Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020046.1 Corchorus olitorius cultivar O-4 contig20079, 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: 20868
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:2650 original size:93 final size:93
Alignment explanation
Indices: 2541--2727 Score: 329
Period size: 93 Copynumber: 2.0 Consensus size: 93
2531 GCTTTTTAAT
* *
2541 TAAATTAGTAATATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
* *
2606 AGTTTTTAGTTGAGTAAAACTATGAAAG
66 AGTTTTTAGTTGACTAAAACTATAAAAG
*
2634 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
2699 AGTTTTTAGTTGACTAAAACTATAAAAG
66 AGTTTTTAGTTGACTAAAACTATAAAAG
2727 T
1 T
2728 TTAAACAATG
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (93 bp):
TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:4291 original size:19 final size:19
Alignment explanation
Indices: 4267--4309 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
4257 TCGGAAGAGC
4267 CAAGGTAGAGGACATTGGT
1 CAAGGTAGAGGACATTGGT
*
4286 CAAGGTAGAGGACGTTGGT
1 CAAGGTAGAGGACATTGGT
4305 CAAGG
1 CAAGG
4310 AGGACCGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.12, G:0.40, T:0.19
Consensus pattern (19 bp):
CAAGGTAGAGGACATTGGT
Found at i:9981 original size:19 final size:19
Alignment explanation
Indices: 9941--9977 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9931 AATTTTTAAG
9941 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
9960 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
9978 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:12091 original size:222 final size:225
Alignment explanation
Indices: 11699--12144 Score: 702
Period size: 222 Copynumber: 2.0 Consensus size: 225
11689 ATTTTATCTT
* *
11699 AGCAATCAAGTTAAATGAAAGGAAATATTGTAAGAATTATAATGTCTATTGAAATAATTATCTAC
1 AGCAATCAAGTTAAATGAAAGGAAATATTCTAAGAATTATAATGTCTATTCAAATAA-TATCTA-
11764 TTTTAACAAAAAAAATAATCATCTATTGAAAAAAAGAAATGAAGTTTTACTTTGATTATAATTCA
64 -TTTAACAAAAAAAATAATCATCTATTGAAAAAAAGAAATGAAGTTTTACTTTGATTATAATTCA
*
11829 ATGTTGTGAAATATTATTTGAAATTCTAAATATATAATAATATATATTGGTTTTCTTTCAACCAA
128 ATGTTGTAAAATATTATTTGAAATTCTAAATATATAATAATATATATTGGTTTTCTTTCAACCAA
*
11894 TCAACTTTTGACAAATGTCAGCATAAGAAGAGC
193 TCAACTTTAGACAAATGTCAGCATAAGAAGAGC
* *
11927 AGCAATCAAGTTAAATGGAAGGAAATATTCTTAGAATTATAATGTCTATTCAAAT-A-AT-TA-T
1 AGCAATCAAGTTAAATGAAAGGAAATATTCTAAGAATTATAATGTCTATTCAAATAATATCTATT
* * * * *
11988 TAACAAAAAAAATAATTATCTCTTGGAAAAAAAGATATGGAGTTTTACTTTGATTATATTTCAAT
66 TAACAAAAAAAATAATCATCTATT-GAAAAAAAGAAATGAAGTTTTACTTTGATTATAATTCAAT
*
12053 GTTGTAAAATATTATTTGAAATTCTAAATATATAATAATATATATTGGTTTTCTTTCAATCAATC
130 GTTGTAAAATATTATTTGAAATTCTAAATATATAATAATATATATTGGTTTTCTTTCAACCAATC
* *
12118 AACTTTAGACAAATGTTAGCATGAGAA
195 AACTTTAGACAAATGTCAGCATAAGAA
12145 AGGCAAATAC
Statistics
Matches: 203, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
221 23 0.11
222 124 0.61
224 2 0.01
225 2 0.01
227 1 0.00
228 51 0.25
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (225 bp):
AGCAATCAAGTTAAATGAAAGGAAATATTCTAAGAATTATAATGTCTATTCAAATAATATCTATT
TAACAAAAAAAATAATCATCTATTGAAAAAAAGAAATGAAGTTTTACTTTGATTATAATTCAATG
TTGTAAAATATTATTTGAAATTCTAAATATATAATAATATATATTGGTTTTCTTTCAACCAATCA
ACTTTAGACAAATGTCAGCATAAGAAGAGC
Found at i:16149 original size:18 final size:18
Alignment explanation
Indices: 16106--16142 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
16096 CTTGGACGGC
16106 GATGAAGAAGAAGATCGA
1 GATGAAGAAGAAGATCGA
16124 GATGAAGAAGAAGATCGA
1 GATGAAGAAGAAGATCGA
16142 G
1 G
16143 GAGAAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.35, T:0.11
Consensus pattern (18 bp):
GATGAAGAAGAAGATCGA
Found at i:17943 original size:25 final size:25
Alignment explanation
Indices: 17909--17965 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
17899 CCCCATGGTT
*
17909 CAATACAAAGCCCACACCTATGTGG
1 CAATACAAAGCCCACACCTACGTGG
17934 CAATACAAAGCCCACACCTACGTGG
1 CAATACAAAGCCCACACCTACGTGG
17959 CAATACA
1 CAATACA
17966 TTGGTGACCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.39, C:0.33, G:0.14, T:0.14
Consensus pattern (25 bp):
CAATACAAAGCCCACACCTACGTGG
Done.