Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011381.1 Corchorus capsularis cultivar CVL-1 contig11402, 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: 5005
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Found at i:367 original size:6 final size:6
Alignment explanation
Indices: 354--404 Score: 59
Period size: 6 Copynumber: 8.0 Consensus size: 6
344 TATATATATC
354 AAAA-A AAAAGA AAAAGA AAAAGGAA AAAAGA AAAAGGGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAA-G-A AAAAGA AAAA--GA AAAAGA AAAAGA
405 GTGCAAATGG
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
5 4 0.10
6 24 0.59
7 2 0.05
8 11 0.27
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:380 original size:20 final size:20
Alignment explanation
Indices: 357--402 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 20
347 ATATATCAAA
357 AAAAAAGAAAAA-GAAAAAGG
1 AAAAAAGAAAAAGGAAAAA-G
377 AAAAAAGAAAAAGGGAAAAAG
1 AAAAAAGAAAAA-GGAAAAAG
398 AAAAA
1 AAAAA
403 GAGTGCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.50
21 6 0.25
22 6 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAAGGAAAAAG
Found at i:381 original size:14 final size:14
Alignment explanation
Indices: 364--403 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
354 AAAAAAAAAG
364 AAAAAGAAAAAGGA
1 AAAAAGAAAAAGGA
*
378 AAAAAGAAAAAGGG
1 AAAAAGAAAAAGGA
392 AAAAAGAAAAAG
1 AAAAAGAAAAAG
404 AGTGCAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGGA
Found at i:397 original size:8 final size:7
Alignment explanation
Indices: 357--403 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
347 ATATATCAAA
*
357 AAAAAAG
1 AAAAAGG
364 AAAAA-G
1 AAAAAGG
370 AAAAAGG
1 AAAAAGG
*
377 AAAAAAG
1 AAAAAGG
384 AAAAAGGG
1 AAAAA-GG
392 AAAAA-G
1 AAAAAGG
398 AAAAAG
1 AAAAAG
404 AGTGCAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 12 0.34
7 17 0.49
8 6 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:1610 original size:97 final size:96
Alignment explanation
Indices: 1323--2032 Score: 811
Period size: 97 Copynumber: 7.3 Consensus size: 96
1313 GAAAAGGCAT
* * * * ** * *
1323 TTTGGGAAATGGCAGGTAAGAATAAATATCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAAG
1 TTTGGGAAATAGCAAGCAAAAATAAATGGCTTCCGT-CTGGAAGGGCGTTTTGGGAAATAGCAAG
* * * * *
1388 TAAAGATAAACGGTTTCCGTCCGGAAAGGGCGT
65 TAAAAATAAATGGCTTCCGTCTGG-AAGGGCGC
* * * * * *
1421 TTTGGGGAGATAGCAAGCAAAACTTATTGGCTTCCGTCTGGAAGGGCATTTTAGGAAATAGCAAG
1 TTT-GGGAAATAGCAAGCAAAAATAAATGGCTTCCGTCTGGAAGGGCGTTTTGGGAAATAGCAAG
** * *
1486 CGAAAATTAATGGCTTCCGTTTGGGAAGGGCGC
65 TAAAAATAAATGGCTTCCGTCT-GGAAGGGCGC
* * *
1519 TTTGGGAAATAGCAAGCAAAAATAAACGGCTTCCGTCTGGAAGGGCATTTTCGGGAGATAGCAAG
1 TTTGGGAAATAGCAAGCAAAAATAAATGGCTTCCGTCTGGAAGGGCGTTTT-GGGAAATAGCAAG
* * **
1584 CAAAAATAAATGGCTTACGTCTGGAAGGGCAT
65 TAAAAATAAATGGCTTCCGTCTGGAAGGGCGC
* * *
1616 TTTGGGAAATAGCAAGCGAAAATAAATGGCTTCCGTCTAGAAGGGCGCTTTGGGAAATAGCAAGT
1 TTTGGGAAATAGCAAGCAAAAATAAATGGCTTCCGTCTGGAAGGGCGTTTTGGGAAATAGCAAGT
*
1681 AAAAATAAATGGCTTCCGTCAGGGAAGGGCGC
66 AAAAATAAATGGCTTCCGTC-TGGAAGGGCGC
* *
1713 TTTGGGAAATAGCAAG-TAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAG
1 TTTGGGAAATAGCAAGCAAAAATAAATGGCTTCCGTCT-GGAAGGGCGTTTTGGGAAATAGCAAG
