Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008254.1 Corchorus capsularis cultivar CVL-1 contig08275, 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: 9520
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Found at i:1743 original size:7 final size:7
Alignment explanation
Indices: 1731--1777 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
1721 ACCAACCGCC
1731 TAATATA
1 TAATATA
*
1738 TAATATT
1 TAATATA
1745 TAATATA
1 TAATATA
1752 T-AT-TA
1 TAATATA
1757 TAATATCA
1 TAATAT-A
1765 T-ATATA
1 TAATATA
1771 TAATATA
1 TAATATA
1778 ATTTATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
5 3 0.09
6 6 0.18
7 23 0.68
8 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (7 bp):
TAATATA
Found at i:1784 original size:14 final size:14
Alignment explanation
Indices: 1735--1785 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
1725 ACCGCCTAAT
1735 ATATAATAT-T-TA
1 ATATAATATATATA
1747 ATAT-ATAT-TATA
1 ATATAATATATATA
*
1759 ATATCATATATATA
1 ATATAATATATATA
*
1773 ATATAATTTATAT
1 ATATAATATATAT
1786 TTATTTGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 5 0.15
12 10 0.29
13 4 0.12
14 15 0.44
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATAATATATATA
Found at i:1814 original size:12 final size:12
Alignment explanation
Indices: 1733--1832 Score: 59
Period size: 12 Copynumber: 8.2 Consensus size: 12
1723 CAACCGCCTA
1733 ATATATAATATTT
1 ATATAT-ATATTT
1746 A-ATATATA-TT
1 ATATATATATTT
*
1756 ATA-ATATCATAT
1 ATATATAT-ATTT
1768 ATATAATATAATTT
1 ATAT-ATAT-ATTT
1782 ATAT-T-TATTT
1 ATATATATATTT
* *
1792 GATTCTTTATATTT
1 -A-TATATATATTT
1806 ATATATATATTT
1 ATATATATATTT
*
1818 TTATA-ATAATTT
1 ATATATAT-ATTT
1830 ATA
1 ATA
1833 AAATAAATGT
Statistics
Matches: 69, Mismatches: 8, Indels: 21
0.70 0.08 0.21
Matches are distributed among these distances:
10 11 0.16
11 9 0.13
12 30 0.43
13 3 0.04
14 16 0.23
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (12 bp):
ATATATATATTT
Found at i:3376 original size:113 final size:113
Alignment explanation
Indices: 3178--3404 Score: 454
Period size: 113 Copynumber: 2.0 Consensus size: 113
3168 CGACCGATAC
3178 TCACCCCTAATAGTAGAGGGACCGCCTTGTTACTTTTAAAGTCTGTTTGGAAGTTTCTATAGCAG
1 TCACCCCTAATAGTAGAGGGACCGCCTTGTTACTTTTAAAGTCTGTTTGGAAGTTTCTATAGCAG
3243 GTAAAAAGGTAGAAAGTTTTTCTATAGAAAGTTTAGGAAAAGAAAGTT
66 GTAAAAAGGTAGAAAGTTTTTCTATAGAAAGTTTAGGAAAAGAAAGTT
3291 TCACCCCTAATAGTAGAGGGACCGCCTTGTTACTTTTAAAGTCTGTTTGGAAGTTTCTATAGCAG
1 TCACCCCTAATAGTAGAGGGACCGCCTTGTTACTTTTAAAGTCTGTTTGGAAGTTTCTATAGCAG
3356 GTAAAAAGGTAGAAAGTTTTTCTATAGAAAGTTTAGGAAAAGAAAGTT
66 GTAAAAAGGTAGAAAGTTTTTCTATAGAAAGTTTAGGAAAAGAAAGTT
3404 T
1 T
3405 TTTCTTAAGA
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.32
Consensus pattern (113 bp):
TCACCCCTAATAGTAGAGGGACCGCCTTGTTACTTTTAAAGTCTGTTTGGAAGTTTCTATAGCAG
GTAAAAAGGTAGAAAGTTTTTCTATAGAAAGTTTAGGAAAAGAAAGTT
Found at i:6660 original size:201 final size:198
Alignment explanation
Indices: 6041--6820 Score: 952
Period size: 201 Copynumber: 4.0 Consensus size: 198
6031 CTTTATAATA
* *
