Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1828
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: 4082
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Found at i:3860 original size:474 final size:476
Alignment explanation
Indices: 30--4082 Score: 4941
Period size: 473 Copynumber: 8.6 Consensus size: 476
20 CGCGAATGAC
* * *** *
30 TTGCTTGTCTTATTTAAAGGTTGAGCTTTTGATTTTAAGGAAAACTAAGGGCAAAG-AAAGATTT
1 TTGCTTGTCTGATTTAAGGGTT-AAAATTTGATTTTAAGGAAAA-TAAGGGTAAAGAAAAGATTT
* * * ** * *
94 CCATG-AAAGAAAAACATCAAT-TCATTT-CTCCTAATGAGGATAACGTGTTTATAAGGTGCCCA
64 CCATGAAAAGAAAATCATCAATATCATTTACTGC-AATGAGCATATTGTGTTTAT-A-GTTCCTA
* **** * * * * *
156 TTCACAAGGTGAGTGAAGATCAATACTAGATTCCTTGTTTGGCACATTTTAGGCACAGACATAGA
126 ATCACAAAACAAATGAAGAACAATACTAGAATCCATGTTTGGCACATTTTAGGCACGGACATAGA
* *
221 CTCTTATAATAATAGGTCGAAAG-AAACC-TTCTTGAGAAACCAAA-CTTCATTATCATGCATAC
191 CT-TTATAATAATTGGTCGAAAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATCC
* ** * * *
283 TTATGAGAAGGACTATATTTATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTTTGACCATTCA
255 CTATGAGAA-GACTACGTTTATGGTGCCTAATCC-CAAAAGAATGGGGATTAGTATGACGATTCA
* * * * * *
348 TGTTTTGTCTTATTTAAGAGGCAAACTTTCATTCTCTCAAAAATGG-CGAATGACAAGTTTTTCT
318 TG-TTTGTCTTTTTTAAGAGGCAAACTTTCATTCTATCAAAAACGGTGGAATGAAAAGCTTTTCT
* * * * *
412 TTGTGACACCAAAGCATCAATGTCGTGTAT-CTAACG-AGGAGAATGTGTTTTTGGGTGCAAATC
382 TAG-GACACCAAAGCGTCAATGTCGTGTATCCTAATGAAGG-GAATGTGTTTTTGGGTCCCAATC
* * *
475 -TGAAAAG-AATGG-GATTGTTACGAGGAATTG
445 TTGAAAAGAAATGGAGAATGTTTCGA-AAATTG
* * * * ** *
505 ATGCTTGTCTTATTTAAAGGTT-GAGCTTGATTTTAAGGCAAAATAAGGG-CAAGAAAAGATTTC
1 TTGCTTGTCTGATTTAAGGGTTAAAATTTGATTTTAAGG-AAAATAAGGGTAAAGAAAAGATTTC
* * ** * * *
568 CATGAAAAGAAAATCATCAATATCATTTA-TCCTAATGAGGATAACGTTGTTTATAAG-GCCCAT
65 CATGAAAAGAAAATCATCAATATCATTTACTGC-AATGAGCATATTG-TGTTTAT-AGTTCCTAA
**** * * * * * *
631 TCACAAGGTGTGAGTG-AGATCAATACTAGATTCCTTCTTTGGCACATTTTAGGCACAGACATAG
127 TCACAA--AACAAATGAAGAACAATACTAGAATCCATGTTTGGCACATTTTAGGCACGGACATAG
* * *
695 ACTTTCTAATAATAGGTCGAAAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATAC
190 ACTTTATAATAATTGGTCGAAAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATCC
* * *
