Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011323.1 Corchorus capsularis cultivar CVL-1 contig11344, 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: 29074
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:43 original size:30 final size:29
Alignment explanation
Indices: 7--108 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 29
1 GTTATA
*
7 TGTGTTTGGGGACTTTATTATAGATGCCTC
1 TGTGTTTAGGGACTTTA-TATAGATGCCTC
*
37 TGTGTTTAGGGACTTTAATATGGATGCC-C
1 TGTGTTTAGGGACTTT-ATATAGATGCCTC
* *
66 TTGTGCTT-GAGGACTTTGATGTAGATGCCTC
1 -TGTGTTTAG-GGACTTT-ATATAGATGCCTC
97 TGTGTTTAGGGA
1 TGTGTTTAGGGA
109 TGAATACCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
29 2 0.03
30 55 0.92
31 3 0.05
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.40
Consensus pattern (29 bp):
TGTGTTTAGGGACTTTATATAGATGCCTC
Found at i:132 original size:52 final size:53
Alignment explanation
Indices: 63--245 Score: 237
Period size: 53 Copynumber: 3.4 Consensus size: 53
53 AATATGGATG
*
63 CCCTTGTGCTTGAGGACTTTGATGTAGA-TGCCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGTTTGAGGACTTTGATGTAGAGTGCCTCTGTGTTTAGGGATGAATA
115 CCCTTGTGTTTGAGGACTTTTGA-G-AGAGGTGCCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGTTTGAGGAC-TTTGATGTAGA-GTGCCTCTGTGTTTAGGGATGAATA
* * * *
168 CCCTTGTGTTTGAGGACTTTGATATAGAATTGCCTCTGTGTTTAGGGACTTATAAATG
1 CCCTTGTGTTTGAGGACTTTGATGTAG-AGTGCCTCTGTGTTTAGGG----ATGAATA
226 CCCTTGTGTTTGAGGACTTT
1 CCCTTGTGTTTGAGGACTTT
246 AATTATTGGG
Statistics
Matches: 116, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
51 3 0.03
52 22 0.19
53 46 0.40
54 19 0.16
55 1 0.01
58 25 0.22
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (53 bp):
CCCTTGTGTTTGAGGACTTTGATGTAGAGTGCCTCTGTGTTTAGGGATGAATA
Found at i:1634 original size:31 final size:31
Alignment explanation
Indices: 1596--1669 Score: 148
Period size: 31 Copynumber: 2.4 Consensus size: 31
1586 TTGAAAAAGT
1596 ACCAAATTGGACTATTTATCAAACGTTTGCC
1 ACCAAATTGGACTATTTATCAAACGTTTGCC
1627 ACCAAATTGGACTATTTATCAAACGTTTGCC
1 ACCAAATTGGACTATTTATCAAACGTTTGCC
1658 ACCAAATTGGAC
1 ACCAAATTGGAC
1670 GAAATTAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (31 bp):
ACCAAATTGGACTATTTATCAAACGTTTGCC
Found at i:3796 original size:21 final size:21
Alignment explanation
Indices: 3770--3809 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3760 ATAAATGTGG
*
3770 TGGACACGGGAGGGACACGCC
1 TGGACACGGCAGGGACACGCC
*
3791 TGGACACGGCATGGACACG
1 TGGACACGGCAGGGACACG
3810 ACAAAACCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.40, T:0.07
Consensus pattern (21 bp):
TGGACACGGCAGGGACACGCC
Found at i:4188 original size:2 final size:2
Alignment explanation
Indices: 4181--4206 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4171 TTAATATTTA
4181 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4207 TGCCGTGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4565 original size:30 final size:31
Alignment explanation
Indices: 4529--4594 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
4519 TATTTCTGTC
4529 TTTATTTT-AGATTTAGGTTAGT-ATAAGGCT
1 TTTATTTTCAGATTTAGGTTAGTCAT-AGGCT
** *
4559 TTTATTTTCTTATTTAGGTTAGTCATGGGCT
1 TTTATTTTCAGATTTAGGTTAGTCATAGGCT
4590 TTTAT
1 TTTAT
4595 GGGCTGTTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 8 0.26
31 21 0.68
32 2 0.06
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.55
Consensus pattern (31 bp):
TTTATTTTCAGATTTAGGTTAGTCATAGGCT
Found at i:15746 original size:12 final size:12
Alignment explanation
Indices: 15725--15756 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
15715 TTGACTATCC
*
15725 GTAGCTAAGCTT
1 GTAGCAAAGCTT
15737 GTAGCAAAGCTT
1 GTAGCAAAGCTT
15749 GTAGCAAA
1 GTAGCAAA
15757 ACTTCTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (12 bp):
GTAGCAAAGCTT
Found at i:15813 original size:27 final size:27
Alignment explanation
Indices: 15776--15835 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
15766 TTCATAAAAT
15776 TTCAT-TTAATTACAAAAGAAATTACA
1 TTCATATTAATTACAAAAGAAATTACA
15802 TTCATATTAATTACAAAAGAAATTACA
1 TTCATATTAATTACAAAAGAAATTACA
15829 TTCATAT
1 TTCATAT
15836 GAGATATACG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.37
Consensus pattern (27 bp):
TTCATATTAATTACAAAAGAAATTACA
Found at i:19504 original size:12 final size:12
Alignment explanation
Indices: 19487--19511 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19477 CTTTTTCATC
19487 CTAAACCCGTAG
1 CTAAACCCGTAG
19499 CTAAACCCGTAG
1 CTAAACCCGTAG
19511 C
1 C
19512 AGATATTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (12 bp):
CTAAACCCGTAG
Found at i:22665 original size:33 final size:33
Alignment explanation
Indices: 22621--22727 Score: 119
Period size: 33 Copynumber: 3.2 Consensus size: 33
22611 AGCACAAGTG
22621 ACCGGCCACGCGACATGGAGATGACCGACCATC
1 ACCGGCCACGCGACATGGAGATGACCGACCATC
* * *
22654 ACCGGCTACGCGAC-TCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACAT-GGAGATGACCGACCATC
* * * *
22687 ATCGGCCACGCGACATGGACATGTCCGGCCA-C
1 ACCGGCCACGCGACATGGAGATGACCGACCATC
22719 AACCGGCCA
1 -ACCGGCCA
22728 TCGCTTGGCG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
32 2 0.03
33 60 0.95
34 1 0.02
ACGTcount: A:0.23, C:0.38, G:0.28, T:0.10
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGAGATGACCGACCATC
Found at i:23705 original size:8 final size:8
Alignment explanation
Indices: 23692--23725 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
23682 ACCCTTCTTG
23692 AAAAATTC
1 AAAAATTC
23700 AAAAATTC
1 AAAAATTC
*
23708 AGAAACTTC
1 A-AAAATTC
23717 AAAAATTC
1 AAAAATTC
23725 A
1 A
23726 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Done.