Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g02149.F1
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, 752
Length: 1254
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Found at i:628 original size:15 final size:15
Alignment explanation
Indices: 580--900 Score: 67
Period size: 15 Copynumber: 21.0 Consensus size: 15
570 TGACCTGCCT
580 TCATGTAAATGCAGC
1 TCATGTAAATGCAGC
* ** *
595 TCGTGCGATTGCA-C
1 TCATGTAAATGCAGC
609 TTCATGTAAATGCAGC
1 -TCATGTAAATGCAGC
* * *
625 TCATGCAACTGCA-A
1 TCATGTAAATGCAGC
*
639 TCCGTGTAAATGCAGC
1 T-CATGTAAATGCAGC
* ** * *
655 TCGTGCGACTGCA-A
1 TCATGTAAATGCAGC
*
669 TCCGTGTAAATGCAGC
1 T-CATGTAAATGCAGC
* * * *
685 TCGTGCAACTGCA-A
1 TCATGTAAATGCAGC
* *
699 TCCGTGTAAATGCGGC
1 T-CATGTAAATGCAGC
** * *
715 TCATGCGACTGCA-A
1 TCATGTAAATGCAGC
729 TCCATGTAAATGCAGC
1 T-CATGTAAATGCAGC
* * * * * *
745 CCGTGTGACTGTAGT
1 TCATGTAAATGCAGC
760 TCATGTAAATGCAGC
1 TCATGTAAATGCAGC
* * * *
775 AGTTTATGTGACTGCAGT
1 ---TCATGTAAATGCAGC
*
793 TCATGTAATTGCAGC
1 TCATGTAAATGCAGC
* * * *
808 TCATGCAACTGTAGT
1 TCATGTAAATGCAGC
823 TCATGTAAATGCAGC
1 TCATGTAAATGCAGC
* ** * *
838 AGTTTATGCGACTGCAGT
1 ---TCATGTAAATGCAGC
* *
856 TCTTGTAAATGCATC
1 TCATGTAAATGCAGC
* * *
871 TCATGCAACTGCAGT
1 TCATGTAAATGCAGC
886 TCATGTAAATGCAGC
1 TCATGTAAATGCAGC
901 AGTTTATGCG
Statistics
Matches: 202, Mismatches: 88, Indels: 32
0.63 0.27 0.10
Matches are distributed among these distances:
14 5 0.02
15 172 0.85
16 4 0.02
18 21 0.10
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.28
Consensus pattern (15 bp):
TCATGTAAATGCAGC
Found at i:794 original size:33 final size:33
Alignment explanation
Indices: 751--933 Score: 234
Period size: 33 Copynumber: 5.7 Consensus size: 33
741 CAGCCCGTGT
* *
751 GACTGTAGTTCATGTAAATGCAGCAGTTTATGT
1 GACTGCAGTTCATGTAAATGCAGCAGTTTATGC
* *
784 GACTGCAGTTCATGTAATTGCAGC---TCATGC
1 GACTGCAGTTCATGTAAATGCAGCAGTTTATGC
* *
814 AACTGTAGTTCATGTAAATGCAGCAGTTTATGC
1 GACTGCAGTTCATGTAAATGCAGCAGTTTATGC
* * *
847 GACTGCAGTTCTTGTAAATGCATC---TCATGC
1 GACTGCAGTTCATGTAAATGCAGCAGTTTATGC
*
877 AACTGCAGTTCATGTAAATGCAGCAGTTTATGC
1 GACTGCAGTTCATGTAAATGCAGCAGTTTATGC
910 GACTGCAGTTCATGTAAATGCAGC
1 GACTGCAGTTCATGTAAATGCAGC
934 TCGTGTGACT
Statistics
Matches: 126, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
30 51 0.40
33 75 0.60
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (33 bp):
GACTGCAGTTCATGTAAATGCAGCAGTTTATGC
Found at i:931 original size:15 final size:15
Alignment explanation
Indices: 757--932 Score: 84
Period size: 15 Copynumber: 11.1 Consensus size: 15
747 GTGTGACTGT
757 AGTTCATGTAAATGCAGC
1 AGTTCATGTAAAT---GC
* * *
775 AGTTTATGTGACTGC
1 AGTTCATGTAAATGC
*
790 AGTTCATGTAATTGC
1 AGTTCATGTAAATGC
* * * *
805 AGCTCATGCAACTGT
1 AGTTCATGTAAATGC
820 AGTTCATGTAAATGCAGC
1 AGTTCATGTAAAT---GC
* ** *
838 AGTTTATGCGACTGC
1 AGTTCATGTAAATGC
*
853 AGTTCTTGTAAATGC
1 AGTTCATGTAAATGC
* *
868 A-TCTCATGCAACTGC
1 AGT-TCATGTAAATGC
883 AGTTCATGTAAATGCAGC
1 AGTTCATGTAAAT---GC
* ** *
901 AGTTTATGCGACTGC
1 AGTTCATGTAAATGC
916 AGTTCATGTAAATGC
1 AGTTCATGTAAATGC
931 AG
1 AG
933 CTCGTGTGAC
