Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 54 of 216
Found at i:15847375 original size:57 final size:58
Alignment explanation
Indices: 15847302--15847422 Score: 174
Period size: 57 Copynumber: 2.1 Consensus size: 58
15847292 TCATTTTCAT
* * *
15847302 TTTTGATTTTCATTTTGAATAAAA-CTACATTCATTTCCAAATATTTCCC-TTTCTCCC
1 TTTTCATTTTCATTTTGAAGAAAACCT-CATTCATTTCCAAATATTTCCCATTTCTCCA
* *
15847359 TTTTCATTTTCATTTTGGAGAAAACCTCATTCATTTCCAAATGTTTCCCATTTCTCCA
1 TTTTCATTTTCATTTTGAAGAAAACCTCATTCATTTCCAAATATTTCCCATTTCTCCA
15847417 TTTTCA
1 TTTTCA
15847423 CCATTTCTGT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
57 42 0.74
58 15 0.26
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.47
Consensus pattern (58 bp):
TTTTCATTTTCATTTTGAAGAAAACCTCATTCATTTCCAAATATTTCCCATTTCTCCA
Found at i:15848836 original size:14 final size:14
Alignment explanation
Indices: 15848790--15848836 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
15848780 TGTATTATTT
*
15848790 TTATAATCTTAAATA
1 TTAT-ATCTAAAATA
*
15848805 TTAAATCTAAAA-A
1 TTATATCTAAAATA
*
15848818 TTATATGTAAAATA
1 TTATATCTAAAATA
15848832 TTATA
1 TTATA
15848837 ATATACAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 11 0.41
14 13 0.48
15 3 0.11
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (14 bp):
TTATATCTAAAATA
Found at i:15857940 original size:69 final size:69
Alignment explanation
Indices: 15857829--15857998 Score: 241
Period size: 69 Copynumber: 2.5 Consensus size: 69
15857819 ATCAGATGTG
* * * ** *
15857829 ATCGAGTAGTTTTAGGAGTTACGATATTAAATCAGGTAACCTTTATAATATCAGCTGTGAACGTA
1 ATCGAGTTGTTTTAGGAGTTGCGATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTA
15857894 GGTC
66 GGTC
* *
15857898 ATCGAGTTGTTTTATGAGTTGCAATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTA
1 ATCGAGTTGTTTTAGGAGTTGCGATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTA
15857963 GGTC
66 GGTC
** *
15857967 ATCGAACTATTTTAGGAGTTGCGATCTTAAAT
1 ATCGAGTTGTTTTAGGAGTTGCGATCTTAAAT
15857999 TACCTAACTC
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 88 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (69 bp):
ATCGAGTTGTTTTAGGAGTTGCGATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTA
GGTC
Found at i:15858103 original size:106 final size:106
Alignment explanation
Indices: 15857915--15858164 Score: 383
Period size: 106 Copynumber: 2.4 Consensus size: 106
15857905 TGTTTTATGA
* ** * *
15857915 GTTGCAATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTAGGTCATCGAACTATTTT
1 GTTGCAATCTTAAATCAGCTAACCTTTATAATATCAGTTGTGAACGTAGGTCATCAAACTATTTC
* * *
15857980 AGGAGTTGCGATCTTAAATTACCTAACTCAAAGAAACTTAG
66 AAGAGTTGCGATATTAAATCACCTAACTCAAAGAAACTTAG
* *
15858021 GTTGCAATCTTAAATCGGCTAACCTTTATAATACCAGTTGTGAACGTAGGTCATCAAACTATTTC
1 GTTGCAATCTTAAATCAGCTAACCTTTATAATATCAGTTGTGAACGTAGGTCATCAAACTATTTC
* *
15858086 AAGAGTTGCGATATTAAATCAGCTAACTCAAAGAAACTTCG
66 AAGAGTTGCGATATTAAATCACCTAACTCAAAGAAACTTAG
*
15858127 GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGT
1 GTTGCAATCTTAAATCAGCTAACCTTTATAATATCAGT
15858165 ACTTGTATAG
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 129 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (106 bp):
GTTGCAATCTTAAATCAGCTAACCTTTATAATATCAGTTGTGAACGTAGGTCATCAAACTATTTC
AAGAGTTGCGATATTAAATCACCTAACTCAAAGAAACTTAG
Found at i:15875165 original size:15 final size:15
Alignment explanation
Indices: 15875107--15875182 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 15
15875097 CCGAATAAGC
*
15875107 TTGAACTCAAAAATAC
1 TTGAACTCAAAAA-AT
* *
15875123 TTGAACATGATAAAAT
1 TTGAAC-TCAAAAAAT
**
15875139 TTGAACAAAAAAAAT
1 TTGAACTCAAAAAAT
15875154 TTGAACTCAAAAAAT
1 TTGAACTCAAAAAAT
* * *
15875169 CTGCACTTAAAAAA
1 TTGAACTCAAAAAA
15875183 ATCCAAACCC
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
15 30 0.62
16 13 0.27
17 5 0.10
ACGTcount: A:0.54, C:0.13, G:0.08, T:0.25
Consensus pattern (15 bp):
TTGAACTCAAAAAAT
Found at i:15875167 original size:16 final size:16
Alignment explanation
Indices: 15875107--15875167 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
15875097 CCGAATAAGC
* *
15875107 TTGAACTCAAAAATAC
1 TTGAACTCAAAAAAAT
* *
15875123 TTGAACAT-GATAAAAT
1 TTGAAC-TCAAAAAAAT
*
15875139 TTGAAC-AAAAAAAAT
1 TTGAACTCAAAAAAAT
15875154 TTGAACTCAAAAAA
1 TTGAACTCAAAAAA
15875168 TCTGCACTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 12 0.34
16 22 0.63
17 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.25
Consensus pattern (16 bp):
TTGAACTCAAAAAAAT
Found at i:15876806 original size:26 final size:26
Alignment explanation
Indices: 15876774--15876827 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
15876764 CCTCCTCTAC
15876774 CACTAGTTTTTAACAATGAAAACTAT
1 CACTAGTTTTTAACAATGAAAACTAT
15876800 CACTAGTTTTTAACAATGAAAACTAT
1 CACTAGTTTTTAACAATGAAAACTAT
15876826 CA
1 CA
15876828 TATTTGGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (26 bp):
CACTAGTTTTTAACAATGAAAACTAT
Found at i:15879804 original size:26 final size:26
Alignment explanation
Indices: 15879733--15879807 Score: 93
Period size: 25 Copynumber: 2.9 Consensus size: 26
15879723 AAATATTTTC
15879733 TCAAAATTTTACTAGAG-GTAAAATCA
1 TCAAAATTTTACTAG-GTGTAAAATCA
* *
15879759 TCAAAA-TTTACT-GATGGTAAAATCG
1 TCAAAATTTTACTAGGT-GTAAAATCA
15879784 TCAAAATTTTACTAGGTGTAAAAT
1 TCAAAATTTTACTAGGTGTAAAAT
15879808 AGGGTTGAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.02
25 20 0.48
26 19 0.45
27 2 0.05
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTACTAGGTGTAAAATCA
Found at i:15881985 original size:25 final size:25
Alignment explanation
Indices: 15881951--15882091 Score: 107
Period size: 25 Copynumber: 5.6 Consensus size: 25
15881941 GTACATGTAT
*
15881951 GCTCATACGAGCTATGAATCGGTAT
1 GCTCATACGAGCTATGAATCGGTAA
* *
15881976 GCTC-TCACGAGCTGTAAATCGGTAA
1 GCTCAT-ACGAGCTATGAATCGGTAA
15882001 GCTCATA-GAAGCTGA-GAATCGGTAA
1 GCTCATACG-AGCT-ATGAATCGGTAA
*
15882026 GCTC-TCATGAG-T-TGCAAATCGGTAA
1 GCTCAT-ACGAGCTATG--AATCGGTAA
* * *
15882051 GCTC-TCACAAGCTGTAAATCGGTAA
1 GCTCAT-ACGAGCTATGAATCGGTAA
15882076 GCTCATACGAGCTATG
1 GCTCATACGAGCTATG
15882092 GTGTGTCCGC
Statistics
Matches: 93, Mismatches: 11, Indels: 24
0.73 0.09 0.19
Matches are distributed among these distances:
23 1 0.01
24 4 0.04
25 83 0.89
26 4 0.04
27 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (25 bp):
GCTCATACGAGCTATGAATCGGTAA
Found at i:15882020 original size:50 final size:51
Alignment explanation
Indices: 15881966--15882088 Score: 155
Period size: 50 Copynumber: 2.5 Consensus size: 51
15881956 TACGAGCTAT
* * *
15881966 GAATCGGTATGCTCTCACGAGCTGTAAATCGGTAAGCTCAT-AGAAGCTG-A
1 GAATCGGTAAGCTCTCACGAGCTGCAAATCGGTAAGCTC-TCACAAGCTGTA
* *
15882016 GAATCGGTAAGCTCTCATGAGTTGCAAATCGGTAAGCTCTCACAAGCTGTA
1 GAATCGGTAAGCTCTCACGAGCTGCAAATCGGTAAGCTCTCACAAGCTGTA
15882067 -AATCGGTAAGCTCAT-ACGAGCT
1 GAATCGGTAAGCTC-TCACGAGCT
15882089 ATGGTGTGTC
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
49 1 0.02
50 60 0.95
51 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (51 bp):
GAATCGGTAAGCTCTCACGAGCTGCAAATCGGTAAGCTCTCACAAGCTGTA
Found at i:15886399 original size:25 final size:25
Alignment explanation
Indices: 15886346--15886458 Score: 99
Period size: 25 Copynumber: 4.5 Consensus size: 25
15886336 GTACATGTAT
* *
15886346 GCTCATACGAGCTATGAATTCG-TAT
1 GCTCATACGAGCTAT-AAATCGATAA
15886371 GCTC-TCACGAGCTATAAATCGATAA
1 GCTCAT-ACGAGCTATAAATCGATAA
* * * *
15886396 GCTCATACAAGTCGA-GAATCGGTAA
1 GCTCATACGAG-CTATAAATCGATAA
*
15886421 GCTC-TAGCGAGCTACAAATCGATAA
1 GCTCATA-CGAGCTATAAATCGATAA
15886446 GCTCATACGAGCT
1 GCTCATACGAGCT
15886459 GTGGTGTGTC
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
24 10 0.14
25 56 0.79
26 5 0.07
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTATAAATCGATAA
Found at i:15891607 original size:21 final size:22
Alignment explanation
Indices: 15891583--15891630 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
15891573 AAGTCAAATC
15891583 GAAACAAA-TTAGAAAA-TTTCA
1 GAAACAAAGTT-GAAAATTTTCA
15891604 GAAA-AAAGTTGAAAATTTTCA
1 GAAACAAAGTTGAAAATTTTCA
15891625 -AAACAA
1 GAAACAA
15891631 GGATCACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.23
Consensus pattern (22 bp):
GAAACAAAGTTGAAAATTTTCA
Found at i:15907063 original size:16 final size:16
Alignment explanation
Indices: 15907044--15907076 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
15907034 TCACATCAAT
15907044 AAATTTTATAAAATTA
1 AAATTTTATAAAATTA
*
15907060 AAATTTTATAATATTA
1 AAATTTTATAAAATTA
15907076 A
1 A
15907077 CTGAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTTTATAAAATTA
Found at i:15907984 original size:19 final size:18
Alignment explanation
Indices: 15907962--15908003 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
15907952 AATTCAAAAA
15907962 TAAAAATA-AAAATATTTTT
1 TAAAAATATAAAA-A-TTTT
15907981 TAAAAATATAAAAATTTT
1 TAAAAATATAAAAATTTT
15907999 TAAAA
1 TAAAA
15908004 TTCAATGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 9 0.41
20 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAATATAAAAATTTT
Found at i:15911363 original size:16 final size:16
Alignment explanation
Indices: 15911327--15911373 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
15911317 CTCATCACTT
* *
15911327 TATGGTGTGTTGGGGG
1 TATGGTGTGTTTGGAG
15911343 T-TGGTGTGTTTGGAG
1 TATGGTGTGTTTGGAG
*
15911358 TATGGTTTGTTTGGAG
1 TATGGTGTGTTTGGAG
15911374 GACATGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.09, C:0.00, G:0.47, T:0.45
Consensus pattern (16 bp):
TATGGTGTGTTTGGAG
Found at i:15913028 original size:13 final size:14
Alignment explanation
Indices: 15912994--15913083 Score: 66
Period size: 13 Copynumber: 6.7 Consensus size: 14
15912984 CCAATGTTTC
* *
15912994 ATTTCATAT-ATCT
1 ATTTCATATAACCG
