Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019735.1 Corchorus olitorius cultivar O-4 contig19768, 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: 34036
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Found at i:7484 original size:20 final size:18
Alignment explanation
Indices: 7443--7478 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
7433 CGAAGCATGG
7443 GTTATATATATTCTAGTA
1 GTTATATATATTCTAGTA
7461 GTTATATATATTCTAGTA
1 GTTATATATATTCTAGTA
7479 AAGTTACGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (18 bp):
GTTATATATATTCTAGTA
Found at i:7987 original size:32 final size:32
Alignment explanation
Indices: 7950--8013 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
7940 AATTCCAGCC
* *
7950 TACCTAGACCATGAGGTCTTAGGTTCAACTCT
1 TACCTAAACCATGAGGTCTTAGCTTCAACTCT
7982 TACCTAAACCATGAGGTCTTAGCTTCAACTCT
1 TACCTAAACCATGAGGTCTTAGCTTCAACTCT
8014 CACGGAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (32 bp):
TACCTAAACCATGAGGTCTTAGCTTCAACTCT
Found at i:9008 original size:29 final size:29
Alignment explanation
Indices: 8954--9009 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
8944 TAATAACTTC
***
8954 TAAAGCTTTTTAATTTAATTTTTTTAAAA
1 TAAAGCTTTTTAATTTAATCAGTTTAAAA
8983 TAAAGCTTTTTAATTTTAA-CAGTTTAA
1 TAAAGCTTTTTAA-TTTAATCAGTTTAA
9010 TCTTTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (29 bp):
TAAAGCTTTTTAATTTAATCAGTTTAAAA
Found at i:27313 original size:10 final size:10
Alignment explanation
Indices: 27300--27333 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
27290 TAGAACTTAG
27300 AAAGTAAAGA
1 AAAGTAAAGA
*
27310 AAAGAAAAGAA
1 AAAGTAAAG-A
27321 AAAGTAAAGA
1 AAAGTAAAGA
27331 AAA
1 AAA
27334 TATACCCTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (10 bp):
AAAGTAAAGA
Found at i:30021 original size:15 final size:15
Alignment explanation
Indices: 30001--30031 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29991 AAAAAGGTTC
30001 CATTTCTTTTTCTCA
1 CATTTCTTTTTCTCA
30016 CATTTCTTTTTCTCA
1 CATTTCTTTTTCTCA
30031 C
1 C
30032 TTTTATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.29, G:0.00, T:0.58
Consensus pattern (15 bp):
CATTTCTTTTTCTCA
Found at i:30307 original size:31 final size:31
Alignment explanation
Indices: 30272--30406 Score: 171
Period size: 31 Copynumber: 4.4 Consensus size: 31
30262 TTTGTGCACG
**
30272 TGGCATGCCACGTGTCACTTTTTGAAACACA
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
30303 TGGCATGCCACGTGTCACTTTTTGGTACACA
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
* ** * *
30334 TGGCGTGATATGTGTCACTTTTTGGTACACG
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
* * * *
30365 TGGCGTGCCACATGTCGCTTTTTGGTACACG
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
30396 TGGCATGCCAC
1 TGGCATGCCAC
30407 CGTCGGACAC
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 91 1.00
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (31 bp):
TGGCATGCCACGTGTCACTTTTTGGTACACA
Found at i:30859 original size:30 final size:30
Alignment explanation
Indices: 30822--30884 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
30812 CCTTGCCATT
30822 TTTTTTTTCCTGAAGAATCTTGCCATTAATA
1 TTTTTTTTCCTGAA-AATCTTGCCATTAATA
** *
30853 TTTTTTTTGGTTAAAATCTTGCCATTAATA
1 TTTTTTTTCCTGAAAATCTTGCCATTAATA
30883 TT
1 TT
30885 ATTATTAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (30 bp):
TTTTTTTTCCTGAAAATCTTGCCATTAATA
Found at i:32867 original size:2 final size:2
Alignment explanation
