Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 64 of 185
Found at i:18620984 original size:29 final size:29
Alignment explanation
Indices: 18620951--18621012 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
18620941 GTTTTCTTGA
18620951 TTATGGAC-TT-TCATTTTATTTTGGGACTT
1 TTATGGACTTTATCATTTTA-TTTGGG-CTT
*
18620980 TTATGGACTTTATGATTTTATTTGGGCTT
1 TTATGGACTTTATCATTTTATTTGGGCTT
18621009 TTAT
1 TTAT
18621013 TTTTGTGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 15 0.50
30 8 0.27
31 7 0.23
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.56
Consensus pattern (29 bp):
TTATGGACTTTATCATTTTATTTGGGCTT
Found at i:18622971 original size:16 final size:17
Alignment explanation
Indices: 18622940--18622972 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18622930 TACCATTTCG
*
18622940 TAACTAAACAACATTTT
1 TAACCAAACAACATTTT
18622957 TAACCAAAC-ACATTTT
1 TAACCAAACAACATTTT
18622973 ACTTGCTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
TAACCAAACAACATTTT
Found at i:18623998 original size:32 final size:32
Alignment explanation
Indices: 18623943--18624229 Score: 260
Period size: 32 Copynumber: 9.0 Consensus size: 32
18623933 AATCAAATCA
* *
18623943 GCAATAT-A-TATACAAATAAAATTCAATTCG
1 GCAATATAAGTATACATATACAATTCAATTCG
* *
18623973 ACAATATAAGTATACATATATAATTCAATT--
1 GCAATATAAGTATACATATACAATTCAATTCG
* * * *
18624003 -CAATAATAGGTGCATACCTATACAATTCATTTTG
1 GCAAT-ATAAGT--ATACATATACAATTCAATTCG
* *
18624037 GCAATATAAGTATATATATACATTTCAATTCG
1 GCAATATAAGTATACATATACAATTCAATTCG
*** * *
18624069 GCAATAGGTGTATACCTATACAATTCATTTCG
1 GCAATATAAGTATACATATACAATTCAATTCG
* * *
18624101 GCAATATAAGTATATATATACATTTAAATTCG
1 GCAATATAAGTATACATATACAATTCAATTCG
*** *
18624133 GCAATAGGTGTATACCTATACAATTCAATTCG
1 GCAATATAAGTATACATATACAATTCAATTCG
* *
18624165 GCAATATAAGTATATATATACATTTCAATTCG
1 GCAATATAAGTATACATATACAATTCAATTCG
*** *
18624197 GCAATAGGTGTATACCTATACAATTCAATTCG
1 GCAATATAAGTATACATATACAATTCAATTCG
18624229 G
1 G
18624230 TGATGTATAT
Statistics
Matches: 202, Mismatches: 47, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
29 4 0.02
30 11 0.05
31 1 0.00
32 177 0.88
34 5 0.02
35 4 0.02
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (32 bp):
GCAATATAAGTATACATATACAATTCAATTCG
Found at i:18624042 original size:64 final size:64
Alignment explanation
Indices: 18623962--18624229 Score: 419
Period size: 64 Copynumber: 4.2 Consensus size: 64
18623952 ATACAAATAA
* * * * * *** *
18623962 AATTCAATTCGACAATATAAGTATACATATATAATTCAATTCAATAATAGGTGCATACCTATAC
1 AATTCATTTCGGCAATATAAGTATATATATACATTTCAATTCGGCAATAGGTGTATACCTATAC
*
18624026 AATTCATTTTGGCAATATAAGTATATATATACATTTCAATTCGGCAATAGGTGTATACCTATAC
1 AATTCATTTCGGCAATATAAGTATATATATACATTTCAATTCGGCAATAGGTGTATACCTATAC
*
18624090 AATTCATTTCGGCAATATAAGTATATATATACATTTAAATTCGGCAATAGGTGTATACCTATAC
1 AATTCATTTCGGCAATATAAGTATATATATACATTTCAATTCGGCAATAGGTGTATACCTATAC
*
18624154 AATTCAATTCGGCAATATAAGTATATATATACATTTCAATTCGGCAATAGGTGTATACCTATAC
1 AATTCATTTCGGCAATATAAGTATATATATACATTTCAATTCGGCAATAGGTGTATACCTATAC
*
18624218 AATTCAATTCGG
1 AATTCATTTCGG
18624230 TGATGTATAT
Statistics
Matches: 190, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 190 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (64 bp):
AATTCATTTCGGCAATATAAGTATATATATACATTTCAATTCGGCAATAGGTGTATACCTATAC
Found at i:18638269 original size:19 final size:18
Alignment explanation
Indices: 18638226--18638271 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
18638216 AGATTGTATC
18638226 CATGTATCTGTGACGTTA
1 CATGTATCTGTGACGTTA
* *
18638244 GATTGTATCTGTGACGTTTT
1 CA-TGTATCTGTGACG-TTA
18638264 CATGTATC
1 CATGTATC
18638272 CATTTTAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 19 0.83
20 3 0.13
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (18 bp):
CATGTATCTGTGACGTTA
Found at i:18643778 original size:22 final size:22
Alignment explanation
Indices: 18643753--18643807 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
18643743 AGAACTCTAA
*
18643753 TTAACCTAAACAAGAAGTAGTT
1 TTAAACTAAACAAGAAGTAGTT
18643775 TTAAACTAAACAAGAAGTAGTT
1 TTAAACTAAACAAGAAGTAGTT
18643797 TTAAACTAAAC
1 TTAAACTAAAC
18643808 TTTCTTGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (22 bp):
TTAAACTAAACAAGAAGTAGTT
Found at i:18648951 original size:73 final size:73
Alignment explanation
Indices: 18648864--18649020 Score: 289
Period size: 73 Copynumber: 2.2 Consensus size: 73
18648854 GAATGAATCC
18648864 CAAACCATCCATTCCCTCT-AACCCTTCTCCCTTGAATCAAGCATGAATCAAGCTAATATCCTTC
1 CAAACCATCCATTCCCT-TGAACCCTTCTCCCTTGAATCAAGCATGAATCAAGCTAATATCCTTC
18648928 CCAAAATAG
65 CCAAAATAG
*
18648937 CAAACCATCTATTCCCTTGAACCCTTCTCCCTTGAATCAAGCATGAATCAAGCTAATATCCTTCC
1 CAAACCATCCATTCCCTTGAACCCTTCTCCCTTGAATCAAGCATGAATCAAGCTAATATCCTTCC
18649002 CAAAATAG
66 CAAAATAG
18649010 CAAACCATCCA
1 CAAACCATCCA
18649021 CCCACCTTCT
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
72 1 0.01
73 80 0.99
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (73 bp):
CAAACCATCCATTCCCTTGAACCCTTCTCCCTTGAATCAAGCATGAATCAAGCTAATATCCTTCC
CAAAATAG
Found at i:18651088 original size:18 final size:18
Alignment explanation
Indices: 18651065--18651101 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
18651055 TGCGGCTTGG
18651065 TTCGACTGTAGATCAGAC
1 TTCGACTGTAGATCAGAC
18651083 TTCGACTGTAGATCAGAC
1 TTCGACTGTAGATCAGAC
18651101 T
1 T
18651102 ACACGTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (18 bp):
TTCGACTGTAGATCAGAC
Found at i:18659600 original size:19 final size:19
Alignment explanation
Indices: 18659576--18659620 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
18659566 GATAAAACCA
18659576 TATCATTTTCCTTTTTACT
1 TATCATTTTCCTTTTTACT
18659595 TATCATTTTCCTTTTTACT
1 TATCATTTTCCTTTTTACT
18659614 TATCATT
1 TATCATT
18659621 CAACATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (19 bp):
TATCATTTTCCTTTTTACT
Found at i:18665141 original size:17 final size:19
Alignment explanation
Indices: 18665119--18665157 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
18665109 GGTAAGATTA
18665119 TGATTTGT-TCCATGA-AT
1 TGATTTGTGTCCATGATAT
*
18665136 TGATTTGTGTTCATGATAT
1 TGATTTGTGTCCATGATAT
18665155 TGA
1 TGA
18665158 ATATCGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.49
Consensus pattern (19 bp):
TGATTTGTGTCCATGATAT
Found at i:18666509 original size:19 final size:19
Alignment explanation
Indices: 18666485--18666529 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
18666475 GATAAAACCA
18666485 TATCATTTTCCTTTTTACT
1 TATCATTTTCCTTTTTACT
18666504 TATCATTTTCCTTTTTACT
1 TATCATTTTCCTTTTTACT
18666523 TATCATT
1 TATCATT
18666530 CAACATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (19 bp):
TATCATTTTCCTTTTTACT
Found at i:18668363 original size:63 final size:63
Alignment explanation
Indices: 18668277--18668414 Score: 258
Period size: 63 Copynumber: 2.2 Consensus size: 63
18668267 AGTTACTATG
*
18668277 GTTAAGTTGATGCATGATTTGATAACCAAATTGGTAAGTGATGGTATGTTTGCAAGGTGGTTAA
1 GTTAGGTT-ATGCATGATTTGATAACCAAATTGGTAAGTGATGGTATGTTTGCAAGGTGGTTAA
18668341 GTTAGGTTATGCATGATTTGATAACCAAATTGGTAAGTGATGGTATGTTTGCAAGGTGGTTAA
1 GTTAGGTTATGCATGATTTGATAACCAAATTGGTAAGTGATGGTATGTTTGCAAGGTGGTTAA
18668404 GTTAGGTTATG
1 GTTAGGTTATG
18668415 TTTTGAGATA
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
63 66 0.90
64 7 0.10
ACGTcount: A:0.28, C:0.06, G:0.29, T:0.37
Consensus pattern (63 bp):
GTTAGGTTATGCATGATTTGATAACCAAATTGGTAAGTGATGGTATGTTTGCAAGGTGGTTAA
Found at i:18672593 original size:51 final size:51
Alignment explanation
Indices: 18672468--18672603 Score: 186
Period size: 50 Copynumber: 2.7 Consensus size: 51
18672458 AGTGAAAATG
* *
18672468 ATGGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACTAGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTAGAATGAT
* * * *
18672519 A-GGTCGCATGTGTAGTACTATGTGCAGGCTACTACGTGTA-TCGGATGGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTAGAATGAT
*
18672568 AATGGTCACATGTGTAGTACAATGTGCAGGCTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
18672604 TGTGAACCGA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
49 6 0.08
50 37 0.49
51 32 0.43
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACTAGAATGAT
Found at i:18672667 original size:45 final size:45
Alignment explanation
Indices: 18672616--18672702 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
18672606 TGAACCGAAC
* *
18672616 ATCATTGATTAGTAAGGTGGTTGCTATATGCTGATTCCACCGGAT
1 ATCATTGATTAATAAGGTGGTTGCTATATGCTGAATCCACCGGAT
*
18672661 ATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
1 ATCATTGATTAATAAGGTGGTTGCTATATGCTGAATCCACCG
18672703 AGTATCTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (45 bp):
ATCATTGATTAATAAGGTGGTTGCTATATGCTGAATCCACCGGAT
Found at i:18675584 original size:4 final size:4
Alignment explanation
Indices: 18675575--18675638 Score: 119
Period size: 4 Copynumber: 15.8 Consensus size: 4
18675565 CATCAATTTG
18675575 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
18675623 ATGT ATGT ATGAT ATG
1 ATGT ATGT ATG-T ATG
18675639 AAATAGGTAA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 55 0.93
5 4 0.07
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:18677865 original size:18 final size:18
Alignment explanation
Indices: 18677842--18677899 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 18
18677832 TATTGAGGTT
18677842 AAATACAACTCAAATATA
1 AAATACAACTCAAATATA
*
18677860 AAATAC-TCATCAAA-ATA
1 AAATACAAC-TCAAATATA
*
18677877 AAAT-TAACTCAAATATA
1 AAATACAACTCAAATATA
18677894 AAATAC
1 AAATAC
