Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017157.1 Corchorus olitorius cultivar O-4 contig17190, 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: 34932
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1986 original size:5 final size:5
Alignment explanation
Indices: 1976--2025 Score: 100
Period size: 5 Copynumber: 10.0 Consensus size: 5
1966 ACCAACAGAA
1976 ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT
1 ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT
2026 TGTTAATTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ACTAT
Found at i:8934 original size:54 final size:54
Alignment explanation
Indices: 8867--9009 Score: 196
Period size: 54 Copynumber: 2.6 Consensus size: 54
8857 AGATGAAGTT
* * * *
8867 GACGGGGTGCCAAACGCCGGAGTCGAAGATGGAGTACCAAAAGCTGGAGTAGAA
1 GACGGAGTGCCAAACGCCGGCGTCGAAGAAGGAGTACCAAAAGCCGGAGTAGAA
* * *
8921 GACGGAGTTCCAAACGCCGGCGTCGAAGAGGGAGTACCAAATGCCGGAGTAGAA
1 GACGGAGTGCCAAACGCCGGCGTCGAAGAAGGAGTACCAAAAGCCGGAGTAGAA
* * *
8975 GAGGGAGTGCCAAACGCTGGCGTAGAAGAAGGAGT
1 GACGGAGTGCCAAACGCCGGCGTCGAAGAAGGAGT
9010 GCCGAAGGCG
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 78 1.00
ACGTcount: A:0.32, C:0.19, G:0.38, T:0.11
Consensus pattern (54 bp):
GACGGAGTGCCAAACGCCGGCGTCGAAGAAGGAGTACCAAAAGCCGGAGTAGAA
Found at i:9010 original size:27 final size:27
Alignment explanation
Indices: 8873--9012 Score: 154
Period size: 27 Copynumber: 5.2 Consensus size: 27
8863 AGTTGACGGG
* *
8873 GTGCCAAACGCCGGAGTCGAAGATGGA
1 GTGCCAAACGCCGGAGTAGAAGAGGGA
* * * *
8900 GTACCAAAAGCTGGAGTAGAAGACGGA
1 GTGCCAAACGCCGGAGTAGAAGAGGGA
* * *
8927 GTTCCAAACGCCGGCGTCGAAGAGGGA
1 GTGCCAAACGCCGGAGTAGAAGAGGGA
* *
8954 GTACCAAATGCCGGAGTAGAAGAGGGA
1 GTGCCAAACGCCGGAGTAGAAGAGGGA
* * *
8981 GTGCCAAACGCTGGCGTAGAAGAAGGA
1 GTGCCAAACGCCGGAGTAGAAGAGGGA
9008 GTGCC
1 GTGCC
9013 GAAGGCGGAA
Statistics
Matches: 93, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.32, C:0.20, G:0.36, T:0.11
Consensus pattern (27 bp):
GTGCCAAACGCCGGAGTAGAAGAGGGA
Found at i:9751 original size:45 final size:45
Alignment explanation
Indices: 9700--9790 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
9690 ATAGTAAAGT
* *
9700 TTTAGGGACCTGACATGTTCCCTTACATAATACTGATAATTGAGA
1 TTTAGGGACCTGACATGTTCCCATACAGAATACTGATAATTGAGA
* * *
9745 TTTAGGGACCTGACTTGTTCCCATACAGCATACTGATAATTTAGA
1 TTTAGGGACCTGACATGTTCCCATACAGAATACTGATAATTGAGA
9790 T
1 T
9791 AACAAACATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (45 bp):
TTTAGGGACCTGACATGTTCCCATACAGAATACTGATAATTGAGA
Found at i:15940 original size:29 final size:30
Alignment explanation
Indices: 15897--15976 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 30
15887 GCATTAGTGT
*
15897 GTATAGGATAATTTTGATGATTAAAATGAAA
1 GTAT-GGATATTTTTGATGATTAAAATGAAA
* * *
15928 GTAT-GATATTTTTTGTTCA-AAAAATGAAA
1 GTATGGATA-TTTTTGATGATTAAAATGAAA
*
15957 GTATGGAT-TTTTTAATGATT
1 GTATGGATATTTTTGATGATT
15977 TGTCAGTCCA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
28 7 0.18
29 17 0.45
30 10 0.26
31 4 0.11
ACGTcount: A:0.39, C:0.01, G:0.17, T:0.42
Consensus pattern (30 bp):
GTATGGATATTTTTGATGATTAAAATGAAA
Found at i:18661 original size:30 final size:31
Alignment explanation
Indices: 18603--18669 Score: 118
Period size: 32 Copynumber: 2.2 Consensus size: 31
18593 ATTACAAACC
18603 ATTTTCAAATCAATAACCCTACACACACACTT
1 ATTTTCAAATCAATAACCCTA-ACACACACTT
18635 ATTTTCAAATCAATAACCCT-ACACACACTT
1 ATTTTCAAATCAATAACCCTAACACACACTT
18665 ATTTT
1 ATTTT
18670 ATGGTGATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 15 0.43
32 20 0.57
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (31 bp):
ATTTTCAAATCAATAACCCTAACACACACTT
Found at i:24234 original size:17 final size:17
Alignment explanation
Indices: 24194--24235 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
24184 CTGATTGGGT
24194 AAAGAGAAAGAAAAATA
1 AAAGAGAAAGAAAAATA
*
24211 AAA-AGAAA-AGAAATGA
1 AAAGAGAAAGAAAAAT-A
24227 AAAGAGAAA
