Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1679
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: 68618
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:11979 original size:23 final size:23
Alignment explanation
Indices: 11928--11984 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
11918 TTTTATGTTT
11928 TTATTTTTATTCTATTTTAAGAC
1 TTATTTTTATTCTATTTTAAGAC
* * *
11951 TAATTTTTATTTTTTCTTTAA-AC
1 TTATTTTTATTCTAT-TTTAAGAC
*
11974 TTATTTCTATT
1 TTATTTTTATT
11985 AGATTTTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.65
Consensus pattern (23 bp):
TTATTTTTATTCTATTTTAAGAC
Found at i:13799 original size:38 final size:38
Alignment explanation
Indices: 13757--13885 Score: 177
Period size: 38 Copynumber: 3.4 Consensus size: 38
13747 TTTAAGCTCA
* * * *
13757 GATATAATACCACCACTAGGCCTGTGGGATTTAACCCG
1 GATATAATACCAGCACGAAGCCTGCGGGATTTAACCCG
* *
13795 GATATAATACCAGCACGAAGCCTGCAGGATTTAACCCA
1 GATATAATACCAGCACGAAGCCTGCGGGATTTAACCCG
* *
13833 GATATATTACTAGCACGAAGCCTGCGGGATTTAACCCG
1 GATATAATACCAGCACGAAGCCTGCGGGATTTAACCCG
*
13871 GATATAATTCCAGCA
1 GATATAATACCAGCA
13886 TATAGCCTGC
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 78 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (38 bp):
GATATAATACCAGCACGAAGCCTGCGGGATTTAACCCG
Found at i:21829 original size:38 final size:38
Alignment explanation
Indices: 21784--21914 Score: 181
Period size: 38 Copynumber: 3.4 Consensus size: 38
21774 ACTTTAAGCT
* *
21784 CAGATATAATACCAGCACTAGGCCTGCGGGATTTAACC
1 CAGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
*
21822 CAGATATAATACCAGCACGAAGCCTGCAGGATTTAACC
1 CAGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
* * *
21860 CGGATATATTACTAGCACGAAGCCTGCGGGATTTAACC
1 CAGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
** *
21898 TGGATATAATTCCAGCA
1 CAGATATAATACCAGCA
21915 TATAGTCTGC
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 82 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (38 bp):
CAGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
Found at i:30520 original size:23 final size:23
Alignment explanation
Indices: 30449--30535 Score: 67
Period size: 21 Copynumber: 4.0 Consensus size: 23
30439 ACCTGATCAG
*
30449 AATACGACACATAA-GTGCCT-A
1 AATACGACACACAAGGTGCCTGA
* * *
30470 AA-ATGACACACGAGGTGTCTG-
1 AATACGACACACAAGGTGCCTGA
* *
30491 -CTGCGACACACAAGGTGCCTGA
1 AATACGACACACAAGGTGCCTGA
* *
30513 AATACGACACATAAAGTGCCTGA
1 AATACGACACACAAGGTGCCTGA
30536 TTAGTAAAGC
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
20 8 0.17
21 22 0.46
23 18 0.38
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (23 bp):
AATACGACACACAAGGTGCCTGA
Found at i:30793 original size:28 final size:26
Alignment explanation
Indices: 30724--30837 Score: 132
Period size: 23 Copynumber: 4.4 Consensus size: 26
30714 AAATGTCCAA
30724 CCAAAACACACCAG---TATAATCCT
1 CCAAAACACACCAGATATATAATCCT
30747 CCAAAACACACCAG---TATAATCCT
1 CCAAAACACACCAGATATATAATCCT
30770 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG-AT-ATATAATCCT
*
30798 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG-AT-ATATAATCC-T
30827 CCAAAACACAC
1 CCAAAACACAC
30838 TAGAATAGCA
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
23 37 0.46
28 33 0.41
29 11 0.14
ACGTcount: A:0.46, C:0.34, G:0.04, T:0.17
Consensus pattern (26 bp):
CCAAAACACACCAGATATATAATCCT
Found at i:30843 original size:29 final size:28
Alignment explanation
Indices: 30738--30844 Score: 134
Period size: 28 Copynumber: 4.0 Consensus size: 28
30728 AACACACCAG
30738 TATAATCCTCCAAAACACACCAG-----
1 TATAATCCTCCAAAACACACCAGAATAA
* *
30761 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
30789 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
*
30817 TATAATCCATCCAAAACACACTAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
30845 GCACAAAGTG
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
23 23 0.32
28 33 0.45
29 17 0.23
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.20
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:31528 original size:16 final size:16
Alignment explanation
Indices: 31507--31540 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31497 GAGTTACCGA
*
31507 TTCATTTATCAGATAT
1 TTCATTAATCAGATAT
*
31523 TTCATTAATCCGATAT
1 TTCATTAATCAGATAT
31539 TT
1 TT
31541 TCTTTTCCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (16 bp):
TTCATTAATCAGATAT
Found at i:34266 original size:28 final size:28
Alignment explanation
Indices: 34235--34295 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
34225 AAAATAATTA
34235 AAATTTAA-TATGTTAATAATTTAAGTGT
1 AAATTTAATTAT-TTAATAATTTAAGTGT
* *
34263 AAA-TTAATTATTTTATAATTTATGTGT
1 AAATTTAATTATTTAATAATTTAAGTGT
*
34290 GAATTT
1 AAATTT
34296 TGACAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (28 bp):
AAATTTAATTATTTAATAATTTAAGTGT
Found at i:42398 original size:39 final size:40
Alignment explanation
Indices: 42298--42482 Score: 189
Period size: 40 Copynumber: 4.7 Consensus size: 40
42288 TCGAATGATG
* * * *
42298 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
42338 TTCAGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
42378 TCTGGGCTAAG-CCCGAAGGCATTGGTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42417 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
42458 -CCGAGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42483 AACGAGTAGC
Statistics
Matches: 118, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
39 33 0.28
40 75 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42515 original size:79 final size:79
Alignment explanation
Indices: 42351--42507 Score: 176
Period size: 79 Copynumber: 2.0 Consensus size: 79
42341 AGACTAAGAT
* * * **
42351 CCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGCCCGAAGGCATTGGTGCAAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGAGCTAAGCCCGAAGGCATTGGAACAAGTTACTAA
*
42416 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
42430 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGAGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGAGCTAAG-CCCGAAGGCATTGGAACAAGTTA-C
*
42493 TATATCC-GGTTAAAT
63 TAAATCCGGGTTAAAT
42508 TCTGAAGGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 40 0.62
80 23 0.35
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGAGCTAAGCCCGAAGGCATTGGAACAAGTTACTAA
ATCCGGGTTAAATC
Done.