Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014513.1 Corchorus olitorius cultivar O-4 contig14546, 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: 49499
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:531 original size:30 final size:33
Alignment explanation
Indices: 491--563 Score: 80
Period size: 34 Copynumber: 2.3 Consensus size: 33
481 TTATATAATC
* * *
491 AAATTTATA-TTATGGAATAA-AA-AACTCTTT
1 AAATTAATATTTATCGAATAATAATAACTCTCT
*
521 AAATTAATATTTATCGATTAATTAATAACTCTCT
1 AAATTAATATTTATCGAATAA-TAATAACTCTCT
555 AAATTAATA
1 AAATTAATA
564 AATTTTCATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
30 8 0.23
31 9 0.26
33 2 0.06
34 16 0.46
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (33 bp):
AAATTAATATTTATCGAATAATAATAACTCTCT
Found at i:8582 original size:14 final size:15
Alignment explanation
Indices: 8565--8593 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
8555 AATAATATAT
8565 ATATATAT-TTAATA
1 ATATATATGTTAATA
8579 ATATATATGTTAATA
1 ATATATATGTTAATA
8594 TTTAAATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATATATATGTTAATA
Found at i:8598 original size:22 final size:20
Alignment explanation
Indices: 8544--8586 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
8534 AATGAGTACC
*
8544 TATATATTTTTAATAATATA
1 TATATATATTTAATAATATA
8564 TATATATATTTAATAATATA
1 TATATATATTTAATAATATA
8584 TAT
1 TAT
8587 GTTAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATATATTTAATAATATA
Found at i:40367 original size:31 final size:32
Alignment explanation
Indices: 40324--40388 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
40314 AAAAAAATAA
*
40324 AATTTGGCTCTATCATTATTG-AGTCGAACTC
1 AATTAGGCTCTATCATTATTGTAGTCGAACTC
*
40355 AATTAGGCTCTATCATTATTGTCGTCGAACTC
1 AATTAGGCTCTATCATTATTGTAGTCGAACTC
40387 AA
1 AA
40389 ACTCGAGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 20 0.65
32 11 0.35
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (32 bp):
AATTAGGCTCTATCATTATTGTAGTCGAACTC
Found at i:44611 original size:25 final size:24
Alignment explanation
Indices: 44581--44642 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
44571 GTGGATTGTA
*
44581 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
44606 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
44630 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
44643 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:47973 original size:206 final size:206
Alignment explanation
Indices: 47619--48032 Score: 776
Period size: 206 Copynumber: 2.0 Consensus size: 206
47609 AGAGAAGCTC
47619 ATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACTCTTTAAATGTTGAGGCCT
1 ATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACTCTTTAAATGTTGAGGCCT
* *
47684 CCAAATCTTGACACGTGTCTCTAATTAATTCTAATATTCATTATATTAATATATTTATTAGAAAA
66 CCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTAATATATTGATTAGAAAA
*
47749 AAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTTTAA-ATTTTAATTA
131 AAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAA-TATTTAAGATTTTAATTA
47813 AAAAATAAAGAA
195 AAAAATAAAGAA
47825 ATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACTCTTTAAATGTTGAGGCCT
1 ATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACTCTTTAAATGTTGAGGCCT
*
47890 CCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTGATATATTGATTAGAAAA
66 CCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTAATATATTGATTAGAAAA
47955 AAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATATTTAAGATTTTAATTAA
131 AAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATATTTAAGATTTTAATTAA
48020 AAAATAAAGAA
196 AAAATAAAGAA
48031 AT
1 AT
48033 TAATAATGAA
Statistics
Matches: 203, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
205 6 0.03
206 197 0.97
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (206 bp):
ATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACTCTTTAAATGTTGAGGCCT
CCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTAATATATTGATTAGAAAA
AAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATATTTAAGATTTTAATTAA
AAAATAAAGAA
Done.