Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 166 of 172
Found at i:49146354 original size:37 final size:37
Alignment explanation
Indices: 49146309--49146379 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
49146299 TCATTTTTTT
49146309 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
49146346 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
49146380 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:49146608 original size:20 final size:18
Alignment explanation
Indices: 49146580--49146618 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
49146570 ATTCCCCTTC
*
49146580 AACTCATTTTTTATTTAAT
1 AACTCA-TTTTAATTTAAT
49146599 AACTCTATTTTAATTTAAT
1 AACTC-ATTTTAATTTAAT
49146618 A
1 A
49146619 TACTATCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (18 bp):
AACTCATTTTAATTTAAT
Found at i:49146680 original size:18 final size:19
Alignment explanation
Indices: 49146631--49146689 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
49146621 CTATCCTCAT
49146631 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
49146650 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
*
49146668 TTAAATTAAAATAGAGCTA
1 TTAAATTAAAATAGAGTTA
49146687 TTA
1 TTA
49146690 CTTAATTAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:49146926 original size:37 final size:37
Alignment explanation
Indices: 49146884--49146954 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
49146874 AGTATTACTT
49146884 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
49146921 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
49146955 AAAAAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.39
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:49146959 original size:19 final size:19
Alignment explanation
Indices: 49146890--49146958 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
49146880 ACTTAATAGT
49146890 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
49146909 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
49146927 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
49146946 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
49146959 AAATGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:49147065 original size:27 final size:27
Alignment explanation
Indices: 49147034--49147092 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
49147024 ATTTTAGTCA
**
49147034 TTTGGCACCATTAGTGCCGGCAATCAC
1 TTTGGCACCATTAGTGCCACCAATCAC
* *
49147061 TTTGGCACCATTGGTGCCACCAATCTC
1 TTTGGCACCATTAGTGCCACCAATCAC
49147088 TTTGG
1 TTTGG
49147093 TAAATTTTCG
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:0.19, C:0.29, G:0.22, T:0.31
Consensus pattern (27 bp):
TTTGGCACCATTAGTGCCACCAATCAC
Found at i:49149856 original size:13 final size:13
Alignment explanation
Indices: 49149838--49149862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49149828 AAGTTCTTTT
49149838 AAAAAAAAACAAA
1 AAAAAAAAACAAA
49149851 AAAAAAAAACAA
1 AAAAAAAAACAA
49149863 TGATAGGTCA
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:49161330 original size:26 final size:29
Alignment explanation
Indices: 49161277--49161344 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
49161267 TGAACTAATT
*
49161277 TAACACTATAAAAATATTAAAGTCATT-AA
1 TAACATTATAAAAATATTAAAG-CATTAAA
*
49161306 TAACATTATAAAAATA-TAGAG-ATTAAA
1 TAACATTATAAAAATATTAAAGCATTAAA
*
49161333 TTACATT-TAAAA
1 TAACATTATAAAA
49161345 TTAAAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 8 0.23
27 8 0.23
28 4 0.11
29 15 0.43
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.32
Consensus pattern (29 bp):
TAACATTATAAAAATATTAAAGCATTAAA
Found at i:49161359 original size:26 final size:28
Alignment explanation
Indices: 49161341--49161403 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
49161331 AATTACATTT
49161341 AAAATTAAA-ATATAAAAATTAAATCTC
1 AAAATTAAACATATAAAAATTAAATCTC
* * * *
49161368 AAATTTAAACATATTAAAATTAAAACTG
1 AAAATTAAACATATAAAAATTAAATCTC
49161396 AAAATTAA
1 AAAATTAA
49161404 CCATTTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAATTAAACATATAAAAATTAAATCTC
Found at i:49161852 original size:14 final size:14
Alignment explanation
Indices: 49161833--49161866 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
49161823 CATGATATAA
*
49161833 TTAAAAAATAGAAT
1 TTAAAAAATAAAAT
49161847 TTAAAAAATAAAAT
1 TTAAAAAATAAAAT
49161861 TCTAAA
1 T-TAAA
49161867 TGAAGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (14 bp):
TTAAAAAATAAAAT
Found at i:49170742 original size:22 final size:22
Alignment explanation
Indices: 49170684--49170742 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
49170674 AAATGGTATC
49170684 TACAAATCAAATCTCTAAGATT
1 TACAAATCAAATCTCTAAGATT
*
49170706 TACAAAATCATATCTCCTAAGA-T
1 TAC-AAATCAAATCT-CTAAGATT
*
49170729 TACATATCAAATCT
1 TACAAATCAAATCT
49170743 ACGATTGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 12 0.38
23 14 0.44
24 6 0.19
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.32
Consensus pattern (22 bp):
TACAAATCAAATCTCTAAGATT
Found at i:49175885 original size:22 final size:22
Alignment explanation
Indices: 49175827--49175885 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
49175817 GAATGGTATC
49175827 TACAAATCAAATCTCTAAGATT
1 TACAAATCAAATCTCTAAGATT
*
49175849 TACAAAATCATATCTCCTAAGA-T
1 TAC-AAATCAAATCT-CTAAGATT
*
49175872 TACATATCAAATCT
1 TACAAATCAAATCT
49175886 ACGATTGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 12 0.38
23 14 0.44
24 6 0.19
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.32
Consensus pattern (22 bp):
TACAAATCAAATCTCTAAGATT
Found at i:49176108 original size:75 final size:75
Alignment explanation
Indices: 49175985--49176135 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
49175975 CGGGCCAAAT
49175985 GACCTCCTTCCCACTTGATGGATCACACGAATGTGTCATGGTTGCGGGCTCCCATGCGCAACCCA
1 GACCTCCTTCCCACTTGATGGATCACACGAATGTGTCATGGTTGCGGGCTCCCATGCGCAACCCA
49176050 TGACACTAGG
66 TGACACTAGG
49176060 GACCTCCTTCCCACTTGATGGATCACACGAATGTGTCATGGTTGCGGGCTCCCATGCGCAACCCA
1 GACCTCCTTCCCACTTGATGGATCACACGAATGTGTCATGGTTGCGGGCTCCCATGCGCAACCCA
49176125 TGACACTAGG
66 TGACACTAGG
49176135 G
1 G
49176136 CCCGGATGAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.21, C:0.32, G:0.25, T:0.23
Consensus pattern (75 bp):
GACCTCCTTCCCACTTGATGGATCACACGAATGTGTCATGGTTGCGGGCTCCCATGCGCAACCCA
TGACACTAGG
Found at i:49176862 original size:24 final size:24
Alignment explanation
Indices: 49176826--49176876 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
49176816 AACGAAGGAT
*
49176826 GGACCTTTCGGTGATGGAATATCA
1 GGACCTTTAGGTGATGGAATATCA
* *
49176850 GGACTTTTAGGTGGTGGAATATCA
1 GGACCTTTAGGTGATGGAATATCA
49176874 GGA
1 GGA
49176877 GGGATGCTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.29
Consensus pattern (24 bp):
GGACCTTTAGGTGATGGAATATCA
Found at i:49177870 original size:26 final size:26
Alignment explanation
Indices: 49177841--49177896 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
49177831 TATTCTTTAT
*
49177841 ATATGT-AATTTTTATAATTTTTAAAA
1 ATATGTAAATTTTGA-AATTTTTAAAA
*
49177867 ATATGTAAATTTTGAAATTTTTATAA
1 ATATGTAAATTTTGAAATTTTTAAAA
49177893 ATAT
1 ATAT
49177897 TTTGAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (26 bp):
ATATGTAAATTTTGAAATTTTTAAAA
Found at i:49179614 original size:11 final size:11
Alignment explanation
Indices: 49179600--49179624 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
49179590 AAATAATAAC
49179600 AACAATATAGT
1 AACAATATAGT
49179611 AACAATATAGT
1 AACAATATAGT
49179622 AAC
1 AAC
49179625 GAAACAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (11 bp):
AACAATATAGT
Found at i:49179672 original size:23 final size:24
Alignment explanation
Indices: 49179626--49179685 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
49179616 TATAGTAACG
*
49179626 AAACAGCACCAAAATAGTAAAAAA
1 AAACAGCACAAAAATAGTAAAAAA
* *
49179650 AAACAACACAAAAATAGT-GAAAA
1 AAACAGCACAAAAATAGTAAAAAA
*
49179673 CAACAGCA-AAAAA
1 AAACAGCACAAAAA
49179686 GAACAGGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 5 0.16
23 10 0.32
24 16 0.52
ACGTcount: A:0.68, C:0.17, G:0.08, T:0.07
