Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011914.1 Corchorus olitorius cultivar O-4 contig11947, 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: 4867
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.30
Found at i:2794 original size:40 final size:38
Alignment explanation
Indices: 2714--2838 Score: 159
Period size: 36 Copynumber: 3.3 Consensus size: 38
2704 AAAAGGAGCT
2714 AAAAAA-AAAAACTGGACCTAAAATAGAAAGAGGTC--
1 AAAAAAGAAAAACTGGACCTAAAATAGAAAGAGGTCAA
*
2749 GAAAAAGAAAAACTGGACCTAAAATAGAAAGAGGTCAAAA
1 AAAAAAGAAAAACTGGACCTAAAATAGAAAGAGGTC--AA
* *
2789 AAAAAAGAAAAACTTGG-CCTAAAACAGAGAGAGGTCAGA
1 AAAAAAGAAAAAC-TGGACCTAAAATAGAAAGAGGTCA-A
2828 AAAAAAGAAAA
1 AAAAAAGAAAA
2839 TAAATAAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
35 5 0.06
36 29 0.37
38 1 0.01
39 12 0.15
40 29 0.37
41 3 0.04
ACGTcount: A:0.61, C:0.10, G:0.19, T:0.10
Consensus pattern (38 bp):
AAAAAAGAAAAACTGGACCTAAAATAGAAAGAGGTCAA
Found at i:3759 original size:59 final size:59
Alignment explanation
Indices: 3687--4192 Score: 843
Period size: 59 Copynumber: 8.6 Consensus size: 59
3677 ATTTCCCTTT
* *
3687 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGTGTTTTCAGTTCAAAATCTTA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA
* * *
3746 CCGTGTTTATAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA
*
3805 CCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA
* *
3864 TCTTGCTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTCCAATTCAAAATCTTA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA
* *
3923 CCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA
* *
3982 TCTTGTTTCTAAAATCCTATTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA
* *
4041 TCTTGTTTTTAAAAATCCTGTTTGAGGTCTCAGTTAGAGAGTTTTCAATTCAAAATCTTA
1 TCTTGTTTTT-AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA
*
4101 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTTA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA
* *
4160 TCTTG-TTTTAAACTCCTGGTCGAGGTCTCTGTT
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTT
4193 TAAGAGTCAG
Statistics
Matches: 419, Mismatches: 27, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
58 26 0.06
59 337 0.80
60 56 0.13
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.43
Consensus pattern (59 bp):
TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTA
Found at i:4468 original size:29 final size:29
Alignment explanation
Indices: 4435--4807 Score: 437
Period size: 29 Copynumber: 12.9 Consensus size: 29
4425 TTCGCACGCT
*
4435 CAGGGGAATTTTGGTCATTTTTGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * * *
4464 CAGGGGTATTTTGGTCATTTTCGCACATT
1 CAGGGGCATTTTGGTCATTTTTGCATATC
*
4493 CAGGGGCATTTTGGTCATTTTCGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * *
4522 CGGGGGCATTTTGATCATTTTTGCACATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
4551 CAGGGGCATTTTGGTCATTTTTGCATAT-
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* *
4579 CTGGGG-AGTTTTGGTCATTTTTGCACATC
1 CAGGGGCA-TTTTGGTCATTTTTGCATATC
* *
4608 CAGGGGTATTTTGGTCATTTTCGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * *
4637 CGGGGGCATTTTGATCATTTTTGCACATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* *
4666 CAGGGGCATTTTGGTCATTATTGCATATA
1 CAGGGGCATTTTGGTCATTTTTGCATATC
4695 C-GGGGCATTTTGGTCATTTTTGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* ** * *
4723 CGGGGGCATTTTGGTCATTTTTATACATT
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * * * * *
4752 CAGGGGCATTTCGGTCATCTGTACACATT
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* *
4781 CTGGGGCAGTTTGGTCATTTTTGCATA
1 CAGGGGCATTTTGGTCATTTTTGCATA
4808 CTCTAGGTTC
Statistics
Matches: 293, Mismatches: 47, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
27 1 0.00
28 50 0.17
29 241 0.82
30 1 0.00
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (29 bp):
CAGGGGCATTTTGGTCATTTTTGCATATC
Found at i:4638 original size:115 final size:115
Alignment explanation
Indices: 4435--4807 Score: 498
Period size: 115 Copynumber: 3.2 Consensus size: 115
4425 TTCGCACGCT
* * * * *
4435 CAGGGGAATTTTGGTCATTTTTGCATATCCAGGGGTATTTTGGTCATTTTCGCACATTCAGGGGC
1 CAGGGGCATTTTGGTCATTTTTGCATATAC-GGGGCATTTTGGTCATTTTTGCACATCCAGGGGC
4500 ATTTTGGTCATTTTCGCATATCCGGGGGCATTTTGATCATTTTTGCACATC
65 ATTTTGGTCATTTTCGCATATCCGGGGGCATTTTGATCATTTTTGCACATC
4551 CAGGGGCATTTTGGTCATTTTTGCATAT-CTGGGG-AGTTTTGGTCATTTTTGCACATCCAGGGG
1 CAGGGGCATTTTGGTCATTTTTGCATATAC-GGGGCA-TTTTGGTCATTTTTGCACATCCAGGGG
*
4614 TATTTTGGTCATTTTCGCATATCCGGGGGCATTTTGATCATTTTTGCACATC
64 CATTTTGGTCATTTTCGCATATCCGGGGGCATTTTGATCATTTTTGCACATC
* * *
4666 CAGGGGCATTTTGGTCATTATTGCATATACGGGGCATTTTGGTCATTTTTGCATATCCGGGGGCA
1 CAGGGGCATTTTGGTCATTTTTGCATATACGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCA
*** * * * * * * * * *
4731 TTTTGGTCATTTTTATACATTCAGGGGCATTTCGGTCATCTGTACACATT
66 TTTTGGTCATTTTCGCATATCCGGGGGCATTTTGATCATTTTTGCACATC
* *
4781 CTGGGGCAGTTTGGTCATTTTTGCATA
1 CAGGGGCATTTTGGTCATTTTTGCATA
4808 CTCTAGGTTC
Statistics
Matches: 230, Mismatches: 24, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
114 1 0.00
115 200 0.87
116 29 0.13
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (115 bp):
CAGGGGCATTTTGGTCATTTTTGCATATACGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCA
TTTTGGTCATTTTCGCATATCCGGGGGCATTTTGATCATTTTTGCACATC
Done.