Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 91 of 316
Found at i:27555618 original size:52 final size:50
Alignment explanation
Indices: 27555504--27555620 Score: 144
Period size: 50 Copynumber: 2.3 Consensus size: 50
27555494 ATCGGGTATG
* **
27555504 CATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACCATCTGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCTGAAACA
* * * * *
27555554 CGTAGTAGCCTGCACTTAGTACTGCACACGTGACCTAAAACCATTTTAAACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCT--AACCATCTGAAACA
27555606 CATAGTAGCCTGCAC
1 CATAGTAGCCTGCAC
27555621 ATGTGTTCTC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 32 0.57
52 24 0.43
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (50 bp):
CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCTGAAACA
Found at i:27558521 original size:51 final size:51
Alignment explanation
Indices: 27558445--27558546 Score: 134
Period size: 51 Copynumber: 2.0 Consensus size: 51
27558435 AATTATATAA
* **
27558445 AGTCCATCTTAGAAAGATGTGACTATCAGCTTTGCCTTAAAGAAGTGAATT
1 AGTCCATCTTAGAAAGATGTGACTATCAACTTCACCTTAAAGAAGTGAATT
* * *
27558496 AGTCCATCTTA-AAGAGGTGTGACTATGAACTTCACCTTAAAGAGGTGAATT
1 AGTCCATCTTAGAA-AGATGTGACTATCAACTTCACCTTAAAGAAGTGAATT
27558547 CTATAAAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
50 2 0.05
51 42 0.95
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (51 bp):
AGTCCATCTTAGAAAGATGTGACTATCAACTTCACCTTAAAGAAGTGAATT
Found at i:27558591 original size:57 final size:57
Alignment explanation
Indices: 27558422--27558939 Score: 509
Period size: 57 Copynumber: 9.2 Consensus size: 57
27558412 CCACTTAAAA
* *
27558422 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAGAA-AGATGTGACTATCAGCTTTG
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTA-AAGAGGTGTGACTATCAACTTTG
* * **
27558479 CCTTAAAGAAGTG-A--AT-T--AGTCCATCTTAAAGAGGTGTGACTATGAACTTCA
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAAGAGGTGTGACTATCAACTTTG
* * * * *
27558530 CCTTAAAGAGGTGAATTCTATAAAGTACATCTTAAAAAGGCGTGACTATCAATTTTG
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAAGAGGTGTGACTATCAACTTTG
* * ** * * *
27558587 CCTTAAAGAGGCGAATTATATAAAGTCCATTTTAAAGAGGCATGATTATCAAATTTC
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAAGAGGTGTGACTATCAACTTTG
* * * * * * *
27558644 CCTCAAAGAGATGAATTATATAAAGTCCATGTTAAAGAGGTATGATTATCGA-TGTCG
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAAGAGGTGTGACTATCAACT-TTG
* * *
27558701 CCTTAAAGAGGTGAATTATATAAAGTCCATCTT-AAGGGGCTGTGATTATCAACTTTA
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAAGAGG-TGTGACTATCAACTTTG
* * * **
27558758 CTTTAAAAAGGTGAACTATATAAAGTCCATCTTAAAGAGGCATGACTATCAACTTTG
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAAGAGGTGTGACTATCAACTTTG
* ** * * * *
27558815 CCTTAAAGAGGTGAATTATATAGAGTCCAAGTTAAAGATGTGTGACTATTAGCTTCG
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAAGAGGTGTGACTATCAACTTTG
* * * * *
27558872 CTTTAAATAGGTGAATTATATAAAGTCCATCTTAAGGAAGTGTGAC-ATC-ATTTTCG
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAAGAGGTGTGACTATCAACTTT-G
*
27558928 TCTTAAAGAGGT
1 CCTTAAAGAGGT
27558940 AAATCATCCT
Statistics
Matches: 375, Mismatches: 74, Indels: 25
0.79 0.16 0.05
Matches are distributed among these distances:
50 2 0.01
51 38 0.10
52 1 0.00
53 1 0.00
54 3 0.01
55 3 0.01
56 19 0.05
57 302 0.81
58 6 0.02
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (57 bp):
CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAAGAGGTGTGACTATCAACTTTG
Found at i:27558681 original size:29 final size:29
Alignment explanation
Indices: 27558588--27558735 Score: 87
Period size: 29 Copynumber: 5.2 Consensus size: 29
27558578 TCAATTTTGC
**
27558588 CTTAAAGAGGCGAATTATATAAAGTCCAT
1 CTTAAAGAGATGAATTATATAAAGTCCAT
* **
27558617 TTTAAAGAGGCATG-ATTATCA-AATTTCC--
1 CTTAAAGA-G-ATGAATTAT-ATAAAGTCCAT
*
27558645 CTCAAAGAGATGAATTATATAAAGTCCAT
1 CTTAAAGAGATGAATTATATAAAGTCCAT
* ** *
27558674 GTTAAAGAGGTATG-ATTAT-CGATGTCGC--
1 CTTAAAGA-G-ATGAATTATATAAAGTC-CAT
*
27558702 CTTAAAGAGGTGAATTATATAAAGTCCAT
1 CTTAAAGAGATGAATTATATAAAGTCCAT
27558731 CTTAA
1 CTTAA
27558736 GGGGCTGTGA
Statistics
Matches: 86, Mismatches: 19, Indels: 28
0.65 0.14 0.21
Matches are distributed among these distances:
26 6 0.07
27 18 0.21
28 17 0.20
29 22 0.26
30 18 0.21
31 5 0.06
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (29 bp):
CTTAAAGAGATGAATTATATAAAGTCCAT
Found at i:27558907 original size:171 final size:169
Alignment explanation
Indices: 27558421--27558908 Score: 569
Period size: 171 Copynumber: 2.9 Consensus size: 169
27558411 TCCACTTAAA
* *
27558421 ACCTTAAAGAGGTGAATTATATAAAGTCCATCTTAGAAAGATG--TGACTATCAGCTTTGCCTTA
1 ACCTTAAAGAGGTGAATTATATAAAGTCCATCTT--AAAGAGGCATGACTATCAACTTTGCCTTA
* * * * *
27558484 AAGAAGTG-A--AT-T-AGTCCATCTTAAAGAGGTGTGACTATGAACTTCACCTTAAAGAGGTGA
64 AAGAGGTGAATTATATAAGTCCATGTTAAAGAGGTGTGACTATTAGCTTCGCCTTAAAGAGGTGA
* * ** *
27558544 ATTCTATAAAGTACATCTTAAAAAGGCGTGACTATCAATTTT
129 ATTATATAAAGTCCATCTT-AAGGGGCGTGACTATCAACTTT
* * * * * * *
27558586 GCCTTAAAGAGGCGAATTATATAAAGTCCATTTTAAAGAGGCATGATTATCAAATTTCCCTCAAA
1 ACCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAAGAGGCATGACTATCAACTTTGCCTTAAA
* * * * *
27558651 GAGATGAATTATATAAAGTCCATGTTAAAGAGGTATGATTA-TCGATGTCGCCTTAAAGAGGTGA
66 GAGGTGAATTATAT-AAGTCCATGTTAAAGAGGTGTGACTATTAGCT-TCGCCTTAAAGAGGTGA
*
27558715 ATTATATAAAGTCCATCTTAAGGGGCTGTGATTATCAACTTT
129 ATTATATAAAGTCCATCTTAAGGGGC-GTGACTATCAACTTT
* * *
27558757 ACTTTAAAAAGGTGAACTATATAAAGTCCATCTTAAAGAGGCATGACTATCAACTTTGCCTTAAA
1 ACCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAAGAGGCATGACTATCAACTTTGCCTTAAA
* * * *
27558822 GAGGTGAATTATATAGAGTCCAAGTTAAAGATGTGTGACTATTAGCTTCGCTTTAAATAGGTGAA
66 GAGGTGAATTATATA-AGTCCATGTTAAAGAGGTGTGACTATTAGCTTCGCCTTAAAGAGGTGAA
27558887 TTATATAAAGTCCATCTTAAGG
130 TTATATAAAGTCCATCTTAAGG
27558909 AAGTGTGACA
Statistics
Matches: 267, Mismatches: 44, Indels: 18
0.81 0.13 0.05
Matches are distributed among these distances:
163 6 0.02
165 52 0.19
166 1 0.00
168 2 0.01
169 1 0.00
170 7 0.03
171 195 0.73
172 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (169 bp):
ACCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAAGAGGCATGACTATCAACTTTGCCTTAAA
GAGGTGAATTATATAAGTCCATGTTAAAGAGGTGTGACTATTAGCTTCGCCTTAAAGAGGTGAAT
TATATAAAGTCCATCTTAAGGGGCGTGACTATCAACTTT
Found at i:27559766 original size:35 final size:35
Alignment explanation
Indices: 27559719--27559792 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
27559709 CTGGTTTTTC
27559719 GGGGTGACACCATGTAAATGATATACAGGTCCTTT
1 GGGGTGACACCATGTAAATGATATACAGGTCCTTT
* * *
27559754 GGGGTGATACCATGTAAATGGTATATAGGTCCTTT
1 GGGGTGACACCATGTAAATGATATACAGGTCCTTT
27559789 GGGG
1 GGGG
27559793 CGAAATTGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.30
Consensus pattern (35 bp):
GGGGTGACACCATGTAAATGATATACAGGTCCTTT
Found at i:27559805 original size:35 final size:35
Alignment explanation
Indices: 27559727--27559815 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 35
27559717 TCGGGGTGAC
* * *
27559727 ACCATGTAAATGATATACAGGTCCTTTGGGGTGAT
1 ACCATGTAAATGGTATACAGGTCCTTTGGGGCGAA
*
27559762 ACCATGTAAATGGTATATAGGTCCTTTGGGGCGAA
1 ACCATGTAAATGGTATACAGGTCCTTTGGGGCGAA
***
27559797 ATTGTGTAAATGGTATACA
1 ACCATGTAAATGGTATACA
27559816 TGTAAAATCT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.31
Consensus pattern (35 bp):
ACCATGTAAATGGTATACAGGTCCTTTGGGGCGAA
Found at i:27561470 original size:14 final size:14
Alignment explanation
Indices: 27561451--27561479 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27561441 ATAAGTCTAT
27561451 AATCAAGGATGTAC
1 AATCAAGGATGTAC
27561465 AATCAAGGATGTAC
1 AATCAAGGATGTAC
27561479 A
1 A
27561480 TACTCGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AATCAAGGATGTAC
Found at i:27568472 original size:24 final size:24
Alignment explanation
Indices: 27568429--27568481 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
27568419 CACAAACGCA
*
27568429 GCTCTTCATAAGCGTCCTGATATAG
1 GCTCTTCATAAGCGTCCTGACAT-G
* *
27568454 GCTCTT-ATGAGCTTCCTGACATG
1 GCTCTTCATAAGCGTCCTGACATG
27568477 GCTCT
1 GCTCT
27568482 CTTGAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.24
24 13 0.52
25 6 0.24
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (24 bp):
GCTCTTCATAAGCGTCCTGACATG
Found at i:27570272 original size:21 final size:21
Alignment explanation
Indices: 27570246--27570310 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
27570236 GTAGCTTGGT
* *
27570246 CACACGGGCATGTGTCTCTTC
1 CACACGGGCACGTGTCTCCTC
*
27570267 CACACGGGTACGTGTCTCCTC
1 CACACGGGCACGTGTCTCCTC
* **
27570288 TACACGGGTGCGTGTCTCCTC
1 CACACGGGCACGTGTCTCCTC
27570309 CA
1 CA
27570311 TATGGGCGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.14, C:0.35, G:0.25, T:0.26
Consensus pattern (21 bp):
CACACGGGCACGTGTCTCCTC
Found at i:27573206 original size:22 final size:22
Alignment explanation
Indices: 27573181--27573228 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
27573171 ATCGTGTATA
*
27573181 TAAATAT-AAGCAAATTAAAACT
