Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020246.1 Corchorus olitorius cultivar O-4 contig20279, 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: 39941
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:7846 original size:8 final size:8
Alignment explanation
Indices: 7821--7854 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
7811 CGAATGTCCA
*
7821 TTGTGCAG
1 TTGTGCTG
7829 TTGTGCTG
1 TTGTGCTG
*
7837 TTGTGTTG
1 TTGTGCTG
7845 TTGTGCTG
1 TTGTGCTG
7853 TT
1 TT
7855 CAATTCGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.03, C:0.09, G:0.35, T:0.53
Consensus pattern (8 bp):
TTGTGCTG
Found at i:10874 original size:30 final size:32
Alignment explanation
Indices: 10840--10913 Score: 107
Period size: 30 Copynumber: 2.3 Consensus size: 32
10830 TTTTGTATTG
10840 AATTTGTGGACTGTTATTG-CCTTA-TTGGAT
1 AATTTGTGGACTGTTATTGACCTTATTTGGAT
*
10870 AATTTGTGGACTGTTATTGACTTTATTGTTGGAT
1 AATTTGTGGACTGTTATTGACCTTA-T-TTGGAT
10904 AATTTGTGGA
1 AATTTGTGGA
10914 TTTTTCATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 19 0.49
31 4 0.10
34 16 0.41
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.47
Consensus pattern (32 bp):
AATTTGTGGACTGTTATTGACCTTATTTGGAT
Found at i:15157 original size:14 final size:13
Alignment explanation
Indices: 15132--15156 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15122 TCTTCGTTTA
15132 TTTTTTTTAAAAT
1 TTTTTTTTAAAAT
15145 TTTTTTTTAAAA
1 TTTTTTTTAAAA
15157 AATACTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTTTAAAAT
Found at i:15712 original size:26 final size:26
Alignment explanation
Indices: 15683--15733 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
15673 AATTATATAA
15683 TTCTTCCCAAGTCCCAAGCAAATTAT
1 TTCTTCCCAAGTCCCAAGCAAATTAT
***
15709 TTCTTTGGAAGTCCCAAGCAAATTA
1 TTCTTCCCAAGTCCCAAGCAAATTA
15734 AGCAAAGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (26 bp):
TTCTTCCCAAGTCCCAAGCAAATTAT
Found at i:16030 original size:21 final size:21
Alignment explanation
Indices: 16006--16077 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
15996 GAGAGAAAGG
*
16006 AGGAGGAAAAGAAGGAGAAG-A
1 AGGAGGAAGAGAAGGA-AAGAA
* *
16027 AGGAGGAGGAGAAGGCAAGAA
1 AGGAGGAAGAGAAGGAAAGAA
* *
16048 AGGAGGATGATAAGGAAAGAA
1 AGGAGGAAGAGAAGGAAAGAA
16069 AGGAGGAAG
1 AGGAGGAAG
16078 TGAGGGCGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 3 0.07
21 40 0.93
ACGTcount: A:0.51, C:0.01, G:0.44, T:0.03
Consensus pattern (21 bp):
AGGAGGAAGAGAAGGAAAGAA
Found at i:16040 original size:12 final size:12
Alignment explanation
Indices: 15991--16041 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
15981 GGTGATGAGG
15991 AGGAGGA-GAGAA
1 AGGAGGAGGAG-A
*
16003 AGGAGGAGGAAA
1 AGGAGGAGGAGA
* *
16015 AGAAGGAGAAGA
1 AGGAGGAGGAGA
16027 AGGAGGAGGAGA
1 AGGAGGAGGAGA
16039 AGG
1 AGG
16042 CAAGAAAGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 30 0.94
13 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (12 bp):
AGGAGGAGGAGA
Found at i:16075 original size:24 final size:21
Alignment explanation
Indices: 15988--16075 Score: 55
Period size: 21 Copynumber: 4.3 Consensus size: 21
15978 GATGGTGATG
*
15988 AGGAGGAGGAG--A-GAAAGG
1 AGGAGGAGGAGAAAGGAAAGA
**
16006 AGGAGGAAAAG-AAGGAGAAGA
1 AGGAGGAGGAGAAAGGA-AAGA
*
16027 AGGAGGAGGAG-AAGGCAAGA
1 AGGAGGAGGAGAAAGGAAAGA
16047 A--AGGAGGATGATAAGGAAAGAA
1 AGGAGGAGGA-GA-AAGGAAAG-A
16069 AGGAGGA
1 AGGAGGA
16076 AGTGAGGGCG
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
18 16 0.30
19 2 0.04
20 7 0.13
21 23 0.43
22 2 0.04
24 4 0.07
ACGTcount: A:0.50, C:0.01, G:0.47, T:0.02
Consensus pattern (21 bp):
AGGAGGAGGAGAAAGGAAAGA
Found at i:19449 original size:34 final size:35
Alignment explanation
Indices: 19399--19466 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 35
19389 AAAATACTTA
*
19399 AAATATAGATGAAAATATAACCTTTCTAACCCTTG
1 AAATATAGATGAAAATATAACATTTCTAACCCTTG
*
19434 AAATATGGAT-AAAATATAACATTTCTAACCCTT
1 AAATATAGATGAAAATATAACATTTCTAACCCTT
19467 TTGGGAGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 22 0.71
35 9 0.29
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.32
Consensus pattern (35 bp):
AAATATAGATGAAAATATAACATTTCTAACCCTTG
Found at i:24701 original size:17 final size:16
Alignment explanation
Indices: 24647--24697 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
24637 ATCAACCCCC
*
24647 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
24664 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
24681 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
24697 A
1 A
24698 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:30763 original size:2 final size:2
Alignment explanation
Indices: 30756--30780 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30746 CAAAAATTGT
30756 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 T
30781 TATTCCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33909 original size:42 final size:42
Alignment explanation
Indices: 33846--33926 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
33836 GCTAAGTCTT
*
33846 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAAGTAAGAAATACTCAACTCAAATCATA
*
33888 GAAAATTCTTTGTAAAGTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAAGTAAGAAATACTCAACTCAAATC
33927 TTGATCCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (42 bp):
GAAAATTCTCTGTAAAGTAAGAAATACTCAACTCAAATCATA
Found at i:34069 original size:51 final size:51
Alignment explanation
Indices: 34007--34106 Score: 191
Period size: 51 Copynumber: 2.0 Consensus size: 51
33997 AATTAAGTAG
*
34007 AGATTGTGGGGATAGGATTTATTATAACATTTATTGTGTGAAAGGAAACGA
1 AGATAGTGGGGATAGGATTTATTATAACATTTATTGTGTGAAAGGAAACGA
34058 AGATAGTGGGGATAGGATTTATTATAACATTTATTGTGTGAAAGGAAAC
1 AGATAGTGGGGATAGGATTTATTATAACATTTATTGTGTGAAAGGAAAC
34107 AGATAATTAC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (51 bp):
AGATAGTGGGGATAGGATTTATTATAACATTTATTGTGTGAAAGGAAACGA
Found at i:36548 original size:19 final size:19
Alignment explanation
Indices: 36524--36564 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
36514 TCCCACTAAC
*
36524 AAATTTAAGGACTGATAGA
1 AAATTTAAGGACTAATAGA
36543 AAATTTAAGGACTAATAGA
1 AAATTTAAGGACTAATAGA
36562 AAA
1 AAA
36565 GTATTACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.17, T:0.24
Consensus pattern (19 bp):
AAATTTAAGGACTAATAGA
Done.