Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009836.1 Corchorus olitorius cultivar O-4 contig09868, 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: 2344
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Found at i:964 original size:329 final size:330
Alignment explanation
Indices: 17--1762 Score: 947
Period size: 329 Copynumber: 5.3 Consensus size: 330
7 ATATATATAT
* * * * * *
17 ATATATATATTCATCGAACCAAATCTCGGCTAC-ATACGATATAAGGATTTGTTTTTACGAGCAT
1 ATATATATAATCATCAAACCAAATCCCAGCCACAAT-GGATATAAGGATTTGTTTTTACGAGCAT
* * * * * * * *
81 CTGAATCTTGTTTCGATTTAATTAGAAAGTAATTCGGAAAAAAAATGGAAAAACGATATTAAAAG
65 CTAAATATTATTTCAATTTAATTAGAAAGTAATT--G-AAAAAAA-GGATAAACAATATTAGATG
* * * * * *
146 CGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTATATATTT-TTCCTGAGTATTGTGGCAAAA
126 CATGAAAAACCCGTCAATCCTTTTGGCATTGAATTATATATTTCTT-ATGACTATTATGGCAAAA
* * * *
210 AATTCA-TAAAAAAATTATTCGGGTCA------G-----TTTTAGTCGAAATCGTGTA-T---CA
190 AATTGAGTAAAAATA-T-TTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCA
* * * * * * *
259 TCAC-GATTTTTGGGTTAAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGACTTTTGGCAG
253 TCACAGGTTTTT-GGATAAAAACGCGTTCCGAGACCCCGGCTTACTTTTGCATGATTTTTGGC-G
* *
323 -AAAGAA-TTCTCGAA
316 CAAA-AACTCCTTGAA
* ** * * * * * * * * *
337 ATATATATATTCATCTTACCAAATCTCAACCACATTGGATTTAAGGGTATGGTTGTACAAGCATC
1 ATATATATAATCATCAAACCAAATCCCAGCCACAATGGATATAAGGATTTGTTTTTACGAGCATC
* * * * * * ** * ** *
402 TGAATCTTGTATCGATTTAACTAG-AAGTAAATTCAGAAAGAAAAAAAAAAAACGTTATTAGAAG
66 TAAATATTATTTCAATTTAATTAGAAAGT-AATT--G-AA-AAAAAGGATAAACAATATTAGATG
* * ** ** * *
466 CGTGAAAAACCC-TTAATTTTTTTTTCAGTTGAATTATATATTTCTTGTGAGTATTATGGCAAAA
126 CATGAAAAACCCGTCAATCCTTTTGGCA-TTGAATTATATATTTCTTATGACTATTATGGCAAAA
* * * * * *
530 AATTGAGTAAAAATTTTTCGGGTCAGTTTTTTCAAACTTTTAGTCGAAATCGTGTGCTAACCATC
190 AATTGAGTAAAAATATTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATC
* * * * * * * *
595 ACAGTTTTTTTGCTAAAAACGCGTTCCGGGTCCCCGGCTTAGTTTTGCATGATTTTTGGTGTAAA
255 ACAGGTTTTTGGATAAAAACGCGTTCCGAGACCCCGGCTTACTTTTGCATGATTTTTGGCGCAAA
* * *
660 GACTTCTTGAT
320 AACTCCTTGAA
* * * **
671 ATATCTATAATCTTCAGACCAAATCCCAGCCACTTTGGAT-TGAAGGATTTGTTTTTACGAGCAT
1 ATATATATAATCATCAAACCAAATCCCAGCCACAATGGATAT-AAGGATTTGTTTTTACGAGCAT
* * * *
