Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009887.1 Corchorus olitorius cultivar O-4 contig09919, 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: 4404
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Found at i:1908 original size:27 final size:26
Alignment explanation
Indices: 1853--1914 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
1843 TCTAATTTTC
1853 TATTATTTTAATAATGGAATAATTAAAA
1 TATTA-TTTAATAATGGAAT-ATTAAAA
1881 TATTATTTAATAATGGCAAT-TTAGAAA
1 TATTATTTAATAATGG-AATATTA-AAA
1908 TA-TATTT
1 TATTATTT
1915 GAAAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.25
27 16 0.50
28 8 0.25
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (26 bp):
TATTATTTAATAATGGAATATTAAAA
Found at i:2085 original size:6 final size:6
Alignment explanation
Indices: 2076--2102 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2066 CTTTATATAT
2076 ATACTA ATACTA ATACTA ATACTA ATA
1 ATACTA ATACTA ATACTA ATACTA ATA
2103 AATAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACTA
Found at i:4162 original size:332 final size:325
Alignment explanation
Indices: 3028--4189 Score: 1085
Period size: 332 Copynumber: 3.6 Consensus size: 325
3018 GCTTTGTTAC
* * * * * * * *
3028 CAAAAACCGTGATGGTTAATACACGATTTCGGTTAAAATTTTGTGAAAATTTACCCAAAAGAAAT
1 CAAAAACTGTGAT-GTTAGTACATGATTTCAGCTAAAATTTTGTAAAAATTGACTC--AAGAAAT
* ** ** * ** * *
3093 T-TCCTAAATTTTTTGCCATGATACTCATAAAAAATATATAATTCAACGTAAAAAAAAATTGAAA
63 TCTCCTCAATTTTCGGCCACAATACTCATAAAAAATATATAACTCAACG-CCAAAAAGATTGAAG
* * * * *
3157 GGTTTTTCGCGCTTCTAATATCGGTTTTCTTATTTTTTTCCGAATCAATTTCTAATTAAATCGAA
127 GGCTTCTCACGCTTCTAATATC-GTTTTCCTA-TTTTTTCCGAATTAATTTCTAATTAAATCGAA
* * *
3222 ACATGATAGAGATGCTTGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGG
190 ACATGAT-CAGATG--TGTAAAAACAAATCCTTAAATCCAATGTGGTTAAGATTTGGTTAGATAG
* * * * * * *
3287 ATATAGATATTTCAATGTGACTTGGCGCAAAAAATCATGCAAAACAGAGCCGGGACCCCGAAATG
252 ATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAATAGAGCCGGG-GCCTGGAACG
3352 CGTTTTTAGT
316 CGTTTTTAGT
* * *
3362 CAAAAACTGTGA---T-G--CATGATTTCAGCTAAAATTTTGTAAAAATTGACATGAAGGATTTC
1 CAAAAACTGTGATGTTAGTACATGATTTCAGCTAAAATTTTGTAAAAATTGAC-TCAAGAAATTC
* * * * * * *
3421 TCCTCAATTTCCCGACACCATATTCATAAAAAATATGTAACTCAACGCCAAAAAAATTGAAGGGC
65 TCCTCAATTTTCGGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAGGGC
* * * *
3486 TTCTGACACTTCTAAAATTG-TTT--T-TTTTTTCCGAATTAATTTCTAATTAAATCGAAAC---
130 TTCTCACGCTTCTAATATCGTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATG
* * ** * *
3544 --CGGAT-TG-AAAAACAAATCCTTAAATCCAATGTGGCTGAA-ATTTTTTTAAATAAATATAGA
195 ATCAGATGTGTAAAAACAAATCCTTAAATCCAATGTGG-TTAAGATTTGGTTAGATAGATATAGA
* * * *
3604 TATTTCAATGACTA-TTGACGTCAAAAATCATGCAAAACT-GAGCCGGGGCCATGGAACGCATTT
259 TATTTCAATGA-GACTTGGCGCCAAAAATCATGCAAAA-TAGAGCCGGGGCC-TGGAACGCGTTT
*
3667 TTAGC
321 TTAGT
* * * *
3672 CAAAAACCGTGATAGTTAGTACATGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAA-AGAAT
1 CAAAAACTGTGAT-GTTAGTACATGATTTCAGCTAAAATTTTGTAAAAATTGACTC-AAGA-AAT
* * * * * * * *
3736 TTTTCTCAATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACACAAAAAAGATTGAAAG
63 TCTCCTCAATTTTCGGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAGG
* * * *
3801 GCTAT-TCACGCTTCCAATATCGTTTTTCCTATTTTTTTCGAATTAATTCCTAATTGAATCGAAA
128 GCT-TCTCACGCTTCTAATATCG-TTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAA
* ** *
3865 CATGATTCATATGGTCGTAAAAACAAATATTTAAATCCAATGTGGTTAAGATTTGGTTAGATTGA
191 CATGA-TCAGAT-GT-GTAAAAACAAATCCTTAAATCCAATGTGGTTAAGATTTGGTTAGATAGA
* * *
3930 TATATATATTTCAATGAGACTTGGCGCCAAAAATCGTGTAAAATAGAGCCGGGGCTCTGGAACGC
253 TATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAATAGAGCCGGGGC-CTGGAACGC
3995 GTTTTTAGT
317 GTTTTTAGT
* * * * *
4004 CAAAAATTGTGATGGTTAGTACACGATTTCAGCTAAATTTTTGCAAAAGTTGACTCAAGAAATAT
1 CAAAAACTGTGAT-GTTAGTACATGATTTCAGCTAAAATTTTGTAAAAATTGACTCAAGAAAT-T
* * *
4069 CTCCTCAATTTTGGGCCACAATACT-ATAAAAAAATATATAACTCAATGCCAAAAAGACTGAAGG
64 CTCCTCAATTTTCGGCCACAATACTCAT-AAAAAATATATAACTCAACGCCAAAAAGATTGAAGG
*
4133 GCTTCTCACGCTTCTAATATCGCTTTTCCTACCTTTTTCCGAATTAATTTCTAATTA
128 GCTTCTCACGCTTCTAATATCG-TTTTCCTA-TTTTTTCCGAATTAATTTCTAATTA
4190 TAAAAATTAT
Statistics
Matches: 662, Mismatches: 126, Indels: 81
0.76 0.14 0.09
Matches are distributed among these distances:
309 2 0.00
310 104 0.16
311 5 0.01
314 4 0.01
315 1 0.00
317 101 0.15
318 1 0.00
319 3 0.00
320 33 0.05
321 1 0.00
322 32 0.05
324 3 0.00
325 1 0.00
326 33 0.05
327 65 0.10
328 3 0.00
330 2 0.00
331 14 0.02
332 221 0.33
333 22 0.03
334 11 0.02
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (325 bp):
CAAAAACTGTGATGTTAGTACATGATTTCAGCTAAAATTTTGTAAAAATTGACTCAAGAAATTCT
CCTCAATTTTCGGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAGGGCT
TCTCACGCTTCTAATATCGTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGA
TCAGATGTGTAAAAACAAATCCTTAAATCCAATGTGGTTAAGATTTGGTTAGATAGATATAGATA
TTTCAATGAGACTTGGCGCCAAAAATCATGCAAAATAGAGCCGGGGCCTGGAACGCGTTTTTAGT
Done.