Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 79 of 208
Found at i:28111608 original size:22 final size:23
Alignment explanation
Indices: 28111598--28111651 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
28111588 TTACTAACAA
* * *
28111598 TTAATTTTA-ATAACAATTAGTT
1 TTAATTTTATATAAAAAATAATT
*
28111620 TTAATTTTATTTAAAAAATAATT
1 TTAATTTTATATAAAAAATAATT
28111643 TTAATTTTA
1 TTAATTTTA
28111652 ATGCAAAACG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TTAATTTTATATAAAAAATAATT
Found at i:28114024 original size:4 final size:4
Alignment explanation
Indices: 28114015--28114048 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
28114005 AAAGAAGTAA
28114015 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
28114049 CAGATTACGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:28120910 original size:25 final size:25
Alignment explanation
Indices: 28120862--28120910 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
28120852 TATAATTGAA
* * *
28120862 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
28120887 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
28120911 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:28122680 original size:41 final size:43
Alignment explanation
Indices: 28122620--28122736 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
28122610 GATTTGAGAT
* * *
28122620 TTACGTGTAAGACCATGTCTGGGA-ATTGGCATCG-TATATGA
1 TTACATGTAAGACCATGTCTAGGACAGTGGCATCGTTATATGA
* * *
28122661 TTACATGTAAGACCCTGTCTAGGACAGTGGTATCGTTATTTGA
1 TTACATGTAAGACCATGTCTAGGACAGTGGCATCGTTATATGA
28122704 TTACATGTAAGACCATGTCTAGGAC-GTTGGCAT
1 TTACATGTAAGACCATGTCTAGGACAG-TGGCAT
28122737 TGTACGAGCT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
41 21 0.32
42 9 0.14
43 35 0.54
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (43 bp):
TTACATGTAAGACCATGTCTAGGACAGTGGCATCGTTATATGA
Found at i:28123165 original size:14 final size:14
Alignment explanation
Indices: 28123146--28123196 Score: 66
Period size: 14 Copynumber: 3.4 Consensus size: 14
28123136 TGTTAAAAAA
28123146 TATTATTAAATTAT
1 TATTATTAAATTAT
*
28123160 TATTATTAAATTGT
1 TATTATTAAATTAT
28123174 TAAATTATTATAATTAT
1 T--ATTATTA-AATTAT
28123191 TATTAT
1 TATTAT
28123197 ATTATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 14 0.44
15 5 0.16
16 7 0.22
17 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TATTATTAAATTAT
Found at i:28123345 original size:16 final size:17
Alignment explanation
Indices: 28123324--28123355 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28123314 TATTATATTA
28123324 TATTATA-TTATTAAAG
1 TATTATATTTATTAAAG
28123340 TATTATATTTATTAAA
1 TATTATATTTATTAAA
28123356 TAATAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTATATTTATTAAAG
Found at i:28123348 original size:5 final size:5
Alignment explanation
Indices: 28123308--28123334 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28123298 ATATAAGAAA
28123308 ATATT ATATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT AT
28123335 TAAAGTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:28123420 original size:17 final size:17
Alignment explanation
Indices: 28123371--28123410 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
28123361 AACAAAACAT
*
28123371 AAACTAAAAGAATAAAAG
1 AAAC-AAAAGAAGAAAAG
28123389 AAACAAAAGAAGAAAAG
1 AAACAAAAGAAGAAAAG
28123406 AAACA
1 AAACA
28123411 GAATAGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.75, C:0.07, G:0.12, T:0.05
Consensus pattern (17 bp):
AAACAAAAGAAGAAAAG
Found at i:28123841 original size:24 final size:23
Alignment explanation
Indices: 28123808--28123854 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
28123798 ATTTGAATAG
28123808 AAATAGAGTGTGAATTGAGTTAGGA
1 AAATAGA--GTGAATTGAGTTAGGA
*
28123833 AAATA-AGTGAATTTAGTTAGGA
1 AAATAGAGTGAATTGAGTTAGGA
28123855 TTAAATTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 15 0.71
24 1 0.05
25 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.28, T:0.30
Consensus pattern (23 bp):
AAATAGAGTGAATTGAGTTAGGA
Found at i:28124122 original size:6 final size:6
Alignment explanation
Indices: 28124111--28124187 Score: 127
Period size: 6 Copynumber: 12.8 Consensus size: 6
28124101 TAAGTATGAA
28124111 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
* * *
28124159 TATTAG TATTAT TATTAT TATTAT TATTA
1 TATTAG TATTAG TATTAG TATTAG TATTA
28124188 AAATGAGTGG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.55
Consensus pattern (6 bp):
TATTAG
Found at i:28124328 original size:17 final size:18
Alignment explanation
Indices: 28124296--28124329 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28124286 AATTGAATGG
*
28124296 AAATGTATTGAGTTGTGA
1 AAATGTATTGAATTGTGA
28124314 AAATGTA-TGAATTGTG
1 AAATGTATTGAATTGTG
28124330 GATTAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.38
Consensus pattern (18 bp):
AAATGTATTGAATTGTGA
Found at i:28129232 original size:26 final size:26
Alignment explanation
Indices: 28129203--28129285 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
28129193 TATGAACACG
28129203 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
* *
28129229 TGTGTA-T-CGATAGAT-AATGG-TCAC-A
1 TGTGTAGTACTA-AG-TGCA-GGCT-ACTA
*
28129254 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
28129280 TGTGTA
1 TGTGTA
28129286 CCGGATGGCC
Statistics
Matches: 43, Mismatches: 5, Indels: 18
0.65 0.08 0.27
Matches are distributed among these distances:
24 2 0.05
25 17 0.40
26 22 0.51
27 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.34
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGCAGGCTACTA
Found at i:28129279 original size:51 final size:50
Alignment explanation
Indices: 28129203--28129423 Score: 237
Period size: 51 Copynumber: 4.4 Consensus size: 50
28129193 TATGAACACG
*
28129203 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATC-GATAGATAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATAGAT--TGGTCACA
* * * *
28129254 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATGGCCTTGGTCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATAG-ATTGGTCACA
* * * * * * **
28129305 TGTGTAGTACTATGTGCAGGCTACTACGTGAATCGAAAAGCTTGATCATG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATAGATTGGTCACA
* * *
28129355 TGTGTAGTACTATGTGTAGGCTACTATGTGTATCGGATGACAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGAT-AGATTGGTCACA
* *
28129406 TGGGTGGTACTATGTGCA
1 TGTGTAGTACTATGTGCA
28129424 AACCACTGAA
Statistics
Matches: 140, Mismatches: 27, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
50 41 0.29
51 94 0.67
52 4 0.03
53 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATAGATTGGTCACA
Found at i:28129392 original size:101 final size:101
Alignment explanation
Indices: 28129199--28129423 Score: 281
Period size: 101 Copynumber: 2.2 Consensus size: 101
28129189 TACCTATGAA
* * * * *
28129199 CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTATCGATAGATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGAATCGAAAGAT-ATGATCACATGTGTAGTAC
* **
28129264 TATGTGCAGGCTACTATGTGTACCGGATGGCCTTGGT
65 TATGTGCAGGCTACTATGTGTACCGGATGACAATGGT
* **
28129301 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGAATCGAAAAGCT-TGATCATGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGAATCG-AAAGATATGATCACATGTGTAGTAC
* *
28129365 TATGTGTAGGCTACTATGTGTATCGGATGACAATGGT
65 TATGTGCAGGCTACTATGTGTACCGGATGACAATGGT
* * *
28129402 CACATGGGTGGTACTATGTGCA
1 CACGTGTGTAGTACTATGTGCA
28129424 AACCACTGAA
Statistics
Matches: 106, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
101 66 0.62
102 36 0.34
103 4 0.04
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.31
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGAATCGAAAGATATGATCACATGTGTAGTACT
ATGTGCAGGCTACTATGTGTACCGGATGACAATGGT
Found at i:28132426 original size:34 final size:34
Alignment explanation
Indices: 28132379--28132447 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
28132369 TTTTCAACCC
* *
28132379 TAAACTTTTCGATCTTATCAATTAGAGGTCGTCA
1 TAAACTTTCCGATCTTATCAATTAAAGGTCGTCA
28132413 TAAACTTTCCGATCTTATCAATTAAAGGTCGTCA
1 TAAACTTTCCGATCTTATCAATTAAAGGTCGTCA
28132447 T
1 T
28132448 GCATTTTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (34 bp):
TAAACTTTCCGATCTTATCAATTAAAGGTCGTCA
Found at i:28132775 original size:16 final size:16
Alignment explanation
Indices: 28132749--28132786 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
28132739 ACACTATCAC
28132749 AGGTT-AATACGCGCT
1 AGGTTCAATACGCGCT
28132764 AGGTTCAATACGCGCT
1 AGGTTCAATACGCGCT
28132780 AGGTTCA
1 AGGTTCA
28132787 GTCCTAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (16 bp):
AGGTTCAATACGCGCT
Found at i:28139556 original size:13 final size:14
Alignment explanation
Indices: 28139538--28139571 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28139528 TTGTTAAAAG
28139538 TTATTTTAA-TTAA
1 TTATTTTAATTTAA
*
28139551 TTATTTTAATTTAT
1 TTATTTTAATTTAA
28139565 TTATTTT
1 TTATTTT
28139572 GTTGAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTTTAATTTAA
Found at i:28142539 original size:23 final size:24
Alignment explanation
Indices: 28142509--28142555 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28142499 ATTTTGAAAA
*
28142509 AAAAAAAACT-TCACCAGTAAAGT
1 AAAAAAAACTCTCACCAATAAAGT
*
28142532 AAAAAAAACTCTTACCAATAAAGT
1 AAAAAAAACTCTCACCAATAAAGT
28142556 TAGAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.57, C:0.17, G:0.06, T:0.19
Consensus pattern (24 bp):
AAAAAAAACTCTCACCAATAAAGT
Found at i:28144765 original size:21 final size:22
Alignment explanation
Indices: 28144726--28144767 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
28144716 ACGACTGTAA
*
28144726 TAAAAATATTATAATTTAATAAT
1 TAAAAATA-TATAAATTAATAAT
28144749 TAAAAATA-ATAAATTAATA
1 TAAAAATATATAAATTAATA
28144768 TAGTATCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAATATATAAATTAATAAT
Found at i:28148444 original size:14 final size:14
Alignment explanation
Indices: 28148425--28148467 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
28148415 TACCAATACA
28148425 TTATCCTGGCCCGG
1 TTATCCTGGCCCGG
*
28148439 TTATCCTGGCCCAG
1 TTATCCTGGCCCGG
28148453 TTATCCTGGCCCGG
1 TTATCCTGGCCCGG
28148467 T
1 T
28148468 GCTTGATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.09, C:0.35, G:0.26, T:0.30
Consensus pattern (14 bp):
TTATCCTGGCCCGG
Found at i:28149285 original size:22 final size:22
Alignment explanation
Indices: 28149257--28149298 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28149247 CGGCTGGGTA
*
28149257 GATTTTTATAAT-TTTTATTTTT
1 GATTTTT-TAATAATTTATTTTT
28149279 GATTTTTTAATAATTTATTT
1 GATTTTTTAATAATTTATTT
28149299 GCTTTGAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
GATTTTTTAATAATTTATTTTT
Found at i:28152191 original size:22 final size:22
Alignment explanation
Indices: 28152166--28152213 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
28152156 ACAAGAGCAA
*
28152166 AAACCCAATGTAAGATAACACC
1 AAACCCAATGTAAGACAACACC
28152188 AAACCCAATGTAAGACAACACC
1 AAACCCAATGTAAGACAACACC
28152210 AAAC
1 AAAC
28152214 TTAATTACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.52, C:0.29, G:0.08, T:0.10
Consensus pattern (22 bp):
AAACCCAATGTAAGACAACACC
Found at i:28154878 original size:43 final size:43
Alignment explanation
Indices: 28154812--28154933 Score: 125
Period size: 39 Copynumber: 2.9 Consensus size: 43
28154802 ATAGGATTTC
28154812 CGATATGTG-TTATCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGTTTA-CGTGTAAGACCACGTCTGGGACGTTGGCAT
* *
28154855 CGACT-TGTGTTTACGTGTAAGA-C-C--CTGGTATAG-TGGCAT
1 CGA-TATGTGTTTACGTGTAAGACCACGTCTGGGA-CGTTGGCAT
*
28154894 CGATATGT-TATTACATGTAAGACCACGTCTGGGACGTTGG
1 CGATATGTGT-TTACGTGTAAGACCACGTCTGGGACGTTGG
28154934 TATTGTACGA
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
38 2 0.03
39 28 0.44
40 2 0.03
41 2 0.03
42 2 0.03
43 24 0.38
44 4 0.06
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (43 bp):
CGATATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:28155604 original size:14 final size:15
Alignment explanation
Indices: 28155585--28155613 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28155575 AATCATGGAA
28155585 TAGTATTT-TATGGT
1 TAGTATTTATATGGT
28155599 TAGTATTTATATGGT
1 TAGTATTTATATGGT
28155614 AATGTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (15 bp):
TAGTATTTATATGGT
Found at i:28157494 original size:20 final size:22
Alignment explanation
Indices: 28157442--28157500 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
28157432 ATGTGTGTAC
**
28157442 GTATACATTTTTATATTTCGTAA
1 GTATACATACTTATATTTC-TAA
*
28157465 GTATATATACTTATATTT-TAA
1 GTATACATACTTATATTTCTAA
*
28157486 -TATACATACTCATAT
1 GTATACATACTTATAT
28157501 ATATATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 13 0.42
21 3 0.10
23 15 0.48
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (22 bp):
GTATACATACTTATATTTCTAA
Found at i:28158653 original size:16 final size:16
Alignment explanation
Indices: 28158632--28158663 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28158622 TGTCAACATA
28158632 TATGCTGTCAAATTTT
1 TATGCTGTCAAATTTT
28158648 TATGCTGTCAAATTTT
1 TATGCTGTCAAATTTT
28158664 GATGTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (16 bp):
TATGCTGTCAAATTTT
Found at i:28158772 original size:92 final size:93
Alignment explanation
Indices: 28158648--28158850 Score: 381
Period size: 92 Copynumber: 2.2 Consensus size: 93
28158638 GTCAAATTTT
28158648 TATGCTGTCAAATTTTGATGTATAAATACAGTCCAATTATATATGTATATGCTGTCAAATTTTGA
1 TATGCTGTCAAATTTTGATGTATAAATACAGTCCAATTATATATGTATATGCTGTCAAATTTTGA
28158713 TGTATAAATGCAGTCCAATT-TTGTATA
66 TGTATAAATGCAGTCCAATTGTTGTATA
*
28158740 TATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGTATATGCTGTCAAATTTTGA
1 TATGCTGTCAAATTTTGATGTATAAATACAGTCCAATTATATATGTATATGCTGTCAAATTTTGA
28158805 TGTATAAATGCAGTCCAATTGTTGTATA
66 TGTATAAATGCAGTCCAATTGTTGTATA
28158833 TATGCTGTCCAAATTTTG
1 TATGCTGT-CAAATTTTG
28158851 GTGTGAAAAT
Statistics
Matches: 108, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
92 84 0.78
93 15 0.14
94 9 0.08
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (93 bp):
TATGCTGTCAAATTTTGATGTATAAATACAGTCCAATTATATATGTATATGCTGTCAAATTTTGA
TGTATAAATGCAGTCCAATTGTTGTATA
Found at i:28158861 original size:47 final size:47
Alignment explanation
Indices: 28158648--28158850 Score: 322
Period size: 47 Copynumber: 4.4 Consensus size: 47
28158638 GTCAAATTTT
* *
28158648 TATGCTGTCAAATTTTGATGTATAAATACAGTCCAATTATATATGTA
1 TATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATATA
*
28158695 TATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATT-T-TGTATA
1 TATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATATA
*
28158740 TATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGTA
1 TATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATATA
* *
28158787 TATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTGT-TGTATA
1 TATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATATA
28158833 TATGCTGTCCAAATTTTG
1 TATGCTGT-CAAATTTTG
28158851 GTGTGAAAAT
Statistics
Matches: 145, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
45 42 0.29
46 14 0.10
47 89 0.61
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (47 bp):
TATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATATA
Found at i:28158903 original size:23 final size:23
Alignment explanation
Indices: 28158709--28158904 Score: 65
Period size: 23 Copynumber: 8.5 Consensus size: 23
28158699 CTGTCAAATT
28158709 TTGATGTATAAATGCA-GTCC-AA
1 TTGATGTATAAATG-ATGTCCAAA
* * *
28158731 TT-TTGTATATATGCTGT-CAAA
1 TTGATGTATAAATGATGTCCAAA
28158752 TTTTGATGTATAAATGCA-GTCCAATTA
1 --TTGATGTATAAATG-ATGTCCAA--A
*
28158779 TAT-ATGTAT--ATGCTGT-CAAA
1 T-TGATGTATAAATGATGTCCAAA
28158799 TTTTGATGTATAAATGCA-GTCC-AA
1 --TTGATGTATAAATG-ATGTCCAAA
* * *
28158823 TTGTTGTATATATGCTGTCCAAA
1 TTGATGTATAAATGATGTCCAAA
* * * **
28158846 TTTTGGTGTGA-AAATGTTGTCTAGT
1 --TTGATGT-ATAAATGATGTCCAAA
* *
28158871 TTGGTATATAAATGATGTCCAAA
1 TTGATGTATAAATGATGTCCAAA
28158894 TTGATGTATAA
1 TTGATGTATAA
28158905 TAGTTGTCCA
Statistics
Matches: 126, Mismatches: 24, Indels: 47
0.64 0.12 0.24
Matches are distributed among these distances:
20 2 0.02
21 14 0.11
22 29 0.23
23 34 0.27
24 18 0.14
25 26 0.21
26 2 0.02
27 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.41
Consensus pattern (23 bp):
TTGATGTATAAATGATGTCCAAA
Found at i:28168520 original size:30 final size:30
Alignment explanation
Indices: 28168469--28168525 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
28168459 AAATAGATAA
* *
28168469 ATATAAATAAATATTTATATATATAATGAC
1 ATATAAATAAACAATTATATATATAATGAC
*
28168499 ATATAAATAGAACAATT-TATATTTAAT
1 ATATAAATA-AACAATTATATATATAAT
28168526 TTTCGAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (30 bp):
ATATAAATAAACAATTATATATATAATGAC
Found at i:28169856 original size:16 final size:16
Alignment explanation
Indices: 28169835--28169869 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
28169825 TATAAATAAA
28169835 TTTTATTTAAATTTAT
1 TTTTATTTAAATTTAT
28169851 TTTTATTTAAATTTAT
1 TTTTATTTAAATTTAT
28169867 TTT
1 TTT
28169870 GTAAATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTTAAATTTAT
Found at i:28171624 original size:28 final size:28
Alignment explanation
Indices: 28171563--28171625 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 28
28171553 ATAGTAACGT
28171563 TTATTAAAATAAATATTCATAAAATTTAA
1 TTATT-AAATAAATATTCATAAAATTTAA
* **
28171592 -AATTAAA-AAATATTTTTAAAATTTTAA
1 TTATTAAATAAATATTCATAAAA-TTTAA
28171619 TTATTAA
1 TTATTAA
28171626 TATACCGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
26 12 0.43
27 8 0.29
28 8 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
TTATTAAATAAATATTCATAAAATTTAA
Found at i:28186862 original size:11 final size:11
Alignment explanation
Indices: 28186846--28186872 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28186836 TTTCAAGCAT
28186846 TTAATTTTTAA
1 TTAATTTTTAA
28186857 TTAATTTTTAA
1 TTAATTTTTAA
28186868 TTAAT
1 TTAAT
28186873 ATATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTAATTTTTAA
Found at i:28186948 original size:17 final size:17
Alignment explanation
Indices: 28186916--28186949 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28186906 TTTTTTAGCT
28186916 TTTAAATAATATATAAA
1 TTTAAATAATATATAAA
28186933 TTTAGAATAATA-ATAAA
1 TTTA-AATAATATATAAA
28186950 AAGTAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TTTAAATAATATATAAA
Found at i:28188377 original size:22 final size:23
Alignment explanation
Indices: 28188336--28188379 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
28188326 TAACTTTTTG
28188336 TCAATAATCAAGTAACATAACTT
1 TCAATAATCAAGTAACATAACTT
28188359 TCAATAAT-AA-TAAACATAACT
1 TCAATAATCAAGT-AACATAACT
28188380 CATTAGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 1 0.05
22 11 0.55
23 8 0.40
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (23 bp):
TCAATAATCAAGTAACATAACTT
Found at i:28188928 original size:3 final size:3
Alignment explanation
Indices: 28188920--28188969 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
28188910 TACTTAGTGT
28188920 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28188968 TT
1 TT
28188970 TTCTTTCTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28190141 original size:9 final size:9
Alignment explanation
Indices: 28190038--28190140 Score: 134
Period size: 9 Copynumber: 11.4 Consensus size: 9
28190028 GTAGTGATTC
*
28190038 AATTTGGTT
1 AATTCGGTT
28190047 AATTCGGTT
1 AATTCGGTT
*
28190056 AATTCGGGT
1 AATTCGGTT
*
28190065 AATTCGGGT
1 AATTCGGTT
*
28190074 AATTCGGGT
1 AATTCGGTT
28190083 AATTCGGTT
1 AATTCGGTT
*
28190092 AATTCGGGT
