Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 43 of 198
Found at i:12858553 original size:61 final size:61
Alignment explanation
Indices: 12858488--12858798 Score: 226
Period size: 61 Copynumber: 5.2 Consensus size: 61
12858478 TTATAATTAA
* * *
12858488 AATATATAATTTAATAAAATTCTTAATAAATAAAATTCTTATATGAATTTACTGAAATCAT
1 AATATATAATTTAATAAAATTATTAATAAATAAAATTATTATATGAATTTACTTAAATCAT
* * * * * * * * * *
12858549 AATATATGATACT-ATAAAA-TATAAATTAACATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTATTAATAAATAAAATTATTATATGAATTTACTTA-AATCAT
* ** * * *
12858608 AATATATAATTTAATAAAATTCTTAATAGTTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTATTAATAAATAAAATTATTATATGAATTTACTTAAATCAT
* * * * * * * * * * *
12858669 AATATATGATACT-ATAAAA-TATAAATTAAAT-TAATTATT-TTTAAATATAATTTAATAAA
1 AATATATAAT-TTAATAAAATTATTAA-TAAATAAAATTATTATATGAATTTACTTAAATCAT
* *
12858728 AATATATAATTTAATAAAATTATTAAT-ATTAAATATTATTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTATTAATAAATAAA-ATTATTATATGAATTTACTTAAATCAT
12858789 AATATATAAT
1 AATATATAAT
12858799 ACTATAAAAT
Statistics
Matches: 178, Mismatches: 59, Indels: 26
0.68 0.22 0.10
Matches are distributed among these distances:
58 6 0.03
59 54 0.30
60 49 0.28
61 65 0.37
62 4 0.02
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTATTAATAAATAAAATTATTATATGAATTTACTTAAATCAT
Found at i:12858621 original size:14 final size:15
Alignment explanation
Indices: 12858572--12858623 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
12858562 ATAAAATATA
12858572 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
12858587 TATTAAATATATTAT
1 AATTAAATATATTAT
12858602 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
12858615 AATTTAATA
1 AATTAAATA
12858624 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:12858669 original size:120 final size:119
Alignment explanation
Indices: 12858456--12858823 Score: 578
Period size: 120 Copynumber: 3.1 Consensus size: 119
12858446 ATCATATTTA
*
12858456 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT-ATTAA
* *
12858521 AATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATT
65 TATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAATT
12858576 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAGTTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA-TTAA
*
12858641 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
65 TATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAATT
* * *
12858696 AA-ATTAATTATTTTTAAATATAATT-TAATAAAAATATATAATTTAATAAAATTATTAATATTA
1 AACA-TAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATTCTTAATATT-
* * *
12858759 AATATTATTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTT
63 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAATT
*
12858816 AAAATAAT
1 AACATAAT
12858824 AAAATTTGAA
Statistics
Matches: 233, Mismatches: 10, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
119 4 0.02
120 225 0.97
121 4 0.02
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (119 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATATTAAT
ATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAATT
Found at i:12858736 original size:18 final size:18
Alignment explanation
Indices: 12858713--12858759 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
12858703 TTATTTTTAA
12858713 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
12858731 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
12858749 AT-TAATATTAA
1 ATATAAT-TTAA
12858760 ATATTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:12858868 original size:20 final size:20
Alignment explanation
Indices: 12858821--12858859 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12858811 AATTTAAAAT
*
12858821 AATAAAATTTGAATCGATTA
1 AATAATATTTGAATCGATTA
* *
12858841 AATGATATTTGAATTGATT
1 AATAATATTTGAATCGATT
12858860 TGATAATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (20 bp):
AATAATATTTGAATCGATTA
Found at i:12859163 original size:11 final size:12
Alignment explanation
Indices: 12859133--12859168 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
12859123 TGTATTAAAT
12859133 TTATTTTTCATA
1 TTATTTTTCATA
*
12859145 TTATTTTTGATA
1 TTATTTTTCATA
12859157 TTA-TTTTCATA
1 TTATTTTTCATA
12859168 T
1 T
12859169 CATGTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (12 bp):
TTATTTTTCATA
Found at i:12859183 original size:23 final size:23
Alignment explanation
Indices: 12859121--12859184 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
12859111 TAATTTATTG
12859121 CATGTATTAAATTTATTTTTCATAT
1 CATGTATT-AATTTA-TTTTCATAT
* * *
12859146 TAT-TTTTGATATTATTTTCATAT
1 CATGTATTAAT-TTATTTTCATAT
12859169 CATGTATTAATTTATT
1 CATGTATTAATTTATT
12859185 GCATGTTTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
23 18 0.58
24 11 0.35
25 2 0.06
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.59
Consensus pattern (23 bp):
CATGTATTAATTTATTTTCATAT
Found at i:12869080 original size:16 final size:17
Alignment explanation
Indices: 12869059--12869092 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12869049 GAAATATAAT
12869059 ATAAAAACAAGAA-AAA
1 ATAAAAACAAGAAGAAA
*
12869075 ATAAAAATAAGAAGAAA
1 ATAAAAACAAGAAGAAA
12869092 A
1 A
12869093 ATAAGAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (17 bp):
ATAAAAACAAGAAGAAA
Found at i:12869319 original size:6 final size:6
Alignment explanation
Indices: 12869308--12869365 Score: 82
Period size: 6 Copynumber: 9.3 Consensus size: 6
12869298 AACGTAGATT
12869308 AATAAA AAT-AA AATAAA CGAATAACA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA --AATAA-A AATAAA AATAAA AATAAA AATAAA
12869358 AATAAA AA
1 AATAAA AA
12869366 AGAAACACAA
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.10
6 32 0.67
7 5 0.10
8 5 0.10
9 1 0.02
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:12872835 original size:25 final size:25
Alignment explanation
Indices: 12872807--12873056 Score: 276
Period size: 25 Copynumber: 10.4 Consensus size: 25
12872797 GGAGTTTAGC
12872807 GTGCTCTCTGATTATTAGCACATCA
1 GTGCTCTCTGATTATTAGCACATCA
12872832 GTGCTCTCTGATTATTAGCACATCA
1 GTGCTCTCTGATTATTAGCACATCA
12872857 GTGCTCTCTGATTATTAGCACATCA
1 GTGCTCTCTGATTATTAGCACATCA
*
12872882 GTGCTCTCTGATTATTAGCACATTA
1 GTGCTCTCTGATTATTAGCACATCA
* *
12872907 GTGCTCTCTGATTACTAGCACGTCA
1 GTGCTCTCTGATTATTAGCACATCA
12872932 GTGCTCTCTGATT-TCTAGCA-AGTCA
1 GTGCTCTCTGATTAT-TAGCACA-TCA
12872957 GTGCTCTCT-A--ATTA-CTACA-C-
1 GTGCTCTCTGATTATTAGC-ACATCA
* * *
12872977 --GCTCTCTGATT-TCTAGAACGTTA
1 GTGCTCTCTGATTAT-TAGCACATCA
* *
12873000 GTGCTCTCCGATTATTAGCACATTA
1 GTGCTCTCTGATTATTAGCACATCA
* *
12873025 GTGCTCTCT-A-TA-TAGCACTTTA
1 GTGCTCTCTGATTATTAGCACATCA
12873047 GTGCTCTCTG
1 GTGCTCTCTG
12873057 TTTTATAGTG
Statistics
Matches: 195, Mismatches: 14, Indels: 34
0.80 0.06 0.14
Matches are distributed among these distances:
18 7 0.04
19 1 0.01
20 1 0.01
21 6 0.03
22 21 0.11
23 4 0.02
24 2 0.01
25 152 0.78
26 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATCA
Found at i:12873738 original size:2 final size:2
Alignment explanation
Indices: 12873733--12873757 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12873723 GTTATGTGTG
12873733 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 T
12873758 GAAAGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12873787 original size:16 final size:16
Alignment explanation
Indices: 12873766--12873797 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12873756 ATGAAAGTTA
12873766 AATTTTGAGGCTTTAT
1 AATTTTGAGGCTTTAT
12873782 AATTTTGAGGCTTTAT
1 AATTTTGAGGCTTTAT
12873798 GACCTCTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (16 bp):
AATTTTGAGGCTTTAT
Found at i:12882467 original size:23 final size:24
Alignment explanation
Indices: 12882423--12882468 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
12882413 TTTCTCACAT
* **
12882423 TTTCAATTCAATCATTTTTCCACC
1 TTTCAATTCAATAATTAATCCACC
12882447 TTTCAA-TCAATAATTAATCCAC
1 TTTCAATTCAATAATTAATCCAC
12882469 AAATTCACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTCAATTCAATAATTAATCCACC
Found at i:12882625 original size:6 final size:6
Alignment explanation
Indices: 12882614--12882693 Score: 97
Period size: 6 Copynumber: 13.3 Consensus size: 6
12882604 TCACTCATCT
* *
12882614 TAATAA TAATAA TAATAA TAATAA TAATAA TGATAA TAATAA TACTAA
1 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA
* * * * *
12882662 TACTAA TACTAA TACTAA TACTAA TATTAA TA
1 TAATAA TAATAA TAATAA TAATAA TAATAA TA
12882694 CTTACCTCAC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (6 bp):
TAATAA
Found at i:12882967 original size:14 final size:14
Alignment explanation
Indices: 12882948--12882977 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12882938 AATTTAATCC
12882948 TAACTAAGTTTTCT
1 TAACTAAGTTTTCT
12882962 TAACTAAGTTTTCT
1 TAACTAAGTTTTCT
12882976 TA
1 TA
12882978 CTTTCCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (14 bp):
TAACTAAGTTTTCT
Found at i:12883448 original size:16 final size:16
