Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015206.1 Kokia drynarioides strain JFW-HI SEQ_130250, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 388724
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 703 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:6192 original size:20 final size:20
Alignment explanation
Indices: 6141--6193 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
6131 AAAAACTCTT
6141 TAAAA-TTCAAAA-ATAAAA
1 TAAAATTTCAAAATATAAAA
*
6159 TAAAATATTAAAAATATAAACA
1 TAAAAT-TTCAAAATATAAA-A
6181 -AAAATTTCAAAAT
1 TAAAATTTCAAAAT
6194 TCAATATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 5 0.17
20 13 0.45
21 10 0.34
22 1 0.03
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAATTTCAAAATATAAAA
Found at i:8460 original size:29 final size:29
Alignment explanation
Indices: 8392--8449 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
8382 TTGTGTGATT
8392 ACATAGTAATATCTGTTTATATTTTCTTA
1 ACATAGTAATATCTGTTTATATTTTCTTA
8421 ACATAGTAATATCTGTTTATATTTTCTTA
1 ACATAGTAATATCTGTTTATATTTTCTTA
8450 CTTTTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (29 bp):
ACATAGTAATATCTGTTTATATTTTCTTA
Found at i:9409 original size:21 final size:21
Alignment explanation
Indices: 9362--9431 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
9352 TGTTAAATCA
9362 TACAAAATATA-TAAAAAAAT
1 TACAAAATATATTAAAAAAAT
*
9382 CTA-AAAATATATTTAAAAAAT
1 -TACAAAATATATTAAAAAAAT
*
9403 TACAAAA-AAATTGAAAAAAAT
1 TACAAAATATATT-AAAAAAAT
9424 TACAAAAT
1 TACAAAAT
9432 CTAATAGTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
20 14 0.33
21 28 0.67
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.26
Consensus pattern (21 bp):
TACAAAATATATTAAAAAAAT
Found at i:9410 original size:11 final size:11
Alignment explanation
Indices: 9396--9430 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
9386 AAATATATTT
9396 AAAAAATTACA
1 AAAAAATTACA
*
9407 AAAAAATT-GA
1 AAAAAATTACA
9417 AAAAAATTACA
1 AAAAAATTACA
9428 AAA
1 AAA
9431 TCTAATAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAAAATTACA
Found at i:15019 original size:32 final size:34
Alignment explanation
Indices: 14950--15026 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 34
14940 GTCTATACTA
14950 AAAAAATTAATCTTATTTGCTTCAGAATAAAAAAT
1 AAAAAATTAATCTTATTTGC-TCAGAATAAAAAAT
*
14985 AAAAAATGTAATCTTATTTGC-C-TAA-AAAAAAT
1 AAAAAAT-TAATCTTATTTGCTCAGAATAAAAAAT
15017 AAAAAATTAA
1 AAAAAATTAA
15027 ATTAAATTCG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
31 3 0.08
32 14 0.35
33 2 0.05
34 1 0.03
35 7 0.17
36 13 0.32
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (34 bp):
AAAAAATTAATCTTATTTGCTCAGAATAAAAAAT
Found at i:20092 original size:8 final size:8
Alignment explanation
Indices: 20079--20131 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 8
20069 AGGAAAAAAC
*
20079 AAAGAAAG
1 AAAGAAGG
20087 AAAGAAGG
1 AAAGAAGG
20095 AAAGAAGG
1 AAAGAAGG
20103 AAA-AAGG
1 AAAGAAGG
*
20110 AGAAGAAGA
1 A-AAGAAGG
20119 AGAAGAA-G
1 A-AAGAAGG
20127 AAAGA
1 AAAGA
20132 GAAAAAGGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
7 9 0.22
8 21 0.52
9 10 0.25
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (8 bp):
AAAGAAGG
Found at i:20241 original size:17 final size:18
Alignment explanation
Indices: 20209--20242 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20199 AATGTGATTG
*
20209 ATTTGTTATTATAAATTT
1 ATTTGTTATAATAAATTT
20227 ATTTGTT-TAATAAATT
1 ATTTGTTATAATAAATT
20243 AATTAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (18 bp):
ATTTGTTATAATAAATTT
Found at i:20297 original size:18 final size:18
Alignment explanation
Indices: 20274--20308 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20264 GGAAGAAATG
20274 TAAGTTTGATTAATTTTT
1 TAAGTTTGATTAATTTTT
*
20292 TAAGTTTGGTTAATTTT
1 TAAGTTTGATTAATTTT
20309 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (18 bp):
TAAGTTTGATTAATTTTT
Found at i:20506 original size:21 final size:20
Alignment explanation
Indices: 20480--20522 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
20470 TAATTTACTT
20480 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAG-TAG
*
20501 TAATTTTATTTTGTTAGTAG
1 TAATTTAATTTTGTTAGTAG
20521 TA
1 TA
20523 GTAAGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (20 bp):
TAATTTAATTTTGTTAGTAG
Found at i:20935 original size:30 final size:30
Alignment explanation
Indices: 20901--20995 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 30
20891 GTGTTTAATA
*
20901 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTAGT
** *** * *
20931 AAAT-AAT-GGTGCGTGGATACCATTTTGGT
1 AAATAAATATATATTTTG-TACCATTTTAGT
* *
20960 ATATAAATATATATTTTGTACCATTTTAGG
1 AAATAAATATATATTTTGTACCATTTTAGT
20990 AAATAA
1 AAATAA
20996 CTCATTTTGA
Statistics
Matches: 45, Mismatches: 17, Indels: 6
0.66 0.25 0.09
Matches are distributed among these distances:
28 3 0.07
29 17 0.38
30 22 0.49
31 3 0.07
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (30 bp):
AAATAAATATATATTTTGTACCATTTTAGT
Found at i:22239 original size:43 final size:43
Alignment explanation
Indices: 22156--22240 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
22146 ATTAACATGT
* * *
22156 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGATTGAATGTTAC
* *
22199 TAAATTATATTACTTTACTCTTATTAATAT-ATTGAAATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGATTG-AATGTTA
22241 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGATTGAATGTTAC
Found at i:22897 original size:45 final size:45
Alignment explanation
Indices: 22808--22899 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
22798 CCCTAGCTCA
*
22808 TCAAGCCAAAGATATCAGCCTCAGTTTGACAAGCCACTACAATAC
1 TCAAGCCAAAGATATCAGCCTCAGTTTGACAAGCCACCACAATAC
* * * * **
22853 TCAAGCCAAGGATATCAGGCTGAGTTTGACGAGCCACCGTAATAC
1 TCAAGCCAAAGATATCAGCCTCAGTTTGACAAGCCACCACAATAC
22898 TC
1 TC
22900 TACTCTTCCG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (45 bp):
TCAAGCCAAAGATATCAGCCTCAGTTTGACAAGCCACCACAATAC
Found at i:24927 original size:4 final size:4
Alignment explanation
Indices: 24918--24965 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
24908 TCTCTCCTTC
* * *
24918 TTCT TTCTT TTCT ATCT TTCT TTCT TTCT TTTT TTCT TACT TTCT TTC
1 TTCT TTC-T TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
24966 GTTCCCGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (4 bp):
TTCT
Found at i:25129 original size:13 final size:13
Alignment explanation
Indices: 25111--25135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25101 GTGTCAAAAC
25111 ACCCCTTAGTGTT
1 ACCCCTTAGTGTT
25124 ACCCCTTAGTGT
1 ACCCCTTAGTGT
25136 GTAACATCCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
ACCCCTTAGTGTT
Found at i:27001 original size:23 final size:23
Alignment explanation
Indices: 26975--27086 Score: 129
Period size: 23 Copynumber: 4.8 Consensus size: 23
26965 ACACTAGCGC
*
26975 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
26998 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
27021 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
*
27044 GCTCTCTG-TTGCCCAGCAC-TTATGT
1 GCTCTCTGATT----AGCACTTTGTGT
*
27069 GCTCTCTGATTAGTACTT
1 GCTCTCTGATTAGCACTT
27087 CGGTACTATC
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
22 6 0.08
23 51 0.66
25 13 0.17
26 7 0.09
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTTGTGT
Found at i:29254 original size:30 final size:32
Alignment explanation
Indices: 29202--29296 Score: 81
Period size: 31 Copynumber: 3.1 Consensus size: 32
29192 TATTTATTTC
*
29202 TTTAAATTTATATGATTAAATCA-AATTAAAAT
1 TTTAAATATATAT-ATTAAATCACAATTAAAAT
* *
29234 TTTAAATATATAT-TTGAATCACAGTTAAAAT
1 TTTAAATATATATATTAAATCACAATTAAAAT
* ** * *
29265 TTCACGTATATA-ATTACA-CAAAATTAAAAT
1 TTTAAATATATATATTAAATCACAATTAAAAT
29295 TT
1 TT
29297 ATATATACAA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
30 19 0.37
31 20 0.39
32 12 0.24
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.41
Consensus pattern (32 bp):
TTTAAATATATATATTAAATCACAATTAAAAT
Found at i:29303 original size:29 final size:29
Alignment explanation
Indices: 29271--29332 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
29261 AAATTTCACG
* *
29271 TATATAATTACACAAAATTAAAATTTATA
1 TATACAATAACACAAAATTAAAATTTATA
* ** *
29300 TATACAATAATATTAAATTAAACTTTATA
1 TATACAATAACACAAAATTAAAATTTATA
29329 TATA
1 TATA
29333 ATTTTAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (29 bp):
TATACAATAACACAAAATTAAAATTTATA
Found at i:31003 original size:5 final size:5
Alignment explanation
Indices: 30970--31001 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
30960 AAAGTTGTTT
