Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 42 of 190
Found at i:11712000 original size:11 final size:11
Alignment explanation
Indices: 11711978--11712049 Score: 53
Period size: 10 Copynumber: 6.6 Consensus size: 11
11711968 TTATTAGAAC
*
11711978 TTATTATATTT
1 TTATAATATTT
11711989 TTATAA-ATTT
1 TTATAATATTT
11711999 TTATAATATTTAT
1 TTATAATA-TT-T
* *
11712012 GTTTTATTATTT
1 -TTATAATATTT
*
11712024 TTAT--GATTT
1 TTATAATATTT
11712033 TTATAA-ATTT
1 TTATAATATTT
11712043 TTATAAT
1 TTATAAT
11712050 TTATTAGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
9 8 0.16
10 20 0.41
11 9 0.18
12 3 0.06
13 3 0.06
14 6 0.12
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (11 bp):
TTATAATATTT
Found at i:11712018 original size:16 final size:17
Alignment explanation
Indices: 11711997--11712042 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
11711987 TTTTATAAAT
11711997 TTTTATAATATTTATG-
1 TTTTATAATATTTATGA
* *
11712013 TTTTATTATTTTTATGA
1 TTTTATAATATTTATGA
11712030 TTTTTATAA-ATTT
1 -TTTTATAATATTT
11712043 TTATAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 14 0.58
17 3 0.12
18 7 0.29
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (17 bp):
TTTTATAATATTTATGA
Found at i:11712025 original size:9 final size:9
Alignment explanation
Indices: 11711961--11712090 Score: 79
Period size: 9 Copynumber: 14.3 Consensus size: 9
11711951 TATTAAAAAA
11711961 TTATAATTT
1 TTATAATTT
* *
11711970 ATTAGAACTTA
1 -TTATAA-TTT
11711981 TTAT-ATTT
1 TTATAATTT
11711989 TTATAAATTT
1 TTAT-AATTT
*
11711999 TTATAATAT
1 TTATAATTT
*
11712008 TTAT--GTT
1 TTATAATTT
*
11712015 TTATTATTT
1 TTATAATTT
*
11712024 TTATGATTT
1 TTATAATTT
11712033 TTATAAATTT
1 TTAT-AATTT
11712043 TTATAATTT
1 TTATAATTT
*
11712052 ATTA-GATTT
1 -TTATAATTT
**
11712061 TTATAAAGT
1 TTATAATTT
* *
11712070 TTATAAATC
1 TTATAATTT
*
11712079 TTATGATTT
1 TTATAATTT
11712088 TTA
1 TTA
11712091 ACGAGAGAAT
Statistics
Matches: 93, Mismatches: 19, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
7 5 0.05
8 9 0.10
9 50 0.54
10 27 0.29
11 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.60
Consensus pattern (9 bp):
TTATAATTT
Found at i:11712065 original size:18 final size:19
Alignment explanation
Indices: 11712020--11712066 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
11712010 ATGTTTTATT
* *
11712020 ATTTTTATGATTTTTATAA
1 ATTTTTATAATTTATATAA
*
11712039 ATTTTTATAATTTAT-TAG
1 ATTTTTATAATTTATATAA
11712057 ATTTTTATAA
1 ATTTTTATAA
11712067 AGTTTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
ATTTTTATAATTTATATAA
Found at i:11716520 original size:9 final size:9
Alignment explanation
Indices: 11716506--11716536 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
11716496 GTTAAACGAA
11716506 TCGAGTTAT
1 TCGAGTTAT
*
11716515 TCGAGTTAA
1 TCGAGTTAT
11716524 TCGAGTTAT
1 TCGAGTTAT
11716533 TCGA
1 TCGA
11716537 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:11716609 original size:9 final size:9
Alignment explanation
Indices: 11716590--11716644 Score: 83
Period size: 9 Copynumber: 6.1 Consensus size: 9
11716580 TGAGTTTTCG
*
11716590 AATTTGAAT
1 AATTCGAAT
*
11716599 AACTCGAAT
1 AATTCGAAT
11716608 AATTCGAAT
1 AATTCGAAT
*
11716617 AACTCGAAT
1 AATTCGAAT
11716626 AATTCGAAT
1 AATTCGAAT
11716635 AATTCGAAT
1 AATTCGAAT
11716644 A
1 A
11716645 TCAAACTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (9 bp):
AATTCGAAT
Found at i:11716611 original size:18 final size:18
Alignment explanation
Indices: 11716590--11716644 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
11716580 TGAGTTTTCG
*
11716590 AATTTGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
11716608 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
*
11716626 AATTCGAATAATTCGAAT
1 AATTCGAATAACTCGAAT
11716644 A
1 A
11716645 TCAAACTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (18 bp):
AATTCGAATAACTCGAAT
Found at i:11716902 original size:30 final size:31
Alignment explanation
Indices: 11716854--11716913 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
11716844 AAACCTTTTA
*
11716854 TTTTCCCCAAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCAAAAACTTTTACTCCCTTCCCAC
* * *
11716884 TTTTCTCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCAAAAACTTTTACTCCCTTCCCA
11716914 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCAAAAACTTTTACTCCCTTCCCAC
Found at i:11722313 original size:27 final size:26
Alignment explanation
Indices: 11722275--11722343 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 26
11722265 GTGGAGGGTA
*
11722275 TCCCATGCGCGGCACCAAAGGTGCCTT
1 TCCCATG-GCGGCACCAAAGGTGCCAT
* *
11722302 TCCCATAGGCGGCACCGATGGTGCCAT
1 TCCCAT-GGCGGCACCAAAGGTGCCAT
11722329 TCCCATGGGCGGCAC
1 TCCCAT-GGCGGCAC
11722344 TGCCCATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.17, C:0.36, G:0.29, T:0.17
Consensus pattern (26 bp):
TCCCATGGCGGCACCAAAGGTGCCAT
Found at i:11722434 original size:5 final size:5
Alignment explanation
Indices: 11722406--11722514 Score: 59
Period size: 5 Copynumber: 22.4 Consensus size: 5
11722396 GAAAGAAGAA
* * * * *
11722406 GAAA- GAAAG AAAAC GAAAG AAAAG GAAAG GAGAG GAAA- GAAAG AAAAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
* * *
11722454 GAAAG GAGAAG AAGAAA- -AAA- GAAAG AAAAA G-AAG GAAAG AAAAG
1 GAAAG GA-AAG --GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
* *
11722498 GAAAG GAGAG GAGAG GA
1 GAAAG GAAAG GAAAG GA
11722515 GAAAAAAAAA
Statistics
Matches: 80, Mismatches: 17, Indels: 15
0.71 0.15 0.13
Matches are distributed among these distances:
3 3 0.04
4 14 0.17
5 56 0.70
6 3 0.04
7 2 0.03
8 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.34, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:11722447 original size:24 final size:24
Alignment explanation
Indices: 11722396--11722506 Score: 110
Period size: 24 Copynumber: 4.8 Consensus size: 24
11722386 GAAGGAGAGG
11722396 GAAAGAAGAA-GAAA-GA-AAGAAAA
1 GAAAGAA-AAGGAAAGGAGAAG-AAA
*
11722419 CGAAAGAAAAGGAAAGGAGAGGAAA
1 -GAAAGAAAAGGAAAGGAGAAGAAA
11722444 GAAAGAAAAGGAAAGGAGAAG-AA
1 GAAAGAAAAGGAAAGGAGAAGAAA
* * *
11722467 G-AA-AAAA-GAAAGAAAAAGAAG
1 GAAAGAAAAGGAAAGGAGAAGAAA
11722488 GAAAGAAAAGGAAAGGAGA
1 GAAAGAAAAGGAAAGGAGA
11722507 GGAGAGGAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
20 9 0.12
21 6 0.08
22 4 0.05
23 9 0.12
24 38 0.52
25 5 0.07
26 2 0.03
ACGTcount: A:0.68, C:0.01, G:0.32, T:0.00
Consensus pattern (24 bp):
GAAAGAAAAGGAAAGGAGAAGAAA
Found at i:11722490 original size:48 final size:48
Alignment explanation
Indices: 11722438--11722535 Score: 135
Period size: 48 Copynumber: 2.0 Consensus size: 48
11722428 AGGAAAGGAG
*
11722438 AGGAAAG-AAAGAAAAGGAAAGGAGAAGAAGAAAAAAGAAAGAAAAAGA
1 AGGAAAGAAAAGAAAAGGAAAGGAG-AGAAGAAAAAAAAAAGAAAAAGA
* * * *
11722486 AGGAAAGAAAAGGAAAGGAGAGGAGAGGAGAAAAAAAAAAGAAGAAGA
1 AGGAAAGAAAAGAAAAGGAAAGGAGAGAAGAAAAAAAAAAGAAAAAGA
11722534 AG
1 AG
11722536 AAGAGGGAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 29 0.66
49 15 0.34
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (48 bp):
AGGAAAGAAAAGAAAAGGAAAGGAGAGAAGAAAAAAAAAAGAAAAAGA
Found at i:11722495 original size:14 final size:14
Alignment explanation
Indices: 11722444--11722496 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
11722434 GGAGAGGAAA
*
11722444 GAAAGAAAAGGAAAG
1 GAAAGAAAAAG-AAG
*
11722459 GAGAAGAAGAAA-AAA
1 GA-AAGAA-AAAGAAG
11722474 GAAAGAAAAAGAAG
1 GAAAGAAAAAGAAG
11722488 GAAAGAAAA
1 GAAAGAAAA
11722497 GGAAAGGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 3 0.09
14 16 0.50
15 6 0.19
16 5 0.16
17 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
GAAAGAAAAAGAAG
Found at i:11722502 original size:68 final size:67
Alignment explanation
Indices: 11722404--11722565 Score: 188
Period size: 68 Copynumber: 2.4 Consensus size: 67
11722394 GGGAAAGAAG
* *
11722404 AAGAAAGAAAGAA-AACGAAAGAAAAGGAAAGGAGAGGA-A-AGAAAGAAAAGGAAAGGAGAAGA
1 AAGAAAGAAA-AAGAAAGAAAGAAAAGGAAAGGAGAGGAGAGAGAAA-AAAA--AAAGAAGAAGA
11722466 AGAAAA
62 AGAAAA
*
11722472 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGAGAGGAGAAAAAAAAAAGAAGAAGAAGA
1 AAGAAAGAAAAAGAAAGAAAGAAAAGGAAAGGAGAGGAGA-GAGAAAAAAAAAAGAAGAAGAAGA
*
11722537 AGA
65 AAA
** *
11722540 GGGAAGGAAAAAGAAAGAAA-AAAAGG
1 AAGAAAGAAAAAGAAAGAAAGAAAAGG
11722566 TAATTTTTAA
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
67 8 0.10
68 65 0.78
69 1 0.01
70 4 0.05
71 5 0.06
ACGTcount: A:0.67, C:0.01, G:0.32, T:0.00
Consensus pattern (67 bp):
AAGAAAGAAAAAGAAAGAAAGAAAAGGAAAGGAGAGGAGAGAGAAAAAAAAAAGAAGAAGAAGAA
AA
Found at i:11722520 original size:24 final size:24
Alignment explanation
Indices: 11722421--11722526 Score: 92
Period size: 24 Copynumber: 4.4 Consensus size: 24
11722411 AAAGAAAACG
11722421 AAAGAAAAGGAAAGGAGAGGA-AA
1 AAAGAAAAGGAAAGGAGAGGAGAA
*
11722444 GAAAGAAAAGGAAAGGAGAAGAAGAA
1 -AAAGAAAAGGAAAGGAG-AGGAGAA
* * *
11722470 AAA-AGAAAGAAAAAGA-AGGAAAGA
1 AAAGA-AAAGGAAAGGAGAGGAGA-A
* *
11722494 AAAGGAAAGGAGAGGAGAGGAGAA
1 AAAGAAAAGGAAAGGAGAGGAGAA
*
11722518 AAAAAAAAG
1 AAAGAAAAG
11722527 AAGAAGAAGA
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
23 4 0.06
24 38 0.59
25 20 0.31
26 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (24 bp):
AAAGAAAAGGAAAGGAGAGGAGAA
Found at i:11722534 original size:54 final size:50
Alignment explanation
Indices: 11722412--11722556 Score: 132
Period size: 49 Copynumber: 2.8 Consensus size: 50
11722402 AGAAGAAAGA
** * * *
11722412 AAGAAAACGAAAGAAAAGGAAAGGAGAGGAAAG-AAAGAAAAGGAAAGGAG
1 AAGAAAAAAAAAGAAAAGAAAAAGA-AGGAAAGAAAAGGAAAGGAAAGGAG
* *
11722462 AAGAAGAAAAAAG-AAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGAG
1 AAGAAAAAAAAAGAAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAAAGGAG
* * * *
11722511 AGGAGAAAAAAAAAAGAAGAAGAAGAAGAGGGAAGGAAAAAGAAAG
1 A--AG-AAAAAAAAAGAA-AAGAAAAAGAAGGAAAGAAAAGGAAAG
11722557 AAAAAAAGGT
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
48 7 0.09
49 25 0.32
50 10 0.13
51 2 0.03
52 9 0.12
53 1 0.01
54 23 0.30
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (50 bp):
AAGAAAAAAAAAGAAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAAAGGAG
Found at i:11723677 original size:16 final size:15
Alignment explanation
Indices: 11723651--11723680 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
11723641 GTACTGAAAT
11723651 AATATAAAATAATAA
1 AATATAAAATAATAA
11723666 AATATGAAAATAATA
1 AATAT-AAAATAATA
11723681 TTTTTTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AATATAAAATAATAA
Found at i:11723715 original size:285 final size:285
Alignment explanation
Indices: 11722930--11723788 Score: 1501
Period size: 286 Copynumber: 3.0 Consensus size: 285
11722920 AAATAAAGTA
11722930 AAATTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGAG-AAAAAATACGAAGA
1 AAATTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGAGAAAAAAATACGAAGA
* *
11722994 AATGACCGAAGTAAGAGTGTTTTA-TAAAATTTTTTAAAAATTCAGAAATAATTATTGCAAATAT
66 AATGACCGAAGTAAGAGTGTTTTACTAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATAT
11723058 TTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGAAA
131 TTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGAAA
* * *
11723123 GTAATAAAATTTGGGAAAATAATACGAGCAAATGACAGGAATAAGGGTTTTTTT-ACACTAAATT
196 GTAATAAAATTCGGGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTGACACTAAATT
11723187 AATTTAAAAAACACACTAAATTAAT
261 AATTTAAAAAACACACTAAATTAAT
** *
11723212 AAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATATAGAGAAAAAAATATGAA
1 AAA-TTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAAT-GCGAGAAAAAAATACGAA
* * *
11723277 GAAATGACTGAATTAAGAGTGTTTTACTAAAATTTTTTCAAAATTCAGAAATAATTAATACAAAT
64 GAAATGACCGAAGTAAGAGTGTTTTACTAAAATTTTTTAAAAATTCAGAAATAATTAATACAAAT
*
11723342 ATTTCAAACAAAATGTATTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGA
129 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGA
*
11723407 AAGTAACAAAATTCGGGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTGACACTAAA
194 AAGTAATAAAATTCGGGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTGACACTAAA
11723472 TTAATTTAAAAAACACACTAAATTAAT
259 TTAATTTAAAAAACACACTAAATTAAT
11723499 AAATTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAG
1 AAATTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGC-GAGAAAAAAATACGAAG
*
11723564 AAATGGCCGAAGTAAGAGTGTTTTACT-AAATTTTTTAAAAATTCAGAAATAATTAATACAAATA
65 AAATGACCGAAGTAAGAGTGTTTTACTAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATA
*
11723628 TTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATATGAAAATAATATTTTTTATTGAA
130 TTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGAA
* *
11723693 AGTAATAAAATTCGGAAAAATAATACGAGCAAAGGGCAGGAATAAGAGTTTTTTTGACACTAAAT
195 AGTAATAAAATTCGGGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTGACACTAAAT
*
11723758 TAATTTTAAAAACACACTAAATTAAT
260 TAATTTAAAAAACACACTAAATTAAT
11723784 AAATT
1 AAATT
11723789 TCAAACATAA
Statistics
Matches: 545, Mismatches: 26, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
282 3 0.01
283 42 0.08
284 3 0.01
285 226 0.41
286 233 0.43
287 38 0.07
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.31
Consensus pattern (285 bp):
AAATTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGAGAAAAAAATACGAAGA
AATGACCGAAGTAAGAGTGTTTTACTAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATAT
TTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGAAA
GTAATAAAATTCGGGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTGACACTAAATT
AATTTAAAAAACACACTAAATTAAT
Found at i:11723877 original size:159 final size:153
Alignment explanation
Indices: 11723499--11723917 Score: 440
Period size: 159 Copynumber: 2.6 Consensus size: 153
11723489 CTAAATTAAT
*
11723499 AAATTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAG
1 AAATTATAAAATTAGAAA-TATGATATTTTTTAAAATAATAAAATGCGGAGAAAAAAATACG-AG
* *
11723564 AAATGGCCGAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAATAT
64 AAAGGGCCGAAGTAAGAGTGTTTTACTAAATTTTTTAAAAA-TCACAAATAATTAAT--AAATAT
*
11723629 TTCAAACAAAATGTACTGAAATAATATA
126 TTCAAACAAAATGCACTGAAATAATATA
* * * *
11723657 AAATAATAAAA-TATGAAA-ATAATATTTTTTATTGAAAGTAATAAAATTCGGA-AAAATAATAC
1 AAATTATAAAATTA-GAAATATGATATTTTTTA---AAA-TAATAAAATGCGGAGAAAAAAATAC
* * *
11723719 GAGCAAAGGGCAGGAA-TAAGAGTTTTTTTGACACTAAATTAATTTTAAAAA-CAC-ACTAAATT
61 GAG-AAAGGGC-CGAAGTAAGAG-TGTTTT---ACTAAATT--TTTTAAAAATCACAAAT-AATT
* * *
11723781 AAT-AA-ATTTCAAACATAATGCACTTAAATAATGTA
117 AATAAATATTTCAAACAAAATGCACTGAAATAATATA
11723816 AAATTATAAAAATTAGAAACTATGATATTTTTTAAAATAATAAAATGCGGAGAAAAAAATACGAA
1 AAATTAT-AAAATTAGAAA-TATGATATTTTTTAAAATAATAAAATGCGGAGAAAAAAATACG-A
* *
11723881 GAAATGGCCGAAGTAAGAGTGTTTTACTAACTTTTTT
63 GAAAGGGCCGAAGTAAGAGTGTTTTACTAAATTTTTT
11723918 TCAACATGCA
Statistics
Matches: 218, Mismatches: 22, Indels: 47
0.76 0.08 0.16
Matches are distributed among these distances:
153 4 0.02
155 7 0.03
156 12 0.06
157 2 0.01
158 37 0.17
159 81 0.37
160 33 0.15
161 2 0.01
162 14 0.06
163 17 0.08
165 9 0.04
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (153 bp):
AAATTATAAAATTAGAAATATGATATTTTTTAAAATAATAAAATGCGGAGAAAAAAATACGAGAA
AGGGCCGAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATCACAAATAATTAATAAATATTTCAA
ACAAAATGCACTGAAATAATATA
Found at i:11727195 original size:40 final size:40
Alignment explanation
Indices: 11727080--11727195 Score: 112
Period size: 40 Copynumber: 2.8 Consensus size: 40
11727070 CCACTAATCC
* *
11727080 TAATAACTAACACAATAAAAATAATAATAGTTTTATACTCAAAA
1 TAATAACTAAC-C-ATAATAATAATAATAG-TTT-TACTAAAAA
*
11727124 TAAT-AGTAA-C-TAATAATAATAATTAGGGTTTTACTAAAAA
1 TAATAACTAACCATAATAATAATAA-TA--GTTTTACTAAAAA
*
11727164 TAATAACTAACCATAATAATAATACTAGTTTT
1 TAATAACTAACCATAATAATAATAATAGTTTT
11727196 TTACTAACTA
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
39 11 0.18
40 19 0.31
41 8 0.13
42 4 0.07
43 15 0.25
44 4 0.07
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (40 bp):
TAATAACTAACCATAATAATAATAATAGTTTTACTAAAAA
Found at i:11727524 original size:27 final size:27
Alignment explanation
Indices: 11727484--11727549 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
11727474 TAACACGAGT
*
11727484 GGTGCCGCCCATGGGAATGGCACCATC
1 GGTGCCGCCTATGGGAATGGCACCATC
* *
11727511 GGTGCCGCCTATGGGAATGGCACCTTT
1 GGTGCCGCCTATGGGAATGGCACCATC
11727538 GGTGCCGCCTAT
1 GGTGCCGCCTAT
11727550 CAGTCTCTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.21
Consensus pattern (27 bp):
GGTGCCGCCTATGGGAATGGCACCATC
Found at i:11728606 original size:2 final size:2
Alignment explanation
Indices: 11728599--11728631 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11728589 CTGTTAATAT
11728599 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
11728632 ATCTTTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11732649 original size:4 final size:4
Alignment explanation
Indices: 11732640--11732667 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
11732630 AACTTAAGCC
11732640 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
11732668 CAAGCGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:11763121 original size:36 final size:36
Alignment explanation
Indices: 11763076--11763149 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
11763066 AATGTGCAAC
*
11763076 ATTTAGCTTTGCGT-GCAAAAACCATATAAGGATAAT
1 ATTTAGCTTTGC-TCGCAAAAACCATATAAAGATAAT
*
11763112 ATTTTGCTTTGCTCGCAAAAACCATATAAAGATAAT
1 ATTTAGCTTTGCTCGCAAAAACCATATAAAGATAAT
11763148 AT
1 AT
11763150 ACAAAGTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 1 0.03
36 34 0.97
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (36 bp):
ATTTAGCTTTGCTCGCAAAAACCATATAAAGATAAT
Found at i:11768493 original size:3 final size:3
Alignment explanation
Indices: 11768485--11768526 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
11768475 GAGAAGCTTA
11768485 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
11768527 CACCATACTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TAC
Found at i:11775502 original size:18 final size:19
Alignment explanation
Indices: 11775475--11775511 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
11775465 GAGATAACAA
11775475 GGATGAGAAATGG-ATATG
1 GGATGAGAAATGGAATATG
*
11775493 GGATGGGAAATGGAATATG
1 GGATGAGAAATGGAATATG
11775512 AAATGACGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.22
Consensus pattern (19 bp):
GGATGAGAAATGGAATATG
Found at i:11779917 original size:321 final size:323
Alignment explanation
Indices: 11779063--11780004 Score: 1613
Period size: 325 Copynumber: 2.9 Consensus size: 323
11779053 CTGGAATGTA
* **
11779063 AGGATTATTCTGTAGTTTTTTATTT-CCTCTATTATCAACAACTTGATCTATATAATAGTTAAAA
1 AGGATTATTCTGCAGTTTTTCCTTTCCCTCTATTATCAACAACTTGATCTATATAATAGTTAAAA
*
11779127 TTCAAATTATCAATTCAAAAATCATTATATCACTCAAATACATGCATATGACCTTTTAATTTCAT
66 TTCAAATTATCAATTCAAAAAGCATTATATCACTCAAATACATGCATATGACCTTTTAATTTCAT
11779192 TTTACATAATTTCCCTAAACTTTTATATTTTATTCAATTTAATCCCTAAAACCAAGACTATTATA
131 TTTACATAATTTCCCTAAACTTTTATATTTTATTCAATTTAATCCCTAAAACCAAGACTATTATA
*
11779257 ACTTTCACAATTAAAC-TCAATTTTTCATTCCAATTTCAATTACATCCTTCTACAGCTCTCTAAA
196 ACTTTCACAATTAAACTTC-ATTTTTCATTCCAATTTCAATTACATCCTTCTACAGCCCTCTAAA
*
11779321 CTCTAAATTTATAGAATTTTCATGTCACTTTTATCATAACACAACCAACTAACGAGCTGAAACGT
260 CTCTAAATTTATAGAATTTTCATGTCACTTTTATCATAACACAACCAACTAACGAACTGAAAC-T
* *
11779386 AGGGACTATTCTGCAGTTTTTCCTTTCCCTCGATTATCAACAACTTGATCTATATAATAGTTAAA
1 A-GGATTATTCTGCAGTTTTTCCTTTCCCTCTATTATCAACAACTTGATCTATATAATAGTTAAA
*
11779451 ATTCAAATTATCAATTCAAAAAGCATTATATCACTCAAATACATGCATATGATCTTTTAATTTCA
65 ATTCAAATTATCAATTCAAAAAGCATTATATCACTCAAATACATGCATATGACCTTTTAATTTCA
11779516 TTTTACATAATTTCCCTAAACTTTTATATTTTATTCAATTTAATCCCTAAAACCAAGACTATTAT
130 TTTTACATAATTTCCCTAAACTTTTATATTTTATTCAATTTAATCCCTAAAACCAAGACTATTAT
* *
11779581 AACTTTCACAATTAAACTTCATTTTTCATTCCAATTTCAATTACATCCTTCTACAGCCCTGTAAG
195 AACTTTCACAATTAAACTTCATTTTTCATTCCAATTTCAATTACATCCTTCTACAGCCCTCTAAA
*
11779646 CTCTAAATTTATAGAATTTTCATGTCACTTTTATCATAACACAACCGACTAACGAACTGAAA-T
260 CTCTAAATTTATAGAATTTTCATGTCACTTTTATCATAACACAACCAACTAACGAACTGAAACT
* *
11779709 -GTATTATTCTGCAGTTTTTCCTTTCCCCCTATTATCAACAACTTGATCTATATAATAGTTAAAA
1 AGGATTATTCTGCAGTTTTTCCTTTCCCTCTATTATCAACAACTTGATCTATATAATAGTTAAAA
* *
11779773 TTTAAATTATCAATTCAAAAAGAATTATATCACTCAAATACATGCATATGACCTTTTAATTTCAT
66 TTCAAATTATCAATTCAAAAAGCATTATATCACTCAAATACATGCATATGACCTTTTAATTTCAT
* * * * *
11779838 TTTACACAATTTCCTTGAACTTTTATATTTTATTCAAGTTAATCTCTAAAACCAAGACTATTATA
131 TTTACATAATTTCCCTAAACTTTTATATTTTATTCAATTTAATCCCTAAAACCAAGACTATTATA
* * *
11779903 AATTTCACAATTAAACTTCATTTTTCATTCCAATTTCAATTATATCCTTCTACATCCCTCTAAAC
196 ACTTTCACAATTAAACTTCATTTTTCATTCCAATTTCAATTACATCCTTCTACAGCCCTCTAAAC
11779968 TCTAAATTTATAGAATTTTCATGTCACTTTTATCATA
261 TCTAAATTTATAGAATTTTCATGTCACTTTTATCATA
11780005 TTCACAATTT
Statistics
Matches: 587, Mismatches: 29, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
321 279 0.48
323 2 0.00
324 20 0.03
325 284 0.48
326 2 0.00
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (323 bp):
AGGATTATTCTGCAGTTTTTCCTTTCCCTCTATTATCAACAACTTGATCTATATAATAGTTAAAA
TTCAAATTATCAATTCAAAAAGCATTATATCACTCAAATACATGCATATGACCTTTTAATTTCAT
TTTACATAATTTCCCTAAACTTTTATATTTTATTCAATTTAATCCCTAAAACCAAGACTATTATA
ACTTTCACAATTAAACTTCATTTTTCATTCCAATTTCAATTACATCCTTCTACAGCCCTCTAAAC
TCTAAATTTATAGAATTTTCATGTCACTTTTATCATAACACAACCAACTAACGAACTGAAACT
Found at i:11784624 original size:18 final size:17
Alignment explanation
Indices: 11784585--11784629 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
11784575 AAGAATTATG
11784585 AATTTTTCTTATTTTTT
1 AATTTTTCTTATTTTTT
*
11784602 CATTTTT-TTATATTTTT
1 AATTTTTCTTAT-TTTTT
11784619 AAATTTTTCTT
1 -AATTTTTCTT
11784630 CAAAAGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 6 0.26
19 2 0.09
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (17 bp):
AATTTTTCTTATTTTTT
Found at i:11785665 original size:17 final size:18
Alignment explanation
Indices: 11785643--11785686 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