1 TAAATATAAAACAAA-TAAAACT
*
27573203 TAAA-ATAAAACGAATAAAACT
1 TAAATATAAAACAAATAAAACT
27573224 TAAAT
1 TAAAT
27573229 CAAAATTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.25
Consensus pattern (22 bp):
TAAATATAAAACAAATAAAACT
Found at i:27587579 original size:24 final size:24
Alignment explanation
Indices: 27587551--27587598 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
27587541 ATGATAACTT
27587551 ATCCAAGCTCTTTAGAACAATATG
1 ATCCAAGCTCTTTAGAACAATATG
*
27587575 ATCCAAGCTTTTTAGAACAATATG
1 ATCCAAGCTCTTTAGAACAATATG
27587599 TAATTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (24 bp):
ATCCAAGCTCTTTAGAACAATATG
Found at i:27589719 original size:49 final size:49
Alignment explanation
Indices: 27589647--27589746 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
27589637 ACAGTATGGG
*
27589647 AAAACATTCAATACCGTGAAAGGAATCGTTCCGTTTGCATTAAGCTCTA
1 AAAACATTCAATACCGAGAAAGGAATCGTTCCGTTTGCATTAAGCTCTA
* *
27589696 AAAACATTCAATACCGAGAAAGGAATCGTTCTGTTTTCATTAAGCTCTA
1 AAAACATTCAATACCGAGAAAGGAATCGTTCCGTTTGCATTAAGCTCTA
27589745 AA
1 AA
27589747 GTAACAATTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (49 bp):
AAAACATTCAATACCGAGAAAGGAATCGTTCCGTTTGCATTAAGCTCTA
Found at i:27595239 original size:8 final size:8
Alignment explanation
Indices: 27595226--27595263 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
27595216 TTAATCTTTA
27595226 TTTATTTC
1 TTTATTTC
27595234 TTTATTTC
1 TTTATTTC
27595242 -TTATTTTC
1 TTTA-TTTC
27595250 TTTATTTC
1 TTTATTTC
27595258 TTTATT
1 TTTATT
27595264 ATTTATTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 3 0.11
8 22 0.79
9 3 0.11
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTATTTC
Found at i:27596951 original size:6 final size:6
Alignment explanation
Indices: 27596936--27596985 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
27596926 CCATTTATCA
* * *
27596936 TTTA-T TTTATT TTTATT TTTATT TTTATG TTTATG TTTATT ATTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
27596983 TTT
1 TTT
27596986 TTAGACTTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
5 4 0.10
6 36 0.90
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:27598861 original size:17 final size:16
Alignment explanation
Indices: 27598831--27598865 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
27598821 CCACATGGGC
*
27598831 TGAGCACATGCCCATG
1 TGAGCACATACCCATG
27598847 TGAGCCACATACCCATG
1 TGAG-CACATACCCATG
27598864 TG
1 TG
27598866 CCAGCCTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (16 bp):
TGAGCACATACCCATG
Found at i:27616856 original size:26 final size:27
Alignment explanation
Indices: 27616827--27616893 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
27616817 TTAATAAAAA
* *
27616827 TAATAATAAATAAT-TTAATTATATTT
1 TAATAATAAATAATATTAAATATAATT
* *
27616853 TAAT-ATAATTATTATTAAATATAATT
1 TAATAATAAATAATATTAAATATAATT
27616879 TAATAA-AAATAATAT
1 TAATAATAAATAATAT
27616894 ATAATTTAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 7 0.21
26 25 0.76
27 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TAATAATAAATAATATTAAATATAATT
Found at i:27616863 original size:61 final size:58
Alignment explanation
Indices: 27616783--27616922 Score: 199
Period size: 61 Copynumber: 2.3 Consensus size: 58
27616773 GATTATTTTT
* * *
27616783 ATTAAATTTTAATAGAATTATTATTAAATATGATTTAATAAAAATAATAATAAATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAAT-AT--ATAATTTA
27616844 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTA
* *
27616902 GTAATATTCTTAATATAATTA
1 ATTATATT-TTAATATAATTA
27616923 CTTTTATATT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
58 14 0.19
59 12 0.16
60 2 0.03
61 45 0.62
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (58 bp):
ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTA
Found at i:27616873 original size:16 final size:16
Alignment explanation
Indices: 27616793--27616878 Score: 54
Period size: 16 Copynumber: 5.6 Consensus size: 16
27616783 ATTAAATTTT
*
27616793 AATAGAATTATTATTA
1 AATATAATTATTATTA
* *
27616809 AATATGA-T-TTAATA
1 AATATAATTATTATTA
* * * *
27616823 AAAATAATAATAAAT-
1 AATATAATTATTATTA
* *
27616838 AATTTAATTA-TATTTT
1 AATATAATTATTA-TTA
27616854 AATATAATTATTATTA
1 AATATAATTATTATTA
27616870 AATATAATT
1 AATATAATT
27616879 TAATAAAAAT
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
14 11 0.22
15 9 0.18
16 29 0.57
17 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
AATATAATTATTATTA
Found at i:27616949 original size:32 final size:31
Alignment explanation
Indices: 27616913--27616980 Score: 91
Period size: 32 Copynumber: 2.2 Consensus size: 31
27616903 TAATATTCTT
*
27616913 AATATAATTACTTTTATATTAAATTATATTAA
1 AATATAATTACTTTTATATTAAAATAT-TTAA
** *
27616945 AATATTTTTATTTTTATATTAAAATATTTAA
1 AATATAATTACTTTTATATTAAAATATTTAA
27616976 AATAT
1 AATAT
27616981 TTTATTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 9 0.28
32 23 0.72
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
AATATAATTACTTTTATATTAAAATATTTAA
Found at i:27616984 original size:30 final size:32
Alignment explanation
Indices: 27616924--27616987 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
27616914 ATATAATTAC
*
27616924 TTTTATATTAAATTATATTAAAATATTTTTAT
1 TTTTATATTAAAATATATTAAAATATTTTTAT
27616956 TTTTATATTAAAATAT-TTAAAATA-TTTTAT
1 TTTTATATTAAAATATATTAAAATATTTTTAT
27616986 TT
1 TT
27616988 AATACATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 8 0.26
31 8 0.26
32 15 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
TTTTATATTAAAATATATTAAAATATTTTTAT
Found at i:27616999 original size:24 final size:24
Alignment explanation
Indices: 27616936--27617003 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 24
27616926 TTATATTAAA
**
27616936 TTATATTAAAATATTT-TTAT-TT
1 TTATATTAAAATATTTAAAATATT
27616958 TTATATTAAAATATTTAAAATATT
1 TTATATTAAAATATTTAAAATATT
27616982 TTAT-TTAATACATA-TTAAAATA
1 TTATATTAA-A-ATATTTAAAATA
27617004 ATGAACTATC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
22 16 0.40
23 6 0.15
24 15 0.38
25 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (24 bp):
TTATATTAAAATATTTAAAATATT
Found at i:27622591 original size:21 final size:21
Alignment explanation
Indices: 27622567--27622607 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
27622557 CAAATAAAAG
27622567 GAAAAAAAACCTAAAAATGGT
1 GAAAAAAAACCTAAAAATGGT
**
27622588 GAAAACGAACCTAAAAATGG
1 GAAAAAAAACCTAAAAATGG
27622608 ACAAATCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.17, T:0.12
Consensus pattern (21 bp):
GAAAAAAAACCTAAAAATGGT
Found at i:27624917 original size:20 final size:20
Alignment explanation
Indices: 27624892--27624929 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27624882 ATGCAAATTA
27624892 TTATTCCTAGAAAATAAAAT
1 TTATTCCTAGAAAATAAAAT
*
27624912 TTATTCTTAGAAAATAAA
1 TTATTCCTAGAAAATAAA
27624930 TTCTCACTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (20 bp):
TTATTCCTAGAAAATAAAAT
Found at i:27625397 original size:30 final size:30
Alignment explanation
Indices: 27625362--27625419 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
27625352 TAGACACTTC
*
27625362 CACACGGGT-GATCCATACGCCCGTGTGTGA
1 CACACGGGTAGA-CCACACGCCCGTGTGTGA
27625392 CACACGGGTAGACCACACGCCCGTGTGT
1 CACACGGGTAGACCACACGCCCGTGTGT
27625420 CATGGCTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.21, C:0.33, G:0.29, T:0.17
Consensus pattern (30 bp):
CACACGGGTAGACCACACGCCCGTGTGTGA
Found at i:27630263 original size:6 final size:6
Alignment explanation
Indices: 27630248--27630298 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
27630238 AGTCCATTTA
* * * * *
27630248 TTTA-T TTTATT TTTATT TTTCTT TTTCTT TTTAAT TTTATC TTTCTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
27630295 TTTA
1 TTTA
27630299 ATTATTTTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:27630278 original size:18 final size:18
Alignment explanation
Indices: 27630248--27630301 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
27630238 AGTCCATTTA
* *
27630248 TTTA-TTTTATTTTTATT
1 TTTATTTTTCTTTTTAAT
*
27630265 TTTCTTTTTCTTTTTAAT
1 TTTATTTTTCTTTTTAAT
*
27630283 TTTATCTTTCTTTTTAAT
1 TTTATTTTTCTTTTTAAT
27630301 T
1 T
27630302 ATTTTTGAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 3 0.10
18 28 0.90
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATTTTTCTTTTTAAT
Found at i:27630285 original size:24 final size:24
Alignment explanation
Indices: 27630252--27630297 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
27630242 CATTTATTTA
* *
27630252 TTTTATTTTTATTTTTCTTTTTCT
1 TTTTAATTTTATCTTTCTTTTTCT
27630276 TTTTAATTTTATCTTTCTTTTT
1 TTTTAATTTTATCTTTCTTTTT
27630298 AATTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTAATTTTATCTTTCTTTTTCT
Found at i:27634629 original size:25 final size:25
Alignment explanation
Indices: 27634595--27634652 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
27634585 ACAAAGTTAC
27634595 TTAGTTCAGTCACATCTTACTTTGG
1 TTAGTTCAGTCACATCTTACTTTGG
27634620 TTAGTTCAGTCACATCTTACTTTGG
1 TTAGTTCAGTCACATCTTACTTTGG
27634645 TTATGTTC
1 TTA-GTTC
