Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2636
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: 13439
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Found at i:4212 original size:40 final size:40
Alignment explanation
Indices: 3980--4203 Score: 326
Period size: 40 Copynumber: 5.6 Consensus size: 40
3970 TGGATGATAA
*
3980 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* *
4021 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
4061 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
4101 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
4141 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
4181 CCGGGCTATGTCCTGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
4204 CGAACGAGTA
Statistics
Matches: 169, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
40 141 0.83
41 24 0.14
42 4 0.02
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:4221 original size:80 final size:79
Alignment explanation
Indices: 3975--4238 Score: 293
Period size: 80 Copynumber: 3.3 Consensus size: 79
3965 ATATTTGGAT
* * * *
3975 GATAACCGGGCTAAGTCCCGAAGGCATTTTGCGCTAGTGACTAGT-TCCGGGCTAAGTCCCGAAG
1 GATATCCGGGCTAAGTCCCGAAGGCATTGTGCG--AGTTACTA-TATCCGGGCTAAGTCCTGAAG
* *
4039 GCATTTGTGCGAGTTAT
63 GCATTTGTGCGAGCTAC
* * *
4056 TACATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGT-CTCGAAGG
1 GATATCCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATATCCGGGCTAAGTCCT-GAAGG
4120 CATTTGTGCGAGCTAC
64 CATTTGTGCGAGCTAC
* *
4136 TATATCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCCGGGCTATGTCCTGAAGGC
1 GATATCCGGGCTAAGTCCCGAAGGCATT-GTGCGAGTTACTATATCCGGGCTAAGTCCTGAAGGC
* **
4201 ATTCGAACGAG-TAGC
65 ATTTGTGCGAGCTA-C
* *
4216 GATATCC-GGTTAAATCCCGAAGG
1 GATATCCGGGCTAAGTCCCGAAGG
4239 TACTTGGCTT
Statistics
Matches: 159, Mismatches: 18, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
79 20 0.13
80 108 0.68
81 25 0.16
82 6 0.04
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (79 bp):
GATATCCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATATCCGGGCTAAGTCCTGAAGGCA
TTTGTGCGAGCTAC
Found at i:4221 original size:120 final size:120
Alignment explanation
Indices: 3975--4238 Score: 331
Period size: 120 Copynumber: 2.2 Consensus size: 120
3965 ATATTTGGAT
*
3975 GATAACCGGGCTAAGTCCCGAAGGCATTTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGG
1 GATATCCGGGCTAAGTCCCGAAGGCATTTTGCGC-AGTGACTAGTTCCGGGCTAAGTCCCGAAGG
* * * **
4040 CATTTGTGCGAGTTATTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTAC
65 CATTGGTGCGAGTTACTACATCCGGGCTAAGTCCCGAAGGCATTCGAACGAGCTAC
* *
4096 TATATCCGGGCTAAGTCTCGAAGGCATTTGTGCG-AGCT-ACTA-TATCCGGGCTAAGTCCCGAA
1 GATATCCGGGCTAAGTCCCGAAGGCATTT-TGCGCAG-TGACTAGT-TCCGGGCTAAGTCCCGAA
* * *
4158 GGCATTGGTGCGAGTTACTATATCCGGGCTATGTCCTGAAGGCATTCGAACGAG-TAGC
63 GGCATTGGTGCGAGTTACTACATCCGGGCTAAGTCCCGAAGGCATTCGAACGAGCTA-C
* *
4216 GATATCC-GGTTAAATCCCGAAGG
1 GATATCCGGGCTAAGTCCCGAAGG
4239 TACTTGGCTT
Statistics
Matches: 124, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
119 16 0.13
120 77 0.62
121 27 0.22
122 4 0.03
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (120 bp):
GATATCCGGGCTAAGTCCCGAAGGCATTTTGCGCAGTGACTAGTTCCGGGCTAAGTCCCGAAGGC
ATTGGTGCGAGTTACTACATCCGGGCTAAGTCCCGAAGGCATTCGAACGAGCTAC
Found at i:12228 original size:40 final size:40
Alignment explanation
Indices: 12074--12365 Score: 370
Period size: 39 Copynumber: 7.5 Consensus size: 40
12064 TGGATGATAA
*
12074 CCGGGCTAAGTCCCGAAGGCATTT-TGC--GCTAGTGATAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACT-ATA-T
* * * *
12113 TCGGGCTAAGT-CCGAAGGCATTTGTG-GAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
12151 CCGGGCTAAGTCCCGAAGG-ATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
*
12190 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTGCTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
12229 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
* *
12269 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
* * *
12309 CCGGGCTATGT-CCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTA-CTATAT
* *
12348 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
12366 TACTTGGCTT
Statistics
Matches: 226, Mismatches: 18, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
38 37 0.16
39 119 0.53
40 70 0.31
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
Found at i:12282 original size:79 final size:80
Alignment explanation
Indices: 12074--12365 Score: 379
Period size: 79 Copynumber: 3.7 Consensus size: 80
12064 TGGATGATAA
* *
12074 CCGGGCTAAGTCCCGAAGGCATTT-TGC--GCTAGTGATAGTTCGGGCTAAGT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACT-ATA-TCCGGGCTAAGTCCCGAAGGCATT
* *
12135 TGTG-GAGTTATTACAT
64 TGTGCGAGTTACTATAT
12151 CCGGGCTAAGTCCCGAAGG-ATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
* *
12215 TGCGAGCTGCTATA-
66 TGCGAGTTACTATAT
*
12229 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
12294 TGCGAGTTACTATAT
66 TGCGAGTTACTATAT
* * * * *
12309 CCGGGCTATGT-CCGAAGGCATTCGAGCGAG-TAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTA-CTATATCCGGGCTAAGTCCCGAAGG
12366 TACTTGGCTT
Statistics
Matches: 193, Mismatches: 14, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
76 4 0.02
77 33 0.17
78 53 0.27
79 93 0.48
80 10 0.05
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTATAT
Done.