11785633 TATCAAGATA
11785643 AATATTAGAT-TAAATTT
1 AATATTAGATATAAATTT
*
11785660 AATATTAAGATAATCAATTT
1 AATATT-AGAT-ATAAATTT
11785680 AATATTA
1 AATATTA
11785687 AATTTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 4 0.17
19 1 0.04
20 12 0.52
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (18 bp):
AATATTAGATATAAATTT
Found at i:11785681 original size:68 final size:68
Alignment explanation
Indices: 11785602--11785732 Score: 192
Period size: 68 Copynumber: 1.9 Consensus size: 68
11785592 TAATTAAACT
* * * * *
11785602 TAATCACTTTAATATTAAATTAATATAAA-CTTATCAAGATAAATATTAGATTAAATTTAATATT
1 TAATCAATTTAATATTAAATTAATA-AAATATTATCAAAATAAATATTAAATTAAATTAAATATT
11785666 AAGA
65 AAGA
*
11785670 TAATCAATTTAATATTAAATTTATAAAATATTATCAAAATAAATATTAAATTAAATTAAATAT
1 TAATCAATTTAATATTAAATTAATAAAATATTATCAAAATAAATATTAAATTAAATTAAATAT
11785733 GAAATTTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 3 0.05
68 53 0.95
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (68 bp):
TAATCAATTTAATATTAAATTAATAAAATATTATCAAAATAAATATTAAATTAAATTAAATATTA
AGA
Found at i:11786882 original size:16 final size:16
Alignment explanation
Indices: 11786851--11786910 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
11786841 TCTTCAGGTG
* *
11786851 AAGAAAGAATATGCTC
1 AAGAAAGAGTACGCTC
*
11786867 AATAAAGAGTACGCTC
1 AAGAAAGAGTACGCTC
11786883 AAGAAAGAGTACGC-C
1 AAGAAAGAGTACGCTC
*
11786898 TAAGGAAGAGTAC
1 -AAGAAAGAGTAC
11786911 ACCCTAAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
15 1 0.03
16 37 0.97
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.15
Consensus pattern (16 bp):
AAGAAAGAGTACGCTC
Found at i:11787389 original size:12 final size:12
Alignment explanation
Indices: 11787374--11787399 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11787364 ATGATTCAAC
11787374 CTTCTAGTAAGT
1 CTTCTAGTAAGT
11787386 CTTCTAGTAAGT
1 CTTCTAGTAAGT
11787398 CT
1 CT
11787400 ATTTTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (12 bp):
CTTCTAGTAAGT
Found at i:11794891 original size:51 final size:49
Alignment explanation
Indices: 11794774--11794951 Score: 205
Period size: 51 Copynumber: 3.5 Consensus size: 49
11794764 GATGGTCATG
* *
11794774 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-ATGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA-G-TTGGTCACA
* * * * *
11794824 TGTGTAGTACTATGTGCAAGCTACTATGCGTACCAGATAGCTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAG-TT-GGTCACA
***
11794875 TGTGTAGTACTATGTGCAGGCTACTACGTGTATTGGATAGTGATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGT--TGGTCACA
11794926 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
11794952 TGTGAACCGG
Statistics
Matches: 108, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
50 37 0.34
51 70 0.65
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTTGGTCACA
Found at i:11794955 original size:26 final size:26
Alignment explanation
Indices: 11794875--11794955 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
11794865 TTCGATCACG
11794875 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *
11794901 CGTGTATTGGA-TA-GTG-ATGG-TCAC-A
1 TGTGTA--GTACTATGTGCA-GGCT-ACTA
11794926 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
11794952 TGTG
1 TGTG
11794956 AACCGGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
23 2 0.05
24 2 0.05
25 15 0.36
26 19 0.45
27 2 0.05
28 2 0.05
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:11795038 original size:46 final size:43
Alignment explanation
Indices: 11794957--11795055 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 43
11794947 TACTATGTGA
* *
11794957 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTACTATGTGCTGAAT-CC
* *
11795000 ACCGGATATCATTGATTACAAAGGGTGGTTACTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTACTATGTGCTGAATCC
11795046 ACCGTGTATC
1 ACCG-GTATC
11795056 TGTTATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.11
44 11 0.23
45 2 0.04
46 26 0.55
47 3 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTACTATGTGCTGAATCC
Found at i:11795200 original size:16 final size:16
Alignment explanation
Indices: 11795179--11795210 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11795169 TGATTGAAAG
*
11795179 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
11795195 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
11795211 GGAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:11797119 original size:8 final size:8
Alignment explanation
Indices: 11797108--11797150 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
11797098 GAAGTTAAGA
11797108 GTTAGTGG
1 GTTAGTGG
11797116 GTTAGTGG
1 GTTAGTGG
11797124 GTTAGTGG
1 GTTAGTGG
*
11797132 GATTTAG-CG
1 G--TTAGTGG
11797141 GTTAGTGG
1 GTTAGTGG
11797149 GT
1 GT
11797151 GGTTAAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 4 0.13
8 20 0.67
9 2 0.07
10 4 0.13
ACGTcount: A:0.14, C:0.02, G:0.47, T:0.37
Consensus pattern (8 bp):
GTTAGTGG
Found at i:11799987 original size:50 final size:50
Alignment explanation
Indices: 11799918--11800088 Score: 166
Period size: 50 Copynumber: 3.4 Consensus size: 50
11799908 CAAACCACAC
* * * * *
11799918 AAAGCCTTTTTGGCAAGTTATTTGAATGGCCTGTGTGGCATA-TAGTCTGG
1 AAAGCCTTTGTGGCGAGTTATTTGAAAGGCCTATGTGGCATATTA-TCTAG
* * *
11799968 AAAGCCTTTGTGGTGAGTTATCTGAAAGGCTTATGTGGCATATTATCTAG
1 AAAGCCTTTGTGGCGAGTTATTTGAAAGGCCTATGTGGCATATTATCTAG
* * * * * *
11800018 AAAGCC-TTGTGGCGAGTTATTTAAAAGGCCTTTATGACATATTATTTGG
1 AAAGCCTTTGTGGCGAGTTATTTGAAAGGCCTATGTGGCATATTATCTAG
* *
11800067 GAAGCCTTAGTGGCGAAGTTAT
1 AAAGCCTTTGTGGCG-AGTTAT
11800089 CTGGAAAGCC
Statistics
Matches: 99, Mismatches: 19, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
49 39 0.39
50 52 0.53
51 8 0.08
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (50 bp):
AAAGCCTTTGTGGCGAGTTATTTGAAAGGCCTATGTGGCATATTATCTAG
Found at i:11799991 original size:25 final size:25
Alignment explanation
Indices: 11799963--11800121 Score: 103
Period size: 25 Copynumber: 6.4 Consensus size: 25
11799953 TGGCATATAG
*
11799963 TCTGGAAAGCCTTTGTGGTGAGTTA
1 TCTGGAAAGCCTTTGTGGCGAGTTA
* *
11799988 TCT-GAAAGGCTTATGTGGC-ATATTA
1 TCTGGAAAGCCTT-TGTGGCGA-GTTA
*
11800013 TCTAGAAAGCC-TTGTGGCGAGTTA
1 TCTGGAAAGCCTTTGTGGCGAGTTA
** * * *
11800037 T-TTAAAAGGCCTTTATGAC-ATATTA
1 TCTGGAAA-GCCTTTGTGGCGA-GTTA
* * *
11800062 TTTGGGAAGCCTTAGTGGCGAAGTTA
1 TCTGGAAAGCCTTTGTGGCG-AGTTA
* * *
11800088 TCTGGAAAGCCTTTGCGGCAAGTCA
1 TCTGGAAAGCCTTTGTGGCGAGTTA
11800113 TCTGGAAAG
1 TCTGGAAAG
11800122 TCTATATGGC
Statistics
Matches: 101, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
23 4 0.04
24 23 0.23
25 46 0.46
26 27 0.27
27 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.32
Consensus pattern (25 bp):
TCTGGAAAGCCTTTGTGGCGAGTTA
Found at i:11800030 original size:24 final size:24
Alignment explanation
Indices: 11799946--11800030 Score: 61
Period size: 25 Copynumber: 3.5 Consensus size: 24
11799936 TATTTGAATG
*
11799946 GCCTGTGTGGCATA-TAGTCTGGAAA
1 GCCTATGTGGCATATTA-TCT-GAAA
*
11799971 GCCTTTGTGG--TGAGTTATCTGAAA
1 GCCTATGTGGCAT-A-TTATCTGAAA
*
11799995 GGCTTATGTGGCATATTATCTAGAAA
1 -GCCTATGTGGCATATTATCT-GAAA
11800021 GCCT-TGTGGC
1 GCCTATGTGGC
11800031 GAGTTATTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
23 1 0.02
24 11 0.22
25 29 0.59
26 7 0.14
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.33
Consensus pattern (24 bp):
GCCTATGTGGCATATTATCTGAAA
Found at i:11808486 original size:149 final size:149
Alignment explanation
Indices: 11808162--11808487 Score: 389
Period size: 149 Copynumber: 2.2 Consensus size: 149
11808152 AAAAAAAAAG
* ** *
11808162 AAAGCAGAAAGTTTAGATTTTGGAAAATAAAAATCTGCTTTTTTTAGTCATTTTAAAGAAAAGTT
1 AAAGGAGAAAGTTTAGATTTTAAAAAATAAAAATCTACTTTTTTTAGTCATTTTAAAGAAAAGTT
* *
11808227 TAAAATTTTAAAACAACGTTTTGATTTTTTTCAATTACTTAAAAATAAAAGCTTTAATCTTTAAG
66 TAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTACTTAAAAATAAAAGCTTTAATCTTTAAG
*
11808292 AAAAATAGTGTTTTTTTTA
131 AAAAATAATGTTTTTTTTA
* * *
11808311 AAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTTTTAGTCATTTTAAAGGAAAGTT
1 AAAGGAGAAAGTTTAGATTTTAAAAAATAAAAATCTACTTTTTTTAGTCATTTTAAAGAAAAGTT
* * ** * * * *
11808376 TAAAGTTTTAAAACAAAGTTTTGA-TTTTTT-AACTATTTTGAAAT-AAGGTTTTGATTTTTAAG
66 TAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTACTTAAAAATAAAAGCTTTAATCTTTAAG
*
11808438 AAAATTAATGATTTTTTTCT-
131 AAAAATAATG-TTTTTTT-TA
11808458 AAA-GA-AAAGTTT-GATTCTGTAAAAAA-AAAA
1 AAAGGAGAAAGTTTAGATT-T-TAAAAAATAAAA
11808488 TCCAGCCACC
Statistics
Matches: 155, Mismatches: 18, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
144 4 0.03
145 12 0.08
146 30 0.19
147 20 0.13
148 7 0.05
149 82 0.53
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (149 bp):
AAAGGAGAAAGTTTAGATTTTAAAAAATAAAAATCTACTTTTTTTAGTCATTTTAAAGAAAAGTT
TAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTACTTAAAAATAAAAGCTTTAATCTTTAAG
AAAAATAATGTTTTTTTTA
Found at i:11812173 original size:28 final size:28
Alignment explanation
Indices: 11812133--11812189 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
11812123 GGGCTTCATG
11812133 TAAAATTCTCTATGCAAATTCTGAATTC
1 TAAAATTCTCTATGCAAATTCTGAATTC
*
11812161 TAAAATTCTCTATGCAAGTTCTGAATTC
1 TAAAATTCTCTATGCAAATTCTGAATTC
11812189 T
1 T
11812190 TCGGTACACA
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:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (28 bp):
TAAAATTCTCTATGCAAATTCTGAATTC
Found at i:11820303 original size:4 final size:4
Alignment explanation
Indices: 11820294--11820342 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
11820284 TGACCCAATA
* * * * *
11820294 TCAT TCAT TCAT TCAT TTAT TCAT CCAT TCGT TCAC TCAT TCGT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
11820342 T
1 T
11820343 TGTTTATTCA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.20, C:0.27, G:0.04, T:0.49
Consensus pattern (4 bp):
TCAT
Found at i:11825189 original size:14 final size:15
Alignment explanation
Indices: 11825165--11825193 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
11825155 TATTTGAGAC
11825165 CTTTATTTTTCTTTT
1 CTTTATTTTTCTTTT
11825180 CTTT-TTTTTCTTTT
1 CTTTATTTTTCTTTT
11825194 TTCCTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTATTTTTCTTTT
Found at i:11826024 original size:148 final size:150
Alignment explanation
Indices: 11825604--11826250 Score: 811
Period size: 148 Copynumber: 4.3 Consensus size: 150
11825594 GGAAAAGTTT
* * * *
11825604 TGATTTTTTTTAAAAAAAGAAAAAGCTTATATTTT-AACAAATAAAAATCTTTTTTTGTTTTAGT
1 TGATTTTTTTT---AAAAGAGAAAGTTTAGATTTTGAA-AAATAAAAATC-TATTTT-TTTTAGT
* * * *
11825668 TATTTTAAAGGAAAGTTTAAATTTTTAAAACAAAATTTTGA--TTTTTTTCAACTATTTCAAAGT
60 CATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGATTTTTTTTTCAACTACTTCAAAAT
11825731 AAAAGCTTTAATCTTTAA-AAAAATA
125 AAAAGCTTTAATCTTTAAGAAAAATA
11825756 -GTATTTTTTTCTAAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTTTTAGT
1 TG-ATTTTTTT-T---AAAA-GAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTTTTAGT
*
11825820 CATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTTTCAACTACTTCAAAA
60 CATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGA-TTTTTTTTTCAACTACTTCAAAA
11825885 TAAAAGCTTTAATCTTTAAGAAAAATA
124 TAAAAGCTTTAATCTTTAAGAAAAATA
*
11825912 -G-TTTTTTTT-AAAGAGAAAGTTTAGATTTTGAAAAATAAAAATTTATTTTTTCTTAGTCATTT
1 TGATTTTTTTTAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTT-TTAGTCATTT
*
11825974 TAAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGATTTTTTTTTCAACTACTTCAAAATAAAAA
65 TAAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGATTTTTTTTTCAACTACTTCAAAATAAAAG
*
11826039 CTTTAATCTTTAAGAAAAGTA
130 CTTTAATCTTTAAGAAAAATA
* *
11826060 GTG-TTTTTTTTAAAAGGAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTTAAGTCATT
1 -TGATTTTTTTTAAAA-GAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTTTTAGTCATT
* * * * *
11826124 TTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTT-AATTTTTTTT-AACTATTTCGAAAT-AAG
64 TTAAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGATTTTTTTTTCAACTACTTCAAAATAAAA
* *
11826186 GTTTTAATTTTTAAGAAAAATAA
129 GCTTTAATCTTTAAGAAAAAT-A
* * *
11826209 TGATTTTTTCT-AAAGA-AAACTTT-GATTTTGCAAAAAAAAAAA
1 TGATTTTTTTTAAAAGAGAAAGTTTAGATTTTG-AAAAATAAAAA
11826251 AATTGACCAC
Statistics
Matches: 450, Mismatches: 29, Indels: 38
0.87 0.06 0.07
Matches are distributed among these distances:
145 6 0.01
146 16 0.04
147 2 0.00
148 110 0.24
149 68 0.15
150 18 0.04
151 46 0.10
152 90 0.20
153 14 0.03
154 32 0.07
155 40 0.09
156 8 0.02
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (150 bp):
TGATTTTTTTTAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTTTTAGTCATTTT
AAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGATTTTTTTTTCAACTACTTCAAAATAAAAGC
TTTAATCTTTAAGAAAAATA
Found at i:11826254 original size:300 final size:299
Alignment explanation
Indices: 11825646--11826250 Score: 877
Period size: 300 Copynumber: 2.0 Consensus size: 299
11825636 TTTAACAAAT
* * *
11825646 AAAAATCTTTTTTTGTTTTAGTTATTTTAAAGGAAAGTTTAAATTTTTAAAACAAAATTTTGATT
1 AAAAAT-TTTTTTTGTCTTAGTCATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGATT
* * *
11825711 TTTTTCAACTATTTCAAAGTAAAAGCTTTAATCTTTAAAAAAATAGTATTTTTTTCTAAAAAAAG
65 TTTTTCAACTACTTCAAAATAAAAACTTTAATCTTTAAAAAAATAGTATTTTTTTCT--AAAAAG
*
11825776 GAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTTTTAGTCATTTTAAAGGAAAGTTTAAA
128 GAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTTTAAGTCATTTTAAAGGAAAGTTTAAA
*
11825841 ATTTTAAAACAAAGTTTTGATTTTTTTTTTCAACTACTTCAAAATAAAAGCTTTAATCTTTAAGA
193 ATTTTAAAACAAAGTTTTGATATTTTTTTTCAACTACTTCAAAATAAAAGCTTTAATCTTTAAGA
* * *
11825906 AAAATAGTTTTTTTTAAAGAGAAAGTTTAGATTTTGAAAAAT
258 AAAATAGTTTTTTCTAAAGAGAAACTTTAGATTTTGAAAAAA
11825948 AAAAATTTATTTTT-TCTTAGTCATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGATT
1 AAAAATTT-TTTTTGTCTTAGTCATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGA--
* *
11826012 TTTTTTTCAACTACTTCAAAATAAAAACTTTAATCTTTAAGAAAAGTAGTGTTTTTTT-T-AAAA
63 TTTTTTTCAACTACTTCAAAATAAAAACTTTAATCTTTAA-AAAAATAGTATTTTTTTCTAAAAA
*
11826075 GGAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTTAAGTCATTTTAAAGGAAAGTTTAA
127 GGAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTTTAAGTCATTTTAAAGGAAAGTTTAA
* * * * *
11826140 AATTTTAAAACAAAGTTTT-A-ATTTTTTTT-AACTATTTCGAAAT-AAGGTTTTAATTTTTAAG
192 AATTTTAAAACAAAGTTTTGATATTTTTTTTCAACTACTTCAAAATAAAAGCTTTAATCTTTAAG
11826201 AAAAATAATGATTTTTTCTAAAGA-AAACTTT-GATTTTGCAAAAAA
257 AAAAAT-A-G-TTTTTTCTAAAGAGAAACTTTAGATTTTG-AAAAAA
11826246 AAAAA
1 AAAAA
11826251 AATTGACCAC
Statistics
Matches: 276, Mismatches: 19, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
296 21 0.08
297 20 0.07
298 25 0.09
299 13 0.05
300 86 0.31
301 47 0.17
302 11 0.04
303 38 0.14
304 15 0.05
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (299 bp):
AAAAATTTTTTTTGTCTTAGTCATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGATTT
TTTTCAACTACTTCAAAATAAAAACTTTAATCTTTAAAAAAATAGTATTTTTTTCTAAAAAGGAG
AAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTTTAAGTCATTTTAAAGGAAAGTTTAAAATT
TTAAAACAAAGTTTTGATATTTTTTTTCAACTACTTCAAAATAAAAGCTTTAATCTTTAAGAAAA
ATAGTTTTTTCTAAAGAGAAACTTTAGATTTTGAAAAAA
Found at i:11826684 original size:13 final size:13
Alignment explanation
Indices: 11826666--11826704 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
11826656 TATACTAGTT
11826666 AGTTTTAGTTTTA
1 AGTTTTAGTTTTA
*
11826679 AGTTTTAAGTTTTT
1 AGTTTT-AGTTTTA
*
11826693 AGCTTTAGTTTT
1 AGTTTTAGTTTT
11826705 CACTTCCCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.21, C:0.03, G:0.15, T:0.62
Consensus pattern (13 bp):
AGTTTTAGTTTTA
Found at i:11828661 original size:35 final size:35
Alignment explanation
Indices: 11828604--11828781 Score: 110
Period size: 35 Copynumber: 4.9 Consensus size: 35
11828594 GATTTTACTA
* *
11828604 ACAATTAATAATTTGATAATTTTACTAACAATTAAT
1 ACAATTAACAA-TTAATAATTTTACTAACAATTAAT
11828640 ACAATTAACAATTAATAATTTTACTAACAA--AAT
1 ACAATTAACAATTAATAATTTTACTAACAATTAAT
* * ** * ** *
11828673 GTCAGATTTTACAAAATGTTTTGACTGGTAGTAACAATTAAT
1 -ACA-A--TTA-ACAAT-TAAT-AATTTTACTAACAATTAAT
* * * *
11828715 A-ATTTGATATAATTTGATAATTTTACTAACAATTAGT
1 ACAATT-A-ACAA-TTAATAATTTTACTAACAATTAAT
11828752 ACAATTAACAATTAATAATTTTACTAACAA
1 ACAATTAACAATTAATAATTTTACTAACAA
11828782 AATGTTAGAT
Statistics
Matches: 106, Mismatches: 24, Indels: 25
0.68 0.15 0.16
Matches are distributed among these distances:
33 3 0.03
34 2 0.02
35 37 0.35
36 13 0.12
37 21 0.20
38 13 0.12
39 3 0.03
40 11 0.10
42 3 0.03
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.39
Consensus pattern (35 bp):
ACAATTAACAATTAATAATTTTACTAACAATTAAT
Found at i:11828667 original size:19 final size:19
Alignment explanation
Indices: 11828619--11828669 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
11828609 TAATAATTTG
11828619 ATAATTTTACTAACAATTA
1 ATAATTTTACTAACAATTA
*
11828638 ATACA----ATTAACAATTA
1 ATA-ATTTTACTAACAATTA
11828654 ATAATTTTACTAACAA
1 ATAATTTTACTAACAA
11828670 AATGTCAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
15 1 0.04
16 13 0.52
19 10 0.40
20 1 0.04
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAATTTTACTAACAATTA
Found at i:11828716 original size:59 final size:58
Alignment explanation
Indices: 11828645--11828831 Score: 192
Period size: 59 Copynumber: 3.3 Consensus size: 58
11828635 TTAATACAAT
11828645 TAACAATTAATAATTTTACTAACAAAATGTCAGATTTTACAAAATGTTTTGACTGGTAG
1 TAACAATTAATAATTTTACTAACAAAATGT-AGATTTTACAAAATGTTTTGACTGGTAG
* * ** ** * *
11828704 TAACAATTAATAATTTGA-T-ATAATTTGATA-ATTTTACTAACAAT-TAGT-AC---AAT
1 TAACAATTAATAATTTTACTAACAAAATG-TAGATTTTAC-AA-AATGTTTTGACTGGTAG
*
11828757 TAACAATTAATAATTTTACTAACAAAATGTTAGATTTTACAAAATGTTTTGAGTGGTAG
1 TAACAATTAATAATTTTACTAACAAAATG-TAGATTTTACAAAATGTTTTGACTGGTAG
11828816 TAACAATTAATAATTT
1 TAACAATTAATAATTT
11828832 GATAATTTTA
Statistics
Matches: 99, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
53 18 0.18
54 4 0.04
55 11 0.11
56 17 0.17
57 10 0.10
58 5 0.05
59 34 0.34
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.40
Consensus pattern (58 bp):
TAACAATTAATAATTTTACTAACAAAATGTAGATTTTACAAAATGTTTTGACTGGTAG
Found at i:11828757 original size:112 final size:110
Alignment explanation
Indices: 11828608--11828932 Score: 515
Period size: 112 Copynumber: 3.0 Consensus size: 110
11828598 TTACTAACAA
11828608 TTAATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAAT
1 TTAATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAAT
*
11828673 GTCAGATTTTACAAAATGTTTTGACTGGTAGTAACAATTAATAAT
66 GTTAGATTTTACAAAATGTTTTGACTGGTAGTAACAATTAATAAT
*
11828718 TTGATATAATTTGATAATTTTACTAACAATTAGTACAATTAACAATTAATAATTTTACTAACAAA
1 TT-A-ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAA
*
11828783 ATGTTAGATTTTACAAAATGTTTTGAGTGGTAGTAAC-------AA-
64 ATGTTAGATTTTACAAAATGTTTTGACTGGTAGTAACAATTAATAAT
* **
11828822 TTAATAATTTGATAATTTTACTAACAACTAATACAATTAACAAGCAATAATTTTACTAACAAAAT
1 TTAATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAAT
11828887 GTTAGATTTTACAAAATGTTTTGACTGGT-GTAACAATTAATAAT
66 GTTAGATTTTACAAAATGTTTTGACTGGTAGTAACAATTAATAAT
11828931 TT
1 TT
11828933 TACTATCAAA
Statistics
Matches: 197, Mismatches: 8, Indels: 21
0.87 0.04 0.09
Matches are distributed among these distances:
101 5 0.03
102 86 0.44
103 1 0.01
104 2 0.01
105 2 0.01
108 2 0.01
109 2 0.01
110 2 0.01
111 1 0.01
112 94 0.48
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (110 bp):
TTAATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAAT
GTTAGATTTTACAAAATGTTTTGACTGGTAGTAACAATTAATAAT
Found at i:11828929 original size:58 final size:58
Alignment explanation
Indices: 11828867--11829085 Score: 263
Period size: 58 Copynumber: 3.8 Consensus size: 58
11828857 ATTAACAAGC
11828867 AATAATTTTACTAACAAAATGTTAGATTTTACAAAATGTTTTGACTGGTGTAACAATT
1 AATAATTTTACTAACAAAATGTTAGATTTTACAAAATGTTTTGACTGGTGTAACAATT
* *
11828925 AATAATTTTACTATCAAAATGTTAGATTTTACAAAATATTTTGACTGGTAGTAACAATT
1 AATAATTTTACTAACAAAATGTTAGATTTTACAAAATGTTTTGACTGGT-GTAACAATT
* * ** * ** **
11828984 AATAATTTGA-T-ATAATTTGATA-ATTTTACTAACAAT-TAAT-AC-AAT-TAACAATT
1 AATAATTTTACTAACAAAATGTTAGATTTTAC-AA-AATGTTTTGACTGGTGTAACAATT
11829037 AATAATTTTACTAACAAAATGTTAGATTTTACAAAATGTTTTGACTGGT
1 AATAATTTTACTAACAAAATGTTAGATTTTACAAAATGTTTTGACTGGT
11829086 ACAAAAAAAT
Statistics
Matches: 131, Mismatches: 21, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
53 17 0.13
54 4 0.03
55 12 0.09
56 18 0.14
57 11 0.08
58 51 0.39
59 18 0.14
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.41
Consensus pattern (58 bp):
AATAATTTTACTAACAAAATGTTAGATTTTACAAAATGTTTTGACTGGTGTAACAATT
Found at i:11828935 original size:160 final size:164
Alignment explanation
Indices: 11828757--11829085 Score: 522
Period size: 170 Copynumber: 2.0 Consensus size: 164
11828747 TTAGTACAAT
* *
11828757 TAACAATTAATAATTTTACTAACAAAATGTTAGATTTTACAAAATGTTTTGAGTGGTAGTAAC-A
1 TAACAATTAATAATTTTACTAACAAAATGTTAGATTTTACAAAATATTTTGACTGGTAGTAACAA
11828821 A-TT-A-ATAATTTGATAATTTTACTAACAACTAATACAATTAACAAGCAATAATTTTACTAACA
66 ATTTGATATAATTTGATAATTTTACTAACAACTAATACAATTAACAAGCAATAATTTTACTAACA
11828883 AAATGTTAGATTTTACAAAATGTTTTGACTGGTG
131 AAATGTTAGATTTTACAAAATGTTTTGACTGGTG
*
11828917 TAACAATTAATAATTTTACTATCAAAATGTTAGATTTTACAAAATATTTTGACTGGTAGTAACAA
1 TAACAATTAATAATTTTACTAACAAAATGTTAGATTTTACAAAATATTTTGACTGGTAGTAAC--
* **
11828982 TTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTA
64 ---A-AATTTGATATAATTTGATAATTTTACTAACAACTAATACAATTAACAAGCAATAATTTTA
11829047 CTAACAAAATGTTAGATTTTACAAAATGTTTTGACTGGT
125 CTAACAAAATGTTAGATTTTACAAAATGTTTTGACTGGT
11829086 ACAAAAAAAT
Statistics
Matches: 153, Mismatches: 6, Indels: 10
0.91 0.04 0.06
Matches are distributed among these distances:
160 60 0.39
167 2 0.01
168 2 0.01
169 1 0.01
170 88 0.58
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (164 bp):
TAACAATTAATAATTTTACTAACAAAATGTTAGATTTTACAAAATATTTTGACTGGTAGTAACAA
ATTTGATATAATTTGATAATTTTACTAACAACTAATACAATTAACAAGCAATAATTTTACTAACA