1 AATTCGGTT
*
28190101 AATTCGGGT
1 AATTCGGTT
28190110 AATTCGGTT
1 AATTCGGTT
*
28190119 AATTCGATT
1 AATTCGGTT
*
28190128 AATTTGGTT
1 AATTCGGTT
28190137 AATT
1 AATT
28190141 TTTAACCAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 86 1.00
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:28197036 original size:18 final size:19
Alignment explanation
Indices: 28197007--28197065 Score: 95
Period size: 18 Copynumber: 3.2 Consensus size: 19
28196997 TTCTAGGTCC
*
28197007 TTTTCATTTTTCTTTTTCA
1 TTTTCATTTTTCATTTTCA
28197026 TTTTC-TTTTTCATTTTCA
1 TTTTCATTTTTCATTTTCA
28197044 TTTTCATTTTT-ATTTTCA
1 TTTTCATTTTTCATTTTCA
28197062 TTTT
1 TTTT
28197066 TGAGAAAACC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
18 28 0.74
19 10 0.26
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTCATTTTTCATTTTCA
Found at i:28197064 original size:6 final size:6
Alignment explanation
Indices: 28197007--28197065 Score: 82
Period size: 6 Copynumber: 9.7 Consensus size: 6
28196997 TTCTAGGTCC
* * *
28197007 TTTTCA TTTTTCT TTTTCA TTTTCT TTTTCA TTTTCA TTTTCA TTTTTA
1 TTTTCA -TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA
28197056 TTTTCA TTTT
1 TTTTCA TTTT
28197066 TGAGAAAACC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
6 41 0.89
7 5 0.11
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTCA
Found at i:28197110 original size:57 final size:58
Alignment explanation
Indices: 28197041--28197171 Score: 178
Period size: 57 Copynumber: 2.3 Consensus size: 58
28197031 TTTTTCATTT
* * * *
28197041 TCATTT-T-CATTTTTATTTTCATTTTTGAGAAAACCACATTCATTTCCAAATGATTC
1 TCATTTCTCCATTTTCATTTTCATTTTGGAAAAAACCACAATCATTTCCAAATGATTC
* * *
28197097 -CATTTCTCCATTTTCATTTTTATTTTGGAAAAAACCATAATCATTTCCAAATGTTTC
1 TCATTTCTCCATTTTCATTTTCATTTTGGAAAAAACCACAATCATTTCCAAATGATTC
28197154 TCATTTCTCCATTTTCAT
1 TCATTTCTCCATTTTCAT
28197172 CATTTCTATC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
55 5 0.08
56 1 0.02
57 42 0.65
58 17 0.26
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (58 bp):
TCATTTCTCCATTTTCATTTTCATTTTGGAAAAAACCACAATCATTTCCAAATGATTC
Found at i:28205353 original size:28 final size:28
Alignment explanation
Indices: 28205302--28205396 Score: 72
Period size: 28 Copynumber: 3.3 Consensus size: 28
28205292 TCTTTATAAA
* *
28205302 TTTAAATTTTAGTTTTTATATTTT-TAT
1 TTTAAAATTTAGTTTCTATATTTTATAT
28205329 TTTAGAAATTTAGTCTTCTAT-TTTTCATAT
1 TTTA-AAATTTAGT-TTCTATATTTT-ATAT
* *
28205359 TTTAAATTTTAG-ATCTA-ATTATTAATAT
1 TTTAAAATTTAGTTTCTATATT-TT-ATAT
28205387 TGTTAAAATT
1 T-TTAAAATT
28205397 ATTTTTTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
27 10 0.18
28 19 0.35
29 19 0.35
30 7 0.13
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (28 bp):
TTTAAAATTTAGTTTCTATATTTTATAT
Found at i:28205983 original size:21 final size:21
Alignment explanation
Indices: 28205950--28205993 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
28205940 AAAATTCTAT
* *
28205950 AAAAATCATAAAAATTATAAA
1 AAAAATCAAAAAAAGTATAAA
* *
28205971 AAAAATTAAAAAAAGTATTAA
1 AAAAATCAAAAAAAGTATAAA
28205992 AA
1 AA
28205994 TTGATATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (21 bp):
AAAAATCAAAAAAAGTATAAA
Found at i:28206019 original size:9 final size:9
Alignment explanation
Indices: 28205925--28206021 Score: 68
Period size: 9 Copynumber: 9.9 Consensus size: 9
28205915 ATTTAATTTT
28205925 TTATAAAAA
1 TTATAAAAA
*
28205934 TGTATTAAAAT
1 T-TA-TAAAAA
28205945 TCTATAAAAA
1 T-TATAAAAA
*
28205955 TCATAAAAA
1 TTATAAAAA
28205964 TTATAAAAAAAA
1 TTAT---AAAAA
*
28205976 TTAAAAAAA
1 TTATAAAAA
* *
28205985 GTATTAAAA
1 TTATAAAAA
*
28205994 TTGATATAAAC
1 TT-ATA-AAAA
28206005 TTATAAAAA
1 TTATAAAAA
28206014 TTATAAAA
1 TTATAAAA
28206022 TAAATCATAA
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
9 34 0.50
10 13 0.19
11 13 0.19
12 8 0.12
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:28206034 original size:50 final size:51
Alignment explanation
Indices: 28205927--28206034 Score: 139
Period size: 50 Copynumber: 2.1 Consensus size: 51
28205917 TTAATTTTTT
* *
28205927 ATAAAAATGTATTAAAATTCTATAAAAATCATAAAAATTATAAAAAAAATT
1 ATAAAAATGTATTAAAATTATATAAAAATCATAAAAATTATAAAAAAAATC
* * * *
28205978 A-AAAAAAGTATTAAAATTGATAT-AAACTTATAAAAATTATAAAATAAATC
1 ATAAAAATGTATTAAAATT-ATATAAAAATCATAAAAATTATAAAAAAAATC
28206028 ATAAAAA
1 ATAAAAA
28206035 CTTGAATTGG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
50 40 0.82
51 9 0.18
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.30
Consensus pattern (51 bp):
ATAAAAATGTATTAAAATTATATAAAAATCATAAAAATTATAAAAAAAATC
Found at i:28206522 original size:19 final size:18
Alignment explanation
Indices: 28206500--28206544 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
28206490 TATTTTTAAG
* *
28206500 AATTTTAATACGTTTTTTT
1 AATTTTAATAAG-TTTATT
28206519 AATTTTAAATAAGTTTATT
1 AATTTT-AATAAGTTTATT
28206538 AATTTTA
1 AATTTTA
28206545 TATTTTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 17 0.74
20 5 0.22
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (18 bp):
AATTTTAATAAGTTTATT
Found at i:28206550 original size:26 final size:27
Alignment explanation
Indices: 28206514--28206587 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 27
28206504 TTAATACGTT
28206514 TTTTTA-ATTTTAAATAAGTTTATT-AA
1 TTTTTATATTTTAAATAA-TTTATTAAA
*
28206540 -TTTTATATTTT-CATAATTTATTAAAA
1 TTTTTATATTTTAAATAATTTATT-AAA
28206566 TTTTTATATTTTATAAT-ATTTA
1 TTTTTATATTTTA-AATAATTTA
28206588 CAAGTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
24 6 0.15
25 9 0.22
26 7 0.17
27 11 0.28
28 5 0.12
29 2 0.05
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (27 bp):
TTTTTATATTTTAAATAATTTATTAAA
Found at i:28206596 original size:27 final size:28
Alignment explanation
Indices: 28206540--28206605 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
28206530 AGTTTATTAA
*
28206540 TTTTATATTTTCATAATTTATTAAA-AT
1 TTTTATATTTTCATAATATATTAAATAT
*
28206567 TTTTATATTTT-ATAATAT-TTACAAGTTT
1 TTTTATATTTTCATAATATATTA-AA-TAT
28206595 TTTTATATTTT
1 TTTTATATTTT
28206606 TTTATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 3 0.09
26 8 0.24
27 11 0.32
28 12 0.35
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTATATTTTCATAATATATTAAATAT
Found at i:28206651 original size:111 final size:108
Alignment explanation
Indices: 28206456--28206654 Score: 240
Period size: 111 Copynumber: 1.8 Consensus size: 108
28206446 AGTTTATACC
* * * * *
28206456 AATTTTAATATTTTATATTTTTTCCAATTTTTATTATTTTTAAGAATTTTAATACGTTTTTTTAA
1 AATTTTAATATTTTATAATATTTACAATTTTTATTATTTTTAAGAATTTTAATAAGTTTTATTAA
*
28206521 TTTTAAATAAGTTTATTAATTTTATATTTTCATAATTTATTAA
66 TTCTAAATAAGTTTATTAATTTTATATTTTCATAATTTATTAA
* * * *
28206564 AATTTTTATATTTTATAATATTTACAAGTTTTTTTATATTTTTTTATAATTTTAATAAGTTTATA
1 AATTTTAATATTTTATAATATTTACAA-TTTTTAT-TA-TTTTTAAGAATTTTAATAAGTTT-TA
*
28206629 TTAATTCT-AATATA-TTTTTTAATTTT
62 TTAATTCTAAATA-AGTTTATTAATTTT
28206655 TTAATGTTTA
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
108 23 0.31
109 6 0.08
110 2 0.03
111 35 0.47
112 9 0.12
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (108 bp):
AATTTTAATATTTTATAATATTTACAATTTTTATTATTTTTAAGAATTTTAATAAGTTTTATTAA
TTCTAAATAAGTTTATTAATTTTATATTTTCATAATTTATTAA
Found at i:28206679 original size:31 final size:31
Alignment explanation
Indices: 28206639--28206721 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
28206629 TTAATTCTAA
*
28206639 TATATTTTTTAATTTTTTAATGTTTAATATAT
1 TATATTTTTTAATTTTTTAAT-TATAATATAT
*
28206671 T-TATTTTTTAATTATTTT--TTATAATTTAT
1 TATATTTTTTAATT-TTTTAATTATAATATAT
*
28206700 TATAATTTTTAATATTTTTAAT
1 TATATTTTTTAAT-TTTTTAAT
28206722 CATTTTTATG
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
29 9 0.21
30 15 0.35
31 13 0.30
32 6 0.14
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (31 bp):
TATATTTTTTAATTTTTTAATTATAATATAT
Found at i:28206729 original size:10 final size:10
Alignment explanation
Indices: 28206593--28206729 Score: 64
Period size: 10 Copynumber: 14.6 Consensus size: 10
28206583 ATTTACAAGT
* *
28206593 TTTTTTATAT
1 TTTTTAATAA
*
28206603 TTTTTTATAA
1 TTTTTAATAA
28206613 -TTTTAATAA
1 TTTTTAATAA
* *
28206622 GTTTATATTAA
1 -TTTTTAATAA
*
28206633 -TTCTAATATA
1 TTTTTAATA-A
28206643 TTTTT--TAA
1 TTTTTAATAA
28206651 TTTTT--TAA
1 TTTTTAATAA
*
28206659 TGTTTAAT-A
1 TTTTTAATAA
*
28206668 TATTT-AT--
1 TTTTTAATAA
*
28206675 TTTTTAATTA
1 TTTTTAATAA
*
28206685 TTTTTTATAA
1 TTTTTAATAA
28206695 TTTATT-ATAA
1 TTT-TTAATAA
28206705 TTTTTAAT-A
1 TTTTTAATAA
*
28206714 TTTTTAATCA
1 TTTTTAATAA
28206724 TTTTTA
1 TTTTTA
28206730 TGAGAAAAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
7 4 0.04
8 17 0.17
9 32 0.31
10 38 0.37
11 12 0.12
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:28217220 original size:11 final size:10
Alignment explanation
Indices: 28217203--28217264 Score: 81
Period size: 10 Copynumber: 6.1 Consensus size: 10
28217193 TCGTTTATAC
28217203 ATTTTAATTA
1 ATTTTAATTA
*
28217213 GTTTTTAATTA
1 -ATTTTAATTA
28217224 ATTTTAATTA
1 ATTTTAATTA
*
28217234 GTTTTTAATTA
1 -ATTTTAATTA
28217245 ATTTTAATTA
1 ATTTTAATTA
28217255 A-TTTAATTA
1 ATTTTAATTA
28217264 A
1 A
28217265 CCTAAGTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
9 9 0.20
10 19 0.41
11 18 0.39
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (10 bp):
ATTTTAATTA
Found at i:28217229 original size:21 final size:21
Alignment explanation
Indices: 28217203--28217254 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
28217193 TCGTTTATAC
28217203 ATTTTAATTAGTTTTTAATTA
1 ATTTTAATTAGTTTTTAATTA
28217224 ATTTTAATTAGTTTTTAATTA
1 ATTTTAATTAGTTTTTAATTA
28217245 ATTTTAATTA
1 ATTTTAATTA
28217255 ATTTAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
ATTTTAATTAGTTTTTAATTA
Found at i:28217855 original size:26 final size:27
Alignment explanation