735 CTAAATATTGTTTCGATTTAATTAGAAATTAATT-AAAAAATGGA-AATACAATATTAGATGCAT
65 CTAAATATTATTTCAATTTAATTAGAAAGTAATTGAAAAAAAGGATAA-ACAATATTAGATGCAT
*
798 GAAAAATCC-TCCAATCCTTTTGGCATTGAATTATATATTT-TATATGACTATT-TCGGCAAAAA
129 GAAAAACCCGT-CAATCCTTTTGGCATTGAATTATATATTTCT-TATGACTATTAT-GGCAAAAA
* * **
860 ATTGTG-AAATCATATTTCGGGTTTGTTTTTGCAAAATTTTAGCCGCAAATCATGTACTAACCAT
191 ATTGAGTAAA-AATATTTCGGGTCAGTTTTTGCAAAATTTTAGCCG-AAATCATGTACTAACCAT
* *
924 CAC-GGTTTTTGGATAAAAACGCGTTTCGAGACCTCGGCTTACTTTTGCATGATTTTTGGCGCAA
254 CACAGGTTTTTGGATAAAAACGCGTTCCGAGACCCCGGCTTACTTTTGCATGATTTTTGGCGCAA
988 AAACTCCTTGAA
319 AAACTCCTTGAA
* * * *
1000 ATATATATAATCATGAAACCAAATCTCGGCCACAATGGATATAAGGATTTGTTTTTACGAGCATT
1 ATATATATAATCATCAAACCAAATCCCAGCCACAATGGATATAAGGATTTGTTTTTACGAGCATC
* * * * *
1065 TGAATCTTATTTTAATTTAATTAGAAAGTAATTCGGAAAAAAAGGATAAACGATATTAGATGCGT
66 TAAATATTATTTCAATTTAATTAGAAAGTAATT--GAAAAAAAGGATAAACAATATTAGATGCAT
* * ** * * * *
1130 GAAAAGCCCGTCAATCTTTTTGGTGTTGAATTATATATTTAGCCTA--AGTGTTATGGCAAATAA
129 GAAAAACCCGTCAATCCTTTTGGCATTGAATTATATATTT--CTTATGACTATTATGGCAAAAAA
* * * *
1193 TTCAG-AAAGAATTTTTCGGGTCA------G-----TTTTAGCCGAAATCGTGTACTAATCATCA
192 TTGAGTAAA-AATATTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCA
* * * * * * * * * *
1246 C-GATTTTTGGGTTAAAAACGCGTTTCGGGGCCCCAGCTCAGTATTGCATGACTTTTGGCAG-AA
256 CAGGTTTTT-GGATAAAAACGCGTTCCGAGACCCCGGCTTACTTTTGCATGATTTTTGGC-GCAA
* *
1309 AGACTCCTCGAA
319 AAACTCCTTGAA
* * * * * * * *
1321 ATATCTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGGTTTTACGAGCATC
1 ATATATATAATCATCAAACCAAATCCCAGCCACAATGGATATAAGGATTTGTTTTTACGAGCATC
** * * * ** *
1386 CGAATCTTATTTCGATTTACTTAG-AAGTAAATTCAGAAAAAAAAAATTTAAAAAAAAACGATAT
66 TAAATATTATTTCAATTTAATTAGAAAGT-AATT--GAAAAAAAGGA--T------AAACAATAT
* * * ** * * ** * * ** * * *
1450 GAGAAGCTTGAAAAACCATTAAAT-TTTTTTTCAGTTGGATTATATATTACTTGGGAGTATTGTT
120 TAGATGCATGAAAAACCCGTCAATCCTTTTGGCA-TTGAATTATATATTTCTTATGACTATTATG
* * * * * * * *
1514 GCAAAGAATTAAGTAAAAATTTTTCGGATCAGTTTTTTCAAAATTTTAGCTGAAATCGTGTGC--
184 GCAAAAAATTGAGTAAAAATATTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACTA
* * * ** * *
1577 ACCATCACCA--TTTTTGGCTAAAAACACGTTCCCGGGTTCCCGGCTCAGTTTTGCATGATTTTT
249 ACCATCA-CAGGTTTTTGGATAAAAACGCGTT-CCGAGACCCCGGCTTACTTTTGCATGATTTTT
