Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010374.1 Corchorus capsularis cultivar CVL-1 contig10395, 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: 6600
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:863 original size:327 final size:326
Alignment explanation
Indices: 4--2612 Score: 3249
Period size: 325 Copynumber: 8.1 Consensus size: 326
1 CAT
* **
4 AAAAATTGAAGGGTTTTT-ACGCATACAATATCGTTTTACCA---TTTTTTCCGAATTTA-TTCT
1 AAAAATTGAAGGGTTTTTCACGCATCCAATATCGTTTTTTCATTTTTTTTTCCGAATTTATTTCT
* * * ** * *
64 AA-TAAATCG-AACAAAATTCAGATGCTTGTAAAAT-GAATTCTTATTTCTAATGTGGATGAGAT
66 AATTAAATCGAAACAAAATTCAGATACTCGTAAAATCGAATCCTTAAATCCAATGTGGCTGAGAT
* * * * *
126 TTAGTTTGATGAATAGAGATATTTCAAGGAGGTTATTTGCCAAAAATCACGGAAAACTTAGCCGA
131 TTAGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAAATCACGCAAAACTGAGCCGA
* *
191 GGCTCCGAAACGCATTTTTAGCCCAATAACAGTGATGGTTAGTATACGATTTCGGCTAAGAATTG
196 GGGTCCGAAACGCATTTTTAGCCCAATAACAGTGATGGTTAGTACACGATTTCGGCTAAGAATTG
**
256 A-CCAAAAAAAAATTTTCTGAAATTTTTGCCACAATACTCGGAAAAATAATATAATTGAATGCAT
261 ACCCAAAAAATTATTTTCTGAAATTTTTGCCACAATACTCGGAAAAATAATATAATTGAATGCAT
320 A
326 A
*
321 AAAAATTGAAGGGTTTTTCACGCATCCAATATCGTTTGTTCAATTTTTTTTTCCGAATTTATTT-
1 AAAAATTGAAGGGTTTTTCACGCATCCAATATCGTTTTTTC-ATTTTTTTTTCCGAATTTATTTC
* * * * * *
385 TAATTAAATCGAAAGAAAATTTAAATGCTCGTAAAAACGAATCCTTAAATCTAATGTGGCTGAGA
65 TAATTAAATCGAAACAAAATTCAGATACTCGTAAAATCGAATCCTTAAATCCAATGTGGCTGAGA
* * * * * * *
450 TTTAGTTCGGTGGATAAAGATAATTCAAGGAGGCTATCTGCCAATAATAACGCCAAACTGAGCCG
130 TTTAGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAAATCACGCAAAACTGAGCCG
* * * * *
515 GGGGTCCGAAACGCGTTTTTAGCGCAATAACAATGATGGTTAGTACACGATTTTGGCTAAGAATT
195 AGGGTCCGAAACGCATTTTTAGCCCAATAACAGTGATGGTTAGTACACGATTTCGGCTAAGAATT
* * * * *
580 GACCCGAAAATTTTTTTTCTGAAATTTTTTCCACAATACTCGGAAAAATAATATTATTGAATGCA
260 GACCCAAAAAATTATTTTCTGAAATTTTTGCCACAATACTCGGAAAAATAATATAATTGAATGCA
645 TA
325 TA
* * *
647 AAAAAATGAAAGGTTTTTCACGCATCCAATATCGTTTTTTCATTGTTTTTTTCCGTATTTATTTC
1 AAAAATTGAAGGGTTTTTCACGCATCCAATATCGTTTTTTCATT-TTTTTTTCCGAATTTATTTC
* ** * *
712 TAATTAAATCGAAACAAAATTCAGATGCTCGTAAAATCGAATTGTTAAATCCAATGTAGCCGAGA
65 TAATTAAATCGAAACAAAATTCAGATACTCGTAAAATCGAATCCTTAAATCCAATGTGGCTGAGA
* *
777 TTTAGTTCGATGAATAGAGATATTTCAAGGAGGTTATTTGCCAAAAATCACGCAAAACTGAGCCG
130 TTTAGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAAATCACGCAAAACTGAGCCG
*
842 AGGGTCCGAAACGCATTTTTAGCCCAATAACAGTGATGGTTAGTATACGATTTCGGCTAAGAATT
195 AGGGTCCGAAACGCATTTTTAGCCCAATAACAGTGATGGTTAGTACACGATTTCGGCTAAGAATT
