Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020194.1 Corchorus olitorius cultivar O-4 contig20227, 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: 6700
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:251 original size:27 final size:28
Alignment explanation
Indices: 221--284 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
211 CTTGACGCTT
* *
221 AAGGGCAAAATTGTAA-TTTAGTCAACC
1 AAGGGCAAAATGGTAATTTTAGCCAACC
* *
248 AAGGGTAAAATGGTAATTTTAGCCGACC
1 AAGGGCAAAATGGTAATTTTAGCCAACC
*
276 AAGGACAAA
1 AAGGGCAAA
285 TACGTAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 14 0.47
28 16 0.53
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (28 bp):
AAGGGCAAAATGGTAATTTTAGCCAACC
Found at i:1084 original size:35 final size:35
Alignment explanation
Indices: 1039--1138 Score: 141
Period size: 35 Copynumber: 2.9 Consensus size: 35
1029 ACTTTCGTAG
1039 GCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTT
1 GCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTT
1074 GCTTTGTTGTTGCTTTGTTGATGGAGAA-AACTTT
1 GCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTT
** *
1108 GCTGCAGAT-TTGCTTTGCTTGATGGAGAAGA
1 GCT-TTGTTGTTGCTTTG-TTGATGGAGAAGA
1139 GTTTTGCCTT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 17 0.29
35 41 0.69
36 1 0.02
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (35 bp):
GCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTT
Found at i:1768 original size:28 final size:28
Alignment explanation
Indices: 1737--1793 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1727 ATTCTAAAAA
* **
1737 TTACTCATCAAAGGGTAATTTAGTAATT
1 TTACCCATCAAAGGGTAAAATAGTAATT
* *
1765 TTACCCCTCCAAGGGTAAAATAGTAATT
1 TTACCCATCAAAGGGTAAAATAGTAATT
1793 T
1 T
1794 CACTTTCCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (28 bp):
TTACCCATCAAAGGGTAAAATAGTAATT
Found at i:1883 original size:12 final size:12
Alignment explanation
Indices: 1868--1946 Score: 81
Period size: 12 Copynumber: 6.7 Consensus size: 12
1858 TTATTTTTTA
*
1868 TTTTTCCTTCTC
1 TTTTTCTTTCTC
*
1880 TTTTCCTTT-TCC
1 TTTTTCTTTCT-C
*
1892 TTTTTCTTTTTC
1 TTTTTCTTTCTC
1904 TTTTTCTTTCTC
1 TTTTTCTTTCTC
*
1916 TTTCTCTTTCTC
1 TTTTTCTTTCTC
* *
1928 TCTTTCTTT-TT
1 TTTTTCTTTCTC
1939 TTTTTCTT
1 TTTTTCTT
1947 ATTTTTTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
11 9 0.16
12 46 0.82
13 1 0.02
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTCTTTCTC
Found at i:1889 original size:18 final size:18
Alignment explanation
Indices: 1868--1918 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1858 TTATTTTTTA
1868 TTTTTCCTTCTCTTTTCC
1 TTTTTCCTTCTCTTTTCC
* *
1886 -TTTTCCTTTTTCTTTTTC
1 TTTTTCC-TTCTCTTTTCC
*
1904 TTTTTCTTTCTCTTT
1 TTTTTCCTTCTCTTT
1919 CTCTTTCTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 6 0.22
18 16 0.59
19 5 0.19
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTCCTTCTCTTTTCC
Found at i:1909 original size:36 final size:33
Alignment explanation
Indices: 1849--1944 Score: 95
Period size: 36 Copynumber: 2.7 Consensus size: 33
1839 AATTTTCTTA
1849 TTTTCCTATTTAT-TTTTTATTTTTCCTTCTCTTTTCC
1 TTTTCCT-TTT-TCTTTTT-TTTTTCCTTCTC-TTT-C
*
1886 TTTTCCTTTTTCTTTTTCTTTTTCTTTCTCTTTC
1 TTTTCCTTTTTCTTTTT-TTTTTCCTTCTCTTTC
*
1920 TCTTTCTCTCTTTCTTTTTTTTTTC
1 T-TTTC-CTTTTTCTTTTTTTTTTC
1945 TTATTTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
34 2 0.04
35 14 0.26
36 30 0.57
37 7 0.13
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (33 bp):
TTTTCCTTTTTCTTTTTTTTTTCCTTCTCTTTC
Found at i:1917 original size:6 final size:6
Alignment explanation
Indices: 1887--1928 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1877 CTCTTTTCCT
* * *
1887 TTTC-C TTTTTC TTTTTC TTTTTC TTTCTC TTTCTC TTTCTC T
1 TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC T
1929 CTTTCTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 3 0.09
6 31 0.91
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTCTC
Found at i:3165 original size:20 final size:20
Alignment explanation
Indices: 3140--3178 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3130 CCAAGGAACA
3140 CTTAACCATAACCATATACG
1 CTTAACCATAACCATATACG
*
3160 CTTAACTATAACCATATAC
1 CTTAACCATAACCATATAC
3179 TACAAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.28, G:0.03, T:0.28
Consensus pattern (20 bp):
CTTAACCATAACCATATACG
Found at i:4765 original size:18 final size:19
Alignment explanation
Indices: 4742--4779 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
4732 TTGTTGTCGT
4742 TTATTCTTACAC-TAAAAA
1 TTATTCTTACACTTAAAAA
4760 TTATTCTTACACTTAAAAA
1 TTATTCTTACACTTAAAAA
4779 T
1 T
4780 CCTATTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (19 bp):
TTATTCTTACACTTAAAAA
Done.