Consensus pattern (24 bp):
AAACAGCACAAAAATAGTAAAAAA
Found at i:49181225 original size:20 final size:20
Alignment explanation
Indices: 49181184--49181225 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
49181174 ATTTTTGGAC
* *
49181184 AAAAATCTATTTTATTATTT
1 AAAAATATATTTTATTAATT
49181204 AAAAATATA-TTTATATAATT
1 AAAAATATATTTTAT-TAATT
49181224 AA
1 AA
49181226 TTTTTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAAATATATTTTATTAATT
Found at i:49187092 original size:216 final size:208
Alignment explanation
Indices: 49186699--49187095 Score: 462
Period size: 216 Copynumber: 1.9 Consensus size: 208
49186689 GCCTTGAGAT
* * *
49186699 TTTAGGGGGGTTTGGATAGGAGGTTGTCATTGGTGAAGTTCAATATGAATTTAATGGTTTTTGTA
1 TTTAGGGGGATTTGGATAGGAGGTTGTCATTGATGAAGTTCAATATGAATTTAATGCTTTTTGTA
** * * * *
49186764 TTGGAGTTCCAAAAATGAATTATCAACAGGTGATCAGAGAAAGTGGCAGTGGACATCTCCCTAGG
66 TTGGAGTTCCAAAAACAAATTACCAACAGGTGATCAAAGAAAGTGGCAGCGGACATCTCCCCAGG
* ** **
49186829 CATTTGGACTGAATTTGAATCTAGGAGTCATCACTATTGGGAGGGCTTTACCTGAATACCACTCT
131 CATTTAGACTGAATTCAAATCTAGGAGTCATCACTATTGAAAGGGCTTTACCTGAATACCACTCT
49186894 GGCCTGAACAAGA
196 GGCCTGAACAAGA
* * *
49186907 TTTAGGGGGATTTGGATATGAGGGGTTGTCATTGATGAAGTTTATATTTGAATTTAATGCTTTTT
1 TTTAGGGGGATTTGGATA-G-GAGGTTGTCATTGATGAAGTTCA-ATATGAATTTAATGCTTTTT
*
49186972 GTATTGGTGAAGTT-CAAAAGACAAATTACCAACAGGTGATCAAA-AGAAGTGGC-GCGGTACTT
63 GTATT-G-G-AGTTCCAAAA-ACAAATTACCAACAGGTGATCAAAGA-AAGTGGCAGCGG-ACAT
* *
49187034 CTTCCCCCGGGCATTTAGA-TTAAGTTCAAATCTTA-GAGTCATCACTATTGAAAGGGCTTTAC
122 C-T-CCCCAGGCATTTAGACTGAA-TTCAAATC-TAGGAGTCATCACTATTGAAAGGGCTTTAC
49187096 TAAATACTAC
Statistics
Matches: 156, Mismatches: 20, Indels: 18
0.80 0.10 0.09
Matches are distributed among these distances:
208 17 0.11
209 1 0.01
210 20 0.13
211 23 0.15
212 1 0.01
213 10 0.06
214 35 0.22
215 4 0.03
216 43 0.28
217 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (208 bp):
TTTAGGGGGATTTGGATAGGAGGTTGTCATTGATGAAGTTCAATATGAATTTAATGCTTTTTGTA
TTGGAGTTCCAAAAACAAATTACCAACAGGTGATCAAAGAAAGTGGCAGCGGACATCTCCCCAGG
CATTTAGACTGAATTCAAATCTAGGAGTCATCACTATTGAAAGGGCTTTACCTGAATACCACTCT
GGCCTGAACAAGA
Found at i:49189474 original size:21 final size:20
Alignment explanation
Indices: 49189450--49189492 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
49189440 ATCATTTCTT
* *
49189450 ATTTAATTATTTCATATTAAA
1 ATTTAAATATTT-AAATTAAA
49189471 ATTTAAATATTTAAATTAAA
1 ATTTAAATATTTAAATTAAA
49189491 AT
1 AT
49189493 AAACTAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTAAATATTTAAATTAAA
Found at i:49200366 original size:26 final size:25
Alignment explanation
Indices: 49200297--49200367 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 25
49200287 TAAATTTATA
*
49200297 AAAATTATTTAAATATATAAAAGCCT
1 AAAA-TATATAAATATATAAAAGCCT
* *
49200323 ATAATATATAAAAAATATAAAA-CCTT
1 AAAATATAT-AAATATATAAAAGCC-T
*
49200349 AGAAATTTATAAATATATA
1 A-AAATATATAAATATATA
49200368 TTATAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
25 6 0.17
26 24 0.67
27 6 0.17
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.34
Consensus pattern (25 bp):
AAAATATATAAATATATAAAAGCCT
Found at i:49201813 original size:31 final size:31
Alignment explanation
Indices: 49201773--49201874 Score: 78
Period size: 29 Copynumber: 3.5 Consensus size: 31
49201763 TTTTTCTCTC
* *
49201773 TTTTATAATAAATTTTAACAAATG-TTTTTATG
1 TTTT-TAATAAATTTTAA-AAATGATTTCTATA
49201805 TTTTTAAT--ATTTTAAAAATGATTTCTATA
1 TTTTTAATAAATTTTAAAAATGATTTCTATA
* *
49201834 TTGTTTTATAAA-TTT-AAAAT--TTT-TCTA
1 TT-TTTAATAAATTTTAAAAATGATTTCTATA
49201861 TTTTT-ATAAATTTT
1 TTTTTAATAAATTTT
49201875 CTATTTTATA
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
25 5 0.08
26 6 0.10
27 5 0.08
28 8 0.13
29 15 0.25
30 10 0.16
31 7 0.11
32 5 0.08
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (31 bp):
TTTTTAATAAATTTTAAAAATGATTTCTATA
Found at i:49201888 original size:19 final size:17
Alignment explanation
Indices: 49201854--49201904 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
49201844 AATTTAAAAT
49201854 TTTTCTATTTTTATAAA
1 TTTTCTATTTTTATAAA
49201871 TTTTCTATTTTATAATAAA
1 TTTTCTATTTT-T-ATAAA
* *
49201890 TTTTGTTTTTTTATA
1 TTTTCTATTTTTATA
49201905 TCTCTAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 14 0.47
18 2 0.07
19 14 0.47
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTCTATTTTTATAAA
Found at i:49201949 original size:29 final size:29
Alignment explanation
Indices: 49201917--49202002 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
49201907 TCTAACAAAT
49201917 TTTTAATAATTTTTATAATTTTTTATAAA
1 TTTTAATAATTTTTATAATTTTTTATAAA
*
49201946 TTTTAACAATTTTTATAATTTTTTAT--A
1 TTTTAATAATTTTTATAATTTTTTATAAA
* * * *
49201973 TTTCAAATATTTTTTTTAAATTTTTATAAA
1 TTT-TAATAATTTTTATAATTTTTTATAAA
49202003 AAAAAAGTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
27 4 0.08
28 18 0.38
29 25 0.52
30 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTTAATAATTTTTATAATTTTTTATAAA
Found at i:49201975 original size:9 final size:10
Alignment explanation
Indices: 49201914--49201972 Score: 68
Period size: 10 Copynumber: 6.1 Consensus size: 10
49201904 ATCTCTAACA
*
49201914 AATTTTTAAT
1 AATTTTTTAT
49201924 AA-TTTTTAT
1 AATTTTTTAT
49201933 AATTTTTTAT
1 AATTTTTTAT
* * *
49201943 AAATTTTAAC
1 AATTTTTTAT
49201953 AA-TTTTTAT
1 AATTTTTTAT
49201962 AATTTTTTAT
1 AATTTTTTAT
49201972 A
1 A
49201973 TTTCAAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
9 15 0.37
10 26 0.63
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:49202143 original size:36 final size:36
Alignment explanation
Indices: 49202102--49202171 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
49202092 TGAAGCTCAT
*
49202102 AATAACAAATAAAATACGGCTTGGACGGCTTGGCAA
1 AATAACAAATAAAATACGGCTTGGACAGCTTGGCAA
49202138 AATAACAAATAAAATACGGCTTGGACAGCTTGGC
1 AATAACAAATAAAATACGGCTTGGACAGCTTGGC
49202172 TCGGAAAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.20
Consensus pattern (36 bp):
AATAACAAATAAAATACGGCTTGGACAGCTTGGCAA
Found at i:49205068 original size:163 final size:163
Alignment explanation
Indices: 49204798--49205124 Score: 654
Period size: 163 Copynumber: 2.0 Consensus size: 163
49204788 AAGATTGCCA
49204798 ATATGCTGGAGTAAACATCAAAATGATCACTGGTGACAATGTTTTCACTGCAATAGCCATAGCTA
1 ATATGCTGGAGTAAACATCAAAATGATCACTGGTGACAATGTTTTCACTGCAATAGCCATAGCTA
49204863 CCGAATGTGGGATTCTCAAACCAGGTCAAGACTTGTCTAGTGGTGCAGTGGTAGAAGGTGAGGAA
66 CCGAATGTGGGATTCTCAAACCAGGTCAAGACTTGTCTAGTGGTGCAGTGGTAGAAGGTGAGGAA
49204928 TTCAGAAACTATACATCATAAGAAAGGATGGAG
131 TTCAGAAACTATACATCATAAGAAAGGATGGAG
49204961 ATATGCTGGAGTAAACATCAAAATGATCACTGGTGACAATGTTTTCACTGCAATAGCCATAGCTA
1 ATATGCTGGAGTAAACATCAAAATGATCACTGGTGACAATGTTTTCACTGCAATAGCCATAGCTA
49205026 CCGAATGTGGGATTCTCAAACCAGGTCAAGACTTGTCTAGTGGTGCAGTGGTAGAAGGTGAGGAA
66 CCGAATGTGGGATTCTCAAACCAGGTCAAGACTTGTCTAGTGGTGCAGTGGTAGAAGGTGAGGAA
49205091 TTCAGAAACTATACATCATAAGAAAGGATGGAG
131 TTCAGAAACTATACATCATAAGAAAGGATGGAG
49205124 A
1 A
49205125 AAGTTGAGAA
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 164 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (163 bp):
ATATGCTGGAGTAAACATCAAAATGATCACTGGTGACAATGTTTTCACTGCAATAGCCATAGCTA
CCGAATGTGGGATTCTCAAACCAGGTCAAGACTTGTCTAGTGGTGCAGTGGTAGAAGGTGAGGAA
TTCAGAAACTATACATCATAAGAAAGGATGGAG
Found at i:49205472 original size:59 final size:59
Alignment explanation
Indices: 49205388--49205505 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
49205378 TATTTATTCC
49205388 AACATCCAAAAATTCATTCAGTTTCTGCTCACCGCAAATGTGGCTACACTTTGTATCAA
1 AACATCCAAAAATTCATTCAGTTTCTGCTCACCGCAAATGTGGCTACACTTTGTATCAA
49205447 AACATCCAAAAATTCATTCAGTTTCTGCTCACCGCAAATGTGGCTACACTTTGTATCAA
1 AACATCCAAAAATTCATTCAGTTTCTGCTCACCGCAAATGTGGCTACACTTTGTATCAA
49205506 CTTTATAGCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (59 bp):
AACATCCAAAAATTCATTCAGTTTCTGCTCACCGCAAATGTGGCTACACTTTGTATCAA
Found at i:49205874 original size:27 final size:27
Alignment explanation
Indices: 49205836--49205889 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
49205826 AATTTAACTC
49205836 AAGAAAGCTCGAAAAGAAGAACGTATT
