Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017762.1 Corchorus olitorius cultivar O-4 contig17795, 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: 51012
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:23676 original size:2 final size:2
Alignment explanation
Indices: 23671--23699 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
23661 AAAAAAAAAG
23671 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23700 CCCATACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:23692 original size:13 final size:13
Alignment explanation
Indices: 23674--23699 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23664 AAAAAAGTAT
23674 ATATATATATATA
1 ATATATATATATA
23687 ATATATATATATA
1 ATATATATATATA
23700 CCCATACAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:23939 original size:11 final size:11
Alignment explanation
Indices: 23923--23949 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
23913 TTTTATCCAA
23923 CATTAAATATT
1 CATTAAATATT
23934 CATTAAATATT
1 CATTAAATATT
23945 CATTA
1 CATTA
23950 GTGGCAATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (11 bp):
CATTAAATATT
Found at i:24167 original size:21 final size:19
Alignment explanation
Indices: 24109--24168 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
24099 TTCATTTATG
*
24109 TACTGTATAGATGATATTA
1 TACTGTATAAATGATATTA
* *
24128 TACTGTATAAATCAAATTA
1 TACTGTATAAATGATATTA
* *
24147 GGTAGTGTATATATGATATTA
1 --TACTGTATAAATGATATTA
24168 T
1 T
24169 TAAAACAACG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
19 17 0.53
21 15 0.47
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (19 bp):
TACTGTATAAATGATATTA
Found at i:28638 original size:34 final size:34
Alignment explanation
Indices: 28587--28657 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
28577 AAATTAACTT
28587 AAAAAAGCATTAAAAATAGTCAGAAAAGAGAGGA
1 AAAAAAGCATTAAAAATAGTCAGAAAAGAGAGGA
* * * *
28621 AAAAAAGTATTAGAAATAGTCAGAAAGGTGAGGA
1 AAAAAAGCATTAAAAATAGTCAGAAAAGAGAGGA
28655 AAA
1 AAA
28658 GAATCAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.59, C:0.04, G:0.23, T:0.14
Consensus pattern (34 bp):
AAAAAAGCATTAAAAATAGTCAGAAAAGAGAGGA
Found at i:31691 original size:13 final size:14
Alignment explanation
Indices: 31673--31703 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
31663 GCTTAAACTT
31673 AGAAAA-AAAAAAA
1 AGAAAACAAAAAAA
31686 AGAAAACAAAAAAA
1 AGAAAACAAAAAAA
31700 AGAA
1 AGAA
31704 GCTCTCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (14 bp):
AGAAAACAAAAAAA
Found at i:37322 original size:21 final size:19
Alignment explanation
Indices: 37290--37328 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
37280 TAATGAGGAT
37290 GCCAATGTTGCTCTAGTTG
1 GCCAATGTTGCTCTAGTTG
*
37309 GCCACATGTATGCTTTAGTT
1 GCCA-ATGT-TGCTCTAGTT
37329 TCCTATACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (19 bp):
GCCAATGTTGCTCTAGTTG
Found at i:44548 original size:19 final size:19
Alignment explanation
Indices: 44524--44560 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
44514 GGTACTGGGT
*
44524 ACTGTACAGATGAAATTAC
1 ACTGTACAGATCAAATTAC
44543 ACTGTACAGATCAAATTA
1 ACTGTACAGATCAAATTA
44561 AGTATTGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (19 bp):
ACTGTACAGATCAAATTAC
Found at i:48228 original size:2 final size:2
Alignment explanation
Indices: 48221--48259 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
48211 GGAAATTATG
48221 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48260 CATACAACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.