Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 97 of 207
Found at i:28782458 original size:10 final size:10
Alignment explanation
Indices: 28782412--28782459 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
28782402 TAGATCTTCA
28782412 TTTTTTTCTT
1 TTTTTTTCTT
*
28782422 TTCTTTTCTT
1 TTTTTTTCTT
**
28782432 TCCTTTTCTT
1 TTTTTTTCTT
*
28782442 TTGTTTTTGTT
1 TT-TTTTTCTT
28782453 TTTTTTT
1 TTTTTTT
28782460 TTGCAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 24 0.75
11 8 0.25
ACGTcount: A:0.00, C:0.12, G:0.04, T:0.83
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:28782461 original size:5 final size:5
Alignment explanation
Indices: 28782415--28782448 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
28782405 ATCTTCATTT
* *
28782415 TTTTC TTTTC TTTTC TTTCC TTTTC TTTTG TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
28782449 TGTTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:28784242 original size:26 final size:26
Alignment explanation
Indices: 28784213--28784290 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
28784203 TTTTTGATGT
**
28784213 AATATGAAAGAAAGCCTTTGTGGTGG
1 AATATGAAAGAAAGCCTTTGTGGCAG
*
28784239 AATATGAAAGAAAACCTTTGTGGCAG
1 AATATGAAAGAAAGCCTTTGTGGCAG
* *
28784265 AATATGAAAGGAATGTCTTTGTGGCA
1 AATATGAAA-GAAAGCCTTTGTGGCA
28784291 AACTCCGTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
26 32 0.71
27 13 0.29
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.27
Consensus pattern (26 bp):
AATATGAAAGAAAGCCTTTGTGGCAG
Found at i:28788496 original size:35 final size:33
Alignment explanation
Indices: 28788442--28788506 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
28788432 GAAAAAATTA
*
28788442 TTTCAAAAAATTGTCAAATA-TCAAAAAGTATTT
1 TTTCAAAAAATTATCAAATACT-AAAAAGTATTT
28788475 TTTCAAAAAAATTATCTAAATACTAAAAAGTA
1 TTTC-AAAAAATTATC-AAATACTAAAAAGTA
28788507 CTTAACTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 4 0.14
34 10 0.36
35 13 0.46
36 1 0.04
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (33 bp):
TTTCAAAAAATTATCAAATACTAAAAAGTATTT
Found at i:28797145 original size:13 final size:13
Alignment explanation
Indices: 28797124--28797185 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
28797114 ACACTCAAAT
28797124 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
28797137 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
28797150 ATTTCCACAA-CAC
1 -TTTTCAAAAGCAC
28797163 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
28797176 TTTTCAAAAG
1 TTTTCAAAAG
28797186 TAATGAAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
12 7 0.17
13 28 0.68
14 6 0.15
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:28802274 original size:38 final size:40
Alignment explanation
Indices: 28802205--28802293 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 40
28802195 TTAAAAATAT
* *
28802205 TTATATTAAAAAACACTACCATAAATATAATAAATG-TTTTG
1 TTATATT-AAAAACACTACAATAAATATAATAAA-GATTTTA
28802246 TTATATTAAAAACAC-A-AATAAATATAATAAAGATTTTA
1 TTATATTAAAAACACTACAATAAATATAATAAAGATTTTA
*
28802284 TTGTATTAAA
1 TTATATTAAA
28802294 TATAAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
37 1 0.02
38 27 0.61
39 1 0.02
40 8 0.18
41 7 0.16
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (40 bp):
TTATATTAAAAACACTACAATAAATATAATAAAGATTTTA
Found at i:28802402 original size:6 final size:6
Alignment explanation
Indices: 28802391--28802438 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
28802381 TTAGTGATTT
28802391 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
28802439 CATAATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:28805872 original size:12 final size:12
Alignment explanation
Indices: 28805855--28805881 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28805845 TCGTCCTTGC
28805855 AAAAAAAAAGAA
1 AAAAAAAAAGAA
28805867 AAAAAAAAAGAA
1 AAAAAAAAAGAA
28805879 AAA
1 AAA
28805882 TAATGACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:28811787 original size:20 final size:21
Alignment explanation
Indices: 28811749--28811799 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
28811739 AACGTAGTGG
28811749 AAATT-TATTTTCTAAGAAT-
1 AAATTCTATTTTCTAAGAATC
**
28811768 AAATTCTATTTTCTGGGAATC
1 AAATTCTATTTTCTAAGAATC
28811789 ACAATTCTATT
1 A-AATTCTATT
28811800 GGTTTCTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 12 0.44
21 1 0.04
22 9 0.33
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (21 bp):
AAATTCTATTTTCTAAGAATC
Found at i:28816175 original size:37 final size:37
Alignment explanation
Indices: 28816125--28816201 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
28816115 TAATAGAAAG
28816125 TATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGA
1 TATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGA
28816162 TATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGA
1 TATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGA
28816199 TAT
1 TAT
28816202 CCATATGGCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (37 bp):
TATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGA
Found at i:28818968 original size:45 final size:44
Alignment explanation
Indices: 28818900--28818984 Score: 125
Period size: 45 Copynumber: 1.9 Consensus size: 44
28818890 ATAGATACTC
* *
28818900 GGTGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTTT
1 GGTGGAATCAACACATAGCAACCACCTTA-TAATAAATGATGTTT
* *
28818945 GGTGGAATCGACACATAGTAACCACCTTATAATAAATGAT
1 GGTGGAATCAACACATAGCAACCACCTTATAATAAATGAT
28818985 ACCTGATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 10 0.28
45 26 0.72
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (44 bp):
GGTGGAATCAACACATAGCAACCACCTTATAATAAATGATGTTT
Found at i:28819048 original size:51 final size:50
Alignment explanation
Indices: 28818993--28819181 Score: 184
Period size: 51 Copynumber: 3.7 Consensus size: 50
28818983 ATACCTGATT
** * * *
28818993 CACATAGTAGCCTGGACATAGTACTACACATGTGACCATTTTCATCTGATA
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCA-TATCATCCGATA
* * * *
28819044 CACATAGTAGCCTACACATAATACTACACACGTGATCGA-AGCTATCCGGTA
1 CACATAGTAGCCTACACATAGTACTACACACGTGA-CCATATC-ATCCGATA
* * * * *
28819095 CGCATAGTAGCCTACACATAGTGCTACACATGCGACC-TATCATTCCGGTA
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCATATCA-TCCGATA
* *
28819145 CACGTAGTAGCCTGCACATAGTACTACACACGTGACC
1 CACATAGTAGCCTACACATAGTACTACACACGTGACC
28819182 TAGCAACTTC
Statistics
Matches: 112, Mismatches: 22, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
49 1 0.01
50 42 0.38
51 67 0.60
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTACACATAGTACTACACACGTGACCATATCATCCGATA
Found at i:28819172 original size:101 final size:101
Alignment explanation
Indices: 28818995--28819179 Score: 255
Period size: 101 Copynumber: 1.8 Consensus size: 101
28818985 ACCTGATTCA
** * * *
28818995 CATAGTAGCCTGGACATAGTACTACACATGTGACCATTTTCATCTGATACACATAGTAGCCTACA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCA-TATCATCCGATACACATAGTAGCCTACA
28819060 CATAATACTACACACGTGATCGAAGCTATCCGGTACG
65 CATAATACTACACACGTGATCGAAGCTATCCGGTACG
* * * *
28819097 CATAGTAGCCTACACATAGTGCTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATATCA-TCCGATACACATAGTAGCCTACA
*
28819161 CATAGTACTACACACGTGA
65 CATAATACTACACACGTGA
28819180 CCTAGCAACT
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
100 4 0.06
101 37 0.51
102 31 0.43
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATATCATCCGATACACATAGTAGCCTACAC
ATAATACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:28823033 original size:21 final size:21
Alignment explanation
Indices: 28822999--28823039 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28822989 GCGTAAAAGC
28822999 AAAGAGAAAGGAGAGGATGAT
1 AAAGAGAAAGGAGAGGATGAT
*
28823020 AAAGAAGAAA-GAGATGATGA
1 AAAG-AGAAAGGAGAGGATGA
28823040 AATGGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.34, T:0.10
Consensus pattern (21 bp):
AAAGAGAAAGGAGAGGATGAT
Found at i:28827880 original size:5 final size:5
Alignment explanation
Indices: 28827870--28827918 Score: 98
Period size: 5 Copynumber: 9.8 Consensus size: 5
28827860 TTACTAACAG
28827870 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
28827919 TCATAACAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:28828504 original size:18 final size:19
Alignment explanation
Indices: 28828483--28828523 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
28828473 ATTAAATGTT
*
28828483 ATAAGTTATAAT-TAATAA
1 ATAAGTTATAATATAAAAA
*
28828501 ATAATTTATAATATAAAAA
1 ATAAGTTATAATATAAAAA
28828520 ATAA
1 ATAA
28828524 AAAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAAGTTATAATATAAAAA
Found at i:28829768 original size:20 final size:19
Alignment explanation
Indices: 28829745--28829789 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
28829735 AATATGAATT
*
28829745 ATGAAATTTATATATGTGAA
1 ATGAAATGTA-ATATGTGAA
28829765 ATGAAAATGTAATATGTGAA
1 ATG-AAATGTAATATGTGAA
28829785 ATGAA
1 ATGAA
28829790 TTAGAATGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 15 0.65