Alignment explanation
Indices: 12883427--12883465 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12883417 TTTGCTTTGT
* *
12883427 TTTTATTTCCTTTTTA
1 TTTTATTTACTTTATA
12883443 TTTTATTTACTTTATA
1 TTTTATTTACTTTATA
*
12883459 TTATATT
1 TTTTATT
12883466 AATTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTATTTACTTTATA
Found at i:12883901 original size:21 final size:21
Alignment explanation
Indices: 12883877--12883919 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
12883867 AATAATAACT
12883877 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
12883898 AATATCTTATACTAAGTAATA
1 AATAACTAATAATAAATAATA
12883919 A
1 A
12883920 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:12884051 original size:25 final size:23
Alignment explanation
Indices: 12884007--12884067 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
12883997 ATTTTGATTT
*
12884007 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
12884031 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
12884055 ATATAAATTATAT
1 AT-TTAATTATAT
12884068 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:12884070 original size:35 final size:35
Alignment explanation
Indices: 12884015--12884094 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
12884005 TTATTTAATA
* *
12884015 ATATAATAT-CATTATAATTTAATTATCATAAATT
1 ATATAATATAAATTATAATTTAAATATCATAAATT
*
12884049 CATATAATATAAATTAT-ATTTAAATATCATTAATT
1 -ATATAATATAAATTATAATTTAAATATCATAAATT
12884084 ATATAAT-TAAA
1 ATATAATATAAA
12884095 CAAATAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 25 0.61
36 5 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (35 bp):
ATATAATATAAATTATAATTTAAATATCATAAATT
Found at i:12891440 original size:17 final size:16
Alignment explanation
Indices: 12891413--12891445 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
12891403 TAATTGGTAG
12891413 CTAATCACTCTAAACC
1 CTAATCACTCTAAACC
12891429 CTAATACACTCTAAACC
1 CTAAT-CACTCTAAACC
12891446 ACTCTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.24
Consensus pattern (16 bp):
CTAATCACTCTAAACC
Found at i:12910914 original size:25 final size:25
Alignment explanation
Indices: 12910880--12910927 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
12910870 TCTTGAATTG
*
12910880 TTAATGAAGTGATTGCATCGAGCAT
1 TTAATAAAGTGATTGCATCGAGCAT
12910905 TTAATAAAGTGATTGCATCGAGC
1 TTAATAAAGTGATTGCATCGAGC
12910928 TTCATGGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (25 bp):
TTAATAAAGTGATTGCATCGAGCAT
Found at i:12917189 original size:15 final size:15
Alignment explanation
Indices: 12917177--12917216 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
12917167 CGGAGGTGAT
12917177 GGATACATCGGTGGC
1 GGATACATCGGTGGC
12917192 GGATACATCGGTGGC
1 GGATACATCGGTGGC
12917207 GGATACATCG
1 GGATACATCG
12917217 ATGTTACCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.23, C:0.20, G:0.38, T:0.20
Consensus pattern (15 bp):
GGATACATCGGTGGC
Found at i:12921875 original size:17 final size:18
Alignment explanation
Indices: 12921855--12921894 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
12921845 TAAGATGACT
*
12921855 ATAAAAAA-ATTCAATAA
1 ATAAAAAATATTAAATAA
*
12921872 ATAAAAAATATTAAATTA
1 ATAAAAAATATTAAATAA
12921890 ATAAA
1 ATAAA
12921895 TATCAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAAAAATATTAAATAA
Found at i:12921895 original size:15 final size:15
Alignment explanation
Indices: 12921877--12921917 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
12921867 AATAAATAAA
12921877 AAATATTAAATTAAT
1 AAATATTAAATTAAT
*
12921892 AAATATCAAATTAAT
1 AAATATTAAATTAAT
12921907 ATAATA-TAAAT
1 A-AATATTAAAT
12921918 ATTTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATATTAAATTAAT
Found at i:12949776 original size:18 final size:18
Alignment explanation
Indices: 12949744--12949787 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
12949734 GGCCCCCAAG
*
12949744 TTTTTTATAATTTTAT-T
1 TTTTTTATAAATTTATAT
12949761 TTTTTTATAAAATTTATAAT
1 TTTTTTAT-AAATTTAT-AT
12949781 TTTTTTA
1 TTTTTTA
12949788 ATGATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
18 7 0.30
20 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTTATAAATTTATAT
Found at i:12950839 original size:13 final size:13
Alignment explanation
Indices: 12950821--12950845 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12950811 TAATTTAATA
12950821 TTATTTTGTGTGT
1 TTATTTTGTGTGT
12950834 TTATTTTGTGTG
1 TTATTTTGTGTG
12950846 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:12951825 original size:2 final size:2
Alignment explanation
Indices: 12951818--12951858 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
12951808 TTAAATCAGC
*
12951818 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12951859 ACTATTGTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12952183 original size:114 final size:114
Alignment explanation
Indices: 12951838--12952166 Score: 563
Period size: 114 Copynumber: 2.9 Consensus size: 114
12951828 ATATATATAT
* * * *
12951838 ATATATATATATATATGTATAACTATTGTACATTTGATGAGCTATAATTAAAAGTATACGAATTG
1 ATATGTATATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATATGAATTG
*
12951903 AAATTAGTTAAGTATGAATGATATATATATG--CATAAATGAAGTTCGA
66 AAATTAGTTAAGTATGAATGTTATATATATGCACATAAATGAAGTTCGA
12951950 ATATGTGTATATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATATGAAT
1 ATA--TGTATATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATATGAAT
*
12952015 TGAAATTAGTTAAGTATGAATGTTATATATATACACATAAATGAAGTTCGA
64 TGAAATTAGTTAAGTATGAATGTTATATATATGCACATAAATGAAGTTCGA
*
12952066 ATATGTATATATATATGTCTATCTATTGTATATTTGATGAGCTATAATTAAAAGTATATGAATTG
1 ATATGTATATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATATGAATTG
12952131 AAATTAGTTAAGTATGAATGTTATATATATGCACAT
66 AAATTAGTTAAGTATGAATGTTATATATATGCACAT
12952167 GTGTGAGGTT
Statistics
Matches: 205, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
112 3 0.01
114 183 0.89
116 19 0.09
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.40
Consensus pattern (114 bp):
ATATGTATATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATATGAATTG
AAATTAGTTAAGTATGAATGTTATATATATGCACATAAATGAAGTTCGA
Found at i:12952558 original size:41 final size:40
Alignment explanation
Indices: 12952504--12952643 Score: 217
Period size: 41 Copynumber: 3.4 Consensus size: 40
12952494 TTTCGGACTT
*
12952504 TAAGTCTAGCAGGCTAAGTGCAGGTGATCTGAATCAGGTTA
1 TAAGCCTAGCAGGCTAAGTGC-GGTGATCTGAATCAGGTTA
12952545 TAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTA
1 TAAGCCTAGCAGGCTAAGTG-CGGTGATCTGAATCAGGTTA
* *
12952586 TAAACCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTA
1 TAAGCCTAGCAGGCTAAGTG-CGGTGATCTGAATCAGGTTA
*
12952627 TAAGCTTAGCAGGCTAA
1 TAAGCCTAGCAGGCTAA
12952644 ATGCTTAGCA
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
41 91 0.99
42 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (40 bp):
TAAGCCTAGCAGGCTAAGTGCGGTGATCTGAATCAGGTTA
Found at i:12952641 original size:16 final size:16
Alignment explanation
Indices: 12952620--12952663 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
12952610 TGATCTGAAT
12952620 CAGGCTATAA-GCTTAG
1 CAGGCTA-AATGCTTAG
12952636 CAGGCTAAATGCTTAG
1 CAGGCTAAATGCTTAG
*
12952652 CAAGCTAAATGC
1 CAGGCTAAATGC
12952664 CGGTGAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 2 0.08
16 24 0.92
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (16 bp):
CAGGCTAAATGCTTAG
Found at i:12962698 original size:20 final size:20
Alignment explanation
Indices: 12962670--12962707 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12962660 TCATAAAATT
*
12962670 TAAATAAATTAAACATATTA
1 TAAAAAAATTAAACATATTA
*
12962690 TAAAAAAATTAATCATAT
1 TAAAAAAATTAAACATAT
12962708 ACTTTTTGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAAAATTAAACATATTA
Found at i:12965599 original size:34 final size:34
Alignment explanation
Indices: 12965506--12965739 Score: 147
Period size: 34 Copynumber: 6.9 Consensus size: 34
12965496 ATGTTATAAC
* *
12965506 AGATCAATACGGTAGTAATAA-CATGCTTATAACA
1 AGATCAATACAGTAGTAATAATCATGCTTA-AAAA
* *
12965540 A-ATCAATACAGTAGCAATTATCATGCTTAAAAA
1 AGATCAATACAGTAGTAATAATCATGCTTAAAAA
* * * * *
12965573 AGATCATTATATTAGTAATAAACATGCTT-ATAA
1 AGATCAATACAGTAGTAATAATCATGCTTAAAAA
* * * * *
12965606 CGAGTCAATACAATAGCAATTATCATGCTTAAAAC
1 AGA-TCAATACAGTAGTAATAATCATGCTTAAAAA
* * *
12965641 ATATCATTACAGTAGTAATAATCATGCTT-ATAA
1 AGATCAATACAGTAGTAATAATCATGCTTAAAAA
* * * * *
12965674 TGAGTCGATA-ATATAGCAATTATCATGCTTAAAACA
1 AGA-TCAATACA-GTAGTAATAATCATGCTTAAAA-A
* * * *
12965710 A-ATCATTACAGTAGCAATAAGCTTGCTTAA
1 AGATCAATACAGTAGTAATAATCATGCTTAA
12965740 CATGTATTTA
Statistics
Matches: 148, Mismatches: 43, Indels: 18
0.71 0.21 0.09
Matches are distributed among these distances:
33 29 0.20
34 111 0.75
35 7 0.05
36 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.30
Consensus pattern (34 bp):
AGATCAATACAGTAGTAATAATCATGCTTAAAAA
Found at i:12965614 original size:68 final size:67
