Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020839.1 Corchorus olitorius cultivar O-4 contig20872, 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: 48471
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1802 original size:332 final size:333
Alignment explanation
Indices: 1194--2519 Score: 1776
Period size: 332 Copynumber: 4.0 Consensus size: 333
1184 TTTTCCTCAT
* * ** *
1194 TTTTTCGCCACAACACTCTTAAAAAATATATAACTCAATGCAAAAAAAATTGCAGGGCTTTTCAC
1 TTTTTCGCCACAACACTCTTAAAAAATATATAAATCAATGCAAAAAAGATTAAATGGCTTTTCAC
* * *
1259 GATTTTAATATCGTTTTTCCTATTTTTTTTTCGAATTAATTTCAAATAAAATCAAAACAAGATTC
66 GCTTCTAATATCATTTTTCCTA--TTTTTTTCGAATTAATTTCAAATAAAATCAAAACAAGATTC
* * * * *
1324 TGATAATTGTAAAAATAAATCTTTAAATCCAATGTGCCTGACATTTGGTTATATGGATATATAGA
129 TGATGATTGTAAAAACAAATCCTTAAATCCAATGTGGCTGATATTTGGTTATATGGATATATAGA
* * *
1389 T-TTTTCAATGTGTCTTGGCGTTAAAAATCATGCAAAACTGAGACGGGGCCTTGGAACACGTTTT
194 TATTTT-AGTGTATCTTGGCGTTAAAAATCATGCAAAACTGAGACGGGGCCTCGGAACACGTTTT
* *
1453 AAGCCAAAAACTGTGATGGTTGGTACATGATTTCGGTTAAAATTTTGC-AAAACTGACCCG-AAA
258 AAGCCAAAAACTGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTGACCCGTAAA
*
1516 ACATTTCTACAG
323 A-ATTTCTACAA
* * *
1528 TTTTTCGCCACAACACTCTTTAAAAATATATAAATCAATGCATAAAATATTAAATGGCTTTTCAC
1 TTTTTCGCCACAACACTCTTAAAAAATATATAAATCAATGCAAAAAAGATTAAATGGCTTTTCAC
* *
1593 GCTTCTAATATCATTTTTCCTATTTCTTTCGAATTAATTTCTAATAAAATCAAAACAAGATTCTG
66 GCTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTTCAAATAAAATCAAAACAAGATTCTG
*
1658 ATGATTGTAAAAACAAATCCTTAAATCCAATGTGGCTGATATTTGGTTATATGGACATATAGATA
131 ATGATTGTAAAAACAAATCCTTAAATCCAATGTGGCTGATATTTGGTTATATGGATATATAGATA
* *
1723 TTTTAGTGTATCTTGGCGTTAAAAATCATGCAAAAATGAGACGGGGCCTCGGAACGCGTTTTAAG
196 TTTTAGTGTATCTTGGCGTTAAAAATCATGCAAAACTGAGACGGGGCCTCGGAACACGTTTTAAG
* * *
1788 TCAAAAACTGTGATGATTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTTACCCGTAAAAAT
261 CCAAAAACTGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTGACCCGTAAAAAT
1853 TGTCCT-CAA
326 T-T-CTACAA
* * * * * ** *
1862 TTTTTTGCCACAACACTC-TATAAACATCTATAATTCAAAGCAAAAAAGATTGCATGACTTTTCA
1 TTTTTCGCCACAACACTCTTA-AAAAATATATAAATCAATGCAAAAAAGATTAAATGGCTTTTCA
* * * * *
1926 CGCTTCTAATATCGTTTTACCTA-TTTTTCCTAATTAATTTCAAATAAAATCGAAAA-ATGATTC
65 CGCTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTTCAAATAAAATC-AAAACAAGATTC
* * * * *
1989 TGATGCTCGTAAAAGCAAATCCTTAAATCCAATGTGGCTTATATTTGGTTAGATGG--ATATAGA
129 TGATGATTGTAAAAACAAATCCTTAAATCCAATGTGGCTGATATTTGGTTATATGGATATATAGA
* * ** * * * ***
2052 TATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTGAGCCGGGATCC-CGGATTGCGTTTT
194 TATTTTAGTGTATCTTGGCGTTAAAAATCATGCAAAACTGAGACGGG-GCCTCGGAACACGTTTT
* * * * * * * * *
2116 TAGCAAAAAACAGTAATGGTTAATATACGATTTCGGCCAAAATTTTGCAAAAAACTGATCCG-AA
