Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2430
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: 11768
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Found at i:1696 original size:20 final size:19
Alignment explanation
Indices: 1673--1724 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
1663 GAGGGAATAG
1673 AAAAAATCATGAGGACGTAC
1 AAAAAATCATGAGGA-GTAC
1693 AAAAAATTC-T-AGGGAGTAC
1 AAAAAA-TCATGA-GGAGTAC
*
1712 AGAAAATCATGAG
1 AAAAAATCATGAG
1725 ATAATATCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
18 2 0.07
19 12 0.44
20 11 0.41
21 2 0.07
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.17
Consensus pattern (19 bp):
AAAAAATCATGAGGAGTAC
Found at i:3518 original size:23 final size:23
Alignment explanation
Indices: 3492--3552 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 23
3482 TTTTTACATA
3492 TTATTAATATTATTACTATTATT
1 TTATTAATATTATTACTATTATT
3515 TTATTAATA-TATTA--ATTATT
1 TTATTAATATTATTACTATTATT
*
3535 TT-TAAAGTATTATTACTA
1 TTATTAA-TATTATTACTA
3553 CTAATGATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 3 0.09
20 10 0.30
21 5 0.15
22 5 0.15
23 10 0.30
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (23 bp):
TTATTAATATTATTACTATTATT
Found at i:3822 original size:12 final size:11
Alignment explanation
Indices: 3807--3937 Score: 55
Period size: 10 Copynumber: 11.9 Consensus size: 11
3797 GTATATAAGT
3807 TTTAATATTATA
1 TTTAATA-TATA
3819 TTT-ATATATA
1 TTTAATATATA
*
3829 -TTATTATATA
1 TTTAATATATA
3839 TTTTAATAT-TA
1 -TTTAATATATA
*
3850 -TTAGT-TATA
1 TTTAATATATA
*
3859 TTT-TTATACTA
1 TTTAATATA-TA
3870 TTATATATATATA
1 TT-TA-ATATATA
*
3883 TCTAATAT-TA
1 TTTAATATATA
* **
3893 TATGGTATAT-
1 TTTAATATATA
3903 TTCTAATACTATTA
1 TT-TAATA-TA-TA
3917 TTTATATATATA
1 TTTA-ATATATA
3929 TTT-ATATAT
1 TTTAATATAT
3938 GTATGTATGT
Statistics
Matches: 91, Mismatches: 12, Indels: 34
0.66 0.09 0.25
Matches are distributed among these distances:
8 1 0.01
9 9 0.10
10 28 0.31
11 17 0.19
12 19 0.21
13 8 0.09
14 9 0.10
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAATATATA
Found at i:3835 original size:18 final size:19
Alignment explanation
Indices: 3812--3895 Score: 75
Period size: 18 Copynumber: 4.4 Consensus size: 19
3802 TAAGTTTTAA
3812 TATTATATTTATATA-TAT
1 TATTATATTTATATACTAT
* *
3830 TATTATATATTTTAATATTAT
1 TATTATAT-TTAT-ATACTAT
*
3851 TAGTTATATTTTTATACTAT
1 TA-TTATATTTATATACTAT
* *
3871 TA-TATATATATAT-CTAA
1 TATTATATTTATATACTAT
3888 TATTATAT
1 TATTATAT
3896 GGTATATTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
17 5 0.09
18 22 0.39
19 3 0.05
20 11 0.20
21 9 0.16
22 6 0.11
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (19 bp):
TATTATATTTATATACTAT
Found at i:3840 original size:20 final size:19
Alignment explanation
Indices: 3815--3877 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 19
3805 GTTTTAATAT
3815 TATATTTATATATATTATTA
1 TATATTT-TATATATTATTA
3835 TATATTTTA-ATATTATTA
1 TATATTTTATATATTATTA
*
3853 GTTATATTTT-TATACTATTA
1 --TATATTTTATATATTATTA
3873 TATAT
1 TATAT
3878 ATATATCTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
18 14 0.36
19 2 0.05
20 23 0.59
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TATATTTTATATATTATTA
Done.