Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold622
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, 927
Length: 1545
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Found at i:1447 original size:470 final size:473
Alignment explanation
Indices: 1--1545 Score: 2666
Period size: 470 Copynumber: 3.3 Consensus size: 473
1 ATGTCATGTATCCTAATGACAAGGAATGTGTTTTTGGTTCCTAATCTTG-AAA-AATGGAGACTT
1 ATGTCATGTATCCTAATGA-AAGGAATGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTT
* * *
64 TTACGAGAATC-ATGCATGTCTCA-TTAAAGTGCAAACTTTGATTTTATGAAAATAAGGC-AAGA
65 TAACAAGAATCAATGCATATCTCATTTAAAGTGCAAACTTTGATTTTATGAAAATAAGGCAAAGA
126 GAAAGATTTCAATGCAAAAGAAAACCATCAATATCTGCATCCTGAGGAGGAGAATGTGTTTATAG
130 -AAAGATTTCAATGCAAAAGAAAACCATCAATATCTGCATCCTGAGGAGGAGAATGTGTTTATAG
* *
191 TGCCTAA-CATGAAATGAGTGAAGATCCATACTAGAATCCATGTTTGTCT-ATTTGAGGCGCGGA
194 TGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTTTGTCTCATTTGAGGCACGGA
254 CTTAGATTTTACACAAATTGGT-GGA--AAAGCGTATCTTGCGAAACCAAAGCATCAATATCATG
259 CTTAGATTTTACACAAATTGGTGGGACGAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATG
* *
316 TATCCATATAAGAAGACTATGTTTATGGTGCCAACTCCAGAAAAGAATGGGGATTAGT-AGAGTA
324 TATCCATATAAGAAGACTATGTTTATGGTGCCAAATACAGAAAAGAATGGGGATTAGTAAGAGTA
* * * *
380 TT-ATGTTTTGTCTTATTAAATAAGAGACAA-TTTGATTCTATCAATAATGGTGGAAAGACAAGC
389 TTCATG-TTTGTCTTATT---TAAAAGACAACGTTGATTCTATCAATAACGGCGGAAAGACAAGC
*
443 TTCTCTTGCGACA-CAAAGCATCA
450 TTTTCTTGCGACACCAAAGCATCA
466 ATGTCATGTATCCTAATGAAAGGAATGTGTTTTTTGGTCTCCTAATCTTGAAAAGAATGGAGACT
1 ATGTCATGTATCCTAATGAAAGGAATGTG-TTTTTGGT-TCCTAATCTTGAAAAGAATGGAGACT
* *
531 GTT-ACGAGAATCAATGCATGTCTCATTTAAAGTGCAAACTTTGATTTTATGAAAATAAGGCAAA
64 -TTAACAAGAATCAATGCATATCTCATTTAAAGTGCAAACTTTGATTTTATGAAAATAAGGCAAA
595 GAAAAGATTTCAATGCAAAAGAAAAACCATCAATATCTTGCATCCTGAGGAGGAGAATGTGTTTA
128 GAAAAGATTTCAATGCAAAAG-AAAACCATCAATATC-TGCATCCTGAGGAGGAGAATGTGTTTA
660 TAGTGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTTTGTCTCATTTGAGGCAC
191 TAGTGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTTTGTCTCATTTGAGGCAC
725 GGACTTAGATTTTACACAAATTGGTGGGACGAAAGCGTATCTTGCGAAACCAAAGCATCAATATC
256 GGACTTAGATTTTACACAAATTGGTGGGACGAAAGCGTATCTTGCGAAACCAAAGCATCAATATC
*
790 ATGTATCCGTATAAGAAGACTATGTTTATGGTGCCAAATACAGAAAAGAATGGGGATTAGTAAGA
321 ATGTATCCATATAAGAAGACTATGTTTATGGTGCCAAATACAGAAAAGAATGGGGATTAGTAAGA
855 GTATTCATGTTTGTCTTATTTAAAAGACAACGTTGATTCTATCAATAACGGCGGAAAGACAAGC-
386 GTATTCATGTTTGTCTTATTTAAAAGACAACGTTGATTCTATCAATAACGGCGGAAAGACAAGCT
