Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1824
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: 53184
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Found at i:6134 original size:39 final size:39
Alignment explanation
Indices: 6082--6252 Score: 202
Period size: 39 Copynumber: 4.3 Consensus size: 39
6072 GGACTAAGAT
*
6082 CCGAAGGCATTTGTGCGAGATACAAGTTCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGATACAA-ATCCGGGTTAAGTC
*
6121 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
* * *
6161 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
6201 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
6240 CCGAAGGCATTTG
1 CCGAAGGCATTTG
6253 AACGAGGAGC
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
39 65 0.57
40 50 0.43
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:6165 original size:79 final size:79
Alignment explanation
Indices: 6029--6252 Score: 222
Period size: 79 Copynumber: 2.8 Consensus size: 79
6019 TTGAATGCTG
* * * * * * *
6029 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
*
6092 TTGTGCGAGATA-CAAGT
63 TTGTGCGAGATATCAA-A
* * * *
6109 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTT
* *
6173 GTGCGAGTTATTAAA
65 GTGCGAGATATCAAA
* * *
6188 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
6253 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 90 0.74
80 30 0.25
81 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:6270 original size:79 final size:80
Alignment explanation
Indices: 6109--6285 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
6099 AGATACAAGT
* * *
6109 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
6173 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
6188 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
6252 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
6267 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
6286 TATGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 16 0.19
79 59 0.71
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:14028 original size:40 final size:39
Alignment explanation
Indices: 13991--14165 Score: 203
Period size: 39 Copynumber: 4.5 Consensus size: 39
13981 ATATCCGGAC
*
13991 TAAGATCCGAAGGCATTTGTGCGAGATAC-AAGTTCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAA-ATCCGGGT
* *
14031 TAAGCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGT
1 TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * *
14070 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * *
14110 TAAGTCCGAAGGCA-TTGTGTGAGTTACTAAA-CCGGGC
1 TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
*
14147 TATGTCCCGAAGGCATTTG
1 TAAGT-CCGAAGGCATTTG
14166 AACGAGGAGC
Statistics
Matches: 118, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
37 9 0.08
38 23 0.19
39 45 0.38
40 41 0.35
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (39 bp):
TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
Found at i:14080 original size:79 final size:77
Alignment explanation
Indices: 13997--14165 Score: 214
Period size: 79 Copynumber: 2.2 Consensus size: 77
13987 GGACTAAGAT
* *
13997 CCGAAGGCATTTGTGCGAGATA-CAAGTTCCGGGTTAAGCCCGAAGGCCTTTGTGCGAGATACTA
1 CCGAAGGCATTTGTGCGAGATATCAA-ATCCGGGTTAAGCCCGAAGG-CATTGTGCGAGATACTA
*
14061 AATCCGGGTTAAGTC
64 AA-CCGGGCTAAGTC
* * * * * *
14076 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCGAAGGCATTGTGTGAGTTACTAAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCGAAGGCATTGTGCGAGATACTAAA
*
14141 CCGGGCTATGTC
66 CCGGGCTAAGTC
14153 CCGAAGGCATTTG
1 CCGAAGGCATTTG
14166 AACGAGGAGC
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
77 22 0.28
78 16 0.21
79 38 0.49
80 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (77 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCGAAGGCATTGTGCGAGATACTAAA
CCGGGCTAAGTC
Found at i:14157 original size:38 final size:39
Alignment explanation
Indices: 13944--14163 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
13934 TTGAATGCTG
* * * * * *
13944 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
13984 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* *
14024 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
14063 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
14103 TCCGGGTTAAGT-CCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
14141 -CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
14164 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
37 9 0.06
38 24 0.16
39 46 0.30
40 66 0.43
41 7 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:14183 original size:77 final size:79
Alignment explanation
Indices: 14024--14197 Score: 194
Period size: 77 Copynumber: 2.2 Consensus size: 79
14014 AGATACAAGT
* * *
14024 TCCGGGTTAAGCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGTTAAGTCCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCG
** * *
14089 TGCGAGTTATTAAA
66 AACGAGTGACTAAA
* * * *
14103 TCCGGGTTAAGTCCGAAGG-CATTGTGTGAGTTACTAAA-CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCG
*
14166 AACGAG-GAGCTATA
66 AACGAGTGA-CTAAA
*
14180 TCC-GGTTAAATCCGAAGG
1 TCCGGGTTAAGTCCGAAGG
14198 TACGTGATTT
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
76 15 0.19
77 32 0.40
78 16 0.20
79 18 0.22
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCGAAGGCCATTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCG
AACGAGTGACTAAA
Found at i:19942 original size:46 final size:46
Alignment explanation
Indices: 19795--19965 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
19785 AACCCGCCCC
* * *
19795 TAAGTGAACTCGGACTCAACTCAACGAGCT-GGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
19840 TAAGTGAACTC-GACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
