Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 235 of 343
Found at i:77383766 original size:19 final size:19
Alignment explanation
Indices: 77383742--77383778 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
77383732 CTCCCCCCCC
77383742 AAAAAAAAAACCTAACCCA
1 AAAAAAAAAACCTAACCCA
77383761 AAAAAAAAAACCTAACCC
1 AAAAAAAAAACCTAACCC
77383779 CCCCCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.27, G:0.00, T:0.05
Consensus pattern (19 bp):
AAAAAAAAAACCTAACCCA
Found at i:77384636 original size:24 final size:24
Alignment explanation
Indices: 77384581--77384636 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
77384571 AATCATGTTA
*
77384581 TATATGTAATATTGTTATCACTAT
1 TATATTTAATATTGTTATCACTAT
* *
77384605 TATTTTTATATATTGTTATTA-TAT
1 TATATTTA-ATATTGTTATCACTAT
77384629 TATATTTA
1 TATATTTA
77384637 GCTATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (24 bp):
TATATTTAATATTGTTATCACTAT
Found at i:77384831 original size:15 final size:17
Alignment explanation
Indices: 77384803--77384834 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
77384793 TTGTATATAT
77384803 TATATTTATATTATGTA
1 TATATTTATATTATGTA
77384820 TATATTT-T-TTATGTA
1 TATATTTATATTATGTA
77384835 CGTTTCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TATATTTATATTATGTA
Found at i:77386118 original size:22 final size:21
Alignment explanation
Indices: 77386081--77386123 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
77386071 AATAATAACG
*
77386081 ATATATAAACATATAA-ATGT
1 ATATATAAAAATATAATATGT
77386101 ATATATTAAAAATAATAATATGT
1 ATATA-TAAAAAT-ATAATATGT
77386124 GTACATAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 4 0.21
23 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (21 bp):
ATATATAAAAATATAATATGT
Found at i:77386378 original size:12 final size:12
Alignment explanation
Indices: 77386357--77386387 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
77386347 TTAATAATGC
77386357 TATATA-ACATA
1 TATATATACATA
77386368 TATATATACATA
1 TATATATACATA
77386380 TATATATA
1 TATATATA
77386388 TAATGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATACATA
Found at i:77386399 original size:23 final size:23
Alignment explanation
Indices: 77386373--77386421 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
77386363 ACATATATAT
77386373 ATACATA-TATATATATAATGAAA
1 ATACATACTAT-TATATAATGAAA
* * *
77386396 ATACGTACTATTATGTAATGATA
1 ATACATACTATTATATAATGAAA
77386419 ATA
1 ATA
77386422 GAAATACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (23 bp):
ATACATACTATTATATAATGAAA
Found at i:77390125 original size:17 final size:18
Alignment explanation
Indices: 77390088--77390125 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
77390078 GATTGAGAGT
* *
77390088 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
77390106 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
77390123 GAA
1 GAA
77390126 GTTGAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:77390138 original size:12 final size:12
Alignment explanation
Indices: 77390107--77390160 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
77390097 TGTGAAACAG
*
77390107 AAAAGAAATTGA
1 AAAAGAAGTTGA
77390119 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
77390131 AAAAGAAG-AGA
1 AAAAGAAGTTGA
*
77390142 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
77390154 AAAAGAA
1 AAAAGAA
77390161 ACAAAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 25 0.74
13 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:77390143 original size:23 final size:23
Alignment explanation
Indices: 77390117--77390160 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
77390107 AAAAGAAATT
77390117 GAAAAAGAAGTT-GAAAAAGAAGA
1 GAAAAAG-AGTTAGAAAAAGAAGA
*
77390140 GAAAATGAGTTAGAAAAAGAA
1 GAAAAAGAGTTAGAAAAAGAA
77390161 ACAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (23 bp):
GAAAAAGAGTTAGAAAAAGAAGA
Found at i:77390166 original size:22 final size:22
Alignment explanation
Indices: 77390125--77390166 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
77390115 TTGAAAAAGA
*
77390125 AGTTGAAAAAGAAGAGAAAATG
1 AGTTGAAAAAGAAGACAAAATG
77390147 AGTTAGAAAAAGAA-ACAAAA
1 AGTT-GAAAAAGAAGACAAAA
77390167 AAAAAGACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.64, C:0.02, G:0.21, T:0.12
Consensus pattern (22 bp):
AGTTGAAAAAGAAGACAAAATG
Found at i:77393331 original size:18 final size:18
Alignment explanation
Indices: 77393261--77393366 Score: 87
Period size: 17 Copynumber: 5.8 Consensus size: 18
77393251 TGTTGTAAAC
* *
77393261 TTTTCGTGTTTCCAAAAT
1 TTTTCGTGTTTTCAAAAA
77393279 TTTTCGTGTTTTTCTAAAAAAAA
1 TTTTCGTG-TTTTC----AAAAA
*
77393302 ATTTCAG-G-TTTCAAAAA
1 TTTTC-GTGTTTTCAAAAA
77393319 TTTTCGTGTTTTC-AAAA
1 TTTTCGTGTTTTCAAAAA
77393336 TTTTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
77393353 TTTTCAT-TTTTCAA
1 TTTTCGTGTTTTCAA
77393367 TTGGATCATG
Statistics
Matches: 73, Mismatches: 5, Indels: 21
0.74 0.05 0.21
Matches are distributed among these distances:
16 5 0.07
17 38 0.52
18 12 0.16
19 4 0.05
21 4 0.05
23 9 0.12
24 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.50
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:77397818 original size:24 final size:25
Alignment explanation
Indices: 77397782--77397845 Score: 94
Period size: 24 Copynumber: 2.5 Consensus size: 25
77397772 TACTAAAAAA
77397782 AATATGTTGAATAATAATAATACTTAT
1 AATAT-TT-AATAATAATAATACTTAT
*
77397809 -ATCTTTAATAATAATAATACTTAT
1 AATATTTAATAATAATAATACTTAT
77397833 AATATTTAATAAT
1 AATATTTAATAAT
77397846 CATACTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 18 0.53
25 13 0.38
26 3 0.09
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (25 bp):
AATATTTAATAATAATAATACTTAT
Found at i:77397834 original size:9 final size:9
Alignment explanation
Indices: 77397798--77397879 Score: 50
Period size: 9 Copynumber: 9.7 Consensus size: 9
77397788 TTGAATAATA
77397798 ATAATACTT
1 ATAATACTT
77397807 AT-AT-CTT
1 ATAATACTT
* *
77397814 -TAATAATA
1 ATAATACTT
77397822 ATAATACTT
1 ATAATACTT
77397831 ATAATA-TT
1 ATAATACTT
* *
77397839 -TAATAATC
1 ATAATACTT
* *
77397847 ATACTA-TA
1 ATAATACTT
77397855 ATAATACTT
1 ATAATACTT
*
77397864 ATAATATTT
1 ATAATACTT
77397873 AATAATA
1 -ATAATA
77397880 ATACAATAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
6 1 0.02
7 10 0.18
8 12 0.21
9 27 0.48
10 6 0.11
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (9 bp):
ATAATACTT
Found at i:77397844 original size:19 final size:19
Alignment explanation
Indices: 77397820--77397879 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
77397810 TCTTTAATAA
77397820 TAATAATACTTATAATATT
1 TAATAATACTTATAATATT
*
77397839 TAATAAT-C--ATACTA--
1 TAATAATACTTATAATATT
77397853 TAATAATACTTATAATATT
1 TAATAATACTTATAATATT
77397872 TAATAATA
1 TAATAATA
77397880 ATACAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 7 0.21
15 1 0.03
16 5 0.15
17 5 0.15
18 1 0.03
19 15 0.44
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (19 bp):
TAATAATACTTATAATATT
Found at i:77397856 original size:33 final size:33
Alignment explanation
Indices: 77397818--77397891 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
77397808 TATCTTTAAT
*
77397818 AATAATAATACTTATAATATTTAATAATCATAC
1 AATAATAATACTTATAATATTTAATAATAATAC
*
77397851 TATAATAATACTTATAATATTTAATAATAATAC
1 AATAATAATACTTATAATATTTAATAATAATAC
77397884 AATAATAA
1 AATAATAA
77397892 AAATATGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (33 bp):
AATAATAATACTTATAATATTTAATAATAATAC
Found at i:77401779 original size:22 final size:23
Alignment explanation
Indices: 77401747--77401790 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
77401737 ATTCATAAAA
*
77401747 AATTATAAGTATAAATACAATGT
1 AATTATAAGTACAAATACAATGT
*
77401770 AATTAT-AGTACAATTACAATG
1 AATTATAAGTACAAATACAATG
77401791 GTATGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (23 bp):
AATTATAAGTACAAATACAATGT
Found at i:77403647 original size:18 final size:19
Alignment explanation
Indices: 77403598--77403647 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
77403588 AATTTTTTAT
*
77403598 TCGAATTAATTCAAATAAC
1 TCGAATTAATTTAAATAAC
* *
77403617 TTG-ATTAACTTAAATAAC
1 TCGAATTAATTTAAATAAC
77403635 TCGAATT-ATTTAA
1 TCGAATTAATTTAA
77403648 TTTAGAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (19 bp):
TCGAATTAATTTAAATAAC
Found at i:77404306 original size:14 final size:14
Alignment explanation
Indices: 77404289--77404335 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
77404279 ATATTCAAAC
77404289 AATAATAACAAAAT
1 AATAATAACAAAAT
*
77404303 AATAACAACAAAAT
1 AATAATAACAAAAT
* *
77404317 AATAGTAACATAAT
1 AATAATAACAAAAT
77404331 AATAA
1 AATAA
77404336 AATGGTAACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.21
Consensus pattern (14 bp):
AATAATAACAAAAT
Found at i:77404385 original size:21 final size:21
Alignment explanation
Indices: 77404356--77404395 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
77404346 AAATAAGGAG
77404356 AAAACAATAAAAAAATAACATT
1 AAAACAAT-AAAAAATAACATT
77404378 AAAA-AATAAAAAATAACA
1 AAAACAATAAAAAATAACA
77404396 GATTTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 3 0.17
22 4 0.22
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (21 bp):
AAAACAATAAAAAATAACATT
Found at i:77405657 original size:56 final size:59
Alignment explanation
Indices: 77405569--77405700 Score: 171
Period size: 56 Copynumber: 2.3 Consensus size: 59
77405559 AAATTAAATT
* *
77405569 TTTTTGAAAACTTAAATTTGATTTGTTTTGAATTTAAATTTTTGAAAA-AAAA-CTAAAA
1 TTTTTG-AAAGTTAAATTTGATTTATTTTGAATTTAAATTTTTGAAAACAAAAGCTAAAA
* * *
77405627 TTTTT-AAAGTTAATTTTTATTTATTTTGAATTTAAATTTTTGAAAAGCAAAAGCTTAAA
1 TTTTTGAAAGTTAAATTTGATTTATTTTGAATTTAAATTTTTGAAAA-CAAAAGCTAAAA
*
77405686 TTTTTGAAATTTAAA
1 TTTTTGAAAGTTAAA
77405701 AAATTTTGGA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
56 37 0.59
58 9 0.14
59 10 0.16
60 7 0.11
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (59 bp):
TTTTTGAAAGTTAAATTTGATTTATTTTGAATTTAAATTTTTGAAAACAAAAGCTAAAA
Found at i:77406012 original size:37 final size:38
