Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022533.1 Corchorus olitorius cultivar O-4 contig22566, 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: 16106
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Found at i:2025 original size:9 final size:9
Alignment explanation
Indices: 1971--2043 Score: 85
Period size: 9 Copynumber: 8.1 Consensus size: 9
1961 AACCTTCTTC
1971 ATAATACAT-
1 ATAATA-ATA
*
1980 ATAACAATA
1 ATAATAATA
*
1989 CTAATAATA
1 ATAATAATA
1998 ATAATAATA
1 ATAATAATA
2007 ATAATAATA
1 ATAATAATA
2016 ATAATAATA
1 ATAATAATA
* *
2025 AAAATAAAA
1 ATAATAATA
*
2034 ATAAAAATA
1 ATAATAATA
2043 A
1 A
2044 ATAAGGATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
8 2 0.04
9 52 0.96
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.27
Consensus pattern (9 bp):
ATAATAATA
Found at i:2044 original size:6 final size:6
Alignment explanation
Indices: 1971--2043 Score: 85
Period size: 6 Copynumber: 12.2 Consensus size: 6
1961 AACCTTCTTC
* *
1971 ATAATA CAT-ATA ACAATA CTAATA ATAATA ATAATA ATAATA ATAATA
1 ATAATA -ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * *
2019 ATAATA AAAATA AAAATA AAAATA A
1 ATAATA ATAATA ATAATA ATAATA A
2044 ATAAGGATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
5 1 0.02
6 57 0.95
7 2 0.03
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.27
Consensus pattern (6 bp):
ATAATA
Found at i:8851 original size:441 final size:439
Alignment explanation
Indices: 7942--8902 Score: 1453
Period size: 441 Copynumber: 2.2 Consensus size: 439
7932 GCATTAAATG
* * * * *
7942 GTCCAACCCATAATTATGAGGGATTAAATAGCATAAAGCATAAAAATCTTAGGATCATTTGATAA
1 GTCCAACCCAAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTCTAAGGATCATTTGATAA
*
8007 ATAATCCAGC-AAGAAAAATATTTGTTTATGGAGACCAAACATAAAAATTCCCTTCTGAACCCTC
66 ATAATCCAGCAAAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATTCCCTTCTGAACCCTC
* *
8071 TACGAAACTCATTAATCAAATTCAGCTTTGAGACCCTTAACGAAAATCGTAGATCACACAATAAC
131 TACGAAACTCATTAATCAAATTCAGCTTTGAGACCCTTAACGAAAACCATAGATCACACAATAAC
8136 CTTTTAACCGACACTTGAATAACCTCAATCGGACAAGTGGGAAAAAAATTATACGTATCAAATAG
196 CTTTTAACCGACACTTGAATAACCTCAATCGGACAAGTGGGAAAAAAATTATACGTATCAAATAG
* *
8201 ACCGGAAATCAAGACCACAAAATTTCAAAAGCATTTTTTAAAATCAAAACATTAAATTTGGCTTT
261 ACCGGAAATCAAGACCACAAAATTTCAAAAGCATTTTTTAAAATCAAAACATTAAAATTGACTTT
* * * *
8266 TGAGTTCTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATACACACTTGAATCACCTTGAT
326 TGAGTCCTTCATGAAAGTTGTAAATCACGAAATTACCTTTTAATACACACTTGAATCACCTTGAT
*
8331 CAGACAAGCAAAAGAAAAAATAAAAGAATTAAAGCCAAAACGTTCAGTC
391 CAGACAAGCAAAACAAAAAATAAAAGAATTAAAGCCAAAACGTTCAGTC
* ** * *
8380 GTCCAACCGAGAAATTGTTCGGGGCTAAATAGCATAAAGCATAAAAGTCTAAGGATAATTTGATA
1 GTCCAACCCA-AAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTCTAAGGATCATTTGATA
* *
8445 AATAATCCAGCAAAAAAAAATATTTGTTTATGGAGACTAAACATAAAAATTCCC-TCTTGAATCC
65 AATAATCCAGCAAAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATTCCCTTC-TGAACCC
* *
8509 TCTACGAAACTCATTAATCAAATTCAGTTTTGA-AGCCCTTAACGAAACCCATAGATCACACAAT
129 TCTACGAAACTCATTAATCAAATTCAGCTTTGAGA-CCCTTAACGAAAACCATAGATCACACAAT
* *
8573 AATCTTTTAACCGACACTTGAATAACCTCAATCGGACAAGT-GGAATAAAAATTATAGGATATCA
193 AACCTTTTAACCGACACTTGAATAACCTCAATCGGACAAGTGGGAA-AAAAATTATACG-TATCA
* * *
8637 AATAGACCGGTAATCAAGACCATAAAATTTTAAAAGCATTTTTTAAAATCAAAACATTAAAATTG
256 AATAGACCGGAAATCAAGACCACAAAATTTCAAAAGCATTTTTTAAAATCAAAACATTAAAATTG
* *
8702 ACTTTTGAGTCCTTCATGAAAGTTGTAAATCACGAAATTACGTTTTAATAGACACTTGAATCACC
321 ACTTTTGAGTCCTTCATGAAAGTTGTAAATCACGAAATTACCTTTTAATACACACTTGAATCACC
* * * ** *
8767 TTGATCGGACCAGCAAAACAAAAACTAAAAGAATTAAAGCCGGAACGTTTAGTC
386 TTGATCAGACAAGCAAAACAAAAAATAAAAGAATTAAAGCCAAAACGTTCAGTC
* * * *
8821 GTCCAACCCAAAACTTGTGAGGGACTAAATAGCATAAAGTATAAAAGTATATGAATCATTTGATA
1 GTCCAACCCAAAA-TTGTGAGGGACTAAATAGCATAAAGCATAAAAGTCTAAGGATCATTTGATA
* *
8886 AATAAACCAACAAAAAA
65 AATAATCCAGCAAAAAA
8903 TGATTTATTT
Statistics
Matches: 468, Mismatches: 48, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
438 9 0.02
439 63 0.13
440 158 0.34
441 238 0.51
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (439 bp):
GTCCAACCCAAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTCTAAGGATCATTTGATAA
ATAATCCAGCAAAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATTCCCTTCTGAACCCTC
TACGAAACTCATTAATCAAATTCAGCTTTGAGACCCTTAACGAAAACCATAGATCACACAATAAC
CTTTTAACCGACACTTGAATAACCTCAATCGGACAAGTGGGAAAAAAATTATACGTATCAAATAG
ACCGGAAATCAAGACCACAAAATTTCAAAAGCATTTTTTAAAATCAAAACATTAAAATTGACTTT
TGAGTCCTTCATGAAAGTTGTAAATCACGAAATTACCTTTTAATACACACTTGAATCACCTTGAT
CAGACAAGCAAAACAAAAAATAAAAGAATTAAAGCCAAAACGTTCAGTC
Done.