Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012622.1 Corchorus capsularis cultivar CVL-1 contig12643, 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: 25441
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:194 original size:9 final size:8
Alignment explanation
Indices: 181--222 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
171 TAAACTTATT
181 AAAAAAGA
1 AAAAAAGA
189 ATAAAAAGA
1 A-AAAAAGA
198 GAAAAAAGA
1 -AAAAAAGA
207 AAAAGAA-A
1 AAAA-AAGA
215 AAAAAAGA
1 AAAAAAGA
223 CACGTGACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
7 2 0.07
8 11 0.37
9 16 0.53
10 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:4839 original size:2 final size:2
Alignment explanation
Indices: 4832--4864 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4822 CAAAGCTTAC
4832 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4865 GTAATAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5154 original size:36 final size:36
Alignment explanation
Indices: 5112--5220 Score: 98
Period size: 36 Copynumber: 3.0 Consensus size: 36
5102 TTATGACGAC
5112 TAACATAAACAATTGCTTCAAGCATATAATGAACTG
1 TAACATAAACAATTGCTTCAAGCATATAATGAACTG
* * * * * *
5148 TGACATACAAAAATTGC-GCATGCGA-AGTTATG-ACTAC
1 TAACATA-AACAATTGCTTCAAGC-ATA-TAATGAACT-G
*
5185 TAATATAAACAATTGCTTCAAGCATATAATGAACTG
1 TAACATAAACAATTGCTTCAAGCATATAATGAACTG
5221 CGACCAACAT
Statistics
Matches: 53, Mismatches: 13, Indels: 14
0.66 0.16 0.17
Matches are distributed among these distances:
36 27 0.51
37 26 0.49
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (36 bp):
TAACATAAACAATTGCTTCAAGCATATAATGAACTG
Found at i:8504 original size:6 final size:6
Alignment explanation
Indices: 8495--8551 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
8485 ATCAACATCA
8495 TCAGGC TCAGGC TCAGGC TCAGGC TCAGGC TCAGGC TCAGGC TCAGGC
1 TCAGGC TCAGGC TCAGGC TCAGGC TCAGGC TCAGGC TCAGGC TCAGGC
8543 TCAGGC TCA
1 TCAGGC TCA
8552 ACCAAATCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.18
Consensus pattern (6 bp):
TCAGGC
Found at i:14246 original size:36 final size:36
Alignment explanation
Indices: 14197--14270 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
14187 CTCGACTCCT
14197 TGACTCTAAACTGGAGTCCAGGTGGTGCTGCAGGTG
1 TGACTCTAAACTGGAGTCCAGGTGGTGCTGCAGGTG
* *
14233 TGACTCTAGACTGGAGTCCAGGTGGTGGTGCAGGTG
1 TGACTCTAAACTGGAGTCCAGGTGGTGCTGCAGGTG
14269 TG
1 TG
14271 GAGGATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.18, C:0.18, G:0.39, T:0.26
Consensus pattern (36 bp):
TGACTCTAAACTGGAGTCCAGGTGGTGCTGCAGGTG
Found at i:15220 original size:156 final size:150
Alignment explanation
Indices: 14927--15236 Score: 370
Period size: 156 Copynumber: 2.0 Consensus size: 150
14917 ATTGCCGCTG
* * *
14927 CACTCGTCTTGAGTCTTTAAAGATTTATTCTTGTCCTGGATTGACAATGCTTCCAAAGGAGGTGA
1 CACTCGTCTTGAGTCTTTAAAGATTAAATATTGTCCTGGATTGACAATGCTTCCAAAGGAGGTGA
** ** * * *
14992 ATGCCAATGCCCTCCCCTCTTTACAAATTTTGGAAATTAGGGAATGTAGCAATTTGATGGCTTTG
66 ATGCCAATGCCCTAACCTCTTTACAAAAGTTGAAAATTAGCGAATGTACCAATTTGATGGCTTTG
*
15057 CCAAACTGGATACTCAATCT
131 CCAAACTGGATACCCAATCT
* *
15077 CACTCGTCTTGAGTCTTTAGAGATTAAATATTGTGCTGGATTGACAATGCTTCCAAAGGTTAAGG
1 CACTCGTCTTGAGTCTTTAAAGATTAAATATTGTCCTGGATTGACAATGCTTCC--A----AAGG
* *** *
15142 AGGTGAATGCCACTGCCCTAACCTCTTTACAAAAGTTGAAAATCTA-CTCTTGTTCCAATTTGAT
60 AGGTGAATGCCAATGCCCTAACCTCTTTACAAAAGTTGAAAAT-TAGCGAATGTACCAATTTGAT
* *
15206 GGGTTTGCCCAACTGGATACCCAATCT
124 GGCTTTGCCAAACTGGATACCCAATCT
15233 CACT
1 CACT
15237 TCCCTCCAAG
Statistics
Matches: 133, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
150 49 0.37
152 1 0.01
156 81 0.61
157 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (150 bp):
CACTCGTCTTGAGTCTTTAAAGATTAAATATTGTCCTGGATTGACAATGCTTCCAAAGGAGGTGA
ATGCCAATGCCCTAACCTCTTTACAAAAGTTGAAAATTAGCGAATGTACCAATTTGATGGCTTTG
CCAAACTGGATACCCAATCT
Found at i:19750 original size:2 final size:2
Alignment explanation
Indices: 19743--19824 Score: 92
Period size: 2 Copynumber: 41.0 Consensus size: 2
19733 TTAAGAATTG
*
19743 CA CA CA CA CA CA CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
* * * * * * *
19785 CA CA CA CA TA TA TA TA TA TA CA CA CA CA CG CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
19825 GAAAACCCTT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.41, G:0.01, T:0.07
Consensus pattern (2 bp):
CA
Found at i:22491 original size:1 final size:1
Alignment explanation
Indices: 22485--22519 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
22475 TGATGATGAT
22485 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22520 GATGTTAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.