27634653 CGTAAGTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 28 0.88
26 4 0.12
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.47
Consensus pattern (25 bp):
TTAGTTCAGTCACATCTTACTTTGG
Found at i:27635781 original size:22 final size:22
Alignment explanation
Indices: 27635756--27635806 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
27635746 AGCCTATCTT
27635756 GAGACATC-GTTCTCTATGTCTC
1 GAGACA-CGGTTCTCTATGTCTC
27635778 GAGACACGGTTCTCTATGTCTC
1 GAGACACGGTTCTCTATGTCTC
*
27635800 GAAACAC
1 GAGACAC
27635807 AACATTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (22 bp):
GAGACACGGTTCTCTATGTCTC
Found at i:27637970 original size:43 final size:43
Alignment explanation
Indices: 27637909--27638067 Score: 141
Period size: 43 Copynumber: 3.7 Consensus size: 43
27637899 AAAGCTCGTA
27637909 CAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAT
1 CAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAT
* * *
27637952 CAATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAAT-G
1 CAATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAATCAAATAT
* * * * *
27637994 CGATGCCGATGTCCCCA-ACATGGTCTTACACT-TAAATCTCAA-AT
1 CAATGCCAACGT-CCCAGACGTGGTCTTACA-TGT-AATC-AAATAT
*
27638038 CGATGCCAACGTCCCAGACGTGGTCTTACA
1 CAATGCCAACGTCCCAGACGTGGTCTTACA
27638068 AGAAAACACA
Statistics
Matches: 93, Mismatches: 13, Indels: 19
0.74 0.10 0.15
Matches are distributed among these distances:
42 21 0.23
43 47 0.51
44 25 0.27
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (43 bp):
CAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAT
Found at i:27641112 original size:37 final size:36
Alignment explanation
Indices: 27641046--27641147 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 36
27641036 ATTTGAATAT
** * *
27641046 TTTATAA-G-ATTTTTAAAATTTTAATAATTTTTTAA
1 TTTATAATGTATTTTTTTAATTTTTAGAATTTTTT-A
27641081 TTCTATAAT-TATTTTTTTATATTTTT-GAATTTTTTA
1 TT-TATAATGTATTTTTTTA-ATTTTTAGAATTTTTTA
*
27641117 TTTATAATGTTTTTTTTTAATTTTTAGAATT
1 TTTATAATGTATTTTTTTAATTTTTAGAATT
27641148 AGGATAAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
35 14 0.25
36 22 0.39
37 15 0.27
38 5 0.09
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (36 bp):
TTTATAATGTATTTTTTTAATTTTTAGAATTTTTTA
Found at i:27656229 original size:28 final size:30
Alignment explanation
Indices: 27656198--27656262 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
27656188 AGTCAAACTT
*
27656198 AAAAAAAA-TT-AATAGACTAGTGATTTAA
1 AAAAAAAATTTGAATAGACTAGTGAATTAA
**
27656226 AAAAAAAATTTGAATAGTTTAGTGAATTAA
1 AAAAAAAATTTGAATAGACTAGTGAATTAA
*
27656256 ATAAAAA
1 AAAAAAA
27656263 CTTTCAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 8 0.26
29 2 0.06
30 21 0.68
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (30 bp):
AAAAAAAATTTGAATAGACTAGTGAATTAA
Found at i:27656278 original size:31 final size:30
Alignment explanation
Indices: 27656215--27656279 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
27656205 ATTAATAGAC
* * *
27656215 TAGTGATTTAAAAAAAAAATTTGAATAGTT
1 TAGTGAATTAAAAAAAAAATTTAAATAATT
* *
27656245 TAGTGAATTAAATAAAAACTTTCAAATAATT
1 TAGTGAATTAAAAAAAAAATTT-AAATAATT
27656276 TAGT
1 TAGT
27656280 AATCATTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (30 bp):
TAGTGAATTAAAAAAAAAATTTAAATAATT
Found at i:27656440 original size:33 final size:33
Alignment explanation
Indices: 27656398--27656460 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
27656388 GTCACTTAAC
27656398 AATTAGATTTAGGTTTAATTGTTTGTAATTACA
1 AATTAGATTTAGGTTTAATTGTTTGTAATTACA
* *
27656431 AATTAGATTTGGGTTTACTTGTTTGTAATT
1 AATTAGATTTAGGTTTAATTGTTTGTAATT
27656461 GAGAGATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.51
Consensus pattern (33 bp):
AATTAGATTTAGGTTTAATTGTTTGTAATTACA
Found at i:27685779 original size:13 final size:13
Alignment explanation
Indices: 27685757--27685789 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
27685747 AAGGATTTGT
27685757 TTAT-TAAACTAA
1 TTATCTAAACTAA
27685769 TTATCTAAACTAA
1 TTATCTAAACTAA
*
27685782 TTAACTAA
1 TTATCTAA
27685790 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:27688769 original size:25 final size:25
Alignment explanation
Indices: 27688676--27688767 Score: 75
Period size: 26 Copynumber: 3.7 Consensus size: 25
27688666 TATGTTTTTC
* * *
27688676 AAAATAAAATAATAAAATTGAAA-TG
1 AAAATAAAATAAAAAAAAT-AAAGTA
* *
27688701 AAAATAAAAATCAAAAGAA-AAAG-A
1 AAAAT-AAAATAAAAAAAATAAAGTA
27688725 AAAAT-AAATAAAATAAAATAAAGTA
1 AAAATAAAATAAAA-AAAATAAAGTA
27688750 AAAATAAGAATAAAAAAA
1 AAAATAA-AATAAAAAAA
27688768 TAGGAGGATT
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
22 7 0.13
23 3 0.06
24 12 0.23
25 11 0.21
26 13 0.25
27 7 0.13
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.16
Consensus pattern (25 bp):
AAAATAAAATAAAAAAAATAAAGTA
Found at i:27693519 original size:28 final size:28
Alignment explanation
Indices: 27693453--27693580 Score: 175
Period size: 28 Copynumber: 4.5 Consensus size: 28
27693443 CATGAGATTG
* * **
27693453 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
27693482 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
27693510 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
27693539 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
27693567 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
27693581 GACTTACTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 45 0.51
29 44 0.49
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:27693542 original size:57 final size:57
Alignment explanation
Indices: 27693453--27693580 Score: 186
Period size: 57 Copynumber: 2.2 Consensus size: 57
27693443 CATGAGATTG
*
27693453 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
* * * *
27693510 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATATA
*
27693567 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
27693581 GACTTACTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
Found at i:27697461 original size:39 final size:40
Alignment explanation
Indices: 27697416--27697587 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
27697406 GCTCCTCGTT
* * *
27697416 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
27697456 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
27697495 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
27697535 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
27697575 CAAATGCCTTCGG
1 CAAATGCCTTCGG
27697588 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:27697516 original size:40 final size:39
Alignment explanation
Indices: 27697418--27697640 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
27697408 TCCTCGTTCA
* * * *
27697418 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
27697457 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
27697496 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
27697536 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
27697576 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
27697617 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
27697641 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:27697600 original size:80 final size:79
Alignment explanation
Indices: 27697416--27697640 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
27697406 GCTCCTCGTT
* * * * *
27697416 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
27697480 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
27697495 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
27697560 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
27697575 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
27697639 GA
63 GA
27697641 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:27697649 original size:41 final size:41
Alignment explanation
Indices: 27697572--27697649 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
27697562 TTTGTATCTC
* * *
27697572 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
27697613 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
27697650 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:27703850 original size:40 final size:40
Alignment explanation
Indices: 27703750--27703920 Score: 222
Period size: 39 Copynumber: 4.3 Consensus size: 40
27703740 AGCTCCTGTT
* * *
27703750 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
27703790 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
27703829 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
27703869 CAAAGGCCTTCGGG-CTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
27703908 CAAATGCCTTCGG
1 CAAATGCCTTCGG
27703921 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
39 67 0.56
40 52 0.44
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:27703933 original size:79 final size:79
Alignment explanation
Indices: 27703750--27703963 Score: 227
Period size: 79 Copynumber: 2.7 Consensus size: 79
27703740 AGCTCCTGTT
* * *
27703750 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGA
27703815 TTTAATAACTCGCA
66 TTTAATAACTCGCA
* * * * *
