Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold720
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: 35359
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Found at i:2074 original size:47 final size:47
Alignment explanation
Indices: 1935--2322 Score: 514
Period size: 46 Copynumber: 8.4 Consensus size: 47
1925 GTATATTTGA
* * *
1935 ATGAATGTGAAAGTTATATATATGTGATAA-GCCTAATGGCCGATGTG
1 ATGAATGTGAAAG-TGTATATATGTGATAAGGCCGAATGGCCAATGTG
* * *
1982 ATGAATGTGAAAGTGTATATAT-TGATAAGGCCTAATAGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
2028 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
2075 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTG
*
2124 ATGAATGTGAACA-TG--TATGTGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
* * *
2169 ATGCATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
* *
2216 ATGAATG-GAACA-TGCATATATGAGATAAGGCCGAAT-GCCAATGTG
1 ATGAATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
2261 ATGAATGTGAAAGTGTATATATGT-ATAA-GCCGAATGGCCAATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
*
2306 ATGGATGT--AAGTGTATA
1 ATGAATGTGAAAGTGTATA
2323 AATATTATAA
Statistics
Matches: 318, Mismatches: 13, Indels: 24
0.90 0.04 0.07
Matches are distributed among these distances:
43 9 0.03
44 7 0.02
45 86 0.27
46 87 0.27
47 83 0.26
49 45 0.14
50 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.28
Consensus pattern (47 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
Found at i:2103 original size:141 final size:141
Alignment explanation
Indices: 1935--2322 Score: 530
Period size: 141 Copynumber: 2.8 Consensus size: 141
1925 GTATATTTGA
* *
1935 ATGAATGTGAAAGT-TATATATATGTGATAA-GCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGT
* * * *
1998 ATATATTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGA
66 ATATA-TGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGGCCGA
2063 ATGGCCAATGTG
130 ATGGCCAATGTG
2075 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG
* * * *
2139 TATGTGTGATAAGGCCGAATGGCCAATGTGATGCATGTGAACA-TGCATATATGAGATAAGGCCG
65 TATATATGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTATATATGAGATAAGGCCG
2203 AATGGCCAATGTG
129 AATGGCCAATGTG
* *
2216 ATGAATG-GAACA-TG--CATATATGAGATAAGGCCGAAT-GCCAATGTGATGAATGTGAAAGTG
1 ATGAATGTGAA-AGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
*
2276 TATATATGTATAA-GCCGAATGGCCAATGTGATGGATGT--AAGTGTATA
65 TATATATG-ATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
2323 AATATTATAA
Statistics
Matches: 224, Mismatches: 16, Indels: 21
0.86 0.06 0.08
Matches are distributed among these distances:
134 1 0.00
135 6 0.03
136 1 0.00
137 52 0.23
138 24 0.11
140 19 0.08
141 87 0.39
142 33 0.15
143 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.28
Consensus pattern (141 bp):
ATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGT
ATATATGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGGCCGAA
TGGCCAATGTG
Found at i:2162 original size:45 final size:46
Alignment explanation
Indices: 1935--2313 Score: 472
Period size: 45 Copynumber: 8.2 Consensus size: 46
1925 GTATATTTGA
* * *
1935 ATGAATGTGAAAGTTATATATATGTGATAA-GCCTAATGGCCGATGTG
1 ATGAATGTGAAAG-T-GATATATGTGATAAGGCCGAATGGCCAATGTG
* * *
1982 ATGAATGTGAAAGTGTATATAT-TGATAAGGCCTAATAGCCGATGTG
1 ATGAATGTGAAAGTG-ATATATGTGATAAGGCCGAATGGCCAATGTG
2028 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAAAGTG-ATATATGTGATAAGGCCGAATGGCCAATGTG
2075 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAAAGTG---ATATATGTGATAAGGCCGAATGGCCAATGTG
*
2124 ATGAATGTGAACA-TG-TATGTGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAA-AGTGATATATGTGATAAGGCCGAATGGCCAATGTG
* *
2169 ATGCATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAA-AGTG-ATATATGTGATAAGGCCGAATGGCCAATGTG
*
2216 ATGAATG-GAACA-TGCATATATGAGATAAGGCCGAAT-GCCAATGTG
