Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008269.1 Hibiscus syriacus cultivar Beakdansim tig00110926_pilon, whole genome shotgun sequence
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: 799769
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:195136 original size:18 final size:18
Alignment explanation
Indices: 195106--195165 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
195096 TATAATATAA
195106 ATTTATA-TATAAACTAT
1 ATTTATATTATAAACTAT
195123 ATTTATATTATAAACTAT
1 ATTTATATTATAAACTAT
* *
195141 A-TAATTATTATAAGCTAT
1 ATTTA-TATTATAAACTAT
*
195159 ATATATA
1 ATTTATA
195166 AATTATGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 9 0.25
18 26 0.72
19 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTATATTATAAACTAT
Found at i:195245 original size:14 final size:15
Alignment explanation
Indices: 195218--195255 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
195208 AAACGATAAA
*
195218 AAATATATAGTTTAT
1 AAATATATAATTTAT
195233 AAAT-TATAATTTAT
1 AAATATATAATTTAT
*
195247 ATATATATA
1 AAATATATA
195256 TATATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATATATAATTTAT
Found at i:195586 original size:2 final size:2
Alignment explanation
Indices: 195579--195671 Score: 61
Period size: 2 Copynumber: 47.5 Consensus size: 2
195569 TACTTTTAAC
* * *
195579 TA TA TA TA TA TA TA TA TA CA TA TA TA TA AA CTA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
195622 -A AA TA TA TA -A AA TA TA TA GTT TA TA AA T- TA TA T- TA -A TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
195660 TA GTA TA TA TA T
1 TA -TA TA TA TA T
195672 GTATGTTAAC
Statistics
Matches: 71, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
1 5 0.07
2 62 0.87
3 4 0.06
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:195637 original size:31 final size:31
Alignment explanation
Indices: 195576--195637 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
195566 AATTACTTTT
* *
195576 AACTATATATATATATATATACATATATATA
1 AACTATATATATATAAATATACATAAATATA
* *
195607 AACTATATATGTATAAA-ATATATAAAATATA
1 AACTATATATATATAAATATACAT-AAATATA
195638 TAGTTTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (31 bp):
AACTATATATATATAAATATACATAAATATA
Found at i:196223 original size:101 final size:101
Alignment explanation
Indices: 196094--196293 Score: 319
Period size: 101 Copynumber: 2.0 Consensus size: 101
196084 TAAAACCTTA
* **
196094 AACCCTAAACAATATGCATAAACCCTAAATCATAAATCATACGCATTAAAATATAAACCCTAAAT
1 AACCCTAAACAATATACATAAACCCTAAATCATAAATCATAAACATTAAAATATAAACCCTAAAT
* * *
196159 CATAAAACCTAAGCTATAAATCAAAAACCCTAAATT
66 CATAAAACCCAAACCATAAATCAAAAACCCTAAATT
* * *
196195 AACCCTAAACAATATACATAAACTCTAAATCCTAAATCTTAAACATTAAAATATAAACCCTAAAT
1 AACCCTAAACAATATACATAAACCCTAAATCATAAATCATAAACATTAAAATATAAACCCTAAAT
196260 CATAAAACCCAAACCATAAATCAAAAACCCTAAA
66 CATAAAACCCAAACCATAAATCAAAAACCCTAAA
196294 CCCTAAATAT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 90 1.00
ACGTcount: A:0.53, C:0.23, G:0.01, T:0.22
Consensus pattern (101 bp):
AACCCTAAACAATATACATAAACCCTAAATCATAAATCATAAACATTAAAATATAAACCCTAAAT
CATAAAACCCAAACCATAAATCAAAAACCCTAAATT
Found at i:196273 original size:21 final size:21
Alignment explanation
Indices: 196248--196301 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
196238 CATTAAAATA
196248 TAAACCCTAAATCATAAAACCC
1 TAAACCCTAAATCA-AAAACCC
*
196270 -AAACCATAAATCAAAAACCC
1 TAAACCCTAAATCAAAAACCC
196290 TAAACCCTAAAT
1 TAAACCCTAAAT
196302 ATTATGCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.17
Consensus pattern (21 bp):
TAAACCCTAAATCAAAAACCC
Found at i:196412 original size:20 final size:19
Alignment explanation
Indices: 196387--196479 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 19
196377 TACATGTATG
*
196387 TATAAACTATGTATACTATA
1 TATAAACTATATATA-TATA
196407 TATAAACTATATATATATA
1 TATAAACTATATATATATA
* * *
196426 -ACCTATAGTATATGTATATA
1 TA--TAAACTATATATATATA
* * * *
196446 TACAATCTATTTATATGTTA
1 TATAAACTATATATAT-ATA
196466 TATAAACTATATAT
1 TATAAACTATATAT
196480 GTAACTTATA
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
18 1 0.02
19 12 0.22
20 41 0.75
21 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (19 bp):
TATAAACTATATATATATA
Found at i:196420 original size:57 final size:57
Alignment explanation
Indices: 196354--196491 Score: 174
Period size: 57 Copynumber: 2.4 Consensus size: 57
196344 TGTATACATG
*
196354 TAAACTATATATGTAACTTATAGTACATGTATGTATA-AA-CTATGTATACT-ATATA
1 TAAACTATATATGTAACTTATAGTACATGTATATATACAATCTATGTATA-TGATATA
* * * * *
196409 TAAACTATATATATATAACCTATAGTATATGTATATATACAATCTATTTATATGTTATA
1 TAAAC--TATATATGTAACTTATAGTACATGTATATATACAATCTATGTATATGATATA
196468 TAAACTATATATGTAACTTATAGT
1 TAAACTATATATGTAACTTATAGT
196492 TTATAAACAA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
55 5 0.07
57 45 0.64
58 3 0.04
59 17 0.24
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (57 bp):
TAAACTATATATGTAACTTATAGTACATGTATATATACAATCTATGTATATGATATA
Found at i:196423 original size:15 final size:16
Alignment explanation
Indices: 196398--196438 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
196388 ATAAACTATG
196398 TATACTATATATAAAC
1 TATACTATATATAAAC
*
196414 TATA-TATATATAACC
1 TATACTATATATAAAC
*
196429 TATAGTATAT
1 TATACTATAT
196439 GTATATATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (16 bp):
TATACTATATATAAAC
Found at i:196426 original size:35 final size:39
Alignment explanation
Indices: 196387--196461 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 39
196377 TACATGTATG
196387 TATAAACTAT-GTATA-CTATATATA-AA-CTATATATA
1 TATAAACTATAGTATATCTATATATACAATCTATATATA
* * *
196422 TATAACCTATAGTATATGTATATATACAATCTATTTATA
1 TATAAACTATAGTATATCTATATATACAATCTATATATA
196461 T
1 T
196462 GTTATATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 9 0.27
36 5 0.15
37 8 0.24
38 2 0.06
39 9 0.27
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (39 bp):
TATAAACTATAGTATATCTATATATACAATCTATATATA
Found at i:196443 original size:24 final size:22
Alignment explanation
Indices: 196418--196476 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
196408 ATAAACTATA
*
196418 TATATATAACCTATAGTATATG
1 TATATATAAACTATAGTATATG
*
196440 TATATATACAATCTAT-TTATATG
1 TATATATA-AA-CTATAGTATATG
196463 T-TATATAAACTATA
1 TATATATAAACTATA
196477 TATGTAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
22 14 0.44
23 8 0.25
24 4 0.12
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (22 bp):
TATATATAAACTATAGTATATG
Found at i:196510 original size:21 final size:20
Alignment explanation
Indices: 196485--196576 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 20
196475 TATATGTAAC
196485 TTATAGTTTATAAACAATAGT
1 TTATA-TTTATAAACAATAGT
** *
196506 TTATA-TTAGTGTACTATATAAT
1 TTATATTTA-TAAAC-A-ATAGT
* *
196528 TTATATTTTATAACCTATAGT
1 TTATA-TTTATAAACAATAGT
* *
196549 ATATAATTTATAAACTATAGT
1 TTAT-ATTTATAAACAATAGT
196570 TTATATT
1 TTATATT
196577 AATGTACTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.06
20 6 0.11
21 30 0.56
22 10 0.19
23 2 0.04
24 3 0.06
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (20 bp):
TTATATTTATAAACAATAGT
Found at i:196587 original size:20 final size:21
Alignment explanation
Indices: 196501--196603 Score: 75
Period size: 22 Copynumber: 4.8 Consensus size: 21
196491 TTTATAAACA
*
196501 ATAGTTTATATTAGTGTACTAT
1 ATAGTTTATATTAATGTAC-AT
* * * *
196523 ATAATTTATATTTTAT-AACCT
1 ATAGTTTATA-TTAATGTACAT
* * **
196544 ATAGTATATAATTTATAAAC-T
1 ATAGTTTAT-ATTAATGTACAT
196565 ATAGTTTATATTAATGTACTAT
1 ATAGTTTATATTAATGTAC-AT
196587 ATAGTTTATATTAATGT
1 ATAGTTTATATTAATGT
196604 TAATTATCTT
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
20 7 0.11
21 22 0.34
22 33 0.51
23 3 0.05
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.50
Consensus pattern (21 bp):
ATAGTTTATATTAATGTACAT
Found at i:196656 original size:14 final size:14
Alignment explanation
Indices: 196639--196699 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
196629 TAATATAGTA
196639 TATAGTTTATAAAC
1 TATAGTTTATAAAC
* * *
196653 TATACTATATTAA-
1 TATAGTTTATAAAC
* *
196666 TATTAATTATATTAAC
1 TA-TAGTT-TATAAAC
196682 TATAGTTTATAAAC
1 TATAGTTTATAAAC
196696 TATA
1 TATA
196700 CTATATAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
13 2 0.05
14 23 0.62
15 10 0.27
16 2 0.05
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (14 bp):
TATAGTTTATAAAC
Found at i:196672 original size:65 final size:65
Alignment explanation
Indices: 196550--196738 Score: 188
Period size: 65 Copynumber: 2.9 Consensus size: 65
196540 ACCTATAGTA
* * * * * * *
196550 TATAATTTATAAACTATAGTTTAT-ATTAATGTACTATATAGTTTATATTAATGTTAATTATCTT
1 TATAATTTATAAACTATACTATATAATTTAT-AAC-ATATAG-CTATATTAATATTAATTATATT
196614 AAC
63 AAC
* *
196617 TATAATTTATATTAA-TATAGTATATAGTTTATAA-ACTATA-CTATATTAATATTAATTATATT
1 TATAATTTATA--AACTATACTATATAATTTATAACA-TATAGCTATATTAATATTAATTATATT
196679 AAC
63 AAC
* *
196682 TATAGTTTATAAACTATACTATATAATTTATAACATATAGTTTATATTAATATTAAT
1 TATAATTTATAAACTATACTATATAATTTATAACATATAG-CTATATTAATATTAAT
196739 ATTAATTTTA
Statistics
Matches: 103, Mismatches: 11, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
63 2 0.02
64 21 0.20
65 33 0.32
66 16 0.16
67 15 0.15
68 10 0.10
69 6 0.06
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (65 bp):
TATAATTTATAAACTATACTATATAATTTATAACATATAGCTATATTAATATTAATTATATTAAC
Found at i:196683 original size:29 final size:30
Alignment explanation
Indices: 196593--196685 Score: 80
Period size: 34 Copynumber: 2.9 Consensus size: 30
196583 CTATATAGTT
