Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003651.1 Hibiscus syriacus cultivar Beakdansim tig00007758_pilon, whole genome shotgun sequence
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: 79003
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:558 original size:51 final size:51
Alignment explanation
Indices: 439--569 Score: 147
Period size: 51 Copynumber: 2.6 Consensus size: 51
429 AAAAAGATAC
* * *
439 TTAAAGAATATTTAATAAATTGAATAAAGAATTGATGTTGAAGAAGAAAAG
1 TTAAAGAATCTTTAATAAATTGAAGAATGAATTGATGTTGAAGAAGAAAAG
* * * *
490 TTAAAGAATCTTAAATAAATTGAAGAATGGATTGATATTTG-AGAAGAATAG
1 TTAAAGAATCTTTAATAAATTGAAGAATGAATTGAT-GTTGAAGAAGAAAAG
** * *
541 TTAAATTATTTTTAATAAATTAAAGAATG
1 TTAAAGAATCTTTAATAAATTGAAGAATG
570 TGTTTTGAGA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
51 64 0.96
52 3 0.04
ACGTcount: A:0.50, C:0.01, G:0.16, T:0.34
Consensus pattern (51 bp):
TTAAAGAATCTTTAATAAATTGAAGAATGAATTGATGTTGAAGAAGAAAAG
Found at i:3724 original size:55 final size:55
Alignment explanation
Indices: 3685--4007 Score: 501
Period size: 55 Copynumber: 5.9 Consensus size: 55
3675 TAATTTGTTT
*
3685 ATGAATTTCCGTATGGACACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
** *
3740 ATGAATTTTAGCATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
*
3795 ATGAATTTCCGTAT-GGCACTTTATGTGTAAACTTATGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
3849 ATGAA-TTCACGTGTGGGCACTTTATGTGTAAACTTATGAAATTCATACTAAGTGG
1 ATGAATTTC-CGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
3904 ATGAATTCCCGTGTGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
3959 ATGAATTTTCGTATGGG-ACTTTATGTGTAAAAC-TAGGAAATTCATACTA
1 ATGAATTTCCGTATGGGCACTTTATGTGT-AAACTTAAGAAATTCATACTA
4008 GGTGTACAAA
Statistics
Matches: 249, Mismatches: 15, Indels: 9
0.91 0.05 0.03
Matches are distributed among these distances:
53 3 0.01
54 74 0.30
55 170 0.68
56 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (55 bp):
ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
Found at i:3855 original size:109 final size:109
Alignment explanation
Indices: 3685--4007 Score: 508
Period size: 109 Copynumber: 3.0 Consensus size: 109
3675 TAATTTGTTT
3685 ATGAATTTCCGTATGGACACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTA
1 ATGAATTTCCGTATGG-CACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTA
*
3750 GCATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
65 GTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
3795 ATGAATTTCCGTATGGCACTTTATGTGTAAACTTATGAAATTCATACTAAGTGGATGAA-TTCAC
1 ATGAATTTCCGTATGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTA-
* *
3859 GTGTGGGCACTTTATGTGTAAACTTATGAAATTCATACTAAGTGG
65 GTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * *
3904 ATGAATTCCCGTGTGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTC
1 ATGAATTTCCGTAT-GGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTA
*
3969 GTATGGG-ACTTTATGTGTAAAAC-TAGGAAATTCATACTA
65 GTATGGGCACTTTATGTGT-AAACTTAAGAAATTCATACTA
4008 GGTGTACAAA
Statistics
Matches: 197, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
108 3 0.02
109 122 0.62
110 70 0.36
111 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (109 bp):
ATGAATTTCCGTATGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTAG
TATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
Found at i:3938 original size:164 final size:164
Alignment explanation
Indices: 3685--4007 Score: 515
Period size: 164 Copynumber: 2.0 Consensus size: 164
3675 TAATTTGTTT
**
3685 ATGAATTTCCGTATGGACACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTA
1 ATGAATTTCCGTATGGACACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTCCA
3750 GCATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGCACT
66 GCATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGCACT
*
3815 TTATGTGT-AAACTTATGAAATTCATACTAAGTGG
131 TTATGTGTAAAAC-TAGGAAATTCATACTAAGTGG
* * *
3849 ATGAA-TTCACGTGTGGGCACTTTATGTGTAAACTTATGAAATTCATACTAAGTGGATGAATTCC
1 ATGAATTTC-CGTATGGACACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTCC
* ** * *
3913 CGTGTGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGAC
65 AGCATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGCAC
3978 TTTATGTGTAAAACTAGGAAATTCATACTA
130 TTTATGTGTAAAACTAGGAAATTCATACTA
4008 GGTGTACAAA
Statistics
Matches: 146, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
163 3 0.02
164 139 0.95
165 4 0.03
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (164 bp):
ATGAATTTCCGTATGGACACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTCCA
GCATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGCACT
TTATGTGTAAAACTAGGAAATTCATACTAAGTGG
Found at i:10122 original size:19 final size:20
Alignment explanation
Indices: 10098--10156 Score: 84
Period size: 19 Copynumber: 2.9 Consensus size: 20
10088 TGCAAAAATG
10098 GTATCGATACCATAATAG-A
1 GTATCGATACCATAATAGTA
10117 GTATCGATACCATAGTATAGTA
1 GTATCGATACCATA--ATAGTA
*
10139 GTATCGATACCATGATAG
1 GTATCGATACCATAATAG
10157 GGATATTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 14 0.39
20 4 0.11
21 4 0.11
22 14 0.39
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (20 bp):
GTATCGATACCATAATAGTA
Found at i:10643 original size:55 final size:55
Alignment explanation
Indices: 10529--10929 Score: 592
Period size: 55 Copynumber: 7.3 Consensus size: 55
10519 TAATTTGTTT
** * *
10529 ATGAATTTCCGTATGGGCACTTTATGCAATAAACTTAAGAAATTTATACCAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATG-TGTAAACTTAAGAAATTCATACTAAGTGG
** *
10585 ATGAATTTTTGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTAG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
*
10640 ATGAATTTCTGTATGGGCACTTTATGTGTAAACTTAA-AAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
10694 ATGAATTTCCGTATGGGCACTTTATGTGTAACCTTAAGAAATTCATACTAAATGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
10749 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
*
10804 ATGAATTTCCGTATGGGCGCTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * * * *
10859 ATGAATTTCCGTAAT-GACACTTTATGTGCAAAAC-TAGGAAATTCATACTAGGTGT
1 ATGAATTTCCGT-ATGGGCACTTTATGTG-TAAACTTAAGAAATTCATACTAAGTGG
* *
10914 ATAAATTTCTGTATGG
1 ATGAATTTCCGTATGG
10930 TTAGTGGGTG
Statistics
Matches: 318, Mismatches: 23, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
54 53 0.17
55 235 0.74
56 30 0.09
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (55 bp):
ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
Found at i:10784 original size:164 final size:165
Alignment explanation
Indices: 10529--10908 Score: 586
Period size: 164 Copynumber: 2.3 Consensus size: 165
10519 TAATTTGTTT
** * * * *
10529 ATGAATTTCCGTATGGGCACTTTATGCAATAAACTTAAGAAATTTATACCAAGTGGATGAATTTT
1 ATGAATTTCCGTATGGGCACTTTATG-TGTAAACTTAAGAAATTCATACTAAATGGATGAATTTC
* *
10594 TGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTAGATGAATTTCTGTATGGGCA
65 CGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTAGATGAATTTCCGTATGGGCA
10659 CTTTATGTGTAAACTTAA-AAATTCATACTAAGTGG
130 CTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
*
10694 ATGAATTTCCGTATGGGCACTTTATGTGTAACCTTAAGAAATTCATACTAAATGGATGAATTTCC
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAATGGATGAATTTCC
* *
10759 GTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCGC
66 GTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTAGATGAATTTCCGTATGGGCAC
10824 TTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
131 TTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * *
10859 ATGAATTTCCGTAAT-GACACTTTATGTGCAAAAC-TAGGAAATTCATACTA
1 ATGAATTTCCGT-ATGGGCACTTTATGTG-TAAACTTAAGAAATTCATACTA
10909 GGTGTATAAA
Statistics
Matches: 197, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
164 110 0.56
165 82 0.42
166 5 0.03
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (165 bp):
ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAATGGATGAATTTCC
GTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTAGATGAATTTCCGTATGGGCAC
TTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
Found at i:19079 original size:54 final size:54
Alignment explanation
Indices: 18992--19164 Score: 265
Period size: 54 Copynumber: 3.2 Consensus size: 54
18982 CTATTTGTAC
* * *
18992 TATAAGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGTTGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCG
* * *
19046 TATAGGCACTAAGTGTGGAACCCACGAAATTCATCATGTGTTGATGAACAACCA
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCG
* *
19100 TATAGACACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCG
*
19154 TATACGCACTA
1 TATAGGCACTA
19165 TACGTGCGAA
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCG
Found at i:19185 original size:54 final size:53
Alignment explanation
Indices: 18992--19218 Score: 233
Period size: 54 Copynumber: 4.2 Consensus size: 53
18982 CTATTTGTAC
* * * * *
18992 TATAAGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGTTGAACAACCG
1 TATAGGCACTAAGTGCG-AACCCACGAAATTCATCATATGTTGATGAACAACCA
* *
19046 TATAGGCACTAAGTGTGGAACCCACGAAATTCATCATGTGTTGATGAACAACCA
1 TATAGGCACTAAGTG-CGAACCCACGAAATTCATCATATGTTGATGAACAACCA
* * * *
19100 TATAGACACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACAACCG
1 TATAGGCACTAAGTGCG-AACCCACGAAATTCATCATATGTTGATGAACAACCA
* * * * **
19154 TATACGCACTATACGTGCGAA-CCA-TAGAATTCATAATATGTTTATGAATGACCA
1 TATAGGCACTA-A-GTGCGAACCCACGA-AATTCATCATATGTTGATGAACAACCA
19208 TATAGGCACTA
1 TATAGGCACTA
19219 TGTGTATATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
53 2 0.01
54 136 0.93
55 4 0.03
56 4 0.03
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (53 bp):
TATAGGCACTAAGTGCGAACCCACGAAATTCATCATATGTTGATGAACAACCA
Found at i:19187 original size:108 final size:108
Alignment explanation
Indices: 18998--19223 Score: 287
Period size: 108 Copynumber: 2.1 Consensus size: 108
18988 GTACTATAAG
* * * * *
18998 CACTAAGTGTGCAACCCACGGAATTCATCATATGTTGTTGAACAACCGTATAGGCACTAAGTGTG
1 CACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACAACCGTATACGCACTAAGTGTC
* * *
19063 GAACCCACGAAATTCATCATGTGTTGATGAACAACCATATAGA
66 GAACCCAAGAAATTCATAATATGTTGATGAACAACCATATAGA
19106 CACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACAACCGTATACGCACTATACGTG
1 CACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACAACCGTATACGCACTA-A-GTG
* ** *
19171 -CGAA-CCATAG-AATTCATAATATGTTTATGAATGACCATATAGG
64 TCGAACCCA-AGAAATTCATAATATGTTGATGAACAACCATATAGA
*
19214 CACTATGTGT
1 CACTAAGTGT
19224 ATATCTCAAT
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
108 94 0.92
109 5 0.05
110 3 0.03
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (108 bp):
CACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACAACCGTATACGCACTAAGTGTC
GAACCCAAGAAATTCATAATATGTTGATGAACAACCATATAGA
Found at i:23467 original size:14 final size:14
Alignment explanation
Indices: 23450--23494 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
23440 GACCCGCTTG
23450 ACCCGACTGAGTCA
1 ACCCGACTGAGTCA
*
23464 ACCCGCATTGAGTCA
1 ACCCG-ACTGAGTCA
* *
23479 ACTCGGCTGAGTCA
1 ACCCGACTGAGTCA
23493 AC
1 AC
23495 TTGTTGACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.18
Consensus pattern (14 bp):
ACCCGACTGAGTCA
Found at i:25852 original size:39 final size:39
Alignment explanation
Indices: 25798--25880 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
25788 TTCCCTATTT
* * * * *
25798 TTACCGCAGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCC
1 TTACCGCAGGCTCCTCGGCTGTATGCACAGGATAAGACC
*
25837 TTACCGCAGGCTCCTCTGCTGTATGCACAGGATAAGACC
1 TTACCGCAGGCTCCTCGGCTGTATGCACAGGATAAGACC
25876 TTACC
1 TTACC
25881 ATTTCCCCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (39 bp):
TTACCGCAGGCTCCTCGGCTGTATGCACAGGATAAGACC
Found at i:25924 original size:45 final size:45
Alignment explanation
Indices: 25853--25969 Score: 157
Period size: 45 Copynumber: 2.6 Consensus size: 45
25843 CAGGCTCCTC
*
25853 TGCTGTATGCACAGGATAAGACCTTACCATTTCCCCATGCTCATCG
1 TGCTGTATGCACAGGATAAGACCTTACCATTTCCCCATACTCAT-G
* * *
25899 T-CTGTGTGCACAGGATAAGACCTTACCATTTCCCCATACTCCTT
1 TGCTGTATGCACAGGATAAGACCTTACCATTTCCCCATACTCATG
* *
25943 TGCTATCTGCA-AGGATAAGACCTTACC
1 TGCTGTATGCACAGGATAAGACCTTACC
25970 GTTACCTTAG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
44 17 0.27
45 46 0.72
46 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (45 bp):
TGCTGTATGCACAGGATAAGACCTTACCATTTCCCCATACTCATG
Found at i:25985 original size:44 final size:42
Alignment explanation
Indices: 25843--26097 Score: 197
Period size: 44 Copynumber: 5.9 Consensus size: 42
25833 GTCCTTACCG
* * * *
25843 CAGGCTCCTCTGCTGTATGCACAGGATAAGACCTTACCATTTCCC
1 CAGGCTCCTTTGCTATGTGCA-AGGATAAGACCTTACC-GTT-CC
* * * * *
25888 CATGCT-CATCGTCTGTGTGCACAGGATAAGACCTTACCATTTCCC
1 CAGGCTCCTTTG-CTATGTGCA-AGGATAAGACCTTACC-GTT-CC
** *
25933 CATACTCCTTTGCTATCTGCAAGGATAAGACCTTACCGTTACC
1 CAGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCGTT-CC
* * * * *
25976 TTAGGCTCCTCTGCTATATGCAAGGGTAAGTCCTTACCGTTCC
1 -CAGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCGTTCC
* * * *
26019 CATGCTCCTTTGTTATGTGCAAGCATAAGACCTTACCGTTTCA
1 CAGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCG-TTCC
* * *
26062 AAGGCTCTTTTGCTATGTGCAAGGGTAAGACCTTAC
1 CAGGCTCCTTTGCTATGTGCAAGGATAAGACCTTAC
26098 TGTTTTTGCA
Statistics
Matches: 172, Mismatches: 34, Indels: 10
0.80 0.16 0.05
Matches are distributed among these distances:
42 30 0.17
43 39 0.23
44 51 0.30
45 49 0.28
46 3 0.02