Indices: 28217818--28217869 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
28217808 CAACAAAACT
* *
28217818 AAAATACGTGCTATTAGAAGTAGACTG
1 AAAATACGTGCTATTAAAAGCAGACTG
28217845 AAAA-ACGTGCTATTAAAAGCAGACT
1 AAAATACGTGCTATTAAAAGCAGACT
28217870 CGATGAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.23
Consensus pattern (27 bp):
AAAATACGTGCTATTAAAAGCAGACTG
Found at i:28218620 original size:17 final size:17
Alignment explanation
Indices: 28218593--28218638 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
28218583 CCGATATAAT
* * *
28218593 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
*
28218610 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
28218627 AAATATTTTTAA
1 AAATATTTTTAA
28218639 AATACTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:28218636 original size:11 final size:11
Alignment explanation
Indices: 28218622--28218719 Score: 50
Period size: 11 Copynumber: 9.4 Consensus size: 11
28218612 ATTTTTTTAA
28218622 TTTTAAAATAT
1 TTTTAAAATAT
28218633 TTTTAAAATACT
1 TTTTAAAATA-T
** *
28218645 TTTTTTATTAT
1 TTTTAAAATAT
*
28218656 TTTT----TAA
1 TTTTAAAATAT
28218663 TTTTAAAATACT
1 TTTTAAAATA-T
*
28218675 TTTTAAACT-T
1 TTTTAAAATAT
* *
28218685 TTTT---TTAA
1 TTTTAAAATAT
28218693 TTTTAAAATAT
1 TTTTAAAATAT
28218704 TTTTAAAATACT
1 TTTTAAAATA-T
28218716 TTTT
1 TTTT
28218720 TTAATTTTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 21
0.68 0.10 0.22
Matches are distributed among these distances:
7 7 0.11
8 4 0.06
10 5 0.08
11 29 0.44
12 21 0.32
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:28218649 original size:41 final size:40
Alignment explanation
Indices: 28218604--28218728 Score: 128
Period size: 30 Copynumber: 3.4 Consensus size: 40
28218594 AATATATTTA
* *
28218604 TTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTATTTTTTTTAATTTTAAAATATTTTTAAAATAC
28218644 TTTTTTTATTATTTTTTAATTTTAAAATACTTTTT--AA-AC
1 TTTTTTTATT-TTTTTTAATTTTAAAATA-TTTTTAAAATAC
28218683 --------TTTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTATTTTTTTTAATTTTAAAATATTTTTAAAATAC
*
28218715 TTTTTTTAATTTTT
1 TTTTTTTATTTTTT
28218729 AAAATAAATT
Statistics
Matches: 69, Mismatches: 3, Indels: 26
0.70 0.03 0.27
Matches are distributed among these distances:
29 5 0.07
30 18 0.26
31 4 0.06
32 2 0.03
39 2 0.03
40 15 0.22
41 18 0.26
42 5 0.07
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTTTTATTTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:28218740 original size:21 final size:21
Alignment explanation
Indices: 28218702--28218741 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28218692 ATTTTAAAAT
**
28218702 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
28218723 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
28218742 AGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:28218748 original size:22 final size:21
Alignment explanation
Indices: 28218701--28218759 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
28218691 AATTTTAAAA
* *
28218701 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
28218721 TAATTTTTAAAATAAATTTTTAG
1 T-ATTTTTAAAATAAATTTTT-G
28218744 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
28218760 GGGCCGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:28219713 original size:28 final size:28
Alignment explanation
Indices: 28219673--28219729 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
28219663 ACTATGACAG
*
28219673 TAAGGCGCCCACACTCTTTTTTACTTGT
1 TAAGGCGCCCACACTCCTTTTTACTTGT
28219701 TAAGGCGCCCACACTCCTTTTTACTTGT
1 TAAGGCGCCCACACTCCTTTTTACTTGT
28219729 T
1 T
28219730 CTTGTTCCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.39
Consensus pattern (28 bp):
TAAGGCGCCCACACTCCTTTTTACTTGT
Found at i:28224363 original size:66 final size:66
Alignment explanation
Indices: 28224230--28224363 Score: 146
Period size: 67 Copynumber: 2.0 Consensus size: 66
28224220 TTTAATAAAA
*** * * * *
28224230 TTTTTTCTCATTTTCTCTCTTGTTAAAAACCACTTTTTTTTCTTCATAATACATGGTTGTTGCCA
1 TTTTTTCTCATTTTCTCTCTTACCAAAAACCACTTTTTCTTCTTCAAAACACATGATTG-TGCCA
28224295 TT
65 TT
* *
28224297 TTTTTCTCTCATTTTCTCTCTTACCAAACACCA-TTTTTCTTCTTCAAAACATATGATTG-GCTC
1 TTTTT-TCTCATTTTCTCTCTTACCAAAAACCACTTTTTCTTCTTCAAAACACATGATTGTGC-C
28224360 ATT
64 ATT
28224363 T
1 T
28224364 CATCTACAAG
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
65 2 0.04
66 5 0.09
67 26 0.46
68 23 0.41
ACGTcount: A:0.21, C:0.22, G:0.06, T:0.51
Consensus pattern (66 bp):
TTTTTTCTCATTTTCTCTCTTACCAAAAACCACTTTTTCTTCTTCAAAACACATGATTGTGCCAT
T
Found at i:28224531 original size:21 final size:21
Alignment explanation
Indices: 28224491--28224546 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
28224481 TTTTCTCTCA
* *
28224491 TTTTCTCTCTTGCTAAACACTAT
1 TTTTCT-TCTT-CAAAACACCAT
28224514 TTTTCTTCTTCAAAACACCAT
1 TTTTCTTCTTCAAAACACCAT
28224535 TTTTCTTCTTCA
1 TTTTCTTCTTCA
28224547 GTACCTAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 21 0.68
22 4 0.13
23 6 0.19
ACGTcount: A:0.21, C:0.27, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTTCTTCTTCAAAACACCAT
Found at i:28225586 original size:66 final size:66
Alignment explanation
Indices: 28225480--28225605 Score: 191
Period size: 66 Copynumber: 1.9 Consensus size: 66
28225470 GAAATGAGCC
* * *
28225480 AACCATATGTTTTGAAGAAGAAAAATGGTGTTTGGCAAGAGAGAAAATGAGAGAAAAAATGCCAA
1 AACCATATGTTTTGAAGAAGAAAAATGGTGGTAGGAAAGAGAGAAAATGAGAGAAAAAATGCCAA
28225545 T
66 T
* *
28225546 AACCATGTGTTTTGAAGAA-AAAAAGTGTTGGTAGGAAAGAGAGAAAATGAGAGAAAAAAT
1 AACCATATGTTTTGAAGAAGAAAAA-TGGTGGTAGGAAAGAGAGAAAATGAGAGAAAAAAT
28225606 TTTATTAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 5 0.09
66 49 0.91
ACGTcount: A:0.48, C:0.06, G:0.25, T:0.21
Consensus pattern (66 bp):
AACCATATGTTTTGAAGAAGAAAAATGGTGGTAGGAAAGAGAGAAAATGAGAGAAAAAATGCCAA
T
Found at i:28234414 original size:14 final size:14
Alignment explanation
Indices: 28234395--28234422 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28234385 AACTACAAAG
28234395 GCTAATTGTATTTA
1 GCTAATTGTATTTA
28234409 GCTAATTGTATTTA
1 GCTAATTGTATTTA
28234423 TTACCTCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (14 bp):
GCTAATTGTATTTA
Found at i:28237803 original size:24 final size:24
Alignment explanation
Indices: 28237771--28237820 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
28237761 GAACGGACCT
28237771 TATTTTGAGTTACAGCAAGTACAA
1 TATTTTGAGTTACAGCAAGTACAA
28237795 TATTTTGAGTTACAGCAAGTACAA
1 TATTTTGAGTTACAGCAAGTACAA
28237819 TA
1 TA
28237821 CTTCACATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (24 bp):
TATTTTGAGTTACAGCAAGTACAA
Found at i:28242496 original size:35 final size:35
Alignment explanation
Indices: 28242450--28242682 Score: 298
Period size: 35 Copynumber: 6.8 Consensus size: 35
28242440 ATCAAATGAT
*
28242450 GTGAACAGGAGAGATTCCCTGCAACAAAATAATCC
1 GTGAACAGGAGAGATTCCCTGCAACAAAATAATGC
* *
28242485 GTGAACAGGAGAGATTCCCTGCAA-GAAATGAT--
1 GTGAACAGGAGAGATTCCCTGCAACAAAATAATGC
* *
28242517 GTGAACAGGAAAGATTCCCTGCAACAAAATAATGT
1 GTGAACAGGAGAGATTCCCTGCAACAAAATAATGC
*
28242552 GTGAACAGGAGAGATTCCCTACAACAAAATAATGC
1 GTGAACAGGAGAGATTCCCTGCAACAAAATAATGC
* *
28242587 GTGAACAGGAGAGATTCCCTGCAA-GAAATGAT--
1 GTGAACAGGAGAGATTCCCTGCAACAAAATAATGC
* * *
28242619 GTGAACAGTAAAGATTCCCTGCAACAGAATAATGC
1 GTGAACAGGAGAGATTCCCTGCAACAAAATAATGC
* * *
28242654 GTGAACAGGAAATATTCCCTGCAAGAAAA
1 GTGAACAGGAGAGATTCCCTGCAACAAAA
28242683 GACAAGTGAA
Statistics
Matches: 172, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
32 45 0.26
33 11 0.06
34 12 0.07
35 104 0.60
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.18
Consensus pattern (35 bp):
GTGAACAGGAGAGATTCCCTGCAACAAAATAATGC
Found at i:28242556 original size:67 final size:67
Alignment explanation
Indices: 28242450--28242682 Score: 274
Period size: 67 Copynumber: 3.4 Consensus size: 67
28242440 ATCAAATGAT
* * * *
28242450 GTGAACAGGAGAGATTCCCTGCAACAAAATAATCCGTGAACAGGAGAGATTCCCTGCAAGAAATG
1 GTGAACAGGAAAGATTCCCTGCAACAAAATAAT-TGTGAACAGGAGAGATTCCCTGCAAAAAATA
28242515 AT-
65 ATC
*
28242517 GTGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTACAACAAAAT
1 GTGAACAGGAAAGATTCCCTGCAACAAAATAAT-TGTGAACAGGAGAGATTCCCTGCAA-AAAAT
28242582 AATGC
64 AAT-C
* * * * * *
28242587 GTGAACAGGAGAGATTCCCTGCAA-GAAATGA-TGTGAACAGTAAAGATTCCCTGCAACAGAATA
1 GTGAACAGGAAAGATTCCCTGCAACAAAATAATTGTGAACAGGAGAGATTCCCTGCAA-AAAATA
28242650 ATGC
65 AT-C
* *
28242654 GTGAACAGGAAATATTCCCTGCAAGAAAA
1 GTGAACAGGAAAGATTCCCTGCAACAAAA
28242683 GACAAGTGAA
Statistics
Matches: 146, Mismatches: 16, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
67 109 0.75
68 9 0.06
69 5 0.03
70 23 0.16
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.18
Consensus pattern (67 bp):
GTGAACAGGAAAGATTCCCTGCAACAAAATAATTGTGAACAGGAGAGATTCCCTGCAAAAAATAA
TC
Found at i:28242625 original size:102 final size:102
Alignment explanation
Indices: 28242444--28242682 Score: 397
Period size: 102 Copynumber: 2.3 Consensus size: 102
28242434 ATATTTATCA
28242444 AATGATGTGAACAGGAGAGATTCCCTGCAACAAAATAATCCGTGAACAGGAGAGATTCCCTGCAA
1 AATG-TGTGAACAGGAGAGATTCCCTGCAACAAAATAATCCGTGAACAGGAGAGATTCCCTGCAA
28242509 GAAATGATGTGAACAGGAAAGATTCCCTGCAACAAAAT
65 GAAATGATGTGAACAGGAAAGATTCCCTGCAACAAAAT
* *
28242547 AATGTGTGAACAGGAGAGATTCCCTACAACAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAG
1 AATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATCCGTGAACAGGAGAGATTCCCTGCAAG
* *
28242612 AAATGATGTGAACAGTAAAGATTCCCTGCAACAGAAT
66 AAATGATGTGAACAGGAAAGATTCCCTGCAACAAAAT
* * * *
28242649 AATGCGTGAACAGGAAATATTCCCTGCAAGAAAA
1 AATGTGTGAACAGGAGAGATTCCCTGCAACAAAA
28242683 GACAAGTGAA
Statistics
Matches: 127, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
102 123 0.97
103 4 0.03
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (102 bp):
AATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATCCGTGAACAGGAGAGATTCCCTGCAAG