27703829 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGG-CTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG
* *
27703893 AATTT-GTATCTCGCA
65 -ATTTAATAACTCGCA
* * * * * *
27703908 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGAC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCA-CACAAGGCCTTCGGGAC
27703964 TTAGCTCGGA
Statistics
Matches: 110, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
78 3 0.03
79 88 0.80
80 19 0.17
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGA
TTTAATAACTCGCA
Found at i:27710129 original size:39 final size:40
Alignment explanation
Indices: 27710084--27710255 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
27710074 GCTCCTCGTT
* * *
27710084 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
27710124 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
27710163 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
27710203 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
27710243 CAAATGCCTTCGG
1 CAAATGCCTTCGG
27710256 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:27710184 original size:40 final size:39
Alignment explanation
Indices: 27710086--27710308 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
27710076 TCCTCGTTCA
* * * *
27710086 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
27710125 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
27710164 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
27710204 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
27710244 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
27710285 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
27710309 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:27710268 original size:80 final size:79
Alignment explanation
Indices: 27710084--27710308 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
27710074 GCTCCTCGTT
* * * * *
27710084 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
27710148 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
27710163 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
27710228 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
27710243 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
27710307 GA
63 GA
27710309 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:27710317 original size:41 final size:41
Alignment explanation
Indices: 27710240--27710317 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
27710230 TTTGTATCTC
* * *
27710240 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
27710281 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
27710318 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:27716468 original size:39 final size:40
Alignment explanation
Indices: 27716423--27716594 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
27716413 GCTCCTCGTT
* * *
27716423 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
27716463 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
27716502 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
27716542 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
27716582 CAAATGCCTTCGG
1 CAAATGCCTTCGG
27716595 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:27716523 original size:40 final size:39
Alignment explanation
Indices: 27716425--27716647 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
27716415 TCCTCGTTCA
* * * *
27716425 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
27716464 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
27716503 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
27716543 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
27716583 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
27716624 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
27716648 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:27716607 original size:80 final size:79
Alignment explanation
Indices: 27716423--27716647 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
27716413 GCTCCTCGTT
* * * * *
27716423 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
27716487 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
27716502 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
27716567 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
27716582 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
27716646 GA
63 GA
27716648 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:27716656 original size:41 final size:41
Alignment explanation
Indices: 27716579--27716656 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
27716569 TTTGTATCTC
* * *
27716579 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
27716620 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
27716657 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:27725891 original size:21 final size:21
Alignment explanation
Indices: 27725846--27725895 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
27725836 GGGTCTATAA
*
27725846 GCCCATGTGAAGGCTACACAC
1 GCCCATGTGAAGGCGACACAC
* * *
27725867 GCCCATGTGAAGGGGAGACAT
1 GCCCATGTGAAGGCGACACAC
27725888 GCCCATGT
1 GCCCATGT
27725896 AACTCACTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.30, T:0.16
Consensus pattern (21 bp):
GCCCATGTGAAGGCGACACAC
Found at i:27726171 original size:17 final size:17
Alignment explanation
Indices: 27726149--27726184 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
27726139 TCGAAATGAT
27726149 CCCTAACCATTGGTGAC
1 CCCTAACCATTGGTGAC
27726166 CCCTAACCATTGGTGAC
1 CCCTAACCATTGGTGAC
27726183 CC
1 CC
27726185 AGAATTATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.22
Consensus pattern (17 bp):
CCCTAACCATTGGTGAC
Found at i:27730306 original size:17 final size:16
Alignment explanation
Indices: 27730270--27730305 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
27730260 CTTTTAAAAC
27730270 AAAAATAATATAATAT
1 AAAAATAATATAATAT
27730286 AAAAATAA-ATAATAT
1 AAAAATAATATAATAT
27730301 AAAAA
1 AAAAA
27730306 ACGCTCATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAAATAATATAATAT
Found at i:27739811 original size:31 final size:30
Alignment explanation
Indices: 27739755--27739812 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
27739745 GACTAGTTAT
** *
27739755 TTAAAAAAAACTTTTGAATAGTTTAGTGAA
1 TTAAAAAAAACTTTCAAATAATTTAGTGAA
27739785 TTAAATAAAAACTTTCAAATAATTTAGT
1 TTAAA-AAAAACTTTCAAATAATTTAGT
27739813 AATCATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (30 bp):
TTAAAAAAAACTTTCAAATAATTTAGTGAA
Found at i:27754883 original size:32 final size:32
Alignment explanation
Indices: 27754847--27754908 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
27754837 AGCTTTTGGT
27754847 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
* *
27754879 TTTTTCGTGTTGTCAAATAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
27754909 AAAATAGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:27755719 original size:46 final size:47
Alignment explanation
Indices: 27755575--27755822 Score: 171
Period size: 46 Copynumber: 5.3 Consensus size: 47
27755565 TTTGTGTGCT
* * * *
27755575 AGTGTAAGACATGTCTGGGACATGCATTGGCCACATTATG-AGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCATGATGTAGAGCC
* * * * *
27755621 AATGTAAGACCATGTCTGGAACATGACATCGGCAT--TGA-GACCAGAGCT
1 AGTGTAAGA-CATGTCTGGGACATG-CATCGGCCTCATGATG--TAGAGCC
*
27755669 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGA-GATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTC-ATGATGTAGAGCC
* *
27755715 AGTGTAAAACATGTCTGGGACATGCATTGG-CTACATGATGT---GCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CATGATGTAGAGCC
* * * *
27755759 AGTGTAAGACCATGTTTGGGACATTACATCGACCT-A-G-TGTGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACA-TGCATCGGCCTCATGATGT-AGAGCC
27755806 AGTGTAAGACCATGTCT
1 AGTGTAAGA-CATGTCT
27755823 CAGACATGGC
Statistics
Matches: 162, Mismatches: 22, Indels: 35
0.74 0.10 0.16
Matches are distributed among these distances:
43 3 0.02
44 12 0.07
45 17 0.10
46 59 0.36
47 48 0.30
48 22 0.14
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCATGATGTAGAGCC
Found at i:27761116 original size:40 final size:40
Alignment explanation
Indices: 27761037--27761253 Score: 273
Period size: 40 Copynumber: 5.5 Consensus size: 40
27761027 AAGCCAATTA
* * * *
27761037 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
27761076 CCTTCGGGACTTAGCCTGGATATAGT-ACTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAAC-TCGCACAAATG
27761116 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
27761156 CCTTCGGGACTTTGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
** * * *
27761196 CCTTCGACACTT-GCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
27761235 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
27761254 TTATCATCCA
Statistics
Matches: 159, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
38 1 0.01
39 47 0.30
40 109 0.69
41 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:27762378 original size:92 final size:93
Alignment explanation
Indices: 27762224--27762395 Score: 233
Period size: 92 Copynumber: 1.9 Consensus size: 93
27762214 TTACGAGAGC
* *
