Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016996.1 Corchorus olitorius cultivar O-4 contig17029, 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: 26472
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:10119 original size:23 final size:22
Alignment explanation
Indices: 10093--10170 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
10083 CAGGAATTAA
*
10093 TATGTTTTATTTATGTAATTTTT
1 TATGTTTTA-TTATGTAATTTTC
*
10116 TATGTTTTAATAATG-ACACTCTTTC
1 TATGTTTT-ATTATGTA-A-T-TTTC
10141 TATGTTTTATTATGTAATTTTC
1 TATGTTTTATTATGTAATTTTC
*
10163 TATTTTTT
1 TATGTTTT
10171 TGGTGAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
22 12 0.26
23 14 0.30
24 8 0.17
25 12 0.26
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.63
Consensus pattern (22 bp):
TATGTTTTATTATGTAATTTTC
Found at i:11273 original size:7 final size:8
Alignment explanation
Indices: 11256--11289 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
11246 TATATTAATT
11256 AAAAGGAA
1 AAAAGGAA
11264 AAAAGGAA
1 AAAAGGAA
11272 AAAAGGAA
1 AAAAGGAA
*
11280 AAAATGAA
1 AAAAGGAA
11288 AA
1 AA
11290 GGGTTGGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (8 bp):
AAAAGGAA
Found at i:16598 original size:12 final size:12
Alignment explanation
Indices: 16581--16614 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
16571 TTAAGCATAT
16581 TAATAGATTTGC
1 TAATAGATTTGC
*
16593 TAATAGATTAGC
1 TAATAGATTTGC
16605 TAATA-ATTTG
1 TAATAGATTTG
16615 GCACATGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (12 bp):
TAATAGATTTGC
Found at i:18095 original size:19 final size:18
Alignment explanation
Indices: 18066--18108 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
18056 AAATTAATTA
18066 ATTTAATATTAAATTTTT
1 ATTTAATATTAAATTTTT
*
18084 ATTTATATATTATATTTTT
1 ATTTA-ATATTAAATTTTT
*
18103 ACTTAA
1 ATTTAA
18109 AAATTACTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTAATATTAAATTTTT
Found at i:22745 original size:13 final size:13
Alignment explanation
Indices: 22712--22768 Score: 68
Period size: 12 Copynumber: 4.7 Consensus size: 13
22702 CCCGTTGAGG
22712 AAATG-TTT-TAT
1 AAATGTTTTATAT
*
22723 AACTGTTTTATAT
1 AAATGTTTTATAT
*
22736 AAATGCTTTATA-
1 AAATGTTTTATAT
22748 AAATGTTTTA-AT
1 AAATGTTTTATAT
22760 AAATGTTTT
1 AAATGTTTT
22769 GGGTGCATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
11 5 0.13
12 21 0.54
13 13 0.33
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (13 bp):
AAATGTTTTATAT
Done.