Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007789.1 Corchorus olitorius cultivar O-4 contig07816, 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: 3098
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:1686 original size:32 final size:32
Alignment explanation
Indices: 1641--2408 Score: 792
Period size: 32 Copynumber: 23.6 Consensus size: 32
1631 GATTTCGAAG
*
1641 TTCCAGACCTCAGACAGGTCTTTCTCAGTTCAA
1 TTCC-GACCTCAGACAGGTCTTTCTCAGTTTAA
1674 TTCCGACCTCAGACAGGTCTTTCTCAGTTTAA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTAA
* *
1706 TTTCGACCTCAGACAGGTCTTTCTCAGTTCAA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTAA
*
1738 TTCCGACCTCAGACAAGTCTTTCTCAGTTTAA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTAA
* *
1770 TTTCGACCTCAGACAGGTCTTTCTCAGTTTTA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTAA
*
1802 TCCCGACCTCAGACAGGTCTTTCTCAGCTTT-A
1 TTCCGACCTCAGACAGGTCTTTCTCAG-TTTAA
* *
1834 TTTCGACCTCAGACAGGTCTTTCTCAGTTTTTA
1 TTCCGACCTCAGACAGGTCTTTCTCAG-TTTAA
**
1867 TTTTGACCTCAGACAGGTCTTTCTCAGCTTTTAA
1 TTCCGACCTCAGACAGGTCTTTCTCAG--TTTAA
* *
1901 TTTCGACCTCAGACAGGTCTTTAT-A-TTTCAA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTT-AA
*
1932 TTCCGACCTCATACAGGTCTTTCTCAGCTTTTAA
1 TTCCGACCTCAGACAGGTCTTTCTCAG--TTTAA
* *
1966 TTTCGACCTCAGACAGGTCTTTATC--TTTCAAA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTT--AA
* *
1998 TTCCGGCCTCAGACAGGTCTTTATC--TTTCAAA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTT--AA
2030 TTCCGACCTCAGACAGGTCTTTCTCAGCTTTTAA
1 TTCCGACCTCAGACAGGTCTTTCTCAG--TTTAA
* *
2064 TTTCGACCTCAGACAGGTCTTTATC--TTTCAA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTT-AA
* * *
2095 TTCCGGCCTCAGACAGGTCTTTTTCAGTTAAA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTAA
* *
2127 TTCCGACCTCAGACAAGTCCTTCTCAGTTTCAA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTT-AA
* * *
2160 TTTCGACCTCAGAAAGGTCTTTATC--TTTCAA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTT-AA
* *
2191 TTCCGGCCTCAGACAGGTCTTTATC--TTTCAAA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTT--AA
*
2223 TTCCGACCTCAGATAGGTCTTTCTCAGCTTTTAA
1 TTCCGACCTCAGACAGGTCTTTCTCAG--TTTAA
* * * *
2257 TTTCAACCTTAGACAGGTCTTTATC--TTTCAA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTT-AA
*
2288 TTCCGACTTCAGACAGGTCTTTATCTTTCTCAGTTTAA
1 TTCCGACCTCAGACAGG------TCTTTCTCAGTTTAA
* *
2326 TTTCGACCTTAGACAGGTCTTTCTCAGTTTAA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTAA
**
2358 TTTTGACCTCAGACAGGTCTTTCTCAGTTTTAA
1 TTCCGACCTCAGACAGGTCTTTCTCAG-TTTAA
* *
2391 TTTCGACCTCAGATAGGT
1 TTCCGACCTCAGACAGGT
2409 TTTTATCTTT
Statistics
Matches: 634, Mismatches: 68, Indels: 66
0.83 0.09 0.09
Matches are distributed among these distances:
30 12 0.02