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (42 bp):
CAGGCTCCTTTGCTATGTGCAAGGATAAGACCTTACCGTTCC
Found at i:26040 original size:86 final size:85
Alignment explanation
Indices: 25905--26097 Score: 233
Period size: 86 Copynumber: 2.2 Consensus size: 85
25895 ATCGTCTGTG
* * *
25905 TGCACAGGATAAGACCTTACCATTTCCCCATACTCCTTTGCTATCTGCAAGGATAAGACCTTACC
1 TGCA-AGGGTAAGACCTTACC-GTT-CCCATACTCCTTTGCTATCTGCAAGCATAAGACCTTACC
**
25970 GTTACCTTAGGCTCCTCTGCTATA
63 GTT-CCAAAGGCTCCTCTGCTATA
* * * *
25994 TGCAAGGGTAAGTCCTTACCGTTCCCATGCTCCTTTGTTATGTGCAAGCATAAGACCTTACCGTT
1 TGCAAGGGTAAGACCTTACCGTTCCCATACTCCTTTGCTATCTGCAAGCATAAGACCTTACCGTT
* * * *
26059 TCAAAGGCTCTTTTGCTATG
66 CCAAAGGCTCCTCTGCTATA
26079 TGCAAGGGTAAGACCTTAC
1 TGCAAGGGTAAGACCTTAC
26098 TGTTTTTGCA
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
85 32 0.36
86 38 0.42
87 2 0.02
88 14 0.16
89 4 0.04
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (85 bp):
TGCAAGGGTAAGACCTTACCGTTCCCATACTCCTTTGCTATCTGCAAGCATAAGACCTTACCGTT
CCAAAGGCTCCTCTGCTATA
Found at i:26111 original size:129 final size:135
Alignment explanation
Indices: 25842--26119 Score: 313
Period size: 129 Copynumber: 2.1 Consensus size: 135
25832 AGTCCTTACC
* * *
25842 GCAGGCTCCTCTGCTGTATGCACAGGATAAGACCTTACCATTTCCCCATGCTCATCGTCTGTGTG
1 GCAGGCTCCTCTGCTATATGCACAGGATAAGACCTTACCAGTTCCCCATGCTCATCGTCTATGTG
* ** *
25907 CACAGGATAAGACCTTACCATTTCCCCATACTCCTTTGCTATCTGCAAGGATAAGACCTTACCGT
66 CACAGCATAAGACCTTACCATTTCCAAAGACTCCTTTGCTATCTGCAAGGATAAGACCTTACCGT
25972 TACCTT
131 TA-CTT
* * * *
25978 --AGGCTCCTCTGCTATATGCA-AGGGTAAGTCCTTACC-GTT-CCCATGCTCCTTTGT-TATGT
1 GCAGGCTCCTCTGCTATATGCACAGGATAAGACCTTACCAGTTCCCCATGCT-CATCGTCTATGT
* * * * * *
26037 GCA-AGCATAAGACCTTACCGTTT-CAAAGGCTCTTTTGCTATGTGCAAGGGTAAGACCTTACTG
65 GCACAGCATAAGACCTTACCATTTCCAAAGACTCCTTTGCTATCTGCAAGGATAAGACCTTACCG
*
26100 TT-TTT
130 TTACTT
26105 GCAGGCTCCTCTGCT
1 GCAGGCTCCTCTGCT
26120 TTGCGCATAG
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
127 2 0.02
129 47 0.39
130 18 0.15
131 15 0.12
132 6 0.05
133 14 0.12
134 19 0.16
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (135 bp):
GCAGGCTCCTCTGCTATATGCACAGGATAAGACCTTACCAGTTCCCCATGCTCATCGTCTATGTG
CACAGCATAAGACCTTACCATTTCCAAAGACTCCTTTGCTATCTGCAAGGATAAGACCTTACCGT
TACTT
Found at i:28354 original size:165 final size:164
Alignment explanation
Indices: 28083--28397 Score: 463
Period size: 165 Copynumber: 1.9 Consensus size: 164
28073 ATATGAAAAT
* *
28083 TCATCAACTCATGATGAATTCCGTGGGTTGCACACATAGAGCATGTATGGTTACTCATCAACTCA
1 TCATCAACTCATGATGAATTCCGTGGGTTGCACACATAGAGCATGTACGGTTACTCATCAACCCA
* * *
28148 TGATGAATCCCGTGGGTTTGCACACATAGTGCTTGTACGGTTATTCATCAACTGATGATAAATTT
66 TGATGAATCCCGTGGATTTGCACACATACTGCTTGTACGGTTATTCATCAACTGATGATAAATTC
28213 TGTAGATTTGCACACATAGTACATGTATGGTTAA
131 TGTAGATTTGCACACATAGTACATGTATGGTTAA
* * ** *
28247 TCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTTTGTACGGTTATTCATCAACCC
1 TCATCAACTCATGATGAATTCCGTGG-GTTGCACACATAGAGCATGTACGGTTACTCATCAACCC
* *
28312 ATGATGAATTCCC-TGGATTTGCACGCATACTG-TCTGTACGGTTATTCATCAACTTATGATAAA
65 ATGATGAA-TCCCGTGGATTTGCACACATACTGCT-TGTACGGTTATTCATCAACTGATGATAAA
* *
28375 TTCTGTGGATTTGTACACATAGT
128 TTCTGTAGATTTGCACACATAGT
28398 GACTGTAGTA
Statistics
Matches: 134, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
164 27 0.20
165 103 0.77
166 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (164 bp):
TCATCAACTCATGATGAATTCCGTGGGTTGCACACATAGAGCATGTACGGTTACTCATCAACCCA
TGATGAATCCCGTGGATTTGCACACATACTGCTTGTACGGTTATTCATCAACTGATGATAAATTC
TGTAGATTTGCACACATAGTACATGTATGGTTAA
Found at i:28404 original size:55 final size:55
Alignment explanation
Indices: 28081--28398 Score: 388
Period size: 55 Copynumber: 5.8 Consensus size: 55
28071 CTATATGAAA
* * *
28081 ATTCATCAACTCATGATGAATTCCGTGG-GTTGCACACATAGAGCATGTATGGTT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
* * * *
28135 ACTCATCAACTCATGATGAATCCCGTGGGTTTGCACACATAGTGCTTGTACGGTT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
* * ** * * *
28190 ATTCATCAACTGATGATAAATTTTGTAGATTTGCACACATAGTACATGTATGGTT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
* **
28245 AATCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTTTGTACGGTT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
* * * *
28300 ATTCATCAACCCATGATGAATTCCCTGGATTTGCACGCATACTGTC-TGTACGGTT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTG-CATGTACGGTT
* * * *
28355 ATTCATCAACTTATGATAAATTCTGTGGATTTGTACACATAGTG