1 AAAGAGAAA
24236 CTTAAAAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.23
16 9 0.41
17 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (17 bp):
AAAGAGAAAGAAAAATA
Found at i:24487 original size:4 final size:4
Alignment explanation
Indices: 24478--24502 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
24468 TAACAGAAGG
24478 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
24503 AGAAATGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:29227 original size:9 final size:9
Alignment explanation
Indices: 29206--29236 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
29196 TCTTCCTTTC
29206 TTCTTTCTCT
1 TTCTTTCT-T
29216 TTCTTTCTT
1 TTCTTTCTT
29225 TTCTTTCTT
1 TTCTTTCTT
29234 TTC
1 TTC
29237 CGCTTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (9 bp):
TTCTTTCTT
Found at i:29234 original size:13 final size:13
Alignment explanation
Indices: 29191--29234 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
29181 CGACTCCATA
*
29191 TTCTTTC-TTCCT
1 TTCTTTCTTTTCT
29203 TTC-TTCTTTCTCT
1 TTCTTTCTTT-TCT
29216 TTCTTTCTTTTCT
1 TTCTTTCTTTTCT
29229 TTCTTT
1 TTCTTT
29235 TCCGCTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 3 0.11
12 5 0.18
13 14 0.50
14 6 0.21
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TTCTTTCTTTTCT
Found at i:29414 original size:23 final size:20
Alignment explanation
Indices: 29369--29418 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
29359 CATATAATAA
29369 AAAATTATAATTTCTTTTAT
1 AAAATTATAATTTCTTTTAT
*
29389 AAAATTTTAATATTCTTCCTTAT
1 AAAATTATAAT-TTCTT--TTAT
29412 AAAATTA
1 AAAATTA
29419 ATTTATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.40
21 5 0.20
23 10 0.40
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATTATAATTTCTTTTAT
Found at i:31349 original size:25 final size:25
Alignment explanation
Indices: 31327--31373 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
31317 ACTTTACGTT
31327 TATTACATA-GA-AAAGAAATTACG
1 TATTACATATGACAAAGAAATTACG
*
31350 TATTACATATTACAAAGAAATTAC
1 TATTACATATGACAAAGAAATTAC
31374 ATTTTACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 1 0.05
25 11 0.52
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.30
Consensus pattern (25 bp):
TATTACATATGACAAAGAAATTACG
Found at i:32623 original size:15 final size:16
Alignment explanation
Indices: 32603--32632 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
32593 CATATAACTA
32603 TTCTTTC-TTCCTTTC
1 TTCTTTCTTTCCTTTC
32618 TTCTTTCTTTCCTTT
1 TTCTTTCTTTCCTTT
32633 ATTTTCCGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTTTCTTTCCTTTC
Found at i:33017 original size:93 final size:94
Alignment explanation
Indices: 32915--33095 Score: 310
Period size: 94 Copynumber: 1.9 Consensus size: 94
32905 TTATTTAAAT
*
32915 TTTTATAGTTTTAGTCAACTAAAAACTCTA-TTTTTATTTAATTAAATCTAATATCCTTATAACT
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACT
*
32979 ATTTTATTTTTACCATTTTACTATTTTAC
66 ATTTTATTTTTACCATATTACTATTTTAC
* *
33008 TTTTATAGTTTTACTTAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATACCT
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACT
*
33073 ATTTTATTTTTACGATATTACTA
66 ATTTTATTTTTACCATATTACTA
33096 ATCTATATCT
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 28 0.34
94 54 0.66
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.52
Consensus pattern (94 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACT
ATTTTATTTTTACCATATTACTATTTTAC
Found at i:34347 original size:13 final size:13
Alignment explanation
Indices: 34314--34366 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
34304 GCACCCAAAA
*
34314 CATTTAT-TAAAA
1 CATTTATATAAAG
34326 CATTT-TATAAAG
1 CATTTATATAAAG
34338 CATTTATATAAAG
1 CATTTATATAAAG
*
34351 CAGTTATA-AAA-
1 CATTTATATAAAG
34362 CATTT
1 CATTT
34367 CCTCAACGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 14 0.39
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
CATTTATATAAAG
Done.