18677900 TCATCAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 5 0.16
17 16 0.50
18 11 0.34
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATACAACTCAAATATA
Found at i:18677886 original size:19 final size:17
Alignment explanation
Indices: 18677851--18677914 Score: 78
Period size: 17 Copynumber: 3.7 Consensus size: 17
18677841 TAAATACAAC
18677851 TCAAATATAAAATACTCA
1 TCAAA-ATAAAATACTCA
18677869 TCAAAATAAAATTAACTCA
1 TCAAAATAAAA-T-ACTCA
*
18677888 --AATATAAAATACTCA
1 TCAAAATAAAATACTCA
18677903 TCAAAATAAAAT
1 TCAAAATAAAAT
18677915 TTTGGTTGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 5 0.12
16 1 0.03
17 23 0.57
18 6 0.15
19 5 0.12
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (17 bp):
TCAAAATAAAATACTCA
Found at i:18677889 original size:34 final size:34
Alignment explanation
Indices: 18677848--18677915 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
18677838 GGTTAAATAC
18677848 AACTCAAATATAAAATACTCATCAAAATAAAATT
1 AACTCAAATATAAAATACTCATCAAAATAAAATT
18677882 AACTCAAATATAAAATACTCATCAAAATAAAATT
1 AACTCAAATATAAAATACTCATCAAAATAAAATT
18677916 TTGGTTGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (34 bp):
AACTCAAATATAAAATACTCATCAAAATAAAATT
Found at i:18688426 original size:17 final size:17
Alignment explanation
Indices: 18688400--18688435 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
18688390 TCCCCAAGTG
18688400 TTAAACCTCCATACATC
1 TTAAACCTCCATACATC
*
18688417 TTAAATCTCCATACATC
1 TTAAACCTCCATACATC
18688434 TT
1 TT
18688436 TAAGAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAACCTCCATACATC
Found at i:18698175 original size:42 final size:42
Alignment explanation
Indices: 18698124--18698227 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 42
18698114 ACCCTAATAG
* * *
18698124 GTTTATGTTCAGCTCTTTTGAAC-TTCTTTTTAACCCTTATGA
1 GTTTCTGTTCAGCTCTTATGAACTTTC-GTTTAACCCTTATGA
* *
18698166 GTTTCTGTTCAGCTCTTATGAGCTTTCGTTTAACCCTTATGG
1 GTTTCTGTTCAGCTCTTATGAACTTTCGTTTAACCCTTATGA
* * *
18698208 GTTTCTATTTAGCACTTATG
1 GTTTCTGTTCAGCTCTTATG
18698228 TGCTTCTGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 50 0.94
43 3 0.06
ACGTcount: A:0.17, C:0.19, G:0.15, T:0.48
Consensus pattern (42 bp):
GTTTCTGTTCAGCTCTTATGAACTTTCGTTTAACCCTTATGA
Found at i:18698183 original size:21 final size:21
Alignment explanation
Indices: 18698159--18698241 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
18698149 CTTTTTAACC
*
18698159 CTTATGAGTTTCTGTTCAGCT
1 CTTATGAGTTTCTGTTCAGCA
* * *
18698180 CTTATGAGCTTTC-GTTTAACC
1 CTTATGAG-TTTCTGTTCAGCA
* * *
18698201 CTTATGGGTTTCTATTTAGCA
1 CTTATGAGTTTCTGTTCAGCA
* *
18698222 CTTATGTGCTTCTGTTCAGC
1 CTTATGAGTTTCTGTTCAGC
18698242 CTTCGGGATT
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
20 4 0.08
21 41 0.84
22 4 0.08
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (21 bp):
CTTATGAGTTTCTGTTCAGCA
Found at i:18701005 original size:28 final size:29
Alignment explanation
Indices: 18700941--18701009 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
18700931 TTGACAGAGA
*
18700941 TCACCACAAAGGTGTGTTCTTTCAAAGAT
1 TCACCACAAAGGTGTGTCCTTTCAAAGAT
** *
18700970 TTGCCACAAAGGT-TGTCCTTT-AATAGGT
1 TCACCACAAAGGTGTGTCCTTTCAA-AGAT
18700998 TCACCACAAAGG
1 TCACCACAAAGG
18701010 CTTACCTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 2 0.06
28 20 0.61
29 11 0.33
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (29 bp):
TCACCACAAAGGTGTGTCCTTTCAAAGAT
Found at i:18701034 original size:57 final size:57
Alignment explanation
Indices: 18700890--18701164 Score: 238
Period size: 57 Copynumber: 4.8 Consensus size: 57
18700880 GAGATTGCCT
* * * * *
18700890 CAAAGGCTTTCCTATCTAGAG-TTTTCCACAGAGGCTT-TCCTTTGACAGAGATCACCA
1 CAAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGG-TTGTCCTTTAACAG-GTTCACCA
** * * * *
18700947 CAAAGG-TGTGTTCTTTC-AAAGATTTGCCACAAAGGTTGTCCTTTAATAGGTTCACCA
1 CAAAGGCT-T-ACCTTTCTAGAGTTTTTCCACAAAGGTTGTCCTTTAACAGGTTCACCA
* **
18701004 CAAAGGCTTACCTTTCTAGAGTTTTTCCACAAATGCTT-TCCTTTAACAGGTT-TGCA
1 CAAAGGCTTACCTTTCTAGAGTTTTTCCACAAA-GGTTGTCCTTTAACAGGTTCACCA
* * * * * *
18701060 AAAAGGCTTACTTTTCTAGAGTTTTTCCATAAAGGATGTCCTTTAACAAGTTCGCCA
1 CAAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGTTGTCCTTTAACAGGTTCACCA
* * * **
18701117 CAAATGCTTACCTTTCCAGAGTTTTGCCACAAAGAATGTCCTTTAACA
1 CAAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGTTGTCCTTTAACA
18701165 AAGATTGCCA
Statistics
Matches: 177, Mismatches: 32, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
55 2 0.01
56 51 0.29
57 95 0.54
58 29 0.16
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (57 bp):
CAAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGTTGTCCTTTAACAGGTTCACCA
Found at i:18701041 original size:29 final size:29
Alignment explanation
Indices: 18701001--18701150 Score: 96
Period size: 29 Copynumber: 5.3 Consensus size: 29
18700991 AATAGGTTCA
18701001 CCACAAAGGCTTACCTTTCTAGAGTTTTT
1 CCACAAAGGCTTACCTTTCTAGAGTTTTT
* * * * *
18701030 CCACAAATGCTTTCCTTT-AACAG-GTTT
1 CCACAAAGGCTTACCTTTCTAGAGTTTTT
* * *
18701057 GCAAAAAGGCTTACTTTTCTAGAGTTTTT
1 CCACAAAGGCTTACCTTTCTAGAGTTTTT
* * **
18701086 CCATAAAGGATGT-CCTTTAAC-A-AG-TTCG
1 CCACAAAGGCT-TACCTTT--CTAGAGTTTTT
* * *
18701114 CCACAAATGCTTACCTTTCCAGAGTTTTG
1 CCACAAAGGCTTACCTTTCTAGAGTTTTT
18701143 CCACAAAG
1 CCACAAAG
18701151 AATGTCCTTT
Statistics
Matches: 88, Mismatches: 24, Indels: 18
0.68 0.18 0.14
Matches are distributed among these distances:
26 1 0.01
27 18 0.20
28 23 0.26
29 43 0.49
30 2 0.02
31 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (29 bp):
CCACAAAGGCTTACCTTTCTAGAGTTTTT
Found at i:18701388 original size:53 final size:52
Alignment explanation
Indices: 18701301--18701459 Score: 194
Period size: 53 Copynumber: 3.0 Consensus size: 52
18701291 TTAATTTTTC
18701301 CTATATGATGCCATAACCCACCAATTACAATCTTACACGATATGGTCTTCTTT
1 CTATATGATGCCATAACCCACC-ATTACAATCTTACACGATATGGTCTTCTTT
* * ** * *
18701354 CTATATCATGCCATAACCCACTAGTTACGGTCTTACA-TAGTATGGTATTCTTT
1 CTATATGATGCCATAACCCACCA-TTACAATCTTACACGA-TATGGTCTTCTTT
* * * *
18701407 CCATATGATGACATAACCCACCATTACAATCTTTCACGATACGGTCTTCTTT
1 CTATATGATGCCATAACCCACCATTACAATCTTACACGATATGGTCTTCTTT
18701459 C
1 C
18701460 CTATTTATAA
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
52 24 0.28
53 63 0.72
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (52 bp):
CTATATGATGCCATAACCCACCATTACAATCTTACACGATATGGTCTTCTTT
Found at i:18708941 original size:17 final size:17
Alignment explanation
Indices: 18708919--18708951 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18708909 TAGAATTAGG
18708919 TTGAGAAGATT-ATTTAA
1 TTGAGAA-ATTAATTTAA
18708936 TTGAGAAATTAATTTA
1 TTGAGAAATTAATTTA
18708952 TTAACTTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (17 bp):
TTGAGAAATTAATTTAA
Found at i:18711190 original size:45 final size:45
Alignment explanation
Indices: 18711134--18711221 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 45
18711124 TAATTTGGAC
** *
18711134 AAAAAAATTTAAATTTAAATATAAAAATAATTATCAAGTTTAAAT
1 AAAAAAATTTAAACCTAAATATAAAAATAATTATCAAATTTAAAT
* * * *
18711179 AAAAAGATTTAAACCTAAATTTAAACATAATTATTAAATTTAA
1 AAAAAAATTTAAACCTAAATATAAAAATAATTATCAAATTTAA
18711222 GAAGTAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (45 bp):
AAAAAAATTTAAACCTAAATATAAAAATAATTATCAAATTTAAAT
Found at i:18711848 original size:16 final size:18
Alignment explanation
Indices: 18711827--18711862 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
18711817 TTTTATGTAT
18711827 TATAAAT-T-ATATAATA
1 TATAAATATAATATAATA
18711843 TATAAATATAATATAATA
1 TATAAATATAATATAATA
18711861 TA
1 TA
18711863 AAACATCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TATAAATATAATATAATA
Found at i:18717786 original size:33 final size:33
Alignment explanation
Indices: 18717764--18717835 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
18717754 GAAACCTTGG
* * *
18717764 GTGAAGAAACTCCATCTGTTCCTCCAATATTCA
1 GTGAAGAAACTCCAGCTGTTCCTCAAACATTCA
***
18717797 GTGAAGAAACTCCAGCTGTTCCTCCGTCATTCA
1 GTGAAGAAACTCCAGCTGTTCCTCAAACATTCA
18717830 GTGAAG
1 GTGAAG
18717836 GAACCACTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (33 bp):
GTGAAGAAACTCCAGCTGTTCCTCAAACATTCA
Found at i:18717851 original size:30 final size:32
Alignment explanation
Indices: 18717764--18717869 Score: 83
Period size: 33 Copynumber: 3.3 Consensus size: 32
18717754 GAAACCTTGG
* * *
18717764 GTGAAGAAACTCCATCTGTTCCTCCAAT-ATTCA
1 GTGAAGAAAC-CCAGCTATTCCTCC-GTCATTCA
*
18717797 GTGAAGAAACTCCAGCTGTTCCTCCGTCATTCA
1 GTGAAGAAAC-CCAGCTATTCCTCCGTCATTCA
* * *
18717830 GTGAAGGAA-CCA-CTATTCCTCCTTCCTTCA
1 GTGAAGAAACCCAGCTATTCCTCCGTCATTCA
* *
18717860 ATGAGGAAAC
1 GTGAAGAAAC
18717870 TCCTACTGTT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
30 21 0.34
31 3 0.05
32 1 0.02
33 37 0.60
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (32 bp):
GTGAAGAAACCCAGCTATTCCTCCGTCATTCA
Found at i:18732304 original size:12 final size:12
Alignment explanation
Indices: 18732283--18732343 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
18732273 TAATAATAAT
18732283 ATTA-TATTAAA
1 ATTATTATTAAA
18732294 ATTATTATT-AA
1 ATTATTATTAAA
18732305 A-TATTATTAATA
1 ATTATTATTAA-A
18732317 ATTA-TATTAAGA
1 ATTATTATTAA-A
*
18732329 A-TGTTATT-AA
1 ATTATTATTAAA
18732339 ATTAT
1 ATTAT
18732344 ATATATTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
10 9 0.22
11 12 0.29
12 18 0.44
13 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (12 bp):
ATTATTATTAAA
Found at i:18732312 original size:13 final size:13