** ** *
1640 GGCATAAAGAA-TTGTTGAT
312 GGCGCAAA-AACTCCTTGAA
* * * * * *
1659 ATATCTATATTCATCAAACCAAATCCCAACCACATTGGATTTAAGGATTTTTTTTTACGAGCATC
1 ATATATATAATCATCAAACCAAATCCCAGCCACAATGGATATAAGGATTTGTTTTTACGAGCATC
* * * * *
1724 TAAATATTGTTTCGATTAAATTAG-AATTAATTCAAAAAA
66 TAAATATTATTTCAATTTAATTAGAAAGTAATTGAAAAAA
1763 TTGGAAATAC
Statistics
Matches: 1137, Mismatches: 216, Indels: 131
0.77 0.15 0.09
Matches are distributed among these distances:
319 24 0.02
320 173 0.15
321 165 0.15
322 1 0.00
323 1 0.00
326 1 0.00
327 2 0.00
328 12 0.01
329 300 0.26
330 52 0.05
331 1 0.00
332 84 0.07
333 7 0.01
334 133 0.12
335 15 0.01
337 17 0.01
338 129 0.11
339 2 0.00
340 18 0.02
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (330 bp):
ATATATATAATCATCAAACCAAATCCCAGCCACAATGGATATAAGGATTTGTTTTTACGAGCATC
TAAATATTATTTCAATTTAATTAGAAAGTAATTGAAAAAAAGGATAAACAATATTAGATGCATGA
AAAACCCGTCAATCCTTTTGGCATTGAATTATATATTTCTTATGACTATTATGGCAAAAAATTGA
GTAAAAATATTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACAGGT
TTTTGGATAAAAACGCGTTCCGAGACCCCGGCTTACTTTTGCATGATTTTTGGCGCAAAAACTCC
TTGAA
Found at i:1903 original size:142 final size:142
Alignment explanation
Indices: 1644--1925 Score: 467
Period size: 142 Copynumber: 2.0 Consensus size: 142
1634 ATTTTTGGCA
* *
1644 TAAAGAATTGTTGATATATCTATATTCATCAAACCAAATCCCAACCACATTGGATTTAAGGATTT
1 TAAAGAATTCTTGATATATCTATATTCATCAAACCAAATCCCAACCACATTGGATTAAAGGATTT
* *
1709 TTTTTTACGAGCATCTAAATATTGTTTCGATTAAATTAGAATTAATTCAAAAAATTGGAAATACG
66 GTTTTTACGAGCATCTAAATATTGTTTCGATTAAATTAGAATTAATTCAAAAAAATGGAAATACG
1774 ATATTAGATGAG
131 ATATTAGATGAG
* * *
1786 TAAAGACTTCTTGATATATCTATATTCTTCAAACCAAATCCCAACCACTTTGGATTAAAGGATTT
1 TAAAGAATTCTTGATATATCTATATTCATCAAACCAAATCCCAACCACATTGGATTAAAGGATTT
* *
1851 GTTTTTACGAGTATCTAAATATTGTTTCGATTTAATTAGAAATTAATT-AAAAAAATGGAAATAC
66 GTTTTTACGAGCATCTAAATATTGTTTCGATTAAATTAG-AATTAATTCAAAAAAATGGAAATAC
1915 GATATTAGATG
130 GATATTAGATG
1926 CATGAAAAAC
Statistics
Matches: 130, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
142 122 0.94
143 8 0.06
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (142 bp):
TAAAGAATTCTTGATATATCTATATTCATCAAACCAAATCCCAACCACATTGGATTAAAGGATTT
GTTTTTACGAGCATCTAAATATTGTTTCGATTAAATTAGAATTAATTCAAAAAAATGGAAATACG
ATATTAGATGAG
Done.