* * *
196593 TATATTAATGTTAATTATCTTAACTATAATT
1 TATATTAATATTAATTATATTAACTAT-ATC
* *
196624 TATATTAATATAGTATATAGTTTATAAACTATA-C
1 TATATTAATAT--TA-AT--TATATTAACTATATC
196658 TATATTAATATTAATTATATTAACTATA
1 TATATTAATATTAATTATATTAACTATA
196686 GTTTATAAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
29 11 0.22
31 12 0.24
32 2 0.04
33 2 0.04
34 13 0.26
35 1 0.02
36 9 0.18
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (30 bp):
TATATTAATATTAATTATATTAACTATATC
Found at i:196689 original size:43 final size:40
Alignment explanation
Indices: 196615--196727 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 40
196605 AATTATCTTA
*
196615 ACTATAATTTATATTAATATAGTATATAGTTTATAAACTAT
1 ACTAT-ATTAATATTAATATAGTATATAGTTTATAAACTAT
*
196656 ACTATATTAATATTAATTATATTAACTATAGTTTATAAACTAT
1 ACTATATTAATATTAA-TATAGT-A-TATAGTTTATAAACTAT
*
196699 ACTATA-TAAT-TT-ATA-A-CATATAGTTTATA
1 ACTATATTAATATTAATATAGTATATAGTTTATA
196728 TTAATATTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
35 11 0.17
36 1 0.02
38 1 0.02
39 2 0.03
40 11 0.17
41 12 0.18
42 5 0.08
43 23 0.35
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (40 bp):
ACTATATTAATATTAATATAGTATATAGTTTATAAACTAT
Found at i:196706 original size:14 final size:14
Alignment explanation
Indices: 196646--196707 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
196636 GTATATAGTT
196646 TATAAACTATACTA
1 TATAAACTATACTA
* *
196660 TATTAA-TATTAATTA
1 TATAAACTA-T-ACTA
* * *
196675 TATTAACTATAGTT
1 TATAAACTATACTA
196689 TATAAACTATACTA
1 TATAAACTATACTA
196703 TATAA
1 TATAA
196708 TTTATAACAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 2 0.05
14 24 0.63
15 10 0.26
16 2 0.05
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.44
Consensus pattern (14 bp):
TATAAACTATACTA
Found at i:196736 original size:6 final size:6
Alignment explanation
Indices: 196725--196824 Score: 63
Period size: 6 Copynumber: 17.3 Consensus size: 6
196715 CATATAGTTT
* * * *
196725 ATATTA ATATTA ATATTA ATTTTA TAGACT- ATATTCT ATATT- ATATTA
1 ATATTA ATATTA ATATTA ATATTA -ATATTA ATATT-A ATATTA ATATTA
*
196773 ATA-TA A-GTTA ATATTA ATATT- A-ATTA A-ATTA ATATTA AT-TATA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATAT-TA
196816 ATATATA AT
1 ATAT-TA AT
196825 TATTTTTATA
Statistics
Matches: 76, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
4 3 0.04
5 22 0.29
6 38 0.50
7 13 0.17
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (6 bp):
ATATTA
Found at i:196757 original size:58 final size:58
Alignment explanation
Indices: 196687--196796 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
196677 TTAACTATAG
*
196687 TTTATAAACTATACTATATAATT-TATAACATAT-AGTTTATATTAATATTAATATTAAT
1 TTTATAAACTATACTATAT-ATTATATAA-ATATAAGTTAATATTAATATTAATATTAAT
* * * *
196745 TTTATAGACTATATTCTATATTATATTAATATAAGTTAATATTAATATTAAT
1 TTTATAAACTATACTATATATTATATAAATATAAGTTAATATTAATATTAAT
196797 TAAATTAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
57 7 0.16
58 38 0.84
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (58 bp):
TTTATAAACTATACTATATATTATATAAATATAAGTTAATATTAATATTAATATTAAT
Found at i:196788 original size:16 final size:15
Alignment explanation
Indices: 196767--196869 Score: 76
Period size: 15 Copynumber: 7.0 Consensus size: 15
196757 ATTCTATATT
196767 ATATTAATATAAGTTA
1 ATATTAATATAA-TTA
196783 ATATTAATATTAATTA
1 ATATTAATA-TAATTA
196799 A-ATTAATATTAATT-
1 ATATTAATA-TAATTA
*
196813 ATAAT-ATATAATT-
1 ATATTAATATAATTA
* *
196826 ATTTTTATATTAATT-
1 ATATTAATA-TAATTA
196841 ATATT-ATATAATTA
1 ATATTAATATAATTA
*
196855 TTA-TAATATTAATTA
1 ATATTAATA-TAATTA
196870 TAAATACTCT
Statistics
Matches: 75, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
13 14 0.19
14 15 0.20
15 30 0.40
16 13 0.17
17 3 0.04
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
ATATTAATATAATTA
Found at i:196804 original size:21 final size:22
Alignment explanation
Indices: 196762--196869 Score: 84
Period size: 22 Copynumber: 5.0 Consensus size: 22
196752 ACTATATTCT
*
196762 ATATT-ATATTAATATAAGTTA
1 ATATTAATATTAATATAAATTA
196783 ATATTAATATTAAT-TAAATTA
1 ATATTAATATTAATATAAATTA
196804 ATATTAAT-TATAATATATAATT-
1 ATATTAATAT-TAATATA-AATTA
* * *
196826 ATTTTTATATTAAT-TATATTA
1 ATATTAATATTAATATAAATTA
* *
196847 TATAATTATTA-TAATATTAATTA
1 -AT-ATTAATATTAATATAAATTA
196870 TAAATACTCT
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
20 4 0.06
21 25 0.36
22 26 0.38
23 14 0.20
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
ATATTAATATTAATATAAATTA
Found at i:196835 original size:28 final size:28
Alignment explanation
Indices: 196787--196872 Score: 120
Period size: 28 Copynumber: 3.1 Consensus size: 28
196777 AAGTTAATAT
**
196787 TAATAT-TAATTAAATTAATATTAATTA
1 TAATATATAATTATTTTAATATTAATTA
*
196814 TAATATATAATTATTTTTATATTAATTA
1 TAATATATAATTATTTTAATATTAATTA
* *
196842 TATTATATAATTATTATAATATTAATTA
1 TAATATATAATTATTTTAATATTAATTA
196870 TAA
1 TAA
196873 ATACTCTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 6 0.12
28 45 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TAATATATAATTATTTTAATATTAATTA
Found at i:196836 original size:43 final size:43
Alignment explanation
Indices: 196789--196870 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
196779 GTTAATATTA
196789 ATATTAATTAAATTA-AT-ATTAATTATAATATATAATTATTTTT
1 ATATTAATTAAATTATATAATT-ATTATAATAT-TAATTATTTTT
*
196832 ATATTAATTATATTATATAATTATTATAATATTAATTAT
1 ATATTAATTAAATTATATAATTATTATAATATTAATTAT
196871 AAATACTCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
43 21 0.58
44 12 0.33
45 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (43 bp):
ATATTAATTAAATTATATAATTATTATAATATTAATTATTTTT
Found at i:197070 original size:101 final size:101
Alignment explanation
Indices: 196892--197093 Score: 296
Period size: 101 Copynumber: 2.0 Consensus size: 101
196882 TAATATAAAT
** * * *
196892 TATATAAGGCGGTGACGTCAAATAACCAAACAAGAATTGTCATTTCCCTCCTATTTTTATTTTTC
1 TATATAACACGGTGACGCCAAATAACCAAACAAGAATTATCATTTCCCTCATATTTTTATTTTTC
* *
196957 TTCTGCTCTTAATTATTTTCCTCTTTCCAAACAACC
66 TTCTGCTATTAATTATTTTCCTCTCTCCAAACAACC
* * * *
196993 TATATAACACGGTGGCGCCAAATAACTAAACCATAATTATCATTTCCCTCATATTTTTATTTTTC
1 TATATAACACGGTGACGCCAAATAACCAAACAAGAATTATCATTTCCCTCATATTTTTATTTTTC
*
197058 TTCTGCTATTAATTGTTTTCCTCTCTCCAAACAACC
66 TTCTGCTATTAATTATTTTCCTCTCTCCAAACAACC
197094 CATCGCTCCA
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 89 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (101 bp):
TATATAACACGGTGACGCCAAATAACCAAACAAGAATTATCATTTCCCTCATATTTTTATTTTTC
TTCTGCTATTAATTATTTTCCTCTCTCCAAACAACC
Found at i:199710 original size:23 final size:23
Alignment explanation
Indices: 199680--199725 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
199670 TTTTTCTTTA
199680 ATATAAATTAAACTATATAAATT
1 ATATAAATTAAACTATATAAATT
*
199703 ATATAAATTAAACTATATTAATT
1 ATATAAATTAAACTATATAAATT
199726 TTCCTTTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATAAATTAAACTATATAAATT
Found at i:199797 original size:13 final size:13
Alignment explanation
Indices: 199765--199791 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
199755 TAATTTACAT
199765 TTAAATAATTTTA
1 TTAAATAATTTTA
199778 TTAAATAATTTTA
1 TTAAATAATTTTA
199791 T
1 T
199792 ATAATAGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:200082 original size:16 final size:16
Alignment explanation
Indices: 199981--200098 Score: 157
Period size: 16 Copynumber: 7.4 Consensus size: 16
199971 CAGATCATTT
*
199981 ACAGGCCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
**
199997 ACATATCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
200013 ACAAGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* *
200029 ACAAGTCAGGTTTAAA
1 ACAGGTCAGGTTAAAA
200045 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
200061 ATAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
200077 ACAGGTCAGGTT-GAA
1 ACAGGTCAGGTTAAAA
200092 ACAGGTC
1 ACAGGTC
200099 GGGTAATACC
Statistics
Matches: 91, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
15 9 0.10
16 82 0.90
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:201025 original size:24 final size:24
Alignment explanation
Indices: 200998--201047 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
200988 AAAATTTAAG
200998 ATACTAAGAAACAAGAAATATATC
1 ATACTAAGAAACAAGAAATATATC
201022 ATACTAAGAAACAAGAAATATATC
1 ATACTAAGAAACAAGAAATATATC
201046 AT
1 AT
201048 TTATTGTCCA
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:0.58, C:0.12, G:0.08, T:0.22
Consensus pattern (24 bp):
ATACTAAGAAACAAGAAATATATC
Found at i:202687 original size:17 final size:18
Alignment explanation
Indices: 202665--202705 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
202655 TGTTTCTAAG
202665 GGAATT-AAATCTGTGAA
1 GGAATTAAAATCTGTGAA
202682 GGAATTAAAATCTGTGAA
1 GGAATTAAAATCTGTGAA
*
202700 TGAATT
1 GGAATT
202706 GGAATCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (18 bp):
GGAATTAAAATCTGTGAA
Found at i:202711 original size:18 final size:18
Alignment explanation
Indices: 202672--202728 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
202662 AAGGGAATTA
**
202672 AATCTGTGAAGGAATTAA
1 AATCTGTGAAGGAATTGG
*
202690 AATCTGTGAATGAATTGG
1 AATCTGTGAAGGAATTGG
*
202708 AATCTGT-TAGGAATTGG
1 AATCTGTGAAGGAATTGG
202725 AATC
1 AATC
202729 CAATTCCATA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 12 0.35
18 22 0.65
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.32
Consensus pattern (18 bp):
AATCTGTGAAGGAATTGG
Found at i:203516 original size:270 final size:258
Alignment explanation