30970 AAAGA AAAGA AAAGA AAAGA AAAGA AAA-A AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
31002 AAGAGTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:31408 original size:27 final size:28
Alignment explanation
Indices: 31378--31430 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
31368 ATTTTATAAT
* *
31378 ATCTAATAAA-TTCATGTACCAAATTGA
1 ATCTAAAAAAGTTCAGGTACCAAATTGA
*
31405 ATCTAAAAAAGTTTAGGTACCAAATT
1 ATCTAAAAAAGTTCAGGTACCAAATT
31431 AAGAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.32
Consensus pattern (28 bp):
ATCTAAAAAAGTTCAGGTACCAAATTGA
Found at i:46702 original size:101 final size:101
Alignment explanation
Indices: 46527--46731 Score: 392
Period size: 101 Copynumber: 2.0 Consensus size: 101
46517 ATTTAAAATG
46527 TTAAAAGGATAAAAATGGTGTAAACCGTGATAAAAAAGTCCAAGCGGTGGTGATATTATTAAATC
1 TTAAAAGGATAAAAATGGTGTAAACCGTGATAAAAAAGTCCAAGCGGTGGTGATATTATTAAATC
*
46592 CACTAACTTTTGGGTTATTTGCTCATTAAGTCTTAA
66 CACTAACTTTTGGGCTATTTGCTCATTAAGTCTTAA
46628 TTAAAAGGATAAAAATGGTGTAAACCGTGATAAAAAAGTCCAAGCGGTGGTGATATTATTAAATC
1 TTAAAAGGATAAAAATGGTGTAAACCGTGATAAAAAAGTCCAAGCGGTGGTGATATTATTAAATC
*
46693 CACTAACTTTTGGGCTATTTGCTCATTTAGTCTTAA
66 CACTAACTTTTGGGCTATTTGCTCATTAAGTCTTAA
46729 TTA
1 TTA
46732 GTTTAAGGTT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (101 bp):
TTAAAAGGATAAAAATGGTGTAAACCGTGATAAAAAAGTCCAAGCGGTGGTGATATTATTAAATC
CACTAACTTTTGGGCTATTTGCTCATTAAGTCTTAA
Found at i:47558 original size:16 final size:16
Alignment explanation
Indices: 47539--47571 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47529 CTAATTTTGG
47539 TGTTAAA-TGATTAAAA
1 TGTTAAAGTGA-TAAAA
47555 TGTTAAAGTGATAAAA
1 TGTTAAAGTGATAAAA
47571 T
1 T
47572 TATAAGGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (16 bp):
TGTTAAAGTGATAAAA
Found at i:49723 original size:23 final size:23
Alignment explanation
Indices: 49696--49846 Score: 146
Period size: 23 Copynumber: 6.5 Consensus size: 23
49686 ACACTAGCGC
*
49696 GCTCTCTGTTTAGCACTATGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
49719 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* * *
49744 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
49767 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
49790 GCTCTCTGTTGCCCAGCACT-TATGT
1 GCTCTCTGTT---TAGCACTGTGTGT
* *
49815 GCTCTCTG-TTAGTACTTTG-GT
1 GCTCTCTGTTTAGCACTGTGTGT
*
49836 ACTCTCTGTTT
1 GCTCTCTGTTT
49847 GTTCCGTATA
Statistics
Matches: 106, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
21 14 0.13
22 3 0.03
23 48 0.45
24 2 0.02
25 33 0.31
26 6 0.06
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:49772 original size:48 final size:46
Alignment explanation
Indices: 49696--49797 Score: 150
Period size: 48 Copynumber: 2.2 Consensus size: 46
49686 ACACTAGCGC
* *
49696 GCTCTCTGTTTAGCACTATGTGTGCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTATGTGTACTCTCTG-T-TTAGCACTGTGTGT
* *
49744 GCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTATGTGTACTCTCTGTTTAGCACTGTGTGT
49790 GCTCTCTG
1 GCTCTCTG
49798 TTGCCCAGCA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 22 0.44
47 1 0.02
48 27 0.54
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.44
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTATGTGTACTCTCTGTTTAGCACTGTGTGT
Found at i:49816 original size:71 final size:69
Alignment explanation
Indices: 49697--49846 Score: 221
Period size: 71 Copynumber: 2.1 Consensus size: 69
49687 CACTAGCGCG
** *
49697 CTCTCTGTTTAGCACTATGTGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGTACTT
1 CTCTCTGTTTAGCACTATGTGTGCTCTCTGTTACCAGCACTGTATGTGCTCTCTG-TTAGTACTT
49762 TGTGTA
65 TG-GTA
* *
49768 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACT-TATGTGCTCTCTGTTAGTACTT
1 CTCTCTGTTTAGCACTATGTGTGCTCTCTGTT-ACCAGCACTGTATGTGCTCTCTGTTAGTACTT
49832 TGGTA
65 TGGTA
49837 CTCTCTGTTT
1 CTCTCTGTTT
49847 GTTCCGTATA
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
69 13 0.18
70 11 0.15
71 43 0.59
72 6 0.08
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (69 bp):
CTCTCTGTTTAGCACTATGTGTGCTCTCTGTTACCAGCACTGTATGTGCTCTCTGTTAGTACTTT
GGTA
Found at i:50994 original size:16 final size:16
Alignment explanation
Indices: 50975--51007 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
50965 CTAATTTTGG
50975 TGTTAAA-TGATTAAAA
1 TGTTAAAGTGA-TAAAA
50991 TGTTAAAGTGATAAAA
1 TGTTAAAGTGATAAAA
51007 T
1 T
51008 TATAAGGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (16 bp):
TGTTAAAGTGATAAAA
Found at i:53159 original size:23 final size:23
Alignment explanation
Indices: 53132--53282 Score: 146
Period size: 23 Copynumber: 6.5 Consensus size: 23
53122 ACACTAGCGC
*
53132 GCTCTCTGTTTAGCACTATGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
53155 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* * *
53180 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
53203 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
53226 GCTCTCTGTTGCCCAGCACT-TATGT
1 GCTCTCTGTT---TAGCACTGTGTGT
* *
53251 GCTCTCTG-TTAGTACTTTG-GT
1 GCTCTCTGTTTAGCACTGTGTGT
*
53272 ACTCTCTGTTT
1 GCTCTCTGTTT
53283 GTTCCGTATA
Statistics
Matches: 106, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
21 14 0.13
22 3 0.03
23 48 0.45
24 2 0.02
25 33 0.31
26 6 0.06
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:53208 original size:48 final size:46
Alignment explanation
Indices: 53132--53233 Score: 150
Period size: 48 Copynumber: 2.2 Consensus size: 46
53122 ACACTAGCGC
* *
53132 GCTCTCTGTTTAGCACTATGTGTGCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTATGTGTACTCTCTG-T-TTAGCACTGTGTGT
* *
53180 GCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTATGTGTACTCTCTGTTTAGCACTGTGTGT
53226 GCTCTCTG
1 GCTCTCTG
53234 TTGCCCAGCA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 22 0.44
47 1 0.02
48 27 0.54
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.44
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTATGTGTACTCTCTGTTTAGCACTGTGTGT
Found at i:53252 original size:71 final size:69
Alignment explanation
Indices: 53133--53282 Score: 221
Period size: 71 Copynumber: 2.1 Consensus size: 69
53123 CACTAGCGCG
** *
53133 CTCTCTGTTTAGCACTATGTGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGTACTT
1 CTCTCTGTTTAGCACTATGTGTGCTCTCTGTTACCAGCACTGTATGTGCTCTCTG-TTAGTACTT
53198 TGTGTA
65 TG-GTA
* *
53204 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACT-TATGTGCTCTCTGTTAGTACTT
1 CTCTCTGTTTAGCACTATGTGTGCTCTCTGTT-ACCAGCACTGTATGTGCTCTCTGTTAGTACTT
53268 TGGTA
65 TGGTA
53273 CTCTCTGTTT
1 CTCTCTGTTT
53283 GTTCCGTATA
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
69 13 0.18
70 11 0.15
71 43 0.59
72 6 0.08
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (69 bp):
CTCTCTGTTTAGCACTATGTGTGCTCTCTGTTACCAGCACTGTATGTGCTCTCTGTTAGTACTTT
GGTA
Found at i:53875 original size:38 final size:38
Alignment explanation
Indices: 53824--53909 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 38
53814 GGGTGTTACA
*
53824 AGTGTATATCGGGCTTAATACCTAGCAGGCTTCGTGCC
1 AGTGTTTATCGGGCTTAATACCTAGCAGGCTTCGTGCC
** ** *
53862 AGTGTTTATCGGGCTTTGTGTCTAGCAGGCTTCGTGCT
1 AGTGTTTATCGGGCTTAATACCTAGCAGGCTTCGTGCC
*
53900 GGTGTTTATC
1 AGTGTTTATC
53910 TAGTAGGCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (38 bp):
AGTGTTTATCGGGCTTAATACCTAGCAGGCTTCGTGCC
Found at i:53918 original size:26 final size:27
Alignment explanation
Indices: 53882--53971 Score: 103
Period size: 27 Copynumber: 3.4 Consensus size: 27
53872 GGGCTTTGTG
* *
53882 TCTAGCAGGCT-TCGTGCTGGTGTTTA
1 TCTAGCAGGCTATCGAGCAGGTGTTTA
* *
53908 TCTAGTAGGCTATTGAGCAGGTGTTTA
1 TCTAGCAGGCTATCGAGCAGGTGTTTA
* *
53935 TCTAGCAAGCTATTGAGCCA-GTGTTTA
1 TCTAGCAGGCTATCGAG-CAGGTGTTTA
53962 TCTAGCAGGC
1 TCTAGCAGGC
53972 CTTGGGCCGG
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
26 10 0.18
27 43 0.78
28 2 0.04
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (27 bp):
TCTAGCAGGCTATCGAGCAGGTGTTTA
Found at i:53936 original size:27 final size:28
Alignment explanation
Indices: 53900--53971 Score: 112
Period size: 27 Copynumber: 2.6 Consensus size: 28
53890 GCTTCGTGCT
*
53900 GGTGTTTATCTAGTAGGCTATTGAG-CA
1 GGTGTTTATCTAGCAGGCTATTGAGCCA
*
53927 GGTGTTTATCTAGCAAGCTATTGAGCCA
1 GGTGTTTATCTAGCAGGCTATTGAGCCA
53955 -GTGTTTATCTAGCAGGC
1 GGTGTTTATCTAGCAGGC
53972 CTTGGGCCGG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 39 0.95
28 2 0.05
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (28 bp):
GGTGTTTATCTAGCAGGCTATTGAGCCA
Found at i:55610 original size:18 final size:18
Alignment explanation
Indices: 55566--55610 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