760 TTATGAGAAGACTACGTTTATAGTGCCTAAT-CCAAAATGAATGGGGATTCGTATGACCG-TTCA
255 CTATGAGAAGACTACGTTTATGGTGCCTAATCCCAAAA-GAATGGGGATTAGTATGA-CGATTCA
* *
823 TGTTTGTCTTATTTAAGAGGCAAACTTTCATT-TATCAAAAATGGTTGGAATGAAAAAG-TTTTC
318 TGTTTGTCTTTTTTAAGAGGCAAACTTTCATTCTATCAAAAACGG-TGGAATG-AAAAGCTTTTC
* * * * *
886 TT-GTGACACCAAAGCATCAATGTCGTGTATCCGAACGAAAGGGAATGTGTTTTTGGGTGCAAAT
381 TTAG-GACACCAAAGCGTCAATGTCGTGTATCCTAATG-AAGGGAATGTGTTTTTGGGTCCCAAT
* * *
950 C-TGAAAAG-AATGGAGATTGTTACGAGAATTG
444 CTTGAAAAGAAATGGAGAATGTTTCGAAAATTG
* * * * ** **
981 ATGCTTGTCTTATTTTAAAGGTTGAGCTTTGATTTTAAGGAAAAATAAGGGCGAAGAAAAGATTT
1 TTGCTTGTCTGA-TTTAAGGGTTAAAATTTGATTTTAAGG-AAAATAAGGGTAAAGAAAAGATTT
* * * ** **
1046 CCATGAAAAGAAAATCATCAATATC-TTTA-TCCCAATAAGGATAACGTGTTTATAAGGCCCCT-
64 CCATGAAAAGAAAATCATCAATATCATTTACT-GCAATGAGCATATTGTGTTTAT-A-GTTCCTA
****** ** * *
1108 -TC-CAAGGTGTGTGAAGATTAATACTAGATTCCTTGTTTGGCACATTTTAGGCA-GGACATAGA
126 ATCACAAAACAAATGAAGAACAATACTAGAATCCATGTTTGGCACATTTTAGGCACGGACATAGA
*
1170 CTTTAT-ATAATTGGTCGAAAGAAAACCTCTCTTGAGAAACCAAAGCTTC-TTATCATGCATCCC
191 CTTTATAATAATTGGTCGAAAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATCCC
* * *
1233 TATCAGAAGACTACGTTTATTGTGCCTAATCCC-AAGGAATGGGGATTAGTATGACGATTCATGT
256 TATGAGAAGACTACGTTTATGGTGCCTAATCCCAAAAGAATGGGGATTAGTATGACGATTCATGT
*
1297 TTGTCTTTTTTTAGAGGCAAACTTTCCATTCTATC-AAAACGGTGGAATGAAAAGCTTTTCTTTA
321 TTGTCTTTTTTAAGAGGCAAACTTT-CATTCTATCAAAAACGGTGGAATGAAAAGCTTTTC-TTA
*
1361 GGACACCAAAGCGTCAATGTCGTGTATCCTAATGAAGGGAAGGGAATGTGTTTTGGGTCCC-AT-
384 GGACACCAAAGCGTCAATGTCGTGTATCCTAATGAAGGGAA-TG--TGT-TTTTGGGTCCCAATC
1424 TTG-AAAGAAAT-GAGAATGTTTCGAAAATTG
445 TTGAAAAGAAATGGAGAATGTTTCGAAAATTG
* *
1454 TTGCTTGTCTGATTT-AGGGATACAAATTTGATTAT-AGGAAAATAAGGGTAAAGAAAAGATTTC
1 TTGCTTGTCTGATTTAAGGGTTA-AAATTTGATTTTAAGGAAAATAAGGGTAAAGAAAAGATTTC
*
1517 CATGAAAAAGAAAATCATCAATATCATTTACTGTAATGAGC-TATTGTG-TTATAGTTCCTAAT-
65 CATG-AAAAGAAAATCATCAATATCATTTACTGCAATGAGCATATTGTGTTTATAGTTCCTAATC
*
1579 -CAAAACAAATGAAGAACAATACTAGAATCCATGTTTTGCACATTTTTAGGCACGGACCATAGAC
129 ACAAAACAAATGAAGAACAATACTAGAATCCATGTTTGGCACA-TTTTAGGCACGGA-CATAGAC
* *
1643 TTTATAATAACTGGTCGAAAGAAAACCTCTCTTGAGAAACCAAAGCTTCATTATCAT-CATCCCT
192 TTTATAATAATTGGTCGAAAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATCCCT
* *
1707 ATCAGAAAGACTACGTTTATGGTGCCTAATCCCGAAAGGAATGGGGATTAGTATGACGATTCATG
257 ATGAG-AAGACTACGTTTATGGTGCCTAATCCC-AAAAGAATGGGGATTAGTATGACGATTCATG
*
1772 TTTGTC-TTTTTAAAAGGCAAACTTTC-TTCTATC-AAAACGGTGGAATGAAAAGCTTTTCTTAG
320 TTTGTCTTTTTTAAGAGGCAAACTTTCATTCTATCAAAAACGGTGGAATGAAAAGCTTTTCTTAG
* *
1834 GACACCAAAGCCTCAATGTCGTGTATCCTAATGAAGGGTATGTG-TTTTGGTGTCCCAATCTTG-
385 GACACCAAAGCGTCAATGTCGTGTATCCTAATGAAGGGAATGTGTTTTTGG-GTCCCAATCTTGA
1897 AAAGAAATGAGAGAATGTTTCG-AAATTG
449 AAAGAAATG-GAGAATGTTTCGAAAATTG
* * *
1925 TTGCTTGTCTGATTTAAGGGATAAAATTTGATTATAAGGAAAATAAGGGTTAAGAAAAGATTTTC
1 TTGCTTGTCTGATTTAAGGGTTAAAATTTGATTTTAAGGAAAATAAGGGTAAAGAAAAGA-TTTC
* *
1990 CATGAAAAGAAAATCAGCAATATCATTTACTGTAATGAGCATATTGTGTTTATAGTTCCTAATCA
65 CATGAAAAGAAAATCATCAATATCATTTACTGCAATGAGCATATTGTGTTTATAGTTCCTAATCA
2055 CAAAACAAATGAAGAAC-ATACTAGAATCCATGTTTGGCACATTTTAGGCACGGACATAGACTTT
130 CAAAACAAATGAAGAACAATACTAGAATCCATGTTTGGCACATTTTAGGCACGGACATAGACTTT
*
2119 ATAATAATTGGTCGAAAGAAAACC-TTCTTGAGAAACCAAAGCTTCATTCTCATGCATCCCTATG
195 ATAATAATTGGTCGAAAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATCCCTATG
* *
2183 AGAAGACTACGTTTATGGTGCCTAATTCCCAAAGGAATGGGGATTAGCATTGACGATTCATG-TT
260 AGAAGACTACGTTTATGGTGCCTAA-TCCCAAAAGAATGGGGATTAGTA-TGACGATTCATGTTT
2247 GTCTTTTTTAAGAGGC-AACTTTCATTCTATCAAAAACCGGTGGAATGACAAAAGCTTTTCTTAG
323 GTCTTTTTTAAGAGGCAAACTTTCATTCTATCAAAAA-CGGTGGAATG--AAAAGCTTTTCTTAG
*
2311 GACACCAAAGCGTCAATGTCGTGTATCCTAATAGGGAATGGGAATGTGTTTTTGGGTCCCAATTT
385 GACACCAAAGCGTCAATGTCGTGTATCCTAAT---GAA-GGGAATGTGTTTTTGGGTCCCAATCT
2376 TGAAAAGAAAT-GAGAATGTTTCGAAAATTG
446 TGAAAAGAAATGGAGAATGTTTCGAAAATTG
2406 TTGCTTGTCTGATTTAAGGGATTCAAAATTTGA--TTAAGGAAAATAAGGGTAAAG-AAAGATTT
1 TTGCTTGTCTGATTTAAGGG-TT-AAAATTTGATTTTAAGGAAAATAAGGGTAAAGAAAAGATTT
*
2468 CCATGAAAAG-AAATCATCAAT-TCATTTACTGTAATGAGCATATTGTGTTTATAGTTCCTAATC
64 CCATGAAAAGAAAATCATCAATATCATTTACTGCAATGAGCATATTGTGTTTATAGTTCCTAATC
2531 ACAAAACAAATG-AGAACAATACTAGAATCCATGTTTGG-ACATTTTAGGCACGGACATAGACTT
129 ACAAAACAAATGAAGAACAATACTAGAATCCATGTTTGGCACATTTTAGGCACGGACATAGACTT
* *
2594 TATAATAACTGGTCGAAAGAAAACCTCTCTTGAGAAACCAAAAGCTTCATTATCATGCATCCCTA
