Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1367
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: 50830
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3249 original size:40 final size:39
Alignment explanation
Indices: 3205--3387 Score: 188
Period size: 39 Copynumber: 4.6 Consensus size: 39
3195 AAGTGAATAT
* * *
3205 ATCCGGATTAAGATCCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCGAAGGCATTCGTGCGAGATACTAA
* *
3245 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGATACTAA
* * **
3285 ATCCGGGTTAAGTCCGAAGGCAGTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCGAAGGCATTCGTGCGAGATACTAA
* * *
3324 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGATACTAA
* * *
3363 AACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGT-CCGAAGGCATT
3388 TGAACGAGGA
Statistics
Matches: 127, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
39 71 0.56
40 56 0.44
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (39 bp):
ATCCGGGTTAAGTCCGAAGGCATTCGTGCGAGATACTAA
Found at i:3313 original size:39 final size:40
Alignment explanation
Indices: 3166--3387 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
3156 TTGAATGCTG
* * * * * *
3166 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
* * * *
3206 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
3246 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* **
3286 TCCGGGTTAAGT-CCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
3325 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
3364 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
3388 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
39 71 0.45
40 78 0.50
41 8 0.05
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:3331 original size:79 final size:78
Alignment explanation
Indices: 3166--3385 Score: 233
Period size: 79 Copynumber: 2.8 Consensus size: 78
3156 TTGAATGCTG
* * * * * * ** *
3166 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGTTAAG-TCCGAAGGCAGTC
3231 GTGCGAGATACTAAA
64 GTGCGAGATACTAAA
*
3246 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCGAAGGCAGTCG
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGTTAAGTCCGAAGGCAGTCG
* **
3311 TGCGAGTTGTTAAA
65 TGCGAGATACTAAA
* * * * * *
3325 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGTTAAGT-CCGAAGGCA
3386 TTTGAACGAG
Statistics
Matches: 119, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
78 22 0.18
79 54 0.45
80 39 0.33
81 4 0.03
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGTTAAGTCCGAAGGCAGTCGT
GCGAGATACTAAA
Found at i:3407 original size:79 final size:79
Alignment explanation
Indices: 3241--3422 Score: 206
Period size: 79 Copynumber: 2.3 Consensus size: 79
3231 GTGCGAGATA
* * *
3241 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCGAAGGC
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCGAAGGC
** **
3306 AGTCGTGCGAGTTG
66 AGTCGAACGAGGAG
* * * *
3320 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGT-CCGAAGG
* *
3384 CATTTGAACGAGGAG
65 CAGTCGAACGAGGAG
* *
3399 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
3423 TACGTGATTT
Statistics
Matches: 85, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
78 36 0.42
79 49 0.58
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (79 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCGAAGGC
AGTCGAACGAGGAG
Found at i:13208 original size:8 final size:9
Alignment explanation
Indices: 13157--13215 Score: 66
Period size: 10 Copynumber: 6.3 Consensus size: 9
13147 TATTTAAGTC
13157 TAAAAATTA
1 TAAAAATTA
13166 TTAAAATATTA
1 -TAAAA-ATTA
*
13177 TAAGAATTA
1 TAAAAATTA
*
13186 TTAAAAACTA
1 -TAAAAATTA
13196 TAAAAATTA
1 TAAAAATTA
13205 -AAAAATTA
1 TAAAAATTA
13213 TAA
1 TAA
13216 TTTTTGTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 8 0.19
9 14 0.33
10 16 0.38
11 4 0.10
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:19442 original size:25 final size:26
Alignment explanation
Indices: 19410--19464 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
19400 TTATTAAATT
*
19410 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
19435 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
19460 A-ATAT
1 ATATAT
19465 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:19651 original size:44 final size:45
Alignment explanation
Indices: 19602--19696 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
19592 TTACACCTCT
* *
19602 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
19646 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
19691 ATTACA
1 ATTACA
19697 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:19696 original size:16 final size:16
Alignment explanation
Indices: 19677--19744 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
19667 GATTTGCTAT
* *
19677 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
19693 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19709 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19725 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19741 TACA
1 TACA
19745 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:24060 original size:27 final size:28
Alignment explanation
Indices: 24023--24077 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
24013 GTGTTTGAAT
*
24023 ACAGGGACTCACTTATA-GAGGTTCGCA
1 ACAGGGACTCACCTATAGGAGGTTCGCA
* *
24050 ACAGGGGCTCACCTATAGGGGGTTCGCA
1 ACAGGGACTCACCTATAGGAGGTTCGCA
24078 TTCAAGGGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.25, C:0.24, G:0.31, T:0.20
Consensus pattern (28 bp):
ACAGGGACTCACCTATAGGAGGTTCGCA
Found at i:28058 original size:37 final size:37
Alignment explanation
Indices: 28008--28082 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
27998 ACTCAAAGCA
28008 ATTCGAGATTTAAAGATAGCGTAGAAGATCATTTGGT
1 ATTCGAGATTTAAAGATAGCGTAGAAGATCATTTGGT
28045 ATTCGAGATTTAAAGATAGCGTAGAAGATCATTTGGT
1 ATTCGAGATTTAAAGATAGCGTAGAAGATCATTTGGT
28082 A
1 A
28083 AAAAGTTGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (37 bp):
ATTCGAGATTTAAAGATAGCGTAGAAGATCATTTGGT
Found at i:40777 original size:40 final size:40
Alignment explanation
Indices: 40694--40956 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
40684 TTGAATGCTG
* * * * * *
40694 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
40734 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
40774 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
40814 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
40854 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40894 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40933 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40957 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:40976 original size:79 final size:80
Alignment explanation
Indices: 40733--40991 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
40723 AAGTGAATAT
* * * * * * *
40733 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
40797 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
40813 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
40878 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
40893 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
40957 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
40972 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
40992 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Found at i:48701 original size:40 final size:39
Alignment explanation
Indices: 48619--48876 Score: 272
Period size: 40 Copynumber: 6.6 Consensus size: 39
48609 TTGAATGCTG
* * * * * *
48619 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
48658 TCCGGATTAAGATCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCGAAGGCATTCGTGCGAGTTATTAAA
48698 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTATTAAA
48738 T-CGGGTTAAGTCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTATTAAA
* *
48776 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTATTAAA
* * *
48816 TCCGGGTTATGTCCGAAGGC-TT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
48853 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGT-CCGAAGGCATT
48877 TGAACGAGGA
Statistics
Matches: 191, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
37 22 0.12
38 37 0.19
39 40 0.21
40 85 0.45
41 7 0.04
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (39 bp):
TCCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:48776 original size:78 final size:77
Alignment explanation
Indices: 48657--48876 Score: 298
Period size: 78 Copynumber: 2.8 Consensus size: 77
48647 AAGTGAATAT
* *
48657 ATCCGGATTAAGATCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAG-TCCGAAGG-C-TTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
48722 CGTGCGAGTTATTAA
63 CGTGCGAGTTATTAA
* *
48737 AT-CGGGTTAAGTCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGTC
1 ATCCGGGTTAAGTCCGAAGGC-TT-GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
*
48801 GTGCGAGTTGTTAA
64 GTGCGAGTTATTAA
* * * * *
48815 ATCCGGGTTATGTCCGAAGGCTTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCGAAGGCTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
48877 TGAACGAGGA
Statistics
Matches: 125, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
77 36 0.29
78 62 0.50
79 25 0.20
80 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.27
Consensus pattern (77 bp):
ATCCGGGTTAAGTCCGAAGGCTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGT
GCGAGTTATTAA
Done.