Alignment explanation
Indices: 77405951--77406058 Score: 112
Period size: 37 Copynumber: 2.9 Consensus size: 38
77405941 TTTATAAAAA
**
77405951 AATCTTTACTATTCTTCTCCGTCTTTTCTTTGCAG-AG
1 AATCTTTACTATTGATCTCCGTCTTTTCTTTGCAGTAG
** * *
77405988 AATCTTTACTATTGATCTTTGTCTTTTTTTTTC-GTAG
1 AATCTTTACTATTGATCTCCGTCTTTTCTTTGCAGTAG
** * *
77406025 AAAATTTATTACTGATCTCCGTCTTTTCTTTGCA
1 AATCTTTACTATTGATCTCCGTCTTTTCTTTGCA
77406059 TAATTGTTCT
Statistics
Matches: 55, Mismatches: 14, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
36 1 0.02
37 54 0.98
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (38 bp):
AATCTTTACTATTGATCTCCGTCTTTTCTTTGCAGTAG
Found at i:77408847 original size:50 final size:49
Alignment explanation
Indices: 77408735--77408908 Score: 240
Period size: 49 Copynumber: 3.5 Consensus size: 49
77408725 CTGGTACGCA
77408735 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTAGTACACG
* * * * *
77408784 TAGTAGCCTGCACTTAGTACTACACAGGTGACCTCACCATCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AACAATCTAGTACACG
* ** *
77408834 TAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTAGTACACG
* *
77408883 TAGTAGCTTGCATTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
77408909 CGTGACCTCA
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
49 66 0.61
50 43 0.39
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTAGTACACG
Found at i:77408906 original size:99 final size:99
Alignment explanation
Indices: 77408735--77408919 Score: 307
Period size: 99 Copynumber: 1.9 Consensus size: 99
77408725 CTGGTACGCA
* *
77408735 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTAGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGCAACCAACAATCCAGTACACGTAGTAGCCTGCACTTA
*
77408800 GTACTACACAGGTGACCTCACCATCTAATACACG
66 GTACTACACACGTGACCTCACCATCTAATACACG
** * *
77408834 TAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCCAGTACACGTAGTAGCTTGCATTTA
1 TAGTAGCCTGCACTTAGTACTACACATGCAACCAACAATCCAGTACACGTAGTAGCCTGCACTTA
77408899 GTACTACACACGTGACCTCAC
66 GTACTACACACGTGACCTCAC
77408920 AATAGCTCAT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 79 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACATGCAACCAACAATCCAGTACACGTAGTAGCCTGCACTTA
GTACTACACACGTGACCTCACCATCTAATACACG
Found at i:77414541 original size:33 final size:33
Alignment explanation
Indices: 77414498--77414565 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
77414488 AAACAAACCT
*
77414498 AAATTAGGCTTCTTTCATCATAATACAACAAAA
1 AAATCAGGCTTCTTTCATCATAATACAACAAAA
77414531 AAATCAGGCTTCTTTCATCATAATACAACAAAA
1 AAATCAGGCTTCTTTCATCATAATACAACAAAA
77414564 AA
1 AA
77414566 GGTCTAGGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (33 bp):
AAATCAGGCTTCTTTCATCATAATACAACAAAA
Found at i:77416733 original size:13 final size:13
Alignment explanation
Indices: 77416715--77416741 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
77416705 GCTCGGTAGG
77416715 GACACGCCCGTGT
1 GACACGCCCGTGT
77416728 GACACGCCCGTGT
1 GACACGCCCGTGT
77416741 G
1 G
77416742 CGATTGCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:77423958 original size:15 final size:16
Alignment explanation
Indices: 77423926--77423959 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
77423916 CTTACTGAGG
77423926 GTTCATCACATAATGA
1 GTTCATCACATAATGA
*
77423942 GTTCATCACGT-ATGA
1 GTTCATCACATAATGA
77423957 GTT
1 GTT
77423960 TTTTTGTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (16 bp):
GTTCATCACATAATGA
Found at i:77429053 original size:16 final size:16
Alignment explanation
Indices: 77429032--77429062 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
77429022 GTATGGATAA
*
77429032 ATAAGTAAATTAAATC
1 ATAAGTAAATAAAATC
77429048 ATAAGTAAATAAAAT
1 ATAAGTAAATAAAAT
77429063 ATATTATTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.29
Consensus pattern (16 bp):
ATAAGTAAATAAAATC
Found at i:77436105 original size:15 final size:16
Alignment explanation
Indices: 77436085--77436114 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
77436075 AAGATATTAA
77436085 AATCATAA-CTTACTC
1 AATCATAACCTTACTC
77436100 AATCATAACCTTACT
1 AATCATAACCTTACT
77436115 GAGGGTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (16 bp):
AATCATAACCTTACTC
Found at i:77436392 original size:42 final size:42
Alignment explanation
Indices: 77436345--77436441 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
77436335 ATAGCCTAAC
*
77436345 TATGGTCTTACACGAAATATCAGATCGATGCCATATCCCAGA
1 TATGGTCTTACACGAAATATCACATCGATGCCATATCCCAGA
* * * *
77436387 TATGGTTTTACACGAAGTTTCACATTGATGCCATATCCCAGA
1 TATGGTCTTACACGAAATATCACATCGATGCCATATCCCAGA
77436429 TATGGTCTTACAC
1 TATGGTCTTACAC
77436442 ATAGTCTTAG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (42 bp):
TATGGTCTTACACGAAATATCACATCGATGCCATATCCCAGA
Found at i:77437892 original size:15 final size:15
Alignment explanation
Indices: 77437869--77437921 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
77437859 GATGAACCCT
*
77437869 TATGACGAACTCACC
1 TATGGCGAACTCACC
77437884 TATGGCGAAC-C-CC
1 TATGGCGAACTCACC
* *
77437897 TATGGCAAACTCACA
1 TATGGCGAACTCACC
77437912 TATGGCGAAC
1 TATGGCGAAC
77437922 CCCTATCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 11 0.34
14 2 0.06
15 19 0.59
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (15 bp):
TATGGCGAACTCACC
Found at i:77437894 original size:28 final size:28
Alignment explanation
Indices: 77437862--77437927 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
77437852 TATCATTGAT
* * *
77437862 GAACCCTTATGACGAACTCACCTATGGC
1 GAACCCCTATGACAAACTCACATATGGC
*
77437890 GAACCCCTATGGCAAACTCACATATGGC
1 GAACCCCTATGACAAACTCACATATGGC
77437918 GAACCCCTAT
1 GAACCCCTAT
77437928 CATGAACTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (28 bp):
GAACCCCTATGACAAACTCACATATGGC
Found at i:77437900 original size:13 final size:13
Alignment explanation
Indices: 77437862--77437927 Score: 60
Period size: 15 Copynumber: 4.8 Consensus size: 13
77437852 TATCATTGAT
* *
77437862 GAACCCTTATGAC
1 GAACCCCTATGGC
77437875 GAACTCACCTATGGC
1 GAAC-C-CCTATGGC
77437890 GAACCCCTATGGC
1 GAACCCCTATGGC
* *
77437903 AAACTCACATATGGC
1 GAAC-C-CCTATGGC
77437918 GAACCCCTAT
1 GAACCCCTAT
77437928 CATGAACTGC
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 19 0.44
14 4 0.09
15 20 0.47
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (13 bp):
GAACCCCTATGGC
Found at i:77437935 original size:28 final size:28
Alignment explanation
Indices: 77437862--77437935 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
77437852 TATCATTGAT
* *
77437862 GAACCCTTATG-ACGAACTCACCTATGGC
1 GAACCCCTATGCA-GAACTCACATATGGC
77437890 GAACCCCTATGGCA-AACTCACATATGGC
1 GAACCCCTAT-GCAGAACTCACATATGGC
77437918 GAACCCCTAT-CATGAACT
1 GAACCCCTATGCA-GAACT
77437936 GCCTTAATCC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 2 0.05
28 36 0.90
29 1 0.03
30 1 0.03
ACGTcount: A:0.31, C:0.32, G:0.16, T:0.20
Consensus pattern (28 bp):
GAACCCCTATGCAGAACTCACATATGGC
Found at i:77446944 original size:21 final size:22
Alignment explanation
Indices: 77446919--77446966 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
77446909 AACAGAGAAT
* *
77446919 GAAAACGAAATAGAAAGAAAA-
1 GAAAACGAAAAAAAAAGAAAAG
*
77446940 GAAAAGGAAAAAAAAAGAAAAG
1 GAAAACGAAAAAAAAAGAAAAG
77446962 GAAAA
1 GAAAA
77446967 ATTAGGGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (22 bp):
GAAAACGAAAAAAAAAGAAAAG
Found at i:77446955 original size:16 final size:16
Alignment explanation
Indices: 77446936--77446967 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
77446926 AAATAGAAAG
77446936 AAAAGAAAAGGAAAAA
1 AAAAGAAAAGGAAAAA
77446952 AAAAGAAAAGGAAAAA
1 AAAAGAAAAGGAAAAA
77446968 TTAGGGTTTT
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGGAAAAA
Found at i:77454719 original size:88 final size:85
Alignment explanation
Indices: 77454627--77454896 Score: 190
Period size: 88 Copynumber: 3.1 Consensus size: 85
77454617 GTGGCTTAAA
77454627 TCTGCTCCATTGCCGATACATGGAGATAAGATTCACCGTCTTCGATCTGCTCTGCTACTGCTTAG
1 TCTGCTCCATTG-CGATACATGGAGATAAGATTC-CCGTCTTCGATCTGCTCTGCTACT-CTTAG
77454692 GGAGATAAATCTGTGATTTTCAG
63 GGAGATAAATCTGTGATTTTCAG
** * ** * * * * *
77454715 TCTGCTCCACCGCAACTTTAGGGAGATAAGACTT---GTATATTGAGCTTGCTCCATTGCAACT-
1 TCTGCTCCATTGCGA-TACATGGAGATAAGA-TTCCCGTCT-TCGATC-TGCT-C--TGCTACTC
* ** ** * *
77454776 TCAGGGAGATAAGGCTTGTG-GCTTAAA
59 TTAGGGAGATAAATC-TGTGATTTTCAG
* * *
77454803 TTTGCTCCATTGTCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCGCTACTACTTAG
1 TCTGCTCCATTG-CGATACATGGAGATAAGATTC-CCGTCTTCGATCTGCTCTGCTACT-CTTAG
*
77454868 GGAGATAAATCTGAGATTTTCAG
63 GGAGATAAATCTGTGATTTTCAG
77454891 TCTGCT
1 TCTGCT
77454897 TTCTTGCTAC
Statistics
Matches: 127, Mismatches: 39, Indels: 32
0.64 0.20 0.16
Matches are distributed among these distances:
85 3 0.02
86 9 0.07
87 11 0.09
88 80 0.63
89 12 0.09
90 10 0.08
91 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (85 bp):
TCTGCTCCATTGCGATACATGGAGATAAGATTCCCGTCTTCGATCTGCTCTGCTACTCTTAGGGA
GATAAATCTGTGATTTTCAG
Found at i:77454812 original size:176 final size:176
Alignment explanation
Indices: 77454089--77455066 Score: 1033
Period size: 176 Copynumber: 5.5 Consensus size: 176
77454079 GGTTGATGGG
* * * * ** *
77454089 TTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTTACCATTTTCGACCTACTCCATTGCAA
1 TTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTGCTCCGCTACAA
* * * * * * * *
77454154 CTTCAGGGAGACAAGATCTT-AATCTTCAATCTGATTTCTTGCTATCTCAGAAAGATAAGACTCA
66 CTTCAGGGAGATAA-ATCTTAAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTA
* * * * * * *
77454218 TTCTTCAACCTGCTCTCTTACTACCTCAAAGAGATAAGG-TAAGTAGC
130 ATCTTCAACCTGCTCTCTTGCAACTTCAGAGAGATAAGGCT-TGTGGC
* * * *
77454265 TAAAATCTGCTCCATTGCTGATACATGGAGATAAGATTCACCATCTTCGATCTACTCCACTACAA
1 TTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTGCTCCGCTACAA
* * *
77454330 CTTCAGGGAGATAAGATCTTCAATCTTT-AGTCTACTTCCTTGCTACCTCAGGAAGATAAGACTC
66 CTTCAGGGAGATAA-ATCTTAAAT-TTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTT
* * * *
77454394 AATCTTTAACTTGCTCTCTTGCTACCTT-AGAGAGATAAGGCTTGGGGC