21 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (19 bp):
ATGAAATGTAATATGTGAA
Found at i:28830806 original size:54 final size:54
Alignment explanation
Indices: 28830747--28830874 Score: 159
Period size: 54 Copynumber: 2.4 Consensus size: 54
28830737 CGCGGCATGC
* * * *
28830747 GACACGGCTGTGTGACCCAAGTCAGTAAGTTACAC-AGGTAGAGACACGGGCTGG
1 GACACGGCCGTGTGTCCCAAGTCAGTAAGTTACACTA-GTAGAGACACGGCCTAG
* * ** *
28830801 GACACGACCGTGTGTCTCAAGTTTGTGAGTTACACTAGTAGAGACACGGCCTAG
1 GACACGGCCGTGTGTCCCAAGTCAGTAAGTTACACTAGTAGAGACACGGCCTAG
28830855 GACACGGCCGTGTGTCCCAA
1 GACACGGCCGTGTGTCCCAA
28830875 ATTCGAAAGC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
54 61 0.98
55 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (54 bp):
GACACGGCCGTGTGTCCCAAGTCAGTAAGTTACACTAGTAGAGACACGGCCTAG
Found at i:28833659 original size:50 final size:50
Alignment explanation
Indices: 28833548--28833793 Score: 230
Period size: 50 Copynumber: 4.8 Consensus size: 50
28833538 ATTTGGGTAA
* *
28833548 AGAGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGGTTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
* *
28833604 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *** * * *
28833654 AGAGGTCCCCCATAAGACCATGTCTGGGATATGGCATGGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
28833704 AGA-ACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACA-G
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * * *
28833752 AAACATCTCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28833794 TGTTATTATC
Statistics
Matches: 164, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
48 37 0.23
49 3 0.02
50 81 0.49
52 1 0.01
53 2 0.01
55 1 0.01
56 39 0.24
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:28842076 original size:24 final size:24
Alignment explanation
Indices: 28842040--28842177 Score: 161
Period size: 24 Copynumber: 5.8 Consensus size: 24
28842030 TAACACACCA
*
28842040 CGTTGTGGACAAGCCACTGTATAT
1 CGTTGTGGTCAAGCCACTGTATAT
* *
28842064 CGTTGTAGTCAAGCCACTAG-ATAA
1 CGTTGTGGTCAAGCCACT-GTATAT
* *
28842088 CGTTGTGGTTAAGCCATTGTATAT
1 CGTTGTGGTCAAGCCACTGTATAT
* *
28842112 CATTGTGGTCAAGCCACTATATAT
1 CGTTGTGGTCAAGCCACTGTATAT
* * * *
28842136 CCTTGTGGTCAAGTCACTGAATAA
1 CGTTGTGGTCAAGCCACTGTATAT
28842160 CGTTGTGGTCAAGCCACT
1 CGTTGTGGTCAAGCCACT
28842178 TTCTATTGCA
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
23 1 0.01
24 92 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (24 bp):
CGTTGTGGTCAAGCCACTGTATAT
Found at i:28842110 original size:48 final size:48
Alignment explanation
Indices: 28842039--28842177 Score: 179
Period size: 48 Copynumber: 2.9 Consensus size: 48
28842029 ATAACACACC
* *
28842039 ACGTTGTGGACAAGCCACTGTATATCGTTGTAGTCAAGCCACTAGATA
1 ACGTTGTGGTCAAGCCACTGTATATCGTTGTGGTCAAGCCACTAGATA
* * * *
28842087 ACGTTGTGGTTAAGCCATTGTATATCATTGTGGTCAAGCCACTATATA
1 ACGTTGTGGTCAAGCCACTGTATATCGTTGTGGTCAAGCCACTAGATA
* * * * *
28842135 TCCTTGTGGTCAAGTCACTGAATAACGTTGTGGTCAAGCCACT
1 ACGTTGTGGTCAAGCCACTGTATATCGTTGTGGTCAAGCCACT
28842178 TTCTATTGCA
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 77 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (48 bp):
ACGTTGTGGTCAAGCCACTGTATATCGTTGTGGTCAAGCCACTAGATA
Found at i:28842160 original size:72 final size:72
Alignment explanation
Indices: 28842042--28842175 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 72
28842032 ACACACCACG
* * *
28842042 TTGTGGACAAGCCACTGTATATCGTTGTAGTCAAGCCACTAGATAACGTTGTGGTTAAGCCATTG
1 TTGTGGACAAGCCACTATATATCCTTGTAGTCAAGCCACTAGATAACGTTGTGGTCAAGCCATTG
28842107 TATATCA
66 TATATCA
* * *
28842114 TTGTGGTCAAGCCACTATATATCCTTGTGGTCAAGTCACT-GAATAACGTTGTGGTCAAGCCA
1 TTGTGGACAAGCCACTATATATCCTTGTAGTCAAGCCACTAG-ATAACGTTGTGGTCAAGCCA
28842176 CTTTCTATTG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 1 0.02
72 54 0.98
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (72 bp):
TTGTGGACAAGCCACTATATATCCTTGTAGTCAAGCCACTAGATAACGTTGTGGTCAAGCCATTG
TATATCA
Found at i:28850385 original size:16 final size:15
Alignment explanation
Indices: 28850366--28850408 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
28850356 TTTATTCTTT
28850366 TTATTTTATATTTTGA
1 TTATTTTAT-TTTTGA
*
28850382 TTATTTTATTTTTGG
1 TTATTTTATTTTTGA
28850397 TT-TGTTTATTTT
1 TTAT-TTTATTTT
28850409 GCTTTTCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 1 0.04
15 15 0.60
16 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.74
Consensus pattern (15 bp):
TTATTTTATTTTTGA
Found at i:28861263 original size:61 final size:58
Alignment explanation
Indices: 28861156--28861355 Score: 204
Period size: 61 Copynumber: 3.2 Consensus size: 58
28861146 ATTACTTTAA
* *
28861156 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
28861214 TATTAAATTAATAGAATACTTATGTACAAGATAAATATTAAATTAAATTTAATATTAGGATAATC
1 TATTAAATTAATAGAATACTTA--T-CAAGATAAATATTAAATTAAATTTAATATT---A-AAT-
28861279 AC
58 -C
* * * *
28861281 TTTAATATTAAATTAATAAAATA-TTATCAAGATAAGTATTAAACTAAATTTAATATTAAAAC
1 -----TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
*
28861343 TATTAAAATAATA
1 TATTAAATTAATA
28861356 TTATTTTTGA
Statistics
Matches: 121, Mismatches: 7, Indels: 29
0.77 0.04 0.18
Matches are distributed among these distances:
57 12 0.10
58 21 0.17
60 1 0.01
61 29 0.24
62 1 0.01
64 3 0.02
65 4 0.03
67 1 0.01
68 28 0.23
69 1 0.01
71 3 0.02
72 17 0.14
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
Found at i:28861297 original size:20 final size:18
Alignment explanation
Indices: 28861247--28861298 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
28861237 GTACAAGATA
28861247 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
*
28861264 AATATTAGGA-TAATCACTTT
1 AATATTA-AATTAAT-A-TTT
28861284 AATATTAAATTAATA
1 AATATTAAATTAATA
28861299 AAATATTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 10 0.36
18 1 0.04
19 3 0.11
20 14 0.50
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:28861355 original size:68 final size:71
Alignment explanation
Indices: 28861214--28861358 Score: 163
Period size: 68 Copynumber: 2.1 Consensus size: 71
28861204 ATATTAAATC
* * **
28861214 TATTAAATTAATAGAATACTTATGTACAAGATAAATATTAAATTAAATTTAATATTAGGATAATC
1 TATTAAATTAATAAAATACTTA-GTACAAGATAAATATTAAACTAAATTTAATATTAAAATAATC
***
28861279 ACTTTAA
65 AAAATAA
* *
28861286 TATTAAATTAATAAAATA-TTA-T-CAAGATAAGTATTAAACTAAATTTAATATTAAAACT-ATT
1 TATTAAATTAATAAAATACTTAGTACAAGATAAATATTAAACTAAATTTAATATTAAAA-TAATC
28861347 AAAATAA
65 AAAATAA
28861354 TATTA
1 TATTA
28861359 TTTTTGAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
68 41 0.65
69 2 0.03
71 3 0.05
72 17 0.27
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (71 bp):
TATTAAATTAATAAAATACTTAGTACAAGATAAATATTAAACTAAATTTAATATTAAAATAATCA
AAATAA
Found at i:28864064 original size:3 final size:3
Alignment explanation
Indices: 28864056--28864115 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
28864046 ATTTTGGAGG
28864056 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28864104 TAT TAT TAT TAT
1 TAT TAT TAT TAT
28864116 ATAACATGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:28866344 original size:19 final size:19
Alignment explanation
Indices: 28866286--28866345 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
28866276 AGGCCCTTTT
*
28866286 AAAATTTAAAATTAATTTAAA
1 AAAAATTAAAATT--TTTAAA
* * *
28866307 AAATCA-TAAAAATTATAAA
1 AAA-AATTAAAATTTTTAAA
28866326 AAAAATTAAAATTTTTAAA
1 AAAAATTAAAATTTTTAAA
28866345 A
1 A
28866346 TTATAAAAGT
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
18 1 0.03
19 20 0.67
21 9 0.30
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTAAAATTTTTAAA
Found at i:28868446 original size:19 final size:19
Alignment explanation
Indices: 28868403--28868461 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
28868393 ATTACAAAAA
28868403 AAAAATTCCAAAATAATTT-T
1 AAAAATT-CAAAAT-ATTTAT
28868423 CAAAAATTCAAAATATTTAT
1 -AAAAATTCAAAATATTTAT
*
28868443 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
28868461 A
1 A
28868462 TATTTTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 7 0.19
19 15 0.42
20 7 0.19
21 7 0.19
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:28868463 original size:20 final size:20
Alignment explanation
Indices: 28868403--28868456 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
28868393 ATTACAAAAA
28868403 AAAAATTCCAAAATAATTT-T
1 AAAAATTCCAAAAT-ATTTAT
28868423 CAAAAATT-CAAAATATTTAT
1 -AAAAATTCCAAAATATTTAT
28868443 AAAAATTCCAAAAT
1 AAAAATTCCAAAAT
28868457 TTATATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.35
20 13 0.42
21 7 0.23
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATTCCAAAATATTTAT
Found at i:28869481 original size:19 final size:19
Alignment explanation
Indices: 28869453--28869494 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28869443 GAAAATTAAT
*
28869453 ATTTTATCTATTATATTAC
1 ATTTTATCTATTAGATTAC
* *
28869472 ATTTTTTCTATTAGATTCC
1 ATTTTATCTATTAGATTAC
28869491 ATTT
1 ATTT
28869495 GAAATATAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTATCTATTAGATTAC
Found at i:28870152 original size:25 final size:25
