Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012389.1 Corchorus olitorius cultivar O-4 contig12422, 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: 22495
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--42 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
43 TAAAAAGTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2829 original size:15 final size:16
Alignment explanation
Indices: 2795--2831 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2785 TGACAGTTTT
2795 TTTTTAAATGGATAGC
1 TTTTTAAATGGATAGC
2811 TTTTTAAGATGG-TAG-
1 TTTTTAA-ATGGATAGC
2826 TTTTTA
1 TTTTTA
2832 TTTTGTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 10 0.50
17 4 0.20
ACGTcount: A:0.27, C:0.03, G:0.19, T:0.51
Consensus pattern (16 bp):
TTTTTAAATGGATAGC
Found at i:12465 original size:24 final size:24
Alignment explanation
Indices: 12433--12479 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
12423 AAAACCATAT
*
12433 TTAGTCCATTCTAAAGTGAGGATC
1 TTAGTCCATACTAAAGTGAGGATC
12457 TTAGTCCATACTAAAGTGAGGAT
1 TTAGTCCATACTAAAGTGAGGAT
12480 GCCTGAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (24 bp):
TTAGTCCATACTAAAGTGAGGATC
Found at i:16815 original size:45 final size:45
Alignment explanation
Indices: 16764--16870 Score: 105
Period size: 45 Copynumber: 2.4 Consensus size: 45
16754 CATACTATCA
*
16764 TATCAAAAAATTTATAGGGAGATTAAT-AAAATTTCATAGAGAGGT
1 TATCAAAAAATTTATAGGGAGATT-ATCAAAATTTCATAGAAAGGT
* * * *
16809 TATCAAAGAAA-TCATATGGAGGTTTTCAAAATTTCATAGAAAGGT
1 TATCAAA-AAATTTATAGGGAGATTATCAAAATTTCATAGAAAGGT
16854 T-T-ATAAAAATTTCATAG
1 TATCA-AAAAATTT-ATAG
16871 TTAGGTTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
43 4 0.08
44 5 0.10
45 38 0.76
46 3 0.06
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.33
Consensus pattern (45 bp):
TATCAAAAAATTTATAGGGAGATTATCAAAATTTCATAGAAAGGT
Found at i:16853 original size:22 final size:22
Alignment explanation
Indices: 16791--16870 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 22
16781 GGAGATTAAT
*
16791 AAAATTTCATAGAGAGGTTATC
1 AAAATTTCATAGAGAGGTTTTC
**
16813 AAAGAAATCATATG-GAGGTTTTC
1 AAA-ATTTCATA-GAGAGGTTTTC
* *
16836 AAAATTTCATAGAAAGGTTTATA
1 AAAATTTCATAGAGAGGTTT-TC
16859 AAAATTTCATAG
1 AAAATTTCATAG
16871 TTAGGTTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
21 1 0.02
22 15 0.32
23 30 0.64
24 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (22 bp):
AAAATTTCATAGAGAGGTTTTC
Found at i:16946 original size:22 final size:22
Alignment explanation
Indices: 16770--16957 Score: 105
Period size: 22 Copynumber: 8.5 Consensus size: 22
16760 ATCATATCAA
* *
16770 AAAATTT-ATAGGGAGATTAAT-
1 AAAATTTCATAGTGAGGTT-ATC
*
16791 AAAATTTCATAGAGAGGTTATC
1 AAAATTTCATAGTGAGGTTATC
** *
16813 AAAGAAATCATA-TGGAGGTTTTC
1 AAA-ATTTCATAGT-GAGGTTATC
** *
16836 AAAATTTCATAGAAAGGTTTATA
1 AAAATTTCATAGTGAGG-TTATC
* *
16859 AAAATTTCATAGTTAGGTTATT
1 AAAATTTCATAGTGAGGTTATC
** * * *
16881 AGTATTTCATTGGGAGTTTATC
1 AAAATTTCATAGTGAGGTTATC
* * * **
16903 ACAATTTTATAGGGTA-AATATC
1 AAAATTTCATAGTG-AGGTTATC
*
16925 AAAATTTCATAGTGTGGTTATC
1 AAAATTTCATAGTGAGGTTATC
16947 AAAATTTCATA
1 AAAATTTCATA
16958 AAAATATTTA
Statistics
Matches: 125, Mismatches: 34, Indels: 15
0.72 0.20 0.09
Matches are distributed among these distances:
21 9 0.07
22 80 0.64
23 36 0.29
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.37
Consensus pattern (22 bp):
AAAATTTCATAGTGAGGTTATC
Found at i:19939 original size:23 final size:23
Alignment explanation
Indices: 19896--19939 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
19886 TAAGTTTTTT
*
19896 AATAAAATTAGTAGAATGATAAA
1 AATAAAATTAGTAGAAGGATAAA
*
19919 AATAAAA-TAGGTATAAGGATA
1 AATAAAATTA-GTAGAAGGATA
19940 TTAGATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (23 bp):
AATAAAATTAGTAGAAGGATAAA
Done.