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTG
28399 ACTGTAGTAC
Statistics
Matches: 221, Mismatches: 41, Indels: 3
0.83 0.15 0.01
Matches are distributed among these distances:
54 26 0.12
55 195 0.88
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTT
Found at i:28804 original size:22 final size:22
Alignment explanation
Indices: 28763--28815 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
28753 GGCTCCTTAA
28763 TATCGATAC--CCATACCATGG
1 TATCGATACTACCATACCATGG
*
28783 TATCGATACTACCATACTATGG
1 TATCGATACTACCATACCATGG
28805 TA-CTGATACTA
1 TATC-GATACTA
28816 TGCTATGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 9 0.31
21 1 0.03
22 19 0.66
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (22 bp):
TATCGATACTACCATACCATGG
Found at i:28894 original size:20 final size:20
Alignment explanation
Indices: 28871--28908 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28861 TTGATACTTT
*
28871 CCCTTCAGTATCTATATTCC
1 CCCTTCAGTATCGATATTCC
*
28891 CCCTTCGGTATCGATATT
1 CCCTTCAGTATCGATATT
28909 GATTGAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.32, G:0.11, T:0.39
Consensus pattern (20 bp):
CCCTTCAGTATCGATATTCC
Found at i:34122 original size:55 final size:55
Alignment explanation
Indices: 34012--34224 Score: 279
Period size: 55 Copynumber: 3.9 Consensus size: 55
34002 AGTTTAAAAA
* *
34012 ATTCATCAACTCATGATGAATTCCGTGG-GTTGCACACATAGTGCATGTACGGTT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATATTGCATGTACGGTT
** * * * **
34066 ATTTTTCAACTCATGATGAATCCCATGGGTTTGCACACATATTGGTTGTACGGTT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATATTGCATGTACGGTT
*
34121 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACAT-TGTGCATGTACGATT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAT-TGCATGTACGGTT
* * *
34176 ATTCATCAACTC-TGATGAATTCCGTGGATTTACACACACAGTGCATGTA
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATATTGCATGTA
34225 GTACACATAG
Statistics
Matches: 137, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
54 58 0.42
55 79 0.58
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATATTGCATGTACGGTT
Found at i:34141 original size:109 final size:109
Alignment explanation
Indices: 34012--34213 Score: 307
Period size: 109 Copynumber: 1.9 Consensus size: 109
34002 AGTTTAAAAA
* **
34012 ATTCATCAACTCATGATGAATTCCGTGG-GTTGCACACATAGTGCATGTACGGTTATTTTTCAAC
1 ATTCATCAACTCATGATGAATTCCGTGGAGTTGCACACATAGTGCATGTACGATTATTCATCAAC
* *
34076 TCATGATGAATCCCATGGGTTTGCACACATATTGGTTGTACGGTT
66 TC-TGATGAATCCCATGGATTTACACACATATTGGTTGTACGGTT
* *
34121 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATTGTGCATGTACGATTATTCATCAAC
1 ATTCATCAACTCATGATGAATTCCGTGGAGTTGCACACATAGTGCATGTACGATTATTCATCAAC
* *
34186 TCTGATGAATTCCGTGGATTTACACACA
66 TCTGATGAATCCCATGGATTTACACACA
34214 CAGTGCATGT
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
109 50 0.60
110 33 0.40
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (109 bp):
ATTCATCAACTCATGATGAATTCCGTGGAGTTGCACACATAGTGCATGTACGATTATTCATCAAC
TCTGATGAATCCCATGGATTTACACACATATTGGTTGTACGGTT
Found at i:34594 original size:22 final size:22
Alignment explanation
Indices: 34552--34622 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 22
34542 TGGCTCCTCA
*
34552 GTATCGATAC--CTATACCATG
1 GTATCGATACTACTATACTATG
*
34572 GTATCGATACTACCATACTATG
1 GTATCGATACTACTATACTATG
* *
34594 GTA-CCA-A-TACTATGCTATG
1 GTATCGATACTACTATACTATG
34613 GTATCGATAC
1 GTATCGATAC
34623 CATTGTTGCA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 13 0.32
20 13 0.32
21 3 0.08
22 11 0.28
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (22 bp):
GTATCGATACTACTATACTATG
Found at i:34671 original size:19 final size:20
Alignment explanation
Indices: 34647--34697 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
34637 GTTTCGAAAT
**
34647 GGTATCGATAC-CTTCCTTC
1 GGTATCGATACTCCCCCTTC
*
34666 GGTATCGCTACTCCCCCTTC
1 GGTATCGATACTCCCCCTTC
34686 GGTATCGATACT
1 GGTATCGATACT
34698 GATTGAATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.33
Consensus pattern (20 bp):
GGTATCGATACTCCCCCTTC
Found at i:37703 original size:54 final size:54
Alignment explanation
Indices: 37583--37815 Score: 269
Period size: 54 Copynumber: 4.4 Consensus size: 54
37573 TTATTTGTAC
* *
37583 TATAAGCACTAAGTGCGCAACCCAC-ATAATTCATC--ATGTTGATGAATAACCG
1 TATAGGCACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAATAACCG
*
37635 TATAGGCACAAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAATAACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAATAACCG
* * * * *
37689 TATAGGAACTAAGTGTGAAACCCACAAAATTCATCATATGTTGATGAACAACTG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAATAACCG
* * * * * *
37743 TATAGGCACTATA-TGTACGAA-CCATGGAATTCATAATATGTTTATGAATGACCG
1 TATAGGCACTA-AGTGTGC-AACCCACGAAATTCATCATATGTTGATGAATAACCG
*
37797 TATAGGCACTACGTGTGCA
1 TATAGGCACTAAGTGTGCA
37816 GCTCAATGAA
Statistics
Matches: 153, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
52 30 0.20
53 2 0.01
54 118 0.77
55 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAATAACCG
Found at i:41541 original size:153 final size:152
Alignment explanation
Indices: 41263--41570 Score: 580
Period size: 153 Copynumber: 2.0 Consensus size: 152
41253 AAACACGTAA
*
41263 TTTACTCAATAAAATAATGGGACCCATAAATTTATTAATGTGTCAATTATCTTTATAAAATTTTA
1 TTTACTCAATAAAATAATGGGACCCATAAATTTATTAATATGTCAATTATCTTTATAAAATTTTA
41328 TATTAACGTTAATAAATTGTTCTTCCATAAAATACTAATTTAATATTTCTTTCTCAAAATTAAAA
66 TATTAACGTTAATAAATTGTTCTTCCATAAAATACTAATTTAATATTTCTTTCTCAAAATTAAAA
41393 AAAAAATCAATTAAACTCTTTAG
131 AAAAAAT-AATTAAACTCTTTAG
41416 TTTACTCAATAAAATAATGGGACCCATAAATTTATTAATATGTCAATTATCTTTATAAAATTTTA
1 TTTACTCAATAAAATAATGGGACCCATAAATTTATTAATATGTCAATTATCTTTATAAAATTTTA
*
41481 TATTAACGTTAATAAATTGTTCTTCCATAAAATACTAATTTAATATTTCTTTCTCAAAATTCAAA
66 TATTAACGTTAATAAATTGTTCTTCCATAAAATACTAATTTAATATTTCTTTCTCAAAATTAAAA
*
41546 AAAAAATAATTAAACTTTTTAG
131 AAAAAATAATTAAACTCTTTAG
41568 TTT
1 TTT
41571 TGATCTTTCC
Statistics
Matches: 152, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
152 17 0.11
153 135 0.89
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (152 bp):
TTTACTCAATAAAATAATGGGACCCATAAATTTATTAATATGTCAATTATCTTTATAAAATTTTA
TATTAACGTTAATAAATTGTTCTTCCATAAAATACTAATTTAATATTTCTTTCTCAAAATTAAAA
AAAAAATAATTAAACTCTTTAG
Found at i:44802 original size:33 final size:33
Alignment explanation
Indices: 44757--44823 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
44747 CTTATATTTT
* *
44757 ACTACTTCTGAGGACAAGCATTCAAGGACTTGA
1 ACTACTTATGAGGACAAGAATTCAAGGACTTGA
44790 ACTACTTATGAGGACAAGAATTCAAGGACTTGA
1 ACTACTTATGAGGACAAGAATTCAAGGACTTGA
44823 A
1 A
44824 ACTTACCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (33 bp):
ACTACTTATGAGGACAAGAATTCAAGGACTTGA
Found at i:44901 original size:21 final size:22
Alignment explanation
Indices: 44857--44901 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
44847 AGTTTCTTTA
* *
44857 TTGTTCTTTGTTTCATACTGTT
1 TTGTTCTTAGTTTCAAACTGTT
*
44879 TTGTTCTTAGTTT-AAAGTGTT
1 TTGTTCTTAGTTTCAAACTGTT
44900 TT
1 TT
44902 CTTTCTAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.13, C:0.09, G:0.16, T:0.62
Consensus pattern (22 bp):
TTGTTCTTAGTTTCAAACTGTT
Found at i:50867 original size:26 final size:25
Alignment explanation
Indices: 50829--50878 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
50819 TAAGATACAA
50829 CAACAACACCATCTCCATTTCATCAT
1 CAACAACACCATCTCCA-TTCATCAT
* * *
50855 CAACACCATCATCTTCATTCATCA
1 CAACAACACCATCTCCATTCATCA
50879 AGACCATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (25 bp):
CAACAACACCATCTCCATTCATCAT
Found at i:50879 original size:22 final size:21
Alignment explanation
Indices: 50847--50887 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
50837 CCATCTCCAT
50847 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
50868 TTCATTCATCAAGACCATCA
1 TTCA-TCATCAACACCATCA
50888 ATTCCGTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.34, C:0.34, G:0.02, T:0.29
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:51220 original size:10 final size:9
Alignment explanation
Indices: 51204--51266 Score: 63
Period size: 10 Copynumber: 6.2 Consensus size: 9
51194 ATTGGAGTGC
51204 AAAAAGAAA
1 AAAAAGAAA
51213 AGAAAAGACAA
1 A-AAAAGA-AA
51224 AAAGAAGAAAA
1 AAA-AAG-AAA
51235 AAAATCAGAAA
1 AAAA--AGAAA
51246 AAAAAGAAAA
1 AAAAAG-AAA
51256 AAAAAGAAA
1 AAAAAGAAA
51265 AA
1 AA
51267 GAAATTCAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
9 8 0.17
10 18 0.38
11 18 0.38
12 3 0.06
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:51231 original size:21 final size:19
Alignment explanation
Indices: 51204--51266 Score: 81
Period size: 21 Copynumber: 3.1 Consensus size: 19
51194 ATTGGAGTGC
*
51204 AAAAAGAAAAGAAAAGACAA
1 AAAAAGAAAAAAAAAGA-AA
51224 AAAGAAGAAAAAAAATCAGAAA
1 AAA-AAGAAAAAAAA--AGAAA
51246 AAAAAGAAAAAAAAAGAAA
1 AAAAAGAAAAAAAAAGAAA
51265 AA
1 AA
51267 GAAATTCAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 7 0.18
