Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015607.1 Corchorus olitorius cultivar O-4 contig15640, 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: 4949
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Found at i:1650 original size:35 final size:35
Alignment explanation
Indices: 1606--2347 Score: 243
Period size: 35 Copynumber: 21.6 Consensus size: 35
1596 ATATTAACCT
* *
1606 AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGATCC
* ** * *
1641 AGGGTGGTCTTTTTTTCAGTTTATGGCAGAATGATCG
1 AGGGTGGTC-TTTCTTCAGTTTATTTCAG-TTGATCC
* *
1678 AGGGTGGTCTTTCTTCAATTCATTTCAGTTGA-CC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGATCC
* *
1712 TAGGGCGGTCTTTTCTTCAG-TTATTTTCAATTGA-CC
1 -AGGGTGGTC-TTTCTTCAGTTTA-TTTCAGTTGATCC
* * *
1748 TAGGCTGGTCTTTCTTTAGTTTATTTCAGTCGATCC
1 -AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGATCC
** * * * * *
1784 AGGGTGACCTCTCTTAAG-TGACTTTCAATTGACCC
1 AGGGTGGTCTTTCTTCAGTTTA-TTTCAGTTGATCC
** * **
1819 AAAGCGGTCCATCTTC----TA----A-TTGATCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGATCC
* * * * *
1845 AGGGCGGTCTATC-TCTAGTTTACTTCGGAATGATCC
1 AGGGTGGTCTTTCTTC-AGTTTATTTCAG-TTGATCC
* * * *
1881 AGGGCGATC-TTCTTTTAGTTTATTTCAGTTGACCC
1 AGGGTGGTCTTTC-TTCAGTTTATTTCAGTTGATCC
* * *** * *
1916 AGGATGGTCTTTCTTCAGTTCAAAACAGAATGATCA
1 AGGGTGGTCTTTCTTCAGTTTATTTCAG-TTGATCC
* * **** * * * *
1952 AAGGTAGT-TGTTCTTCAGTACGGTCCGGAATGATCA
1 AGGGTGGTCT-TTCTTCAGTTTATTTCAG-TTGATCC
* * * *
1988 AGGGTGGTCATAT-TTCAG-TT-TCT-AGTCGACCC
1 AGGGTGGTC-TTTCTTCAGTTTATTTCAGTTGATCC
* * * * *
2020 AGGGTGGTCTCTT-TTCAG-TTGTGTCGGAATGATCG
1 AGGGTGGTCT-TTCTTCAGTTTATTTCAG-TTGATCC
* * ** **
2055 AGGGTGGTCGTTCTTCAGTTCATTTTTGTTGGCCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGATCC
* * * *
2090 AGGGTAGTCTTTCTTCAATTTATTTTAGTTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGATCC
* * * * * * *
2125 AGGGTGGTCTCTCTTTAG-TTGTGTCGGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATTTCAG-TTGATCC
* * * *
2160 AGGGTGGTCGTTCTCCAGTTTATTTCTGTTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGATCC
* *
2195 AGGGTGGTCTTTCCTCA----A----AG-TGATCG
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGATCC
*
2221 AGGGTGGTCATTCTTCAGTTTATTTCAGTTGATCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGATCC
*** * *
2256 AGGGTGGTCTTTCTTCAACCTATGTTCAATGTGATCG
1 AGGGTGGTCTTTCTTCAGTTTAT-TTCAGT-TGATCC
* * *
2293 AGGGTGGTCATTCTTCAGTTAATTTCAGTTGATTC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGATCC
*
2328 AGGGTAGTCTTTCTTCAGTT
1 AGGGTGGTCTTTCTTCAGTT
2348 ACTTATTCTA
Statistics
Matches: 506, Mismatches: 156, Indels: 90
0.67 0.21 0.12
Matches are distributed among these distances:
25 2 0.00
26 35 0.07
27 2 0.00
30 3 0.01
31 2 0.00
32 21 0.04
33 3 0.01
34 13 0.03
35 237 0.47
36 149 0.29
37 38 0.08
38 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (35 bp):
AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGATCC
Found at i:1659 original size:36 final size:36
Alignment explanation
Indices: 1606--1789 Score: 169