AAATGATGTGAACAGGAAAGATTCCCTGCAACAAAAT
Found at i:28246657 original size:41 final size:41
Alignment explanation
Indices: 28246599--28246731 Score: 194
Period size: 41 Copynumber: 3.2 Consensus size: 41
28246589 ACTGGCACTT
** * *
28246599 AGCCTGCTAGAAATAAAGTCTGAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCAGCATCA
28246640 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCAGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCAGCATCA
** * *
28246681 AGCCTGCTAGACTTAAAGTCTGAAACATATCACTAGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCAGCATCA
28246722 AGCCTGCTAG
1 AGCCTGCTAG
28246732 GCACCGAGCC
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (41 bp):
AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCAGCATCA
Found at i:28247646 original size:2 final size:2
Alignment explanation
Indices: 28247639--28247668 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28247629 AATACAATAG
*
28247639 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28247669 TAATTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28251173 original size:4 final size:4
Alignment explanation
Indices: 28251164--28251189 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
28251154 AGAATTTTGA
28251164 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
28251190 CCCAAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:28259864 original size:10 final size:10
Alignment explanation
Indices: 28259836--28259865 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
28259826 GAGTTATAGC
*
28259836 ATGTATGTAT
1 ATGTATGTGT
28259846 ATGTATGTGT
1 ATGTATGTGT
28259856 ATGTATGTGT
1 ATGTATGTGT
28259866 GTATTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (10 bp):
ATGTATGTGT
Found at i:28264310 original size:31 final size:30
Alignment explanation
Indices: 28264275--28264351 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 30
28264265 TGCTTGTATC
*
28264275 ATTTAAATATTATTTATTATTATA-TTAAA
1 ATTTAAATATAATTTATTATTATATTTAAA
*
28264304 TTATTTAAATATAATTTATTTTTATATTTAAA
1 --ATTTAAATATAATTTATTATTATATTTAAA
28264336 ATTTAAA-ATAATTTAT
1 ATTTAAATATAATTTAT
28264352 GTGTCATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 9 0.21
30 7 0.16
31 22 0.51
32 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTTAAATATAATTTATTATTATATTTAAA
Found at i:28272300 original size:10 final size:10
Alignment explanation
Indices: 28272281--28272314 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
28272271 TGGTCACCGC
28272281 AAAA-AAAAA
1 AAAAGAAAAA
28272290 AAAAGAAAAA
1 AAAAGAAAAA
28272300 AAAAGAAAAA
1 AAAAGAAAAA
28272310 GAAAA
1 -AAAA
28272315 ATGGTCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 4 0.17
10 15 0.65
11 4 0.17
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:28272302 original size:16 final size:16
Alignment explanation
Indices: 28272281--28272315 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28272271 TGGTCACCGC
28272281 AAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAGAA
*
28272297 AAAAAAAGAAAAAGAA
1 AAAAAAAAAAAAAGAA
28272313 AAA
1 AAA
28272316 TGGTCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAGAA
Found at i:28282236 original size:117 final size:116
Alignment explanation
Indices: 28282107--28282348 Score: 423
Period size: 117 Copynumber: 2.1 Consensus size: 116
28282097 TCTAAGTGTC
28282107 GATTTGATAATTGATATATTAGATCAGTGTCTATCAATAAATACAAAAATATACTTTAGATCTAA
1 GATTTGATAATTGATATATTAGATCAGTGTCTATCAATAAATACAAAAATATACTTTAGATCTAA
* *
28282172 GTTAATCTAACAGTCTATGACAGAAATTAGAGAAAAAAACTGTTTGAATTTT
66 GTTAATCTAACAGTCTATGACAGAAATTAGAG-AAAAAACTATTTAAATTTT
*
28282224 GATTTGATAATTGATATATTAGATCAGTGTCTATCAATAAATACAAAAATATACTTTAGATTTAA
1 GATTTGATAATTGATATATTAGATCAGTGTCTATCAATAAATACAAAAATATACTTTAGATCTAA
*
28282289 GTTAATCTAACAGTCTATGACCGAAATTAGAGAAAAAACTATTTAAATTTT
66 GTTAATCTAACAGTCTATGACAGAAATTAGAGAAAAAACTATTTAAATTTT
*
28282340 AATTT-ATAA
1 GATTTGATAA
28282349 ATGTATGACG
Statistics
Matches: 120, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
115 4 0.03
116 21 0.17
117 95 0.79
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (116 bp):
GATTTGATAATTGATATATTAGATCAGTGTCTATCAATAAATACAAAAATATACTTTAGATCTAA
GTTAATCTAACAGTCTATGACAGAAATTAGAGAAAAAACTATTTAAATTTT
Found at i:28286796 original size:14 final size:14
Alignment explanation
Indices: 28286766--28286803 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28286756 ATAATAAAAG
28286766 ATAAA-ATA-AAAT
1 ATAAATATATAAAT
28286778 A-AAATATATAAAT
1 ATAAATATATAAAT
28286791 ATAAATATATAAA
1 ATAAATATATAAA
28286804 AAATATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.13
12 4 0.17
13 5 0.22
14 11 0.48
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
ATAAATATATAAAT
Found at i:28286968 original size:17 final size:18
Alignment explanation
Indices: 28286943--28286978 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
28286933 AATTGAAAAT
28286943 AAATAAATAAATCAAACA
1 AAATAAATAAATCAAACA
*
28286961 AAAT-AATAAATGAAACA
1 AAATAAATAAATCAAACA
28286978 A
1 A
28286979 TTTAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATAAATAAATCAAACA
Found at i:28287105 original size:17 final size:16
Alignment explanation
Indices: 28287067--28287105 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 16
28287057 TAAATTATAA
28287067 AAAATAAGGATAAAAT
1 AAAATAAGGATAAAAT
28287083 AGAAATAAGGATAAAAAT
1 A-AAATAAGGAT-AAAAT
28287101 AAAAT
1 AAAAT
28287106 GCTCGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 14 0.67
18 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (16 bp):
AAAATAAGGATAAAAT
Found at i:28288440 original size:3 final size:3
Alignment explanation
Indices: 28288408--28288473 Score: 60
Period size: 3 Copynumber: 21.0 Consensus size: 3
28288398 TGCTATTTTT
* * *
28288408 TTA TTAA TTA ATA TTA ATA TTA TTA CTA TTA TTA TCGTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA T--TA TTA TTA TTA
* *
28288456 GTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA
28288474 CTGCTATTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
3 44 0.88
4 3 0.06
5 3 0.06
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:28288450 original size:20 final size:20
Alignment explanation
Indices: 28288425--28288462 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28288415 TTAATATTAA
*
28288425 TATTATTACTATTATTATCG
1 TATTATTACTAGTATTATCG
*
28288445 TATTATTATTAGTATTAT
1 TATTATTACTAGTATTAT
28288463 TATTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (20 bp):
TATTATTACTAGTATTATCG
Found at i:28288800 original size:19 final size:19
Alignment explanation
Indices: 28288776--28288841 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 19
28288766 ATGTATATAC
* **
28288776 ATACTTATATATTTTTTTT
1 ATACTTATATAATTTTAAT
28288795 ATACTT-TATAATTTTAAT
1 ATACTTATATAATTTTAAT
* *
28288813 ATACATATATACA-TATAA-
1 ATACTTATATA-ATTTTAAT
28288831 ATACTTATATA
1 ATACTTATATA
28288842 TCTTCTTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 24 0.62
19 14 0.36
20 1 0.03
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.52
Consensus pattern (19 bp):
ATACTTATATAATTTTAAT
Found at i:28292399 original size:7 final size:7
Alignment explanation
Indices: 28292387--28292448 Score: 103
Period size: 7 Copynumber: 9.3 Consensus size: 7
28292377 CAGTGGAGGC
28292387 AACAAAA
1 AACAAAA
28292394 AACAAAA
1 AACAAAA
28292401 AACAAAA
1 AACAAAA
28292408 AACAAAA
1 AACAAAA
28292415 AACAAAA
1 AACAAAA
28292422 AAC--AA
1 AACAAAA
28292427 AA-AAAA
1 AACAAAA
28292433 AACAAAA
1 AACAAAA
28292440 AACAAAA
1 AACAAAA
28292447 AA
1 AA
28292449 AACTCTACCG
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.08
6 4 0.08
7 44 0.85
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (7 bp):
AACAAAA
Found at i:28292401 original size:1 final size:1
Alignment explanation
Indices: 28292390--28292450 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
28292380 TGGAGGCAAC
* * * * * * *
28292390 AAAAAACAAAAAACAAAAAACAAAAAACAAAAAACAAAAAAAAAACAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28292451 CTCTACCGGA
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28294070 original size:131 final size:131
Alignment explanation
Indices: 28293833--28294404 Score: 826
Period size: 131 Copynumber: 4.4 Consensus size: 131
28293823 ATATCAAGTA
* *
28293833 TTATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAATG
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTG
* * * *
28293898 GAGTAGATCGAGGACGGGGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAGGCCACCAGC
66 GAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCACCAGC
28293963 C
131 C
* * * *
28293964 TTATCTCCCTGAGCAACAGTAGAGTAAGTTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTG
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTG
* * * *
28294029 GAGTAGATCGAAGACGGTGAATCTTATCTTCCTGAGATAGTAGGAAGCAGATTTAAGCCACCAGT
66 GAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCACCAG-
28294094 CC
130 CC
* * *
28294096 -TATCTCCCTAAGCAGTAGTGGAGTAGGTTAAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTG
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTG
** *
28294160 GAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAGCAGATTTAAGCCACCTAT
66 GAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCACC-AG
28294225 CC
130 CC
*
28294227 -TATCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTG
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTG
* * * * *
28294291 GAGCAGATCAAAGATGGCGAATCTTATCTTTCC-AAGGTAGTAGGGAAACAGATTTAAACCACTA
66 GAGCAGATCGAAGACGGCGAATCTTATC-TTCCTAAGGTAGTA-GGAAGCAGATTTAAGCCACCA
28294355 GCC
129 GCC
* * *
28294358 TTATCTCCCTGAGCAGTAGTGGAGTAGGTCGAAGATTGTAGATCTTA
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTA
28294405 CCTTCCTGTA
Statistics
Matches: 398, Mismatches: 38, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