20 3 0.08
21 21 0.54
22 5 0.13
23 3 0.08
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAAAAAAAGAAA
Found at i:51237 original size:12 final size:12
Alignment explanation
Indices: 51222--51260 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
51212 AAGAAAAGAC
51222 AAAAAGAAGAAA
1 AAAAAGAAGAAA
**
51234 AAAAATCAGAAA
1 AAAAAGAAGAAA
51246 AAAAAGAA-AAA
1 AAAAAGAAGAAA
51257 AAAA
1 AAAA
51261 GAAAAAGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 7 0.30
12 16 0.70
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (12 bp):
AAAAAGAAGAAA
Found at i:51245 original size:33 final size:34
Alignment explanation
Indices: 51208--51284 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 34
51198 GAGTGCAAAA
*
51208 AGAAAAGAAAAGACAAAAAGAAGAAAAA-AAA-TC
1 AGAAAAGAAAAGA-AAAAAAAAGAAAAAGAAATTC
51241 AGAAAA-AAAAGAAAAAAAAAGAAAAAGAAATTC
1 AGAAAAGAAAAGAAAAAAAAAGAAAAAGAAATTC
51274 AGAAAGAGAAA
1 AGAAA-AGAAA
51285 GCAAGCCAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
31 13 0.33
32 9 0.23
33 13 0.33
34 1 0.03
35 3 0.08
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.04
Consensus pattern (34 bp):
AGAAAAGAAAAGAAAAAAAAAGAAAAAGAAATTC
Found at i:55301 original size:22 final size:21
Alignment explanation
Indices: 55269--55309 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
55259 CCATCTCTAT
55269 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
55290 TTCATTCATCAAGACCATCA
1 TTCA-TCATCAACACCATCA
55310 ATTCCGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.34, C:0.34, G:0.02, T:0.29
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:56872 original size:29 final size:30
Alignment explanation
Indices: 56836--56974 Score: 94
Period size: 29 Copynumber: 4.8 Consensus size: 30
56826 TGGGATGAAG
56836 TTAGAATGTTCAAAAGTTTAATGACT-AAT
1 TTAGAATGTTCAAAAGTTTAATGACTAAAT
* * * *
56865 TTAGAATGAGTC-ATAGTTTGAGGA-TGAAA-
1 TTAGAATG-TTCAAAAGTTTAATGACT-AAAT
* *
56894 TTGGAATGTTCAAAAGTTTAATGAAT-AAT
1 TTAGAATGTTCAAAAGTTTAATGACTAAAT
* * ** *
56923 TTAGAATGATC-ATAGTTT-GGGACTAAAG
1 TTAGAATGTTCAAAAGTTTAATGACTAAAT
* *
56951 TTGGAATGTTTAAAAGTTTAATGA
1 TTAGAATGTTCAAAAGTTTAATGA
56975 GGATCATAGT
Statistics
Matches: 79, Mismatches: 22, Indels: 17
0.67 0.19 0.14
Matches are distributed among these distances:
27 3 0.04
28 21 0.27
29 48 0.61
30 7 0.09
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (30 bp):
TTAGAATGTTCAAAAGTTTAATGACTAAAT
Found at i:56890 original size:58 final size:57
Alignment explanation
Indices: 56803--56974 Score: 256
Period size: 57 Copynumber: 3.0 Consensus size: 57
56793 GTTTGGGACC
* *
56803 AATTTAGAATGAGAGTCATAGTTTGGGATGAAGTTAGAATGTTCAAAAGTTTAATGACT
1 AATTTAGAAT--GAGTCATAGTTTGGGATGAAGTTGGAATGTTCAAAAGTTTAATGAAT
*
56862 AATTTAGAATGAGTCATAGTTTGAGGATGAAATTGGAATGTTCAAAAGTTTAATGAAT
1 AATTTAGAATGAGTCATAGTTTG-GGATGAAGTTGGAATGTTCAAAAGTTTAATGAAT
* *
56920 AATTTAGAATGA-TCATAGTTTGGGACTAAAGTTGGAATGTTTAAAAGTTTAATGA
1 AATTTAGAATGAGTCATAGTTTGGGA-TGAAGTTGGAATGTTCAAAAGTTTAATGA
56975 GGATCATAGT
Statistics
Matches: 105, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
56 3 0.03
57 49 0.47
58 43 0.41
59 10 0.10
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (57 bp):
AATTTAGAATGAGTCATAGTTTGGGATGAAGTTGGAATGTTCAAAAGTTTAATGAAT
Found at i:56936 original size:57 final size:57
Alignment explanation
Indices: 56765--56974 Score: 257
Period size: 58 Copynumber: 3.6 Consensus size: 57
56755 TTTGGATGAA
* ** *
56765 TTTGAGGATGAAATTGGAA-GATTAAAAAGTTT-GGGACCAATTTAGAATGAGAGTCATAG
1 TTTG-GGATGAAATTGGAATG-TTCAAAAGTTTAATGACTAATTTAGAAT--GAGTCATAG
* *
56824 TTTGGGATGAAGTTAGAATGTTCAAAAGTTTAATGACTAATTTAGAATGAGTCATAG
1 TTTGGGATGAAATTGGAATGTTCAAAAGTTTAATGACTAATTTAGAATGAGTCATAG
*
56881 TTTGAGGATGAAATTGGAATGTTCAAAAGTTTAATGAATAATTTAGAATGA-TCATAG
1 TTTG-GGATGAAATTGGAATGTTCAAAAGTTTAATGACTAATTTAGAATGAGTCATAG
*
56938 TTTGGGACT-AAAGTTGGAATGTTTAAAAGTTTAATGA
1 TTTGGGA-TGAAA-TTGGAATGTTCAAAAGTTTAATGA
56975 GGATCATAGT
Statistics
Matches: 136, Mismatches: 10, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
56 6 0.04
57 47 0.35
58 65 0.48
59 18 0.13
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (57 bp):
TTTGGGATGAAATTGGAATGTTCAAAAGTTTAATGACTAATTTAGAATGAGTCATAG
Found at i:59108 original size:4 final size:4
Alignment explanation
Indices: 59099--59144 Score: 65
Period size: 4 Copynumber: 10.8 Consensus size: 4
59089 GAAAAAATAA