55556 CATTTTGTGC
55566 TATTTATA-T-TATTGAA
1 TATTTATATTATATTGAA
*
55582 T-TTTTTAATTATATTGAA
1 TATTTAT-ATTATATTGAA
55600 TATTTATATTA
1 TATTTATATTA
55611 AAATTGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
15 4 0.17
16 2 0.09
17 1 0.04
18 12 0.52
19 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
TATTTATATTATATTGAA
Found at i:62168 original size:15 final size:16
Alignment explanation
Indices: 62148--62186 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
62138 AATTCGAAAA
*
62148 TAAAAATTAAATTCT-
1 TAAAAATTAAATTATG
*
62163 TAAAAATAAAATTATG
1 TAAAAATTAAATTATG
62179 TAAAAATT
1 TAAAAATT
62187 TTGAGTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (16 bp):
TAAAAATTAAATTATG
Found at i:62770 original size:35 final size:35
Alignment explanation
Indices: 62715--62783 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
62705 ATACACCTTG
*
62715 ACTGCTCATAACTGCTACTAACTGATTAACTACTA
1 ACTGCTCACAACTGCTACTAACTGATTAACTACTA
* *
62750 ACTGTTCACAACTGCTACTAATTGATTAACTACT
1 ACTGCTCACAACTGCTACTAACTGATTAACTACT
62784 TAATAATTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (35 bp):
ACTGCTCACAACTGCTACTAACTGATTAACTACTA
Found at i:70264 original size:14 final size:14
Alignment explanation
Indices: 70216--70266 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
70206 ATTTCAAATT
70216 TATAAA-ATATTTAA
1 TATAAATATATTT-A
* *
70230 TATATATATATATA
1 TATAAATATATTTA
70244 TATAAATATATTTA
1 TATAAATATATTTA
70258 TATAAATAT
1 TATAAATAT
70267 CAAATTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 27 0.84
15 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATAAATATATTTA
Found at i:70279 original size:28 final size:29
Alignment explanation
Indices: 70201--70280 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 29
70191 AGATGATATG
* *
70201 ATAT-AATTTCAAATTTATAAAATATTTA
1 ATATAAATATCAAATTTATAATATATTTA
* * *
70229 ATATATATAT-ATATATATAAATATATTT-
1 ATATAAATATCAAATTTAT-AATATATTTA
70257 ATATAAATATCAAATTTATAATAT
1 ATATAAATATCAAATTTATAATAT
70281 TAAATATATT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
28 24 0.59
29 17 0.41
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (29 bp):
ATATAAATATCAAATTTATAATATATTTA
Found at i:70312 original size:18 final size:19
Alignment explanation
Indices: 70291--70334 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
70281 TAAATATATT
70291 TCAA-ATATAAAAAATTCA
1 TCAATATATAAAAAATTCA
**
70309 TCAATTATATAAATTATTCA
1 TCAA-TATATAAAAAATTCA
70329 TCAATA
1 TCAATA
70335 AACTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 2 0.09
20 16 0.73
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (19 bp):
TCAATATATAAAAAATTCA
Found at i:70318 original size:20 final size:20
Alignment explanation
Indices: 70295--70333 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
70285 TATATTTCAA
70295 ATATAAAAAATTCATCAATT
1 ATATAAAAAATTCATCAATT
**
70315 ATATAAATTATTCATCAAT
1 ATATAAAAAATTCATCAAT
70334 AAACTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAAAAAATTCATCAATT
Found at i:70958 original size:43 final size:43
Alignment explanation
Indices: 70897--70984 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
70887 CCCTTTATTT
70897 CATACTTTTTTTTGGTGGTCCTCCAACTAGAGCCATCCATGAC
1 CATACTTTTTTTTGGTGGTCCTCCAACTAGAGCCATCCATGAC
*
70940 CATACTTTTTTTTGGTGGTCCTCCAACTAGAGCCATTCATGAC
1 CATACTTTTTTTTGGTGGTCCTCCAACTAGAGCCATCCATGAC
70983 CA
1 CA
70985 ACCATTCATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (43 bp):
CATACTTTTTTTTGGTGGTCCTCCAACTAGAGCCATCCATGAC
Found at i:77184 original size:23 final size:23
Alignment explanation
Indices: 77158--77204 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
77148 AATTGAATAG
77158 AAATGTCATGCCAACATAAGCTA
1 AAATGTCATGCCAACATAAGCTA
*
77181 AAATGTCATGTCAACATAAGCTA
1 AAATGTCATGCCAACATAAGCTA
77204 A
1 A
77205 CGGTATTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (23 bp):
AAATGTCATGCCAACATAAGCTA
Found at i:87168 original size:7 final size:7
Alignment explanation
Indices: 87156--87190 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
87146 TCTTTATTAA
87156 AATTATT
1 AATTATT
87163 AATTATT
1 AATTATT
87170 AATTATT
1 AATTATT
87177 AATT-TT
1 AATTATT
87183 AAATTATT
1 -AATTATT
87191 TCACATGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 2 0.08
7 22 0.85
8 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATTATT
Found at i:87553 original size:87 final size:86
Alignment explanation
Indices: 87451--87617 Score: 273
Period size: 88 Copynumber: 1.9 Consensus size: 86
87441 CTAGAATACA
* * *
87451 TCAAGGTGTAAAAAT-AAAATCAGAATTTCTCACCATGATCACACTAAACTGTAAAAAAAAACTA
1 TCAAGGTGTAAAAATAAAAATAAAAAATTCTCACCATGATCACACTAAAC--TAAAAAAAAACTA
87515 TTAATTACAACTATAGTTCATAT
64 TTAATTACAACTATAGTTCATAT
*
87538 TCAAGGTGTAAAAATAAAAATAAAAAATTCTCACCATGATCACACTAAACTATAAAAAAACTATT
1 TCAAGGTGTAAAAATAAAAATAAAAAATTCTCACCATGATCACACTAAACTAAAAAAAAACTATT
87603 AATTACAACTATAGT
66 AATTACAACTATAGT
87618 CCATTCAATT
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
86 29 0.39
87 15 0.20
88 31 0.41
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.28
Consensus pattern (86 bp):
TCAAGGTGTAAAAATAAAAATAAAAAATTCTCACCATGATCACACTAAACTAAAAAAAAACTATT
AATTACAACTATAGTTCATAT
Found at i:101181 original size:18 final size:18
Alignment explanation
Indices: 101158--101194 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
101148 CGCAATCTAT
101158 TCACAATTGTCTTCGTAA
1 TCACAATTGTCTTCGTAA
101176 TCACAATTGTCTTCGTAA
1 TCACAATTGTCTTCGTAA
101194 T
1 T
101195 AGTCTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (18 bp):
TCACAATTGTCTTCGTAA
Found at i:118180 original size:23 final size:23
Alignment explanation
Indices: 118154--118202 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
118144 AATTCATGTC
*
118154 TTAATATAATAATAATATTGAGT
1 TTAATATAAGAATAATATTGAGT
*
118177 TTAATATAAGAATAATTTTGAGT
1 TTAATATAAGAATAATATTGAGT
118200 TTA
1 TTA
118203 GAGATTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (23 bp):
TTAATATAAGAATAATATTGAGT
Found at i:122745 original size:30 final size:30
Alignment explanation
Indices: 122706--122763 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
122696 CCAAATTTTA
122706 AAAAATTACAATATAATCACTAACGTTATC
1 AAAAATTACAATATAATCACTAACGTTATC
* * * *
122736 AAAAGTTACAATATGATTACTAATGTTA
1 AAAAATTACAATATAATCACTAACGTTA
122764 CTGGTTTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (30 bp):
AAAAATTACAATATAATCACTAACGTTATC
Found at i:126441 original size:15 final size:15
Alignment explanation
Indices: 126417--126446 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
126407 TTAAGTTTAT
*
126417 ACTTTTATTTTGATC
1 ACTTTCATTTTGATC
126432 ACTTTCATTTTGATC
1 ACTTTCATTTTGATC
126447 GTCCAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.57
Consensus pattern (15 bp):
ACTTTCATTTTGATC
Found at i:130151 original size:2 final size:2
Alignment explanation
Indices: 130144--130176 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
130134 ATTTTCTTTT
130144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
130177 GCATATGCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:142977 original size:13 final size:13
Alignment explanation
Indices: 142959--142983 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
142949 GTTGGATACT
142959 ATAAAAAAAAAAA
1 ATAAAAAAAAAAA
142972 ATAAAAAAAAAA
1 ATAAAAAAAAAA
142984 GCATATACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (13 bp):
ATAAAAAAAAAAA
Found at i:155228 original size:23 final size:23
Alignment explanation
Indices: 155202--155255 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
155192 TTAACTTAAT
* *
155202 CGAATATGCTCATGAACATCAAG
1 CGAACATGCTCATGAACATCAAA
155225 CGAACATGCTCATGAACATCAAA
1 CGAACATGCTCATGAACATCAAA
155248 CGAACATG
1 CGAACATG
155256 TTCACGAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.19
Consensus pattern (23 bp):
CGAACATGCTCATGAACATCAAA
Found at i:158690 original size:29 final size:31
Alignment explanation
Indices: 158655--158721 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
158645 ATCTTTATAT
*
158655 TTTTTAAAGA-ATTAAATCA-AATTTTATCA
1 TTTTTAAAGAGATCAAATCACAATTTTATCA
* *
158684 TTTTTAAAGAGATCAAATTACAATTTTATTA
1 TTTTTAAAGAGATCAAATCACAATTTTATCA
*
158715 TTATTAA
1 TTTTTAA
158722 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 10 0.31
30 7 0.22
31 15 0.47
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (31 bp):
TTTTTAAAGAGATCAAATCACAATTTTATCA
Found at i:159400 original size:155 final size:151
Alignment explanation
Indices: 159122--159429 Score: 481
Period size: 155 Copynumber: 2.0 Consensus size: 151