15913007 ATTTCCATATAACCG
1 ATTT-CATATAACCG
**
15913022 A-TTCATATAA-AT
1 ATTTCATATAACCG
* *
15913034 ATTTCATAT-ATCT
1 ATTTCATATAACCG
15913047 ATTTTCATATAACCG
1 A-TTTCATATAACCG
15913062 A-TTCATATAACC-
1 ATTTCATATAACCG
15913074 ATTTCATATA
1 ATTTCATATA
15913084 TCTATATTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
12 3 0.05
13 39 0.62
14 15 0.24
15 6 0.10
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (14 bp):
ATTTCATATAACCG
Found at i:15913039 original size:40 final size:39
Alignment explanation
Indices: 15912993--15913097 Score: 165
Period size: 40 Copynumber: 2.6 Consensus size: 39
15912983 TCCAATGTTT
15912993 CATTTCATATATCTATTTCCATATAACCGATTCATATAAA
1 CATTTCATATATCTATTT-CATATAACCGATTCATATAAA
* *
15913033 TATTTCATATATCTATTTTCATATAACCGATTCATATAAC
1 CATTTCATATATCTA-TTTCATATAACCGATTCATATAAA
15913073 CATTTCATATATCTATATTCATATA
1 CATTTCATATATCTAT-TTCATATA
15913098 TTCATTTTCA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
39 1 0.02
40 56 0.93
41 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.44
Consensus pattern (39 bp):
CATTTCATATATCTATTTCATATAACCGATTCATATAAA
Found at i:15913092 original size:27 final size:26
Alignment explanation
Indices: 15912993--15913097 Score: 97
Period size: 27 Copynumber: 3.9 Consensus size: 26
15912983 TCCAATGTTT
*
15912993 CATTTCATATATCTATTTCCATATAAC
1 CATTTCATATAACTATTT-CATATAAC
* *
15913020 CGA-TTCATATAAATATTTCATATATC
1 C-ATTTCATATAACTATTTCATATAAC
* *
15913046 TATTTTCATATAACCGA-TTCATATAAC
1 CA-TTTCATATAA-CTATTTCATATAAC
*
15913073 CATTTCATATATCTATATTCATATA
1 CATTTCATATAACTAT-TTCATATA
15913098 TTCATTTTCA
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
25 3 0.05
26 16 0.26
27 41 0.66
28 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.44
Consensus pattern (26 bp):
CATTTCATATAACTATTTCATATAAC
Found at i:15913107 original size:14 final size:14
Alignment explanation
Indices: 15912995--15913107 Score: 60
Period size: 13 Copynumber: 8.4 Consensus size: 14
15912985 CAATGTTTCA
15912995 TTTCATATATCTAT
1 TTTCATATATCTAT
* * *
15913009 TTCCATATAACCGA-
1 TTTCATAT-ATCTAT
**
15913023 -TTCATATAAATA-
1 TTTCATATATCTAT
15913035 TTTCATATATCTAT
1 TTTCATATATCTAT
* *
15913049 TTTCATATAACCGA-
1 TTTCATAT-ATCTAT
* *
15913063 -TTCATATAACCA-
1 TTTCATATATCTAT
15913075 TTTCATATATCTAT
1 TTTCATATATCTAT
*
15913089 ATTCATATAT-TCAT
1 TTTCATATATCT-AT
15913103 TTTCA
1 TTTCA
15913108 CACGATGAAC
Statistics
Matches: 75, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
12 5 0.07
13 34 0.45
14 30 0.40
15 6 0.08
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.46
Consensus pattern (14 bp):
TTTCATATATCTAT
Found at i:15915539 original size:23 final size:25
Alignment explanation
Indices: 15915512--15915563 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
15915502 TTTTTTTAGC
15915512 TATTTCATTATTTAGTTATT-TT-T
1 TATTTCATTATTTAGTTATTGTTAT
* * *
15915535 TATTTCTTTTTTTTGTTATTGTTAT
1 TATTTCATTATTTAGTTATTGTTAT
15915560 TATT
1 TATT
15915564 ATTATTGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.71
24 2 0.08
25 5 0.21
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (25 bp):
TATTTCATTATTTAGTTATTGTTAT
Found at i:15915610 original size:26 final size:23
Alignment explanation
Indices: 15915581--15915638 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
15915571 TTATTATTTC
*
15915581 TATATTTATACACGCATTTTTTA
1 TATATATATACACGCATTTTTTA
* *
15915604 TAGTATATATATATGCATTTTTTA
1 TA-TATATATACACGCATTTTTTA
15915628 TATATAATATA
1 TATAT-ATATA
15915639 TATATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (23 bp):
TATATATATACACGCATTTTTTA
Found at i:15915621 original size:24 final size:24
Alignment explanation
Indices: 15915594--15915641 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
15915584 ATTTATACAC
15915594 GCATTTTTTATAGTAT-ATATATAT
1 GCATTTTTTATA-TATAATATATAT
15915618 GCATTTTTTATATATAATATATAT
1 GCATTTTTTATATATAATATATAT
15915642 ATTTTTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.54
Consensus pattern (24 bp):
GCATTTTTTATATATAATATATAT
Found at i:15920660 original size:5 final size:6
Alignment explanation
Indices: 15920645--15920678 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
15920635 TGAAAGTGAT
15920645 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
15920679 TGGAGAGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:15920668 original size:18 final size:17
Alignment explanation
Indices: 15920645--15920678 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
15920635 TGAAAGTGAT
15920645 AAAAAGAAAAAGAAAAAG
1 AAAAAG-AAAAGAAAAAG
15920663 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
15920679 TGGAGAGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAG
Found at i:15930692 original size:34 final size:35
Alignment explanation
Indices: 15930558--15930711 Score: 93
Period size: 34 Copynumber: 4.5 Consensus size: 35
15930548 TTCAATTACG
* *
15930558 TCCCGCCATAATGCCAGAACTTCATT-TATCAATCA
1 TCCCGCCACAATGCCAGAACTTCATTCAATCAA-CA
* * ** *
15930593 TCCAGCCACAATGCCA-ATAATTTTTTCAATTAACA
1 TCCCGCCACAATGCCAGA-ACTTCATTCAATCAACA
* * * **
15930628 TTCTG-TACAACCCCA-ATACTTCATTCAATCAACA
1 TCCCGCCACAATGCCAGA-ACTTCATTCAATCAACA
* *
15930662 TCCCGCCACAATGCCAGAATTTCATT-AATCAATA
1 TCCCGCCACAATGCCAGAACTTCATTCAATCAACA
* * *
15930696 TCTCTCCACAACGCCA
1 TCCCGCCACAATGCCA
15930712 ATAGATCAAA
Statistics
Matches: 89, Mismatches: 26, Indels: 9
0.72 0.21 0.07
Matches are distributed among these distances:
34 46 0.52
35 38 0.43
36 5 0.06
ACGTcount: A:0.34, C:0.32, G:0.06, T:0.28
Consensus pattern (35 bp):
TCCCGCCACAATGCCAGAACTTCATTCAATCAACA
Found at i:15930954 original size:9 final size:9
Alignment explanation
Indices: 15930940--15930964 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
15930930 CACTCAATAG
15930940 AACAACATC
1 AACAACATC
15930949 AACAACATC
1 AACAACATC
15930958 AACAACA
1 AACAACA
15930965 ACAAAGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.32, G:0.00, T:0.08
Consensus pattern (9 bp):
AACAACATC
Found at i:15933734 original size:17 final size:18
Alignment explanation
Indices: 15933712--15933747 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15933702 TAAGGTTTTC
15933712 ATAATA-AAAAAAATAAA
1 ATAATATAAAAAAATAAA
*
15933729 ATAATATAAAAAGATAAA
1 ATAATATAAAAAAATAAA
15933747 A
1 A
15933748 ATTAAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (18 bp):
ATAATATAAAAAAATAAA
Found at i:15952187 original size:35 final size:34
Alignment explanation
Indices: 15952148--15952232 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 34
15952138 TTAACATTTC
* **
15952148 GCCACAACCCCAATACTTAATTAAATTTACATCCT
1 GCCACAACACCAATACTTAATT-AATCAACATCCT
* *
15952183 GCCACAACACCAGA-ACTTTATTAATCAATATCCT
1 GCCACAACACCA-ATACTTAATTAATCAACATCCT
*
15952217 GCCACAACGCCAATAC
1 GCCACAACACCAATAC
15952233 ATCATAACAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
33 1 0.02
34 22 0.52
35 18 0.43
36 1 0.02
ACGTcount: A:0.38, C:0.33, G:0.06, T:0.24
Consensus pattern (34 bp):
GCCACAACACCAATACTTAATTAATCAACATCCT
Found at i:15962812 original size:87 final size:87
Alignment explanation
Indices: 15962660--15962822 Score: 231
Period size: 87 Copynumber: 1.9 Consensus size: 87
15962650 CATGTATAAC
* * *
15962660 GTTGAGTTCTTACTCTTGATGAATTCATAGCCCCCGAGTTTTGGTGATCACATTGAGACGAACTT
1 GTTGAGTTCTTACTCTTAATGAATTCATAGCCCCAGAGTTTGGGTGATCACATTGAGACGAACTT
15962725 GATGAATTCACCGACATGTGAG
66 GATGAATTCACCGACATGTGAG
* * * *
15962747 GTTGAGTTTCTTACTCTTAATGAGTTCATA-TCCCAGAGTTTGGGTGGTC-CTATTGAGACGTAC
1 GTTGAG-TTCTTACTCTTAATGAATTCATAGCCCCAGAGTTTGGGTGATCAC-ATTGAGACGAAC
15962810 TTGATGAATTCAC
64 TTGATGAATTCAC
15962823 TGAATTTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
86 1 0.01
87 45 0.67
88 21 0.31
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (87 bp):
GTTGAGTTCTTACTCTTAATGAATTCATAGCCCCAGAGTTTGGGTGATCACATTGAGACGAACTT
GATGAATTCACCGACATGTGAG
Found at i:15963712 original size:24 final size:25
Alignment explanation
Indices: 15963685--15963736 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
15963675 CACATGTTTC
*
15963685 TTTTCAG-TATATTTTTTGATTATT
1 TTTTCAGCTATATTTTTCGATTATT
*
15963709 TTTTCAGCTCTATTTTTCGATTATT
1 TTTTCAGCTATATTTTTCGATTATT
15963734 TTT
1 TTT
15963737 CTTTTCTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.17, C:0.10, G:0.08, T:0.65
Consensus pattern (25 bp):
TTTTCAGCTATATTTTTCGATTATT
Found at i:15964275 original size:20 final size:21
Alignment explanation
Indices: 15964237--15964275 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
15964227 AATCTAAAAA
*
15964237 AAAAAGAATAATAGCTAAATT
1 AAAAAGAATAAAAGCTAAATT
*
15964258 AAAAA-AATAAAAGTTAAA
1 AAAAAGAATAAAAGCTAAA
15964276 GGCTAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (21 bp):
AAAAAGAATAAAAGCTAAATT
Found at i:15967399 original size:23 final size:23
Alignment explanation
Indices: 15967372--15967416 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
15967362 CGAAAATATT
15967372 AAATATATATA-TTTTTATTTTTA
1 AAATATA-ATAGTTTTTATTTTTA
15967395 AAATATAATAGTTTTTTATTTT
1 AAATATAATAG-TTTTTATTTT
15967417 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 7 0.35
24 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
AAATATAATAGTTTTTATTTTTA
Found at i:15967546 original size:59 final size:59
Alignment explanation
Indices: 15967483--15967661 Score: 223
Period size: 68 Copynumber: 2.9 Consensus size: 59
15967473 TCAAGTTTGT
* *
15967483 TTTACTAATCAAATGTTAAATTTTGTTACAACAATTAATATAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATATAATTAATAATTTGATAAA
*
15967542 TTTACTAATTAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAA-T--T--AA-T-AT--AATTAATAATTTGAT
15967607 AAA
57 AAA
* * *
15967610 TTTACTAATCAAATGTTAGATTTTATTACAATAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATATAATTAATAATT
15967662 AATAATTTGA
Statistics
Matches: 104, Mismatches: 7, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
59 41 0.39
60 1 0.01
61 1 0.01
62 2 0.02
63 2 0.02
64 2 0.02
65 2 0.02
66 2 0.02
67 1 0.01
68 50 0.48
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATATAATTAATAATTTGATAAA
Found at i:15967584 original size:9 final size:9
Alignment explanation
Indices: 15967572--15967599 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
15967562 TTTTATTACA
15967572 ACAATTAAT
1 ACAATTAAT
15967581 ACAATTAAT
1 ACAATTAAT
15967590 ACAATTAAT
1 ACAATTAAT
15967599 A
1 A
15967600 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:15967587 original size:68 final size:68
Alignment explanation
Indices: 15967513--15967683 Score: 292
Period size: 68 Copynumber: 2.5 Consensus size: 68
15967503 TTTTGTTACA
* *
15967513 ACAATTAATATAATTAATAATTTGATAAATTTACTAATTAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
15967578 AAT
66 AAT
*
15967581 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAATAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
15967646 AAT
66 AAT
*
15967649 ACAATT-A-ACAATTAATAATTTGATAATTTTACTAA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAA
15967684 CAATTAATTT
Statistics
Matches: 99, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
66 27 0.27
67 1 0.01
68 71 0.72
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (68 bp):
ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
AAT
Found at i:15967693 original size:16 final size:16
Alignment explanation
Indices: 15967672--15967713 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
15967662 AATAATTTGA
*
15967672 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
15967688 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
15967704 TAGTTTTAAT
1 TAATTTTAAT
15967714 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:15967697 original size:22 final size:23
Alignment explanation
Indices: 15967687--15967742 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
15967677 TTACTAACAA
* * *
15967687 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAACTAATT
*
15967709 TTAATTTTATTAAAAAACTAATT
1 TTAATTTTAATAAAAAACTAATT
15967732 TTAATTTTAAT
1 TTAATTTTAAT
15967743 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAACTAATT
Found at i:15987819 original size:50 final size:50
Alignment explanation
Indices: 15987728--15987865 Score: 188
Period size: 50 Copynumber: 2.8 Consensus size: 50
15987718 CGGGTTGCAA
* * *
15987728 AGGCTTTCCAGATAACTTCACCACTAAGGCTTCCCAAATAATATGACACGT
1 AGGCTTTTCAGATAAC-TCACCACAAAGGCTTTCCAAATAATATGACACGT
* *
15987779 AGGCTTTTCAGATAACTCACCACAAAGGCTTTCCAGATAATATGCCACGT
1 AGGCTTTTCAGATAACTCACCACAAAGGCTTTCCAAATAATATGACACGT
* * *
15987829 AGGC-CTTCAGATAACTCGCCATAAAGGCTTTCCAAAT
1 AGGCTTTTCAGATAACTCACCACAAAGGCTTTCCAAAT
15987866 GACTTGTCAC
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
49 29 0.37
50 34 0.44
51 15 0.19
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (50 bp):
AGGCTTTTCAGATAACTCACCACAAAGGCTTTCCAAATAATATGACACGT
Found at i:15987856 original size:24 final size:24
Alignment explanation
Indices: 15987785--15987856 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
15987775 ACGTAGGCTT
* *
15987785 TTCAGATAACTCACCACAAAGGCT
1 TTCAGATAACTCGCCACAAAGGCC
* **
15987809 TTCCAGATAA-TATGCCACGTAGGCC
1 TT-CAGATAACT-CGCCACAAAGGCC
*
15987834 TTCAGATAACTCGCCATAAAGGC
1 TTCAGATAACTCGCCACAAAGGC
15987857 TTTCCAAATG
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
24 18 0.50
25 18 0.50
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (24 bp):
TTCAGATAACTCGCCACAAAGGCC
Found at i:15987879 original size:25 final size:26
Alignment explanation
Indices: 15987725--15987918 Score: 121
Period size: 25 Copynumber: 7.7 Consensus size: 26
15987715 ACTCGGGTTG
* **
15987725 CAAAGGCTTTCCAGATAACTTCACCA
1 CAAAGGCTTTCCAAATAACTTTGCCA
* * * *
15987751 CTAAGGCTTCCCAAATAA-TATGACA
1 CAAAGGCTTTCCAAATAACTTTGCCA
** * * **
15987776 CGTAGGCTTTTCAGATAAC-TCACCA
1 CAAAGGCTTTCCAAATAACTTTGCCA
* *
15987801 CAAAGGCTTTCCAGATAA-TATGCCA
1 CAAAGGCTTTCCAAATAACTTTGCCA
** * * *
15987826 CGTAGGCCTT-CAGATAAC-TCGCCA
1 CAAAGGCTTTCCAAATAACTTTGCCA
* * *
15987850 TAAAGGCTTTCCAAATGAC-TTGTCA
1 CAAAGGCTTTCCAAATAACTTTGCCA
15987875 CAAAGGCTTTCCAAATAACTTTGCCA
1 CAAAGGCTTTCCAAATAACTTTGCCA
* *
15987901 CTAAGGCTTCCCAAATAA
1 CAAAGGCTTTCCAAATAA
15987919 TATGTCACAT
Statistics
Matches: 123, Mismatches: 40, Indels: 10
0.71 0.23 0.06
Matches are distributed among these distances:
24 17 0.14
25 70 0.57
26 36 0.29
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (26 bp):
CAAAGGCTTTCCAAATAACTTTGCCA
Found at i:15993390 original size:48 final size:48
Alignment explanation
Indices: 15993321--15993519 Score: 245
Period size: 48 Copynumber: 4.1 Consensus size: 48
15993311 TCAGAATAAA
* * *
15993321 AACAGATTTCTCGGTGGCCTGCACACAGTCCATTCCACCTTTGTATAAT
1 AACAGA-TTCTCGGTGGCCTGCACACAGTCCATGCCACCCTTGTATCAT
* * * *
15993370 AATAGATTCTCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCTT
1 AACAGATTCTCGGTGGCCTGCACACAGTCCATGCCACCCTTGTATCAT
* * * * *
15993418 AACAGGTTGTTGGTGGCCTGCACACAGTCCGTGCCACCCTTATATCAT
1 AACAGATTCTCGGTGGCCTGCACACAGTCCATGCCACCCTTGTATCAT
* * * *
15993466 AACAGAATATCGGTGGCCAGCACACAGTCCATGCCACCCTTGTGTCAT
1 AACAGATTCTCGGTGGCCTGCACACAGTCCATGCCACCCTTGTATCAT
15993514 AACAGA
1 AACAGA
15993520 ATATCGGTAC
Statistics
Matches: 128, Mismatches: 22, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
48 123 0.96
49 5 0.04
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (48 bp):
AACAGATTCTCGGTGGCCTGCACACAGTCCATGCCACCCTTGTATCAT
Found at i:15995018 original size:15 final size:16
Alignment explanation
Indices: 15994998--15995032 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
15994988 ATTTAACGGT
15994998 AAATTTTATA-TTTGA
1 AAATTTTATATTTTGA
*
15995013 AAATTTTTTATTTTGA
1 AAATTTTATATTTTGA
15995029 AAAT
1 AAAT
15995033 GCCATTAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (16 bp):
AAATTTTATATTTTGA
Found at i:15995027 original size:16 final size:17
Alignment explanation
Indices: 15995001--15995032 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
15994991 TAACGGTAAA
15995001 TTTTATATTTGAAAATT
1 TTTTATATTTGAAAATT
15995018 TTTTAT-TTTGAAAAT
1 TTTTATATTTGAAAAT
15995033 GCCATTAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TTTTATATTTGAAAATT
Found at i:16002875 original size:23 final size:22
Alignment explanation
Indices: 16002836--16002878 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
16002826 GATTGAATTG
16002836 AATTTTTAATATCTTATTTTAT
1 AATTTTTAATATCTTATTTTAT
16002858 AATTTTATAATAAT-TTATTTT
1 AATTTT-TAAT-ATCTTATTTT
16002879 TATTGAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 11 0.58
24 2 0.11
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
AATTTTTAATATCTTATTTTAT
Found at i:16005286 original size:28 final size:28
Alignment explanation
Indices: 16005225--16005286 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
16005215 TCTAAAAAGG
* * *
16005225 TTTTTAAATTTAAAGTTTTTTTTTCAAT
1 TTTTAAAATTTAAAGTTTTTTTTTAAAA
16005253 TATTTAAAATTTAAA-TATTTTTTTTAAAA
1 T-TTTAAAATTTAAAGT-TTTTTTTTAAAA
16005282 TTTTA
1 TTTTA
16005287 TAACAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTAAAATTTAAAGTTTTTTTTTAAAA
Found at i:16005368 original size:23 final size:22
Alignment explanation
Indices: 16005342--16005390 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 22
16005332 TATAATTATA
16005342 TATTTTAGAA-TTTTATAAAAAAT
1 TATTTTA-AACTTTTA-AAAAAAT
16005365 TATTTTTAAACTTTTAAAAAAAT
1 TA-TTTTAAACTTTTAAAAAAAT
16005388 TAT
1 TAT
16005391 ATTTTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 1 0.04
23 13 0.54
24 10 0.42
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTTTAAACTTTTAAAAAAAT
Found at i:16005379 original size:24 final size:24
Alignment explanation
Indices: 16005340--16005396 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
16005330 TTTATAATTA
16005340 TATATTTTAGAATTTTATAAAAAAT
1 TATATTTTAGAATTTTA-AAAAAAT
16005365 TAT-TTTTA-AACTTTTAAAAAAAT
1 TATATTTTAGAA-TTTTAAAAAAAT
16005388 TATATTTTA
1 TATATTTTA
16005397 TATATGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 12 0.40
24 15 0.50
25 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TATATTTTAGAATTTTAAAAAAAT
Found at i:16005664 original size:32 final size:31
Alignment explanation
Indices: 16005610--16005669 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
16005600 AATTATCACA
16005610 TGGCACATTTTCATCAGCCAAAATATGCCATG
1 TGGCACATTTTCATCAGCCAAAAT-TGCCATG
* ** *
16005642 TGGCACCTTTTCATTTGTCAAAATTGCC
1 TGGCACATTTTCATCAGCCAAAATTGCC
16005670 TAACAATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 4 0.17
32 20 0.83
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (31 bp):
TGGCACATTTTCATCAGCCAAAATTGCCATG
Found at i:16006831 original size:19 final size:19
Alignment explanation
Indices: 16006769--16006837 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 19
16006759 GACATTTTCC
*
16006769 ATTAAGTGTAATTAATGGTTGG
1 ATTAAGT-TAATTAA--GTTAG
* **
16006791 ATTATGTTAATTAA-CAATG
1 ATTAAGTTAATTAAGTTA-G
16006810 ATTAAGTTAATTAAGTTAG
1 ATTAAGTTAATTAAGTTAG
16006829 ATTAA-TTAA
1 ATTAAGTTAA
16006838 GTCTTAATCA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 4 0.11
19 20 0.53
20 1 0.03
21 7 0.18
22 6 0.16
ACGTcount: A:0.41, C:0.01, G:0.16, T:0.42
Consensus pattern (19 bp):
ATTAAGTTAATTAAGTTAG
Found at i:16008658 original size:6 final size:6
Alignment explanation
Indices: 16008644--16008682 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
16008634 GGATTGCAAG
* * *
16008644 TTTCCA TTTCTA TTTTCA TTTTCA TTTCCA TTTCCA TTT
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTT
16008683 TTGGAAACCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (6 bp):
TTTCCA
Found at i:16012891 original size:30 final size:30
Alignment explanation
Indices: 16012868--16013127 Score: 378
Period size: 30 Copynumber: 8.7 Consensus size: 30
16012858 GTATATGTTT
* * *
16012868 TATATATTTCCGAATTGA-TTGTATATGGG
1 TATACATTGCCGAATTGATTTGTATATGGA
16012897 TATACATTGCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
16012927 TATACATTGTCAAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
16012957 TATACATTGCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
16012987 TATACATTGCCGAATTAATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
** **
16013017 TATACATTGCTAAATTGATTTGTATATCAA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
16013047 TATAGATTGCCGAATTGATTTGTATATAGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
16013077 TATACATTGTCGAATTGATTTGTATATGTA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
16013107 TATATATTGCCGAATTGATTT
1 TATACATTGCCGAATTGATTT
16013128 AAGCATTGGA
Statistics
Matches: 206, Mismatches: 24, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
29 16 0.08
30 190 0.92
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (30 bp):
TATACATTGCCGAATTGATTTGTATATGGA
Found at i:16022821 original size:86 final size:86
Alignment explanation
Indices: 16022648--16022813 Score: 226
Period size: 86 Copynumber: 1.9 Consensus size: 86
16022638 CTTTTTAAAC
* * * *
16022648 ATTTAAATTTTAAATTATTCCAAATACTTTTTGGGAATATTTGAGATACAGTTTATAAATAAATA
1 ATTTAAAATTTAAATTATTCCAAATACTTTTTGGGAATATTTGAAATACAGTGTATAAAGAAATA
* ***
16022713 AAAATTATATGTATGACGTAT
66 AAAATTAAAAAAATGACGTAT
*
16022734 ATTTAAAATTTAAATTATTCCAAATACTTTTTGGGAATATTTGAAATACGGTGTATAAAGAAA-A
1 ATTTAAAATTTAAATTATTCCAAATACTTTTTGGGAATATTTGAAATACAGTGTATAAAGAAATA
16022798 AAAAGTTGAAAAAAAT
66 AAAA-TT-AAAAAAAT
16022814 ATTTATATAA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
85 5 0.07
86 60 0.87
87 4 0.06
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.38
Consensus pattern (86 bp):
ATTTAAAATTTAAATTATTCCAAATACTTTTTGGGAATATTTGAAATACAGTGTATAAAGAAATA
AAAATTAAAAAAATGACGTAT
Found at i:16031208 original size:25 final size:25
Alignment explanation
Indices: 16031179--16031230 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
16031169 TTTAACGACT
16031179 TCCTTCATAATAGGATTCAATCTTC
1 TCCTTCATAATAGGATTCAATCTTC
16031204 TCCTTCATAATAGGATTCAATCTTC
1 TCCTTCATAATAGGATTCAATCTTC
16031229 TC
1 TC
16031231 TATTGCTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (25 bp):
TCCTTCATAATAGGATTCAATCTTC
Found at i:16065826 original size:19 final size:20
Alignment explanation
Indices: 16065804--16065850 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
16065794 TCAAAACAAG
*
16065804 TTCAAAATAATTT-TTAAAA-
1 TTCAAAAT-ATTTATAAAAAT
*
16065823 TTCATAATATTTATAAAAAT
1 TTCAAAATATTTATAAAAAT
16065843 TTCAAAAT
1 TTCAAAAT
16065851 TTATATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 12 0.52
20 7 0.30
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (20 bp):
TTCAAAATATTTATAAAAAT
Found at i:16070881 original size:29 final size:29
Alignment explanation
Indices: 16070848--16071457 Score: 878
Period size: 29 Copynumber: 21.3 Consensus size: 29
16070838 AAATAAATTA
* *
16070848 GGTTAGGGTTTTTAAATAAATTAGGGTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
16070877 GGTTAGGATTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
16070906 GGTTAGAGTTTTTAAATAAATTAGGTTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
16070935 GGTTAGGGTTTTTAATTAAATTAGGGTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
16070964 GGTTAGGATTTTTAATTAAATTAGGTTTA-
1 GGTTAGGGTTTTTAATTAAATTAGG-TTAG
*
16070993 AGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
16071022 GGTTAGGGTTTTTAAATAAATTAGGTTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
16071051 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
16071080 GGTTAGGGTTTTTAAATAAATTAGGCTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
16071109 GGTTAGGGTTTTTAATTAAATTAGGGTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
16071138 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
16071167 AGTTAGGGTTTTTAAATAAATTAGGTTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
16071196 GGTTAGGGTTTTTAATT-AA--A--TTA-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
16071219 GGTTAGGGTTTTTAAATAAATTAGGCTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
16071248 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
16071277 GGTTAGGGTTTTTAAATAAATTAGGTTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
16071306 TGTTAGGG-TTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
16071334 GGTTAAGGTTTTTAAATAAATTAGGTTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
16071363 GGTTAGGGTTTTTAATTAAATTAGGTTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
16071392 GGTTAGGG-TTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
16071420 GGTTAGGGTTTTTAATTAAATCAGGTTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
16071449 GGTTAGGGT
1 GGTTAGGGT
16071458 ATGAAATAAA
Statistics
Matches: 520, Mismatches: 51, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
23 16 0.03
24 5 0.01
26 2 0.00
28 58 0.11
29 437 0.84
30 2 0.00
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:16071388 original size:23 final size:23
Alignment explanation
Indices: 16071362--16071423 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 23
16071352 AATTAGGTTA
16071362 AGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
16071385 AGGTTAAGGTTAGGGTTTTAATTAAATT
1 AGGTT-A-G---GGTTTTTAATTAAATT
16071413 AGGTTAGGGTT
1 AGGTTAGGGTT
16071424 AGGGTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
23 8 0.25
24 1 0.03
25 1 0.03
26 1 0.03
27 1 0.03
28 20 0.62
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (23 bp):
AGGTTAGGGTTTTTAATTAAATT
Found at i:16071491 original size:26 final size:25
Alignment explanation
Indices: 16071461--16071518 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
16071451 TTAGGGTATG
16071461 AAATAAA-TTACGATTTTTATTACATC
1 AAATAAACTT-CGA-TTTTATTACATC
* *
16071487 AAATAGAACTTCTATTTTATTATATC
1 AAATA-AACTTCGATTTTATTACATC
16071513 AAATAA
1 AAATAA
16071519 TATCTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 1 0.04
26 21 0.75
27 4 0.14
28 2 0.07
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.41
Consensus pattern (25 bp):
AAATAAACTTCGATTTTATTACATC
Found at i:16073908 original size:22 final size:21
Alignment explanation
Indices: 16073883--16073933 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
16073873 TAATATGGAT
*
16073883 TTGAGAGATTTTTGGAATGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
16073905 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGA-GATTTTGGAAGGAAA
16073927 TTGAGAG
1 TTGAGAG
16073934 TTTAAGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 24 0.89
23 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.31
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:16073958 original size:52 final size:52
Alignment explanation
Indices: 16073886--16073984 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
16073876 TATGGATTTG
* * *
16073886 AGAGATTTTTGGAATGAAATTGAGAGGATTTTGGAAGGAAATTGAGAGTTTA
1 AGAGAATTTTGAAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGAGTTTA
16073938 AGAGAATTTTGAAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGA
1 AGAGAATTTTGAAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGA
16073985 TAGGATTTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.29
Consensus pattern (52 bp):
AGAGAATTTTGAAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGAGTTTA
Found at i:16073997 original size:27 final size:22
Alignment explanation
Indices: 16073938--16073984 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
16073928 TGAGAGTTTA
*
16073938 AGAGAATTTTGAAAGGAAATTG
1 AGAGGATTTTGAAAGGAAATTG
*
16073960 AGAGGATTTTGGAAGGAAATTG
1 AGAGGATTTTGAAAGGAAATTG
16073982 AGA
1 AGA
16073985 TAGGATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.26
Consensus pattern (22 bp):
AGAGGATTTTGAAAGGAAATTG
Found at i:16076721 original size:21 final size:22
Alignment explanation
Indices: 16076684--16076726 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
16076674 ATTATTTTTA
*
16076684 ATTTTTAAAATTCAAAAAATAT
1 ATTTTTAAAAATCAAAAAATAT
16076706 ATTTTTAAAAAT-AAAAAATAT
1 ATTTTTAAAAATCAAAAAATAT
16076727 TACATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTTTTAAAAATCAAAAAATAT
Found at i:16076734 original size:22 final size:22
Alignment explanation
Indices: 16076687--16076734 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
16076677 ATTTTTAATT
* **
16076687 TTTAAAATTCAAAAAATATATT
1 TTTAAAAATCAAAAAATATACA
16076709 TTTAAAAAT-AAAAAATATTACA
1 TTTAAAAATCAAAAAATA-TACA
16076731 TTTA
1 TTTA
16076735 TTAAAGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAAATCAAAAAATATACA
Found at i:16079031 original size:18 final size:19
Alignment explanation
Indices: 16079010--16079052 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
16079000 TATATGAGAA
*
16079010 TTAAAAAATTTT-AATATT
1 TTAAAAAATTTTAAAAATT
16079028 TT-AAAAATTTTAAAAATT
1 TTAAAAAATTTTAAAAATT
16079046 TTAAAAA
1 TTAAAAA
16079053 TTAATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 9 0.41
19 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAAAAATTTTAAAAATT
Found at i:16079053 original size:9 final size:9
Alignment explanation
Indices: 16079013--16079054 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
16079003 ATGAGAATTA
16079013 AAAAATTTT
1 AAAAATTTT
*
16079022 -AATATTTT
1 AAAAATTTT
16079030 AAAAATTTT
1 AAAAATTTT
16079039 AAAAATTTT
1 AAAAATTTT
16079048 AAAAATT
1 AAAAATT
