Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1932
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: 20367
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Found at i:3044 original size:19 final size:20
Alignment explanation
Indices: 3014--3090 Score: 84
Period size: 19 Copynumber: 3.9 Consensus size: 20
3004 TTTTACCCAG
*
3014 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
3034 ATGTAT-GATACATGTGTGA
1 ATGTATCGATACATTTTTCA
*
3053 ATGTATCGATACATTCTTCAA
1 ATGTATCGATACATTTTTC-A
*
3074 ATGTATCAATACATTTT
1 ATGTATCGATACATTTT
3091 GTCTTTTACC
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.35
20 14 0.30
21 16 0.35
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3120 original size:90 final size:90
Alignment explanation
Indices: 2964--3137 Score: 242
Period size: 90 Copynumber: 1.9 Consensus size: 90
2954 TTTTACCCAG
* * * **
2964 ATGTATCAATATATTTTTCAATGTATCGATACATTCTATCTTTTACCCAGATGTATTGATACATT
1 ATGTATCAATACATTCTTCAATGTATCAATACATTCTATCTTTTACCCAGATGTATCAATACATT
3029 TTTCAATGTAT-GATACATGTGTGA
66 TTTCAATGTATCGATACATGTGTGA
* * * * *
3053 ATGTATCGATACATTCTTCAAATGTATCAATACATTTTGTCTTTTACCGAGATGTATCAATATAT
1 ATGTATCAATACATTCTTC-AATGTATCAATACATTCTATCTTTTACCCAGATGTATCAATACAT
3118 TTTTCAATGTATCGATACAT
65 TTTTCAATGTATCGATACAT
3138 CTAGTTAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
89 16 0.22
90 50 0.68
91 7 0.10
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (90 bp):
ATGTATCAATACATTCTTCAATGTATCAATACATTCTATCTTTTACCCAGATGTATCAATACATT
TTTCAATGTATCGATACATGTGTGA
Found at i:7546 original size:6 final size:6
Alignment explanation
Indices: 7537--7607 Score: 51
Period size: 6 Copynumber: 12.3 Consensus size: 6
7527 GAGTTAGATA
* ** *
7537 ATTTAT ATTTAT -TATAT ATTTAT ATAAAT -TTTA- ATATAT ATTTAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
* *
7582 ATTTAT -GTTAT GTATTAT ATTTAT AT
1 ATTTAT ATTTAT AT-TTAT ATTTAT AT
7608 CGGGTAAGTT
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
5 13 0.27
6 31 0.63
7 5 0.10
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (6 bp):
ATTTAT
Found at i:7567 original size:10 final size:10
Alignment explanation
Indices: 7540--7607 Score: 55
Period size: 11 Copynumber: 6.1 Consensus size: 10
7530 TTAGATAATT
7540 TATATTTATTA
1 TATATTTA-TA
7551 TATATTTATA
1 TATATTTATA
*
7561 TAAATTTTAATA
1 TATA-TTT-ATA
7573 TATATTTATA
1 TATATTTATA
*
7583 TTTATGTTATGTA
1 TATAT-TTA--TA
7596 TTATATTTATA
1 -TATATTTATA
7607 T
1 T
7608 CGGGTAAGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
10 13 0.28
11 19 0.40
12 6 0.13
13 5 0.11
14 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (10 bp):
TATATTTATA
Found at i:7569 original size:22 final size:22
Alignment explanation
Indices: 7544--7607 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
7534 ATAATTTATA
7544 TTTATTATATATTTATATAAAT
1 TTTATTATATATTTATATAAAT
* **
7566 TTTAATATATATTTATATTTAT
1 TTTATTATATATTTATATAAAT
*
7588 GTTATGTATTATATTTATAT
1 TTTAT-TA-TATATTTATAT
7608 CGGGTAAGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 22 0.63
23 2 0.06
24 11 0.31
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (22 bp):
TTTATTATATATTTATATAAAT
Found at i:8346 original size:2 final size:2
Alignment explanation
Indices: 8339--8368 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8329 ATAGCAAAGC
8339 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
8369 GGATTCTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:14803 original size:14 final size:15
Alignment explanation
Indices: 14784--14812 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
14774 ACTAACAAAG
14784 TGTTAAT-AAATAAA
1 TGTTAATAAAATAAA
14798 TGTTAATAAAATAAA
1 TGTTAATAAAATAAA
14813 AGGCCATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (15 bp):
TGTTAATAAAATAAA
Found at i:15265 original size:24 final size:23
Alignment explanation
Indices: 15238--15305 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 23
15228 ATAACATAAA
*
15238 TAAAATATAAATATATAAATATTT
1 TAAAATATAAATATATAAAT-TAT
* *
15262 TAAAATTTATATAATATAAATTAT
1 TAAAATATAAAT-ATATAAATTAT
15286 TAATAA-ATAAAATATATAAA
1 TAA-AATAT-AAATATATAAA
15306 ATTGTGGGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
24 23 0.64
25 13 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAAATATAAATATATAAATTAT
Found at i:19348 original size:27 final size:26
Alignment explanation
Indices: 19277--19348 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 26
19267 TTTTAAAAAT
19277 TAATTAATATATTTTTTATAATAATAA
1 TAATTAATA-ATTTTTTATAATAATAA
* *
19304 TAA-TAATAATATTGTTATGAAT-GTAA
1 TAATTAATAAT-TTTTTAT-AATAATAA
19330 TAATTAATAATTTTATTAT
1 TAATTAATAATTTT-TTAT
19349 TTAATATTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
25 2 0.05
26 19 0.50
27 17 0.45
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (26 bp):
TAATTAATAATTTTTTATAATAATAA
Done.