131 332 0.83
132 66 0.17
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (131 bp):
TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATCGAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCACCAGC
C
Found at i:28294296 original size:87 final size:87
Alignment explanation
Indices: 28293918--28294298 Score: 208
Period size: 87 Copynumber: 4.4 Consensus size: 87
28293908 AGGACGGGGA
* * * *
28293918 ATCTTATCTTCCTAAG--GTAGTAGGAAGCAGATTTAGGCCACC-AGCCTTATCTCCCTGAGCAA
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTTAAGCCACCTATCC-TATCTCCCTGAGCAG
* * * *
28293980 CAGTAGAGTA-AGTTGAAGATTGAAG
63 CAGTGGAGCAGA-TTGAAGACTGCAG
* ** * * *
28294005 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAG--ACGGTGAATCTTATCTTCCTGAG-A-
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTTAAGCCAC-CT--ATCCTATCTCCCTGAGCAG
* * * **
28294066 TAGTAGGAAGCAGATTTAAGCCACCAG
63 CAGT-GG-AGCAGATTGAAGACTGCAG
* * * * *** ** * * *
28294093 -TCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTAAAGATTGCAGATCTTATCTCCCTAAGCAGTA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTTAAG-CCACCTATCCTATCTCCCTGAGCAGCA
* *
28294157 GTGGAGCAGATCGAAGACGGC-G
65 GTGGAGCAGATTGAAGACTGCAG
* * * *
28294179 AATCTTATCTTCCCGAGGTAGTAG-GAAGCAGATTTAAGCCACCTATCCTATCTCCCTGAGCAGC
1 -ATCTTATC-TCCCTAAGCAGTAGTGGAGCAGATTTAAGCCACCTATCCTATCTCCCTGAGCAGC
* * * *
28294243 AGCGGAGTAGGTTGAAGATTGCAG
64 AGTGGAGCAGATTGAAGACTGCAG
28294267 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
28294299 CAAAGATGGC
Statistics
Matches: 217, Mismatches: 58, Indels: 38
0.69 0.19 0.12
Matches are distributed among these distances:
85 2 0.01
86 15 0.07
87 133 0.61
88 43 0.20
89 23 0.11
90 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (87 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTTAAGCCACCTATCCTATCTCCCTGAGCAGCAG
TGGAGCAGATTGAAGACTGCAG
Found at i:28294305 original size:44 final size:44
Alignment explanation
Indices: 28293833--28294298 Score: 220
Period size: 44 Copynumber: 10.7 Consensus size: 44
28293823 ATATCAAGTA
* * * * *
28293833 TTATCTCCCTGAGCAGCAGTGAAGTAGGTTGAAGATTGCAGATC
1 TTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATC
* * * * * **
28293877 TTATCTCCCTAAGCAGTAATGGAGTAGATCGAGGA-CGGGGAATC
1 TTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAG-ATC
* * * **** *
28293921 TTATCTTCCTAAG--GTAGTAGGAAGCAGATTTAGGCCACCAG-CC
1 TTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTGCAGATC
* ** * * *
28293964 TTATCTCCCTGAGCAACAGTAGAGTA-AGTTGAAGATTGAAGATC
1 TTATCTCCCTAAGCAGTAGTGGAGCAGA-TTGAAGATTGCAGATC
* * *
28294008 TTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTG-A-ATC
1 TTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA--TTGCAGATC
* * * ****
28294052 TTATCTTCCTGAG-A-TAGTAGGAAGCAGATTTAAGCCACCAG-TC
1 TTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATTGCAGATC
* * * *
28294095 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTAAAGATTGCAGATC
1 TTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATC
* **
28294139 TTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGC-GAATC
1 TTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAG-ATC
* * * * * *** **
28294183 TTATCTTCCCGAGGTAGTAG-GAAGCAGATTTAAG-CCACCTATC
1 TTATC-TCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATC
* * * * * *
28294226 CTATCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGCAGATC
1 TTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATC
28294270 TTATCTCCCTAAGCAGTAGTGGAGCAGAT
1 TTATCTCCCTAAGCAGTAGTGGAGCAGAT
28294299 CAAAGATGGC
Statistics
Matches: 302, Mismatches: 97, Indels: 46
0.68 0.22 0.10
Matches are distributed among these distances:
42 18 0.06
43 73 0.24
44 188 0.62
45 21 0.07
46 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (44 bp):
TTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATC
Found at i:28294805 original size:220 final size:219
Alignment explanation
Indices: 28294227--28294807 Score: 865
Period size: 220 Copynumber: 2.6 Consensus size: 219
28294217 CCACCTATCC
*
28294227 TATCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
28294292 AGCAGATCAAAGATGGCGAATCTTATCTTTCCAAGGTAGTAGGGAAACAGATTTAAACCACTAGC
66 AGCAGATCAAAGACGGCGAATCTTATC-TTCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
* * ** *
28294357 CTTATCTCCCTGAGCAGTAGTGGAGTAGGTCGAAGATTGTAGATCTTACCTTCCTGTACTAGCAG
130 CTTATCTCTCTGAGAAAAAGTGGAGTAGGTCGAAGATTGTAAATCTTACCTTCCTGTACTAGCAG
28294422 TAAAACAGATCGAAAGCGCCAGCCT
195 TAAAACAGATCGAAAGCGCCAGCCT
* * * *
28294447 TATCTCCCTGAACAGCGGTGGAGTAGGTTGAAGATTGCAGATCCTATGTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
28294512 AGTAGATCGAAGACGGCGAATCTTATTTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
66 AGCAGATCAAAGACGGCGAATCTTATCTT-CCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
* ** * *
28294577 CTTATCTCTCTGAGAAAAAGTGGAGTAGGTCGAAGATTTTAAATCTTGTCTTCTTGTACTGGCAG
130 CTTATCTCTCTGAGAAAAAGTGGAGTAGGTCGAAGATTGTAAATCTTACCTTCCTGTACTAGCAG
* * *
28294642 TGAAGCAGATCGAAAGCTCCAGCCT
195 TAAAACAGATCGAAAGCGCCAGCCT
*
28294667 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTGTCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
** * * *
28294732 AGCAGATCAAAGACGATGAATCTTATCTTCCTAAGGTAGTCGGGAAGCAGATTTAAGCCACAAGT
66 AGCAGATCAAAGACGGCGAATCTTATCTTCC-AAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
28294797 CTTATCTCTCT
130 CTTATCTCTCT
28294808 AATGTTGCAG
Statistics
Matches: 322, Mismatches: 37, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
219 4 0.01
220 318 0.99
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (219 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCAAAGACGGCGAATCTTATCTTCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCC
TTATCTCTCTGAGAAAAAGTGGAGTAGGTCGAAGATTGTAAATCTTACCTTCCTGTACTAGCAGT
AAAACAGATCGAAAGCGCCAGCCT
Found at i:28294911 original size:51 final size:45
Alignment explanation
Indices: 28294796--28294913 Score: 112
Period size: 45 Copynumber: 2.5 Consensus size: 45
28294786 AAGCCACAAG
*
28294796 TCTTATCTCTCT-AATGTTGCAGTGGAGCAGACTGAAGATAGTGAA
1 TCTTATCTCTCTGAA-GTTGCAGTGGAACAGACTGAAGATAGTGAA
* * * * *
28294841 TCTTATTTCCCTGATGTTGCAGTGGAACAGATTGAAGCTATATAGTGCTGA
1 TCTTATCTCTCTGAAGTTGCAGTGGAACAGACTGAAG----ATAGTG--AA
28294892 TCTTATCTCTCTGAAGTTGCAG
1 TCTTATCTCTCTGAAGTTGCAG
28294914 AAGAGCATAT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
45 30 0.53
46 1 0.02
49 6 0.11
51 20 0.35
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (45 bp):
TCTTATCTCTCTGAAGTTGCAGTGGAACAGACTGAAGATAGTGAA
Found at i:28295026 original size:44 final size:44
Alignment explanation
Indices: 28294978--28295137 Score: 143
Period size: 44 Copynumber: 3.7 Consensus size: 44
28294968 AATTGAAAAC
*
28294978 CTTATCTCCTTAAAGTTGCAGTGGAGCGGATTAAAATGATTAAT
1 CTTATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAATGATTAAT
* *
28295022 CTTATCT-CTCTAAAGTTGCAGTAGAGCAGATT-CAA-G-TTAAT
1 CTTATCTCCT-TAAAGTTGCAGTGGAGCAGATTAAAATGATTAAT
* * * * * **
28295063 -TCAATCTCCTTGAAGTTACAGTGGAGCAAATTAAAACGATGGAT
1 CT-TATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAATGATTAAT
* *
28295107 CTTATCT-CTCTGAAGTTGCAGTAGAGCAGAT
1 CTTATCTCCT-TAAAGTTGCAGTGGAGCAGAT
28295138 CGAGTGGAGT
Statistics
Matches: 93, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
40 1 0.01
41 27 0.29
42 5 0.05
43 7 0.08
44 52 0.56
45 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (44 bp):
CTTATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAATGATTAAT
Found at i:28295208 original size:44 final size:41
Alignment explanation
Indices: 28294990--28295219 Score: 114
Period size: 44 Copynumber: 5.4 Consensus size: 41
28294980 TATCTCCTTA
* ** *
28294990 AAGTTGCAGTGGAGCGGATTAAAATGATTAATCTTATCTCTCTA
1 AAGTTGCAGT-GAGC-AATTAAAA-GATGGATCTTATCTCTCTG
* ** *
28295034 AAGTTGCAGTAGAGCAGATT-CAAG-TTAAT-TCAATCTC-CTTG
1 AAGTTGCAGT-GAGCA-ATTAAAAGATGGATCT-TATCTCTC-TG
*
28295075 AAGTTACAGTGGAGCAAATTAAAACGATGGATCTTATCTCTCTG
1 AAGTTGCAGT-GAGC-AATTAAAA-GATGGATCTTATCTCTCTG
** * * *
28295119 AAGTTGCAGTAGAGCAGA-T-CGAG-TGGAGTTTTATCTCCCTA
1 AAGTTGCAGT-GAGCA-ATTAAAAGATGGA-TCTTATCTCTCTG
*
28295160 AAGTTGCAGTGTAGCGAATTAAAATGATGGATCTTATCTATCTG
1 AAGTTGCAGTG-AGC-AATTAAAA-GATGGATCTTATCTCTCTG
*
28295204 AAGTTCCAGTAGAGCA
1 AAGTTGCAGT-GAGCA
28295220 GATCGCATCA
Statistics
Matches: 143, Mismatches: 25, Indels: 37
0.70 0.12 0.18
Matches are distributed among these distances:
40 7 0.05
41 52 0.36
42 7 0.05
43 7 0.05
44 63 0.44
45 7 0.05
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (41 bp):
AAGTTGCAGTGAGCAATTAAAAGATGGATCTTATCTCTCTG
Found at i:28295223 original size:85 final size:84
Alignment explanation
Indices: 28294979--28295224 Score: 321
Period size: 85 Copynumber: 2.9 Consensus size: 84
28294969 ATTGAAAACC
* ** *
28294979 TTATCTCCTTAAAGTTGCAGTGGAGCGGATTAAAATGATTAATCTTATCTCTCTAAAGTTGCAGT
1 TTATCTCCTTAAAGTTGCAGTGGAGCGAATTAAAATGATGGATCTTATCTCTCTGAAGTTGCAGT
* *
28295044 AGAGCAGATTCAAGTTAATT
66 AGAGCAGA-TCGAGTGAATT
** * * * *
28295064 CAATCTCCTTGAAGTTACAGTGGAGCAAATTAAAACGATGGATCTTATCTCTCTGAAGTTGCAGT
1 TTATCTCCTTAAAGTTGCAGTGGAGCGAATTAAAATGATGGATCTTATCTCTCTGAAGTTGCAGT
*
28295129 AGAGCAGATCGAGTGGAGTT
66 AGAGCAGATCGAGT-GAATT
* * * *
28295149 TTATCTCCCTAAAGTTGCAGTGTAGCGAATTAAAATGATGGATCTTATCTATCTGAAGTTCCAGT
1 TTATCTCCTTAAAGTTGCAGTGGAGCGAATTAAAATGATGGATCTTATCTCTCTGAAGTTGCAGT
28295214 AGAGCAGATCG
66 AGAGCAGATCG
28295225 CATCAGACTT
Statistics
Matches: 137, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
84 5 0.04
85 132 0.96
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (84 bp):
TTATCTCCTTAAAGTTGCAGTGGAGCGAATTAAAATGATGGATCTTATCTCTCTGAAGTTGCAGT
AGAGCAGATCGAGTGAATT
Found at i:28295254 original size:85 final size:85
Alignment explanation
Indices: 28295081--28295254 Score: 208
Period size: 85 Copynumber: 2.0 Consensus size: 85