AAATGTTAGATTTTACAAAATGTTTTGACTGGTG
Found at i:11829132 original size:22 final size:22
Alignment explanation
Indices: 11829122--11829181 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
11829112 TTAATAACAA
**
11829122 TTAATTTTAATAAAA-ATTGTTT
1 TTAATTTTAATAAAATA-TAATT
11829144 TTAATTTTAATAAAATATAATT
1 TTAATTTTAATAAAATATAATT
11829166 TTAATTTTAATCAAAA
1 TTAATTTTAAT-AAAA
11829182 AACGGGCCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 29 0.85
23 5 0.15
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTAATTTTAATAAAATATAATT
Found at i:11829148 original size:16 final size:16
Alignment explanation
Indices: 11829107--11829139 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11829097 TAATTTGATA
*
11829107 TAATTTTAATAACAAT
1 TAATTTTAATAAAAAT
11829123 TAATTTTAATAAAAAT
1 TAATTTTAATAAAAAT
11829139 T
1 T
11829140 GTTTTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTTTAATAAAAAT
Found at i:11831082 original size:17 final size:17
Alignment explanation
Indices: 11831047--11831079 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11831037 TCAAGATAAG
*
11831047 TATTAAATTTAATTTAA
1 TATTAAATTTAATTAAA
11831064 TATTAAATTT-ATTAAA
1 TATTAAATTTAATTAAA
11831080 ATAATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAAATTTAATTAAA
Found at i:11831391 original size:19 final size:20
Alignment explanation
Indices: 11831367--11831409 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
11831357 TTCGACCAGT
11831367 TTTTGG-GTCTC-AGCCTCAA
1 TTTTGGAGTCTCGAGCC-CAA
*
11831386 TTTTGGATTCTCGAGCCCAA
1 TTTTGGAGTCTCGAGCCCAA
11831406 TTTT
1 TTTT
11831410 CAAGTTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (20 bp):
TTTTGGAGTCTCGAGCCCAA
Found at i:11831504 original size:19 final size:19
Alignment explanation
Indices: 11831472--11831510 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
11831462 AAACATCGTG
*
11831472 TTAATTTTAATTTATTTGA
1 TTAATTTTAATTTACTTGA
11831491 TTAA-TTTAATTTTACTTGA
1 TTAATTTTAA-TTTACTTGA
11831510 T
1 T
11831511 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
TTAATTTTAATTTACTTGA
Found at i:11832283 original size:5 final size:5
Alignment explanation
Indices: 11832265--11832308 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
11832255 AATAAATAAG
*
11832265 TATTA TATTA -ATTA TATTA TTATAA TATTA TATTA TATATA TAT
1 TATTA TATTA TATTA TATTA -TATTA TATTA TATTA TAT-TA TAT
11832309 ATAAAAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
4 4 0.12
5 21 0.62
6 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:11833318 original size:47 final size:46
Alignment explanation
Indices: 11833247--11833371 Score: 164
Period size: 47 Copynumber: 2.7 Consensus size: 46
11833237 GAACTCTAGC
*
11833247 GCGCTCTCTGATATTTAGCACGTCAGTGCTCTCTATTTAGCAGATCT
1 GCGCTCTCTGATA-TTAGCACGTCAGTGCTCTCTATTTAGCACATCT
* *
11833294 GTGCTCTCTGATTATTAGCACGTCAGTGCTCTCTGTTTAGCACATCT
1 GCGCTCTCTGA-TATTAGCACGTCAGTGCTCTCTATTTAGCACATCT
* * *
11833341 GCGCTCTTTG-CA-TAGCACTTCAGTGCTCTCT
1 GCGCTCTCTGATATTAGCACGTCAGTGCTCTCT
11833372 GTTCATTAGT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
44 18 0.26
45 1 0.01
47 49 0.70
48 2 0.03
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (46 bp):
GCGCTCTCTGATATTAGCACGTCAGTGCTCTCTATTTAGCACATCT
Found at i:11833322 original size:25 final size:24
Alignment explanation
Indices: 11833249--11833372 Score: 109
Period size: 22 Copynumber: 5.3 Consensus size: 24
11833239 ACTCTAGCGC
11833249 GCTCTCTGATATTTAGCACGTCAGT
1 GCTCTCTGATA-TTAGCACGTCAGT
*
11833274 GCTCTCT-AT-TTAGCA-GATCTGT
1 GCTCTCTGATATTAGCACG-TCAGT
11833296 GCTCTCTGATTATTAGCACGTCAGT
1 GCTCTCTGA-TATTAGCACGTCAGT
* * *
11833321 GCTCTCTG-T-TTAGCACATCTGC
1 GCTCTCTGATATTAGCACGTCAGT
* * *
11833343 GCTCTTTG-CA-TAGCACTTCAGT
1 GCTCTCTGATATTAGCACGTCAGT
11833365 GCTCTCTG
1 GCTCTCTG
11833373 TTCATTAGTG
Statistics
Matches: 82, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
21 1 0.01
22 50 0.61
23 2 0.02
24 3 0.04
25 25 0.30
26 1 0.01
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (24 bp):
GCTCTCTGATATTAGCACGTCAGT
Found at i:11835454 original size:19 final size:20
Alignment explanation
Indices: 11835414--11835456 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
11835404 ATTACAAAGT
*
11835414 AATTCAAAATAATTTTTAAA
1 AATTCAAAATAATTTATAAA
*
11835434 AATTCAAAAT-CTTTATAAA
1 AATTCAAAATAATTTATAAA
11835453 AATT
1 AATT
11835457 TTAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTCAAAATAATTTATAAA
Found at i:11836414 original size:22 final size:20
Alignment explanation
Indices: 11836388--11836428 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
11836378 TTAAAATCTT
*
11836388 ATTTAAGTAATTATTATTTTAA
1 ATTTAAATAA-TA-TATTTTAA
11836410 ATTTAAATAATATATTTTA
1 ATTTAAATAATATATTTTA
11836429 GGGATTCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTTAAATAATATATTTTAA
Found at i:11838435 original size:50 final size:50
Alignment explanation
Indices: 11838368--11838462 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 50
11838358 ACGGTATTAC
* *
11838368 AGGAGGTATGGATGGAGAAGACCTTATCCGCCTTGTGGAAAAGGTATTGT
1 AGGAGGTATGGATGGAGAAGACCTCATCCGCCTTGTGAAAAAGGTATTGT
*
11838418 AGGAGGTATTGATGGAGAAGACCTCATCCGCCTTGTGAAAAAGGT
1 AGGAGGTATGGATGGAGAAGACCTCATCCGCCTTGTGAAAAAGGT
11838463 TAGAAACTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (50 bp):
AGGAGGTATGGATGGAGAAGACCTCATCCGCCTTGTGAAAAAGGTATTGT
Found at i:11845770 original size:21 final size:21
Alignment explanation
Indices: 11845736--11845775 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11845726 TGATACTAGT
**
11845736 TACTATAGTGGTAAAATTACA
1 TACTATAGCAGTAAAATTACA
*
11845757 TACTATAGCAGTAAGATTA
1 TACTATAGCAGTAAAATTA
11845776 AAATCCGTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (21 bp):
TACTATAGCAGTAAAATTACA
Found at i:11852176 original size:11 final size:11
Alignment explanation
Indices: 11852162--11852212 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
11852152 CTCACAATAT
11852162 TCTCTCAAAAA
1 TCTCTCAAAAA
11852173 TCTCTC-AAAA
1 TCTCTCAAAAA
*
11852183 T-TCTCAAACCA
1 TCTCTCAAA-AA
*
11852194 -CTCTCAAAAT
1 TCTCTCAAAAA
11852204 TCTCTCAAA
1 TCTCTCAAA
11852213 TTCTCTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
9 4 0.12
10 7 0.21
11 22 0.67
ACGTcount: A:0.39, C:0.31, G:0.00, T:0.29
Consensus pattern (11 bp):
TCTCTCAAAAA
Found at i:11852209 original size:22 final size:22
Alignment explanation
Indices: 11852151--11852212 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 22
11852141 CTTACTCATT
* *
11852151 TCTCACAATATTCTCTCAAAAA
1 TCTCTCAAAATTCTCTCAAAAA
*
11852173 TCTCTCAAAA-T-TCTCAAACCA
1 TCTCTCAAAATTCTCTCAAA-AA
11852194 -CTCTCAAAATTCTCTCAAA
1 TCTCTCAAAATTCTCTCAAA
11852213 TTCTCTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 16 0.47
21 3 0.09
22 15 0.44
ACGTcount: A:0.39, C:0.31, G:0.00, T:0.31
Consensus pattern (22 bp):
TCTCTCAAAATTCTCTCAAAAA
Found at i:11856108 original size:12 final size:15
Alignment explanation
Indices: 11856078--11856111 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
11856068 ATGGTTGCAT
11856078 CACCGATGCCCACAC
1 CACCGATGCCCACAC
11856093 CACCGATGCCCACAC
1 CACCGATGCCCACAC
11856108 CACC
1 CACC
11856112 TACCAGTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.56, G:0.12, T:0.06
Consensus pattern (15 bp):
CACCGATGCCCACAC
Found at i:11858348 original size:30 final size:30
Alignment explanation
Indices: 11858309--11858376 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
11858299 TTTTATAAAT
* * *
11858309 AATTAATATTT-ATTGCTTAAAAATATTTAC
1 AATTTATATTTCATTGATT-AAAATATTAAC
*
11858339 AATTTATATTTCATTTATTAAAATATTAAC
1 AATTTATATTTCATTGATTAAAATATTAAC
*
11858369 AAGTTATA
1 AATTTATA
11858377 ATAAATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (30 bp):
AATTTATATTTCATTGATTAAAATATTAAC
Found at i:11858576 original size:26 final size:26
Alignment explanation
Indices: 11858537--11858600 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
11858527 TTTAAACCAA
*
11858537 ACTTTTCAAAAGTACTTCTCAAAATC
1 ACTTTTCAAAAGTACTTCTCAAAAGC
* * * *
11858563 ACTTTTCTACAGTACTTTTTAAAAGC
1 ACTTTTCAAAAGTACTTCTCAAAAGC
11858589 ACTTTTCAAAAG
1 ACTTTTCAAAAG
11858601 CAATGAAGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (26 bp):
ACTTTTCAAAAGTACTTCTCAAAAGC
Found at i:11858601 original size:13 final size:13
Alignment explanation
Indices: 11858537--11858602 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
11858527 TTTAAACCAA
*
11858537 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
* *
11858550 ACTTCTCAAAATC
1 ACTTTTCAAAAGC
* * *
11858563 ACTTTTCTACAGT
1 ACTTTTCAAAAGC
*
11858576 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
11858589 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
11858602 A
1 A
11858603 ATGAAGAATT
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:11859981 original size:24 final size:24
Alignment explanation
Indices: 11859945--11859993 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
11859935 AGTATGTAGC
*
11859945 ATCATTCACAATAGTGGAATTTAT
1 ATCATTCAAAATAGTGGAATTTAT
11859969 ATCATTCAAAATAGTGGAATTTAT
1 ATCATTCAAAATAGTGGAATTTAT
11859993 A
1 A
11859994 GCCCAACCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (24 bp):
ATCATTCAAAATAGTGGAATTTAT
Found at i:11860664 original size:36 final size:36
Alignment explanation
Indices: 11860621--11860692 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
11860611 TTAATTGGTC
*
11860621 ATTGTGAATCCATTGAATATATAAATTAAATATATT
1 ATTGTGAATCCATTAAATATATAAATTAAATATATT
11860657 ATTGTGAATCCATTAAATATATAAATTAAATATATT
1 ATTGTGAATCCATTAAATATATAAATTAAATATATT
11860693 TTCTCATAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.42
Consensus pattern (36 bp):
ATTGTGAATCCATTAAATATATAAATTAAATATATT
Found at i:11866009 original size:24 final size:24
Alignment explanation
Indices: 11865982--11866054 Score: 137
Period size: 24 Copynumber: 3.0 Consensus size: 24
11865972 AAATAAACTC
11865982 AACTAATTTCATGGAAAAAAATGT
1 AACTAATTTCATGGAAAAAAATGT
11866006 AACTAATTTCATGGAAAAAAATGT
1 AACTAATTTCATGGAAAAAAATGT
*
11866030 AACTAATTTCAAGGAAAAAAATGT
1 AACTAATTTCATGGAAAAAAATGT
11866054 A
1 A
11866055 TCATTTTATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.27
Consensus pattern (24 bp):
AACTAATTTCATGGAAAAAAATGT
Found at i:11873937 original size:21 final size:23
Alignment explanation
Indices: 11873896--11873940 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
11873886 AATTTATATA
11873896 ATTTTTTAAAATATAACTTAATT
1 ATTTTTTAAAATATAACTTAATT
11873919 ATTTTATT-AAAT-TAA-TTAATT
1 ATTTT-TTAAAATATAACTTAATT
11873940 A
1 A
11873941 AAATTTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
23 9 0.43
24 2 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTTTTAAAATATAACTTAATT
Found at i:11878696 original size:5 final size:5
Alignment explanation
Indices: 11878683--11878720 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
11878673 TGCATTACAA
*
