Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1906
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: 24750
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:439 original size:13 final size:13
Alignment explanation
Indices: 421--449 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
411 AATAGTTGTG
421 TGTTATTTAATTA
1 TGTTATTTAATTA
434 TGTTATTTAATTA
1 TGTTATTTAATTA
447 TGT
1 TGT
450 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:3943 original size:21 final size:20
Alignment explanation
Indices: 3909--3951 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
3899 GGATGAGCTG
3909 AAACGAGCTAAATTTGAACTC
1 AAACGAGCTAAA-TTGAACTC
* * *
3930 AAACGAGTTGAATTGAGCTC
1 AAACGAGCTAAATTGAACTC
3950 AA
1 AA
3952 GTGAGCTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (20 bp):
AAACGAGCTAAATTGAACTC
Found at i:8600 original size:30 final size:30
Alignment explanation
Indices: 8552--8633 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
8542 TACGGAATAG
* *
8552 AGATGACATGAAAACCAAGATAAAGAAGTCCA
1 AGAT-ACA-GAAATCCAAGATAAAGAAATCCA
*
8584 GGATGA-AGAAATCCAAGATAAAGAAATCCA
1 AGAT-ACAGAAATCCAAGATAAAGAAATCCA
8614 AGATACAGAAATCCAAGATA
1 AGATACAGAAATCCAAGATA
8634 CAATATCATA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 1 0.02
30 38 0.84
31 1 0.02
32 5 0.11
ACGTcount: A:0.54, C:0.15, G:0.18, T:0.13
Consensus pattern (30 bp):
AGATACAGAAATCCAAGATAAAGAAATCCA
Found at i:8635 original size:15 final size:15
Alignment explanation
Indices: 8561--8633 Score: 101
Period size: 15 Copynumber: 4.9 Consensus size: 15
8551 GAGATGACAT
*
8561 GAAAACCAAGATAAA
1 GAAATCCAAGATAAA
* * *
8576 GAAGTCCAGGATGAA
1 GAAATCCAAGATAAA
8591 GAAATCCAAGATAAA
1 GAAATCCAAGATAAA
*
8606 GAAATCCAAGATACA
1 GAAATCCAAGATAAA
8621 GAAATCCAAGATA
1 GAAATCCAAGATA
8634 CAATATCATA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 50 1.00
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (15 bp):
GAAATCCAAGATAAA
Found at i:12226 original size:40 final size:39
Alignment explanation
Indices: 12142--12326 Score: 160
Period size: 40 Copynumber: 4.6 Consensus size: 39
12132 TTGAATGATG
* * *
12142 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-T-ACTAAA
* *
12182 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAA
* *
12222 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
* * * *
12261 TCCGGGTTAAGTCCCAAAGGCAATTGTGCGAGTTAC-AATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGATACTAA-A
* * *
12301 ACCGAGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
12327 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 37 0.31
40 73 0.60
41 10 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:12281 original size:79 final size:81
Alignment explanation
Indices: 12142--12326 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
12132 TTGAATGATG
* * *
12142 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCAAAGGCAAT
12206 TGTGCGAGATACTAAT-
66 TGTGCGAGATAC-AATA
* * * **
12222 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCAAAGGCAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCAAAGGCAA
*
12284 TTGTGCGAGTTACAATA
65 TTGTGCGAGATACAATA
* * *
12301 ACCGAGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
12327 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 4 0.04
79 53 0.60
80 32 0.36
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCAAAGGCAAT
TGTGCGAGATACAATA
Found at i:20182 original size:39 final size:41
Alignment explanation
Indices: 20081--20264 Score: 206
Period size: 39 Copynumber: 4.6 Consensus size: 41
20071 TTGAATGATG
* *
20081 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
20121 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
20161 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
20200 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
20239 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20265 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.01
39 69 0.55
40 43 0.34
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:20217 original size:79 final size:80
Alignment explanation
Indices: 20081--20264 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 80
20071 TTGAATGATG
*
20081 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-T
20145 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
20160 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
20222 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
20239 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20265 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 49 0.54
80 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
GTGCGAGATACTATA
Found at i:20287 original size:78 final size:79
Alignment explanation
Indices: 20134--20297 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 79
20124 GGACTAAGAT
* **
20134 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
20199 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
20213 CCGAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
20275 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
20291 CCGAAGG
1 CCGAAGG
20298 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 38 0.51
79 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.