Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017271.1 Corchorus olitorius cultivar O-4 contig17304, 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: 2492
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Found at i:743 original size:18 final size:18
Alignment explanation
Indices: 722--779 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
712 AACTGGGCCT
722 AAAACAGAAAGAGGTCGG
1 AAAACAGAAAGAGGTCGG
* * * **
740 AAAACAAAAACAGGGCCT
1 AAAACAGAAAGAGGTCGG
* *
758 AAAATAGAAAGAGGTAGG
1 AAAACAGAAAGAGGTCGG
776 AAAA
1 AAAA
780 GAAAATACTG
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.26, T:0.07
Consensus pattern (18 bp):
AAAACAGAAAGAGGTCGG
Found at i:756 original size:36 final size:36
Alignment explanation
Indices: 704--810 Score: 151
Period size: 36 Copynumber: 2.9 Consensus size: 36
694 AAAAAAAAAA
704 AAAAAAAAAACTGGGCCTAAAACAGAAAGAGGTCGG
1 AAAAAAAAAACTGGGCCTAAAACAGAAAGAGGTCGG
* * * *
740 AAAACAAAAACAGGGCCTAAAATAGAAAGAGGTAGG
1 AAAAAAAAAACTGGGCCTAAAACAGAAAGAGGTCGG
* *
776 AAAAGAAAATACTGGACCTAAAACAGAAAGAGGTC
1 AAAA-AAAAAACTGGGCCTAAAACAGAAAGAGGTC
811 ATAAAAACTA
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
36 36 0.60
37 24 0.40
ACGTcount: A:0.54, C:0.13, G:0.23, T:0.09
Consensus pattern (36 bp):
AAAAAAAAAACTGGGCCTAAAACAGAAAGAGGTCGG
Found at i:905 original size:45 final size:45
Alignment explanation
Indices: 838--946 Score: 209
Period size: 45 Copynumber: 2.4 Consensus size: 45
828 GGGGTTCAGG
838 TTGAAAACCCGCAAAGGGCAGCCTGAATCCAAAGGGGGTTCTTGAA
1 TTGAAAACCCG-AAAGGGCAGCCTGAATCCAAAGGGGGTTCTTGAA
884 TTGAAAACCCGAAAGGGCAGCCTGAATCCAAAGGGGGTTCTTGAA
1 TTGAAAACCCGAAAGGGCAGCCTGAATCCAAAGGGGGTTCTTGAA
929 TTGAAAACCCGAAAGGGC
1 TTGAAAACCCGAAAGGGC
947 GATTCAAGCA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 52 0.83
46 11 0.17
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (45 bp):
TTGAAAACCCGAAAGGGCAGCCTGAATCCAAAGGGGGTTCTTGAA
Found at i:1788 original size:57 final size:57
Alignment explanation
Indices: 1691--2271 Score: 766
Period size: 57 Copynumber: 10.0 Consensus size: 57
1681 TTAGTTTCAG
* * *
1691 TTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
1 TTTCAATTCAAAATCTCATCTCG-TT-TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
** *
1750 TTTCAAAACAAAATCTCATCTCATTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
1 TTTCAATTCAAAATCTCATCTCGTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* * *
1807 TTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
1 TTTCAATTCAAAATCTCATCTCG-TT-TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
**
1866 TTTCAAAACAAAATCTCATCTCGTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
1 TTTCAATTCAAAATCTCATCTCGTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* * * *
1923 TTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAAAGAGT
1 TTTCAATTCAAAATCTCATCTCG-TT-TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
**
1982 TTTCAAAACAAAATCTCATCTCGTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
1 TTTCAATTCAAAATCTCATCTCGTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* *
2039 TTTCAATTCAAAATCTTATCTTGTTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
1 TTTCAATTCAAAATCTCATCTCG--TT-TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* * *
2099 TTTCAATTCAAAATCTCATCTTGTCTTAAAATCTTGTTCGAGGTCTCTGTTAGGGAGT
1 TTTCAATTCAAAATCTCATCTCGT-TTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* * ***
2157 TTTCAATTCAAAATCTTATCTTGTTTTTGATCCTGTTCGAGGTCTCTGTTAGAGAGT
1 TTTCAATTCAAAATCTCATCTCGTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* * * * * *
2214 TTTCAATTCAAAATTTTATCTTGTTTTAAACTCCTGGTCGAGGTCTCTGTTTGAGAGT
1 TTTCAATTCAAAATCTCATCTCG-TTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
2272 CTATATTTCA
Statistics
Matches: 464, Mismatches: 49, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
57 199 0.43
58 92 0.20
59 119 0.26
60 54 0.12
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (57 bp):
TTTCAATTCAAAATCTCATCTCGTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
Found at i:1839 original size:116 final size:116
Alignment explanation
Indices: 1691--2271 Score: 932
