Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007176.1 Corchorus capsularis cultivar CVL-1 contig07197, 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: 42931
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1723 original size:27 final size:27
Alignment explanation
Indices: 1665--1733 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
1655 AGGTGAACTT
* * *
1665 AAAAATGACTAAAATGCCCCCGAGTGT
1 AAAAATGACCAAAATGCCCCCGAGCGC
*
1692 AAAAATGACCAAAATGCCCCCGGGCGC
1 AAAAATGACCAAAATGCCCCCGAGCGC
*
1719 GAAAATGACCAAAAT
1 AAAAATGACCAAAAT
1734 ACCCTTGGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.43, C:0.25, G:0.19, T:0.13
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCCGAGCGC
Found at i:4882 original size:15 final size:15
Alignment explanation
Indices: 4862--4900 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4852 GAAAACAAAC
**
4862 AAATAATTAACTAGA
1 AAATAATTAAAGAGA
4877 AAATAATTAAAGAGA
1 AAATAATTAAAGAGA
4892 AAATCAATT
1 AAAT-AATT
4901 GATAAAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (15 bp):
AAATAATTAAAGAGA
Found at i:11282 original size:85 final size:85
Alignment explanation
Indices: 11139--11310 Score: 326
Period size: 85 Copynumber: 2.0 Consensus size: 85
11129 AGTTGAATTT
*
11139 CAAAGCAAGAAAACATGTCAAGAAGTGTCATAGCACTGGAGTACATGGGTCGCGAGGCAAACCAC
1 CAAAGCAAGAAAACATGTCAAGAAGTGTCATAGCACGGGAGTACATGGGTCGCGAGGCAAACCAC
*
11204 ATGGGGCGCCAAGCATAGCA
66 ATGGAGCGCCAAGCATAGCA
11224 CAAAGCAAGAAAACATGTCAAGAAGTGTCATAGCACGGGAGTACATGGGTCGCGAGGCAAACCAC
1 CAAAGCAAGAAAACATGTCAAGAAGTGTCATAGCACGGGAGTACATGGGTCGCGAGGCAAACCAC
11289 ATGGAGCGCCAAGCATAGCA
66 ATGGAGCGCCAAGCATAGCA
11309 CA
1 CA
11311 TGGGCACCCA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.37, C:0.23, G:0.28, T:0.12
Consensus pattern (85 bp):
CAAAGCAAGAAAACATGTCAAGAAGTGTCATAGCACGGGAGTACATGGGTCGCGAGGCAAACCAC
ATGGAGCGCCAAGCATAGCA
Found at i:20236 original size:39 final size:39
Alignment explanation
Indices: 20174--20248 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
20164 AGGAAAAGGG
20174 AGAAGAGAAATCTGAGGAGACTAAAGAAGAGGAGGAAGA
1 AGAAGAGAAATCTGAGGAGACTAAAGAAGAGGAGGAAGA
*
20213 AGAAGAGAAATCTTAGG-GTACTAAAGAAGAGGAGGA
1 AGAAGAGAAATCTGAGGAG-ACTAAAGAAGAGGAGGA
20249 GGATGACGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.49, C:0.05, G:0.35, T:0.11
Consensus pattern (39 bp):
AGAAGAGAAATCTGAGGAGACTAAAGAAGAGGAGGAAGA
Found at i:23382 original size:21 final size:21
Alignment explanation
Indices: 23358--23453 Score: 80
Period size: 21 Copynumber: 4.9 Consensus size: 21
23348 AATTAAGTTG
23358 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
*
23379 ATTACCAATTTACTTAA-TT-
1 ATTACCAAATTACTTAATTTA
** * * *
23398 -GCACC-GA--A-TTAAGTTG
1 ATTACCAAATTACTTAATTTA
23414 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
*
23435 ATTACCAATTTACTTAATT
1 ATTACCAAATTACTTAATT
23454 GCACCGAATT
Statistics
Matches: 57, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
14 4 0.07
15 3 0.05
17 3 0.05
18 4 0.07
20 3 0.05
21 40 0.70
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.42
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:23390 original size:56 final size:56
Alignment explanation
Indices: 23330--23477 Score: 269
Period size: 56 Copynumber: 2.6 Consensus size: 56
23320 CCAATTACTG
**
23330 ATTTACTTAATCACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTACCA
1 ATTTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTACCA
23386 ATTTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTACCA
1 ATTTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTACCA
*
23442 ATTTACTTAATTGCACCGAATTAAGTTAATTACCAA
1 ATTTACTTAATTGCACCGAATTAAGTTGATTACCAA