Alignment explanation
Indices: 28870105--28870152 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
28870095 TCAGTTTATA
* *
28870105 TTATAATAGTATATATATCTAATCT
1 TTATAATAGTATAAATATATAATCT
28870130 TTAT-ATAGTATAAATTATATAAT
1 TTATAATAGTATAAA-TATATAAT
28870153 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (25 bp):
TTATAATAGTATAAATATATAATCT
Found at i:28870174 original size:20 final size:21
Alignment explanation
Indices: 28870146--28870187 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28870136 AGTATAAATT
28870146 ATATAATA-TATAAAAATAAA
1 ATATAATATTATAAAAATAAA
* *
28870166 ATATTATATTATAAAATTAAA
1 ATATAATATTATAAAAATAAA
28870187 A
1 A
28870188 AGTAAAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATAATATTATAAAAATAAA
Found at i:28871836 original size:5 final size:5
Alignment explanation
Indices: 28871804--28871857 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
28871794 GTTATATATG
* * *
28871804 TATAA TA-AA TAT-A TAAAA TTTAAA TATAA TATAA TATAA TATAA AAT-A
1 TATAA TATAA TATAA TATAA TAT-AA TATAA TATAA TATAA TATAA TATAA
28871852 TATAA T
1 TATAA T
28871858 GACATAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
4 10 0.26
5 25 0.64
6 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:28872131 original size:28 final size:28
Alignment explanation
Indices: 28872093--28872157 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
28872083 GTTTTGAATA
28872093 AAGTTTAAATTGG-ACTTAAGCTTGAGTTT
1 AAGTTT-AATTGGTA-TTAAGCTTGAGTTT
**
28872122 AAGTTTAATTGGTATTGGGCTTGAGTTT
1 AAGTTTAATTGGTATTAAGCTTGAGTTT
*
28872150 AGGTTTAA
1 AAGTTTAA
28872158 ATCTATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 25 0.78
29 7 0.22
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.43
Consensus pattern (28 bp):
AAGTTTAATTGGTATTAAGCTTGAGTTT
Found at i:28873062 original size:18 final size:19
Alignment explanation
Indices: 28873039--28873091 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
28873029 AATCGTGTCG
28873039 TTCATTTTCAAAAT-ATTA
1 TTCATTTTCAAAATCATTA
*
28873057 TTCATTTAC-AAATCATTA
1 TTCATTTTCAAAATCATTA
*
28873075 TTCAATTTCAAAA-CATT
1 TTCATTTTCAAAATCATT
28873092 TTTTTTATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 4 0.13
18 23 0.77
19 3 0.10
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (19 bp):
TTCATTTTCAAAATCATTA
Found at i:28877134 original size:22 final size:22
Alignment explanation
Indices: 28877106--28877147 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28877096 AATAAACTAT
*
28877106 TAATTAATTAATTAA-CTATGAC
1 TAATTAA-CAATTAACCTATGAC
28877128 TAATTAACAATTAACCTATG
1 TAATTAACAATTAACCTATG
28877148 TATAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (22 bp):
TAATTAACAATTAACCTATGAC
Found at i:28884804 original size:59 final size:59
Alignment explanation
Indices: 28884732--28885064 Score: 302
Period size: 59 Copynumber: 5.7 Consensus size: 59
28884722 TTAACAGAGG
*
28884732 TCGCCAC-AAGGCTTTCCTTTTAGAGATTTTCCACGAAGGCATCTTTTTCATTCAGTAC
1 TCGCCACAAAGGCTTTCCTTTTAGAGATTTTCCACAAAGGCATCTTTTTCATTCAGTAC
** * * * * *
28884790 TCAG-CACAAAGGCTTTATTTTTAAAGATTTTCCATAAAGACATCATTTTCATTCGGTAC
1 TC-GCCACAAAGGCTTTCCTTTTAGAGATTTTCCACAAAGGCATCTTTTTCATTCAGTAC
* * ** * * * * * *
28884849 TCACCATAAAGATTTTCCTTTCAGATATTTTCCACAAAGACAACCTTTTCTTTCAGTAC
1 TCGCCACAAAGGCTTTCCTTTTAGAGATTTTCCACAAAGGCATCTTTTTCATTCAGTAC
* *
28884908 TCGCCACAAAGGCTTTCCTTTTAGAGGTTTGCCACAAAGGCATCCTTTGTT--TT-AGTAC
1 TCGCCACAAAGGCTTTCCTTTTAGAGATTTTCCACAAAGGCAT-CTTT-TTCATTCAGTAC
* * * * * *
28884966 TCGCCACAAAGGCTTT-CTTTTCAAATATTTGCCACAAAGGCAAC-CTTTCTTTCAGTAC
1 TCGCCACAAAGGCTTTCCTTTT-AGAGATTTTCCACAAAGGCATCTTTTTCATTCAGTAC
* * * * *
28885024 TCGCCACAAGGGCTTTCCTTTCAAATATTTGCCACAAAGGC
1 TCGCCACAAAGGCTTTCCTTTTAGAGATTTTCCACAAAGGC
28885065 TTTCCTTTCA
Statistics
Matches: 225, Mismatches: 40, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
55 2 0.01
56 1 0.00
57 8 0.04
58 82 0.36
59 127 0.56
60 3 0.01
61 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.35
Consensus pattern (59 bp):
TCGCCACAAAGGCTTTCCTTTTAGAGATTTTCCACAAAGGCATCTTTTTCATTCAGTAC
Found at i:28884974 original size:30 final size:29
Alignment explanation
Indices: 28884880--28885032 Score: 87
Period size: 28 Copynumber: 5.2 Consensus size: 29
28884870 CAGATATTTT
* * *
28884880 CCACAAAGACAACCTTTTCTTTCAGTACTCG
1 CCACAAAGGCATCC-TTT-TTTAAGTACTCG
* ** * *
28884911 CCACAAAGGCTTTCCTTTTAGAGGT--TTG
1 CCACAAAGGC-ATCCTTTTTTAAGTACTCG
*
28884939 CCACAAAGGCATCCTTTGTTTTAGTACTCG
1 CCACAAAGGCATCCTTT-TTTAAGTACTCG
* * * * * *
28884969 CCACAAAGGCTTTC-TTTTCAAATATTTG
1 CCACAAAGGCATCCTTTTTTAAGTACTCG
* *
28884997 CCACAAAGGCAACCTTTCTTTCAGTACTCG
1 CCACAAAGGCATCCTTT-TTTAAGTACTCG
28885027 CCACAA
1 CCACAA
28885033 GGGCTTTCCT
Statistics
Matches: 87, Mismatches: 29, Indels: 13
0.67 0.22 0.10
Matches are distributed among these distances:
27 6 0.07
28 33 0.38
29 4 0.05
30 30 0.34
31 12 0.14
32 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (29 bp):
CCACAAAGGCATCCTTTTTTAAGTACTCG
Found at i:28885006 original size:28 final size:28
Alignment explanation
Indices: 28884968--28885090 Score: 124
Period size: 28 Copynumber: 4.3 Consensus size: 28
28884958 TTTAGTACTC
*
28884968 GCCACAAAGGCTTTCTTTTCAAATATTT
1 GCCACAAAGGCTTTCCTTTCAAATATTT
* * *
28884996 GCCACAAAGGCAACCTTT-CTTTC-AGTACTC
1 GCCACAAAGG----CTTTCCTTTCAAATATTT
*
28885026 GCCACAAGGGCTTTCCTTTCAAATATTT
1 GCCACAAAGGCTTTCCTTTCAAATATTT
* *
28885054 GCCACAAAGGCTTTCCTTTCAGAGATTT
1 GCCACAAAGGCTTTCCTTTCAAATATTT
*
28885082 TCCACAAAG
1 GCCACAAAG
28885091 ACATCCTTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
26 4 0.05
27 5 0.06
28 47 0.61
30 13 0.17
31 4 0.05
32 4 0.05
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (28 bp):
GCCACAAAGGCTTTCCTTTCAAATATTT
Found at i:28885938 original size:14 final size:14
Alignment explanation
Indices: 28885919--28885945 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28885909 ACAAAAAAAC
28885919 CCAATTTTATTGAG
1 CCAATTTTATTGAG
28885933 CCAATTTTATTGA
1 CCAATTTTATTGA
28885946 TAAAAAATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (14 bp):
CCAATTTTATTGAG
Found at i:28886022 original size:10 final size:10
Alignment explanation
Indices: 28886007--28886037 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28885997 AAACATTTAA
28886007 AAAATAACAT
1 AAAATAACAT
*
28886017 AAAATAAGAT
1 AAAATAACAT
28886027 AAAATAACAT
1 AAAATAACAT
28886037 A
1 A
28886038 TAACACAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.19
Consensus pattern (10 bp):
AAAATAACAT
Found at i:28889418 original size:4 final size:4
Alignment explanation
Indices: 28889411--28889454 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
28889401 TAATCATTAA
*
28889411 TTAT TTAT TTAT TTAT TTAT TTAT TTTT TGTGAT TTAT TT-T TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T-T-AT TTAT TTAT TTA
28889455 GGAGTTTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 3 0.09
4 28 0.80
5 2 0.06
6 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:28889463 original size:15 final size:14
Alignment explanation
Indices: 28889417--28889453 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
28889407 TTAATTATTT
*
28889417 ATTTATTTATT-T-
1 ATTTATTTTTTGTG
28889429 ATTTATTTTTTGTG
1 ATTTATTTTTTGTG
28889443 ATTTATTTTTT
1 ATTTATTTTTT
28889454 AGGAGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.45
13 1 0.05
14 11 0.50
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (14 bp):
ATTTATTTTTTGTG
Found at i:28890910 original size:40 final size:41
Alignment explanation
Indices: 28890841--28890925 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 41
28890831 AGCAATTCTG
* *
28890841 ACTTATTTGAAAATCATTTTTGATGTGTTAAAATGATTTTA
1 ACTTAATTGAAAATCATTTTTGATGTGTTAAAATCATTTTA
* *
28890882 ACTTAATTG-AAATCA-TTTTGACTTTGTTAAAATCATTTTC
1 ACTTAATTGAAAATCATTTTTGA-TGTGTTAAAATCATTTTA
28890922 ACTT
1 ACTT
28890926 GATTTTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
39 6 0.15
40 25 0.64
41 8 0.21
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (41 bp):
ACTTAATTGAAAATCATTTTTGATGTGTTAAAATCATTTTA
Found at i:28890914 original size:20 final size:20
Alignment explanation
Indices: 28890850--28890925 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
28890840 GACTTATTTG
*
28890850 AAAATCATTTTTGA-TGTGTT
1 AAAATCA-TTTTGACTTTGTT
* * **
28890870 AAAATGATTTTAACTTAATT
1 AAAATCATTTTGACTTTGTT
*
28890890 GAAATCATTTTGACTTTGTT
1 AAAATCATTTTGACTTTGTT
*
28890910 AAAATCATTTTCACTT
1 AAAATCATTTTGACTT
28890926 GATTTTAAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 5 0.12
20 38 0.88
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (20 bp):
AAAATCATTTTGACTTTGTT
Found at i:28897752 original size:22 final size:20
Alignment explanation
Indices: 28897683--28897742 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
28897673 ATTTTGATGT
* * *
28897683 GTTAAAATGATTTTAACTTA
1 GTTAAAATCATTTTCACTTG
* * *
28897703 ATTGAAATCATTTTGACTTG
1 GTTAAAATCATTTTCACTTG
28897723 GTTAAAATCATTTTCACTTG
1 GTTAAAATCATTTTCACTTG
28897743 ATTTTAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
