Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold291
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: 18994
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Found at i:1852 original size:40 final size:40
Alignment explanation
Indices: 1795--2050 Score: 369
Period size: 40 Copynumber: 6.5 Consensus size: 40
1785 GGATTGATAA
1795 CCGGGCTAA--CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1833 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
1873 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
1913 CCGGGCCAAGTCCCGAAGGCAATTGTGTGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
1953 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
*
1994 -CGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
**
2033 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
2051 TACTTGGTTT
Statistics
Matches: 202, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
38 9 0.04
39 18 0.09
40 174 0.86
41 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:9444 original size:40 final size:40
Alignment explanation
Indices: 9381--9600 Score: 331
Period size: 40 Copynumber: 5.6 Consensus size: 40
9371 ATTCGGATTG
9381 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
9420 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
9460 ATAACCGGGCCAAGT-CCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
9499 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
9539 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* **
9579 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
9601 TACTTGGTTT
Statistics
Matches: 168, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
39 66 0.39
40 102 0.61
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.22
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:9512 original size:79 final size:79
Alignment explanation
Indices: 9381--9600 Score: 336
Period size: 79 Copynumber: 2.8 Consensus size: 79
9371 ATTCGGATTG
* *
9381 ATAACCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCAA
9446 TTGTGCGAGTTACT
66 TTGTGCGAGTTACT
* * *
9460 ATAACCGGGCCAAGTCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCAA
1 ATAACCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCAA
9525 TTGTGCGAGTTACT
66 TTGTGCGAGTTACT
* **
9539 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
9601 TACTTGGTTT
Statistics
Matches: 128, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
79 104 0.81
80 24 0.19
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.22
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCAA
TTGTGCGAGTTACT
Found at i:11878 original size:39 final size:38
Alignment explanation
Indices: 11804--11878 Score: 123
Period size: 38 Copynumber: 1.9 Consensus size: 38
11794 TGTTTTTACT
* *
11804 TCCATCAAGGTAACCGTTAAATTTCCCATATTTTTTCA
1 TCCATCAAGGTAACCGTTAAAATTCCCATAATTTTTCA
11842 TCCATCAAGGTAACCGTTAAAATTCCCATTAATTTTT
1 TCCATCAAGGTAACCGTTAAAATTCCCA-TAATTTTT
11879 AATGTTATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 27 0.79
39 7 0.21
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.39
Consensus pattern (38 bp):
TCCATCAAGGTAACCGTTAAAATTCCCATAATTTTTCA
Found at i:14391 original size:39 final size:41
Alignment explanation
Indices: 14290--14472 Score: 197
Period size: 39 Copynumber: 4.6 Consensus size: 41
14280 TTGAATGATG
* *
14290 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
14330 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
14370 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
14408 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
14447 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
14473 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
38 26 0.21
39 53 0.42
40 33 0.26
41 12 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:14429 original size:78 final size:79
Alignment explanation
Indices: 14290--14470 Score: 217
Period size: 78 Copynumber: 2.3 Consensus size: 79
14280 TTGAATGATG
* *
14290 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-TT
14355 GTGCGAGATACTA-A
65 GTGCGAGATACTATA
* * * **
14369 TTCCGGGCTAAG-CCCGAAGGCATTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
*
14431 TGTGCGAGTTACTATA
64 TGTGCGAGATACTATA
* *
14447 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
14471 TGAACGAGTA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
77 24 0.27
78 38 0.43
79 15 0.17
80 11 0.12
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTG
TGCGAGATACTATA
Found at i:14494 original size:78 final size:78
Alignment explanation
Indices: 14291--14505 Score: 199
Period size: 78 Copynumber: 2.7 Consensus size: 78
14281 TGAATGATGT
* * * * * **
14291 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTT
1 CCGGGCTAAG-CCCGAAGGCATTGTGC-GAGTTACTAAATCCGGGTTAA-ATCCCGAAGGCATTT
*
14355 GTGCGAGATACTAATT
63 GTGCGAGATACTAATA
*
14371 CCGGGCTAAGCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCA-TTGTG
1 CCGGGCTAAGCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTTGTG
*
14435 CGAGTTACT-ATAA
66 CGAGATACTAAT-A
* * *
14448 CCGGGCTATGTCCCGAAGGCATT-TGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTGTG--CGAGTTA-CTAAATCCGGGTTAAATCCCGAAGG
14506 TACGTGATTT
Statistics
Matches: 115, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
76 2 0.02
77 25 0.22
78 52 0.45
79 26 0.23
80 10 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (78 bp):
CCGGGCTAAGCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTTGTG
CGAGATACTAATA
Done.