23478 TTTGTTTTTT
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 89 1.00
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.38
Consensus pattern (56 bp):
ATTTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTACCA
Found at i:24725 original size:2 final size:2
Alignment explanation
Indices: 24718--24748 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24708 ACAAACCCCT
24718 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24749 GAAACTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27549 original size:89 final size:90
Alignment explanation
Indices: 27431--27762 Score: 303
Period size: 80 Copynumber: 3.8 Consensus size: 90
27421 GAAGAAATTT
* *
27431 GAGAATATGCTGCACCGAGCTCACTGAATCCAATCTTGAAGTAATAATGCACCG-ATTAACTTGG
1 GAGAATATGCTGCACCGAGCTCACCGAATCCAATCTTGAAGTAATAATGCACCGCATTAACTTGA
*
27495 TCCACCAAATTACCCTGAACTGTCTG
66 TCCACCAAATCACCCTGAACTG-CTG
* * * * *
27521 GA-AATACGCTGCACTGAACTCACCGAATCTAATCTTGAAGTAATAATGCACCGCGTTAACTTGA
1 GAGAATATGCTGCACCGAGCTCACCGAATCCAATCTTGAAGTAATAATGCACCGCATTAACTTGA
* ** * *
27585 TTCACTGAATCACCCTGGACTGCTT
66 TCCACCAAATCACCCTGAACTGCTG
*
27610 GAGAATGTGCTGCACCGAGCTCACCGAAT-C---C-------AATAATGCACCGCATTAAACTTG
1 GAGAATATGCTGCACCGAGCTCACCGAATCCAATCTTGAAGTAATAATGCACCGCATT-AACTTG
* ** ** ** *
27664 ATTCACTGAATCGTCCTGAACTATTT
65 ATCCACCAAATCACCCTGAACTGCTG
* * *
27690 GAAAATATGCTACACCGAGCTCACCGAATTCCAATCTTTGAAGAAATAATGCACCGCATTAACTT
1 GAGAATATGCTGCACCGAGCTCACCGAA-TCCAATC-TTGAAGTAATAATGCACCGCATTAACTT
*
27755 GATTCACC
64 GATCCACC
27763 GAATAACCAT
Statistics
Matches: 198, Mismatches: 28, Indels: 30
0.77 0.11 0.12
Matches are distributed among these distances:
79 15 0.08
80 52 0.26
81 1 0.01
82 1 0.01
85 1 0.01
86 1 0.01
89 50 0.25
90 49 0.25
92 12 0.06
93 16 0.08
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (90 bp):
GAGAATATGCTGCACCGAGCTCACCGAATCCAATCTTGAAGTAATAATGCACCGCATTAACTTGA
TCCACCAAATCACCCTGAACTGCTG
Found at i:28532 original size:4 final size:4
Alignment explanation
Indices: 28523--28553 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
28513 AAGGAATTTA
28523 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
28554 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:28804 original size:27 final size:27
Alignment explanation
Indices: 28774--28857 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
28764 TCTTCCACAT
28774 AAGCCGCCCTTTTCGGGTTTTCAACTC
1 AAGCCGCCCTTTTCGGGTTTTCAACTC
** * *
28801 AAGCTC-CTCCTTTTC-CATCCTTC-ACTT
1 AAGC-CGC-CCTTTTCGGGT-TTTCAACTC
*
28828 GAGCCGCCCTTTTCGGGTTTTCAACTC
1 AAGCCGCCCTTTTCGGGTTTTCAACTC
28855 AAG
1 AAG
28858 TGACCCTCAA
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
26 11 0.27
27 19 0.46
28 11 0.27
ACGTcount: A:0.15, C:0.35, G:0.15, T:0.35
Consensus pattern (27 bp):
AAGCCGCCCTTTTCGGGTTTTCAACTC
Found at i:41568 original size:35 final size:35
Alignment explanation
Indices: 41529--41610 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 35
41519 CCATTTGATT
41529 ATTTACTTAATTACACCGAATTAAGCTAATTACCA
1 ATTTACTTAATTACACCGAATTAAGCTAATTACCA
* * *
41564 ATTTACTTAATTGCACCGAATTAAGTTGATTACCA
1 ATTTACTTAATTACACCGAATTAAGCTAATTACCA
*
41599 AATTACTTAATT
1 ATTTACTTAATT
41611 TAATTACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (35 bp):
ATTTACTTAATTACACCGAATTAAGCTAATTACCA
Found at i:41616 original size:21 final size:21
Alignment explanation
Indices: 41592--41631 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41582 AATTAAGTTG
*
41592 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTAAATTTA
*
41613 ATTACCAATTTACTAAATT
1 ATTACCAAATTACTAAATT
41632 GCACCGGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTACCAAATTACTAAATTTA
Done.