Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007865.1 Corchorus capsularis cultivar CVL-1 contig07886, 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: 16930
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:1844 original size:42 final size:42
Alignment explanation
Indices: 1785--1868 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
1775 GGGGGGTGAA
1785 CTTCTAAACTAGGATTGATATAGTATACTGTATACATGATTT
1 CTTCTAAACTAGGATTGATATAGTATACTGTATACATGATTT
1827 CTTCTAAACTAGGATTGATATAGTATACTGTATACATGATTT
1 CTTCTAAACTAGGATTGATATAGTATACTGTATACATGATTT
1869 TTTTTTTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (42 bp):
CTTCTAAACTAGGATTGATATAGTATACTGTATACATGATTT
Found at i:4352 original size:34 final size:34
Alignment explanation
Indices: 4309--4374 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
4299 AATTCTGTTA
*
4309 CATGGATGAGCAGAAACCTCATAGTGCAAAAATC
1 CATGGATGAGCAGAAACCTCACAGTGCAAAAATC
*
4343 CATGGATGAGCAGAAACCTTACAGTGCAAAAA
1 CATGGATGAGCAGAAACCTCACAGTGCAAAAA
4375 CCCTTTTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.17
Consensus pattern (34 bp):
CATGGATGAGCAGAAACCTCACAGTGCAAAAATC
Found at i:12262 original size:33 final size:33
Alignment explanation
Indices: 12181--12304 Score: 135
Period size: 33 Copynumber: 3.7 Consensus size: 33
12171 CCGCGCAACA
*
12181 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
* *
12216 CGGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* ** *
12249 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC
12282 CCGGCCACAACCGGCCACGCGAC
1 CCGGCCACAACCGGCCACGCGAC
12305 CCTTTGTCTA
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
32 2 0.03
33 66 0.88
35 6 0.08
36 1 0.01
ACGTcount: A:0.23, C:0.41, G:0.28, T:0.07
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Found at i:13334 original size:5 final size:5
Alignment explanation
Indices: 13314--13348 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
13304 GTTATATCGA
13314 AAAAT ATAAA- AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT
13349 TTCGACCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 3 0.11
5 22 0.79
6 3 0.11
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:14742 original size:33 final size:33
Alignment explanation
Indices: 14700--14809 Score: 132
Period size: 33 Copynumber: 3.3 Consensus size: 33
14690 GATTGTTTTG
14700 ATGATACTAAACCTAATTTGAGTGTTGTTTGCA
1 ATGATACTAAACCTAATTTGAGTGTTGTTTGCA
* * * * *
14733 ATGACACTAAATCT-GTTTTAGATGTTGTTTGCG
1 ATGATACTAAACCTAATTTGAG-TGTTGTTTGCA
*
14766 ATGATACTAAACCTAATTTGAGTGTTGTATGCA
1 ATGATACTAAACCTAATTTGAGTGTTGTTTGCA
* *
14799 ATAAAACTAAA
1 ATGATACTAAA
14810 TCTGTTTTGG
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
32 5 0.08
33 52 0.84
34 5 0.08
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (33 bp):
ATGATACTAAACCTAATTTGAGTGTTGTTTGCA
Found at i:14775 original size:66 final size:66
Alignment explanation
Indices: 14699--14822 Score: 212
Period size: 66 Copynumber: 1.9 Consensus size: 66
14689 TGATTGTTTT
* * *
14699 GATGATACTAAACCTAATTTGAGTGTTGTTTGCAATGACACTAAATCTGTTTTAGATGTTGTTTG
1 GATGATACTAAACCTAATTTGAGTGTTGTATGCAATAAAACTAAATCTGTTTTAGATGTTGTTTG
14764 C
66 C
*
14765 GATGATACTAAACCTAATTTGAGTGTTGTATGCAATAAAACTAAATCTGTTTTGGATG
1 GATGATACTAAACCTAATTTGAGTGTTGTATGCAATAAAACTAAATCTGTTTTAGATG
14823 CTAATTGTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (66 bp):
GATGATACTAAACCTAATTTGAGTGTTGTATGCAATAAAACTAAATCTGTTTTAGATGTTGTTTG
C
Found at i:14835 original size:66 final size:66
Alignment explanation
Indices: 14698--14835 Score: 204
Period size: 66 Copynumber: 2.1 Consensus size: 66
14688 ATGATTGTTT
* * * * **
14698 TGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATGACACTAAATCTGTTTTAGATGTTGTTT
1 TGATGATACTAAACCTAATTTGAGTGTTGTATGCAATAAAACTAAATCTGTTTTAGATGCTAATT
14763 G
66 G
* *
14764 CGATGATACTAAACCTAATTTGAGTGTTGTATGCAATAAAACTAAATCTGTTTTGGATGCTAATT
1 TGATGATACTAAACCTAATTTGAGTGTTGTATGCAATAAAACTAAATCTGTTTTAGATGCTAATT
14829 G
66 G
14830 TGATGA
1 TGATGA
14836 AAACAATTCT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (66 bp):
TGATGATACTAAACCTAATTTGAGTGTTGTATGCAATAAAACTAAATCTGTTTTAGATGCTAATT
G
Found at i:14928 original size:30 final size:31
Alignment explanation
Indices: 14833--14946 Score: 122
Period size: 33 Copynumber: 3.6 Consensus size: 31
14823 CTAATTGTGA
* *
14833 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
1 TGAAAATAATCCTGTTTTGGTTG-A-ATAGCAT
* * *
14866 TAAAAACAATTCTGTTTTGGTTGATTATAGCAT
1 TGAAAATAATCCTGTTTTGGTTGA--ATAGCAT
*
14899 TGCAAATAATCCTGTTTTGGTTG-ATAGCAT
1 TGAAAATAATCCTGTTTTGGTTGAATAGCAT
*
14929 TGAAAATAAACCTGTTTT
1 TGAAAATAATCCTGTTTT
14947 AGGTGACGAG
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
30 23 0.32
32 1 0.01
33 48 0.67
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.39
Consensus pattern (31 bp):
TGAAAATAATCCTGTTTTGGTTGAATAGCAT
Found at i:16855 original size:33 final size:33
Alignment explanation
Indices: 16774--16897 Score: 126
Period size: 33 Copynumber: 3.7 Consensus size: 33
16764 CCGCGCAACA
*
16774 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
* *
16809 CGGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* * ** *
16842 CTGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC
16875 CCGGCCACAACCGGCCACGCGAC
1 CCGGCCACAACCGGCCACGCGAC
16898 CCTTTGTCTA
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
32 2 0.03
33 65 0.88
35 6 0.08
36 1 0.01
ACGTcount: A:0.23, C:0.40, G:0.28, T:0.08
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Done.