Alignment explanation
Indices: 18732280--18732313 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
18732270 TCTTAATAAT
18732280 AATATTA-TATTA
1 AATATTATTATTA
18732292 AA-ATTATTATTA
1 AATATTATTATTA
18732304 AATATTATTA
1 AATATTATTA
18732314 ATAATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 9 0.45
13 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATATTATTATTA
Found at i:18732599 original size:44 final size:46
Alignment explanation
Indices: 18732539--18732631 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 46
18732529 TACAACATCT
* *
18732539 ATTCTATTTAACCAAACACA-AGAATT-CT-ATTACAGCTCTATTCC
1 ATTCAATTCAACCAAACA-ATAGAATTACTGATTACAGCTCTATTCC
* * *
18732583 ATTCAATTCAACCAAACAATTGAATTACTGGTTACAGCTCTATTTC
1 ATTCAATTCAACCAAACAATAGAATTACTGATTACAGCTCTATTCC
18732629 ATT
1 ATT
18732632 ACAACTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.51
45 2 0.05
46 17 0.41
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.35
Consensus pattern (46 bp):
ATTCAATTCAACCAAACAATAGAATTACTGATTACAGCTCTATTCC
Found at i:18732642 original size:16 final size:16
Alignment explanation
Indices: 18732629--18732682 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
18732619 GCTCTATTTC
*
18732629 ATTACAACTTTATTCT
1 ATTACAACTTTATTCA
*
18732645 ATTACAACTCTATTCA
1 ATTACAACTTTATTCA
*
18732661 ATTACAACTTTATTCT
1 ATTACAACTTTATTCA
18732677 ATTACA
1 ATTACA
18732683 GTGAATCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTACAACTTTATTCA
Found at i:18732656 original size:32 final size:32
Alignment explanation
Indices: 18732614--18732682 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
18732604 GAATTACTGG
*
18732614 TTACAGCTCTATTTC-ATTACAACTTTATTCTA
1 TTACAACTCTA-TTCAATTACAACTTTATTCTA
18732646 TTACAACTCTATTCAATTACAACTTTATTCTA
1 TTACAACTCTATTCAATTACAACTTTATTCTA
18732678 TTACA
1 TTACA
18732683 GTGAATCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 3 0.09
32 32 0.91
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.45
Consensus pattern (32 bp):
TTACAACTCTATTCAATTACAACTTTATTCTA
Found at i:18733901 original size:22 final size:22
Alignment explanation
Indices: 18733876--18733923 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 22
18733866 TAAGTTCATT
*
18733876 TTTTTTAATTTGTTTT-TGTTTA
1 TTTTTT-ATTAGTTTTATGTTTA
18733898 -TTTTTATTAGTTTTCATGTTTA
1 TTTTTTATTAGTTTT-ATGTTTA
18733920 TTTT
1 TTTT
18733924 GATTTCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 8 0.36
21 5 0.23
22 6 0.27
23 3 0.14
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (22 bp):
TTTTTTATTAGTTTTATGTTTA
Found at i:18733996 original size:25 final size:25
Alignment explanation
Indices: 18733963--18734042 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
18733953 TTTAGATTTT
18733963 TTTTA-TATTATTTCA-TGTAAACAA
1 TTTTATTATTATTT-ATTGTAAACAA
* * *
18733987 TTTTATTATTATTTATTTTAAAGAT
1 TTTTATTATTATTTATTGTAAACAA
*
18734012 TTTTATGTATTATTTATAT-TAAACAG
1 TTTTAT-TATTATTTAT-TGTAAACAA
18734038 TTTTA
1 TTTTA
18734043 GTTTATATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
24 6 0.13
25 20 0.43
26 20 0.43
27 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (25 bp):
TTTTATTATTATTTATTGTAAACAA
Found at i:18734033 original size:26 final size:26
Alignment explanation
Indices: 18733980--18734056 Score: 88
Period size: 26 Copynumber: 3.1 Consensus size: 26
18733970 TTATTTCATG
* *
18733980 TAAACAATTTTAT-TATTATTTATTT
1 TAAACAGTTTTATGTATTATTTATAT
* *
18734005 TAAAGATTTTTATGTATTATTTATAT
1 TAAACAGTTTTATGTATTATTTATAT
*
18734031 TAAACAGTTTTA-GT-TTATATATAT
1 TAAACAGTTTTATGTATTATTTATAT
18734055 TA
1 TA
18734057 CTCTAAGTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 11 0.24
25 13 0.29
26 21 0.47
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (26 bp):
TAAACAGTTTTATGTATTATTTATAT
Found at i:18734587 original size:12 final size:11
Alignment explanation
Indices: 18734570--18734604 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
18734560 AACAAATCCT
18734570 CTCTCATATTTC
1 CTCTCA-ATTTC
18734582 CTCTCAA-TTC
1 CTCTCAATTTC
18734592 CTCTCAATTTC
1 CTCTCAATTTC
18734603 CT
1 CT
18734605 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:18734652 original size:51 final size:51
Alignment explanation
Indices: 18734585--18734707 Score: 194
Period size: 51 Copynumber: 2.4 Consensus size: 51
18734575 ATATTTCCTC
* * *
18734585 TCAA-TTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCTATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATATAATT
*
18734635 TCAATTTCCTCTTAATTTCCTTCAAAAATTCTCTCAAATCCATATATAATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATATAATT
*
18734686 TCAATTTCTTCTCAATTTCCTT
1 TCAATTTCCTCTCAATTTCCTT
18734708 TTTTTAAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
50 4 0.06
51 62 0.94
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.46
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATATAATT
Found at i:18737028 original size:44 final size:45
Alignment explanation
Indices: 18736976--18737062 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 45
18736966 ATATTTTGAA
*
18736976 TATTTTGATATTATTTTATGTAAAAAAATAGAAATTT-TTTGAGT
1 TATTTTGATATTATTTGATGTAAAAAAATAGAAATTTATTTGAGT
* *
18737020 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAAAAAAATAGAAATTTATTTGA
18737063 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 34 0.87
45 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAAAAAAATAGAAATTTATTTGAGT
Found at i:18737098 original size:23 final size:23
Alignment explanation
Indices: 18737068--18737677 Score: 615
Period size: 23 Copynumber: 26.5 Consensus size: 23
18737058 TTTGATGTAA
*
18737068 TAAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
18737091 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
18737114 TAAAAACCCTAGCCTAACCTAATTTAAT
1 TAAAAA--C---CCTAACCTAATTTAAT
18737142 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
18737165 TAAAAACCCTAAACC---CTTAACT
1 TAAAAACCCT-AACCTAATTTAA-T
*
18737187 TAAAAACCCTAACCTAA-TTGAT
1 TAAAAACCCTAACCTAATTTAAT
18737209 TAAAAACCCTAGCCTAACCTAATTTAAT
1 TAAAAA--C---CCTAACCTAATTTAAT
18737237 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
18737260 TAAAAACCCTAAACC---CTTAACT
1 TAAAAACCCT-AACCTAATTTAA-T
*
18737282 TAAAAACCCTAACCTAATTTGAT
1 TAAAAACCCTAACCTAATTTAAT
*
18737305 TAAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
18737328 TAAAAACCCTAATCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
18737351 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
18737374 TAAAAACCCTAAACC---CTTAACT
1 TAAAAACCCT-AACCTAATTTAA-T
*
18737396 T-AAAACCCTAACCTAATTCAAT
1 TAAAAACCCTAACCTAATTTAAT
18737418 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
18737441 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* *
18737464 T-AAAACCCTAACCTTAATTAAAAA
1 TAAAAACCCTAACC-TAATT-TAAT
***
18737488 TCCTAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* *
18737511 T-AAAACTCTAAACC---CTTAACT
1 TAAAAACCCT-AACCTAATTTAA-T
* *
18737532 TAAAAA----AACTTAATTCAAT
1 TAAAAACCCTAACCTAATTTAAT
18737551 TAAAAACCCTAACCTAA-TTAAT
1 TAAAAACCCTAACCTAATTTAAT
18737573 T-AAAA-CCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
18737594 TAAAAACCATAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
18737617 T-AAAACCCTAAACCCTTAA-TTAA-
1 TAAAAACCCT-AA-CC-TAATTTAAT
* *
18737640 AAACCATAACCCTAACCTAATTCAAT
1 TAA--A-AACCCTAACCTAATTTAAT
18737666 TAAAAACCCTAA
1 TAAAAACCCTAA
18737678 ACCCTTAACT
Statistics
Matches: 499, Mismatches: 36, Indels: 104
0.78 0.06 0.16
Matches are distributed among these distances:
17 3 0.01
19 7 0.01
20 21 0.04
21 40 0.08
22 70 0.14
23 249 0.50
24 35 0.07
25 19 0.04
26 7 0.01
27 16 0.03
28 32 0.06
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.29
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:18737233 original size:95 final size:94
Alignment explanation
Indices: 18737086--18737650 Score: 606
Period size: 95 Copynumber: 6.2 Consensus size: 94
18737076 CTAGCCTAAT
18737086 TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAACCTAATTTAATTAAAAACCC
1 TTAATTAAAAACCCTAACCTAA-TTAATTAAAAACCCTAGCCTAACCTAATTTAATTAAAAACCC
18737151 TAACCTAATTTAATTAAAAACCCTAAACCC
65 TAACCTAATTTAATTAAAAACCCTAAACCC
*
18737181 TTAACTTAAAAACCCTAACCTAATTGATTAAAAACCCTAGCCTAACCTAATTTAATTAAAAACCC
1 TTAA-TTAAAAACCCTAACCTAATTAATTAAAAACCCTAGCCTAACCTAATTTAATTAAAAACCC
18737246 TAACCTAATTTAATTAAAAACCCTAAACCC
65 TAACCTAATTTAATTAAAAACCCTAAACCC
*
18737276 TTAACTTAAAAACCCTAACCTAATTTGATTAAAAACCCTAG-----CCTAATTTAATTAAAAACC
1 TTAA-TTAAAAACCCTAACCTAA-TTAATTAAAAACCCTAGCCTAACCTAATTTAATTAAAAACC
* *
18737336 CTAATCTAATTTAATTAAAAACCCT-AACCTAAT
64 CTAACCTAATTTAATTAAAAACCCTAAACC---C
* *
18737369 TTAATTAAAAACCCTAAACC--CTTAACTT-AAAA--C---CCTAACCTAATTCAATTAAAAACC
1 TTAATTAAAAACCCT-AACCTAATTAA-TTAAAAACCCTAGCCTAACCTAATTTAATTAAAAACC
*
18737426 CTAACCTAATTTAATTAAAAACCCT-AACCTAAT
64 CTAACCTAATTTAATTAAAAACCCTAAACC---C
* * *
18737459 TTAATT-AAAACCCTAACC---TTAATTAAAAATCCTAACCCTAACCTAATTTAATT-AAAACTC
1 TTAATTAAAAACCCTAACCTAATTAATTAAAAACCCT-AGCCTAACCTAATTTAATTAAAAACCC
* *
18737519 TAAACCCTTAACTTAA--AAAAA--CTTAA---
65 T-AA-CC-TAATTTAATTAAAAACCCTAAACCC
*
18737545 TTCAATTAAAAACCCTAACCTAATTAATT--AAA----A-CCTAACCTAATTTAATTAAAAACCA
1 TT-AATTAAAAACCCTAACCTAATTAATTAAAAACCCTAGCCTAACCTAATTTAATTAAAAACCC
18737603 TAACCTAATTTAATT-AAAACCCTAAACCC
65 TAACCTAATTTAATTAAAAACCCTAAACCC
*
18737632 TTAATTAAAAACCATAACC
1 TTAATTAAAAACCCTAACC
18737651 CTAACCTAAT
Statistics
Matches: 419, Mismatches: 15, Indels: 81
0.81 0.03 0.16
Matches are distributed among these distances:
81 7 0.02
82 6 0.01
83 19 0.05
84 11 0.03
86 20 0.05
87 14 0.03
88 17 0.04
89 12 0.03
90 67 0.16
91 53 0.13
92 20 0.05
93 31 0.07
94 2 0.00
95 105 0.25
96 35 0.08
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.29
Consensus pattern (94 bp):
TTAATTAAAAACCCTAACCTAATTAATTAAAAACCCTAGCCTAACCTAATTTAATTAAAAACCCT
AACCTAATTTAATTAAAAACCCTAAACCC
Found at i:18737650 original size:20 final size:20
Alignment explanation
Indices: 18737589--18737652 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
18737579 CTAACCTAAT
*
18737589 TTAATTAAAAACCATAACCTAAT
1 TTAATTAAAAACCATAACC---C
*
18737612 TTAATT-AAAACCCTAAACCC
1 TTAATTAAAAACCAT-AACCC
18737632 TTAATTAAAAACCATAACCC
1 TTAATTAAAAACCATAACCC
18737652 T
1 T
18737653 AACCTAATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 12 0.33
21 7 0.19
22 7 0.19
23 10 0.28
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.28
Consensus pattern (20 bp):
TTAATTAAAAACCATAACCC
Found at i:18737685 original size:50 final size:50
Alignment explanation
Indices: 18737598--18737700 Score: 163
Period size: 49 Copynumber: 2.1 Consensus size: 50
18737588 TTTAATTAAA
*
18737598 AACCATAACCTAATTTAATTAAAACCCTAAACCCTTAA-TTAAAAACCAT
1 AACCATAACCTAATTCAATTAAAACCCTAAACCCTTAACTTAAAAACCAT
* *
18737647 AACCCTAACCTAATTCAATTAAAAACCCTAAACCCTTAACTTAAAAACCCT
1 AACCATAACCTAATTCAATT-AAAACCCTAAACCCTTAACTTAAAAACCAT
18737698 AAC
1 AAC
18737701 TTTAATGTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
49 18 0.37
50 18 0.37
51 13 0.27
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (50 bp):
AACCATAACCTAATTCAATTAAAACCCTAAACCCTTAACTTAAAAACCAT
Found at i:18737850 original size:116 final size:116
Alignment explanation
Indices: 18737708--18737925 Score: 382
Period size: 116 Copynumber: 1.9 Consensus size: 116
18737698 AACTTTAATG
*
18737708 TAATGTTAGATTTGGAAAATTGTTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
1 TAATGTTAGATTTGGAAAATTGTTTTGACTGGTACTAACAAATAATAATTGTACATAATTTGATA
*
18737773 ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
66 ATTTTACTAACCATTAATACAATTTTTTAACTTAATAATTTTACATTCACA
* ** *
18737824 TAATGTTAGATTTGGAAAATTTTTTTGACTGGTACTAACATTTAATAATTGTATATAATTTGATA
1 TAATGTTAGATTTGGAAAATTGTTTTGACTGGTACTAACAAATAATAATTGTACATAATTTGATA
18737889 ATTTTACTAACCATTAATACAATTTTTTAACTTAATA
66 ATTTTACTAACCATTAATACAATTTTTTAACTTAATA
18737926 CAATTTATCA
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 96 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (116 bp):
TAATGTTAGATTTGGAAAATTGTTTTGACTGGTACTAACAAATAATAATTGTACATAATTTGATA
ATTTTACTAACCATTAATACAATTTTTTAACTTAATAATTTTACATTCACA
Found at i:18737942 original size:17 final size:17
Alignment explanation
Indices: 18737901--18737942 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
18737891 TTTACTAACC
* *
18737901 ATTAATACAATTTTTTA
1 ATTAATACAATTTATCA
18737918 ACTTAATACAATTTATCA
1 A-TTAATACAATTTATCA
18737936 ATTAATA
1 ATTAATA
18737943 ATTTCACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTAATACAATTTATCA
Found at i:18741251 original size:126 final size:125
Alignment explanation
Indices: 18740955--18741306 Score: 528
Period size: 126 Copynumber: 2.8 Consensus size: 125
18740945 CCCAAACATG
* * * *
18740955 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAAGTTCTTCTCAAATAGCATCTTGG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
18741020 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTC-AAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
* * * *
18741079 CTACTGTAGCAAAAGCGC-ACTGACGAGGCCGCAATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* * * *
18741143 CTAGAACCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
65 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTACATGAC
* *
18741205 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGTGATTTCACAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
**
18741270 TAGAAGCGATTTTATATTATTTTATCAGAAACGTCAA
66 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAA
18741307 CTCGAAATTA
Statistics
Matches: 202, Mismatches: 22, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
123 1 0.00
124 88 0.44
125 6 0.03
126 106 0.52
127 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
Found at i:18743453 original size:24 final size:24
Alignment explanation
Indices: 18743403--18743453 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
18743393 AGTTTTGACC
* *
18743403 TTTGACTATTGGGTAAATTTTAAA
1 TTTGAATATTGGGTAAATTATAAA
*
18743427 TTTGAATATT-GGTATAATTATATA
1 TTTGAATATTGGGTA-AATTATAAA
18743451 TTT
1 TTT
18743454 ATTTTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (24 bp):
TTTGAATATTGGGTAAATTATAAA
Found at i:18753386 original size:29 final size:29
Alignment explanation
Indices: 18753292--18753379 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
18753282 TGTTAAGTAT
18753292 TGTTTTGAAAGAAATAAATTTGAC-AAGATG
1 TGTTTTGAAA-AAATAAATTTGACGAA-ATG
* * * **
18753322 GGATATGAAAAAATAAATTTGACGTGATG
1 TGTTTTGAAAAAATAAATTTGACGAAATG
* *
18753351 TGTTTTGAAAAAATTATTTTGACGAAATG
1 TGTTTTGAAAAAATAAATTTGACGAAATG
18753380 GATTTTGTTT
Statistics
Matches: 45, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
29 38 0.84
30 7 0.16
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.34
Consensus pattern (29 bp):
TGTTTTGAAAAAATAAATTTGACGAAATG
Found at i:18758739 original size:40 final size:40
Alignment explanation
Indices: 18758594--18758726 Score: 187
Period size: 40 Copynumber: 3.3 Consensus size: 40
18758584 GCTCCTCGTT
* * * *
18758594 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
*
18758634 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
* *
18758674 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTATCTCGCA
18758714 CAAATGCCTTCGG
1 CAAATGCCTTCGG
18758727 ATCTTAGTCC
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 79 0.95
41 4 0.05
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
Found at i:18764789 original size:58 final size:60
Alignment explanation
Indices: 18764727--18764841 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 60
18764717 TCACTTTAAT
* * *
18764727 ATTAAATTAATATAATACTTA-T-CAAGATTAATACTAGATTAAATTTAATATTAATTCC
1 ATTAAATTAATAGAATACTTACTACAAGATAAATACTAAATTAAATTTAATATTAATTCC
* *
18764785 ATTAAATTAATAGAATACTTATCTACAAGATAAATATTAAATTGAATTTAATATTAA
1 ATTAAATTAATAGAATACTTA-CTACAAGATAAATACTAAATTAAATTTAATATTAA
18764842 GGTAATCACT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 20 0.41
60 1 0.02
61 28 0.57
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (60 bp):
ATTAAATTAATAGAATACTTACTACAAGATAAATACTAAATTAAATTTAATATTAATTCC
Found at i:18768155 original size:43 final size:43
Alignment explanation
Indices: 18768095--18768185 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
18768085 CTTTGAGTTC
* * * *
18768095 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
*
18768137 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATATTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
18768180 ATTACC
1 ATTACC
18768186 TTGCATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
Found at i:18768564 original size:43 final size:43
Alignment explanation
Indices: 18768459--18768815 Score: 468
Period size: 43 Copynumber: 8.3 Consensus size: 43
18768449 AAGATATATT
*
18768459 TTTAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTAT--TC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-ATGGTC
* *
18768501 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
18768544 TTTAGCGACGTTTGTGGGAAAAACGCCACTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
18768587 TTTAGCGGCGTTTATAGGAAAAGCGCTGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * * *
18768630 TTTAGCGGCGTTTTTTTGTAAAAGTGTCGCTAAAAGTCATGGTC
1 TTTAGCGGCG-TTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
18768674 TTTTAGCGGCGTTTGTGGG-AAAGCGCTGCTAAAGGTCATGGTC
1 -TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
18768717 TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTTATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
18768760 TTTAGCGGCGTTTGTTGGAAAAGCGCTGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
18768803 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
18768816 ATTTATAAAA
Statistics
Matches: 275, Mismatches: 35, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.00
42 52 0.19
43 182 0.66
44 30 0.11
45 10 0.04
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:18768793 original size:173 final size:174
Alignment explanation
Indices: 18768503--18768825 Score: 524
Period size: 173 Copynumber: 1.9 Consensus size: 174
18768493 GTCTATTCTA
* *
18768503 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGACGTTTGTGGGAAAAAC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTAGGAAAAAC
*
18768568 GCCACTAAAGGTCTTGGTCTTTAGCGGCGTTTATAGGAAAAGCGCTGCTAAAGGTCTTGGTCTTT
66 GCCACTAAAGGTCTTGGTCTTTAGCGGCGTTTATAGGAAAAGCGCTGCTAAAGGTCATGGTCTTT
* *
18768633 AGCGGCGTTTTTTTGTAAAAGTGTCGCTAAAAGTCATGGTCTTT
131 AGCGGCGTTTATTTATAAAAGTGTCGCTAAAAGTCATGGTCTTT
* * *
18768677 TAGCGGCGTTTGTGGG-AAAGCGCTGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTAGGAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTAGGAAAAAC
* * *
18768741 GCCGCTAAAGGT-TATGGTCTTTAGCGGCGTTTGTTGGAAAAGCGCTGCTAAAGGTCATGGTCTT
66 GCCACTAAAGGTCT-TGGTCTTTAGCGGCGTTTATAGGAAAAGCGCTGCTAAAGGTCATGGTCTT
18768805 TAGCGGCGTTTATTTATAAAA
130 TAGCGGCGTTTATTTATAAAA
18768826 ACGCCGCTAA
Statistics
Matches: 137, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
172 1 0.01
173 120 0.88
174 16 0.12