59099 AAAT AAAT AAAT AAAT AAAT AGAAAT AAAT AAAT AAAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT --AAAT AAAT AAAT -AAAT AAAT AAA
59145 AAAGTATACT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
4 31 0.79
5 4 0.10
6 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:59116 original size:18 final size:18
Alignment explanation
Indices: 59093--59144 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
59083 GACCTAGAAA
59093 AAATAAAAATAAATAAAT
1 AAATAAAAATAAATAAAT
* *
59111 AAATAAATAGAAATAAAT
1 AAATAAAAATAAATAAAT
59129 AAAT-AAAATAAATAAA
1 AAATAAAAATAAATAAA
59145 AAAGTATACT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 10 0.33
18 20 0.67
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
AAATAAAAATAAATAAAT
Found at i:59124 original size:22 final size:23
Alignment explanation
Indices: 59093--59146 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
59083 GACCTAGAAA
59093 AAATAAAAATAAATAAAT-AAAT
1 AAATAAAAATAAATAAATAAAAT
*
59115 AAATAGAAATAAATAAATAAAAT
1 AAATAAAAATAAATAAATAAAAT
59138 AAATAAAAA
1 AAATAAAAA
59147 AGTATACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATAAAAATAAATAAATAAAAT
Found at i:59250 original size:37 final size:37
Alignment explanation
Indices: 59193--59706 Score: 681
Period size: 37 Copynumber: 13.8 Consensus size: 37
59183 AAACCTAAAC
59193 ATGTTTTCTAAAA-TATATATTATATATATTTTCCAAAA
1 ATGTTTTC-AAAACTATATATTATATATATTTT-CAAAA
* * * * * * *
59231 ACGATGT-AAAATTATATATTATACACATTTTCGAAA
1 ATGTTTTCAAAACTATATATTATATATATTTTCAAAA
* *
59267 ATGTTTTCAAAACCATATATTATATATATTTT-GAAA
1 ATGTTTTCAAAACTATATATTATATATATTTTCAAAA
*
59303 ATGTTTTCACAACTATATATTATATATATTTTCAAAA
1 ATGTTTTCAAAACTATATATTATATATATTTTCAAAA
* *
59340 ATGTTTTCAAAACCATATATTATATATATTTTGAAAA
1 ATGTTTTCAAAACTATATATTATATATATTTTCAAAA
*
59377 ATGTTTTCACAACTATATATTATATATATTTTCAAAA
1 ATGTTTTCAAAACTATATATTATATATATTTTCAAAA
59414 ATGTTTTCAAAACTATATATTATATATATTTTCGAAAA
1 ATGTTTTCAAAACTATATATTATATATATTTTC-AAAA
*
59452 ATGTTTTCAAAACTATATATTATATAATTTTTTTCAAAA
1 ATGTTTTCAAAACTATATATTATAT-A-TATTTTCAAAA
*
59491 AT-ATTTCAAAACTATATATTATATATATTTTCAAAA
1 ATGTTTTCAAAACTATATATTATATATATTTTCAAAA
59527 ATG-TTTCAAAAACTATATA-T-TATATATTTTCAAAAAA
1 ATGTTTTC-AAAACTATATATTATATATATTTTC--AAAA
59564 ATGTTTTCAAAACTATATA-T-TATATATTTTCAAAAA
1 ATGTTTTCAAAACTATATATTATATATATTTTC-AAAA
59600 ATGTTTTCAAAACTATATA-T-TATATATTTTCAAAA
1 ATGTTTTCAAAACTATATATTATATATATTTTCAAAA
*
59635 ATGTTTTCAAAATTATATATATATATATATATATTTTCAAAA
1 ATGTTTTC-AAA--A-CTATATAT-TATATATATTTTCAAAA
59677 ATGTTTTCAAAACTATATATTATATATATT
1 ATGTTTTCAAAACTATATATTATATATATT
59707 ATATACTGAA
Statistics
Matches: 430, Mismatches: 28, Indels: 37
0.87 0.06 0.07
Matches are distributed among these distances:
35 23 0.05
36 102 0.24
37 192 0.45
38 66 0.15
39 14 0.03
40 6 0.01
41 4 0.01
42 23 0.05
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (37 bp):
ATGTTTTCAAAACTATATATTATATATATTTTCAAAA
Found at i:59660 original size:43 final size:44
Alignment explanation
Indices: 59613--59711 Score: 175
Period size: 42 Copynumber: 2.3 Consensus size: 44
59603 TTTTCAAAAC
*
59613 TATATATTATATATTTTCAAAAATGTTTTCAAAATTATATA-TA
1 TATATATTATATATTTTCAAAAATGTTTTCAAAACTATATATTA
59656 TATATA-TATATATTTTCAAAAATGTTTTCAAAACTATATATTA
1 TATATATTATATATTTTCAAAAATGTTTTCAAAACTATATATTA
59699 TATATATTATATA
1 TATATATTATATA
59712 CTGAATAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
42 33 0.62
43 14 0.26
44 6 0.11
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.48
Consensus pattern (44 bp):
TATATATTATATATTTTCAAAAATGTTTTCAAAACTATATATTA
Found at i:70689 original size:20 final size:21
Alignment explanation
Indices: 70664--70703 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
70654 AAGAAATAGA
70664 TTCTGGATT-AGT-AGTATCGG
1 TTCTGG-TTGAGTGAGTATCGG
70684 TTCTGGTTGAGTGAGTATCG
1 TTCTGGTTGAGTGAGTATCG
70704 ATACTACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 9 0.50
21 7 0.39
ACGTcount: A:0.17, C:0.10, G:0.33, T:0.40
Consensus pattern (21 bp):
TTCTGGTTGAGTGAGTATCGG
Found at i:76753 original size:17 final size:17
Alignment explanation
Indices: 76728--76774 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
76718 ATTTCTTCTC
*
76728 TTTTCTTCTTTTCTG-AT
1 TTTTTTTCTTTT-TGTAT
76745 TTTTTTTCTTTTTGTAT
1 TTTTTTTCTTTTTGTAT
76762 TTTCTTTTCTTTT
1 TTT-TTTTCTTTT
76775 GTACTCCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 2 0.07
17 16 0.59
18 9 0.33
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.79
Consensus pattern (17 bp):
TTTTTTTCTTTTTGTAT
Done.