* *
907 GACCCAAAAAA--AATTTCTGAAACTTTTGCCACAATACTCGGAAAAATAATATAATTGAATGCA
260 GACCCAAAAAATTATTTTCTGAAATTTTTGCCACAATACTCGGAAAAATAATATAATTGAATGCA
970 TA
325 TA
* *
972 AAAAATTGAAGGGTTTTTCACGCATCCAATATCG-TTTTTC----CTTTTTCGGCAATTTATTTC
1 AAAAATTGAAGGGTTTTTCACGCATCCAATATCGTTTTTTCATTTTTTTTTCCG-AATTTATTTC
* * * * ** * *
1032 TAA-TAAATCGAAACAAAATTCAGATCCTTGTAAAATTGAATTCTTATTTCCAATGTAGATGAGA
65 TAATTAAATCGAAACAAAATTCAGATACTCGTAAAATCGAATCCTTAAATCCAATGTGGCTGAGA
* *
1096 TTTAGTTTGATGAATAGAGATATTTCAAGGAGGTTATCTGCCAAAAATCACGCAAAACTGAGCCG
130 TTTAGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAAATCACGCAAAACTGAGCCG
* *
1161 GGGGTCCGAAACGCATTTTT-GCCCAATAACAGTGATGGTTAGTACACGATTCCGGCTAAGAATT
195 AGGGTCCGAAACGCATTTTTAGCCCAATAACAGTGATGGTTAGTACACGATTTCGGCTAAGAATT
* * *
1225 GACCCAAAAAA--ATTTTCTGAAAATTTTGCCAAAATACTCGGAAAAATAAAATAAATTGAATGC
260 GACCCAAAAAATTATTTTCTGAAATTTTTGCCACAATACTCGGAAAAATAATAT-AATTGAATGC
1288 ATA
324 ATA
* *
1291 AAAAATTGAAGGGTTTTTCACGCATCCAATATCGTTTGTTCAAATTTTTTTTCCGAATTTATTTC
1 AAAAATTGAAGGGTTTTTCACGCATCCAATATCGTTTTTTC-ATTTTTTTTTCCGAATTTATTTC
* * * * * *
1356 TAATTAAATCGAAATAAAATTCAGATACTCGTAAAATCGAATCGTTAAATCCAAAGTAGTTGGGA
65 TAATTAAATCGAAACAAAATTCAGATACTCGTAAAATCGAATCCTTAAATCCAATGTGGCTGAGA
* * * * ** *
1421 TTTGGTTCGATGAATAGAAATATTTCAAGGAGGGTATGTGATAAAAATCACGCAAAACTGAGCTG
130 TTTAGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAAATCACGCAAAACTGAGCCG
* ** * *
1486 GGGGTCCGAAACGCGGTTTTAGCCCGATAACATTGATGGTTAGTACACGATTTCGGCTAAGAATT
195 AGGGTCCGAAACGCATTTTTAGCCCAATAACAGTGATGGTTAGTACACGATTTCGGCTAAGAATT
* * *
1551 GATCCAAAAAATTCTTTTCTGAAATTTTTGCCACAATACTCAGAAAAATAATATAATTGAATGCA
260 GACCCAAAAAATTATTTTCTGAAATTTTTGCCACAATACTCGGAAAAATAATATAATTGAATGCA
1616 TA
325 TA
* * * * *
1618 AAAAATTGAGGGGTTTTTTACACATCCAATATCGTTTTTCCATTTGTTTTTTCCGAATTTAATTC
1 AAAAATTGAAGGGTTTTTCACGCATCCAATATCGTTTTTTCATTT-TTTTTTCCGAATTTATTTC
* * * * *
1683 CAATAAAATCGAAACAAAATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGA
65 TAATTAAATCGAAACAAAATTCAGATACTCGTAAAATCGAATCCTTAAATCCAATGTGGCTGAGA
* * * * *
1748 TTTGGTTC----AATAAATATATTTTAAGGAGGCTATCTGCCAAAAATCACGCAGAACTGAGCCG
130 TTTAGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAAATCACGCAAAACTGAGCCG
* * * *** *
1809 A--GTCCGAAACGCGTATGTAGCCCAATAACAGTGATGGTTAGTACACGATTTCAATTACGAATT
195 AGGGTCCGAAACGCATTTTTAGCCCAATAACAGTGATGGTTAGTACACGATTTCGGCTAAGAATT
* * * * * *
1872 GACCC---GAATT-TTTTTTCAAATTTTTTTTCCACAATACTCGTAAAAATAAAATAATTGAATG