Alignment explanation
Indices: 12965508--12965738 Score: 286
Period size: 68 Copynumber: 3.4 Consensus size: 67
12965498 GTTATAACAG
* * * * *
12965508 ATCAATACGGTAGTAAT-AACATGCTTATAACAAATCAATACAGTAGCAATTATCATGCTTAAAA
1 ATCATTACAGTAGTAATAAACATGCTTATAACGAGTCAATACAATAGCAATTATCATGCTTAAAA
12965572 AA
66 AA
* *
12965574 GATCATTATATTAGTAATAAACATGCTTATAACGAGTCAATACAATAGCAATTATCATGCTTAAA
1 -ATCATTACAGTAGTAATAAACATGCTTATAACGAGTCAATACAATAGCAATTATCATGCTTAAA
*
12965639 ACAT
65 A-AA
* * *
12965643 ATCATTACAGTAGTAATAATCATGCTTATAATGAGTCGATA-ATATAGCAATTATCATGCTTAAA
1 ATCATTACAGTAGTAATAAACATGCTTATAACGAGTCAATACA-ATAGCAATTATCATGCTTAAA
12965707 ACAA
65 A-AA
* * *
12965711 ATCATTACAGTAGCAATAAGCTTGCTTA
1 ATCATTACAGTAGTAATAAACATGCTTA
12965739 ACATGTATTT
Statistics
Matches: 144, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
67 14 0.10
68 129 0.90
69 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (67 bp):
ATCATTACAGTAGTAATAAACATGCTTATAACGAGTCAATACAATAGCAATTATCATGCTTAAAA
AA
Found at i:12965737 original size:102 final size:101
Alignment explanation
Indices: 12965494--12965739 Score: 246
Period size: 102 Copynumber: 2.4 Consensus size: 101
12965484 ATGCAACATG
* * * *
12965494 ACATG-TTATAACAGATCAATACGGTAGTAATAACATGCTTATAACAAATCAATACAGTAGCAAT
1 ACATGCTTATAACAAATCAATACAGTAGCAATAACATGCTTAAAACAAATCAATACAGTAGCAAT
* * *
12965558 TATCATGCTTAAAAAAGATCATTATATTAGTAATAA
66 AATCATGCTTAAAAAAGATCATAATATTAGCAATAA
* * * * * * *
12965594 ACATGCTTATAACGAGTCAATACAATAGCAATTATCATGCTTAAAACATATCATTACAGTAGTAA
1 ACATGCTTATAACAAATCAATACAGTAGCAA-TAACATGCTTAAAACAAATCAATACAGTAGCAA
* * *
12965659 TAATCATGCTT-ATAATGAGTCGATAATA-TAGCAATTA
65 TAATCATGCTTAAAAAAGA-TC-ATAATATTAGCAATAA
* * * *
12965696 TCATGCTTAAAACAAATCATTACAGTAGCAATAAGCTTGCTTAA
1 ACATGCTTATAACAAATCAATACAGTAGCAATAA-CATGCTTAA
12965740 CATGTATTTA
Statistics
Matches: 116, Mismatches: 25, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
100 5 0.04
101 26 0.22
102 80 0.69
103 5 0.04
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.30
Consensus pattern (101 bp):
ACATGCTTATAACAAATCAATACAGTAGCAATAACATGCTTAAAACAAATCAATACAGTAGCAAT
AATCATGCTTAAAAAAGATCATAATATTAGCAATAA
Found at i:12975412 original size:21 final size:19
Alignment explanation
Indices: 12975368--12975412 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
12975358 ACAGAGAAAT
12975368 GGTGTGTTTTCACAAACTC
1 GGTGTGTTTTCACAAACTC
*
12975387 GGTGTGTTTTCGCAAACTC
1 GGTGTGTTTTCACAAACTC
*
12975406 AGTGTGT
1 GGTGTGT
12975413 AATCTCCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (19 bp):
GGTGTGTTTTCACAAACTC
Found at i:12978026 original size:41 final size:41
Alignment explanation
Indices: 12977981--12978065 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
12977971 TTAATTATTT
* *
12977981 CCTGAATTGCACATACGTGTTC-TTGTTTGTACTTTGGTACC
1 CCTGAATTACACATACGTG-CCGTTGTTTGTACTTTGGTACC
*
12978022 CCTGAATTACACATACGTGCCGTTGTTTGTACTTTGGTGCC
1 CCTGAATTACACATACGTGCCGTTGTTTGTACTTTGGTACC
12978063 CCT
1 CCT
12978066 ATTTGTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 1 0.03
41 39 0.98
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (41 bp):
CCTGAATTACACATACGTGCCGTTGTTTGTACTTTGGTACC
Found at i:12979106 original size:12 final size:12
Alignment explanation
Indices: 12979089--12979114 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12979079 AAACGAAACA
12979089 GAAAGAAAGAAG
1 GAAAGAAAGAAG
12979101 GAAAGAAAGAAG
1 GAAAGAAAGAAG
12979113 GA
1 GA
12979115 GAAAGGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (12 bp):
GAAAGAAAGAAG
Found at i:12979486 original size:20 final size:20
Alignment explanation
Indices: 12979450--12979487 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12979440 GTGAAATTTG
*
12979450 TGTGAAAATATAGAATTAAT
1 TGTGAAAATATAAAATTAAT
12979470 TGTGAAGAA-ATAAAATTA
1 TGTGAA-AATATAAAATTA
12979488 GTCTCGGTTT
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:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (20 bp):
TGTGAAAATATAAAATTAAT
Found at i:12980043 original size:40 final size:39
Alignment explanation
Indices: 12979996--12980093 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 39
12979986 CGACTTCGAG
* *
12979996 TCGATGAG-ACAGGTGTGTCAATTTATTACTTCGAATTAAT
1 TCGATGAGCACAGG-GTGTCAATCTATTACTTAGAATT-AT
* *
12980036 TTGATGAGGCACTGGGTGTCAATCTATTACTTAGAATTAT
1 TCGATGA-GCACAGGGTGTCAATCTATTACTTAGAATTAT
*
12980076 TCGATGAGGCACTGGGTG
1 TCGATGA-GCACAGGGTG
12980094 CCAAACTGGT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 25 0.49
41 22 0.43
42 4 0.08
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.35
Consensus pattern (39 bp):
TCGATGAGCACAGGGTGTCAATCTATTACTTAGAATTAT
Found at i:12980055 original size:41 final size:40
Alignment explanation
Indices: 12980010--12980093 Score: 132
Period size: 41 Copynumber: 2.1 Consensus size: 40
12980000 TGAGACAGGT
* * *
12980010 GTGTCAATTTATTACTTCGAATTAATTTGATGAGGCACTGG
1 GTGTCAATCTATTACTTAGAATT-ATTCGATGAGGCACTGG
12980051 GTGTCAATCTATTACTTAGAATTATTCGATGAGGCACTGG
1 GTGTCAATCTATTACTTAGAATTATTCGATGAGGCACTGG
12980091 GTG
1 GTG
12980094 CCAAACTGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 19 0.47
41 21 0.52
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (40 bp):
GTGTCAATCTATTACTTAGAATTATTCGATGAGGCACTGG
Found at i:12981764 original size:20 final size:21
Alignment explanation
Indices: 12981731--12981770 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12981721 CCCCTGCAGT
*
12981731 TCAATTTTTAAAAT-TTTTCC
1 TCAATGTTTAAAATGTTTTCC
*
12981751 TCAATGTTTCAAATGTTTTC
1 TCAATGTTTAAAATGTTTTC
12981771 GATTTCGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.53
Consensus pattern (21 bp):
TCAATGTTTAAAATGTTTTCC
Found at i:12985683 original size:3 final size:3
Alignment explanation
Indices: 12985675--12985700 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12985665 ATATTATAAA
12985675 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
12985701 ATTGTGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:12996886 original size:34 final size:35
Alignment explanation
Indices: 12996819--12996941 Score: 124
Period size: 35 Copynumber: 3.5 Consensus size: 35
12996809 AGTAAATTAA
* * * *
12996819 CAATCCAACCAAAACACACTAGATGCGCATAAGAGC
1 CAATCCATCCGAAACACACCA-ATGCTCATAAGAGC
*
12996855 CAATCCATCCG-AACACATCAATGCTCATAAGAGC
1 CAATCCATCCGAAACACACCAATGCTCATAAGAGC
* * *
12996889 TAATCCCTCCGAAACACACCAGTGCTCATAAGAGC
1 CAATCCATCCGAAACACACCAATGCTCATAAGAGC
* *
12996924 TAGTCCAAT-CGAAACACA
1 CAATCC-ATCCGAAACACA
12996942 TCGAGACAGA
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
34 22 0.30
35 42 0.57
36 10 0.14
ACGTcount: A:0.40, C:0.32, G:0.13, T:0.15
Consensus pattern (35 bp):
CAATCCATCCGAAACACACCAATGCTCATAAGAGC
Found at i:12996905 original size:35 final size:35
Alignment explanation
Indices: 12996841--12996943 Score: 129
Period size: 35 Copynumber: 3.0 Consensus size: 35
12996831 AACACACTAG
* *
12996841 ATGCGCATAAGAGCCAATCCATCCG-AACACATCA
1 ATGCTCATAAGAGCTAATCCATCCGAAACACATCA
* *
12996875 ATGCTCATAAGAGCTAATCCCTCCGAAACACACCA
1 ATGCTCATAAGAGCTAATCCATCCGAAACACATCA
* *
12996910 GTGCTCATAAGAGCTAGTCCAAT-CGAAACACATC
1 ATGCTCATAAGAGCTAATCC-ATCCGAAACACATC
12996944 GAGACAGAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
34 22 0.37
35 36 0.61
36 1 0.02
ACGTcount: A:0.37, C:0.31, G:0.15, T:0.17
Consensus pattern (35 bp):
ATGCTCATAAGAGCTAATCCATCCGAAACACATCA
Found at i:12997885 original size:10 final size:10
Alignment explanation
Indices: 12997870--12997894 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12997860 TTTTTTATTC
12997870 TTTAATTTTG
1 TTTAATTTTG
12997880 TTTAATTTTG
1 TTTAATTTTG
12997890 TTTAA
1 TTTAA
12997895 ACTTTCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (10 bp):
TTTAATTTTG
Found at i:12999215 original size:16 final size:16
Alignment explanation
Indices: 12999194--12999235 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
12999184 CTTTCCATTT
12999194 CAAATTCATATATGCA
1 CAAATTCATATATGCA
* *
12999210 CAAATTCAAATATTCA
1 CAAATTCATATATGCA
*
12999226 -AGATTCATAT
1 CAAATTCATAT
12999236 TAGTTCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (16 bp):
CAAATTCATATATGCA
Found at i:13001180 original size:12 final size:14
Alignment explanation
Indices: 13001142--13001179 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
13001132 AAAATTATAA
13001142 AATAATAAAAATTC
1 AATAATAAAAATTC
13001156 AATAATTAAAAATTC
1 AATAA-TAAAAATTC
13001171 AATAA-AAAA
1 AATAATAAAA
13001180 TGTGGTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 5 0.22
15 14 0.61
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAATAAAAATTC
Found at i:13001425 original size:20 final size:18
Alignment explanation
Indices: 13001396--13001435 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
13001386 ATTTTAAGTT
13001396 TTTAAATTTATTCGATTTAG
1 TTTAAATTTA-T-GATTTAG
*
13001416 TTTAATTTTATGATTTAG
1 TTTAAATTTATGATTTAG
13001434 TT
1 TT
13001436 CTTGTACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 1 0.05
