Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015483.1 Corchorus capsularis cultivar CVL-1 contig15504, 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: 4064
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.32
Found at i:1669 original size:109 final size:109
Alignment explanation
Indices: 1522--1796 Score: 455
Period size: 109 Copynumber: 2.5 Consensus size: 109
1512 AAAAAACCTA
1522 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1585 AAAAAATTTTAATATATCCAAATATTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATATTTTGGTAAAAATAAAGTAAT
1630 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
* *
1695 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATATTTTGGTAAAAATAAAGTAAT
*
1739 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTTTAGTAGAATAAAA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA
1797 CTATAATAGT
Statistics
Matches: 157, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
108 6 0.04
109 118 0.75
110 3 0.02
111 1 0.01
114 29 0.18
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.38
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATATTTTGGTAAAAATAAAGTAAT
Found at i:2928 original size:70 final size:70
Alignment explanation
Indices: 2852--3076 Score: 315
Period size: 70 Copynumber: 3.1 Consensus size: 70
2842 TAATTAAAAT
*
2852 AGTAAAATGGTAAAATATAATAGTAATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
1 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
2917 AGTTGAG
66 AGTT--G
*
2924 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATCATATAAAAATAGA
1 ------AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
2989 GTTTTTAGTTG
60 GTTTTTAGTTG
* * * * *
3000 AGTAAAATAGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
3065 AGTTG
66 AGTTG
3070 AGTAAAA
1 AGTAAAA
3077 CTATAAAAAC
Statistics
Matches: 139, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
70 71 0.51
76 1 0.01
78 67 0.48
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.36
Consensus pattern (70 bp):
AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:2933 original size:78 final size:77
Alignment explanation
Indices: 2846--3084 Score: 352
Period size: 78 Copynumber: 3.2 Consensus size: 77
2836 GTTTTTTAAT
2846 TAAAATAGTAAAATGGTAAAATATAATAGTAATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGT-ATAAGGATATTAGATTTAATTATATAAAAATAGA
2911 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
*
2924 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATCATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAG-TATAAGGATATTAGATTTAATTATATAAAAATAGA
2989 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* *
3002 TAAAATAGTAAAA---TAAAATAGT--TA-TA-AA-GATATTATATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATA-TAATAGTATAAGGATATTAGATTTAATTATATAAAAATAGA
3059 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
3072 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
3085 ACCTAAACAA
Statistics
Matches: 154, Mismatches: 4, Indels: 14
0.90 0.02 0.08
Matches are distributed among these distances:
70 49 0.32
71 4 0.03
72 2 0.01
74 2 0.01
75 7 0.05
76 1 0.01
78 88 0.57
79 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.13, T:0.36
Consensus pattern (77 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:3135 original size:148 final size:148
Alignment explanation
Indices: 2852--3125 Score: 329
Period size: 148 Copynumber: 1.9 Consensus size: 148
2842 TAATTAAAAT
* * * *
2852 AGTAAAATGGTAAAATATAATAGTAATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAGTAATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
*** * * ** * *
2917 AGTTGAGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATCATATAA
66 AGTTGAGTAAAATAGTAAAAACCTAAAATATAATAGTTAGAAAGATATTAGATCAAATAAGATAA
2982 AAATAGAGTTTTTAGTTG
131 AAATAGAGTTTTTAGTTG
* *
3000 AGTAAAATAGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAGTAATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
** * *
3065 AGTTGAGTAAAACTA-TAAAAACCTAAACA-ATGGTAAGTTAGAAATATATTTGA-CAAATAAG
66 AGTTGAGTAAAA-TAGTAAAAACCTAAA-ATATAAT-AGTTAGAAAGATATTAGATCAAATAAG
3126 GATATAATAG
Statistics
Matches: 104, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
148 87 0.84
149 17 0.16
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (148 bp):
AGTAAAATAGTAAAATAAAATAGTAATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTGAGTAAAATAGTAAAAACCTAAAATATAATAGTTAGAAAGATATTAGATCAAATAAGATAA
AAATAGAGTTTTTAGTTG
Done.