11878683 AAAAT AAAAG AAAAG AAAAG AAAAG AAAAG -AAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
11878721 AACAACATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:11891309 original size:9 final size:9
Alignment explanation
Indices: 11891280--11891322 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
11891270 CAGATTCAAT
*
11891280 GAAAAAAAG
1 GAAAAAAAA
*
11891289 GAAAAAAGA
1 GAAAAAAAA
11891298 GAAAAAAAA
1 GAAAAAAAA
11891307 GAACAAAAAA
1 GAA-AAAAAA
*
11891317 CAAAAA
1 GAAAAA
11891323 GAAATAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:11891998 original size:42 final size:42
Alignment explanation
Indices: 11891939--11892039 Score: 150
Period size: 42 Copynumber: 2.4 Consensus size: 42
11891929 CCCGAAAAGG
*
11891939 GCAGCTCAAATTTTGATCAG-GATAGGGCTGGAAGTGATCAGA
1 GCAGCTCAAATTTTGATCAGAG-TAGGGCTGGAAGTGATCAAA
11891981 GCAGCTCAAATTTTGATCAGAGTAGGGCTGGAAGTGATCAAA
1 GCAGCTCAAATTTTGATCAGAGTAGGGCTGGAAGTGATCAAA
** *
11892023 GTGGCTCAGATTTTGAT
1 GCAGCTCAAATTTTGAT
11892040 TGGAATGGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 53 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (42 bp):
GCAGCTCAAATTTTGATCAGAGTAGGGCTGGAAGTGATCAAA
Found at i:11892018 original size:21 final size:21
Alignment explanation
Indices: 11891952--11892020 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
11891942 GCTCAAATTT
11891952 TGATCAG-GATAGGGCTGGAAG
1 TGATCAGAG-TAGGGCTGGAAG
* ** *
11891973 TGATCAGAGCA--GCTCAAATTT
1 TGATCAGAGTAGGGCTGGAA--G
11891994 TGATCAGAGTAGGGCTGGAAG
1 TGATCAGAGTAGGGCTGGAAG
11892015 TGATCA
1 TGATCA
11892021 AAGTGGCTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
19 5 0.14
21 24 0.69
22 1 0.03
23 5 0.14
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.23
Consensus pattern (21 bp):
TGATCAGAGTAGGGCTGGAAG
Found at i:11893409 original size:50 final size:50
Alignment explanation
Indices: 11893349--11893773 Score: 248
Period size: 50 Copynumber: 8.5 Consensus size: 50
11893339 TTAAAAAGAA
*
11893349 TGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAGCAGAT
1 TGAAGCCACAACGGCAGATCTTACTTCCCTGACGGTGCAATGGAGCAGAT
* * * * * *
11893399 TGAAGTCACAACGGCAGATC-TAGTTTCCCCGACAGCGCAAT-TA-CAAGGAT
1 TGAAGCCACAACGGCAGATCTTA-CTTCCCTGACGGTGCAATGGAGC-A-GAT
* * * *
11893449 TGAAGCCACAGCGGCAGATTTTACTTTCCTGACGGTGCAGTGGAGCAGAT
1 TGAAGCCACAACGGCAGATCTTACTTCCCTGACGGTGCAATGGAGCAGAT
* ** *** * * * *
11893499 TGAAGTCACAACGGTGGATCTGGTTTCCCCGACAGCGCAAT-TA-CAAAGAT
1 TGAAGCCACAACGGCAGATCTTACTTCCCTGACGGTGCAATGGAGC--AGAT
* * * *
11893549 TGAAGCCACTATGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGAT
1 TGAAGCCACAACGGCAGATCTTACTTCCCTGACGGTGCAATGGAGCAGAT
* * * *** * * * ** ** *
11893599 TGAAGTCACAATGGTAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGAC
1 TGAAGCCACAACGGCAGATCTTACTTCCCTGACGGTGCAATGGAGCAGAT
* * *
11893649 TGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGTAGTGGAGCATGAT
1 TGAAGCCACAACGGCAGATCTTACTTCCCTGACGGTGCAATGGAGCA-GAT
** * * *** * * * ** **
11893700 TGAAATCATAACGGCGGATCTGGTTTCCTTGACAGCGCAATTAAAAAGAT
1 TGAAGCCACAACGGCAGATCTTACTTCCCTGACGGTGCAATGGAGCAGAT
*
11893750 TGAAGCCACAACGGCGGATCTTAC
1 TGAAGCCACAACGGCAGATCTTAC
11893774 CTCCTTAGCT
Statistics
Matches: 263, Mismatches: 101, Indels: 22
0.68 0.26 0.06
Matches are distributed among these distances:
48 2 0.01
49 5 0.02
50 217 0.83
51 37 0.14
52 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (50 bp):
TGAAGCCACAACGGCAGATCTTACTTCCCTGACGGTGCAATGGAGCAGAT
Found at i:11893473 original size:100 final size:100
Alignment explanation
Indices: 11893338--11893804 Score: 655
Period size: 100 Copynumber: 4.7 Consensus size: 100
11893328 TTTGGCATTG
* *
11893338 ATTAAAAAGAATGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAGCAGATTGAA
1 ATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAA
*
11893403 GTCACAACGGCAGATCTAGTTTCCCCGACAGCGCA
66 GTCACAACGGCAGATCTGGTTTCCCCGACAGCGCA
* * * * * *
11893438 ATTACAAGGATTGAAGCCACAGCGGCAGATTTTACTTTCCTGACGGTGCAGTGGAGCAGATTGAA
1 ATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAA
**
11893503 GTCACAACGGTGGATCTGGTTTCCCCGACAGCGCA
66 GTCACAACGGCAGATCTGGTTTCCCCGACAGCGCA
* * *
11893538 ATTACAAAGATTGAAGCCACTATGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAA
1 ATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAA
* *
11893603 GTCACAATGGTAGATCTGGTTTCCCCGACAGCGCA
66 GTCACAACGGCAGATCTGGTTTCCCCGACAGCGCA
* *
11893638 ATTAAAAAGACTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGTAGTGGAGCATGATTGA
1 ATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGCA-GATTGA
* * * **
11893703 AATCATAACGGCGGATCTGGTTTCCTTGACAGCGCA
65 AGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCA
* * * * * * *
11893739 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACCTCCTTAGCTGTGCAGTTGAACAGATTGAA
1 ATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAA
11893804 G
66 G
11893805 CTACGACGGC
Statistics
Matches: 324, Mismatches: 42, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
100 240 0.74
101 84 0.26
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (100 bp):
ATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAA
GTCACAACGGCAGATCTGGTTTCCCCGACAGCGCA
Found at i:11893779 original size:50 final size:50
Alignment explanation
Indices: 11893338--11893833 Score: 170
Period size: 50 Copynumber: 9.9 Consensus size: 50
11893328 TTTGGCATTG
* * * * * *
11893338 ATTAAAAAGAATGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCA
1 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTGACAGCGCA
** ** * * * **
11893388 ATGGAGCAGATTGAAGTCACAACGGCAGATC-TAGTTTCCCCGACAGCGCA
1 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTA-CTTCCTTGACAGCGCA
* * * * * * *
11893438 ATTACAAGGATTGAAGCCACAGCGGCAGATTTTACTTTCC-TGACGGTGCA
1 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTAC-TTCCTTGACAGCGCA
* ** ** * * *** **
11893488 GTGGAGCAGATTGAAGTCACAACGGTGGATCTGGTTTCCCCGACAGCGCA
1 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTGACAGCGCA
* * * * * * * *
11893538 ATTACAAAGATTGAAGCCACTATGGCAGATCTTACTTCCCTGGCGGTGCA
1 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTGACAGCGCA
* ** ** * * ** *** **
11893588 GTGGAGCAGATTGAAGTCACAATGGTAGATCTGGTTTCCCCGACAGCGCA
1 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTGACAGCGCA
* * * * * * *
11893638 ATTAAAAAGACTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGTA
1 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTGACAGCGCA
* * ** * ** * ***
11893688 GTGGAGCATGATTGAAATCATAACGGCGGATCTGGTTTCCTTGACAGCGCA
1 AT-TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTGACAGCGCA
* * *
11893739 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACCTCCTT-AGCTGTGCA
1 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTGA-CAGCGCA
* * * * * * **
11893789 GTTGAACAGATTGAAGCTACGACGGCGGATTTTGTTTCCTTGACA
1 ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTGACA
11893834 TTGTAATTGG
Statistics
Matches: 304, Mismatches: 135, Indels: 14
0.67 0.30 0.03
Matches are distributed among these distances:
49 7 0.02
50 258 0.85
51 39 0.13
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (50 bp):
ATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTGACAGCGCA
Found at i:11898223 original size:27 final size:27
Alignment explanation
Indices: 11898131--11898228 Score: 110
Period size: 27 Copynumber: 3.7 Consensus size: 27
11898121 TTTTATATCA
* * *
11898131 CCAC-AAGTCTTCTATTTCATAGATTA
1 CCACAAAGGCTTCCATTTCATAGATTT
* *
11898157 CCACAAAGGCTTTCTTTTCATAGATTGT
1 CCACAAAGGCTTCCATTTCATAGATT-T
* *
11898185 -CACAAAGACTTCCATTTCATGGATTT
1 CCACAAAGGCTTCCATTTCATAGATTT
11898211 CCACAAAGGCTTCCATTT
1 CCACAAAGGCTTCCATTT
11898229 TTTGGCGTGT
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
26 5 0.08
27 54 0.92
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (27 bp):
CCACAAAGGCTTCCATTTCATAGATTT
Found at i:11900594 original size:29 final size:29
Alignment explanation
Indices: 11900534--11900597 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
11900524 CCAAAAATAT
* *
11900534 AAAAA-ATAAAAAAATAATTAATTTTAAT
1 AAAAATATAAAAAAATAATTAATATTAAA
*
11900562 AAAAATATAAAAAAATTATTAA-ATTAGAA
1 AAAAATATAAAAAAATAATTAATATTA-AA
11900591 AAAAATA
1 AAAAATA
11900598 AATTATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (29 bp):
AAAAATATAAAAAAATAATTAATATTAAA
Found at i:11900678 original size:25 final size:26
Alignment explanation
Indices: 11900644--11900694 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
11900634 AAATGCATCA
11900644 AAAAAAAT-CCTTTAACCATTAATTT
1 AAAAAAATCCCTTTAACCATTAATTT
11900669 AAAAAAATCCCTTTAACCATTAATTT
1 AAAAAAATCCCTTTAACCATTAATTT
11900695 TAACCGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAAAAATCCCTTTAACCATTAATTT
Found at i:11900955 original size:28 final size:28
Alignment explanation
Indices: 11900878--11900965 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
11900868 TTCTTTACAT
*
11900878 TTTTATAATTTTCTTACGACTTTATAAAA
1 TTTTATAATTTT-TTACGAATTTATAAAA
* *
11900907 TTTTAT-ATTTTTT-CTATATTTCTAAATA
1 TTTTATAATTTTTTACGA-ATTTATAAA-A
11900935 TTTTATAATTTTTTAC-AATTTTTATAAAA
1 TTTTATAATTTTTTACGAA--TTTATAAAA
11900964 TT
1 TT
11900966 CTATTTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
26 2 0.04
27 9 0.18
28 13 0.27
29 17 0.35
30 8 0.16
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (28 bp):
TTTTATAATTTTTTACGAATTTATAAAA
Found at i:11900957 original size:19 final size:19
Alignment explanation
Indices: 11900840--11900961 Score: 76
Period size: 19 Copynumber: 6.5 Consensus size: 19
11900830 AATACGATAG
*
11900840 TTTTTATACTTTTTTACGAA
1 TTTTTATAATTTTTTAC-AA
11900860 -TTTTAT-ATTTCTTTAC-A
1 TTTTTATAATTT-TTTACAA
*
11900877 TTTTTATAATTTTCTTACGA
1 TTTTTATAATTTT-TTACAA
* ** * *
11900897 -CTTTATAAAATTTTATAT
1 TTTTTATAATTTTTTACAA
* *
11900915 TTTTTCT-ATATTTCTA-AA
1 TTTTTATAAT-TTTTTACAA
11900933 TATTTTATAATTTTTTACAA
1 T-TTTTATAATTTTTTACAA
11900953 TTTTTATAA
1 TTTTTATAA
11900962 AATTCTATTT
Statistics
Matches: 77, Mismatches: 15, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
17 1 0.01
18 16 0.21
19 54 0.70
20 6 0.08
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTATAATTTTTTACAA
Found at i:11900959 original size:57 final size:55
Alignment explanation
Indices: 11900876--11901003 Score: 150
Period size: 57 Copynumber: 2.3 Consensus size: 55
11900866 ATTTCTTTAC
* * * *
11900876 ATTTTTATAATTTTCTTACGACTTTATAAAATTTTATATTTTTTCTATA-TTTCTAA
1 ATTTTTATAATTTT-TTACAACTTTATAAAATTCTATATTTTTTATAAATTTTC-AA
* *
11900932 ATATTTTATAATTTTTTACAATTTTTATAAAATTCTATTTTTTTTATAAATTTTCAA
1 AT-TTTTATAATTTTTTACAA-CTTTATAAAATTCTATATTTTTTATAAATTTTCAA
*
11900989 ATTTTTATAGTTTTT
1 ATTTTTATAATTTTT
11901004 AATTAAAATT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
56 19 0.31
57 39 0.63
58 4 0.06
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (55 bp):
ATTTTTATAATTTTTTACAACTTTATAAAATTCTATATTTTTTATAAATTTTCAA
Found at i:11900968 original size:38 final size:37
Alignment explanation