20 9 0.47
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.60
Consensus pattern (18 bp):
TTTAAATTTATGATTTAG
Found at i:13004091 original size:21 final size:21
Alignment explanation
Indices: 13004048--13004092 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13004038 AACACGGCAC
*
13004048 TGTGGCTACTCCACACGCCCG
1 TGTGGCTACTCCACACACCCG
* * *
13004069 TGTGGCTATTTCACACACTCG
1 TGTGGCTACTCCACACACCCG
13004090 TGT
1 TGT
13004093 ACGTAGACCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.33, G:0.22, T:0.29
Consensus pattern (21 bp):
TGTGGCTACTCCACACACCCG
Found at i:13006211 original size:2 final size:2
Alignment explanation
Indices: 13006204--13006241 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
13006194 ATTTGTTTCT
13006204 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13006242 CTTTTAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13010377 original size:26 final size:26
Alignment explanation
Indices: 13010348--13010435 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 26
13010338 TATAACAATC
13010348 ATTTTACCTTATAGGGTATTTCAGTA
1 ATTTTACCTTATAGGGTATTTCAGTA
**
13010374 ATTTTATCCTTCA-AGGGTATTTTGGTA
1 ATTTTA-CCTT-ATAGGGTATTTCAGTA
* * *
13010401 CTTTTACC-CATCGAGGGTATTTCAGTC
1 ATTTTACCTTAT--AGGGTATTTCAGTA
13010428 ATTTTACC
1 ATTTTACC
13010436 CATCAAGGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
24 1 0.02
26 8 0.16
27 39 0.80
28 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (26 bp):
ATTTTACCTTATAGGGTATTTCAGTA
Found at i:13010384 original size:27 final size:25
Alignment explanation
Indices: 13010348--13010461 Score: 77
Period size: 27 Copynumber: 4.3 Consensus size: 25
13010338 TATAACAATC
13010348 ATTTTACCTTATAGGGTATTTCAGTA
1 ATTTTACCTTA-AGGGTATTTCAGTA
**
13010374 ATTTTATCCTTCAAGGGTATTTTGGTA
1 ATTTTA-CCTT-AAGGGTATTTCAGTA
* ** *
13010401 CTTTTACCCATCGAGGGTATTTCAGTC
1 ATTTTA-CC-TTAAGGGTATTTCAGTA
* *
13010428 ATTTTACCCATCAAGGGTACTTT-AGTT
1 ATTTTA-CC-TTAAGGGTA-TTTCAGTA
13010455 ATTTTAC
1 ATTTTAC
13010462 AACCTTTCCA
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
26 7 0.10
27 60 0.83
28 5 0.07
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.44
Consensus pattern (25 bp):
ATTTTACCTTAAGGGTATTTCAGTA
Found at i:13022066 original size:18 final size:18
Alignment explanation
Indices: 13022022--13022069 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
13022012 AAATAAAAAA
13022022 AATATTTTGAAATTGAAT
1 AATATTTTGAAATTGAAT
*
13022040 AACGA-TTTGTAAA-TGAAT
1 AA-TATTTTG-AAATTGAAT
13022058 AATATTTTGAAA
1 AATATTTTGAAA
13022070 ACAAACAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (18 bp):
AATATTTTGAAATTGAAT
Found at i:13028554 original size:18 final size:18
Alignment explanation
Indices: 13028510--13028557 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
13028500 CAATAAAAAA
13028510 AATGTTTTGAAATTAAAT
1 AATGTTTTGAAATTAAAT
* * *
13028528 AACGATTTGTAAA-TGAAT
1 AATGTTTTG-AAATTAAAT
13028546 AATGTTTTGAAA
1 AATGTTTTGAAA
13028558 ACGAACAACA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.40
Consensus pattern (18 bp):
AATGTTTTGAAATTAAAT
Found at i:13032318 original size:27 final size:28
Alignment explanation
Indices: 13032276--13032328 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
13032266 ATTTTTTATA
13032276 ATATTTTTTACAA-TTTTATAAAAAATT
1 ATATTTTTTACAATTTTTATAAAAAATT
*
13032303 ATATTTTTTACGATTTTTATAAAAAA
1 ATATTTTTTACAATTTTTATAAAAAA
13032329 ATACATTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (28 bp):
ATATTTTTTACAATTTTTATAAAAAATT
Found at i:13032320 original size:28 final size:27
Alignment explanation
Indices: 13032276--13032328 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
13032266 ATTTTTTATA
13032276 ATATTTTTTACAATTTTATAAAAAATT
1 ATATTTTTTACAATTTTATAAAAAATT
*
13032303 ATATTTTTTACGATTTTTATAAAAAA
1 ATATTTTTTAC-AATTTTATAAAAAA
13032329 ATACATTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (27 bp):
ATATTTTTTACAATTTTATAAAAAATT
Found at i:13032397 original size:30 final size:30
Alignment explanation
Indices: 13032354--13032411 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
13032344 ATTCATTAAG
*
13032354 ATTTTTATAATTTTT-TCTATTTTAAATAAA
1 ATTTTAATAATTTTTATC-ATTTTAAATAAA
* *
13032384 ATTTTAATGATTTTTATCATTTTTAATA
1 ATTTTAATAATTTTTATCATTTTAAATA
13032412 TTTTCTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (30 bp):
ATTTTAATAATTTTTATCATTTTAAATAAA
Found at i:13032414 original size:39 final size:39
Alignment explanation
Indices: 13032349--13032444 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 39
13032339 TATAAATTCA
* **
13032349 TTAA-GATTTTTATAATTTTTTCTATTTTAAATAAAATT
1 TTAATGATTTTTATCATTTTTAATATTTTAAATAAAATT
** **
13032387 TTAATGATTTTTATCATTTTTAATATTTTCTATAACTTT
1 TTAATGATTTTTATCATTTTTAATATTTTAAATAAAATT
*
13032426 TTATTGATTTTTATC-TTTT
1 TTAATGATTTTTATCATTTT
13032445 ATCATTTTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 8 0.16
39 41 0.84
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (39 bp):
TTAATGATTTTTATCATTTTTAATATTTTAAATAAAATT
Found at i:13032895 original size:11 final size:11
Alignment explanation
Indices: 13032850--13032932 Score: 61
Period size: 11 Copynumber: 7.8 Consensus size: 11
13032840 TTATTTTAAA
13032850 ATTTTAAAAA-
1 ATTTTAAAAAT
13032860 A--TTAAAAAT
1 ATTTTAAAAAT
* *
13032869 AATTAATAAAAGT
1 -ATT-TTAAAAAT
13032882 ATTTTAAAAAT
1 ATTTTAAAAAT
13032893 ATTTT--AAA-
1 ATTTTAAAAAT
**
13032901 ATTAAAAAAAGT
1 ATTTTAAAAA-T
13032913 ATTTTAAAAAT
1 ATTTTAAAAAT
13032924 ATTTTAAAA
1 ATTTTAAAA
13032933 TTAAAAAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
8 10 0.18
9 3 0.05
10 5 0.09
11 21 0.38
12 11 0.20
13 6 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:13032904 original size:31 final size:31
Alignment explanation
Indices: 13032869--13032941 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
13032859 AATTAAAAAT
*
13032869 AATTAATAAAAGTATTTTAAAAATATTTTAA
1 AATTAAAAAAAGTATTTTAAAAATATTTTAA
13032900 AATTAAAAAAAGTATTTTAAAAATATTTTAA
1 AATTAAAAAAAGTATTTTAAAAATATTTTAA
13032931 AATTAAAAAAA
1 AATTAAAAAAA
13032942 ATTAAAAAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (31 bp):
AATTAAAAAAAGTATTTTAAAAATATTTTAA
Found at i:13032919 original size:71 final size:71
Alignment explanation
Indices: 13032841--13032981 Score: 205
Period size: 71 Copynumber: 2.0 Consensus size: 71
13032831 GGCCTATTTT
* * * *
13032841 TATTTT-AAAAT-TTTAAAAAATTAAAAATAATTAATAAAAGTATTTTAAAAATATTTTAAAATT
1 TATTTTAAAAATATTT-AAAAATTAAAAAAAATTAA-AAAAGTAATGTAAAAAAATTTTAAAATT
13032904 AAAAAAAG
64 AAAAAAAG
*
13032912 TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAGTAATGTAAAAAAATTTTAAAATTAA
1 TATTTTAAAAATATTTAAAAATTAAAAAAAATTAAAAAAGTAATGTAAAAAAATTTTAAAATTAA
13032977 AAAAA
66 AAAAA
13032982 TAAATATATT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
71 38 0.60
72 22 0.35
73 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (71 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAAATTAAAAAAGTAATGTAAAAAAATTTTAAAATTAA
AAAAAG
Found at i:13032961 original size:40 final size:40
Alignment explanation
Indices: 13032841--13032981 Score: 103
Period size: 40 Copynumber: 3.5 Consensus size: 40
13032831 GGCCTATTTT
**
13032841 TATTTTAAAATTTTAAAAAATT-AAAAA-TAATTAATAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAGTAATTAA-AAAA
* *** *
13032880 GTATTTTAAAAATATTTTAAAATTAAAAAAAGTATTTTAAAAATA
1 -TATTTTAAAATTA-AAAAAAATT-AAAAAAGTA-ATTAAAAA-A
* *
13032925 T-TTTAAAAT-TAAAAAAAATTAAAAAAGTAATGTAAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAGTAAT-TAAAAAA
13032964 -ATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
13032982 TAAATATATT
Statistics
Matches: 79, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
39 8 0.10
40 34 0.43
41 13 0.16
42 2 0.03
43 11 0.14
44 6 0.08
45 5 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAGTAATTAAAAAA
Found at i:13034383 original size:19 final size:20
Alignment explanation
Indices: 13034350--13034396 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
13034340 TCAGGAAAAT
13034350 ATTTTCTGAAAAATGATTTA
1 ATTTTCTGAAAAATGATTTA
*
13034370 CTTTTCTG-AAAATGATTTA
1 ATTTTCTGAAAAATGATTTA
13034389 ATTTTCTG
1 ATTTTCTG
13034397 GTGTTTGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (20 bp):
ATTTTCTGAAAAATGATTTA
Found at i:13034440 original size:36 final size:36
Alignment explanation
Indices: 13034397--13034467 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
13034387 TAATTTTCTG
13034397 GTGTTTGGATAAATCTATGTAAAATATTTTCTGTTT
1 GTGTTTGGATAAATCTATGTAAAATATTTTCTGTTT
* *
13034433 GTGTTTGGATGAATTTATGTAAAATATTTTCTGTT
1 GTGTTTGGATAAATCTATGTAAAATATTTTCTGTT
13034468 GTTTAGCAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (36 bp):
GTGTTTGGATAAATCTATGTAAAATATTTTCTGTTT
Found at i:13036409 original size:27 final size:27
Alignment explanation
Indices: 13036371--13036423 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
13036361 TATTAACAGC
