Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018824.1 Corchorus olitorius cultivar O-4 contig18857, 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: 4334
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:3076 original size:21 final size:22
Alignment explanation
Indices: 3045--3085 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
3035 AGAAGTATAC
3045 AAAAAACTT-GGA-AGAAAACT
1 AAAAAACTTGGGAGAGAAAACT
3065 AAAAAACTTTGGGAGAGAAAA
1 AAAAAAC-TTGGGAGAGAAAA
3086 AAAGAGAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 3 0.17
23 6 0.33
ACGTcount: A:0.59, C:0.07, G:0.20, T:0.15
Consensus pattern (22 bp):
AAAAAACTTGGGAGAGAAAACT
Found at i:3727 original size:331 final size:325
Alignment explanation
Indices: 3113--4330 Score: 1148
Period size: 331 Copynumber: 3.7 Consensus size: 325
3103 GGGCAATATA
* * * * *
3113 AGAAATACGATATTAAAAGCGTGAAAAACCC-TCAAATCTTTTTGGCGTTTAATTATATATTT-C
1 AGAAAAACGATATTAAAA-CAT-AAAAGCCCTTC-AATCTTTTTGGCG-TTAAATATATATTTAT
* *
3176 TATGAGTATTTTAGCCAAAAATTGAGGAGAA-ATCTTTCGTGTCAATTTTTGCAAAATTTTAGCC
62 TATGAGTATTTTAG-CAAAAATTGA-GAAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCC
* * * ** * * *
3240 GAAATAGTGTACCAACTAACCATCACGGTTTTTCACTAAAAACGCA-TTCCGGAGACCCGCCTCA
125 AAAATCGTGT---AA-TAACCATCACAGTTTTTGGCTAAAAAAG-AGTTCCGGAGCCCCGACTCA
* * * * * *
3304 ATTTTGTATGATTTTTGA-ATCCAAGACTACTTGAAATATCTGTATCCATCTAATCAAATATCAG
185 GTTTTGCATGATTTTTGACA-CCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
*
3368 CCACATTGGATTTAA-AGATTTGTTTTTACAAGCATCTGAATCTTGTTTTGATTTAATTAGAAAT
249 CCACATTGGATTTAAGA-ATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
3432 TAATTCGGAAAAAT
313 TAATTC-GAAAAAT
* *
3446 AGGAAAACCGATATTAGAAACATCAAAAGCCCTTCAATCTTTTTAGCGTTAAAATATATAATTT-
1 A-GAAAAACGATATTA-AAACAT-AAAAGCCCTTCAATCTTTTTGGCGTT-AAATATAT-ATTTA
* * * **
3510 TTATGAGTATTTTAGCAAAAATTTAGAAAATATCTTTCGGATCAAATTTTTACAAAATTTTAGTT
61 TTATGAGTATTTTAGCAAAAATTGAGAAAATATCTTTCGGGTC-AATTTTTGCAAAATTTTAGCC
* * *
3575 AAAATCGTGTAATAACCATCACAATTTTTGGGTAAAAAAGAGTTCTGTG-GCCCCGACTCAGTTT
125 AAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAAAGAGTTCCG-GAGCCCCGACTCAGTTT
** * * *
3639 TATATGATTTTTGACACCAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCTACA
189 TGCATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACA
* *
3704 TTGGATTTAAGAATTTCTTTTTACAAGCA-CTGGAATCTTGTTTCGATTCAATTAGAAATTAATT
254 TTGGATTTAAGAATTTGTTTTTACAAGCATCT-GAATCTTGTTTCGATTTAATTAGAAATTAATT
3768 CAGAAAAAGT
318 C-GAAAAA-T
* * *
3778 ATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATCTTTTTGGTGTTAAAT-TATATTTATT
1 A-GAAAAACGATATTAAAA-CAT-AAAAGCCCTTCAATCTTTTTGGCGTTAAATATATATTTATT
* * * *
3842 ATGAGTATTTTATCCAAAAACTGAGAAAAAAAT-TTTCGGGTCATTTTTTGCAAAATTTTAGCCA
63 ATGAGTATTTTA-GCAAAAATTGAG-AAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCA
* * *
3906 AAATC--GT-AT-ACCATCACGGTTTTTGGCTAAAAACACA-TTTCGGAG-CCCGACTCAGTTTT
126 AAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAA-AGAGTTCCGGAGCCCCGACTCAGTTTT
** * * *
3965 GCATGATTTTTGACGTCGAGACTCCTTGAAGA-ATCTATATTCATCTAATAAAATCTTAGCCACA
190 GCATGATTTTTGACACCAAGACTCCTTGAA-ATATCTATATTCATCTAATCAAATCTCAGCCACA
* ** * * *
4029 TTGCATTTAAGGCTTTGATTTTACGAGCATCTGAATCTTATTTCGATTTAATTCAGAAA--AA-T
254 TTGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATT-AGAAATTAATT
4091 ------AT
318 CGAAAAAT
* * * * * *
4093 -GAAAAACGATATTAAAAACGTGAAAGCCCTTCAATATTTTTGGTGTTGAATTATATATTTGTTA
1 AGAAAAACGATATT-AAAACATAAAAGCCCTTCAATCTTTTTGGCGTT-AAATATATATTTATTA
* * * * **
4157 TGCGTATTGTGGCTAAAAAATTGATG-AAATATCTTTCGGGTCAATTTCTGCAAAATTTTAGCTG
64 TGAGTATTTTAGC--AAAAATTGA-GAAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCA
* * * * * *
4221 AAATCGTGTAATAATCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCAG-TTCA-TTTTG
126 AAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAAAGAGTTCCGGAGCCCCGACTCAGTTTTG
*** *
4284 CATGATTTTTGGTGCCAAGACTCCTTGAAATATCTATATTCGTCTAA
191 CATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAA
4331 CCAA
Statistics
Matches: 739, Mismatches: 110, Indels: 87
0.79 0.12 0.09
Matches are distributed among these distances:
312 22 0.03
313 19 0.03
314 27 0.04
315 41 0.06
316 2 0.00
317 3 0.00
318 47 0.06
319 31 0.04
320 3 0.00
323 1 0.00
324 2 0.00
325 109 0.15
326 33 0.04
327 4 0.01
328 2 0.00
329 4 0.01
330 43 0.06
331 180 0.24
332 51 0.07
333 7 0.01
334 59 0.08
335 49 0.07
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (325 bp):
AGAAAAACGATATTAAAACATAAAAGCCCTTCAATCTTTTTGGCGTTAAATATATATTTATTATG
AGTATTTTAGCAAAAATTGAGAAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATC
GTGTAATAACCATCACAGTTTTTGGCTAAAAAAGAGTTCCGGAGCCCCGACTCAGTTTTGCATGA
TTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATT
TAAGAATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAT
Done.