28295071 CTTGAAGTTA
* * *
28295081 CAGTGGAGCAAATTAAAACGATGGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGAGTGGA
1 CAGTGGAGCAAATTAAAACGATGGATCTTATCTATCTGAAGTTCCAGTAGAGCAGATCGAGTAGA
* **
28295146 GTTTTATCTCCCTAAAGTTG
66 GCTTTATCTCCCTAAAGACG
* * *
28295166 CAGTGTAGCGAATTAAAATGATGGATCTTATCTATCTGAAGTTCCAGTAGAGCAGATCGCA-TCA
1 CAGTGGAGCAAATTAAAACGATGGATCTTATCTATCTGAAGTTCCAGTAGAGCAGATCG-AGT-A
* * *
28295230 GA-CTTTATTTTCTTAAAGACG
64 GAGCTTTATCTCCCTAAAGACG
28295251 CAGT
1 CAGT
28295255 AAATCAAGTT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
85 72 0.96
86 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (85 bp):
CAGTGGAGCAAATTAAAACGATGGATCTTATCTATCTGAAGTTCCAGTAGAGCAGATCGAGTAGA
GCTTTATCTCCCTAAAGACG
Found at i:28295469 original size:130 final size:130
Alignment explanation
Indices: 28295151--28295471 Score: 543
Period size: 130 Copynumber: 2.5 Consensus size: 130
28295141 GTGGAGTTTT
* * * * * *
28295151 ATCTCCCTAAAGTTGCAGTGTAGCGAATTAAAATGATGGATCTTATCTATCTGAAGTTCCAGTAG
1 ATCTCCCTGAAGTTGTAGTGGAGCGAATTAAAATGATGGATCTTATCTATCTGAAGTTGCAATAA
28295216 AGCAGATCGCATCAGACTTTATTTTCTTAAAGACGCAGTAAATCAAGTTGAAGCTACCAAGTCCC
66 AGCAGATCGCATCAGACTTTATTTTCTTAAAGACGCAGTAAATCAAGTTGAAGCTACCAAGTCCC
* *
28295281 ATCTCCCTGAAATTGTAGTGGAGCGAATTAAAATGATGGATATTATCTATCTGAAGTTGCAATAA
1 ATCTCCCTGAAGTTGTAGTGGAGCGAATTAAAATGATGGATCTTATCTATCTGAAGTTGCAATAA
*
28295346 AGCAGATCGCATCAGACTTTATTTTCTTAAAGACGCAGTAGATCAAGTTGAAGCTACCAAGTCCC
66 AGCAGATCGCATCAGACTTTATTTTCTTAAAGACGCAGTAAATCAAGTTGAAGCTACCAAGTCCC
* *
28295411 ATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAATGATGGATCTTATCTATCTCAAGTTGCA
1 ATCTCCCTGAAGTTGTAGTGGAGCGAATTAAAATGATGGATCTTATCTATCTGAAGTTGCA
28295472 TTAGGTCGGA
Statistics
Matches: 178, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 178 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (130 bp):
ATCTCCCTGAAGTTGTAGTGGAGCGAATTAAAATGATGGATCTTATCTATCTGAAGTTGCAATAA
AGCAGATCGCATCAGACTTTATTTTCTTAAAGACGCAGTAAATCAAGTTGAAGCTACCAAGTCCC
Found at i:28297089 original size:3 final size:3
Alignment explanation
Indices: 28297057--28297122 Score: 60
Period size: 3 Copynumber: 21.0 Consensus size: 3
28297047 TGCTATTTTT
* * *
28297057 TTA TTAA TTA ATA TTA ATA TTA TTA CTA TTA TTA TCGTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA T--TA TTA TTA TTA
* *
28297105 GTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA
28297123 CTGCTATTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
3 44 0.88
4 3 0.06
5 3 0.06
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:28297099 original size:20 final size:20
Alignment explanation
Indices: 28297074--28297111 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28297064 TTAATATTAA
*
28297074 TATTATTACTATTATTATCG
1 TATTATTACTAGTATTATCG
*
28297094 TATTATTATTAGTATTAT
1 TATTATTACTAGTATTAT
28297112 TATTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (20 bp):
TATTATTACTAGTATTATCG
Found at i:28298917 original size:51 final size:51
Alignment explanation
Indices: 28298841--28298991 Score: 194
Period size: 51 Copynumber: 3.0 Consensus size: 51
28298831 GTAATAAGAT
* * *
28298841 TTGTAGCCTCTATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAAC
1 TTGTAGCTTCAATCTGTTCCACTGCAACTTTAGGGAGATAAGATTTGTAAC
*
28298892 TTGTAGCTTCAATCTGTTGCACTGCAACTTTAGGGAGATAAGATTTGTAAC
1 TTGTAGCTTCAATCTGTTCCACTGCAACTTTAGGGAGATAAGATTTGTAAC
* * * * * * * *
28298943 TTTTAGCTTCAATATTTTCCACTGAAACTTCAGTGAAATTAGATTTGTA
1 TTGTAGCTTCAATCTGTTCCACTGCAACTTTAGGGAGATAAGATTTGTA
28298992 GTTTTAATTT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 87 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (51 bp):
TTGTAGCTTCAATCTGTTCCACTGCAACTTTAGGGAGATAAGATTTGTAAC
Found at i:28299442 original size:44 final size:44
Alignment explanation
Indices: 28298960--28299702 Score: 445
Period size: 44 Copynumber: 16.7 Consensus size: 44
28298950 TTCAATATTT
* * * * * **
28298960 TCCACTGAAACTTCAGTGAAATTAGATTTGTAGT-TTTAATTTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTA-TATTTAATCTAC
* * * *
28299004 TCTACTGCAACTTCAGGGAGATGAGATTTATA-ACTTTAATATAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATA-TTTAATCTAC
* * * ** *
28299048 TCTACTGTAACTTCAGAGAGATAAGATTCACTATTTTTAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATT-TGTATATTTAATCTAC
* * *
28299093 TCCACTGCAACTTCAAGAAGATAAGATTTGTA-ACTTCAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATA-TTTAATCTAC
** * * * * * * *
28299137 TAGATTGCGACTTCAGAGAGATAATATTAGTATATTCAAACTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATATTTAATCTAC
* * * *
28299181 TCCACTGCAACTTCAGAGAGATAAGATTAGTATATTCAAACTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATATTTAATCTAC
* *
28299225 TCCACTGCAACTTTAGGGAGATAAGATTTGTGT-TTTCAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATATTT-AATCTAC
* * * * *
28299269 TCCACTACAACTTCAAGGAGATAAGATTAGTATATTCAATCTAT
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATATTTAATCTAC
* * *
28299313 TCCACTGCAACTTTAGGGAGATAGGATTTGTGT-TTTCAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATATTT-AATCTAC
* * * * * *
28299357 TCCACTACAACTTTAAGGAGATAAGATTAGTATATTCAATCTAT
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATATTTAATCTAC
* *** **
28299401 TCCACTGCAACTTTAGGGAGATAAGATTTGTGGCTTTAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATATTTAATCTAC
* * * * *
28299445 TCCTCTGCAACTTTAGGGAGATAAGATTCGCCATAATGACTTCAATCT-G
1 TCCACTGCAACTTCAGGGAGATAAGATTTG---T-AT-A-TTTAATCTAC
* * * *
28299494 TCCCACTACAACTTCAGGG-GTATAGGATTTATGGTTTGTAGCTTTAATCTAT
1 T-CCACTGCAACTTCAGGGAG-ATAAGA-TT-T-G--TATA--TTTAATCTAC
* * * *
28299546 TCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATATTTAATCTAC
* * * *
28299591 TCTACTGTAAATTCAGGGAAATAAGA--T-T-TA-TT--TCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATATTTAATCTAC
* * ** * * **
28299628 TCCAATACAACTTCAATGAGATAACATTTGTGA-CTTTAATCTTT
1 TCCACTGCAACTTCAGGGAGATAAGATTTGT-ATATTTAATCTAC
*
28299672 TCCGCTGCAACTTCAGGGAGATAAGATTTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTTGT
28299703 CATGGTGACA
Statistics
Matches: 541, Mismatches: 126, Indels: 64
0.74 0.17 0.09
Matches are distributed among these distances:
37 22 0.04
39 2 0.00
40 2 0.00
41 1 0.00
42 2 0.00
43 4 0.01
44 368 0.68
45 70 0.13
47 3 0.01
48 1 0.00
49 2 0.00
50 29 0.05
51 32 0.06
52 2 0.00
53 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTGTATATTTAATCTAC
Found at i:28299442 original size:132 final size:132
Alignment explanation
Indices: 28299007--28299428 Score: 490
Period size: 132 Copynumber: 3.2 Consensus size: 132
28298997 AATTTGTTCT
* * * * *
28299007 ACTGCAACTTCAGGGAGATGAGATT--TATAACTTTAATATACTCTACTGTAACTTCAGAGAGAT
1 ACTGCAACTTCAGGGAGATAAGATTAGTAT-A-TTCAATCTACTCCACTGCAACTTCAGAGAGAT
* * * *
28299070 AAGATTCACTATTTTTAATCTACTCCACTGCAACTTCAAGAAGATAAGATTTGTA-ACTTCAATC
64 AAGATT-AGTATTTTCAATCTACTCCACTGCAACTTTAAGGAGATAAGATTTGTATA-TTCAATC
**
28299134 TACTAG
127 TACTCC
* * * * *
28299140 ATTGCGACTTCAGAGAGATAATATTAGTATATTCAAACTACTCCACTGCAACTTCAGAGAGATAA
1 ACTGCAACTTCAGGGAGATAAGATTAGTATATTCAATCTACTCCACTGCAACTTCAGAGAGATAA
* * * * *
28299205 GATTAGTATATTCAAACTACTCCACTGCAACTTTAGGGAGATAAGATTTGTGTTTTCAATCTACT
66 GATTAGTATTTTCAATCTACTCCACTGCAACTTTAAGGAGATAAGATTTGTATATTCAATCTACT
28299270 CC
131 CC
* * * * * *
28299272 ACTACAACTTCAAGGAGATAAGATTAGTATATTCAATCTATTCCACTGCAACTTTAGGGAGATAG
1 ACTGCAACTTCAGGGAGATAAGATTAGTATATTCAATCTACTCCACTGCAACTTCAGAGAGATAA
* * * * *
28299337 GATTTGTGTTTTCAATCTACTCCACTACAACTTTAAGGAGATAAGATTAGTATATTCAATCTATT
66 GATTAGTATTTTCAATCTACTCCACTGCAACTTTAAGGAGATAAGATTTGTATATTCAATCTACT
28299402 CC
131 CC
*
28299404 ACTGCAACTTTAGGGAGATAAGATT
1 ACTGCAACTTCAGGGAGATAAGATT
28299429 TGTGGCTTTA
Statistics
Matches: 241, Mismatches: 45, Indels: 7
0.82 0.15 0.02
Matches are distributed among these distances:
132 184 0.76
133 53 0.22
134 1 0.00
135 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (132 bp):
ACTGCAACTTCAGGGAGATAAGATTAGTATATTCAATCTACTCCACTGCAACTTCAGAGAGATAA
GATTAGTATTTTCAATCTACTCCACTGCAACTTTAAGGAGATAAGATTTGTATATTCAATCTACT
CC
Found at i:28300601 original size:3 final size:3
Alignment explanation
Indices: 28300593--28300642 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
28300583 CCTATCCTTT
28300593 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
28300641 TT
1 TT
28300643 TTACATGAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:28306226 original size:3 final size:3
Alignment explanation
Indices: 28306205--28306255 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
28306195 TAGAACAATG
*
28306205 ATA ATA ATGA A-A ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28306250 ATA ATA
1 ATA ATA
28306256 TTATTATTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:28309963 original size:14 final size:14
Alignment explanation
Indices: 28309940--28309971 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28309930 CAGCATTTAT
28309940 TTATGATTAATTAA
1 TTATGATTAATTAA
*
28309954 TTATGTTTAATTAA
1 TTATGATTAATTAA
28309968 TTAT
1 TTAT
28309972 CTCATTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (14 bp):
TTATGATTAATTAA
Found at i:28313044 original size:14 final size:14
Alignment explanation
Indices: 28313027--28313058 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28313017 TAAAAAAATG
*
28313027 TTATTAAATTATTA
1 TTATTAAATTAGTA
28313041 TTATTAAATTAGTA
1 TTATTAAATTAGTA
28313055 TTAT
1 TTAT
28313059 ATTATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TTATTAAATTAGTA
Found at i:28313195 original size:3 final size:3
Alignment explanation
Indices: 28313189--28313238 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
28313179 TATTAAAATA
28313189 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28313237 TA
1 TA
28313239 ACTAGGAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28313588 original size:16 final size:16
