Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020469.1 Corchorus olitorius cultivar O-4 contig20502, 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: 23428
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Found at i:1658 original size:18 final size:19
Alignment explanation
Indices: 1630--1667 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1620 CAGCCCTCCT
*
1630 TATTCTTCTTCTTTCTTCC
1 TATTCTTCTTCTTCCTTCC
1649 TATT-TTCTTCTTCCTTCC
1 TATTCTTCTTCTTCCTTCC
1667 T
1 T
1668 CATCTTCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTCTTCTTCTTCCTTCC
Found at i:3852 original size:26 final size:26
Alignment explanation
Indices: 3800--3905 Score: 88
Period size: 26 Copynumber: 3.9 Consensus size: 26
3790 TTAAGAGTGT
**
3800 ACTTAAAATGACCAACGTGCCCCTGA
1 ACTTAAAATGACCAAAATGCCCCTGA
* *
3826 ACTTAAAATGACCAAAATGTCCTTGA
1 ACTTAAAATGACCAAAATGCCCCTGA
* *
3852 A-TATGCAAATGACTAAAATGCCCCTAGA
1 ACT-T-AAAATGACCAAAATGCCCCT-GA
* *
3880 TTCTTGAGAATGACCAAAATGCCCCT
1 -ACTT-AAAATGACCAAAATGCCCCT
3906 AGTTGATCCT
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
25 1 0.02
26 24 0.38
27 16 0.25
28 2 0.03
29 19 0.30
30 1 0.02
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.24
Consensus pattern (26 bp):
ACTTAAAATGACCAAAATGCCCCTGA
Found at i:13075 original size:15 final size:15
Alignment explanation
Indices: 13055--13089 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
13045 TAGGATAGAA
13055 AATTGTTTGTTTTTG
1 AATTGTTTGTTTTTG
13070 AATTGTTTGTTTTTG
1 AATTGTTTGTTTTTG
*
13085 GATTG
1 AATTG
13090 ATTATTCCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63
Consensus pattern (15 bp):
AATTGTTTGTTTTTG
Found at i:18040 original size:125 final size:125
Alignment explanation
Indices: 17804--18468 Score: 1051
Period size: 125 Copynumber: 5.3 Consensus size: 125
17794 TTTGTAGAAG
* * * *
17804 ATTATAAATAGCGGCGTCTACTATAGAAACGCCACTATTTAGCGACGTCTGTCATGAGAAACACC
1 ATTATATATAGCGGCGTCTACTATCGAAACGCCACTATTTAGCGGCGTCTGTCATGAGAAACGCC
* * *
17869 GCTATTCATAACATAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTCGGAAGAC
66 GCTATTCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAAC
* * * *
17929 ATCATATATACCGGCGTCTACTCTCGAAACGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCC
1 ATTATATATAGCGGCGTCTACTATCGAAACGCCACTATTTAGCGGCGTCTGTCATGAGAAACGCC
* * *
17994 GCTATGCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAAATTCTATTCTTTGGAAAAAT
66 GCTATTCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGG-AAAAC
* * *
18055 ATTATATATAGTGGCGTCTACTATCGAAACGCCACTATTTAGCGACGTCTGTCATGAGAAATGCC
1 ATTATATATAGCGGCGTCTACTATCGAAACGCCACTATTTAGCGGCGTCTGTCATGAGAAACGCC
* *
18120 ACTATTCATAACAAAGAAATTGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAAC
66 GCTATTCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAAC
* * *
18180 ATTATATATAGCGGCGTCTACTATCGAAACGCCACTATTTTGCGGCGTATGTCATGAGAAACGTC
1 ATTATATATAGCGGCGTCTACTATCGAAACGCCACTATTTAGCGGCGTCTGTCATGAGAAACGCC
*
18245 GCTATTCATAATAAAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAAC
66 GCTATTCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAAC
