Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold925
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: 4177
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Found at i:65 original size:18 final size:18
Alignment explanation
Indices: 7--67 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 18
1 TATTTT
* *
7 TATTTTTTAATTTTAAAA
1 TATTTTTTATTTTTAATA
** *
25 TACTTTTAAATTTTT-TTA
1 TA-TTTTTTATTTTTAATA
43 T-TTTTTTATTTTTAATA
1 TATTTTTTATTTTTAATA
60 TATTTTTT
1 TATTTTTT
68 TTGTGTTTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
16 10 0.31
17 3 0.09
18 10 0.31
19 9 0.28
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTTTTTATTTTTAATA
Found at i:699 original size:50 final size:50
Alignment explanation
Indices: 626--810 Score: 145
Period size: 50 Copynumber: 3.7 Consensus size: 50
616 GCAATTAAAT
* * * * * * *
626 AGATTGAAGCTGCAACGGTGAATCTCAATTCCCTGGCAGTACAGTGGAGC
1 AGATTAAAGCTACGACGGCGAATCTCACTTCCCTAGCACTACAGTGGAGC
* * ** * * * ** **
676 AGATTAAAGCTACGACGACGAATCTTACTTCCCTAATATTGCAATTTAAA
1 AGATTAAAGCTACGACGGCGAATCTCACTTCCCTAGCACTACAGTGGAGC
* * * *
726 AGATTGAAGCCACAACGGTGAATCTCACTTCCCTAGCACTACAGTGGAGC
1 AGATTAAAGCTACGACGGCGAATCTCACTTCCCTAGCACTACAGTGGAGC
* **
776 AGATTAAAGTTACGACGGCGAATCTTGCTTCCCTA
1 AGATTAAAGCTACGACGGCGAATCTCACTTCCCTA
811 ATATTGCAAT
Statistics
Matches: 96, Mismatches: 39, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
50 96 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (50 bp):
AGATTAAAGCTACGACGGCGAATCTCACTTCCCTAGCACTACAGTGGAGC
Found at i:830 original size:50 final size:50
Alignment explanation
Indices: 676--959 Score: 183
Period size: 50 Copynumber: 5.7 Consensus size: 50
666 ACAGTGGAGC
*
676 AGATTAAAGCTACGACGACGAATCTTACTTCCCTAATATTGCAATTTAAA
1 AGATTAAAGCTACGACGGCGAATCTTACTTCCCTAATATTGCAATTTAAA
* * * * * ** * * * ** **
726 AGATTGAAGCCACAACGGTGAATCTCACTTCCCTAGCACTACAGTGGAGC
1 AGATTAAAGCTACGACGGCGAATCTTACTTCCCTAATATTGCAATTTAAA
* *
776 AGATTAAAGTTACGACGGCGAATCTTGCTTCCCTAATATTGCAATTTAAA
1 AGATTAAAGCTACGACGGCGAATCTTACTTCCCTAATATTGCAATTTAAA
* * * * ** ** * ** **
826 AGATTGAAGCCACAACGGTGAATCTTACTTTTCTAGCGA-TGCAGTAGAGC
1 AGATTAAAGCTACGACGGCGAATCTTACTTCCCTA-ATATTGCAATTTAAA
* ** * ** *
876 AGATTAAAGCTACAACGGTAAATCTTGCTTCCCCGACATTGCAATTTAAA
1 AGATTAAAGCTACGACGGCGAATCTTACTTCCCTAATATTGCAATTTAAA
* ** *
926 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCT
1 AGATTAAAGCTACGACGGCGAATCTTACTTCCCT
960 GAGGTTGTAG
Statistics
Matches: 164, Mismatches: 68, Indels: 4
0.69 0.29 0.02
Matches are distributed among these distances:
49 1 0.01
50 162 0.99
51 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (50 bp):
AGATTAAAGCTACGACGGCGAATCTTACTTCCCTAATATTGCAATTTAAA
Found at i:973 original size:100 final size:101
Alignment explanation
Indices: 546--962 Score: 517
Period size: 100 Copynumber: 4.2 Consensus size: 101
536 TTTACATTAG
*
546 GAATCTTACTTCCCTGA-CGATGTAGTGGAGCAGATTAAAGCTACAACGGCGAATCTTG-TTCCC
1 GAATCTTACTTCCCTGAGCGATGCAGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCC
* **
609 CGACATTGCAA-TTAAATAGATTGAAGCTGCAACGGT
66 CAACATTGCAATTTAAA-AGATTGAAGCCACAACGGT
* * * * * *
645 GAATCTCAATTCCCTG-GC-AGTACAGTGGAGCAGATTAAAGCTACGACGACGAATCTTACTTCC
1 GAATCTTACTTCCCTGAGCGA-TGCAGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCC
* *
708 CTAATATTGCAATTTAAAAGATTGAAGCCACAACGGT
65 CCAACATTGCAATTTAAAAGATTGAAGCCACAACGGT
* * * *
745 GAATCTCACTTCCCT-AGC-ACTACAGTGGAGCAGATTAAAGTTACGACGGCGAATCTTGCTTCC
1 GAATCTTACTTCCCTGAGCGA-TGCAGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCC
* *
808 CTAATATTGCAATTTAAAAGATTGAAGCCACAACGGT
65 CCAACATTGCAATTTAAAAGATTGAAGCCACAACGGT
** * **
845 GAATCTTACTTTTCT-AGCGATGCAGTAGAGCAGATTAAAGCTACAACGGTAAATCTTGCTTCCC
1 GAATCTTACTTCCCTGAGCGATGCAGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCC
* * *
909 CGACATTGCAATTTAAAAGATTGAAGCCGCAACGGC
66 CAACATTGCAATTTAAAAGATTGAAGCCACAACGGT
945 GAATCTTACTTCCCTGAG
1 GAATCTTACTTCCCTGAG
963 GTTGTAGTAG
Statistics
Matches: 278, Mismatches: 33, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
98 1 0.00
99 48 0.17
100 221 0.79
101 8 0.03
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (101 bp):
GAATCTTACTTCCCTGAGCGATGCAGTGGAGCAGATTAAAGCTACAACGGCGAATCTTGCTTCCC
CAACATTGCAATTTAAAAGATTGAAGCCACAACGGT
Done.