Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017994.1 Corchorus olitorius cultivar O-4 contig18027, 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: 13895
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Found at i:402 original size:2 final size:2
Alignment explanation
Indices: 395--429 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
385 GAGCTAGCTA
395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
430 AACACTTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:663 original size:20 final size:20
Alignment explanation
Indices: 638--686 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
628 CAGAGGCAGG
638 TGTTGATTTAGAAAG-CCAGC
1 TGTTGATTTA-AAAGCCCAGC
* *
658 TGTTGATTCATAAGCCCAGC
1 TGTTGATTTAAAAGCCCAGC
678 TGTTGATTT
1 TGTTGATTT
687 GTGGTTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.37
Consensus pattern (20 bp):
TGTTGATTTAAAAGCCCAGC
Found at i:10940 original size:6 final size:6
Alignment explanation
Indices: 10924--10984 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
10914 GCTAGAAGGG
* * *
10924 AAAAG- AAAAGA AAAAGA AATAGG AAAAGAA AAAAGG AAAAG- AAAAGTA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAG-A AAAAGA AAAAGA AAAAG-A
10972 AAAA-A AAAAGA AA
1 AAAAGA AAAAGA AA
10985 TAGGAAAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
5 15 0.33
6 22 0.48
7 9 0.20
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:10960 original size:13 final size:13
Alignment explanation
Indices: 10929--10968 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
10919 AAGGGAAAAG
*
10929 AAAAGAAAAAG-A
1 AAAAGGAAAAGAA
*
10941 AATAGGAAAAGAA
1 AAAAGGAAAAGAA
10954 AAAAGGAAAAGAA
1 AAAAGGAAAAGAA
10967 AA
1 AA
10969 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (13 bp):
AAAAGGAAAAGAA
Found at i:10967 original size:18 final size:17
Alignment explanation
Indices: 10923--11011 Score: 83
Period size: 18 Copynumber: 4.9 Consensus size: 17
10913 AGCTAGAAGG
10923 GAAAAGAAAAG-AAAAA
1 GAAAAGAAAAGAAAAAA
10939 GAAATAGGAAAAGAAAAAA
1 GAAA-A-GAAAAGAAAAAA
10958 GGAAAAGAAAAGTAAAAAA
1 -GAAAAGAAAAG-AAAAAA
10977 -AAAAGAAATAGGAAAATAA
1 GAAAAGAAA-A-GAAAA-AA
**
10996 GAAAATTAAAGAAAAA
1 GAAAAGAAAAGAAAAA
11012 TTTGGAAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 17
0.77 0.02 0.21
Matches are distributed among these distances:
16 4 0.06
17 10 0.16
18 22 0.35
19 16 0.26
20 10 0.16
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (17 bp):
GAAAAGAAAAGAAAAAA
Found at i:10992 original size:13 final size:11
Alignment explanation
Indices: 10922--10984 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
10912 AAGCTAGAAG
10922 GGAAAAGAAAA
1 GGAAAAGAAAA
*
10933 GAAAAAGAAATA
1 GGAAAAGAAA-A
10945 GGAAAAGAAAAAA
1 GGAAAAG--AAAA
10958 GGAAAAGAAAA
1 GGAAAAGAAAA
* *
10969 GTAAAAAAAAA
1 GGAAAAGAAAA
*
10980 AGAAA
1 GGAAA
10985 TAGGAAAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
11 25 0.58
12 7 0.16
13 8 0.19
14 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (11 bp):
GGAAAAGAAAA
Found at i:12201 original size:24 final size:24
Alignment explanation
Indices: 12174--12230 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
12164 CCCGTTTAGG
* * *
12174 AAATGTTTTAT-TACTGTTTTATAT
1 AAATGTTTTATAAAATGTTTT-GAT
*
12198 AAATGATTTATAAAATGTTTTGAT
1 AAATGTTTTATAAAATGTTTTGAT
12222 AAATGTTTT
1 AAATGTTTT
12231 GGGTGCATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.53
Consensus pattern (24 bp):
AAATGTTTTATAAAATGTTTTGAT
Found at i:12231 original size:12 final size:11
Alignment explanation
Indices: 12174--12230 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 11
12164 CCCGTTTAGG
12174 AAATGTTTTAT
1 AAATGTTTTAT
* *
12185 TACTGTTTTATAT
1 AAATG-TTT-TAT
*
12198 AAATGATTTAT
1 AAATGTTTTAT
12209 AAAATGTTTTGAT
1 -AAATGTTTT-AT
12222 AAATGTTTT
1 AAATGTTTT
12231 GGGTGCATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
11 6 0.17
12 22 0.61
13 8 0.22
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.53
Consensus pattern (11 bp):
AAATGTTTTAT
Done.