1 AAGAAAGCTCGAAAAGAAGAACGTATT
49205863 AAGAAAGCTCGAAAAGAAGAACGTATT
1 AAGAAAGCTCGAAAAGAAGAACGTATT
49205890 TGATGATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.11, G:0.22, T:0.15
Consensus pattern (27 bp):
AAGAAAGCTCGAAAAGAAGAACGTATT
Found at i:49206917 original size:7 final size:7
Alignment explanation
Indices: 49206905--49206929 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49206895 AAAATATAAT
49206905 TAATTTA
1 TAATTTA
49206912 TAATTTA
1 TAATTTA
49206919 TAATTTA
1 TAATTTA
49206926 TAAT
1 TAAT
49206930 AAAACTAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TAATTTA
Found at i:49209384 original size:28 final size:28
Alignment explanation
Indices: 49209325--49209385 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
49209315 AAAAGCCCAT
*
49209325 TTTTTTAATAATTACGGAAATGGGCCGG
1 TTTTTTAATAATTACGGAAATGGGCCGA
*
49209353 TTTTTTAATTATTTACCGG-AATGGGCC-A
1 TTTTTTAA-TAATTA-CGGAAATGGGCCGA
49209381 TTTTT
1 TTTTT
49209386 CGTGAAATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 13 0.45
29 13 0.45
30 3 0.10
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (28 bp):
TTTTTTAATAATTACGGAAATGGGCCGA
Found at i:49209385 original size:29 final size:28
Alignment explanation
Indices: 49209321--49209385 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
49209311 TAATAAAAGC
49209321 CCATTTTTTTAATAATTACGGAAATGGG
1 CCATTTTTTTAATAATTACGGAAATGGG
** *
49209349 CCGGTTTTTTAATTATTTACCGG-AATGGG
1 CCATTTTTTTAA-TAATTA-CGGAAATGGG
49209378 CCATTTTT
1 CCATTTTT
49209386 CGTGAAATCG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 10 0.33
29 17 0.57
30 3 0.10
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (28 bp):
CCATTTTTTTAATAATTACGGAAATGGG
Found at i:49209638 original size:23 final size:21
Alignment explanation
Indices: 49209608--49209685 Score: 111
Period size: 23 Copynumber: 3.6 Consensus size: 21
49209598 TTTCACAATC
49209608 AAATTCTCTCAATTTCTTCAA
1 AAATTCTCTCAATTTCTTCAA
*
49209629 AAATTCTCTCAATTCCCTTCAA
1 AAATTCTCTCAATT-TCTTCAA
*
49209651 AAATTCTCTCAATTTTCCTTCCA
1 AAATTCTCTCAA-TTT-CTTCAA
49209674 AAATTCTCTCAA
1 AAATTCTCTCAA
49209686 ACTCTCAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
21 14 0.27
22 18 0.35
23 19 0.37
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTCTCTCAATTTCTTCAA
Found at i:49209651 original size:22 final size:21
Alignment explanation
Indices: 49209608--49209685 Score: 111
Period size: 22 Copynumber: 3.6 Consensus size: 21
49209598 TTTCACAATC
*
49209608 AAATTCTCTCAATTTCTTCAA
1 AAATTCTCTCAATTCCTTCAA
49209629 AAATTCTCTCAATTCCCTTCAA
1 AAATTCTCTCAATT-CCTTCAA
*
49209651 AAATTCTCTCAATTTTCCTTCCA
1 AAATTCTCTCAA--TTCCTTCAA
49209674 AAATTCTCTCAA
1 AAATTCTCTCAA
49209686 ACTCTCAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
21 14 0.27
22 18 0.35
23 18 0.35
24 2 0.04
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTCTCTCAATTCCTTCAA
Found at i:49209692 original size:53 final size:51
Alignment explanation
Indices: 49209634--49209737 Score: 138
Period size: 53 Copynumber: 2.0 Consensus size: 51
49209624 TTCAAAAATT
* * *
49209634 CTCTC-AATTCCCTTCAAAAATTCTCTCAATTTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATT-CCTTCAAAAATCCTCTCAA-TTTCCTTCAAAAAATCTC-CAAA
*
49209687 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
49209738 TCCATATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
51 4 0.09
52 16 0.35
53 22 0.48
54 4 0.09
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:49209701 original size:30 final size:31
Alignment explanation
Indices: 49209656--49209715 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
49209646 TTCAAAAATT
* *
49209656 CTCTCAATTTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATATTCCTTCCAAAATCCTCTCAAA
49209687 CTCTCAA-ATTCCTTCCAAAATCCTCTCAA
1 CTCTCAATATTCCTTCCAAAATCCTCTCAA
49209716 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (31 bp):
CTCTCAATATTCCTTCCAAAATCCTCTCAAA
Found at i:49209726 original size:21 final size:22
Alignment explanation
Indices: 49209687--49209728 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
49209677 TTCTCTCAAA
49209687 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
49209709 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
49209729 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:49209954 original size:14 final size:15
Alignment explanation
Indices: 49209925--49209958 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
49209915 AAATTTTAAA
49209925 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
49209940 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
49209954 TTTTA
1 TTTTA
49209959 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:49213210 original size:125 final size:123
Alignment explanation
Indices: 49212989--49213254 Score: 354
Period size: 125 Copynumber: 2.1 Consensus size: 123
49212979 CCACGAGGGC
49212989 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAATTATTTCCAACATGACCAACTGTAGCGA
1 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAATTATTTCCAACATGACCAACTGTAGCGA
* * * * **
49213054 AATCGCGTCCACGTGGGCGCGATTTAACAATTTCTGCCCAATATAGCATCCTTGTATCA
66 AATCGCGTCCACGAGGCCACGATTTAACAATTTCTGCCCAA-ATAGCATCCTAGTAGAA
* * * **
49213113 GCGATTTTATACTATTTGCTTAGAAAACGTCAAAAAAAATTATTTCTTACATGACC-ACTGTAGC
1 GCGATTTGACACTATTTGCTCAG-AAACGTC-AAAAAAATTATTTCCAACATGACCAACTGTAGC
* * *
49213177 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
64 GAAATCGCGTCCACGAGGCCACGATTTAACAATTTCTGCCCAAATAGCATCCTAGTAGAA
**
49213237 GCGATTTCCCACTATTTG
1 GCGATTTGACACTATTTG
49213255 ACCGGATACG
Statistics
Matches: 123, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
124 49 0.40
125 52 0.42
126 22 0.18
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (123 bp):
GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAATTATTTCCAACATGACCAACTGTAGCGA
AATCGCGTCCACGAGGCCACGATTTAACAATTTCTGCCCAAATAGCATCCTAGTAGAA
Found at i:49214666 original size:11 final size:11
Alignment explanation
Indices: 49214627--49214668 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
49214617 ATTTTAAAAA
49214627 TAAAAAA-ATT
1 TAAAAAATATT
*
49214637 AAAAAAAGTATT
1 TAAAAAA-TATT
*
49214649 TTAAAAATATT
1 TAAAAAATATT
49214660 TAAAAAATA
1 TAAAAAATA
49214669 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 6 0.23
11 12 0.46
12 8 0.31
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
TAAAAAATATT
Found at i:49215294 original size:31 final size:31
Alignment explanation
Indices: 49215248--49215322 Score: 143
Period size: 31 Copynumber: 2.5 Consensus size: 31
49215238 TAACAAAATT
49215248 AACAATAA-AACAAGAGATATATAATATCCA
1 AACAATAACAACAAGAGATATATAATATCCA
49215278 AACAATAACAACAAGAGATATATAATATCCA
1 AACAATAACAACAAGAGATATATAATATCCA
49215309 AACAATAACAACAA
1 AACAATAACAACAA
49215323 AATAGTAGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 8 0.18
31 36 0.82
ACGTcount: A:0.61, C:0.16, G:0.05, T:0.17
Consensus pattern (31 bp):
AACAATAACAACAAGAGATATATAATATCCA
Found at i:49220147 original size:22 final size:21
Alignment explanation
Indices: 49220114--49220208 Score: 65
Period size: 22 Copynumber: 4.6 Consensus size: 21
49220104 TTATTTTTTA
49220114 TTTTTAAA-TTTTAAAATACTT
1 TTTTTAAATTTTTAAAATA-TT
*
49220135 TTTTTAAATTTTT----TAAT
1 TTTTTAAATTTTTAAAATATT
**
49220152 TTTAAAATATTTTTAAAATATT
1 TTTTTAA-ATTTTTAAAATATT
** *
49220174 TTTAAAATATTTTTAAAATACT
1 TTTTTAA-ATTTTTAAAATATT
*
49220196 TTTTTAATTTTTT
1 TTTTTAAATTTTT
49220209 TAATTTTAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
17 6 0.10
18 8 0.13
21 13 0.22
22 33 0.55
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTAAATTTTTAAAATATT
Found at i:49220165 original size:11 final size:11
Alignment explanation
Indices: 49220151--49220230 Score: 91
Period size: 11 Copynumber: 7.7 Consensus size: 11
49220141 AATTTTTTAA
49220151 TTTTAAAATAT
1 TTTTAAAATAT
49220162 TTTTAAAATAT
1 TTTTAAAATAT
49220173 TTTTAAAATAT
1 TTTTAAAATAT
49220184 TTTTAAAATACT
1 TTTTAAAATA-T
*
49220196 TTTT-TAAT-T
1 TTTTAAAATAT
*
49220205 TTTT----TAA
1 TTTTAAAATAT
49220212 TTTTAAAATAT
1 TTTTAAAATAT
49220223 TTTTAAAA
1 TTTTAAAA
