Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019651.1 Corchorus olitorius cultivar O-4 contig19684, 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: 7012
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1794 original size:23 final size:23
Alignment explanation
Indices: 1764--1807 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1754 ATAATCAAAC
1764 AAATTAAATCCAG-TTCTAGCCCT
1 AAATTAAATCCAGATT-TAGCCCT
1787 AAATTAAATCCAGATTTAGCC
1 AAATTAAATCCAGATTTAGCC
1808 GTTATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (23 bp):
AAATTAAATCCAGATTTAGCCCT
Found at i:5892 original size:335 final size:325
Alignment explanation
Indices: 4673--7000 Score: 2171
Period size: 333 Copynumber: 7.1 Consensus size: 325
4663 TCATGATGGT
* * * *
4673 AAAAA-TGACCCGAAAGACTTTTCCTCAATTTTTGGCAAAAATACTCA-AAAAATATATATAATT
1 AAAAATTGA-CCGAAATATTTTTCCTCAATTTTTAGC-CAAATACTCATAAAAA-ATATATAATT
* * * **
4736 CAACGCCAAAAAGATTGGAA-GACTTTTCATGCTTTTAATATCATTTTTCATATTTTTTCAGAAT
63 CAAAGCCAAAAAGATT-GAAGGACTTTTCACGCTTCTAATATTGTTTTTCATATTTTTTC--AAT
* * *
4800 TAATTTCTAATTAAATCAAAACAAAATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTG
125 TAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* ***
4865 GCTGAGATTTGATTAGAAGAATA-A-AGATATTTCAAGGAGTCTCAACGCCAAAAATCATGCAAA
190 GCTGAGATTTGATTAGATGAATATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAA
* * * * * * *
4928 ACAGAGTCGTGGCCCTGCAACGCATTTTTAGCC-AAAAACCGTGATGATTAGTACACGATTTCAG
255 ACTGA-CCG-GGCCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATG----GTAAACGATTTCGG
4992 CTAAAATTTTGC
314 CTAAAATTTTGC
* * * *
5004 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTTGCTTAAATACTCATAAAAAATATATAATTC
1 AAAAATTGA-CCGAAATATTTTTCCTCAATTTTTAGC-CAAATACTCATAAAAAATATATAATTC
* * * **
5069 GACA-TCAAAAAGATTGAAGGACTTTTAACATTTCTAATATTGTTTTTCATATTCTTTTCCGAAT
64 -AAAGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATTGTTTTTCATATT-TTTT-C-AAT
*
5133 TAATTTCGAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
125 TAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * *
5198 TCTGAGATTTGGTTAGATG-A-ATATAGATATTTCAAGGAGTTTTGGCACCAAAAATCATGCAAA
190 GCTGAGATTTGATTAGATGAATATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAA
* *
5261 ACTGAGCCGGGCCCCGGAACGCGTTTTTAGCC-GAAAACCGTGATGGTTAGTACACGATTTCGGC
255 ACTGA-CCGGGCCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGG-TA--A-ACGATTTCGGC
5325 T-AAATTTTGC
315 TAAAATTTTGC
* * ** *
5335 AAAAATTGACCCGAAAGT-TTTTTCCTCGATTTCTAGTGAAAATACACATAAAAAATATATAATT
1 AAAAATTGA-CCGAAA-TATTTTTCCTCAATTTTTAG-CCAAATACTCATAAAAAATATATAATT
* * * * * * *
5399 CAACGCCAAAAAAATTGAAAGCCTTTTTCATGCTTCTAATATCGTTTTTCCTATTTTATTTCAAT
63 CAAAGCCAAAAAGATTGAAGGAC-TTTTCACGCTTCTAATATTGTTTTTCATA-TTT-TTTC-A-
* * *
5464 ATTAATTTCTAATTAAATCAAAACAAGATTTAGATACTCGTAAAAACAAATCCTTAAATACAATG
123 ATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * * **
5529 TGGCTGAGATTTGATTAGTTGAATATATAAATATTTTAAGGAGTCTTGTTGCCAAAAATCATGCA
188 TGGCTGAGATTTGATTAGATGAATATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCA
* * *
5594 AAATTGACCTAGGGCCCCGAAATGCGTTTTTAGCCAAAAAAACCATGATGGTAAACGATTTCGGC
253 AAACTGACC--GGGCCCCGAAACGCGTTTTTAGCC-AAAAAACCGTGATGGTAAACGATTTCGGC
5659 TAAAATTTTGC
315 TAAAATTTTGC
* ** *
5670 AAAAATTGACACGAAATATTTTTCTTCTAATTTAAAGCCACAATACTCATAAATAATATATAATT
1 AAAAATTGAC-CGAAATATTTTTCCTC-AATTTTTAGCCA-AATACTCATAAAAAATATATAATT
* * * *
5735 CAAAGCCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATGGTTTTTCCTATTGTTTTCAATTT
63 CAAAGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATTGTTTTTCATATT-TTTTCAA-TT
*** ** * * *
5800 AATTAGAAATTAAATTGAAACATGATTCAAATGCTCGTAAAAACAAACCCTTAAATCCAATGTGG
126 AATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * *
5865 CTGAGATTTGGTTAGATGAATATAT--ATATTTCAAGGAGTGTTGCCACAAAAAATCATGCAAAA
191 CTGAGATTTGATTAGATGAATATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAA
* * *
5928 CTGACCCGGGGCACC-AGAACGCGTTTTTAGCTAAAAAACCGTGATGGT--ACGATTTCGGCTTA
256 CTGA-CC-GGGCCCCGA-AACGCGTTTTTAGCCAAAAAACCGTGATGGTAAACGATTTCGGCTAA
5990 AATTTTGC
318 AATTTTGC
* * *
5998 AAAAATTAATCCGAAATATTTTTCCTCAATTTTAAGCCACAATACTCAT--AGAATATATAATT-
1 AAAAATTGA-CCGAAATATTTTTCCTCAATTTTTAGCCA-AATACTCATAAAAAATATATAATTC
* * * * *
6060 AAACGCCAAAAAGATTGGAGGACTCTTCACACTTTTAATATTGTTTTTCATATTTTTCTGAATTA
64 AAA-GCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATTGTTTTTCATATTTTT-TCAATTA
* *
6125 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGC
127 ATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * *
6190 TGAAATTTGATTAGATGAA-AT-TAGATGTTTCAAGGAGTCTTGGTGCCGAAAATCATGCAAAAC
192 TGAGATTTGATTAGATGAATATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAC
*
6253 TGAGCCGGAGCCCCGAAACGCGTTTTTAGCAAAAAAACCCCGTGATGGTTAATCTACGATTTCGG
257 TGA-CCGG-GCCCCGAAACGCGTTTTTAGCCAAAAAA--CCGTGATGG-TAA---ACGATTTCGG
6318 CTAAAATTTTGC
314 CTAAAATTTTGC
* * * *
6330 -AAAATATGACCAGAAA-AGTATTTCCTCAATTTTTAGCTTAAATACTCATGAAATATATATAAT
1 AAAAAT-TGACC-GAAATA-TTTTTCCTCAATTTTTAGC-CAAATACTCATAAAAAATATATAAT
* * * * * ** *
6393 TTAACGCCAAAAAAATTGGAGGACTTTTCACGCTTTTTTTTATTGTTTTTCATATTTTTATGAAT
62 TCAAAGCCAAAAAGATTGAAGGACTTTTCACGC-TTCTAATATTGTTTTTCATATTTTT-TCAAT
* * * *
6458 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATATA
125 TAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * *
6523 GCTGAGATTTGATTAGATG-A-ATATGGATATCTCAAGTAGTCTCGGCGCCAAAAATCATGCAAA
190 GCTGAGATTTGATTAGATGAATATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAA
* * * * * *
6586 ACTGAACTGGGGACCTGGAACACGTTTTTAGCC-AAAAA-C-TCA---T----GA--T-GGC---
255 ACTG-AC-CGGGCCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTAAACGATTTCGGCTAA
6635 -A------
318 AATTTTGC
* * * * ** ** *
6636 AAAAA-TGACCCGAAAAAGTTTT-CTTAATTTTTGGATAAAATACTCATAAACTATATATAATTT
1 AAAAATTGA-CCGAAATATTTTTCCTCAATTTTTAG-CCAAATACTCATAAAAAATATATAATTC
* * * * * * *
6699 AACGGCAAAAAGATTCG-AGGACTTTTCACGTTTTTAATGTCGTTTTTCATATTTTTCTGAATTA
64 AAAGCCAAAAAGATT-GAAGGACTTTTCACGCTTCTAATATTGTTTTTCATATTTTT-TCAATTA
* * *
6763 ATTTCTAATTAAATCGAAACAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGGC
127 ATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * *
6828 TGAGATATGATTAGAAGAATA-A-AGATATTTCAAGGAGTCTCGGCGCCAAAAATCATTCAAAA-
192 TGAGATTTGATTAGATGAATATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAC
* * ** * *
6890 TGAACCGGG-CCCAAGAACACGTTTTTAG-CAAAAAACCGTGATATTAATTACACAATTTCGGAT
257 TG-ACCGGGCCCCGA-AACGCGTTTTTAGCCAAAAAACCGTGATGGT-A--A-ACGATTTCGGCT
6953 AAAATTTTGC
316 AAAATTTTGC
*
6963 AAAAATTGATCCGAAAGATATTTT-CTCAATTTTTAGCC
1 AAAAATTGA-CCGAAATAT-TTTTCCTCAATTTTTAGCC
7001 GTAATACTTA
Statistics
Matches: 1679, Mismatches: 221, Indels: 197
0.80 0.11 0.09
Matches are distributed among these distances:
300 3 0.00
301 21 0.01
302 6 0.00
303 141 0.08
304 62 0.04
305 12 0.01
306 4 0.00
307 4 0.00
312 1 0.00
314 1 0.00
316 4 0.00
317 3 0.00
319 2 0.00
321 1 0.00
322 1 0.00
323 4 0.00
324 144 0.09
325 58 0.03
326 10 0.01
327 27 0.02
328 55 0.03
329 17 0.01
330 19 0.01
331 150 0.09
332 212 0.13
333 297 0.18
334 68 0.04
335 266 0.16
336 72 0.04
337 2 0.00
338 12 0.01
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (325 bp):
AAAAATTGACCGAAATATTTTTCCTCAATTTTTAGCCAAATACTCATAAAAAATATATAATTCAA
AGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATTGTTTTTCATATTTTTTCAATTAATTT
CTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
ATTTGATTAGATGAATATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAC
CGGGCCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTAAACGATTTCGGCTAAAATTTTGC
Done.