Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 31 of 85
Found at i:10320106 original size:11 final size:11
Alignment explanation
Indices: 10320092--10320119 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
10320082 TTCTTATCTT
10320092 TTTTTTTTTTG
1 TTTTTTTTTTG
10320103 TTTTTTTTTTG
1 TTTTTTTTTTG
10320114 TTTTTT
1 TTTTTT
10320120 GCCTAAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:10322175 original size:37 final size:36
Alignment explanation
Indices: 10322110--10322190 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 36
10322100 TATTTAGAAT
*
10322110 ATATATTAATTTAAAACAATATATAATAA-ATAATGAA
1 ATATA-TAACTTAAAACAATATATAATAACAT-ATGAA
*
10322147 ATGTATAACTTAAAACTAAT-TAATAATAACATATGAA
1 ATATATAACTTAAAAC-AATAT-ATAATAACATATGAA
10322184 ATATATA
1 ATATATA
10322191 CAATATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
36 11 0.29
37 25 0.66
38 2 0.05
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.35
Consensus pattern (36 bp):
ATATATAACTTAAAACAATATATAATAACATATGAA
Found at i:10323903 original size:11 final size:11
Alignment explanation
Indices: 10323889--10323933 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
10323879 AGATAAATAT
10323889 TATTTTATTAA
1 TATTTTATTAA
*
10323900 TATTTTAATGATA
1 TATTTT-ATTA-A
*
10323913 TATTTTACTAA
1 TATTTTATTAA
10323924 TATTTTATTA
1 TATTTTATTA
10323934 TAAATAGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 16 0.57
12 5 0.18
13 7 0.25
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:10326355 original size:19 final size:19
Alignment explanation
Indices: 10326308--10326359 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
10326298 AAAAATTAGA
*
10326308 AAAAAATTATAAAAATTGT
1 AAAAAATTATAAAAATCGT
*** *
10326327 AAACTTTTATAAAAGTCGT
1 AAAAAATTATAAAAATCGT
10326346 AAAAAATTATAAAA
1 AAAAAATTATAAAA
10326360 TATATAGAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (19 bp):
AAAAAATTATAAAAATCGT
Found at i:10326951 original size:92 final size:89
Alignment explanation
Indices: 10326841--10327105 Score: 354
Period size: 92 Copynumber: 2.9 Consensus size: 89
10326831 ACCCACCTCT
*
10326841 GGCCTTTTTGATGTATTTTGACAATTTAAGTACCCAATTGAGTGAAAAAAAATAGCAAAGGGCTT
1 GGCCTTTTTGATGCATTTTGACAATTTAAGTACCCAATTGAGTGAAAAAAAA-AGC-AAGGGCTT
* *
10326906 AATTGCTTTTTATGAAAA-GTTTGAA
64 AATTACTTTTTTTGAAAACGTTTGAA
* * * * *
10326931 GGCCTTTTTTTTATGCATTTTGGCAATTCAAGTACCCAATTGAGTGCAAAAAAAAAAGTAGGGGC
1 GGCC--TTTTTGATGCATTTTGACAATTTAAGTACCCAATTGAGTG--AAAAAAAAAGCAAGGGC
*
10326996 TTAATTACTTTTTTTTAAAACGTTTGAA
62 TTAATTACTTTTTTTGAAAACGTTTGAA
*
10327024 GGCCTTTTTGATGCATTTTGA-AAGTTTAAGTACCCAATTGAGTGGAAAAAAAAAGCATGGGCTT
1 GGCCTTTTTGATGCATTTTGACAA-TTTAAGTACCCAATTGAGT-GAAAAAAAAAGCAAGGGCTT
10327088 AATTACTTTTTTTGAAAA
64 AATTACTTTTTTTGAAAA
10327106 AGATTGAGGG
Statistics
Matches: 153, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
90 40 0.26
91 33 0.22
92 59 0.39
93 13 0.08
94 8 0.05
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (89 bp):
GGCCTTTTTGATGCATTTTGACAATTTAAGTACCCAATTGAGTGAAAAAAAAAGCAAGGGCTTAA
TTACTTTTTTTGAAAACGTTTGAA
Found at i:10327996 original size:19 final size:19
Alignment explanation
Indices: 10327949--10328000 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
10327939 AAAAATTAGA
*
10327949 AAAAAATTATAAAAATTGT
1 AAAAAATTATAAAAATCGT
*** *
10327968 AAACTTTTATAAAAGTCGT
1 AAAAAATTATAAAAATCGT
10327987 AAAAAATTATAAAA
1 AAAAAATTATAAAA
10328001 TATATAGAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (19 bp):
AAAAAATTATAAAAATCGT
Found at i:10328592 original size:92 final size:91
Alignment explanation
Indices: 10328482--10328723 Score: 330
Period size: 92 Copynumber: 2.7 Consensus size: 91
10328472 ACCCACCTCT
* *
10328482 GGCCTTTTTGATGTATTTTGACAATTTAAGTACCCAATTGAGTG-AAAAAAAATAGCAAAGGGCT
1 GGCCTTTTTGATGCATTTTGACAATTTAAGTACCCAATTGAGTGCAAAAAAAAAAG-AAAGGGCT
*
10328546 TAATTGCTTTTTATGAAAA-GTTTGAA
65 TAATTACTTTTTATGAAAACGTTTGAA
* * * * *
10328572 GGCCTTTTTTTTATGCATTTTGGCAATTCAAGTACCCAATTGAGTGCAAAAAAAAAAGTAGGGGC
1 GGCC--TTTTTGATGCATTTTGACAATTTAAGTACCCAATTGAGTGCAAAAAAAAAAGAAAGGGC
* *
10328637 TTAATTACTTTTTTTTAAAACGTTTGAA
64 TTAATTACTTTTTATGAAAACGTTTGAA
10328665 GGCCTTTTTGATGCATTTTGA-AAGTTTAAGTACCCAATTGAGTGC-AAAAAAAAAGAAAG
1 GGCCTTTTTGATGCATTTTGACAA-TTTAAGTACCCAATTGAGTGCAAAAAAAAAAGAAAG
10328724 AGCAGGGGCT
Statistics
Matches: 132, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
90 18 0.14
91 35 0.27
92 58 0.44
93 21 0.16
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (91 bp):
GGCCTTTTTGATGCATTTTGACAATTTAAGTACCCAATTGAGTGCAAAAAAAAAAGAAAGGGCTT
AATTACTTTTTATGAAAACGTTTGAA
Found at i:10329373 original size:4 final size:4
Alignment explanation
Indices: 10329364--10329455 Score: 57
Period size: 4 Copynumber: 22.2 Consensus size: 4
10329354 AAAACAAATA
**
10329364 AAAG AAAG AAAG AAAG AAAG AAAAG AAAG CCAAAG CCAAAG CCA- AAAG
1 AAAG AAAG AAAG AAAG AAAG -AAAG AAAG --AAAG --AAAG AAAG AAAG
* *
10329412 AAA- ACAG AAAGG GAAG AAAG AAA- AAAG AAA- AAGAG AAAG AAAG A
1 AAAG AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AA-AG AAAG AAAG A
10329456 CCCATGTCAA
Statistics
Matches: 71, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
3 8 0.11
4 44 0.62
5 9 0.13
6 10 0.14
ACGTcount: A:0.70, C:0.08, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:10329379 original size:12 final size:12
Alignment explanation
Indices: 10329364--10329455 Score: 57
Period size: 13 Copynumber: 7.4 Consensus size: 12
10329354 AAAACAAATA
10329364 AAAGAAAGAAAG
1 AAAGAAAGAAAG
10329376 AAAGAAAGAAAAG
1 AAAGAAAG-AAAG
10329389 AAAGCCAAAGCCAAAG
1 AAAG--AAAG--AAAG
**
10329405 CCA-AAAGAAA-
1 AAAGAAAGAAAG
* *
10329415 ACAGAAAGGGAAG
1 AAAGAAA-GAAAG
10329428 AAAGAAA-AAAG
1 AAAGAAAGAAAG
10329439 AAA-AAGAGAAAG
1 AAAGAA-AGAAAG
10329451 AAAGA
1 AAAGA
10329456 CCCATGTCAA
Statistics
Matches: 63, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
10 4 0.06
11 13 0.21
12 18 0.29
13 19 0.30
15 4 0.06
16 5 0.08
ACGTcount: A:0.70, C:0.08, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAG
Found at i:10330323 original size:40 final size:40
Alignment explanation
Indices: 10330202--10330339 Score: 97
Period size: 40 Copynumber: 3.5 Consensus size: 40
10330192 CTTCGAGTTC
* * * *
10330202 ATGAGACACTAGGTGTCAATTTACTGCTTC-AGATTAAT-TCG
1 ATGAGACACTGGGTGTCAAATTATTACTTCGA-ATT-ATCT-G
* * ** * *
10330243 ATGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTAGCCG
1 ATGAGACACTGGGTGTCAAATTATTACTTCGAATTATCTG
10330280 ATGAGACACTGGGTGTCAAATTATTACTTCGAATTATCTG
1 ATGAGACACTGGGTGTCAAATTATTACTTCGAATTATCTG
* * *
10330320 ATGAGCCAGTGGGTGCCAAA
1 ATGAGACACTGGGTGTCAAA
10330340 CTGGTGTGTT
Statistics
Matches: 73, Mismatches: 19, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
37 16 0.22
38 10 0.14
39 2 0.03
40 32 0.44
41 13 0.18
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAAATTATTACTTCGAATTATCTG
Found at i:10331842 original size:13 final size:12
Alignment explanation
Indices: 10331824--10331853 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
10331814 AAAATAACTA
10331824 ATATATTAATACT
1 ATATATTAAT-CT
10331837 ATATATTAATCT
1 ATATATTAATCT
10331849 ATATA
1 ATATA
10331854 AGTAGTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATTAATCT
Found at i:10331880 original size:18 final size:18
Alignment explanation
Indices: 10331853--10331887 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10331843 TAATCTATAT
*
10331853 AAGTAGTATATATAAAAG
1 AAGTAATATATATAAAAG
10331871 AAGTAATATATATAAAA
1 AAGTAATATATATAAAA
10331888 TGGAGAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
AAGTAATATATATAAAAG
Found at i:10332235 original size:16 final size:15
Alignment explanation
Indices: 10332210--10332249 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
10332200 AAAGAGAAAT
*
10332210 TTTAAAATAAATTAA
1 TTTAAAATAAATAAA
10332225 TTTAAAGATAAATAAA
1 TTTAAA-ATAAATAAA
10332241 TTTAAAATA
1 TTTAAAATA
10332250 TCATATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TTTAAAATAAATAAA
Found at i:10348227 original size:15 final size:16
Alignment explanation
Indices: 10348207--10348236 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10348197 TGGTGGCTCG
10348207 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
10348222 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
10348237 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:10348576 original size:17 final size:17
Alignment explanation
Indices: 10348554--10348595 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
10348544 TATGGTCAAG
10348554 TATGTATAAGTTAGATA
1 TATGTATAAGTTAGATA
10348571 TATGTATAAGTTAGATA
1 TATGTATAAGTTAGATA
10348588 TATGTATA
1 TATGTATA
10348596 TTTGGGATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (17 bp):
TATGTATAAGTTAGATA
Found at i:10350882 original size:41 final size:40
Alignment explanation
Indices: 10350837--10351140 Score: 351
Period size: 41 Copynumber: 7.5 Consensus size: 40
10350827 TCTCAAATCT
* * *
10350837 ATGAAAAGGTTGAAAAGGAAGTTATCCAAAAAGGATAACAA
1 ATGAAAAGGTTGAAAAGGACGATATCCAAAAA-GATATCAA
** **
10350878 ATGAAAATATTGAAAAGGACGATATTTGAAAAAGATATCAA
1 ATGAAAAGGTTGAAAAGGACGATA-TCCAAAAAGATATCAA
*
10350919 ATGAAAAGGTTGAAAAGGACGATATTCGAAAAAGATATCAA
1 ATGAAAAGGTTGAAAAGGACGATA-TCCAAAAAGATATCAA
* * *
10350960 ATGAAAAGGTTGAAAAGAACGATATCCAAAAAATATATCAC
1 ATGAAAAGGTTGAAAAGGACGATATCC-AAAAAGATATCAA
10351001 ATGAAAAGGTTGAAAAGGACGATATCCGAAAAAGATATCAA
1 ATGAAAAGGTTGAAAAGGACGATATCC-AAAAAGATATCAA
** **
10351042 ATGAAAATATTGAAAAGGACGATATTAAAAAAAGATATCAA
1 ATGAAAAGGTTGAAAAGGACGATA-TCCAAAAAGATATCAA
* **
10351083 ATGAAAAGGTTGAAAATGACGATATTTGAAGAAA-ATATC-A
1 ATGAAAAGGTTGAAAAGGACGATA-TCCAA-AAAGATATCAA
*
10351123 ATGAAAAGGTCGAAAAGG
1 ATGAAAAGGTTGAAAAGG
10351141 TTAGGAATGA
Statistics
Matches: 230, Mismatches: 29, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
40 19 0.08
41 201 0.87
42 10 0.04
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (40 bp):
ATGAAAAGGTTGAAAAGGACGATATCCAAAAAGATATCAA
Found at i:10351121 original size:82 final size:82
Alignment explanation
Indices: 10350837--10351129 Score: 403
Period size: 82 Copynumber: 3.6 Consensus size: 82
10350827 TCTCAAATCT
* * * *
10350837 ATGAAAAGGTTGAAAAGGAAGTTA-TCCAAAAAGGATAACAAATGAAAATATTGAAAAGGACGAT
1 ATGAAAAGGTTGAAAAGGACGATATTCGAAAAA-GATATCAAATGAAAATATTGAAAAGGACGAT
**
10350901 ATTTGAAAAAGATATCAA
65 ATTAAAAAAAGATATCAA
** *
10350919 ATGAAAAGGTTGAAAAGGACGATATTCGAAAAAGATATCAAATGAAAAGGTTGAAAAGAACGATA
1 ATGAAAAGGTTGAAAAGGACGATATTCGAAAAAGATATCAAATGAAAATATTGAAAAGGACGATA