Indices: 32860--32892 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32850 ATGAATGATT
32860 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32893 TTGACTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33102 original size:60 final size:62
Alignment explanation
Indices: 33029--33175 Score: 237
Period size: 60 Copynumber: 2.4 Consensus size: 62
33019 TGTAGAGTAT
* *
33029 ACTATTCAATTCTACAATTTTAATTTGTTAACGTTATTAACG-T-TATATTCAATTTTATTA
1 ACTATTCAATTCTACAATTTTAATTTGTTAACGTTATCAACGTTATATATTCAAATTTATTA
*
33089 ACTATTCAATTCTACAACTTTAATTTGTTAACGTTATCAACGTTATATATTCAAATTTATTA
1 ACTATTCAATTCTACAATTTTAATTTGTTAACGTTATCAACGTTATATATTCAAATTTATTA
*
33151 ACTATTCAATTCTA-TATTTTAATTT
1 ACTATTCAATTCTACAATTTTAATTT
33176 TTATGTTTAA
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
60 40 0.50
61 10 0.12
62 30 0.38
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (62 bp):
ACTATTCAATTCTACAATTTTAATTTGTTAACGTTATCAACGTTATATATTCAAATTTATTA
Found at i:33120 original size:30 final size:29
Alignment explanation
Indices: 33029--33120 Score: 73
Period size: 30 Copynumber: 3.1 Consensus size: 29
33019 TGTAGAGTAT
33029 ACTATTCAATTCTACAATTTTAATTTGTTA
1 ACTATTCAATTCTACAA-TTTAATTTGTTA
* * * *
33059 ACGTTATT-AACGT-TA-TATTCAATTTTATTA
1 AC--TATTCAA-TTCTACAATTTAA-TTTGTTA
33089 ACTATTCAATTCTACAACTTTAATTTGTTA
1 ACTATTCAATTCTACAA-TTTAATTTGTTA
33119 AC
1 AC
33121 GTTATCAACG
Statistics
Matches: 46, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
28 5 0.11
29 8 0.17
30 20 0.43
31 8 0.17
32 5 0.11
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.48
Consensus pattern (29 bp):
ACTATTCAATTCTACAATTTAATTTGTTA
Found at i:33208 original size:62 final size:62
Alignment explanation
Indices: 33029--33213 Score: 206
Period size: 60 Copynumber: 3.0 Consensus size: 62
33019 TGTAGAGTAT
*
33029 ACTATTCAATTCTACAATTTTAATTTGTTAACGTTA--TTAACGTTA-TATTCAATTTTATTA
1 ACTATTCAATTCTACAACTTTAATTTGTTAACGTTATCTTAACGTTATTATTCAA-TTTATTA
33089 ACTATTCAATTCTACAACTTTAATTTGTTAACGTTATC--AACGTTATATATTCAAATTTATTA
1 ACTATTCAATTCTACAACTTTAATTTGTTAACGTTATCTTAACGTTAT-TATTC-AATTTATTA
* * * * *
33151 ACTATTCAATTCTA-TATTTTAATTT-TT-ATGTTTAATTCTTAACATTATTATTCAATTTTTTA
1 ACTATTCAATTCTACAACTTTAATTTGTTAACG-TT-A-TCTTAACGTTATTATTCAATTTATTA
33213 A
1 A
33214 ATATGATTAT
Statistics
Matches: 109, Mismatches: 6, Indels: 18
0.82 0.05 0.14
Matches are distributed among these distances:
59 2 0.02
60 46 0.42
61 10 0.09
62 37 0.34
63 7 0.06
64 7 0.06
ACGTcount: A:0.34, C:0.12, G:0.04, T:0.51
Consensus pattern (62 bp):
ACTATTCAATTCTACAACTTTAATTTGTTAACGTTATCTTAACGTTATTATTCAATTTATTA
Found at i:33936 original size:43 final size:44
Alignment explanation
Indices: 33846--33947 Score: 120
Period size: 43 Copynumber: 2.3 Consensus size: 44
33836 TCACAATTTA
* * * *
33846 TATCACAATTTCATAGTTAGGTTATCAAAGTTTCATATGGAGTT
1 TATCACAATTTCATAGATAGATTATCAAAATTTCATAGGGAGTT
33890 TATCACAATTTCATAGATA-ATTATCAAAATTT-AGTAGGGTAG-T
1 TATCACAATTTCATAGATAGATTATCAAAATTTCA-TAGGG-AGTT
*
33933 TATCAAAATTTCATA
1 TATCACAATTTCATA
33948 AAAATATTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
42 1 0.02
43 30 0.59
44 20 0.39
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (44 bp):
TATCACAATTTCATAGATAGATTATCAAAATTTCATAGGGAGTT
Found at i:34013 original size:2 final size:2
Alignment explanation
Indices: 34006--34035 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33996 TTAAAACTAG
34006 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34036 A
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.