Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021045.1 Corchorus olitorius cultivar O-4 contig21078, 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: 2984
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Found at i:1445 original size:72 final size:70
Alignment explanation
Indices: 1197--2072 Score: 694
Period size: 71 Copynumber: 12.2 Consensus size: 70
1187 CAATCAACCT
* * * * * * *
1197 AGGGTGGTCTTTCTTCAGTTGT-TTTCAAGTTGATCCAGGGCGATCCTTCTTCAATTCATTTTAG
1 AGGGTGGTCTTTCTTCAGTT-TATGTC-AGTTGATCCAGGGTGGTCTTTCTTCAGTTTATTTCAG
*
1261 TCGACCC
64 TTGACCC
* * *
1268 AGGGTGGTCTTTCTTCAGCTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAGT
1 AGGGTGGTCTTTCTTCAGTTTATGTCAGTTGATCCAGGGTGGTC-TTTCTTCAGTTTATTTCAGT
1333 TGACCC
65 TGACCC
* * * ** * * *
1339 AGGGCGGTCTTTCTTCAGCTTATTTTGGATTGATCCAGGGCGGTCTTTCTTTAGTTTATTGCAGT
1 AGGGTGGTCTTTCTTCAGTTTATGTCAG-TTGATCCAGGGTGGTCTTTCTTCAGTTTATTTCAGT
*
1404 TGACCT
65 TGACCC
* *
1410 AGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCTTTCTTCAGTTTATTTCAG
1 AGGGTGGTC-TTTCTTCAGTTTATGTCAG-TTGATCCAGGGTGGTCTTTCTTCAGTTTATTTCAG
1475 TTGACCC
64 TTGACCC
** * * * *
1482 AGGGCAGT-TTTTTTCAGTTTAT-TGCAGTTGACCCAGGGTGGTCTATTCTTTAGTTTATGTCAG
1 AGGGTGGTCTTTCTTCAGTTTATGT-CAGTTGATCCAGGGTGGTCT-TTCTTCAGTTTATTTCA-
* * *
1545 GATGATCG
63 GTTGACCC
* *
1553 AGGGTGGTCTTTCTTCAGTTTAT-TGCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAG
1 AGGGTGGTCTTTCTTCAGTTTATGT-CAGTTGATCCAGGGTGGTC-TTTCTTCAGTTTATTTCAG
* * *
1617 AATGATCG
64 -TTGACCC
* * * *
1625 AGGGTGGT-TTTCCTTTAGTTTATTTCAGTTGA-CCTAGGGCGGTCTTTCTTCAGTTTATTGCAG
1 AGGGTGGTCTTT-CTTCAGTTTATGTCAGTTGATCC-AGGGTGGTCTTTCTTCAGTTTATTTCAG
1688 TTGACCC
64 TTGACCC
* * *
1695 AGGGTGGTCTTTTCTTCAGCTTATGTCAGAATGATCGAGGGTGGTCTTTCTTCAGTTTATTTCAG
1 AGGGTGGTC-TTTCTTCAGTTTATGTCAG-TTGATCCAGGGTGGTCTTTCTTCAGTTTATTTCAG
*
1760 TTAACCCC
64 TTGA-CCC
* * *
1768 AGGGTGGTCTTTTTCTTCAGTTTATGTCAGTCGACCCAGGGGGGGTCTTTTCTTC-GTTTTATTT
1 AGGGTGGTC--TTTCTTCAGTTTATGTCAGTTGATCCA-GGGTGGTC-TTTCTTCAG-TTTATTT
*
1832 CAGTTGACCT
61 CAGTTGACCC
* * * * * * * * * *
1842 ATGGTAGTCTTTCTTCAGTTTGTGTCGGAATGATCAAGGGTGGT-TGTTCCTCAGTTCAATTCGG
1 AGGGTGGTCTTTCTTCAGTTTATGTCAG-TTGATCCAGGGTGGTCT-TTCTTCAGTTTATTTCAG
* * *
1906 AATGATCG
64 -TTGACCC
* * * ** * ** * * *
1914 AGGGTGGTCGTTCTGCAGTTTATTTCAGTTGGCCCAGGGTGGTCTTTCTTTAGTTGGTGTCGGAA
1 AGGGTGGTCTTTCTTCAGTTTATGTCAGTTGATCCAGGGTGGTCTTTCTTCAGTTTATTTCAG-T
* *
1979 TGATCG
65 TGACCC
* * **
1985 AGGGTGGTCATTT-TTCAGTTTATTTCAAG-TGA-CCTAGGGTGGTCTTGCTTCAACTTATTTCA
1 AGGGTGGTC-TTTCTTCAGTTTATGTC-AGTTGATCC-AGGGTGGTCTTTCTTCAGTTTATTTCA
*
2047 GAATGACCC
63 G-TTGACCC
2056 AGGGTGGTCTTTCTTCA
1 AGGGTGGTCTTTCTTCA
2073 ATTCTTCAAG
Statistics
Matches: 662, Mismatches: 112, Indels: 62
0.79 0.13 0.07
Matches are distributed among these distances:
69 15 0.02
70 65 0.10
71 252 0.38
72 251 0.38
73 23 0.03
74 36 0.05
75 20 0.03
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (70 bp):
