15.8 Consensus size: 9
1669 ATAATAAAAC
1679 ATATATAAT
1 ATATATAAT
*
1688 ATATTTTAA-
1 ATA-TATAAT
*
1697 ATATAT-TT
1 ATATATAAT
*
1705 ATATAAAAT
1 ATATATAAT
1714 ATATTTATAAT
1 ATA--TATAAT
1725 ATATATAAT
1 ATATATAAT
* *
1734 ATATTTTAAA
1 ATA-TATAAT
* *
1744 ATTTAT-TT
1 ATATATAAT
*
1752 ATTTAT-AT
1 ATATATAAT
*
1760 ATATA-AAA
1 ATATATAAT
*
1768 ACATAT-AT
1 ATATATAAT
1776 A-ATATAAT
1 ATATATAAT
1784 ATATATAAT
1 ATATATAAT
* *
1793 ATTTTTAA-
1 ATATATAAT
1801 ATATATAAT
1 ATATATAAT
1810 ATTATATA
1 A-TATATA
1818 TAAAAATATC
Statistics
Matches: 97, Mismatches: 21, Indels: 23
0.69 0.15 0.16
Matches are distributed among these distances:
7 4 0.04
8 34 0.35
9 35 0.36
10 16 0.16
11 8 0.08
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (9 bp):
ATATATAAT
Found at i:1731 original size:15 final size:14
Alignment explanation
Indices: 1686--1730 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
1676 AACATATATA
1686 ATATATTT-TAAAT
1 ATATATTTATAAAT
1699 ATAT-TTATATAAA-
1 ATATATT-TATAAAT
1712 ATATATTTAT-AAT
1 ATATATTTATAAAT
1725 ATATAT
1 ATATAT
1731 AATATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 4 0.14
13 18 0.64
14 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATTTATAAAT
Found at i:1787 original size:14 final size:13
Alignment explanation
Indices: 1664--1820 Score: 75
Period size: 12 Copynumber: 12.7 Consensus size: 13
1654 TTTATTAATT
*
1664 TATATATAATAAAA
1 TATATATAAT-ATA
*
1678 CATATATAATATA
1 TATATATAATATA
*
1691 T-TTTA-AATATA
1 TATATATAATATA
*
1702 TTTATATAA-A-A
1 TATATATAATATA
*
1713 TATAT-TTATA-A
1 TATATATAATATA
1724 TATATATAATATA
1 TATATATAATATA
* * *
1737 T-TTTAAAATTTA
1 TATATATAATATA
* *
1749 TTTAT-TTATATA
1 TATATATAATATA
* *
1761 TATA-AAAACATA
1 TATATATAATATA
1773 TATAATATAATATA
1 TAT-ATATAATATA
* *
1787 TATA-ATATTTTTA
1 TATATATA-ATATA
*
1800 AATATATAATAT-
1 TATATATAATATA
1812 TATATATAA
1 TATATATAA
1821 AAATATCTAT
Statistics
Matches: 105, Mismatches: 27, Indels: 24
0.67 0.17 0.15
Matches are distributed among these distances:
10 2 0.02
11 19 0.18
12 45 0.43
13 18 0.17
14 21 0.20
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATATAATATA
Found at i:1806 original size:26 final size:26
Alignment explanation
Indices: 1679--1817 Score: 81
Period size: 26 Copynumber: 5.3 Consensus size: 26
1669 ATAATAAAAC
*
1679 ATATATAATATATTTTAAATATAT-TT
1 ATATATAATAT-TTTTAAATATATAAT
*
1705 ATATAAAATATATTTATAATATATATAAT
1 ATATATAATAT-TTT-TAA-ATATATAAT
* * * *
1734 ATATTTTAAAATTTATT-TATTTAT-AT
1 ATA-TATAATATTT-TTAAATATATAAT
* ** * *
1760 ATATA-AAAACATATATA-ATATAAT
1 ATATATAATATTTTTAAATATATAAT
1784 ATATATAATATTTTTAAATATATAAT
1 ATATATAATATTTTTAAATATATAAT
1810 ATTATATA
1 A-TATATA
1818 TAAAAATATC
Statistics
Matches: 86, Mismatches: 17, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
23 4 0.05
24 14 0.16
25 8 0.09
26 27 0.31
27 14 0.16
28 6 0.07
29 7 0.08
30 6 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATATAATATTTTTAAATATATAAT
Found at i:1807 original size:91 final size:91
Alignment explanation
Indices: 1642--1820 Score: 242
Period size: 91 Copynumber: 2.0 Consensus size: 91
1632 ATATTTAAAC
* * *
1642 TATATTTTAAATTTTATTAATTTATATATAATAAAACATATATAATATATTTTAAATATATTTAT
1 TATATTTTAAAATTTATTAATTTATATATAATAAAACATATATAATATAATATAAATATATTTAT
1707 ATAAAATATATTTATAATATATATAA
66 ATAAAATATATTTATAATATATATAA
* *
1733 TATATTTTAAAATTTATTTATTTATATAT-ATAAAAACATATATAATATAATATATATAATATTT
1 TATATTTTAAAATTTATTAATTTATATATAAT-AAAACATATATAATATAATATAAAT-ATATTT
* *
1797 -T-T-AAATATA-TAATATTATATATAA
64 ATATAAAATATATTTATAATATATATAA
1821 AAATATCTAT
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
88 13 0.16
89 7 0.09
90 3 0.04
91 50 0.63
92 6 0.08
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (91 bp):
TATATTTTAAAATTTATTAATTTATATATAATAAAACATATATAATATAATATAAATATATTTAT
ATAAAATATATTTATAATATATATAA
Found at i:1818 original size:59 final size:58
Alignment explanation
Indices: 1697--1819 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 58
1687 TATATTTTAA
* * * * *
1697 ATATATTTATATAAAATATATTTATAATATATATAATATATTTTAAAATTTATTTATT
1 ATATATATATAAAAAATATATATATAATATATATAATATATTTTAAAATATATATATT
1755 -TATATATATAAAAACATATATAATATAATATATATAATAT-TTTT-AAATATATAATATT
1 ATATATATATAAAAA-ATATAT-ATATAATATATATAATATATTTTAAAATATAT-ATATT
1813 ATATATA
1 ATATATA
1820 AAAATATCTA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
57 19 0.34
58 14 0.25
59 23 0.41
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (58 bp):
ATATATATATAAAAAATATATATATAATATATATAATATATTTTAAAATATATATATT
Done.