Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1473
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: 53377
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:554 original size:1 final size:1
Alignment explanation
Indices: 548--574 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
538 CTCTCCAAAG
548 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
575 AGGAAGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11737 original size:42 final size:44
Alignment explanation
Indices: 11650--11742 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 44
11640 ATAAATAAAG
* * ** *
11650 ATATATATATATGAATTACAAAACATGAAAATATAAGTATTTAC
1 ATATATAAATATGAATTAAAAAACATGAAAATATAAACATGTAC
* *
11694 ATATATAAATA-GATTTAAAAAATAT-AAAATATAAACATGTAC
1 ATATATAAATATGAATTAAAAAACATGAAAATATAAACATGTAC
11736 AT-TATAA
1 ATATATAA
11743 GAACGTAGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 5 0.12
42 16 0.38
43 11 0.26
44 10 0.24
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (44 bp):
ATATATAAATATGAATTAAAAAACATGAAAATATAAACATGTAC
Found at i:13224 original size:16 final size:17
Alignment explanation
Indices: 13205--13238 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13195 ATTAATGTTT
13205 TGGGCTA-TTTGGGCTG
1 TGGGCTAGTTTGGGCTG
*
13221 TGGGTTAGTTTGGGCTG
1 TGGGCTAGTTTGGGCTG
13238 T
1 T
13239 TAATTTGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.06, C:0.09, G:0.44, T:0.41
Consensus pattern (17 bp):
TGGGCTAGTTTGGGCTG
Found at i:13418 original size:24 final size:25
Alignment explanation
Indices: 13385--13434 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
13375 GATTTGAATT
13385 TTAAAATTTTGAAAAATAAAG-AAA
1 TTAAAATTTTGAAAAATAAAGTAAA
* * *
13409 TTAAACTTTTGGAAATTAAAGTAAA
1 TTAAAATTTTGAAAAATAAAGTAAA
13434 T
1 T
13435 GGACTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (25 bp):
TTAAAATTTTGAAAAATAAAGTAAA
Found at i:14128 original size:19 final size:19
Alignment explanation
Indices: 14094--14138 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
14084 ACAAATGACC
* *
14094 TAAATTTTTATTTTAT-AT
1 TAAATTCTTATATTATAAT
14112 TAATATTCTTATATTATAAT
1 TAA-ATTCTTATATTATAAT
14132 TAAATTC
1 TAAATTC
14139 AAGTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 15 0.65
20 5 0.22
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
TAAATTCTTATATTATAAT
Found at i:17313 original size:21 final size:21
Alignment explanation
Indices: 17258--17313 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
17248 TGAAAATATT
*
17258 AAATATTAAT-AT-TTTAATAA
1 AAATATTAATAATAATT-ATAA
* *
17278 AAATATTTATTATAATTATAA
1 AAATATTAATAATAATTATAA
*
17299 ATATATTAATAATAA
1 AAATATTAATAATAA
17314 ATATTTTGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.31
21 18 0.62
22 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATATTAATAATAATTATAA
Found at i:23154 original size:23 final size:23
Alignment explanation
Indices: 23110--23197 Score: 88
Period size: 23 Copynumber: 3.8 Consensus size: 23
23100 TTAATGTTCA
**
23110 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-CGAACATTAAT
* *
23133 CGAACATGTTCACGGACATTAAA
1 CGAACATGTTCACGAACATTAAT
*
23156 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCACGAACAT-TAAT
**
23180 TAAACATGTTCACGAACA
1 CGAACATGTTCACGAACA
23198 ATGTTAATAA
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 2 0.04
23 33 0.62
24 18 0.34
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (23 bp):
CGAACATGTTCACGAACATTAAT
Found at i:23408 original size:12 final size:12
Alignment explanation
Indices: 23379--23432 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
23369 ATCATTAATA
23379 AATAAACGAGTC
1 AATAAACGAGTC
23391 -ATAAACGAGTC
1 AATAAACGAGTC
23402 AATAAACGAG-C
1 AATAAACGAGTC
* *
23413 TTATAAACGAGCC
1 -AATAAACGAGTC
23426 AATAAAC
1 AATAAAC
23433 AAGCTTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
11 12 0.32
12 24 0.65
13 1 0.03
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.17
Consensus pattern (12 bp):
AATAAACGAGTC
Found at i:23423 original size:24 final size:24
Alignment explanation
Indices: 23379--23446 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
23369 ATCATTAATA
* *
23379 AATAAACGAG-TCATAAACGAGTC
1 AATAAACGAGCTTATAAACGAGCC
23402 AATAAACGAGCTTATAAACGAGCC
1 AATAAACGAGCTTATAAACGAGCC
* *
23426 AATAAACAAGCTTTTAAACGA
1 AATAAACGAGCTTATAAACGA
23447 ACTCGTTCGT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 10 0.25
24 30 0.75
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.19
Consensus pattern (24 bp):
AATAAACGAGCTTATAAACGAGCC
Found at i:28501 original size:27 final size:25
Alignment explanation
Indices: 28463--28514 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
28453 TAATTTTAAT
28463 TTAAAATAAGAATAATTTTTTAATATA
1 TTAAAATAAGAAT--TTTTTTAATATA
28490 TTAACAAT-AGAATTTTTTTAATATA
1 TTAA-AATAAGAATTTTTTTAATATA
28515 AAAGGTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 12 0.50
27 9 0.38
28 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
TTAAAATAAGAATTTTTTTAATATA
Found at i:30187 original size:29 final size:29
Alignment explanation
Indices: 30124--30195 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
30114 ATTCACAATA
* *
30124 AATTGAGCCTTCAACATCTATTTTCATGC
1 AATTGACCCTTCAACATCTATTTTCATCC
*
30153 ATTTGAACCCTTCAA-ATCTATTTTCATCC
1 AATTG-ACCCTTCAACATCTATTTTCATCC
*
30182 AATTGAGCCTTCAA
1 AATTGACCCTTCAA
30196 TCTGACAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.22
29 21 0.57
30 8 0.22
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (29 bp):
AATTGACCCTTCAACATCTATTTTCATCC
Found at i:40792 original size:14 final size:15
Alignment explanation
Indices: 40759--40806 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
40749 AACCTTCTGA
*
40759 TGATTCTCTACCAAT
1 TGATTCTCTACCAGT
40774 TGATTCTCTA-CAGT
1 TGATTCTCTACCAGT
40788 TGATTCTCTACCAGT
1 TGATTCTCTACCAGT
40803 TGAT
1 TGAT
40807 GCAATGGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 13 0.42
15 18 0.58
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (15 bp):
TGATTCTCTACCAGT
Found at i:50852 original size:19 final size:17
Alignment explanation
Indices: 50818--50870 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
50808 GCTTAGAAAT
* *
50818 TATTTTTATCACATTAA
1 TATTTTTATAAAATTAA
50835 TAATTTTTATAATAATTAA
1 T-ATTTTTATAA-AATTAA
*
50854 TATTTTTTTAAAATTAA
1 TATTTTTATAAAATTAA
50871 ATTATATAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 7 0.23
18 18 0.58
19 6 0.19
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTTTATAAAATTAA
Found at i:51262 original size:19 final size:17
Alignment explanation
Indices: 51225--51269 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
51215 AATTTAAATA
51225 ATATTAAAAATTATTTT
1 ATATTAAAAATTATTTT
*
51242 ATATTTAAAATATATTTT
1 ATATTAAAAAT-TATTTT
51260 -TA-TAAAAATT
1 ATATTAAAAATT
51270 TTAAAACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 1 0.04
16 6 0.24
17 12 0.48
18 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTAAAAATTATTTT
Done.