GTTAAAATCATTTTCACTTG
Found at i:28901951 original size:20 final size:20
Alignment explanation
Indices: 28901926--28901969 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
28901916 AATTATGATA
28901926 GAAAGGTCTATCAATGTTAG
1 GAAAGGTCTATCAATGTTAG
28901946 GAAAGGTCTATCAATGTTAG
1 GAAAGGTCTATCAATGTTAG
28901966 GAAA
1 GAAA
28901970 ATTATTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (20 bp):
GAAAGGTCTATCAATGTTAG
Found at i:28906730 original size:15 final size:15
Alignment explanation
Indices: 28906712--28906744 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28906702 AAATAATAAG
28906712 AAAGGAAATAAATGA
1 AAAGGAAATAAATGA
*
28906727 AAAGTAAATAAATGA
1 AAAGGAAATAAATGA
28906742 AAA
1 AAA
28906745 ACGAGAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (15 bp):
AAAGGAAATAAATGA
Found at i:28910265 original size:52 final size:52
Alignment explanation
Indices: 28910208--28910327 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 52
28910198 CTCAGACAGA
* * *
28910208 GATCATACAAAACATAATAAA-CAAATCAGAGTAACACAGAGAATTTGGTAAC
1 GATCATA-AAAACAGAACAAAGCAAATCAGAGTAACACAGAGAATTTGATAAC
* * * * *
28910260 GATCATAAAACCAGAACAAAGCAAATCAGAGTATCATAGAGATTTTGATAAT
1 GATCATAAAAACAGAACAAAGCAAATCAGAGTAACACAGAGAATTTGATAAC
*
28910312 GATCATATAAACAGAA
1 GATCATAAAAACAGAA
28910328 TAGAGAATGC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 10 0.18
52 47 0.82
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.21
Consensus pattern (52 bp):
GATCATAAAAACAGAACAAAGCAAATCAGAGTAACACAGAGAATTTGATAAC
Found at i:28910377 original size:25 final size:26
Alignment explanation
Indices: 28910349--28910397 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
28910339 TAACTATGCT
28910349 AATGCGAGA-TTTTTC-GAAAAATCAG
1 AATG-GAGATTTTTTCAGAAAAATCAG
*
28910374 AATGTAGATTTTTTCAGAAAAATC
1 AATGGAGATTTTTTCAGAAAAATC
28910398 CTACCCAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 10 0.48
26 8 0.38
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (26 bp):
AATGGAGATTTTTTCAGAAAAATCAG
Found at i:28917298 original size:30 final size:30
Alignment explanation
Indices: 28917262--28917322 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
28917252 AACTTAACAA
28917262 CAGACTTGAAATAAACAAAAAAAAATCACC
1 CAGACTTGAAATAAACAAAAAAAAATCACC
*
28917292 CAGACTTGAAATAAACAAAATAAAATCACC
1 CAGACTTGAAATAAACAAAAAAAAATCACC
28917322 C
1 C
28917323 TACACCCCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.21, G:0.07, T:0.15
Consensus pattern (30 bp):
CAGACTTGAAATAAACAAAAAAAAATCACC
Found at i:28921428 original size:21 final size:19
Alignment explanation
Indices: 28921397--28921435 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
28921387 TTTATAAAAG
28921397 TTAAGGCATTCAAAAGTGT
1 TTAAGGCATTCAAAAGTGT
*
28921416 TTAATGGCAATTCGAAAGTG
1 TTAA-GGC-ATTCAAAAGTG
28921436 AAAGTGTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 3 0.18
21 10 0.59
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (19 bp):
TTAAGGCATTCAAAAGTGT
Found at i:28922969 original size:30 final size:30
Alignment explanation
Indices: 28922933--28923010 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
28922923 ATCCGTATTT
* * **
28922933 ATGGAAAGTCAAATATATGTTTATCAAATA
1 ATGGAAAATCAAAGATATGGGTATCAAATA
*
28922963 ATGGAAATTCAAAGATATGGGTATCAAATA
1 ATGGAAAATCAAAGATATGGGTATCAAATA
*
28922993 TTGGAAAATCAAAGATAT
1 ATGGAAAATCAAAGATAT
28923011 AAGTATCGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.29
Consensus pattern (30 bp):
ATGGAAAATCAAAGATATGGGTATCAAATA
Found at i:28923017 original size:30 final size:30
Alignment explanation
Indices: 28922954--28923027 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
28922944 AATATATGTT
* * **
28922954 TATCAAATAATGGAAATTCAAAGATATGGG
1 TATCAAATATTGGAAAATCAAAGATATAAG
28922984 TATCAAATATTGGAAAATCAAAGATATAAG
1 TATCAAATATTGGAAAATCAAAGATATAAG
*
28923014 TATCGAGATATTGG
1 TATC-AAATATTGG
28923028 CATAAGAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 30 0.79
31 8 0.21
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (30 bp):
TATCAAATATTGGAAAATCAAAGATATAAG
Found at i:28931921 original size:12 final size:11
Alignment explanation
Indices: 28931903--28931937 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
28931893 TAACTATGTG
28931903 AATAACAAATA
1 AATAACAAATA
28931914 AATGAACAAATA
1 AAT-AACAAATA
*
28931926 AATAACTAATA
1 AATAACAAATA
28931937 A
1 A
28931938 TACTATGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.69, C:0.09, G:0.03, T:0.20
Consensus pattern (11 bp):
AATAACAAATA
Found at i:28938100 original size:27 final size:26
Alignment explanation
Indices: 28938070--28938238 Score: 142
Period size: 26 Copynumber: 6.3 Consensus size: 26
28938060 AAAATGACCA
**
28938070 AAATACCCCCAAAAGACAAAATAACTG
1 AAATA-CCCCAAAAGGTAAAATAACTG
* *
28938097 AAATATCCCAAAAGGGTAAAATGA-TCG
1 AAATACCCCAAAA-GGTAAAATAACT-G
* *
28938124 AAATACCCCAAAGGGTAAAATAACCG
1 AAATACCCCAAAAGGTAAAATAACTG
* * *
28938150 AAAGACCCCAAAGGGTGAAATAACTG
1 AAATACCCCAAAAGGTAAAATAACTG
* * * *
28938176 AAATACCCCTAAAGTATAAAATGACCG
1 AAATACCCCAAAAG-GTAAAATAACTG
*
28938203 AAATACCCCCATAAGGTAAAATAACTG
1 AAATA-CCCCAAAAGGTAAAATAACTG
**
28938230 CTATACCCC
1 AAATACCCC
28938239 TAGGAGTCGA
Statistics
Matches: 112, Mismatches: 25, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
26 56 0.50
27 49 0.44
28 7 0.06
ACGTcount: A:0.48, C:0.23, G:0.14, T:0.15
Consensus pattern (26 bp):
AAATACCCCAAAAGGTAAAATAACTG
Found at i:28938143 original size:26 final size:26
Alignment explanation
Indices: 28938059--28938224 Score: 145
Period size: 27 Copynumber: 6.2 Consensus size: 26
28938049 GTAGGGTCAA
* * *
28938059 TAAAATGACCAAAATACCCCCAAAAGA
1 TAAAATGACCGAAATA-CCCCAAAGGG
* * * *
28938086 CAAAATAACTGAAATATCCCAAAAGGG
1 TAAAATGACCGAAATA-CCCCAAAGGG
*
28938113 TAAAATGATCGAAATACCCCAAAGGG
1 TAAAATGACCGAAATACCCCAAAGGG
* *
28938139 TAAAATAACCGAAAGACCCCAAAGGG
1 TAAAATGACCGAAATACCCCAAAGGG
* * * **
28938165 TGAAATAACTGAAATACCCCTAAAGTA
1 TAAAATGACCGAAATACCCC-AAAGGG
28938192 TAAAATGACCGAAATACCCCCATAA-GG
1 TAAAATGACCGAAATA-CCCCA-AAGGG
28938219 TAAAAT
1 TAAAAT
28938225 AACTGCTATA
Statistics
Matches: 110, Mismatches: 26, Indels: 6
0.77 0.18 0.04
Matches are distributed among these distances:
26 49 0.45
27 55 0.50
28 6 0.05
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.15
Consensus pattern (26 bp):
TAAAATGACCGAAATACCCCAAAGGG
Found at i:28938236 original size:54 final size:53
Alignment explanation
Indices: 28938070--28938240 Score: 159
Period size: 53 Copynumber: 3.2 Consensus size: 53
28938060 AAAATGACCA
* * * * * * *
28938070 AAATACCCCCAAAAGACAAAATAACTGAAATATCCCAAAAGGGTAAAATGA-TCG
1 AAATACCCCTAAAGGATAAAATAACCGAAAGA-CCCCAAAGGGTAAAATAACT-G
* *
28938124 AAATACCCC-AAAGGGTAAAATAACCGAAAGACCCCAAAGGGTGAAATAACTG
1 AAATACCCCTAAAGGATAAAATAACCGAAAGACCCCAAAGGGTAAAATAACTG
* * *
28938176 AAATACCCCTAAAGTATAAAATGACCGAAATACCCCCATAA-GGTAAAATAACTG
1 AAATACCCCTAAAGGATAAAATAACCGAAAGA-CCCCA-AAGGGTAAAATAACTG
**
28938230 CTATACCCCTA
1 AAATACCCCTA
28938241 GGAGTCGAAA
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
52 25 0.26
53 36 0.37
54 35 0.36
55 2 0.02
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.16
Consensus pattern (53 bp):
AAATACCCCTAAAGGATAAAATAACCGAAAGACCCCAAAGGGTAAAATAACTG
Found at i:28938600 original size:28 final size:28
Alignment explanation
Indices: 28938537--28938601 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
28938527 GGTTACATTA
* *
28938537 CCACACTATTACTGTATTGGGCTAAGAC
1 CCACACTGTTACTGTATCGGGCTAAGAC
*
28938565 CCACACTGTTACTGTATCGGGCTAAGGC
1 CCACACTGTTACTGTATCGGGCTAAGAC
28938593 CCACACTGT
1 CCACACTGT
28938602 ACTATCATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (28 bp):
CCACACTGTTACTGTATCGGGCTAAGAC
Found at i:28939797 original size:27 final size:26
Alignment explanation
Indices: 28939730--28939814 Score: 98
Period size: 27 Copynumber: 3.2 Consensus size: 26
28939720 ATTTATGAGT
*
28939730 AAATTACCGAAATACCCTCGAAGGGTA
1 AAATTACC-AAATACCCTCAAAGGGTA
**
28939757 AAATTATTGAAATACCCTCAAAGGGTA
1 AAATTA-CCAAATACCCTCAAAGGGTA
* *
28939784 AAATTACCATAATACCCCCTAAGGGTA
1 AAATTACCA-AATACCCTCAAAGGGTA
28939811 AAAT
1 AAAT
28939815 GATCTTTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
26 1 0.02
27 48 0.98
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (26 bp):
AAATTACCAAATACCCTCAAAGGGTA
Found at i:28940192 original size:28 final size:28
Alignment explanation
Indices: 28940152--28940239 Score: 124
Period size: 28 Copynumber: 3.2 Consensus size: 28
28940142 ACTGAAATGA
* *
28940152 TACTGTATGGGGTTAAGGCCCACACTGC
1 TACTGAATTGGGTTAAGGCCCACACTGC
28940180 TACTGAATTGGGTTAAGGCCCACACTGC
1 TACTGAATTGGGTTAAGGCCCACACTGC
* * *
28940208 TACTGAAATAGGTTAAGGCCCTCACTG-
1 TACTGAATTGGGTTAAGGCCCACACTGC
28940235 TACTG
1 TACTG
28940240 TCACTGAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 5 0.09
28 50 0.91
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (28 bp):
TACTGAATTGGGTTAAGGCCCACACTGC
Found at i:28942396 original size:21 final size:20
Alignment explanation