159112 CATTAACCCA
159122 AAGATTCAATATCTTTTATTCCAATATCTTCTTCCCGTTAAGTTTTTTTGGGTTAATGAATTTCA
1 AAGATTCAATATCTTTTATTCCAATATCTTCTTCCCGTTAAGTTTTTTTGGGTTAATGAATTTCA
* * * *
159187 AATATTCAAGCTTTGAGACAGATTTGTAACAAAAGATATTGGAATCAAAAGGGAAGAAGATGAAG
66 AAGATTCAAGCTTTGAGACAAATTTGTAACAAAAGATATTGAAATCAAAAGGAAAGAAGATGAAG
*
159252 ATGAAGAAGAGAGGTGTGTGG
131 ATGAAGAAGAAAGGTGTGTGG
* * **
159273 AAGATTCAATATTTTTTATTCCAATATCTTCTTCCTGTTAAGTTTTTTGTTTTGGGTTAATGGGT
1 AAGATTCAATATCTTTTATTCCAATATCTTCTTCCCGTTAAG---TTT-TTTTGGGTTAATGAAT
* *
159338 TTTAAAGATTCAAGCTTTGAGACAAATTTGTAACTAAAGATATTGAAATCAAAAGGAAAGAAGAT
62 TTCAAAGATTCAAGCTTTGAGACAAATTTGTAACAAAAGATATTGAAATCAAAAGGAAAGAAGAT
159403 GAAGATGAAGAAGAAAGGTGTGTGG
127 GAAGATGAAGAAGAAAGGTGTGTGG
159428 AA
1 AA
159430 ATGAGTTTAG
Statistics
Matches: 142, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
151 40 0.28
154 3 0.02
155 99 0.70
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (151 bp):
AAGATTCAATATCTTTTATTCCAATATCTTCTTCCCGTTAAGTTTTTTTGGGTTAATGAATTTCA
AAGATTCAAGCTTTGAGACAAATTTGTAACAAAAGATATTGAAATCAAAAGGAAAGAAGATGAAG
ATGAAGAAGAAAGGTGTGTGG
Found at i:160708 original size:20 final size:21
Alignment explanation
Indices: 160651--160708 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 21
160641 ATAATTTTAG
*
160651 ATAAATTAATTAAAT-ATAAAT
1 ATAAA-TAAATAAATAATAAAT
*
160672 ATAAAT-AAT-TATGAATAAA-
1 ATAAATAAATAAAT-AATAAAT
160691 ATAAATAAATAAATAATA
1 ATAAATAAATAAATAATA
160709 TTATTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
18 2 0.07
19 8 0.27
20 13 0.43
21 7 0.23
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAATAAATAAATAATAAAT
Found at i:164052 original size:10 final size:10
Alignment explanation
Indices: 164037--164063 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
164027 TTACTAATTT
164037 AAAATTTTAA
1 AAAATTTTAA
164047 AAAATTTTAA
1 AAAATTTTAA
164057 AAAATTT
1 AAAATTT
164064 AAATGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:165585 original size:17 final size:17
Alignment explanation
Indices: 165563--165597 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
165553 AAGAAATTAT
165563 TAAAAAAT-TTATAAAAA
1 TAAAAAATATT-TAAAAA
165580 TAAAAAATATTTAAAAA
1 TAAAAAATATTTAAAAA
165597 T
1 T
165598 TGGTTCAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAATATTTAAAAA
Found at i:166431 original size:33 final size:31
Alignment explanation
Indices: 166373--166436 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
166363 TAAAATTAGT
*
166373 AATGATAAAATTATAATTTGACTTTTTAAAAA
1 AATGATAAAATTATAATTTAAC-TTTTAAAAA
*
166405 AATGATAAAAATT-TGATTTAATCTTTTAAAAA
1 AATGAT-AAAATTATAATTTAA-CTTTTAAAAA
166437 TTATAAAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (31 bp):
AATGATAAAATTATAATTTAACTTTTAAAAA
Found at i:175873 original size:2 final size:2
Alignment explanation
Indices: 175864--175911 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
175854 CATTTGGGTA
* * *
175864 AC AC -C AC AC AT AC AC TC GC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
175905 AC AC AC A
1 AC AC AC A
175912 TATATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.46, C:0.48, G:0.02, T:0.04
Consensus pattern (2 bp):
AC
Found at i:177472 original size:97 final size:97
Alignment explanation
Indices: 177298--177480 Score: 282
Period size: 97 Copynumber: 1.9 Consensus size: 97
177288 AAGATATTTG
177298 ATTATCTCGATTTGAAGAAAATTCGCACATAGTAAGTTAAGGCACAAATTTTCAAAATCAGAAAT
1 ATTATCTCGATTTGAAGAAAATTCGCACATAGTAAGTTAAGGCACAAATTTTCAAAATCAGAAAT
177363 AAAGAAACATTGCCTCGATTTAAGGGTATTCA
66 AAAGAAACATTGCCTCGATTTAAGGGTATTCA
* * *
177395 ATTATTTCGATTTGAAGAAAAATT-GCACCTAGTAAGTTAAGGCACAAATTTTCAAAA-CTTGAA
1 ATTATCTCGATTTGAAG-AAAATTCGCACATAGTAAGTTAAGGCACAAATTTTCAAAATC-AGAA
*
177458 ATAAA-AGAATATTGCCTCGATTT
64 ATAAAGA-AACATTGCCTCGATTT
177481 TAAAGTTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
96 2 0.03
97 71 0.90
98 6 0.08
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (97 bp):
ATTATCTCGATTTGAAGAAAATTCGCACATAGTAAGTTAAGGCACAAATTTTCAAAATCAGAAAT
AAAGAAACATTGCCTCGATTTAAGGGTATTCA
Found at i:177795 original size:30 final size:30
Alignment explanation
Indices: 177735--177868 Score: 82
Period size: 29 Copynumber: 4.5 Consensus size: 30
177725 CACTTGGGGG
* * * *
177735 AAAATTGGTAATTTTGGGAAAGATT-AAGGT
1 AAAAATGGTAATTTT-TGAAAAATTCGAGGT
*
177765 -AAAATGGTAATTTTTGAAAAAAATCGAGGT
1 AAAAATGGTAATTTTTG-AAAAATTCGAGGT
* *
177795 AAAAAATAG-AATTTTT-AGAAATTCGAGGGT
1 -AAAAATGGTAATTTTTGAAAAATTCGA-GGT
* *
177825 -AAAATGGTAGTTTTTGGAAAAATTAG-GGT
1 AAAAATGGTAATTTTT-GAAAAATTCGAGGT
* *
177854 CAAAATGGAAATTTT
1 AAAAATGGTAATTTT
177869 GGGAGTTCGG
Statistics
Matches: 81, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
28 7 0.09
29 35 0.43
30 19 0.23
31 14 0.17
32 6 0.07
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.32
Consensus pattern (30 bp):
AAAAATGGTAATTTTTGAAAAATTCGAGGT
Found at i:177935 original size:59 final size:60
Alignment explanation
Indices: 177762--177959 Score: 214
Period size: 58 Copynumber: 3.4 Consensus size: 60
177752 GAAAGATTAA
* * * * *
177762 GGTAAAATGGTAATTTTT-GAAAAAAATCGAGGTAAAAAAT-AGAATTTTTAGAAATTCGAG
1 GGTAAAATGGTAATTTTTGGAAAAAAATAG-GGTTAAAAATGA-AATTTTTGGAAGTTCGGG
* * * *
177822 GGTAAAATGGTAGTTTTTGG-AAAAATTAGGG-TCAAAATGGAAA-TTTTGGGAGTTCGGG
1 GGTAAAATGGTAATTTTTGGAAAAAAATAGGGTTAAAAAT-GAAATTTTTGGAAGTTCGGG
*
177880 GGTAAAATGATAATTTTTGGAAAAAAAT-GGGTTAAAAATGAAATTTTTGGAAGTTCGGG
1 GGTAAAATGGTAATTTTTGGAAAAAAATAGGGTTAAAAATGAAATTTTTGGAAGTTCGGG
*
177939 GTTAAAATGG-AA-TTTTGGAAA
1 GGTAAAATGGTAATTTTTGGAAA
177960 GTTTAGGGGT
Statistics
Matches: 116, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
57 9 0.08
58 43 0.37
59 38 0.33
60 25 0.22
61 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.31
Consensus pattern (60 bp):
GGTAAAATGGTAATTTTTGGAAAAAAATAGGGTTAAAAATGAAATTTTTGGAAGTTCGGG
Found at i:177941 original size:29 final size:28
Alignment explanation
Indices: 177850--177997 Score: 95
Period size: 30 Copynumber: 5.1 Consensus size: 28
177840 GGAAAAATTA
* * *
177850 GGGTCAAAATGGAAA-TTTTGGGAGTTCG
1 GGGTTAAAAT-GAAATTTTTGGAAGTTAG
* *** *
177878 GGGGTAAAATGATAATTTTTGGAAAAAAAT
1 GGGTTAAAATGA-AATTTTTGG-AAGTTAG
*
177908 GGGTTAAAAATGAAATTTTTGGAAGTTCG
1 GGGTT-AAAATGAAATTTTTGGAAGTTAG
*
177937 GGGTTAAAATGGAA-TTTTGGAAAGTTTAG
1 GGGTTAAAATGAAATTTTTGG-AAG-TTAG
*
177966 GGG-TAGAAATGTAATTTTTGGAAAGTTTAG
1 GGGTTA-AAATGAAATTTTTGG-AAG-TTAG
177996 GG
1 GG
177998 ACCTTCAAGG
Statistics
Matches: 95, Mismatches: 17, Indels: 14
0.75 0.13 0.11
Matches are distributed among these distances:
27 8 0.08
28 23 0.24
29 26 0.27
30 31 0.33
31 7 0.07
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.32
Consensus pattern (28 bp):
GGGTTAAAATGAAATTTTTGGAAGTTAG
Found at i:177987 original size:30 final size:30
Alignment explanation
Indices: 177835--177997 Score: 110
Period size: 29 Copynumber: 5.6 Consensus size: 30
177825 AAAATGGTAG
** *
177835 TTTTTGGAAAAATTA-GGGTCAAAATGGAAA
1 TTTTTGGAAAGTTTAGGGGTTAAAAT-GAAA
* * *
177865 -TTTTGG-GAG-TTCGGGGGTAAAATGATAA
1 TTTTTGGAAAGTTTAGGGGTTAAAATGA-AA
*** *
177893 TTTTTGGAAA-AAAATGGGTTAAAAATGAAA
1 TTTTTGGAAAGTTTAGGGGTT-AAAATGAAA
* *
177923 TTTTTGG-AAG-TTCGGGGTTAAAATGGAA
1 TTTTTGGAAAGTTTAGGGGTTAAAATGAAA
*
177951 -TTTTGGAAAGTTTAGGGG-TAGAAATGTAA
1 TTTTTGGAAAGTTTAGGGGTTA-AAATGAAA
177980 TTTTTGGAAAGTTTAGGG
1 TTTTTGGAAAGTTTAGGG
177998 ACCTTCAAGG
Statistics
Matches: 104, Mismatches: 18, Indels: 22
0.72 0.12 0.15
Matches are distributed among these distances:
27 10 0.10
28 24 0.23
29 32 0.31
30 31 0.30
31 7 0.07
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.34
Consensus pattern (30 bp):
TTTTTGGAAAGTTTAGGGGTTAAAATGAAA
Found at i:179765 original size:30 final size:29
Alignment explanation
Indices: 179729--179857 Score: 99
Period size: 30 Copynumber: 4.3 Consensus size: 29
179719 GTAGAAGGGT
179729 AATTTTTGAGAGTTTCAGGGTGAAAAATGG
1 AATTTTTG-GAGTTTCAGGGTGAAAAATGG
*
179759 AATTTTTGGAGGTTCGAGGGT--AAAATGG
1 AATTTTTGGAGTTTC-AGGGTGAAAAATGG
179787 TAATTTTTGGAAGTTT-AGGG-GTAAAAATTGGG
1 -AATTTTTGG-AGTTTCAGGGTG-AAAAA-T-GG
* * *
179819 ATTTTTTGGAAGTTT--GGGGGTAAAATGG
1 AATTTTTGG-AGTTTCAGGGTGAAAAATGG
179847 TAATTTTTGGA
1 -AATTTTTGGA
179858 AGTATTGGGG
Statistics
Matches: 84, Mismatches: 5, Indels: 22
0.76 0.05 0.20
Matches are distributed among these distances:
28 14 0.17
29 24 0.29
30 28 0.33
31 16 0.19
32 2 0.02
ACGTcount: A:0.29, C:0.02, G:0.32, T:0.37
Consensus pattern (29 bp):
AATTTTTGGAGTTTCAGGGTGAAAAATGG
Found at i:179802 original size:59 final size:60
Alignment explanation
Indices: 179714--179913 Score: 207