27762224 CAGTGTAAGACCATGTCCGGGACATGGCATCAACATTGAGACGAGAGCTAGTGTAAGACATGTCT
1 CAGTGTAAGACCATGTCCGGGACATGGCATCAACATTGAGACGAGAGCCAATGTAAGACATGTCT
27762289 GGGACAT-GCATCGGCTACATGATGTGT
66 GGGACATGGCATCGGCTACATGATGTGT
* * * * **
27762316 CAGTGTAAGATCATGTCTGGGACATGGCGTCGAC-TT-AGTGTGAGAGCCAATGTAAGACCATGT
1 CAGTGTAAGACCATGTCCGGGACATGGCATCAACATTGAG-ACGAGAGCCAATGTAAGA-CATGT
27762379 CTGGGACATGGCATCGG
64 CTGGGACATGGCATCGG
27762396 TATTATACCC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
90 2 0.03
91 16 0.23
92 44 0.64
93 7 0.10
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (93 bp):
CAGTGTAAGACCATGTCCGGGACATGGCATCAACATTGAGACGAGAGCCAATGTAAGACATGTCT
GGGACATGGCATCGGCTACATGATGTGT
Found at i:27762381 original size:47 final size:46
Alignment explanation
Indices: 27762218--27762394 Score: 189
Period size: 47 Copynumber: 3.8 Consensus size: 46
27762208 GCCAAATTAC
* * *
27762218 GAGAGCCAGTGTAAGACCATGTCCGGGACATGGCATCAACATTGAGAC
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TT-AGAT
* * *
27762266 GAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TACAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTAGAT
* * * * *
27762309 GATGTGTCAGTGTAAGATCATGTCTGGGACATGGCGTCGACTTAGTGT
1 GA-GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTAG-AT
*
27762357 GAGAGCCAATGTAAGACCATGTCTGGGACATGGCATCG
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
27762395 GTATTATACC
Statistics
Matches: 106, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
43 4 0.04
44 12 0.11
45 14 0.13
46 12 0.11
47 46 0.43
48 18 0.17
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (46 bp):
GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTAGAT
Found at i:27768959 original size:23 final size:23
Alignment explanation
Indices: 27768933--27768979 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
27768923 CATTCTCTTG
*
27768933 TCATACCCATGCCATTACTATGC
1 TCATACCCATGCCATTACCATGC
* * *
27768956 TCATTCTCATGCTATTACCATGC
1 TCATACCCATGCCATTACCATGC
27768979 T
1 T
27768980 AATGTCACGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (23 bp):
TCATACCCATGCCATTACCATGC
Found at i:27785807 original size:13 final size:13
Alignment explanation
Indices: 27785767--27785807 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
27785757 GAAGTACGAT
27785767 TCACACGGGCATG
1 TCACACGGGCATG
* *
27785780 TAACACAGGCATG
1 TCACACGGGCATG
*
27785793 TCACACGGGCGTG
1 TCACACGGGCATG
27785806 TC
1 TC
27785808 CCTGGCGAGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.17
Consensus pattern (13 bp):
TCACACGGGCATG
Found at i:27789164 original size:46 final size:48
Alignment explanation
Indices: 27789077--27789179 Score: 147
Period size: 46 Copynumber: 2.2 Consensus size: 48
27789067 TACATAAATT
* *
27789077 ATTCCTGTCTCCAATGCCATATATATATAATATGGGCTTACATGGCTC
1 ATTCCTGTCTCCAAAGCCATATATATATAATATGGACTTACATGGCTC
* *
27789125 ATTCCTGTCTCCAAAGCCATATA-A-CTGATATGGACTTACATGGCTC
1 ATTCCTGTCTCCAAAGCCATATATATATAATATGGACTTACATGGCTC
*
27789171 ATTTCTGTC
1 ATTCCTGTC
27789180 CTGTCCTGTC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
46 27 0.54
47 1 0.02
48 22 0.44
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (48 bp):
ATTCCTGTCTCCAAAGCCATATATATATAATATGGACTTACATGGCTC
Found at i:27792208 original size:46 final size:45
Alignment explanation
Indices: 27792141--27792315 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 45
27792131 TGTAACCCGC
*
27792141 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCAT
* *
27792187 CCATAAGTGAACTCGGACTCAACTCAACGAGCCCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* *** * *
27792233 ACATCTCTCGAACTCGGACTCAACTCAAAGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCAT
* *
27792280 CTATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
27792316 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 65 0.62
47 29 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:27792277 original size:93 final size:93
Alignment explanation
Indices: 27792149--27792319 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
27792139 GCCCATAAGT
* *
27792149 GAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAAGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
27792214 CGAGCCCGGATGCCTAGTTACATCTCTC
66 CGAGCCCGGATGCCTAGTTACATCTCTC
* *
27792242 GAACTCGGACTCAACTCAAAGAGTTC-GGACATTCGCATCTATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAAAGAGCTCAGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
**
27792306 ACGAGTTCGGATGC
65 ACGAGCCCGGATGC
27792320 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAAAGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCCCGGATGCCTAGTTACATCTCTC
Found at i:27792335 original size:46 final size:46
Alignment explanation
Indices: 27792146--27792335 Score: 110
Period size: 46 Copynumber: 4.1 Consensus size: 46
27792136 CCCGCCCATA
* * *
27792146 AGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTC--GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGCTC-GGATGCTCAACCATCC-T
*
27792191 AAGTGAACTCGGACTCAACTCAACGAGCCCGGATGC-CTAGTTA-CATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTC-A---ACCATC-CT
* * * * * * * *
27792241 --CGAACTCGGACTCAACTCAAAGAGTTCGGACATTCGCATCTAT--A
1 AGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGCTCAACCATCCT
*
27792285 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACCATCCT
27792331 AGTGA
1 AGTGA
27792336 CATGTCACTT
Statistics
Matches: 110, Mismatches: 18, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
44 8 0.07
45 3 0.03
46 61 0.55
47 27 0.25
49 4 0.04
50 6 0.05
51 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACCATCCT
Found at i:27807847 original size:25 final size:25
Alignment explanation
Indices: 27807819--27807867 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
27807809 TGGGATAGAG
*
27807819 TTCCTATTCTATTTGAGTCTCTAAT
1 TTCCTAGTCTATTTGAGTCTCTAAT
*
27807844 TTCCTGGTCTATTTGAGTCTCTAA
1 TTCCTAGTCTATTTGAGTCTCTAA
27807868 CTCACTGTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.49
Consensus pattern (25 bp):
TTCCTAGTCTATTTGAGTCTCTAAT
Found at i:27810815 original size:20 final size:20
Alignment explanation
Indices: 27810790--27810830 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
27810780 AAGAATTAAG
27810790 AATGACGGTGTCCGTAAGAT
1 AATGACGGTGTCCGTAAGAT
27810810 AATGACGGTGTCCGTAAGAT
1 AATGACGGTGTCCGTAAGAT
27810830 A
1 A
27810831 TTTTGTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (20 bp):
AATGACGGTGTCCGTAAGAT
Found at i:27815863 original size:6 final size:6
Alignment explanation
Indices: 27815854--27815892 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
27815844 AAATAAAACG
** *
27815854 AAAATA AAAATA AAAATA AAAATA ATCATA ATAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
27815893 CTAATAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:27815897 original size:18 final size:18
Alignment explanation
Indices: 27815863--27815897 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27815853 GAAAATAAAA
27815863 ATAAAAATAAAAATAATC
1 ATAAAAATAAAAATAATC
* *
27815881 ATAATAATAAAACTAAT
1 ATAAAAATAAAAATAAT
27815898 AATTATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAAAATAAAAATAATC
Found at i:27821434 original size:3 final size:3
Alignment explanation
Indices: 27821426--27821460 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
27821416 ACAAGCTTTA
27821426 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27821461 AGAGTAATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:27826000 original size:16 final size:16
Alignment explanation
Indices: 27825962--27826037 Score: 89
Period size: 16 Copynumber: 4.4 Consensus size: 16
27825952 GATTAAACAT
*
27825962 AATTACTTTAATATTA
1 AATTAATTTAATATTA
27825978 AATTTAATTTAATATTA
1 AA-TTAATTTAATATTA
27825995 AATTAATTTAATATTA
1 AATTAATTTAATATTA
*
27826011 AGATAATCATTTTAATATTA
1 A-AT--T-AATTTAATATTA
27826031 AATTAAT
1 AATTAAT
27826038 AAAATACTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
16 19 0.37
17 18 0.35
19 3 0.06
20 12 0.23
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (16 bp):
AATTAATTTAATATTA
Found at i:27826036 original size:11 final size:11
Alignment explanation
Indices: 27825969--27826038 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
27825959 CATAATTACT
27825969 TTAATATTAAA
1 TTAATATTAAA
27825980 TTTAAT-TTAATA
1 -TTAATATTAA-A
*
27825992 TTAA-ATTAAT
1 TTAATATTAAA
27826002 TTAATATTAAGA
1 TTAATATTAA-A
27826014 -TAATCATT---
1 TTAAT-ATTAAA
27826022 TTAATATTAAA
1 TTAATATTAAA
27826033 TTAATA
1 TTAATA
27826039 AAATACTATC
Statistics
Matches: 47, Mismatches: 2, Indels: 19
0.69 0.03 0.28
Matches are distributed among these distances:
8 3 0.06
9 4 0.09
10 4 0.09
11 27 0.57
12 9 0.19
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:27834323 original size:40 final size:40
Alignment explanation
Indices: 27834246--27834463 Score: 289
Period size: 40 Copynumber: 5.5 Consensus size: 40
27834236 CAACTAAGTA
* * * *
27834246 CCTTCGGGATTTA-TCCGGACATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
