Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020391.1 Corchorus olitorius cultivar O-4 contig20424, 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: 18055
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:2996 original size:20 final size:20
Alignment explanation
Indices: 2971--3010 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2961 GTACTAGTTT
2971 GGCATGGTACCTATAACCCA
1 GGCATGGTACCTATAACCCA
2991 GGCATGGTACCTATAACCCA
1 GGCATGGTACCTATAACCCA
3011 AATTTGATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (20 bp):
GGCATGGTACCTATAACCCA
Found at i:3049 original size:2 final size:2
Alignment explanation
Indices: 3044--3094 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
3034 CTCAATTTTA
*
3044 AC AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
3086 AC AC AC AC A
1 AC AC AC AC A
3095 GAGATATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.47, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:3454 original size:3 final size:3
Alignment explanation
Indices: 3448--3483 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
3438 TGGAATAATA
*
3448 ATT ATT ATT -TT ATA ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3484 AGTCATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3462 original size:17 final size:18
Alignment explanation
Indices: 3442--3478 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
3432 TAATTATGGA
3442 ATAATAATTATTATT-TT
1 ATAATAATTATTATTATT
*
3459 ATAATTATTATTATTATT
1 ATAATAATTATTATTATT
3477 AT
1 AT
3479 TATTAAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATAATAATTATTATTATT
Found at i:6187 original size:18 final size:18
Alignment explanation
Indices: 6164--6201 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6154 TTTCGGTAGA
6164 AAAATGTTATAGAAA-GAT
1 AAAATG-TATAGAAATGAT
*
6182 AAAATGTCTAGAAATGAT
1 AAAATGTATAGAAATGAT
6200 AA
1 AA
6202 GTTGCGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.55, C:0.03, G:0.16, T:0.26
Consensus pattern (18 bp):
AAAATGTATAGAAATGAT
Found at i:8105 original size:18 final size:18
Alignment explanation
Indices: 8071--8105 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
8061 CACCGCTATG
8071 AAATTAAGAAATCAAAGA
1 AAATTAAGAAATCAAAGA
8089 AAATATAAGAAAT-AAAG
1 AAAT-TAAGAAATCAAAG
8106 GAGAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.69, C:0.03, G:0.11, T:0.17
Consensus pattern (18 bp):
AAATTAAGAAATCAAAGA
Found at i:8887 original size:13 final size:13
Alignment explanation
Indices: 8869--8893 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8859 TGCAGAAAAA
8869 ATATATATAATAT
1 ATATATATAATAT
8882 ATATATATAATA
1 ATATATATAATA
8894 ATGTTAGAAC
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATATATAATAT
Found at i:10654 original size:17 final size:17
Alignment explanation
Indices: 10634--10686 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
10624 GAAGCGACTC
10634 AAATTCGTAGCATAAAT
1 AAATTCGTAGCATAAAT
* * * *
10651 AAATTCCCTA-AAAAAAA
1 AAATT-CGTAGCATAAAT
10668 AAATTCGTAGCATAAAT
1 AAATTCGTAGCATAAAT
10685 AA
1 AA
10687 TTACAAAGAG
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.77
18 3 0.12
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.25
Consensus pattern (17 bp):
AAATTCGTAGCATAAAT
Found at i:11248 original size:15 final size:17
Alignment explanation
Indices: 11228--11262 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
11218 TGAAGAAGAC
11228 TAATTAATTA-AT-TAT
1 TAATTAATTATATATAT
11243 TAATTAATTATATATAT
1 TAATTAATTATATATAT
11260 TAA
1 TAA
