Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023351.1 Corchorus olitorius cultivar O-4 contig23384, 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: 4961
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:32 original size:1 final size:1
Alignment explanation
Indices: 28--67 Score: 71
Period size: 1 Copynumber: 40.0 Consensus size: 1
18 AAAGGGNGTT
*
28 AAAAAAAAAAAAANAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
68 CTGGGCCTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:104 original size:36 final size:36
Alignment explanation
Indices: 57--163 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 36
47 AAAAAAAAAA
* *
57 AAAAAAAAAAACTGGGCCTAAAATAGAAAGAGGTTG
1 AAAAAAAAAAACTGGACCTAAAATAGAAAGAGGTCG
* *
93 AAAAACAAAAACAGGACCTAAAATAGAAAGAGGTCG
1 AAAAAAAAAAACTGGACCTAAAATAGAAAGAGGTCG
* * * * *
129 GAAAAGAAAGACTGGACCTAAAACAGAGAGAGGTC
1 AAAAAAAAAAACTGGACCTAAAATAGAAAGAGGTC
164 ATAAAAGCTA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.54, C:0.12, G:0.23, T:0.10
Consensus pattern (36 bp):
AAAAAAAAAAACTGGACCTAAAATAGAAAGAGGTCG
Found at i:1016 original size:58 final size:58
Alignment explanation
Indices: 948--1418 Score: 682
Period size: 58 Copynumber: 8.1 Consensus size: 58
938 GATTGCATTA
* *
948 TCTTGTTTTAAAATCCTATTCGAGGTCTCTGTTAGAGAGTTTTAAATTCAAAATATCT
1 TCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCT
* *
1006 TCTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATAT-T
1 TCTTG-TTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCT
*
1064 ATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTAAATTCAAAATATCT
1 -TCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCT
* * *
1123 TC-T-TTTAAAAATCCTGTTCAAGGTCTCTGCTAGAGAGTTTTCAATTCAAAATATCT
1 TCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCT
* *
1179 TCTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCA
1 TCTTG-TTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCT
*
1238 TCTTGTTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCA
1 TCTTG--TTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCT
**
1298 TCTTGCGTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATAT-T
1 TCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCT
** * * *
1355 ATCTTGCGTTAAAATCCTGTTCGAGGTCT-TCGTTAGAGAGTTTTCAATTTAAAATTTTT
1 -TCTTGTTTTAAAATCCTGTTCGAGGTCTCT-GTTAGAGAGTTTTCAATTCAAAATATCT
1414 TCTTG
1 TCTTG
1419 GTCGAGATCT
Statistics
Matches: 382, Mismatches: 21, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
56 51 0.13
57 3 0.01
58 162 0.42
59 109 0.29
60 57 0.15
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (58 bp):
TCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATCT
Found at i:1718 original size:29 final size:28
Alignment explanation
Indices: 1682--1855 Score: 152
Period size: 29 Copynumber: 6.0 Consensus size: 28
1672 TTTTTCTTGT
1682 ACATCCAAAGGCATTTTGGTCATTTTTGC
1 ACATCC-AAGGCATTTTGGTCATTTTTGC
* *
1711 ACATCCAAGAGCATTTTAGTCATTTCTGC
1 ACATCCAAG-GCATTTTGGTCATTTTTGC
** *
1740 ACAATCCGGGGCATTTTGATCATTTTT-C
1 AC-ATCCAAGGCATTTTGGTCATTTTTGC
* ** *
1768 ACCCACCCGTGGGCATTTTGGTCATTTTCGC
1 A--CATCC-AAGGCATTTTGGTCATTTTTGC
* *
1799 ACATCCAAGAGCATTTTAGTCATTTCTGC
1 ACATCCAAG-GCATTTTGGTCATTTTTGC
**
1828 ACAATCCGGGGCATTTTGGTCATTTTTG
1 AC-ATCCAAGGCATTTTGGTCATTTTTG
1856 TTTTATTTTT
Statistics
Matches: 116, Mismatches: 21, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
28 6 0.05
29 80 0.69
30 28 0.24
31 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (28 bp):
ACATCCAAGGCATTTTGGTCATTTTTGC
Found at i:1840 original size:88 final size:88
Alignment explanation
Indices: 1691--1854 Score: 310
Period size: 88 Copynumber: 1.9 Consensus size: 88
1681 TACATCCAAA
*
1691 GGCATTTTGGTCATTTTTGCACATCCAAGAGCATTTTAGTCATTTCTGCACAATCCGGGGCATTT
1 GGCATTTTGGTCATTTTCGCACATCCAAGAGCATTTTAGTCATTTCTGCACAATCCGGGGCATTT
1756 TGATCATTTTTCACCCACCCGTG
66 TGATCATTTTTCACCCACCCGTG
1779 GGCATTTTGGTCATTTTCGCACATCCAAGAGCATTTTAGTCATTTCTGCACAATCCGGGGCATTT
1 GGCATTTTGGTCATTTTCGCACATCCAAGAGCATTTTAGTCATTTCTGCACAATCCGGGGCATTT
*
1844 TGGTCATTTTT
66 TGATCATTTTT
1855 GTTTTATTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 74 1.00
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (88 bp):
GGCATTTTGGTCATTTTCGCACATCCAAGAGCATTTTAGTCATTTCTGCACAATCCGGGGCATTT
TGATCATTTTTCACCCACCCGTG
Found at i:2844 original size:17 final size:17
Alignment explanation
Indices: 2822--2854 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2812 AAACTCAGAA
2822 AGCAGAGTTCTAAATGC
1 AGCAGAGTTCTAAATGC
2839 AGCAGAGTTCTAAATG
1 AGCAGAGTTCTAAATG
2855 GCAAGGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (17 bp):
AGCAGAGTTCTAAATGC
Done.