Indices: 203087--203871 Score: 1094
Period size: 270 Copynumber: 3.0 Consensus size: 258
203077 CCATCCCAAC
203087 CCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACCCG
1 CCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACCCG
*
203152 A--AA-T---AATAA-AAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATT
66 ACCAACTCGAAATAATAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATT
*
203210 ATATATA-AAGGGATATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTCG
131 ATATATATAAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTCG
*
203274 GGTCGGGTTTTTTCACCCTAAACTCGAACCCGACCCGACCCGAATATCACACTTAAAAAAAACTG
196 GGTCGGGTTTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAAA---
203339 A
258 A
203340 CCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACCCG
1 CCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACCCG
203405 ACTCAACTCGAAATAATAATAAAATATTTTTATTCAAT-AAAACAGTGACTTAATTGAAAAAATA
66 AC-CAACTCGAAATAATAA-AAAATATTTTTATTCAATAAAAACAGTGACTTAATTG--AAAA-A
203469 TATATATATATATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATA
126 -A-A-AT-TATATATATA-AGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATA
203534 TATTTTTTCGGGTCAGTCGGGTTTTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCAC
186 TATTTTTTC-GG---GTCGGG-TTTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCAC
203599 ACTT--AAAAAAA
246 ACTTAAAAAAAAA
* * * *
203610 CCGACCCGACCAAAATAAAGTTTCACCCGACCCGATCCGAATATATGAATTAAAAACCCTA-ACG
1 CCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACCCG
* * *
203674 ACCCGACCCGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGATTTAATTG-AAAAAA
66 A-CCAACTCGAAATAAT--AAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
*
203738 ATTATATATAT-AGGGGTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATATTTTT
128 ATTATATATATAAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA-TTTT
* * *
203802 TTCGGGTCGAGTCAGGTATTTTTCACCCTAAACCCGAACCCGACTCAACCCGAATATCATACTTA
192 TTCGGGTC--G---GGT-TTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTA
203867 AAAAA
251 AAAAA
203872 CCCGACCCGA
Statistics
Matches: 482, Mismatches: 14, Indels: 60
0.87 0.03 0.11
Matches are distributed among these distances:
253 66 0.14
256 2 0.00
257 1 0.00
258 3 0.01
260 6 0.01
261 69 0.14
262 25 0.05
263 58 0.12
264 3 0.01
265 6 0.01
266 2 0.00
267 3 0.01
268 11 0.02
269 16 0.03
270 132 0.27
271 21 0.04
273 6 0.01
274 6 0.01
275 46 0.10
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (258 bp):
CCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACCCG
ACCAACTCGAAATAATAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATT
ATATATATAAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTCG
GGTCGGGTTTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAAAA
Found at i:213534 original size:31 final size:29
Alignment explanation
Indices: 213489--213559 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 29
213479 AAATGAATGT
*
213489 TTTAGGTACCTATTTTGACCAAAAAGATAAC
1 TTTAGGTACTTATTTTGACCAAAAA-AT-AC
* *
213520 TTTAAGTACTTATTTTGACCAAACAATAC
1 TTTAGGTACTTATTTTGACCAAAAAATAC
213549 TTTAGGTACTT
1 TTTAGGTACTT
213560 GAATGAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 12 0.33
30 2 0.06
31 22 0.61
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (29 bp):
TTTAGGTACTTATTTTGACCAAAAAATAC
Found at i:220695 original size:6 final size:6
Alignment explanation
Indices: 220684--220710 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
220674 TTAGTTACAA
220684 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
220711 ACATCCGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:220783 original size:13 final size:13
Alignment explanation
Indices: 220765--220804 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
220755 CTAAAAAGTC
*
220765 AAAAATATTAGAT
1 AAAAATATTAAAT
220778 AAAAATATTAAAT
1 AAAAATATTAAAT
220791 --AAATATTAAAT
1 AAAAATATTAAAT
220802 AAA
1 AAA
220805 TTAAGAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 11 0.46
13 13 0.54
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AAAAATATTAAAT
Found at i:220796 original size:11 final size:11
Alignment explanation
Indices: 220780--220805 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
220770 TATTAGATAA
220780 AAATATTAAAT
1 AAATATTAAAT
220791 AAATATTAAAT
1 AAATATTAAAT
220802 AAAT
1 AAAT
220806 TAAGAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATATTAAAT
Found at i:222586 original size:2 final size:2
Alignment explanation
Indices: 222573--222603 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
222563 ATAAAATAAA
222573 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
222604 TTAAAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:222651 original size:35 final size:35
Alignment explanation
Indices: 222587--222819 Score: 170
Period size: 36 Copynumber: 6.5 Consensus size: 35
222577 ACTATATATA
* *
222587 TATATATATATATATATTTAAAAATTATTTTAAAAC
1 TATATATA-ATATATATTTAAAAAATGTTTTAAAAC
* *
222623 TATATATAATATATATTTCAAAAATATTTTCAAAAC
1 TATATATAATATATATTTAAAAAATGTTTT-AAAAC
* * *
222659 CATATATTATATA-ATTTTAAAAAAATGTTTTCAAAC
1 TATATATAATATATA-TTT-AAAAAATGTTTTAAAAC
* *
222695 TATATGTTATATAGT-TTTAAAAAATGTTTTAAAA-
1 TATATATAATATA-TATTTAAAAAATGTTTTAAAAC
* ** * *
222729 -ATATATCATAGGT-TCTCAAAAATGTTTTTTTAAAAC
1 TATATATAATATATATTTAAAAAATG---TTTTAAAAC
* * *
222765 TATATATTATACATATTTTAAAAATGTCTTTAAAATC
1 TATATATAATATATATTTAAAAAATGT-TTTAAAA-C
222802 TATAATATATATATATAT
1 TAT-ATATA-ATATATAT
222820 ATATATATAT
Statistics
Matches: 159, Mismatches: 23, Indels: 27
0.76 0.11 0.13
Matches are distributed among these distances:
32 10 0.06
33 8 0.05
35 45 0.28
36 52 0.33
37 24 0.15
38 13 0.08
39 7 0.04
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (35 bp):
TATATATAATATATATTTAAAAAATGTTTTAAAAC
Found at i:222813 original size:2 final size:2
Alignment explanation
Indices: 222802--222843 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
222792 CTTTAAAATC
222802 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
222843 T
1 T
222844 CGGACGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:232505 original size:10 final size:10
Alignment explanation
Indices: 232476--232509 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
232466 ATGAAGATCG
232476 AAAACGAAGAT
1 AAAA-GAAGAT
232487 AACAAGAAGAT
1 AA-AAGAAGAT
232498 AAAAGAAGAT
1 AAAAGAAGAT
232508 AA
1 AA
232510 GATGGCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 10 0.45
12 2 0.09
ACGTcount: A:0.68, C:0.06, G:0.18, T:0.09
Consensus pattern (10 bp):
AAAAGAAGAT
Found at i:233175 original size:42 final size:42
Alignment explanation
Indices: 233116--233553 Score: 592
Period size: 42 Copynumber: 10.5 Consensus size: 42
233106 ATCATTAAAT
* *
233116 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* *
233158 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* * * *
233200 GGCATCAGTAAGTCTTTTGAGCATGATGATGAAGTCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
233242 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* *
233284 GTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
*
233326 GCCATCAGTAATTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* * *
233368 GTCATCAGTAAGTGTTTCGAGCATGATGATTAAATCATTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* * * *
233410 GCCATCAGTAAGTATTTCGAGCATGATTATTAAATCATTCGA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
*
233452 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
** *** * * *
233494 GTTATTTTTGAGTCTTTCGAGCAAGAT-AATAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* *
233535 GTCATCCA-TAAGTCCTTCG
1 GCCAT-CAGTAAGTCTTTCG
233554 GGTAGGATGT
Statistics
Matches: 359, Mismatches: 36, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
41 25 0.07
42 334 0.93
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
Found at i:233453 original size:22 final size:22
Alignment explanation
Indices: 233257--233492 Score: 98
Period size: 22 Copynumber: 11.2 Consensus size: 22
233247 CAGTAAGTCT
* *
233257 TTCGAGCATGATGATTAAATCC
1 TTCGAGCATGATCATTAAATCA
* * * * *
233279 TTCG-G-GTCATCAGTAAGTCT
1 TTCGAGCATGATCATTAAATCA
*
233299 TTCGAGCATGATGATTAAATCA
1 TTCGAGCATGATCATTAAATCA
* * * * *
233321 TTCGGGC--CATCAGTAATTCT
1 TTCGAGCATGATCATTAAATCA
* *
233341 TTCGAGCATGATGATTAAATCC
1 TTCGAGCATGATCATTAAATCA
* * * * **
233363 TTCG-G-GTCATCAGTAAGTGT
1 TTCGAGCATGATCATTAAATCA
*
233383 TTCGAGCATGATGATTAAATCA
1 TTCGAGCATGATCATTAAATCA
* * * *
233405 TTCGGGC--CATCAGTAAGT-A
1 TTCGAGCATGATCATTAAATCA
*
233424 TTTCGAGCATGATTATTAAATCA
1 -TTCGAGCATGATCATTAAATCA
* * * *
233447 TTCGAGC--CATCAGTAAGTCT
1 TTCGAGCATGATCATTAAATCA
*
233467 TTCGAGCATGATGATTAAATCA
1 TTCGAGCATGATCATTAAATCA
233489 TTCG
1 TTCG
233493 GGTTATTTTT
Statistics
Matches: 144, Mismatches: 58, Indels: 24
0.64 0.26 0.11
Matches are distributed among these distances:
19 1 0.01
20 67 0.47
21 4 0.03
22 71 0.49
23 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (22 bp):
TTCGAGCATGATCATTAAATCA
Found at i:234054 original size:53 final size:53
Alignment explanation
Indices: 233974--234098 Score: 232
Period size: 53 Copynumber: 2.4 Consensus size: 53
233964 ATAATCACAC
*
233974 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGAGAACCCGTAGG
*
234027 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGAGAACTCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGAGAACCCGTAGG
234080 CAGAAGATTGTTCGAGTTC
1 CAGAAGATTGTTCGAGTTC
234099 GTAAGCAGAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 70 1.00