919 TTTCTTGCGACACC-AAGCATCA
451 TTTCTTGCGACACCAAAGCATCA
*
941 ATGTCGTGTATCCTAATGAAAGGAATGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTTT
1 ATGTCATGTATCCTAATGAAAGGAATGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTTT
1006 AACAAGAATCAATGCATATCTC-TTTAAAGTGCAAAC-TTGATTTTATGGAAAATAAGGCAAAGA
66 AACAAGAATCAATGCATATCTCATTTAAAGTGCAAACTTTGATTTTAT-GAAAATAAGGCAAAGA
1069 AAAGATTTCAATGCAAAAGAAAACCATCAATATCATGCATCCTGAGGAGGAGAATGTGTTTATAG
130 AAAGATTTCAATGCAAAAGAAAACCATCAATATC-TGCATCCTGAGGAGGAGAATGTGTTTATAG
1134 TGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCAT-TTTGTCTCATTTGAGGCACGGA
194 TGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTTTGTCTCATTTGAGGCACGGA
1198 CTTAGATTTTACACAAATTGGTGGGACGAAAGCGTATCTTGCGAAACCAAAGCATC-ATATCA-G
259 CTTAGATTTTACACAAATTGGTGGGACGAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATG
1261 TATCCATATAAGAAGACTATGTTTATGGTGCCAAATACAGAAAAGAATGGGGATTAGTAAGAGTA
324 TATCCATATAAGAAGACTATGTTTATGGTGCCAAATACAGAAAAGAATGGGGATTAGTAAGAGTA
1326 TTCATGTTTGTCTTATTTAAAAGACAACGTTGATTCTATCAATAACGGCGGAAAGACAAGCTTTT
389 TTCATGTTTGTCTTATTTAAAAGACAACGTTGATTCTATCAATAACGGCGGAAAGACAAGCTTTT
1391 CTTGCGACACCAAAGCATCA
454 CTTGCGACACCAAAGCATCA
1411 ATGTCATGTATCCTAATGAAAGGAATGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTTT
1 ATGTCATGTATCCTAATGAAAGGAATGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTTT
1476 AACAAGAATCAATGCATATCTCATTTAAAGTGCAAACTTTGATTTTATGGAAAATAAGGCAAAGA
66 AACAAGAATCAATGCATATCTCATTTAAAGTGCAAACTTTGATTTTAT-GAAAATAAGGCAAAGA
1541 AAAGA
130 AAAGA
Statistics
Matches: 1039, Mismatches: 16, Indels: 43
0.95 0.01 0.04
Matches are distributed among these distances:
464 10 0.01
465 27 0.03
466 11 0.01
467 3 0.00
468 145 0.14
469 34 0.03
470 226 0.22
471 130 0.13
472 120 0.12
473 86 0.08
474 43 0.04
475 59 0.06
476 31 0.03
477 92 0.09
478 19 0.02
479 3 0.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (473 bp):
ATGTCATGTATCCTAATGAAAGGAATGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTTT
AACAAGAATCAATGCATATCTCATTTAAAGTGCAAACTTTGATTTTATGAAAATAAGGCAAAGAA
AAGATTTCAATGCAAAAGAAAACCATCAATATCTGCATCCTGAGGAGGAGAATGTGTTTATAGTG
CCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTTTGTCTCATTTGAGGCACGGACT
TAGATTTTACACAAATTGGTGGGACGAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATGTA
TCCATATAAGAAGACTATGTTTATGGTGCCAAATACAGAAAAGAATGGGGATTAGTAAGAGTATT
CATGTTTGTCTTATTTAAAAGACAACGTTGATTCTATCAATAACGGCGGAAAGACAAGCTTTTCT
TGCGACACCAAAGCATCA
Done.