Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012669.1 Corchorus olitorius cultivar O-4 contig12702, 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: 15090
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Found at i:683 original size:36 final size:36
Alignment explanation
Indices: 636--705 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
626 TTCAATAACC
* *
636 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
672 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
706 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:1554 original size:203 final size:200
Alignment explanation
Indices: 1216--1623 Score: 719
Period size: 203 Copynumber: 2.0 Consensus size: 200
1206 GCTTAATAAC
1216 TTTATCAATGGTGAATGTTATTAAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTAATAAG
1 TTTATCAATGGTGAATGTTATTAAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTAATAAG
* * * *
1281 ATACAACACATTATTATTATATATAAAACTATACCAAAAAAATTAGTTGAATATTAGTGGTTGAT
66 ATACAACACATTACTATTATATATAAAACTATACAAAAAAAATCAGTTGAACATTAGTGGTTGAT
*
1346 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGCTATTAAAGATCCG
131 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCG
1411 ATTTA
196 ATTTA
1416 TTTATCAATGGTGAATGTTATT-AATGTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATCAATGGTGAATGTTATTAAAT-TTTTAAGTCTAAGATTACTAACAAAGTTGTAGT-AATA
1480 AGATACAACACATTACTATTATATATATAGAACTATACAAAAAAAATCAGTTGAACATTAGTGGT
64 AGATACAACACATTACTATTATATATA-A-AACTATACAAAAAAAATCAGTTGAACATTAGTGGT
*
1545 TGATTTATTAAATTAAATTAGATCAATGTCAAACGAAATTTCAAAATTATAAAAGATATTAAAGA
127 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
1610 TCCGATTTA
192 TCCGATTTA
1619 TTTAT
1 TTTAT
1624 TATTAAGGAA
Statistics
Matches: 198, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
199 3 0.02
200 55 0.28
201 30 0.15
202 1 0.01
203 109 0.55
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (200 bp):
TTTATCAATGGTGAATGTTATTAAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTAATAAG
ATACAACACATTACTATTATATATAAAACTATACAAAAAAAATCAGTTGAACATTAGTGGTTGAT
TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCG
ATTTA
Found at i:1794 original size:39 final size:40
Alignment explanation
Indices: 1740--1820 Score: 155
Period size: 39 Copynumber: 2.0 Consensus size: 40
1730 CTACCTAAGA
1740 ATTTAATTAATGTAAGTATTTTAGTTATTATAT-TATTAC
1 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1779 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1819 AT
1 AT
1821 AGGAATTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 33 0.80
40 8 0.20
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
Found at i:4335 original size:24 final size:24
Alignment explanation
Indices: 4306--4351 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
4296 ACTCTCTTAA
*
4306 TTGACTAAATAGAAGCAAAAAAGT
1 TTGACTAAATAGAAGAAAAAAAGT
*
4330 TTGACTAAATTGAAGAAAAAAA
1 TTGACTAAATAGAAGAAAAAAA
4352 AGTAGAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.22
Consensus pattern (24 bp):
TTGACTAAATAGAAGAAAAAAAGT
Found at i:4818 original size:226 final size:227
Alignment explanation
Indices: 4423--4880 Score: 882
Period size: 226 Copynumber: 2.0 Consensus size: 227
4413 AAAATTAATT
4423 AAATACTCACCAACGTAACCAATTTCTCCTTTCCAATTTTTTCCTAAAAAAAACTTCAAAAGATT
1 AAATACTCACCAACGTAACCAATTTCTCCTTTCCAATTTTTTCCTAAAAAAAACTTCAAAAGATT
*
4488 TATGTAATTTTTTCTTTTAATATGTAAACGTTTTATGAATTACGAATTACCAATTTTTTTATATT
66 TATGTAATTTTTTCTTTTAATATGTAAACGTTTTATGAATTACAAATTACCAATTTTTTTATATT
4553 TATTAAAGTTAAATAAAAATTCCCCACCAATTAGTTAATTAAAAGTTTAAGAAGAAGTAAATTAC
131 TATTAAAGTTAAATAAAAATTCCCCACCAATTAGTTAATTAAAAGTTTAAGAAGAAGTAAATTAC
*
4618 TTATTAACAATTAAAATTAATAGGTTTTGATG
196 TTATTAACAATTAAAATTAACAGGTTTTGATG
4650 AAATACTCACCAACGTAACCAATTTCTCCTTTCCAATTTTTTCCT-AAAAAAACTTCAAAAGATT
1 AAATACTCACCAACGTAACCAATTTCTCCTTTCCAATTTTTTCCTAAAAAAAACTTCAAAAGATT
4714 TATGTAATTTTTTCTTTTAATATGTAAACGTTTTATGAATTACAAATTACCAATTTTTTTATATT
66 TATGTAATTTTTTCTTTTAATATGTAAACGTTTTATGAATTACAAATTACCAATTTTTTTATATT
*
4779 TATTAAAGTTAAATAAAAGTTCCCCACCAATTAGTTAATTAAAAGTTTAAGAAGAAGTAAATTAC
131 TATTAAAGTTAAATAAAAATTCCCCACCAATTAGTTAATTAAAAGTTTAAGAAGAAGTAAATTAC
4844 TTATTAACAATTAAAATTAACAGGTTTTGATG
196 TTATTAACAATTAAAATTAACAGGTTTTGATG
4876 AAATA
1 AAATA
4881 AAAATACATG
Statistics
Matches: 228, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
226 183 0.80
227 45 0.20
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.39
Consensus pattern (227 bp):
AAATACTCACCAACGTAACCAATTTCTCCTTTCCAATTTTTTCCTAAAAAAAACTTCAAAAGATT
TATGTAATTTTTTCTTTTAATATGTAAACGTTTTATGAATTACAAATTACCAATTTTTTTATATT
TATTAAAGTTAAATAAAAATTCCCCACCAATTAGTTAATTAAAAGTTTAAGAAGAAGTAAATTAC
TTATTAACAATTAAAATTAACAGGTTTTGATG
Found at i:12253 original size:62 final size:62
Alignment explanation
Indices: 12146--12265 Score: 188
Period size: 62 Copynumber: 1.9 Consensus size: 62
12136 ATAATATTGA
* * *
12146 AAGATAACTAAAATAGATTCCATTATATAGGAGAAGCATGGTAGGGTACAATTGGCCCTTGG
1 AAGATAACTAAAATAGATTCCATTATATAGGAGAAACATGATAGGGTACAATGGGCCCTTGG
*
12208 AAGATAACTTAAATAGATTCCATTATATAGG-GAAAACATGATAGGGTACAATGGGCCC
1 AAGATAACTAAAATAGATTCCATTATATAGGAG-AAACATGATAGGGTACAATGGGCCC
12266 GGGCCAATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 1 0.02
62 52 0.98
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (62 bp):
AAGATAACTAAAATAGATTCCATTATATAGGAGAAACATGATAGGGTACAATGGGCCCTTGG
Done.