16079055 AATTAAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AAAAATTTT
Found at i:16079053 original size:18 final size:17
Alignment explanation
Indices: 16078964--16079054 Score: 69
Period size: 18 Copynumber: 5.1 Consensus size: 17
16078954 AAAAAAATAT
*
16078964 TTTTAAAA-ATTAAAAA
1 TTTTAAAATTTTAAAAA
16078980 TTATTAAAATTATTAAAAAA
1 TT-TTAAAATT-TT-AAAAA
* * *
16079000 TATATGAGAA-TTAAAAAA
1 T-T-TTAAAATTTTAAAAA
*
16079018 TTTTAATATTTTAAAAA
1 TTTTAAAATTTTAAAAA
16079035 TTTTAAAAATTTTAAAAA
1 TTTT-AAAATTTTAAAAA
16079053 TT
1 TT
16079055 AATTAAATGT
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
16 5 0.08
17 18 0.31
18 20 0.34
19 3 0.05
20 7 0.12
21 6 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTTAAAATTTTAAAAA
Found at i:16079828 original size:30 final size:30
Alignment explanation
Indices: 16079769--16079832 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
16079759 TTTTCTTTAG
*
16079769 TTTTCTTCTCTTCTTCTTCGTTACCTTTCT
1 TTTTCTTCTCTTCTTATTCGTTACCTTTCT
*
16079799 TTTTCTTCTTCTTCATTATTC-TT-CTTTTCT
1 TTTTCTTC-TCTTC-TTATTCGTTACCTTTCT
16079829 TTTT
1 TTTT
16079833 ATTTTTGCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 18 0.60
31 7 0.23
32 5 0.17
ACGTcount: A:0.05, C:0.25, G:0.02, T:0.69
Consensus pattern (30 bp):
TTTTCTTCTCTTCTTATTCGTTACCTTTCT
Found at i:16092180 original size:26 final size:24
Alignment explanation
Indices: 16092147--16092207 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
16092137 AGCCATGATT
*
16092147 GGTAAGCTCATTTCGAGCTAAAGAAC
1 GGTAAGCTCATATCGAGCT-AA-AAC
* *
16092173 GGTAAGCTC-TATCTAGCTGAAAC
1 GGTAAGCTCATATCGAGCTAAAAC
16092196 GGTAAGCTCATA
1 GGTAAGCTCATA
16092208 AGAGTTGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 12 0.39
24 3 0.10
25 7 0.23
26 9 0.29
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (24 bp):
GGTAAGCTCATATCGAGCTAAAAC
Found at i:16096528 original size:20 final size:20
Alignment explanation
Indices: 16096503--16096542 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16096493 GATGCATAGT
* *
16096503 AGAGGCATCGAAGTGCAAAC
1 AGAGGCACCAAAGTGCAAAC
16096523 AGAGGCACCAAAGTGCAAAC
1 AGAGGCACCAAAGTGCAAAC
16096543 CTGTACAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.28, T:0.07
Consensus pattern (20 bp):
AGAGGCACCAAAGTGCAAAC
Found at i:16096851 original size:10 final size:10
Alignment explanation
Indices: 16096836--16096868 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
16096826 TATCACAAGT
*
16096836 TATATAAATA
1 TATATAATTA
16096846 TATATAATTA
1 TATATAATTA
16096856 TATATAATTA
1 TATATAATTA
16096866 TAT
1 TAT
16096869 TTATCTATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TATATAATTA
Found at i:16108076 original size:21 final size:25
Alignment explanation
Indices: 16108025--16108076 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 25
16108015 AAAAAATAAA
16108025 AAAAATTTGAAGCATATTGTAATCT
1 AAAAATTTGAAGCATATTGTAATCT
**
16108050 TTAAATTT-AA-C-TATT-TAATCT
1 AAAAATTTGAAGCATATTGTAATCT
16108071 AAAAAT
1 AAAAAT
16108077 AATTATCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
21 10 0.43
22 4 0.17
23 1 0.04
24 2 0.09
25 6 0.26
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (25 bp):
AAAAATTTGAAGCATATTGTAATCT
Found at i:16109384 original size:75 final size:75
Alignment explanation
Indices: 16109304--16109454 Score: 230
Period size: 75 Copynumber: 2.0 Consensus size: 75
16109294 ATTTTAACTC
* * * *
16109304 AATTAATTTTCATGTTTTGGGCTTTATCTTGTCCAAATATCTCCAAAACAGATAGCACAATGCTT
1 AATTAATTTTCATATTTTGGGCTTTAACTTATCCAAATATCTCAAAAACAGATAGCACAATGCTT
16109369 TTACTTTAAA
66 TTACTTTAAA
* * *
16109379 AATTAATTTTCATATTTTGGGTTTTAACTTATCCAAATATCTCAAAAACAGATAGCCCATTGCTT
1 AATTAATTTTCATATTTTGGGCTTTAACTTATCCAAATATCTCAAAAACAGATAGCACAATGCTT
*
16109444 TTATTTTAAA
66 TTACTTTAAA
16109454 A
1 A
16109455 TTTGCCAATT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 68 1.00
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (75 bp):
AATTAATTTTCATATTTTGGGCTTTAACTTATCCAAATATCTCAAAAACAGATAGCACAATGCTT
TTACTTTAAA
Found at i:16110988 original size:49 final size:49
Alignment explanation
Indices: 16110916--16111025 Score: 220
Period size: 49 Copynumber: 2.2 Consensus size: 49
16110906 GGTTGGACGA
16110916 TTGAAGGATTGGAACATCGAGAGTAAGGGTTAGAGTGAACGATTGAAGG
1 TTGAAGGATTGGAACATCGAGAGTAAGGGTTAGAGTGAACGATTGAAGG
16110965 TTGAAGGATTGGAACATCGAGAGTAAGGGTTAGAGTGAACGATTGAAGG
1 TTGAAGGATTGGAACATCGAGAGTAAGGGTTAGAGTGAACGATTGAAGG
16111014 TTGAAGGATTGG
1 TTGAAGGATTGG
16111026 TATTTTCGTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 61 1.00
ACGTcount: A:0.34, C:0.05, G:0.37, T:0.24
Consensus pattern (49 bp):
TTGAAGGATTGGAACATCGAGAGTAAGGGTTAGAGTGAACGATTGAAGG
Found at i:16110992 original size:21 final size:21
Alignment explanation
Indices: 16110919--16110992 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 21
16110909 TGGACGATTG
16110919 AAGGATTGGAACATCGAGAGT
1 AAGGATTGGAACATCGAGAGT
* *
16110940 AAGGGTTAGAGTGAACGATTGA-AGGTT
1 AAGGATT---G-GAAC-ATCGAGA-G-T
16110967 GAAGGATTGGAACATCGAGAGT
1 -AAGGATTGGAACATCGAGAGT
16110989 AAGG
1 AAGG
16110993 GTTAGAGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
21 10 0.25
22 1 0.03
23 5 0.12
24 6 0.15
25 6 0.15
26 5 0.12
27 1 0.03
28 6 0.15
ACGTcount: A:0.36, C:0.07, G:0.36, T:0.20
Consensus pattern (21 bp):
AAGGATTGGAACATCGAGAGT
Found at i:16111779 original size:184 final size:183
Alignment explanation
Indices: 16111402--16111761 Score: 598
Period size: 186 Copynumber: 2.0 Consensus size: 183
16111392 ATGGCCTGCT
* *
16111402 ATGTGCATACAGATAGCCTTAGGGTTTAGTGACATCATTTTTTATTGAATTATTTGAAACTGTGT
1 ATGTGCATACAGATAGCATTAGGGTTTAGTGAAATCATTTTTTATTGAATTATTTGAAACTGTGT
16111467 ATGTCATTGAATTATTCAAATATGATACAAAATATTTTTAAATGTTGATTGAAATATGATTTTAT
66 ATGTCATTGAATTATTCAAATATGATACAAAATATTTTTAAATGTTGATTGAAATATGA-TTTAT
* *
16111532 TGTTTGTATCAAACTGAATTGTAGGTTTGGATTTTTGTAAACTTATGGTCTACC
130 TGTTTGTATCAAACTGAATTGCAGGTTTGGATTTATGTAAACTTATGGTCTACC
16111586 ATGTGCATACAGATAGCATTAGGGTTTAGTGATAAATCATTTTTTATTGAATTATTTGAAACTGT
1 ATGTGCATACAGATAGCATTAGGGTTTAGTG--AAATCATTTTTTATTGAATTATTTGAAACTGT
** * *
16111651 GTATGTCATTGAATTATTCAAATATGATTTATGAGTA-TTTTAAATGTTGATTGAAATATGA-TT
64 GTATGTCATTGAATTATTCAAATATGATACA-AAATATTTTTAAATGTTGATTGAAATATGATTT
16111714 ATTGTTTGTATCAAACTGAATTGCAGGTTTGGATTTATGTAAACTTAT
128 ATTGTTTGTATCAAACTGAATTGCAGGTTTGGATTTATGTAAACTTAT
16111762 TGTTCGCCAT
Statistics
Matches: 165, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
184 78 0.47
186 84 0.51
187 3 0.02
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (183 bp):
ATGTGCATACAGATAGCATTAGGGTTTAGTGAAATCATTTTTTATTGAATTATTTGAAACTGTGT
ATGTCATTGAATTATTCAAATATGATACAAAATATTTTTAAATGTTGATTGAAATATGATTTATT
GTTTGTATCAAACTGAATTGCAGGTTTGGATTTATGTAAACTTATGGTCTACC
Found at i:16116410 original size:44 final size:42
Alignment explanation
Indices: 16116250--16116407 Score: 163
Period size: 44 Copynumber: 3.6 Consensus size: 42
16116240 CACTTTAATT
* * * *
16116250 TGCTTCACTGCAACTTTAGGGAGATAGGATTAGTAGCTTCAGCC
1 TGCTCCACTGCAACTTTAGAGAGATAGGATT-GTA-TTTCAACC
*
16116294 TGCTCCACTGCAACTTTAGGGAGATAGGAATTGTATCTTCAACC
1 TGCTCCACTGCAACTTTAGAGAGATAGG-ATTGTAT-TTCAACC
* * * *
16116338 TGCCCCACTGCAACTTCAGAGGGATAAGGCTTGTTATTTCAACC
1 TGCTCCACTGCAACTTTAGAGAGAT-AGGATTG-TATTTCAACC
* *
16116382 TACTCTACTGCAACTTTAGAGAGATA
1 TGCTCCACTGCAACTTTAGAGAGATA
16116408 AGGTTTGATA
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
43 1 0.01
44 87 0.90
45 9 0.09
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (42 bp):
TGCTCCACTGCAACTTTAGAGAGATAGGATTGTATTTCAACC
Found at i:16116997 original size:85 final size:86
Alignment explanation
Indices: 16116888--16117191 Score: 292
Period size: 85 Copynumber: 3.5 Consensus size: 86
16116878 ATTTTAATCG
* * *
16116888 GCTCCACTGAAACTTCAGGGAGATAAGACTC-GTAATTTCAACCTGCCCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGAGAGATAAGACTCTGTAATTTCAACCTGCCCCACTGCAACTTTAGGG
16116952 AGATGAGGTTTGATATGATCT
66 AGATGAGGTTTGATATGATCT
* * **
16116973 GCTCTACTGCAACTTCAGAGAGATAAGAC-CTGTAATTTATAGCTTCAATCTGTTCCACTGCAAC
1 GCTCCACTGCAACTTCAGAGAGATAAGACTCTGT-A---AT---TTCAACCTGCCCCACTGCAAC
* * * * * * *
16117037 TTTAGGGAAATAAGATTCGCTTCCTTCAGTCT
59 TTTAGGGAGATGAGGTTTG-AT--ATGA-TCT
* * * * * *
16117069 GCTCCACTGCAACTTCAGAGAGGTGAGACT-TGTATTTTCAACCTGCCCCACTACAACTTTAAGA
1 GCTCCACTGCAACTTCAGAGAGATAAGACTCTGTAATTTCAACCTGCCCCACTGCAACTTTAGGG
16117133 AGATGAGGTTTGATATGATCT
66 AGATGAGGTTTGATATGATCT
*
16117154 GCTCTACTGCAACTTCAGAGAGATAAGA-TCTGTAATTT
1 GCTCCACTGCAACTTCAGAGAGATAAGACTCTGTAATTT
16117192 ATCTCTTTAA
Statistics
Matches: 170, Mismatches: 35, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
84 2 0.01
85 63 0.37
86 3 0.02
88 1 0.01
89 32 0.19
92 33 0.19
93 1 0.01
95 3 0.02
96 32 0.19
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (86 bp):
GCTCCACTGCAACTTCAGAGAGATAAGACTCTGTAATTTCAACCTGCCCCACTGCAACTTTAGGG
AGATGAGGTTTGATATGATCT
Found at i:16117088 original size:96 final size:93
Alignment explanation
Indices: 16116970--16117261 Score: 260
Period size: 96 Copynumber: 3.2 Consensus size: 93
16116960 TTTGATATGA
*
16116970 TCTGCTCTACTGCAACTTCAGAGAGATAAGACCTGTAATTTATAGCTTCAATCTGTTCCACTGCA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACCTGTAATTTAT--CTTCAATCTGTTCCACTGCA
16117035 ACTTTAGGGAAATAAGATTCGCTTCCTTCAG
64 ACTTTAGGGAAATAAGATTCGCTT-CTTCAG
* * * * ** *
16117066 TCTGCTCCACTGCAACTTCAGAGAGGTGAGACTTGT-A--T-T-TTCAACCTGCCCCACTACAAC
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACCTGTAATTTATCTTCAATCTGTTCCACTGCAAC
* * * * * * *
16117126 TTTA-AGAAGATGAGGTTTG-AT-ATGA-
66 TTTAGGGAA-ATAAGATTCGCTTCTTCAG
* * *
16117151 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATCTCTTTAATCTGTTCCACTGCA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACCTGTAATTTA--TCTTCAATCTGTTCCACTGCA