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (174 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTAGGAAAAAC
GCCACTAAAGGTCTTGGTCTTTAGCGGCGTTTATAGGAAAAGCGCTGCTAAAGGTCATGGTCTTT
AGCGGCGTTTATTTATAAAAGTGTCGCTAAAAGTCATGGTCTTT
Found at i:18768940 original size:22 final size:21
Alignment explanation
Indices: 18768907--18768951 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
18768897 TTTAGCGGCG
*
18768907 CTAAAAAACGCCGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAGC
18768928 CTAAAAAAGCGCCGCTAAAAGC
1 CTAAAAAA-CGCCGCTAAAAGC
18768950 CT
1 CT
18768952 TTTTTGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.42, C:0.29, G:0.18, T:0.11
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:18772627 original size:11 final size:10
Alignment explanation
Indices: 18772589--18772629 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
18772579 AACTATCATA
*
18772589 AAATGTGACT
1 AAATGTGATT
*
18772599 GAATGTGATT
1 AAATGTGATT
18772609 AAATGTGATT
1 AAATGTGATT
18772619 AATATGTGATT
1 AA-ATGTGATT
18772630 GGATATATGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.39
Consensus pattern (10 bp):
AAATGTGATT
Found at i:18782473 original size:5 final size:5
Alignment explanation
Indices: 18782463--18782493 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
18782453 ACTTTTATAT
18782463 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
18782494 CTGATATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:18786012 original size:20 final size:21
Alignment explanation
Indices: 18785977--18786017 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
18785967 CACCAGTTAA
18785977 AATTAATTAGCTAATACTTGC
1 AATTAATTAGCTAATACTTGC
* *
18785998 AATTTATTA-CTAATATTTGC
1 AATTAATTAGCTAATACTTGC
18786018 TGATTTCTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (21 bp):
AATTAATTAGCTAATACTTGC
Found at i:18789410 original size:20 final size:21
Alignment explanation
Indices: 18789382--18789422 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
18789372 CAAGAAATCA
18789382 GCAAATATTAG-TAATAAATT
1 GCAAATATTAGCTAATAAATT
* *
18789402 GCAAGTATTAGCTAATTAATT
1 GCAAATATTAGCTAATAAATT
18789423 TTAACTGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (21 bp):
GCAAATATTAGCTAATAAATT
Found at i:18794366 original size:35 final size:36
Alignment explanation
Indices: 18794299--18794375 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 36
18794289 CGTGAAAGAG
* * *
18794299 AATATATGGGTATGTTATTCATGCCATGTGACAGTA
1 AATATATGAGTATGTTATTCATACCATATGACAGTA
*
18794335 AATATGTGAGTATGTT-TTCATACCATATGACAGTA
1 AATATATGAGTATGTTATTCATACCATATGACAGTA
*
18794370 ACTATA
1 AATATA
18794376 ATGTGCTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
35 21 0.60
36 14 0.40
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (36 bp):
AATATATGAGTATGTTATTCATACCATATGACAGTA
Found at i:18797397 original size:5 final size:5
Alignment explanation
Indices: 18797387--18797415 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
18797377 CGCCTTATAG
18797387 TGTGA TGTGA TGTGA TGTGA TGTGA TGTG
1 TGTGA TGTGA TGTGA TGTGA TGTGA TGTG
18797416 TTGAGGTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.41, T:0.41
Consensus pattern (5 bp):
TGTGA
Found at i:18798549 original size:24 final size:24
Alignment explanation
Indices: 18798517--18798565 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
18798507 GTAAAATTCA
*
18798517 TGATAAAATCTCATTATTCTTACC
1 TGATAAAATCTCAATATTCTTACC
18798541 TGATAAAATCTCAATATTCTTACC
1 TGATAAAATCTCAATATTCTTACC
18798565 T
1 T
18798566 TACTTTCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (24 bp):
TGATAAAATCTCAATATTCTTACC
Found at i:18802265 original size:18 final size:19
Alignment explanation
Indices: 18802235--18802271 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
18802225 CGGTCTGAGG
18802235 ATGAAATGCAGTA-CTAAA
1 ATGAAATGCAGTACCTAAA
18802253 ATGAAAT-CGAGTACCTAAA
1 ATGAAATGC-AGTACCTAAA
18802272 GTTTCGTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.06
18 11 0.65
19 5 0.29
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.22
Consensus pattern (19 bp):
ATGAAATGCAGTACCTAAA
Found at i:18811135 original size:121 final size:121
Alignment explanation
Indices: 18810957--18811206 Score: 482
Period size: 121 Copynumber: 2.1 Consensus size: 121
18810947 TTAAGCTCGT
18810957 ATTTCATCCGTATTTCATGCTAGCCAAATTCACTAGGGACCTACACTAACCCATACAAATCAGCA
1 ATTTCATCCGTATTTCATGCTAGCCAAATTCACTAGGGACCTACACTAACCCATACAAATCAGCA
18811022 TTTCACAATTTTACCATGGAATTTTACTACTTTTATAAATAAGTCCCTAAATGAAA
66 TTTCACAATTTTACCATGGAATTTTACTACTTTTATAAATAAGTCCCTAAATGAAA
*
18811078 ATTTCATCTGTATTTCATGCTAGCCAAATTCACTAGGGACCTACACTAACCCATACAAATCAGCA
1 ATTTCATCCGTATTTCATGCTAGCCAAATTCACTAGGGACCTACACTAACCCATACAAATCAGCA
*
18811143 TTTCACAATTTTACCATGGAATTTTACTACTTTTATAAATAAGTCCCTAAATGACA
66 TTTCACAATTTTACCATGGAATTTTACTACTTTTATAAATAAGTCCCTAAATGAAA
18811199 ATTTCATC
1 ATTTCATC
18811207 AAAAAATTCC
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 127 1.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (121 bp):
ATTTCATCCGTATTTCATGCTAGCCAAATTCACTAGGGACCTACACTAACCCATACAAATCAGCA
TTTCACAATTTTACCATGGAATTTTACTACTTTTATAAATAAGTCCCTAAATGAAA
Found at i:18814005 original size:77 final size:76
Alignment explanation
Indices: 18813785--18814069 Score: 292
Period size: 78 Copynumber: 3.7 Consensus size: 76
18813775 GATTGTATTA
* * * *
18813785 TGTTTCAAACAAAAATTCAAATGAACAATCCTATTTTAGGA-TTTATTCCTACCGTTTTAACAGG
1 TGTTTCAAACAAAAATACAATTGAACAATCCTGTTTCAGGATTTTATTCCT---GTTTTAACAGG
18813849 ATTTGTTTAATTTT
63 ATTTGTTTAATTTT
* * *
18813863 TGTTTCAAACAGAAAATA-AATTGAACAATCCTGTTTCAAGATTTTATTCTTGCCATTTAACAGG
1 TGTTTCAAACA-AAAATACAATTGAACAATCCTGTTTCAGGATTTTATTCCTG--TTTTAACAGG
*
18813927 ATTTGTTTGATTTT
63 ATTTGTTTAATTTT
** *
18813941 TGTTTCAAACAAAAA-ACAATTGAACAATTTTGTTTCAGGATTTTATTCCTGTTGCTTAATAGGA
1 TGTTTCAAACAAAAATACAATTGAACAATCCTGTTTCAGGATTTTATTCCTGTT--TTAACAGGA
*
18814005 TTTGTTCAATTTTTT
64 TTTGTTTAA--TTTT
* * **
18814020 TGTTTCAAACAGAAAT-CAATTGAATAATATTGTTTCAGGATTCTT-TTCCT
1 TGTTTCAAACAAAAATACAATTGAACAATCCTGTTTCAGGATT-TTATTCCT
18814070 ACTGCTCAAC
Statistics
Matches: 177, Mismatches: 19, Indels: 21
0.82 0.09 0.10
Matches are distributed among these distances:
75 1 0.01
76 2 0.01
77 49 0.28
78 63 0.36
79 60 0.34
80 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (76 bp):
TGTTTCAAACAAAAATACAATTGAACAATCCTGTTTCAGGATTTTATTCCTGTTTTAACAGGATT
TGTTTAATTTT
Found at i:18814081 original size:156 final size:154
Alignment explanation
Indices: 18813785--18814086 Score: 324
Period size: 156 Copynumber: 1.9 Consensus size: 154
18813775 GATTGTATTA
* *
18813785 TGTTTCAAACAAAAATTCAAATGAACAATCCTATTTTAGGATTTATTCCTACCGTTTTAACAGGA
1 TGTTTCAAACAAAAATACAAATGAACAATCCTATTTCAGGATTTATTCCT--CGTTTTAACAGGA
* * * *
18813850 TTTGTTTAATTTTTGTTTCAAACAGAAAATAAATTGAACAATCCTGTTTCAAGATTTTATTCTTG
64 TTTGTTCAATTTTTGTTTCAAACAGAAAATAAATTGAACAATACTGTTTCAAGATTTTATTCCTA
* * *
18813915 CCATTTAACAGGATTTGTTTGATTTT
129 CCACTCAACAGAATTTGTTTGATTTT
* ** * *
18813941 TGTTTCAAACAAAAA-ACAATTGAACAATTTTGTTTCAGGATTTTATTCCT-GTTGCTTAATAGG
1 TGTTTCAAACAAAAATACAAATGAACAATCCTATTTCAGGA-TTTATTCCTCGTT--TTAACAGG
* * * *
18814004 ATTTGTTCAATTTTTTTGTTTCAAACAG-AAATCAATTGAATAATATTGTTTCAGGATTCTT-TT
63 ATTTGTTCAA--TTTTTGTTTCAAACAGAAAATAAATTGAACAATACTGTTTCAAGATT-TTATT
**
18814067 CCTACTGCTCAACAGAATTT
125 CCTACCACTCAACAGAATTT
18814087 ATTCAATTTC
Statistics
Matches: 120, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
153 3 0.03
155 35 0.29
156 64 0.53
157 18 0.15
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (154 bp):
TGTTTCAAACAAAAATACAAATGAACAATCCTATTTCAGGATTTATTCCTCGTTTTAACAGGATT
TGTTCAATTTTTGTTTCAAACAGAAAATAAATTGAACAATACTGTTTCAAGATTTTATTCCTACC
ACTCAACAGAATTTGTTTGATTTT
Found at i:18814092 original size:79 final size:79
Alignment explanation
Indices: 18813785--18814095 Score: 213
Period size: 79 Copynumber: 4.0 Consensus size: 79
18813775 GATTGTATTA
* * ** * * * * * *
18813785 TGTTTCAAACAAAAATTCAAATGAACAATCCTATTTTAGGA-TTTATTCCTACCGTTTTAACAGG
1 TGTTTCAAACAAAAA-ACAATTGAACAATATTGTTTCAGGATTTTATTCCTACTG-CTCAACAGA
* *
18813849 ATTTGTTTAA--TTTT
64 ATTTATTCAATTTTTT
** * * * *** * *
18813863 TGTTTCAAACAGAAAATA-AATTGAACAATCCTGTTTCAAGATTTTATTCTTGCCATTTAACAGG
1 TGTTTCAAACA-AAAA-ACAATTGAACAATATTGTTTCAGGATTTTATTCCTACTGCTCAACAGA
* **
18813927 ATTTGTTTGA--TTTT
64 ATTTATTCAATTTTTT
* ** * * *
18813941 TGTTTCAAACAAAAAACAATTGAACAATTTTGTTTCAGGATTTTATTCCTGTTGCTTAATAGGAT
1 TGTTTCAAACAAAAAACAATTGAACAATATTGTTTCAGGATTTTATTCCTACTGCTCAACAGAAT
*
18814006 TTGTTCAATTTTTT
66 TTATTCAATTTTTT
* * *
18814020 TGTTTCAAACAGAAATCAATTGAATAATATTGTTTCAGGATTCTT-TTCCTACTGCTCAACAGAA
1 TGTTTCAAACAAAAAACAATTGAACAATATTGTTTCAGGATT-TTATTCCTACTGCTCAACAGAA
18814084 TTTATTCAATTT
65 TTTATTCAATTT
18814096 CTATTGTTAA
Statistics
Matches: 197, Mismatches: 30, Indels: 11
0.83 0.13 0.05
Matches are distributed among these distances:
76 1 0.01
77 49 0.25
78 63 0.32
79 82 0.42
80 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.43
Consensus pattern (79 bp):
TGTTTCAAACAAAAAACAATTGAACAATATTGTTTCAGGATTTTATTCCTACTGCTCAACAGAAT
TTATTCAATTTTTT
Found at i:18814107 original size:27 final size:27
Alignment explanation
Indices: 18814077--18814137 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
18814067 CCTACTGCTC
*
18814077 AACAGAATTTATTCAATTTCTATTGTT
1 AACAAAATTTATTCAATTTCTATTGTT
* *
18814104 AACAAAATTTATTCGATTTCTGTTGTT
1 AACAAAATTTATTCAATTTCTATTGTT
*
18814131 ACCAAAA
1 AACAAAA
18814138 ATTGATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (27 bp):