11263 GTCTAAACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 2 0.11
17 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATTAATTATATATAT
Found at i:11963 original size:13 final size:13
Alignment explanation
Indices: 11945--11969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11935 AGGCCTTAAA
11945 AATAAATTTCCTC
1 AATAAATTTCCTC
11958 AATAAATTTCCT
1 AATAAATTTCCT
11970 TTTTAAGTTT
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:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
AATAAATTTCCTC
Found at i:12699 original size:11 final size:11
Alignment explanation
Indices: 12675--12726 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
12665 AGAAATGAAA
12675 TTTATAATTAAT
1 TTTATAATT-AT
*
12687 TTTATAAGTAT
1 TTTATAATTAT
*
12698 TTGATAATTTAT
1 TTTATAA-TTAT
12710 TTTATAGAATTAT
1 TTTAT--AATTAT
12723 TTTA
1 TTTA
12727 GTAAAATGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
11 8 0.24
12 15 0.45
13 8 0.24
14 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (11 bp):
TTTATAATTAT
Found at i:13238 original size:11 final size:11
Alignment explanation
Indices: 13224--13261 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13214 ATTCATAACA
13224 AATTTATAATT
1 AATTTATAATT
13235 AATTTATAATT
1 AATTTATAATT
13246 -ATTTGATAATT
1 AATTT-ATAATT
*
13257 TATTT
1 AATTT
13262 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:15185 original size:29 final size:30
Alignment explanation
Indices: 15125--15196 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
15115 AATACCGTAA
* * *
15125 GGTCCCTCTACTTACAAAAAGGGATCGATTT
1 GGTCCCCCTAC-TACAAAAAGCGATCAATTT
*
15156 GGTCCCCCTACTACAAAAA-CTATCAATTT
1 GGTCCCCCTACTACAAAAAGCGATCAATTT
*
15185 GGTCTCCCTACT
1 GGTCCCCCTACT
15197 TATAATTTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 18 0.50
30 8 0.22
31 10 0.28
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (30 bp):
GGTCCCCCTACTACAAAAAGCGATCAATTT
Found at i:15468 original size:2 final size:2
Alignment explanation
Indices: 15461--15510 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
15451 AACTCCCTTT
* * *
15461 TA TA TA TA TA TA TA TA TA TA TA TG TA TG CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15503 TA TA TA TA
1 TA TA TA TA
15511 ATTCAAGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:16198 original size:31 final size:30
Alignment explanation
Indices: 16162--16281 Score: 104
Period size: 31 Copynumber: 3.9 Consensus size: 30
16152 ATATATAATC
16162 AATTGACAGATTTTGTCAAGTAGAGGGACTC-
1 AATTGACAGATTTTGT-AAGTAGAGGGAC-CA
* ** *
16193 AATTGACACCAAATTGTAAGTAAAGGGACCA
1 AATTGACA-GATTTTGTAAGTAGAGGGACCA
16224 AATTGACAG-TTTT-TATAGTAGAGGGACCA
1 AATTGACAGATTTTGTA-AGTAGAGGGACCA
**
16253 AATTGATTC-TTTTTTGTAAGTAGAGGGAC
1 AATTGA--CAGATTTTGTAAGTAGAGGGAC
16282 ATGTACGGTA
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
28 2 0.03
29 20 0.27
30 1 0.01
31 43 0.59
32 7 0.10
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (30 bp):
AATTGACAGATTTTGTAAGTAGAGGGACCA
Found at i:16265 original size:29 final size:31
Alignment explanation
Indices: 16209--16281 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
16199 CACCAAATTG
* *
16209 TAAGTAAAGGGACCAAATTGACA-GTTTTTA
1 TAAGTAGAGGGACCAAATTGACACTTTTTTA
** *
16239 T-AGTAGAGGGACCAAATTGATTCTTTTTTG
1 TAAGTAGAGGGACCAAATTGACACTTTTTTA
16269 TAAGTAGAGGGAC
1 TAAGTAGAGGGAC
16282 ATGTACGGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 18 0.50
30 7 0.19
31 11 0.31
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.32
Consensus pattern (31 bp):
TAAGTAGAGGGACCAAATTGACACTTTTTTA
Done.