* * *
16117216 ACTTCAGGGAAATAAGATTCGCTATCTGCTG
64 ACTTTAGGGAAATAAGATTCGCT-TCTTCAG
*
16117247 CCTGCTCCACTGCAA
1 TCTGCTCCACTGCAA
16117262 ACTTAGGGAG
Statistics
Matches: 146, Mismatches: 37, Indels: 26
0.70 0.18 0.12
Matches are distributed among these distances:
85 31 0.21
86 3 0.02
88 5 0.03
89 28 0.19
91 1 0.01
92 27 0.18
93 4 0.03
94 1 0.01
95 1 0.01
96 45 0.31
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (93 bp):
TCTGCTCCACTGCAACTTCAGAGAGATAAGACCTGTAATTTATCTTCAATCTGTTCCACTGCAAC
TTTAGGGAAATAAGATTCGCTTCTTCAG
Found at i:16117192 original size:181 final size:181
Alignment explanation
Indices: 16116888--16117261 Score: 570
Period size: 181 Copynumber: 2.1 Consensus size: 181
16116878 ATTTTAATCG
* * * * *
16116888 GCTCCACTGAAACTTCAGGGAGATAAGACTCGTAATTTCAACCTGCCCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGAGAGATAAGACTCGTAATTTCAACCTGCCCCACTACAACTTCAAGAA
16116953 GATGAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGACCTGTAATTTATAGCTT
66 GATGAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGACCTGTAATTTATAGCTT
* * *
16117018 CAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTCGCT-TCCTTCAGTCT
131 CAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTAT-CTGCAGCCT
* * * * *
16117069 GCTCCACTGCAACTTCAGAGAGGTGAGACTTGTATTTTCAACCTGCCCCACTACAACTTTAAGAA
1 GCTCCACTGCAACTTCAGAGAGATAAGACTCGTAATTTCAACCTGCCCCACTACAACTTCAAGAA
* **
16117134 GATGAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATCTCTT
66 GATGAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGACCTGTAATTTATAGCTT
* *
16117199 TAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTGCTGCCT
131 CAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTGCAGCCT
16117250 GCTCCACTGCAA
1 GCTCCACTGCAA
16117262 ACTTAGGGAG
Statistics
Matches: 174, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
181 173 0.99
182 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (181 bp):
GCTCCACTGCAACTTCAGAGAGATAAGACTCGTAATTTCAACCTGCCCCACTACAACTTCAAGAA
GATGAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGACCTGTAATTTATAGCTT
CAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTGCAGCCT
Found at i:16118299 original size:45 final size:45
Alignment explanation
Indices: 16118247--16118333 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
16118237 AGTTCGAAAT
* *
16118247 GAATAAATTAATGAAGATAACAAATTTTTCCAAGATACGAAATGA
1 GAATAAATTAATCAAGATAACAAATTTTTCCAAAATACGAAATGA
* ** *
16118292 GAATAAATTGATCAAGATGGCATATTTTTCCAAAATACGAAA
1 GAATAAATTAATCAAGATAACAAATTTTTCCAAAATACGAAA
16118334 ACGAATAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (45 bp):
GAATAAATTAATCAAGATAACAAATTTTTCCAAAATACGAAATGA
Found at i:16118627 original size:5 final size:5
Alignment explanation
Indices: 16118613--16118676 Score: 67
Period size: 5 Copynumber: 12.4 Consensus size: 5
16118603 GGCCTCTACT
* * *
16118613 TTTTC TTTTTC TTTTC TTTT- TCTTC TCTTC TCTTC TTTTC TTTTC TTTTTTC
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC --TTTTC
16118665 TTTTC TTTTC TT
1 TTTTC TTTTC TT
16118677 CTTTTTTTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
4 3 0.06
5 40 0.75
6 5 0.09
7 5 0.09
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:16118649 original size:30 final size:31
Alignment explanation
Indices: 16118615--16118682 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 31
16118605 CCTCTACTTT
16118615 TTCTTTTTCTTTTC-TTTTTCTTCTCTTCTC
1 TTCTTTTTCTTTTCTTTTTTCTTCTCTTCTC
* *
16118645 TTC-TTTTCTTTTCTTTTTTCTTTTCTTTTC
1 TTCTTTTTCTTTTCTTTTTTCTTCTCTTCTC
16118675 TTCTTTTT
1 TTCTTTTT
16118683 TTTGTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 10 0.29
30 20 0.59
31 4 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (31 bp):
TTCTTTTTCTTTTCTTTTTTCTTCTCTTCTC
Found at i:16118652 original size:35 final size:35
Alignment explanation
Indices: 16118613--16118691 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
16118603 GGCCTCTACT
16118613 TTTTCTTTTTCTTTTCT-TTTTCTTCTCTTCTCTTC
1 TTTTCTTTTTCTTTTCTCTTTTCTTCTCTTCT-TTC
* * *
16118648 TTTTC-TTTTCTTTTTTCTTTTCTTTTCTTCTTTT
1 TTTTCTTTTTCTTTTCTCTTTTCTTCTCTTCTTTC
*
16118682 TTTTGTTTTT
1 TTTTCTTTTT
16118692 TAACATTCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
34 16 0.42
35 22 0.58
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (35 bp):
TTTTCTTTTTCTTTTCTCTTTTCTTCTCTTCTTTC
Found at i:16118683 original size:10 final size:10
Alignment explanation
Indices: 16118618--16118692 Score: 66
Period size: 10 Copynumber: 7.5 Consensus size: 10
16118608 CTACTTTTTC
*
16118618 TTTTTCTTTT
1 TTTTTCTTCT
16118628 CTTTTTCTTCT
1 -TTTTTCTTCT
* *
16118639 CTTCTCTTCT
1 TTTTTCTTCT
16118649 TTTCTT-TTCT
1 TTT-TTCTTCT
16118659 TTTTTCTT-T
1 TTTTTCTTCT
16118668 TCTTTTCTTCT
1 T-TTTTCTTCT
*
16118679 TTTTT-TTGT
1 TTTTTCTTCT
16118688 TTTTT
1 TTTTT
16118693 AACATTCTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
9 12 0.22
10 30 0.56
11 12 0.22
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:16118692 original size:30 final size:29
Alignment explanation
Indices: 16118615--16118692 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
16118605 CCTCTACTTT
*
16118615 TTCTTTTTCTTTTCTTTTTCTTCTCTTCTC
1 TTCTTTTT-TTTTTTTTTTCTTCTCTTCTC
* * *
16118645 TTCTTTTCTTTTCTTTTTTCTTTTCTTTTC
1 TTCTTTT-TTTTTTTTTTTCTTCTCTTCTC
*
16118675 TTCTTTTTTTTGTTTTTT
1 TTCTTTTTTTTTTTTTTT
16118693 AACATTCTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 10 0.24
30 31 0.74
31 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.79
Consensus pattern (29 bp):
TTCTTTTTTTTTTTTTTTCTTCTCTTCTC
Found at i:16124177 original size:5 final size:5
Alignment explanation
Indices: 16124167--16124194 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
16124157 GTATACAGAG
16124167 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
16124195 GAACAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:16126639 original size:16 final size:15
Alignment explanation
Indices: 16126599--16126639 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
16126589 CCATATTGAA
* *
16126599 TATTTTTTATATATT
1 TATTTTTAATATAAT
16126614 TATTTTTAATATAAT
1 TATTTTTAATATAAT
16126629 TATTTTCTAAT
1 TATTTT-TAAT
16126640 TTTGAGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTTTTAATATAAT
Found at i:16129078 original size:19 final size:19
Alignment explanation
Indices: 16129056--16129094 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
16129046 TTTTCATGTA
*
16129056 ATCATCATACATACTTATG
1 ATCACCATACATACTTATG
* *
16129075 ATCACCATGCATGCTTATG
1 ATCACCATACATACTTATG
16129094 A
1 A
16129095 ATATTCTCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (19 bp):
ATCACCATACATACTTATG
Found at i:16130374 original size:45 final size:44
Alignment explanation
Indices: 16130287--16130440 Score: 132
Period size: 45 Copynumber: 3.4 Consensus size: 44
16130277 ATATAGTACT
* *
16130287 CGGTGTAATCAGCACATAGCAACCACCTTTATACTCAATGGTA-C
1 CGGTGAAATCAGCACATAGCAATCA-CTTTATACTCAATGGTATC
* * *
16130331 CGGATGAATTCAGCACATAACAATCACTTATATAAC-CATTGGTATC
1 CGG-TGAAATCAGCACATAGCAATCACTT-TAT-ACTCAATGGTATC
* ** * **
16130377 CGGTGAAATCAACACATAGCAATCACCTTTATTTTCATTAATATC
1 CGGTGAAATCAGCACATAGCAATCA-CTTTATACTCAATGGTATC
* *
16130422 TGGTGGAATCAGCACATAG
1 CGGTGAAATCAGCACATAG
16130441 TATCCACCTA
Statistics
Matches: 89, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
44 6 0.07
45 74 0.83
46 9 0.10
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (44 bp):
CGGTGAAATCAGCACATAGCAATCACTTTATACTCAATGGTATC
Found at i:16130998 original size:50 final size:49
Alignment explanation
Indices: 16130878--16131059 Score: 208
Period size: 50 Copynumber: 3.7 Consensus size: 49
16130868 CACATATCGA
* * * * *
16130878 TGCCGATTCCATGTCCCAGACATGGTCTTACACTGGCACT-CAT-CTCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCCTTGCTCG
* * *
16130925 AGCCGATGCCATGTCCCAGACATGGTCCTACACTGACTCTCCTTTGTTCG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCC-TTGCTCG
* * * *
16130975 TGCCGATGCCATGTCCCAGACATGGTCTTAGACT-AGTACTCCTCGGTCTG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACT-CTCCTTGCTC-G
16131025 TGCCGATGCCATGTCCCAGACATGGTCTTACACTG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTG
16131060 GCACACTCAT
Statistics
Matches: 114, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
47 35 0.31
48 1 0.01
49 7 0.06
50 71 0.62
ACGTcount: A:0.19, C:0.32, G:0.21, T:0.27
Consensus pattern (49 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCCTTGCTCG
Found at i:16131057 original size:100 final size:97
Alignment explanation
Indices: 16130878--16131059 Score: 265
Period size: 97 Copynumber: 1.8 Consensus size: 97
16130868 CACATATCGA
* *
16130878 TGCCGATTCCATGTCCCAGACATGGTCTTACACTGGCACTCATCTCAAGCCGATGCCATGTCCCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCAAGCCGATGCCATGTCCCA
16130943 GACATGGTCCTACACTGACTCTCCTTTGTTCG
66 GACATGGTCCTACACTGACTCTCCTTTGTTCG
* * * **
16130975 TGCCGATGCCATGTCCCAGACATGGTCTTAGACTAGTACTCCTCGGTCTGTGCCGATGCCATGTC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATC--TC-AAGCCGATGCCATGTC
*
16131040 CCAGACATGGTCTTACACTG
63 CCAGACATGGTCCTACACTG
16131060 GCACACTCAT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
97 39 0.53
99 2 0.03
100 33 0.45
ACGTcount: A:0.19, C:0.32, G:0.21, T:0.27
Consensus pattern (97 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCAAGCCGATGCCATGTCCCA
GACATGGTCCTACACTGACTCTCCTTTGTTCG
Found at i:16134283 original size:43 final size:43
Alignment explanation
Indices: 16134197--16134344 Score: 165
Period size: 43 Copynumber: 3.5 Consensus size: 43
16134187 CCGAGATTAA
* * * ** *
16134197 GTGTAAGACCATATCTAGGATA-TGAAATCGATATGAGAATTC
1 GTGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTTC
*