258 AAGCCAAAAACTGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGC-AAAAACTGACCCGTAA
*
2180 AAATTTTCTACAT
322 AAA-TTTCTACAA
2193 TTTTTCGCCACAACACTCTTAAAAAATATATAAATCAATGCAAAAAAGATTAAATGGCTTTTCAC
1 TTTTTCGCCACAACACTCTTAAAAAATATATAAATCAATGCAAAAAAGATTAAATGGCTTTTCAC
* * *
2258 ACTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTTCTAATAAAATCAAAACAAGATTATG
66 GCTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTTCAAATAAAATCAAAACAAGATTCTG
* *
2323 ATGATTGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGT-TTTGGTTTTATGGATATATAGAT
131 ATGATTGTAAAAACAAATCCTTAAATCCAATGTGGCTGA-TATTTGGTTATATGGATATATAGAT
*
2387 ATTTTAGTGTATCTTGGCGTTAAAAATCATGCAAAACTGAGACGGGGCCTCGGATCACGTTTTAA
195 ATTTTAGTGTATCTTGGCGTTAAAAATCATGCAAAACTGAGACGGGGCCTCGGAACACGTTTTAA
* *
2452 GCCAAAAACTGTGATGGTTAGTACATGATTTCGACTAAAATTTTGCAAAAATTGACCCGTAAAAA
260 GCCAAAAACTGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTGACCCGTAAAAA
2517 TTT
325 TTT
2520 TCCTCAAGGA
Statistics
Matches: 855, Mismatches: 118, Indels: 39
0.84 0.12 0.04
Matches are distributed among these distances:
330 2 0.00
331 181 0.21
332 290 0.34
333 117 0.14
334 263 0.31
335 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (333 bp):
TTTTTCGCCACAACACTCTTAAAAAATATATAAATCAATGCAAAAAAGATTAAATGGCTTTTCAC
GCTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTTCAAATAAAATCAAAACAAGATTCTG
ATGATTGTAAAAACAAATCCTTAAATCCAATGTGGCTGATATTTGGTTATATGGATATATAGATA
TTTTAGTGTATCTTGGCGTTAAAAATCATGCAAAACTGAGACGGGGCCTCGGAACACGTTTTAAG
CCAAAAACTGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTGACCCGTAAAAAT
TTCTACAA
Found at i:4640 original size:11 final size:11
Alignment explanation
Indices: 4610--4661 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
4600 ATACATGTAT
**
4610 ATTTATAACAA
1 ATTTATAATTA
4621 ATTTATAATTA
1 ATTTATAATTA
4632 ATTTATAATT-
1 ATTTATAATTA
4642 ATTTGATAATATA
1 ATTT-ATAAT-TA
*
4655 TTTTATA
1 ATTTATA
4662 TAGGAAAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 4 0.11
11 24 0.69
12 4 0.11
13 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
ATTTATAATTA
Found at i:8247 original size:13 final size:13
Alignment explanation
Indices: 8229--8254 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8219 ATATTATGTG
8229 CTAAGAAACAAAA
1 CTAAGAAACAAAA
8242 CTAAGAAACAAAA
1 CTAAGAAACAAAA
8255 TTAAATTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.15, G:0.08, T:0.08
Consensus pattern (13 bp):
CTAAGAAACAAAA
Found at i:20960 original size:14 final size:15
Alignment explanation
Indices: 20932--20964 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
20922 TCATCATCTT
20932 TATATAAAGTATAAG
1 TATATAAAGTATAAG
20947 TATATAAA-TATAAG
1 TATATAAAGTATAAG
20961 TATA
1 TATA
20965 GATGTCATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (15 bp):
TATATAAAGTATAAG
Found at i:22308 original size:13 final size:13