27834285 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
27834325 CCTTCGGGACTTAGCTCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
27834365 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
27834405 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
* *
27834445 CCGTCGGGGCTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
27834464 TTATCATCCG
Statistics
Matches: 162, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
39 14 0.09
40 148 0.91
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:27838651 original size:55 final size:55
Alignment explanation
Indices: 27838556--27838674 Score: 143
Period size: 55 Copynumber: 2.2 Consensus size: 55
27838546 CTTAAACTTT
* * * * * *
27838556 TAAA-TCAATATTGTCCACGGTTAGGGCACACGGACGTGTGTCATCGCCGTG-TC
1 TAAAGTCAGTATTGCCCACGGGTAGGCCACACGGACATGTGTCATCGCCGTGCCC
* *
27838609 TATAAGTCAGTATTGCCCACGGGTAGGCCACACGGGCATGTGTCATGGCCGTGCCC
1 TA-AAGTCAGTATTGCCCACGGGTAGGCCACACGGACATGTGTCATCGCCGTGCCC
27838665 TAAAGTCAGT
1 TAAAGTCAGT
27838675 GTCTCATACT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 2 0.04
54 2 0.04
55 48 0.87
56 3 0.05
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (55 bp):
TAAAGTCAGTATTGCCCACGGGTAGGCCACACGGACATGTGTCATCGCCGTGCCC
Found at i:27845020 original size:47 final size:46
Alignment explanation
Indices: 27844950--27845118 Score: 150
Period size: 47 Copynumber: 3.7 Consensus size: 46
27844940 TATGTAAGAG
* * *
27844950 CCAGTATAAGACCATGTCTGGGACATGGCATTGGCTTAGAGACGA-CTT-
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTAGA-A-GATCTTA
* *
27844998 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAAGATGTTA
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGAAGATCTTA
* * * *
27845044 GCCAGTGTAAGACATGTCTGGGACATTCATCGG-CT--AAGTTTTGTG
1 -CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGAAGATCT-TA
* *
27845089 CTAGTGTAAGACATGTCTAGGACATGCATC
1 CCAGTGTAAGACATGTCTGGGACATGCATC
27845119 AGCACGTATA
Statistics
Matches: 105, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
44 34 0.32
45 4 0.04
46 12 0.11
47 45 0.43
48 10 0.10
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (46 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGAAGATCTTA
Found at i:27845112 original size:44 final size:46
Alignment explanation
Indices: 27844998--27845118 Score: 158
Period size: 44 Copynumber: 2.7 Consensus size: 46
27844988 GAGACGACTT
27844998 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAAGATGTTAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTC-AAGATGTTAG
* * *
27845045 CCAGTGTAAGACATGTCTGGGACATTCATCGG-CT-AAG-TTTTGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGTT-AG
* *
27845089 CTAGTGTAAGACATGTCTAGGACATGCATC
1 CCAGTGTAAGACATGTCTGGGACATGCATC
27845119 AGCACGTATA
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
43 3 0.04
44 31 0.46
46 2 0.03
47 31 0.46
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (46 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGTTAG
Found at i:27852378 original size:48 final size:48
Alignment explanation
Indices: 27852255--27852439 Score: 173
Period size: 49 Copynumber: 3.9 Consensus size: 48
27852245 TTGGCCACAT
* * * * * *
27852255 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATTGGA-ATTGAG-
1 TATGAAAGCTAGTGTAAGACCTGTCTGGGACATGCA-TCGACCTCGAGA
* * *
27852302 -ACGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGA
1 TATGAAAGCTAGTGTAAGACCTGTCTGGGACATGCATCGACCTCGAGA
* * * *
27852349 TAT-ACAAGCTAGTGTAAGACCTGTCTGGGACACAGCATCGTCCTTGATA
1 TATGA-AAGCTAGTGTAAGACCTGTCTGGGACA-TGCATCGACCTCGAGA
27852398 TATGAAAG-TCAGTGTAAGACCTGTCTGGGACATGACATCGAC
1 TATGAAAGCT-AGTGTAAGACCTGTCTGGGACATG-CATCGAC
27852440 TTTGATGTGT
Statistics
Matches: 116, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
45 3 0.03
46 37 0.32
47 1 0.01
48 28 0.24
49 46 0.40
50 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (48 bp):
TATGAAAGCTAGTGTAAGACCTGTCTGGGACATGCATCGACCTCGAGA
Found at i:27860211 original size:30 final size:30
Alignment explanation
Indices: 27860168--27860229 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
27860158 TTTTTTTAAA
27860168 TTAACTCTTATTTGAACATTTTAAAAAAAT
1 TTAACTCTTATTTGAACATTTTAAAAAAAT
* *
27860198 TTAACT-TTCATTTGAGCATTTTATAAAAAT
1 TTAACTCTT-ATTTGAACATTTTAAAAAAAT
27860228 TT
1 TT
27860230 GACCCAACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.47
Consensus pattern (30 bp):
TTAACTCTTATTTGAACATTTTAAAAAAAT
Found at i:27864899 original size:30 final size:30
Alignment explanation
Indices: 27864876--27864934 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
27864866 GTCTATCTCG
*
27864876 TTTGGGTCACATGGGCATGTGTCTAGCCCA
1 TTTGGGTCACATAGGCATGTGTCTAGCCCA
*
27864906 TTTGGGTCACATAGGCATGTGCCTAGCCC
1 TTTGGGTCACATAGGCATGTGTCTAGCCC
27864935 GTGTGGCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (30 bp):
TTTGGGTCACATAGGCATGTGTCTAGCCCA
Found at i:27866800 original size:12 final size:11
Alignment explanation
Indices: 27866744--27866821 Score: 52
Period size: 11 Copynumber: 7.0 Consensus size: 11
27866734 AAATAAGTCT
*
27866744 AAGAAAATAAA
1 AAGAAAACAAA
* *
27866755 AATAAAACAAC
1 AAGAAAACAAA
* *
27866766 TA-AAAATAAA
1 AAGAAAACAAA
*
27866776 AA-TAAACATAA
1 AAGAAAACA-AA
27866787 AAGGAAAACAAA
1 AA-GAAAACAAA
*
27866799 AAGAAAGCTAAA
1 AAGAAAAC-AAA
27866811 AAGAAAACAAA
1 AAGAAAACAAA
27866822 TAAAATCTAC
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
10 11 0.22
11 21 0.41
12 14 0.27
13 5 0.10
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.09
Consensus pattern (11 bp):
AAGAAAACAAA
Found at i:27867775 original size:15 final size:15
Alignment explanation
Indices: 27867755--27867785 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27867745 TACGATAGCT
27867755 AAAATAAGAATAAAA
1 AAAATAAGAATAAAA
*
27867770 AAAATAAGTATAAAA
1 AAAATAAGAATAAAA
27867785 A
1 A
27867786 TTAATAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (15 bp):
AAAATAAGAATAAAA
Found at i:27867839 original size:13 final size:12
Alignment explanation
Indices: 27867763--27867878 Score: 69
Period size: 12 Copynumber: 9.5 Consensus size: 12
27867753 CTAAAATAAG
27867763 AATAAAAAAAAT
1 AATAAAAAAAAT
* *
27867775 AAGTATAAAAATT
1 AA-TAAAAAAAAT
* *
27867788 AATAAACATAAT
1 AATAAAAAAAAT
27867800 AATAACACAAAAA-
1 AATAA-A-AAAAAT
*
27867813 AAGGAAAAAAAAT
1 AA-TAAAAAAAAT
**
27867826 -A-AAACTAAAT
1 AATAAAAAAAAT
27867836 AATAATAAAAAAT
1 AATAA-AAAAAAT
27867849 AATAAAAAATAA-
1 AATAAAAAA-AAT
* *
27867861 AATAAAATAAAG
1 AATAAAAAAAAT
27867873 AATAAA
1 AATAAA
27867879 GAAATCGAGG
Statistics
Matches: 80, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
10 7 0.09
11 3 0.04
12 39 0.49
13 26 0.32
14 5 0.06
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.18
Consensus pattern (12 bp):
AATAAAAAAAAT
Found at i:27867856 original size:27 final size:26
Alignment explanation
Indices: 27867817--27867877 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
27867807 CAAAAAAAGG
*
27867817 AAAAAA-AATAAAACT-AAATAATAAT
1 AAAAAATAATAAAAATAAAATAA-AAT
27867842 AAAAAATAATAAAAAATAAAATAAAAT
1 AAAAAATAAT-AAAAATAAAATAAAAT
*
27867869 AAAGAATAA
1 AAAAAATAA
27867878 AGAAATCGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 6 0.19
26 3 0.10
27 16 0.52
28 6 0.19
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (26 bp):
AAAAAATAATAAAAATAAAATAAAAT
Found at i:27867859 original size:17 final size:17
Alignment explanation
Indices: 27867839--27867883 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
27867829 ACTAAATAAT
27867839 AATAAAAAATAATAAAA
1 AATAAAAAATAATAAAA
*
27867856 AATAAAATAA-AATAAAG
1 AATAAAA-AATAATAAAA
27867873 AATAAAGAAAT
1 AATAAA-AAAT
27867884 CGAGGAAGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (17 bp):
AATAAAAAATAATAAAA
Found at i:27867859 original size:20 final size:20
Alignment explanation
Indices: 27867754--27867870 Score: 55
Period size: 20 Copynumber: 5.7 Consensus size: 20
27867744 ATACGATAGC
27867754 TAAAATAAGAATAA-AAAAAA
1 TAAAATAA-AATAATAAAAAA
* *
27867774 TAAGTATAAAAATTAAT-AAACA
1 TAA-AAT-AAAA-TAATAAAAAA
* * *
27867796 TAATAATAACACAA-AAAAAG
1 TAA-AATAAAATAATAAAAAA
* *
27867816 GAAAA-AAAATAA-AACTAAA
1 TAAAATAAAATAATAA-AAAA
27867835 TAATAATAAAAAATAATAAAAAA
1 TAA-AAT--AAAATAATAAAAAA
27867858 TAAAATAAAATAA
1 TAAAATAAAATAA
27867871 AGAATAAAGA
Statistics
Matches: 71, Mismatches: 15, Indels: 22
0.66 0.14 0.20
Matches are distributed among these distances:
18 7 0.10
19 6 0.08
20 19 0.27
21 7 0.10
22 17 0.24
23 13 0.18
24 2 0.03
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.19
Consensus pattern (20 bp):
TAAAATAAAATAATAAAAAA
Found at i:27872789 original size:19 final size:18
Alignment explanation
Indices: 27872767--27872820 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
27872757 AACAAAAGAA
27872767 AAATTAGAAAGTAAAAAT-T
1 AAATTA-AAA-TAAAAATAT
*
27872786 AAATTAAAAACAAAAATAT
1 AAATT-AAAATAAAAATAT
*
27872805 AAAATAAAATAAAAAT
1 AAATTAAAATAAAAAT
27872821 GGCTAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 16 0.53
19 13 0.43
20 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (18 bp):