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.22
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGAGAACCCGTAGG
Found at i:234100 original size:24 final size:24
Alignment explanation
Indices: 234073--234122 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
234063 GGGAGAGAAC
*
234073 TCGTAGGCAGAAGATTGTTCGAGT
1 TCGTAAGCAGAAGATTGTTCGAGT
234097 TCGTAAGCAGAAGATTGTTCGAGT
1 TCGTAAGCAGAAGATTGTTCGAGT
234121 TC
1 TC
234123 TACTCCCTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (24 bp):
TCGTAAGCAGAAGATTGTTCGAGT
Found at i:234161 original size:77 final size:77
Alignment explanation
Indices: 234021--234175 Score: 256
Period size: 77 Copynumber: 2.0 Consensus size: 77
234011 GGAGCGAACC
* * **
234021 CGTAGGCAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGAGAACTCGTAGGCAGAAG
1 CGTAAGCAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGAGAACCCGTAAACAGAAG
*
234086 ATTGTTCGAGTT
66 ATTGTTCAAGTT
*
234098 CGTAAGCAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAACAGAAG
1 CGTAAGCAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGAGAACCCGTAAACAGAAG
234163 ATTGTTCAAGTT
66 ATTGTTCAAGTT
234175 C
1 C
234176 TACTCCCTGA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (77 bp):
CGTAAGCAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGAGAACCCGTAAACAGAAG
ATTGTTCAAGTT
Found at i:234178 original size:53 final size:53
Alignment explanation
Indices: 234098--234202 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
234088 TGTTCGAGTT
* *
234098 CGTAAGCAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACC
1 CGTAAACAGAAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACC
*
234151 CGTAAACAGAAGATTGTTCAAGTTCTACTCCCTGAAGCAATAGGGAGCGAAC
1 CGTAAACAGAAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAAC
234203 TCATTTTTAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (53 bp):
CGTAAACAGAAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACC
Found at i:235894 original size:3 final size:3
Alignment explanation
Indices: 235886--235950 Score: 114
Period size: 3 Copynumber: 21.7 Consensus size: 3
235876 TGTCCTTAGG
235886 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
235933 TTA TTA TTTA TTA TTA TT
1 TTA TTA -TTA TTA TTA TT
235951 TTGTCATGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:242705 original size:18 final size:18
Alignment explanation
Indices: 242682--242723 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
242672 TTCGTTTCAG
242682 TACCTATTTTCAAAACAA
1 TACCTATTTTCAAAACAA
242700 TACCTATTTTCAAAACAA
1 TACCTATTTTCAAAACAA
242718 TACCTA
1 TACCTA
242724 AAGTTTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (18 bp):
TACCTATTTTCAAAACAA
Found at i:245913 original size:23 final size:23
Alignment explanation
Indices: 245887--245941 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
245877 ATAATGGCTC
245887 TCAGCACTGTTTTACTGAATTAG
1 TCAGCACTGTTTTACTGAATTAG
245910 TCAGCACTGTTTTACTGAATTAG
1 TCAGCACTGTTTTACTGAATTAG
*
245933 TTAGCACTG
1 TCAGCACTG
245942 AATCATTCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (23 bp):
TCAGCACTGTTTTACTGAATTAG
Found at i:246216 original size:16 final size:15
Alignment explanation
Indices: 246186--246247 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
246176 AAAAACATGT
246186 TATTTAATAATAAAA
1 TATTTAATAATAAAA
*
246201 TATTTAAATGATAAAA
1 TATTT-AATAATAAAA
246217 -ATTATAA-AATAAAA
1 TATT-TAATAATAAAA
**
246231 -A-GAAATAATAAAA
1 TATTTAATAATAAAA
246244 TATT
1 TATT
246248 AGTTTTTACC
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
12 2 0.05
13 7 0.19
14 8 0.22
15 10 0.27
16 10 0.27
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
TATTTAATAATAAAA
Found at i:247282 original size:2 final size:2
Alignment explanation
Indices: 247275--247319 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
247265 TTTAAAAATA
*
247275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT A- AT -T A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
247314 AT AT AT
1 AT AT AT
247320 TTAATTAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:250091 original size:62 final size:62
Alignment explanation
Indices: 250025--250148 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
250015 GCTTAACTCA
*
250025 CATCATTAATAAAAATAAAACCAAAATTAAATAAATAGTTAGTTATAAGATAATTTGTGCTT
1 CATCATTAATAAAAATAAAACAAAAATTAAATAAATAGTTAGTTATAAGATAATTTGTGCTT
250087 CATCATTAATAAAAATAAAACAAAAATTAAATAAATAGTTAGTTATAAGATAATTTGTGCTT
1 CATCATTAATAAAAATAAAACAAAAATTAAATAAATAGTTAGTTATAAGATAATTTGTGCTT
250149 AATAAAAATA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.34
Consensus pattern (62 bp):
CATCATTAATAAAAATAAAACAAAAATTAAATAAATAGTTAGTTATAAGATAATTTGTGCTT
Found at i:253817 original size:56 final size:57
Alignment explanation
Indices: 253731--253845 Score: 223
Period size: 56 Copynumber: 2.0 Consensus size: 57
253721 TAATGAATTT
253731 GTGGAAAATCCTTAGTGTGGATAGCTAAGGTT-TGGACGTAGACTTTGGTTGAGAAA
1 GTGGAAAATCCTTAGTGTGGATAGCTAAGGTTGTGGACGTAGACTTTGGTTGAGAAA
253787 GTGGAAAATCCTTAGTGTGGATAGCTAAGGTTGTGGACGTAGACTTTGGTTGAGAAA
1 GTGGAAAATCCTTAGTGTGGATAGCTAAGGTTGTGGACGTAGACTTTGGTTGAGAAA
253844 GT
1 GT
253846 CGAACCACTC
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 32 0.55
57 26 0.45
ACGTcount: A:0.28, C:0.09, G:0.33, T:0.30
Consensus pattern (57 bp):
GTGGAAAATCCTTAGTGTGGATAGCTAAGGTTGTGGACGTAGACTTTGGTTGAGAAA
Found at i:259064 original size:23 final size:23
Alignment explanation
Indices: 259021--259102 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 23
259011 ATAGGGCAGA
* * *
259021 GGGAATCGATACCCCC-ATGAAG
1 GGGAACCGATTCCCCCTTTGAAG
* *
259043 GGGAACTGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAG
*
259066 GGGAACCGATTCCCCCCTT--AG
1 GGGAACCGATTCCCCCTTTGAAG
* *
259087 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
259103 AAGGGTTCTG
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 15 0.31
22 13 0.27
23 21 0.43
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:259804 original size:21 final size:20
Alignment explanation
Indices: 259765--259805 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
259755 AATCAAACCC
*
259765 TCCTCCAAATCCTCCTCCTA
1 TCCTCCAAATCCTACTCCTA
*
259785 TCCTACCAAATCCTATTCCTA
1 TCCT-CCAAATCCTACTCCTA
259806 ATCCCATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (20 bp):
TCCTCCAAATCCTACTCCTA
Found at i:262699 original size:18 final size:19
Alignment explanation
Indices: 262664--262700 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
262654 CACGGAATGT
262664 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
262684 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
262701 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:263833 original size:14 final size:14
Alignment explanation
Indices: 263810--263839 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
263800 AGAAAAAATA
*
263810 ATATAGTTTAATTT
1 ATATAATTTAATTT
263824 ATATAATTTAATTT
1 ATATAATTTAATTT
263838 AT
1 AT
263840 GTAAAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
ATATAATTTAATTT
Found at i:265111 original size:29 final size:30
Alignment explanation
Indices: 265079--265153 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
265069 ATTTTATATG
265079 AATTTTTTAAAATTTTA-GAGATCAAATTA-
1 AATTTTTTAAAATTTTATGAGAT-AAATTAT
** *
265108 AATTGTTTTAAAATTAAATGATATAAATTAT
1 AATT-TTTTAAAATTTTATGAGATAAATTAT
265139 AA-TTTTTAAAATTTT
1 AATTTTTTAAAATTTT
265154 GGGTCATGTC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 14 0.37
30 18 0.47
31 6 0.16
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.48
Consensus pattern (30 bp):
AATTTTTTAAAATTTTATGAGATAAATTAT
Found at i:266109 original size:60 final size:60
Alignment explanation
Indices: 266002--266159 Score: 158
Period size: 60 Copynumber: 2.6 Consensus size: 60
265992 TTAGGACAAC
* * **
266002 ATTGAAATGTTCAAAAAATTTAGGGACTAATTTAGAA-TTAATGTCATAATTTGGGGATGAA
1 ATTGAAATGTT-TAAAAATTTAGGGACTAATTTAAAATTTAA-GTCATAATTTAAGGATGAA
* * * *
266063 ATTGAAATGTTTAAAATTTTAAGGACTAATTTAAAATTGTAA-TCATAGTTTAAGGATGGA
1 ATTGAAATGTTTAAAAATTTAGGGACTAATTTAAAATT-TAAGTCATAATTTAAGGATGAA
* * * * *
266123 ACTGAAATATTTTAAAGTTTGGGGACTAATTTAAAAT
1 ATTGAAATGTTTAAAAATTTAGGGACTAATTTAAAAT
266160 GAGGGTCATA
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
60 66 0.81
61 12 0.15
62 3 0.04
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (60 bp):
ATTGAAATGTTTAAAAATTTAGGGACTAATTTAAAATTTAAGTCATAATTTAAGGATGAA
Found at i:271910 original size:14 final size:14
Alignment explanation
Indices: 271891--271932 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
271881 AAATAAAGGG
271891 AATGATTGAAATAA
1 AATGATTGAAATAA
271905 AATGATTGAAATAA
1 AATGATTGAAATAA
271919 AATGATTGAAATAA
1 AATGATTGAAATAA
271933 TTATATCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (14 bp):
AATGATTGAAATAA
Found at i:272423 original size:14 final size:14
Alignment explanation
Indices: 272406--272432 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
272396 TAATAAAAAA
272406 GAAGCAAAAAATGT
1 GAAGCAAAAAATGT
272420 GAAGCAAAAAATG
1 GAAGCAAAAAATG
272433 AGAGGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.11
Consensus pattern (14 bp):
GAAGCAAAAAATGT
Found at i:272443 original size:13 final size:14
Alignment explanation
Indices: 272405--272435 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
272395 GTAATAAAAA
272405 AGAAGCAAAAAATG
1 AGAAGCAAAAAATG
*
272419 TGAAGCAAAAAATG
1 AGAAGCAAAAAATG
272433 AGA
1 AGA
272436 GGAAAAAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.23, T:0.10
Consensus pattern (14 bp):
AGAAGCAAAAAATG
