Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020109.1 Corchorus olitorius cultivar O-4 contig20142, 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: 21199
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:1854 original size:223 final size:218
Alignment explanation
Indices: 1458--1898 Score: 697
Period size: 223 Copynumber: 2.0 Consensus size: 218
1448 TACATTCATA
*
1458 GCACCAATCCTTTGGAATTCCGAAAGAGGAGTCGAACCGGTAAATCCTAATTTCCACACACAATT
1 GCACCAATCCTTTGGAATTCCGAAAGAGGAGTCGAACCGGTAAATCCTAATATCCACACACAATT
*
1523 AATATTTAATTAAAACACATTTAATCATAAATATTAGTCAACTTAGCTTAAAATTACTTTCAAAA
66 AATATGTAATTAAAACACATTTAATCATAAATATTAGTCAACTTAGCTTAAAATTACTTTCAAAA
* * * *
1588 CCAAACACACCCAATACTCACTATAACAATCATAAGGATTATTGGGTATTGGTAATTAACCAAGT
131 CCAAACACACCCAATACACACTACAACAATCATAAGAATTATT--G----GGTAATTAACCAAGC
*
1653 GAGAAAAGACGAAAA-GGGGCGAAAAGGT
190 GAAAAAAGACGAAAAGGGGGCGAAAAGGT
* **
1681 GCACCAATCCTTTGGAATTCTGGCAGAGGAGTCGAACCGGTAAATCCTAATATCCACACACAATT
1 GCACCAATCCTTTGGAATTCCGAAAGAGGAGTCGAACCGGTAAATCCTAATATCCACACACAATT
1746 AATATGTAATTAAAACACATTTAATCATAAATATTAGTCAACTTAGCTTAAAATTACTTTCAAAA
66 AATATGTAATTAAAACACATTTAATCATAAATATTAGTCAACTTAGCTTAAAATTACTTTCAAAA
*
1811 CCAAACACACCCAATACACACTACAACAATTATACA-AATTATTGGGTAATTAACCAAGCGAAAA
131 CCAAACACACCCAATACACACTACAACAATCATA-AGAATTATTGGGTAATTAACCAAGCGAAAA
*
1875 AAGATGAAAAGGGGGCGAAAAGGT
195 AAGACGAAAAGGGGGCGAAAAGGT
1899 TGATCCTCAT
Statistics
Matches: 204, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
217 27 0.13
218 13 0.06
221 1 0.00
223 162 0.79
224 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (218 bp):
GCACCAATCCTTTGGAATTCCGAAAGAGGAGTCGAACCGGTAAATCCTAATATCCACACACAATT
AATATGTAATTAAAACACATTTAATCATAAATATTAGTCAACTTAGCTTAAAATTACTTTCAAAA
CCAAACACACCCAATACACACTACAACAATCATAAGAATTATTGGGTAATTAACCAAGCGAAAAA
AGACGAAAAGGGGGCGAAAAGGT
Found at i:2575 original size:168 final size:172
Alignment explanation
Indices: 2376--2718 Score: 613
Period size: 173 Copynumber: 2.0 Consensus size: 172
2366 ATCATTTTTT
*
2376 TTTCATTGTTGTTAGAGTTTCCTACATGCATATTTAGGACTCA-TTT-T-CATGTTTGTACATTA
1 TTTCATTGTTGTTAGAGTTTCCGACATGCATATTTAGGACTCATTTTATGCATGTTTGTACATTA
2438 AGAGAAACAATTAATGTT-TTTTTAATTTAATTTTTCTTATATAATCCCATTATTTCTTAATTTT
66 AGAGAAACAATTAATGTTCTTTTTAATTTAATTTTTCTTATATAATCCCATTATTTCTTAATTTT
2502 GATTTCGATAACCTTAGAAATTATTCTTTGTATTCGCAATGA
131 GATTTCGATAACCTTAGAAATTATTCTTTGTATTCGCAATGA
2544 TTTCATTGTTGTTAGAGTTTCCGACATGCATATTTAGGACTCATTTTCATGCATGTTTGTACATT
1 TTTCATTGTTGTTAGAGTTTCCGACATGCATATTTAGGACTCATTTT-ATGCATGTTTGTACATT
*
2609 AAGAGAAACAATTAATGTTCTTTTTAATTTAATTTTTCTTTTATAATCCCATTATTTCTTAATTT
65 AAGAGAAACAATTAATGTTCTTTTTAATTTAATTTTTCTTATATAATCCCATTATTTCTTAATTT
* *
2674 TGATTTTGATAACCTTGGAAATTATTCTTTGTATTCGCAATGA
130 TGATTTCGATAACCTTAGAAATTATTCTTTGTATTCGCAATGA
2717 TT
1 TT
2719 ACAAGTATAT
Statistics
Matches: 166, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
168 42 0.25
169 3 0.02
171 1 0.01
172 33 0.20
173 87 0.52
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (172 bp):
TTTCATTGTTGTTAGAGTTTCCGACATGCATATTTAGGACTCATTTTATGCATGTTTGTACATTA
AGAGAAACAATTAATGTTCTTTTTAATTTAATTTTTCTTATATAATCCCATTATTTCTTAATTTT
GATTTCGATAACCTTAGAAATTATTCTTTGTATTCGCAATGA
Found at i:5150 original size:13 final size:14
Alignment explanation
Indices: 5129--5166 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
5119 CCCAAAAATA
5129 ATTTAATAAAAAAC
1 ATTTAATAAAAAAC
*
5143 ATTT-ATAAAACAC
1 ATTTAATAAAAAAC
5156 -TTTAATAAAAA
1 ATTTAATAAAAA
5167 CAATAATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 3 0.14
13 14 0.67
14 4 0.19
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (14 bp):
ATTTAATAAAAAAC
Found at i:5168 original size:14 final size:15
Alignment explanation
