Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3212
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: 19271
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:5594 original size:46 final size:44
Alignment explanation
Indices: 5496--5711 Score: 204
Period size: 46 Copynumber: 4.6 Consensus size: 44
5486 GTAAGGTGCC
* * *
5496 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTCGTA-GCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGC--TCGTCTC-AAGGCT
*
5544 GATGCATGTCCCAGACATATCTTACACTGGCTTACGTCTCAAGGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGC-T-CGTCTCAAGGCT
* * * *
5590 GATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGATGTT
1 GATGCATGTCCCAGACATGTCTTACACT-G-GCTCGTCTCAAGGCT
5636 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCAT-AATGTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCGTC-TCAA---GGCT
5684 GATGCATGTCCCAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
5712 AGCCTACAAT
Statistics
Matches: 144, Mismatches: 14, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
45 5 0.03
46 73 0.51
47 45 0.31
48 21 0.15
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (44 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTCGTCTCAAGGCT
Found at i:5695 original size:94 final size:92
Alignment explanation
Indices: 5496--5714 Score: 261
Period size: 94 Copynumber: 2.3 Consensus size: 92
5486 GTAAGGTGCC
*
5496 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTCGTAGCCGATGCATGTCCCAGACA
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTATCATCTCGTAGCCGATGCATGTCCCAGACA
5561 TATCTTACACTGGCTTACGTCTCAAGGCT
64 TATCTTACACTGGCTTACGTCTCAAGGCT
* **
5590 GATGCATGTCCCAGACATGTCTTACACTAGC-ACTCGTCTCG-ATGTTGATGCCATGTCCCAGAC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTA-TCATCTCGTA-GCCGATG-CATGTCCCAGAC
*
5653 ATGGTCTTACACTGGC-T-C-TCAT-AATGTGGCT
63 AT-ATCTTACACTGGCTTACGTC-TCAA---GGCT
5684 GATGCATGTCCCAGACATGTCTTACACTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
5715 CTACAATAAC
Statistics
Matches: 112, Mismatches: 5, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
91 6 0.05
92 26 0.23
93 29 0.26
94 51 0.46
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTATCATCTCGTAGCCGATGCATGTCCCAGACATA
TCTTACACTGGCTTACGTCTCAAGGCT
Found at i:12667 original size:46 final size:46
Alignment explanation
Indices: 12617--12792 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
12607 TGGTTGAGCA
12617 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
12663 TCCGAACTCGTTGAGTTGAGTTCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
12708 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-C
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
12755 ACCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12793 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 61 0.56
47 28 0.26
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:12773 original size:93 final size:93
Alignment explanation
Indices: 12614--12784 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
12604 GGATGGTTGA
**
12614 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATCACCGAACTCGTTGAGT
*
12679 TGAGTTCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
12707 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-CACCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATCACC-GAACTCGTTGAG
12771 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
12785 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATCACCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.