129 AATCTTCAACCTGCTCTCTTGC-AACTTCAGAGAGATAAGGCTTGTGGC
* * ** * *
77454442 TTCAGTCTGCTCCATTGCCGATACATGGAGATAAGATTTGCCATCTTCGATGATCTGCTCTGCTG
1 TTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTC---GATCTGCTCCGCTA
* *
77454507 CAAATTCAGGGAGATAAAATCTTAAATTCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGAC
63 CAACTTCAGGGAGAT-AAATCTTAAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGAC
* * * *
77454572 TCATTCTTCAACCTGCTCTCTTGCTA-TCTCAGAGAGATAAGACTTGTGGC
127 TTAATCTTCAACCTGCTCTCTTGCAACT-TCAGAGAGATAAGGCTTGTGGC
* * **
77454622 TTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCGTCTTCGATCTGCTCTGCTACTG
1 TTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTGCTCCGCTACAA
* ** * * * *
77454687 CTT-AGGGAGATAAATCTGT-GATTTTCAGTCTGC-TCCACCGCAACTTTAGGGAGATAAGACTT
66 CTTCAGGGAGATAAATCT-TAAATTTTCAGTCTGCTTCC-TTGCTACCTCAGGAAGATAAGACTT
* * * * * *
77454749 GTATATTGAGCTTGCTC-CATTGCAACTTCAGGGAGATAAGGCTTGTGGC
129 -AATCTTCAACCTGCTCTC-TTGCAACTTCAGAGAGATAAGGCTTGTGGC
* * * *
77454798 TTAAATTTGCTCCATTGTCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCGCTACTA
1 TTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTGCTCCGCTACAA
* * * *
77454863 CTT-AGGGAGATAAATCTGAGATTTTCAGTCTGCTTTCTTGCTACCTCAGAAAGATAAGACTTAA
66 CTTCAGGGAGATAAATCTTAAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTAA
* * *
77454927 TTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGG-
131 -TCTTCAACCTGCTCTCTTGCAACTTCAGAGAGATAAGGCTTGTGGC
* * * *
77454973 TAAAATCTGCTCCATTTCCGATACATAGAGATAAGATTCACCATCTTCGATCTGCTCCGCTGCAA
1 TTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTGCTCCGCTACAA
*
77455038 CTTCAGGGAGATAAGATCTTCAATTTTCA
66 CTTCAGGGAGATAA-ATCTTAAATTTTCA
77455067 CCAATATCGC
Statistics
Matches: 671, Mismatches: 109, Indels: 43
0.82 0.13 0.05
Matches are distributed among these distances:
174 3 0.00
175 98 0.15
176 274 0.41
177 138 0.21
178 6 0.01
179 3 0.00
180 147 0.22
181 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (176 bp):
TTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTGCTCCGCTACAA
CTTCAGGGAGATAAATCTTAAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTAA
TCTTCAACCTGCTCTCTTGCAACTTCAGAGAGATAAGGCTTGTGGC
Found at i:77455049 original size:88 final size:89
Alignment explanation
Indices: 77454769--77455052 Score: 214
Period size: 88 Copynumber: 3.2 Consensus size: 89
77454759 CTTGCTCCAT
* * *
77454769 TGCAACTTCAGGGAGATAAGGCTTGTGGCTTAAATTTGCTCCATTGT-CGATACATGGAGATAAG
1 TGCAACTTCAGGGAGATAAGGCTGGTGG-TTAAATCTGCTCCATTGTCCGATACATAGAGATAAG
*
77454833 ATTCGCCATCTTCGATCTGCTCCGC
65 ATTCACCATCTTCGATCTGCTCCGC
* * ** * * * * * *
77454858 TACTACTT-AGGGAGATAAATCTGAGAT-TTTCAGTCTGCTTTC-TTGCTACC--T-CAGAAAGA
1 TGCAACTTCAGGGAGATAAGGCTG-G-TGGTTAAATCTGC-TCCATTG-T-CCGATACATAGAGA
* * *
77454917 TAAGACTT-A--ATTCTTCAACCTGCTCTC-T
61 TAAGA-TTCACCA-TCTTCGATCTGCTC-CGC
* * * *
77454945 TGCTACCTCAGAGAGATAAGGCTGGTGGTAAAATCTGCTCCATT-TCCGATACATAGAGATAAGA
1 TGCAACTTCAGGGAGATAAGGCTGGTGGTTAAATCTGCTCCATTGTCCGATACATAGAGATAAGA
77455009 TTCACCATCTTCGATCTGCTCCGC
66 TTCACCATCTTCGATCTGCTCCGC
77455033 TGCAACTTCAGGGAGATAAG
1 TGCAACTTCAGGGAGATAAG
77455053 ATCTTCAATT
Statistics
Matches: 141, Mismatches: 35, Indels: 39
0.66 0.16 0.18
Matches are distributed among these distances:
84 2 0.01
85 1 0.01
86 7 0.05
87 41 0.29
88 74 0.52
89 14 0.10
90 1 0.01
91 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (89 bp):
TGCAACTTCAGGGAGATAAGGCTGGTGGTTAAATCTGCTCCATTGTCCGATACATAGAGATAAGA
TTCACCATCTTCGATCTGCTCCGC
Found at i:77463300 original size:12 final size:12
Alignment explanation
Indices: 77463267--77463317 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
77463257 TCTTAGCCAG
77463267 TTGCTCTTGCAT
1 TTGCTCTTGCAT
*
77463279 TTG-TGATTGCAT
1 TTGCT-CTTGCAT
77463291 TTGCTCTTGCAT
1 TTGCTCTTGCAT
* * *
77463303 ATCCTTTTGCAT
1 TTGCTCTTGCAT
77463315 TTG
1 TTG
77463318 TTCTAACTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
11 1 0.03
12 28 0.93
13 1 0.03
ACGTcount: A:0.12, C:0.20, G:0.18, T:0.51
Consensus pattern (12 bp):
TTGCTCTTGCAT
Found at i:77463476 original size:19 final size:19
Alignment explanation
Indices: 77463452--77463491 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
77463442 TATTGCCTTT
*
77463452 AATGCATATG-ATGTAATGC
1 AATGCAAATGCATG-AATGC
77463471 AATGCAAATGCATGAATGC
1 AATGCAAATGCATGAATGC
77463490 AA
1 AA
77463492 ATGAGGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (19 bp):
AATGCAAATGCATGAATGC
Found at i:77473671 original size:6 final size:6
Alignment explanation
Indices: 77473656--77473712 Score: 69
Period size: 6 Copynumber: 9.5 Consensus size: 6
77473646 TGTGTACCAC
* * * *
77473656 TACTGC TACTAT TACTGT TACTGT TACTGT TAATGT TACTGT TACTAT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT
*
77473704 TACTAT TAC
1 TACTGT TAC
77473713 GGTGTATTCC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.47
Consensus pattern (6 bp):
TACTGT
Found at i:77473683 original size:18 final size:18
Alignment explanation
Indices: 77473656--77473712 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
77473646 TGTGTACCAC
*
77473656 TACTGCTACTATTACTGT
1 TACTGTTACTATTACTGT
* *
77473674 TACTGTTACTGTTAATGT
1 TACTGTTACTATTACTGT
*
77473692 TACTGTTACTATTACTAT
1 TACTGTTACTATTACTGT
77473710 TAC
1 TAC
77473713 GGTGTATTCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.47
Consensus pattern (18 bp):
TACTGTTACTATTACTGT
Found at i:77482186 original size:43 final size:42
Alignment explanation
Indices: 77482151--77482239 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
77482141 CTTACATGAT
*
77482151 ATCAAATATCGATGCCACTGT-TCCAGACAGGGTCTTACACAAA
1 ATCAAATA-CGATGCCAATGTCT-CAGACAGGGTCTTACACAAA
* * *
77482194 ATCATATACGATGCCAATGTCTCAGACATGGTCTTACACAAT
1 ATCAAATACGATGCCAATGTCTCAGACAGGGTCTTACACAAA
77482236 ATCA
1 ATCA
77482240 CATCTCGGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
42 33 0.80
43 8 0.20
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.26
Consensus pattern (42 bp):
ATCAAATACGATGCCAATGTCTCAGACAGGGTCTTACACAAA
Found at i:77489803 original size:42 final size:42
Alignment explanation
Indices: 77489755--77489837 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 42
77489745 TCTAGACAGG
* *
77489755 GTCTTACATGAAAT-CATATACGATGCCAATGTCCCAGACACA
1 GTCTTACACGAAATCCAGAT-CGATGCCAATGTCCCAGACACA
*
77489797 GTCTTACACGTAATCGCAGATCGATGCCAATGTCCCAGACA
1 GTCTTACACGAAATC-CAGATCGATGCCAATGTCCCAGACA
77489838 TGGTCTGACA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 12 0.33
43 20 0.56
44 4 0.11
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.23
Consensus pattern (42 bp):
GTCTTACACGAAATCCAGATCGATGCCAATGTCCCAGACACA
Found at i:77497636 original size:17 final size:18
Alignment explanation
Indices: 77497614--77497648 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
77497604 TAAGAGTTGA
*
77497614 CAAA-TTTATTTTTCTAG
1 CAAATTTTATTATTCTAG
77497631 CAAATTTTATTATTCTAG
1 CAAATTTTATTATTCTAG
77497649 AATGTGAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (18 bp):
CAAATTTTATTATTCTAG
Found at i:77500174 original size:6 final size:6
Alignment explanation
Indices: 77500163--77500187 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
77500153 CCCTATTCAA
77500163 TATCAG TATCAG TATCAG TATCAG T
1 TATCAG TATCAG TATCAG TATCAG T
77500188 TTGGCCTTAG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (6 bp):
TATCAG
Found at i:77501946 original size:40 final size:40
Alignment explanation
Indices: 77501694--77501939 Score: 404
Period size: 40 Copynumber: 6.2 Consensus size: 40
77501684 AACCCAAGTA
* *
77501694 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
77501733 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
77501773 CCTTCGGGACTTGGCTCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
77501813 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
77501853 CCTTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
77501893 CCTTCGGGGCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
77501933 CCTTCGG
1 CCTTCGG
77501940 ATCTTAGTCC
Statistics
Matches: 193, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
39 13 0.07
40 180 0.93
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:77503265 original size:13 final size:13
Alignment explanation
Indices: 77503242--77503275 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
77503232 TTATTTTATT
77503242 ATTTCTAACACAAA
1 ATTT-TAACACAAA
77503256 ATTTTAACACAAA
1 ATTTTAACACAAA
77503269 ATGTTTA
1 AT-TTTA
77503276 TAATATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (13 bp):
ATTTTAACACAAA
Found at i:77511378 original size:79 final size:81
Alignment explanation
Indices: 77511241--77511425 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
77511231 TTGAATGATG
* *
77511241 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
*
77511306 GTGCGAGATACTA-AT
66 GTGCGAGATACTATAA
* * * * **
77511321 TCCGGGCTAAG-CCCGAAGGCTTTTGTGC-GAGTTACTAAATCTGGGTTAAG-TCCCGAAGGCAA
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAA
*
77511383 TTGTGCGAGTTACTATAA
64 TTGTGCGAGATACTATAA
*
77511401 T-CGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGC-TTTG
77511426 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 55 0.62
80 33 0.37
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTATAA
Found at i:77511432 original size:40 final size:39
Alignment explanation
Indices: 77511243--77511425 Score: 192
Period size: 40 Copynumber: 4.6 Consensus size: 39
77511233 GAATGATGTC
* * * *
77511243 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAAT
* * *
77511282 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATT
1 -CGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
77511322 CCGGGCTAAG-CCCGAAGGCTTTTGTGCGAGTTACTAAAT
1 -CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
77511361 CTGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAAT
1 C-GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AAT
*
77511402 CGGGCTATGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTG
