Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3437
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: 28823
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Found at i:8120 original size:40 final size:40
Alignment explanation
Indices: 8058--8275 Score: 266
Period size: 40 Copynumber: 5.5 Consensus size: 40
8048 AAACCAAGTA
* * * *
8058 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
**
8097 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
8137 CCTTCGGGACTTAGCCCGGATATAGTAACTCCCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
8177 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCA-ACAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACA-AATG
* * *
8217 CCTTCGGGACTTAGCTCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
8257 CCTTCAGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
8276 TTATCATCCG
Statistics
Matches: 159, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 15 0.09
40 143 0.90
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:14181 original size:56 final size:56
Alignment explanation
Indices: 14095--14251 Score: 305
Period size: 56 Copynumber: 2.8 Consensus size: 56
14085 ATGATGGGCA
*
14095 AAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAAACATGTCATG
1 AAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAAAACATGTCATG
14151 AAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAAAACATGTCATG
1 AAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAAAACATGTCATG
14207 AAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAA
1 AAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAA
14252 TAAACTAATA
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 100 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (56 bp):
AAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAAAACATGTCATG
Found at i:15868 original size:47 final size:47
Alignment explanation
Indices: 15817--16180 Score: 595
Period size: 47 Copynumber: 7.7 Consensus size: 47
15807 TTAGGATTCT
* * *
15817 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
15864 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
15911 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
15958 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
16005 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
16052 ATGTGATAAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
16099 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
16146 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
16181 TCCCGAAGGG
Statistics
Matches: 299, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
46 1 0.00
47 298 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:16355 original size:37 final size:37
Alignment explanation
Indices: 16299--16377 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
16289 CCGAGCTCTA
* * *
16299 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
16336 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
16373 AAGAC
1 AAGAC
16378 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:28503 original size:40 final size:40
Alignment explanation
Indices: 28363--28547 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
28353 TTGAATGATG
* * * * *
28363 TCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
28404 TCCGGACTAAGAT-CCGAAGGCA-TTGTCCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28443 TCCAGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28482 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
28523 -CAGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28548 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
38 9 0.08
39 37 0.31
40 53 0.44
41 20 0.17
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28504 original size:78 final size:81
Alignment explanation
Indices: 28366--28547 Score: 203
Period size: 79 Copynumber: 2.3 Consensus size: 81
28356 AATGATGTCC
* *
28366 GGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCA-TTGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGT
**
28430 CCGAGATACTAATTCCA
66 CCGAGATACT-ATAACA
* * * **
28447 -GGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATTTG
* *
28508 TGCGAGTTACTATAACA
65 TCCGAGATACTATAACA
*
28525 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
28548 AACGAGTAGC
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
77 1 0.01
78 29 0.34
79 34 0.40
80 21 0.25
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGT
CCGAGATACTATAACA
Found at i:28577 original size:78 final size:78
Alignment explanation
Indices: 28416--28579 Score: 174
Period size: 78 Copynumber: 2.1 Consensus size: 78
28406 CGGACTAAGA
** **
28416 TCCGAAGGCATTGTCCGAGATACTAATTCCAGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 TCCGAAGGCATTGTCCGAGATACTAATAACAGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28481 ATCCGGGTTAAGT
66 ATCCGGGTTAAAT
* * * *
28494 CCCGAAGGCATTTGTGCGAGTTACT-ATAACAGGGCTATGTCCCGAAGGCATTTGAACGAG-TAG
1 TCCGAAGGCA-TTGTCCGAGATACTAATAACA-GGCTAAG-CCCGAAGGCATTTGAACGAGTTA-
*
28557 CTATAT-C-GGTTAAAT
62 CTAAATCCGGGTTAAAT
28572 TCCGAAGG
1 TCCGAAGG
28580 TACGTGATTT
Statistics
Matches: 71, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
78 27 0.38
79 21 0.30
80 23 0.32
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (78 bp):
TCCGAAGGCATTGTCCGAGATACTAATAACAGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAAT
Done.