16134239 GTGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTC
1 GTGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTTC
* * *
16134282 GTGTAAGACCATGGCTGGG-CTATTGGCATCGATACGAGATTAC
1 GTGTAAGACCATGTCTGGGAC-ATTGGCATCGATATGAGATTTC
* *
16134325 ATGTAAGACCATTTCTGGGA
1 GTGTAAGACCATGTCTGGGA
16134345 TATGACATTG
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 20 0.22
43 69 0.78
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTTC
Found at i:16140926 original size:16 final size:16
Alignment explanation
Indices: 16140905--16140937 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16140895 ATTGAAAAAA
16140905 TAAAT-ATAAATGACAT
1 TAAATAATAAATG-CAT
16140921 TAAATAATAAATGCAT
1 TAAATAATAAATGCAT
16140937 T
1 T
16140938 CTTTCAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAATAATAAATGCAT
Found at i:16142419 original size:23 final size:20
Alignment explanation
Indices: 16142393--16142451 Score: 55
Period size: 23 Copynumber: 2.7 Consensus size: 20
16142383 TAGTTTTTTA
16142393 AATATATAAAAAAATAAAGAGAT
1 AATATATAAAAAAAT--AGA-AT
* *
16142416 AATAAATAAATAAATAGAAT
1 AATATATAAAAAAATAGAAT
16142436 AACGTATATAAAAAAA
1 AA--TATATAAAAAAA
16142452 GTCTATAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 4 0.13
21 3 0.10
22 10 0.33
23 13 0.43
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (20 bp):
AATATATAAAAAAATAGAAT
Found at i:16152387 original size:29 final size:30
Alignment explanation
Indices: 16152328--16152385 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
16152318 TCCGAGTCTT
*
16152328 GGGGCAAAAATGTAATTATGCAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
16152358 GGGGC-AAAATCGTAAATT-TGAAAAAGTT
1 GGGGCAAAAAT-GT-AATTATGAAAAAGTT
16152386 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 5 0.20
30 16 0.64
31 4 0.16
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:16152614 original size:13 final size:13
Alignment explanation
Indices: 16152596--16152627 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16152586 TTTCCAGAAA
16152596 TTATGAATTTATT
1 TTATGAATTTATT
16152609 TTATGAATTTATT
1 TTATGAATTTATT
*
16152622 TGATGA
1 TTATGA
16152628 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:16152835 original size:50 final size:50
Alignment explanation
Indices: 16152722--16152970 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
16152712 ATTTGGGTAA
* *
16152722 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--AAGA-C--G
*
16152778 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACG
* * *
16152828 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACG
* * * * * *
16152878 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGTACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACG
** * *
16152928 AGAACATCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16152971 TGTTATTATC
Statistics
Matches: 172, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 94 0.55
51 32 0.19
52 1 0.01
53 3 0.02
55 2 0.01
56 40 0.23
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACG
Found at i:16152923 original size:100 final size:103
Alignment explanation
Indices: 16152722--16152971 Score: 335
Period size: 100 Copynumber: 2.4 Consensus size: 103
16152712 ATTTGGGTAA
16152722 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGAGA--ATGAGAGGTCCC
* * * *
16152787 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGACG
63 ATATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * *
16152828 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GAG-ATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGAATGAGAGGTCCCATA
* *
16152890 TAAGACCATGTCTGGGACATGGCATGGGTACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * *
16152928 AGAACATCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
16152972 GTTATTATCA
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
100 48 0.37
101 36 0.28
103 3 0.02
105 2 0.02
106 40 0.31
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGAATGAGAGGTCCCATA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:16159379 original size:29 final size:29
Alignment explanation
Indices: 16159346--16159404 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
16159336 TGAAGAGAGG
*
16159346 TCTTAGGACCAAGATAGCTAGTACCGCAT
1 TCTTAGGACCAAGATAACTAGTACCGCAT
*
16159375 TCTTAGTACCAAGATAACTAGTACCGCAT
1 TCTTAGGACCAAGATAACTAGTACCGCAT
16159404 T
1 T
16159405 AGTGAGTGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (29 bp):
TCTTAGGACCAAGATAACTAGTACCGCAT
Found at i:16159534 original size:23 final size:25
Alignment explanation
Indices: 16159508--16159564 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
16159498 ATTTATATTT
16159508 TAATATTTAA-AAATATTAAATA-A
1 TAATATTTAATAAATATTAAATATA
* *
16159531 TAATATTAAATAAATTTTAAATATA
1 TAATATTTAATAAATATTAAATATA
*
16159556 AAATATTTA
1 TAATATTTA
16159565 TCAATTATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 9 0.32
24 11 0.39
25 8 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TAATATTTAATAAATATTAAATATA
Found at i:16159537 original size:13 final size:13
Alignment explanation
Indices: 16159519--16159543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16159509 AATATTTAAA
16159519 AATATTAAATAAT
1 AATATTAAATAAT
16159532 AATATTAAATAA
1 AATATTAAATAA
16159544 ATTTTAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATTAAATAAT
Found at i:16159848 original size:23 final size:23
Alignment explanation
Indices: 16159818--16159888 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
16159808 GGCCCAGCCC
*
16159818 ATAT-TAAATATATATTTTTAAT
1 ATATATAAATATATATATTTAAT
*
16159840 ATATATAAATATATATATTTGAT
1 ATATATAAATATATATATTTAAT
16159863 -TA-A-AAATAATATATATTTAAT
1 ATATATAAAT-ATATATATTTAAT
16159884 ATATA
1 ATATA
16159889 ATTCGGGTCG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
20 4 0.10
21 13 0.31
22 8 0.19
23 17 0.40
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (23 bp):
ATATATAAATATATATATTTAAT
Found at i:16160297 original size:11 final size:11
Alignment explanation
Indices: 16160283--16160308 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16160273 AAAATAAAAA
16160283 AAAAGTATTTT
1 AAAAGTATTTT
16160294 AAAAGTATTTT
1 AAAAGTATTTT
16160305 AAAA
1 AAAA
16160309 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:16160656 original size:20 final size:20
Alignment explanation
Indices: 16160620--16160657 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16160610 GAGGGGAATT
*
16160620 TTTTATTTATTATAATTTGG
1 TTTTATTTATTAAAATTTGG
16160640 TTTTATATT-TTAAAATTT
1 TTTTAT-TTATTAAAATTT
16160658 AAAGTTTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTTATTTATTAAAATTTGG
Found at i:16162869 original size:17 final size:17
Alignment explanation
Indices: 16162844--16162882 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
16162834 TTACCGATTC
*
16162844 AAAACAAATAA-ATTATT
1 AAAAAAAATAAGATTA-T
16162861 AAAAAAAATAAGATTAT
1 AAAAAAAATAAGATTAT
16162878 AAAAA
1 AAAAA
16162883 TTGGTTCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAAAAAATAAGATTAT
Found at i:16162981 original size:77 final size:79
Alignment explanation
Indices: 16162841--16162991 Score: 209
Period size: 77 Copynumber: 1.9 Consensus size: 79
16162831 TGGTTACCGA
* *
16162841 TTCAAAACAAATAAATTATTAAAAAAAATAAGATTATAAAAATTGGTTCTACTACCAATTCAAAT
1 TTCAAAACAAATAAATTATTAAAAAAAATAAGA-TATAAAAATTGGTTCAACGACCAATTCAAAT
16162906 GGTTTTTTAGCTTGG
65 GGTTTTTTAGCTTGG
* * * *
16162921 TTCAAATCAAATAAATTATT-AAAAAATTGAA-A-ATAAAAATTGTTTCAACGGCCAATTCAAAT
1 TTCAAAACAAATAAATTATTAAAAAAAAT-AAGATATAAAAATTGGTTCAACGACCAATTCAAAT
16162983 GGTTTTTTA
65 GGTTTTTTA
16162992 ACCCTATTCA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
77 35 0.55
79 8 0.12
80 21 0.33
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (79 bp):
TTCAAAACAAATAAATTATTAAAAAAAATAAGATATAAAAATTGGTTCAACGACCAATTCAAATG
GTTTTTTAGCTTGG
Found at i:16168846 original size:16 final size:17
Alignment explanation
Indices: 16168809--16168845 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
16168799 ACTATAATGG
16168809 AAAAAGAATGGAGAGTA
1 AAAAAGAATGGAGAGTA
*
16168826 CAAAAG-ATGGAGA-TA
1 AAAAAGAATGGAGAGTA
16168841 AAAAA
1 AAAAA
16168846 ACTAAACCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.33
16 7 0.39
17 5 0.28
ACGTcount: A:0.62, C:0.03, G:0.24, T:0.11
Consensus pattern (17 bp):
AAAAAGAATGGAGAGTA
Found at i:16169481 original size:13 final size:13
Alignment explanation
Indices: 16169463--16169488 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16169453 AAAGATAAGG
16169463 AAAAATAAAAAAT
1 AAAAATAAAAAAT
16169476 AAAAATAAAAAAT
1 AAAAATAAAAAAT
16169489 TGTCAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:16172751 original size:13 final size:13
Alignment explanation
Indices: 16172733--16172761 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16172723 GCCCAAACTT
16172733 AATTACCCAACCC
1 AATTACCCAACCC
16172746 AATTACCCAACCC
1 AATTACCCAACCC
16172759 AAT
1 AAT
16172762 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.17
Consensus pattern (13 bp):
AATTACCCAACCC
Found at i:16172786 original size:31 final size:31
Alignment explanation
Indices: 16172748--16172807 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
16172738 CCCAACCCAA
16172748 TTACCCAACCCAATAAAACTAAAACTAAAGT
1 TTACCCAACCCAATAAAACTAAAACTAAAGT
*
16172779 TTACCCAATCCAATAAAACTAAAACTAAA
1 TTACCCAACCCAATAAAACTAAAACTAAA
16172808 AGACAACCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.53, C:0.25, G:0.02, T:0.20
Consensus pattern (31 bp):
TTACCCAACCCAATAAAACTAAAACTAAAGT
Found at i:16172906 original size:9 final size:9
Alignment explanation
Indices: 16172894--16172952 Score: 66
Period size: 9 Copynumber: 6.4 Consensus size: 9
16172884 AAATAAAAAA
16172894 AATTCGGGT
