Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009245.1 Corchorus olitorius cultivar O-4 contig09273, 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: 1815
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:974 original size:322 final size:315
Alignment explanation
Indices: 18--1148 Score: 1079
Period size: 330 Copynumber: 3.5 Consensus size: 315
8 TAAATATAGA
*** * *
18 TTTTGATTTAATTAGAAATAAATTC-TTTAAAAAATTGAAAAACGATATTAGAAGCTTGTAAAAC
1 TTTTGATTTAATTAGAAATAAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGCGTG-AAAAC
* * * *
82 CCTTCAATATTTTTAGCGTTGAATTATATAATTTTGTGAGTATTTTGGAAAAAAAATTGAGAAAA
65 CCTTCAATATTTTTGGCATTGAATTATATATTTTTCTGAGTA-TTT-GAAAAAAAATTGAG-AAA
* * * *
147 AATTTCTTCGTGTCAGTTTTTAGCCGAAATCGTTTACTAACCATCACGGTTTTTTGGTAAAAACG
127 AATAT-TTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTTGCTAAAAACG
* *
212 CGTTTTAGGGCCCCGACTCAGTTTTGCATGATTTCTTGCAGAAAGGCTCCTTGAAATATCTATAT
190 CG-TTTCGGGCCCCGACTCAGTTTTGCATGATTT-TTGCAGAAAGACTCCTTGAAATATCTATAT
* * *
277 TCATCTAACCAAATCTCAGCCACAATGGATCTAAGGATTGGTATATACGAGCATCTGAATCTTG
253 TCATCTAACCAAATCTCAGCCACAATGGATATAAGGATT-GTTTTTACGAGCATCTGAATCTTG
* *
341 TTTTGATTTAATTAGAAATAAATTC--TAAAAAAATGGAAAAACGATATTAGAAGCTTGAAAACC
1 TTTTGATTTAATTAGAAATAAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAACC
* **
404 CTTCAATATTTTTGGCATTGAATTACATATTTTTTCTGAGTATTCTGGTAAAAAATTGAGGAAAA
66 CTTCAATATTTTTGGCATTGAATTATATA-TTTTTCTGAGTATT-TGAAAAAAAATTGA-GAAAA
* * * * *
469 A-ATTTTCGGCTCATTTTCTGAAAAATTTTAGCCGAAATCGTGCATTAACCATCACGATTTTTGG
128 ATA-TTTCGGGTCA------G----TTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT-G
** * * * * * * *
533 CTAAAAACGCGTTTCGGAGTGCGGGCTCAATTTTGCAGGATTATTGGCACAAAAACTCCTTGAAA
181 CTAAAAACGCGTTTCGG-GCCCCGACTCAGTTTTGCATGATT-TTTGCAGAAAGACTCCTTGAAA
* * * * ** *
598 TATCTTTATTCATCGAACCAAATGTCAGCCACATTGGATATAAAAATTTGTTTTTACGACCATCT
244 TATCTATATTCATCTAACCAAATCTCAGCCACAATGGATATAAGGA-TTGTTTTTACGAGCATCT
*
663 CAATCTTG
308 GAATCTTG
* * *
671 TTTTGATTTAATTAGAAATTAATTC-GGAAACAAATGGAAAAACGATATTAGAAACGTGAAAAGC
1 TTTTGATTTAATTAGAAATAAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA-C
* * * * * * * * *
735 CCGTCAATCTTTGTGGCATTGAATTATATATTTATTCTAAATATTTCACAAAAGATTGAGTAAAA
65 CCTTCAATATTTTTGGCATTGAATTATATATTT-TTCTGAGTATTTGAAAAAAAATTGAGAAAAA
* *
800 TCATTTCGGGTCAGTTTTTAGCGGAAATCGTGTACCTAACTATCACGGTTTTCTGCTAAAAACGC
129 T-ATTTCGGGTCAGTTTTTAGCCGAAATCGTGTA-CTAACCATCACGGTTTT-TGCTAAAAACGC
*
865 GTTTCGGGCCCCGACTCAGTTTTGCATGAATTTTTGACAGAAAGACTCCTTAAAATATCTATATT
191 GTTTCGGGCCCCGACTCAGTTTTGCATG-ATTTTTG-CAGAAAGACTCCTTGAAATATCTATATT
* * * * * *
930 CAAT-TAACTAAATTTAAGCCTCAATGGATTTAAGGATATGTTTTTACGAGCATCTGATTCTTG