1 ATGAATGTGAA-AGTG-ATATATGTGATAAGGCCGAATGGCCAATGTG
2261 ATGAATGTGAAAGTGTATATATGT-ATAA-GCCGAATGGCCAATGTG
1 ATGAATGTGAAAGTG-ATATATGTGATAAGGCCGAATGGCCAATGTG
*
2306 ATGGATGT
1 ATGAATGT
2314 AAGTGTATAA
Statistics
Matches: 308, Mismatches: 13, Indels: 24
0.89 0.04 0.07
Matches are distributed among these distances:
44 7 0.02
45 86 0.28
46 86 0.28
47 83 0.27
49 45 0.15
50 1 0.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (46 bp):
ATGAATGTGAAAGTGATATATGTGATAAGGCCGAATGGCCAATGTG
Found at i:2339 original size:45 final size:46
Alignment explanation
Indices: 1935--2339 Score: 429
Period size: 47 Copynumber: 8.8 Consensus size: 46
1925 GTATATTTGA
* *
1935 ATGAATGTGAAAGT-TATATATATGTGATAA-GCCTAATGGCCGATGTG
1 ATGAATGTG-AAGTGTATATATA--TGATAAGGCCGAATGGCCAATGTG
* * *
1982 ATGAATGTGAAAGTGTATATAT-TGATAAGGCCTAATAGCCGATGTG
1 ATGAATGTG-AAGTGTATATATATGATAAGGCCGAATGGCCAATGTG
*
2028 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTG-AAGTGTATATATATGATAAGGCCGAATGGCCAATGTG
2075 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTG-AAGTGTATATATA--TGATAAGGCCGAATGGCCAATGTG
* * *
2124 ATGAATGTGAACATG--TATGTGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAA-GTGTATATATATGATAAGGCCGAATGGCCAATGTG
* * *
2169 ATGCATGTGAACATGCATATATGA-GATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAA-GTGTATATAT-ATGATAAGGCCGAATGGCCAATGTG
* *
2216 ATGAATG-GAACATGCATATATGA-GATAAGGCCGAAT-GCCAATGTG
1 ATGAATGTGAA-GTGTATATAT-ATGATAAGGCCGAATGGCCAATGTG
*
2261 ATGAATGTGAAAGTGTATATATGT-ATAA-GCCGAATGGCCAATGTG
1 ATGAATGTG-AAGTGTATATATATGATAAGGCCGAATGGCCAATGTG
* * * *
2306 ATGGATGT-AAGTGTATAAATATTATAAGTCCGAA
1 ATGAATGTGAAGTGTATATATATGATAAGGCCGAA
2340 GGGCAATTGT
Statistics
Matches: 324, Mismatches: 19, Indels: 32
0.86 0.05 0.09
Matches are distributed among these distances:
43 12 0.04
44 11 0.03
45 85 0.26
46 76 0.23
47 96 0.30
48 9 0.03
49 35 0.11
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (46 bp):
ATGAATGTGAAGTGTATATATATGATAAGGCCGAATGGCCAATGTG
Found at i:3925 original size:21 final size:21
Alignment explanation
Indices: 3879--3919 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3869 ATGAAATACG
*
3879 AATGTGCCATGATTATTGTTA
1 AATGTGCCATGATTATTGTGA
3900 AATGTG-CATGATTATT-TGA
1 AATGTGCCATGATTATTGTGA
3919 A
1 A
3920 TGATGTCCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 10 0.53
21 6 0.32
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (21 bp):
AATGTGCCATGATTATTGTGA
Found at i:4032 original size:38 final size:40
Alignment explanation
Indices: 3925--4144 Score: 246
Period size: 39 Copynumber: 5.7 Consensus size: 40
3915 TTGAATGATG
*
3925 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC--AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
3963 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
4004 TCCGGGCTAAG-CCCGAA-GCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
4042 TCCGGG-TAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
4080 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-TTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
4118 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
4145 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 9, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
37 10 0.06
38 53 0.33
39 57 0.35
40 39 0.24
41 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:11888 original size:39 final size:40
Alignment explanation
Indices: 11793--11976 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
11783 TTGAATGATG
*
11793 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATA
*
11832 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA
* *
11871 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
* *
11911 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
* *
11951 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