Period size: 60 Copynumber: 3.4 Consensus size: 60
179704 TTTGGTCATC
* * *
179714 CGAGGGTAGAAGGGTAATTTTT-GAGAGTTTCA-GGGTGAAAAA-T-GGAATTTTTGGAGGTT
1 CGAGGGTAAAATGGTAATTTTTGGA-AGTTT-AGGGGT-AAAAATTGGGAATTTTTGGAAGTT
*
179773 CGAGGGTAAAATGGTAATTTTTGGAAGTTTAGGGGTAAAAATTGGGATTTTTTGGAAGTT
1 CGAGGGTAAAATGGTAATTTTTGGAAGTTTAGGGGTAAAAATTGGGAATTTTTGGAAGTT
* * * * *
179833 TGGGGGTAAAATGGTAATTTTTGGAAGTATT-GGGGTCAAATTTGAG-ATTTTTGGAAGTT
1 CGAGGGTAAAATGGTAATTTTTGGAAGT-TTAGGGGTAAAAATTGGGAATTTTTGGAAGTT
* * *
179892 TGGGGGT-AAATGATAATTTTTG
1 CGAGGGTAAAATGGTAATTTTTG
179914 AATGTTTCGA
Statistics
Matches: 125, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
58 20 0.16
59 49 0.39
60 54 0.43
61 2 0.02
ACGTcount: A:0.28, C:0.02, G:0.33, T:0.36
Consensus pattern (60 bp):
CGAGGGTAAAATGGTAATTTTTGGAAGTTTAGGGGTAAAAATTGGGAATTTTTGGAAGTT
Found at i:179867 original size:29 final size:29
Alignment explanation
Indices: 179717--179913 Score: 170
Period size: 29 Copynumber: 6.7 Consensus size: 29
179707 GGTCATCCGA
* *
179717 GGGTAGAAGGGTAATTTTT-GAGAGTTTCAGG
1 GGGTAAAATGGTAATTTTTGGA-AGTTT--GG
* * * * *
179748 GTGAAAAATGG-AATTTTTGGAGGTTCGA
1 GGGTAAAATGGTAATTTTTGGAAGTTTGG
*
179776 GGGTAAAATGGTAATTTTTGGAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAGTTTGG
* *
179805 GGGTAAAAATTGGGATTTTTTGGAAGTTTGG
1 GGGT-AAAA-TGGTAATTTTTGGAAGTTTGG
179836 GGGTAAAATGGTAATTTTTGGAAGTATT-G
1 GGGTAAAATGGTAATTTTTGGAAGT-TTGG
* *
179865 GGGTCAAAT-TTGAGATTTTTGGAAGTTTGG
1 GGGTAAAATGGT-A-ATTTTTGGAAGTTTGG
*
179895 GGGT-AAATGATAATTTTTG
1 GGGTAAAATGGTAATTTTTG
179914 AATGTTTCGA
Statistics
Matches: 136, Mismatches: 21, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
28 18 0.13
29 49 0.36
30 38 0.28
31 31 0.23
ACGTcount: A:0.28, C:0.02, G:0.33, T:0.37
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGGAAGTTTGG
Found at i:179953 original size:59 final size:58
Alignment explanation
Indices: 179828--179972 Score: 161
Period size: 58 Copynumber: 2.5 Consensus size: 58
179818 GATTTTTTGG
* * * * * **
179828 AAGTTTGGGGGTAAAATGGTAATTTTTGGAAGTATTGGGGTCAAATTTGAGATTTTTGG
1 AAGTTTGGGGGTAAAATGATAATTTTT-GAAGTATTGAGGTCAAAATCGAGACTTTTAA
179887 AAGTTTGGGGGT-AAATGATAATTTTTGAATGT-TTCGAGGTCAAAATCGAGACTTTTAA
1 AAGTTTGGGGGTAAAATGATAATTTTTGAA-GTATT-GAGGTCAAAATCGAGACTTTTAA
*
179945 AAGTTTTGGGGTAAAAAT-ATAATTTTTG
1 AAGTTTGGGGGT-AAAATGATAATTTTTG
179973 GATAATTTAG
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
57 5 0.07
58 43 0.58
59 22 0.30
60 4 0.05
ACGTcount: A:0.31, C:0.03, G:0.27, T:0.39
Consensus pattern (58 bp):
AAGTTTGGGGGTAAAATGATAATTTTTGAAGTATTGAGGTCAAAATCGAGACTTTTAA
Found at i:182808 original size:21 final size:23
Alignment explanation
Indices: 182658--182806 Score: 128
Period size: 23 Copynumber: 6.4 Consensus size: 23
182648 AGCAAGTCTC
*
182658 GTGCTCTCTGTTATTAGCACTGT-T
1 GTGCTCTCTG--ATTAGCACTTTGT
182682 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
182705 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* * * *
182728 GTACTCTCTGTTTAGCACTGTGC
1 GTGCTCTCTGATTAGCACTTTGT
*
182751 GTGCTCTCTG-TTGCCCAGCAC-TTAT
1 GTGCTCTCTGATT----AGCACTTTGT
*
182776 GTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATTAGCACTTTGT
*
182797 GTACTCTCTG
1 GTGCTCTCTG
182807 TTTGTTCCGT
Statistics
Matches: 105, Mismatches: 14, Indels: 15
0.78 0.10 0.11
Matches are distributed among these distances:
21 13 0.12
22 14 0.13
23 50 0.48
24 10 0.10
25 13 0.12
26 5 0.05
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.43
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:184459 original size:97 final size:97
Alignment explanation
Indices: 184274--184467 Score: 268
Period size: 97 Copynumber: 2.0 Consensus size: 97
184264 AACTTTGGAA
*
184274 AAGGATATTCGATTATCTCGATTTGAAGAAAATTCACACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAATTCACACCTAGTAAGTTAAGGAACAAATTTTCA
184339 AAATCAGAAATAAAGAAACATTGCCTCGATTT
66 AAATCAGAAATAAAGAAACATTGCCTCGATTT
* * * * *
184371 AAGGGTATTTGATTATTTCGATTTGAAGAAAAATT-GCACGTAGTAAGTTAAGGAACAAATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAG-AAAATTCACACCTAGTAAGTTAAGGAACAAATTTTC
**
184435 AAAACTC-GAAATAAA-ATATTATTGCCTCGATTT
65 AAAA-TCAGAAATAAAGA-AACATTGCCTCGATTT
184468 TAAAGTTTTC
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
96 1 0.01
97 77 0.90
98 8 0.09
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAATTCACACCTAGTAAGTTAAGGAACAAATTTTCA
AAATCAGAAATAAAGAAACATTGCCTCGATTT
Found at i:184906 original size:29 final size:29
Alignment explanation
Indices: 184700--185014 Score: 146
Period size: 29 Copynumber: 10.9 Consensus size: 29
184690 AGATACCCAA
* ** **
184700 GGGGGCAAAATGGTAA-TTTTGGTCACTT
1 GGGGGTAAAATGGTAATTTTTGGAAAAAT
* **
184728 GGGGGTAAAATGGTAA-TTTTGGGAAGTT
1 GGGGGTAAAATGGTAATTTTTGGAAAAAT
***
184756 CAAGGTAAAATGGTAATTTTTGGAAAAAAT
1 GGGGGTAAAATGGTAATTTTTGG-AAAAAT
* * **
184786 -GGGGTCAAAAATAG-AATTTTTAGAAATTT
1 GGGGGT--AAAATGGTAATTTTTGGAAAAAT
* *
184815 GAGGGTAAAATGGTAGTTTTTGGAAAAAT
1 GGGGGTAAAATGGTAATTTTTGGAAAAAT
* * * ***
184844 CGGGGTCAAAAATAG-AATTTTTGGGAGTCT
1 GGGGGT--AAAATGGTAATTTTTGGAAAAAT
* *
184874 GGGGGTAAAATGGTATTTTTTGGAAAAAA
1 GGGGGTAAAATGGTAATTTTTGGAAAAAT
* * **
184903 GGGGTTAAAAAT-GAAATTTTTGG-AAGTT
1 GGGGGT-AAAATGGTAATTTTTGGAAAAAT
* **
184931 CGAGGGTAAAATGGTAATTTTTGGAAAGTT
1 -GGGGGTAAAATGGTAATTTTTGGAAAAAT
* * **
184961 AGAGGTCAAAAATGG-AA-TTTTGGAAAGTT
1 GGGGGT--AAAATGGTAATTTTTGGAAAAAT
184990 CGGGGGTAAAAT-GTAATTTTTGGAA
1 -GGGGGTAAAATGGTAATTTTTGGAA
185015 GTTTAAGGAC
Statistics
Matches: 217, Mismatches: 52, Indels: 35
0.71 0.17 0.12
Matches are distributed among these distances:
27 1 0.00
28 63 0.29
29 88 0.41
30 46 0.21
31 19 0.09
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (29 bp):
GGGGGTAAAATGGTAATTTTTGGAAAAAT
Found at i:184921 original size:58 final size:58
Alignment explanation
Indices: 184742--185014 Score: 313
Period size: 59 Copynumber: 4.7 Consensus size: 58
184732 GTAAAATGGT
* *
184742 AATTTTGGGAAGTTC-AAGGTAAAATGGTAATTTTTGGAAAAAATGGGGTCAAAAATAG
1 AATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAAA-GGGGTCAAAAATAG
* * * * *
184800 AATTTTTAGAAATTTGAGGGTAAAATGGTAGTTTTTGGAAAAATCGGGGTCAAAAATAG
1 AATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAA-AGGGGTCAAAAATAG
* * * *
184859 AATTTTTGGGAG-TCTGGGGGTAAAATGGTATTTTTTGGAAAAAAGGGGTTAAAAAT-G
1 AATTTTTGGAAGTTC-GAGGGTAAAATGGTAATTTTTGGAAAAAAGGGGTCAAAAATAG
** * *
184916 AAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAGTTAGAGGTCAAAAATGG
1 -AATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAA-AAAGGGGTCAAAAATAG
*
184976 AA-TTTTGGAAAGTTCGGGGGTAAAAT-GTAATTTTTGGAA
1 AATTTTTGG-AAGTTCGAGGGTAAAATGGTAATTTTTGGAA
185015 GTTTAAGGAC
Statistics
Matches: 184, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
57 1 0.01
58 77 0.42
59 105 0.57
60 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (58 bp):
AATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAAAGGGGTCAAAAATAG
Found at i:186544 original size:17 final size:18
Alignment explanation
Indices: 186510--186545 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
186500 TGAATTTCTA
186510 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
186528 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
186545 T
1 T
186546 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:189760 original size:20 final size:21
Alignment explanation
Indices: 189735--189777 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
189725 TACTTACTAC
189735 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
*
189755 TACTAACTAACAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
189776 TA
1 TA
189778 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:190129 original size:3 final size:3
Alignment explanation
Indices: 190123--190163 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
190113 ACCTTTTTTT
* * *
190123 TTC TTC TCC TTC TTC CTC TTC TTC TCC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
190164 TCTTTCTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
TTC
Found at i:190146 original size:18 final size:18
Alignment explanation
Indices: 190123--190180 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
190113 ACCTTTTTTT
190123 TTCTTCTCCTTCTTCCTC
1 TTCTTCTCCTTCTTCCTC
*
190141 TTCTTCTCCTTCTTCTTC
1 TTCTTCTCCTTCTTCCTC
* *
190159 TTCTT-TCTTTCTTTCT-
1 TTCTTCTCCTTCTTCCTC
190175 TTCTTC
1 TTCTTC
190181 CTCTTTTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
16 5 0.14
17 8 0.23
18 22 0.63
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (18 bp):
TTCTTCTCCTTCTTCCTC
Found at i:190168 original size:4 final size:4
Alignment explanation