31 93 0.15
32 316 0.50
33 80 0.13
34 98 0.15
35 3 0.00
36 6 0.01
37 7 0.01
38 16 0.03
39 3 0.00
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.37
Consensus pattern (32 bp):
TTCCGACCTCAGACAGGTCTTTCTCAGTTTAA
Found at i:1761 original size:96 final size:96
Alignment explanation
Indices: 1641--2415 Score: 893
Period size: 96 Copynumber: 7.9 Consensus size: 96
1631 GATTTCGAAG
* * *
1641 TTCCAGACCTCAGACAGGTCTTTCTCAG-TTCAATTCCGACCTCAGACAGGTCTTTCTCAGTTT-
1 TTCC-GACCTCAGACAGGTCTTTCTCAGTTTTAATTTCGACCTCAGACAGGTCTTTATC--TTTC
* *
1704 AATTTCGACCTCAGACAGGTCTTTCTCAGTTCAA
63 AATTCCGACCTCAGACAGGTCTTTATCAGTTCAA
* * *
1738 TTCCGACCTCAGACAAGTCTTTCTCAG-TTTAATTTCGACCTCAGACAGGTCTTTCTCAGTTT-T
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTTAATTTCGACCTCAGACAGGTCTTTATC--TTTCA
* * *
1801 ATCCCGACCTCAGACAGGTCTTTCTCAGCTT-TA
64 ATTCCGACCTCAGACAGGTCTTTATCAG-TTCAA
* * * * *
1834 TTTCGACCTCAGACAGGTCTTTCTCAGTTTTTATTTTGACCTCAGACAGGTCTTTCTCAGCTTTT
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTTAATTTCGACCTCAGACAGGTC-TT-T-ATCTTTC
* *
1899 AATTTCGACCTCAGACAGGTCTTTAT-ATTTCAA
63 AATTCCGACCTCAGACAGGTCTTTATCAGTTCAA
*
1932 TTCCGACCTCATACAGGTCTTTCTCAGCTTTTAATTTCGACCTCAGACAGGTCTTTATCTTTCAA
1 TTCCGACCTCAGACAGGTCTTTCTCAG-TTTTAATTTCGACCTCAGACAGGTCTTTATCTTTC-A
* *
1997 ATTCCGGCCTCAGACAGGTCTTTATC-TTTCAAA
64 ATTCCGACCTCAGACAGGTCTTTATCAGTTC-AA
2030 TTCCGACCTCAGACAGGTCTTTCTCAGCTTTTAATTTCGACCTCAGACAGGTCTTTATCTTTCAA
1 TTCCGACCTCAGACAGGTCTTTCTCAG-TTTTAATTTCGACCTCAGACAGGTCTTTATCTTTCAA
* * *
2095 TTCCGGCCTCAGACAGGTCTTTTTCAGTTAAA
65 TTCCGACCTCAGACAGGTCTTTATCAGTTCAA
* * * *
2127 TTCCGACCTCAGACAAGTCCTTCTCAGTTTCAATTTCGACCTCAGAAAGGTCTTTATCTTTCAAT
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTTAATTTCGACCTCAGACAGGTCTTTATCTTTCAAT
* *
2192 TCCGGCCTCAGACAGGTCTTTATC-TTTCAAA
66 TCCGACCTCAGACAGGTCTTTATCAGTTC-AA
* * *
2223 TTCCGACCTCAGATAGGTCTTTCTCAGCTTTTAATTTCAACCTTAGACAGGTCTTTATCTTTCAA
1 TTCCGACCTCAGACAGGTCTTTCTCAG-TTTTAATTTCGACCTCAGACAGGTCTTTATCTTTCAA
* *
2288 TTCCGACTTCAGACAGGTCTTTATCTTTCTCAGTTTAA
65 TTCCGACCTCAGACAGGTCTTTA------TCAGTTCAA
* * * * *
2326 TTTCGACCTTAGACAGGTCTTTCTCAG-TTTAATTTTGACCTCAGACAGGTCTTTCTCAGTTTTA
1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTTAATTTCGACCTCAGACAGGTCTTTATC--TTTCA
* * *
2390 ATTTCGACCTCAGATAGGTTTTTATC
64 ATTCCGACCTCAGACAGGTCTTTATC
2416 TTTTAATAGC
Statistics
Matches: 594, Mismatches: 61, Indels: 46
0.85 0.09 0.07
Matches are distributed among these distances:
95 2 0.00
96 197 0.33
97 168 0.28
98 100 0.17
99 46 0.08
100 1 0.00
101 26 0.04
103 52 0.09
104 2 0.00
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.37
Consensus pattern (96 bp):
TTCCGACCTCAGACAGGTCTTTCTCAGTTTTAATTTCGACCTCAGACAGGTCTTTATCTTTCAAT
TCCGACCTCAGACAGGTCTTTATCAGTTCAA
Done.