49220231 CAAATTTTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
6 1 0.02
7 4 0.07
9 5 0.08
11 45 0.75
12 5 0.08
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:49220260 original size:61 final size:59
Alignment explanation
Indices: 49220114--49220261 Score: 181
Period size: 61 Copynumber: 2.4 Consensus size: 59
49220104 TTATTTTTTA
* ** *
49220114 TTTTTAAATTTTAAAATACTTTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATAT
1 TTTTTAATTTTTAAAATAAATTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAAAAT
* * *
49220173 TTTTAAAATATTTTTAAAAT-ACTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAACAAAT
1 TTTT--TA-ATTTTTAAAATAAATTTTTTAAATTTTTTAATTTTAAAATATTTTT-AAA-AAAT
49220236 TTTTTAATTTTTAAAATAAATTTTTT
1 TTTTTAATTTTTAAAATAAATTTTTT
49220262 GTATTTATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
59 4 0.05
60 11 0.15
61 40 0.53
62 13 0.17
63 7 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (59 bp):
TTTTTAATTTTTAAAATAAATTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAAAAT
Found at i:49220278 original size:22 final size:21
Alignment explanation
Indices: 49220221--49220261 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
49220211 ATTTTAAAAT
*
49220221 ATTTTTAAAACAAATTTTTTA
1 ATTTTTAAAATAAATTTTTTA
49220242 ATTTTTAAAATAAATTTTTT
1 ATTTTTAAAATAAATTTTTT
49220262 GTATTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:49238071 original size:23 final size:23
Alignment explanation
Indices: 49238045--49238090 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
49238035 CTTGGTATTT
* *
49238045 CAAGTGGCAGCGATCAGACAACC
1 CAAGTGACAGCAATCAGACAACC
49238068 CAAGTGACAGCAATCAGACAACC
1 CAAGTGACAGCAATCAGACAACC
49238091 GGTTCGAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.30, G:0.22, T:0.09
Consensus pattern (23 bp):
CAAGTGACAGCAATCAGACAACC
Found at i:49240260 original size:100 final size:101
Alignment explanation
Indices: 49240079--49240274 Score: 313
Period size: 100 Copynumber: 2.0 Consensus size: 101
49240069 GGTAAAAACA
* ** * *
49240079 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGGTGTCCATACCATGT
1 TGCCAAAGCCATGTCCCAGACATAGTCTTACATGGGATCCTCTCATCTCGGTGCCCATACCATGT
*
49240144 CCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
49240180 TGCCAACGCCATGTCCCAGACATAGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATGT
1 TGCCAAAGCCATGTCCCAGACATAGTCTTACATGGGATCCTCTCATCTCGGTGCCCATACCATGT
49240244 CCCAGACATGGTCTTACAGGGGACCTCTCAT
66 CCCAGACATGGTCTTACAGGGGACCTCTCAT
49240275 GATCTCAAGG
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
100 52 0.60
101 35 0.40
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (101 bp):
TGCCAAAGCCATGTCCCAGACATAGTCTTACATGGGATCCTCTCATCTCGGTGCCCATACCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:49240309 original size:56 final size:50
Alignment explanation
Indices: 49240079--49240317 Score: 273
Period size: 50 Copynumber: 4.6 Consensus size: 50
49240069 GGTAAAAACA
* * ** *
49240079 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
49240130 TGTCC-ATACCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
49240180 TGCCAACGCCATGTCCCAGACATAGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
49240230 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATCTC--GG
* * *
49240285 ATGCCAATGTCATGTCCCAAACATGGTTTTACA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACA
49240318 TGAGATCTCT
Statistics
Matches: 160, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
49 2 0.01
50 91 0.57
51 30 0.19
52 2 0.01
53 5 0.03
55 2 0.01
56 28 0.17
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:49247459 original size:16 final size:16
Alignment explanation
Indices: 49247438--49247489 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
49247428 TTTGGTTCGC
*
49247438 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
49247454 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
49247470 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
49247486 TGTA
1 TGTA
49247490 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:49247745 original size:16 final size:16
Alignment explanation
Indices: 49247705--49247746 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
49247695 TTAATCATAT
49247705 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATTA
*
49247721 TT-AAATATATTTTTA
1 TTAAAATATATTATTA
49247736 TTAAAATATAT
1 TTAAAATATAT
49247747 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAATATATTATTA
Found at i:49247866 original size:18 final size:17
Alignment explanation
Indices: 49247845--49247879 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
49247835 TTATTATTAA
*
49247845 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
49247863 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
49247880 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:49247921 original size:120 final size:120
Alignment explanation
Indices: 49247708--49247970 Score: 517
Period size: 120 Copynumber: 2.2 Consensus size: 120
49247698 ATCATATTTA
*
49247708 AACATAATTATTATTAAATATATTTTTATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
49247773 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
49247828 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
49247893 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
49247948 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
49247971 AACTTGAAAA
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 142 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:49248108 original size:47 final size:46
Alignment explanation
Indices: 49248055--49248193 Score: 144
Period size: 47 Copynumber: 3.0 Consensus size: 46
49248045 TTAATAATAA
*
49248055 TATATAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATT
1 TATATAATTTCATAAAATTCTTAATAATAAATTTTCTTATAT-AATT
** * * *
49248102 TATATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-ATAATGA
1 TATATAATTTCATAAAATTCTTAATAATAAAT-T-TTCTTATATAAT-T
*
49248146 TATATAATTTCATAAAATTCTTAATAATAAATATTCTTATATAATT
1 TATATAATTTCATAAAATTCTTAATAATAAATTTTCTTATATAATT
49248192 TA
1 TA
49248194 CTAAAATCAT
Statistics
Matches: 72, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
43 3 0.04
44 25 0.35
45 7 0.10
46 8 0.11
47 29 0.40
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (46 bp):
TATATAATTTCATAAAATTCTTAATAATAAATTTTCTTATATAATT
Found at i:49248150 original size:44 final size:43
Alignment explanation
Indices: 49248033--49248155 Score: 106
Period size: 44 Copynumber: 2.7 Consensus size: 43
49248023 TTATATTTTA
** *
49248033 ATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTGAT
1 ATTAAATATAATTTAATAAT-ATATATAA-TT--TAAAATAATTAAT
* * *
49248080 AATAAAT-T-TTCTTATATGAATTTATATAATTTAAAATAATTAAT
1 ATTAAATATAAT-TTA-AT-AATATATATAATTTAAAATAATTAAT
49248124 ATTAAATATAATTTAATAATGATATATAATTT
1 ATTAAATATAATTTAATAAT-ATATATAATTT
49248156 CATAAAATTC
Statistics
Matches: 61, Mismatches: 9, Indels: 15
0.72 0.11 0.18
Matches are distributed among these distances:
43 3 0.05
44 28 0.46
45 5 0.08
46 7 0.11
47 15 0.25
48 3 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (43 bp):
ATTAAATATAATTTAATAATATATATAATTTAAAATAATTAAT
Found at i:49248183 original size:16 final size:16
Alignment explanation
Indices: 49248157--49248190 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
49248147 ATATAATTTC
49248157 ATAAAATTCTTA-ATA
1 ATAAAATTCTTATATA
49248172 ATAAATATTCTTATATA
1 ATAAA-ATTCTTATATA
49248189 AT
1 AT
49248191 TTACTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAAATTCTTATATA
Found at i:49248537 original size:66 final size:66
Alignment explanation
Indices: 49248431--49248561 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
49248421 CGCAAATGTG
* *
49248431 ATTTGAGTTCAAATTAGATTCATAGTAAGCTCAAATTTTTATTAATGCCAATGCCAACACTACCA
1 ATTTGAGTTCAAATTAGACTCATAGTAAGCTCAAACTTTTATTAATGCCAATGCCAACACTACCA
49248496 C
66 C
* *
49248497 ATTTGGGTTCAAATTATACTCATAGTAAGCTCAAACTTTTATTAATGCCAATGCCAACACTACCA
1 ATTTGAGTTCAAATTAGACTCATAGTAAGCTCAAACTTTTATTAATGCCAATGCCAACACTACCA
49248562 AAACCTTTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.33
Consensus pattern (66 bp):
