Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020764.1 Corchorus olitorius cultivar O-4 contig20797, 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: 7246
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:5199 original size:333 final size:333
Alignment explanation
Indices: 4618--5467 Score: 885
Period size: 334 Copynumber: 2.5 Consensus size: 333
4608 ATAAGCTTCC
*
4618 GAATCATGTTTCGATTTAATTAAAAATTAATTCAGAAAATAATAGGAAAAAC-AATATTAGAAGC
1 GAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAA-AATAGGAAAAACGAA-ATTAGAAGC
* * * * * * *
4682 ATGAAAAGCCATTCAATTTTTTTGGCGTTGAATTATATAATTTTTATGATTATTGTGGCTAAAAA
64 GTGAAAAACCATCCAATCTTTTTGGCGTTAAATTATATAATTTTTATGAGTATTGTAGCTAAAAA
* *
4747 ATTGAGGAAATAACTTTCGAGTCAATTTTTGCAAAATTCTAGCCGAAATTGTGTAATAATCAGCA
129 ATTGAGGAAATAACTTTCAAGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAA-CAGCA
4812 CAGTTATTTGACTAAAAACGTATTCCGCGGCCCCGACTAAGTTTTGTATGA-TTTTTGGTGCCAA
193 CAGTTATTTGACTAAAAACGTATTCCGCGGCCCCGACTAAGTTTTGTATGATTTTTTGGTG-CAA
* * * * *
4876 GAGTCTTTGAGATATCCATATTCATCTAATCAAAT-TTCAGCTACATTGGATTTAAAAATTTATT
257 AACTCCTTGAAATATCCATATTCATCTAATCAAATCTT-AGCCACATTGGATTTAAAAATTTATT
4940 TTTACGAGCATCT
321 TTTACGAGCATCT
* * * *
4953 GAATCTTGTTTTGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGAAATTAAAAGCGT
1 GAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATAGGAAAAACGAAATTAGAAGCGT
* * *
5017 GAAAAATC-TGCCAATCTTTTTGGCGTTAAATTATAT-ATATTTTATGAGTATTTTAGC-CAAAA
66 GAAAAACCAT-CCAATCTTTTTGGCGTTAAATTATATAAT-TTTTATGAGTATTGTAGCTAAAAA
** *
5079 ATTGACGGAAA-ATTTTTTCAAGTCATTTTTTTGCAAAAATTGC-AGCCGAAATCGTGT-ATAA-
129 ATTGA-GGAAATA-ACTTTCAAGTCA-ATTTTTGC-AAAATT-CTAGCCGAAATCGTGTAATAAC
* * * * * * *
5140 ATCACAGTTTTTTGGCTAAAGACGTGTTCCG-GGACCCCGAGTTAGTTTTTGCT-TGATTTTTTT
189 AGCACAGTTATTTGACTAAAAACGTATTCCGCGG-CCCCGACTAAG-TTTTG-TATGA-TTTTTT
* * * **
5203 GTTGCAAAACTCCTTGAAATATCTATTTTCATCTAATCAAATCTTAGCCACATTGGATTTAAGGA
250 GGTGCAAAACTCCTTGAAATATCCATATTCATCTAATCAAATCTTAGCCACATTGGATTTAAAAA
* *
5268 TTTGTTTTTACGAGCATTT
315 TTTATTTTTACGAGCATCT
* *
5287 GAAT-TATGTTTCGATTTAATTAAAAATTAATT-AGAAAAAATAGGGAAAACGATATTAGAAGCG
1 GAATCT-TGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATAGGAAAAACGAAATTAGAAGCG
* * * * * * * **
5350 TGAGAAGCCCTTCAATCTTTTTTTTGTGTTGAATTATAT-ATTTTTATGAGTATTGGGGCT-AAA
65 TGAAAAACCATCCAATC--TTTTTGGCGTTAAATTATATAATTTTTATGAGTATTGTAGCTAAAA
* * * *
5413 AATTGAGGAAA-ATA-TTTC-GGATCAATTTTTGCAAAATTTTAGCAGAAATCTTGTA
128 AATTGAGGAAATA-ACTTTCAAG-TCAATTTTTGCAAAATTCTAGCCGAAATCGTGTA
5468 CCATCATGGT
Statistics
Matches: 431, Mismatches: 61, Indels: 49
0.80 0.11 0.09
Matches are distributed among these distances:
331 20 0.05
332 56 0.13
333 96 0.22
334 153 0.35
335 86 0.20
336 20 0.05
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (333 bp):
GAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATAGGAAAAACGAAATTAGAAGCGT
GAAAAACCATCCAATCTTTTTGGCGTTAAATTATATAATTTTTATGAGTATTGTAGCTAAAAAAT
TGAGGAAATAACTTTCAAGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAACAGCACAG
TTATTTGACTAAAAACGTATTCCGCGGCCCCGACTAAGTTTTGTATGATTTTTTGGTGCAAAACT
CCTTGAAATATCCATATTCATCTAATCAAATCTTAGCCACATTGGATTTAAAAATTTATTTTTAC
GAGCATCT
Found at i:6988 original size:24 final size:24
Alignment explanation
Indices: 6943--6990 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
6933 TTACTTTATT
*
6943 TTCTTCAAACTTCAAAATTTTCAA
1 TTCTTCAAACTTCAAAACTTTCAA
*
6967 TTCTCTCAACCTTC-AAACTTTCAA
1 TTCT-TCAAACTTCAAAACTTTCAA
6991 AACTCAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (24 bp):
TTCTTCAAACTTCAAAACTTTCAA
Done.