Alignment explanation
Indices: 22290--22322 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
22280 TTGTGATGAA
22290 TTAATTAGAGTAT
1 TTAATTAGAGTAT
22303 TTAATTAGAGTAT
1 TTAATTAGAGTAT
*
22316 GTAATTA
1 TTAATTA
22323 TAATTGGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (13 bp):
TTAATTAGAGTAT
Found at i:22610 original size:34 final size:34
Alignment explanation
Indices: 22567--22634 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
22557 AGTGAATGTA
22567 GGCATCATCTCATCGTGTAAAACCCAAAGTCTTG
1 GGCATCATCTCATCGTGTAAAACCCAAAGTCTTG
22601 GGCATCATCTCATCGTGTAAAACCCAAAGTCTTG
1 GGCATCATCTCATCGTGTAAAACCCAAAGTCTTG
22635 CTGATGAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (34 bp):
GGCATCATCTCATCGTGTAAAACCCAAAGTCTTG
Found at i:28556 original size:17 final size:17
Alignment explanation
Indices: 28534--28572 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
28524 AATTATAAGC
28534 TCAAATGAACTTTGGGT
1 TCAAATGAACTTTGGGT
*
28551 TCAAATGAAGTTTGGGT
1 TCAAATGAACTTTGGGT
28568 TCAAA
1 TCAAA
28573 ATTGATTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (17 bp):
TCAAATGAACTTTGGGT
Found at i:29640 original size:3 final size:3
Alignment explanation
Indices: 29632--29666 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
29622 AACATGGCTA
* *
29632 CTT CTT CTT CTT CTT CTT CCT CTG CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
29667 CTTTGGATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.37, G:0.03, T:0.60
Consensus pattern (3 bp):
CTT
Found at i:36172 original size:102 final size:104
Alignment explanation
Indices: 35989--36198 Score: 334
Period size: 102 Copynumber: 2.0 Consensus size: 104
35979 TGATTCGGAA
35989 AAAGAGCTAAAGTCATCTCCAGTGCAAAATGCTGGTGTCAAAGCCTATGAGAATTCAAAAGTAAA
1 AAAGAGCTAAAGTCATCTCCAGTGCAAAATGCTGGTGT--AAGCCTATGAGAATTCAAAAGTAAA
*
36054 TGTTGATGAAGAGAAGGAACTGATCCATTCTTCTTCTG-TG
64 TGTTGATGAAGAGAAGGAACTGATCCATTCTTCTGCTGCTG
* * * *
36094 AAAGAGCTTAAGTCATCTCCGGTGCAAAATGCTGGTGT-GGGCTATGAGAATTCAAAAGTAAATG
1 AAAGAGCTAAAGTCATCTCCAGTGCAAAATGCTGGTGTAAGCCTATGAGAATTCAAAAGTAAATG
*
36158 TTGATGAAGGGAAGGAACTGATCCATTCTTCTGCTGCTG
66 TTGATGAAGAGAAGGAACTGATCCATTCTTCTGCTGCTG
36197 AA
1 AA
36199 TCTATCGAGG
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
102 58 0.59
103 4 0.04
105 36 0.37
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (104 bp):
AAAGAGCTAAAGTCATCTCCAGTGCAAAATGCTGGTGTAAGCCTATGAGAATTCAAAAGTAAATG
TTGATGAAGAGAAGGAACTGATCCATTCTTCTGCTGCTG
Found at i:47466 original size:16 final size:15
Alignment explanation
Indices: 47430--47464 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
47420 TTTTATAATT
47430 ATTTTATTTTTTACC
1 ATTTTATTTTTTACC
*
47445 ATTTTATTTTTTACT
1 ATTTTATTTTTTACC
47460 ATTTT
1 ATTTT
47465 TAATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTATTTTTTACC
Done.