ATTTGAGTTCAAATTAGACTCATAGTAAGCTCAAACTTTTATTAATGCCAATGCCAACACTACCA
C
Found at i:49255200 original size:15 final size:15
Alignment explanation
Indices: 49255180--49255234 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 15
49255170 GGGGAAATTC
49255180 GAGTTAAGTACTAAT
1 GAGTTAAGTACTAAT
49255195 GAGTTAAGTACGACTCAAT
1 GAGTTAAGT---ACT-AAT
*
49255214 GAGTTAAATACTAAT
1 GAGTTAAGTACTAAT
49255229 GAGTTA
1 GAGTTA
49255235 CCCATTAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 18 0.51
16 3 0.09
18 3 0.09
19 11 0.31
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (15 bp):
GAGTTAAGTACTAAT
Found at i:49265971 original size:42 final size:41
Alignment explanation
Indices: 49265924--49266009 Score: 136
Period size: 42 Copynumber: 2.1 Consensus size: 41
49265914 TTTAAAAATT
*
49265924 AAAAAAGTATTTTTAAAATATTTTAAAATTAAAAAATAATAA
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAA-AATAA
* *
49265966 AAAAAAGTATTTTAAAAATATTTTACAATTAAAAAAATTAA
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATAA
49266007 AAA
1 AAA
49266010 TAAATATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 7 0.17
42 34 0.83
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (41 bp):
AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATAA
Found at i:49266448 original size:12 final size:12
Alignment explanation
Indices: 49266431--49266461 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
49266421 CTTTATTTGT
*
49266431 TATTTATATATA
1 TATTTATAAATA
49266443 TATTTATAAATA
1 TATTTATAAATA
49266455 TATTTAT
1 TATTTAT
49266462 TAGATAATTT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTTATAAATA
Found at i:49266988 original size:31 final size:30
Alignment explanation
Indices: 49266948--49267041 Score: 77
Period size: 31 Copynumber: 3.1 Consensus size: 30
49266938 GAAAATTGAA
* *
49266948 TTATAATTTTTTAAAAGATTAAAATATAATT
1 TTATTATTTTTAAAAAGA-TAAAATATAATT
*
49266979 TTATTATTTTTAAAAACCACT-AAATA-AATT
1 TTATTATTTTTAAAAA-GA-TAAAATATAATT
* * *
49267009 GTCTTCATTTTTGAAAAG-TAAAATATAATT
1 TTATT-ATTTTTAAAAAGATAAAATATAATT
49267039 TTA
1 TTA
49267042 GTATACTAGA
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
28 1 0.02
29 5 0.10
30 12 0.24
31 29 0.59
32 2 0.04
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (30 bp):
TTATTATTTTTAAAAAGATAAAATATAATT
Found at i:49280385 original size:24 final size:25
Alignment explanation
Indices: 49280332--49280385 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
49280322 ATTGTAAAAT
* *
49280332 ATAATTTTATTTTACTTATTTTTTT
1 ATAATATTATTTTACTTATTTTTTA
49280357 A-AATATTATTTTA-TT-TTTATTTA
1 ATAATATTATTTTACTTATTT-TTTA
49280380 ATAATA
1 ATAATA
49280386 ATTCTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 3 0.12
23 6 0.24
24 15 0.60
25 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
ATAATATTATTTTACTTATTTTTTA
Found at i:49284721 original size:6 final size:6
Alignment explanation
Indices: 49284710--49284738 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
49284700 AAATATCGTA
49284710 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
49284739 ATATATATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:49289914 original size:19 final size:19
Alignment explanation
Indices: 49289890--49289958 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
49289880 AAAATATAAA
49289890 ATTTAGAATTTTTATAAA-T
1 ATTTAGAATTTTTA-AAATT
49289909 ATTTAGAA-TTTTAAAATT
1 ATTTAGAATTTTTAAAATT
49289927 ATTTTA-AATTTTTGAAAATT
1 A-TTTAGAATTTTT-AAAATT
*
49289947 ATTTTGAATTTT
1 ATTTAGAATTTT
49289959 GGTTGAGAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
17 3 0.07
18 9 0.20
19 19 0.43
20 13 0.30
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
ATTTAGAATTTTTAAAATT
Found at i:49289946 original size:20 final size:19
Alignment explanation
Indices: 49289891--49289958 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 19
49289881 AAATATAAAA
49289891 TTTAGAATTTTTATAAA-TA-
1 TTTA-AATTTTTA-AAATTAT
49289910 TTTAGAA-TTTTAAAATTAT
1 TTTA-AATTTTTAAAATTAT
49289929 TTTAAATTTTTGAAAATTAT
1 TTTAAATTTTT-AAAATTAT
*
49289949 TTTGAATTTT
1 TTTAAATTTT
49289959 GGTTGAGAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
17 3 0.07
18 9 0.20
19 15 0.34
20 17 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTAAATTTTTAAAATTAT
Found at i:49291531 original size:40 final size:39
Alignment explanation
Indices: 49291458--49291575 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 39
49291448 AATGTTCATG
49291458 CCACGTCAGCAAATCGCGTCCTAGA-G-GGA-GCGATTTCCTT
1 CCACGTCAGCAAATCGCG--CT-GACGTGGACGCGATTTCC-T
49291498 CCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCCT
1 CCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCCT
* * * *
49291537 GCGCGT-ACCCTGACATCGCGCTGACGTGGACGCGATTTC
1 CCACGTCA-GC--AAATCGCGCTGACGTGGACGCGATTTC
49291576 GCGGAAAATG
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
37 2 0.03
38 4 0.06
39 9 0.13
40 27 0.40
41 26 0.38
ACGTcount: A:0.19, C:0.32, G:0.27, T:0.21
Consensus pattern (39 bp):
CCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCCT
Found at i:49291640 original size:29 final size:28
Alignment explanation
Indices: 49291580--49291639 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
49291570 GATTTCGCGG
*
49291580 AAAATGGCCCATTCCGGTCAATAATTAA
1 AAAATGGCCCATTCCGGTAAATAATTAA
* *
49291608 AAAATCGGCCCATTTCGGTAAAT-TTTAA
1 AAAAT-GGCCCATTCCGGTAAATAATTAA
49291636 AAAA
1 AAAA
49291640 AACGGGCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (28 bp):
AAAATGGCCCATTCCGGTAAATAATTAA
Found at i:49294507 original size:34 final size:35
Alignment explanation
Indices: 49294463--49294529 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
49294453 CAGTAAAATA
*
49294463 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
49294497 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
49294530 TTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:49299135 original size:21 final size:21
Alignment explanation
Indices: 49299106--49299212 Score: 106
Period size: 21 Copynumber: 5.1 Consensus size: 21
49299096 AGTTAACTCA
49299106 TATGAGTTTCAGTTTAACCCT
1 TATGAGTTTCAGTTTAACCCT
* * * *
49299127 TCTGGGTTTCAGTTTAGCTCT
1 TATGAGTTTCAGTTTAACCCT
* *
49299148 TTTGAGCTTCAGTTTAACCCT
1 TATGAGTTTCAGTTTAACCCT
* * * *
49299169 TATGGGTTTCTGTTTAGCTCT
1 TATGAGTTTCAGTTTAACCCT
* *
49299190 TATGAGCTTCCGTTTAACCCT
1 TATGAGTTTCAGTTTAACCCT
49299211 TA
1 TA
49299213 CGGATTTCCG
Statistics
Matches: 66, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.45
Consensus pattern (21 bp):
TATGAGTTTCAGTTTAACCCT
Found at i:49299160 original size:42 final size:42
Alignment explanation
Indices: 49299106--49299241 Score: 175
Period size: 42 Copynumber: 3.2 Consensus size: 42
49299096 AGTTAACTCA
*
49299106 TATGAGTTTCAGTTTAACCCTTCTGGGTTTCAGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTCTGGGTTTCAGTTTAGCTCT
* * *
49299148 TTTGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTCTGGGTTTCAGTTTAGCTCT
* * * *
49299190 TATGAGCTTCCGTTTAACCCTTAC-GGATTTCCGTTTAGCACT
1 TATGAGCTTCAGTTTAACCCTT-CTGGGTTTCAGTTTAGCTCT
*
49299232 TATGTGCTTC
1 TATGAGCTTC
49299242 TGTGCAGCCT
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTCTGGGTTTCAGTTTAGCTCT
Found at i:49302956 original size:31 final size:31
Alignment explanation
Indices: 49302918--49302981 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
49302908 ATTTTGATGC
49302918 TAGGGTAAAAGTACCACTAAGGCTCTTATAT
1 TAGGGTAAAAGTACCACTAAGGCTCTTATAT
49302949 TAGGGTAAAAGTACCACTAAGGCTCTTATAT
1 TAGGGTAAAAGTACCACTAAGGCTCTTATAT
49302980 TA
1 TA
49302982 AGAGTGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (31 bp):
TAGGGTAAAAGTACCACTAAGGCTCTTATAT
Found at i:49314166 original size:15 final size:15
Alignment explanation
Indices: 49314143--49314207 Score: 67
Period size: 15 Copynumber: 4.1 Consensus size: 15
49314133 GAAATGTAGA
49314143 AACAATAATAATAAT
1 AACAATAATAATAAT
*
49314158 AACATTAATAATAAT
1 AACAATAATAATAAT
* * *
49314173 AGCAATAAAAACAAT
1 AACAATAATAATAAT
49314188 GAACTAAATAATAATAAT
1 -AAC--AATAATAATAAT
49314206 AA
1 AA
49314208 AGGGACTAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 25 0.64