77511426 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 1 0.01
39 32 0.27
40 75 0.62
41 12 0.10
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:77511458 original size:79 final size:79
Alignment explanation
Indices: 77511294--77511449 Score: 181
Period size: 79 Copynumber: 2.0 Consensus size: 79
77511284 GGACTAAGAT
* * * **
77511294 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCTTTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
77511359 ATCTGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
77511373 CCGAAGGCAATTGTGCGAGTTACTATAAT-CGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTA-AATCCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
77511436 TATATCCGGTTTAA
63 TAAATCCGGGTTAA
77511450 TTCTGAAGGT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
79 33 0.52
80 31 0.48
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:77513793 original size:21 final size:22
Alignment explanation
Indices: 77513767--77513812 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
77513757 AAGATCTCGG
77513767 GAAAGTCT-TTCAACAGGCATC
1 GAAAGTCTCTTCAACAGGCATC
*
77513788 GAAAGTCTCTTCAATAGGCATC
1 GAAAGTCTCTTCAACAGGCATC
77513810 GAA
1 GAA
77513813 GAAATTTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (22 bp):
GAAAGTCTCTTCAACAGGCATC
Found at i:77515617 original size:15 final size:16
Alignment explanation
Indices: 77515579--77515620 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
77515569 TTTTGCTCTC
*
77515579 CATTTTGGTTGTTGTTA
1 CATTTTTGTT-TTGTTA
77515596 C-TTTTTGTTTT-TTA
1 CATTTTTGTTTTGTTA
77515610 CATTTTTGTTT
1 CATTTTTGTTT
77515621 GAGGCCGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 4 0.17
15 11 0.48
16 7 0.30
17 1 0.04
ACGTcount: A:0.10, C:0.07, G:0.14, T:0.69
Consensus pattern (16 bp):
CATTTTTGTTTTGTTA
Found at i:77526431 original size:33 final size:34
Alignment explanation
Indices: 77526389--77526453 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
77526379 GCATATCTGT
* *
77526389 ACTGTTACTGTTACTG-AATAGGCTAAGGCCCAC
1 ACTGATACTGATACTGTAATAGGCTAAGGCCCAC
*
77526422 ACTGATACTGATACTGTAATGGGCTAAGGCCC
1 ACTGATACTGATACTGTAATAGGCTAAGGCCC
77526454 TAACGGAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 14 0.50
34 14 0.50
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (34 bp):
ACTGATACTGATACTGTAATAGGCTAAGGCCCAC
Found at i:77526466 original size:34 final size:33
Alignment explanation
Indices: 77526395--77526466 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 33
77526385 CTGTACTGTT
* * *
77526395 ACTGTTACTGAATAGGCTAAGGCCCACACTGAT
1 ACTGATACTGAATAGGCTAAGGCCCACACGGAA
*
77526428 ACTGATACTGTAATGGGCTAAGGCCCTA-ACGGAA
1 ACTGATACTG-AATAGGCTAAGGCCC-ACACGGAA
77526462 ACTGA
1 ACTGA
77526467 ACTATTACTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 9 0.27
34 23 0.70
35 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (33 bp):
ACTGATACTGAATAGGCTAAGGCCCACACGGAA
Found at i:77531208 original size:49 final size:50
Alignment explanation
Indices: 77531126--77531360 Score: 260
Period size: 49 Copynumber: 4.7 Consensus size: 50
77531116 TGATCTATTG
* *
77531126 TTAGGTCACGTGTGTAGTACTAAGTACAGGCTACTACGTGTACAGGATAA
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGGATAA
* * * **
77531176 TT-GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAA
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGGATAA
* * * * * * **
77531225 CTTCGATCACGTGTGTAGTACTAAGTGTAGGCTACTACATGTATTA-GATGG
1 -TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CAGGATAA
* * *
77531276 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAA
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGGATAA
*
77531326 TT-GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
77531361 TGCGTACCAG
Statistics
Matches: 152, Mismatches: 29, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
49 71 0.47
50 46 0.30
51 35 0.23
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (50 bp):
TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGGATAA
Found at i:77531319 original size:101 final size:98
Alignment explanation
Indices: 77531131--77531360 Score: 284
Period size: 100 Copynumber: 2.3 Consensus size: 98
77531121 TATTGTTAGG
* * *
77531131 TCACGTGTGTAGTACTAAGTACAGGCTACTACGTGTACAGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACAGGATAATTGGTCACATGTGTAGTACT
*
77531196 AAGTGCAGGCTACTATGCGTACCCG-ATAACTTCGA
66 AAGTGCAGGCTACTACGCGTA-CCGAATAA-TT-GA
* * ** *
77531231 TCACGTGTGTAGTACTAAGTGTAGGCTACTACATGTATTA-GATGGTTAGGTCACGTGTGTAGTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTA-CAGGATAATT-GGTCACATGTGTAGTA
* *
77531295 CTAAGTGCAGGCTACTACGTGTACCGAATAATTGG
64 CTAAGTGCAGGCTACTACGCGTACCGAATAATTGA
* *
77531330 TCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTA
77531361 TGCGTACCAG
Statistics
Matches: 113, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
99 29 0.26
100 44 0.39
101 40 0.35
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (98 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACAGGATAATTGGTCACATGTGTAGTACT
AAGTGCAGGCTACTACGCGTACCGAATAATTGA
Found at i:77534059 original size:57 final size:58
Alignment explanation
Indices: 77533928--77534073 Score: 163
Period size: 57 Copynumber: 2.5 Consensus size: 58
77533918 GTTGTTAACG
* * **
77533928 GGATTTAGCCTGGATTGGTAATCCTGATATAATTCCTTTCGAGCATATGTTACAATTA
1 GGATTTAGCCTGGATTGGTAATCCTGATATAACTCCTTTCGAGCATATATTACAAAAA
* * *
77533986 GGATTTAGCCTGGATTGGTAATCTTGAT-TGAGCT-C-TTCTGAGCATATATTGCAAAAA
1 GGATTTAGCCTGGATTGGTAATCCTGATAT-AACTCCTTTC-GAGCATATATTACAAAAA
* * *
77534043 GGATTTAGCCTAGATTGGTAACCCTGTTATA
1 GGATTTAGCCTGGATTGGTAATCCTGATATA
77534074 TGTTATAAGG
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
56 3 0.04
57 41 0.55
58 30 0.41
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (58 bp):
GGATTTAGCCTGGATTGGTAATCCTGATATAACTCCTTTCGAGCATATATTACAAAAA
Found at i:77542270 original size:39 final size:39
Alignment explanation
Indices: 77542216--77542296 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
77542206 ATAATTTGTG
*
77542216 ATAGTGTGATGACTCCAGATCATTTTAAATGTGTTTTTC
1 ATAGTGTGATGACTCCAGATCATTTTAAATATGTTTTTC
*
77542255 ATAGTGTGATGACTCCTGATCATTTTAAATATGTTTTTC
1 ATAGTGTGATGACTCCAGATCATTTTAAATATGTTTTTC
77542294 ATA
1 ATA
77542297 TAGTAATGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.44
Consensus pattern (39 bp):
ATAGTGTGATGACTCCAGATCATTTTAAATATGTTTTTC
Found at i:77548018 original size:25 final size:25
Alignment explanation
Indices: 77547989--77548036 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
77547979 TTATAATATG
* * *
77547989 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
77548014 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
77548037 GTTTCTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:77548103 original size:20 final size:20
Alignment explanation
Indices: 77548080--77548138 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
77548070 TAAACATGGT
77548080 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
77548100 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
77548120 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
77548139 GGTATTCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:77548120 original size:11 final size:11
Alignment explanation
Indices: 77548084--77548138 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
77548074 CATGGTATGT
77548084 ATGATATGCAC
1 ATGATATGCAC
* *
77548095 ATGACATG--T
1 ATGATATGCAC
77548104 ATGATATGCAC
1 ATGATATGCAC
*
77548115 ATGATATG--T
1 ATGATATGCAC
77548124 ATGATATGCAC
1 ATGATATGCAC
77548135 ATGA
1 ATGA
77548139 GGTATTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:77548220 original size:24 final size:24
Alignment explanation
Indices: 77548189--77548332 Score: 164
Period size: 24 Copynumber: 6.0 Consensus size: 24
77548179 GAGGAAGTGC
77548189 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
77548213 AAATGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* * *
77548237 AAAAGGGCTTATGCCCTAATTATC
1 AAAAGGGCTTATGCCCCAGTTATT
* *
77548261 AAAAAGGTTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* * * *
77548285 CAAAGGGCTTTTGTCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
77548309 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
77548333 ATGATAAAGC
Statistics
Matches: 98, Mismatches: 20, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
24 87 0.89
25 11 0.11
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:77552518 original size:150 final size:150
Alignment explanation
Indices: 77552243--77552544 Score: 577
Period size: 150 Copynumber: 2.0 Consensus size: 150
77552233 CCTCGAAAGA
77552243 TTGAGGCAATTTTGAAATGGAAGCCACCGAAGTCGGTAATAGAGATCCGAAGTTTTCTAGGGTTG
1 TTGAGGCAATTTTGAAATGGAAGCCACCGAAGTCGGTAATAGAGATCCGAAGTTTTCTAGGGTTG
* *
77552308 GCAGGTTATTATCGGAGATTCGTGGAAGGATTTTCTGTGTTGGTAGCACCGTTAATGAAACATAT
66 GCAGATTATTATCGGAGATTCGTGGAAGGATTTTCTGTGTTGGTAGCACCGTTAACGAAACATAT
77552373 AAGGAAGGGAGCACCTTTTG
131 AAGGAAGGGAGCACCTTTTG
*
77552393 TTGAGGCAATTTTGAAATGGAAGCCACCGAAGTCGGTAATAGAGATCCGAAGTTTTCTGGGGTTG
1 TTGAGGCAATTTTGAAATGGAAGCCACCGAAGTCGGTAATAGAGATCCGAAGTTTTCTAGGGTTG
77552458 GCAGATTATTATCGGAGATTCGTGGAAGGATTTTCTGTGTTGGTAGCACCGTTAACGAAACATAT
66 GCAGATTATTATCGGAGATTCGTGGAAGGATTTTCTGTGTTGGTAGCACCGTTAACGAAACATAT
77552523 AAGGAAGGGAGCACCTTTTG
131 AAGGAAGGGAGCACCTTTTG
77552543 TT
1 TT
77552545 TGGACAAATA
Statistics
Matches: 149, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 149 1.00
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (150 bp):
TTGAGGCAATTTTGAAATGGAAGCCACCGAAGTCGGTAATAGAGATCCGAAGTTTTCTAGGGTTG
GCAGATTATTATCGGAGATTCGTGGAAGGATTTTCTGTGTTGGTAGCACCGTTAACGAAACATAT
AAGGAAGGGAGCACCTTTTG
Found at i:77556270 original size:25 final size:25
Alignment explanation
Indices: 77556241--77556288 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
77556231 TTATAATATG
* * *
77556241 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
77556266 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
77556289 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:77556355 original size:20 final size:20
