Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021764.1 Corchorus olitorius cultivar O-4 contig21797, 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: 25049
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3942 original size:18 final size:17
Alignment explanation
Indices: 3900--3942 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
3890 CCCAGTACCA
* *
3900 TTGTTTGCATCGTTAAC
1 TTGTTTGCACCATTAAC
3917 TTGATTTGCACCATTCAAC
1 TTG-TTTGCACCATT-AAC
3936 TTGTTTG
1 TTGTTTG
3943 TGCCGTTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 13 0.59
19 6 0.27
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.47
Consensus pattern (17 bp):
TTGTTTGCACCATTAAC
Found at i:6111 original size:10 final size:11
Alignment explanation
Indices: 6092--6120 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
6082 GTAATTATCA
6092 TAGCTTTAGTT
1 TAGCTTTAGTT
6103 TAG-TTTAGTT
1 TAGCTTTAGTT
6113 TAGCTTTA
1 TAGCTTTA
6121 ATTTTAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (11 bp):
TAGCTTTAGTT
Found at i:12615 original size:36 final size:34
Alignment explanation
Indices: 12575--12644 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 34
12565 CTATTTCCAA
*
12575 TTGGGTACCTTTTATGATTTGGGCTTTTATTCTATT
1 TTGGGCACCTTTTATGATTTGGGC-TTTATT-TATT
*
12611 TTGGGCATCTTTTATGATTTGGGCTTTATTTATT
1 TTGGGCACCTTTTATGATTTGGGCTTTATTTATT
12645 ACTTTGGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 4 0.12
35 6 0.19
36 22 0.69
ACGTcount: A:0.14, C:0.10, G:0.20, T:0.56
Consensus pattern (34 bp):
TTGGGCACCTTTTATGATTTGGGCTTTATTTATT
Found at i:12642 original size:18 final size:19
Alignment explanation
Indices: 12585--12678 Score: 83
Period size: 18 Copynumber: 5.1 Consensus size: 19
12575 TTGGGTACCT
12585 TTTATGATTTGGGCTTTTA
1 TTTATGATTTGGGCTTTTA
* *
12604 TTCTAT--TTTGGGCATCT-
1 TT-TATGATTTGGGCTTTTA
12621 TTTATGATTTGGGC-TTTA
1 TTTATGATTTGGGCTTTTA
*
12639 TTTATTACTTT-GGCTTTTA
1 TTTATGA-TTTGGGCTTTTA
*
12658 TTTATGCA-TTGGGTTTTTA
1 TTTATG-ATTTGGGCTTTTA
12677 TT
1 TT
12679 ATTGGGCCTA
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
16 3 0.05
17 4 0.07
18 27 0.44
19 23 0.38
20 4 0.07
ACGTcount: A:0.15, C:0.09, G:0.18, T:0.59
Consensus pattern (19 bp):
TTTATGATTTGGGCTTTTA
Found at i:12810 original size:18 final size:20
Alignment explanation
Indices: 12786--12829 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
12776 AAATTCTAGA
12786 ATTAGTTTAA-TGTC-ATAG
1 ATTAGTTTAATTGTCAATAG
*
12804 TTTAGTTTAATTGTCAATAG
1 ATTAGTTTAATTGTCAATAG
12824 ATTAGT
1 ATTAGT
12830 AAAAGAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 4 0.18
20 9 0.41
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.48
Consensus pattern (20 bp):
ATTAGTTTAATTGTCAATAG
Found at i:15314 original size:18 final size:19
Alignment explanation
Indices: 15291--15330 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
15281 CTAGCCCTAA
15291 AACTAG-GAGAAAAACTAG
1 AACTAGAGAGAAAAACTAG
*
15309 AACTAGAAGAGAAAAAGTAG
1 AACTAG-AGAGAAAAACTAG
15329 AA
1 AA
15331 GAGAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
20 13 0.68
ACGTcount: A:0.60, C:0.07, G:0.23, T:0.10
Consensus pattern (19 bp):
AACTAGAGAGAAAAACTAG
Found at i:17941 original size:18 final size:19
Alignment explanation
Indices: 17918--17954 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
17908 CACCCTAGCC
17918 CTAAAACTAGAAGA-AAAA
1 CTAAAACTAGAAGAGAAAA
*
17936 CTAAAACTATAAGAGAAAA
1 CTAAAACTAGAAGAGAAAA
17955 AGAAGAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.65, C:0.11, G:0.11, T:0.14
Consensus pattern (19 bp):
CTAAAACTAGAAGAGAAAA
Found at i:17963 original size:14 final size:14
Alignment explanation
Indices: 17946--17982 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
17936 CTAAAACTAT
17946 AAGAGAAAAAGAAG
1 AAGAGAAAAAGAAG
17960 AAGAGAAAAAGAAG
1 AAGAGAAAAAGAAG
*
17974 ATGAGAAAA
1 AAGAGAAAA
17983 TTATCTAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (14 bp):
AAGAGAAAAAGAAG
Found at i:19369 original size:31 final size:30
Alignment explanation
Indices: 19334--19392 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
19324 CTCTTTTGAT
*
19334 TTTCTGATTTTTCCATTTTTTATTTTTTTCC
1 TTTCTGATTTTTCCA-TTTTCATTTTTTTCC
** *
19365 TTTCTTCTTTTTTCATTTTCATTTTTTT
1 TTTCTGATTTTTCCATTTTCATTTTTTT
19393 TTCAACTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75
Consensus pattern (30 bp):
TTTCTGATTTTTCCATTTTCATTTTTTTCC
Done.