AGGGTGGTCTTTCTTCAGTTTATGTCAGTTGATCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTT
GACCC
Found at i:2057 original size:107 final size:106
Alignment explanation
Indices: 1197--2072 Score: 741
Period size: 107 Copynumber: 8.2 Consensus size: 106
1187 CAATCAACCT
* * * * * * * * *
1197 AGGGTGGTCTTTCTTCAGTTGT-TTTCAAGTTGATCCAGGGCGATCCTTCTTCAATTCATTTTAG
1 AGGGTGGTCTTTCTTCAGTT-TATGTC-AGATGATCGAGGGTGGTCTTTCTTCAGTTTATTTCAG
* * *
1261 TCGACCCAGGGTGGTC-TTTCTTCAGCTTATTTCAGTTGACCC
64 TTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAGATGACCC
* * * * * * **
1303 AGGGTGGTCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGCTTATTTTGGA
1 AGGGTGGTC-TTTCTTCAGTTTATGTCAGATGATCGAGGGTGGTCTTTCTTCAGTTTATTTCAG-
* * * * * *
1368 TTGATCCAGGGCGGTC-TTTCTTTAGTTTATTGCAGTTGACCT
64 TTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAGATGACCC
1410 AGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCTTTCTTCAGTTTATTTCAG
1 AGGGTGGTC-TTTCTTCAGTTTATGTCAG-ATGATCGAGGGTGGTCTTTCTTCAGTTTATTTCAG
** * *
1475 TTGACCCAGGGCAGT-TTTT-TTCAGTTTATTGCAGTTGACCC
64 TTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAGATGACCC
* *
1516 AGGGTGGTCTATTCTTTAGTTTATGTCAGGATGATCGAGGGTGGTCTTTCTTCAGTTTATTGCAG
1 AGGGTGGTCT-TTCTTCAGTTTATGTCA-GATGATCGAGGGTGGTCTTTCTTCAGTTTATTTCAG
* * *
1581 TTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCG
64 TTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAG-ATGACCC
* * * * * * *
1625 AGGGTGGT-TTTCCTTTAGTTTATTTCAGTTGACCTAGGGCGGTCTTTCTTCAGTTTATTGCAGT
1 AGGGTGGTCTTT-CTTCAGTTTATGTCAGATGATCGAGGGTGGTCTTTCTTCAGTTTATTTCAGT
* * * *
1689 TGACCCAGGGTGGTCTTTTCTTCAGCTTATGTCAGAATGATCG
65 TGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAG-ATGACCC
* * * * * *
1732 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTAACCCCAGGGTGGTCTTTTTCTTCAGTTTATGTCA
1 AGGGTGGTCTTTCTTCAGTTTATGTCAGATGA-TCGAGGGTGGTC--TTTCTTCAGTTTATTTCA
* * * *
1797 GTCGACCCAGGGGGGGTCTTTTCTTC-GTTTTATTTCAGTTGACCT
63 GTTGACCCA-GGGTGGTCTTTTCTTCAG-TTTATTTCAGATGACCC
* * * * * * * * *
1842 ATGGTAGTCTTTCTTCAGTTTGTGTCGGAATGATCAAGGGTGGT-TGTTCCTCAGTTCAATTCGG
1 AGGGTGGTCTTTCTTCAGTTTATGTCAG-ATGATCGAGGGTGGTCT-TTCTTCAGTTTATTTCAG
* * * * * * *
1906 AATGATCGAGGGTGGTC-GTTCTGCAGTTTATTTCAGTTGGCCC
64 -TTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAGATGACCC
* ** *
1949 AGGGTGGTCTTTCTTTAGTTGGTGTCGGAATGATCGAGGGTGGTCATTT-TTCAGTTTATTTCAA
1 AGGGTGGTCTTTCTTCAGTTTATGTCAG-ATGATCGAGGGTGGTC-TTTCTTCAGTTTATTTC-A
* * **
2013 G-TGACCTAGGGTGGTC-TTGCTTCAACTTATTTCAGAATGACCC
63 GTTGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAG-ATGACCC
2056 AGGGTGGTCTTTCTTCA
1 AGGGTGGTCTTTCTTCA
2073 ATTCTTCAAG
Statistics
Matches: 649, Mismatches: 96, Indels: 49
0.82 0.12 0.06
Matches are distributed among these distances:
105 1 0.00
106 159 0.24
107 293 0.45
108 93 0.14
109 17 0.03
110 61 0.09
111 25 0.04
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (106 bp):
AGGGTGGTCTTTCTTCAGTTTATGTCAGATGATCGAGGGTGGTCTTTCTTCAGTTTATTTCAGTT
GACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAGATGACCC
Found at i:2073 original size:36 final size:35
Alignment explanation
Indices: 1197--2072 Score: 740
Period size: 36 Copynumber: 24.5 Consensus size: 35
1187 CAATCAACCT
*
1197 AGGGTGGTCTTTCTTCAGTTGT-TTTCAAGTTGATCC
1 AGGGTGGTCTTTCTTCAGTT-TATTTC-AGTTGACCC
* * * * * * *
1233 AGGGCGATCCTTCTTCAATTCATTTTAGTCGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
*
1268 AGGGTGGTCTTTCTTCAGCTTATTTCAGTTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
1303 AGGGTGGTCTTTTCTTCAGTTTATTTCAGTTGACCC
1 AGGGTGGTC-TTTCTTCAGTTTATTTCAGTTGACCC
* * ** *
1339 AGGGCGGTCTTTCTTCAGCTTATTTTGGATTGATCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAG-TTGACCC
* * * *
1375 AGGGCGGTCTTTCTTTAGTTTATTGCAGTTGACCT
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
* * * *
1410 AGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCG
1 AGGGTGGTC-TTTCTTCAGTTTATTTCAG-TTGACCC
1447 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
** * *
1482 AGGGCAGT-TTTTTTCAGTTTATTGCAGTTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
* * * * *
1516 AGGGTGGTCTATTCTTTAGTTTATGTCAGGATGATCG
1 AGGGTGGTCT-TTCTTCAGTTTATTTCA-GTTGACCC
*
1553 AGGGTGGTCTTTCTTCAGTTTATTGCAGTTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
* * * *
1588 AGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCG
1 AGGGTGGTC-TTTCTTCAGTTTATTTCAG-TTGACCC
* *
1625 AGGGTGGT-TTTCCTTTAGTTTATTTCAGTTGACCT
1 AGGGTGGTCTTT-CTTCAGTTTATTTCAGTTGACCC
* *
1660 AGGGCGGTCTTTCTTCAGTTTATTGCAGTTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
* * * * *
1695 AGGGTGGTCTTTTCTTCAGCTTATGTCAGAATGATCG
1 AGGGTGGTC-TTTCTTCAGTTTATTTCAG-TTGACCC
*
1732 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTAACCCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGA-CCC
* *
1768 AGGGTGGTCTTTTTCTTCAGTTTATGTCAGTCGACCC
1 AGGGTGGTC--TTTCTTCAGTTTATTTCAGTTGACCC
* *
1805 AGGGGGGGTCTTTTCTTC-GTTTTATTTCAGTTGACCT
1 A-GGGTGGTC-TTTCTTCAG-TTTATTTCAGTTGACCC
* * * * * * * *
1842 ATGGTAGTCTTTCTTCAGTTTGTGTCGGAATGATCA
1 AGGGTGGTCTTTCTTCAGTTTATTTCAG-TTGACCC
* * * * * * *
1878 AGGGTGGT-TGTTCCTCAGTTCAATTCGGAATGATCG
1 AGGGTGGTCT-TTCTTCAGTTTATTTCAG-TTGACCC
* * *
1914 AGGGTGGTCGTTCTGCAGTTTATTTCAGTTGGCCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
* ** * * * * *
1949 AGGGTGGTCTTTCTTTAGTTGGTGTCGGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATTTCAG-TTGACCC
*
1985 AGGGTGGTCATTT-TTCAGTTTATTTCAAG-TGACCT
1 AGGGTGGTC-TTTCTTCAGTTTATTTC-AGTTGACCC
* ** *
2020 AGGGTGGTCTTGCTTCAACTTATTTCAGAATGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAG-TTGACCC
2056 AGGGTGGTCTTTCTTCA
1 AGGGTGGTCTTTCTTCA
2073 ATTCTTCAAG
Statistics
Matches: 668, Mismatches: 143, Indels: 58
0.77 0.16 0.07
Matches are distributed among these distances:
34 34 0.05
35 204 0.31
36 319 0.48
37 84 0.13
38 27 0.04
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (35 bp):
AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
Done.