Indices: 5129--5168 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
5119 CCCAAAAATA
5129 ATTTAATAAAAA-AC
1 ATTTAATAAAAACAC
5143 ATTT-AT-AAAACAC
1 ATTTAATAAAAACAC
5156 -TTTAATAAAAACA
1 ATTTAATAAAAACA
5169 ATAATGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 7 0.30
13 6 0.26
14 10 0.43
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTTAATAAAAACAC
Found at i:8684 original size:42 final size:43
Alignment explanation
Indices: 8633--8726 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
8623 AGTGCATTAT
*
8633 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
8674 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
8719 CTAATATT
1 CTAATATT
8727 AATTGTTGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:10114 original size:25 final size:25
Alignment explanation
Indices: 10065--10114 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
10055 ATTAATAAGT
* **
10065 CAAACAAATTAATTAATGATTTCTC
1 CAAACAAATTAATTAATAAAGTCTC
*
10090 CAAACAAATTAATTGATAAAGTCTC
1 CAAACAAATTAATTAATAAAGTCTC
10115 TACTTTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.32
Consensus pattern (25 bp):
CAAACAAATTAATTAATAAAGTCTC
Found at i:12325 original size:26 final size:26
Alignment explanation
Indices: 12264--12330 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
12254 ATTTGATATG
*
12264 TGAAAGGTTACTAAAATTTGTAAGAA
1 TGAAAGGTTACTAAAATTTCTAAGAA
*
12290 TGAAAAGTTACTGAAAA-TTCTAAGAA
1 TGAAAGGTTACT-AAAATTTCTAAGAA
**
12316 TGTGAGGTTACTAAA
1 TGAAAGGTTACTAAA
12331 TTTATGTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 3 0.09
26 28 0.80
27 4 0.11
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.30
Consensus pattern (26 bp):
TGAAAGGTTACTAAAATTTCTAAGAA
Found at i:13874 original size:16 final size:16
Alignment explanation
Indices: 13855--13896 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
13845 ACCCGCCCGA
*
13855 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
*
13871 ACCCGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
13887 ACCCGAACCC
1 ACCCGAACCC
13897 AAGGCAGCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.43, G:0.14, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:14160 original size:2 final size:2
Alignment explanation
Indices: 14119--14151 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14109 AAACTACTAA
14119 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14152 ACTTATATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14800 original size:16 final size:16
Alignment explanation
Indices: 14775--14897 Score: 160
Period size: 16 Copynumber: 7.8 Consensus size: 16
14765 CCGACCCGAG
14775 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
14791 CCCGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
**
14807 CCCGAACCCG-ACTTAA
1 CCCGAACCCGAAAAT-A
*
14823 CCCGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
*
14839 CCCAAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
14855 CCCAAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
14871 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
14886 CCCGAACCCGAA
1 CCCGAACCCGAA
14898 CCCGCCCGAG
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
15 16 0.17
16 75 0.81
17 2 0.02
ACGTcount: A:0.40, C:0.40, G:0.14, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:16151 original size:21 final size:21
Alignment explanation
Indices: 16122--16170 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
16112 TAGAAGTTTA
16122 ACAAGTTACTAAAATACTTAAT
1 ACAA-TTACTAAAATACTTAAT
* *
16144 ACAATTACTAAATTGCTTAAT
1 ACAATTACTAAAATACTTAAT
16165 A-AATTA
1 ACAATTA
16171 TAGATAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.20
21 16 0.64
22 4 0.16
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (21 bp):
ACAATTACTAAAATACTTAAT
Done.