Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015981.1 Corchorus olitorius cultivar O-4 contig16014, 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, 997
Length: 1662
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:613 original size:211 final size:211
Alignment explanation
Indices: 232--633 Score: 678
Period size: 211 Copynumber: 1.9 Consensus size: 211
222 TTCTATTTTT
232 TCTGAATTTATTTCTAATTAAATCTTAACAAGATTCAGATGCTCGTAAAAACAAATCCGTAAATC
1 TCTGAATTTATTTCTAATTAAATCTTAACAAGATTCAGATGCTCGTAAAAACAAATCCGTAAATC
* * * **
297 CAATGTGGCTGAGATTTGTTTAGATGAATATAGATATTTCCAGGAGTCTTTCTGGTAAAAATCAT
66 CAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCAT
* *
362 GCAAAACTGAGCCAGGGCCCCGAAACACGTTTTAAGCCAAAATTGTGATGGTTAGTACACGTTTT
131 GCAAAACTGAGCCAGGGCCCAGAAACACGTTTTAAGCCAAAACTGTGATGGTTAGTACACGTTTT
427 AAGCCAAAATTGGTGC
196 AAGCCAAAATTGGTGC
443 TCTGAATTTATTTCTAATTAAATCTTAACAAGATTCAGATGCTCGTAAAAACAAATCCGTAAATC
1 TCTGAATTTATTTCTAATTAAATCTTAACAAGATTCAGATGCTCGTAAAAACAAATCCGTAAATC
* *
508 CAATGTGGTTGAGATTTGGTTAGATAAATATAGATATTTCAAGGTGTCTTTCTGCCAAAAATCAT
66 CAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCAT
* * * * *
573 TCAAAATTGAGCCATGGCCCAGAAACGCGTTTTTAGCCAAAACTGTGATGGTTAGTACACG
131 GCAAAACTGAGCCAGGGCCCAGAAACACGTTTTAAGCCAAAACTGTGATGGTTAGTACACG
634 ATTTCGGCTA
Statistics
Matches: 177, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
211 177 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (211 bp):
TCTGAATTTATTTCTAATTAAATCTTAACAAGATTCAGATGCTCGTAAAAACAAATCCGTAAATC
CAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCAT
GCAAAACTGAGCCAGGGCCCAGAAACACGTTTTAAGCCAAAACTGTGATGGTTAGTACACGTTTT
AAGCCAAAATTGGTGC
Found at i:1075 original size:335 final size:332
Alignment explanation
Indices: 443--1662 Score: 1662
Period size: 333 Copynumber: 3.6 Consensus size: 332
433 AAATTGGTGC
* ** * *
443 TCTGAATTTATTTCTAATTAAATCTTAACAAGATTCAGATGCTCGTAAAAACAAATCCGTAAATC
1 TCTGAATTTATTTCAAATTAAATCGAAACAAAATTCAGATACTCGTAAAAACAAATCCGTAAATC
* * * ** *
508 CAATGTGG-TTGAGATTTGGTTAGATAAATATAGATATTTCAAGGTGTCTTTCTGCCAAAAATCA
66 CATTGTGGCTAGAGATTTGATTAGATAAATATAGATATTTCAAGAAGTCATTCTGCCAAAAATCA
* * * *
572 TTCAAAATTGAGCCATGGCCCAGAAACGCGTTTTTAGCCAAAACTGTGATGGTTAGTACACGATT
131 TGCAAAATTGAGCCAGGGCCC-GAAACGCATTTTTAGCCAAAACCGTGATGGTTAGTACACGATT
637 TCGGCT-AAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCCCAATTTTTTATCACAATACAT-
195 TCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCCCAATTTTTTATCACAATAC-TC
* *
700 AGAAAACTCATATAATTCAACGCCAAAACTATTTTAGGGTTTTTCACGCTTCTAATATCGTTATT
259 AGAAAAATCATATAATTCAACGCCAAAACTATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTT
765 CCATTTTTT
324 CCATTTTTT
* * * *
774 TCTGAATTTATTTCAAATTAAATAGAAACAAAATTCAGATACTTGTAAAAATAAATCCGTAAATG