Indices: 11900926--11900997 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 37
11900916 TTTTCTATAT
* *
11900926 TTCTAAATATTTTATAATTTTTTACAATTTTTATAAAA
1 TTCTAAATATTTTATAAATTTTCA-AATTTTTATAAAA
** *
11900964 TTCTATTTTTTTTATAAATTTTCAAATTTTTATA
1 TTCTAAATATTTTATAAATTTTCAAATTTTTATA
11900998 GTTTTTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 10 0.34
38 19 0.66
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (37 bp):
TTCTAAATATTTTATAAATTTTCAAATTTTTATAAAA
Found at i:11901013 original size:30 final size:30
Alignment explanation
Indices: 11900968--11901044 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
11900958 ATAAAATTCT
* *
11900968 ATTTTTTTTATAAATTTTCA-AATTTTTATA
1 ATTTTTATTA-AAATTTTAATAATTTTTATA
*
11900998 GTTTTTAATTAAAA-TTTAATAATTTTTATA
1 ATTTTT-ATTAAAATTTTAATAATTTTTATA
11901028 ATTTTTATTAAAATTTT
1 ATTTTTATTAAAATTTT
11901045 TTTATCATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 11 0.28
30 26 0.65
31 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (30 bp):
ATTTTTATTAAAATTTTAATAATTTTTATA
Found at i:11901030 original size:9 final size:9
Alignment explanation
Indices: 11900907--11901035 Score: 64
Period size: 9 Copynumber: 13.7 Consensus size: 9
11900897 CTTTATAAAA
*
11900907 TTTTATATT
1 TTTTATAAT
*
11900916 TTTTCTATAT
1 TTTTATA-AT
*
11900926 TTCTA-AAT
1 TTTTATAAT
11900934 ATTTTATAATT
1 -TTTTATAA-T
*
11900945 TTTTACAAT
1 TTTTATAAT
*
11900954 TTTTATAAAA
1 TTTTAT-AAT
* **
11900964 TTCTATTTT
1 TTTTATAAT
11900973 TTTTATAAAT
1 TTTTAT-AAT
*
11900983 TTTCA-AAT
1 TTTTATAAT
*
11900991 TTTTATAGT
1 TTTTATAAT
*
11901000 TTTTAATTAAAA
1 TTTT-A-T-AAT
*
11901012 TTTAATAAT
1 TTTTATAAT
11901021 TTTTATAAT
1 TTTTATAAT
11901030 TTTTAT
1 TTTTAT
11901036 TAAAATTTTT
Statistics
Matches: 87, Mismatches: 23, Indels: 20
0.67 0.18 0.15
Matches are distributed among these distances:
8 9 0.10
9 44 0.51
10 27 0.31
11 3 0.03
12 4 0.05
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:11904700 original size:30 final size:28
Alignment explanation
Indices: 11904644--11904701 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
11904634 TTTGGGAAAT
*
11904644 GGAAGAGAAAAGTTTTGGGAGGAAAGTA
1 GGAAGAGAAAAGTTTTGGGAGAAAAGTA
11904672 GGAAGGAGTAAAAGTTTTGAGG-GAAAAGTA
1 GGAA-GAG-AAAAGTTTTG-GGAGAAAAGTA
11904702 AAAAAGTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.15
29 3 0.12
30 17 0.65
31 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.38, T:0.19
Consensus pattern (28 bp):
GGAAGAGAAAAGTTTTGGGAGAAAAGTA
Found at i:11905116 original size:3 final size:3
Alignment explanation
Indices: 11905108--11905172 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
11905098 AATGTTTTAA
* *
11905108 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11905156 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
11905173 ATGTATATTC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11905327 original size:16 final size:16
Alignment explanation
Indices: 11905306--11905388 Score: 68
Period size: 16 Copynumber: 5.2 Consensus size: 16
11905296 ATGAATATAG
11905306 TAATTATAATAAAATC
1 TAATTATAATAAAATC
11905322 TAATTA-ACATAAAAATC
1 TAATTATA-AT-AAAATC
*
11905339 --CTTATAATAAAATC
1 TAATTATAATAAAATC
11905353 TAATTA-ACATAAAAT-
1 TAATTATA-ATAAAATC
**
11905368 TCCTTATAATAAAAATC
1 TAATTATAAT-AAAATC
11905385 TAAT
1 TAAT
11905389 AAGCATAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
14 6 0.12
15 13 0.25
16 25 0.48
17 8 0.15
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATTATAATAAAATC
Found at i:11905344 original size:31 final size:31
Alignment explanation
Indices: 11905309--11905396 Score: 142
Period size: 31 Copynumber: 2.8 Consensus size: 31
11905299 AATATAGTAA
11905309 TTATAATAAAATCTAATTAACATAAAAATCC
1 TTATAATAAAATCTAATTAACATAAAAATCC
*
11905340 TTATAATAAAATCTAATTAACATAAAATTCC
1 TTATAATAAAATCTAATTAACATAAAAATCC
11905371 TTATAATAAAAATCTAA-TAAGCATAA
1 TTATAAT-AAAATCTAATTAA-CATAA
11905397 TTTTTAAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 40 0.74
32 14 0.26
ACGTcount: A:0.55, C:0.11, G:0.01, T:0.33
Consensus pattern (31 bp):
TTATAATAAAATCTAATTAACATAAAAATCC
Found at i:11905350 original size:15 final size:15
Alignment explanation
Indices: 11905330--11905384 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
11905320 TCTAATTAAC
11905330 ATAAAAATCCTTATA
1 ATAAAAATCCTTATA
*
11905345 AT-AAAAT-CTAATTAA
1 ATAAAAATCCTTA-T-A
*
11905360 CATAAAATTCCTTATA
1 -ATAAAAATCCTTATA
11905376 ATAAAAATC
1 ATAAAAATC
11905385 TAATAAGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
13 3 0.10
14 6 0.19
15 11 0.35
16 3 0.10
17 5 0.16
18 3 0.10
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAAAAATCCTTATA
Found at i:11913160 original size:9 final size:9
Alignment explanation
Indices: 11913146--11913291 Score: 150
Period size: 9 Copynumber: 16.0 Consensus size: 9
11913136 GGATCTTTTG
11913146 AGTTATGTA
1 AGTTATGTA
*
11913155 AGTTATTTA
1 AGTTATGTA
*
11913164 ATTTATGTA
1 AGTTATGTA
*
11913173 GGTTATGTA
1 AGTTATGTA
*
11913182 AGTTATTTA
1 AGTTATGTA
*
11913191 ATTTATGTA
1 AGTTATGTA
11913200 AGTTAT-TA
1 AGTTATGTA
*
11913208 AGTTATTTA
1 AGTTATGTA
*
11913217 ATTTATGTA
1 AGTTATGTA
*
11913226 GGTTATGTA
1 AGTTATGTA
11913235 AGTTATGTA
1 AGTTATGTA
*
11913244 AGTTATTTA
1 AGTTATGTA
*
11913253 ATTTATGTA
1 AGTTATGTA
*
11913262 AGTTATGCA
1 AGTTATGTA
*
11913271 AGCTTATATACA
1 AG-TTATGT--A
11913283 AGTTATGTA
1 AGTTATGTA
11913292 TTATAACATA
Statistics
Matches: 110, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
8 8 0.07
9 90 0.82
10 4 0.04
11 5 0.05
12 3 0.03
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (9 bp):
AGTTATGTA
Found at i:11913185 original size:27 final size:27
Alignment explanation
Indices: 11913146--11913267 Score: 183
Period size: 27 Copynumber: 4.6 Consensus size: 27
11913136 GGATCTTTTG
11913146 AGTTATGTAAGTTATTTAATTTATGTA
1 AGTTATGTAAGTTATTTAATTTATGTA
*
11913173 GGTTATGTAAGTTATTTAATTTATGTA
1 AGTTATGTAAGTTATTTAATTTATGTA
11913200 AGTTAT-TAAGTTATTTAATTTATGTA
1 AGTTATGTAAGTTATTTAATTTATGTA
* * * *
11913226 GGTTATGTAAGTTATGTAAGTTATTTA
1 AGTTATGTAAGTTATTTAATTTATGTA
*
11913253 ATTTATGTAAGTTAT
1 AGTTATGTAAGTTAT
11913268 GCAAGCTTAT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
26 25 0.29
27 61 0.71
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (27 bp):
AGTTATGTAAGTTATTTAATTTATGTA
Found at i:11913394 original size:116 final size:116
Alignment explanation
Indices: 11913260--11913500 Score: 439
Period size: 116 Copynumber: 2.1 Consensus size: 116
11913250 TTAATTTATG
11913260 TAAGTTATGCAAGCTTATATACAAGTTATGTATTATAACATAAAGTATTATGTAATTTAT-TATG
1 TAAGTTATGCAAGCTTATATACAAGTTATGTATTATAACATAAAGTATTATGTAATTTATGT-TG
11913324 CTATTATATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
65 CTATTATATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
* *
11913376 TAAGTTATGCAAGCTTATATCCAAGTTATGTATTATAACATAAAGTATTATGTAATTTATGTTGT
1 TAAGTTATGCAAGCTTATATACAAGTTATGTATTATAACATAAAGTATTATGTAATTTATGTTGC
*
11913441 TATTATATATAAGTTCTGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
66 TATTATATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
11913492 TAAGTTATG
1 TAAGTTATG
11913501 TATTATATAA
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
116 120 0.99
117 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (116 bp):
TAAGTTATGCAAGCTTATATACAAGTTATGTATTATAACATAAAGTATTATGTAATTTATGTTGC
TATTATATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
Found at i:11913401 original size:21 final size:21
Alignment explanation
Indices: 11913356--11913405 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
11913346 ATTATTATGT
*
11913356 AAGTTATGCAAGCTTAAATAT
1 AAGTTATGCAAGCTTAAATAC
* *
11913377 AAGTTATGCAAGCTTATATCC
1 AAGTTATGCAAGCTTAAATAC
11913398 AAGTTATG
1 AAGTTATG
11913406 TATTATAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (21 bp):
AAGTTATGCAAGCTTAAATAC
Found at i:11913647 original size:62 final size:62
Alignment explanation
Indices: 11913562--11913680 Score: 141
Period size: 62 Copynumber: 1.9 Consensus size: 62
11913552 AGAAAACTTA
* * * *** *
11913562 TAAACTTAATACACATATATTTTATTTCTCCCAAATTTAGAACACTTATTTAGAAAATGAAG
1 TAAACTTAATACACATAAATTTTAATACAAACAAATTTAGAAAACTTATTTAGAAAATGAAG
* *
11913624 TAAATTTAATACTA-ATAAATTTTAATACAAATAAATTTAGAAAACTTATTTAGAAAA
1 TAAACTTAATAC-ACATAAATTTTAATACAAACAAATTTAGAAAACTTATTTAGAAAA
11913681 CTTACAAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 46 0.98
63 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (62 bp):
TAAACTTAATACACATAAATTTTAATACAAACAAATTTAGAAAACTTATTTAGAAAATGAAG
Found at i:11913649 original size:16 final size:16
Alignment explanation
Indices: 11913624--11913661 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
11913614 GAAAATGAAG
*
11913624 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
11913639 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
11913655 TAAATTT
1 TAAATTT
11913662 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:11913676 original size:13 final size:13
Alignment explanation
Indices: 11913658--11913707 Score: 64
Period size: 13 Copynumber: 3.5 Consensus size: 13
11913648 ATACAAATAA
11913658 ATTTAGAAAACTT
1 ATTTAGAAAACTT
11913671 ATTTAGAAAACTT
1 ATTTAGAAAACTT
11913684 ACAAATTTAGAAAACTT
1 ----ATTTAGAAAACTT
11913701 ATTTAGA
1 ATTTAGA
11913708 TATTAAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 20 0.61
17 13 0.39
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:11913693 original size:17 final size:16
Alignment explanation
Indices: 11913656--11913701 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 16
11913646 TAATACAAAT
11913656 AAATTTAGAAAACTT-
1 AAATTTAGAAAACTTA
11913671 --ATTTAGAAAACTTA
1 AAATTTAGAAAACTTA
11913685 CAAATTTAGAAAACTTA
1 -AAATTTAGAAAACTTA
11913702 TTTAGATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 13 0.48
17 14 0.52
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (16 bp):
AAATTTAGAAAACTTA
Found at i:11915521 original size:23 final size:24
Alignment explanation
Indices: 11915495--11915547 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
11915485 AATAAGAAAG
11915495 CAAAATCAAAAT-TAAAAATACGA
1 CAAAATCAAAATCTAAAAATACGA
** *
11915518 CAAAA-CCCAATCTATAAATACGA
1 CAAAATCAAAATCTAAAAATACGA
11915541 -AAAATCA
1 CAAAATCA
11915548 GACATTCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.60, C:0.19, G:0.04, T:0.17
Consensus pattern (24 bp):
CAAAATCAAAATCTAAAAATACGA
Found at i:11917891 original size:114 final size:114
Alignment explanation
Indices: 11917688--11918242 Score: 785
Period size: 114 Copynumber: 4.9 Consensus size: 114
11917678 AATATTTTTT
* *
11917688 GCGGCGCTTT-TCCAAAAACGCCGCTAAATCACCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
1 GCGGCGCTTTCT-TAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* *
11917752 GGTTTTTTTGTGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTAAGCATTA
65 GGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTA
* * **
