Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold899
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: 4515
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Found at i:285 original size:18 final size:19
Alignment explanation
Indices: 264--301 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
254 TATGTTTAAA
*
264 TAAAATTGT-TATTATTTT
1 TAAAATTCTCTATTATTTT
282 T-AAATTCTCTATTATTTT
1 TAAAATTCTCTATTATTTT
300 TA
1 TA
302 TTTTAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 3
0.81 0.05 0.14
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (19 bp):
TAAAATTCTCTATTATTTT
Found at i:702 original size:18 final size:19
Alignment explanation
Indices: 681--718 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
671 TATGTTTAAA
*
681 TAAAATTGT-TATTATTTT
1 TAAAATTCTCTATTATTTT
699 T-AAATTCTCTATTATTTT
1 TAAAATTCTCTATTATTTT
717 TA
1 TA
719 TTTTAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 3
0.81 0.05 0.14
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (19 bp):
TAAAATTCTCTATTATTTT
Found at i:949 original size:417 final size:418
Alignment explanation
Indices: 162--998 Score: 1658
Period size: 417 Copynumber: 2.0 Consensus size: 418
152 AACCTTAAAC
162 ATTATATTAAAGTCTAAACTTAAGACATTAAATCCTAAAATCGAGAGTTATTATTATTTTATTTA
1 ATTATATTAAAG-CTAAACTTAAGACATTAAATCCTAAAATCGAGAGTTATTATTATTTTATTTA
227 TAATTATTATAATTAAAAATAATCAATTATGTTTAAATAAAATTGTTATTATTTTTAAATTCTCT
65 TAATTATTATAATTAAAAATAATCAATTATGTTTAAATAAAATTGTTATTATTTTTAAATTCTCT
292 ATTATTTTTATTTTAATCAATAATAAAATGTTATTTCTCTAACAAAATATCCAATTCTTTCCTAT
130 ATTATTTTTATTTTAATCAATAATAAAATGTTATTTCTCTAACAAAATATCCAATTCTTTCCTAT
357 AATCCACATTTGTGAATGATCACTATTTATTTTAGATTTATATAATTAAAAGGAAATGTTTGGGA
195 AATCCACATTTGTGAATGATCACTATTTATTTTAGATTTATATAATTAAAAGGAAATGTTTGGGA
422 GAAAGTGATGCAACTTTTTAATATATACCAGTACTACATTTTAAAAAGGAAATTTCTTTCCAATA
260 GAAAGTGATGCAACTTTTTAATATATACCAGTACTACATTTTAAAAAGGAAATTTCTTTCCAATA
487 ATTCACTATTTTCTTCTCAACCTATTACTCTGGAATTACATAAAATTTAGGTAGATTTCTGTAGT
325 ATTCACTATTTTCTTCTCAACCTATTACTCTGGAATTACATAAAATTTAGGTAGATTTCTGTAGT
552 TTTAACAAAGATTAGTTATGTTCTCATGA
390 TTTAACAAAGATTAGTTATGTTCTCATGA
581 ATTATATTAAA-CTAAACTTAAGACATTAAATCCTAAAATCGAGAGTTATTATTATTTTATTTAT
1 ATTATATTAAAGCTAAACTTAAGACATTAAATCCTAAAATCGAGAGTTATTATTATTTTATTTAT
645 AATTATTATAATTAAAAATAATCAATTATGTTTAAATAAAATTGTTATTATTTTTAAATTCTCTA
66 AATTATTATAATTAAAAATAATCAATTATGTTTAAATAAAATTGTTATTATTTTTAAATTCTCTA
710 TTATTTTTATTTTAATCAATAATAAAATGTTATTTCTCTAACAAAATATCCAATTCTTTCCTATA
131 TTATTTTTATTTTAATCAATAATAAAATGTTATTTCTCTAACAAAATATCCAATTCTTTCCTATA
775 ATCCACATTTGTGAATGATCACTATTTATTTTAGATTTATATAATTAAAAGGAAATGTTTGGGAG
196 ATCCACATTTGTGAATGATCACTATTTATTTTAGATTTATATAATTAAAAGGAAATGTTTGGGAG
840 AAAGTGATGCAACTTTTTAATATATACCAGTACTACATTTTAAAAAGGAAATTTCTTTCCAATAA
261 AAAGTGATGCAACTTTTTAATATATACCAGTACTACATTTTAAAAAGGAAATTTCTTTCCAATAA
905 TTCACTATTTTCTTCTCAACCTATTACTCTGGAATTACATAAAATTTAGGTAGATTTCTGTAGTT
326 TTCACTATTTTCTTCTCAACCTATTACTCTGGAATTACATAAAATTTAGGTAGATTTCTGTAGTT
970 TTAACAAAGATTAGTTATGTTCTCATGA
391 TTAACAAAGATTAGTTATGTTCTCATGA
998 A
1 A
999 AATGACCATA
Statistics
Matches: 418, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
417 407 0.97
419 11 0.03
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (418 bp):
ATTATATTAAAGCTAAACTTAAGACATTAAATCCTAAAATCGAGAGTTATTATTATTTTATTTAT
AATTATTATAATTAAAAATAATCAATTATGTTTAAATAAAATTGTTATTATTTTTAAATTCTCTA
TTATTTTTATTTTAATCAATAATAAAATGTTATTTCTCTAACAAAATATCCAATTCTTTCCTATA
ATCCACATTTGTGAATGATCACTATTTATTTTAGATTTATATAATTAAAAGGAAATGTTTGGGAG
AAAGTGATGCAACTTTTTAATATATACCAGTACTACATTTTAAAAAGGAAATTTCTTTCCAATAA
TTCACTATTTTCTTCTCAACCTATTACTCTGGAATTACATAAAATTTAGGTAGATTTCTGTAGTT
TTAACAAAGATTAGTTATGTTCTCATGA
Done.