** * *
10350984 TCCAAAAAATATATCAC
66 TTAAAAAAAGATATCAA
*
10351001 ATGAAAAGGTTGAAAAGGACGATATCCGAAAAAGATATCAAATGAAAATATTGAAAAGGACGATA
1 ATGAAAAGGTTGAAAAGGACGATATTCGAAAAAGATATCAAATGAAAATATTGAAAAGGACGATA
10351066 TTAAAAAAAGATATCAA
66 TTAAAAAAAGATATCAA
* *
10351083 ATGAAAAGGTTGAAAATGACGATATTTGAAGAAA-ATATC-AATGAAAA
1 ATGAAAAGGTTGAAAAGGACGATATTCGAA-AAAGATATCAAATGAAAA
10351130 GGTCGAAAAG
Statistics
Matches: 186, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
81 8 0.04
82 168 0.90
83 10 0.05
ACGTcount: A:0.54, C:0.07, G:0.19, T:0.20
Consensus pattern (82 bp):
ATGAAAAGGTTGAAAAGGACGATATTCGAAAAAGATATCAAATGAAAATATTGAAAAGGACGATA
TTAAAAAAAGATATCAA
Found at i:10351121 original size:123 final size:122
Alignment explanation
Indices: 10350837--10351140 Score: 398
Period size: 123 Copynumber: 2.5 Consensus size: 122
10350827 TCTCAAATCT
* ** * **
10350837 ATGAAAAGGTTGAAAAGGAA-GTTATCCAAAAAGGATAACAAATGAAAATATTGAAAAGGACGAT
1 ATGAAAAGGTTGAAAA-GAACGATATCCAAAAAATATATC-AATGAAAAGGTTGAAAAGGACGAT
** * **
10350901 ATTTGAAAAAGATATCAAATGAAAAGGTTGAAAAGGACGATATTCGAAAAAGATATCAA
64 ATCCGAAAAAGATATCAAATGAAAAGATTGAAAAGGACGATATTAAAAAAAGATATCAA
10350960 ATGAAAAGGTTGAAAAGAACGATATCCAAAAAATATATCACATGAAAAGGTTGAAAAGGACGATA
1 ATGAAAAGGTTGAAAAGAACGATATCCAAAAAATATATCA-ATGAAAAGGTTGAAAAGGACGATA
*
10351025 TCCGAAAAAGATATCAAATGAAAATATTGAAAAGGACGATATTAAAAAAAGATATCAA
65 TCCGAAAAAGATATCAAATGAAAAGATTGAAAAGGACGATATTAAAAAAAGATATCAA
** * *
10351083 ATGAAAAGGTTGAAAATG-ACGATATTTGAAGAAA-ATATCAATGAAAAGGTCGAAAAGG
1 ATGAAAAGGTTGAAAA-GAACGATA-TCCAAAAAATATATCAATGAAAAGGTTGAAAAGG
10351141 TTAGGAATGA
Statistics
Matches: 161, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
122 21 0.13
123 133 0.83
124 7 0.04
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (122 bp):
ATGAAAAGGTTGAAAAGAACGATATCCAAAAAATATATCAATGAAAAGGTTGAAAAGGACGATAT
CCGAAAAAGATATCAAATGAAAAGATTGAAAAGGACGATATTAAAAAAAGATATCAA
Found at i:10352916 original size:18 final size:18
Alignment explanation
Indices: 10352893--10352932 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
10352883 AGTCGCCACC
10352893 GATCTTTTATTGAGGTGT
1 GATCTTTTATTGAGGTGT
10352911 GATCTTTTATTGAGGTGT
1 GATCTTTTATTGAGGTGT
10352929 GATC
1 GATC
10352933 GGATCACCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.47
Consensus pattern (18 bp):
GATCTTTTATTGAGGTGT
Found at i:10361750 original size:18 final size:18
Alignment explanation
Indices: 10361727--10361762 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10361717 CCCCACCGCT
*
10361727 GCCATGACCCTCTCCATA
1 GCCATGACCCTCGCCATA
*
10361745 GCCATGCCCCTCGCCATA
1 GCCATGACCCTCGCCATA
10361763 ACTTTCACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.47, G:0.14, T:0.19
Consensus pattern (18 bp):
GCCATGACCCTCGCCATA
Found at i:10361980 original size:12 final size:12
Alignment explanation
Indices: 10361965--10362001 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
10361955 ACTTGAACTG
*
10361965 GAACTGGAACCA
1 GAACCGGAACCA
10361977 GAACCGGAACCA
1 GAACCGGAACCA
10361989 GAACCGGAACCA
1 GAACCGGAACCA
10362001 G
1 G
10362002 CCCCAGCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.41, C:0.30, G:0.27, T:0.03
Consensus pattern (12 bp):
GAACCGGAACCA
Found at i:10362038 original size:22 final size:20
Alignment explanation
Indices: 10362000--10362039 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
10361990 AACCGGAACC
*
10362000 AGCCCCAGCTCCAGACCCTG
1 AGCCCCACCTCCAGACCCTG
10362020 AGCCACCACCTCCGAGACCC
1 AGCC-CCACCTCC-AGACCC
10362040 AGCCCTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.23, C:0.53, G:0.17, T:0.07
Consensus pattern (20 bp):
AGCCCCACCTCCAGACCCTG
Found at i:10365824 original size:60 final size:60
Alignment explanation
Indices: 10365727--10365852 Score: 180
Period size: 60 Copynumber: 2.1 Consensus size: 60
10365717 GCCTCGTCCT
* * * *
10365727 GACCCAGCTCGAGAGCCAGCATAGGAACCGGCAGATGAACCGGCTTCTGAACCTGCACCA
1 GACCCAGCTCGAGACCCAGCATAAGAACCGGCAGATGAACCAGCTTCAGAACCTGCACCA
* * * *
10365787 GACCCGGCTCGAGACCCAGCGTAAGAACCTGCGGATGAACCAGCTTCAGAACCTGCACCA
1 GACCCAGCTCGAGACCCAGCATAAGAACCGGCAGATGAACCAGCTTCAGAACCTGCACCA
10365847 GACCCA
1 GACCCA
10365853 CCAGATGAAC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.29, C:0.35, G:0.25, T:0.11
Consensus pattern (60 bp):
GACCCAGCTCGAGACCCAGCATAAGAACCGGCAGATGAACCAGCTTCAGAACCTGCACCA
Found at i:10367169 original size:18 final size:18
Alignment explanation
Indices: 10367136--10367188 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 18
10367126 TTTTTATTTT
*
10367136 AAAAATTTTAAAAAAATAA
1 AAAAATTTT-TAAAAATAA
10367155 AAAAATATTTTAAAAATAA
1 AAAAAT-TTTTAAAAATAA
10367174 AAAAATTTTTAAAAA
1 AAAAATTTTTAAAAA
10367189 AAGTATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 9 0.28
19 20 0.62
20 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATTTTTAAAAATAA
Found at i:10367214 original size:11 final size:11
Alignment explanation
Indices: 10367130--10367215 Score: 60
Period size: 11 Copynumber: 8.2 Consensus size: 11
10367120 GGCCCATTTT
10367130 TATTTT-AAAA
1 TATTTTAAAAA
10367140 -ATTTTAAAAA
1 TATTTTAAAAA
* **
10367150 -AATAAAAAAA
1 TATTTTAAAAA
10367160 TATTTTAAAAA
1 TATTTTAAAAA
*
10367171 TA---AAAAAA
1 TATTTTAAAAA
10367179 T-TTTTAAAAAAA
1 TATTTT--AAAAA
10367191 GTATTTTAAAAA
1 -TATTTTAAAAA
10367203 TATTTTAAAAA
1 TATTTTAAAAA
10367214 TA
1 TA
10367216 AAAAATAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
8 6 0.10
9 5 0.08
10 11 0.19
11 22 0.37
12 10 0.17
13 1 0.02
14 4 0.07
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:10367221 original size:7 final size:7
Alignment explanation
Indices: 10367209--10367233 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
10367199 AAAATATTTT
10367209 AAAAATA
1 AAAAATA
10367216 AAAAATA
1 AAAAATA
10367223 AAAAATA
1 AAAAATA
10367230 AAAA
1 AAAA
10367234 TATTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:10367544 original size:29 final size:30
Alignment explanation
Indices: 10367490--10367559 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
10367480 ATCTCAAAAT
*
10367490 TATACATGAACTATGGTTTAATGTATAATTG
1 TATACATGAACTATGATTT-ATGTATAATTG
* *
10367521 TATACATGAACTTTGATTT-TGTATAATTT
1 TATACATGAACTATGATTTATGTATAATTG
10367550 TATACATGAA
1 TATACATGAA
10367560 ATTTTAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 19 0.53
31 17 0.47
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (30 bp):
TATACATGAACTATGATTTATGTATAATTG
Found at i:10367570 original size:29 final size:29
Alignment explanation
Indices: 10367511--10367570 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
10367501 TATGGTTTAA
* *
10367511 TGTATAATTGTATACATGAACTTTGATTT
1 TGTATAATTGTATACATGAAATTTGAATT
* *
10367540 TGTATAATTTTATACATGAAATTTTAATT
1 TGTATAATTGTATACATGAAATTTGAATT
10367569 TG
1 TG
10367571 ATCCATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (29 bp):
TGTATAATTGTATACATGAAATTTGAATT
Found at i:10367737 original size:29 final size:29
Alignment explanation
Indices: 10367675--10367775 Score: 89
Period size: 29 Copynumber: 3.3 Consensus size: 29
10367665 AAATAAATCG
* *
10367675 ATGTATACATTTGAACCACAATTAGAGTTTCAT
1 ATGTATA-A-TTGTACCA-AATTAAAG-TTCAT
10367708 ATGTATAATTGTACCAAATTAAAGTTCAT
1 ATGTATAATTGTACCAAATTAAAGTTCAT
* * *
10367737 ATATATAATTGTACATTAAATAAAAGTT--T
1 ATGTATAATTGTAC--CAAATTAAAGTTCAT
10367766 ATGTATAATT
1 ATGTATAATT
10367776 TTGAGATTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
29 28 0.47
30 7 0.12
31 17 0.28
32 1 0.02
33 7 0.12
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.40
Consensus pattern (29 bp):
ATGTATAATTGTACCAAATTAAAGTTCAT
Found at i:10371489 original size:25 final size:25
Alignment explanation
Indices: 10371450--10371499 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
10371440 GGCAAAGCAA
* *
10371450 GGATCACTAGTGGGCCTGGCGAGTT
1 GGATCACCAGCGGGCCTGGCGAGTT
* *
10371475 GGATCACCAGCGGGCTTGGTGAGTT
1 GGATCACCAGCGGGCCTGGCGAGTT
10371500 TTTATTGCTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.40, T:0.24
Consensus pattern (25 bp):
GGATCACCAGCGGGCCTGGCGAGTT
Found at i:10406630 original size:21 final size:22
Alignment explanation
Indices: 10406601--10406644 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
10406591 AAACTTTCGT
*
10406601 ACTTTTAA-TTTTATTTTTGGG
1 ACTTATAATTTTTATTTTTGGG
10406622 ACTTATAATTTTTATTTTTGGG
1 ACTTATAATTTTTATTTTTGGG
10406644 A
1 A
10406645 TGATTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.23, C:0.05, G:0.14, T:0.59
Consensus pattern (22 bp):
ACTTATAATTTTTATTTTTGGG
Found at i:10406656 original size:22 final size:23
Alignment explanation
Indices: 10406603--10406656 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
10406593 ACTTTCGTAC
*
10406603 TTTTAATTTTATTTTTGGGACTTA
1 TTTT-ATTTTATTTTTGGGACTGA
**
10406627 TAAT-TTTTATTTTTGGGA-TGA
1 TTTTATTTTATTTTTGGGACTGA
10406648 TTTTATTTT
1 TTTTATTTT
10406657 GTTGGGAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.17
22 18 0.75
24 2 0.08
ACGTcount: A:0.20, C:0.02, G:0.13, T:0.65
Consensus pattern (23 bp):
TTTTATTTTATTTTTGGGACTGA
Found at i:10410007 original size:26 final size:26
Alignment explanation
Indices: 10409971--10410039 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
10409961 TTCTCTAAAT
*
10409971 TTTACCAGGGGTAAAATCGTCAAAAC
1 TTTACTAGGGGTAAAATCGTCAAAAC
* *
10409997 TTTATCT-GGGGTAAAATCGTCCAAAT
1 TTTA-CTAGGGGTAAAATCGTCAAAAC
*
10410023 TTTACTAGGGATAAAAT
1 TTTACTAGGGGTAAAAT
10410040 AGGGATGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.05
26 34 0.92
27 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (26 bp):
TTTACTAGGGGTAAAATCGTCAAAAC
Found at i:10417752 original size:46 final size:46
Alignment explanation
Indices: 10417641--10418127 Score: 657
Period size: 46 Copynumber: 10.7 Consensus size: 46
10417631 ATGATTGAAG
* * ** *
10417641 GATGCCATGGTGTCTTTCAACCATGGTCTTATTTA-TACTCGGCT-T
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTC-GATAT
* * *
10417686 GATGCCATAATGTCTTTCAACCATGGTCTTATTCACTTTCCGGTAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCGATAT
10417732 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCGATAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCGATAT
10417778 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCGATAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCGATAT
* *
10417824 GATGCCATAGTGT-TTTCAACCATAGTATTATTCACTTTTCGATAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCGATAT
10417869 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCGATAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCGATAT
* *
10417915 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTCCAATAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCGATAT
* *
10417961 GATGCCATAGTGTCATTCAACCATGGTCTTATTCAC-TTTCTAATAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTC-GATAT
* *
10418007 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCA-TTTTCGATAG
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCGATAT
*** * * *
10418052 GATGTTGTCGTGTCTTTCAACTATGGTCTTACTCA--TTT-GAATCAT
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCG-AT-AT
* * *
10418097 GATGCCATAGCGTCTTTCAGCTATGGTCTTA
1 GATGCCATAGTGTCTTTCAACCATGGTCTTA
10418128 CTTGTCTAAA
Statistics
Matches: 401, Mismatches: 34, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
43 1 0.00
44 5 0.01
45 139 0.35
46 256 0.64
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (46 bp):
GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCGATAT
Found at i:10417887 original size:137 final size:137
Alignment explanation
Indices: 10417641--10418127 Score: 653
Period size: 137 Copynumber: 3.6 Consensus size: 137
10417631 ATGATTGAAG
* * ** * *
10417641 GATGCCATGGTGTCTTTCAACCATGGTCTTATTTATACTCGGCT-TGATGCCATAATGTCTTTCA
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTC-GATATGATGCCATAGTGTCTTTCA
* *
10417705 ACCATGGTCTTATTCACTTTCCGGTATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTT
65 ACCATGGTCTTATTCACTTTTCGATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTT
10417770 TTCGATAT
130 TTCGATAT
10417778 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCGATATGATGCCATAGTGT-TTTCA
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCA-TTTTCGATATGATGCCATAGTGTCTTTCA
* *
10417842 ACCATAGTATTATTCACTTTTCGATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTT
65 ACCATGGTCTTATTCACTTTTCGATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTT
10417907 TTCGATAT
130 TTCGATAT
* * *
10417915 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTCCAATATGATGCCATAGTGTCATTCA
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCA-TTTTCGATATGATGCCATAGTGTCTTTCA
* *
10417980 ACCATGGTCTTATTCAC-TTTCTAATATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCA-T
65 ACCATGGTCTTATTCACTTTTC-GATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACT
*
10418043 TTTCGATAG
129 TTTCGATAT
*** * * * *
10418052 GATGTTGTCGTGTCTTTCAACTATGGTCTTACTCA-TTT-GAATCATGATGCCATAGCGTCTTTC
1 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCG-AT-ATGATGCCATAGTGTCTTTC
* *
10418115 AGCTATGGTCTTA
64 AACCATGGTCTTA
10418128 CTTGTCTAAA
Statistics
Matches: 314, Mismatches: 30, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
135 4 0.01
136 29 0.09
137 208 0.66
138 73 0.23
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (137 bp):
GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCGATATGATGCCATAGTGTCTTTCAA
CCATGGTCTTATTCACTTTTCGATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTT
TCGATAT
Found at i:10417949 original size:183 final size:183
Alignment explanation
Indices: 10417641--10418127 Score: 644
Period size: 183 Copynumber: 2.7 Consensus size: 183
10417631 ATGATTGAAG
* * * * ** * *
10417641 GATGCCATGGTGTCTTTCAACCATGGTCTTATTTATACTCGGCT-TGATGCCATAATGTCTTTCA
1 GATGCCATAGTGTCTTTCAACCATAGTATTATTCATTTTC-GATATGATGCCATAGTGTCTTTCA
* *
10417705 ACCATGGTCTTATTCACTTTCCGGTATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTT
65 ACCATGGTCTTATTCACTTTTCGATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTT
* * * *
10417770 TTCGATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTT-TCGATAT
130 TCCAATATGATGCCATAGTGTCATTCAACCATGGTCTTATTCACTTTCT-AATAT
10417824 GATGCCATAGTGT-TTTCAACCATAGTATTATTCACTTTTCGATATGATGCCATAGTGTCTTTCA
1 GATGCCATAGTGTCTTTCAACCATAGTATTATTCA-TTTTCGATATGATGCCATAGTGTCTTTCA
10417888 ACCATGGTCTTATTCACTTTTCGATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTT
65 ACCATGGTCTTATTCACTTTTCGATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTT
10417953 TCCAATATGATGCCATAGTGTCATTCAACCATGGTCTTATTCACTTTCTAATAT
130 TCCAATATGATGCCATAGTGTCATTCAACCATGGTCTTATTCACTTTCTAATAT
* * * * *** *
10418007 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCGATAGGATGTTGTCGTGTCTTTCAA
1 GATGCCATAGTGTCTTTCAACCATAGTATTATTCATTTTCGATATGATGCCATAGTGTCTTTCAA
* * * * *
10418072 CTATGGTCTTACTCA--TTT-GAATCATGATGCCATAGCGTCTTTCAGCTATGGTCTTA
66 CCATGGTCTTATTCACTTTTCG-AT-ATGATGCCATAGTGTCTTTCAACCATGGTCTTA
10418128 CTTGTCTAAA
Statistics
Matches: 271, Mismatches: 27, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
180 1 0.00
181 5 0.02
182 50 0.18
183 196 0.72
184 19 0.07
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (183 bp):
GATGCCATAGTGTCTTTCAACCATAGTATTATTCATTTTCGATATGATGCCATAGTGTCTTTCAA
CCATGGTCTTATTCACTTTTCGATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTT
CCAATATGATGCCATAGTGTCATTCAACCATGGTCTTATTCACTTTCTAATAT
Found at i:10418031 original size:24 final size:24
Alignment explanation
Indices: 10417912--10418031 Score: 63
Period size: 24 Copynumber: 5.2 Consensus size: 24
10417902 CACTTTTCGA
10417912 TATGATGCCATAGTGTCTTTCAAC
1 TATGATGCCATAGTGTCTTTCAAC
* * * * **
10417936 CATG--GTCTTATTCACTTTCCAA-
1 TATGATGCCATAGTGTCTTT-CAAC
*
10417958 TATGATGCCATAGTGTCATTCAAC
1 TATGATGCCATAGTGTCTTTCAAC
* * * * **
10417982 CATG--GTCTTATTCACTTTCTAA-
1 TATGATGCCATAGTGTCTTTC-AAC
10418004 TATGATGCCATAGTGTCTTTCAAC
1 TATGATGCCATAGTGTCTTTCAAC
10418028 TATG
1 TATG
10418032 GTCTTATTCA
Statistics
Matches: 62, Mismatches: 26, Indels: 16
0.60 0.25 0.15
Matches are distributed among these distances:
22 24 0.39
23 10 0.16
24 28 0.45
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (24 bp):
TATGATGCCATAGTGTCTTTCAAC
Found at i:10418190 original size:45 final size:45
Alignment explanation
Indices: 10417867--10418190 Score: 165
Period size: 45 Copynumber: 7.1 Consensus size: 45
10417857 ACTTTTCGAT
* * * * * * *
10417867 ATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTTTTCGAT-
1 ATGATGCCATAGCGTCTTTCAGCTATGGTCTTACTC-GTCTT-AATC
* * * * *
10417913 ATGATGCCATAGTGTCTTTCAACCATGGTCTTATTC-ACTTTCCAAT-
1 ATGATGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTC-TT--AATC
* * * * * * *
10417959 ATGATGCCATAGTGTCATTCAACCATGGTCTTATTCACTTTCTAAT-
1 ATGATGCCATAGCGTCTTTCAGCTATGGTCTTACTC-GTCT-TAATC
* * * * * *
10418005 ATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCGAT-
1 ATGATGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTCTT-AATC
* *** * * * *
10418050 AGGATGTTGTCGTGTCTTTCAACTATGGTCTTACTCAT-TTGAATC
1 ATGATGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTCTT-AATC
* * *
10418095 ATGATGCCATAGCGTCTTTCAGCTATGGTCTTACTTGTCTAAATA
1 ATGATGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTCTTAATC
* * *
10418140 ATGATGTCATAGCTTCTTTCAGCTATGGTCTTACTCGTCTTCATC
1 ATGATGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTCTTAATC
*
10418185 CTGATG
1 ATGATG
10418191 AACCTACTCA
Statistics
Matches: 234, Mismatches: 36, Indels: 17
0.82 0.13 0.06
Matches are distributed among these distances:
44 5 0.02
45 115 0.49
46 112 0.48
47 1 0.00
48 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (45 bp):
ATGATGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTCTTAATC
Found at i:10424362 original size:44 final size:44
Alignment explanation
Indices: 10424313--10424408 Score: 147
Period size: 44 Copynumber: 2.2 Consensus size: 44
10424303 ATGTATATTG
* *
10424313 GTAGTGAATCTGACAAATTCAAGTATATGATGATTGGTGTCTGA
1 GTAGTGAATATGACAAATTCAAGTATATGATGATTGGTGTATGA
* *
10424357 GTAGTGAATATGATAAATTCAAGTATGTGATGATTGGTGTATGA
1 GTAGTGAATATGACAAATTCAAGTATATGATGATTGGTGTATGA
*
10424401 GTACTGAA
1 GTAGTGAA
10424409 ACGATGAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.34
Consensus pattern (44 bp):
GTAGTGAATATGACAAATTCAAGTATATGATGATTGGTGTATGA
Found at i:10429774 original size:18 final size:18
Alignment explanation
Indices: 10429751--10429794 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
10429741 CTCTTGAACT
10429751 AATAATGTTTACATTAGG
1 AATAATGTTTACATTAGG
*
10429769 AATAATGTTTCCATTAGG
1 AATAATGTTTACATTAGG
*
10429787 AATGATGT
1 AATAATGT
10429795 AGGGAAGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (18 bp):
AATAATGTTTACATTAGG
Found at i:10431318 original size:15 final size:15
Alignment explanation
Indices: 10431288--10431326 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
10431278 AAATCCTAAT
10431288 AAATACTAAT--AAA
1 AAATACTAATAGAAA
*
10431301 AAATCCTAATAGAAA
1 AAATACTAATAGAAA
10431316 AAATACTAATA
1 AAATACTAATA
10431327 TAATTAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 9 0.41
15 13 0.59
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (15 bp):
AAATACTAATAGAAA
Found at i:10441418 original size:3 final size:3
Alignment explanation
Indices: 10441410--10441437 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10441400 CTTGAATTCA
10441410 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
10441438 CTCCTCTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:10443664 original size:19 final size:20
Alignment explanation
Indices: 10443626--10443665 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
10443616 TTTTAAAAAA
*
10443626 AAAGAAAGAACTATTTTTTT
1 AAAGAAAAAACTATTTTTTT
10443646 AAAGAAAAAACTATTTTTTT
1 AAAGAAAAAACTATTTTTTT
10443666 GGATTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (20 bp):
AAAGAAAAAACTATTTTTTT
Found at i:10444273 original size:103 final size:104
Alignment explanation
Indices: 10444120--10444421 Score: 421
Period size: 107 Copynumber: 2.9 Consensus size: 104
10444110 CAAAACAAGA
*
10444120 TAATATTTTGCGTTTTGAAAATCGAGAAAACGTGCCCTAA-AGTGCTGGGTTTCGATTTCTCGTT
1 TAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACA-TGCTGGGTTTCGATTTCTCGTT
*
10444184 TGACCAAATAAGCCAAATATCCTTTTAAAATTTC-A-AAGG
65 CGACCAAAT-AGCCAAATATCCTTTTAAAATTTCAAGAAGG
* * * *
10444223 TAATATTTTGCGTTTGGAAAATCGAGAGAATGTGCCCTAACATGCTGGGTTTCGATTTCTCATAC
1 TAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACATGCTGGGTTTCGATTTCTCGTTC
* * *
10444288 GACCAAATAGCCGAATATCATTTTTAAACTTTCAAAGTAAGG
66 GACCAAATAGCCAAATATC-CTTTTAAAATTTC-AAG-AAGG
* * * *
10444330 CAATATTTTACGTTTGGAAAATCGAGAAAACATGCCCTAACGTGCTGGGTTTCGATTTCTCGTTC
1 TAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACATGCTGGGTTTCGATTTCTCGTTC
10444395 GACCAAATAGCCAAATATCCTTTTAAA
66 GACCAAATAGCCAAATATCCTTTTAAA
10444422 TCTAAATCCA
Statistics
Matches: 174, Mismatches: 19, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
