Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022593.1 Corchorus olitorius cultivar O-4 contig22626, 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: 12344
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Found at i:1047 original size:294 final size:292
Alignment explanation
Indices: 517--1100 Score: 915
Period size: 294 Copynumber: 2.0 Consensus size: 292
507 AATCTTGATT
*
517 GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACTAATCCTTTGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACCAATCCTTTGGAATTCCGGCA
**
582 GAGGAGTTGAACTGATAAATCCTAATATCCACACACAATCAATATGTAATTAAAACACACTTAAT
66 GAGGAGTTGAACTGATAAATCCTAATATCCACACACAATCAATACATAATTAAAACACACTTAAT
* *
647 CATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTGAGGGAGAAAATTCATCG
131 CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGAAAATTCATCG
*
712 AAGGCCTTTTTAGTCATCCAAAAAGTGAGAAAAGACAAAAAAAGGACAAAAGGAAGCACCACATT
196 AAGGCCTTTTTAGTCACCCAAAAAGTGAGAAAAGACAAAAAAA-GACAAAAGGAAGCACCACATT
* *
777 AATTCTCAATTTGGCCTTTTAGTTAATTTCCAAA
260 AATCCTCAATTTGGCCTTTAAG-TAATTTCCAAA
* * *
811 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACCAATCCTTTGGAATTCCGGCA
* *
876 GAGGAGTTGAA-TCGGTAAATCCTAATATCCACACACAATTAATACATAATTAAAACACACTTAA
66 GAGGAGTTGAACT-GATAAATCCTAATATCCACACACAATCAATACATAATTAAAACACACTTAA
* * *
940 TCATAAATACAAAAATATTAAATTACAAAAAA-GGCAGGAGGAAAAGTAAGGGATG-AAATTTAT
130 TCATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGA-GAAAATTCAT
* * *
1003 C-AAGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCAC
194 CGAA-GGCCTTTTTAGTCACCCAAAAAGTGAGAAAAGA-CAAAAAAAGACAAAAGGAAGCACCAC
1067 ATTAATCCTCAATTTGGCCTTTAAGTAATTTCCA
257 ATTAATCCTCAATTTGGCCTTTAAGTAATTTCCA
1101 TATTCACTAA
Statistics
Matches: 267, Mismatches: 19, Indels: 10
0.90 0.06 0.03
Matches are distributed among these distances:
292 11 0.04
293 98 0.37
294 158 0.59
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (292 bp):
GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACCAATCCTTTGGAATTCCGGCA
GAGGAGTTGAACTGATAAATCCTAATATCCACACACAATCAATACATAATTAAAACACACTTAAT
CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGAAAATTCATCG
AAGGCCTTTTTAGTCACCCAAAAAGTGAGAAAAGACAAAAAAAGACAAAAGGAAGCACCACATTA
ATCCTCAATTTGGCCTTTAAGTAATTTCCAAA
Found at i:6278 original size:20 final size:20
Alignment explanation
Indices: 6255--6298 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
6245 ACATATAACA
6255 TTTTT-ATAACTTATTTAGC
1 TTTTTGATAACTTATTTAGC
6274 TTTTTGATAACTTATTTAGC
1 TTTTTGATAACTTATTTAGC
6294 TTTTT
1 TTTTT
6299 CAATATTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTTTGATAACTTATTTAGC
Found at i:10172 original size:2 final size:2
Alignment explanation
Indices: 10165--10206 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
10155 GTTATAGTCA
10165 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10204 AT A
1 AT A
10207 ACATAACATA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:10407 original size:89 final size:89
Alignment explanation
Indices: 10254--10522 Score: 475
Period size: 89 Copynumber: 3.0 Consensus size: 89
10244 GAATTATCCT
* * *
10254 TTTGTCGAGTTATAAGATACAACACATTCACCGAAGAACAAATTGTTAGGGGTATTTCGTTACTT
1 TTTGTCGAGCTATAAGATACACCACATTCACCGAAGAACAAATTGTTAGGGGTATTTCGGTACTT
*
10319 TCATGTTCGGTATTTTTGTTATTA
66 TCATGCTCGGTATTTTTGTTATTA
*
10343 TTTGTCGAGCTATAAGATACACCACATTCACCGAAGAACAAATTGTTAGGGGCATTTCGGTACTT
1 TTTGTCGAGCTATAAGATACACCACATTCACCGAAGAACAAATTGTTAGGGGTATTTCGGTACTT
*
10408 TCATGCTCGATATTTTTGTTATTA
66 TCATGCTCGGTATTTTTGTTATTA
10432 TTTGTCGAGCTATAAGATACACCACATTCACCGAAGAACAAATTGTTAGGGGTATTTCGGTACTT
1 TTTGTCGAGCTATAAGATACACCACATTCACCGAAGAACAAATTGTTAGGGGTATTTCGGTACTT
*
10497 TCATGCTCGGTATTTTTATTATTA
66 TCATGCTCGGTATTTTTGTTATTA
10521 TT
1 TT
10523 GTTGATTGTT
Statistics
Matches: 171, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 171 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (89 bp):
TTTGTCGAGCTATAAGATACACCACATTCACCGAAGAACAAATTGTTAGGGGTATTTCGGTACTT
TCATGCTCGGTATTTTTGTTATTA
Found at i:12078 original size:127 final size:130
Alignment explanation
Indices: 11876--12135 Score: 391
Period size: 127 Copynumber: 2.0 Consensus size: 130
11866 GCCATTAGAC
11876 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* * * * *
11941 TTTAATTTTTACCATTTTACTATTTTAATT-AAAAACTT-ATATATTAGAATTTTTTAAATATAT
66 TTTAATTTTTACCAATTTAATAATTTAATTAAAAAACTTAATATATTAGAAATTTTAAAATATAT
* * * *
12004 TTTTATAGTTTTACTCAACTAAAAACTCT-TTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* *
12068 TTTTATTTTTATCAATTTAATAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
66 TTTAATTTTTACCAATTTAATAATTTAATTAAAAAACTTA-ATATATTAGAAATTTTAAAATATA
12133 T
130 T
12134 TT
1 TT
12136 CTTAAATGAC
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
127 56 0.47
128 37 0.31
130 25 0.21
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (130 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
TTTAATTTTTACCAATTTAATAATTTAATTAAAAAACTTAATATATTAGAAATTTTAAAATATAT
Done.