Period size: 36 Copynumber: 5.2 Consensus size: 36
1596 ATATTAACCT
*
1606 AGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGACCC
1 AGGGTGGTCTTTTCTTCAGTTTATTTCAGTTGACCC
* ** * * *
1641 AGGGTGGTCTTTTTTTCAGTTTATGGCAGAATGATCG
1 AGGGTGGTCTTTTCTTCAGTTTATTTCAG-TTGACCC
* * *
1678 AGGGTGGTC-TTTCTTCAATTCATTTCAGTTGACCT
1 AGGGTGGTCTTTTCTTCAGTTTATTTCAGTTGACCC
* * *
1713 AGGGCGGTCTTTTCTTCAG-TTATTTTCAATTGACCT
1 AGGGTGGTCTTTTCTTCAGTTTA-TTTCAGTTGACCC
* * * *
1749 AGGCTGGTC-TTTCTTTAGTTTATTTCAGTCGATCC
1 AGGGTGGTCTTTTCTTCAGTTTATTTCAGTTGACCC
1784 AGGGTG
1 AGGGTG
1790 ACCTCTCTTA
Statistics
Matches: 117, Mismatches: 27, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
35 44 0.38
36 60 0.51
37 13 0.11
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (36 bp):
AGGGTGGTCTTTTCTTCAGTTTATTTCAGTTGACCC
Found at i:2145 original size:105 final size:105
Alignment explanation
Indices: 2010--2212 Score: 327
Period size: 105 Copynumber: 1.9 Consensus size: 105
2000 TTTCAGTTTC
*
2010 TAGTCGACCCAGGGTGGTCTCTTTTCAGTTGTGTCGGAATGATCGAGGGTGGTCGTTCTTCAGTT
1 TAGTCGACCCAGGGTGGTCTCTTTTCAGTTGTGTCGGAATGATCGAGGGTGGTCGTTCTCCAGTT
* * *
2075 CATTTTTGTTGGCCCAGGGTAGTCTTTCTTCAATTTATTT
66 CATTTCTGTTGACCCAGGGTAGTCTTTCCTCAATTTATTT
*
2115 TAGTTGACCCAGGGTGGTCTCTCTTT-AGTTGTGTCGGAATGATCGAGGGTGGTCGTTCTCCAGT
1 TAGTCGACCCAGGGTGGTCTCT-TTTCAGTTGTGTCGGAATGATCGAGGGTGGTCGTTCTCCAGT
* *
2179 TTATTTCTGTTGACCCAGGGTGGTCTTTCCTCAA
65 TCATTTCTGTTGACCCAGGGTAGTCTTTCCTCAA
2213 AGTGATCGAG
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
105 87 0.97
106 3 0.03
ACGTcount: A:0.14, C:0.19, G:0.28, T:0.39
Consensus pattern (105 bp):
TAGTCGACCCAGGGTGGTCTCTTTTCAGTTGTGTCGGAATGATCGAGGGTGGTCGTTCTCCAGTT
CATTTCTGTTGACCCAGGGTAGTCTTTCCTCAATTTATTT
Found at i:2252 original size:61 final size:61
Alignment explanation
Indices: 2154--2273 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 61
2144 TGTGTCGGAA
* *
2154 TGATCGAGGGTGGTCGTTCTCCAGTTTATTTCTGTTGACCCAGGGTGGTCTTTCCTCAAAG
1 TGATCGAGGGTGGTCATTCTCCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCCTCAAAG
* * *
2215 TGATCGAGGGTGGTCATTCTTCAGTTTATTTCAGTTGATCCAGGGTGGTCTTTCTTCAA
1 TGATCGAGGGTGGTCATTCTCCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCCTCAA
2274 CCTATGTTCA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.38
Consensus pattern (61 bp):
TGATCGAGGGTGGTCATTCTCCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCCTCAAAG
Found at i:2331 original size:72 final size:72
Alignment explanation
Indices: 2209--2344 Score: 236
Period size: 72 Copynumber: 1.9 Consensus size: 72
2199 TGGTCTTTCC
* *
2209 TCAAAGTGATCGAGGGTGGTCATTCTTCAGTTTATTTCAGTTGATCCAGGGTGGTCTTTCTTCAA
1 TCAAAGTGATCGAGGGTGGTCATTCTTCAGTTAATTTCAGTTGATCCAGGGTAGTCTTTCTTCAA
2274 CCTATGT
66 CCTATGT
* *
2281 TCAATGTGATCGAGGGTGGTCATTCTTCAGTTAATTTCAGTTGATTCAGGGTAGTCTTTCTTCA
1 TCAAAGTGATCGAGGGTGGTCATTCTTCAGTTAATTTCAGTTGATCCAGGGTAGTCTTTCTTCA
2345 GTTACTTATT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.40
Consensus pattern (72 bp):
TCAAAGTGATCGAGGGTGGTCATTCTTCAGTTAATTTCAGTTGATCCAGGGTAGTCTTTCTTCAA
CCTATGT
Done.