102 10 0.06
103 76 0.44
104 1 0.01
105 1 0.01
106 7 0.04
107 79 0.45
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (104 bp):
TAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACATGCTGGGTTTCGATTTCTCGTTC
GACCAAATAGCCAAATATCCTTTTAAAATTTCAAGAAGG
Found at i:10456097 original size:40 final size:41
Alignment explanation
Indices: 10456051--10456290 Score: 265
Period size: 40 Copynumber: 5.8 Consensus size: 41
10456041 AAGATAGTAT
10456051 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
* * * * *
10456092 -TCTTATCTCCCTAAGCAGCAGTGGAGCAGATGAAAGAAACCAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT--CA-CATCAAG
*
10456135 ATCCTATCTCCCTAAGCAGTAGTGGAGC-GAATCACATCAAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAG-ATCACATCAAG
* * * *
10456176 -TCTTATCTCCCTAAGCAGTAGTGGAGCAAACGA-AAGAAACTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGC--A-GATCA-CATCAAG
* *
10456219 ATCTTATCTACCTAAGCAGTAGTGGAGCAAATCACATC-AG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
10456259 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
10456291 GAAAAAAAAA
Statistics
Matches: 164, Mismatches: 23, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
40 88 0.54
41 7 0.04
42 5 0.03
43 10 0.06
44 54 0.33
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (41 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG
Found at i:10456158 original size:84 final size:84
Alignment explanation
Indices: 10456055--10456294 Score: 385
Period size: 84 Copynumber: 2.9 Consensus size: 84
10456045 TAGTATATCT
*
10456055 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGCAGTGGAGCA
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
10456120 GATGAAAGAAACCAGATCC
66 GATGAAAGAAACCAGATCC
10456139 TATCTCCCTAAGCAGTAGTGGAGC-GAATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGC
1 TATCTCCCTAAGCAGTAGTGGAGCAG-ATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGC
* * * *
10456203 AAACGAAAGAAACTAGATCT
65 AGATGAAAGAAACCAGATCC
* *
10456223 TATCTACCTAAGCAGTAGTGGAGCAAATCACATC-AGATCTTATCTCCCTAAGCAGTAGTGGAGC
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAG-TCTTATCTCCCTAAGCAGTAGTGGAGC
10456287 AGATGAAA
65 AGATGAAA
10456295 AAAAAACAAT
Statistics
Matches: 144, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
83 3 0.02
84 141 0.98
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (84 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
GATGAAAGAAACCAGATCC
Found at i:10458516 original size:107 final size:107
Alignment explanation
Indices: 10458318--10458618 Score: 487
Period size: 107 Copynumber: 2.8 Consensus size: 107
10458308 TCAAAACAAA
* *
10458318 GCAATATTTTGCGTTTAGAAAATCGAGAAAATGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTT
1 GCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTT
* *
10458383 TGACCAAATAAGCCAAATATCC-TTTTAAAATTTGAAAGTAAG
66 CGACCAAAT-AGCCAAATATCCTTTTTAAAATTTCAAAGTAAG
* * * * *
10458425 GTAATATTTTGCGTTTGGAAAATCAAGAGAACGTGCCCTAACGTGCTGGGTTTCAATTTCTCGTA
1 GCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTT
*
10458490 CGACCAAATAGCCAAATATCCTTTTTAAACTTTCAAAGTAAG
66 CGACCAAATAGCCAAATATCCTTTTTAAAATTTCAAAGTAAG
*
10458532 GCAATATTTTGCGTTTGGAAAATCGAGAAAACATGCCCTAACGTGCTGGGTTTCGATTTCTCGTT
1 GCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTT
10458597 CGACCAAATAGCCAAATATCCT
66 CGACCAAATAGCCAAATATCCT
10458619 CTTAAATCTA
Statistics
Matches: 177, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
106 12 0.07
107 165 0.93
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (107 bp):
GCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTT
CGACCAAATAGCCAAATATCCTTTTTAAAATTTCAAAGTAAG
Found at i:10459083 original size:81 final size:81
Alignment explanation
Indices: 10458948--10459110 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
10458938 CGACCCCGTT
10458948 TTCATCAAAAAATGGTGTCAACACCACCAACTTAAGCCATTTGCAATTCCTTTTTCAAATTCCCT
1 TTCATCAAAAAATGGTGTCAACACCACCAACTTAAGCCATTTGCAATTCCTTTTTCAAATTCCCT
10459013 TTTCATTTCCAGTAGC
66 TTTCATTTCCAGTAGC
10459029 TTCATCAAAAAATGGTGTCAACACCACCAACTTAAGCCATTTGCAATTCCTTTTTCAAATTCCCT
1 TTCATCAAAAAATGGTGTCAACACCACCAACTTAAGCCATTTGCAATTCCTTTTTCAAATTCCCT
10459094 TTTCATTTCCAGTAGC
66 TTTCATTTCCAGTAGC
10459110 T
1 T
10459111 AACCATCCGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.35
Consensus pattern (81 bp):
TTCATCAAAAAATGGTGTCAACACCACCAACTTAAGCCATTTGCAATTCCTTTTTCAAATTCCCT
TTTCATTTCCAGTAGC
Found at i:10465325 original size:49 final size:49
Alignment explanation
Indices: 10465210--10465331 Score: 140
Period size: 49 Copynumber: 2.5 Consensus size: 49
10465200 ACTCAGTATA
* * *
10465210 CAGATACGATGGACCACTAGTAGGGCATGTTTGTTGCTAACTAAAATGG
1 CAGATAAGATGGACCACTAGTAGGGCATGCTAGTTGCTAACTAAAATGG
** *
10465259 CAGATGTGATGGACCACTAGTAGGGCATGCTAGTTGCTAAC-CAAATGG
1 CAGATAAGATGGACCACTAGTAGGGCATGCTAGTTGCTAACTAAAATGG
* *
10465307 GAGAATAAGAT-GAGCCACTAATAGG
1 CAG-ATAAGATGGA-CCACTAGTAGG
10465332 TCATTTTAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 10 0.16
49 52 0.84
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (49 bp):
CAGATAAGATGGACCACTAGTAGGGCATGCTAGTTGCTAACTAAAATGG
Found at i:10471643 original size:42 final size:42
Alignment explanation
Indices: 10471584--10471663 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
10471574 GTATCAACTG
10471584 TTGGAACAACTTCTGTAGCCATGGCCCCCCCAAAAAAAATTT
1 TTGGAACAACTTCTGTAGCCATGGCCCCCCCAAAAAAAATTT
* *
10471626 TTGGAACAACTTCTGTAGTCATGGCCCCCCCCAAAAAA
1 TTGGAACAACTTCTGTAGCCATGGCCCCCCCAAAAAAA
10471664 TTTACACCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (42 bp):
TTGGAACAACTTCTGTAGCCATGGCCCCCCCAAAAAAAATTT
Found at i:10473240 original size:21 final size:21
Alignment explanation
Indices: 10473215--10473255 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10473205 GTGAAATGAC
*
10473215 AACAAAACAGTGGAAAACAAT
1 AACAAAACAGTGAAAAACAAT
*
10473236 AACAAAATAGTGAAAAACAA
1 AACAAAACAGTGAAAAACAA
10473256 CAAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.66, C:0.12, G:0.12, T:0.10
Consensus pattern (21 bp):
AACAAAACAGTGAAAAACAAT
Found at i:10482888 original size:19 final size:19
Alignment explanation
Indices: 10482864--10482908 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
10482854 TTTTTCATTC
10482864 TCTTTTTTCGAATTTTC-TT
1 TCTTTTTTC-AATTTTCTTT
*
10482883 TCTTTTTTTCATTTTTCTTT
1 TC-TTTTTTCAATTTTCTTT
10482903 TCTTTT
1 TCTTTT
10482909 GTATTTTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.76
Consensus pattern (19 bp):
TCTTTTTTCAATTTTCTTT
Found at i:10482891 original size:20 final size:19
Alignment explanation
Indices: 10482855--10482908 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
10482845 TCTCACTTTT
*
10482855 TTTTCATTCTCTTTTTTCGAA
1 TTTTCTTTCT-TTTTTTC-AA
*
10482876 TTTTCTTTCTTTTTTTCAT
1 TTTTCTTTCTTTTTTTCAA
10482895 TTTTCTTTTCTTTT
1 TTTTC-TTTCTTTT
10482909 GTATTTTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 6 0.20
20 15 0.50
21 9 0.30
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTCTTTCTTTTTTTCAA
Found at i:10485658 original size:41 final size:42
Alignment explanation
Indices: 10485595--10485677 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 42
10485585 AGTCTTACGG
10485595 GTCTCGTACGAAATTTGAGAGAAAATGCCTCACAAATTTGGT
1 GTCTCGTACGAAATTTGAGAGAAAATGCCTCACAAATTTGGT
10485637 GTCTCGTACG-AATTTGAGAGAAAATGCCTCACAAATTTGGT
1 GTCTCGTACGAAATTTGAGAGAAAATGCCTCACAAATTTGGT
10485678 AGCAATTCGA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 31 0.76
42 10 0.24
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (42 bp):
GTCTCGTACGAAATTTGAGAGAAAATGCCTCACAAATTTGGT
Found at i:10488703 original size:18 final size:18
Alignment explanation
Indices: 10488627--10488705 Score: 67
Period size: 18 Copynumber: 4.5 Consensus size: 18
10488617 ATAAAAAATT
10488627 TAAAATAT-AATATTATA
1 TAAAATATAAATATTATA
*
10488644 TATAAA-ATAAATTTTA-A
1 TA-AAATATAAATATTATA
* * *
10488661 GTAAAAAATAATTA-CATA
1 -TAAAATATAAATATTATA
*
10488679 CAAAATATAAATATTATA
1 TAAAATATAAATATTATA
10488697 TAAAATATA
1 TAAAATATA
10488706 TTATAAGAGT
Statistics
Matches: 47, Mismatches: 9, Indels: 11
0.70 0.13 0.16
Matches are distributed among these distances:
17 19 0.40
18 28 0.60
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (18 bp):
TAAAATATAAATATTATA
Found at i:10490575 original size:59 final size:60
Alignment explanation
Indices: 10490455--10490585 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 60
10490445 TTATTGGTAT
* * * *
10490455 AATAATAAATTTAACCCTCAAATGTTTACAAATTTTCTCAATTTAGTTCTAATTCTAAAA
1 AATAATAAATTTAACCCTCAAATCTTTACAAATTCTATCAATTTAGTTCTAATCCTAAAA
* * * *
10490515 AATTAATAAATTTAGCCCTC-AA-CTTTACACATTCTATCAATTTAG-TCTTGATCCTTAAA
1 AA-TAATAAATTTAACCCTCAAATCTTTACAAATTCTATCAATTTAGTTC-TAATCCTAAAA
*
10490574 AATAAAAAATTT
1 AATAATAAATTT
10490586 TAAAAAATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
58 11 0.18
59 29 0.48
60 4 0.07
61 16 0.27
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.39
Consensus pattern (60 bp):
AATAATAAATTTAACCCTCAAATCTTTACAAATTCTATCAATTTAGTTCTAATCCTAAAA
Found at i:10490670 original size:19 final size:19
Alignment explanation
Indices: 10490615--10490661 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
10490605 TCATTTTTCA
* * *
10490615 ATAAAATTACATAAGATTT
1 ATAAAAATACATAAAAATT
10490634 ATAAAAATACATAAAAATT
1 ATAAAAATACATAAAAATT
10490653 ATAAAAATA
1 ATAAAAATA
10490662 TTTATAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAAAAATACATAAAAATT
Found at i:10497036 original size:39 final size:39
Alignment explanation
Indices: 10496982--10497080 Score: 144
Period size: 39 Copynumber: 2.5 Consensus size: 39
10496972 ATGTTTTTGA
*
10496982 GTATTGTGATATATGCTTGAATGTTATGTGATTATATGG
1 GTATTGTGATATATGCTTAAATGTTATGTGATTATATGG
* *
10497021 GTATTGTGATATATGCTTAAATGTTATGTGATTGTATGT
1 GTATTGTGATATATGCTTAAATGTTATGTGATTATATGG
* **
10497060 GTAATGTGATGCATGCTTAAA
1 GTATTGTGATATATGCTTAAA
10497081 AGTGAATATG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.27, C:0.04, G:0.24, T:0.44
Consensus pattern (39 bp):
GTATTGTGATATATGCTTAAATGTTATGTGATTATATGG
Found at i:10500020 original size:42 final size:42
Alignment explanation
Indices: 10499961--10500089 Score: 190
Period size: 42 Copynumber: 3.1 Consensus size: 42
10499951 TTTATGTGAA
*
10499961 AAACGCCGCTATAGAACATGACCTTTAGCGGTGCTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTCCCAC
**
10500003 AAACGCCGCTATAGAACATGACCTTTAATGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGC-TTTCCCAC