Indices: 28942372--28942428 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
28942362 AAAATCTTAT
28942372 AATATAATTATTTAATTAATA
1 AATATAATTATTTAA-TAATA
** *
28942393 AATATCTTTTACTTAATAATA
1 AATAT-AATTATTTAATAATA
*
28942414 AATAATAAATATTTA
1 AAT-ATAATTATTTA
28942429 TTTACTTAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATAATTATTTAATAATA
Found at i:28942443 original size:30 final size:28
Alignment explanation
Indices: 28942388--28942449 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 28
28942378 ATTATTTAAT
28942388 TAATAAATATCTTTTACTTAATAATAAA
1 TAATAAATATCTTTTACTTAATAATAAA
* *
28942416 TAATAAATATTTATTTACTTAAATAATAAG
1 TAATAAATATCT-TTTACTT-AATAATAAA
28942446 TAAT
1 TAAT
28942450 TTAAATCCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 11 0.37
29 7 0.23
30 12 0.40
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (28 bp):
TAATAAATATCTTTTACTTAATAATAAA
Found at i:28945021 original size:20 final size:20
Alignment explanation
Indices: 28944996--28945041 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
28944986 CTGAAATGGA
* *
28944996 AACAAAAGTAGAAAATAAAG
1 AACAAAAGAAGAAAAAAAAG
28945016 AACAAAAGAAGAAAAAAAAG
1 AACAAAAGAAGAAAAAAAAG
28945036 AA-AAAA
1 AACAAAA
28945042 AAGGATAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.78, C:0.04, G:0.13, T:0.04
Consensus pattern (20 bp):
AACAAAAGAAGAAAAAAAAG
Found at i:28945039 original size:8 final size:9
Alignment explanation
Indices: 28945005--28945044 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
28944995 AAACAAAAGT
*
28945005 AGAAAATAA
1 AGAAAAAAA
28945014 AGAACAAAAGA
1 AGAA-AAAA-A
28945025 AGAAAAAAA
1 AGAAAAAAA
28945034 AGAAAAAAA
1 AGAAAAAAA
28945043 AG
1 AG
28945045 GATAGGGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 16 0.57
10 7 0.25
11 5 0.18
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:28945320 original size:24 final size:24
Alignment explanation
Indices: 28945293--28945339 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
28945283 CGGGGTTTTA
28945293 AATAGAAGACCAAAGGGTAAGCTG
1 AATAGAAGACCAAAGGGTAAGCTG
28945317 AATAGAAGACCAAAGGGTAAGCT
1 AATAGAAGACCAAAGGGTAAGCT
28945340 AACACCTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.28, T:0.13
Consensus pattern (24 bp):
AATAGAAGACCAAAGGGTAAGCTG
Found at i:28949297 original size:23 final size:24
Alignment explanation
Indices: 28949262--28949310 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
28949252 TAGAACTAAT
*
28949262 ACAAACATCGATGCATAGCAGATAC
1 ACAAACA-CGATGCATAACAGATAC
*
28949287 ACAAACA-GATGCATAATAGATAC
1 ACAAACACGATGCATAACAGATAC
28949310 A
1 A
28949311 GATACAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
25 7 0.32
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.16
Consensus pattern (24 bp):
ACAAACACGATGCATAACAGATAC
Found at i:28951729 original size:24 final size:23
Alignment explanation
Indices: 28951697--28951746 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
28951687 ATATATGGGG
* *
28951697 TTGAGAATTCTTCTCTTTTTTCAA
1 TTGACAATTCTTCTCTTATTT-AA
*
28951721 TTGACAATTCTTTTCTTATTTAA
1 TTGACAATTCTTCTCTTATTTAA
28951744 TTG
1 TTG
28951747 TTATTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.56
Consensus pattern (23 bp):
TTGACAATTCTTCTCTTATTTAA
Found at i:28953232 original size:20 final size:20
Alignment explanation
Indices: 28953209--28953251 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
28953199 TAATATTTTA
*
28953209 AACAT-AAATAACTAAAATGT
1 AACATAAAATAAATAAAA-GT
28953229 AACATAAAATAAATAAAAGT
1 AACATAAAATAAATAAAAGT
28953249 AAC
1 AAC
28953252 TATTATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.65, C:0.09, G:0.05, T:0.21
Consensus pattern (20 bp):
AACATAAAATAAATAAAAGT
Found at i:28961025 original size:41 final size:41
Alignment explanation
Indices: 28960973--28961054 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
28960963 ATATTTTATT
* *
28960973 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTAGTTGATTAGAATAAGAGAATTATTTTCC
*
28961014 TTATGTTTTAGTAGTTGATTAGAATAAGAGAATTATTTTCC
1 TTATCTTTTAGTAGTTGATTAGAATAAGAGAATTATTTTCC
28961055 AATTAGGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTGATTAGAATAAGAGAATTATTTTCC
Found at i:28968489 original size:44 final size:47
Alignment explanation
Indices: 28968425--28968549 Score: 157
Period size: 44 Copynumber: 2.7 Consensus size: 47
28968415 GTGGCTGTGC
*
28968425 AGAATCTGCAAGTAGTTGCAGATTCCCCTTGATATTAGGAAGT-T-T
1 AGAATCTGCAAGTAGTTGCAGATTCCCCTTGATATGAGGAAGTATGT
* *
28968470 -GAATCTGCAAGTAGTTGCAGATTTCCATTGATATGAGGAAGTCATGT
1 AGAATCTGCAAGTAGTTGCAGATTCCCCTTGATATGAGGAAGT-ATGT
* * * *
28968517 AGACTTTGCAAGTTGTTGAAGATTCCCCTTGAT
1 AGAATCTGCAAGTAGTTGCAGATTCCCCTTGAT
28968550 TTTTGTGAGA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 39 0.58
46 1 0.01
47 1 0.01
48 26 0.39
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (47 bp):
AGAATCTGCAAGTAGTTGCAGATTCCCCTTGATATGAGGAAGTATGT
Found at i:28973265 original size:12 final size:12
Alignment explanation
Indices: 28973248--28973272 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28973238 TAGATGTCTA
28973248 TTATGTTAAAGG
1 TTATGTTAAAGG
28973260 TTATGTTAAAGG
1 TTATGTTAAAGG
28973272 T
1 T
28973273 GATCTGCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (12 bp):
TTATGTTAAAGG
Found at i:28973384 original size:32 final size:30
Alignment explanation
Indices: 28973335--28973407 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 30
28973325 TCTAAAACTA
*
28973335 AAAACAGAAATAGAAGGAATTTATGCAAAT
1 AAAATAGAAATAGAAGGAATTTATGCAAAT
* *
28973365 GAAAATAGAGAATAGAAGGAATTTTTGTAAAT
1 -AAAATAGA-AATAGAAGGAATTTATGCAAAT
28973397 AAGAATAGAAA
1 AA-AATAGAAA
28973408 GAAATTCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 11 0.30
32 26 0.70
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (30 bp):
AAAATAGAAATAGAAGGAATTTATGCAAAT
Found at i:28983853 original size:21 final size:22
Alignment explanation
Indices: 28983823--28983880 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 22
28983813 GTTCCGCTTT
*
28983823 TTATTATTTTATTTTAAAA-TAA
1 TTATT-TTTTATCTTAAAATTAA
28983845 TTATTTTTTATCTTAAAATTAA
1 TTATTTTTTATCTTAAAATTAA
28983867 TTAGTTTTATTATC
1 TTA-TTTT-TTATC
28983881 ATTATTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 12 0.38
22 11 0.34
23 4 0.12
24 5 0.16
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATTTTTTATCTTAAAATTAA
Found at i:28984496 original size:16 final size:17
Alignment explanation
Indices: 28984475--28984508 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28984465 CATACATATT
*
28984475 TACATATATTTTT-ACA
1 TACATAGATTTTTCACA
28984491 TACATAGATTTTTCACA
1 TACATAGATTTTTCACA
28984508 T
1 T
28984509 TTTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (17 bp):
TACATAGATTTTTCACA
Found at i:28996903 original size:48 final size:47
Alignment explanation
Indices: 28996843--28997117 Score: 163
Period size: 48 Copynumber: 5.7 Consensus size: 47
28996833 GCAATTTAAA
* * *
28996843 AGATCGAAGCTACAGCGGCGAATCTTACTTCGGGCGATGCAGCGGAGC
1 AGATCGAAGCTACAACAGCGAATCTCACTTC-GGCGATGCAGCGGAGC
* ** **** **
28996891 AGATTGAAGCTACAACAGCGAATCTCACTTCCCCGACATTGCAATTTAAA
1 AGATCGAAGCTACAACAGCGAATCTCACTTCGGCG--A-TGCAGCGGAGC
* * * * *
28996941 AGATCGAAGCCACAGCGGTGAATCTTACTTCTGGCGATGCAGCGGAGC
1 AGATCGAAGCTACAACAGCGAATCTCACTTC-GGCGATGCAGCGGAGC
* * ** * **** **
28996989 AGATTGAAGCTACAACAGTGAATCTCACTTCCCCAACATTGCAATTTAAA
1 AGATCGAAGCTACAACAGCGAATCTCACTTCGGC--GA-TGCAGCGGAGC
* * * * *
28997039 AGATCGAAGCCACAGCGGCGAATCTTACTTCTGGCAATGCAGCGGAGC
1 AGATCGAAGCTACAACAGCGAATCTCACTTC-GGCGATGCAGCGGAGC
*
28997087 AGATTGAAGCTACAACAGCGAATCTCACTTC
1 AGATCGAAGCTACAACAGCGAATCTCACTTC
28997118 CCTGACATTG
Statistics
Matches: 159, Mismatches: 60, Indels: 16
0.68 0.26 0.07
Matches are distributed among these distances:
47 3 0.02
48 89 0.56
49 4 0.03
50 60 0.38
51 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (47 bp):
AGATCGAAGCTACAACAGCGAATCTCACTTCGGCGATGCAGCGGAGC
Found at i:28996964 original size:50 final size:50
Alignment explanation
Indices: 28996891--28997416 Score: 350
Period size: 50 Copynumber: 10.6 Consensus size: 50
28996881 GCAGCGGAGC
* *
28996891 AGATTGAAGCTACAACAGCGAATCTCACTTCCCCGACATTGCAATTTAAA
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAATTTAAA
* * * * * * **** **
28996941 AGATCGAAGCCACAGCGGTGAATCTTACTT--CTGGCGA-TGCAGCGGAGC
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCCGAC-ATTGCAATTTAAA
* * * *
28996989 AGATTGAAGCTACAACAGTGAATCTCACTTCCCCAACATTGCAATTTAAA
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAATTTAAA
* * * * * * **** **
28997039 AGATCGAAGCCACAGCGGCGAATCTTACTT--CTGGCAATGCAGCGGAGC
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAATTTAAA
* * *
28997087 AGATTGAAGCTACAACAGCGAATCTCACTTCCCTGACATTGCAATTTAAA
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAATTTAAA
* * ** * * ** *
28997137 AGATCGAAGCCACAACAGTGAATCTTAC-TCCTAG-CGTTGCAGTGGAAT
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAATTTAAA
* * * * *
28997185 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGTAATTAAAA
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAATTTAAA
* * * * * * ** **
28997235 AGATTGAAGCTACAACAGCGGATCTTACTT-TCCTAGCTTTGCAGTGGAGC
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCCGA-CATTGCAATTTAAA
* ** * *
28997285 AGATTGAAGTCACAATGGCGAATCTTGCTTCCCCGACATAGCAA-TTAGAA
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAATTTA-AA
* * *
28997335 AGATTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTTAAA
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAATTTAAA
* * *
28997385 AGATCGAAGCCACAACGGTGAATCTTACTTCC
1 AGATTGAAGCCACAACAGCGAATCTTACTTCC
28997417 AGGCGACACA
Statistics
Matches: 349, Mismatches: 115, Indels: 24
0.72 0.24 0.05
Matches are distributed among these distances:
48 99 0.28
49 13 0.04
50 231 0.66
51 6 0.02
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (50 bp):
AGATTGAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAATTTAAA
Found at i:28997000 original size:98 final size:98
Alignment explanation
Indices: 28996831--28997365 Score: 669
Period size: 98 Copynumber: 5.4 Consensus size: 98
28996821 AAACCATAGT
* * *
28996831 TTGCAATTTAAAAGATCGAAGCTACAGCGGCGAATCTTACTTCGGGCGATGCAGCGGAGCAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
28996896 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* *
28996929 TTGCAATTTAAAAGATCGAAGCCACAGCGGTGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
* *
28996994 GAAGCTACAACAGTGAATCTCACTTCCCCAACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* *
28997027 TTGCAATTTAAAAGATCGAAGCCACAGCGGCGAATCTTACTTCTGGCAATGCAGCGGAGCAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
*
28997092 GAAGCTACAACAGCGAATCTCACTTCCCTGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * * * * * **
28997125 TTGCAATTTAAAAGATCGAAGCCACAACAGTGAATCTTACTCCTAGCGTTGCAGTGGAATAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
* * *
28997190 GAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * * * * * * ** *
28997223 TTGTAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCTTTGCAGTGGAGCAGA
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTAC-TT-CTGGCGATGCAGCGGAGCAGA
** **
28997288 TTGAAG-TCACAATGGCGAATCTTGCTTCCCCGACA
64 TTGAAGCT-ACAACAGCGAATCTCACTTCCCCGACA
* * * *
28997323 TAGCAA-TTAGAAAGATTGAAGCTACAACGGCGAATCTCACTTC
1 TTGCAATTTA-AAAGATCGAAGCCACAACGGCGAATCTTACTTC
28997366 CCCGACATTG
Statistics
Matches: 390, Mismatches: 43, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
98 307 0.79
99 6 0.02
100 77 0.20
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (98 bp):
TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
GAAGCTACAACAGCGAATCTCACTTCCCCGACA
Found at i:28998619 original size:21 final size:22
Alignment explanation
Indices: 28998589--28998646 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 22
28998579 GTTCCGCTGT
*
28998589 TTATTATTTTATTTTAAAA-TAA
1 TTATT-TTTTATCTTAAAATTAA
28998611 TTATTTTTTATCTTAAAATTAA
1 TTATTTTTTATCTTAAAATTAA
28998633 TTAGTTTTATTATC
1 TTA-TTTT-TTATC
28998647 ATTATTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 12 0.38
22 11 0.34
23 4 0.12
24 5 0.16
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATTTTTTATCTTAAAATTAA
Found at i:28999257 original size:16 final size:17
Alignment explanation
Indices: 28999236--28999269 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28999226 CATACATATT
*
28999236 TACATATATTTTT-ACA
1 TACATAGATTTTTCACA
28999252 TACATAGATTTTTCACA
1 TACATAGATTTTTCACA
28999269 T
1 T
28999270 TTTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (17 bp):
TACATAGATTTTTCACA
Found at i:29003639 original size:18 final size:17
Alignment explanation
Indices: 29003618--29003656 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
29003608 AATAAATATT
29003618 ATTTATTAAATTAAATTA
1 ATTTATTAAATTAAA-TA
* *
29003636 ATTTTTTCAATTAAATA
1 ATTTATTAAATTAAATA
29003653 ATTT
1 ATTT
29003657 TATCAACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTATTAAATTAAATA
Found at i:29003654 original size:17 final size:18
Alignment explanation
Indices: 29003626--29003662 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
29003616 TTATTTATTA
*
29003626 AATTAAATTAATTTTTTC
1 AATTAAATTAATTTTATC
29003644 AATTAAA-TAATTTTATC
1 AATTAAATTAATTTTATC
29003661 AA
1 AA
29003663 CCAAATTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTAAATTAATTTTATC
Found at i:29007137 original size:33 final size:33
Alignment explanation
Indices: 29007064--29007137 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
29007054 TACTATCTGT
29007064 TTGGTGTGTTGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTGGTTGGACTAGCTCTTATGAGCA
* * * *
29007097 CTAGTGTGTTGGTTGGATTAGCTCTTCTGAGCA
1 TTGGTGTGTTGGTTGGACTAGCTCTTATGAGCA
29007130 TTGGTGTG
1 TTGGTGTG
29007138 CTGGAGGATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.14, C:0.12, G:0.34, T:0.41
Consensus pattern (33 bp):
TTGGTGTGTTGGTTGGACTAGCTCTTATGAGCA
Found at i:29012205 original size:37 final size:37
Alignment explanation
Indices: 29012155--29012233 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
29012145 TTATTACGAA
* * *
29012155 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
29012192 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
29012229 GTCTT
1 GTCTT
29012234 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:29012429 original size:47 final size:47
Alignment explanation
Indices: 29012351--29012910 Score: 922
Period size: 47 Copynumber: 11.7 Consensus size: 47
29012341 CCCTTCGGGA
* * * * * *
29012351 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29012398 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29012445 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29012492 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29012539 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29012588 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29012637 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29012684 CTTATCACATATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29012733 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29012780 CTTATCACATATATATGCACTTTCAAATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATA--CACTTTCACATTCATCACATCGGCCATTAGGC
*
29012829 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTACGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29012878 CTTATCACATATATACACTTTCACATTCATCAC
1 CTTATCACATATATACACTTTCACATTCATCAC
29012911 GTAGAATCCT
Statistics
Matches: 488, Mismatches: 17, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
47 263 0.54
49 218 0.45
51 7 0.01
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29012580 original size:96 final size:94
Alignment explanation
Indices: 29012351--29012910 Score: 922
Period size: 96 Copynumber: 5.9 Consensus size: 94
29012341 CCCTTCGGGA
* * * * * * * *
29012351 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
29012416 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
29012445 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
29012510 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
29012539 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
29012604 ACACTTTCACATTCATCACATCGGCCATTAGGC
62 ACACTTTCACATTCATCACATCGGCCATTAGGC
29012637 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
29012702 ACTTTCACATTCATCACATCGGCGATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
29012733 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA--C
*
29012798 ACTTTCAAATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
*
29012829 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTACGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
29012894 ACTTTCACATTCATCAC
64 ACTTTCACATTCATCAC
29012911 GTAGAATCCT
Statistics
Matches: 443, Mismatches: 15, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
94 100 0.23
96 244 0.55
98 99 0.22
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:29012646 original size:145 final size:143
Alignment explanation
Indices: 29012351--29012910 Score: 962
Period size: 145 Copynumber: 3.9 Consensus size: 143
29012341 CCCTTCGGGA
* * * * * * * *
29012351 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
29012414 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
29012479 TCGGCCATTAGGC
131 TCGGCCATTAGGC
*
29012492 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
29012557 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
29012622 CATCGGCCATTAGGC
129 CATCGGCCATTAGGC
29012637 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
29012702 ACTTTCACATTCATCACATCGGCGATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
29012767 TCGGCCATTAGGC
131 TCGGCCATTAGGC
*
29012780 CTTATCACATATATATGCACTTTCAAATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATA--CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
*
29012845 ACACTTTCACATTCATCACATCGGCCATTACGCCTTATCACATATATACACTTTCACATTCATCA
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
29012910 C
129 C
29012911 GTAGAATCCT
Statistics
Matches: 399, Mismatches: 14, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
