Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2584
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: 9893
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Found at i:1175 original size:4 final size:4
Alignment explanation
Indices: 1166--1191 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1156 AATAAAAGGA
1166 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
1192 CCAAAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:4181 original size:218 final size:219
Alignment explanation
Indices: 3914--4451 Score: 900
Period size: 218 Copynumber: 2.5 Consensus size: 219
3904 TTTTTTTTAT
* *
3914 ATTCACTTGTCATATATTAATAATTTTATTTTTGAAATATATGTACCTTATAAATAATCAAACCC
1 ATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATATACCTTATAAATAATCAAACCC
*
3979 AAATTGAGAAAAGAAAACTTTATTT-CTAGGATTATCTAATGTTTAATATAACTGAAATCTTATA
66 AAATTGAGAAAAGAAAACTTTATTTACTAGGATTATCTAATGTATAATATAACTGAAATCTTAT-
*
4043 AAAAAATATACATTTAAGATTATTTTTTAGATTTTGTTTGAATAACTTAAATCTTTTTCTCATAT
130 AAAAAATATACATTTAAGATTACTTTTTAGATTTTGTTTGAATAACTTAAATCTTTTTCTCATAT
*
4108 GATTTTATGAAGAT-GTTTCCTTAA
195 AATTTTATGAAGATAGTTTCCTTAA
*
4132 ATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATATACCTTATAAAAAATCAAACCC
1 ATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATATACCTTATAAATAATCAAACCC
* * * *
4197 AAATTGAGAAAAGAAAACCTTATTTACTAGGATTATCTAGTGTATGATATAACTTAAATCTTATA
66 AAATTGAGAAAAGAAAACTTTATTTACTAGGATTATCTAATGTATAATATAACTGAAATCTTATA
** *
4262 AAAAATATATGTTTAAGATTACTTTTTAGATTTTGTTTGAATAACTTAAATCTTTTTTTCATATA
131 AAAAATATACATTTAAGATTACTTTTTAGATTTTGTTTGAATAACTTAAATCTTTTTCTCATATA
* *
4327 ATTTTATGAAGATAGTTTCTTTAC
196 ATTTTATGAAGATAGTTTCCTTAA
*
4351 ATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATATACCTTATAAATAATCAAACTC
1 ATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATATACCTTATAAATAATCAAACCC
*
4416 AAATTGAGAAAAGAAAACTCTATTTACTAGGATTAT
66 AAATTGAGAAAAGAAAACTTTATTTACTAGGATTAT
4452 TTAGTGTCTG
Statistics
Matches: 299, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
218 160 0.54
219 139 0.46
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.43
Consensus pattern (219 bp):
ATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATATACCTTATAAATAATCAAACCC
AAATTGAGAAAAGAAAACTTTATTTACTAGGATTATCTAATGTATAATATAACTGAAATCTTATA
AAAAATATACATTTAAGATTACTTTTTAGATTTTGTTTGAATAACTTAAATCTTTTTCTCATATA
ATTTTATGAAGATAGTTTCCTTAA
Found at i:4432 original size:437 final size:424
Alignment explanation
Indices: 3632--4451 Score: 1148
Period size: 437 Copynumber: 1.9 Consensus size: 424
3622 GGTAATATGT
* *
3632 TTTAAGATTATTATTTTAGATTTGTTTAAATAATTTAAATTTTTTTCTCAGATAAATTTATGAAG
1 TTTAAGATTATTATTTTAGATTTGTTTAAATAACTTAAATCTTTTTCTCAGATAAATTTATGAAG
* * * *
3697 ATGCTTCTTTACATTCACTTATTATATATTAATAGTTTTTATTTTTGAATATATGACCTTATAAA
66 ATGCTTCCTTAAATTCACTTATCATATATTAATAGATTTTATTTTTGAATATATGACCTTATAAA
* * * *
3762 AATCAAACCAAATTGAGAAAAGAAAACTCTATTTTATTAGGATTCTCTAGTATCTTTATATAACT