*
10500046 AAAAC-CCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCC-C
1 -AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTCCCAC
10500087 AAA
1 AAA
10500090 AATGTCGCTA
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
40 3 0.04
41 1 0.01
42 37 0.47
43 34 0.43
44 4 0.05
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.22
Consensus pattern (42 bp):
AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTCCCAC
Found at i:10500056 original size:43 final size:44
Alignment explanation
Indices: 10499960--10500109 Score: 191
Period size: 43 Copynumber: 3.5 Consensus size: 44
10499950 GTTTATGTGA
*
10499960 AAAACGCCGCTATAGAACATGACCTTTAGCGGTGC-TTTCCCAC
1 AAAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
**
10500003 -AAACGCCGCTATAGAACATGACCTTTAATGGCGCTTTTCCCAC
1 AAAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* *
10500046 AAAAC-CCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCA-
1 AAAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
10500088 AAAATGTCGCTAAAGAATATGA
1 AAAACGCCGCTATAGAACATGA
10500110 TTTTTAGTGG
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
42 35 0.37
43 55 0.59
44 4 0.04
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (44 bp):
AAAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:10500511 original size:21 final size:21
Alignment explanation
Indices: 10500468--10500513 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
10500458 TTTCTGCTTA
* * **
10500468 CCTCTGCTTCTCTCGCTGTTG
1 CCTCTACTTCCCTCGCTACTG
10500489 CCTCTACTTCCCTCGCTACTG
1 CCTCTACTTCCCTCGCTACTG
10500510 CCTC
1 CCTC
10500514 CGCTTTAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.04, C:0.46, G:0.13, T:0.37
Consensus pattern (21 bp):
CCTCTACTTCCCTCGCTACTG
Found at i:10501485 original size:467 final size:466
Alignment explanation
Indices: 10500582--10501496 Score: 1456
Period size: 467 Copynumber: 2.0 Consensus size: 466
10500572 GCTGCCTCCG
* * * *
10500582 CTTTAAGTTAAGCAATTTGCTCAATTGTGCTCGCTTGCATCTGAGTCATCTAGTCTTTTAACCTC
1 CTTTAAGTTAAGCAATTTCCTCAACTGTGCTCGCTTGCATCTGAGCCATCTAGTCTCTTAACCTC
* * * * *
10500647 CGAACTTCAGCTTGAGCCTGACTCCCCAAAGGCGTGTACTGCTGTGAGCTGGATCCAAAATATTG
66 CGAACTTCAGCTTGAGCCTAACTCCCCAAAGGCATGTAATGCTGCGAGCTAGATCCAAAATATTG
*
10500712 TATTGGGTTAACAAAAGATCCTTGAAATCAAACCAGACCATACCTTTCAGAACCCAAAACTTCAA
131 GATTGGGTTAACAAAAGATCCTTGAAATCAAACCAGACCATACCTTTCAGAACCCAAAACTTCAA
* *
10500777 TAATAATTTGATTATCAATTTCGTCAAGATTAACAGAACTATCACTCGAAGCGATCGCTTCATAC
196 TAATAATTAGATTATCAATTTCATCAAGATTAACAGAACTATCACTCGAAGCGATCGCTTCATAC
10500842 TCCGCCCTTTTATCCTTTAGTTTCTCCTAATAAATCAACCAAAGAGTTAGAAACGAAATATATAA
261 TCCGCCCTTTTATCCTTTAGTTTCTCCTAATAAATCAACCAAAGAGTTAGAAACGAAATATATAA
* ** *
10500907 TCAAAACAAATGCTACATAACTTGGCATTATTTTCATTAAAAACGACGAATTAAACCATTATAAT
326 TCAAAACAAATGCAACATAACTTAACATTATTTGCATTAAAAACGACGAATTAAACCATTATAAT
* *
10500972 TAAACATAATAAATATTTAAAATAATTCAAATTTTATTAAGTAAATATACCATAATTTCTCTTGA
391 TAAAAATAATAAATATTTAAAATAATTCAAAATTTATTAAGTAAATATACCATAATTTCTCTTGA
10501037 TATTGCCTCTT
456 TATTGCCTCTT
* * *
10501048 CTTTAAGTTGAGCAAATTTCCTCAACTGTGTTCGCTTGCATCTGAGCCATCTGGTCTCTTAACCT
1 CTTTAAGTTAAGC-AATTTCCTCAACTGTGCTCGCTTGCATCTGAGCCATCTAGTCTCTTAACCT
* *
10501113 CTGAACTTCAGCTTGAGCCTAACTCCCCGAAGGCATGTAATGCTGCGAGCTAGATCCAAAATATT
65 CCGAACTTCAGCTTGAGCCTAACTCCCCAAAGGCATGTAATGCTGCGAGCTAGATCCAAAATATT
* ** * *
10501178 GGGTTGGGTTAACAAAAGATCCTTGAAATTGAACCCGACCATACCTTTCAGGACCCAAAACTTCA
130 GGATTGGGTTAACAAAAGATCCTTGAAATCAAACCAGACCATACCTTTCAGAACCCAAAACTTCA
* *
10501243 GTAATAATTCAG-TTATCAATGTT-ATCAAGATTAACAGAACTATCACTCGAAGCGATTGCTTCA
195 ATAATAATT-AGATTATCAAT-TTCATCAAGATTAACAGAACTATCACTCGAAGCGATCGCTTCA
*
10501306 TACTCTGCCCTTTTATCCTTTAGTTTCTCCTAATAAATCAACCAAAGAGTTAGAAACGAAATATA
258 TACTCCGCCCTTTTATCCTTTAGTTTCTCCTAATAAATCAACCAAAGAGTTAGAAACGAAATATA
* ** *
10501371 TAATCAAAACAAATGCAACATAACTTAACATTATTTGCATTACAAACGATTAGTTAAACCATTAT
323 TAATCAAAACAAATGCAACATAACTTAACATTATTTGCATTAAAAACGACGAATTAAACCATTAT
* *
10501436 AATTAAAAATTATAAATATTTAAAATAGTTCAAAATTTATTAAGTAAATATACCATAATTT
388 AATTAAAAATAATAAATATTTAAAATAATTCAAAATTTATTAAGTAAATATACCATAATTT
10501497 TTACAGCTTT
Statistics
Matches: 409, Mismatches: 37, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
466 12 0.03
467 394 0.96
468 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (466 bp):
CTTTAAGTTAAGCAATTTCCTCAACTGTGCTCGCTTGCATCTGAGCCATCTAGTCTCTTAACCTC
CGAACTTCAGCTTGAGCCTAACTCCCCAAAGGCATGTAATGCTGCGAGCTAGATCCAAAATATTG
GATTGGGTTAACAAAAGATCCTTGAAATCAAACCAGACCATACCTTTCAGAACCCAAAACTTCAA
TAATAATTAGATTATCAATTTCATCAAGATTAACAGAACTATCACTCGAAGCGATCGCTTCATAC
TCCGCCCTTTTATCCTTTAGTTTCTCCTAATAAATCAACCAAAGAGTTAGAAACGAAATATATAA
TCAAAACAAATGCAACATAACTTAACATTATTTGCATTAAAAACGACGAATTAAACCATTATAAT
TAAAAATAATAAATATTTAAAATAATTCAAAATTTATTAAGTAAATATACCATAATTTCTCTTGA
TATTGCCTCTT
Found at i:10509287 original size:6 final size:6
Alignment explanation
Indices: 10509276--10509303 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
10509266 TTTATGGAAG
10509276 AAAACA AAAACA AAAACA AAAACA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAA
10509304 ATTTCAAAAT
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:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:10510552 original size:35 final size:33
Alignment explanation
Indices: 10510513--10510679 Score: 93
Period size: 35 Copynumber: 4.8 Consensus size: 33
10510503 CCTATCTTAA
10510513 AAACCCAAGACCCTAAACCTTAAACACCAACCCTT
1 AAACCCAA-ACCCTAAACCTTAAAC-CCAACCCTT
** * * *
10510548 AAACCCTAAACAATAACCCCTAAACCCCATCCCTT
1 AAACCC-AAACCCTAAACCTTAAA-CCCAACCCTT
* * * *
10510583 AACCCCTACCACCTAAACCTTAAACCCTAACCCCT
1 AAACCCAAAC-CCTAAACCTTAAACCC-AACCCTT
** *
10510618 AAACCCTAAACTATAAACCTTTAACCCCTAACACC-T
1 AAACCC-AAACCCTAAACC-TTAAACCC-AAC-CCTT
* * *
10510654 AAACCTTAAACCCCAACCCTTAAACC
1 AAACC-CAAACCCTAAACCTTAAACC
10510680 GTAAACCACA
Statistics
Matches: 98, Mismatches: 26, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
34 5 0.05
35 61 0.62
36 30 0.31
37 2 0.02
ACGTcount: A:0.40, C:0.42, G:0.01, T:0.17
Consensus pattern (33 bp):
AAACCCAAACCCTAAACCTTAAACCCAACCCTT
Found at i:10510554 original size:8 final size:7
Alignment explanation
Indices: 10510513--10510811 Score: 82
Period size: 7 Copynumber: 42.7 Consensus size: 7
10510503 CCTATCTTAA
10510513 AAACCC-
1 AAACCCT
10510519 AAGACCCT
1 AA-ACCCT
*
10510527 AAACCTT
1 AAACCCT
10510534 AAACACC-
1 AAAC-CCT
10510541 -AACCCTT
1 AAACCC-T
10510548 AAACCCT
1 AAACCCT
**
10510555 AAACAAT
1 AAACCCT
*
10510562 AACCCCT
1 AAACCCT
10510569 AAACCC-
1 AAACCCT
* *
10510575 CATCCCTT
1 AAACCC-T
*
10510583 AACCCCT
1 AAACCCT
*
10510590 -ACCACCT
1 AAAC-CCT
*
10510597 AAACCTT
1 AAACCCT
10510604 AAACCCT
1 AAACCCT
*
10510611 AACCCCT
1 AAACCCT
10510618 AAACCCT
1 AAACCCT
**
10510625 AAACTAT
1 AAACCCT
*
10510632 AAACCTTT
1 AAACC-CT
*
10510640 AACCCCT
1 AAACCCT
10510647 -AACACCT
1 AAAC-CCT
*
10510654 AAACCTT
1 AAACCCT
10510661 AAACCC-
1 AAACCCT
*
10510667 CAACCCTT
1 AAACCC-T
*
10510675 AAACCGT
1 AAACCCT
10510682 AAACCAC-
1 AAACC-CT
*
10510689 AAACCAT
1 AAACCCT
*
10510696 AATCCCT
1 AAACCCT
*
10510703 --CCCCT
1 AAACCCT
*
10510708 AAACCTT
1 AAACCCT
* * *
10510715 GAATCAT
1 AAACCCT
* *
10510722 AAAACAT
1 AAACCCT
**
10510729 AAACTAT
1 AAACCCT
**
10510736 AAACTAT
1 AAACCCT
10510743 AAACCCT
1 AAACCCT
10510750 AAACCCCT
1 AAA-CCCT
10510758 -AACCCT
1 AAACCCT
* *
10510764 TAACCTT
1 AAACCCT
*
10510771 CAACACCT
1 AAAC-CCT
*
10510779 AAACCTT
1 AAACCCT
10510786 AAACCC-
1 AAACCCT
*
10510792 CAACCCTT
1 AAACCC-T
*
10510800 AAACCGT
1 AAACCCT
10510807 AAACC
1 AAACC
10510812 ACAAACCATA
Statistics
Matches: 215, Mismatches: 54, Indels: 47
0.68 0.17 0.15
Matches are distributed among these distances:
5 6 0.03
6 28 0.13
7 142 0.66
8 39 0.18
ACGTcount: A:0.41, C:0.39, G:0.01, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:10510646 original size:22 final size:22
Alignment explanation
Indices: 10510617--10510686 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
10510607 CCCTAACCCC
10510617 TAAA-CCCTAA-ACTATAAACCT
1 TAAACCCCTAACAC-ATAAACCT
* *
10510638 TTAACCCCTAACACCTAAACCT
1 TAAACCCCTAACACATAAACCT
* * *
10510660 TAAACCCC-AACCCTTAAACCG
1 TAAACCCCTAACACATAAACCT
10510681 TAAACC
1 TAAACC
10510687 ACAAACCATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 19 0.46
22 20 0.49
23 2 0.05
ACGTcount: A:0.41, C:0.37, G:0.01, T:0.20
Consensus pattern (22 bp):
TAAACCCCTAACACATAAACCT
Found at i:10511349 original size:41 final size:41
Alignment explanation
Indices: 10511273--10511350 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
10511263 TTTGGACAAA
* * * *
10511273 AAATGCCGCTATTGCTTGACCTTTTGCGCCTTTTTTCTCAT
1 AAATGCCGCTACTGCTTGACCTATTACGCCGTTTTTCTCAT
* *
10511314 AAATGCCGCTACTGCTTTACCTATTACGGCGTTTTTC
1 AAATGCCGCTACTGCTTGACCTATTACGCCGTTTTTC
10511351 CGTTAGCGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.17, C:0.27, G:0.15, T:0.41
Consensus pattern (41 bp):
AAATGCCGCTACTGCTTGACCTATTACGCCGTTTTTCTCAT
Found at i:10511755 original size:2 final size:2
Alignment explanation
Indices: 10511748--10511780 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10511738 AAATATCTAT
10511748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10511781 TATGTTGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10520269 original size:59 final size:57
Alignment explanation
Indices: 10520206--10520332 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 57
10520196 ATAAATGGTG
* * *
10520206 AAATGGAGAAATAGGAAACATTCAGGAAATGATTATGGTATTCTCCAAAATGAAAATGA
1 AAATGGAGAAATAGGAAACATT-AGAAAATAAATATGGTATTCT-CAAAATGAAAATGA
* * * * * *
10520265 AAATGGAGAAAAAGGAATCATTTGAAAATAAATGTGGTTTTCTCAAAATGGAAATGA
1 AAATGGAGAAATAGGAAACATTAGAAAATAAATATGGTATTCTCAAAATGAAAATGA
10520322 AAAT-GAGAAAT
1 AAATGGAGAAAT
10520333 GAATTCATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
56 6 0.10
57 17 0.29
58 15 0.26
59 20 0.34
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.24
Consensus pattern (57 bp):
AAATGGAGAAATAGGAAACATTAGAAAATAAATATGGTATTCTCAAAATGAAAATGA
Found at i:10524396 original size:20 final size:21
Alignment explanation
Indices: 10524360--10524410 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
10524350 ACTTATGTCT
*
10524360 GAAAACTTAATTTGAAAATTTG
1 GAAAACTT-ATTTGAAAATTTC
*
10524382 GAAAACTTA-TTGAAACTTTC
1 GAAAACTTATTTGAAAATTTC
10524402 GAAAACTTA
1 GAAAACTTA
10524411 GTATTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 18 0.67
21 1 0.04
22 8 0.30