16 2 0.05
17 2 0.05
18 10 0.26
ACGTcount: A:0.65, C:0.08, G:0.03, T:0.25
Consensus pattern (15 bp):
AACAATAATAATAAT
Found at i:49320992 original size:52 final size:52
Alignment explanation
Indices: 49320914--49321018 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
49320904 TTTATTGCCT
49320914 AATAAAATTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
1 AATAAAATTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
* *
49320966 AATAAATTTTCTCAATTATGATATTATTAGACATGGCACCTGTGGAAGTTCA
1 AATAAAATTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
49321018 A
1 A
49321019 TTGCCTGATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (52 bp):
AATAAAATTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
Found at i:49326274 original size:2 final size:2
Alignment explanation
Indices: 49326267--49326295 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49326257 TCCTGCTGGC
49326267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49326296 GGTATCCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49326878 original size:18 final size:18
Alignment explanation
Indices: 49326857--49326898 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
49326847 TCATGCAATC
*
49326857 CATTTT-TTTACAATTGTT
1 CATTTTCTTTAAAATT-TT
49326875 CATTTTCTTTAAAATTTT
1 CATTTTCTTTAAAATTTT
49326893 CATTTT
1 CATTTT
49326899 GAGCTATACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.24, C:0.12, G:0.02, T:0.62
Consensus pattern (18 bp):
CATTTTCTTTAAAATTTT
Found at i:49327503 original size:24 final size:24
Alignment explanation
Indices: 49327458--49327504 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
49327448 TTAATTAGTG
*
49327458 TATAAAAAATATATTATAAAAACC
1 TATAAAAAATATAATATAAAAACC
49327482 TATAATAAAAT-TAATATTAAAAA
1 TATAA-AAAATATAATA-TAAAAA
49327505 ACAAAAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
TATAAAAAATATAATATAAAAACC
Found at i:49329826 original size:14 final size:14
Alignment explanation
Indices: 49329807--49329837 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
49329797 AAAATTGTTG
49329807 TATATACATACATA
1 TATATACATACATA
*
49329821 TATATACATATATA
1 TATATACATACATA
49329835 TAT
1 TAT
49329838 GATGACTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (14 bp):
TATATACATACATA
Found at i:49336926 original size:22 final size:24
Alignment explanation
Indices: 49336899--49336987 Score: 91
Period size: 22 Copynumber: 3.9 Consensus size: 24
49336889 CACTAATGAA
49336899 CAGAGAGCACTGAA-GTGCTATA-
1 CAGAGAGCACTGAACGTGCTATAC
* *
49336921 CAGAGAGCAC-AAATGTGCTA-AC
1 CAGAGAGCACTGAACGTGCTATAC
*
49336943 CAGAGAGCACTG-ACGTGCTAGTAAT
1 CAGAGAGCACTGAACGTGCTA-T-AC
49336968 CAGAGAGCACT-AACGTGCTA
1 CAGAGAGCACTGAACGTGCTA
49336988 ATAATCAGAG
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
21 3 0.05
22 33 0.59
25 20 0.36
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (24 bp):
CAGAGAGCACTGAACGTGCTATAC
Found at i:49336974 original size:25 final size:24
Alignment explanation
Indices: 49336899--49337000 Score: 106
Period size: 25 Copynumber: 4.3 Consensus size: 24
49336889 CACTAATGAA
49336899 CAGAGAGCACTGAA-GTGCTAT-A-
1 CAGAGAGCACT-AACGTGCTATAAT
* * *
49336921 CAGAGAGCACAAATGTGC--TAAC
1 CAGAGAGCACTAACGTGCTATAAT
*
49336943 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACTAACGTGCTA-TAAT
49336968 CAGAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCT-ATAAT
49336993 CAGAGAGC
1 CAGAGAGC
49337001 GTGCTGAAGT
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.01
21 3 0.04
22 29 0.43
25 33 0.49
26 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (24 bp):
CAGAGAGCACTAACGTGCTATAAT
Found at i:49338047 original size:23 final size:23
Alignment explanation
Indices: 49338013--49338056 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
49338003 AAGTATGTAT
49338013 ATATATTAATTACAAATGTATAC
1 ATATATTAATTACAAATGTATAC
* *
49338036 ATATATTTATTACACATGTAT
1 ATATATTAATTACAAATGTAT
49338057 TTATAATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (23 bp):
ATATATTAATTACAAATGTATAC
Found at i:49338971 original size:5 final size:6
Alignment explanation
Indices: 49338953--49338977 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
49338943 ACAATGTAGC
49338953 TTCTTT TTCTTT TTCTTT TTCTTT T
1 TTCTTT TTCTTT TTCTTT TTCTTT T
49338978 ATGTGTAGAG
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:49343972 original size:47 final size:47
Alignment explanation
Indices: 49343919--49344012 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
49343909 ACTTGTCTCT
49343919 AATTACAACTCATATCATCTACTTCTGCTTTTCATTTTCTGAAACTA
1 AATTACAACTCATATCATCTACTTCTGCTTTTCATTTTCTGAAACTA
49343966 AATTACAACTCATATCATCTACTTCTGCTTTTCATTTTCTGAAACTA
1 AATTACAACTCATATCATCTACTTCTGCTTTTCATTTTCTGAAACTA
49344013 TCGATTGGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.43
Consensus pattern (47 bp):
AATTACAACTCATATCATCTACTTCTGCTTTTCATTTTCTGAAACTA
Found at i:49344505 original size:3 final size:3
Alignment explanation
Indices: 49344497--49344538 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
49344487 TAATTAATTA
*
49344497 ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
49344539 TTGGTTAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:49347275 original size:27 final size:27
Alignment explanation
Indices: 49347245--49347296 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
49347235 TAAAATTAAA
49347245 TAAATTAAAATT-TTAAAATATTATATT
1 TAAATT-AAATTATTAAAATATTATATT
* *
49347272 TAAATTTAATTATTAGAATATTATA
1 TAAATTAAATTATTAAAATATTATA
49347297 AATATTAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TAAATTAAATTATTAAAATATTATATT
Found at i:49348801 original size:19 final size:21
Alignment explanation
Indices: 49348762--49348804 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
49348752 TAATACTCTC
49348762 AAAATAATATTTATTTATTTAT
1 AAAATAATA-TTATTTATTTAT
49348784 AAAATAATA-TATTT-TTTAT
1 AAAATAATATTATTTATTTAT
49348803 AA
1 AA
49348805 TTTCACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
22 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAATAATATTATTTATTTAT
Found at i:49355727 original size:14 final size:14
Alignment explanation
Indices: 49355706--49355739 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
49355696 TGGTATGGGT
49355706 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
49355719 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
49355733 TTATAGG
1 TTATAGG
49355740 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:49362859 original size:10 final size:10
Alignment explanation
Indices: 49362844--49362880 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
49362834 GAACAATTTA
49362844 TTTTTTTCTT-
1 TTTTTTT-TTC
49362854 TTTTTTTTTC
1 TTTTTTTTTC
49362864 TTTTTTTTTC
1 TTTTTTTTTC
49362874 TTTTTTT
1 TTTTTTT
49362881 CTTCCCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 2 0.08
10 24 0.92
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:49362861 original size:12 final size:12
Alignment explanation
Indices: 49362844--49362880 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
49362834 GAACAATTTA
49362844 TTTTTTTCTTTT
1 TTTTTTTCTTTT
49362856 TTTTTTTC--TT
1 TTTTTTTCTTTT
49362866 TTTTTTTCTTTT
1 TTTTTTTCTTTT
49362878 TTT
1 TTT
49362881 CTTCCCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.43
12 13 0.57
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:49362867 original size:18 final size:18
Alignment explanation
Indices: 49362845--49362883 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
49362835 AACAATTTAT
*
49362845 TTTTTTCTTTTTTTTTTTC
1 TTTTTT-TTTCTTTTTTTC
49362864 TTTTTTTTTCTTTTTTTC
1 TTTTTTTTTCTTTTTTTC
49362882 TT
1 TT
49362884 CCCTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (18 bp):
TTTTTTTTTCTTTTTTTC
Found at i:49362869 original size:22 final size:23
Alignment explanation
Indices: 49362844--49362898 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
49362834 GAACAATTTA
**
49362844 TTTTTTTCTTTTTTT-TTTTCTT
1 TTTTTTTCTTTTTTTCTTCCCTT
49362866 TTTTTTTCTTTTTTTCTTCCCTT
1 TTTTTTTCTTTTTTTCTTCCCTT
49362889 TTATTTTTCT