AACAAAATTTATTCAATTTCTATTGTT
Found at i:18826106 original size:18 final size:19
Alignment explanation
Indices: 18826080--18826118 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
18826070 GTCGAGGACA
18826080 AAGTAATATTT-TTTAATT
1 AAGTAATATTTGTTTAATT
* *
18826098 AAGTTATATTTGTTTTATT
1 AAGTAATATTTGTTTAATT
18826117 AA
1 AA
18826119 ATTACTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (19 bp):
AAGTAATATTTGTTTAATT
Found at i:18829666 original size:11 final size:11
Alignment explanation
Indices: 18829650--18829684 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
18829640 AGAACTCCCT
18829650 TTGAAGCTTCC
1 TTGAAGCTTCC
18829661 TTGAAGCTTCC
1 TTGAAGCTTCC
*
18829672 TTTGAAGTTTCC
1 -TTGAAGCTTCC
18829684 T
1 T
18829685 AGCATGAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (11 bp):
TTGAAGCTTCC
Found at i:18829675 original size:23 final size:22
Alignment explanation
Indices: 18829634--18829686 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
18829624 TTCTTGGCAA
18829634 CTTCCTAGAACTCCCTTTGAAG
1 CTTCCTAGAACTCCCTTTGAAG
* *
18829656 CTTCCTTGAAGCTTCCTTTGAAG
1 CTTCCTAGAA-CTCCCTTTGAAG
*
18829679 TTTCCTAG
1 CTTCCTAG
18829687 CATGAGAGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.38
Consensus pattern (22 bp):
CTTCCTAGAACTCCCTTTGAAG
Found at i:18829676 original size:12 final size:12
Alignment explanation
Indices: 18829647--18829684 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
18829637 CCTAGAACTC
18829647 CCTTTGAAGCTT
1 CCTTTGAAGCTT
18829659 CC-TTGAAGCTT
1 CCTTTGAAGCTT
*
18829670 CCTTTGAAGTTT
1 CCTTTGAAGCTT
18829682 CCT
1 CCT
18829685 AGCATGAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (12 bp):
CCTTTGAAGCTT
Found at i:18830822 original size:114 final size:112
Alignment explanation
Indices: 18830619--18830926 Score: 318
Period size: 114 Copynumber: 2.7 Consensus size: 112
18830609 GTGCTCGAGG
* * * *
18830619 ATACTTAGGATTTCTTTTTCATTTTTTGAAAACATCGAAGTCGAAATTGGTATTGATACCAACTA
1 ATACTTAGGATTTATTTTTCATTTTTT-AAAACATCGAAGTCGAAACTGGTATCGATAACAACTA
* * * *
18830684 TGGGTATTGATACTTATGGTCTGGTATCGATACTTTGGTGATTCTATCA
65 TGGGTATCGATACTTA-GGTCTGGTATCGATACCTTAGTGAATCTATCA
*
18830733 ATACTTAGGATTTATTTTTCATTTTCCTT-AAACATCGAAGAT-GAAACTGGTATCGATAACAGC
1 ATACTTAGGATTTATTTTTCATTTT--TTAAAACATCGAAG-TCGAAACTGGTATCGATAACAAC
* * *
18830796 TATGGGTATCGATTCTTA-GTCCCTGGTATCGATACCTTAGTGAATGTATCG
63 TATGGGTATCGATACTTAGGT--CTGGTATCGATACCTTAGTGAATCTATCA
* * * * * * **
18830847 ATACTTAGAATTTATTTTTCAATTTTTCAAAACATTGAAGCCGAAATTGGTATGGAT-ACAAGAA
1 ATACTTAGGATTTATTTTTC-ATTTTTTAAAACATCGAAGTCGAAACTGGTATCGATAACAACTA
*
18830911 TTGGGTATCAATACTT
65 -TGGGTATCGATACTT
18830927 TTGGCACTGG
Statistics
Matches: 162, Mismatches: 23, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
112 2 0.01
113 5 0.03
114 147 0.91
115 6 0.04
116 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (112 bp):
ATACTTAGGATTTATTTTTCATTTTTTAAAACATCGAAGTCGAAACTGGTATCGATAACAACTAT
GGGTATCGATACTTAGGTCTGGTATCGATACCTTAGTGAATCTATCA
Found at i:18835149 original size:6 final size:6
Alignment explanation
Indices: 18835138--18835170 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
18835128 AAGGATTTTC
18835138 TTTCTT TTTCTT TTTC-T TTTCTTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT TTT
18835171 AGAATAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 15 0.60
7 5 0.20
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:18835160 original size:17 final size:17
Alignment explanation
Indices: 18835133--18835170 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
18835123 TAGGTAAGGA
18835133 TTTTCTTTC-TTTTTCT
1 TTTTCTTTCTTTTTTCT
18835149 TTTTCTTTTCTTTTTTCT
1 TTTTC-TTTCTTTTTTCT
18835167 TTTT
1 TTTT
18835171 AGAATAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 4 0.20
18 11 0.55
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTCTTTCTTTTTTCT
Found at i:18839762 original size:174 final size:174
Alignment explanation
Indices: 18839528--18839842 Score: 404
Period size: 174 Copynumber: 1.8 Consensus size: 174
18839518 GAAGCAGTTC
* **
18839528 GTGGTCATGAAGAGTCCAGTAAAGTTGGTTTGGAGGGTAACTTAAGAACCTTAGATAGTGACTGC
1 GTGGTCATGAAGAGTCCAGTAAAGTTGGTTTGGAGGGTAACTCAAGAACCTTAGATAGTGAAGGC
*** * * * *
18839593 CATGC-GGTGGATGGTTTGGGTTCAAGGAATGAGGTTTCAGGTGGTGAAGGTAGGGCTCAGAATG
66 CATGCAGCCAG-TGATTTGGGTTCAAGGAATGAAGTTTCAGGTGGTGAAGCTAAGGCTCAGAATG
18839657 AGGTAAATGGAGGTGTGGTTCGGTCTTGTTCTAATGATGTAATTT
130 AGGTAAATGGAGGTGTGGTTCGGTCTTGTTCTAATGATGTAATTT
* * *
18839702 GTGGTCAT-AATGAGTCC-GATGAAGTTGGTTTGGAGGGTAA-TCCGAGTACCTTAGATAGTGAA
1 GTGGTCATGAA-GAGTCCAG-TAAAGTTGGTTTGGAGGGTAACT-CAAGAACCTTAGATAGTGAA
*** * *
18839764 GGTGGTGCAGCCAGTGATTTGGGTTCAAGGTATGAAGTTTCAGGTGGTGAAGCTAAGGCTCGGAA
63 GGCCATGCAGCCAGTGATTTGGGTTCAAGGAATGAAGTTTCAGGTGGTGAAGCTAAGGCTCAGAA
18839829 TGAGGTAAATGGAG
128 TGAGGTAAATGGAG
18839843 CCAGGGTTTT
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
173 4 0.03
174 113 0.95
175 2 0.02
ACGTcount: A:0.25, C:0.10, G:0.36, T:0.29
Consensus pattern (174 bp):
GTGGTCATGAAGAGTCCAGTAAAGTTGGTTTGGAGGGTAACTCAAGAACCTTAGATAGTGAAGGC
CATGCAGCCAGTGATTTGGGTTCAAGGAATGAAGTTTCAGGTGGTGAAGCTAAGGCTCAGAATGA
GGTAAATGGAGGTGTGGTTCGGTCTTGTTCTAATGATGTAATTT
Found at i:18844151 original size:33 final size:33
Alignment explanation
Indices: 18844114--18844185 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
18844104 CATCGGGTCC
* *
18844114 GGAAACT-CAGACCATTTCTACAACCATGGGTGA
1 GGAAACTACA-ACCATTCCTACAAACATGGGTGA
* *
18844147 GGAAACTACAACCATTCCTGCAAACTTGGGTGA
1 GGAAACTACAACCATTCCTACAAACATGGGTGA
18844180 GGAAAC
1 GGAAAC
18844186 AACTGCTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 32 0.94
34 2 0.06
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (33 bp):
GGAAACTACAACCATTCCTACAAACATGGGTGA
Found at i:18844528 original size:33 final size:33
Alignment explanation
Indices: 18844458--18844577 Score: 91
Period size: 33 Copynumber: 3.6 Consensus size: 33
18844448 ACCATTCCTG
* * * * * **
18844458 CAACCTTAGGTCAAGAAACTCCTACCCTTCCTG
1 CAACCTTGGGTGAAGAAACTCATATCATTCCCA
* *
18844491 CAACCTTGGGTGAAGGAACTCATAGT-ATTCCCT
1 CAACCTTGGGTGAAGAAACTCATA-TCATTCCCA
* * *
18844524 CAACCTCGAGTGAAGAAAGTCATATCATTCCCA
1 CAACCTTGGGTGAAGAAACTCATATCATTCCCA
*
18844557 CTAACC-TGGATGAAGAAACTC
1 C-AACCTTGGGTGAAGAAACTC
18844578 CTACTGATCC
Statistics
Matches: 67, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
32 1 0.01
33 62 0.93
34 4 0.06
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (33 bp):
CAACCTTGGGTGAAGAAACTCATATCATTCCCA
Found at i:18852304 original size:38 final size:38
Alignment explanation
Indices: 18852253--18852330 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 38
18852243 AATATTTAAT
*
18852253 AAAAAATAATTAAATTGATTAAACCTACAAATTAAACC
1 AAAAAATAATTAAATTGATTAAACCAACAAATTAAACC
* * * *
18852291 AAAAATTAGTTAAATTGGTTAATCCAACAAATTAAACC
1 AAAAAATAATTAAATTGATTAAACCAACAAATTAAACC
18852329 AA
1 AA
18852331 GAATATATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (38 bp):
AAAAAATAATTAAATTGATTAAACCAACAAATTAAACC
Found at i:18854701 original size:25 final size:25
Alignment explanation
Indices: 18854667--18854734 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
18854657 CTACTATTTC
18854667 ATTATTATATTACTATTATTTTATT
1 ATTATTATATTACTATTATTTTATT
* *
18854692 GTTATTATATAACTATTATTTTATT
1 ATTATTATATTACTATTATTTTATT
* *
18854717 ATTAATTTTGTTACTATT
1 ATT-ATTATATTACTATT
18854735 TTAGAGTCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 25 0.69
26 11 0.31
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (25 bp):
ATTATTATATTACTATTATTTTATT
Found at i:18854719 original size:11 final size:11
Alignment explanation
Indices: 18854661--18854737 Score: 55
Period size: 11 Copynumber: 6.6 Consensus size: 11
18854651 ATTTTGCTAC
*
18854661 TATTTCATTAT
1 TATTTTATTAT
* *
18854672 TATATTACTAT
1 TATTTTATTAT
*
18854683 TATTTTATTGT
1 TATTTTATTAT
*
18854694 TATTATATAACTAT
1 TATT-T-T-ATTAT
18854708 TATTTTATTAT
1 TATTTTATTAT
* *
18854719 TAATTTTGTTAC
1 T-ATTTTATTAT
18854731 TATTTTA
1 TATTTTA
18854738 GAGTCATTTG
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
11 30 0.60
12 11 0.22
13 2 0.04
14 7 0.14
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:18856226 original size:23 final size:23
Alignment explanation
Indices: 18856206--18856250 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
18856196 TAAAATTTTG
*
18856206 AATTATTTAGTGATAATATTTAA
1 AATTATTTAGTAATAATATTTAA
18856229 AATTATTTAGTAATAATATTTA
1 AATTATTTAGTAATAATATTTA
18856251 GGGAAAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (23 bp):
AATTATTTAGTAATAATATTTAA
Found at i:18859001 original size:59 final size:59
Alignment explanation
Indices: 18858930--18859046 Score: 234
Period size: 59 Copynumber: 2.0 Consensus size: 59
18858920 ATGTGTTTGA
18858930 ATGTGGTTGTTTTAAGCTTAGATGGTGTTTATTACATGATTTTAGTGTCTTATAATGTC
1 ATGTGGTTGTTTTAAGCTTAGATGGTGTTTATTACATGATTTTAGTGTCTTATAATGTC
18858989 ATGTGGTTGTTTTAAGCTTAGATGGTGTTTATTACATGATTTTAGTGTCTTATAATGT
1 ATGTGGTTGTTTTAAGCTTAGATGGTGTTTATTACATGATTTTAGTGTCTTATAATGT
18859047 TTGGAGATGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (59 bp):
ATGTGGTTGTTTTAAGCTTAGATGGTGTTTATTACATGATTTTAGTGTCTTATAATGTC
Found at i:18859048 original size:30 final size:30
Alignment explanation
Indices: 18858955--18859048 Score: 70
Period size: 30 Copynumber: 3.2 Consensus size: 30
18858945 GCTTAGATGG
18858955 TGTTTATTACATGATTTTAGTGTCTTATAA
1 TGTTTATTACATGATTTTAGTGTCTTATAA
* *** * **
18858985 TG-TCATGTGGTTG-TTTTA-AG-CTTAGATGG
