Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014130.1 Corchorus olitorius cultivar O-4 contig14163, 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: 3584
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Found at i:751 original size:321 final size:322
Alignment explanation
Indices: 1--1353 Score: 1548
Period size: 321 Copynumber: 4.1 Consensus size: 322
* * * * *
1 ACCATCACGGTTTTTTTGCTAAAAACGCG-CCTCGGGG-CCTCGGCTCAGTTTTGCATTATTTTT
1 ACCATCACAGTTTTTTGGCTAAAAACGCGTTCT-GGGGCCCT-GACTCAGTTTTGCATGATTTTT
* *
64 GGCAGGAAGACTCCTTAAAAAGATCTATATTCATATAACCAAATCTCAGTCAATTTGGATTTAAG
64 GGCAGAAAGACTCCTT-AAAATATCTATATTCATATAACCAAATCTCAGTCAATTTGGATTTAAG
* * *
129 GATTTCTTTTTAAGATCATCTGAATTTTGTTTCGATTTTATTAGAAATAAATTCGAAAAAAATGG
128 GATTTGTTTTTAAGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGG
*
194 AAAAACGATATTGGAAGCGT-AAAAACCCCTTCAATTTTCTTTGGCGTTGAATTATATATATTTT
193 AAAAACGATATTGGAAGCGTGAAAAA-CCCTTCAATTTTCTTTGGCTTTGAATTATATAT-TTTT
* *
258 TAGAGTTGTGAGGCAAAAAAAATGAGAAAAAAGTTTTCGGGTAAATTTTTAACCGAAATCGTGTA
256 TAGAGTTGTGAGGC-AAAAAAATGAGAAAAAAGTTTTCGGGTAAATTTTTAGCAGAAATCGTGTA
323 CTA
320 CTA
* * * * * * * * *
326 ACCATCAC-GGTTTTTGGCTAAAAACGTGTTCCAGAGCCCCTG-CTAAATTTTGCAAGATTTTAG
1 ACCATCACAGTTTTTTGGCTAAAAACGCGTT-CTGGGGCCCTGACTCAGTTTTGCATGATTTTTG
* * * * *
389 GCAGAAAGTCTCCTTAAAATATTTTTATTCATATAACCAAATCTCAGTCAACTTAGATTTAAGGA
65 GCAGAAAGACTCCTTAAAATATCTATATTCATATAACCAAATCTCAGTCAATTTGGATTTAAGGA
* * * * *
454 TTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGAAAAAAAATCGA
130 TTTGTTTTTAAGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCG-AAAAAAATGGA
*
519 AAAACGATATTGGAAGCGTGAAAAACCCTTCAA-TTT-TTTGGCTTTTAATTATATATATTTTTC
194 AAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTCTTTGGCTTTGAATTATATAT-TTTTT-
* * * * *
582 AGAGTAGTGTGGC--AAAAATTAGAAAAAAAATTTTCGTGTAAATTTTTAGCAGAAATCGTGTAC
257 AGAGTTGTGAGGCAAAAAAATGAG-AAAAAAGTTTTCGGGTAAATTTTTAGCAGAAATCGTGTAC
645 TA
321 TA
*
647 ACTATCACAG-TTTTTGGCTAAAAACGCGTTCTGGGGCCCTGACTCAGTTTTGCATGATTTTTGG
1 ACCATCACAGTTTTTTGGCTAAAAACGCGTTCTGGGGCCCTGACTCAGTTTTGCATGATTTTTGG
* *
711 CAGAAAGGCTCCTTGAAATATCTATATTCATATAACCAAATCTCAG-CTAATTTGGATTTAAGGA
66 CAGAAAGACTCCTTAAAATATCTATATTCATATAACCAAATCTCAGTC-AATTTGGATTTAAGGA
** * *
775 TTTCG-TTTTACTAGCATCTGAATTTTGTTTTGATTTATTTAGAAATAAATTCGAAAAAAATGGA
130 TTT-GTTTTTAAGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGA
* * *
839 AAAATGATATTGGAAGCGTGAAAAACCTTTCAATTTTTTTTGGCTTTGAATTATATATTTTTTCT
194 AAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTCTTTGGCTTTGAATTATATA-TTTTT-T
* * * *
904 AGAGTTGTGTGGCAAACAAAATGAGAAGAAAGTTTTTGGGTCAATTTTTTAGCAGAAATCGTGTA
257 AGAGTTGTGAGGCAAA-AAAATGAGAAAAAAGTTTTCGGGT-AAATTTTTAGCAGAAATCGTGTA
*
969 GTA
320 CTA
972 ACCATCACACGATTTGGATTTAAGGATTTCTTTTTACGACTGCTAAAAACGCGTTTCT-GGGCCC
1 ACCAT--CAC------------A-G---T-TTTTT--G---GCTAAAAACGCG-TTCTGGGGCCC
* *
1036 CGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAAA-ATCTATATTCTTATAACCAA
41 TGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTT-AAAATATCTATATTCATATAACCAA
** * * * *
1100 ATCTCAACCAATTTGGATTTAAGAATTTATTTTTAAGATCATCTGAATTTTGTTTCGATTTTATT
105 ATCTCAGTCAATTTGGATTTAAGGATTTGTTTTTAAGAGCATCTGAATTTTGTTTCGATTTAATT
*
1165 AGAAATAAATTCAGAAAAAAATGGAAAAACGATATTGAAAGCGTG-AAAACCCATTCAATTTTCT
170 AGAAATAAATTC-GAAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCC-TTCAATTTTCT
* * *
1229 TTGGCATTAAATTATATATTTTTTAGAGTTGTGAGGCAAAAAAATGAGAAAAAAGTTTTCGGGTC
233 TTGGCTTTGAATTATATATTTTTTAGAGTTGTGAGGCAAAAAAATGAGAAAAAAGTTTTCGGGTA
* * *
1294 AATTTTTATCCGAAATCGTGTATTA
298 AATTTTTAGCAGAAATCGTGTACTA
*
1319 ACCATCACGGTTTTTTTTTGGCTAAAAACGCGTTC
1 ACCATCACAG---TTTTTTGGCTAAAAACGCGTTC
1354 CGGAGCTCCT
Statistics
Matches: 879, Mismatches: 99, Indels: 100
0.82 0.09 0.09
Matches are distributed among these distances:
320 58 0.07
321 186 0.21
322 60 0.07
323 107 0.12
324 96 0.11
325 54 0.06
326 16 0.02
327 3 0.00
329 1 0.00
331 5 0.01
332 4 0.00
339 1 0.00
340 1 0.00
345 8 0.01
347 27 0.03
348 22 0.03
349 16 0.02
350 150 0.17
351 64 0.07
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (322 bp):
ACCATCACAGTTTTTTGGCTAAAAACGCGTTCTGGGGCCCTGACTCAGTTTTGCATGATTTTTGG
CAGAAAGACTCCTTAAAATATCTATATTCATATAACCAAATCTCAGTCAATTTGGATTTAAGGAT
TTGTTTTTAAGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAA
AACGATATTGGAAGCGTGAAAAACCCTTCAATTTTCTTTGGCTTTGAATTATATATTTTTTAGAG
TTGTGAGGCAAAAAAATGAGAAAAAAGTTTTCGGGTAAATTTTTAGCAGAAATCGTGTACTA
Done.