Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2225
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: 16203
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Found at i:2704 original size:46 final size:46
Alignment explanation
Indices: 2654--2829 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
2644 TGGTTGAGCA
2654 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
*
2700 TCCGAACTCGTTGAGTTGAGTCCGAGTT--C-GA-GAGATGT-AACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGTGAA-T--G
* * * *
2745 CATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
* *
2793 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2830 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 8, Indels: 22
0.79 0.06 0.16
Matches are distributed among these distances:
42 3 0.03
43 7 0.06
44 1 0.01
45 1 0.01
46 63 0.57
47 26 0.23
48 1 0.01
49 1 0.01
50 5 0.05
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
Found at i:2810 original size:93 final size:93
Alignment explanation
Indices: 2651--2821 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
2641 GGATGGTTGA
* * * *
2651 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2716 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
2744 GCATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2809 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
2822 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:4661 original size:64 final size:65
Alignment explanation
Indices: 4560--4689 Score: 235
Period size: 64 Copynumber: 2.0 Consensus size: 65
4550 CCCCTAGGGT
4560 TAAGGTTGACCTAAATGCATGTTTGACTGTTACTATTTACTACATGCCATG-TATTATTATCTGA
1 TAAGGTTGACCTAAATGCATGTTTGACTGTTACTATTTACTACATGCCATGTTATTATTATCTGA
* *
4624 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCTGA
1 TAAGGTTGACCTAAATGCATGTTTGACTGTTACTATTTACTACATGCCATGTTATTATTATCTGA
4689 T
1 T
4690 GTATGGGACT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 49 0.78
65 14 0.22
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (65 bp):
TAAGGTTGACCTAAATGCATGTTTGACTGTTACTATTTACTACATGCCATGTTATTATTATCTGA
Found at i:4675 original size:30 final size:30
Alignment explanation
Indices: 4577--4676 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 30
4567 GACCTAAATG
*
4577 CATGTTTGACTGTTACTATTTACTACATGC
1 CATGTTTGACTGTTACTATTTACTGCATGC
* * *** * *
4607 CATGTATTATTATCTGATAAGGTTGACCTGAATG-
1 CATG--TT-TGA-CTGTTACTATTTA-CTGCATGC
4641 CATGTTTGACTGTTACTATTTACTGCATGC
1 CATGTTTGACTGTTACTATTTACTGCATGC
4671 CATGTT
1 CATGTT
4677 ATTATTATCT
Statistics
Matches: 49, Mismatches: 15, Indels: 12
0.64 0.20 0.16
Matches are distributed among these distances:
29 6 0.12
30 18 0.37
31 2 0.04
32 4 0.08
33 2 0.04
34 12 0.24
35 5 0.10
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (30 bp):
CATGTTTGACTGTTACTATTTACTGCATGC
Found at i:12635 original size:79 final size:81
Alignment explanation
Indices: 12499--12683 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
12489 TTGAATGATG
* *
12499 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
12563 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
12578 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
12640 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
12658 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
12684 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:12697 original size:40 final size:40
Alignment explanation
Indices: 12500--12683 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
12490 TGAATGATGT
* * * *
12500 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
12540 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
12580 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
12618 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
12659 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
12684 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:12705 original size:79 final size:79
Alignment explanation
Indices: 12552--12716 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
12542 GGACTAAGAT
* * **
12552 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
12617 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
12631 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
12694 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
12710 CCGAAGG
1 CCGAAGG
12717 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:16164 original size:1 final size:1
Alignment explanation
Indices: 16158--16187 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
16148 ATCAATGCAT
16158 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16188 TGGCCTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.