11917802 GCGGCGCTTTCTTATAAACGCCGCTAAAGCCTTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
* * **
11917867 GTTTTTTTGCGGCACTTTCCCAAAAACGCCGCTAAAGCTCTGGGCATTA
66 GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTA
* * *
11917916 GCGGCGCTTT-TCCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAATGGCGTCGTTAGGCTTA
1 GCGGCGCTTTCT-TAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* * * * *
11917980 GGTCTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAATG-CTTAGGGCATTA
65 GGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTA-AGCATTA
*
11918030 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
* *
11918095 GTTTTTTTGCGGCGCTTTCCCAAAAGCGCCGCTAAAGCCCTGAGCATTA
66 GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTA
* * * *
11918144 GCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTTAGAAAACGACGTTGTTGGGCTTA-
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
* * *
11918208 GATTTTTTACGGCGCTTTTCCAAAAACGCCGCTAA
66 GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAA
11918243 TGCTTATTTT
Statistics
Matches: 390, Mismatches: 46, Indels: 11
0.87 0.10 0.02
Matches are distributed among these distances:
113 33 0.08
114 353 0.91
115 4 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (114 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTA
Found at i:11918328 original size:12 final size:12
Alignment explanation
Indices: 11918311--11918336 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11918301 TTTTTTATCC
11918311 AAACGCCGCTAA
1 AAACGCCGCTAA
11918323 AAACGCCGCTAA
1 AAACGCCGCTAA
11918335 AA
1 AA
11918337 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:11921843 original size:21 final size:20
Alignment explanation
Indices: 11921817--11921857 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11921807 CTCTAAACCT
*
11921817 TAAACCTCAATCTCCAAGCCC
1 TAAACCT-AAACTCCAAGCCC
*
11921838 TAAACCTAAACTCTAAGCCC
1 TAAACCTAAACTCCAAGCCC
11921858 AGATCACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.37, C:0.39, G:0.05, T:0.20
Consensus pattern (20 bp):
TAAACCTAAACTCCAAGCCC
Found at i:11922413 original size:134 final size:130
Alignment explanation
Indices: 11922206--11922635 Score: 429
Period size: 133 Copynumber: 3.2 Consensus size: 130
11922196 AAACGTTTCT
* * * * *
11922206 GGCGTTTTTTAACATTTCGCAACTAAAG-CATAAAAAGGAAACAACAAAACGGTATCGTTTTGCT
1 GGCGTTTTTTAA-AATGCGCCACTAAAGAAAT-AAAATGAAACAACAAAACGGTA-CGTTTTGCT
* * *
11922270 CAAAATTTTTCCTCAAATTAGATTTCTTTACCGGCGTTTCTACAATAACACCACTATATCCCAAT
63 CAAATTTTTTCCTCAAATTAGATTTCTTTACCGGCGTTTCT-CAA-AACGCCGCTATAT-CCAAT
11922335 ATTTGC
125 ATTTGC
* * * *
11922341 GGCGTTTTTTACAATGCGCCACTAAGGAAATAAAATGAAGCAATAAAACGGTAGCGTTTTG-TCC
1 GGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTA-CGTTTTGCT-C
* * * * * *
11922405 AAATTTTTTCCTCAAATTAGATATCTTTACTGGCGTTTCCCTGAAAACGCCGCTA-ATGCATTCT
64 AAATTTTTTCCTCAAATTAGATTTCTTTACCGGCGTTT--CTCAAAACGCCGCTATATCCAATAT
*
11922469 TGTCC
127 T-TGC
*
11922474 GGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGTTACTGTTTTGCTCA
1 GGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTAC-GTTTTGCTCA
* * *
11922539 GATTTTTTCCTCAAATTCG-TTATCGTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAATT
65 AATTTTTTCCTCAAATTAGATT-TCTTTACCGGCGTTTCTC--AAAACGCCGCTATA-TCCAA-T
*
11922603 TTTTGC
125 ATTTGC
**
11922609 GGCGTTTTTGGGAAA-GCGCCACTAAAG
1 GGCGTTTTT-TAAAATGCGCCACTAAAG
11922636 TCATAAAGTG
Statistics
Matches: 244, Mismatches: 37, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
131 2 0.01
132 7 0.03
133 103 0.42
134 83 0.34
135 41 0.17
136 8 0.03
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (130 bp):
GGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTACGTTTTGCTCAA
ATTTTTTCCTCAAATTAGATTTCTTTACCGGCGTTTCTCAAAACGCCGCTATATCCAATATTTGC
Found at i:11932400 original size:26 final size:24
Alignment explanation
Indices: 11932371--11932419 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
11932361 ATAATGAAAT
11932371 ATTATTTATAGATAAATATATTTATA
1 ATTATTT-TAGATAAATA-ATTTATA
* *
11932397 ATTATTTTATATTAATAATTTAT
1 ATTATTTTAGATAAATAATTTAT
11932420 TATTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 8 0.38
26 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTATTTTAGATAAATAATTTATA
Found at i:11933306 original size:10 final size:8
Alignment explanation
Indices: 11933276--11933316 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
11933266 ATATTTATTA
*
11933276 TAATATAA
1 TAATATAT
11933284 TAA-ATAT
1 TAATATAT
11933291 TAATATAT
1 TAATATAT
11933299 TAATATAT
1 TAATATAT
11933307 TAATATAT
1 TAATATAT
11933315 TA
1 TA
11933317 TAACTTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 6 0.19
8 25 0.81
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
TAATATAT
Found at i:11947120 original size:51 final size:51
Alignment explanation
Indices: 11946942--11947279 Score: 391
Period size: 51 Copynumber: 6.7 Consensus size: 51
11946932 TCATTCGATA
* * * *
11946942 CACGTAGTAGCCTTCACATAGTACTACACACATGATCAAGT-TTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTTCGGTT
* * *
11946992 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTTCGGTT
* *
11947042 CACGTAGTAGCCTTTACATAGTACTACACACGTGACCAAATCTTTTCGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTTCGGTT
* * * *
11947093 CACATAGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATC-TTT-TCGGTT
* * * *
11947144 CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTTCGGTT
* * * * *
11947195 CACATTGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATC-TTT-TCGGTT
*
11947246 CACGTAGTAGCCTTTACATAGTACTACACACGTG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTG
11947280 TTCATCGATA
Statistics
Matches: 247, Mismatches: 34, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
49 5 0.02
50 92 0.37
51 146 0.59
52 2 0.01
53 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (51 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTTCGGTT
Found at i:11947171 original size:102 final size:102
Alignment explanation
Indices: 11946936--11947279 Score: 494
Period size: 102 Copynumber: 3.4 Consensus size: 102
11946926 CTTTTATCAT
* * * * * * *
11946936 TCGATACACGTAGTAGCCTTCACATAGTACTACACACATGATCAAGT-TTTACGGTTCACGTAGT
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTTCGGTACACATAGT
* * * ***
11947000 AGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* *
11947037 -CGGTTCACGTAGTAGCCTTTACATAGTACTACACACGTGACCAAATCTTTTCGGTACACATAGT
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTTCGGTACACATAGT
11947101 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * *
11947138 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGT
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTTCGGTACACATAGT
11947203 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
*
11947240 TCGATTCACGTAGTAGCCTTTACATAGTACTACACACGTG
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTG
11947280 TTCATCGATA
Statistics
Matches: 218, Mismatches: 23, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
100 40 0.18
101 45 0.21
102 133 0.61
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (102 bp):
TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTTCGGTACACATAGT
AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
Found at i:11948710 original size:15 final size:17
Alignment explanation
Indices: 11948684--11948716 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
11948674 TTTAAATTTT
11948684 AAATATATTTATT-TAA
1 AAATATATTTATTATAA
11948700 AAATATA-TTATTATAA
1 AAATATATTTATTATAA
11948716 A
1 A
11948717 TTAATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATATTTATTATAA
Found at i:11949133 original size:17 final size:17
Alignment explanation
Indices: 11949111--11949144 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11949101 TATTTTTATT
11949111 TTTTTAATTTTAAAATA
1 TTTTTAATTTTAAAATA
*
11949128 TTTTTATTTTTAAAATA
1 TTTTTAATTTTAAAATA
11949145 AATTTTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTAATTTTAAAATA
Found at i:11950775 original size:17 final size:17
Alignment explanation
Indices: 11950753--11950791 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
11950743 TTTAAAATGC
*
11950753 TTTATTTGTTTT-TTAAT
1 TTTATTT-TTTTATCAAT
11950770 TTTATTTTTTTATCAAT
1 TTTATTTTTTTATCAAT
11950787 TTTAT
1 TTTAT
11950792 CTACCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTATTTTTTTATCAAT
Found at i:11952379 original size:25 final size:29
Alignment explanation
Indices: 11952344--11952429 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 29
11952334 CATATTTACG
11952344 GAAAGTCAAAGATATGGGTATC-AA-A-T
1 GAAAGTCAAAGATATGGGTATCAAATATT
11952370 -AAAGTCAAAGATATGGGTATCAAATATT
1 GAAAGTCAAAGATATGGGTATCAAATATT
*
11952398 GGAAAGTCAAAGATATGGGTATCGAGATATT
1 -GAAAGTCAAAGATATGGGTATC-AAATATT
11952429 G
1 G
11952430 GCATAAGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
25 21 0.40
26 2 0.04
27 1 0.02
28 1 0.02
30 22 0.42
31 6 0.11
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (29 bp):
GAAAGTCAAAGATATGGGTATCAAATATT
Found at i:11952406 original size:30 final size:30
Alignment explanation
Indices: 11952343--11952430 Score: 123
Period size: 25 Copynumber: 3.1 Consensus size: 30
11952333 CCATATTTAC
11952343 GGAAAGTCAAAGATATGGGTATC-AA-A-T
1 GGAAAGTCAAAGATATGGGTATCAAATATT
11952370 --AAAGTCAAAGATATGGGTATCAAATATT
1 GGAAAGTCAAAGATATGGGTATCAAATATT
*
11952398 GGAAAGTCAAAGATATGGGTATCGAGATATT
1 GGAAAGTCAAAGATATGGGTATC-AAATATT
11952429 GG
1 GG
11952431 CATAAGAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
25 21 0.39
26 2 0.04
27 1 0.02
28 1 0.02
30 21 0.39
31 8 0.15
ACGTcount: A:0.42, C:0.07, G:0.26, T:0.25
Consensus pattern (30 bp):
GGAAAGTCAAAGATATGGGTATCAAATATT
Found at i:11957015 original size:25 final size:29
Alignment explanation
Indices: 11956980--11957065 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 29
11956970 CATATTTATG
11956980 GAAAGTCAAAGATATGGGTATC-AA-A-T
1 GAAAGTCAAAGATATGGGTATCAAATATT
11957006 -AAAGTCAAAGATATGGGTATCAAATATT
1 GAAAGTCAAAGATATGGGTATCAAATATT
*
11957034 GGAAAGTCAAAGATATGGGTATCGAGATATT
1 -GAAAGTCAAAGATATGGGTATC-AAATATT
11957065 G
1 G
11957066 GCATAAGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
25 21 0.40
26 2 0.04
27 1 0.02
28 1 0.02
30 22 0.42
31 6 0.11
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (29 bp):
GAAAGTCAAAGATATGGGTATCAAATATT
Found at i:11957042 original size:30 final size:30
Alignment explanation
Indices: 11956978--11957066 Score: 125
Period size: 25 Copynumber: 3.1 Consensus size: 30
11956968 TCCATATTTA
11956978 TGGAAAGTCAAAGATATGGGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
11957005 T--AAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
11957033 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
11957064 TGG
1 TGG
11957067 CATAAGAAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
25 21 0.38
26 2 0.04
27 2 0.04
28 1 0.02
30 21 0.38
31 8 0.15
ACGTcount: A:0.42, C:0.07, G:0.26, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Done.