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (21 bp):
GAAAACTTATTTGAAAATTTC
Found at i:10524673 original size:34 final size:34
Alignment explanation
Indices: 10524635--10524876 Score: 337
Period size: 34 Copynumber: 7.2 Consensus size: 34
10524625 TCACTTGTCT
* * *
10524635 TTTCTTGCAGGGAATATTTCCTGTTCACGCATCA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
* * *
10524669 TTTCTTGCAGGGAATATTTCCTGTTCACGCATCA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
* * *
10524703 ATTCTTGCAGGGAATCTTTCCTGTTCGCACATCA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
* * *
10524737 TTTCTTGCAAGGAATATCTCCTGTTCGCACATCA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
10524771 -TTCTTGCAGGGAATCTCTCCTGTTCACACATCA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
10524804 -TTCTTGCAGGGAATCTCTCCTGTTCACACATCA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
* *
10524837 -TTCTTGCATGGAATCTCTCCTATTCACACATCA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
10524870 TTTCTTG
1 TTTCTTG
10524877 TATCATTTCT
Statistics
Matches: 194, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
33 94 0.48
34 100 0.52
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (34 bp):
TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
Found at i:10524840 original size:66 final size:67
Alignment explanation
Indices: 10524636--10524876 Score: 358
Period size: 66 Copynumber: 3.6 Consensus size: 67
10524626 CACTTGTCTT
* * * * *
10524636 TTCTTGCAGGGAATATTTCCTGTTCACGCATCATTTCTTGCAGGGAATATTTCCTGTTCACGCAT
1 TTCTTGCAGGGAATCTCTCCTGTTCACACATCATTTCTTGCAGGGAATATCTCCTGTTCACACAT
10524701 CAA
66 C-A
* * * *
10524704 TTCTTGCAGGGAATCTTTCCTGTTCGCACATCATTTCTTGCAAGGAATATCTCCTGTTCGCACAT
1 TTCTTGCAGGGAATCTCTCCTGTTCACACATCATTTCTTGCAGGGAATATCTCCTGTTCACACAT
10524769 CA
66 CA
*
10524771 TTCTTGCAGGGAATCTCTCCTGTTCACACATCA-TTCTTGCAGGGAATCTCTCCTGTTCACACAT
1 TTCTTGCAGGGAATCTCTCCTGTTCACACATCATTTCTTGCAGGGAATATCTCCTGTTCACACAT
10524835 CA
66 CA
* *
10524837 TTCTTGCATGGAATCTCTCCTATTCACACATCATTTCTTG
1 TTCTTGCAGGGAATCTCTCCTGTTCACACATCATTTCTTG
10524877 TATCATTTCT
Statistics
Matches: 158, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
66 61 0.39
67 38 0.24
68 59 0.37
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (67 bp):
TTCTTGCAGGGAATCTCTCCTGTTCACACATCATTTCTTGCAGGGAATATCTCCTGTTCACACAT
CA
Found at i:10527756 original size:21 final size:23
Alignment explanation
Indices: 10527732--10527774 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
10527722 TTAATTTTTT
*
10527732 AAAACATATTT-CTTCT-TTTAG
1 AAAACAGATTTGCTTCTGTTTAG
*
10527753 AAAAGAGATTTGCTTCTGTTTA
1 AAAACAGATTTGCTTCTGTTTA
10527775 TAATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (23 bp):
AAAACAGATTTGCTTCTGTTTAG
Found at i:10535482 original size:90 final size:90
Alignment explanation
Indices: 10535321--10535487 Score: 255
Period size: 90 Copynumber: 1.9 Consensus size: 90
10535311 TTAAAATGTC
* * * *
10535321 AATCCTTCCTTTGTTGTAGGCATGAGAGTTTGGATTCAATCCCAAACAACCCCATTTCCCTCCTT
1 AATCCTTCCTTTGTTGTAGACATGAGAGCTTGGATTCAATACCAAACAACCCCATTCCCCTCCTT
**
10535386 TGATTATCAAAAAGAAAAAAATATT
66 CAATTATCAAAAAGAAAAAAATATT
*
10535411 AATCCTTCCTTTGTTGTCGACATGAGAGCTTGGATTCAATACCAAACAACCCCATTCCCCT-CTT
1 AATCCTTCCTTTGTTGTAGACATGAGAGCTTGGATTCAATACCAAACAACCCCATTCCCCTCCTT
10535475 CCAATTATCAAAA
66 -CAATTATCAAAA
10535488 CAAAAATGTC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
89 3 0.04
90 66 0.96
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (90 bp):
AATCCTTCCTTTGTTGTAGACATGAGAGCTTGGATTCAATACCAAACAACCCCATTCCCCTCCTT
CAATTATCAAAAAGAAAAAAATATT
Found at i:10549304 original size:45 final size:45
Alignment explanation
Indices: 10549239--10549324 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
10549229 CTCGGTAGAT
*
10549239 TCAGCACATAGCAACCACCTTATTAATCAATGATGTCCGGTGGAA
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTGGAA
* *
10549284 TCAGCACATAGCAACTACCTTACTAATCAATGATGTTCGGT
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGT
10549325 TCACATAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (45 bp):
TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTGGAA
Found at i:10549405 original size:12 final size:12
Alignment explanation
Indices: 10549388--10549419 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
10549378 ACGTAGTAGC
10549388 CTGCACATAGTA
1 CTGCACATAGTA
10549400 CTGCACATAGTA
1 CTGCACATAGTA
*
10549412 CTACACAT
1 CTGCACAT
10549420 GTGACGATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.25
Consensus pattern (12 bp):
CTGCACATAGTA
Found at i:10549412 original size:63 final size:63
Alignment explanation
Indices: 10549326--10549464 Score: 226
Period size: 63 Copynumber: 2.2 Consensus size: 63
10549316 ATGTTCGGTT
10549326 CACATAGTAGCATGCACACAGTACTACACATGTGACGATTGCCATCCGATACACGT-AGTAGCCT
1 CACATAGTA-C-TGCACACAGTACTACACATGTGACGATTGCCATCCGATACACGTGA-TAGCCT
10549390 G
63 G
* *
10549391 CACATAGTACTGCACATAGTACTACACATGTGACGATTGCCATCTGATACACGTGATAGCCTG
1 CACATAGTACTGCACACAGTACTACACATGTGACGATTGCCATCCGATACACGTGATAGCCTG
10549454 CACATAGTACT
1 CACATAGTACT
10549465 ATACACGTGA
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
63 60 0.85
64 2 0.03
65 9 0.13
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (63 bp):
CACATAGTACTGCACACAGTACTACACATGTGACGATTGCCATCCGATACACGTGATAGCCTG
Found at i:10549487 original size:51 final size:48
Alignment explanation
Indices: 10549400--10549576 Score: 149
Period size: 51 Copynumber: 3.5 Consensus size: 48
10549390 GCACATAGTA
* ***
10549400 CTGCACATAGTACTACACATGTGACGATTGCCATCTGATACACGT-GATAGC
1 CTGCACATAGTACTACACACGTGAC-A-AAACATCTG-TACACGTAG-TAGC
* ** *
10549451 CTGCACATAGTACTATACACGTGATCAAAACTATCTGGTATGCATAGTAGC
1 CTGCACATAGTACTACACACGTGA-CAAAAC-ATCT-GTACACGTAGTAGC
* * ** *
10549502 CTGCACATAGTACTACACATGCGACCTATCATTCCTGTACACGTAGTAGC
1 CTGCACATAGTACTACACACGTGACAAAACA-T-CTGTACACGTAGTAGC
10549552 CTGCACATAGTACTACACACGTGAC
1 CTGCACATAGTACTACACACGTGAC
10549577 CATCACCTTC
Statistics
Matches: 101, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
49 1 0.01
50 39 0.39
51 58 0.57
52 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (48 bp):
CTGCACATAGTACTACACACGTGACAAAACATCTGTACACGTAGTAGC
Found at i:10549599 original size:101 final size:101
Alignment explanation
Indices: 10549392--10549578 Score: 224
Period size: 101 Copynumber: 1.9 Consensus size: 101
10549382 AGTAGCCTGC
*
10549392 ACATAGTA--CTGCACATAGTACTACACATGTGACGATTGCCATCTGATACACGTGATAGCCTGC
1 ACATAGTAGCCTGCACATAGTACTACACATGCGACGATT-CCATCTGATACACGTGATAGCCTGC
* * **
10549455 ACATAGTACTATACACGTGATCAAAACTATCTGGTAT
65 ACATAGTACTACACACGTGACCAAAACTATCACGTAT
* *
10549492 GCATAGTAGCCTGCACATAGTACTACACATGCGAC-CTAT-CATTCCTG-TACACGT-AGTAGCC
1 ACATAGTAGCCTGCACATAGTACTACACATGCGACGAT-TCCA-T-CTGATACACGTGA-TAGCC
10549553 TGCACATAGTACTACACACGTGACCA
62 TGCACATAGTACTACACACGTGACCA
10549579 TCACCTTCAC
Statistics
Matches: 76, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
100 10 0.13
101 38 0.50
102 28 0.37
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (101 bp):
ACATAGTAGCCTGCACATAGTACTACACATGCGACGATTCCATCTGATACACGTGATAGCCTGCA
CATAGTACTACACACGTGACCAAAACTATCACGTAT
Found at i:10566496 original size:2 final size:2
Alignment explanation
Indices: 10566489--10566514 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10566479 GATAACCCAA
10566489 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
10566515 GCACAGAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:10570997 original size:76 final size:76
Alignment explanation
Indices: 10570900--10571052 Score: 245
Period size: 76 Copynumber: 2.0 Consensus size: 76
10570890 AAATATGAAA
* *
10570900 TCTAACCAAACTACAAGCTAAAACCCTAAAA-TGAACTCCCCAAACTGATAGCTTAATGTAGTAT
1 TCTAACCAAAATACAAGCTAAAACCCTAAAACT-AACTCCCCAAACGGATAGCTTAATGTAGTAT
*
10570964 TTATAGTTTAAG
65 TTATAGTCTAAG
* *
10570976 TCTAACTAAAATACAAGCTAAAACCCTAAAACTAACTCCCCAAACGGATAGTTTAATGTAGTATT
1 TCTAACCAAAATACAAGCTAAAACCCTAAAACTAACTCCCCAAACGGATAGCTTAATGTAGTATT
10571041 TATAGTCTAAG
66 TATAGTCTAAG
10571052 T
1 T
10571053 GTATTATGAC
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
76 70 0.99
77 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.28
Consensus pattern (76 bp):
TCTAACCAAAATACAAGCTAAAACCCTAAAACTAACTCCCCAAACGGATAGCTTAATGTAGTATT
TATAGTCTAAG
Found at i:10572804 original size:23 final size:24
Alignment explanation
Indices: 10572754--10572804 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
10572744 ATTTATTATA
*
10572754 ATAAAAAATAACTATTCACTAAAC
1 ATAATAAATAACTATTCACTAAAC
10572778 -TAATAAATAACTA-TCAC-AAACC
1 ATAATAAATAACTATTCACTAAA-C
10572800 ATAAT
1 ATAAT
10572805 CATTCATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 16 0.67
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.25
Consensus pattern (24 bp):
ATAATAAATAACTATTCACTAAAC
Found at i:10573868 original size:7 final size:8
Alignment explanation
Indices: 10573852--10573878 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
10573842 AATTATTTTT
10573852 AAAATAAA
1 AAAATAAA
10573860 AAAATAAA
1 AAAATAAA
10573868 AAAATAAA
1 AAAATAAA
10573876 AAA
1 AAA
10573879 GTATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:10574250 original size:28 final size:27
Alignment explanation
Indices: 10574181--10574250 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 27
10574171 AATAAACACC
*
10574181 AAAAATTTATTTTAAAAATAAAAAAAT
1 AAAAATATATTTTAAAAATAAAAAAAT
* *
10574208 AAAAAAAGTATTTTAAAATTAAAAAAAT
1 AAAAATA-TATTTTAAAAATAAAAAAAT
10574236 AAAAATATATATTTA
1 AAAAATATAT-TTTA
10574251 TTATATAGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 8 0.22
28 29 0.78
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (27 bp):
AAAAATATATTTTAAAAATAAAAAAAT
Found at i:10574735 original size:22 final size:23
Alignment explanation
Indices: 10574692--10574737 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
10574682 AGCCCGGGTT
* *
10574692 ATTAAAATTATATTTTTATTAAA
1 ATTAAAACTATATTGTTATTAAA
10574715 ATTAAAACTA-ATTGTTATTAAA
1 ATTAAAACTATATTGTTATTAAA
10574737 A
1 A
10574738 CTATATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTAAAACTATATTGTTATTAAA
Found at i:10574861 original size:33 final size:32
Alignment explanation
Indices: 10574793--10574866 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
10574783 ATCTAACATT
* ***
10574793 TTGTTAGTAAAATTATTAATTAATTGTATTAA
1 TTGTTAGTAAAATTATAAATTAATCAAATTAA
10574825 TTGTTAGTAAAATTATCAAATTATATCAAATT-A
1 TTGTTAGTAAAATTAT-AAATTA-ATCAAATTAA