13036371 ACAGCCTTAAATTCTAACAGTTTAGTT
1 ACAGCCTTAAATTCTAACAGTTTAGTT
*
13036398 ACAGCCTTAAATTCTAATAGTTTAGT
1 ACAGCCTTAAATTCTAACAGTTTAGT
13036424 CGGTATCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (27 bp):
ACAGCCTTAAATTCTAACAGTTTAGTT
Found at i:13040547 original size:5 final size:5
Alignment explanation
Indices: 13040534--13040563 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
13040524 TGCAGCTTAG
*
13040534 GTTTG GTTTT GTTTT GTTTT GTTTT GTTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT
13040564 TTCTTTGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (5 bp):
GTTTT
Found at i:13044632 original size:49 final size:49
Alignment explanation
Indices: 13044560--13044683 Score: 144
Period size: 49 Copynumber: 2.5 Consensus size: 49
13044550 ATTGGGCCTA
* * * * *
13044560 CATATGAGAGAGAGTGTAAGTAATATAT-GTTTGGGTAAACTTGGTTTTT
1 CATAT-AGAGAGAGTGCAAGTAATATATCATGTCGGTAAACTTGGTGTTT
13044609 CATATAAGAGAGAGTGCAAGTAATATATCACATGTCGGTAAACTTGGTGTTT
1 CATAT-AGAGAGAGTGCAAGTAATATAT--CATGTCGGTAAACTTGGTGTTT
*
13044661 CATAT-GAGAGTGTGCAAGTAATA
1 CATATAGAGAGAGTGCAAGTAATA
13044684 CGTTTGGAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
49 26 0.40
50 17 0.26
52 22 0.34
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.33
Consensus pattern (49 bp):
CATATAGAGAGAGTGCAAGTAATATATCATGTCGGTAAACTTGGTGTTT
Found at i:13052174 original size:78 final size:78
Alignment explanation
Indices: 13052040--13052197 Score: 271
Period size: 78 Copynumber: 2.0 Consensus size: 78
13052030 AATACTTAAA
* * *
13052040 ATTATTATTTATAAACCCTATGGTTTGCCCTACCTATCTGTCTATTACTCTCCCATGGAATGGAA
1 ATTACTATTTATAAACCCTATGCTTTGCCCTACCTAGCTGTCTATTACTCTCCCATGGAATGGAA
*
13052105 GGTCTTTTGGTGT
66 GATCTTTTGGTGT
*
13052118 ATTACTATTTATAAACCCTATGCTTTGCCCTACCTAGCTGTCTATTACTCTTCCATGGAATGGAA
1 ATTACTATTTATAAACCCTATGCTTTGCCCTACCTAGCTGTCTATTACTCTCCCATGGAATGGAA
13052183 GATCTTTTGGTGT
66 GATCTTTTGGTGT
13052196 AT
1 AT
13052198 GTTTTTCCTT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.41
Consensus pattern (78 bp):
ATTACTATTTATAAACCCTATGCTTTGCCCTACCTAGCTGTCTATTACTCTCCCATGGAATGGAA
GATCTTTTGGTGT
Found at i:13052507 original size:162 final size:163
Alignment explanation
Indices: 13052239--13052565 Score: 566
Period size: 162 Copynumber: 2.0 Consensus size: 163
13052229 TTATTTTTCC
* *
13052239 TATTCTTGTTTTGTTTCTATTATTTACGCCAACTGTTCTATAAGAACACAATAGAAAGATCAATA
1 TATTCTTGTTTTGTTACTATTATTTACACCAACTGTTCTATAAGAACACAATAGAAAGATCAATA
* *
13052304 GAATAACGAAGTAAAACTCTTTGTGGTTTTACCTTCAAAGTTTCTGTCTTCTACCTCTTTTAGAG
66 GAATAACAAAGTAAAACTCTTCGTGGTTTTACCTTCAAAGTTTCTGTCTTCTACCTCTTTTAGAG
*
13052369 TTGGCTTTGTGTAACAGAGTGTTGTTAGGGGTG
131 TTGGCTTTGTGTAACAGAGTGTTGTCAGGGGTG
* *
13052402 TATTCTTGTTTTGTTACTATTATTTACACCTACTGTTCTAT-ATAACACAATAGAAAGATCAATA
1 TATTCTTGTTTTGTTACTATTATTTACACCAACTGTTCTATAAGAACACAATAGAAAGATCAATA
*
13052466 GAATAACAAAGTAAAACTCTTCGTGGTTTTACCTTCAAAGTTTCTGTCTTTTACCTCTTTTAGAG
66 GAATAACAAAGTAAAACTCTTCGTGGTTTTACCTTCAAAGTTTCTGTCTTCTACCTCTTTTAGAG
*
13052531 TTGGCTTTGTGTAACATAGTGTTGTCAGGGGTG
131 TTGGCTTTGTGTAACAGAGTGTTGTCAGGGGTG
13052564 TA
1 TA
13052566 AGGCGCAAAA
Statistics
Matches: 155, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
162 117 0.75
163 38 0.25
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (163 bp):
TATTCTTGTTTTGTTACTATTATTTACACCAACTGTTCTATAAGAACACAATAGAAAGATCAATA
GAATAACAAAGTAAAACTCTTCGTGGTTTTACCTTCAAAGTTTCTGTCTTCTACCTCTTTTAGAG
TTGGCTTTGTGTAACAGAGTGTTGTCAGGGGTG
Found at i:13053761 original size:2 final size:2
Alignment explanation
Indices: 13053756--13053791 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13053746 TCTCTCTCTA
13053756 TG TG TG TG TG 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 TG TG TG TG TG
13053792 CCTGCTTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:13063045 original size:20 final size:20
Alignment explanation
Indices: 13063020--13063061 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
13063010 TTGTTAATGA
*
13063020 AAAATTAATTTAATATAATT
1 AAAATTAAGTTAATATAATT
*
13063040 AAAATTAAGTTAATTTAATT
1 AAAATTAAGTTAATATAATT
13063060 AA
1 AA
13063062 GTAATTAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AAAATTAAGTTAATATAATT
Found at i:13075199 original size:15 final size:15
Alignment explanation
Indices: 13075181--13075221 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
13075171 AACGAGATGG
*
13075181 TTGAGGAAGAAAATA
1 TTGAGAAAGAAAATA
**
13075196 TTGAGAAAGAAGCTA
1 TTGAGAAAGAAAATA
13075211 TTGAGAAAGAA
1 TTGAGAAAGAA
13075222 TCTGCTAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.27, T:0.20
Consensus pattern (15 bp):
TTGAGAAAGAAAATA
Found at i:13079995 original size:21 final size:18
Alignment explanation
Indices: 13079950--13079997 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
13079940 GGTAACAACC
*
13079950 ATTCAATTTACAATTATA
1 ATTCAATTCACAATTATA
13079968 A-TCAATTCACAATTTATCA
1 ATTCAATTCACAA-TTAT-A
13079987 TATTCAATTCA
1 -ATTCAATTCA
13079998 TTAATCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 10 0.40
18 5 0.20
19 1 0.04
20 1 0.04
21 8 0.32
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTCAATTCACAATTATA
Found at i:13080161 original size:24 final size:24
Alignment explanation
Indices: 13080115--13080161 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
13080105 CTTTCATTTC
* *
13080115 AAAAATCAACATTTTCATGCCAAT
1 AAAAATCAACATTATCATCCCAAT
13080139 AAAAATCAAC-TTATCAATCCCAA
1 AAAAATCAACATTATC-ATCCCAA
13080162 CTCCCCTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.49, C:0.23, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAAATCAACATTATCATCCCAAT
Found at i:13083282 original size:109 final size:110
Alignment explanation
Indices: 13083060--13083316 Score: 446
Period size: 109 Copynumber: 2.3 Consensus size: 110
13083050 NNNNNNNNGA
13083060 GCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAATATTTTTGAAAAGGATATT
1 GCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAATATTTTTGAAAAGGATATT
* *
13083125 AAGCCATTTGGTTGAACAAGAACAATCGACACCCAGCACCTTAGG
66 AAGCCATTTGGTTAAACAAGAAAAATCGACACCCAGCACCTTAGG
*
13083170 GCATGTTTTCTCGAATTTTCAAACGCAAAACATTGCCTTATTTTAGA-ATTTTT-AAAAGGATAT
1 GCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTA-ATATTTTTGAAAAGGATAT
*
13083233 TAAGCCATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGG
65 TAAGCCATTTGGTTAAACAAGAAAAATCGACACCCAGCACCTTAGG
*
13083279 GCATATTTTCTCGAATTTCCAAACGCAAAACATTGCCT
1 GCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCT
13083317 CAATTAGAAA
Statistics
Matches: 140, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
109 89 0.64
110 50 0.36
111 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (110 bp):
GCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAATATTTTTGAAAAGGATATT
AAGCCATTTGGTTAAACAAGAAAAATCGACACCCAGCACCTTAGG
Found at i:13083710 original size:33 final size:33
Alignment explanation
Indices: 13083630--13083708 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 33
13083620 GAAGAAAATG
*
13083630 AGTACATAGATATATGTAAATAAATATATATAAA
1 AGTA-ATATATATATGTAAATAAATATATATAAA
* *
13083664 AGTAATATATATAT-TAAATAAAT-TATATGAT
1 AGTAATATATATATGTAAATAAATATATATAAA
13083695 A-TATATATATATAT
1 AGTA-ATATATATAT
13083709 ATAAGCACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 2 0.05
31 17 0.41
32 9 0.22
33 9 0.22
34 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.39
Consensus pattern (33 bp):
AGTAATATATATATGTAAATAAATATATATAAA
Found at i:13083817 original size:21 final size:22
Alignment explanation
Indices: 13083787--13083845 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 22
13083777 TGGAAATATA
*
13083787 ATAATAATAATAATAATA-TTG
1 ATAATAATAATAATAATAGATG
*
13083808 ATATTAATAATAATAA-AGATG
1 ATAATAATAATAATAATAGATG
13083829 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
13083846 GGTAACATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (22 bp):
ATAATAATAATAATAATAGATG
Found at i:13083864 original size:3 final size:3
Alignment explanation
Indices: 13083784--13083845 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
13083774 TAATGGAAAT
* * * *
13083784 ATA ATA ATA ATA ATA ATA ATA TTG ATA TTA ATA ATA ATA A-A GATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
13083829 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
13083846 GGTAACATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 1 0.02
3 48 0.98
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:13084673 original size:17 final size:17
Alignment explanation
Indices: 13084651--13084690 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
13084641 TACGTGCGGC
*
13084651 GCGGCGTCAGAACGGTG
1 GCGGCGACAGAACGGTG
*
13084668 GCGGCGACAGAATGGTG
1 GCGGCGACAGAACGGTG
13084685 GCGGCG
1 GCGGCG
13084691 CCGGGCTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.17, C:0.23, G:0.50, T:0.10
Consensus pattern (17 bp):
GCGGCGACAGAACGGTG
Found at i:13086440 original size:26 final size:26
Alignment explanation