Indices: 190159--190201 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
190149 CTTCTTCTTC
190159 TTCT TTCT TTCT TTCT TTCT TCCTCT TT-T TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT T--TCT TTCT TTCT TTCT TTCT TTC
190202 CTTCATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 6 0.17
4 25 0.71
6 4 0.11
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:190185 original size:18 final size:17
Alignment explanation
Indices: 190122--190196 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 17
190112 TACCTTTTTT
*
190122 TTTCTTCTCCTTCTTCC
1 TTTCTTCTCCTTCTTTC
190139 TCTTCTTCTCCTTC-TTC
1 T-TTCTTCTCCTTCTTTC
*
190156 -TTCTTCTTTCTTTCTTTC
1 TTTCTTC--TCCTTCTTTC
*
190174 TTTCTTC-CTCTTTTTTC
1 TTTCTTCTC-CTTCTTTC
190191 TTTCTT
1 TTTCTT
190197 TTTTCCTTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
15 6 0.12
16 1 0.02
17 20 0.42
18 15 0.31
19 6 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTCTTCTCCTTCTTTC
Found at i:190190 original size:21 final size:21
Alignment explanation
Indices: 190119--190212 Score: 91
Period size: 21 Copynumber: 4.3 Consensus size: 21
190109 CATTACCTTT
*
190119 TTTTTTCTTCTCCTTCTTCCTC
1 TTTTTTCTT-TCTTTCTTCCTC
* * *
190141 TTCTTCTCCTTC-TTCTTCTTC
1 TT-TTTTCTTTCTTTCTTCCTC
190162 TTTCTTTCTTTCTTTCTTCCTC
1 TTT-TTTCTTTCTTTCTTCCTC
*
190184 TTTTTTCTTTCTTTTTTCCTTC
1 TTTTTTCTTTCTTTCTTCC-TC
*
190206 ATTTTTC
1 TTTTTTC
190213 GTTGGTTCCC
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
20 1 0.02
21 31 0.52
22 23 0.38
23 5 0.08
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTTCTTTCTTTCTTCCTC
Found at i:190198 original size:11 final size:11
Alignment explanation
Indices: 190156--190212 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
190146 CTCCTTCTTC
*
190156 TTCTTCTTTCT
1 TTCTTTTTTCT
190167 TTCTTTCTTTCT
1 TTCTTT-TTTCT
190179 TCCTCTTTTTTCT
1 T--TCTTTTTTCT
*
190192 TTCTTTTTTCC
1 TTCTTTTTTCT
*
190203 TTCATTTTTC
1 TTCTTTTTTC
190213 GTTGGTTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 23 0.57
12 6 0.15
13 6 0.15
14 5 0.12
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:190205 original size:25 final size:25
Alignment explanation
Indices: 190115--190201 Score: 83
Period size: 25 Copynumber: 3.5 Consensus size: 25
190105 AACACATTAC
*
190115 CTTT-TTT-TTTCTTCTC-CTTCTTC
1 CTTTCTTTCTTTCTTC-CTCTTCTTT
* *
190138 CTCTTCTTCTCCTTCTTCTTCTTCTTT
1 CT-TTCTT-TCTTTCTTCCTCTTCTTT
*
190165 CTTTCTTTCTTTCTTCCTCTTTTTT
1 CTTTCTTTCTTTCTTCCTCTTCTTT
190190 CTTTCTTT-TTTC
1 CTTTCTTTCTTTC
190202 CTTCATTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
23 2 0.04
24 6 0.11
25 25 0.47
26 6 0.11
27 14 0.26
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (25 bp):
CTTTCTTTCTTTCTTCCTCTTCTTT
Found at i:197291 original size:29 final size:29
Alignment explanation
Indices: 197245--197644 Score: 209
Period size: 29 Copynumber: 13.6 Consensus size: 29
197235 GAACAAAAGG
* *
197245 GTAATTTTTGGAAGGTTCGAGGTCAAAAAT
1 GTAA-TTTTGGAAAGTTTGAGGTCAAAAAT
** *
197275 AG-AATTTTGGAAAGTTCAAGGGCAAAAAT
1 -GTAATTTTGGAAAGTTTGAGGTCAAAAAT
** * * *
197304 GTAATTTTTAAAAATTTTGGGGTTAAAAAT
1 GTAA-TTTTGGAAAGTTTGAGGTCAAAAAT
* * * *
197334 GGAATTTTGAAAAGTTTGGTGGT-GAAAAT
1 GTAATTTTGGAAAGTTT-GAGGTCAAAAAT
* *
197363 GTAATTTTTGGAAAATTTGGGGTCAAAAAT
1 GTAA-TTTTGGAAAGTTTGAGGTCAAAAAT
* * * *
197393 AG-AATTTTAGAAAGTTTGTGATAAAAAAT
1 -GTAATTTTGGAAAGTTTGAGGTCAAAAAT
197422 GTAATTTTCGGAACA-TTTAGAGGT--AAAAT
1 GTAATTTT-GGAA-AGTTT-GAGGTCAAAAAT
* *
197451 GTAATTTTTGAAAAATTTGAGGTC-AAAAT
1 GTAA-TTTTGGAAAGTTTGAGGTCAAAAAT
* *
197480 AG-AATTTTGGAAATTTTAAGGGT--AAAAT
1 -GTAATTTTGGAAAGTTTGA-GGTCAAAAAT
*
197508 GTAATTTTTGGAAAATTT-AGGGTC-AAAAT
1 GTAA-TTTTGGAAAGTTTGA-GGTCAAAAAT
* * *
197537 GGAATTTTGGAAAGTTTAGGGGT-AAAATT
1 GTAATTTTGGAAAGTTT-GAGGTCAAAAAT
* *
197566 GTAATTTTTGGAAAATTTGAGGTTAAAAAT
1 GTAA-TTTTGGAAAGTTTGAGGTCAAAAAT
*
197596 AG-AATTTTGGAAAAGTTTTTGGGGTCAAAATAT
1 -GTAATTTTGG-AAAG--TTTGAGGTCAAAA-AT
* *
197629 G-ATTTTTGGACAGTTT
1 GTAATTTTGGAAAGTTT
197645 ATAGACCTCC
Statistics
Matches: 294, Mismatches: 47, Indels: 58
0.74 0.12 0.15
Matches are distributed among these distances:
27 1 0.00
28 44 0.15
29 141 0.48
30 77 0.26
31 10 0.03
32 19 0.06
33 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (29 bp):
GTAATTTTGGAAAGTTTGAGGTCAAAAAT
Found at i:197334 original size:30 final size:28
Alignment explanation
Indices: 197298--197636 Score: 213
Period size: 29 Copynumber: 11.6 Consensus size: 28
197288 GTTCAAGGGC
*
197298 AAAAATGTAATTTTTAAAAATTTTGGGGTT
1 AAAAATGTAATTTTTGAAAA-TTTGGGG-T
*
197328 AAAAATGGAA-TTTTGAAAAGTTTGGTGGT
1 AAAAATGTAATTTTTGAAAA-TTTGG-GGT
*
197357 GAAAATGTAATTTTTGGAAAATTTGGGGT
1 AAAAATGTAATTTTT-GAAAATTTGGGGT
* * * *
197386 CAAAAATAG-AATTTTAGAAAGTTTGTGAT
1 -AAAAAT-GTAATTTTTGAAAATTTGGGGT
* * *
197415 AAAAAATGTAATTTTCGGAACATTTAGAGGT
1 -AAAAATGTAATTTT-TGAAAATTT-GGGGT
*
197446 -AAAATGTAATTTTTGAAAAATTTGAGGT
1 AAAAATGTAATTTTTG-AAAATTTGGGGT
* * * *
197474 CAAAATAG-AATTTTGGAAATTTTAAGGGT
1 AAAAAT-GTAATTTTTGAAAATTT-GGGGT
*
197503 -AAAATGTAATTTTTGGAAAATTTAGGGT
1 AAAAATGTAATTTTT-GAAAATTTGGGGT
* * * *
197531 CAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAAATGTAATTTTTGAAAATTT-GGGGT
* *
197560 AAAATTGTAATTTTTGGAAAATTTGAGGTT
1 AAAAATGTAATTTTT-GAAAATTTG-GGGT
*
197590 AAAAATAG-AATTTTGGAAAAGTTTTTGGGGT
1 AAAAAT-GTAATTTTTGAAAA---TTTGGGGT
* * *
197621 CAAAATATGATTTTTG
1 AAAAATGTAATTTTTG
197637 GACAGTTTAT
Statistics
Matches: 245, Mismatches: 41, Indels: 45
0.74 0.12 0.14
Matches are distributed among these distances:
27 1 0.00
28 36 0.15
29 121 0.49
30 59 0.24
31 24 0.10
32 4 0.02
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (28 bp):
AAAAATGTAATTTTTGAAAATTTGGGGT
Found at i:197409 original size:59 final size:57
Alignment explanation
Indices: 197245--197439 Score: 187
Period size: 59 Copynumber: 3.3 Consensus size: 57
197235 GAACAAAAGG
** * * * *
197245 GTAATTTTTGGAAGGTTCGAGGTCAAAAATAGAATTTTGGAAAGTTCAAG-GGCAAAAAT
1 GTAATTTTTGGAAAATTTGGGGTCAAAAATAGAATTTT-GAAAGTT--TGTGGTAAAAAT
* * * *
197304 GTAATTTTT-AAAAATTTTGGGGTTAAAAATGGAATTTTGAAAAGTTTGGTGGTGAAAAT
1 GTAATTTTTGGAAAA-TTTGGGGTCAAAAATAGAATTTTG-AAAGTTT-GTGGTAAAAAT
*
197363 GTAATTTTTGGAAAATTTGGGGTCAAAAATAGAATTTTAGAAAGTTTGTGATAAAAAAT
1 GTAATTTTTGGAAAATTTGGGGTCAAAAATAGAATTTT-GAAAGTTTGTGGT-AAAAAT
* *
197422 GTAATTTTCGGAACATTT
1 GTAATTTTTGGAAAATTT
197440 AGAGGTAAAA
Statistics
Matches: 112, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
58 8 0.07
59 99 0.88
60 5 0.04
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (57 bp):
GTAATTTTTGGAAAATTTGGGGTCAAAAATAGAATTTTGAAAGTTTGTGGTAAAAAT
Found at i:197422 original size:88 final size:86
Alignment explanation
Indices: 197328--197492 Score: 224
Period size: 88 Copynumber: 1.9 Consensus size: 86
197318 TTTTGGGGTT
* * * *
197328 AAAAATGGAATTTT-GAAAAGTTTGGTGGTGAAAATGTAATTTTTGGAAAATTTGGGGTCAAAAA
1 AAAAATGGAATTTTCGAAAA-TTTAGAGGT-AAAATGTAATTTTTGAAAAATTTGAGGTC-AAAA
197392 TAGAATTTTAGAAAGTTTGTGATA
63 TAGAATTTTAGAAAGTTTGTGATA
* *
197416 AAAAATGTAATTTTCGGAACATTTAGAGGTAAAATGTAATTTTTGAAAAATTTGAGGTCAAAATA
1 AAAAATGGAATTTTC-GAAAATTTAGAGGTAAAATGTAATTTTTGAAAAATTTGAGGTCAAAATA
*
197481 GAATTTTGGAAA
65 GAATTTTAGAAA
197493 TTTTAAGGGT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
87 17 0.25
88 40 0.59
89 7 0.10
90 4 0.06
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.35
Consensus pattern (86 bp):
AAAAATGGAATTTTCGAAAATTTAGAGGTAAAATGTAATTTTTGAAAAATTTGAGGTCAAAATAG
AATTTTAGAAAGTTTGTGATA
Found at i:197449 original size:118 final size:118
Alignment explanation
Indices: 197245--197469 Score: 256
Period size: 118 Copynumber: 1.9 Consensus size: 118
197235 GAACAAAAGG
** * * *
197245 GTAATTTTTGGAAGGTTCGAGGTCAAAAATAGAATTTTGGAAAGTTCAAGGGCAAAAATGTAATT
1 GTAATTTTTGGAAAATTCGAGGTCAAAAATAGAATTTTAGAAAGTTCAAGAGAAAAAATGTAATT
* * * *
197310 TTTAAAAATTTTGGGGTTAAAAATGGAA-TTTTGAAAAGTTTGGTGGTGAAAAT
66 TTGAAAAATTTAGAGGTT-AAAATGGAATTTTTGAAAAATTTGGTGGTGAAAAT
* * *** *
197363 GTAATTTTTGGAAAATTTGGGGTCAAAAATAGAATTTTAGAAAGTTTGTGATAAAAAATGTAATT
1 GTAATTTTTGGAAAATTCGAGGTCAAAAATAGAATTTTAGAAAGTTCAAGAGAAAAAATGTAATT
* * *
197428 TTCGGAACATTTAGAGG-TAAAATGTAATTTTTGAAAAATTTG
66 TT-GAAAAATTTAGAGGTTAAAATGGAATTTTTGAAAAATTTG
197470 AGGTCAAAAT
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
117 8 0.09
118 70 0.80
119 9 0.10
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (118 bp):
GTAATTTTTGGAAAATTCGAGGTCAAAAATAGAATTTTAGAAAGTTCAAGAGAAAAAATGTAATT
TTGAAAAATTTAGAGGTTAAAATGGAATTTTTGAAAAATTTGGTGGTGAAAAT
Found at i:197516 original size:57 final size:57
Alignment explanation
Indices: 197443--197613 Score: 254