Found at i:273990 original size:45 final size:45
Alignment explanation
Indices: 273920--274742 Score: 675
Period size: 45 Copynumber: 18.6 Consensus size: 45
273910 CTTCAACTTA
* *
273920 ACTTTCTCGTGAAGAGGAGTCAATCTTTCAATGTTGTCATTCTTG
1 ACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATTCTTG
* * * *
273965 ACTTTCTCATGAAGAAGAGTTAATCTTTTAGT-TATGTTATTCTTG
1 ACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGT-TGTCATTCTTG
* * * * *
274010 ACTTTCTCGTGAAGATGAATTAA-CTTTTTAGTGATGTTATTCTTG
1 ACTTTCTCGTGAAGAGGAGTCAATC-TTTTAGTGTTGTCATTCTTG
* * *
274055 ACTTTCTCATGAAGA-GAGTCAATCTTTTAGTGTTTTCACTCTTG
1 ACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATTCTTG
* * * *
274099 ACGTACTCATGAAGAGGAGTCAATCTTTCAGT-TT-T-A------
1 ACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATTCTTG
*
274135 ACTTTATCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCCA-TCTTG
1 ACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGT-CATTCTTG
* * * * *
274180 ACTTTCTCGTGAAGAGAAGCCAA-CTTTTTAGTGATGTTATTCTTA
1 ACTTTCTCGTGAAGAGGAGTCAATC-TTTTAGTGTTGTCATTCTTG
* * *
274225 ACTTTCTCTTGAAGAGGAGTCAATATTTCAGTGTTGTCATTCTTG
1 ACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATTCTTG
* *
274270 A-TGTTCTCATGAAGAGGAGTCAATC------TG-T-T-AGTCTTG
1 ACT-TTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATTCTTG
* *
274306 ACTTTCTCGTGAAGAGGAGTCAATATTTTAGTGTTGTCCTTCTTG
1 ACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATTCTTG
* * * * * *
274351 ACTTTCTCGCGAAAAAGAGT-AAGCATTTTAGTGATGTAATTCTT-
1 ACTTTCTCGTGAAGAGGAGTCAATC-TTTTAGTGTTGTCATTCTTG
* * * * * *
274395 AATTTCTCGAGAAGATGATTCAA-CTTTTTAGTGATGTTATTCTTG
1 ACTTTCTCGTGAAGAGGAGTCAATC-TTTTAGTGTTGTCATTCTTG
* * * *
274440 ACTTTCTCATGAAAAGGAGTCAATCTTTCAGTGTTGTCATTATTG
1 ACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATTCTTG
* *
274485 ACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGTCTTTCTTG
1 ACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATTCTTG
*
274530 ACTTTCTCGTGAAGAGGAGTCAA-CATTTTAGTGATGTCATTCTTG
1 ACTTTCTCGTGAAGAGGAGTCAATC-TTTTAGTGTTGTCATTCTTG
* * * * * * * *
274575 ATTTTCTCGCGAAGAAGAGTCAACCTTTTAGTGATATGATTATTG
1 ACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATTCTTG
* *
274620 ACTTTCTCGCAT-AA-AGGAGTCAACCTTTTAGTGATGAT-ATTCTTG
1 ACTTTCTCG--TGAAGAGGAGTCAATCTTTTAGTGTTG-TCATTCTTG
* * * * * *
274665 ACTTTCTCGGGAAAAAGAGTCAACCTTTTAGTGATATCATTTTCAACTTG
1 ACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCA--TT---CTTG
*
274715 ACTTTCTCGTGGAGAGGAGTCAA-CTTTT
1 ACTTTCTCGTGAAGAGGAGTCAATCTTTT
274743 CTGTAGTATC
Statistics
Matches: 635, Mismatches: 98, Indels: 86
0.78 0.12 0.11
Matches are distributed among these distances:
36 54 0.09
37 4 0.01
38 2 0.00
39 2 0.00
40 1 0.00
42 3 0.00
43 2 0.00
44 82 0.13
45 450 0.71
46 5 0.01
47 2 0.00
49 5 0.01
50 23 0.04
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (45 bp):
ACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTGTCATTCTTG
Found at i:274337 original size:36 final size:36
Alignment explanation
Indices: 274265--274337 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
274255 GTGTTGTCAT
*
274265 TCTTGATGTTCTCATGAAGAGGAGTCAATCTGTTAG
1 TCTTGATGTTCTCATGAAGAGGAGTCAATATGTTAG
* *
274301 TCTTGACT-TTCTCGTGAAGAGGAGTCAATATTTTAG
1 TCTTGA-TGTTCTCATGAAGAGGAGTCAATATGTTAG
274337 T
1 T
274338 GTTGTCCTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (36 bp):
TCTTGATGTTCTCATGAAGAGGAGTCAATATGTTAG
Found at i:275185 original size:38 final size:37
Alignment explanation
Indices: 275143--275323 Score: 132
Period size: 38 Copynumber: 4.8 Consensus size: 37
275133 CATTTTGTAT
*
275143 TTCTTAAGATTGTTTCCCTAGAAACCTCAACTGTGAAC
1 TTCTTAAGATTGTTTCCCTAGAAACCTCAA-TATGAAC
* * * * * *
275181 TTCTTAGGACTTGTATCCC-AGAAAACTCAATTTGGTAT
1 TTCTTAAGA-TTGTTTCCCTAGAAACCTCAATAT-GAAC
*
275219 TTCTTAAGATTGTTTCCCTAGAAACCTCAATTATGACC
1 TTCTTAAGATTGTTTCCCTAGAAACCTCAA-TATGAAC
* * * * * ***
275257 TTCTTAAGACTTATAT-CATAGAAAACTCAATTTGGTTT
1 TTCTTAAGA-TTGTTTCCCTAGAAACCTCAATAT-GAAC
* *
275295 TTCTAAAAATTGTTTCCCTAGAAACCTCA
1 TTCTTAAGATTGTTTCCCTAGAAACCTCA
275324 GCCTTGTCTT
Statistics
Matches: 109, Mismatches: 27, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
37 16 0.15
38 79 0.72
39 14 0.13
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (37 bp):
TTCTTAAGATTGTTTCCCTAGAAACCTCAATATGAAC
Found at i:275268 original size:76 final size:76
Alignment explanation
Indices: 275134--275323 Score: 281
Period size: 76 Copynumber: 2.5 Consensus size: 76
275124 TTGAGAAATC
* * * * *
275134 ATTTTGTATTTCTTAAGATTGTTTCCCTAGAAACCTCAACTGTGAACTTCTTAGGACTTGTATCC
1 ATTTGGTATTTCTTAAGATTGTTTCCCTAGAAACCTCAACTATGAACTTCTTAAGACTTATATCA
275199 CAGAAAACTCA
66 CAGAAAACTCA
* *
275210 ATTTGGTATTTCTTAAGATTGTTTCCCTAGAAACCTCAATTATGACCTTCTTAAGACTTATATCA
1 ATTTGGTATTTCTTAAGATTGTTTCCCTAGAAACCTCAACTATGAACTTCTTAAGACTTATATCA
*
275275 TAGAAAACTCA
66 CAGAAAACTCA
* * *
275286 ATTTGGTTTTTCTAAAAATTGTTTCCCTAGAAACCTCA
1 ATTTGGTATTTCTTAAGATTGTTTCCCTAGAAACCTCA
275324 GCCTTGTCTT
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 103 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (76 bp):
ATTTGGTATTTCTTAAGATTGTTTCCCTAGAAACCTCAACTATGAACTTCTTAAGACTTATATCA
CAGAAAACTCA
Found at i:277920 original size:24 final size:23
Alignment explanation
Indices: 277893--277943 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
277883 AATCAGCAAA
*
277893 AAAATTGAAGCACTCAAAAAGAAG-
1 AAAATTCAAGCACT-AAAAA-AAGC
*
277917 AAAATTCCAGCACTAAAAAAAGC
1 AAAATTCAAGCACTAAAAAAAGC
277940 AAAA
1 AAAA
277944 AATAGAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 3 0.12
23 9 0.38
24 12 0.50
ACGTcount: A:0.61, C:0.16, G:0.12, T:0.12
Consensus pattern (23 bp):
AAAATTCAAGCACTAAAAAAAGC
Found at i:281796 original size:21 final size:21
Alignment explanation
Indices: 281772--281811 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
281762 ATTAAATCTT
* *
281772 ATTAGCTCATAGACATTATAC
1 ATTAGCTCACACACATTATAC
281793 ATTAGCTCACACACATTAT
1 ATTAGCTCACACACATTAT
281812 GAGATGATAT
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:0.23, G:0.07, T:0.33
Consensus pattern (21 bp):
ATTAGCTCACACACATTATAC
Found at i:285968 original size:2 final size:2
Alignment explanation
Indices: 285961--286018 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
285951 AACATATACA
285961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
286003 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
286019 GTTTACAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:286198 original size:30 final size:30
Alignment explanation
Indices: 286152--286431 Score: 279
Period size: 30 Copynumber: 9.4 Consensus size: 30
286142 ATATTTAACC
286152 AAACTTGAAAGG-CTAAAATAGCTAAAACAT
1 AAACTT-AAAGGACTAAAATAGCTAAAACAT
*
286182 AAATTTAAAGGACTAAAATAGC-AAAA-AT
1 AAACTTAAAGGACTAAAATAGCTAAAACAT
*
286210 AGAACTTACAGGACTAAAATAG-TAAAAACAT
1 A-AACTTAAAGGACTAAAATAGCT-AAAACAT
* *
286241 AAGCTTGAAGGACTAAAATAGCTAAAACAT
1 AAACTTAAAGGACTAAAATAGCTAAAACAT
* * * *
286271 AAATTTACAGGACTAAAATAGCAAAAACAG
1 AAACTTAAAGGACTAAAATAGCTAAAACAT
* *
286301 AAACTTACATGACTAAAATAGC-AAAA-AT
1 AAACTTAAAGGACTAAAATAGCTAAAACAT
*
286329 AGAAGCTTAAAGGACTAAAATAGCTAAAA-ACG
1 A-AA-CTTAAAGGACTAAAATAGCTAAAACA-T
* * * *
286361 AAAGTTCAAGGACCAAAATAGCTAAAACAA
1 AAACTTAAAGGACTAAAATAGCTAAAACAT
* *
286391 AAACTTAAAGAACTAAAATAG-AAAAGACAT
1 AAACTTAAAGGACTAAAATAGCTAAA-ACAT
*
286421 AAAGTTAAAGG
1 AAACTTAAAGG
286432 GCTGAACAGT
Statistics
Matches: 208, Mismatches: 30, Indels: 24
0.79 0.11 0.09
Matches are distributed among these distances:
28 5 0.02
29 36 0.17
30 154 0.74
31 12 0.06
32 1 0.00
ACGTcount: A:0.56, C:0.12, G:0.14, T:0.18
Consensus pattern (30 bp):
AAACTTAAAGGACTAAAATAGCTAAAACAT
Found at i:286351 original size:90 final size:89
Alignment explanation
Indices: 286159--286415 Score: 326
Period size: 90 Copynumber: 2.9 Consensus size: 89
286149 ACCAAACTTG
* * *
286159 AAAGG-CTAAAATAGCTAAAACATAAATTTAAAGGACTAAAATAGCAAAAATAG-AACTTACAGG
1 AAAGGACTAAAATAGCTAAAACATAAATTTACAGGACTAAAATAGCAAAAACAGAAACTTACAAG
*
286222 ACTAAAATAGTAAAAACATAAGCTT
66 ACTAAAATAG-AAAAACAGAAGCTT
* *
286247 GAAGGACTAAAATAGCTAAAACATAAATTTACAGGACTAAAATAGCAAAAACAGAAACTTACATG
1 AAAGGACTAAAATAGCTAAAACATAAATTTACAGGACTAAAATAGCAAAAACAGAAACTTACAAG
*
286312 ACTAAAATAGCAAAAATAGAAGCTT
66 ACTAAAATAG-AAAAACAGAAGCTT
* * * * *
286337 AAAGGACTAAAATAGCTAAAA-ACGAAAGTT-CAAGGACCAAAATAGCTAAAACAAAAACTTA-A
1 AAAGGACTAAAATAGCTAAAACA-TAAATTTAC-AGGACTAAAATAGCAAAAACAGAAACTTACA
286399 AGAACTAAAATAGAAAA
64 AG-ACTAAAATAGAAAA
286416 GACATAAAGT
Statistics
Matches: 150, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
88 4 0.03
89 54 0.36
90 92 0.61
ACGTcount: A:0.57, C:0.12, G:0.13, T:0.18
Consensus pattern (89 bp):
AAAGGACTAAAATAGCTAAAACATAAATTTACAGGACTAAAATAGCAAAAACAGAAACTTACAAG
ACTAAAATAGAAAAACAGAAGCTT
Found at i:286996 original size:12 final size:14
Alignment explanation
Indices: 286965--286998 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
286955 AACGAGCGAA
286965 GAGAGAAAGAGTGG
1 GAGAGAAAGAGTGG
286979 GAGAGAAAGAGTGG
1 GAGAGAAAGAGTGG
286993 GAGAGA
1 GAGAGA
286999 GCTCTCTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.50, T:0.06
Consensus pattern (14 bp):
GAGAGAAAGAGTGG
Found at i:290679 original size:14 final size:14
Alignment explanation
Indices: 290660--290688 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
290650 ATTCTAGCCC
290660 ATATGTATATAGAT
1 ATATGTATATAGAT
290674 ATATGTATATAGAT
1 ATATGTATATAGAT
290688 A
1 A
290689 CATATGAACG