1 TGTTTAT-TACATGATTTTAGTGTCTT--ATAA
18859014 TGTTTATTACATGATTTTAGTGTCTTATAA
1 TGTTTATTACATGATTTTAGTGTCTTATAA
18859044 TGTTT
1 TGTTT
18859049 GGAGATGATT
Statistics
Matches: 43, Mismatches: 14, Indels: 14
0.61 0.20 0.20
Matches are distributed among these distances:
27 3 0.07
28 1 0.02
29 15 0.35
30 20 0.47
31 1 0.02
32 3 0.07
ACGTcount: A:0.22, C:0.06, G:0.19, T:0.52
Consensus pattern (30 bp):
TGTTTATTACATGATTTTAGTGTCTTATAA
Found at i:18859482 original size:7 final size:6
Alignment explanation
Indices: 18859456--18859480 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18859446 TTTAATCATT
18859456 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
18859481 ATGAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:18863009 original size:18 final size:18
Alignment explanation
Indices: 18862986--18863100 Score: 67
Period size: 20 Copynumber: 6.2 Consensus size: 18
18862976 ATTAAATCGT
18862986 TTTTTTACATTTTTAATA
1 TTTTTTACATTTTTAATA
*** *
18863004 TTTTTTCACAAACTT-A-C
1 TTTTTT-ACATTTTTAATA
*
18863021 TTTTTTA-ATTTCTAATA
1 TTTTTTACATTTTTAATA
*
18863038 -TTTTTACAACTTTTAATAA
1 TTTTTTAC-ATTTTTAAT-A
18863057 TTCTTTTACATTTTTAATAA
1 TT-TTTTACATTTTTAAT-A
* *
18863077 TTATTTGCAATTTCTTAATA
1 TTTTTTAC-ATTT-TTAATA
18863097 TTTT
1 TTTT
18863101 AATTAATTCT
Statistics
Matches: 72, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
15 2 0.03
16 8 0.11
17 6 0.08
18 14 0.19
19 10 0.14
20 21 0.29
21 11 0.15
ACGTcount: A:0.30, C:0.10, G:0.01, T:0.59
Consensus pattern (18 bp):
TTTTTTACATTTTTAATA
Found at i:18881831 original size:27 final size:27
Alignment explanation
Indices: 18881801--18881870 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
18881791 TGATAATTTG
18881801 ACCCTCAG-TAAAATTTTTAACGATTCT
1 ACCCT-AGATAAAATTTTTAACGATTCT
* * *
18881828 ACCCTGGATAAAATTTTTGACGATTTT
1 ACCCTAGATAAAATTTTTAACGATTCT
* *
18881855 ACCCTTGATATAATTT
1 ACCCTAGATAAAATTT
18881871 CGAGAAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.03
27 36 0.97
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (27 bp):
ACCCTAGATAAAATTTTTAACGATTCT
Found at i:18887078 original size:13 final size:13
Alignment explanation
Indices: 18887048--18887079 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
18887038 TTTCAAACTA
18887048 AAATAC-ATGAGT
1 AAATACAATGAGT
18887060 -AATACAATGAGT
1 AAATACAATGAGT
18887072 AAATACAA
1 AAATACAA
18887080 ATATAACACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 6 0.33
13 7 0.39
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.22
Consensus pattern (13 bp):
AAATACAATGAGT
Found at i:18893278 original size:18 final size:19
Alignment explanation
Indices: 18893241--18893280 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
18893231 TAAATAATCT
18893241 TAAAAAATTCAAAATGTTTA
1 TAAAAAATTCAAAA-GTTTA
18893261 TAAAAAATTCAAAA-TTTA
1 TAAAAAATTCAAAAGTTTA
18893279 TA
1 TA
18893281 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
20 14 0.70
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (19 bp):
TAAAAAATTCAAAAGTTTA
Found at i:18893516 original size:20 final size:20
Alignment explanation
Indices: 18893488--18893530 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
18893478 CTAACATGAA
*
18893488 ATTAATTATACTGTAACAAG
1 ATTAATTATACTATAACAAG
* *
18893508 ATTAGTTATACTATTACAAG
1 ATTAATTATACTATAACAAG
18893528 ATT
1 ATT
18893531 TCATTTCACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (20 bp):
ATTAATTATACTATAACAAG
Found at i:18898441 original size:18 final size:19
Alignment explanation
Indices: 18898401--18898441 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
18898391 CGAACACACC
*
18898401 AAAAAAATATGAAATAATA
1 AAAAAAATATGAAAAAATA
18898420 AAAAAAACTA-GAAAAAATA
1 AAAAAAA-TATGAAAAAATA
18898439 AAA
1 AAA
18898442 CTTATCAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAAAAATATGAAAAAATA
Found at i:18899585 original size:6 final size:6
Alignment explanation
Indices: 18899574--18899601 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
18899564 ATACCTTTTA
18899574 AAAATG AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAA
18899602 ATAATATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:18901359 original size:20 final size:20
Alignment explanation
Indices: 18901334--18901384 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
18901324 TCTGGAAAGA
*
18901334 AGTTGTGAATCATAACCGCC
1 AGTTGTGAATCATAACCACC
18901354 AGTTGTGAATCATAACCACC
1 AGTTGTGAATCATAACCACC
*
18901374 AGTTATGAATC
1 AGTTGTGAATC
18901385 GTATTCGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (20 bp):
AGTTGTGAATCATAACCACC
Found at i:18916694 original size:23 final size:23
Alignment explanation
Indices: 18916659--18916711 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
18916649 AATGTTATTG
* * *
18916659 ATCAGGGGTAGCTTTGGCTACAT
1 ATCAGTGGAAGCTTCGGCTACAT
*
18916682 TTCAGTGGAAGCTTCGGCTACAT
1 ATCAGTGGAAGCTTCGGCTACAT
18916705 ATCAGTG
1 ATCAGTG
18916712 TGACACTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (23 bp):
ATCAGTGGAAGCTTCGGCTACAT
Found at i:18922946 original size:22 final size:22
Alignment explanation
Indices: 18922887--18922943 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 22
18922877 ATCTTCAAGA
18922887 ATATGCAATCTT---AGATATG
1 ATATGCAATCTTAGAAGATATG
18922906 ATATGCAATCTTAGAAGATATG
1 ATATGCAATCTTAGAAGATATG
* *
18922928 ATTTTGTAATCTTAGA
1 A-TATGCAATCTTAGA
18922944 GATTTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 12 0.38
22 8 0.25
23 12 0.38
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
ATATGCAATCTTAGAAGATATG
Found at i:18923191 original size:23 final size:23
Alignment explanation
Indices: 18923147--18923191 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
18923137 TCTTATTTTG
* *
18923147 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
18923170 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
18923192 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:18923883 original size:3 final size:3
Alignment explanation
Indices: 18923877--18923902 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18923867 ATTATTATTA
18923877 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
18923903 CTTGATCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:18932104 original size:23 final size:23
Alignment explanation
Indices: 18932077--18932167 Score: 164
Period size: 23 Copynumber: 4.0 Consensus size: 23
18932067 TAAGTACCTG
18932077 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTGAA
18932100 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTGAA
* *
18932123 ATACGACATACGAGGTGCTTGAA
1 ATACGACACACGAGGTGCCTGAA
18932146 ATACGACACACGAGGTGCCTGA
1 ATACGACACACGAGGTGCCTGA
18932168 TATGACACAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.15
Consensus pattern (23 bp):
ATACGACACACGAGGTGCCTGAA
Found at i:18932178 original size:46 final size:46
Alignment explanation
Indices: 18932073--18932178 Score: 155
Period size: 46 Copynumber: 2.3 Consensus size: 46
18932063 CATATAAGTA
*
18932073 CCTGATACGACAC--ACGAGGTGCCTGAAATACGACACACGAGGTG
1 CCTGATATGACACATACGAGGTGCCTGAAATACGACACACGAGGTG
* *
18932117 CCTGAAAT-ACGACATACGAGGTGCTTGAAATACGACACACGAGGTG
1 CCTGATATGAC-ACATACGAGGTGCCTGAAATACGACACACGAGGTG
18932163 CCTGATATGACACATA
1 CCTGATATGACACATA
18932179 AAGTGCCTGG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
43 2 0.04
44 8 0.15
46 42 0.78
47 2 0.04
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.17
Consensus pattern (46 bp):
CCTGATATGACACATACGAGGTGCCTGAAATACGACACACGAGGTG
Found at i:18932200 original size:23 final size:23
Alignment explanation
Indices: 18932171--18932256 Score: 154
Period size: 23 Copynumber: 3.7 Consensus size: 23
18932161 TGCCTGATAT
18932171 GACACATAAAGTGCCTGGTGTAC
1 GACACATAAAGTGCCTGGTGTAC
*
18932194 GACACATAAAGTGCCTAGTGTAC
1 GACACATAAAGTGCCTGGTGTAC
*
18932217 GACACATAAAGTGCCTGATGTAC
1 GACACATAAAGTGCCTGGTGTAC
18932240 GACACATAAAGTGCCTG
1 GACACATAAAGTGCCTG
18932257 ATCGGCAAAG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (23 bp):
GACACATAAAGTGCCTGGTGTAC
Found at i:18935180 original size:28 final size:28
Alignment explanation
Indices: 18935149--18935207 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
18935139 TTATTTTTAA
18935149 AAAATAAAAAAAT-ATATATTTAAAATAT
1 AAAA-AAAAAAATAATATATTTAAAATAT
** * *
18935177 AAAAAAGCATATAATATTTTTAAAATAT
1 AAAAAAAAAAATAATATATTTAAAATAT
18935205 AAA
1 AAA
18935208 TTTTTTTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAAAAAAAAATAATATATTTAAAATAT
Found at i:18935188 original size:23 final size:23
Alignment explanation
Indices: 18935144--18935189 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
18935134 TATTATTATT
*
18935144 TTTAAAAAATAAAAAAATATATA
1 TTTAAAAAATAAAAAAACATATA
* *
18935167 TTTAAAATATAAAAAAGCATATA
1 TTTAAAAAATAAAAAAACATATA
18935190 ATATTTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
TTTAAAAAATAAAAAAACATATA
Found at i:18951129 original size:32 final size:32
Alignment explanation
Indices: 18951088--18951151 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
18951078 TGCGGGTGTT
18951088 GTATGCCTGCTTGTTAGTATCATTCCTGAGAA
1 GTATGCCTGCTTGTTAGTATCATTCCTGAGAA
18951120 GTATGCCTGCTTGTTAGTATCATTCCTGAGAA
1 GTATGCCTGCTTGTTAGTATCATTCCTGAGAA
18951152 CAGAAGAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (32 bp):
GTATGCCTGCTTGTTAGTATCATTCCTGAGAA
Found at i:18951560 original size:92 final size:91
Alignment explanation
Indices: 18951403--18951611 Score: 260
Period size: 92 Copynumber: 2.3 Consensus size: 91
18951393 TTGATTTTAG
