Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024837.1 Corchorus olitorius cultivar O-4 contig24870, 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: 2170
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Found at i:914 original size:40 final size:40
Alignment explanation
Indices: 870--1700 Score: 677
Period size: 40 Copynumber: 19.7 Consensus size: 40
860 ATAGGAATAG
* * * *
870 CACCTTCCGATGAGCAATGGCAAACTGGGAATATAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGGAATATAAACAA
* * * *
910 CACCTTCCGATGAGGAAGGGCAAACTAGGAATTTAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGGAATATAAACAA
* * * *
950 CATCTTCCGGTGGGGAAGGACTAGA-TGGTAAATTAAACTCAAACAA
1 CACCTTCCGGTGGGGAAGGGC-AAACTGG-GAA-T--A-T-AAACAA
* *
996 CACCTTCCGATGGGGAAGGGCAAACTGTGAATATAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGGAATATAAACAA
* *
1036 CACCTTCCGGTGGGGAAGGGCAAA-TCGGTAAACTAAACTTAAATAA
1 CACCTTCCGGTGGGGAAGGGCAAACT-GG-GAA-T--A--TAAACAA
* *
1082 CACTTTCCGATGGGGAAGGGCAAACTGGGAATATAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGGAATATAAACAA
** *
1122 CACCTTCCGGTGGGGAAGGGCAAGTTGGTAAACTAAACTTAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGG-GAA-T--A--TAAACAA
* * *
1168 CACCTTCCGATTGGGAAAGGCAAACTGGGAATATAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGGAATATAAACAA
* * *
1208 CATCTTCCGGTGGGGAAGGGCAAATTGGAAAACTAAACTTAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGG-GAA-T--A--TAAACAA
* *
1254 CACCTTCCGATGGGGAAGGGCAAACTGGAAAT-TAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGGAATATAAACAA
* *
1293 CACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTAGACTTAAATAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGG--AA-T--A--TAAACAA
* * *
1340 CACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGGAATATAAACAA
* * * *
1380 CACCTTCCGGTGGGGAAGGGAAAATTGGTAA-ACAAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGGAATA-TAAACAA
* *
1420 CACCTTCCGGCGTGGAAGGGCAAACTGGGAACT-TAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGGAA-TATAAACAA
* *
1460 CACCTTCCGGTGGGGAAGGGCAAATTGGGTCAAGCAGACTTAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGG---A--ATA--TAAACAA
* * *
1507 CACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGGAATATAAACAA
* * *
1547 CACCTTCCGGTGGGGAACGGCAAATTGGTAA-ACTAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGGAATA-TAAACAA
*
1587 CACCTTCCGGCGGGGAAGGGCAAACTGGGAACT-TAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGGAA-TATAAACAA
* *
1627 CACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAACAGACTTAAACAA
1 CACCTTCCGGTGGGGAAGGGCAAACTGGG----A-ATA--TAAACAA
* *
1674 CACCTTCCGATGAGGAAGGGCAAACTG
1 CACCTTCCGGTGGGGAAGGGCAAACTG
1701 CCGTCGAAGT
Statistics
Matches: 640, Mismatches: 93, Indels: 109
0.76 0.11 0.13
Matches are distributed among these distances:
39 34 0.05
40 342 0.53
41 13 0.02
42 9 0.01
43 1 0.00
44 10 0.02
45 16 0.03
46 118 0.18
47 97 0.15
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (40 bp):
CACCTTCCGGTGGGGAAGGGCAAACTGGGAATATAAACAA
Found at i:1013 original size:86 final size:86
Alignment explanation
Indices: 903--1700 Score: 1088
Period size: 86 Copynumber: 9.4 Consensus size: 86
893 ACTGGGAATA
* * *
903 TAAACAACACCTTCCGATGAGGAAGGGCAAACTAGGAATTTAAACAACATCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAG
* * *
968 GACTAGA-TGGTAAATTAAACT
66 GGC-AAATTGGTAAACTAAACT
* * *
989 CAAACAACACCTTCCGATGGGGAAGGGCAAACTGTGAATATAAACAACACCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAG
*
1054 GGCAAATCGGTAAACTAAACT
66 GGCAAATTGGTAAACTAAACT
* * *
1075 TAAATAACACTTTCCGATGGGGAAGGGCAAACTGGGAATATAAACAACACCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAG
*
1140 GGCAAGTTGGTAAACTAAACT
66 GGCAAATTGGTAAACTAAACT
* * * *
1161 TAAACAACACCTTCCGATTGGGAAAGGCAAACTGGGAATATAAACAACATCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAG
*
1226 GGCAAATTGGAAAACTAAACT
66 GGCAAATTGGTAAACTAAACT
*
1247 TAAACAACACCTTCCGATGGGGAAGGGCAAACT-GGAAATTAAACAACACCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAG
* *
1311 GGCAAATTGGGTAAAGTAGACT
66 GGCAAATT-GGTAAACTAAACT
* *
1333 TAAATAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAG
*
1398 GGAAAATTGGTAAAC---A--
66 GGCAAATTGGTAAACTAAACT
** * *
1414 -AAACAACACCTTCCGGCGTGGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAG
* *
1478 GGCAAATTGGGTCAAGC-AGACT
66 GGCAAATT-GGT-AAACTAAACT
* *
1500 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAC
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAG
1565 GGCAAATTGG-----TAAAC-
66 GGCAAATTGGTAAACTAAACT
** *
1580 TAAACAACACCTTCCGGCGGGGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAG
*
1645 GGCAAATTGGGTAAAAC-AGACT
66 GGCAAATT-GGT-AAACTAAACT
*
1667 TAAACAACACCTTCCGATGAGGAAGGGCAAACTG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTG
1701 CCGTCGAAGT
Statistics
Matches: 635, Mismatches: 58, Indels: 37
0.87 0.08 0.05
Matches are distributed among these distances:
80 134 0.21
81 8 0.01
82 3 0.00
83 1 0.00
84 1 0.00
85 38 0.06
86 315 0.50
87 135 0.21
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.18
Consensus pattern (86 bp):
TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAG
GGCAAATTGGTAAACTAAACT
Done.