1 TT-TTTTTCT
49362899 CTCTTCTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 15 0.52
23 7 0.24
24 7 0.24
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTTTCTTTTTTTCTTCCCTT
Found at i:49364042 original size:15 final size:16
Alignment explanation
Indices: 49364014--49364045 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
49364004 CTGTTTTAGT
49364014 AATTTAACCAAAATAA
1 AATTTAACCAAAATAA
49364030 AATTTAA-CAAAATAA
1 AATTTAACCAAAATAA
49364045 A
1 A
49364046 TCATTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (16 bp):
AATTTAACCAAAATAA
Found at i:49366527 original size:16 final size:17
Alignment explanation
Indices: 49366508--49366552 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
49366498 TATATATGTA
49366508 TAATAATATTTAAAAT-
1 TAATAATATTTAAAATC
49366524 TAATAAT-TATTAAAATC
1 TAATAATAT-TTAAAATC
49366541 T-ATAA-ATTTAAA
1 TAATAATATTTAAA
49366553 CTTTAATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 6 0.23
16 19 0.73
17 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATAATATTTAAAATC
Found at i:49368650 original size:14 final size:13
Alignment explanation
Indices: 49368633--49368686 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
49368623 ATAATATAAT
49368633 ATTTATAAATATGA
1 ATTTATAAATAT-A
49368647 ATTTATAACATATAA
1 ATTTATAA-ATAT-A
*
49368662 TATTTATAAAAATA
1 -ATTTATAAATATA
49368676 ATTTTATAAAT
1 A-TTTATAAAT
49368687 TGTCCAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 1 0.03
14 17 0.50
15 8 0.24
16 8 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (13 bp):
ATTTATAAATATA
Found at i:49368660 original size:30 final size:30
Alignment explanation
Indices: 49368626--49368684 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
49368616 TTTGTAGATA
*
49368626 ATATAATATTTATAAATATGAA-TTTATAAC
1 ATATAATATTTATAAAAAT-AATTTTATAAC
49368656 ATATAATATTTATAAAAATAATTTTATAA
1 ATATAATATTTATAAAAATAATTTTATAA
49368685 ATTGTCCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (30 bp):
ATATAATATTTATAAAAATAATTTTATAAC
Found at i:49373337 original size:16 final size:18
Alignment explanation
Indices: 49373316--49373348 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
49373306 AACATTAAAA
49373316 TAATATT-TAA-ATTCAT
1 TAATATTATAAGATTCAT
49373332 TAATATTATAAGATTCA
1 TAATATTATAAGATTCA
49373349 ATAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (18 bp):
TAATATTATAAGATTCAT
Found at i:49379160 original size:17 final size:18
Alignment explanation
Indices: 49379119--49379161 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
49379109 GTATAAGATA
49379119 ATATAATTATATTAACTT
1 ATATAATTATATTAACTT
**
49379137 ATA-AATTATA-TATTTT
1 ATATAATTATATTAACTT
49379153 ATATAATTA
1 ATATAATTA
49379162 ATAAAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 12 0.55
18 3 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATAATTATATTAACTT
Found at i:49380180 original size:38 final size:37
Alignment explanation
Indices: 49380120--49380193 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
49380110 ACAATTCACC
*
49380120 AAAAAAAAACATACATATATAAACATGTTTTAAAATATA
1 AAAAAAAAACATACATATATAAA-A-GTTTGAAAATATA
*
49380159 AAAAAAAAAC-TA-ATGTAATAAAAGTTTGAAAATAT
1 AAAAAAAAACATACATAT-ATAAAAGTTTGAAAATAT
49380194 TTCTCTGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 11 0.34
37 4 0.12
38 7 0.22
39 10 0.31
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (37 bp):
AAAAAAAAACATACATATATAAAAGTTTGAAAATATA
Found at i:49398370 original size:4 final size:4
Alignment explanation
Indices: 49398347--49398383 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
49398337 TTGAAGACTT
*
49398347 AGAA AGAA A-AA A-AA AAAA AGAA AGAA AGAA AGAA AGA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGA
49398384 GGGGGAGGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
3 6 0.19
4 25 0.81
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:49407508 original size:27 final size:27
Alignment explanation
Indices: 49407425--49407511 Score: 120
Period size: 27 Copynumber: 3.2 Consensus size: 27
49407415 TATTTCATAA
49407425 GCGCGACTAGTTGAGCCTATCTCAGAG
1 GCGCGACTAGTTGAGCCTATCTCAGAG
* * *
49407452 GCACGACTAGTTGAGCCTATCTGACAG
1 GCGCGACTAGTTGAGCCTATCTCAGAG
* * *
49407479 GCGCGACTAGTTGTGCCTAACACAGAG
1 GCGCGACTAGTTGAGCCTATCTCAGAG
49407506 GCGCGA
1 GCGCGA
49407512 ATGGTGGGGC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.24, C:0.26, G:0.30, T:0.20
Consensus pattern (27 bp):
GCGCGACTAGTTGAGCCTATCTCAGAG
Found at i:49408545 original size:33 final size:33
Alignment explanation
Indices: 49408502--49408566 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
49408492 ATGAACTTGA
* * *
49408502 GCCGGGAGGAGTGGAGTACGGCGGTGGATACGG
1 GCCGGAAGGAGCGGAGTACGGAGGTGGATACGG
*
49408535 GCCGGAAGGAGCGGAGTACTGAGGTGGATACG
1 GCCGGAAGGAGCGGAGTACGGAGGTGGATACG
49408567 AGCTAGGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.51, T:0.12
Consensus pattern (33 bp):
GCCGGAAGGAGCGGAGTACGGAGGTGGATACGG
Found at i:49411571 original size:60 final size:60
Alignment explanation
Indices: 49411498--49411616 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
49411488 ATACTAAACT
* * * *
49411498 AAACACAACAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCAAAATTACTAACAAATTAATTTTAAAATAATTAC
49411558 AAACACAAAAATTTATAACATAATCCAAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAAAAATTTATAACATAATCCAAAATTACTAACAAATTAATTTTAAAATAATTA
49411617 TAAATAGCAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.33
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCAAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:49411991 original size:27 final size:27
Alignment explanation
Indices: 49411953--49412009 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
49411943 CGGGGCAGGG
* *
49411953 GGCTTGATTAGTCGCGCCTGTCTGACA
1 GGCTCGATTAGTCGCGCCTATCTGACA
*
49411980 GGCTCGATTAGTCGCGTCTATCTGACA
1 GGCTCGATTAGTCGCGCCTATCTGACA
49412007 GGC
1 GGC
49412010 GCGACCCGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (27 bp):
GGCTCGATTAGTCGCGCCTATCTGACA
Found at i:49412136 original size:25 final size:25
Alignment explanation
Indices: 49412073--49412136 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 25
49412063 ATATATTTAA
* *
49412073 ATAT-TTTTAA-AAAAATAAAAAAT
1 ATATATTTTAATATAAACAAAAAAT
*
49412096 -TAATATTTT-ATTTAAACAAAAAAT
1 AT-ATATTTTAATATAAACAAAAAAT
49412120 ATATATTTTAATATAAA
1 ATATATTTTAATATAAA
49412137 AAATTGATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
22 1 0.03
23 3 0.09
24 21 0.66
25 7 0.22
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
ATATATTTTAATATAAACAAAAAAT
Found at i:49412811 original size:18 final size:19
Alignment explanation
Indices: 49412769--49412813 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
49412759 ATTCACCTAA
49412769 ACCCAATCCAAACCCAAGT
1 ACCCAATCCAAACCCAAGT
* * *
49412788 ATCCAA-CCCAACCCAATT
1 ACCCAATCCAAACCCAAGT
49412806 ACCCAATC
1 ACCCAATC
49412814 ATAAAAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.40, C:0.44, G:0.02, T:0.13
Consensus pattern (19 bp):
ACCCAATCCAAACCCAAGT
Found at i:49412862 original size:6 final size:6
Alignment explanation
Indices: 49412853--49412895 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
49412843 AAATAAAATT
*
49412853 CTAAAA CTAAAA CTAAAA CTAAAA C-AAAA GTCTAAAA ATAAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA --CTAAAA CTAAAA
49412896 AATATATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
5 4 0.12
6 24 0.73
7 1 0.03
8 4 0.12
ACGTcount: A:0.67, C:0.14, G:0.02, T:0.16
Consensus pattern (6 bp):
CTAAAA
Found at i:49415666 original size:23 final size:23
Alignment explanation
Indices: 49415640--49415683 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
49415630 CCAATTCGAA
49415640 AAATACAAAG-ACAAAAATTAATC
1 AAATA-AAAGTACAAAAATTAATC
*
49415663 AAATAAAAGTATAAAAATTAA
1 AAATAAAAGTACAAAAATTAA
49415684 ATTCACAACT
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:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (23 bp):
AAATAAAAGTACAAAAATTAATC
Found at i:49422907 original size:69 final size:69
Alignment explanation