Alignment explanation
Indices: 77556332--77556390 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
77556322 TAAACATGGT
*
77556332 ATGTATGATATGCACATTAC
1 ATGTATGATATGCACATGAC
*
77556352 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
77556372 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
77556391 GGTACTCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:77556468 original size:24 final size:24
Alignment explanation
Indices: 77556441--77556594 Score: 236
Period size: 24 Copynumber: 6.4 Consensus size: 24
77556431 GAGGAAGTGC
77556441 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
77556465 AAAAGGGCTTATGCCTCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
77556489 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* * *
77556513 AAAAGGGCCTATGCCACAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
* *
77556537 AAAAGGGTTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
77556561 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
77556585 AAAAGAGGCT
1 AAAAG-GGCT
77556595 AGGCCTCTAG
Statistics
Matches: 116, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
24 112 0.97
25 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:77560572 original size:24 final size:24
Alignment explanation
Indices: 77560544--77560619 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
77560534 GAACGTGCGT
77560544 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
* * **
77560568 ATGTGATGA-ATGTG--AACAT-GCGT
1 ATGTG-TGATAAG-GCCGA-ATGGCCA
77560591 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
77560615 ATGTG
1 ATGTG
77560620 ATGAATGTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 17 0.46
25 4 0.11
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (24 bp):
ATGTGTGATAAGGCCGAATGGCCA
Found at i:77560576 original size:47 final size:47
Alignment explanation
Indices: 77560523--77560758 Score: 373
Period size: 47 Copynumber: 5.0 Consensus size: 47
77560513 AGAATTTTAG
*
77560523 GTGATGAATGTGAACGTGCGTATGTGTGATAAGGCCGAATGGCCAAT
1 GTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAAT
77560570 GTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAAT
1 GTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAAT
*
77560617 GTGATGAATGTGAACATGCGTATGTATGATAAGGCCGAATGGCCAAT
1 GTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAAT
* * *
77560664 GTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAAT
1 GTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAAT
** * * * *
77560711 GTGATGAATGTGAACATGTATATATGCGGTAAGGCCGAATGGCTAAT
1 GTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAAT
77560758 G
1 G
77560759 CGAAATGTGT
Statistics
Matches: 179, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 179 1.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.25
Consensus pattern (47 bp):
GTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAAT
Found at i:77560868 original size:46 final size:46
Alignment explanation
Indices: 77560732--77560868 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 46
77560722 GAACATGTAT
* * *
77560732 ATATGCGGTAAGGCCGAATGGCTAATGCGAAATGTGTATGAGATAG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* *
77560778 ATATGTGGTAAAGCCGAATGGCTAATGCAAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * * *
77560824 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATG
77560869 TTTATATATA
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:77563137 original size:40 final size:40
Alignment explanation
Indices: 77563082--77563179 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 40
77563072 CTATCTTGGT
* *
77563082 ATTGCACACTTAGTGCCACATAAAACCAAAGCTATTTC-A
1 ATTGCACACTAAGTGCCACATAAAACCAAAGCTATCTCGA
* * * * *
77563121 ATTTGCACACTAAGTGCTATATATAGCCGAAGCTATCTCGA
1 A-TTGCACACTAAGTGCCACATAAAACCAAAGCTATCTCGA
*
77563162 AATGCACACTAAGTGCCA
1 ATTGCACACTAAGTGCCA
77563180 AACATCGTAG
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.02
40 45 0.94
41 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (40 bp):
ATTGCACACTAAGTGCCACATAAAACCAAAGCTATCTCGA
Found at i:77565354 original size:29 final size:28
Alignment explanation
Indices: 77565299--77565357 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
77565289 TTGAGCATGA
*
77565299 ATATAATGTGATTTGGGCCTCAAGGGCC
1 ATATAATGTGATTTGGGCATCAAGGGCC
77565327 ATATAAATGTGATTTGGGCAT-AATGGGCC
1 ATAT-AATGTGATTTGGGCATCAA-GGGCC
77565356 AT
1 AT
77565358 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.31
Consensus pattern (28 bp):
ATATAATGTGATTTGGGCATCAAGGGCC
Found at i:77579209 original size:46 final size:45
Alignment explanation
Indices: 77579045--77579216 Score: 176
Period size: 43 Copynumber: 3.8 Consensus size: 45
77579035 ATGTAACCCG
77579045 CCATAAGCGAACTCGACTCAACTCAACGAGCTCGG--GTTCGCAT
1 CCATAAGCGAACTCGACTCAACTCAACGAGCTCGGACGTTCGCAT
* *
77579088 CCATAAGTGAACTCGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGACTCAACTCAACGAGCTCGGA---C--GTTCGCAT
* * *
77579137 -C-TCA-CGAACTTGGACTCAACTCAACGAGTTCGGACGTTCGCAT
1 CCATAAGCGAAC-TCGACTCAACTCAACGAGCTCGGACGTTCGCAT
* *
77579180 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTC-GACTCAACTCAACGAGCTCGGA
77579217 TACCCAAATA
Statistics
Matches: 106, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
42 3 0.03
43 37 0.35
44 2 0.02
45 3 0.03
46 30 0.28
47 24 0.23
48 1 0.01
49 3 0.03
50 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (45 bp):
CCATAAGCGAACTCGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:77593186 original size:41 final size:40
Alignment explanation
Indices: 77593059--77593203 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
77593049 CTCGCACAAG
* * * * *
77593059 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
77593099 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
77593139 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
77593180 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
77593204 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:77601104 original size:39 final size:40
Alignment explanation
Indices: 77601059--77601227 Score: 108
Period size: 41 Copynumber: 4.2 Consensus size: 40
77601049 CGGGGTTTAG
* * *
77601059 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
77601098 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
* * * * **
77601138 CCGGATATAGTCCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATA-ACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
77601179 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
77601220 CCGGATAT
1 CCGGATAT
77601228 CATTCGAGTA
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
39 15 0.14
40 30 0.29
41 57 0.54
42 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:77601168 original size:41 final size:40
Alignment explanation
Indices: 77601082--77601227 Score: 186
Period size: 41 Copynumber: 3.6 Consensus size: 40
77601072 CTCGCACAAG
* * * * *
77601082 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
77601122 GCCTTCGGGACTTAGCCCGGATATAGTCCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGT-CGCTAGCACAAAT
* * *
77601163 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
77601204 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
77601228 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
40 30 0.33
41 59 0.64
42 3 0.03
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:77615646 original size:40 final size:40
Alignment explanation
Indices: 77615591--77615852 Score: 375
Period size: 40 Copynumber: 6.6 Consensus size: 40
77615581 TATTCTGATG
77615591 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
77615631 ATAACTGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
77615671 ATAACCGAGCTAAGTCCCGAAGGCATTTGTACGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
77615711 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
77615751 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
77615791 ATAACCGGGCTAAATCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* * *
77615831 ATATCC-GACTAATTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
77615853 TACTTGGTTT
Statistics
Matches: 200, Mismatches: 21, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
39 15 0.08
40 185 0.93
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:77623827 original size:40 final size:40
Alignment explanation
Indices: 77623772--77624033 Score: 402
Period size: 40 Copynumber: 6.6 Consensus size: 40
77623762 TATTCGGATG
77623772 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
77623812 ATAACTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
77623852 ATAACCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
77623892 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
77623932 ATATCCGGGATAAATCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
77623972 ATAACCGGGCTAAATCCTGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* *
77624012 ATATCC-GGCTAATTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
77624034 TACTTGGTTT
Statistics
Matches: 207, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
39 16 0.08
40 191 0.92
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:77628638 original size:31 final size:30
Alignment explanation
Indices: 77628561--77628673 Score: 142
Period size: 31 Copynumber: 3.7 Consensus size: 30
77628551 TTAATCTTGA
*
77628561 CATATACTGGGCCGAAGCC-TTTCATTTAA-
1 CATATACTGGGCCGAAGCCTTTTCA-TAAAT
*
77628590 CAGT-TACTGGGCTGAAGCCTTTTCATAAAT
1 CA-TATACTGGGCCGAAGCCTTTTCATAAAT
77628620 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
*
77628651 CATATCATTGGGCCGAAGCCTTT
1 CATAT-ACTGGGCCGAAGCCTTT
77628674 ACTATAAACG
Statistics
Matches: 75, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
29 20 0.27
30 9 0.12
31 46 0.61
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (30 bp):
CATATACTGGGCCGAAGCCTTTTCATAAAT
Found at i:77628962 original size:26 final size:26
Alignment explanation
Indices: 77628879--77629014 Score: 181
Period size: 26 Copynumber: 5.3 Consensus size: 26
77628869 CTGGAGGCCT