Period size: 57 Copynumber: 2.9 Consensus size: 57
197433 AACATTTAGA
* *
197443 GGTAAAATGTAATTTTTGAAAAATTTGAGGTCAAAATAGAATTTTGGAAATTTTAAG
1 GGTAAAATGTAATTTTTGGAAAATTTGAGGTCAAAATAGAATTTTGGAAAGTTTAAG
* *
197500 GGTAAAATGTAATTTTTGGAAAATTT-AGGGTCAAAATGGAATTTTGGAAAGTTTAGG
1 GGTAAAATGTAATTTTTGGAAAATTTGA-GGTCAAAATAGAATTTTGGAAAGTTTAAG
*
197557 GGTAAAATTGTAATTTTTGGAAAATTTGAGGTTAAAAATAGAATTTTGGAAAAGTTT
1 GGTAAAA-TGTAATTTTTGGAAAATTTGAGG-TCAAAATAGAATTTTGG-AAAGTTT
197614 TTGGGGTCAA
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
56 1 0.01
57 58 0.56
58 21 0.20
59 16 0.16
60 7 0.07
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.37
Consensus pattern (57 bp):
GGTAAAATGTAATTTTTGGAAAATTTGAGGTCAAAATAGAATTTTGGAAAGTTTAAG
Found at i:197985 original size:30 final size:31
Alignment explanation
Indices: 197927--197985 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
197917 GAAAATTAAT
*
197927 TAAAAATATGAAAAGGACCAAATTATAAAAA
1 TAAAAATATGAAAAGGACCAAATCATAAAAA
*
197958 TAAAAA-ATGAAAA-GATCAAATGCATAAA
1 TAAAAATATGAAAAGGACCAAAT-CATAAA
197986 TAGCCCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 12 0.48
31 6 0.24
ACGTcount: A:0.64, C:0.07, G:0.10, T:0.19
Consensus pattern (31 bp):
TAAAAATATGAAAAGGACCAAATCATAAAAA
Found at i:198102 original size:9 final size:9
Alignment explanation
Indices: 198083--198119 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
198073 AATTCAGGTC
198083 TTTCTTTTT
1 TTTCTTTTT
*
198092 TTT-TCTTT
1 TTTCTTTTT
198100 TTTCTTTTT
1 TTTCTTTTT
198109 TTTCTTTTT
1 TTTCTTTTT
198118 TT
1 TT
198120 CTACTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:198107 original size:14 final size:14
Alignment explanation
Indices: 198081--198119 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
198071 GCAATTCAGG
198081 TCTTTCTTTTTTTT
1 TCTTTCTTTTTTTT
*
198095 TCTTT-TTTCTTTT
1 TCTTTCTTTTTTTT
198108 T-TTTCTTTTTTT
1 TCTTTCTTTTTTT
198120 CTACTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 3 0.14
13 14 0.64
14 5 0.23
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TCTTTCTTTTTTTT
Found at i:198121 original size:17 final size:17
Alignment explanation
Indices: 198083--198118 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
198073 AATTCAGGTC
198083 TTTCTTTTTTTTTCTTT
1 TTTCTTTTTTTTTCTTT
198100 TTTC-TTTTTTTTCTTT
1 TTTCTTTTTTTTTCTTT
198116 TTT
1 TTT
198119 TCTACTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTCTTTTTTTTTCTTT
Found at i:199594 original size:11 final size:11
Alignment explanation
Indices: 199578--199620 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
199568 AAACCGTTTC
199578 AAATTTAAACT
1 AAATTTAAACT
*
199589 AAATTTAAATTT
1 AAATTTAAA-CT
* *
199601 AAATTTGAAGT
1 AAATTTAAACT
199612 AAATTTAAA
1 AAATTTAAA
199621 TTTAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (11 bp):
AAATTTAAACT
Found at i:199598 original size:17 final size:18
Alignment explanation
Indices: 199594--199638 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
199584 AAACTAAATT
* *
199594 TAAATTTAAATTT-GAAG
1 TAAATTTAAATTTAAAAA
199611 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAAA
199629 TAAATTTAAA
1 TAAATTTAAA
199639 ACCAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
TAAATTTAAATTTAAAAA
Found at i:199599 original size:6 final size:6
Alignment explanation
Indices: 199540--199638 Score: 67
Period size: 6 Copynumber: 16.0 Consensus size: 6
199530 GTATTTAGAT
* * * *
199540 TTTAAA ATTAAA TTTAAA ATTAAG TTTAAAA CCGTTTCAAA TTTAAA -CTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA ---TTT-AAA TTTAAA TTTAAA
* * **
199592 TTTAAA TTTAAA TTTGAA -GTAAA TTTAAA TTTAAA AATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
199639 ACCAATTTAA
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
5 7 0.10
6 52 0.74
7 5 0.07
10 6 0.09
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:199604 original size:23 final size:23
Alignment explanation
Indices: 199578--199626 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
199568 AAACCGTTTC
199578 AAATTTAAACTAAATTTAAATTT
1 AAATTTAAACTAAATTTAAATTT
* *
199601 AAATTTGAAGTAAATTTAAATTT
1 AAATTTAAACTAAATTTAAATTT
199624 AAA
1 AAA
199627 AATAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
AAATTTAAACTAAATTTAAATTT
Found at i:199645 original size:29 final size:28
Alignment explanation
Indices: 199613--199667 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
199603 ATTTGAAGTA
*
199613 AATTTAAATTTAAAAATAAATTTAAAACC
1 AATTTAAACTT-AAAATAAATTTAAAACC
* *
199642 AATTTAAACTTAATATAATTTTAAAA
1 AATTTAAACTTAAAATAAATTTAAAA
199668 TCAAAAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (28 bp):
AATTTAAACTTAAAATAAATTTAAAACC
Found at i:200613 original size:20 final size:20
Alignment explanation
Indices: 200590--200633 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
200580 TGGAAAAAAA
200590 ATTTCAAAA-AATATAAAATT
1 ATTTCAAAAGAATA-AAAATT
* *
200610 ATTTGAAAAGAATAAAATTT
1 ATTTCAAAAGAATAAAAATT
200630 ATTT
1 ATTT
200634 AATAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (20 bp):
ATTTCAAAAGAATAAAAATT
Found at i:200618 original size:19 final size:18
Alignment explanation
Indices: 200596--200645 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
200586 AAAAATTTCA
200596 AAAAATATAAAATTATTT
1 AAAAATATAAAATTATTT
200614 GAAAAGA-ATAAAATTTATTT
1 -AAAA-ATATAAAA-TTATTT
*
200634 AATAATA-AAAAT
1 AAAAATATAAAAT
200646 ATAATAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
17 1 0.04
18 5 0.19
19 14 0.52
20 7 0.26
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (18 bp):
AAAAATATAAAATTATTT
Found at i:201403 original size:19 final size:19
Alignment explanation
Indices: 201379--201415 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
201369 ATGACACCTT
201379 GGAAAAT-TTGTGTGGAAAA
1 GGAAAATATT-TGTGGAAAA
201398 GGAAAATATTTGTGGAAA
1 GGAAAATATTTGTGGAAA
201416 GCAGTTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (19 bp):
GGAAAATATTTGTGGAAAA
Found at i:211598 original size:21 final size:21
Alignment explanation
Indices: 211574--211617 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
211564 GTTTTTTTGG
211574 GTCTTATAACTCTTTCATTGA
1 GTCTTATAACTCTTTCATTGA
211595 GTCTTATAACTCTTTCATTGA
1 GTCTTATAACTCTTTCATTGA
211616 GT
1 GT
211618 TTGTGTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.48
Consensus pattern (21 bp):
GTCTTATAACTCTTTCATTGA
Found at i:222114 original size:16 final size:15
Alignment explanation
Indices: 222095--222124 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
222085 ACATATTTAA
222095 ATTTATTATTTATTAT
1 ATTTATTA-TTATTAT
222111 ATTTATTATTATTA
1 ATTTATTATTATTA
222125 ATTAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTATTATTATTAT
Found at i:222258 original size:29 final size:30
Alignment explanation
Indices: 222200--222310 Score: 91
Period size: 31 Copynumber: 3.7 Consensus size: 30
222190 ATATCAAAAT
* * *
222200 TATACATG-AACTTTGATTTAATGTGTAATTA
1 TATACATGAAACTTTAATTT--GGTGCAATTA
222231 TATACATG-AACTTTAATTTGGTGCAATTA
1 TATACATGAAACTTTAATTTGGTGCAATTA
* * * * * *
222260 TATACGTGAAACTCTAATCGTGGTTCAAATG
1 TATACATGAAACTTTAAT-TTGGTGCAATTA
*
222291 TATACTTGAAACTTTAATTT
1 TATACATGAAACTTTAATTT
222311 TGATTTAATC
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
29 15 0.23
30 9 0.14
31 42 0.64
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (30 bp):
TATACATGAAACTTTAATTTGGTGCAATTA
Found at i:222494 original size:29 final size:30
Alignment explanation
Indices: 222452--222510 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
222442 AGATTGGATC
* *
222452 AAATCAGAATTTTATGTATAAAATTGCACA
1 AAATCAGAAGTTTATGTATAAAATTACACA
*
222482 AAATCA-AAGTTTATGTATACAATTACACA
1 AAATCAGAAGTTTATGTATAAAATTACACA
222511 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.32
Consensus pattern (30 bp):
AAATCAGAAGTTTATGTATAAAATTACACA
Found at i:224021 original size:53 final size:54
Alignment explanation
Indices: 223963--224069 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 54
223953 ATATTTTTAC
223963 GATCGTAAAAATATAATTTCAAATATTTATATTTTTTTAA-TTTTAAAGAATTA
1 GATCGTAAAAATATAATTTCAAATATTTATATTTTTTTAATTTTTAAAGAATTA
*
224016 GATCGTAAAAATATAATTTCAAATATTTATATTTTTTTAATTTTTAAGGAATTA
1 GATCGTAAAAATATAATTTCAAATATTTATATTTTTTTAATTTTTAAAGAATTA
224070 AATTAAAATT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 40 0.77
54 12 0.23
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.48
Consensus pattern (54 bp):
GATCGTAAAAATATAATTTCAAATATTTATATTTTTTTAATTTTTAAAGAATTA
Found at i:228283 original size:29 final size:30
Alignment explanation
Indices: 228227--228293 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