141 46 0.12
143 101 0.25
145 252 0.63
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (143 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:29013821 original size:29 final size:29
Alignment explanation
Indices: 29013788--29013880 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
29013778 TATTAAATCA
29013788 ACTCATCATGTCCTATTATAATTGAATTT
1 ACTCATCATGTCCTATTATAATTGAATTT
* * * * * **
29013817 ACTCA--ACGTACATCATATCTTATTAAATCA
1 ACTCATCATGT-CCT-AT-TATAATTGAATTT
29013847 ACTCATCATGTCCTATTATAATTGAATTT
1 ACTCATCATGTCCTATTATAATTGAATTT
29013876 ACTCA
1 ACTCA
29013881 ACGTTTAATC
Statistics
Matches: 45, Mismatches: 14, Indels: 10
0.65 0.20 0.14
Matches are distributed among these distances:
27 3 0.07
28 2 0.04
29 20 0.44
30 15 0.33
31 2 0.04
32 3 0.07
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.40
Consensus pattern (29 bp):
ACTCATCATGTCCTATTATAATTGAATTT
Found at i:29013823 original size:34 final size:34
Alignment explanation
Indices: 29013785--29013882 Score: 92
Period size: 34 Copynumber: 3.1 Consensus size: 34
29013775 TCTTATTAAA
29013785 TCAACTCATCATGTCCTATTATAATTGAATTTAC
1 TCAACTCATCATGTCCTATTATAATTGAATTTAC
*
29013819 TCAACGT-A-CA--TCATATCT-T-ATT-AA---A-
1 TCAAC-TCATCATGTCCTAT-TATAATTGAATTTAC
29013844 TCAACTCATCATGTCCTATTATAATTGAATTTAC
1 TCAACTCATCATGTCCTATTATAATTGAATTTAC
29013878 TCAAC
1 TCAAC
29013883 GTTTAATCAC
Statistics
Matches: 49, Mismatches: 2, Indels: 26
0.64 0.03 0.34
Matches are distributed among these distances:
24 1 0.02
25 6 0.12
26 3 0.06
27 1 0.02
28 6 0.12
29 5 0.10
30 5 0.10
31 6 0.12
32 1 0.02
33 3 0.06
34 11 0.22
35 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (34 bp):
TCAACTCATCATGTCCTATTATAATTGAATTTAC
Found at i:29013859 original size:59 final size:59
Alignment explanation
Indices: 29013767--29013884 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
29013757 TATCATGGCC
29013767 ACATCATATCTTATTAAATCAACTCATCATGTCCTATTATAATTGAATTTACTCAACGT
1 ACATCATATCTTATTAAATCAACTCATCATGTCCTATTATAATTGAATTTACTCAACGT
29013826 ACATCATATCTTATTAAATCAACTCATCATGTCCTATTATAATTGAATTTACTCAACGT
1 ACATCATATCTTATTAAATCAACTCATCATGTCCTATTATAATTGAATTTACTCAACGT
29013885 TTAATCACTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (59 bp):
ACATCATATCTTATTAAATCAACTCATCATGTCCTATTATAATTGAATTTACTCAACGT
Found at i:29020353 original size:63 final size:63
Alignment explanation
Indices: 29020275--29020393 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 63
29020265 ACACGGCTTG
* * *
29020275 GACACACGCCCATGTCCCTAGCCCGTGTGACTCTAATTC-CAAAACAGTGAGTTACATGACCTA
1 GACACACGCACATGTCCCTAGCACGTGTGACCCTAATTCAC-AAACAGTGAGTTACATGACCTA
* * * *
29020338 GACACACGCACATGTCCTTGGCACGTGTGACCCTAATTGACAAATAGTGAGTTACA
1 GACACACGCACATGTCCCTAGCACGTGTGACCCTAATTCACAAACAGTGAGTTACA
29020394 CGGCCTGGCA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
63 47 0.98
64 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (63 bp):
GACACACGCACATGTCCCTAGCACGTGTGACCCTAATTCACAAACAGTGAGTTACATGACCTA
Found at i:29025075 original size:18 final size:17
Alignment explanation
Indices: 29025054--29025101 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
29025044 ATTTGGTTTA
29025054 TTTTTATTTTTCTATTAT
1 TTTTTATTTTTCTATT-T
29025072 TTTTTATTTAATT-TATTT
1 TTTTTATTT--TTCTATTT
*
29025090 GTTTTATTTTTC
1 TTTTTATTTTTC
29025102 AAGTGTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 2 0.08
18 18 0.69
19 4 0.15
20 2 0.08
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTTATTTTTCTATTT
Found at i:29031971 original size:14 final size:14
Alignment explanation
Indices: 29031952--29031983 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
29031942 CACAAAAGAA
29031952 ATATCTTAATACAT
1 ATATCTTAATACAT
29031966 ATATCTTAATACAT
1 ATATCTTAATACAT
29031980 ATAT
1 ATAT
29031984 TTTTCCTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATCTTAATACAT
Found at i:29041502 original size:23 final size:24
Alignment explanation
Indices: 29041447--29041502 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
29041437 TGTAAATACA
* *
29041447 CAACAGTCAAATTTTAAATTAGAC
1 CAACAGTAAAATTATAAATTAGAC
* * *
29041471 CAACGGTAAAATTATAAA-TGGTC
1 CAACAGTAAAATTATAAATTAGAC
29041494 CAACAGTAA
1 CAACAGTAA
29041503 CTTTTTTCTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.25
Consensus pattern (24 bp):
CAACAGTAAAATTATAAATTAGAC
Found at i:29047026 original size:28 final size:29
Alignment explanation
Indices: 29046975--29047031 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
29046965 TATTTCACAT
** *
29046975 TTTAGTCCCTTAATTTACACTTTTCTTAA
1 TTTAGTCCCTTAATACACACTTTTATTAA
*
29047004 TTTAGT-CCTTAATACACATTTTTATTAA
1 TTTAGTCCCTTAATACACACTTTTATTAA
29047032 AAATTACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.51
Consensus pattern (29 bp):
TTTAGTCCCTTAATACACACTTTTATTAA
Found at i:29048169 original size:54 final size:54
Alignment explanation
Indices: 29048075--29048189 Score: 133
Period size: 54 Copynumber: 2.1 Consensus size: 54
29048065 TCAAAATTTG
* * * * *
29048075 GGTCACACAACCGTGTCGCAGATCGTGTGCCCACCGGTGTGCA-AATCGAAATAA
1 GGTCACACAACCGTGTCACAGACCGTGTGCCAAACGGTGTG-AGAATCAAAATAA
* ** *
29048129 GGTCACACAACCGTGTCATAGACCGTGTGCCAAATTGTGTGAGATTCAAAATAA
1 GGTCACACAACCGTGTCACAGACCGTGTGCCAAACGGTGTGAGAATCAAAATAA
29048183 GGTCACA
1 GGTCACA
29048190 TGGTCGTGTC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 1 0.02
54 50 0.98
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (54 bp):
GGTCACACAACCGTGTCACAGACCGTGTGCCAAACGGTGTGAGAATCAAAATAA
Found at i:29053888 original size:32 final size:32
Alignment explanation
Indices: 29053852--29053917 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
29053842 TCAATTATTC
29053852 ATGGTTTACAAACATCAAATGATATAACAATA
1 ATGGTTTACAAACATCAAATGATATAACAATA
29053884 ATGGTTTACAAACATCAAATGATATAACAATA
1 ATGGTTTACAAACATCAAATGATATAACAATA
29053916 AT
1 AT
29053918 CACACATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (32 bp):
ATGGTTTACAAACATCAAATGATATAACAATA
Found at i:29056878 original size:25 final size:23
Alignment explanation
Indices: 29056835--29056911 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
29056825 TTGTGGCTAC
* *
29056835 AATGTCTT-TGTGGCATATTTTGT
1 AATGCCTTGTGTGGCGTATTTT-T
*
29056858 AATGCCTTTGTGTGGCGTATTCTAT
1 AATGCC-TTGTGTGGCGTATT-TTT
*
29056883 AAT-ACTTGTGTGGCGTATTCTTT
1 AATGCCTTGTGTGGCGTATT-TTT
29056906 AATGCC
1 AATGCC
29056912 CTTAAGGCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
23 25 0.57
24 4 0.09
25 14 0.32
26 1 0.02
ACGTcount: A:0.18, C:0.14, G:0.22, T:0.45
Consensus pattern (23 bp):
AATGCCTTGTGTGGCGTATTTTT
Found at i:29056891 original size:23 final size:23
Alignment explanation
Indices: 29056865--29056908 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
29056855 TGTAATGCCT
29056865 TTGTGTGGCGTATTCTATAATAC
1 TTGTGTGGCGTATTCTATAATAC
*
29056888 TTGTGTGGCGTATTCTTTAAT
1 TTGTGTGGCGTATTCTATAAT
29056909 GCCCTTAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.11, G:0.23, T:0.48
Consensus pattern (23 bp):
TTGTGTGGCGTATTCTATAATAC
Found at i:29062208 original size:33 final size:33
Alignment explanation
Indices: 29062161--29062227 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
29062151 AAGTTGATGA
*
29062161 AAGTTTGAAATGGGATGCTAAAGGAGTACTAAC
1 AAGTCTGAAATGGGATGCTAAAGGAGTACTAAC
**
29062194 AAGTCTGAAATGGGATGCTAAATTAGTACTAAC
1 AAGTCTGAAATGGGATGCTAAAGGAGTACTAAC
29062227 A
1 A
29062228 GGTTTCGCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.25
Consensus pattern (33 bp):
AAGTCTGAAATGGGATGCTAAAGGAGTACTAAC
Found at i:29076258 original size:25 final size:25
Alignment explanation
Indices: 29076226--29076296 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
29076216 CAAACCCATT
**
29076226 TCACAACTTTTGTAAGCATTTAAAG
1 TCACAACTCGTGTAAGCATTTAAAG
** *
29076251 TCACAACTCGTGTGGGCATTTATAG
1 TCACAACTCGTGTAAGCATTTAAAG
*
29076276 TCACAACTCGTGTGAGCATTT
1 TCACAACTCGTGTAAGCATTT
29076297 TTCCCGCGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (25 bp):
TCACAACTCGTGTAAGCATTTAAAG
Found at i:29078614 original size:28 final size:28
Alignment explanation
Indices: 29078551--29078729 Score: 288
Period size: 28 Copynumber: 6.4 Consensus size: 28
29078541 ATATTAAGTC
*
29078551 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
29078578 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
29078606 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
29078634 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
29078662 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
29078690 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
29078719 CGCACACTTAG
1 CGCACACTTAG
29078730 CGCCAATCTC
Statistics
Matches: 143, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
27 22 0.15
28 105 0.73
29 16 0.11
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:29087464 original size:40 final size:40
Alignment explanation
Indices: 29087419--29087551 Score: 151
Period size: 40 Copynumber: 3.3 Consensus size: 40
29087409 GCTATGTTTA
* * *
29087419 GCACTTAGTATGAAATTTGAGATAGTTTCGGCTATTTATG