* * *
18305 ATTATATATAGCGGCGTCTACTATAGAAATGCCACTATTTAGCGGCGTCTCTCATGAGAAACGCC
1 ATTATATATAGCGGCGTCTACTATCGAAACGCCACTATTTAGCGGCGTCTGTCATGAGAAACGCC
* *
18370 GCTATGCATAACAAATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAAC
66 GCTATTCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAAC
* *
18430 ATTATATATAGCGGCATCTACTATCGAAACGCCGCTATT
1 ATTATATATAGCGGCGTCTACTATCGAAACGCCACTATT
18469 GTATTTAGAA
Statistics
Matches: 491, Mismatches: 48, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
125 379 0.77
126 112 0.23
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (125 bp):
ATTATATATAGCGGCGTCTACTATCGAAACGCCACTATTTAGCGGCGTCTGTCATGAGAAACGCC
GCTATTCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAAC
Found at i:18263 original size:251 final size:250
Alignment explanation
Indices: 17804--18468 Score: 1069
Period size: 251 Copynumber: 2.7 Consensus size: 250
17794 TTTGTAGAAG
* *
17804 ATTATAAATAGCGGCGTCTACTATAGAAACGCCACTATTTAGCGACGTCTGTCATGAGAAACACC
1 ATTATATATAGCGGCGTCTACTATAGAAACGCCACTATTTAGCGACGTCTGTCATGAGAAACGCC
* * * *
17869 GCTATTCATAACATAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTCGGAAGACATCAT
66 GCTATTCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAACATTAT
* * *
17934 ATATACCGGCGTCTACTCTCGAAACGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTAT
131 ATATAGCGGCGTCTACTATCGAAACGCCACTATTTAGCGGCGTATGTCATGAAAAACGCCGCTAT
*
17999 GCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAAATTCTATTCTTTGGAAAAAT
196 GCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAAATTCTATTCTTTGG-AAAAC
* * *
18055 ATTATATATAGTGGCGTCTACTATCGAAACGCCACTATTTAGCGACGTCTGTCATGAGAAATGCC
1 ATTATATATAGCGGCGTCTACTATAGAAACGCCACTATTTAGCGACGTCTGTCATGAGAAACGCC
* *
18120 ACTATTCATAACAAAGAAATTGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAACATTAT
66 GCTATTCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAACATTAT
* * *
18185 ATATAGCGGCGTCTACTATCGAAACGCCACTATTTTGCGGCGTATGTCATGAGAAACGTCGCTAT
131 ATATAGCGGCGTCTACTATCGAAACGCCACTATTTAGCGGCGTATGTCATGAAAAACGCCGCTAT
* * *
18250 TCATAATAAAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAAC
196 GCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAAATTCTATTCTTTGGAAAAC
* * *
18305 ATTATATATAGCGGCGTCTACTATAGAAATGCCACTATTTAGCGGCGTCTCTCATGAGAAACGCC
1 ATTATATATAGCGGCGTCTACTATAGAAACGCCACTATTTAGCGACGTCTGTCATGAGAAACGCC
* *
18370 GCTATGCATAACAAATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAACATTAT
66 GCTATTCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAACATTAT
* *
18435 ATATAGCGGCATCTACTATCGAAACGCCGCTATT
131 ATATAGCGGCGTCTACTATCGAAACGCCACTATT
18469 GTATTTAGAA
Statistics
Matches: 381, Mismatches: 33, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
250 156 0.41
251 225 0.59
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (250 bp):
ATTATATATAGCGGCGTCTACTATAGAAACGCCACTATTTAGCGACGTCTGTCATGAGAAACGCC
GCTATTCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGGAAAACATTAT
ATATAGCGGCGTCTACTATCGAAACGCCACTATTTAGCGGCGTATGTCATGAAAAACGCCGCTAT
GCATAACAAAGAAATGGTGTTTTTAGTTTCACCAAAATTCTATTCTTTGGAAAAC
Done.