Indices: 13086398--13086453 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
13086388 AAAATATTTT
13086398 TTATATTTTAAATAAAA-ACAAAAAAA
1 TTATATTTTAAATAAAATA-AAAAAAA
*
13086424 TTATAATTTTTAA-AAAATAAAAAAAA
1 TTAT-ATTTTAAATAAAATAAAAAAAA
13086450 TTAT
1 TTAT
13086454 GAAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
TTATATTTTAAATAAAATAAAAAAAA
Found at i:13086961 original size:22 final size:22
Alignment explanation
Indices: 13086919--13086961 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
13086909 TTTTTAAATA
*
13086919 AAATATTTTTATTTTTATTTTT
1 AAATATTTTTATGTTTATTTTT
*
13086941 AAATAATTTTTGTGTTT-TTTT
1 AAAT-ATTTTTATGTTTATTTT
13086962 CCATATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (22 bp):
AAATATTTTTATGTTTATTTTT
Found at i:13087017 original size:14 final size:14
Alignment explanation
Indices: 13086977--13087019 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
13086967 TATTTGATTT
13086977 TTTTAAAATATA-A
1 TTTTAAAATATATA
**
13086990 TTTTTATTATATATA
1 -TTTTAAAATATATA
13087005 TTTTAAAATATATA
1 TTTTAAAATATATA
13087019 T
1 T
13087020 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 23 0.96
15 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAAATATATA
Found at i:13087210 original size:12 final size:12
Alignment explanation
Indices: 13087190--13087232 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 12
13087180 GTTGAACTGA
13087190 TTTTT-ATAATT
1 TTTTTAATAATT
13087201 TTTTTAATAATTT
1 TTTTTAATAA-TT
13087214 TATTTTAATAATT
1 T-TTTTAATAATT
*
13087227 TATTTA
1 TTTTTA
13087233 CTTTGAATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 5 0.18
12 8 0.29
13 6 0.21
14 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTTAATAATT
Found at i:13087221 original size:14 final size:13
Alignment explanation
Indices: 13087189--13087231 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
13087179 CGTTGAACTG
*
13087189 ATTTTTATAATTT
1 ATTTTAATAATTT
13087202 -TTTTAATAATTTT
1 ATTTTAATAA-TTT
13087215 ATTTTAATAATTT
1 ATTTTAATAATTT
13087228 ATTT
1 ATTT
13087232 ACTTTGAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 8 0.30
13 10 0.37
14 9 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTAATAATTT
Found at i:13087533 original size:17 final size:17
Alignment explanation
Indices: 13087509--13087547 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
13087499 GTTTTAAAAC
*
13087509 AATTTTTTT-AAATTAA
1 AATTTTTTTAAAAATAA
13087525 AATTTTTTTAAAAATAA
1 AATTTTTTTAAAAATAA
13087542 AATTTT
1 AATTTT
13087548 AAGTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTTTTTAAAAATAA
Found at i:13092151 original size:42 final size:42
Alignment explanation
Indices: 13092104--13092187 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
13092094 TAACCTAATT
13092104 GGGAAAATAATTCCCTTATT-GTAATAAACTACTAAAAGATAA
1 GGGAAAATAATTCCCTTATTCG-AATAAACTACTAAAAGATAA
* **
13092146 GGGAAAGTAATTTTCTTATTCGAATAAACTACTAAAAGATAA
1 GGGAAAATAATTCCCTTATTCGAATAAACTACTAAAAGATAA
13092188 AATAAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 37 0.97
43 1 0.03
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (42 bp):
GGGAAAATAATTCCCTTATTCGAATAAACTACTAAAAGATAA
Found at i:13092233 original size:12 final size:12
Alignment explanation
Indices: 13092216--13092246 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13092206 TATCTCAAAT
*
13092216 GATTTATTCTAA
1 GATTTATTCCAA
13092228 GATTTATTCCAA
1 GATTTATTCCAA
13092240 GATTTAT
1 GATTTAT
13092247 CTACCTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (12 bp):
GATTTATTCCAA
Found at i:13092829 original size:248 final size:248
Alignment explanation
Indices: 13092391--13092886 Score: 992
Period size: 248 Copynumber: 2.0 Consensus size: 248
13092381 ACACTTGGCC
13092391 TTCTTCAATCTTCTCCTTGATGAAATGTCTATCAATCTCTACATGCTTAGTTTTGTCCTGCTGGA
1 TTCTTCAATCTTCTCCTTGATGAAATGTCTATCAATCTCTACATGCTTAGTTTTGTCCTGCTGGA
13092456 CTGGGTTGTGACTTGTGAGCAATACTAATCGCAGCTTTGCTATCATAGTACAACTTCATTGGTGA
66 CTGGGTTGTGACTTGTGAGCAATACTAATCGCAGCTTTGCTATCATAGTACAACTTCATTGGTGA
13092521 AATTATTGGTTTTGTGCTCTTCCATAATTCTTTTTAACCACTTCATTTCACAAATTCCTTGAGCC
131 AATTATTGGTTTTGTGCTCTTCCATAATTCTTTTTAACCACTTCATTTCACAAATTCCTTGAGCC
13092586 ATTGATCTAAACTCAGCCTCTACACTACTTCTTGCTACAACACTTTGTTTTTT
196 ATTGATCTAAACTCAGCCTCTACACTACTTCTTGCTACAACACTTTGTTTTTT
13092639 TTCTTCAATCTTCTCCTTGATGAAATGTCTATCAATCTCTACATGCTTAGTTTTGTCCTGCTGGA
1 TTCTTCAATCTTCTCCTTGATGAAATGTCTATCAATCTCTACATGCTTAGTTTTGTCCTGCTGGA
13092704 CTGGGTTGTGACTTGTGAGCAATACTAATCGCAGCTTTGCTATCATAGTACAACTTCATTGGTGA
66 CTGGGTTGTGACTTGTGAGCAATACTAATCGCAGCTTTGCTATCATAGTACAACTTCATTGGTGA
13092769 AATTATTGGTTTTGTGCTCTTCCATAATTCTTTTTAACCACTTCATTTCACAAATTCCTTGAGCC
131 AATTATTGGTTTTGTGCTCTTCCATAATTCTTTTTAACCACTTCATTTCACAAATTCCTTGAGCC
13092834 ATTGATCTAAACTCAGCCTCTACACTACTTCTTGCTACAACACTTTGTTTTTT
196 ATTGATCTAAACTCAGCCTCTACACTACTTCTTGCTACAACACTTTGTTTTTT
13092887 GCTTCTCCAA
Statistics
Matches: 248, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
248 248 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (248 bp):
TTCTTCAATCTTCTCCTTGATGAAATGTCTATCAATCTCTACATGCTTAGTTTTGTCCTGCTGGA
CTGGGTTGTGACTTGTGAGCAATACTAATCGCAGCTTTGCTATCATAGTACAACTTCATTGGTGA
AATTATTGGTTTTGTGCTCTTCCATAATTCTTTTTAACCACTTCATTTCACAAATTCCTTGAGCC
ATTGATCTAAACTCAGCCTCTACACTACTTCTTGCTACAACACTTTGTTTTTT
Found at i:13097746 original size:12 final size:12
Alignment explanation
Indices: 13097729--13097753 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13097719 AGTATTGTTA
13097729 TTGCAAATTGGC
1 TTGCAAATTGGC
13097741 TTGCAAATTGGC
1 TTGCAAATTGGC
13097753 T
1 T
13097754 AAGTTTGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (12 bp):
TTGCAAATTGGC
Found at i:13098858 original size:168 final size:167
Alignment explanation
Indices: 13098359--13098845 Score: 841
Period size: 168 Copynumber: 2.9 Consensus size: 167
13098349 CATAGGCCTA
* *
13098359 TCATTCCTAAATTTGAGGCAAATGAAGGTGGTGCTAAATACAAATTTATGATGATTAAATTTTGG
1 TCATTCCTAAATTTGAGGCAAATGAAGGTGGTGCTAAACACAAATTTATGATAATTAAATTTTGG
* * * * * *
13098424 AAGTTTTTGGGATTTTTAAT-TCGAATGAGATTGGTAAAAAGTGAATCTTAATGATTATGTTTGG
66 ATGTTTTTGGGCTCTTTAATAT-GAATGAGATTGGTAAGAATTGAATCTTAATGATTAAGTTTGG
13098488 GATCTCTTAGGGATTCTTTAATATGGTTGAGTTCTCATG
130 GATCTCTT-GGGATTCTTTAATATGGTTGAGTTCTCATG
*
13098527 TCATTCCTAAATTTGAGGCAAGTGAAGGTGGTGCTAAACACAAATTTATGATAATTAAATTTTGG
1 TCATTCCTAAATTTGAGGCAAATGAAGGTGGTGCTAAACACAAATTTATGATAATTAAATTTTGG
13098592 ATGTTTTTGGGCTCTTTAATATGAATGAGATTGGTAAGAATTGAATCTTAATGATTAAGTTTGGG
66 ATGTTTTTGGGCTCTTTAATATGAATGAGATTGGTAAGAATTGAATCTTAATGATTAAGTTTGGG
13098657 ATCTCTTGGGGATTCTTTAATATGGTTGAGTTCTCATG
131 ATCTCTT-GGGATTCTTTAATATGGTTGAGTTCTCATG
*
13098695 TCATTCTTAAATTTGAGGCAAATGAAGGTGGTGCTAAACACAAATTTATGATAATTAAATTTTGG
1 TCATTCCTAAATTTGAGGCAAATGAAGGTGGTGCTAAACACAAATTTATGATAATTAAATTTTGG
13098760 ATGTTTTTGGGCTCTTTAATATGAATGAGATTGGTAAGAATTGAATCTTAATGATTAAGTTTGGG
66 ATGTTTTTGGGCTCTTTAATATGAATGAGATTGGTAAGAATTGAATCTTAATGATTAAGTTTGGG
13098825 ATCTCTTGGAGATTCTTTAAT
131 ATCTCTTGG-GATTCTTTAAT
13098846 GTTTTTGAGT
Statistics
Matches: 305, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
167 2 0.01
168 302 0.99
169 1 0.00
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (167 bp):
TCATTCCTAAATTTGAGGCAAATGAAGGTGGTGCTAAACACAAATTTATGATAATTAAATTTTGG
ATGTTTTTGGGCTCTTTAATATGAATGAGATTGGTAAGAATTGAATCTTAATGATTAAGTTTGGG
ATCTCTTGGGATTCTTTAATATGGTTGAGTTCTCATG
Found at i:13099280 original size:15 final size:16
Alignment explanation
Indices: 13099260--13099292 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
13099250 GAAATATTTC
13099260 TTTTAATTCGG-TCGG
1 TTTTAATTCGGTTCGG
13099275 TTTTAATTCGGTTCGG
1 TTTTAATTCGGTTCGG
13099291 TT
1 TT
13099293 AACTGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.52
Consensus pattern (16 bp):
TTTTAATTCGGTTCGG
Found at i:13111233 original size:97 final size:97
Alignment explanation
Indices: 13111064--13111259 Score: 329
Period size: 97 Copynumber: 2.0 Consensus size: 97
13111054 CCCATTTCCA
* *
13111064 TTTTATTTTCCCGATTCTTGTTTTGTTGCTATTATTTACACCAACTGTTCTATAGTAACACAATA
1 TTTTATTTTCCCGATTCTTGTTTTGTTGCTATTATTTACACCAACTGTTCTATAATAAAACAATA
13111129 GAAAGATCAATAGAATAACGAAGTAAAACTCT
66 GAAAGATCAATAGAATAACGAAGTAAAACTCT
* * * *
13111161 TTTTATTTTTCCTATTCTTGTTTTGTTGTTATTATTTACACTAACTGTTCTATAATAAAACAATA
1 TTTTATTTTCCCGATTCTTGTTTTGTTGCTATTATTTACACCAACTGTTCTATAATAAAACAATA
*
13111226 GACAGATCAATAGAATAACGAAGTAAAACTCT
66 GAAAGATCAATAGAATAACGAAGTAAAACTCT
13111258 TT
1 TT
13111260 GTGGTTTTAC
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 92 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (97 bp):
TTTTATTTTCCCGATTCTTGTTTTGTTGCTATTATTTACACCAACTGTTCTATAATAAAACAATA
GAAAGATCAATAGAATAACGAAGTAAAACTCT
Found at i:13115111 original size:140 final size:141
Alignment explanation
Indices: 13114850--13115134 Score: 491
Period size: 140 Copynumber: 2.0 Consensus size: 141
13114840 CTATTTTATT
* *
13114850 TATTAGTTGGTTTTGGAATTGATGTTAACAATAGACATGAGAACAATCCTAAATAGATTTTTTTT