AAATTAAAATAAAAATAT
Found at i:27874972 original size:40 final size:40
Alignment explanation
Indices: 27874893--27875060 Score: 239
Period size: 40 Copynumber: 4.2 Consensus size: 40
27874883 CGGATGATAA
* * *
27874893 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * * * * *
27874933 CCGGGCTATGTCCCGAAGGCATTTATGCTAGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
27874973 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
*
27875013 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
27875053 CC-GGCTAA
1 CCGGGCTAA
27875061 ATCCTGAAGA
Statistics
Matches: 112, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 6 0.05
40 106 0.95
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:27875323 original size:22 final size:22
Alignment explanation
Indices: 27875298--27875342 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
27875288 GAATGTGCAT
*
27875298 ATATGAA-GTTATTCATTTAGTC
1 ATATGAATGTTATAC-TTTAGTC
27875320 ATATGAATGTTATACTTTAGTC
1 ATATGAATGTTATACTTTAGTC
27875342 A
1 A
27875343 AAACTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (22 bp):
ATATGAATGTTATACTTTAGTC
Found at i:27880497 original size:16 final size:18
Alignment explanation
Indices: 27880476--27880516 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
27880466 TTAGTCACCT
27880476 TTTTCTATTT-TT-TTTC
1 TTTTCTATTTATTGTTTC
*
27880492 TTTTCTTTTTATTGTTTC
1 TTTTCTATTTATTGTTTC
27880510 TTCTTCT
1 TT-TTCT
27880517 GTTCTTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.43
17 2 0.10
18 6 0.29
19 4 0.19
ACGTcount: A:0.05, C:0.15, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTCTATTTATTGTTTC
Found at i:27884121 original size:47 final size:46
Alignment explanation
Indices: 27883918--27884196 Score: 190
Period size: 49 Copynumber: 5.9 Consensus size: 46
27883908 GGGATATGTT
* * *
27883918 GCCGATGTCATGTCCCGGACATGGTCTTATACTGGCTATCATCATTGAG
1 GCCGATG-CATGTCCCAGACA-GGTCTTACACTGGCTATCATC-TCGAG
* * * * * ** *
27883967 GCTGATAACATGTCCCAGACATGGTCTTATACTAGCTCTTGTCTATAC-AC
1 GCCGAT-GCATGTCCCAGACA-GGTCTTACACTGGCTATCATC--T-CGAG
* * * * * *
27884017 GCTGATGCATGTCCCAGATATGTCTTACACTAGC-A-CAACTCTTA-
1 GCCGATGCATGTCCCAGACAGGTCTTACACTGGCTATCATCTC-GAG
* *
27884061 GCCGATGCGTGTCCTAGACAGGTCTTACACTGGCTATCATCGTCGAG
1 GCCGATGCATGTCCCAGACAGGTCTTACACTGGCTATCATC-TCGAG
* * * *
27884108 GTCGATGCATGTCCCAGACATGTCTTACACTGGC-ACTCATTCTCTAT
1 GCCGATGCATGTCCCAGACAGGTCTTACACTGGCTA-TCA-TCTCGAG
27884155 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCAT
1 GCCGATG-CATGTCCCAGACA-GGTCTTACACTGGCTATCAT
27884197 ATTGTGGTTG
Statistics
Matches: 183, Mismatches: 33, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
43 1 0.01
44 29 0.16
45 2 0.01
46 6 0.03
47 44 0.24
48 28 0.15
49 63 0.34
50 10 0.05
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACAGGTCTTACACTGGCTATCATCTCGAG
Found at i:27884217 original size:95 final size:91
Alignment explanation
Indices: 27884020--27884239 Score: 271
Period size: 95 Copynumber: 2.4 Consensus size: 91
27884010 TATACACGCT
* * * *
27884020 GATGCATGTCCCAGATATGTCTTACACTAGCACAACTCTTAGCCGATGCGTGTCCTAGACAGGTC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTTAGCCGATGCATGTCCCAGACAGGTC
*
27884085 TTACACTGGCTATCATCGTCGAGGTC
66 TTACACTGGCTATCATCATCGAGGTC
* *
27884111 GATGCATGTCCCAGACATGTCTTACACTGGCACTCATTCTCTATGCCGATGCCATGTCCCAGACA
1 GATGCATGTCCCAGACATGTCTTACACTGGCAC-AACTCT-TA-GCCGATG-CATGTCCCAGACA
* * *
27884176 TGGTCTTACACTGGCTATCAT-ATTGTGGTT
62 -GGTCTTACACTGGCTATCATCATCGAGGTC
* * *
27884206 GGTGCATGTCCCAAACATGTTTTACACTGGCACA
1 GATGCATGTCCCAGACATGTCTTACACTGGCACA
27884240 CAAGTAATCC
Statistics
Matches: 110, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
91 31 0.28
92 4 0.04
93 2 0.02
94 7 0.06
95 46 0.42
96 20 0.18
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (91 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTTAGCCGATGCATGTCCCAGACAGGTC
TTACACTGGCTATCATCATCGAGGTC
Found at i:27887538 original size:16 final size:16
Alignment explanation
Indices: 27887517--27887547 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27887507 TCTCAGAAGA
*
27887517 ATAAAGAATACAAAAC
1 ATAAAGAAAACAAAAC
27887533 ATAAAGAAAACAAAA
1 ATAAAGAAAACAAAA
27887548 AACTCCTGAA
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:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
ATAAAGAAAACAAAAC
Found at i:27891745 original size:55 final size:55
Alignment explanation
Indices: 27891686--27891792 Score: 133
Period size: 55 Copynumber: 1.9 Consensus size: 55
27891676 TTAATTTGAC
** *
27891686 AGGTTCGCCCACGGGTGTTAGACACGGGCGTGTCGCACGCCCATGCTGTTTTAAT
1 AGGTTCGCCCACGGGTCCTAGACACGAGCGTGTCGCACGCCCATGCTGTTTTAAT
* * *** *
27891741 AGGTTCGTCCACGGTTCCTCTTCACGAGCGTGTCGCACGCCCATGTTGTTTT
1 AGGTTCGCCCACGGGTCCTAGACACGAGCGTGTCGCACGCCCATGCTGTTTT
27891793 GGCAGGCTCG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.14, C:0.29, G:0.28, T:0.29
Consensus pattern (55 bp):
AGGTTCGCCCACGGGTCCTAGACACGAGCGTGTCGCACGCCCATGCTGTTTTAAT
Found at i:27894777 original size:30 final size:30
Alignment explanation
Indices: 27894719--27894777 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
27894709 AAGAGAAAGA
* *
27894719 AAAAGTAAATTAATTAGTAATAATAATAAT
1 AAAAGTAAATTAATTAGTAAGAAAAATAAT
*
27894749 AAAATTAAATTAAATT-GTAAGAAAAATAA
1 AAAAGTAAATT-AATTAGTAAGAAAAATAA
27894778 ATGGCTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.31
Consensus pattern (30 bp):
AAAAGTAAATTAATTAGTAAGAAAAATAAT
Found at i:27899613 original size:15 final size:15
Alignment explanation
Indices: 27899593--27899621 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27899583 GTATTGTTGC
27899593 TTGATAACATGGTGA
1 TTGATAACATGGTGA
27899608 TTGATAACATGGTG
1 TTGATAACATGGTG
27899622 TGCGACGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (15 bp):
TTGATAACATGGTGA
Found at i:27910462 original size:30 final size:30
Alignment explanation
Indices: 27910426--27910482 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
27910416 TCACTTCATC
27910426 CCAAAACGACTTTGGTAAACAAGCATTCGA
1 CCAAAACGACTTTGGTAAACAAGCATTCGA
* *
27910456 CCAAAACGACTTTGGTTAATAAGCATT
1 CCAAAACGACTTTGGTAAACAAGCATT
27910483 TGACAACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.25
Consensus pattern (30 bp):
CCAAAACGACTTTGGTAAACAAGCATTCGA
Found at i:27912357 original size:40 final size:40
Alignment explanation
Indices: 27912266--27912435 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 40
27912256 TCCTCGTTCA
* * * * *
27912266 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
27912305 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGGACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
27912345 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
27912385 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
27912425 AAGGCCTTCGG
1 AATGCCTTCGG
27912436 ATCTTAGTCT
Statistics
Matches: 110, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 31 0.28
40 79 0.72
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:27912367 original size:79 final size:80
Alignment explanation
Indices: 27912266--27912412 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 80
27912256 TCCTCGTTCA
* * * * *
27912266 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-CATGCCTTCGGGACGTAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGGAT
27912330 TTAACAACTCGGACG
66 TTAACAACTCGGACG
* * *
27912345 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACGAATGCCCTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGGAT
27912410 TTA
66 TTA
27912413 GTATCTCGCA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 34 0.58
80 25 0.42
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGGAT
TTAACAACTCGGACG
Found at i:27920230 original size:40 final size:40
Alignment explanation
Indices: 27920139--27920361 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
27920129 TCCTCGTTCA
* * * * *
27920139 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
27920178 AATGCCTTCGGGACTTAACCTGGAATTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
27920218 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
27920258 AATGCCTTCAGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
27920298 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
27920338 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
27920362 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 35 0.22
40 114 0.73
41 8 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:27924071 original size:11 final size:12
Alignment explanation
Indices: 27924042--27924084 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
27924032 AAAACAGTGG
27924042 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
27924054 AGAAAAAGGGAA
1 AGAAAAAGAGAA
*
27924066 AG-AAAAGAAAA
1 AGAAAAAGAGAA
27924077 AGGAAAAA
1 A-GAAAAA
27924085 CTAGATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 8 0.31
12 14 0.54
13 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:27924074 original size:17 final size:18
Alignment explanation
Indices: 27924046--27924079 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