194 TATAATAATTGGTCGAAAGAAAACCTTTCTTGAGAAACC-AAAGCTTCATTATCATGCATCCCTA
* *
2659 TCAGAAGACTACGTTTATGGTGCCTAATCCCGAAAGGAATGGGGATTAGTATGACGATTCATGTT
258 TGAGAAGACTACGTTTATGGTGCCTAATCCC-AAAAGAATGGGGATTAGTATGACGATTCATGTT
2724 TGTCTTTTTTAAGAGGCACAACTTTCATTCTATCAAAAACGGTGGAATGAAAAGCTTTTCTTAGG
322 TGTCTTTTTTAAGAGGCA-AACTTTCATTCTATCAAAAACGGTGGAATGAAAAGCTTTTCTTAGG
* *
2789 AC-CCACAAGCCTCAATGTCGTGTATCC-AATGAAGGGTATGTGTTTTTGGGTCCCAATCTTGAA
386 ACACCA-AAGCGTCAATGTCGTGTATCCTAATGAAGGGAATGTGTTTTTGGGTCCCAATCTTGAA
2852 AAGAAAT-GAGAATGTTTCGAAAATTG
450 AAGAAATGGAGAATGTTTCGAAAATTG
* *
2878 TTGCTTGTCTGATTTAAGGGAATAAAATTTGATTATAAGGAAAATAAGGGTAAAGAAAAGATTTC
1 TTGCTTGTCTGATTTAAGGG-TTAAAATTTGATTTTAAGGAAAATAAGGGTAAAGAAAAGATTT-
* *
2943 CCATG-AAAGAAAATCAGC-AT-TCATTTACTGTAATGAGCATATTGGTGTTTATAGTTCCTAAT
64 CCATGAAAAGAAAATCATCAATATCATTTACTGCAATGAGCATATT-GTGTTTATAGTTCCTAAT
3005 CACAAAACAAATGAAGAACAATACTAGAATCCATGTTTGGCA-ATTTTAGGCACGGAC-TAGACT
128 CACAAAACAAATGAAGAACAATACTAGAATCCATGTTTGGCACATTTTAGGCACGGACATAGACT
3068 TT-TAATAA-TGGTCGAAAGAAAACCTTTCTTGAGAAAACC-AAGCTTC-TTATCATGCATCCCT
193 TTATAATAATTGGTCGAAAGAAAACCTTTCTTGAG-AAACCAAAGCTTCATTATCATGCATCCCT
*
3129 ATGAGAAGACTACGTTTATGGTGCCTAAT-CCAAAAGGAATGGGGGATTAGCATGA-G--TCATG
257 ATGAGAAGACTACGTTTATGGTGCCTAATCCCAAAA-GAAT-GGGGATTAGTATGACGATTCATG
*
3190 TTTGTCTTTTTTTAAGAGGCAAACTGTCATTCTATCAAAAACGGTGGAATGAAAAGCTTTTCTTA
320 TTTGTC-TTTTTTAAGAGGCAAACTTTCATTCTATCAAAAACGGTGGAATGAAAAGCTTTTCTTA
3255 GGACACCAAAGCGTCAATGTCGTGTATCCTAATGAAGGGAATGTG-TTTTGGGTCCCAATCTTGA
384 GGACACCAAAGCGTCAATGTCGTGTATCCTAATGAAGGGAATGTGTTTTTGGGTCCCAATCTTGA
**
3319 AAAGAAAT-GAGAATGTTTTAAAAATTG
449 AAAGAAATGGAGAATGTTTCGAAAATTG
* * *
3346 TTGCTTGTCTGATTTAAGGGATAAAATTTGATTATAAGG-AAATAAAGGTAAAGAAAAGATTTCC
1 TTGCTTGTCTGATTTAAGGGTTAAAATTTGATTTTAAGGAAAATAAGGGTAAAGAAAAGATTTCC
* * *
3410 ATGAAAAGAAAATCAGCAATACCATTTACTGCAACGAGCATATTGTGTTTATAGTTCCTAATCAC
66 ATGAAAAGAAAATCATCAATATCATTTACTGCAATGAGCATATTGTGTTTATAGTTCCTAATCAC
* **
3475 AAAACAAATGAAGAACAATAGTAGAATCCATGTTTGGCACATTTTAGGTGCGGACATAGACTTTA
131 AAAACAAATGAAGAACAATACTAGAATCCATGTTTGGCACATTTTAGGCACGGACATAGACTTTA
*
3540 T-ATAATTGGTCGAAAGAAAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATCCTTAT
196 TAATAATTGGTCGAAAG--AAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATCCCTAT
* *
3604 GAGAAGACTACGTTTATGGTGCCTAATCCCGAAAAGAATGGGGA-TAGTGTGACCATTCATG-TT
259 GAGAAGACTACGTTTATGGTGCCTAATCCC-AAAAGAATGGGGATTAGTATGACGATTCATGTTT
* * *
3667 GTCTTATTTAAGAGGCAAACTTTCATTCTATCAAAAATGATGG-ATGAAAAGCTTTTCTT-GTGA
323 GTCTTTTTTAAGAGGCAAACTTTCATTCTATCAAAAACGGTGGAATGAAAAGCTTTTCTTAG-GA
* * * *
3730 CACCAAAGCTTCAATGTCATTGTATCCTAACGAAGGGAATGTGTTTTTGGGTCCAAATCTTGAAA
387 CACCAAAGCGTCAATGTC-GTGTATCCTAATGAAGGGAATGTGTTTTTGGGTCCCAATCTTGAAA
* * *
3795 AG-AATGGAGATTGTTACGAGAATTG
451 AGAAATGGAGAATGTTTCGAAAATTG
* * * ** * *
3820 TTGCTTATCAGATTTAAGGGTTGAGCTTTGATTTTAAGGAAAATCAGGG-CAAGAAAAGATTT-C
1 TTGCTTGTCTGATTTAAGGGTTAAAATTTGATTTTAAGGAAAATAAGGGTAAAGAAAAGATTTCC
* * * ** * * *
3883 ATGAAATGAAAAATCATCAATATCATTTA-TCCTAATGAGGATAACGTGTTTATAAG-GCCCATT
66 ATGAAAAG-AAAATCATCAATATCATTTACTGC-AATGAGCATATTGTGTTTAT-AGTTCCTAAT
*** * * * * *
3946 CAC-AAGTGAGTGAAGATCAATACTAGATTCCTTGTTTGGCACA-TTTAGGCACAGACATAGACT
128 CACAAAACAAATGAAGAACAATACTAGAATCCATGTTTGGCACATTTTAGGCACGGACATAGACT
* * * * * * *
4009 ATATAATAATAGGTCGAAAGAAAACC-TTCTTGAGAAGCCAACGCTTCATTATCATGTATACTTA
193 TTATAATAATTGGTCGAAAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATCCCTA
4073 TGAGAAGACT
258 TGAGAAGACT
Statistics
Matches: 3258, Mismatches: 189, Indels: 267
0.88 0.05 0.07
Matches are distributed among these distances:
465 5 0.00
466 35 0.01
467 86 0.03
468 184 0.06
469 82 0.03
470 121 0.04
471 212 0.07
472 486 0.15
473 513 0.16
474 386 0.12
475 305 0.09
476 266 0.08
477 249 0.08
478 136 0.04
479 64 0.02
480 40 0.01
481 64 0.02
482 15 0.00
483 9 0.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (476 bp):
TTGCTTGTCTGATTTAAGGGTTAAAATTTGATTTTAAGGAAAATAAGGGTAAAGAAAAGATTTCC
ATGAAAAGAAAATCATCAATATCATTTACTGCAATGAGCATATTGTGTTTATAGTTCCTAATCAC
AAAACAAATGAAGAACAATACTAGAATCCATGTTTGGCACATTTTAGGCACGGACATAGACTTTA
TAATAATTGGTCGAAAGAAAACCTTTCTTGAGAAACCAAAGCTTCATTATCATGCATCCCTATGA
GAAGACTACGTTTATGGTGCCTAATCCCAAAAGAATGGGGATTAGTATGACGATTCATGTTTGTC
TTTTTTAAGAGGCAAACTTTCATTCTATCAAAAACGGTGGAATGAAAAGCTTTTCTTAGGACACC
AAAGCGTCAATGTCGTGTATCCTAATGAAGGGAATGTGTTTTTGGGTCCCAATCTTGAAAAGAAA
TGGAGAATGTTTCGAAAATTG
Done.