1 TATTAGTTGGTTTTGGAATTGATGTTAACAATAAACATGAGAACAATCCTAAATAGA-TTTTCTT
* *
13114915 TTAGGGTTTGCTTAAATGGATTTTGTGAAGCATCCTACCTAAAACCAATTGGTAATAGGCGGTGA
65 TTAGGGTTTGCTTAAATGGATTTTGTGAACCATCCTACCTAAAACCAATTGGTAATAGGCAGTGA
*
13114980 GTTCGACTCTAA
130 GTCCGACTCTAA
*
13114992 TATTAGTTGGTTTTGGAATTGATGTTAACAATAAACATGAGAACAATCCTAAGTAGA-TTTCTTT
1 TATTAGTTGGTTTTGGAATTGATGTTAACAATAAACATGAGAACAATCCTAAATAGATTTTCTTT
*
13115056 TAGGGTTTGCTTAAATGGATTTTGTGAACCATCCTACCTAAAACCAATTGGTAATAGGTAGTGAG
66 TAGGGTTTGCTTAAATGGATTTTGTGAACCATCCTACCTAAAACCAATTGGTAATAGGCAGTGAG
13115121 TCCGACTCTAA
131 TCCGACTCTAA
13115132 TAT
1 TAT
13115135 AAGGCCACAA
Statistics
Matches: 136, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
140 81 0.60
142 55 0.40
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.36
Consensus pattern (141 bp):
TATTAGTTGGTTTTGGAATTGATGTTAACAATAAACATGAGAACAATCCTAAATAGATTTTCTTT
TAGGGTTTGCTTAAATGGATTTTGTGAACCATCCTACCTAAAACCAATTGGTAATAGGCAGTGAG
TCCGACTCTAA
Found at i:13120271 original size:185 final size:186
Alignment explanation
Indices: 13119954--13120317 Score: 516
Period size: 185 Copynumber: 2.0 Consensus size: 186
13119944 AGACTAATAT
*
13119954 TTTCTTCTTTAGTAGTGTTGATGATGCTTTAATAGATTTGATCAATAGTCTTCTTAGATTTCAAA
1 TTTCTTCTTTAGTAGTGTTGATGATGCTTTAAGAGATTTGATCAATAGTCTTCTTAGATTTCAAA
* * *
13120019 GAGTGCAAAATCTTAGGACTTACCTAGGAGTGCCTCTTTTTCATGAAAAGGTCACTGACACCACT
66 GAGTGCAAAATCTTAGGACTTACCTAGGAGTGCCTCTTTTTCATGAAAAGGCCACTAACAACACT
* * * *
13120084 TTGCAGTTTGTAGTGGAAAAGGTTAGCAACAAGCTACAAAGTTGGGATGATATGGA
131 TTGCAATTTGTAGTGGAAAAAGTCAGCAACAAACTACAAAGTTGGGATGATATGGA
* * * *
13120140 TTTCTTCTTTAGTAGTGTTGAT-ATGCTTTAGGATATTTGATCAATGGTCTT-TTTGTATTTCAA
1 TTTCTTCTTTAGTAGTGTTGATGATGCTTTAAGAGATTTGATCAATAGTCTTCTTAG-ATTTCAA
* * * ** *
13120203 AGAGTGTAGAATCTTGGGACTTGTCTGGGAGTGCCTCTTTTTCATGAAAAGGCCACTAACAACAC
65 AGAGTGCAAAATCTTAGGACTTACCTAGGAGTGCCTCTTTTTCATGAAAAGGCCACTAACAACAC
* * *
13120268 TTTGCAATTTTTGGTGGAAAAAGTCCGCAACAAACTACAAAGTTGGGATG
130 TTTGCAATTTGTAGTGGAAAAAGTCAGCAACAAACTACAAAGTTGGGATG
13120318 CCATGCAATT
Statistics
Matches: 156, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
184 3 0.02
185 131 0.84
186 22 0.14
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (186 bp):
TTTCTTCTTTAGTAGTGTTGATGATGCTTTAAGAGATTTGATCAATAGTCTTCTTAGATTTCAAA
GAGTGCAAAATCTTAGGACTTACCTAGGAGTGCCTCTTTTTCATGAAAAGGCCACTAACAACACT
TTGCAATTTGTAGTGGAAAAAGTCAGCAACAAACTACAAAGTTGGGATGATATGGA
Found at i:13126511 original size:51 final size:51
Alignment explanation
Indices: 13126399--13126514 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
13126389 GATCAATGCT
* ** ***
13126399 ATCCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTTCC
1 ATCCGGTACACATAATAGCCTGCACATAGTACTACACACATGACCAAGGCC
** * *
13126450 ATCCAATACACGTAATAGCCTGCACATAGTACTACATACATGACCAAGGCC
1 ATCCGGTACACATAATAGCCTGCACATAGTACTACACACATGACCAAGGCC
*
13126501 ATTCGGTACACATA
1 ATCCGGTACACATA
13126515 GTACTACACA
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (51 bp):
ATCCGGTACACATAATAGCCTGCACATAGTACTACACACATGACCAAGGCC
Found at i:13165613 original size:50 final size:50
Alignment explanation
Indices: 13165502--13165798 Score: 328
Period size: 50 Copynumber: 5.8 Consensus size: 50
13165492 ATTTGGGTAA
* *
13165502 AGAGATCCCGTGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
13165558 AGAGGTCCCATGTAAGACCGTGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
13165608 AGAGGTCCCATGTAAGACCAAGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * *
13165658 AAAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
13165708 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** *
13165757 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
13165799 TGTTATTATC
Statistics
Matches: 210, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.00
49 39 0.19
50 127 0.60
53 3 0.01
55 2 0.01
56 38 0.18
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:13175657 original size:21 final size:21
Alignment explanation
Indices: 13175633--13175673 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13175623 CTTTTCAACC
13175633 CTTATGGGTTTCTATTTAGCA
1 CTTATGGGTTTCTATTTAGCA
* *
13175654 CTTATGTGTTTCTGTTTAGC
1 CTTATGGGTTTCTATTTAGC
13175674 CTTCGGGCTT
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:0.15, C:0.15, G:0.20, T:0.51
Consensus pattern (21 bp):
CTTATGGGTTTCTATTTAGCA
Found at i:13177270 original size:7 final size:6
Alignment explanation
Indices: 13177240--13177269 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
13177230 AGGTTTCTCA
13177240 AAATGG AAATGG AAATGG AAATGAG AAATG
1 AAATGG AAATGG AAATGG AAATG-G AAATG
13177270 ATACATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:13179862 original size:26 final size:26
Alignment explanation
Indices: 13179802--13179862 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
13179792 TATTCGGAGC
* *
13179802 TCCTGATTAAAGGCTCTTTGTGAGCT
1 TCCTGATTAAAAGCTCTTTGTGAACT
* *
13179828 TCCTAATTAAAAGTTCTTTGTGAACT
1 TCCTGATTAAAAGCTCTTTGTGAACT
*
13179854 TCTTGATTA
1 TCCTGATTA
13179863 TGGCTCTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (26 bp):
TCCTGATTAAAAGCTCTTTGTGAACT
Found at i:13181990 original size:21 final size:22
Alignment explanation
Indices: 13181946--13182007 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
13181936 TAACAAGTAA
*
13181946 ATAAACAAATAAAAACTAAAACAT
1 ATAAATAAATAAAAA-T-AAACAT
* *
13181970 TTAAA-AAATAATAATAAACAT
1 ATAAATAAATAAAAATAAACAT
13181991 ATAAATAAATAAAAATA
1 ATAAATAAATAAAAATA
13182008 TTTAATAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 11 0.33
23 8 0.24
24 4 0.12
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (22 bp):
ATAAATAAATAAAAATAAACAT
Found at i:13182003 original size:29 final size:29
Alignment explanation
Indices: 13181971--13182037 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
13181961 CTAAAACATT
13181971 TAAAAAATA-ATAATAA-ACATATAAATAAA
1 TAAAAAATATATAATAATA-ATA-AAATAAA
*
13182000 T-AAAAATATTTAATAATAATAAAATAAA
1 TAAAAAATATATAATAATAATAAAATAAA
13182028 T-AAAAATATA
1 TAAAAAATATA
13182038 GAAACGAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 23 0.68
29 10 0.29
30 1 0.03
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.28
Consensus pattern (29 bp):
TAAAAAATATATAATAATAATAAAATAAA
Found at i:13182035 original size:18 final size:17
Alignment explanation
Indices: 13181973--13182068 Score: 59
Period size: 18 Copynumber: 5.2 Consensus size: 17
13181963 AAAACATTTA
*
13181973 AAAAATAATAATAAACAT
1 AAAAATAATAA-AAAAAT
* *
13181991 ATAAATAAATAAAAATATTT
1 AAAAAT-AATAAAAA-A-AT
*
13182011 AATAATAATAAAATAAAT
1 AAAAATAATAAAA-AAAT
13182029 AAAAAT-ATAGAAACGAAAT
1 AAAAATAATA-AAA--AAAT
*
13182048 GAAAATATATAAAAAAAT
1 AAAAATA-ATAAAAAAAT
13182066 AAA
1 AAA
13182069 GATAGTTTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
17 3 0.05
18 23 0.38
19 22 0.37
20 9 0.15
21 3 0.05
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAAATAATAAAAAAAT
Found at i:13183216 original size:23 final size:24
Alignment explanation
Indices: 13183190--13183234 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
13183180 CTAGTTTGAC
* *
13183190 TGTTGGGGTTGGG-ACTTTGGGCT
1 TGTTGGGCTAGGGTACTTTGGGCT
13183213 TGTTGGGCTAGGGTACTTTGGG
1 TGTTGGGCTAGGGTACTTTGGG
13183235 TATTGGGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.07, C:0.09, G:0.47, T:0.38
Consensus pattern (24 bp):
TGTTGGGCTAGGGTACTTTGGGCT
Found at i:13184289 original size:11 final size:11
Alignment explanation
Indices: 13184269--13184329 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
13184259 AGAAAATTAA
13184269 AAAAAGTATTTT
1 AAAAA-TATTTT
13184281 AAAAATATTTT
1 AAAAATATTTT
*
13184292 AAAAATA---A
1 AAAAATATTTT
13184300 AAAAATTATTTT
1 AAAAA-TATTTT
* *
13184312 AAAATTTTTTT
1 AAAAATATTTT
13184323 AAAAATA
1 AAAAATA
13184330 AAAAAATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
8 5 0.13
9 2 0.05
11 23 0.59
12 9 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:13184336 original size:31 final size:31
Alignment explanation
Indices: 13184256--13184345 Score: 117
Period size: 31 Copynumber: 2.8 Consensus size: 31
13184246 AAAAAAAAAA
*
13184256 TTTAGAAAATTAAAAAAAGTATTTTAAAAATAT
1 TTTA-AAAA-TAAAAAAATTATTTTAAAAATAT
* *
13184289 TTTAAAAATAAAAAAATTATTTTAAAATTTT
1 TTTAAAAATAAAAAAATTATTTTAAAAATAT
13184320 TTTAAAAATAAAAAAATATATATTTA
1 TTTAAAAATAAAAAAAT-TAT-TTTA
13184346 TTATATTCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 37 0.71
32 7 0.13
33 8 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (31 bp):
TTTAAAAATAAAAAAATTATTTTAAAAATAT
Found at i:13190382 original size:45 final size:44
Alignment explanation
Indices: 13190313--13190471 Score: 167
Period size: 45 Copynumber: 3.6 Consensus size: 44
13190303 TATACAGTAG
* * * *
13190313 ATCAGCACACAGC-ACCACCCTTATAGTCAATAGCAATCGGTGAA
1 ATCAGCACATAGCAACCACCTTTATAATCAAT-GCAACCGGTGAA
**
13190357 ATCAGCACATAGCAACCACCTTTATAATCAATGGTACCTGGTGAA
1 ATCAGCACATAGCAACCACCTTTATAATCAATGCAACC-GGTGAA