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:0.00, G:0.14, T:0.41
Consensus pattern (14 bp):
ATATGTATATAGAT
Found at i:292485 original size:2 final size:2
Alignment explanation
Indices: 292478--292507 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
292468 GTACATTTTA
292478 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
292508 TAAATTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:292693 original size:18 final size:19
Alignment explanation
Indices: 292666--292702 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
292656 ATTAAAGTTT
*
292666 CAACTTAAAGAAGA-AAAA
1 CAACTCAAAGAAGATAAAA
292684 CAACTCAAAGAAGATAAAA
1 CAACTCAAAGAAGATAAAA
292703 AATCAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.65, C:0.14, G:0.11, T:0.11
Consensus pattern (19 bp):
CAACTCAAAGAAGATAAAA
Found at i:301912 original size:2 final size:2
Alignment explanation
Indices: 301907--301938 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
301897 AAAAAAAAAA
301907 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
301939 TTAAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:302616 original size:42 final size:42
Alignment explanation
Indices: 302563--302719 Score: 132
Period size: 41 Copynumber: 3.8 Consensus size: 42
302553 AAAATGATAC
*
302563 TTTAGCGGCGTTTTTTAAACAAACGCCGTAATAGAGTGGTAA
1 TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* * *
302605 TTTAGCAGCGTTTATAGTT--A-AAACGCCGCAAAAGA-TATGT--
1 TTTAGCGGCGTTT-T--TTAAACAAACGCCGCAATAGAGT-GGTAA
* * *
302645 TTATAGTGGCGTTTTTTCAACAAATGCCGCAATAGAGTGGTAA
1 TT-TAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
* *
302688 -TTAGCGGCG-TTTTTATACAAACGCCGCGATAG
1 TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAG
302720 TGGTGTTTAT
Statistics
Matches: 90, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
38 2 0.02
40 23 0.26
41 32 0.36
42 29 0.32
43 2 0.02
45 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA
Found at i:302631 original size:82 final size:82
Alignment explanation
Indices: 302543--302699 Score: 210
Period size: 83 Copynumber: 1.9 Consensus size: 82
302533 TTTACTATCC
*
302543 AAACGCCACAAAA-ATGATACTT-TAGCGGCGTTTTTTAAACAAACGCCGTAATAGAGTGGTAAT
1 AAACGCCACAAAAGAT-ATACTTATAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAA-
302606 TTAGCAGCGTTTATAGTTA
64 TTAGCAGCGTTTATAGTTA
* ** * * *
302625 AAACGCCGCAAAAGATATGTTTATAGTGGCGTTTTTTCAACAAATGCCGCAATAGAGTGGTAATT
1 AAACGCCACAAAAGATATACTTATAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAATT
*
302690 AGCGGCGTTT
66 AGCAGCGTTT
302700 TTATACAAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
82 27 0.42
83 38 0.58
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (82 bp):
AAACGCCACAAAAGATATACTTATAGCGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGTAATT
AGCAGCGTTTATAGTTA
Found at i:302682 original size:83 final size:81
Alignment explanation
Indices: 302569--302921 Score: 295
Period size: 83 Copynumber: 4.3 Consensus size: 81
302559 ATACTTTAGC
* * * *
302569 GGCGTTTTTTAAACAAACGCCGTAATAGAGTGGTAATTTAGCAGCGTTTATAGTTA-AAACGCCG
1 GGCGTTTGTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTATA--TACAAACGCCG
*
302633 CAAAAGATATGTTTATAGT
64 CAATAG-TATGTTTATAGT
* * * *
302652 GGCGTTTTTTCAACAAATGCCGCAATAGAGTGGTAA-TTAGCGGCGTTTTTATACAAACGCCGCG
1 GGCGTTTGTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTATATACAAACGCCGCA
*
302716 ATAGTGGTGTTTATAGT
66 ATAGT-ATGTTTATAGT
* * * * * ** * * *
302733 GGTGTTTGTTCAGCAAACGACACTATAGAGAAGTAATTTCGCGGTGTTTATCAAACAAACGCCGC
1 GGCGTTTGTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTAT-ATACAAACGCCGC
302798 AATAGTATTGTTTATAGT
65 AATAGTA-TGTTTATAGT
* * ** * * * * *
302816 GGCGTTTGTGCAAGAAACGCCGCAATAGAGTAATAATATAGCGACATTTGTAGGAACAAA-GCCG
1 GGCGTTTGTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTATA--TACAAACGCCG
*
302880 CAATATGT-TGTTTATCGT
64 CAATA-GTATGTTTATAGT
*
302898 GGCGTTTATAT-AA-AAACGCCGCAA
1 GGCGTTTGT-TCAACAAACGCCGCAA
302922 AAATATGCAC
Statistics
Matches: 220, Mismatches: 41, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
80 3 0.01
81 60 0.27
82 44 0.20
83 105 0.48
84 8 0.04
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (81 bp):
GGCGTTTGTTCAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTATATACAAACGCCGCA
ATAGTATGTTTATAGT
Found at i:309286 original size:44 final size:43
Alignment explanation
Indices: 309231--309423 Score: 221
Period size: 44 Copynumber: 4.4 Consensus size: 43
309221 AAATATTAAC
* **
309231 ACCTATTGCGGCGTTTTTATCAAAAAAAACGTCGCTATATACCA-
1 ACCT-TTGCGGCGTTTGTATC-CTAAAAACGTCGCTATATACCAG
*
309275 ACCTTTAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAG
1 ACCTTT-GCGGCGTTTGTATCCTAAAAACGTCGCTATATACCAG
*
309319 ACCTATTGCGGCGTTTGTATCCTAAAAACATCGCTATATACCAG
1 ACCT-TTGCGGCGTTTGTATCCTAAAAACGTCGCTATATACCAG
* * *
309363 ACCTATCGCGGCGTTTGTATCCTAAAAACG-CTGCTAAATACTAG
1 ACCT-TTGCGGCGTTTGTATCCTAAAAACGTC-GCTATATACCAG
309407 A-CTTATCGCGGCGTTTG
1 ACCTT-T-GCGGCGTTTG
309424 AATAAAAATG
Statistics
Matches: 132, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
42 1 0.01
43 24 0.18
44 105 0.80
45 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (43 bp):
ACCTTTGCGGCGTTTGTATCCTAAAAACGTCGCTATATACCAG
Found at i:309323 original size:88 final size:88
Alignment explanation
Indices: 309231--309431 Score: 271
Period size: 88 Copynumber: 2.3 Consensus size: 88
309221 AAATATTAAC
* * *
309231 ACCTATTGCGGCGTTTTTATCAAAAAAAACGTCGCTATATACCA-ACCTTTAGCGGCGTTTGTAT
1 ACCTATTGCGGCGTTTGTATC-AAAAAAACATCGCTATATACCAGACCTATAGCGGCGTTTGTAT
*
309295 CCTAAAAACGCCGCTATATACCAG
65 CCTAAAAACGCCGCTAAATACCAG
** *
309319 ACCTATTGCGGCGTTTGTATCCTAAAAACATCGCTATATACCAGACCTATCGCGGCGTTTGTATC
1 ACCTATTGCGGCGTTTGTATCAAAAAAACATCGCTATATACCAGACCTATAGCGGCGTTTGTATC
* *
309384 CTAAAAACGCTGCTAAATACTAG
66 CTAAAAACGCCGCTAAATACCAG
* * *
309407 ACTTATCGCGGCGTTTGAAT-AAAAA
1 ACCTATTGCGGCGTTTGTATCAAAAA
309432 TGCCGCAAAA
Statistics
Matches: 98, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
87 22 0.22
88 76 0.78
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (88 bp):
ACCTATTGCGGCGTTTGTATCAAAAAAACATCGCTATATACCAGACCTATAGCGGCGTTTGTATC
CTAAAAACGCCGCTAAATACCAG
Found at i:309544 original size:26 final size:26
Alignment explanation
Indices: 309513--309565 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
309503 CGTTTTTAAG
309513 ACAAACATCGCTAAATATCAG-TACCT
1 ACAAACATCGCTAAATATC-GTTACCT
* *
309539 ACAAACGTCGCTATATATCGTTACCT
1 ACAAACATCGCTAAATATCGTTACCT
309565 A
1 A
309566 TTGCGGCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.26
Consensus pattern (26 bp):
ACAAACATCGCTAAATATCGTTACCT
Found at i:320896 original size:21 final size:21
Alignment explanation
Indices: 320854--320897 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
320844 ACCCTGGGAG
*
320854 CTAGCTCTTCATGAGCTGCTC
1 CTAGCTCTTCATGAGCTCCTC
*
320875 CTAGCTCTTC-TCGTGCTCCTC
1 CTAGCTCTTCAT-GAGCTCCTC
320896 CT
1 CT
320898 CCTCCTCCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCATGAGCTCCTC
Found at i:322120 original size:56 final size:57
Alignment explanation
Indices: 322023--322131 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
322013 GATGCACATA
* * *
322023 CCATGCATCGATGCACTGTGGATTTTATGAAAACATTGAATGCATTTGATGCACCAG
1 CCATGCATCGATGCACTCTGGATTTTATGAAAACATCGAATGCACTTGATGCACCAG
*
322080 CCATGCATCGATGCACTCTGGCTATTT-TG-AAACATCGAATGCACTTGATGCA
1 CCATGCATCGATGCACTCTGGAT-TTTATGAAAACATCGAATGCACTTGATGCA
322132 TCCGTGCACT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
56 21 0.45
57 23 0.49
58 3 0.06
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (57 bp):
CCATGCATCGATGCACTCTGGATTTTATGAAAACATCGAATGCACTTGATGCACCAG
Found at i:326674 original size:13 final size:13
Alignment explanation
Indices: 326656--326682 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
326646 TTACAGACGC
326656 GCATATGAAGACT
1 GCATATGAAGACT
326669 GCATATGAAGACT
1 GCATATGAAGACT
326682 G
1 G
326683 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:327084 original size:21 final size:21
Alignment explanation
Indices: 327034--327090 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
327024 TTATTTTAAC
*
327034 TCTTAAAATTTTAATTCGTCC
1 TCTTAAAATTTTAATTCGTCA
*
327055 TCTTAAAATTTTAATTCATTCA
1 TCTTAAAATTTTAATTC-GTCA
327077 TCTT-AAA-TTTAATT
1 TCTTAAAATTTTAATT
327091 TTTTTAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 7 0.21
21 20 0.61
22 6 0.18
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (21 bp):
TCTTAAAATTTTAATTCGTCA
Found at i:330063 original size:21 final size:21
Alignment explanation
Indices: 330034--330086 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
330024 ATTCTGACTA
330034 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
330055 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
330076 TCGCAATGCGA
1 TCGCATTGCGA
330087 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:330101 original size:20 final size:20
Alignment explanation
Indices: 330076--330169 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
330066 TTTTCCTAAT
330076 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
330096 TCGCAATGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
330116 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
330137 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
330157 TCGCAATGCGAAT
1 TCGCAATGCGAAT
330170 CTGACTATCG
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 48 0.73
21 18 0.27
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:330106 original size:41 final size:40
Alignment explanation