6041 AGGATTATTATACAATACAATGTCAAG-GTAAATTTTGGACTCCATAAGCGGGTTAAAAAGTTGA
1 AGGATTATTATACAATACACTGTC-AGTGTAAATTTTGGACTCCATAAGCGGGTTAAAAAGTTAA
* *
6105 CACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTCAGAGG-ACACG
65 CACATACCCCATTTC---A-TAATTAAATATTTAATATTAATACATATTCCCTAAG-GGTACACA
** ** * *
6169 TGTCAACCCCCA--AAACCCCGTGCGTGCAGTCTGCTAAATTCCACTGACGGTGTATTGTATAAT
125 TGTCAACCCAAATTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAA
*
6232 TTTTTTTAT
190 TTTTCTTAT
* * * * **
6241 ATGATTATTATACAATACACTGTCAGAGTAAATTTTGGATTCCATAAACGGGTTAAAAAGTCGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAAAAGTTAAC
** *
6306 ACATA--CC----C-T-ATT-AA-A--TAATATTAATACATATTCCCTAAGGCAATACATGTCAA
66 ACATACCCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAA
*
6359 CCC---TTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGCATTGTATAAATTTTCT
131 CCCAAATTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAATTTTCT
6421 TAT
196 TAT
* * *
6424 AGGATTATTATACAATACACTGTCAGTGAAAATTTTGGATTCCATAAGCGGGTTAAGAAGTTAAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAAAAGTTAAC
* *
6489 ACATACCCTATTTCATAATTAAATATTTAATATTAATACATATTCTCTAAGGGTACACATGTCAA
66 ACATACCCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAA
* * * *
6554 CCCTTAAAGTTAAACTCCGCACGTGTAGTATGCTAAACTCCACTGACGATGTATTGTATAAATTT
131 CCC--AAA-TTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAATTT
6619 TCTTAT
193 TCTTAT
* * * * *
6625 AGGATTGTTATACAATACACTGTTAGTGTAAATTTTGGACTCTATAAGTGGGTTAAGAAGTTAAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAAAAGTTAAC
*
6690 ACATACCCCATTTCATAATTAAATATTTAATATTAATACATACTT-CCTAAGGATACACATGTCA
66 ACATACCCCATTTCATAATTAAATATTTAATATTAATACATA-TTCCCTAAGGGTACACATGTCA
* * *
6754 ACCCTTAAAGTTAAACCCCGCACGTACAGTCTGTTAAACTCCACTGATGGTGTATTGTATAAATT
130 ACCC--AAA-TTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAATT
6819 TT
192 TT
6821 ATGGAAGCAT
Statistics
Matches: 509, Mismatches: 48, Indels: 45
0.85 0.08 0.07
Matches are distributed among these distances:
183 118 0.23
184 35 0.07
185 1 0.00
186 1 0.00
187 2 0.00
188 3 0.01
189 2 0.00
190 1 0.00
191 3 0.01
192 2 0.00
193 1 0.00
194 1 0.00
195 37 0.07
198 2 0.00
199 2 0.00
200 62 0.12
201 234 0.46
202 2 0.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (198 bp):
AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAAAAGTTAAC
ACATACCCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAA
CCCAAATTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAATTTTCT
TAT
Found at i:8011 original size:44 final size:44
Alignment explanation
Indices: 7963--8053 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
7953 ATTGAAAAAA
*
7963 CAAATTTA-ATTACAACG-TAAGCTTTATGATTTCCATGCCACCTT
1 CAAATTTACA-TA-AACGATAAACTTTATGATTTCCATGCCACCTT
* * *
8007 CAAATTTACATAACCGATAAATTTTATGATTTCCCTGCCACCTT
1 CAAATTTACATAAACGATAAACTTTATGATTTCCATGCCACCTT
8051 CAA
1 CAA
8054 GGCTAGGGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 3 0.07
44 37 0.90
45 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (44 bp):
CAAATTTACATAAACGATAAACTTTATGATTTCCATGCCACCTT
Done.