*
1777 TGAAAATAAATGGCTTCCGTCTGGAAGGGCGC
65 TAAAAATAAATGGCTTCCGTCTGGAAGGGCGC
* *
1809 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTT-----ATAGCAAG
1 TTTGGGAAATAGCAAGCAAAAATAAATGGCTTCCGTCT-GGAAGGGCGTTTTGGGAAATAGCAAG
* *
1869 TGAAAATAAATGGCTTTCGTCTGGGAAGGGCGC
65 TAAAAATAAATGGCTTCCGTCT-GGAAGGGCGC
* * * * *
1902 TTTGGGAAATATCAAGTAAAATTAAATGGCTTCCGTCTGGAAATGGTGTTTTGGGAAATAGCAAG
1 TTTGGGAAATAGCAAGCAAAAATAAATGGCTTCCGTCTGG-AAGGGCGTTTTGGGAAATAGCAAG
* **
1967 TAAAAACAAATGGCTTTTGTCTGGGAAGGGCGC
65 TAAAAATAAATGGCTTCCGTCT-GGAAGGGCGC
* * *
2000 TTTGGGAAATAGTAAGTAAAAACAAATGGCTTC
1 TTTGGGAAATAGCAAGCAAAAATAAATGGCTTC
2033 TGTTTGGGAG
Statistics
Matches: 536, Mismatches: 63, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
92 31 0.06
93 54 0.10
96 77 0.14
97 200 0.37
98 149 0.28
99 25 0.05
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (96 bp):
TTTGGGAAATAGCAAGCAAAAATAAATGGCTTCCGTCTGGAAGGGCGTTTTGGGAAATAGCAAGT
AAAAATAAATGGCTTCCGTCTGGAAGGGCGC
Found at i:2041 original size:49 final size:49
Alignment explanation
Indices: 1323--2041 Score: 848
Period size: 49 Copynumber: 14.9 Consensus size: 49
1313 GAAAAGGCAT
* * * ** * **
1323 TTTGGGAAATGGCAGGTAAGAATAAATATCTTCCGTCCGGGAAGGGCAT
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* * * * * *
1372 TTTGGGAAATAGCAAGTAAAGATAAACGGTTTCCGTCCGGAAAGGGCGT
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* * * * * **
1421 TTTGGGGAGATAGCAAGCAAAACTTATTGGCTTCCGTCT-GGAAGGGCAT
1 TTT-GGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* ** * *
1470 TTTAGGAAATAGCAAGCGAAAATTAATGGCTTCCGTTTGGGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* * **
1519 TTTGGGAAATAGCAAGCAAAAATAAACGGCTTCCGTCT-GGAAGGGCAT
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* * * **
1567 TTTCGGGAGATAGCAAGCAAAAATAAATGGCTTACGTCT-GGAAGGGCAT
1 TTT-GGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
** *
1616 TTTGGGAAATAGCAAGCGAAAATAAATGGCTTCCGTCT-AGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
*
1664 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCAGGGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
1713 TTTGGGAAATAGCAAGT-AAAATAAATGGCTTCCGTCTGGGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
*
1761 TTTGGGAAATAGCAAGTGAAAATAAATGGCTTCCGTCT-GGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
1809 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* *
1858 TTT-----ATAGCAAGTGAAAATAAATGGCTTTCGTCTGGGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* * * * * *
1902 TTTGGGAAATATCAAGTAAAATTAAATGGCTTCCGTCTGGAAATGGTGT
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* **
1951 TTTGGGAAATAGCAAGTAAAAACAAATGGCTTTTGTCTGGGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* * * *
2000 TTTGGGAAATAGTAAGTAAAAACAAATGGCTTCTGTTTGGGA
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGA
2042 GAAAGCAGGT
Statistics
Matches: 586, Mismatches: 73, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
44 42 0.07
48 208 0.35
49 310 0.53
50 26 0.04
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.24
Consensus pattern (49 bp):
TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
Done.