11977 AACGAGGAGC
Statistics
Matches: 128, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
39 55 0.43
40 72 0.56
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA
Found at i:11928 original size:79 final size:80
Alignment explanation
Indices: 11793--11976 Score: 234
Period size: 79 Copynumber: 2.3 Consensus size: 80
11783 TTGAATGATG
*
11793 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAAATCCGGACTAAGATCCGAAGGCATTT
11857 GTGCGAGATACTA-A
66 GTGCGAGATACTATA
* * **
11871 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AAATCCGGACTAAGAT-CCGAAGGCA
*
11933 TTTGTGCGAGTTACTATA
63 TTTGTGCGAGATACTATA
* *
11951 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
11977 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
78 15 0.16
79 62 0.67
80 15 0.16
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATA
Found at i:11998 original size:79 final size:79
Alignment explanation
Indices: 11794--12009 Score: 201
Period size: 79 Copynumber: 2.7 Consensus size: 79
11784 TGAATGATGT
** * * **
11794 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-ATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
11856 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
11873 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
11938 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
11952 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
12010 TACGTGATTT
Statistics
Matches: 116, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
78 17 0.15
79 74 0.64
80 25 0.22
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:19726 original size:40 final size:39
Alignment explanation
Indices: 19708--19933 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 39
19698 AAGTGACCAT
19708 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTA
1 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTA
19747 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACT-A
19787 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTA
1 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTA
* *
19826 ATTCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
1 A-TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACT-A
**
19867 ATCCGGGTTAAG-TCCCGAAGGCATTTGTGCGA-ATTACTA
1 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGA-TACTA
* * *
19906 TAACCGGGCTATG-TCCCGAAGGCATTTG
1 -ATCCGGACTAAGAT-CCGAAGGCATTTG
19934 AACGAGGAGC
Statistics
Matches: 174, Mismatches: 7, Indels: 11
0.91 0.04 0.06
Matches are distributed among these distances:
39 42 0.24
40 130 0.75
41 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (39 bp):
ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTA
Found at i:19800 original size:79 final size:79
Alignment explanation
Indices: 19669--19933 Score: 351
Period size: 80 Copynumber: 3.3 Consensus size: 79
19659 TTGAATGATG
* * *
19669 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAATCCGGACTAAGATCCGAAGGCAT
19732 TTGTGCGAGATACTAA
64 TTGTGCGAGATACTAA
*
19748 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATT
19812 TGTGCGAGATACTAA
65 TGTGCGAGATACTAA
* **
19827 TTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGAT-CCGAAGGCAT
19891 TTGTGCGA-ATTACTATA
64 TTGTGCGAGA-TACTA-A
* *
19908 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
19934 AACGAGGAGC
Statistics
Matches: 168, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
79 64 0.38
80 102 0.61
81 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAA
Found at i:19947 original size:40 final size:39
Alignment explanation
Indices: 19670--19933 Score: 256
Period size: 40 Copynumber: 6.6 Consensus size: 39
19660 TGAATGATGT
* * *
19670 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTATAA
* *
19710 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-AT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTATAA
*
19749 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-AA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTATAA
* *
19788 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 -CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTATA-A
19829 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAA
* *
19868 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTATAA
*
19909 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
19934 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 12, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
39 41 0.20
40 150 0.74
41 12 0.06
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAA
Found at i:19951 original size:80 final size:77
Alignment explanation
Indices: 19669--19966 Score: 307
Period size: 80 Copynumber: 3.8 Consensus size: 77
19659 TTGAATGATG
* * * **
19669 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAG-GACTAAATCCGGGTTAAG-TCCGAAGGCATT
19733 TGTGCGAGATACTAA
63 TGTGCGAGATACTAA
* * **
19748 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-GACTAAATCCGGGTTAAG-TCCGAAGGCATT
19812 TGTGCGAGATACTAA
63 TGTGCGAGATACTAA
*
19827 TTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-GACTAAATCCGGGTTAAGT-CCGAAGGCATT
19892 TGTGCGA-ATTACTATA
63 TGTGCGAGA-TACTA-A
* * ** * *
19908 ACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTATATCC-GGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGA-CTAAATCCGGGTT-AAGTCCGAAGG
19967 TACGTGATTT
Statistics
Matches: 193, Mismatches: 17, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
79 78 0.40
80 114 0.59
81 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (77 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGGACTAAATCCGGGTTAAGTCCGAAGGCATTTGT
GCGAGATACTAA
Found at i:21341 original size:29 final size:29
Alignment explanation
Indices: 21308--21407 Score: 78
Period size: 29 Copynumber: 3.4 Consensus size: 29
21298 ATGATTAGAG
*
21308 GCACTGTGTGTGCAAATTCCTTTAACCGA
1 GCACTATGTGTGCAAATTCCTTTAACCGA
* * ** **
21337 GCACTATGTGTACGAGA-T-CGGTAATTGA
1 GCACTATGTGTGC-AAATTCCTTTAACCGA
* * *
21365 GGCATTGTGTGTGCGAATTCCTTTAACCGA
1 -GCACTATGTGTGCAAATTCCTTTAACCGA
21395 GCACTATGTGTGC
1 GCACTATGTGTGC
21408 GAGATCGGTA
Statistics
Matches: 49, Mismatches: 18, Indels: 8
0.65 0.24 0.11
Matches are distributed among these distances:
28 7 0.14
29 34 0.69
30 8 0.16
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (29 bp):
GCACTATGTGTGCAAATTCCTTTAACCGA
Found at i:21427 original size:29 final size:29
Alignment explanation
Indices: 21337--21491 Score: 113
Period size: 29 Copynumber: 5.4 Consensus size: 29
21327 CTTTAACCGA
* *
21337 GCACTATGTGTACGAGATCGGTAATTGAG
1 GCACTATGTGTGCGAGATCGGTAACTGAG
* * ** *
21366 GCATTGTGTGTGCGA-ATTCCTTTAACCGA-
1 GCACTATGTGTGCGAGA-T-CGGTAACTGAG
*
21395 GCACTATGTGTGCGAGATCGGTAATTGAG
1 GCACTATGTGTGCGAGATCGGTAACTGAG
* * * *
21424 GCACTGTGTGTGCGAGTTC-TTCAACCGA-
1 GCACTATGTGTGCGAGATCGGT-AACTGAG
* *
21452 GCACTATGTGTGCGAGATCGGTCAGTG-G
1 GCACTATGTGTGCGAGATCGGTAACTGAG
*
21480 GCACTAAGTGTG
1 GCACTATGTGTG
21492 TGAAATGAGA
Statistics
Matches: 94, Mismatches: 25, Indels: 15
0.70 0.19 0.11
Matches are distributed among these distances:
28 38 0.40
29 49 0.52
30 7 0.07
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (29 bp):
GCACTATGTGTGCGAGATCGGTAACTGAG
Found at i:21483 original size:28 final size:28
Alignment explanation
Indices: 21395--21491 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 28
21385 CTTTAACCGA
* *
21395 GCACTATGTGTGCGAGATCGGTAATTGAG
1 GCACTATGTGTGCGAGATCGGTCACTG-G
* * * * *
21424 GCACTGTGTGTGCGAGTTC-TTCAACCGA
1 GCACTATGTGTGCGAGATCGGTC-ACTGG
*
21452 GCACTATGTGTGCGAGATCGGTCAGTGG
1 GCACTATGTGTGCGAGATCGGTCACTGG
*
21480 GCACTAAGTGTG
1 GCACTATGTGTG
21492 TGAAATGAGA
Statistics