* * * **
13190402 ATCAGCACATAGCAACCACCTATATAATCAATGGTACCCAATGAA
1 ATCAGCACATAGCAACCACCTTTATAATCAAT-GCAACCGGTGAA
* *
13190447 ATCAGCACATAGCAGCCACTTTTAT
1 ATCAGCACATAGCAACCACCTTTAT
13190472 TTTCATTAAT
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
44 15 0.15
45 79 0.81
46 3 0.03
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (44 bp):
ATCAGCACATAGCAACCACCTTTATAATCAATGCAACCGGTGAA
Found at i:13190530 original size:45 final size:45
Alignment explanation
Indices: 13190352--13190530 Score: 193
Period size: 45 Copynumber: 4.0 Consensus size: 45
13190342 ATAGCAATCG
* *
13190352 GTGAAATCAGCACATAGCAACCACCTTTATAATCAATGGTA-CCTG
1 GTGAAATCAGCACATAGCAACCACCTATATAATCAATGGTATCC-A
*
13190397 GTGAAATCAGCACATAGCAACCACCTATATAATCAATGGTACCCA
1 GTGAAATCAGCACATAGCAACCACCTATATAATCAATGGTATCCA
* * * * ** * **
13190442 ATGAAATCAGCACATAGCAGCCACTTTTATTTTCATTAATATCCA
1 GTGAAATCAGCACATAGCAACCACCTATATAATCAATGGTATCCA
*
13190487 GT-AGAATCAGCACATAGCAACCACCTATAT-TTCCAATGGTATCC
1 GTGA-AATCAGCACATAGCAACCACCTATATAAT-CAATGGTATCC
13190531 GGTCTATTCC
Statistics
Matches: 112, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
44 3 0.03
45 107 0.96
46 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (45 bp):
GTGAAATCAGCACATAGCAACCACCTATATAATCAATGGTATCCA
Found at i:13195273 original size:49 final size:50
Alignment explanation
Indices: 13195150--13195277 Score: 145
Period size: 50 Copynumber: 2.6 Consensus size: 50
13195140 GGGTAAAGAG
** * *
13195150 ATCCCATGTAAGACCATGTCTGGGACATGGTATGGGCACCGATATGAGAAC
1 ATCCCATGTAAGACCATGTCTGGGACATGACATGGGCA-CGACAAGAGAAC
* * * *
13195201 -TCCCATGTAAGACCATATTTGGGATATGACATTGGCA-GTACAAGA-AAC
1 ATCCCATGTAAGACCATGTCTGGGACATGACATGGGCACG-ACAAGAGAAC
13195249 ATCCCATGTAAGACCATGTCTGGGACATG
1 ATCCCATGTAAGACCATGTCTGGGACATG
13195278 GCTTTGGCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
48 4 0.06
49 29 0.45
50 31 0.48
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.23
Consensus pattern (50 bp):
ATCCCATGTAAGACCATGTCTGGGACATGACATGGGCACGACAAGAGAAC
Found at i:13195285 original size:49 final size:50
Alignment explanation
Indices: 13195150--13195286 Score: 147
Period size: 49 Copynumber: 2.8 Consensus size: 50
13195140 GGGTAAAGAG
* * *
13195150 ATCCCATGTAAGACCATGTCTGGGACATGG-TATGGGCACCGATATGAGAAC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCT-TTGGCA-CGACAAGAGAAC
* * * * *
13195201 -TCCCATGTAAGACCATATTTGGGATATGACATTGGCA-GTACAAGA-AAC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCACG-ACAAGAGAAC
13195249 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
13195287 TGTTATTATC
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
48 4 0.06
49 36 0.51
50 30 0.43
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (50 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCACGACAAGAGAAC
Found at i:13197795 original size:41 final size:41
Alignment explanation
Indices: 13197750--13197832 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
13197740 TATTGCATGC
* * *
13197750 TTAGTATAATTATTTTTATTACTTTAAAAAATTAAAAAAAT
1 TTAGTACAATTATTTTTATTACTTAAAAAAACTAAAAAAAT
*
13197791 TTAGTACATTTATTTTTATTACTTAAAAAAACTAAAAAAAT
1 TTAGTACAATTATTTTTATTACTTAAAAAAACTAAAAAAAT
13197832 T
1 T
13197833 AAAAATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (41 bp):
TTAGTACAATTATTTTTATTACTTAAAAAAACTAAAAAAAT
Found at i:13198754 original size:24 final size:23
Alignment explanation
Indices: 13198725--13198782 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
13198715 ATTATTATTA
*
13198725 TTTTTTATATTTATTATATTTAG
1 TTTTTTATATTTATTAGATTTAG
13198748 TTGTTTTAT-TATTATTAGATTTAG
1 TT-TTTTATAT-TTATTAGATTTAG
*
13198772 TTTATTATATT
1 TTTTTTATATT
13198783 CTTGTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (23 bp):
TTTTTTATATTTATTAGATTTAG
Found at i:13201045 original size:16 final size:16
Alignment explanation
Indices: 13201024--13201057 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
13201014 CTACCCAAGG
13201024 GTGAAGGCAGAAAATC
1 GTGAAGGCAGAAAATC
*
13201040 GTGAAGGTAGAAAATC
1 GTGAAGGCAGAAAATC
13201056 GT
1 GT
13201058 TTTAGGAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.09, G:0.32, T:0.18
Consensus pattern (16 bp):
GTGAAGGCAGAAAATC
Found at i:13201894 original size:21 final size:20
Alignment explanation
Indices: 13201856--13201918 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
13201846 ATTCAATTTC
13201856 TCAATCC-AAT-ATA-CATT
1 TCAATCCAAATAATATCATT
13201873 TCAATACCACAATAAT-TCATT
1 TCAAT-CCA-AATAATATCATT
*
13201894 T-AATTCAAATAATATCATT
1 TCAATCCAAATAATATCATT
13201913 TGCAAT
1 T-CAAT
13201919 TTCCATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.14
18 8 0.22
19 8 0.22
20 6 0.16
21 10 0.27
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TCAATCCAAATAATATCATT
Found at i:13203447 original size:45 final size:45
Alignment explanation
Indices: 13203379--13203467 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
13203369 AACAGATACT
* * * *
13203379 CGGTGGATTTAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGTC
13203424 CGGTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGT
1 CGGTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGT
13203468 TTGTTCACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGTC
Found at i:13203532 original size:51 final size:50
Alignment explanation
Indices: 13203477--13203660 Score: 217
Period size: 51 Copynumber: 3.6 Consensus size: 50
13203467 TTTGTTCACA
* * *
13203477 TAGTAGTCTGCACATAGTACTACACATGTGACCATTACCATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATCTGGTACACG
* * * * *
13203528 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATCTGGTACACG
* * * * *
13203579 TAGTAGCCTACACATAGTACGACACATGTGACC-TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TCTGGTACACG
13203629 TAGTAGCCTGCACATAGTACTACACACGTGAC
1 TAGTAGCCTGCACATAGTACTACACACGTGAC
13203661 AATCACTTTC
Statistics
Matches: 110, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
49 2 0.02
50 38 0.35
51 68 0.62
52 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATCTGGTACACG
Found at i:13203652 original size:101 final size:101
Alignment explanation
Indices: 13203475--13203659 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
13203465 TGTTTGTTCA
* * * *
13203475 CATAGTAGTCTGCACATAGTACTACACATGTGACCATTACCATCTGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACGACACATGTGACCA-TACCATCCGATACACGTAGTAGCCTGCA
13203540 CATAGTACTACACACGTGATCGAAACTATCTGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCTGGTACG
* *
13203577 CATAGTAGCCTACACATAGTACGACACATGTGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACGACACATGTGACCATACCA-TCCGATACACGTAGTAGCCTGCA
13203641 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
13203660 CAATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 40 0.53
102 32 0.42
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACGACACATGTGACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCTGGTACG
Found at i:13207468 original size:24 final size:25
Alignment explanation
Indices: 13207440--13207486 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
13207430 CCTCAACCTC
13207440 TTTCTCCTTATGCT-TCCTTTCTTT
1 TTTCTCCTTATGCTCTCCTTTCTTT
** *
13207464 TTTCTTGTTATTCTCTCCTTTCT
1 TTTCTCCTTATGCTCTCCTTTCT
13207487 CATCATCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.04, C:0.28, G:0.04, T:0.64
Consensus pattern (25 bp):
TTTCTCCTTATGCTCTCCTTTCTTT
Found at i:13209224 original size:6 final size:6
Alignment explanation
Indices: 13209213--13209237 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13209203 AAGCCTATCA
13209213 CACAAT CACAAT CACAAT CACAAT C
1 CACAAT CACAAT CACAAT CACAAT C
13209238 CTGTTAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:13220091 original size:26 final size:28
Alignment explanation
Indices: 13220055--13220110 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
13220045 CAATTTATTT
*
13220055 ATTAAA-TTTTT-TAAATAA-AATTAATA
1 ATTAAAGTTTTTATAAA-AATATTTAATA
13220081 ATTAAAGTTTTTATAAAAATATTTAATA
1 ATTAAAGTTTTTATAAAAATATTTAATA
13220109 AT
1 AT
13220111 GTTTTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 6 0.23
27 7 0.27
28 13 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
ATTAAAGTTTTTATAAAAATATTTAATA
Found at i:13231939 original size:41 final size:41
Alignment explanation
Indices: 13231894--13232013 Score: 125
Period size: 41 Copynumber: 2.9 Consensus size: 41
13231884 AGCTTATTAA
* * *
13231894 GATACACTGGCATAAAGTCTTCTAGGAACAAAGCCCGATAT
1 GATACACCGGCATAAAGCCTTCTAGGCACAAAGCCCGATAT
* * * *
13231935 GATACACCGGTACAAAGCCTGT-TAGGCATAAAGCCTGATAT
1 GATACACCGGCATAAAGCCT-TCTAGGCACAAAGCCCGATAT
* * * *
13231976 GGTACACCAGCATGAAGCCTGCTAGGCACAAAGCCCGA
1 GATACACCGGCATAAAGCCTTCTAGGCACAAAGCCCGA
13232014 ATATCACTAA
Statistics
Matches: 62, Mismatches: 15, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
41 61 0.98
42 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (41 bp):
GATACACCGGCATAAAGCCTTCTAGGCACAAAGCCCGATAT
Done.