Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024483.1 Corchorus olitorius cultivar O-4 contig24516, 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: 19352
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1078 original size:204 final size:199
Alignment explanation
Indices: 695--1102 Score: 699
Period size: 200 Copynumber: 2.0 Consensus size: 199
685 GCTTAATAAC
* *
695 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTATTAACAAAGTTGTAGTAAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGCAGTAAATAA
*
760 GATACAACACATTATTATCATATATAAAACTATCCAAAAAAAGTAGTTGAACATTAGTGGTTGAT
66 GATACAACACATTACTATCATATATAAAACTATCCAAAAAAAGTAGTTGAACATTAGTGGTTGAT
*
825 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCG
131 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCCA
890 ATTTA
195 ATTTA
*
895 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGCAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGCAGTAAATAA
* * *
960 GATACTACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATCATATATA-A-AACTAT-CC-AAAAAAAGTAGTTGAACATTAGTGGT
1025 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
127 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
1090 CCAATTTA
192 CCAATTTA
1098 TTTAT
1 TTTAT
1103 TATTAAGGAA
Statistics
Matches: 196, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
200 85 0.43
201 1 0.01
202 6 0.03
203 19 0.10
204 85 0.43
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (199 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGCAGTAAATAA
GATACAACACATTACTATCATATATAAAACTATCCAAAAAAAGTAGTTGAACATTAGTGGTTGAT
TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCAA
TTTA
Found at i:1265 original size:39 final size:40
Alignment explanation
Indices: 1211--1290 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
1201 TACCTAAGAC
*
1211 TTTAATTAATGTAAGTATTTCAGTTATTATA-CTATTACA
1 TTTAATTAATGTAAGTATTTCAGTTATTATATATATTACA
*
1250 TTTAATTAATGTAAGTATTTTAGTTATTATATATATTACA
1 TTTAATTAATGTAAGTATTTCAGTTATTATATATATTACA
1290 T
1 T
1291 AGGAATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.51
Consensus pattern (40 bp):
TTTAATTAATGTAAGTATTTCAGTTATTATATATATTACA
Found at i:8108 original size:20 final size:20
Alignment explanation
Indices: 8071--8109 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
8061 CGACTTGAGA
*
8071 AAAATTCGAGTTCGGCTCGG
1 AAAATTCGAGTCCGGCTCGG
8091 AAAATTCGAG-CCGAGCTCG
1 AAAATTCGAGTCCG-GCTCG
8110 AGCCATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (20 bp):
AAAATTCGAGTCCGGCTCGG
Found at i:8966 original size:26 final size:26
Alignment explanation
Indices: 8930--8987 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
8920 TTTCAGTCGA
8930 GCTCGAGTATTGAGATGTTCGGCTCG
1 GCTCGAGTATTGAGATGTTCGGCTCG
8956 GCTCGAGTATTGAGATGTTCGGCTCG
1 GCTCGAGTATTGAGATGTTCGGCTCG
*
8982 ACTCGA
1 GCTCGA
8988 CTCGGTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.17, C:0.21, G:0.33, T:0.29
Consensus pattern (26 bp):
GCTCGAGTATTGAGATGTTCGGCTCG
Found at i:9903 original size:17 final size:17
Alignment explanation
Indices: 9867--9921 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
9857 ATCACCACCC
*
9867 AGATCACTAGTGATCTA
1 AGATCACCAGTGATCTA
9884 AGATCACCAGTGATGC-A
1 AGATCACCAGTGAT-CTA
* * *
9901 AGATTACCGGTGATCAA
1 AGATCACCAGTGATCTA
9918 AGAT
1 AGAT
9922 TACATGGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (17 bp):
AGATCACCAGTGATCTA
Found at i:19334 original size:2 final size:2
Alignment explanation
Indices: 19327--19352 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19317 ATGATAAAGA
19327 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.