77628879 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
** *
77628903 AGCCCTTTTCGGTAAACTGGGGTA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
77628928 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
77628954 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
77628980 AGCCCTTTTCAATAAACTGAGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
77629006 AGCCCTTTT
1 AGCCCTTTT
77629015 GCACTTCCTC
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
23 5 0.05
24 5 0.05
25 31 0.32
26 57 0.58
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:77629004 original size:52 final size:51
Alignment explanation
Indices: 77628879--77629014 Score: 215
Period size: 52 Copynumber: 2.7 Consensus size: 51
77628869 CTGGAGGCCT
*
77628879 AGCCTCTTTT-AAT-AACTGGGGCA-AAGCCCTTTTCGGTAAACTGGGGTAA
1 AGCC-CTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAA
77628928 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCA-A
*
77628980 AGCCCTTTTCAATAAACTGAGGCATAAGCCCTTTT
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
77629015 GCACTTCCTC
Statistics
Matches: 81, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
48 5 0.06
49 7 0.09
50 10 0.12
51 24 0.30
52 35 0.43
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (51 bp):
AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAA
Found at i:77629843 original size:27 final size:27
Alignment explanation
Indices: 77629813--77629891 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 27
77629803 GGGCACATTC
*
77629813 GTCATTTTACCATACAGGGG-TATTACG
1 GTCATTTTACCCTACAGGGGCT-TTACG
*
77629840 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCCTACAGGGGCTTTACG
*
77629867 CTC-TCTTTACCCTACAGGGGCTTTA
1 GTCAT-TTTACCCTACAGGGGCTTTA
77629892 AAGTCTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
27 45 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCTTTACG
Found at i:77630143 original size:53 final size:53
Alignment explanation
Indices: 77630048--77630293 Score: 239
Period size: 53 Copynumber: 4.6 Consensus size: 53
77630038 TTGTAAATCA
* * *
77630048 AGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTTGTAATTTCACAAACC
1 AGGGTATTTTGGTAATTTTACAAATAGAGGGTATTTTGGTAATTTTACAAACC
**
77630101 AGTGGTATTTTGGT-ATTTTACAAACTAG-GGGTATTTTGGTAATTTTACAAATTG
1 AG-GGTATTTTGGTAATTTTACAAA-TAGAGGGTATTTTGGTAATTTTACAAA-CC
* * * * * * *
77630155 AGGGTATTTCGATAATTTTACAAACCA-AGGGTATTTTAGCAATTTTACAGACT
1 AGGGTATTTTGGTAATTTTACAAA-TAGAGGGTATTTTGGTAATTTTACAAACC
** * **
77630208 AGGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAACC
1 AGGGTATTTTGGTAATTTTACAAATAGAGGGTATTTTGGTAATTTTACAAACC
* * *
77630261 GAGGGTATTTTAGTAATTTT-TAAATCGAGGGTA
1 -AGGGTATTTTGGTAATTTTACAAATAGAGGGTA
77630294 AAACAGTAAT
Statistics
Matches: 157, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
53 92 0.59
54 65 0.41
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (53 bp):
AGGGTATTTTGGTAATTTTACAAATAGAGGGTATTTTGGTAATTTTACAAACC
Found at i:77630278 original size:107 final size:106
Alignment explanation
Indices: 77630021--77630280 Score: 283
Period size: 107 Copynumber: 2.4 Consensus size: 106
77630011 TAGAAAGTCA
* * * ***
77630021 AGGGTACTTTT-GTAAGTTTGTAAATCAAGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTT
1 AGGGTA-TTTTGGTAATTTTGTAAATCGAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTT
* * *
77630085 TGTAATTTCACAAACCAGTGGTATTTTGGTATTTTACAAACT
65 AGCAATTTCACAAACCAGTGGTATTTTGGTATTTTACAAACG
** * *
77630127 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTA-TTTCGATAATTTTACAAACCAAGGGTATTT
1 A-GGGTATTTTGGTAATTTTGTAAATCGAGGGTATTTTAG-TAATTTTACAAACCAAGGGTATTT
* * * * *
77630191 TAGCAATTTTACAGACTAG-GGTATTTTGGTAATTTTACTGATCG
64 TAGCAATTTCACAAACCAGTGGTATTTTGGT-ATTTTAC-AAACG
*
77630235 AGGGTATTTTGGTAATTTTGTAAACCGAGGGTATTTTAGTAATTTT
1 AGGGTATTTTGGTAATTTTGTAAATCGAGGGTATTTTAGTAATTTT
77630281 TAAATCGAGG
Statistics
Matches: 126, Mismatches: 22, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
106 20 0.16
107 99 0.79
108 7 0.06
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (106 bp):
AGGGTATTTTGGTAATTTTGTAAATCGAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTA
GCAATTTCACAAACCAGTGGTATTTTGGTATTTTACAAACG
Found at i:77630292 original size:80 final size:79
Alignment explanation
Indices: 77630021--77630293 Score: 304
Period size: 80 Copynumber: 3.4 Consensus size: 79
77630011 TAGAAAGTCA
*
77630021 AGGGTACTTTT-GTAAGTTTGTA-AATCAAGGGTATTTTGGTAATTTTACAAATTGAGGGTATTT
1 AGGGTA-TTTTAGTAA-TTT-TACAATCTAGGGTATTTTGGTAATTTTACAAATTGAGGGTATTT
* *
77630084 TTGTAATTTCACAAACC
63 TGGTAATTTTACAAACC
* * *
77630101 AGTGGTATTTTGGT-ATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTC
1 AG-GGTATTTTAGTAATTTTACAATCTA-GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTT
*
77630165 GATAATTTTACAAACC
64 GGTAATTTTACAAACC
* ** *
77630181 AAGGGTATTTTAGCAATTTTACAGA-CTAGGGTATTTTGGTAATTTTACTGATCGAGGGTATTTT
1 -AGGGTATTTTAGTAATTTTACA-ATCTAGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTT
**
77630245 GGTAATTTTGTAAACC
64 GGTAATTTTACAAACC
*
77630261 GAGGGTATTTTAGTAATTTTTA-AATCGAGGGTA
1 -AGGGTATTTTAGTAA-TTTTACAATCTAGGGTA
77630294 AAACAGTAAT
Statistics
Matches: 166, Mismatches: 18, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
78 2 0.01
79 8 0.05
80 131 0.79
81 24 0.14
82 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (79 bp):
AGGGTATTTTAGTAATTTTACAATCTAGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGG
TAATTTTACAAACC
Found at i:77630417 original size:27 final size:27
Alignment explanation
Indices: 77630021--77630418 Score: 243
Period size: 27 Copynumber: 14.9 Consensus size: 27
77630011 TAGAAAGTCA
* * *
77630021 AGGGTACTTTT-GTAAGTTTGTAAATCA
1 AGGGTA-TTTTGGTAATTTTATAAATCG
* *
77630048 AGGGTATTTTGGTAATTTTACAAATTG
1 AGGGTATTTTGGTAATTTTATAAATCG
* * * *
77630075 AGGGTATTTTTGTAATTTCACAAA-CC
1 AGGGTATTTTGGTAATTTTATAAATCG
* *
77630101 AGTGGTATTTTGGT-ATTTTACAAA-CT
1 AG-GGTATTTTGGTAATTTTATAAATCG
* *
77630127 AGGGGTATTTTGGTAATTTTACAAATTG
1 A-GGGTATTTTGGTAATTTTATAAATCG
* * * * *
77630155 AGGGTATTTCGATAATTTTACAAACCA
1 AGGGTATTTTGGTAATTTTATAAATCG
* * * * *
77630182 AGGGTATTTTAGCAATTTTACAGA-CT
1 AGGGTATTTTGGTAATTTTATAAATCG
*
77630208 AGGGTATTTTGGTAATTTTACT-GATCG
1 AGGGTATTTTGGTAATTTTA-TAAATCG
* *
77630235 AGGGTATTTTGGTAATTTTGTAAACCG
1 AGGGTATTTTGGTAATTTTATAAATCG
*
77630262 AGGGTATTTTAGTAATTTT-TAAATCG
1 AGGGTATTTTGGTAATTTTATAAATCG
***** * * *
77630288 AGGGTAAAACAGTAATTCTGTAAATCA
1 AGGGTATTTTGGTAATTTTATAAATCG
***** *
77630315 AGGGTAAAACAGTAATTCTATAAATCG
1 AGGGTATTTTGGTAATTTTATAAATCG
**** *
77630342 AGGGTAAAACGGTAATTTTGTAAATCG
1 AGGGTATTTTGGTAATTTTATAAATCG
*** * *
77630369 AGGGTAAAATGGTAATTCTATAAATTG
1 AGGGTATTTTGGTAATTTTATAAATCG
*
77630396 AGGGTACTTTGGTAATTTTATAA
1 AGGGTATTTTGGTAATTTTATAA
77630419 TTTAAAGGTA
Statistics
Matches: 309, Mismatches: 53, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
26 70 0.23
27 238 0.77
28 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTATAAATCG
Found at i:77632347 original size:42 final size:43
Alignment explanation
Indices: 77632248--77632405 Score: 178
Period size: 43 Copynumber: 3.7 Consensus size: 43
77632238 AGCTCTTACA
* * * *
77632248 ATGCCAACGTCCCAAACGTGGTCTTACATGAAATCAAATATTG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
* * *
77632291 ATGCCACTGTCCCAGACAG-GGTCTTACACGAGATCATATA-CG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGAAATCAAATATCG
* *
77632333 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCACAA-ATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACAC-GAAATCA-AATATCG
*
77632377 ATGCCAATTTCCCAGACGTGGTCTTACAC
1 ATGCCAATGTCCCAGACGTGGTCTTACAC
77632406 AATAACACAT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
42 27 0.28
43 38 0.40
44 31 0.32
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
Found at i:77632392 original size:44 final size:43
Alignment explanation
Indices: 77632248--77632406 Score: 155
Period size: 44 Copynumber: 3.7 Consensus size: 43
77632238 AGCTCTTACA
* * * *
77632248 ATGCCAACGTCCCAAACGTGGTCTT--ACATGAAATCAAATATTG
1 ATGCCAATGTCCCAGACATGGTCTTACACAT-AAATCAAA-ATCG
* * * * *
77632291 ATGCCACTGTCCCAGACAGGGTCTTACAC-GAGATC-ATATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCAAAAT-CG
77632333 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCACAAATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCA-AAATCG
* *
77632377 ATGCCAATTTCCCAGACGTGGTCTTACACA
1 ATGCCAATGTCCCAGACATGGTCTTACACA
77632407 ATAACACATC
Statistics
Matches: 94, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
41 2 0.02
42 29 0.31
43 28 0.30
44 30 0.32
45 5 0.05
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACATAAATCAAAATCG
Found at i:77632400 original size:86 final size:85
Alignment explanation
Indices: 77632248--77632405 Score: 205
Period size: 86 Copynumber: 1.8 Consensus size: 85
77632238 AGCTCTTACA
* * *
77632248 ATGCCAACGTCCCAAACGTGGTCTTACATGAAATCAAATATTGATGCCACTGTCCCAGACAGGGT
1 ATGCCAACGTCCCAAACATGGTCTTACATGAAATCAAATATCGATGCCAATGTCCCAGACAGGGT
77632313 CTTACACGAGATCATATACG
66 CTTACACGAGATCATATACG
* * *
77632333 ATGCCAATGTCCCAGACATGGTCTTACACAT-AAATCACAA-ATCGATGCCAATTTCCCAGAC-G
1 ATGCCAACGTCCCAAACATGGTCTT--ACATGAAATCA-AATATCGATGCCAATGTCCCAGACAG
77632395 TGGTCTTACAC
63 -GGTCTTACAC
77632406 AATAACACAT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
85 23 0.37
86 34 0.54
87 6 0.10
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (85 bp):
ATGCCAACGTCCCAAACATGGTCTTACATGAAATCAAATATCGATGCCAATGTCCCAGACAGGGT
CTTACACGAGATCATATACG
Found at i:77634489 original size:41 final size:41
Alignment explanation
Indices: 77634396--77634579 Score: 219
Period size: 41 Copynumber: 4.5 Consensus size: 41
77634386 TCGATATTGT
* * * ** **
77634396 GCACACTAAGTGTCGTACATAGCTGAAGCTATCTC-AAATC
1 GCACACTAAGTGCCATATATAGCCAAAGCTATCTCGATCTC
77634436 GCACACTAAGTGCCATATATAGCCAAAGCTATCTCGATCTC
1 GCACACTAAGTGCCATATATAGCCAAAGCTATCTCGATCTC
*
77634477 GCACACTAAGTGCCATATATAGCCAAAGCTATCTTGATCTC
1 GCACACTAAGTGCCATATATAGCCAAAGCTATCTCGATCTC
* * * ** * *
77634518 GTACACTAAGTGGCACATATAGCGGAAGCTATGTCGA-GTC