1 TCTGAATTTATTTCAAATTAAATCGAAACAAAATTCAGATACTCGTAAAAACAAATCCGTAAATC
* *
839 CATTGTGGCTGAGAGATTTGATTAGATAAATATAGATATTTCGAGAAGTCATTCTACCAAAAATC
66 CATTGTGGCT-AGAGATTTGATTAGATAAATATAGATATTTCAAGAAGTCATTCTGCCAAAAATC
*
904 ATGCAAAATTGAGCCAGGGCCACGAAATGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
130 ATGCAAAATTGAGCCAGGGCC-CGAAACGCATTTTTAGCC-AAAACCGTGATGGTTAGTACACGA
* * * * **
969 TTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAACTTTTTTCTCTATTTTTTGCCACAATACT
193 TTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCCCAATTTTTTATCACAATACT
* * *
1034 CAAAAAAATCATCTGAA-TCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTT
258 CAGAAAAATCATAT-AATTCAACGCCAAAACTATTTTAGGGTTTTTCACGCTTCTAATATCGTTT
**
1098 TTCCATTTGTGC
322 TTCCATTT-TTT
* * ** * *
1110 TCTAAATTTATTTCTAATTAAATCTTAACAAGATTCAGATGCTCGTAAAAACAAATCCGTAAATC
1 TCTGAATTTATTTCAAATTAAATCGAAACAAAATTCAGATACTCGTAAAAACAAATCCGTAAATC
* * * *
1175 CAATT-TGGCT-GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATC
66 C-ATTGTGGCTAGAGATTTGATTAGATAAATATAGATATTTCAAGAAGTCATTCTGCCAAAAATC
* * * * * *
1238 ATTCAAAACTGAGCAATGGCGCCGAAACGCGTTTTTAGCCAAAACCGTGAGGGGTTAGTACACGA
130 ATGCAAAATTGAGCCAGGGC-CCGAAACGCATTTTTAGCCAAAACCGTGA-TGGTTAGTACACGA
* *
1303 TTTCGGCTAAAATTTTG-AAAAAATTGACCCGAAAAGTTTTTCCCCAATTTTTTATCACAATACA
193 TTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCCCAATTTTTTATCACAATACT
*
1367 CAGAAAAATCATATAATTCAACTCCAAAACTATTTTAGGGTTTTTCACGCTTCTAATATCGTTTT
258 CAGAAAAATCATATAATTCAACGCCAAAACTATTTTAGGGTTTTTCACGCTTCTAATATCGTTTT
1432 TCCATTTTTTTTT
323 TCCA---TTTTTT
* * * *
1445 TCAGAATTTATTTCAAATTAAATCGAAACAAAATTCAGATACTTGTAAAAATAAATCCGTAAATG
1 TCTGAATTTATTTCAAATTAAATCGAAACAAAATTCAGATACTCGTAAAAACAAATCCGTAAATC
* * *
1510 CATTGTGGCTGAGAGATTTGATTAGATGAATATAGATATTTCGATAAGTCATTCTGCCAAAAATC
66 CATTGTGGCT-AGAGATTTGATTAGATAAATATAGATATTTCAAGAAGTCATTCTGCCAAAAATC
* * * *
1575 ATGCAAAATTGAGCCAGGGCCCCGAGACGCATTTTAAGCCAAAAACCGAGATGGTTAATACACGA
130 ATGCAAAATTGAGCCAGGG-CCCGAAACGCATTTTTAGCC-AAAACCGTGATGGTTAGTACACGA
1640 TTTCGGCTAAAATTTTGCAAAAA
193 TTTCGGCTAAAATTTTGCAAAAA
Statistics
Matches: 771, Mismatches: 97, Indels: 35
0.85 0.11 0.04
Matches are distributed among these distances:
331 63 0.08
332 3 0.00
333 192 0.25
334 145 0.19
335 175 0.23
336 67 0.09
337 111 0.14
338 15 0.02
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (332 bp):
TCTGAATTTATTTCAAATTAAATCGAAACAAAATTCAGATACTCGTAAAAACAAATCCGTAAATC
CATTGTGGCTAGAGATTTGATTAGATAAATATAGATATTTCAAGAAGTCATTCTGCCAAAAATCA
TGCAAAATTGAGCCAGGGCCCGAAACGCATTTTTAGCCAAAACCGTGATGGTTAGTACACGATTT
CGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCCCCAATTTTTTATCACAATACTCAG
AAAAATCATATAATTCAACGCCAAAACTATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCC
ATTTTTT
Done.