Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012101.1 Corchorus capsularis cultivar CVL-1 contig12122, 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: 3857
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Found at i:835 original size:50 final size:50
Alignment explanation
Indices: 766--872 Score: 144
Period size: 50 Copynumber: 2.1 Consensus size: 50
756 AAACAAGAAG
* * ** *
766 TTTCAAAATTAGATGGCATTCCATTTGTGAGTCCATTATCAAGATTCGA-T
1 TTTCAAAATAAGATGGCATTCCACTTGTGAGTCCAAGATCAAAATTC-ACT
*
816 TTTCAAAATAAGATTGCATTCCACTTGTGAGTCCAAGATCAAAATTCACT
1 TTTCAAAATAAGATGGCATTCCACTTGTGAGTCCAAGATCAAAATTCACT
866 TTTCAAA
1 TTTCAAA
873 GGGCATTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
49 1 0.02
50 49 0.98
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (50 bp):
TTTCAAAATAAGATGGCATTCCACTTGTGAGTCCAAGATCAAAATTCACT
Found at i:1288 original size:30 final size:27
Alignment explanation
Indices: 1214--1306 Score: 66
Period size: 30 Copynumber: 3.3 Consensus size: 27
1204 ACAACAAGAG
*
1214 CAAGGAAGC-AAG-TTCAAGGACAAAT
1 CAAGAAAGCAAAGATTCAAGGACAAAT
*
1239 CAAGAAGAACAAAAGGATTCAAGGAAGCAAAGT
1 CAAGAA-AGC-AAA-GATTCAAGG-A-CAAA-T
*
1272 CAAGAAAGCAAAGATTC-AGAACATCAAT
1 CAAGAAAGCAAAGATTCAAGGACA--AAT
1300 CAAGAAA
1 CAAGAAA
1307 TTTTCAGTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
25 5 0.09
26 2 0.04
27 2 0.04
28 11 0.20
29 5 0.09
30 12 0.22
31 4 0.07
32 6 0.11
33 7 0.13
ACGTcount: A:0.54, C:0.15, G:0.20, T:0.11
Consensus pattern (27 bp):
CAAGAAAGCAAAGATTCAAGGACAAAT
Found at i:1529 original size:69 final size:70
Alignment explanation
Indices: 1387--1748 Score: 378
Period size: 69 Copynumber: 5.2 Consensus size: 70
1377 CGAATGCTCC
* ** * *
1387 GGCTTTTCCACTAGCCAAACTCGTTTCCACACGAGTCAG-TTTAGCCTTGGTTCAATCCAAGCAT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAAGCAT
* *
1451 TCAGG
66 ACAGA
1456 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCC-AGACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAAG-CA
*
1520 -AGAGA
65 TACAGA
* * * * * *
1525 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGAT-AGTTTCAGATTTGGTTCCATCCAAGCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAG-TCAGATCCAGCTTTGGTTCCATCCAAGCA
* *
1589 TTCAGG
65 TACAGA
* * *
1595 GGCTTTTTCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCCAGGCA-
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAAGCAT
**
1659 AGGGA
66 ACAGA
* * * * ** *
1664 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGAT-AGTTTAAGATTTGGTTCCATCCAAGCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAG-TCAGATCCAGCTTTGGTTCCATCCAAGCA
*
1728 TTCAG-
65 TACAGA
*
1733 GGCTTTTCCATAAGCC
1 GGCTTTTCCACAAGCC
1749 GAGTTCAATG
Statistics
Matches: 242, Mismatches: 43, Indels: 16
0.80 0.14 0.05
Matches are distributed among these distances:
69 165 0.68
70 77 0.32
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (70 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAAGCAT
ACAGA
Found at i:1636 original size:139 final size:138
Alignment explanation
Indices: 1387--1748 Score: 577
Period size: 139 Copynumber: 2.6 Consensus size: 138
1377 CGAATGCTCC
* * ** *
1387 GGCTTTTCCACT-AGCCAAACTCGTTTCCACACGAG-TCAGTTTAGCCTTGGTTCAATCCAAGCA
1 GGCTTTTCCA-TAAGCCAAACTCGCTTCCACGCGAGAT-AGTTTAGATTTGGTTCCATCCAAGCA
*
1450 TTCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCC
64 TTCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCC
1515 AGACAAGAGA
129 AGACAAGAGA
1525 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTCAGATTTGGTTCCATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTT-AGATTTGGTTCCATCCAAGCAT
*
1590 TCAGGGGCTTTTTCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCCA
65 TCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCCA
* *
1655 GGCAAGGGA
130 GACAAGAGA
1664 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTAAGATTTGGTTCCATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTT-AGATTTGGTTCCATCCAAGCAT
*
1729 TCA-GGGCTTTTCCATAAGCC
65 TCAGGGGCTTTTCCACAAGCC
1749 GAGTTCAATG
Statistics
Matches: 209, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
137 1 0.00
138 51 0.24
139 157 0.75
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (138 bp):
GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTAGATTTGGTTCCATCCAAGCATT
CAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCCAG
ACAAGAGA
Found at i:1985 original size:48 final size:48
Alignment explanation
Indices: 1862--2003 Score: 205
Period size: 47 Copynumber: 3.0 Consensus size: 48
1852 CCAGGCAATC
** *
1862 TTCTCTCGCTTCCATGCGAGTTTTCAAACTAGTGACCAAAGATGGTGT
1 TTCTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGGTCT
* *
1910 TT-TCTCGCTTCCACGCGGGTTTTCAATTTAGTGACCAAAGATGGTCT
1 TTCTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGGTCT
* * *
1957 TTCTCTCGCTTCCATGCGAGTCTGCAATTTAGTGACCAAAGTTGGTC
1 TTCTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGGTC
2004 AACGAGTTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
47 42 0.51
48 41 0.49
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (48 bp):
TTCTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGGTCT
Done.