1 GCACACTAAGTGCCATATATAGCCAAAGCTATCTCGATCTC
77634558 GCACACTAAGTGCCATATATAG
1 GCACACTAAGTGCCATATATAG
77634580 TTGATTTGTC
Statistics
Matches: 124, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
40 51 0.41
41 73 0.59
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (41 bp):
GCACACTAAGTGCCATATATAGCCAAAGCTATCTCGATCTC
Found at i:77639097 original size:7 final size:7
Alignment explanation
Indices: 77639085--77639110 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
77639075 ACATTTCTAC
77639085 TCATCCA
1 TCATCCA
77639092 TCATCCA
1 TCATCCA
77639099 TCATCCA
1 TCATCCA
77639106 TCATC
1 TCATC
77639111 ATTCTCTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.42, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCA
Found at i:77640623 original size:22 final size:22
Alignment explanation
Indices: 77640598--77640640 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
77640588 CACTAAGTCA
* * *
77640598 ACAGAACGGCTTAATGCCGTAG
1 ACAGAACAGCTAAAGGCCGTAG
77640620 ACAGAACAGCTAAAGGCCGTA
1 ACAGAACAGCTAAAGGCCGTA
77640641 AATATTACAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (22 bp):
ACAGAACAGCTAAAGGCCGTAG
Found at i:77640925 original size:27 final size:27
Alignment explanation
Indices: 77640877--77640935 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
77640867 CATAATCGTT
* * *
77640877 ATTTTACCATACAGGGGTATTACGATC
1 ATTTTACCATAAAAGGGCATTACGATC
*
77640904 ATTTTACCCTAAAAGGGCATTACGATC
1 ATTTTACCATAAAAGGGCATTACGATC
77640931 ATTTT
1 ATTTT
77640936 CCAAATCGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (27 bp):
ATTTTACCATAAAAGGGCATTACGATC
Found at i:77641191 original size:18 final size:20
Alignment explanation
Indices: 77641163--77641199 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
77641153 GCATGGGGCC
77641163 CACGAGCCCATT-AGGCCCA
1 CACGAGCCCATTGAGGCCCA
77641182 CACG-GCCCATTGAGGCCC
1 CACGAGCCCATTGAGGCCC
77641200 CAAAACAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.22, C:0.43, G:0.24, T:0.11
Consensus pattern (20 bp):
CACGAGCCCATTGAGGCCCA
Found at i:77648486 original size:38 final size:38
Alignment explanation
Indices: 77648438--77648677 Score: 363
Period size: 38 Copynumber: 6.3 Consensus size: 38
77648428 GGCACGAAGG
* * * *
77648438 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
77648476 CCCGGATATAATACCAGCACGAAGCCTGCGGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGG-ATTTAA
* *
77648515 GCCTGGATATAATACCAGCACGAAGCCTTCGGGATTTAA
1 -CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
77648554 CCCGGATATGATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
77648592 CCCGGATATATTACTAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
77648630 CCCGGATATAATACCAGCACGAAGCCTGTGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
77648668 CCCGGATATA
1 CCCGGATATA
77648678 CATCGAATAT
Statistics
Matches: 183, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
38 144 0.79
39 9 0.05
40 30 0.16
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:77653837 original size:48 final size:48
Alignment explanation
Indices: 77653773--77654095 Score: 176
Period size: 48 Copynumber: 6.8 Consensus size: 48
77653763 AGCCACATTT
* * *
77653773 TGAGAGCCAATGTAAGACCATGTCTGGGACATGGCATCGACATTGAGA
1 TGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGA
* *
77653821 TGAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGA
1 TGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGA
*
77653867 TGTA-AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATC-AGC-TACGAGA
1 TG-AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGA-CAT-CGAGA
* * * * * *
77653913 T-A-TG-TCAGT-TCAAGACCATGTTTGGGGCATGGCATTGGCA-C-ATA
1 TGAGAGCT-AGTGT-AAGACCATGTCTGGGACATGGCATCGACATCGAGA
* * * *
77653957 T-AGAGGTGTCAGTGTAAGACCATGTCTGGGATATGGCATCGGCA-CGGATA
1 TGAGA-G-CT-AGTGTAAGACCATGTCTGGGACATGGCATCGACATC-GAGA
* ** * * **
77654007 TGTGAGAGCTAGTGTAAGACCATGTCT-AGACATTCCGTC-AGCCTCGATT
1 --TGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGA-CATCGAGA
* * *
77654056 TCGATAGCCAATGTAAGACCATGTCTGGGACATGGCATCG
1 T-GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCG
77654096 GCATTATACC
Statistics
Matches: 216, Mismatches: 35, Indels: 46
0.73 0.12 0.15
Matches are distributed among these distances:
43 1 0.00
44 13 0.06
45 14 0.06
46 58 0.27
47 16 0.07
48 67 0.31
49 20 0.09
50 21 0.10
51 1 0.00
52 2 0.01
53 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (48 bp):
TGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGA
Found at i:77653879 original size:46 final size:46
Alignment explanation
Indices: 77653773--77653902 Score: 181
Period size: 46 Copynumber: 2.8 Consensus size: 46
77653763 AGCCACATTT
* *
77653773 TGAGAGCCAATGTAAGACCATGTCTGGGACATGGCATCGACATTGAGA
1 TGAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACATCGAGA
* * *
77653821 TGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGA
1 TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGACATCGAGA
77653867 TGTA-AGCCAGTGTAAGACATGTCTGGGACATGCATC
1 TG-AGAGCCAGTGTAAGACATGTCTGGGACATGCATC
77653903 AGCTACGAGA
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
46 45 0.60
47 15 0.20
48 15 0.20
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.22
Consensus pattern (46 bp):
TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGACATCGAGA
Found at i:77653912 original size:46 final size:48
Alignment explanation
Indices: 77653735--77653913 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 48
77653725 TTTGTGTGCT
* * * * *
77653735 AGTGTAAGACATGTCTAGGACATGAATCAG-CCAC-A-TTTTGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGACTACGAGATGT-AGAGCC
* * *
77653781 AATGTAAGACCATGTCTGGGACATGGCATC-GAC-ATTGAGATG-AGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGACTA-CGAGATGTAGAGCC
* *
77653829 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGACTACGAGATGTAGAGCC
77653875 AGTGTAAGACATGTCTGGGACATGCATCAG-CTACGAGAT
1 AGTGTAAGACATGTCTGGGACATGCATCAGACTACGAGAT
77653914 ATGTCAGTTC
Statistics
Matches: 111, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
45 2 0.02
46 57 0.51
47 32 0.29
48 18 0.16
49 1 0.01
50 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGACTACGAGATGTAGAGCC
Found at i:77655186 original size:15 final size:16
Alignment explanation
Indices: 77655161--77655192 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
77655151 TCCCCTTGTG
77655161 CTTAGGCTATGTGAAC
1 CTTAGGCTATGTGAAC
77655177 CTTA-GCTATGTGAAC
1 CTTAGGCTATGTGAAC
77655192 C
1 C
77655193 ACACAGGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (16 bp):
CTTAGGCTATGTGAAC
Found at i:77658068 original size:14 final size:14
Alignment explanation
Indices: 77658047--77658084 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
77658037 TACATAATTT
77658047 GCAACAAATATCGA
1 GCAACAAATATCGA
*
77658061 GTAACAAATATCGA
1 GCAACAAATATCGA
77658075 GCAACAAATA
1 GCAACAAATA
77658085 AGCTAACTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.18, G:0.13, T:0.16
Consensus pattern (14 bp):
GCAACAAATATCGA
Found at i:77662038 original size:38 final size:38
Alignment explanation
Indices: 77661957--77662114 Score: 217
Period size: 38 Copynumber: 4.1 Consensus size: 38
77661947 TCCAGTCACT
* * * *
77661957 AGCACAAAACCTGCGGGACTTTAAGCTTGAATATAATACC
1 AGCACGAAGCCTGCGGGA-TTTAA-CTCGGATATAATACC
*
77661997 AGCACTAAGCCTGCGGGATTTAACTCGGATATAATACC
1 AGCACGAAGCCTGCGGGATTTAACTCGGATATAATACC
* *
77662035 AGCACGAAGCCTGCGGGATTTAACGCGGCTATAATACC
1 AGCACGAAGCCTGCGGGATTTAACTCGGATATAATACC
* *
77662073 AGCACGAAGCCTGCGGGATTTAACCCGGATATGATACC
1 AGCACGAAGCCTGCGGGATTTAACTCGGATATAATACC
77662111 AGCA
1 AGCA
77662115 TATAGCCTGC
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
38 87 0.81
39 5 0.05
40 16 0.15
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (38 bp):
AGCACGAAGCCTGCGGGATTTAACTCGGATATAATACC
Found at i:77668578 original size:40 final size:40
Alignment explanation
Indices: 77668508--77668673 Score: 149
Period size: 40 Copynumber: 4.2 Consensus size: 40
77668498 TCGGGGTTAG
** * *
77668508 CCGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTAAC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * *
77668547 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
* * *
77668587 CCGGATATAGTCGCTAGCACAAATGCCTTCGGATCTT-AG
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * * * *
77668626 TCGGATGTAGTCGCTTAGCACAAAAGCCTT-GGGACTTAGC
1 CCGGATATAGTCAC-TAGCACAAATGCCTTCGGGTCTTAAC
77668666 CCGGATAT
1 CCGGATAT
77668674 CATTCGAGTA
Statistics
Matches: 100, Mismatches: 24, Indels: 5
0.78 0.19 0.04
Matches are distributed among these distances:
39 32 0.32
40 68 0.68
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:77668664 original size:39 final size:39
Alignment explanation
Indices: 77668531--77668673 Score: 162
Period size: 40 Copynumber: 3.6 Consensus size: 39
77668521 CTCGCACAAG
* * * * *
77668531 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTT-GGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
77668571 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTT-GGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * * *
77668611 GCCTTCGGATCTTAG-TCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
77668651 GCCTTGGGACTTAGCCCGGATAT
1 GCCTTGGGACTTAGCCCGGATAT
77668674 CATTCGAGTA
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 20 0.23
40 68 0.77
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (39 bp):
GCCTTGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:77672131 original size:417 final size:416
Alignment explanation
Indices: 77671358--77672187 Score: 1651
Period size: 417 Copynumber: 2.0 Consensus size: 416
77671348 TTTTAAAGTT
77671358 GTAGCTATAGTTTTCATGCATTGCATATAGTTGTAAGTCACATTTTGTTTAGTACACATTGTCAC
1 GTAGCTATAGTTTTCATGCATTGCATATAGTTGTAAGTCACATTTTGTTTAGTACACATTGTCAC
77671423 TGCATTTTTATTTTCATTATATATTCATGTCAGTGCATTGGGGACAATGCAATCTTTAAGTTTGG
66 TGCATTTTTATTTTCATTATATATTCATGTCAGTGCATTGGGGACAATGCAATCTTTAAGTTTGG
77671488 GGGAATGTATATGGGATTTGGAAATACACCCACATTTCAAAAAAAAAATTGAAGCATGCAAGATT
