Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001421.1 Corchorus olitorius cultivar O-4 contig01421, 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, 825
Length: 1375
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:794 original size:331 final size:325
Alignment explanation
Indices: 1--1375 Score: 1254
Period size: 331 Copynumber: 4.2 Consensus size: 325
*
1 GTTAATACACGATTTCGACTAAAATTTTGCAAAAACTGAACCGAAGGATTTTTACTCAATTTTTG
1 GTTAATACACGATTTCGACTAAAATTTTGCAAAAACTGAACCGAAAGATTTTTACT-AATTTTT-
* * ** * *
66 GCCACAATACTCATAAAAAATATATAATTCAACGTCAAAAATTTTAAAGGGGTTTTCAAGCTTCT
64 TCCACAATACTCATAAAAAATATATAATTCAAC-ACAAAAAGATTAAAGGGCTTTTCACGCTTCT
* * * * *
131 AATATGA-TTTTCCTATTTTTTTACAAATTAATTGCTAATTAAATCGAAA-TAAGATATTGATGC
128 AATATCATTTTTCCTA-TTTTTT-CGAATTAATTGATAATTAAATCGAAACT-AGATTTTGATAC
* * * * * **
194 TCGTAAAAACAAATTCTCAAATCAAATTTGGCTGAGATGTGGTTTTATGAATATAGATATTTCAA
190 TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA
* * * *
259 GGAGTCTTGGCGTAAAAAATCATTCAAAACTGAGCCAGGGGCCCGAAACACGTTTTTAGCTTAAA
255 -TAGTCTTGGCGTCAAAAATCATGCAAAACTGAGCCAGGGGCACG-AACACGTTTTTAGCTTAAA
324 A-C-----
318 ACCTGATG
** * * * * *
326 G----T-CACGATTTCGGTTAAAATTTTGTAAAAATTGAACCAAAAGATTTTTCCTCCATTTTTT
1 GTTAATACACGATTTCGACTAAAATTTTGCAAAAACTGAACCGAAAGATTTTTACT-AATTTTTT
* * *
386 CCACAATACTCATAAAAAATATATAATTCAACACTAAAAAGATTGAAGGACTTTTCACGCTTTTA
65 CCACAATACTCATAAAAAATATATAATTCAACAC-AAAAAGATTAAAGGGCTTTTCACGCTTCTA
* * * * *
451 ATATCATTTTTCC-ATTTTTTCCGAATTATTTTATCATTAAATCGAAATTGGATTTTGATACTCG
129 ATATCATTTTTCCTATTTTTT-CGAATTAATTGATAATTAAATCGAAACTAGATTTTGATACTCG
* *
515 TAAAAA-AAATCCTTAAATTCAATGTGGCTGAGATTTGGTTAGATTAATATAGATATTTCAATAA
193 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAT-A
* * * * **
579 GTCTTGGCGTCAAAACTCATGCAAAACTGAGCC-GGGACACAGAACACATTTTCAGCAAAAAACC
257 GTCTTGGCGTCAAAAATCATGCAAAACTGAGCCAGGGGCAC-GAACACGTTTTTAGCTTAAAACC
643 ATGATG
321 -TGATG
* * *
649 GTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGAACTGAAGGATTTTTACTAGATTTTTT
1 GTTAATACACGATTTCGACTAAAATTTTGCAAAAACTGAACCGAAAGATTTTTACTA-A-TTTTT
* * * *
714 TGCCACAATACTCATAAAAATTTATAAAATTCATCGTCAAAAAGATTAAAGGGCTTTTCACGCTT
64 T-CCACAATACTCATAAAAA-ATATATAATTCAAC-ACAAAAAGATTAAAGGGCTTTTCACGCTT
* * * * ** *
779 CTAATATCGTTTTTCCTAATTTTTCGAATTAATTGCTAATTAAATCGAAACCAGATTCAGATGCT
126 CTAATATCATTTTTCCTATTTTTTCGAATTAATTGATAATTAAATCGAAACTAGATTTTGATACT
* * * * * *
844 CG-AAAAACAAATCCTTAAATCCAGTGTGCCTGTGATTTGGTTTGATAAATATAGATATTTTAAG
191 CGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA-
* ** * *
908 TAGTCTCGATGTCAAAAATCATGCAAATCTGAGCCGGGGGCACGAA-ATGCGTTTTTAGCTTAAA
255 TAGTCTTGGCGTCAAAAATCATGCAAAACTGAGCCAGGGGCACGAACA--CGTTTTTAGCTTAAA
972 ACCGTGATG
318 ACC-TGATG
* * * * * * *
981 GTTAATACACCATTTCAATTATAATTTTGTAAAAATTGAACCGAAAGATTTTTTC-AATTTTTTC
1 GTTAATACACGATTTCGACTAAAATTTTGCAAAAACTGAACCGAAAGATTTTTACTAATTTTTTC
** * * *
1045 CACAATACTCAGGAAAAA-ATATAATTCAACACATGAAAGATTGAAGGGCTTTTCACACTTCTAA
66 CACAATACTCATAAAAAATATATAATTCAACACA-AAAAGATTAAAGGGCTTTTCACGCTTCTAA
* * * * * *
1109 TATCATTTTTCTTTCTTTTTTTTTTTCGAAATATTTTATCATTAAATCGAAACTGGATTTTGATA
130 TATCATTTTTC---C---TATTTTTTCGAATTAATTGATAATTAAATCGAAACTAGATTTTGATA
* *
1174 CTCGTAAAAACAAATCCTTAAATCCAATGTGGGTGATATTTGGTTAGATGAATATAGATATTT-A
189 CTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCA
* * * * * *
1238 AAAGACTCATGGCG-CGAAAAA-CATGCAAAACTGAG-GAGGGGCCCGTAACGCATTTTTAG-TC
254 ATAG--TCTTGGCGTC-AAAAATCATGCAAAACTGAGCCAGGGGCACG-AACACGTTTTTAGCT-
* *
1299 GAAAACTGTGATG
314 TAAAAC-CTGATG
* * * * * * * *
1312 GTTAGTAATATGATTTC-AGTTAAAATTTTGTAAATATTGAACCGAAAGATTTTTCCTCAATTTT
1 GTTAAT-ACACGATTTCGA-CTAAAATTTTGCAAAAACTGAACCGAAAGATTTTTACT-AATTTT
Statistics
Matches: 853, Mismatches: 150, Indels: 85
0.78 0.14 0.08
Matches are distributed among these distances:
316 21 0.02
317 79 0.09
318 46 0.05
319 62 0.07
320 55 0.06
321 1 0.00
323 1 0.00
325 3 0.00
326 47 0.06
327 1 0.00
328 59 0.07
329 13 0.02
330 26 0.03
331 197 0.23
332 176 0.21
333 60 0.07
334 6 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (325 bp):
GTTAATACACGATTTCGACTAAAATTTTGCAAAAACTGAACCGAAAGATTTTTACTAATTTTTTC
CACAATACTCATAAAAAATATATAATTCAACACAAAAAGATTAAAGGGCTTTTCACGCTTCTAAT
ATCATTTTTCCTATTTTTTCGAATTAATTGATAATTAAATCGAAACTAGATTTTGATACTCGTAA
AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAATAGTCT
TGGCGTCAAAAATCATGCAAAACTGAGCCAGGGGCACGAACACGTTTTTAGCTTAAAACCTGATG
Done.