10574858 TTGTTAGTA
1 TTGTTAGTA
10574867 CCAGTCAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 16 0.44
33 15 0.42
34 5 0.14
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (32 bp):
TTGTTAGTAAAATTATAAATTAATCAAATTAA
Found at i:10574877 original size:105 final size:108
Alignment explanation
Indices: 10574733--10574965 Score: 355
Period size: 105 Copynumber: 2.2 Consensus size: 108
10574723 TAATTGTTAT
* * *
10574733 TAAAACTATATCAAATTATTTTTTTTGTACCAATCAAAACATTTTGTAAAATCTAACATTTTGTT
1 TAAAATTATATCAAATTA-TTTGTTAGTACCAATCAAAACATTTTGTAAAATCTAACATTTTGTT
*
10574798 AGTAAAATTATT-A-ATTAATTGTATTAATTGTTAGTAAAATTA
65 AGTAAAATTATTAATATTAATTGCATTAATTGTTAGTAAAATTA
* *
10574840 TCAAATTATATCAAATTA-TTGTTAGTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTA
1 TAAAATTATATCAAATTATTTGTTAGTACCAATCAAAACATTTTGTAAAATCTAACATTTTGTTA
*
10574904 GTTAAATTATTAATTATTAATTGCATTAATTGTTAGTAAAATTA
66 GTAAAATTATTAA-TATTAATTGCATTAATTGTTAGTAAAATTA
*
10574948 TAAAATTATATCAGATTA
1 TAAAATTATATCAAATTA
10574966 GGGTTAGGGT
Statistics
Matches: 114, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
105 53 0.46
106 1 0.01
107 16 0.14
108 44 0.39
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (108 bp):
TAAAATTATATCAAATTATTTGTTAGTACCAATCAAAACATTTTGTAAAATCTAACATTTTGTTA
GTAAAATTATTAATATTAATTGCATTAATTGTTAGTAAAATTA
Found at i:10574974 original size:6 final size:6
Alignment explanation
Indices: 10574963--10574998 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
10574953 TTATATCAGA
*
10574963 TTAGGG TTAGGG TTAGAG TTAGGG TTAGGG TTAGGG
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG
10574999 CTAAGGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.33
Consensus pattern (6 bp):
TTAGGG
Found at i:10575006 original size:18 final size:18
Alignment explanation
Indices: 10574967--10575006 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
10574957 ATCAGATTAG
* *
10574967 GGTTAGGGTTAGAGTTAG
1 GGTTAGGGTTAGAGCTAA
*
10574985 GGTTAGGGTTAGGGCTAA
1 GGTTAGGGTTAGAGCTAA
10575003 GGTT
1 GGTT
10575007 TTTGTTAGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.03, G:0.45, T:0.33
Consensus pattern (18 bp):
GGTTAGGGTTAGAGCTAA
Found at i:10575044 original size:15 final size:15
Alignment explanation
Indices: 10575024--10575101 Score: 67
Period size: 15 Copynumber: 5.2 Consensus size: 15
10575014 GGGTTTTGGT
10575024 GTTTTTAAGTTAAGG
1 GTTTTTAAGTTAAGG
10575039 GTTTTTAAGTTAAGG
1 GTTTTTAAGTTAAGG
10575054 G---TTAGAGTT-AGG
1 GTTTTTA-AGTTAAGG
*
10575066 GTTAGTGTTAGGGTT-AGG
1 GTT--T-TTA-AGTTAAGG
10575084 GTTTTTAAGTTAAGG
1 GTTTTTAAGTTAAGG
10575099 GTT
1 GTT
10575102 AGGGTTAGGG
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
12 7 0.13
13 4 0.08
14 3 0.06
15 25 0.47
16 1 0.02
18 13 0.25
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (15 bp):
GTTTTTAAGTTAAGG
Found at i:10575068 original size:12 final size:12
Alignment explanation
Indices: 10575046--10575082 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
10575036 AGGGTTTTTA
10575046 AGTTAAGGGTTAG
1 AGTT-AGGGTTAG
10575059 AGTTAGGGTTAG
1 AGTTAGGGTTAG
*
10575071 TGTTAGGGTTAG
1 AGTTAGGGTTAG
10575083 GGTTTTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (12 bp):
AGTTAGGGTTAG
Found at i:10575069 original size:6 final size:6
Alignment explanation
Indices: 10575051--10575119 Score: 59
Period size: 6 Copynumber: 11.0 Consensus size: 6
10575041 TTTTAAGTTA
* * *
10575051 AGGGTT AGAGTT AGGGTT AGTGTT AGGGTT AGGGTTTTT A-AGTT AAGGGTT
1 AGGGTT AGGGTT AGGGTT AGGGTT AGGGTT AGGG---TT AGGGTT -AGGGTT
*
10575102 AGGGTT AGGGCT AGGGTT
1 AGGGTT AGGGTT AGGGTT
10575120 TTTGTTAGGG
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
5 2 0.04
6 41 0.82
7 3 0.06
8 1 0.02
9 3 0.06
ACGTcount: A:0.20, C:0.01, G:0.42, T:0.36
Consensus pattern (6 bp):
AGGGTT
Found at i:10575101 original size:33 final size:32
Alignment explanation
Indices: 10575059--10575131 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 32
10575049 TAAGGGTTAG
* *
10575059 AGTTAGGGTTAGTGTTAGGGTTAGGGTTTTTA
1 AGTTAGGGTTAGGGTTAGGGCTAGGGTTTTTA
10575091 AGTTAAGGGTTAGGGTTAGGGCTAGGGTTTTT-
1 AGTT-AGGGTTAGGGTTAGGGCTAGGGTTTTTA
10575123 -GTTAGGGTT
1 AGTTAGGGTT
10575132 TTGGTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 6 0.16
31 3 0.08
32 4 0.11
33 25 0.66
ACGTcount: A:0.18, C:0.01, G:0.40, T:0.41
Consensus pattern (32 bp):
AGTTAGGGTTAGGGTTAGGGCTAGGGTTTTTA
Found at i:10575127 original size:45 final size:45
Alignment explanation
Indices: 10575036--10575133 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
10575026 TTTTAAGTTA
* *
10575036 AGGGTTTTTAAGTTAAGGGTTAGAGTTAGGGTTAGTGTTAGGGTT
1 AGGGTTTTTAAGTTAAGGGTTAGAGTTAGGGCTAGGGTTAGGGTT
* ***
10575081 AGGGTTTTTAAGTTAAGGGTTAGGGTTAGGGCTAGGGTTTTTGTT
1 AGGGTTTTTAAGTTAAGGGTTAGAGTTAGGGCTAGGGTTAGGGTT
10575126 AGGGTTTT
1 AGGGTTTT
10575134 GGTTTTTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.19, C:0.01, G:0.38, T:0.42
Consensus pattern (45 bp):
AGGGTTTTTAAGTTAAGGGTTAGAGTTAGGGCTAGGGTTAGGGTT
Found at i:10575197 original size:7 final size:7
Alignment explanation
Indices: 10575185--10575224 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
10575175 GTTTGTCAAT
10575185 TAAATTA
1 TAAATTA
10575192 TAAATT-
1 TAAATTA
10575198 T-AATTA
1 TAAATTA
10575204 TAAATTA
1 TAAATTA
10575211 TAAATTTA
1 TAAA-TTA
10575219 TAAATT
1 TAAATT
10575225 TTTAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.13
6 2 0.07
7 17 0.57
8 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAAATTA
Found at i:10575270 original size:22 final size:22
Alignment explanation
Indices: 10575239--10575320 Score: 139
Period size: 22 Copynumber: 3.8 Consensus size: 22
10575229 ATAAATTAGG
*
10575239 TTAGAGTTTTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGC
10575260 TTAGGGTTTTTAAGTTAAGGGC
1 TTAGGGTTTTTAAGTTAAGGGC
*
10575282 TTAGGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGC
10575304 TTAGGGTTTTTAAGTTA
1 TTAGGGTTTTTAAGTTA
10575321 TAAGTTAAGG
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
21 20 0.34
22 38 0.66
ACGTcount: A:0.24, C:0.01, G:0.29, T:0.45
Consensus pattern (22 bp):
TTAGGGTTTTTAAGTTAAGGGC
Found at i:10575272 original size:43 final size:44
Alignment explanation
Indices: 10575223--10575318 Score: 126
Period size: 43 Copynumber: 2.2 Consensus size: 44
10575213 AATTTATAAA
10575223 TTTTTAA-TAAATTAGG-TTAGAGTTTTTAAGTTAAGGG-TTAGGG
1 TTTTTAAGTAAA--AGGCTTAGAGTTTTTAAGTTAAGGGTTTAGGG
* * *
10575266 TTTTTAAGTTAAGGGCTTAGGGTTTTTAAGTTAAGGGTTTAGGG
1 TTTTTAAGTAAAAGGCTTAGAGTTTTTAAGTTAAGGGTTTAGGG
10575310 TTTTTAAGT
1 TTTTTAAGT
10575319 TATAAGTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
42 2 0.04
43 27 0.57
44 18 0.38
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.46
Consensus pattern (44 bp):
TTTTTAAGTAAAAGGCTTAGAGTTTTTAAGTTAAGGGTTTAGGG
Found at i:10575384 original size:7 final size:7
Alignment explanation
Indices: 10575372--10575411 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
10575362 GTTTGTCAAT
10575372 TAAATTA
1 TAAATTA
10575379 TAAATT-
1 TAAATTA
10575385 T-AATTA
1 TAAATTA
10575391 TAAATTA
1 TAAATTA
10575398 TAAATTTA
1 TAAA-TTA
10575406 TAAATT
1 TAAATT
10575412 TTTAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.13
6 2 0.07
7 17 0.57
8 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAAATTA
Found at i:10577631 original size:51 final size:51
Alignment explanation
Indices: 10577550--10577649 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
10577540 AAAAAATTAA
*
10577550 AAATAGGGATTTAAGAGAAATTTAAGAGGAAACTGAGAGCAAATTGAGATT
1 AAATAAGGATTTAAGAGAAATTTAAGAGGAAACTGAGAGCAAATTGAGATT
* ** * *
10577601 AAATAAGGATTTGAGA-AAATTTTGGAAGGAAATTGAGAGCAATTTGAGA
1 AAATAAGGATTTAAGAGAAATTTAAG-AGGAAACTGAGAGCAAATTGAGA
10577650 GGAAATTGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 7 0.17
51 35 0.83
ACGTcount: A:0.46, C:0.03, G:0.26, T:0.25
Consensus pattern (51 bp):
AAATAAGGATTTAAGAGAAATTTAAGAGGAAACTGAGAGCAAATTGAGATT
Found at i:10577637 original size:22 final size:22
Alignment explanation
Indices: 10577611--10577671 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
10577601 AAATAAGGAT
10577611 TTGAGA-AAATTTTG-GAAGGAAA
1 TTGAGAGAAA-TTTGAG-AGGAAA
*
10577633 TTGAGAGCAATTTGAGAGGAAA
1 TTGAGAGAAATTTGAGAGGAAA
10577655 TTGAGACGAAA-TTGAGA
1 TTGAGA-GAAATTTGAGA
10577672 AAATAATTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 28 0.82
23 6 0.18
ACGTcount: A:0.43, C:0.03, G:0.30, T:0.25
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:10577649 original size:11 final size:11
Alignment explanation
Indices: 10577630--10577671 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
10577620 TTTTGGAAGG
10577630 AAATTGAGAGC
1 AAATTGAGAGC
* *
10577641 AATTTGAGAGG
1 AAATTGAGAGC
10577652 AAATTGAGA-C
1 AAATTGAGAGC
10577662 GAAATTGAGA
1 -AAATTGAGA
10577672 AAATAATTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.45, C:0.05, G:0.29, T:0.21
Consensus pattern (11 bp):
AAATTGAGAGC
Found at i:10579689 original size:2 final size:2
Alignment explanation
Indices: 10579682--10579708 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10579672 TCAGATGATG
10579682 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
10579709 GTGTTCTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10581380 original size:20 final size:19
Alignment explanation
Indices: 10581337--10581381 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
10581327 TAAGATGAAT
* *
10581337 ATTTAAATATTTTTAATTA
1 ATTTTAATAATTTTAATTA
*
10581356 TTTTTAATAATTTTAATTTA
1 ATTTTAATAATTTTAA-TTA
10581376 ATTTTA
1 ATTTTA
10581382 TATATTATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTAATAATTTTAATTA
Found at i:10582668 original size:17 final size:17
Alignment explanation
Indices: 10582637--10582670 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10582627 ATGATATTTG
*
10582637 AAATATTTCACATATCA
1 AAATATTTCAAATATCA
*
10582654 AAATATTTGAAATATCA
1 AAATATTTCAAATATCA
10582671 TATCCATAAT
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:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (17 bp):
AAATATTTCAAATATCA
Found at i:10583683 original size:81 final size:82
Alignment explanation
Indices: 10583575--10583747 Score: 321
Period size: 81 Copynumber: 2.1 Consensus size: 82
10583565 CGTTCAAATC
10583575 AGTTTCTTAAGAATGGATGCCCCTTTAATTCGCTTCGACGGTAACCATATTTTTGGACCCAAAAT
1 AGTTTCTTAAGAATGGATGCCCCTTTAATTCGCTTCGACGGTAACCATATTTTTGGACCCAAAAT
10583640 GGTAATTCGTTATTTTT
66 GGTAATTCGTTATTTTT
