Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold709
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: 9188
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Found at i:518 original size:3 final size:3
Alignment explanation
Indices: 505--539 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
495 TAATTTTTGA
* *
505 TAT TGT TAT TAT TAT TAT TGT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
540 CTATACTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:525 original size:15 final size:15
Alignment explanation
Indices: 505--538 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
495 TAATTTTTGA
505 TATTGTTATTATTAT
1 TATTGTTATTATTAT
520 TATTGTTATTATTAT
1 TATTGTTATTATTAT
535 TATT
1 TATT
539 ACTATACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTGTTATTATTAT
Found at i:728 original size:2 final size:2
Alignment explanation
Indices: 721--753 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
711 TGGGGAGAGG
721 AT AT AT AT AT AT A- AT GAT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT A
754 ATGATTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:746 original size:20 final size:19
Alignment explanation
Indices: 721--762 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
711 TGGGGAGAGG
721 ATATATATATATAATGATAT
1 ATATATATATATAATGAT-T
741 ATATATATATATAATGATT
1 ATATATATATATAATGATT
760 ATA
1 ATA
763 CATTTAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
ATATATATATATAATGATT
Found at i:1820 original size:10 final size:11
Alignment explanation
Indices: 1805--1870 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 11
1795 TTGATAATAA
1805 TATTTAT-TAT
1 TATTTATATAT
1815 TATTTATAATAT
1 TATTTAT-ATAT
1827 TATTTAATATCAT
1 TATTT-ATAT-AT
* *
1840 ATAATAATATAT
1 -TATTTATATAT
*
1852 TTTTTACTATAT
1 TATTTA-TATAT
1864 TATTTAT
1 TATTTAT
1871 TATAAAATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
10 7 0.16
11 4 0.09
12 22 0.50
13 8 0.18
14 3 0.07
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTTATATAT
Found at i:1824 original size:22 final size:20
Alignment explanation
Indices: 1798--1849 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
1788 TTTTTGTTTG
* *
1798 ATAATAATATTTATTATTATTT
1 ATAATAATATTTAATATCA--T
*
1820 ATAATATTATTTAATATCAT
1 ATAATAATATTTAATATCAT
1840 ATAATAATAT
1 ATAATAATAT
1850 ATTTTTTACT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 10 0.38
22 16 0.62
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATAATATTTAATATCAT
Found at i:3029 original size:41 final size:40
Alignment explanation
Indices: 2953--3036 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 40
2943 TACATAAAAA
** *
2953 TAAAAATAAAAATTATTTGATAAAAATACGATAATTTTTT
1 TAAAAATAAAAATTACATGATAAAAATAAGATAATTTTTT
2993 TAAAAATATAAAATTACATGAGTAAAAATAAG-TAATTTTTT
1 TAAAAATA-AAAATTACATGA-TAAAAATAAGATAATTTTTT
3034 TAA
1 TAA
3037 TTAAATTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 8 0.21
41 22 0.56
42 9 0.23
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (40 bp):
TAAAAATAAAAATTACATGATAAAAATAAGATAATTTTTT
Found at i:4747 original size:2 final size:2
Alignment explanation
Indices: 4740--4782 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4730 GAGGCCCATC
4740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4782 A
1 A
4783 AATAGTATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4880 original size:19 final size:19
Alignment explanation
Indices: 4848--4894 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
4838 AATATAATTT
4848 TTAAAATATATAATAAATAAAA
1 TTAAAA-AT-TAATAAA-AAAA
4870 -TAAAAATTAATAAAAAAA
1 TTAAAAATTAATAAAAAAA
4888 TTAAAAA
1 TTAAAAA
4895 ACAGTACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.17
19 13 0.54
20 2 0.08
21 5 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
TTAAAAATTAATAAAAAAA
Found at i:7841 original size:2 final size:2
Alignment explanation
Indices: 7834--7858 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7824 AGTCACATGC
7834 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
7859 ATAGAATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.