Matches: 52, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
28 31 0.60
29 21 0.40
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.27
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGGTCACTGG
Found at i:21493 original size:58 final size:58
Alignment explanation
Indices: 21305--21473 Score: 286
Period size: 58 Copynumber: 2.9 Consensus size: 58
21295 TGAATGATTA
* *
21305 GAGGCACTGTGTGTGCAAATTCCTTTAACCGAGCACTATGTGTACGAGATCGGTAATT
1 GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
*
21363 GAGGCATTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
1 GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
* *
21421 GAGGCACTGTGTGTGCGAGTT-CTTCAACCGAGCACTATGTGTGCGAGATCGGT
1 GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGT
21474 CAGTGGGCAC
Statistics
Matches: 105, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
57 31 0.30
58 74 0.70
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (58 bp):
GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
Found at i:21767 original size:21 final size:21
Alignment explanation
Indices: 21741--21787 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
21731 TTTGAGTTTG
*
21741 AATTGGGGATTAATAGATATA
1 AATTGGGGATTAATACATATA
21762 AATTGGGGATTAATACATATA
1 AATTGGGGATTAATACATATA
21783 AATTG
1 AATTG
21788 ACGATTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (21 bp):
AATTGGGGATTAATACATATA
Found at i:21793 original size:21 final size:21
Alignment explanation
Indices: 21748--21793 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
21738 TTGAATTGGG
* **
21748 GATTAATAGATATAAATTGGG
1 GATTAATACATATAAATTGAC
21769 GATTAATACATATAAATTGAC
1 GATTAATACATATAAATTGAC
21790 GATT
1 GATT
21794 GATTATTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.35
Consensus pattern (21 bp):
GATTAATACATATAAATTGAC
Found at i:25114 original size:38 final size:38
Alignment explanation
Indices: 25072--25200 Score: 168
Period size: 38 Copynumber: 3.4 Consensus size: 38
25062 ATATGGTAGA
25072 ATTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGT
1 ATTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGT
* *
25110 ATTATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGT
1 ATTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGT
** * *
25148 ATTATATCTAGTTTAAAGTCCCGTAGGCTTCGTGCTGGT
1 ATTATATCCGGGTTAAA-TCCCGCAGGCTTCGTGCTGGT
* * *
25187 GTTATGTTCGGGTT
1 ATTATATCCGGGTT
25201 TTATACCTCG
Statistics
Matches: 76, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
38 50 0.66
39 26 0.34
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (38 bp):
ATTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGT
Found at i:26798 original size:43 final size:43
Alignment explanation
Indices: 26737--26872 Score: 227
Period size: 43 Copynumber: 3.2 Consensus size: 43
26727 GCATGAAATT
26737 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
26780 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* * * **
26823 CGGTGATGTGTATTCAGGTCTTTGTGCCTAGCAGGCTTAATGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
26866 CGGTGAT
1 CGGTGAT
26873 TCGAGCAAGG
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 88 1.00
ACGTcount: A:0.12, C:0.23, G:0.34, T:0.32
Consensus pattern (43 bp):
CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
Found at i:27062 original size:29 final size:29
Alignment explanation
Indices: 27029--27128 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
27019 ATGATTAGAG
27029 GCACTATGTGTGCAAATTTCTTTAACCGA
1 GCACTATGTGTGCAAATTTCTTTAACCGA
* ** **
27058 GCACTATGTGTGCGAGA--TCGGTAATTGA
1 GCACTATGTGTGC-AAATTTCTTTAACCGA
* ** *
27086 GGCACTGTGTGTGTGAATTCCTTTAACCGA
1 -GCACTATGTGTGCAAATTTCTTTAACCGA
27116 GCACTATGTGTGC
1 GCACTATGTGTGC
27129 GAGATCGATA
Statistics
Matches: 51, Mismatches: 16, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
