Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_5155
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: 12078
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Found at i:750 original size:27 final size:27
Alignment explanation
Indices: 712--778 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
702 ATTTACTTGT
*
712 TGCACTAAGTGTGCGAAATGAATATGA
1 TGCACTAAGTGTGCGAAATGAACATGA
* * *
739 TGCACTAAGTGTGCGAATTGACCATGC
1 TGCACTAAGTGTGCGAAATGAACATGA
*
766 GGCACTAAGTGTG
1 TGCACTAAGTGTG
779 TGCATGCGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.25
Consensus pattern (27 bp):
TGCACTAAGTGTGCGAAATGAACATGA
Found at i:786 original size:20 final size:20
Alignment explanation
Indices: 761--798 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
751 GCGAATTGAC
761 CATGCGGCACTAAGTGTGTG
1 CATGCGGCACTAAGTGTGTG
781 CATGCGGCACTAAGTGTG
1 CATGCGGCACTAAGTGTG
799 CGTTTGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (20 bp):
CATGCGGCACTAAGTGTGTG
Found at i:826 original size:73 final size:74
Alignment explanation
Indices: 713--851 Score: 183
Period size: 73 Copynumber: 1.9 Consensus size: 74
703 TTTACTTGTT
*
713 GCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGT
1 GCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCACGCGGCACTAAGTGT
778 GTGCATGCG
66 GTGCATGCG
** * * ** *
787 GCACTAAGTGTGCG-TTTGACTATG-TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCACGCGGCACTAAGTG
850 TG
65 TG
852 CGAGTTGATT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 1 0.02
73 41 0.73
74 14 0.25
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (74 bp):
GCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCACGCGGCACTAAGTGT
GTGCATGCG
Found at i:843 original size:27 final size:27
Alignment explanation
Indices: 787--880 Score: 127
Period size: 27 Copynumber: 3.5 Consensus size: 27
777 TGTGCATGCG
*
787 GCACTAAGTGTGCG-TTTGACTATGTA
1 GCACTAAGTGTGCGATTTGATTATGTA
* *
813 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGATTTGATTATGTA
* *
840 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGATTATGTA
*
867 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
881 GGCTCAATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
26 14 0.24
27 45 0.76
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGATTATGTA
Found at i:871 original size:100 final size:99
Alignment explanation
Indices: 688--878 Score: 233
Period size: 100 Copynumber: 1.9 Consensus size: 99
678 AAATTGTACA
* *
688 GCACTAAGTGTGCGATTTACTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGTGC
1 GCACTAAGTGTGCGATTTACTTGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGTGC
* *
753 GAATTGACCATGCGGCACTAAGTGTGTGCATGCG
66 GAATTGACCATACAGCACTAAGTGTGTGCATGCG
** *
787 GCACTAAGTGTGCG-TTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAGTG
1 GCACTAAGTGTGCGATTT-ACT-TGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGTG
* ** * *
850 TGCGAGTTGATTATATAGCACTGAGTGTG
63 TGCGAATTGACCATACAGCACTAAGTGTG
879 CGGGCTCAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
98 3 0.04
99 18 0.23
100 56 0.73
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (99 bp):
GCACTAAGTGTGCGATTTACTTGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGTGC
GAATTGACCATACAGCACTAAGTGTGTGCATGCG
Found at i:8484 original size:27 final size:26
Alignment explanation
Indices: 8453--8622 Score: 156
Period size: 26 Copynumber: 6.6 Consensus size: 26
8443 TAAATTGTAC
8453 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGA-TATGT
* *
8480 TGCACTAAGTGTGCGA-ATGAATATG-
1 AGCACTAAGTGTGCGATTTG-ATATGT
* * *
8505 ATGCACTAAGTGTGCGAATTGACATGC
1 A-GCACTAAGTGTGCGATTTGATATGT
*
8532 GGCACTAAGTGTGCGAGTTTG--ATG-
1 AGCACTAAGTGTGCGA-TTTGATATGT
8556 AGCACTAAGTG-GCGATTTGAT-TCGT
1 AGCACTAAGTGTGCGATTTGATAT-GT
* *
8581 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGA-TATGT
*
8608 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
8623 GGCTCAATAA
Statistics
Matches: 120, Mismatches: 11, Indels: 24
0.77 0.07 0.15
Matches are distributed among these distances:
22 4 0.03
23 5 0.04
24 11 0.09
25 14 0.12
26 48 0.40
27 37 0.31
28 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTTGATATGT
Found at i:8596 original size:49 final size:48
Alignment explanation
Indices: 8453--8599 Score: 147
Period size: 49 Copynumber: 2.9 Consensus size: 48
8443 TAAATTGTAC
**
8453 AGCACTAAGTGTGCGATTTGACTAT-GTTGCACTAAGTGTGCGAATGAATATG
1 AGCACTAAGTGTGCGATTTGA-T-TCG-TGCACTAAGTGTGCG-A-GTTTATG
* *
8505 ATGCACTAAGTGTGCGAATTGACATGCG-GCACTAAGTGTGCGAGTTTGATG
1 A-GCACTAAGTGTGCGATTTG--ATTCGTGCACTAAGTGTGCGAGTTT-ATG
8556 AGCACTAAGTG-GCGATTTGATTCGTAGCACTAAGTGTGCGAGTT
1 AGCACTAAGTGTGCGATTTGATTCGT-GCACTAAGTGTGCGAGTT
8600 GATTATATAG
Statistics
Matches: 82, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
47 4 0.05
49 25 0.30
50 12 0.15
51 5 0.06
52 15 0.18
53 18 0.22
54 2 0.02
55 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (48 bp):
AGCACTAAGTGTGCGATTTGATTCGTGCACTAAGTGTGCGAGTTTATG
Done.