27924036 CAGTGGAGAA
27924046 AAAGAGAAAGAAAAAGGG
1 AAAGAGAAAGAAAAAGGG
27924064 AAAGA-AAAGAAAAAGG
1 AAAGAGAAAGAAAAAGG
27924080 AAAAACTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AAAGAGAAAGAAAAAGGG
Found at i:27925132 original size:6 final size:6
Alignment explanation
Indices: 27925121--27925164 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
27925111 GTGTGTTCAA
* *
27925121 TACTGT TACTGT TACTGT TACTGC TACCGT TACTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
27925165 TAGGTACTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:27927318 original size:39 final size:39
Alignment explanation
Indices: 27927248--27927431 Score: 237
Period size: 39 Copynumber: 4.7 Consensus size: 39
27927238 ACAAAGCATG
* * * *
27927248 CGGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAACACGAATGCCTT
* *
27927288 CGGGACTTTAGCCCGGATATAACACTAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAACACGAATGCCTT
* *
27927328 CGGGGCTTAGCCCGGATATAACGCCAACACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
*
27927367 CAGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
27927406 CGGGACTTAGCCC-GATTATAACACCA
1 CGGGACTTAGCCCGGA-TATAACACCA
27927432 TTATAAAGTC
Statistics
Matches: 130, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
38 2 0.02
39 108 0.83
40 20 0.15
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
Found at i:27927545 original size:28 final size:28
Alignment explanation
Indices: 27927504--27927568 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
27927494 ATTTAATCAT
27927504 TCAATATTCTGCACACTAAGTGACATTC
1 TCAATATTCTGCACACTAAGTGACATTC
* *
27927532 TCAATA-TCTCGCACATTAAGTGCCATTC
1 TCAATATTCT-GCACACTAAGTGACATTC
27927560 TCAATATTC
1 TCAATATTC
27927569 CGTACACTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 3 0.09
28 28 0.85
29 2 0.06
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (28 bp):
TCAATATTCTGCACACTAAGTGACATTC
Found at i:27927585 original size:28 final size:28
Alignment explanation
Indices: 27927504--27927585 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
27927494 ATTTAATCAT
*
27927504 TCAATATTCTGCACACTAAGTGA-CATTC
1 TCAATATTCCGCACACTAAGT-ACCATTC
* *
27927532 TCAATA-TCTCGCACATTAAGTGCCATTC
1 TCAATATTC-CGCACACTAAGTACCATTC
* *
27927560 TCAATATTCCGTACACTGAGTACCAT
1 TCAATATTCCGCACACTAAGTACCAT
27927586 ATTTGATCGC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
27 2 0.05
28 40 0.91
29 2 0.05
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (28 bp):
TCAATATTCCGCACACTAAGTACCATTC
Found at i:27933236 original size:22 final size:23
Alignment explanation
Indices: 27933203--27933246 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
27933193 AATATTTAAG
*
27933203 TATTAATATATAATATATTATAT
1 TATTAATATATAATATAATATAT
27933226 TATT-ATATATAATATAATATA
1 TATTAATATATAATATAATATA
27933247 ATATATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTAATATATAATATAATATAT
Found at i:27933240 original size:20 final size:20
Alignment explanation
Indices: 27933192--27933254 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
27933182 TATATTAACT
*
27933192 TAATATTTAAGTATTAATATA
1 TAATATATAA-TATTAATATA
* *
27933213 TAATATATTATATTATTATA
1 TAATATATAATATTAATATA
27933233 T-ATAATATAATA-TAATATA
1 TAAT-ATATAATATTAATATA
27933252 TAA
1 TAA
27933255 AACATAAGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 9 0.26
20 18 0.51
21 8 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TAATATATAATATTAATATA
Found at i:27933241 original size:17 final size:17
Alignment explanation
Indices: 27933210--27933254 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
27933200 AAGTATTAAT
27933210 ATATAATATAT--TATA
1 ATATAATATATAATATA
* *
27933225 TTATTATATATAATATA
1 ATATAATATATAATATA
27933242 ATATAATATATAA
1 ATATAATATATAA
27933255 AACATAAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 9 0.38
17 15 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAATATATAATATA
Found at i:27934420 original size:29 final size:30
Alignment explanation
Indices: 27934388--27934444 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
27934378 GCGCTCTCTG
27934388 ATTATTAGCACATT-AGTGCTCTCTGTTCT
1 ATTATTAGCACATTAAGTGCTCTCTGTTCT
*
27934417 ATTATTAGCACGTTAAGTGCTCTCTGTT
1 ATTATTAGCACATTAAGTGCTCTCTGTT
27934445 TAGCACATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (30 bp):
ATTATTAGCACATTAAGTGCTCTCTGTTCT
Found at i:27934461 original size:22 final size:22
Alignment explanation
Indices: 27934432--27934488 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
27934422 TAGCACGTTA
27934432 AGTGCTCTCTGTTTAGCACATCT
1 AGTGCTCTCTGTTTAGCAC-TCT
* *
27934455 -GTGCTCTCTGTATAGCACTTT
1 AGTGCTCTCTGTTTAGCACTCT
27934476 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
27934489 CATTTGTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (22 bp):
AGTGCTCTCTGTTTAGCACTCT
Found at i:27936501 original size:16 final size:16
Alignment explanation
Indices: 27936447--27936509 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
27936437 CACTGTAACA
* *
27936447 GAATAGGGCTATAATT
1 GAATAGAGCTGTAATT
* * *
27936463 GAATAGGGTTGTAAAT
1 GAATAGAGCTGTAATT
27936479 GAATAGAGCTGTAATT
1 GAATAGAGCTGTAATT
*
27936495 GAATAGAACTGTAAT
1 GAATAGAGCTGTAAT
27936510 CAGTAATTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (16 bp):
GAATAGAGCTGTAATT
Found at i:27936508 original size:32 final size:32
Alignment explanation
Indices: 27936438--27936508 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
27936428 CGTTTGATTC
* *
27936438 ACTGTAACAGAATAGGGCTATAATTGAATAGG
1 ACTGTAACAGAATAGAGCTATAATTGAATAGA
** *
27936470 GTTGTAA-ATGAATAGAGCTGTAATTGAATAGA
1 ACTGTAACA-GAATAGAGCTATAATTGAATAGA
27936502 ACTGTAA
1 ACTGTAA
27936509 TCAGTAATTC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
31 1 0.03
32 30 0.97
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (32 bp):
ACTGTAACAGAATAGAGCTATAATTGAATAGA
Found at i:27936579 original size:43 final size:45
Alignment explanation
Indices: 27936495--27936583 Score: 128
Period size: 43 Copynumber: 2.0 Consensus size: 45
27936485 AGCTGTAATT
27936495 GAATAGAACTGTAATCAGTAATTCAACTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATCAG-AATTCAACTGTTTGGTTGAATGGAATG
***
27936541 GAATAGAACTGTAAT-AG-ATTCTTGTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATCAGAATTCAACTGTTTGGTTGAATGGAATG
27936584 ATGTTGTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 23 0.57
45 2 0.05
46 15 0.38
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.35
Consensus pattern (45 bp):
GAATAGAACTGTAATCAGAATTCAACTGTTTGGTTGAATGGAATG
Found at i:27937312 original size:33 final size:33
Alignment explanation
Indices: 27937275--27937341 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
27937265 GATTAAACCA
27937275 ACCAATTTGATCAAATCCAAACATCCATGATGG
1 ACCAATTTGATCAAATCCAAACATCCATGATGG
* *
27937308 ACCAATTTGATCAAGTTCAAACATCCATGATGG
1 ACCAATTTGATCAAATCCAAACATCCATGATGG
27937341 A
1 A
27937342 AACAAGGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.25
Consensus pattern (33 bp):
ACCAATTTGATCAAATCCAAACATCCATGATGG
Found at i:27940513 original size:72 final size:73
Alignment explanation
Indices: 27940423--27940578 Score: 233
Period size: 72 Copynumber: 2.2 Consensus size: 73
27940413 GGATAAAAGC
* *
27940423 ATGAAAAAGAGGGAGAAGGTTTGAAGAAAATGGGAAGAAGAATG-AAAAAAAGAAGATGCTTCAG
1 ATGAAAAAGAGAGAGAAGGTTGGAAGAAAATGGGAAGAAGAATGAAAAAAAAGAAGATGCTTCAG
*
27940487 ACGTGAAA
66 ACATGAAA
* * **
27940495 ATGAAAAAGAGAGTGAAGGTTGGAAGGACTTGGGAAGAAGAATGAAAAAAAAGAAGATGCTTCAG
1 ATGAAAAAGAGAGAGAAGGTTGGAAGAAAATGGGAAGAAGAATGAAAAAAAAGAAGATGCTTCAG
*
27940560 ACATGAGA
66 ACATGAAA
27940568 ATGAAAAAGAG
1 ATGAAAAAGAG
27940579 GGACAAGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
72 38 0.51
73 37 0.49
ACGTcount: A:0.51, C:0.04, G:0.31, T:0.14
Consensus pattern (73 bp):
ATGAAAAAGAGAGAGAAGGTTGGAAGAAAATGGGAAGAAGAATGAAAAAAAAGAAGATGCTTCAG
ACATGAAA
Found at i:27944018 original size:55 final size:55
Alignment explanation
Indices: 27943949--27944071 Score: 160
Period size: 55 Copynumber: 2.2 Consensus size: 55
27943939 AGGTAGTATT
* * * *
27943949 CACACGGCCATGTAACACGCTCGTGTCCA-AGGCCGTGTCAACCACACGACTAAGA
1 CACACGACCATGTAACACACCCGTGTCCACA-GCCGTGTCAACCACACAACTAAGA
*
27944004 CACACGACCGTGTAACACACCCGTGTCCACAGCCGTGTCAACCACACAACTAAGA
1 CACACGACCATGTAACACACCCGTGTCCACAGCCGTGTCAACCACACAACTAAGA
*
27944059 AACAC-ACCCATGT
1 CACACGA-CCATGT
27944072 CTCTGCCCGT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
54 1 0.02
55 57 0.97
56 1 0.02
ACGTcount: A:0.32, C:0.37, G:0.18, T:0.14
Consensus pattern (55 bp):
CACACGACCATGTAACACACCCGTGTCCACAGCCGTGTCAACCACACAACTAAGA
Found at i:27945185 original size:18 final size:18
Alignment explanation
Indices: 27945162--27945197 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27945152 ATATATCATC
27945162 TCACACAAATCAACTCAA
1 TCACACAAATCAACTCAA
* *
27945180 TCACACAATTCAATTCAA
1 TCACACAAATCAACTCAA
27945198 GCATAATAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (18 bp):
TCACACAAATCAACTCAA
Done.