Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2619
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, 537
Length: 896
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.22
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:354 original size:30 final size:29
Alignment explanation
Indices: 318--431 Score: 142
Period size: 29 Copynumber: 3.9 Consensus size: 29
308 CAAAAATCAA
*
318 AAATTACATTTTTGACCCCTAAAGTTTTTG
1 AAATTACA-TTTTGACCCCTAAACTTTTTG
* *
348 AAATTACATTTTGA-CCCTAAACTTTCCTA
1 AAATTACATTTTGACCCCTAAACTTT-TTG
*
377 AAATTATATTTTGACCCCTAAACTTTTTG
1 AAATTACATTTTGACCCCTAAACTTTTTG
* *
406 AAGTTACATTTTGATCCCTAAA-TTTT
1 AAATTACATTTTGACCCCTAAACTTTT
432 CTCAAAATTA
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.19
29 40 0.55
30 19 0.26
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (29 bp):
AAATTACATTTTGACCCCTAAACTTTTTG
Found at i:380 original size:29 final size:29
Alignment explanation
Indices: 317--453 Score: 141
Period size: 29 Copynumber: 4.7 Consensus size: 29
307 ACAAAAATCA
* *
317 AAAATTACATTTTTGACCCCTAAAGTTTTT
1 AAAATTACA-TTTTGACCCCTAAACTTTCT
*
347 GAAATTACATTTTGA-CCCTAAACTTTCCT
1 AAAATTACATTTTGACCCCTAAACTTT-CT
* *
376 AAAATTATATTTTGACCCCTAAACTTTTT
1 AAAATTACATTTTGACCCCTAAACTTTCT
* * * *
405 GAAGTTACATTTTGATCCCTAAATTTTCT
1 AAAATTACATTTTGACCCCTAAACTTTCT
* *
434 CAAAATTATATTTTGGCCCC
1 -AAAATTACATTTTGACCCC
454 AGAAGTTTTG
Statistics
Matches: 87, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
28 10 0.11
29 44 0.51
30 33 0.38
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCTAAACTTTCT
Found at i:396 original size:58 final size:59
Alignment explanation
Indices: 317--462 Score: 199
Period size: 58 Copynumber: 2.5 Consensus size: 59
307 ACAAAAATCA
*
317 AAAATTACATTTTTGACCCCTAAAGTTTTTGAAATTACATTTTGA-CCCTAAACTTTCCT-
1 AAAATTATA-TTTTGACCCCTAAAGTTTTTGAAATTACATTTTGATCCCTAAA-TTTCCTC
* * *
376 AAAATTATATTTTGACCCCTAAACTTTTTGAAGTTACATTTTGATCCCTAAATTTTCTC
1 AAAATTATATTTTGACCCCTAAAGTTTTTGAAATTACATTTTGATCCCTAAATTTCCTC
*
435 AAAATTATATTTTGGCCCC-AGAAGTTTT
1 AAAATTATATTTTGACCCCTA-AAGTTTT
463 GCTGTGTTTG
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
58 39 0.50
59 39 0.50
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (59 bp):
AAAATTATATTTTGACCCCTAAAGTTTTTGAAATTACATTTTGATCCCTAAATTTCCTC
Found at i:863 original size:11 final size:11
Alignment explanation
Indices: 849--879 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
839 AAAAAGTGTC
849 GAAAAAGAAAA
1 GAAAAAGAAAA
860 GAAAAAGAAAA
1 GAAAAAGAAAA
*
871 GGAAAAGAA
1 GAAAAAGAA
880 GAGAGGGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Done.