** *
18951403 TAAATTCATATAAGAACAATTTATTATTGAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
18951468 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
18951495 TAAATTCATATAAGAAAATTTATTATCAAGTATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
*
18951559 TATGTAATAATTATTATTTTAGATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
18951587 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
18951612 GTTATAATTA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
90 1 0.01
91 28 0.27
92 70 0.69
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:18951740 original size:66 final size:61
Alignment explanation
Indices: 18951665--18952233 Score: 305
Period size: 66 Copynumber: 9.4 Consensus size: 61
18951655 AAATATATTT
18951665 AATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTA-AGTATCATATATTATGATTT-AGTAAATT-ATATAA
18951730 G
61 G
* * * **
18951731 AATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-T-AATTA--AAA-TATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTAGTAAATTATATAAG
*
18951784 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTT-AGTAAATT-ATATA
18951848 AG
60 AG
* * * * **
18951850 AATATTAATTA-TTAAGAATTTA-TTAA--ATTATATATT-TTAATTA--AAA-TATAT-TT
1 AATATTAATTATTTAA-ATTTTATTTAAGTATCATATATTATGATTTAGTAAATTATATAAG
*
18951903 AATAATAATTATGTT-AATTTATATTTTATAGTATCATATATTATGATTTCAGTAAATTAATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTT-AGTAAATT-ATATA
18951967 AG
60 AG
* * * * * **
18951969 AATATTAATTATTAAGAATTTCA-TTAA--ATTATATATT-TTAATTA--AAA-TATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTAGTAAATTATATAAG
*
18952023 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTT-AGTAAATT-ATATA
18952087 AG
60 AG
* * * * **
18952089 AATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-TTAATTA--AAA-TATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTAGTAAATTATATAAG
*
18952143 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTT-AGTAAATT-ATATA
18952207 AG
60 AG
*
18952209 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
18952234 AAATTATATA
Statistics
Matches: 379, Mismatches: 57, Indels: 135
0.66 0.10 0.24
Matches are distributed among these distances:
52 5 0.01
53 36 0.09
54 37 0.10
55 17 0.04
56 18 0.05
57 9 0.02
58 11 0.03
59 37 0.10
60 33 0.09
61 31 0.08
62 1 0.00
63 18 0.05
64 15 0.04
65 26 0.07
66 70 0.18
67 15 0.04
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (61 bp):
AATATTAATTATTTAAATTTTATTTAAGTATCATATATTATGATTTAGTAAATTATATAAG
Found at i:18951768 original size:17 final size:17
Alignment explanation
Indices: 18951748--18951781 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18951738 ATTATTAAGA
* *
18951748 ATTTTATTAAATTATAT
1 ATTTAATTAAAATATAT
18951765 ATTTAATTAAAATATAT
1 ATTTAATTAAAATATAT
18951782 TTAATAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTAATTAAAATATAT
Found at i:18952049 original size:120 final size:120
Alignment explanation
Indices: 18951634--18952277 Score: 1154
Period size: 120 Copynumber: 5.4 Consensus size: 120
18951624 TTAAATTATT
* * * *
18951634 TTAAATCATATATTATAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-TTTATAG
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTAT-ATTTTACAG
* *
18951696 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
63 TATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
18951754 TTAAATTATATA-TTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
18951818 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAA-TTTA
66 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
*
18951872 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTAT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
*
18951937 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTCA
66 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
18951992 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
18952057 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
18952112 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
18952177 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
18952232 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
18952278 TAAATATGAT
Statistics
Matches: 509, Mismatches: 10, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
118 22 0.04
119 187 0.37
120 300 0.59
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
Found at i:18952134 original size:18 final size:17
Alignment explanation
Indices: 18952106--18952140 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18952096 ATTATTAAGA
*
18952106 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
18952123 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
18952141 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:18952254 original size:18 final size:17
Alignment explanation
Indices: 18952226--18952260 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18952216 ATTATTAAGA
*
18952226 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
18952243 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
18952261 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:18952474 original size:44 final size:45
Alignment explanation
Indices: 18952425--18952515 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
18952415 ACCTCTATTC
* * *
18952425 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
18952469 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
18952514 CA
1 CA
18952516 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:18952530 original size:17 final size:16
Alignment explanation
Indices: 18952496--18952581 Score: 145
Period size: 16 Copynumber: 5.2 Consensus size: 16
18952486 GATTAGCTAT
18952496 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
18952512 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
18952529 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
18952546 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
18952562 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
18952578 TACA
1 TACA
18952582 GCGAACCAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
16 34 0.51
17 33 0.49
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.24
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:18962717 original size:13 final size:13
Alignment explanation
Indices: 18962701--18962731 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
18962691 ATTTAACCAC
18962701 TTTAATTAATCAA
1 TTTAATTAATCAA
*
18962714 TTTAATTAATTAA
1 TTTAATTAATCAA
18962727 TTTAA
1 TTTAA
18962732 ACCCAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTAATTAATCAA
Found at i:18979363 original size:33 final size:33
Alignment explanation
Indices: 18979318--18979384 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
18979308 TTCCAAACAA
18979318 ATTGGTTAAATAGACACAAATTTTCCAATTTTT
1 ATTGGTTAAATAGACACAAATTTTCCAATTTTT
* *
18979351 ATTGGTTGAATAGACACAAATTTTCTAATTTTT
1 ATTGGTTAAATAGACACAAATTTTCCAATTTTT
18979384 A
1 A
18979385 AATAGAATGG
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:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (33 bp):
ATTGGTTAAATAGACACAAATTTTCCAATTTTT
Found at i:18987525 original size:6 final size:6
Alignment explanation
Indices: 18987514--18987542 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
18987504 ATAATTTATA
18987514 AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
18987543 TGCTTTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:18987850 original size:21 final size:20
Alignment explanation
Indices: 18987799--18987850 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
18987789 AAAATTTTTT
*
18987799 TCGAATCAAATTGAGTCGAG
1 TCGAATCAAATTGAGTCAAG
*
18987819 T-GAAATGAAATTCGAGTCAAG
1 TCG-AATCAAATT-GAGTCAAG
18987840 TCGAATCAAAT
1 TCGAATCAAAT
18987851 AAAATTGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.04
20 9 0.35
21 15 0.58
22 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGAATCAAATTGAGTCAAG
Found at i:18988114 original size:18 final size:19
Alignment explanation
Indices: 18988074--18988115 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
18988064 TATTATTTAG
*
18988074 AATTTTTTAAAAAAATTAT
1 AATTTTTTAAAAAAATTAA
*
18988093 AATTTTTTAAAAATA-TAA
1 AATTTTTTAAAAAAATTAA
18988111 AATTT
1 AATTT
18988116 GAAATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATTTTTTAAAAAAATTAA
Found at i:18988142 original size:18 final size:19
Alignment explanation
Indices: 18988121--18988157 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18988111 AATTTGAAAT
*
18988121 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
18988139 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTGAA
18988158 ATCTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:18994667 original size:20 final size:19
Alignment explanation
Indices: 18994635--18994673 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
18994625 ACCTCTGAAG
18994635 TAATTTTGTTTTTTGTTTTC
1 TAATTTTGTTTTTT-TTTTC
18994655 TAATGTTTGTTTTTTTTTT
1 TAAT-TTTGTTTTTTTTTT
18994674 GAATTCGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.77
Consensus pattern (19 bp):
TAATTTTGTTTTTTTTTTC
Found at i:18996442 original size:23 final size:23
Alignment explanation
Indices: 18996416--18996462 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
18996406 TATGTGATTT
* * *
18996416 AATGTCTGAATTGTTATTGTTAC
1 AATGTATGAATTGTGAATGTTAC
*
18996439 AATGTATGATTTGTGAATGTTAC
1 AATGTATGAATTGTGAATGTTAC
18996462 A
1 A
18996463 TGCCTACTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (23 bp):
AATGTATGAATTGTGAATGTTAC
Done.