1 GCACTTAGTATGAGATTTGAGATAGCTTCGGCTATATATG
* *
29087459 GCACTTAGTGTGAGATTTGAAATAGCTTCGGCTATATATG
1 GCACTTAGTATGAGATTTGAGATAGCTTCGGCTATATATG
* * * * *
29087499 GAACTTAGTGTGCGAGA-CTGAGATAGCTTCGGCTATGTAAG
1 GCACTTAGTAT--GAGATTTGAGATAGCTTCGGCTATATATG
29087540 GCACTTAGTATG
1 GCACTTAGTATG
29087552 CGAGATTATA
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
39 1 0.01
40 45 0.57
41 29 0.37
42 4 0.05
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (40 bp):
GCACTTAGTATGAGATTTGAGATAGCTTCGGCTATATATG
Found at i:29087546 original size:41 final size:42
Alignment explanation
Indices: 29087436--29087557 Score: 151
Period size: 41 Copynumber: 3.0 Consensus size: 42
29087426 GTATGAAATT
* * *
29087436 TGAGATAGTTTCGGCTATTTATGGCACTTAGTGT--GAGATT
1 TGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATC
* *
29087476 TGAAATAGCTTCGGCTATATATGGAACTTAGTGTGCGAGA-C
1 TGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATC
* * *
29087517 TGAGATAGCTTCGGCTATGTAAGGCACTTAGTATGCGAGAT
1 TGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGAT
29087558 TATAATAGCT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
40 30 0.43
41 35 0.51
42 4 0.06
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (42 bp):
TGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATC
Found at i:29088328 original size:24 final size:23
Alignment explanation
Indices: 29088232--29088383 Score: 146
Period size: 23 Copynumber: 6.5 Consensus size: 23
29088222 TGACTGATTG
* *
29088232 ATGCTGCCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGATGTATTA
*
29088255 ATGCTGTCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGATGTATTA
29088278 ATGCTGTCCAATTTGATGTATTA
1 ATGCTGTCCAATTTGATGTATTA
*
29088301 ATGCTGTCCATTTTGA-GCATATTA
1 ATGCTGTCCAATTTGATG--TATTA
* *
29088325 ATGCTGTCCATTTTG-CGCATATTA
1 ATGCTGTCCAATTTGATG--TATTA
* * * *
29088349 ATGTTGTCTAAGTTTGAGGTATAA
1 ATGCTGTCCAA-TTTGATGTATTA
*
29088373 AGGCTGTCCAA
1 ATGCTGTCCAA
29088384 AATAAGGTAG
Statistics
Matches: 113, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
22 1 0.01
23 59 0.52
24 48 0.42
25 4 0.04
26 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (23 bp):
ATGCTGTCCAATTTGATGTATTA
Found at i:29106574 original size:11 final size:11
Alignment explanation
Indices: 29106558--29106582 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29106548 AGTTGGTTGG
29106558 TTTTGGTATGT
1 TTTTGGTATGT
29106569 TTTTGGTATGT
1 TTTTGGTATGT
29106580 TTT
1 TTT
29106583 AAAGTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (11 bp):
TTTTGGTATGT
Found at i:29106985 original size:19 final size:19
Alignment explanation
Indices: 29106960--29107002 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
29106950 CATGTTTCCA
29106960 AAATTTTAAATTTT-TTTC
1 AAATTTTAAATTTTCTTTC
*
29106978 ATAATTTTATATTTTCTTTC
1 A-AATTTTAAATTTTCTTTC
29106998 AAATT
1 AAATT
29107003 GGTCCTAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 16 0.73
20 5 0.23
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (19 bp):
AAATTTTAAATTTTCTTTC
Found at i:29110856 original size:23 final size:23
Alignment explanation
Indices: 29110838--29110915 Score: 93
Period size: 23 Copynumber: 3.4 Consensus size: 23
29110828 TAGGCTTCAT
29110838 AGAATACGCCACAAGGGCTCCAC
1 AGAATACGCCACAAGGGCTCCAC
* ** * *
29110861 AGTATATTCCACAAAGGCTTCAC
1 AGAATACGCCACAAGGGCTCCAC
* *
29110884 AGATTATGCCACAAGGGCTCCAC
1 AGAATACGCCACAAGGGCTCCAC
29110907 AGAATACGC
1 AGAATACGC
29110916 TGCAAAGACG
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (23 bp):
AGAATACGCCACAAGGGCTCCAC
Found at i:29110922 original size:46 final size:46
Alignment explanation
Indices: 29110829--29110970 Score: 135
Period size: 46 Copynumber: 3.1 Consensus size: 46
29110819 CTAGCCATTT
* * * **
29110829 AGGCTTCATAGAATACGCCACAAGGGCTCCACAGTATATTCCACAA
1 AGGCTTCATAGATTATGCCACAAGGGCTCCACAGAATACGCCACAA
* **
29110875 AGGCTTCACAGATTATGCCACAAGGGCTCCACAGAATACGCTGCAA
1 AGGCTTCATAGATTATGCCACAAGGGCTCCACAGAATACGCCACAA
* * * * *
29110921 AGACGTCATAGATTATGCCATAAAGGCAT-CACCA-AATATGCCACAA
1 AGGCTTCATAGATTATGCCACAAGGGC-TCCA-CAGAATACGCCACAA
29110967 AGGC
1 AGGC
29110971 ATTACAGGAT
Statistics
Matches: 77, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
46 74 0.96
47 3 0.04
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (46 bp):
AGGCTTCATAGATTATGCCACAAGGGCTCCACAGAATACGCCACAA
Found at i:29111006 original size:24 final size:23
Alignment explanation
Indices: 29110961--29111017 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
29110951 ACCAAATATG
*
29110961 CCACAAAGGCATTACAGGATACA
1 CCACAAAGGCATTACAGAATACA
** *
29110984 CCACAAAAGGCATTTTAGAATACG
1 CCAC-AAAGGCATTACAGAATACA
*
29111008 CTACAAAGGC
1 CCACAAAGGC
29111018 TCTGTTTGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.42, C:0.25, G:0.18, T:0.16
Consensus pattern (23 bp):
CCACAAAGGCATTACAGAATACA
Found at i:29112675 original size:20 final size:20
Alignment explanation
Indices: 29112573--29112677 Score: 75
Period size: 20 Copynumber: 5.2 Consensus size: 20
29112563 GACAAGCGAG
* *
29112573 CAGTAATGCAAATAAACTGT
1 CAGTAATGCAGATAAACTGC
* *
29112593 CAGTATTGCAGATAAACTAC
1 CAGTAATGCAGATAAACTGC
* *
29112613 CAGTAATGCAGATGAGCTGC
1 CAGTAATGCAGATAAACTGC
* * ** * * **
29112633 TAGTATTGTGGACAAGCCAC
1 CAGTAATGCAGATAAACTGC
*
29112653 CAGTAATGTAGATAAACTGC
1 CAGTAATGCAGATAAACTGC
29112673 CAGTA
1 CAGTA
29112678 CTTCTTCCTT
Statistics
Matches: 62, Mismatches: 23, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (20 bp):
CAGTAATGCAGATAAACTGC
Found at i:29115811 original size:25 final size:25
Alignment explanation
Indices: 29115763--29115814 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
29115753 ATCCCGAGAT
* *
29115763 GAAAACCTCAAATTTTAAGTGGGTG
1 GAAAACCTCAAATTCTAAGCGGGTG
*
29115788 GAAAACCTCAAATTCTACGCGGGTG
1 GAAAACCTCAAATTCTAAGCGGGTG
29115813 GA
1 GA
29115815 TACATTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (25 bp):
GAAAACCTCAAATTCTAAGCGGGTG
Found at i:29116503 original size:13 final size:13
Alignment explanation
Indices: 29116481--29116516 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
29116471 TTTTTGAAAC
29116481 ATCATCACCCTTA
1 ATCATCACCCTTA
*
29116494 ATCTTCACCCTTA
1 ATCATCACCCTTA
29116507 ATCATCACCC
1 ATCATCACCC
29116517 ACAAGTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.28, C:0.42, G:0.00, T:0.31
Consensus pattern (13 bp):
ATCATCACCCTTA
Found at i:29140063 original size:13 final size:13
Alignment explanation
Indices: 29140045--29140070 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29140035 AGACTTAGAC
29140045 TCTAAGTCTTGAG
1 TCTAAGTCTTGAG
29140058 TCTAAGTCTTGAG
1 TCTAAGTCTTGAG
29140071 ACTTGCAGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
TCTAAGTCTTGAG
Found at i:29152898 original size:17 final size:17
Alignment explanation
Indices: 29152876--29152909 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29152866 CTTGAATATT
*
29152876 CTCTCTTGTTGTTGTAG
1 CTCTCTTGTTGGTGTAG
29152893 CTCTCTTGTTGGTGTAG
1 CTCTCTTGTTGGTGTAG
29152910 GACATTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.18, G:0.26, T:0.50
Consensus pattern (17 bp):
CTCTCTTGTTGGTGTAG
Found at i:29153267 original size:20 final size:20
Alignment explanation
Indices: 29153239--29153287 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
29153229 ATAAAGTAAG
*
29153239 GTATTGATAAAATTC-AATAA
1 GTATCGATAAAATTCTAA-AA
* *
29153259 GTATCGATATATTTCTAAAA
1 GTATCGATAAAATTCTAAAA
29153279 GTATCGATA
1 GTATCGATA
29153288 CCTATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (20 bp):
GTATCGATAAAATTCTAAAA
Found at i:29153511 original size:19 final size:21
Alignment explanation
Indices: 29153483--29153522 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
29153473 ATGAATTGTC
*
29153483 CAAAATATTTT-TAAG-TGTT
1 CAAAACATTTTCTAAGATGTT
29153502 CAAAACATTTTCTAAGATGTT
1 CAAAACATTTTCTAAGATGTT
29153523 TGGAAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 4 0.22
21 4 0.22
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (21 bp):
CAAAACATTTTCTAAGATGTT
Found at i:29154271 original size:44 final size:44
Alignment explanation
Indices: 29154218--29154306 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
29154208 TTGAAACCAA
* * *
29154218 AATATAAGTTGTGATAATTATACATTTAAAAATATTTATAATTT
1 AATAGAAGTTGTGATAATTACACATTTAAAAATAATTATAATTT
*
29154262 AATAGAAGTTGTGATAATTGCACATTTAAAAATAATTATAATTT
1 AATAGAAGTTGTGATAATTACACATTTAAAAATAATTATAATTT
29154306 A
1 A
29154307 TTTTACAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (44 bp):
AATAGAAGTTGTGATAATTACACATTTAAAAATAATTATAATTT
Found at i:29156048 original size:20 final size:20
Alignment explanation
Indices: 29156031--29156079 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 20
29156021 AAAACTTTTG
29156031 AATTATTGATAAATCTTTAGA
1 AATT-TTGATAAATCTTTAGA
29156052 AATTTTGATAAATCATCTTAGA
1 AATTTTGATAAATC-T-TTAGA
29156074 AATTTT
1 AATTTT
29156080 AGTAAATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.38
21 5 0.19
22 11 0.42
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (20 bp):
AATTTTGATAAATCTTTAGA
Done.