1 AATTCGGGT
16172903 AATTCGGGT
1 AATTCGGGT
*
16172912 ATTTTTC-GGT
1 A--ATTCGGGT
*
16172922 AATTCGGTT
1 AATTCGGGT
16172931 AATTCGGGT
1 AATTCGGGT
*
16172940 AATTCAGGT
1 AATTCGGGT
16172949 AATT
1 AATT
16172953 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
8 3 0.07
9 32 0.76
10 4 0.10
11 3 0.07
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:16173820 original size:9 final size:9
Alignment explanation
Indices: 16173806--16173836 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16173796 GTTAAACGAA
16173806 TCGAGTTAT
1 TCGAGTTAT
*
16173815 TCGAGTTAA
1 TCGAGTTAT
16173824 TCGAGTTAT
1 TCGAGTTAT
16173833 TCGA
1 TCGA
16173837 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:16173906 original size:9 final size:9
Alignment explanation
Indices: 16173889--16173925 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
16173879 TGAGTTTTCG
16173889 AATTCGAAT
1 AATTCGAAT
*
16173898 AACTCGAAT
1 AATTCGAAT
16173907 AATTCGAAT
1 AATTCGAAT
16173916 AATTCGAAT
1 AATTCGAAT
16173925 A
1 A
16173926 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:16179549 original size:13 final size:13
Alignment explanation
Indices: 16179533--16179570 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
16179523 AAAATTTTTG
16179533 GCTTTTCAAAAGT
1 GCTTTTCAAAAGT
* *
16179546 GCTTTTTAGAAGT
1 GCTTTTCAAAAGT
16179559 GCTTTTCAAAAG
1 GCTTTTCAAAAG
16179571 CACTTTTGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (13 bp):
GCTTTTCAAAAGT
Found at i:16180064 original size:13 final size:13
Alignment explanation
Indices: 16180048--16180087 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
16180038 TTTAAACCAA
16180048 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* * *
16180061 ACTTCTCCATAGC
1 ACTTTTCAAAAGC
16180074 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
16180087 A
1 A
16180088 TTGCCAAACT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:16190872 original size:97 final size:97
Alignment explanation
Indices: 16190676--16190860 Score: 270
Period size: 96 Copynumber: 1.9 Consensus size: 97
16190666 TCTTATGGAA
*
16190676 ATAGCATATATGGCAATATAGACACAATAGCGAGTTCAGGCTAGTAGAATACAAGCAATGGAAAA
1 ATAGCATATATGGCAATAAAGACACAATAGCGAGTTCAGGCTAGTAGAATACAAGCAATGGAAAA
*
16190741 TCAGCATTGTACTCAGAATAGAAAAATCAGAG
66 TCAGCACTGTACTCAGAATAGAAAAATCAGAG
*
16190773 ATAGCA-ATGATGGC-ATAAAGACACAACT-GGGAGTTCAGGAC-AGTAGAATACTAAGCAATGG
1 ATAGCATAT-ATGGCAATAAAGACACAA-TAGCGAGTTCAGG-CTAGTAGAATAC-AAGCAATGG
16190834 AAAAATCAGCACTGTACTCAGAATAGA
62 -AAAATCAGCACTGTACTCAGAATAGA
16190861 TAATTAGAGA
Statistics
Matches: 80, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
96 33 0.41
97 22 0.28
98 25 0.31
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (97 bp):
ATAGCATATATGGCAATAAAGACACAATAGCGAGTTCAGGCTAGTAGAATACAAGCAATGGAAAA
TCAGCACTGTACTCAGAATAGAAAAATCAGAG
Found at i:16193052 original size:353 final size:353
Alignment explanation
Indices: 16192371--16193885 Score: 2085
Period size: 353 Copynumber: 4.3 Consensus size: 353
16192361 ATAAGCAATC
* * * *
16192371 GTTGAGAGATTTGTCGTTGTGCACGGTCAGAT-A-A-TACAACTCTTTGCAAAGTATCCTGATGA
1 GTTGAGAGATATGTCGTTGTGCATGGTCAGATAATACTACAACTCTTTGTAGAGTATCCTGATGA
* * *
16192433 GGAGATTAAGAAGTGCACATTTGTCGTAGGCCTTGCACATAAAATGGAGGAGAGACACCATACAA
66 GAAGATTAAGAAGTGCACATTTTTCGTAGGCCTTGCAAATAAAATGGAGGAGAGACACCATACAA
* * *
16192498 AATGGTTATTTAAAAAAGGACTAATTATGACTATTTCAATTTTA-AGGACTAAATTGAATAAAAT
131 AATGATTAGTT-AAAAAGGACTAGTTATGACTATTTCAATTTTAGA-GACTAAATTGAATAAAAT
* * * * *
16192562 GTAAAACTTTAAGGGGAAGACGAATAATGAAATTGAATTGATAAATACATATAATAGATTTTTAT
194 GTAAAACTTTAAGGGGCATACGAATAATGAAATTGAACTGATACATACATATAATAGATTGTTAT
* *
16192627 AAGATGTTTGGAATTGATAAATTGAACTGAATTGTTATATAGATCGGGAATTGAACCAAGATGAT
259 AAGATGTTTGGAATTGATAAATCGAACTGAATTGTTATATAGATCGAGAATTGAACCAAGATGAT
* *
16192692 CATGCTTTTATATCTACTAATCCAGCAGTT
324 CATGCTTTTATATCTACTAATCCAACAGCT
* * * * *
16192722 GTTGAGAGATGTGTCGTTGTGCATTG-CTAGATAATATTACAACTTTTTGTAGAGTATCCCGATG
1 GTTGAGAGATATGTCGTTGTGCATGGTC-AGATAATACTACAACTCTTTGTAGAGTATCCTGATG
*
16192786 AGAAGATTAAGAAGTGCACATTTTTCGTAGGCCTTGCAAATAAAATGGAGGAGAGACACCATGCA
65 AGAAGATTAAGAAGTGCACATTTTTCGTAGGCCTTGCAAATAAAATGGAGGAGAGACACCATACA
* **
16192851 AAATGATTAGTTAAAAAGAACTAGTTATGACTATTTTGATTTTAGAGACTAAATTGAATAAAATG
130 AAATGATTAGTTAAAAAGGACTAGTTATGACTATTTCAATTTTAGAGACTAAATTGAATAAAATG
* * * * *
16192916 TGAAACTTTAAGGGGTATATGAATAATAAAATTGAACTGATACATACATATAATGGATTGTTATA
195 TAAAACTTTAAGGGGCATACGAATAATGAAATTGAACTGATACATACATATAATAGATTGTTATA
* * *
16192981 AGATGTTTGGAATTGATAAATTGAACTGAATTGTTATATAAATCGAGAACTGAACCAAGATGATC
260 AGATGTTTGGAATTGATAAATCGAACTGAATTGTTATATAGATCGAGAATTGAACCAAGATGATC
* *
16193046 ATGCTTTTATATCTATTAATCCAACAGTT
325 ATGCTTTTATATCTACTAATCCAACAGCT
* * *
16193075 GTTGAGAGATATGTTGTTGTGCATGGTCAGATAATACTACAACTCTTTGTAGAGTATCTTAATG-
1 GTTGAGAGATATGTCGTTGTGCATGGTCAGATAATACTACAACTCTTTGTAGAGTATCCTGATGA
* ** * * *
16193139 GAAGATTAAGAAATGCACAACTGTCGTAGGCCTTGCAAATAAAATGGAGGAGATACACCATGCAA
66 GAAGATTAAGAAGTGCACATTTTTCGTAGGCCTTGCAAATAAAATGGAGGAGAGACACCATACAA
* * *
16193204 AATGATTAGTTAAAAAGGACTAGTTATGACTATTTCGATTTTAGATATTAAATTGAATAAAATGT
131 AATGATTAGTTAAAAAGGACTAGTTATGACTATTTCAATTTTAGAGACTAAATTGAATAAAATGT
* ** * * *
16193269 AAAACTTTAAGGGGCATATGAATAATGAAATCAAACTGATACATACCTATAATAGATTTTTCTAA
196 AAAACTTTAAGGGGCATACGAATAATGAAATTGAACTGATACATACATATAATAGATTGTTATAA
* * * * * *
16193334 GATGTTTGTAATTAATAAATCAAACTGAATTGTTATATAGATCGGGAATTTAACCAAGATTATCA
261 GATGTTTGGAATTGATAAATCGAACTGAATTGTTATATAGATCGAGAATTGAACCAAGATGATCA
*
16193399 TGTTTTTATATCTACTAATCCAACAGCT
326 TGCTTTTATATCTACTAATCCAACAGCT
*
16193427 GTTGAGAGATATGTCGTTGTGCATGGTCAGATAATACTACAAGTCTTTGTAGAGTATCCTGATGA
1 GTTGAGAGATATGTCGTTGTGCATGGTCAGATAATACTACAACTCTTTGTAGAGTATCCTGATGA
* * * * * * *
16193492 GAAGATTAAGAA-TAACACATTTTTCGTAGGCCATGCAAATGAAATAGAAGAGAAACATCATACA
66 GAAGATTAAGAAGT-GCACATTTTTCGTAGGCCTTGCAAATAAAATGGAGGAGAGACACCATACA
* *
16193556 AAATGGTTAGTTAAAAAGGACTAGTTATGACTATTTCAATTTTAGGGACTAAATTGAATAAAATG
130 AAATGATTAGTTAAAAAGGACTAGTTATGACTATTTCAATTTTAGAGACTAAATTGAATAAAATG
* ** * * *
16193621 TGAAACTTTAAAAGGCATACAAATAATGAAATTGAATTGATACATATATATAATAGATTGTTATA
195 TAAAACTTTAAGGGGCATACGAATAATGAAATTGAACTGATACATACATATAATAGATTGTTATA
* * *
16193686 AGATGTTTGAAATTGATAAATCGAACTGAATTATTATATAGATCGAGAATTGAACCAAGATGATT
260 AGATGTTTGGAATTGATAAATCGAACTGAATTGTTATATAGATCGAGAATTGAACCAAGATGATC
**
16193751 ATGCTTTTATAAATACTAA-CTCAACAGCT
325 ATGCTTTTATATCTACTAATC-CAACAGCT
* * * * * *
16193780 ATTGAAAGATATATCATTGTGTATGGTCAAATAATACTACAACTCTTTGTAGAGTATCCTGATGA
1 GTTGAGAGATATGTCGTTGTGCATGGTCAGATAATACTACAACTCTTTGTAGAGTATCCTGATGA
* *
16193845 GAAGATTAAAAAGTGCACATTTGTT-GTAGGCCTTACAAATA
66 GAAGATTAAGAAGTGCACATTT-TTCGTAGGCCTTGCAAATA
16193886 TCGTTCCAAC
Statistics
Matches: 1029, Mismatches: 124, Indels: 20
0.88 0.11 0.02
Matches are distributed among these distances:
350 1 0.00
351 27 0.03
352 321 0.31
353 581 0.56
354 99 0.10
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (353 bp):
GTTGAGAGATATGTCGTTGTGCATGGTCAGATAATACTACAACTCTTTGTAGAGTATCCTGATGA
GAAGATTAAGAAGTGCACATTTTTCGTAGGCCTTGCAAATAAAATGGAGGAGAGACACCATACAA
AATGATTAGTTAAAAAGGACTAGTTATGACTATTTCAATTTTAGAGACTAAATTGAATAAAATGT
AAAACTTTAAGGGGCATACGAATAATGAAATTGAACTGATACATACATATAATAGATTGTTATAA
GATGTTTGGAATTGATAAATCGAACTGAATTGTTATATAGATCGAGAATTGAACCAAGATGATCA
TGCTTTTATATCTACTAATCCAACAGCT
Found at i:16196119 original size:18 final size:18
Alignment explanation
Indices: 16196096--16196164 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
16196086 GATGACAAAT
*
16196096 ATGAGAAATGAATATGAG
1 ATGAGAAATGAATATGAA
16196114 ATGAGAAATGAAATATGAA
1 ATGAGAAATG-AATATGAA
*
16196133 ATGATGAAATGATATGTGAA
1 ATGA-GAAATGA-ATATGAA
* *
16196153 TTGTGAAATGAA
1 ATGAGAAATGAA
16196165 ATCAAGTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
18 11 0.25
19 19 0.43
20 14 0.32
ACGTcount: A:0.49, C:0.00, G:0.25, T:0.26
Consensus pattern (18 bp):
ATGAGAAATGAATATGAA
Found at i:16199166 original size:25 final size:25
Alignment explanation
Indices: 16199132--16199201 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
16199122 CAGACCCATT
*
16199132 TTCACAGCTCATGTGAGCATTTTGA
1 TTCACAGCTCGTGTGAGCATTTTGA
16199157 TTCACAGCTCGTGTGAGCATTTTGA
1 TTCACAGCTCGTGTGAGCATTTTGA
16199182 TTCACAGCTCGTGTGAGCAT
1 TTCACAGCTCGTGTGAGCAT
16199202 ACATTTACAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGCATTTTGA
Found at i:16206058 original size:26 final size:26
Alignment explanation
Indices: 16206027--16206093 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
16206017 CATTCCGACC
16206027 CACAGCTCGTGTGAGCAGA-CTCATTT
1 CACAGCTCGTGTGAGCAGATCT-ATTT
*
16206053 CACAGCTCGTGTGAGCATATCTATTT
1 CACAGCTCGTGTGAGCAGATCTATTT
16206079 CACAGCTCGTGTGAG
1 CACAGCTCGTGTGAG
16206094 GAACGATGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 37 0.95
27 2 0.05
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.28
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCAGATCTATTT
Found at i:16208324 original size:43 final size:44
Alignment explanation
Indices: 16208257--16208384 Score: 133
Period size: 43 Copynumber: 3.0 Consensus size: 44
16208247 GGCTCATACA
* * *
16208257 ATGCCATCGTCCCAGAC-GTGGTCTTACATGTAATCACATATCG
1 ATGCCATTGTCCTAGACAGTGGTCTTACACGTAATCACATATCG
* *
16208300 ATGCCATTGTCCTAGACAGT-GTCTTACACG-AATTAAATA-CG
1 ATGCCATTGTCCTAGACAGTGGTCTTACACGTAATCACATATCG
* * *
16208341 ATGCCAATGT-CTCAGACA-TGGTCTTACACGTAAACACAAATCG
1 ATGCCATTGTCCT-AGACAGTGGTCTTACACGTAATCACATATCG
16208384 A
1 A
16208385 AGGTCCTATT
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
40 3 0.04
41 26 0.37
42 12 0.17
43 27 0.39
44 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (44 bp):
ATGCCATTGTCCTAGACAGTGGTCTTACACGTAATCACATATCG
Done.