Indices: 330076--330169 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 40
330066 TTTTCCTAAT
* *
330076 TCGCAATGCGAATACGTAAATCGCAATGCGATTAAGTAAA
1 TCGCAATGCGAATACGAAAATCGCAATGCGATTACGTAAA
* *
330116 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAA-TACGAAAATCGCAATGCGATTACGTAAA
330157 TCGCAATGCGAAT
1 TCGCAATGCGAAT
330170 CTGACTATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 13 0.27
41 36 0.73
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGAAAATCGCAATGCGATTACGTAAA
Found at i:330180 original size:61 final size:59
Alignment explanation
Indices: 330076--330189 Score: 167
Period size: 61 Copynumber: 1.9 Consensus size: 59
330066 TTTTCCTAAT
*
330076 TCGCAATGCGAATACGTAAATCGCAATGCGATTAAGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGATTAACT-AATCGCAATGC-AATTAGGAAAA
*
330137 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGACT-ATCGCAATGCAATT
1 TCGCAATGCGAATACGTAAATCGCAATGCG-AT-TAACTAATCGCAATGCAATT
330190 TACATAGCAC
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
60 4 0.08
61 40 0.82
62 2 0.04
63 3 0.06
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (59 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGATTAACTAATCGCAATGCAATTAGGAAAA
Found at i:330780 original size:33 final size:33
Alignment explanation
Indices: 330719--330811 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
330709 CGAGAATGAA
**
330719 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
* *
330753 AATCGCAACGCGAAATGAAAATTGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
330786 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
330812 TTGCGATTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 41 0.79
34 11 0.21
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:330858 original size:33 final size:34
Alignment explanation
Indices: 330815--330889 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
330805 AATCGCATTG
* ** *
330815 CGATTCTCTCGTTGCGATTTTCATTT-CGTGTTA
1 CGATTTTCTCGTTGCGATAGTCATTTCCGCGTTA
*
330848 CGATTTTCTCGTTGCGATAGTCATTTCCGCGTTG
1 CGATTTTCTCGTTGCGATAGTCATTTCCGCGTTA
330882 CGATTTTC
1 CGATTTTC
330890 ATTCTCTCGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 23 0.64
34 13 0.36
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (34 bp):
CGATTTTCTCGTTGCGATAGTCATTTCCGCGTTA
Found at i:330891 original size:20 final size:21
Alignment explanation
Indices: 330857--330914 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 21
330847 ACGATTTTCT
**
330857 CGTTGCGATAGTCATTTC-CG
1 CGTTGCGATTTTCATTTCTCG
*
330877 CGTTGCGATTTTCA-TTCTCT
1 CGTTGCGATTTTCATTTCTCG
330897 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
330915 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (21 bp):
CGTTGCGATTTTCATTTCTCG
Found at i:332148 original size:21 final size:20
Alignment explanation
Indices: 332077--332149 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
332067 CTCCACTTCG
332077 AGAGCCATCACCTCAC--CC
1 AGAGCCATCACCTCACAACC
*
332095 AGAGCCATCACCTGATCAACC
1 AGAGCCATCACCTCA-CAACC
* * *
332116 CGA-CTATACACCTCTACAACG
1 AGAGCCAT-CACCTC-ACAACC
332137 AGAGCCATCACCT
1 AGAGCCATCACCT
332150 ATCCCGTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 14 0.33
19 1 0.02
20 3 0.07
21 20 0.48
22 4 0.10
ACGTcount: A:0.32, C:0.41, G:0.12, T:0.15
Consensus pattern (20 bp):
AGAGCCATCACCTCACAACC
Found at i:332734 original size:94 final size:93
Alignment explanation
Indices: 332512--332789 Score: 410
Period size: 94 Copynumber: 3.1 Consensus size: 93
332502 TAGATTGCTT
* *
332512 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
332573 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
* *
332602 AGT--A--TATTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
332663 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
332692 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
332757 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
332785 AGTAA
1 AGTAA
332790 TGCAATCCAT
Statistics
Matches: 169, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
86 26 0.15
88 4 0.02
89 22 0.13
90 32 0.19
92 1 0.01
93 6 0.04
94 78 0.46
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:332928 original size:20 final size:20
Alignment explanation
Indices: 332884--332940 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
332874 GGTTGAAATG
* **
332884 AAAATCGCAACGCGGAA-TG
1 AAAATCGCAACGCGAAACCA
*
332903 AAAATCGCAACGTGAAACCA
1 AAAATCGCAACGCGAAACCA
332923 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
332941 TATAATCGCG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.47, C:0.25, G:0.19, T:0.09
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:332949 original size:19 final size:19
Alignment explanation
Indices: 332884--332949 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
332874 GGTTGAAATG
*
332884 AAAATCGCAACGCGGAA-T
1 AAAATCGCAACGCGAAACT
* *
332902 GAAAATCGCAACGTGAAACCA
1 -AAAATCGCAACGCGAAA-CT
332923 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
*
332942 ATAATCGC
1 AAAATCGC
332950 GTTGCGATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.45, C:0.24, G:0.18, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:332986 original size:19 final size:19
Alignment explanation
Indices: 332946--333020 Score: 78
Period size: 19 Copynumber: 3.8 Consensus size: 19
332936 GAAACTATAA
**
332946 TCGCGTTGCGATTTTTGGTT
1 TCGCGTTGCGA-TTTTCATT
332966 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
332985 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
333006 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
333021 AAGTTCCAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
19 21 0.46
20 11 0.24
21 14 0.30
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:333532 original size:21 final size:21
Alignment explanation
Indices: 333473--333533 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
333463 CTCGAGAGTC
333473 CCCTCCCACCGTTCAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
* ** * *
333494 CACTGTCATCGTTGAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
*
333515 CCCTCCCACCATTCAAGAG
1 CCCTCCCACCGTTCAAGAG
333534 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
CCCTCCCACCGTTCAAGAGGT
Found at i:334900 original size:14 final size:14
Alignment explanation
Indices: 334881--334916 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
334871 ATTGTTTAAT
334881 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
334895 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
334909 TGATTTGT
1 TGATTTGT
334917 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:335068 original size:33 final size:33
Alignment explanation
Indices: 335023--335096 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
335013 AAAAATGACT
* * *
335023 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
335056 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
335089 ATCGCAAC
1 ATCGCAAC
335097 AACAAAATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:335082 original size:19 final size:19
Alignment explanation
Indices: 335023--335083 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
335013 AAAAATGACT
*
335023 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
335042 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
335056 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
335075 ATCGCAACG
1 ATCGCAACG
335084 ACAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:335091 original size:14 final size:14
Alignment explanation
Indices: 335072--335111 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
335062 ACGCGAAATG
335072 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
335086 AAAATCGCAACAAC
1 AAAATCGCAACGAC
*
335100 AAAATCACAACG
1 AAAATCGCAACG
335112 CGAAACTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.55, C:0.28, G:0.10, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:335144 original size:19 final size:18
Alignment explanation
Indices: 335122--335271 Score: 74
Period size: 19 Copynumber: 8.7 Consensus size: 18
335112 CGAAACTAAA
335122 TTCGCGTTGCGATTTACAT
1 TTCGCGTTGCGATTT-CAT
* *
335141 TTCGCTTTGTGA-TTC--
1 TTCGCGTTGCGATTTCAT
* *
335156 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGA-TTTCAT
*
335174 TTCGCATTGCGA-TTC--
1 TTCGCGTTGCGATTTCAT
*
335189 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGA-TTTCAT
*
335207 TTCGCATTGCGA-TTC--
1 TTCGCGTTGCGATTTCAT
335222 TT--CGTTGCGATTTTCAT
1 TTCGCGTTGCGA-TTTCAT
* *
335239 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGAT-TTCAT
335258 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
335272 AGACATTAAG
Statistics
Matches: 96, Mismatches: 17, Indels: 35
0.65 0.11 0.24
Matches are distributed among these distances:
13 7 0.07
14 16 0.17
15 5 0.05
16 6 0.06
17 9 0.09
18 3 0.03
19 40 0.42
20 10 0.10
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (18 bp):
TTCGCGTTGCGATTTCAT
Found at i:335168 original size:33 final size:33
Alignment explanation
Indices: 335126--335251 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
335116 ACTAAATTCG
* * *
335126 CGTTGCGATTTACATTTCGCTTTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
335159 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
335192 CGTTGCGATTTTCATTTCGCATTGCGATT-CTT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
335224 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
335252 AGTCATTTCC
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 29 0.33
33 58 0.67
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:335246 original size:65 final size:66