131 GGGAATGTATATGGGATTTGGAAATACACCCACATTTCAAAAAAAAAATTGAAGCATGCAAGATT
77671553 TATGCACAATTGTTTGAAAATTTTTGTTACATTCGATGCTTAATTCTTGGATCATGTGAATTGTC
196 TATGCACAATTGTTTGAAAATTTTTGTTACATTCGATGCTTAATTCTTGGATCATGTGAATTGTC
77671618 AATGAATGAGTTGGATAAATTTGACTGAATGTTGTATCTTCAATACTTTGATGGATGATTTAGGT
261 AATGAATGAGTTGGATAAATTTGACTGAATGTTGTATCTTCAATACTTTGATGGATGATTTAGGT
77671683 CGCATTAGTAATAAAAAACTAGTAGCATTCCTTGAATCTTGAGTGAAACTACCTTTTTCAGCTGC
326 CGCATTAGTAATAAAAAACTAGTAGCATTCCTTGAATCTTGAGTGAAACTACCTTTTTCAGCTGC
77671748 TTATATATATAGATAGTTATAAACTA
391 TTATATATATAGATAGTTATAAACTA
77671774 GTAGCTATAGTTTTCATGCATTGCATATAGTTGTAAGTCACATTTTGTTTAGTACACATTGTCAC
1 GTAGCTATAGTTTTCATGCATTGCATATAGTTGTAAGTCACATTTTGTTTAGTACACATTGTCAC
77671839 TGCATTTTTATTTTCATTATATATTCATGTCAGTGCATTGGGGACAATGCAATCTTTAAGTTTGG
66 TGCATTTTTATTTTCATTATATATTCATGTCAGTGCATTGGGGACAATGCAATCTTTAAGTTTGG
77671904 GGGAATGTATATGGGATTTGGAAATACACCCACATTTCAAAAAAAAAAATTGAAGCATGCAAGAT
131 GGGAATGTATATGGGATTTGGAAATACACCCACATTTC-AAAAAAAAAATTGAAGCATGCAAGAT
77671969 TTATGCACAATTGTTTGAAAATTTTTGTTACATTCGATGCTTAATTCTTGGATCATGTGAATTGT
195 TTATGCACAATTGTTTGAAAATTTTTGTTACATTCGATGCTTAATTCTTGGATCATGTGAATTGT
77672034 CAATGAATGAGTTGGATAAATTTGACTGAATGTTGTATCTTCAATACTTTGATGGATGATTTAGG
260 CAATGAATGAGTTGGATAAATTTGACTGAATGTTGTATCTTCAATACTTTGATGGATGATTTAGG
77672099 TCGCATTAGTAATAAAAAACTAGTAGCATTCCTTGAATCTTGAGTGAAACTACCTTTTTCAGCTG
325 TCGCATTAGTAATAAAAAACTAGTAGCATTCCTTGAATCTTGAGTGAAACTACCTTTTTCAGCTG
77672164 CTTATATATATAGATAGTTATAAA
390 CTTATATATATAGATAGTTATAAA
77672188 TAAGAGACAC
Statistics
Matches: 413, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
416 168 0.41
417 245 0.59
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (416 bp):
GTAGCTATAGTTTTCATGCATTGCATATAGTTGTAAGTCACATTTTGTTTAGTACACATTGTCAC
TGCATTTTTATTTTCATTATATATTCATGTCAGTGCATTGGGGACAATGCAATCTTTAAGTTTGG
GGGAATGTATATGGGATTTGGAAATACACCCACATTTCAAAAAAAAAATTGAAGCATGCAAGATT
TATGCACAATTGTTTGAAAATTTTTGTTACATTCGATGCTTAATTCTTGGATCATGTGAATTGTC
AATGAATGAGTTGGATAAATTTGACTGAATGTTGTATCTTCAATACTTTGATGGATGATTTAGGT
CGCATTAGTAATAAAAAACTAGTAGCATTCCTTGAATCTTGAGTGAAACTACCTTTTTCAGCTGC
TTATATATATAGATAGTTATAAACTA
Found at i:77679455 original size:32 final size:36
Alignment explanation
Indices: 77679412--77679496 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 36
77679402 TAAAAAAAAC
* *
77679412 TATATTTATATAAATA-ACTA-AATAT-T-TAATTT
1 TATATTAATATAAATATACTATAAAATGTATAATTT
77679444 TATATTAATATATTAATATACTATTAAAATGTATAATTT
1 TATATTAATATA--AATATACTA-TAAAATGTATAATTT
77679483 TAATATTAATATAA
1 T-ATATTAATATAA
77679497 TAAAATAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
32 11 0.26
34 4 0.09
35 4 0.09
37 4 0.09
38 2 0.05
39 7 0.16
40 11 0.26
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (36 bp):
TATATTAATATAAATATACTATAAAATGTATAATTT
Found at i:77679607 original size:28 final size:30
Alignment explanation
Indices: 77679551--77679610 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
77679541 ATTTTATATT
77679551 AAATATATAAAAAATATTTTTTAAAATTAATA
1 AAATATATAAAAAATATTTTTT--AATTAATA
*
77679583 AAATA-ATAAAATATATTTTTT-ATTAATA
1 AAATATATAAAAAATATTTTTTAATTAATA
77679611 TTTATATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 7 0.26
31 15 0.56
32 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
AAATATATAAAAAATATTTTTTAATTAATA
Found at i:77679618 original size:21 final size:21
Alignment explanation
Indices: 77679593--77679635 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
77679583 AAATAATAAA
*
77679593 ATATATTTT-TTATTAATATTT
1 ATATATTTTATAATTAA-ATTT
77679614 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
77679635 A
1 A
77679636 AATAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:77680480 original size:43 final size:43
Alignment explanation
Indices: 77680417--77680503 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
77680407 TGAAAAGTAG
*
77680417 ACTAACTAAATTCCCGAAAATAAAATAAGGAAACTAAATTTCA
1 ACTAACTAAATTCCCAAAAATAAAATAAGGAAACTAAATTTCA
* **
77680460 ACTAACTAAATTCCTAAAAATAATGTAAGGAAACTAAATTTCA
1 ACTAACTAAATTCCCAAAAATAAAATAAGGAAACTAAATTTCA
77680503 A
1 A
77680504 AGGTATGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (43 bp):
ACTAACTAAATTCCCAAAAATAAAATAAGGAAACTAAATTTCA
Found at i:77695961 original size:25 final size:25
Alignment explanation
Indices: 77695890--77695969 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
77695880 GACACACCAC
* *
77695890 AGCTCTTATGAGCGTCCCGATA-AT
1 AGCTCTTATGAGCATCCCGTTATAT
* * * ** *
77695914 AGCTCTCATGAGCTTTCAATTATTT
1 AGCTCTTATGAGCATCCCGTTATAT
77695939 AGCTCTTATGAGCATCCCGTTATAT
1 AGCTCTTATGAGCATCCCGTTATAT
*
77695964 GGCTCT
1 AGCTCT
77695970 CACGAGCTTC
Statistics
Matches: 41, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
24 16 0.39
25 25 0.61
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (25 bp):
AGCTCTTATGAGCATCCCGTTATAT
Found at i:77699360 original size:27 final size:27
Alignment explanation
Indices: 77699343--77699467 Score: 178
Period size: 27 Copynumber: 4.5 Consensus size: 27
77699333 ATATTAAGTC
*
77699343 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
77699370 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
77699397 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
* * * *
77699425 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAACT
77699454 CGCACACTTAGTGC
1 CGCACACTTAGTGC
77699468 CAATCTCATG
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
27 49 0.54
28 23 0.26
29 17 0.19
30 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:77699932 original size:12 final size:12
Alignment explanation
Indices: 77699915--77699941 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
77699905 TGGGCATAGT
77699915 TATGTATATATA
1 TATGTATATATA
77699927 TATGTATATATA
1 TATGTATATATA
77699939 TAT
1 TAT
77699942 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:77707345 original size:27 final size:26
Alignment explanation
Indices: 77707328--77707397 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
77707318 ATATTAAGTC
77707328 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
77707355 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
77707383 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
77707398 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:77707391 original size:28 final size:28
Alignment explanation
Indices: 77707328--77707425 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
77707318 ATATTAAGTC
*
77707328 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
77707355 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
77707383 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
77707412 CGCACACTTAGTGC
1 CGCACACTTAGTGC
77707426 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:77707889 original size:12 final size:12
Alignment explanation
Indices: 77707872--77707898 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
77707862 TGGGCATAGT
77707872 TATGTATATATA
1 TATGTATATATA
77707884 TATGTATATATA
1 TATGTATATATA
77707896 TAT
1 TAT
77707899 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:77712557 original size:22 final size:22
Alignment explanation
Indices: 77712529--77712572 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
77712519 ATAGCTGGGA
77712529 ATAGAGAGAAGAACCAACTATG
1 ATAGAGAGAAGAACCAACTATG
77712551 ATAGAGAGAAGAACCAACTATG
1 ATAGAGAGAAGAACCAACTATG
77712573 CTAAAGTGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.23, T:0.14
Consensus pattern (22 bp):
ATAGAGAGAAGAACCAACTATG
Found at i:77713295 original size:35 final size:32
Alignment explanation
Indices: 77713255--77713321 Score: 80
Period size: 35 Copynumber: 2.0 Consensus size: 32
77713245 CAATCAGTAA
*
77713255 TATTCATTAACAATCAGCTAATCAGAACAATTATT
1 TATTCAATAACAATCAG-TAA-CA-AACAATTATT
* *
77713290 TATTCAATAACAGTCAGTAACAATCAATTATT
1 TATTCAATAACAATCAGTAACAAACAATTATT
77713322 CAATAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 9 0.31
33 2 0.07
34 3 0.10
35 15 0.52
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.34
Consensus pattern (32 bp):
TATTCAATAACAATCAGTAACAAACAATTATT
Found at i:77713354 original size:18 final size:18
Alignment explanation
Indices: 77713303--77713354 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
77713293 TCAATAACAG
* *
77713303 TCAGTAACAATCAATTAT
1 TCAGTATCAATCAGTTAT
* *
77713321 TCAATAAT-AATTAGTTAT
1 TCAGT-ATCAATCAGTTAT
77713339 TCAGTATCAATCAGTT
1 TCAGTATCAATCAGTT
77713355 GATCGGTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
17 2 0.08
18 23 0.88
19 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (18 bp):
TCAGTATCAATCAGTTAT
Found at i:77713659 original size:51 final size:51
Alignment explanation
Indices: 77713595--77713706 Score: 188
Period size: 51 Copynumber: 2.2 Consensus size: 51
77713585 TCTGAAACAG
*
77713595 TAACAGTAACGGTAACAGTAACAATATTCGGCACACAAAGTGCCAAATCGA
1 TAACAGTAACGGTAACAGTAACAATATCCGGCACACAAAGTGCCAAATCGA
* * *
77713646 TAATAGTAACGGTAACAGTAACAATATCCGGCACACAAAGTGCCGAATCGG
1 TAACAGTAACGGTAACAGTAACAATATCCGGCACACAAAGTGCCAAATCGA
77713697 TAACAGTAAC
1 TAACAGTAAC
77713707 CATATTCTGC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (51 bp):
TAACAGTAACGGTAACAGTAACAATATCCGGCACACAAAGTGCCAAATCGA
Found at i:77715072 original size:18 final size:18
Alignment explanation
Indices: 77715051--77715087 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
77715041 AATAATAACT
77715051 ATAATAAAAATCTATTTA
1 ATAATAAAAATCTATTTA
* *
77715069 ATAATAAATATTTATTTA
1 ATAATAAAAATCTATTTA
77715087 A
1 A
77715088 CATTTGTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATAAAAATCTATTTA
Found at i:77715169 original size:13 final size:12
Alignment explanation
Indices: 77715137--77715170 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
77715127 CTTTTATATA
77715137 TATATAATAACT
1 TATATAATAACT
77715149 TA-ATAATATACT
1 TATATAATA-ACT
77715161 TATATAATAA
1 TATATAATAA
77715171 GTAAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.30
12 8 0.40
13 6 0.30
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (12 bp):
TATATAATAACT
Done.