254 C-ATCTAACCAAATCTCAGCCACAATGGATATAAGGAT-TGTTTTTACGAGCATCTGAATCTTG
* * *
993 TTTCGATTTAATTAATTAGAAATAAATTCGGGGGAAAAAAAAGGAAAAACGATATTAGAAGTGTG
1 TTTTGA--T--TTAATTAGAAATAAATTC--GGGAAAAAAATGGAAAAACGATATTAGAAGCGTG
* * * * * ** **
1058 AAAAACCCATCAAT-TCTTTTGACGTCGAATTATATATTTTTTATGAGTATTGTGGCAATGAATT
60 -AAAACCCTTCAATAT-TTTTGGCATTGAATTATATA-TTTTTCTGAGTATT-TGAAAAAAAATT
*
1122 GAGGAAAAAAATTTCGGGTCAGTTTTT
121 GA-GAAAAATATTTCGGGTCAGTTTTT
1149 GCAAAATTTT
Statistics
Matches: 660, Mismatches: 107, Indels: 75
0.78 0.13 0.09
Matches are distributed among these distances:
320 7 0.01
321 87 0.13
322 152 0.23
323 28 0.04
324 1 0.00
325 1 0.00
326 18 0.03
328 1 0.00
329 71 0.11
330 195 0.30
331 62 0.09
332 37 0.06
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (315 bp):
TTTTGATTTAATTAGAAATAAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAACC
CTTCAATATTTTTGGCATTGAATTATATATTTTTCTGAGTATTTGAAAAAAAATTGAGAAAAATA
TTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGCTAAAAACGCGTTTC
GGGCCCCGACTCAGTTTTGCATGATTTTTGCAGAAAGACTCCTTGAAATATCTATATTCATCTAA
CCAAATCTCAGCCACAATGGATATAAGGATTGTTTTTACGAGCATCTGAATCTTG
Found at i:1352 original size:198 final size:200
Alignment explanation
Indices: 1003--1373 Score: 489
Period size: 198 Copynumber: 1.9 Consensus size: 200
993 TTTCGATTTA
* * *
1003 ATTAATTAGAAATAAATTCGGGGGAAAAAAAAGGAAAAACGATATTAGAAGTGTGAAAAACCCAT
1 ATTAATTAGAAATAAATTC-GGGGAAAAAAAACGAAAAACGATAATAGAAGCGTGAAAAACCCAT
* * **
1068 CAATTCTTTTGACGTCGAATTATATATTTTTTATGAGTATTGTGGCAATGAATTGAGGAAAAAAA
65 CAATTCTTTTGACGTCGAATTAAATATTTTTTATGAGTATTCTGGCAAAAAATTGAGGAAAAAAA
* * *
1133 TTTCGGGTCAGTTTTTGCAAAATTTTAGTCAAAATCGTTTACTCATCATGGTTTTCTGAATCTTG
130 TTTCGGGTCAGTTTTTGCAAAAGTTTAGCCAAAATCGTATACTCATCATGGTTTTCTGAATCTTG
1198 TTTCGT
195 TTTCGT
* *
1204 ATTAATTAGAAATAAATTC-GGG-TAAAAAACGAAAAACGATAATAGAAGCGTGAAAAACCCTTC
1 ATTAATTAGAAATAAATTCGGGGAAAAAAAACGAAAAACGATAATAGAAGCGTGAAAAACCCATC
* * * * **
1267 CATTTTTTTG-GGTCGAATTAAATATTTTTTCTGAGTATTCTGTTAAAAAATTGA-GAACAAAAT
66 AATTCTTTTGACGTCGAATTAAATATTTTTTATGAGTATTCTGGCAAAAAATTGAGGAA-AAAA-
* * * *
1330 TTTTTGGGTCATTTTTTGCAAAAGTTTAGCCGAAATCGTATACT
129 ATTTCGGGTCAGTTTTTGCAAAAGTTTAGCCAAAATCGTATACT
1374 AACCATCACA
Statistics
Matches: 146, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
196 3 0.02
197 40 0.27
198 81 0.55
199 3 0.02
201 19 0.13
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (200 bp):
ATTAATTAGAAATAAATTCGGGGAAAAAAAACGAAAAACGATAATAGAAGCGTGAAAAACCCATC
AATTCTTTTGACGTCGAATTAAATATTTTTTATGAGTATTCTGGCAAAAAATTGAGGAAAAAAAT
TTCGGGTCAGTTTTTGCAAAAGTTTAGCCAAAATCGTATACTCATCATGGTTTTCTGAATCTTGT
TTCGT
Done.