Alignment explanation
Indices: 28313563--28313602 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
28313553 GTTGATAAAA
*
28313563 TGATTAAATATGAGGG
1 TGATTGAATATGAGGG
28313579 TGATTGAATATGAGGG
1 TGATTGAATATGAGGG
28313595 TGATTGAA
1 TGATTGAA
28313603 ATTGTTACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (16 bp):
TGATTGAATATGAGGG
Found at i:28316947 original size:19 final size:20
Alignment explanation
Indices: 28316919--28316957 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
28316909 ATATCTAAAT
28316919 TACCACACACACATA-TATA
1 TACCACACACACATACTATA
*
28316938 TACCATACACACATACTATA
1 TACCACACACACATACTATA
28316958 AAACTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (20 bp):
TACCACACACACATACTATA
Found at i:28321694 original size:18 final size:17
Alignment explanation
Indices: 28321661--28321699 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
28321651 TTTTATAAAT
28321661 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
28321679 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
28321696 TGTG
1 TGTG
28321700 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:28321817 original size:8 final size:8
Alignment explanation
Indices: 28321804--28321832 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
28321794 CACTAAAGAT
28321804 CAGTGTTA
1 CAGTGTTA
28321812 CAGTGTTA
1 CAGTGTTA
28321820 CAGTGTTA
1 CAGTGTTA
28321828 CAGTG
1 CAGTG
28321833 AGTCTCGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:28321946 original size:23 final size:23
Alignment explanation
Indices: 28321919--28321971 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
28321909 AGTGTTATTG
28321919 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28321942 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28321965 ATCAGTG
1 ATCAGTG
28321972 TGGCACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:28334210 original size:20 final size:22
Alignment explanation
Indices: 28334163--28334211 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
28334153 GTACATAGAT
*
28334163 ATATATATAGATATGTAAACAA
1 ATATATATAAATATGTAAACAA
*
28334185 AT-TATA-AAATATGTATA-AA
1 ATATATATAAATATGTAAACAA
28334204 ATATATAT
1 ATATATAT
28334212 GAGTACGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 4 0.17
20 13 0.57
21 4 0.17
22 2 0.09
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (22 bp):
ATATATATAAATATGTAAACAA
Found at i:28334263 original size:38 final size:36
Alignment explanation
Indices: 28334219--28334350 Score: 160
Period size: 38 Copynumber: 3.5 Consensus size: 36
28334209 TATGAGTACG
28334219 TATATGTACATATATA-AGTTATAAAAAATATGTATGTA
1 TATATGT--ATATATAGA-TTATAAAAAATATGTATGTA
* *
28334257 TCTATGTATATATAGATTAT-AAAAATGCACGTATGTA
1 TATATGTATATATAGATTATAAAAAAT--ATGTATGTA
28334294 TATATGTATATATAGATTATAAAAAATATACGTATGTA
1 TATATGTATATATAGATTATAAAAAATAT--GTATGTA
*
28334332 TATATGTATATATAAATTA
1 TATATGTATATATAGATTA
28334351 CAATGTATAA
Statistics
Matches: 83, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
35 6 0.07
36 12 0.14
37 28 0.34
38 37 0.45
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (36 bp):
TATATGTATATATAGATTATAAAAAATATGTATGTA
Found at i:28356315 original size:20 final size:19
Alignment explanation
Indices: 28356290--28356327 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
28356280 AAATATAGGT
28356290 AAAAATACGGTCAACGGGTA
1 AAAAAT-CGGTCAACGGGTA
*
28356310 AAAAATGGGTCAACGGGT
1 AAAAATCGGTCAACGGGT
28356328 CGCGCCTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.42, C:0.13, G:0.29, T:0.16
Consensus pattern (19 bp):
AAAAATCGGTCAACGGGTA
Found at i:28356420 original size:20 final size:20
Alignment explanation
Indices: 28356395--28356444 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
28356385 GCTGCTGCCT
*
28356395 TTGTCCCTTCCACCATGG-TG
1 TTGTCCCTTCCACCA-GGCTA
*
28356415 TTGTCCATTCCACCAGGCTA
1 TTGTCCCTTCCACCAGGCTA
28356435 TTGTCCCTTC
1 TTGTCCCTTC
28356445 AATGGGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.12, C:0.36, G:0.16, T:0.36
Consensus pattern (20 bp):
TTGTCCCTTCCACCAGGCTA
Found at i:28357271 original size:16 final size:16
Alignment explanation
Indices: 28357250--28357288 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
28357240 TTAACTCATT
*
28357250 TAATTTTTATATAATG
1 TAATTTTTATATAATA
28357266 TAATTTTTATATAATA
1 TAATTTTTATATAATA
28357282 TAATTTT
1 TAATTTT
28357289 ATTTGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TAATTTTTATATAATA
Found at i:28362862 original size:18 final size:18
Alignment explanation
Indices: 28362841--28362891 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
28362831 ATATATATAC
28362841 ATATATTTTTTAATGTAG
1 ATATATTTTTTAATGTAG
* * *
28362859 ATAT-TATTTTACATATAT
1 ATATATTTTTTA-ATGTAG
*
28362877 ACATATTTTTTAATG
1 ATATATTTTTTAATG
28362892 AATGTTCTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
17 6 0.24
18 13 0.52
19 6 0.24
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (18 bp):
ATATATTTTTTAATGTAG
Found at i:28362896 original size:40 final size:38
Alignment explanation
Indices: 28362825--28362922 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 38
28362815 AATATTTTTC
28362825 ATATTTATATATATACATATATTTTTTAATGTAGATATT
1 ATATTTATATATATACATATATTTTTTAATGT-GATATT
* ** *
28362864 AT-TTTACATATATACATAT-TTTTTAATGAATGTTCTTTT
1 ATATTTATATATATACATATATTTTT--T-AATGTGATATT
28362903 ATATTTATATATATACATAT
1 ATATTTATATATATACATAT
28362923 GTATATTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
37 5 0.10
38 16 0.32
39 8 0.16
40 21 0.42
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.54
Consensus pattern (38 bp):
ATATTTATATATATACATATATTTTTTAATGTGATATT
Found at i:28362912 original size:36 final size:37
Alignment explanation
Indices: 28362828--28362913 Score: 90
Period size: 36 Copynumber: 2.4 Consensus size: 37
28362818 ATTTTTCATA
28362828 TTTATA-TATATACATATATTTTTTAATGTAGATATTAT
1 TTTATATTATATAC--ATATTTTTTAATGTAGATATTAT
* * *
28362866 TTTACA-TATATACATATTTTTTAATG-A-ATGTTCT
1 TTTATATTATATACATATTTTTTAATGTAGATATTAT
28362900 TTTATATTTATATA
1 TTTATA-TTATATA
28362914 TATACATATG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
34 10 0.24
35 1 0.02
36 19 0.45
38 12 0.29
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (37 bp):
TTTATATTATATACATATTTTTTAATGTAGATATTAT
Found at i:28364065 original size:32 final size:34
Alignment explanation
Indices: 28364024--28364086 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
28364014 TCATTTTTTA
28364024 TCGAAAACT-AA-TTTTTGCTTTTT-AAAAAAGGG
1 TCGAAAACTAAATTTTTTG-TTTTTCAAAAAAGGG
*
28364056 TCGACAACTAAATTTTTTGTTTTTCAAAAAA
1 TCGAAAACTAAATTTTTTGTTTTTCAAAAAA
28364087 ATGGTTTCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 8 0.30
33 7 0.26
34 12 0.44
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (34 bp):
TCGAAAACTAAATTTTTTGTTTTTCAAAAAAGGG
Found at i:28367870 original size:17 final size:17
Alignment explanation
Indices: 28367845--28367883 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
28367835 CCTCGAGAGG
*
28367845 GACCTGGTATTAAAGAA
1 GACCCGGTATTAAAGAA
28367862 GACCCGGTATTAAAGAA
1 GACCCGGTATTAAAGAA
28367879 GACCC
1 GACCC
28367884 TTCCCATGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (17 bp):
GACCCGGTATTAAAGAA
Found at i:28369605 original size:123 final size:122
Alignment explanation
Indices: 28369434--28369741 Score: 436
Period size: 132 Copynumber: 2.4 Consensus size: 122
28369424 TTGACAACGA
28369434 AGCAGATCGAAGATGGCGAATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAATTCTACTTCC
1 AGCAGATCGAAGATGGCG-ATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAATTCTACTTCC
* *
28369499 CTGGACAACGGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGTGG
65 CTGGACAACAGAGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGTGG
* *
28369557 AGCAGATCGAGGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAAT
1 AGCAGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTATAGTGGAGTACA-T--------TAAT
*
28369622 TCTACTTCCCTGGGCAACAGAGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGT
56 TCTACTTCCCTGGACAACAGAGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGT
28369687 GG
121 GG
* * *
28369689 AGTAGATCGAAGATGGTGGATTTTACCTCACTGTGGTTATAGTGGAGTACATT
1 AGCAGATCGAAGATGG-CGATTTTACCTCCCTGTGGTTATAGTGGAGTACATT
28369742 GAAGCTAGTA
Statistics
Matches: 164, Mismatches: 10, Indels: 22
0.84 0.05 0.11
Matches are distributed among these distances:
123 48 0.29
124 2 0.01
131 1 0.01
132 113 0.69
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (122 bp):
AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAATTCTACTTCCC
TGGACAACAGAGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGTGG
Found at i:28369695 original size:44 final size:44
Alignment explanation
Indices: 28369509--28369702 Score: 105
Period size: 44 Copynumber: 4.4 Consensus size: 44
28369499 CTGGACAACG
*
28369509 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTA
1 GTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTA
* * * ** * * *
28369553 GTGGAGCAGATCGAGGATGGCAGATTTTACCTCCCT--GTGGTTACA
1 GTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAG-T--A
* * ** * **
28369598 GTGGAGTACATTGAAGCCA-AT-A-AT-TCTA-CTTCCCTGGGCAACA
1 GTGGAGTAGATTGAAG--ATTTCAGATCT-TATC-TCCCTAAGTAGTA
* *
28369641 GAGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTA
1 GTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTA
*
28369685 GTGGAGTAGATCGAAGAT
1 GTGGAGTAGATTGAAGAT
28369703 GGTGGATTTT
Statistics
Matches: 105, Mismatches: 31, Indels: 28
0.64 0.19 0.17
Matches are distributed among these distances:
41 1 0.01
42 4 0.04
43 18 0.17
44 64 0.61
45 16 0.15
46 1 0.01
47 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (44 bp):
GTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTA
Done.