10583657 AGTTTCTTAA-AATGGATGCCCCTTTAATTCGCTTCGACGGTAACCATATTTTTGGACCCAAAAT
1 AGTTTCTTAAGAATGGATGCCCCTTTAATTCGCTTCGACGGTAACCATATTTTTGGACCCAAAAT
10583721 GGTAATTCGTTATTTTT
66 GGTAATTCGTTATTTTT
* *
10583738 AATTTTTTAA
1 AGTTTCTTAA
10583748 TTTTTGTTAT
Statistics
Matches: 89, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
81 79 0.89
82 10 0.11
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (82 bp):
AGTTTCTTAAGAATGGATGCCCCTTTAATTCGCTTCGACGGTAACCATATTTTTGGACCCAAAAT
GGTAATTCGTTATTTTT
Found at i:10583752 original size:9 final size:8
Alignment explanation
Indices: 10583733--10583802 Score: 63
Period size: 8 Copynumber: 8.6 Consensus size: 8
10583723 TAATTCGTTA
10583733 TTTTTAAT
1 TTTTTAAT
10583741 TTTTTAAT
1 TTTTTAAT
*
10583749 TTTTGTTA-
1 TTTT-TAAT
10583757 TTTTTAAT
1 TTTTTAAT
*
10583765 TTTTAAAT
1 TTTTTAAT
*
10583773 TTTTGTTA-
1 TTTT-TAAT
10583781 TTTTTAAT
1 TTTTTAAT
*
10583789 TATGTTAAT
1 T-TTTTAAT
10583798 TTTTT
1 TTTTT
10583803 TGATAAATCT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
7 4 0.08
8 35 0.71
9 10 0.20
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (8 bp):
TTTTTAAT
Found at i:10583757 original size:24 final size:24
Alignment explanation
Indices: 10583729--10583801 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
10583719 ATGGTAATTC
10583729 GTTATTTTTAATTTTTTAATTTTT
1 GTTATTTTTAATTTTTTAATTTTT
*
10583753 GTTATTTTTAATTTTTAAATTTTT
1 GTTATTTTTAATTTTTTAATTTTT
*
10583777 GTTATTTTTAATTATGTTAATTTTT
1 GTTATTTTTAATT-TTTTAATTTTT
10583802 TTGATAAATC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
24 36 0.80
25 9 0.20
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.71
Consensus pattern (24 bp):
GTTATTTTTAATTTTTTAATTTTT
Found at i:10586845 original size:17 final size:18
Alignment explanation
Indices: 10586793--10586845 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
10586783 GAACACTTTC
10586793 AAAAAACT--ATAAGCCCT
1 AAAAAACTCAATAA-CCCT
*
10586810 AAAAAACTCAA-AACACT
1 AAAAAACTCAATAACCCT
*
10586827 AAAAAA-TTAATAACCCT
1 AAAAAACTCAATAACCCT
10586844 AA
1 AA
10586846 CCCTGGAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 3 0.10
17 24 0.80
18 2 0.07
19 1 0.03
ACGTcount: A:0.60, C:0.21, G:0.02, T:0.17
Consensus pattern (18 bp):
AAAAAACTCAATAACCCT
Found at i:10589956 original size:24 final size:25
Alignment explanation
Indices: 10589920--10589967 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
10589910 GATCCCCATA
10589920 TTTTTTTCGTTTTAAGTACTTTAAT
1 TTTTTTTCGTTTTAAGTACTTTAAT
* *
10589945 TTTTTTTC-TTTTATGTTCTTTAA
1 TTTTTTTCGTTTTAAGTACTTTAA
10589968 ACTTTCCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (25 bp):
TTTTTTTCGTTTTAAGTACTTTAAT
Found at i:10590115 original size:14 final size:14
Alignment explanation
Indices: 10590096--10590129 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
10590086 TCATCATTTG
10590096 CCTATAACCAAAAC
1 CCTATAACCAAAAC
*
10590110 CCTATAACTAAAAC
1 CCTATAACCAAAAC
10590124 CC-ATAA
1 CCTATAA
10590130 ACCCATACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:10592446 original size:22 final size:21
Alignment explanation
Indices: 10592421--10592488 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 21
10592411 GATTACTTAC
10592421 AATGAGCTAAAAAAATGACAAA
1 AATGA-CTAAAAAAATGACAAA
10592443 AATGAC-AAATAATAATGACAAA
1 AATGACTAAA-AA-AATGACAAA
10592465 AATGAACTAAAAAAA-GAACAAA
1 AATG-ACTAAAAAAATG-ACAAA
10592487 AA
1 AA
10592489 AATGAAAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.07
21 4 0.10
22 27 0.66
23 4 0.10
24 3 0.07
ACGTcount: A:0.68, C:0.09, G:0.10, T:0.13
Consensus pattern (21 bp):
AATGACTAAAAAAATGACAAA
Found at i:10596469 original size:18 final size:18
Alignment explanation
Indices: 10596446--10596481 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10596436 CCTAAAATAC
10596446 GAGGGTTTTTGGATGCGT
1 GAGGGTTTTTGGATGCGT
10596464 GAGGGTTTTTGGATGCGT
1 GAGGGTTTTTGGATGCGT
10596482 CTAAGACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.06, G:0.44, T:0.39
Consensus pattern (18 bp):
GAGGGTTTTTGGATGCGT
Found at i:10597429 original size:17 final size:17
Alignment explanation
Indices: 10597407--10597440 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
10597397 AAATTTTCAG
10597407 AATT-AATTAAAATTAAA
1 AATTAAATT-AAATTAAA
10597424 AATTAAATTAAATTAAA
1 AATTAAATTAAATTAAA
10597441 TTCCTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTAAATTAAATTAAA
Found at i:10600406 original size:98 final size:99
Alignment explanation
Indices: 10600231--10600421 Score: 312
Period size: 98 Copynumber: 1.9 Consensus size: 99
10600221 AAAAATAATT
* * * *
10600231 AAAAGAATATCCATTTATCCAAGATTTAAGAAATCGCGGCCCAATACGTTAGGGCACAATTCCTT
1 AAAAGAACATCCACTTATCCAAGATTTAAGAAATCACGACCCAATACGTTAGGGCACAATTCCTT
*
10600296 TAAAATCCCAAACTCGGAATATTTCCTTTATTTC
66 TAAAATCCCAAACTCGAAATATTTCCTTTATTTC
10600330 AAAAGAACATCCACTTATCCAAGATTTAAGAAATCAC-ACCCAATACGTTAGGGCACAATTCCTT
1 AAAAGAACATCCACTTATCCAAGATTTAAGAAATCACGACCCAATACGTTAGGGCACAATTCCTT
* *
10600394 TAGAATCTCAAACTCGAAATATTTCCTT
66 TAAAATCCCAAACTCGAAATATTTCCTT
10600422 CATGATTTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
98 51 0.60
99 34 0.40
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (99 bp):
AAAAGAACATCCACTTATCCAAGATTTAAGAAATCACGACCCAATACGTTAGGGCACAATTCCTT
TAAAATCCCAAACTCGAAATATTTCCTTTATTTC
Found at i:10601357 original size:15 final size:16
Alignment explanation
Indices: 10601337--10601370 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
10601327 TTTATTTTCC
10601337 AAACCTTCTTAA-AAA
1 AAACCTTCTTAACAAA
*
10601352 AAACCTTTTTAACAAA
1 AAACCTTCTTAACAAA
10601368 AAA
1 AAA
10601371 AAACTTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (16 bp):
AAACCTTCTTAACAAA
Found at i:10604081 original size:132 final size:126
Alignment explanation
Indices: 10603875--10604245 Score: 350
Period size: 132 Copynumber: 2.8 Consensus size: 126
10603865 TAAGACTTGT
* * *
10603875 CATCTTCGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTG
1 CATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-AAATCTTCAATCTATTCCACTG
**
10603940 TTGTCCAGGGAAGTAGAATTATTGGATTCAATGTACTCCACTATA-ACCACAGAGAGGTAAAATC
65 TACT-CAGGGAAGTAGAATTATTGG-TTCAATGTACTCCACTATATACCA-A-AGA--TAAAATC
10604004 CGC
124 CGC
* *
10604007 CATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAAT-TTTCTCCGCT
1 CATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTA-AATCTTCAATCTAT-TCCACT
** ** ** * * * *** * *
10604071 GCTACTCAGGGAGACAAGGTTTGGTGGCTCAAATCTGCTTCCCACTATATTGGAAAGATAAGATT
64 G-TACTCAGGGA-AGTAGAATTATTGGTTC-AATGTAC-T-CCACTATATACCAAAGATAAAATC
*
10604136 TGC
124 CGC
*
10604139 CATCTTCGATCTGCTCCACTACTGCTTAGGAAGATAAGATCTGAAATCTTCAATCTATTCCACTG
1 CATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-AAATCTTCAATCTATTCCACTG
**
10604204 TTGTTCAGGGAAGTAGAATTATTGGCTTCAATGTACTCCACT
65 -TACTCAGGGAAGTAGAATTATTGG-TTCAATGTACTCCACT
10604246 NNNNNNNNNN
Statistics
Matches: 191, Mismatches: 37, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
129 5 0.03
130 1 0.01
131 15 0.08
132 138 0.72
133 18 0.09
134 4 0.02
135 9 0.05
136 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (126 bp):
CATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTAAATCTTCAATCTATTCCACTGT
ACTCAGGGAAGTAGAATTATTGGTTCAATGTACTCCACTATATACCAAAGATAAAATCCGC
Found at i:10609431 original size:287 final size:286
Alignment explanation
Indices: 10608896--10609457 Score: 962
Period size: 287 Copynumber: 2.0 Consensus size: 286
10608886 AAAAGAGTTG
* * * *
10608896 TTATTTCTAGGATAAATATCAAGTTTGTTTTGAATATTACTCTGAGACAGTTCTAAAGACTTTAG
1 TTATTTCTAGGATAAACAACAAGTTTGTTCTGAACATTACTCTGAGACAGTTCTAAAGACTTTAG
* *
10608961 GTATTTCTTCCGCAGTCCAATTGTCTAGAACACTCCCAGGCTCATAAGGACGAATGTCTAGCTAA
66 GTATTTCTTCCGCAGTCCAATTGTCTAGAACACTCCCAGGCTCATAAGGACGAATGTCTAACCAA
* *
10609026 CTTCTCTCTTCATTCCCAAGTTCATGAATGGCATTAATGTACATATTTCCCAATGTCTCCTCGAT
131 CTTCTCTCTTCATTCCCAAGCTCATGAATGACATTAATGTACATATTTCCCAATGTCTCCTCGAT
* **
10609091 GCTTTCCTCAACCGATTTCTTTCTCTCCTGATGAATGATCCCTCCGGATACGAAGGTTTTGGATA
196 GCTTTCCTCAACCGATTTCTTCCTCTCCTGATGAATGATCCCTCCGGATACGAAAATTTTGGATA
10609156 TGTGGGGAATTATCAAAGAATTCTTT
261 TGTGGGGAATTATCAAAGAATTCTTT
* *
10609182 TTATTTCTAGGCTAAAACAACAAGTTTGTTCTGAACATTACTCTGAGATAGTTCTAAAGACTTTA
1 TTATTTCTAGGAT-AAACAACAAGTTTGTTCTGAACATTACTCTGAGACAGTTCTAAAGACTTTA
*
10609247 GGTATTTCTTCCGCAGTCCAATTGTCTAGAACACTCCCAGGCTCATAAGGTCGAATGTCTAACCA
65 GGTATTTCTTCCGCAGTCCAATTGTCTAGAACACTCCCAGGCTCATAAGGACGAATGTCTAACCA
*
10609312 ACTTCTCTCTTCATTCCCAAGCTCATGAATGACGTTAATGTACATATTTCCCAATGTCTCCTCGA
130 ACTTCTCTCTTCATTCCCAAGCTCATGAATGACATTAATGTACATATTTCCCAATGTCTCCTCGA
* *
10609377 TGCTTTCCTCCATCGATTTCTTCCTCTCCTGATGAATGATCCCTCCGGATACGAAAATTTTGGAT
195 TGCTTTCCTCAACCGATTTCTTCCTCTCCTGATGAATGATCCCTCCGGATACGAAAATTTTGGAT
10609442 ATGTGGGGAATTATCA
260 ATGTGGGGAATTATCA
10609458 TTGGCTCCCA
Statistics
Matches: 258, Mismatches: 17, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
286 12 0.05
287 246 0.95
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (286 bp):
TTATTTCTAGGATAAACAACAAGTTTGTTCTGAACATTACTCTGAGACAGTTCTAAAGACTTTAG
GTATTTCTTCCGCAGTCCAATTGTCTAGAACACTCCCAGGCTCATAAGGACGAATGTCTAACCAA
CTTCTCTCTTCATTCCCAAGCTCATGAATGACATTAATGTACATATTTCCCAATGTCTCCTCGAT
GCTTTCCTCAACCGATTTCTTCCTCTCCTGATGAATGATCCCTCCGGATACGAAAATTTTGGATA
TGTGGGGAATTATCAAAGAATTCTTT
Found at i:10619010 original size:18 final size:17
Alignment explanation
Indices: 10618988--10619021 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
10618978 TGTTCATCTT
10618988 TTTTTTTTACTTTCCCC
1 TTTTTTTTACTTTCCCC
10619005 TTTTTTTTACTTTCCCC
1 TTTTTTTTACTTTCCCC
10619022 AAAATCCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTTTTACTTTCCCC
Found at i:10636872 original size:7 final size:7
Alignment explanation
Indices: 10636862--10636895 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
10636852 ATAAAATAAA
10636862 AAAAATT
1 AAAAATT
10636869 AAAAATT
1 AAAAATT
*
10636876 AATTAATT
1 AA-AAATT
10636884 AAAAATT
1 AAAAATT
10636891 AAAAA
1 AAAAA
10636896 ATGCATAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAAATT
Found at i:10652292 original size:13 final size:14
Alignment explanation
Indices: 10652274--10652306 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
10652264 AGTAGTTTAT
10652274 TTTTCAGAA-ATCA
1 TTTTCAGAAGATCA
*
10652287 TTTTCAGAAGGTCA
1 TTTTCAGAAGATCA
10652301 TTTTCA
1 TTTTCA
10652307 ATAAAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (14 bp):
TTTTCAGAAGATCA
Done.