Period size: 116 Copynumber: 5.0 Consensus size: 116
1681 TTAGTTTCAG
1691 TTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAA
1 TTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAA
*
1756 AACAAAATCTCATCTCATTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
66 AACAAAATCTCATCTCGTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
1807 TTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAA
1 TTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAA
1872 AACAAAATCTCATCTCGTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
66 AACAAAATCTCATCTCGTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
*
1923 TTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAAAGAGTTTTCAA
1 TTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAA
1988 AACAAAATCTCATCTCGTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
66 AACAAAATCTCATCTCGTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* *
2039 TTTCAATTCAAAATCTTATCTTGTTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCA
1 TTTCAATTCAAAATCTAACCTTG-TTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCA
** * * *
2104 ATTCAAAATCTCATCTTGTCTTAAAATCTTGTTCGAGGTCTCTGTTAGGGAGT
65 AAACAAAATCTCATCTCGT-TTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* * **
2157 TTTCAATTCAAAATCTTATCTTGTTT-T-TGATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAA
1 TTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAA
** * * * * * *
2220 TTCAAAATTTTATCTTGTTTTAAACTCCTGGTCGAGGTCTCTGTTTGAGAGT
66 AACAAAATCTCATCTCG-TTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
2272 CTATATTTCA
Statistics
Matches: 443, Mismatches: 19, Indels: 7
0.94 0.04 0.01
Matches are distributed among these distances:
115 77 0.17
116 253 0.57
117 59 0.13
118 54 0.12
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (116 bp):
TTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAA
AACAAAATCTCATCTCGTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
Found at i:1996 original size:175 final size:174
Alignment explanation
Indices: 1691--2271 Score: 837
Period size: 175 Copynumber: 3.3 Consensus size: 174
1681 TTAGTTTCAG
* *
1691 TTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAA
1 TTTCAATTCAAAATCTTATCTTGTTT-TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAA
** **
1756 AACAAAATCTCATC-TCATTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAA
65 TTCAAAATCTCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAA
*
1820 TCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
130 TCTAATCTTGTTT-TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
** * *
1866 TTTCAAAACAAAATCTCATCTCG-TTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAAT
1 TTTCAATTCAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAAT
* * * **
1930 TCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGTTAAAGAGTTTTCAAAACAAAA
66 TCAAAATCTCATCTTGTTT-TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAA
* *
1995 TCTCATCTCG-TTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
130 TCTAATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
2039 TTTCAATTCAAAATCTTATCTTGTTTTCTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCA
1 TTTCAATTCAAAATCTTATCTTG-TTT-TAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCA
* * *
2104 ATTCAAAATCTCATCTTGTCTTAAAATCTTGTTCGAGGTCTCTGTTAGGGAGTTTTCAATTCAAA
64 ATTCAAAATCTCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAA
* **
2169 ATCTTATCTTGTTTT-TGATCCTGTTCGAGGTCTCTGTTAGAGAGT
129 ATCTAATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* * * *
2214 TTTCAATTCAAAATTTTATCTTGTTTTAAACTCCTGGTCGAGGTCTCTGTTTGAGAGT
1 TTTCAATTCAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
2272 CTATATTTCA
Statistics
Matches: 363, Mismatches: 37, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
173 128 0.35
174 10 0.03
175 167 0.46
176 58 0.16
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (174 bp):
TTTCAATTCAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAAT
TCAAAATCTCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
CTAATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
Done.