28 8 0.16
29 35 0.69
30 8 0.16
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (29 bp):
GCACTATGTGTGCAAATTTCTTTAACCGA
Found at i:27148 original size:29 final size:28
Alignment explanation
Indices: 27050--27192 Score: 119
Period size: 29 Copynumber: 5.0 Consensus size: 28
27040 GCAAATTTCT
*
27050 TTAACCGAGCACTATGTGTGCGAGATCG
1 TTAATCGAGCACTATGTGTGCGAGATCG
* * * * *
27078 GTAATTGAGGCACTGTGTGTGTGA-ATTCCT
1 TTAATCGA-GCACTATGTGTGCGAGA-T-CG
*
27108 TTAACCGAGCACTATGTGTGCGAGATCG
1 TTAATCGAGCACTATGTGTGCGAGATCG
* * * *
27136 ATAATTGAGGCACTGTGTGTGCGAGTTC-
1 TTAATCGA-GCACTATGTGTGCGAGATCG
*
27164 TTCAATCGAGTACTATGTGTGCGAGATCG
1 TT-AATCGAGCACTATGTGTGCGAGATCG
27193 GTCAGTGGGC
Statistics
Matches: 86, Mismatches: 22, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
28 29 0.34
29 50 0.58
30 7 0.08
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
TTAATCGAGCACTATGTGTGCGAGATCG
Found at i:27206 original size:28 final size:28
Alignment explanation
Indices: 27116--27212 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 28
27106 CTTTAACCGA
27116 GCACTATGTGTGCGAGATCGAT-AATTGAG
1 GCACTATGTGTGCGAGATCGATCAA-TG-G
* * * *
27145 GCACTGTGTGTGCGAGTTC-TTCAATCGA
1 GCACTATGTGTGCGAGATCGATCAAT-GG
* * *
27173 GTACTATGTGTGCGAGATCGGTCAGTGG
1 GCACTATGTGTGCGAGATCGATCAATGG
*
27201 GCACTAAGTGTG
1 GCACTATGTGTG
27213 TGAAATGAGA
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
28 29 0.55
29 24 0.45
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.29
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGATCAATGG
Found at i:27213 original size:58 final size:57
Alignment explanation
Indices: 27026--27194 Score: 248
Period size: 58 Copynumber: 2.9 Consensus size: 57
27016 CGAATGATTA
* *
27026 GAGGCACTATGTGTGCAAATTTCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
1 GAGGCACTGTGTGTGCGAA-TTCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
* *
27084 GAGGCACTGTGTGTGTGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGATAATT
1 GAGGCACTGTGTGTGCGAATT-CTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
* * * *
27142 GAGGCACTGTGTGTGCGAGTTCTTCAATCGAGTACTATGTGTGCGAGATCGGT
1 GAGGCACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGCGAGATCGGT
27195 CAGTGGGCAC
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
57 30 0.30
58 70 0.70
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (57 bp):
GAGGCACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
Found at i:27488 original size:21 final size:21
Alignment explanation
Indices: 27462--27508 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
27452 TTTGAGTTTG
*
27462 AATTGGGGATTAATAGATATA
1 AATTGGGGATTAATACATATA
27483 AATTGGGGATTAATACATATA
1 AATTGGGGATTAATACATATA
27504 AATTG
1 AATTG
27509 ACGATTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (21 bp):
AATTGGGGATTAATACATATA
Found at i:27514 original size:21 final size:21
Alignment explanation
Indices: 27469--27514 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
27459 TTGAATTGGG
* **
27469 GATTAATAGATATAAATTGGG
1 GATTAATACATATAAATTGAC
27490 GATTAATACATATAAATTGAC
1 GATTAATACATATAAATTGAC
27511 GATT
1 GATT
27515 GATTATTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.35
Consensus pattern (21 bp):
GATTAATACATATAAATTGAC
Found at i:34476 original size:29 final size:28
Alignment explanation
Indices: 34442--34515 Score: 82
Period size: 27 Copynumber: 2.6 Consensus size: 28
34432 TAAATTGTAC
34442 AGCACTAAGTGGTGCGGAGTTTTGATTA-AT
1 AGCACTAAGT-GTGCGGAG--TTGATTATAT
34472 A-CACTAAAGTGTGC-GAGTTGATTATAT
1 AGCACT-AAGTGTGCGGAGTTGATTATAT
*
34499 AGCACTGAGTGTGCGGA
1 AGCACTAAGTGTGCGGA
34516 CTTAATATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
26 7 0.18
27 10 0.26
28 9 0.23
29 8 0.21
30 5 0.13
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGAGTTGATTATAT
Done.