131 AATCAAACCAAATTGAGAAAAGAAAACTCTATTTTACTAGGATTATCTAGTATCATGATATAACT
* *
3827 TAAATTTTATAAAAAATATATATTTAAGATTATTTTTTAGATTTTATTTGAATAACTTAACTATT
196 TAAATCTTATAAAAAATATATATTTAAGATTACTTTTTAGATTTTATTTGAATAACTTAACTATT
* * * * * *
3892 TTTCTCAAGACCTTTTTTTTATATTCACTTGTCATATATTAATAATTTTATTTTTGAAATATATG
261 TTTCTAAAGACATTTTCTTTACATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATA
*
3957 TACCTTATAAATAATCAAACCCAAATTGAGAAAAGAAAACTTTATTT-CTAGGATTATCTAATGT
326 TACCTTATAAATAATCAAACCCAAATTGAGAAAAGAAAACTCTATTTACTAGGATTATCTAATGT
4021 TTAATATAACTGAAATCTTATAAAAAAATATACA
391 TTAATATAACTGAAATCTTATAAAAAAATATACA
* * * *
4055 TTTAAGATTATT-TTTTAGATTTTGTTTGAATAACTTAAATCTTTTTCTCATATGATTTTATGAA
1 TTTAAGATTATTATTTTAGA-TTTGTTTAAATAACTTAAATCTTTTTCTCAGATAAATTTATGAA
* *
4119 GATGTTTCCTTAAATTCACTTATCATATATTAATA-ATTTTATTTTTGAAATATATATACCTTAT
65 GATGCTTCCTTAAATTCACTTATCATATATTAATAGATTTTATTTTTG-AATATAT-GACCTTAT
*
4183 AAAAAATCAAACCCAAATTGAGAAAAGAAAAC-CT-TATTTACTAGGATTATCTAGTGT-ATGAT
128 -AAAAATCAAA-CCAAATTGAGAAAAGAAAACTCTAT-TTTACTAGGATTATCTAGTATCATGAT
* *
4245 ATAACTTAAATCTTATAAAAAATATATGTTTAAGATTACTTTTTAGATTTTGTTTGAATAACTTA
190 ATAACTTAAATCTTATAAAAAATATATATTTAAGATTACTTTTTAGATTTTATTTGAATAACTT-
* *
4310 AATCTTTTTTTCATATAATTTTATGAAGATAGTTTCTTTACATTCACTTATCATATATTAATAAT
254 AA-CTATTTTTC---TAA----A-G-ACAT--TTTCTTTACATTCACTTATCATATATTAATAAT
*
4375 TTTATTTTTGAAATATATATACCTTATAAATAATCAAACTCAAATTGAGAAAAGAAAACTCTATT
307 TTTATTTTTGAAATATATATACCTTATAAATAATCAAACCCAAATTGAGAAAAGAAAACTCTATT
4440 TACTAGGATTAT
372 TACTAGGATTAT
4452 TTAGTGTCTG
Statistics
Matches: 346, Mismatches: 31, Indels: 25
0.86 0.08 0.06
Matches are distributed among these distances:
422 18 0.05
423 88 0.25
424 71 0.21
425 32 0.09
426 28 0.08
429 2 0.01
433 1 0.00
434 1 0.00
435 2 0.01
437 93 0.27
438 10 0.03
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (424 bp):
TTTAAGATTATTATTTTAGATTTGTTTAAATAACTTAAATCTTTTTCTCAGATAAATTTATGAAG
ATGCTTCCTTAAATTCACTTATCATATATTAATAGATTTTATTTTTGAATATATGACCTTATAAA
AATCAAACCAAATTGAGAAAAGAAAACTCTATTTTACTAGGATTATCTAGTATCATGATATAACT
TAAATCTTATAAAAAATATATATTTAAGATTACTTTTTAGATTTTATTTGAATAACTTAACTATT
TTTCTAAAGACATTTTCTTTACATTCACTTATCATATATTAATAATTTTATTTTTGAAATATATA
TACCTTATAAATAATCAAACCCAAATTGAGAAAAGAAAACTCTATTTACTAGGATTATCTAATGT
TTAATATAACTGAAATCTTATAAAAAAATATACA
Found at i:6970 original size:43 final size:43
Alignment explanation
Indices: 6888--6970 Score: 96
Period size: 43 Copynumber: 1.9 Consensus size: 43
6878 AATAATTATT
* * *
6888 ATATTAATAAAATAATATTTTAATAATTATTGTAATATTTAAA
1 ATATTAATAAAATAATATTTTAATAATAATAGCAATATTTAAA
* * *
6931 ATATTAATATAATTAT-TTTTAATAATAAATAGCATTATTT
1 ATATTAATAAAATAATATTTTAATAAT-AATAGCAATATTT
6971 TAAGTATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
42 10 0.30
43 23 0.70
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (43 bp):
ATATTAATAAAATAATATTTTAATAATAATAGCAATATTTAAA
Done.