Statistics
Matches: 114, Mismatches: 36, Indels: 19
0.67 0.21 0.11
Matches are distributed among these distances:
14 1 0.01
15 81 0.71
16 1 0.01
18 31 0.27
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (15 bp):
AGTTCATGTAAATGC
Found at i:946 original size:63 final size:62
Alignment explanation
Indices: 546--935 Score: 380
Period size: 63 Copynumber: 6.3 Consensus size: 62
536 CATCGGAACA
* * * * * * *
546 CAGTTCGTGCAAATGCAGCTCATGTGACCTGC-CTTCATGTAAATGCAGC--TCGTGCGATTG
1 CAGTTCATGTAAATGCAGCTCATG-CAACTGCAGTTCATGTAAATGCAGCGTTCATGCGACTG
* * * * *
606 CACTTCATGTAAATGCAGCTCATGCAACTGCAATCCGTGTAAATGCAGC--TCGTGCGACTG
1 CAGTTCATGTAAATGCAGCTCATGCAACTGCAGTTCATGTAAATGCAGCGTTCATGCGACTG
* * * * * * * *
666 CAATCCGTGTAAATGCAGCTCGTGCAACTGCAATCCGTGTAAATGC-G-GCTCATGCGACTG
1 CAGTTCATGTAAATGCAGCTCATGCAACTGCAGTTCATGTAAATGCAGCGTTCATGCGACTG
* * * * ** * * *
726 CAATCCATGTAAATGCAGCCCGTGTGACTGTAGTTCATGTAAATGCAGCAGTTTATGTGACTG
1 CAGTTCATGTAAATGCAGCTCATGCAACTGCAGTTCATGTAAATGCAGC-GTTCATGCGACTG
* * *
789 CAGTTCATGTAATTGCAGCTCATGCAACTGTAGTTCATGTAAATGCAGCAGTTTATGCGACTG
1 CAGTTCATGTAAATGCAGCTCATGCAACTGCAGTTCATGTAAATGCAGC-GTTCATGCGACTG
* * *
852 CAGTTCTTGTAAATGCATCTCATGCAACTGCAGTTCATGTAAATGCAGCAGTTTATGCGACTG
1 CAGTTCATGTAAATGCAGCTCATGCAACTGCAGTTCATGTAAATGCAGC-GTTCATGCGACTG
915 CAGTTCATGTAAATGCAGCTC
1 CAGTTCATGTAAATGCAGCTC
936 GTGTGACTGC
Statistics
Matches: 285, Mismatches: 39, Indels: 9
0.86 0.12 0.03
Matches are distributed among these distances:
59 6 0.02
60 135 0.47
61 1 0.00
63 143 0.50
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (62 bp):
CAGTTCATGTAAATGCAGCTCATGCAACTGCAGTTCATGTAAATGCAGCGTTCATGCGACTG
Found at i:954 original size:30 final size:30
Alignment explanation
Indices: 546--946 Score: 354
Period size: 30 Copynumber: 13.1 Consensus size: 30
536 CATCGGAACA
* * *
546 CAGTTCGTGCAAATGCAGCTCATGTGACCTG
1 CAGTTCATGTAAATGCAGCTCATGCGA-CTG
* * *
577 C-CTTCATGTAAATGCAGCTCGTGCGATTG
1 CAGTTCATGTAAATGCAGCTCATGCGACTG
* *
606 CACTTCATGTAAATGCAGCTCATGCAACTG
1 CAGTTCATGTAAATGCAGCTCATGCGACTG
* * * *
636 CAATCCGTGTAAATGCAGCTCGTGCGACTG
1 CAGTTCATGTAAATGCAGCTCATGCGACTG
* * * * *
666 CAATCCGTGTAAATGCAGCTCGTGCAACTG
1 CAGTTCATGTAAATGCAGCTCATGCGACTG
* * * *
696 CAATCCGTGTAAATGCGGCTCATGCGACTG
1 CAGTTCATGTAAATGCAGCTCATGCGACTG
* * * * *
726 CAATCCATGTAAATGCAGCCCGTGTGACTG
1 CAGTTCATGTAAATGCAGCTCATGCGACTG
* * *
756 TAGTTCATGTAAATGCAGCAGTTTATGTGACTG
1 CAGTTCATGTAAATGCAGC---TCATGCGACTG
* *
789 CAGTTCATGTAATTGCAGCTCATGCAACTG
1 CAGTTCATGTAAATGCAGCTCATGCGACTG
* *
819 TAGTTCATGTAAATGCAGCAGTTTATGCGACTG
1 CAGTTCATGTAAATGCAGC---TCATGCGACTG
* * *
852 CAGTTCTTGTAAATGCATCTCATGCAACTG
1 CAGTTCATGTAAATGCAGCTCATGCGACTG
*
882 CAGTTCATGTAAATGCAGCAGTTTATGCGACTG
1 CAGTTCATGTAAATGCAGC---TCATGCGACTG
* *
915 CAGTTCATGTAAATGCAGCTCGTGTGACTG
1 CAGTTCATGTAAATGCAGCTCATGCGACTG
945 CA
1 CA
947 AATCATGTTT
Statistics
Matches: 310, Mismatches: 50, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
29 3 0.01
30 228 0.74
31 1 0.00
33 78 0.25
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (30 bp):
CAGTTCATGTAAATGCAGCTCATGCGACTG
Done.