260 GACCCAAAAAATTATTTTCTGAAA--TTTTTGCCACAATACTCGGAAAAATAATATAATTGAATG
1933 CATA
323 CATA
* *
1937 AAAAATTGAAGGGTTTTTCACGCATCCAATATCGTTTTTCCA--TATTTTTCCGAATTTATTTCT
1 AAAAATTGAAGGGTTTTTCACGCATCCAATATCGTTTTTTCATTTTTTTTTCCGAATTTATTTCT
* * *
2000 AA-TAAATCGAAACAAAATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGAT
66 AATTAAATCGAAACAAAATTCAGATACTCGTAAAATCGAATCCTTAAATCCAATGTGGCTGAGAT
* *
2064 TTGGTTC-ATTGAATAGAGATCTTTCAAGGAGGCTATCTGCCAAAAATCACGCAGAAA-TGAGCC
131 TTAGTTCGA-TGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAAATCACGCA-AAACTGAGCC
* *
2127 --GGGTCCCCGAAACGCATTTTTAGCCCATTAACAGTGATGATTAGTACACGATTTCGGCTAAGA
194 GAGGGT--CCGAAACGCATTTTTAGCCCAATAACAGTGATGGTTAGTACACGATTTCGGCTAAGA
* *
2190 TTTGACCCAAAAAATTGTTTTCTGAAATTTTTGCCACAATACTCGGAAAAATAATATAATTGAAT
257 ATTGACCCAAAAAATTATTTTCTGAAATTTTTGCCACAATACTCGGAAAAATAATATAATTGAAT
2255 GCATA
322 GCATA
*
2260 AAAAATTGAAGGGTTTTTAACGCATCCAATATC-TTTTTTC-TTTTTTTTTCCGAATTTATTTCT
1 AAAAATTGAAGGGTTTTTCACGCATCCAATATCGTTTTTTCATTTTTTTTTCCGAATTTATTTCT
* * * *
2323 AACTAAATCGAAACAAAATTCAGATTCTCGTAAAAAT-AAATCCTTAAATCCAATGTGACTGAGA
66 AATTAAATCGAAACAAAATTCAGATACTCGT-AAAATCGAATCCTTAAATCCAATGTGGCTGAGA
* * *
2387 TTT-GATTCGATGAATAGAGATATGTCAAGGAGGCTATCTGCCAAAAATCACGCAGAACTGAGTC
130 TTTAG-TTCGATGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAAATCACGCAAAACTGAGCC
* * * * *
2451 G-GGGCCCCGAAACGCGTTTTTAGCCTAATAAC----A--G-T-G-ACACGATTTCGGCTTAGCA
194 GAGGG-TCCGAAACGCATTTTTAGCCCAATAACAGTGATGGTTAGTACACGATTTCGGCTAAGAA
* ** * * *
2506 TTGACCCGAAAAAA-AAAATTCTAAAATTTTTGTCACAATACTCAGAAAAA-ATATATAATTGAA
258 TTGACCC-AAAAAATTATTTTCTGAAATTTTTGCCACAATACTCGGAAAAATA-ATATAATTGAA
2569 TGCA-A
321 TGCATA
* * * *
2574 ACAAAATTGAAGAGATTTTCACACTTCCAATATCGTTTT
1 A-AAAATTGAAGGGTTTTTCACGCATCCAATATCGTTTT
2613 CAAGCCTTAC
Statistics
Matches: 2006, Mismatches: 233, Indels: 107
0.86 0.10 0.05
Matches are distributed among these distances:
314 3 0.00
315 162 0.08
316 30 0.01
317 28 0.01
318 112 0.06
319 314 0.16
320 20 0.01
321 112 0.06
322 24 0.01
323 150 0.07
324 171 0.09
325 368 0.18
326 167 0.08
327 309 0.15
328 36 0.02
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (326 bp):
AAAAATTGAAGGGTTTTTCACGCATCCAATATCGTTTTTTCATTTTTTTTTCCGAATTTATTTCT
AATTAAATCGAAACAAAATTCAGATACTCGTAAAATCGAATCCTTAAATCCAATGTGGCTGAGAT
TTAGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAAATCACGCAAAACTGAGCCGA
GGGTCCGAAACGCATTTTTAGCCCAATAACAGTGATGGTTAGTACACGATTTCGGCTAAGAATTG
ACCCAAAAAATTATTTTCTGAAATTTTTGCCACAATACTCGGAAAAATAATATAATTGAATGCAT
A
Done.