19887 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
19932 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
19966 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 9, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 19 0.18
45 15 0.14
46 35 0.33
47 24 0.23
48 2 0.02
49 3 0.03
50 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:20421 original size:30 final size:30
Alignment explanation
Indices: 20387--20446 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
20377 ATTTAATACG
20387 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
20417 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
20447 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:25707 original size:39 final size:40
Alignment explanation
Indices: 25606--25829 Score: 255
Period size: 39 Copynumber: 5.7 Consensus size: 40
25596 TTGAATGATG
* *
25606 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
25645 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
25686 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
25725 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
25764 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
25803 AACCGGGCTATGTCCCGAAGGCGTTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
25830 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
39 75 0.46
40 75 0.46
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:25843 original size:40 final size:40
Alignment explanation
Indices: 25607--25829 Score: 235
Period size: 40 Copynumber: 5.6 Consensus size: 40
25597 TGAATGATGT
* * * *
25607 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
25647 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
* *
25687 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-A
25726 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
25764 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
25805 CCGGGCTATGTCCCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
25830 AACGAGTAGC
Statistics
Matches: 162, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
39 74 0.46
40 78 0.48
41 10 0.06
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:25851 original size:79 final size:79
Alignment explanation
Indices: 25659--25862 Score: 218
Period size: 79 Copynumber: 2.6 Consensus size: 79
25649 GGACTAAGAT
** * * * *
25659 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTA
*
25723 ATTCCGGGCTAAGC
66 ATACCGGGCTAAGC
** *
25737 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTA
*
25801 ATAACCGGGCTATGTC
66 AT-ACCGGGCTAAG-C
* * * *
25817 CCGAAGGCGTTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTTA-CTAAATCCGGGTTAAGTCCCGAAGG
25863 TACGTGATTT
Statistics
Matches: 109, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
78 37 0.34
79 48 0.44
80 24 0.22
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTA
ATACCGGGCTAAGC
Found at i:34033 original size:79 final size:78
Alignment explanation
Indices: 33922--34145 Score: 274
Period size: 79 Copynumber: 2.8 Consensus size: 78
33912 GCTACTCGTT
* * *
33922 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
33987 ATTTAGTAACTCGCA
65 A-TTAGTAACTCGCA
* *
34002 CAAATGCCTTCGGGCTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGCTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCG
*
34065 GATTAGTATCTCGCA
64 GATTAGTAACTCGCA
* * * * *
34080 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
34144 GA
64 GA
34146 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
78 29 0.23
79 70 0.56
80 26 0.21
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
TTAGTAACTCGCA
Found at i:34039 original size:39 final size:39
Alignment explanation
Indices: 33922--34145 Score: 267
Period size: 40 Copynumber: 5.7 Consensus size: 39
33912 GCTACTCGTT
* *
33922 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCA
*
33962 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
*
34002 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTAGTAACTCGCA
* *
34041 CAAATGCCTTC-GGATCTTAGTCCGGATTAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTAGTAACTCGCA
* * * *
34080 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA
34121 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
34146 CATCATTCAA
Statistics
Matches: 166, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 73 0.44
40 79 0.48
41 12 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:39892 original size:40 final size:40
Alignment explanation
Indices: 39808--40031 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
39798 TTGAATGATG
* * * *
39808 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
39848 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
39888 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39926 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39966 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40007 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40032 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 25 0.15
39 19 0.12
40 111 0.67
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40026 original size:80 final size:80
Alignment explanation
Indices: 39808--40031 Score: 296
Period size: 78 Copynumber: 2.8 Consensus size: 80
39798 TTGAATGATG
* * * * *
39808 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
39871 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
*
39888 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
39950 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* *
39966 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
40031 G
66 G
40032 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
77 2 0.02
78 49 0.39
79 25 0.20
80 49 0.39
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Done.