Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019245.1 Corchorus olitorius cultivar O-4 contig19278, 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: 22982
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:8584 original size:30 final size:31
Alignment explanation
Indices: 8549--8612 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
8539 TGGTTCGTAT
* *
8549 TATATTGGCCGTTCGTTTT-TTTAAAGGTAA
1 TATATTGGCCGTTCGTTTTGTATAAAGGAAA
8579 TATATTGGCCGTTCGTTTTGTATAAAGGAAA
1 TATATTGGCCGTTCGTTTTGTATAAAGGAAA
8610 TAT
1 TAT
8613 TTCCTTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (31 bp):
TATATTGGCCGTTCGTTTTGTATAAAGGAAA
Found at i:9270 original size:57 final size:56
Alignment explanation
Indices: 9180--9294 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 56
9170 TATCCGTTTC
* *
9180 CTTTCACACAATAAATATTATAATAAATTCTATCCCCTCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCCTATCCCC-CTATCTCTACATAATTATT
9237 CTTTCACACAATAAATATTATAATAAATCCTATCCCCCTATCTCTACATAATTATT
1 CTTTCACACAATAAATATTATAATAAATCCTATCCCCCTATCTCTACATAATTATT
9293 CT
1 CT
9295 ACAAAATAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 20 0.36
57 36 0.64
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (56 bp):
CTTTCACACAATAAATATTATAATAAATCCTATCCCCCTATCTCTACATAATTATT
Found at i:9418 original size:42 final size:42
Alignment explanation
Indices: 9359--9439 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
9349 TGAGGATCAA
* *
9359 GATTTGAGTTGAGTATTTCTTAGTTTACAAATAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
9401 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
9440 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:13867 original size:181 final size:180
Alignment explanation
Indices: 13509--13871 Score: 473
Period size: 181 Copynumber: 2.0 Consensus size: 180
13499 AAATTATGTA
* *
13509 ATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAATTCTTTGGAAGCATTTTTTATAC
1 ATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTTTTGATAC
* *
13574 CTTGAACATTAAATTCAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAACCTTTCAA
66 CTTGAACATTAAATTCAGTTCTCGAGTCCTTCATGAAAGTTGTAGATCATGAAACAACCTTTCAA
* * * * * *
13639 GAAACGCTTGAATGATCTCAATCAGACATCTGGAGCAAAAGTTATATAAT
131 GAAACACTTAAATCACCTCAATCAGAAATCTGGAGCAAAAATTATATAAT
* *
13689 ATATTAAGTGGATCGTCTATTTCCCGTTAACCGAAACAACAAATT-TTTCGGAAGCATTTTTGAT
1 ATATTAAGTAGACCGTCTATTT-CCGTTAACCGAAACAACAAATTCTTT-GGAAGCATTTTTGAT
* *
13753 A-CTTGAAACATTAAATTTAGTTCTCGAGTCCTTCATGAAAGTTGTAGATCATGAAACAATCTTT
64 ACCTTG-AACATTAAATTCAGTTCTCGAGTCCTTCATGAAAGTTGTAGATCATGAAACAACCTTT
* * * * **
13817 TAATAGACACTTAAATCACCTTAATTGGATAATC-GGAG-AGAAAATTATATAAT
128 CAAGAAACACTTAAATCACCTCAATCAGA-AATCTGGAGCA-AAAATTATATAAT
13870 AT
1 AT
13872 TAAATAGATC
Statistics
Matches: 158, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
180 28 0.18
181 127 0.80
182 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (180 bp):
ATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTTTTGATAC
CTTGAACATTAAATTCAGTTCTCGAGTCCTTCATGAAAGTTGTAGATCATGAAACAACCTTTCAA
GAAACACTTAAATCACCTCAATCAGAAATCTGGAGCAAAAATTATATAAT
Found at i:14669 original size:22 final size:23
Alignment explanation
Indices: 14622--14666 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
14612 CCAGATCAAT
14622 TTTCCAGATCTAATAAATAAAAA
1 TTTCCAGATCTAATAAATAAAAA
*
14645 TTTCCAGATCTAATAGATAAAA
1 TTTCCAGATCTAATAAATAAAA
14667 TTTATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (23 bp):
TTTCCAGATCTAATAAATAAAAA
Found at i:15307 original size:23 final size:23
Alignment explanation
Indices: 15260--15323 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
15250 TTATGCTTTC
*
15260 AAAGGAGAAGAAAGGGG-AAAAG
1 AAAGGAGAACAAAGGGGAAAAAG
*
15282 AAAGGAGATCAAAGGGGAAAAAG
1 AAAGGAGAACAAAGGGGAAAAAG
*
15305 AAAGGGGAACAAAGGGGAA
1 AAAGGAGAACAAAGGGGAA
15324 GAATATCTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 15 0.41
23 22 0.59
ACGTcount: A:0.56, C:0.03, G:0.39, T:0.02
Consensus pattern (23 bp):
AAAGGAGAACAAAGGGGAAAAAG
Found at i:16049 original size:25 final size:25
Alignment explanation
Indices: 16015--16063 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
16005 CCAAACAATC
16015 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
16040 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
16064 CAAACTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:16561 original size:30 final size:30
Alignment explanation
Indices: 16527--16587 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
16517 ATTTTTATCT
*
16527 TGACTTTCCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAAATTTAA
*
16557 TGACTTTCCTCTTATACTCTCAAAATTTAA
1 TGACTTTCCTCTTATACCCTCAAAATTTAA
16587 T
1 T
16588 ATCTTACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.25, G:0.03, T:0.44
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAAATTTAA
Found at i:16841 original size:30 final size:30
Alignment explanation
Indices: 16805--16866 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
16795 GTTAATAAGC
*
16805 CATTAAAATTTGAGGGTACAAGAAAAAAGT
1 CATTAAAATTAGAGGGTACAAGAAAAAAGT
* **
16835 CATTAAAATTAGAGGGTATAAGAGGAAAGT
1 CATTAAAATTAGAGGGTACAAGAAAAAAGT
16865 CA
1 CA
16867 AGATAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.23
Consensus pattern (30 bp):
CATTAAAATTAGAGGGTACAAGAAAAAAGT
Done.