Alignment explanation
Indices: 335126--335251 Score: 209
Period size: 65 Copynumber: 1.9 Consensus size: 66
335116 ACTAAATTCG
* *
335126 CGTTGCGATTTACATTTCGCTTTGTGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1 CGTTGCGATTTACATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC
335191 T
66 T
* *
335192 CGTTGCGATTTTCATTTCGCATTGCGATT-CTTCGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTACATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAT
335252 AGTCATTTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
65 30 0.54
66 26 0.46
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (66 bp):
CGTTGCGATTTACATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC
T
Found at i:335270 original size:20 final size:20
Alignment explanation
Indices: 335224--335317 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
335214 TGCGATTCTT
**
335224 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
335243 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
335263 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
335282 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
335304 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
335318 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:338705 original size:20 final size:20
Alignment explanation
Indices: 338682--338869 Score: 220
Period size: 20 Copynumber: 9.3 Consensus size: 20
338672 ATAATCTCGT
*
338682 TGCGATTTAC-TAAATCGTAA
1 TGCGA-TTACGTAAATCGCAA
338702 TGCGATTACGTAAATCG-AA
1 TGCGATTACGTAAATCGCAA
* * * *
338721 GTGTGAATTAGGAAAATCGTAA
1 -TGCG-ATTACGTAAATCGCAA
*
338743 TGTGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
338763 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
* *
338783 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
*
338804 TGTGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
*
338824 TGCGAATACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
*
338844 TGCGAATACGT-AATCGCAA
1 TGCGATTACGTAAATCGCAA
338863 TGCGATT
1 TGCGATT
338870 TTCCTAATTC
Statistics
Matches: 148, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
19 20 0.14
20 94 0.64
21 32 0.22
22 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:338739 original size:41 final size:40
Alignment explanation
Indices: 338688--338869 Score: 217
Period size: 41 Copynumber: 4.5 Consensus size: 40
338678 TCGTTGCGAT
*
338688 TTAC-TAAATCGTAATGCGATTACGTAAATCG-AAGTGTGAA
1 TTACGTAAATCGCAATGCGATTACGTAAATCGCAA-TGTG-A
* * * * *
338728 TTAGGAAAATCGTAATGTGATTACGTAAATCGCAATGCGA
1 TTACGTAAATCGCAATGCGATTACGTAAATCGCAATGTGA
* *
338768 TTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGTGA
1 TTACGTAAATCGCAATGCG-ATTACGTAAATCGCAATGTGA
* *
338809 TTACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGA
1 TTACGTAAATCGCAATGCGATTACGTAAATCGCAATGTGA
*
338849 ATACGT-AATCGCAATGCGATT
1 TTACGTAAATCGCAATGCGATT
338870 TTCCTAATTC
Statistics
Matches: 122, Mismatches: 17, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
39 14 0.11
40 41 0.34
41 65 0.53
42 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.26
Consensus pattern (40 bp):
TTACGTAAATCGCAATGCGATTACGTAAATCGCAATGTGA
Found at i:338790 original size:61 final size:61
Alignment explanation
Indices: 338688--338850 Score: 267
Period size: 61 Copynumber: 2.7 Consensus size: 61
338678 TCGTTGCGAT
* * *
338688 TTAC-TAAATCGTAATGCGATTACGTAAATCG-AAGTGTGAATTAGGAAAATCGTAATGTGA
1 TTACGTAAATCGCAATGCGATTACGTAAATCGCAA-TGCGAATTAGGAAAATCGCAATGTGA
338748 TTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGTGA
1 TTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGTGA
*
338809 TTACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAAT
1 TTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGAAT
338851 ACGTAATCGC
Statistics
Matches: 97, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
60 4 0.04
61 91 0.94
62 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (61 bp):
TTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGTGA
Found at i:338889 original size:20 final size:21
Alignment explanation
Indices: 338857--338948 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
338847 GAATACGTAA
*
338857 TCGCAATGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
338878 TCGCATTG-GATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* * * *
338898 TCTCATTGTGATTTACGTAA-
1 TCGCATTGCGATTTTCCTAAT
* *
338918 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCCTAAT
*
338938 TCTCATTGCGA
1 TCGCATTGCGA
338949 ATTAGAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.73
21 16 0.26
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:338971 original size:21 final size:21
Alignment explanation
Indices: 338945--338990 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
338935 TATTCTCATT
338945 GCGAATTAGAAAAATCGCAAC
1 GCGAATTAGAAAAATCGCAAC
* * *
338966 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGAAAAATCGCAAC
338987 GCGA
1 GCGA
338991 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGAAAAATCGCAAC
Found at i:342058 original size:64 final size:63
Alignment explanation
Indices: 341969--342119 Score: 180
Period size: 64 Copynumber: 2.3 Consensus size: 63
341959 ATGCACATTC
* * *
341969 ATAAGTGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCA-TCGATGCAT
1 ATAA-TGCATCGATGCA-TCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACT-GATGCAC
342032 A
63 A
* *
342033 GATAATGCATCGATGCATCCTTTTAAAATAAAAACATCGAATGCATTTTATGCACTGATGCACA
1 -ATAATGCATCGATGCATCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACTGATGCACA
*
342097 AGTAGTGCATCGATGCATACCTT
1 A-TAATGCATCGATGCAT-CCTT
342120 CATTGAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
63 4 0.05
64 63 0.83
65 9 0.12
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (63 bp):
ATAATGCATCGATGCATCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACTGATGCACA
Found at i:342622 original size:19 final size:21
Alignment explanation
Indices: 342598--342636 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
342588 GATTTACATG
342598 AATACATGT-ATAT-ATATAT
1 AATACATGTGATATGATATAT
342617 AATACATGTGATATGATATA
1 AATACATGTGATATGATATA
342637 AGATATATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.38
Consensus pattern (21 bp):
AATACATGTGATATGATATAT
Found at i:342828 original size:30 final size:30
Alignment explanation
Indices: 342792--342855 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
342782 AAGGAACATA
* *
342792 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
342822 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
342852 TGGA
1 TGGA
342856 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:346259 original size:64 final size:63
Alignment explanation
Indices: 346125--346272 Score: 172
Period size: 64 Copynumber: 2.3 Consensus size: 63
346115 CACATTCATA
* * * *
346125 AGTGCATCGATGCATTCCTTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCATAGAT
1 AGTGCATCGATGCA-TCCTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCAAAGAT
* * * * *
346189 AATGCATTGATGCATCATTTTAAAATAAAAACATCGAATGCATTTTATGCACCGATGCACAAG-T
1 AGTGCATCGATGCATC-CTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCA-AAGAT
346253 AGTGCATCGATGCATACCTT
1 AGTGCATCGATGCAT-CCTT
346273 CATTGAAAGA
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
63 2 0.03
64 64 0.93
65 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (63 bp):
AGTGCATCGATGCATCCTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCAAAGAT
Found at i:346793 original size:19 final size:17
Alignment explanation
Indices: 346756--346798 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
346746 GATTTACATG
*
346756 AATACATGTATATATAT
1 AATATATGTATATATAT
346773 AATATATGTGATATGATAT
1 AATATATGT-ATAT-ATAT
*
346792 AAGATAT
1 AATATAT
346799 ATGGTTACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.40
Consensus pattern (17 bp):
AATATATGTATATATAT
Found at i:346984 original size:30 final size:30
Alignment explanation
Indices: 346948--347011 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
346938 AAGGAACATA
* *
346948 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
346978 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
347008 TGGA
1 TGGA
347012 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:350415 original size:64 final size:63
Alignment explanation
Indices: 350281--350428 Score: 172
Period size: 64 Copynumber: 2.3 Consensus size: 63
350271 CACATTCATA
* * * *
350281 AGTGCATCGATGCATTCCTTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCATAGAT
1 AGTGCATCGATGCA-TCCTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCAAAGAT
* * * * *
350345 AATGCATTGATGCATCATTTTAAAATAAAAACATCGAATGCATTTTATGCACCGATGCACAAG-T
1 AGTGCATCGATGCATC-CTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCA-AAGAT
350409 AGTGCATCGATGCATACCTT
1 AGTGCATCGATGCAT-CCTT
350429 CATTGAAAGA
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
63 2 0.03
64 64 0.93
65 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (63 bp):
AGTGCATCGATGCATCCTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCAAAGAT
Found at i:350934 original size:17 final size:19
Alignment explanation
Indices: 350912--350949 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
350902 GATTTACATG
350912 AATACATGT-ATAT-ATAT
1 AATACATGTGATATGATAT
350929 AATACATGTGATATGATAT
1 AATACATGTGATATGATAT
350948 AA
1 AA
350950 GATATATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 4 0.21
19 6 0.32
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (19 bp):
AATACATGTGATATGATAT
Done.