Indices: 49422795--49422971 Score: 282
Period size: 69 Copynumber: 2.6 Consensus size: 69
49422785 CCAACAATAC
* *
49422795 TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCGAAATGCAGTCA
1 TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAATCA
49422860 ATTA
66 ATTA
* * * *
49422864 TAACTATGATTATAAGTAATTTCTAGACATCAGAGACCCCTCAGTTGCATTCCAAAATGGAATCA
1 TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAATCA
*
49422929 GTTA
66 ATTA
*
49422933 TAACTACGATTTTAAGTAATTTCTAGACATCAGAGACCA
1 TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCA
49422972 TCAATCACAT
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 98 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (69 bp):
TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAATCA
ATTA
Found at i:49425618 original size:84 final size:84
Alignment explanation
Indices: 49425365--49425618 Score: 357
Period size: 84 Copynumber: 3.0 Consensus size: 84
49425355 GTTATAATAT
* **
49425365 TTGGATAAATCATTTTATTATTT-TTCTCAATAAAGCTTTGATCTAATGATCGTCTAAACTTGAT
1 TTGGATAAATCATTTTATT-TTTCTCCTTGATAAAGCTTTGATCTAATGATCGTCTAAACTTGAT
* *
49425429 CTTAGATAAATGTGAGTCGA
65 CTTAGATAAATGTGGGTTGA
* *
49425449 TTGGATAAATCATTTTATTTTTCTCCTTGGTAAAGCTTTGATCTAATGATTGTCTAAACTTGATC
1 TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGATCGTCTAAACTTGATC
* *
49425514 TTAGATAAATATGGGCTGA
66 TTAGATAAATGTGGGTTGA
* * *
49425533 TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGGTCGTATAAACTTGATA
1 TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGATCGTCTAAACTTGATC
* * *
49425598 TTGGATAGACGTGGGTTGA
66 TTAGATAAATGTGGGTTGA
49425617 TT
1 TT
49425619 AAAAGATTAT
Statistics
Matches: 150, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
83 3 0.02
84 147 0.98
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (84 bp):
TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGATCGTCTAAACTTGATC
TTAGATAAATGTGGGTTGA
Found at i:49427902 original size:26 final size:27
Alignment explanation
Indices: 49427859--49427909 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
49427849 TAATAACGGA
*
49427859 TTGCTCTATTCTTATTATTT-TGTTAC
1 TTGCTCTATTATTATTATTTATGTTAC
*
49427885 TTGCTCTATTATTTTTATTTATGTT
1 TTGCTCTATTATTATTATTTATGTT
49427910 TTTATAGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.65
Consensus pattern (27 bp):
TTGCTCTATTATTATTATTTATGTTAC
Found at i:49432141 original size:25 final size:24
Alignment explanation
Indices: 49432113--49432193 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 24
49432103 TATCATGATT
49432113 TTCCCGATATTTGGCTATATTGAGC
1 TTCCCGAT-TTTGGCTATATTGAGC
* * *
49432138 TTCCCGATTAATGGCTCTCTTGAGC
1 TTCCCGATT-TTGGCTATATTGAGC
49432163 TTCCCG-TTTATGGCTAGTA-TGAGC
1 TTCCCGATTT-TGGCTA-TATTGAGC
*
49432187 TTTCCGA
1 TTCCCGA
49432194 CAATTGGCTC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
24 18 0.40
25 27 0.60
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (24 bp):
TTCCCGATTTTGGCTATATTGAGC
Found at i:49432185 original size:24 final size:24
Alignment explanation
Indices: 49432124--49432193 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
49432114 TCCCGATATT
49432124 TGGCTATATTGAGCTTCCCGATTAA
1 TGGCTATA-TGAGCTTCCCGATTAA
* * *
49432149 TGGCTCTCTTGAGCTTCCCG-TTTA
1 TGGCTAT-ATGAGCTTCCCGATTAA
*
49432173 TGGCTAGTATGAGCTTTCCGA
1 TGGCTA-TATGAGCTTCCCGA
49432194 CAATTGGCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
24 18 0.50
25 18 0.50
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (24 bp):
TGGCTATATGAGCTTCCCGATTAA
Found at i:49432186 original size:49 final size:49
Alignment explanation
Indices: 49432124--49432219 Score: 115
Period size: 49 Copynumber: 2.0 Consensus size: 49
49432114 TCCCGATATT
* * **
49432124 TGGCTATATTGAGCTTCCCGATTAA-TGGCTCTCTTGAGCTTCCCGTTTA
1 TGGCTATATTGAGCTTCCCGA-CAATTGGCTCGCAAGAGCTTCCCGTTTA
*
49432173 TGGCTAGTA-TGAGCTTTCCGACAATTGGCTCGCAAGAGCTTCCCGTT
1 TGGCTA-TATTGAGCTTCCCGACAATTGGCTCGCAAGAGCTTCCCGTT
49432220 ATATAGCTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 2 0.05
49 36 0.90
50 2 0.05
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (49 bp):
TGGCTATATTGAGCTTCCCGACAATTGGCTCGCAAGAGCTTCCCGTTTA
Found at i:49435786 original size:22 final size:22
Alignment explanation
Indices: 49435745--49435811 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
49435735 TGCACTAATG
* *
49435745 AACAAAGAGCACTGAGGTGCTA
1 AACAAAGAGCACTAATGTGCTA
* *
49435767 TACAAAGAGCACAAATGTGCTA
1 AACAAAGAGCACTAATGTGCTA
49435789 AACAGAA-AGCACTAATGTGCTA
1 AACA-AAGAGCACTAATGTGCTA
49435811 A
1 A
49435812 TAATCGGAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 36 0.95
23 2 0.05
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (22 bp):
AACAAAGAGCACTAATGTGCTA
Found at i:49438066 original size:30 final size:31
Alignment explanation
Indices: 49438017--49438081 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
49438007 ATATATGAAT
* *
49438017 TATAAAATATATGAAAAAATATGTATGTACA
1 TATAAAATATATGAAAAAATAAGTAAGTACA
* *
49438048 TATAAAGTATAT-AAAAAATAAGTAAGTATA
1 TATAAAATATATGAAAAAATAAGTAAGTACA
49438078 TATA
1 TATA
49438082 TATCAAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (31 bp):
TATAAAATATATGAAAAAATAAGTAAGTACA
Found at i:49439294 original size:3 final size:3
Alignment explanation
Indices: 49439286--49439330 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
49439276 AATCTAGTCC
*
49439286 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
49439331 CTTTTTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:49442614 original size:14 final size:14
Alignment explanation
Indices: 49442595--49442633 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
49442585 TTGTTTCACT
*
49442595 GAAAATGGCTTCCG
1 GAAAATGACTTCCG
* *
49442609 GAAAATGATTTCTG
1 GAAAATGACTTCCG
49442623 GAAAATGACTT
1 GAAAATGACTT
49442634 ACTTTTCTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (14 bp):
GAAAATGACTTCCG
Found at i:49443159 original size:18 final size:18
Alignment explanation
Indices: 49443121--49443156 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
49443111 TAATATTTTT
*
49443121 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
49443139 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
49443157 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:49444499 original size:26 final size:24
Alignment explanation
Indices: 49444470--49444523 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
49444460 TTATGAAATT
*
49444470 TTTTTATACCAAAATTAAATTATATA
1 TTTTTAT-CCAAAATTAAAATATA-A
* *
49444496 TTTTTATCGAGAATTAAAATATAA
1 TTTTTATCCAAAATTAAAATATAA
49444520 TTTT
1 TTTT
49444524 ATTAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.20
25 13 0.52
26 7 0.28
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (24 bp):
TTTTTATCCAAAATTAAAATATAA
Found at i:49449209 original size:4 final size:4
Alignment explanation
Indices: 49449200--49449239 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
49449190 ACAAACACAC
49449200 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
49449240 GTCAAATAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:49449585 original size:22 final size:22
Alignment explanation
Indices: 49449522--49449585 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 22
49449512 TTTTAAATAT
49449522 TATGCAATATAAAAATATATGTAAG
1 TATGCAA-AT-AAAATATATGT-AG
*
49449547 TATGCATATAAACATATATGT-G
1 TATGCAAATAAA-ATATATGTAG
*
49449569 TATGTAAATTAAAATAT
1 TATGCAAA-TAAAATAT
49449586 GTATATATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 11 0.32
23 7 0.21
24 10 0.29
25 6 0.18
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (22 bp):
TATGCAAATAAAATATATGTAG
Found at i:49449792 original size:24 final size:24
Alignment explanation
Indices: 49449765--49449817 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
49449755 GTACGGATTG
* * * *
49449765 TAAAATATGTGCATGTATATATTA
1 TAAAAGATATGCATATATATATAA
*
49449789 TAAAAGATATGTATATATATATAA
1 TAAAAGATATGCATATATATATAA
49449813 TAAAA
1 TAAAA
49449818 CTTGGGATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (24 bp):
TAAAAGATATGCATATATATATAA
Done.