228217 ATCTCAAAAT
*
228227 TATACATGAACTATGGTTTAATATGCAATTG
1 TATACATGAACTATGATTT-ATATGCAATTG
* * *
228258 TATACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTATGATTTATATGCAATTG
228287 TATACAT
1 TATACAT
228294 AAAATTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 15 0.47
31 17 0.53
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (30 bp):
TATACATGAACTATGATTTATATGCAATTG
Found at i:228307 original size:29 final size:29
Alignment explanation
Indices: 228250--228306 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
228240 TGGTTTAATA
*
228250 TGCAATTGTATACATGAACTTTGATTTTG
1 TGCAATTGTATACATAAACTTTGATTTTG
* *
228279 TGCAATTTTATACATAAAATTTTGATTT
1 TGCAATTGTATACAT-AAACTTTGATTT
228307 GATCCAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (29 bp):
TGCAATTGTATACATAAACTTTGATTTTG
Found at i:229345 original size:5 final size:5
Alignment explanation
Indices: 229335--229361 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
229325 CAGTGGACCG
229335 CATCC CATCC CATCC CATCC CATCC CA
1 CATCC CATCC CATCC CATCC CATCC CA
229362 CGCCATTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.59, G:0.00, T:0.19
Consensus pattern (5 bp):
CATCC
Found at i:244438 original size:29 final size:28
Alignment explanation
Indices: 244388--244466 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
244378 AAATAATACT
* *
244388 ACAATAAT-AAAATTAT-TAATAATTTATA
1 ACAAAAATAAAAATTATAT-ATAAATTA-A
244416 A-AAAAATAAAAATTTATATATAAATTAA
1 ACAAAAATAAAAA-TTATATATAAATTAA
*
244444 ACAAAATTAAAAATTATATATAA
1 ACAAAAATAAAAATTATATATAA
244467 CTTCAAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
27 5 0.11
28 17 0.39
29 21 0.48
30 1 0.02
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (28 bp):
ACAAAAATAAAAATTATATATAAATTAA
Found at i:244478 original size:26 final size:27
Alignment explanation
Indices: 244417--244480 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
244407 TAATTTATAA
*
244417 AAAAATAAAAATTTATATATAAATTAAAC
1 AAAATTAAAAATTTATATATAAATT--AC
*
244446 AAAATTAAAAA-TTATATATAACTT-C
1 AAAATTAAAAATTTATATATAAATTAC
244471 AAATATTAAA
1 AAA-ATTAAA
244481 TAATATTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 4 0.12
26 6 0.19
28 12 0.38
29 10 0.31
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (27 bp):
AAAATTAAAAATTTATATATAAATTAC
Found at i:246808 original size:22 final size:22
Alignment explanation
Indices: 246764--246808 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
246754 ATTTTAAAAT
*
246764 TTTTAAATAAAATTTGATTTTG
1 TTTTAAATAAAATTTAATTTTG
*
246786 TTTTAAAT-AATTTTAATTATTG
1 TTTTAAATAAAATTTAATT-TTG
246808 T
1 T
246809 GGGCTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTTAAATAAAATTTAATTTTG
Found at i:248714 original size:12 final size:12
Alignment explanation
Indices: 248697--248723 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
248687 CAAGCCCTAG
248697 CCCAATTACAAA
1 CCCAATTACAAA
248709 CCCAATTACAAA
1 CCCAATTACAAA
248721 CCC
1 CCC
248724 TAACTCGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (12 bp):
CCCAATTACAAA
Found at i:249413 original size:13 final size:15
Alignment explanation
Indices: 249383--249414 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
249373 TTATTTTAGC
249383 AAAAATCATAACAAG
1 AAAAATCATAACAAG
249398 AAAAAT-ATAA-AAG
1 AAAAATCATAACAAG
249411 AAAA
1 AAAA
249415 CAGTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 4 0.24
15 6 0.35
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAAATCATAACAAG
Found at i:251442 original size:91 final size:91
Alignment explanation
Indices: 251341--251522 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 91
251331 TGTAGTGATC
251341 CAATCACACTATATAAAAAGATTGGTGGTGACTCCATATTTCGATTTTTAAAATATTGTTCAAGA
1 CAATCACACTATATAAAAAGATTGGTGGTGACTCCATATTTCGATTTTTAAAATATTGTTCAAGA
*
251406 CCTATTTGTTTTCTCAAAAATAAACG
66 CCTATTTGGTTTCTCAAAAATAAACG
251432 CAATCACACTATATAAAAAGATTGGTGGTGACTCCATATTTCGATTTTTAAAATATTGTTCAAGA
1 CAATCACACTATATAAAAAGATTGGTGGTGACTCCATATTTCGATTTTTAAAATATTGTTCAAGA
251497 CCTATTTGGTTTCTCAAAAATAAACG
66 CCTATTTGGTTTCTCAAAAATAAACG
251523 TTTCGACAAT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (91 bp):
CAATCACACTATATAAAAAGATTGGTGGTGACTCCATATTTCGATTTTTAAAATATTGTTCAAGA
CCTATTTGGTTTCTCAAAAATAAACG
Found at i:252987 original size:6 final size:6
Alignment explanation
Indices: 252978--253046 Score: 76
Period size: 6 Copynumber: 12.2 Consensus size: 6
252968 TTAAATTTGT
*
252978 TTTAAA TTTAAA TTTAAA --TAAA TTTAAA TTT-AA TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
253023 TTTAAA ATT--A TTATAAA TTTAAA T
1 TTTAAA TTTAAA TT-TAAA TTTAAA T
253047 AATATCTCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
4 6 0.11
5 6 0.11
6 38 0.72
7 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:253001 original size:16 final size:16
Alignment explanation
Indices: 252980--253048 Score: 77
Period size: 17 Copynumber: 4.2 Consensus size: 16
252970 AAATTTGTTT
252980 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
*
252996 TAAATTTAAATTTAATT
1 TAAATTTAAATTTAA-A
*
253013 TAAGTTTAAATTTAAA
1 TAAATTTAAATTTAAA
*
253029 -ATTATTATAAATTTAAA
1 TA-AATT-TAAATTTAAA
253046 TAA
1 TAA
253049 TATCTCAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
15 1 0.02
16 17 0.40
17 24 0.56
18 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:253027 original size:17 final size:17
Alignment explanation
Indices: 252950--253027 Score: 88
Period size: 17 Copynumber: 4.6 Consensus size: 17
252940 TCAAACTCAT
*
252950 TTTAAATTTATTTTAAGA
1 TTTAAATTTAATTTAA-A
**
252968 -TTAAATTTGTTTTAAA
1 TTTAAATTTAATTTAAA
*
252984 TTTAAATTTAA-ATAAA
1 TTTAAATTTAATTTAAA
*
253000 TTTAAATTTAATTTAAG
1 TTTAAATTTAATTTAAA
253017 TTTAAATTTAA
1 TTTAAATTTAA
253028 AATTATTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
16 16 0.31
17 36 0.69
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:262223 original size:23 final size:23
Alignment explanation
Indices: 262175--262229 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
262165 AGACTTATTT
* * *
262175 AATTTTTTTATTTGATATTTGTA
1 AATTATTTTATATGATATTTATA
262198 AATTATTTTATATG-TATTTATCA
1 AATTATTTTATATGATATTTAT-A
262221 AA-TATTTTA
1 AATTATTTTA
262230 CAAAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (23 bp):
AATTATTTTATATGATATTTATA
Found at i:270260 original size:26 final size:27
Alignment explanation
Indices: 270212--270263 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
270202 TTCTTCATTA
*
270212 TTTAAATTATTTTTATTATGTTTAAAT
1 TTTAAATTATTTTTATTAGGTTTAAAT
270239 TTTAAATTATTTTTATT-GGTTTAAA
1 TTTAAATTATTTTTATTAGGTTTAAA
270264 AACCTATTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.62
Consensus pattern (27 bp):
TTTAAATTATTTTTATTAGGTTTAAAT
Found at i:270765 original size:16 final size:17
Alignment explanation
Indices: 270744--270778 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
270734 TTTTGATTTG
270744 TTTTTAAA-TATTTTAA
1 TTTTTAAAGTATTTTAA
270760 TTTTTAAATGTATTTTAA
1 TTTTTAAA-GTATTTTAA
270778 T
1 T
270779 AATGTGACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTTTAAAGTATTTTAA
Found at i:271484 original size:20 final size:20
Alignment explanation
Indices: 271461--271500 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
271451 CTGCCGGTAG
271461 AACTTCAGTTCTACCGATAC
1 AACTTCAGTTCTACCGATAC
*
271481 AACTTCAGTTTTACCGATAC
1 AACTTCAGTTCTACCGATAC
271501 CTTGAAGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.33
Consensus pattern (20 bp):
AACTTCAGTTCTACCGATAC
Found at i:271762 original size:20 final size:20
Alignment explanation
Indices: 271739--271780 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
271729 CTATCGGTAG
271739 AACTTCACTTCTACCAATAC
1 AACTTCACTTCTACCAATAC
* * *
271759 AACTTTAGTTCTATCAATAC
1 AACTTCACTTCTACCAATAC
271779 AA
1 AA
271781 GTATGCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.33
Consensus pattern (20 bp):
AACTTCACTTCTACCAATAC
Found at i:276361 original size:19 final size:20
Alignment explanation
Indices: 276337--276380 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
276327 ATTGATGCAA
276337 AAAAATAATTAAATTA-TTT
1 AAAAATAATTAAATTAGTTT
**
276356 AAAAATAATTATTTTAGTTT
1 AAAAATAATTAAATTAGTTT
276376 AAAAA
1 AAAAA
276381 ATCATAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAAATAATTAAATTAGTTT
Found at i:277507 original size:33 final size:34
Alignment explanation
Indices: 277458--277529 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
277448 TTTATTATTA
277458 ATTTTTT--AAAATATTTTTGTATTGTTATAT-T
1 ATTTTTTCAAAAATATTTTTGTATTGTTATATAT
* *
277489 -TTTTTTCAAAAATTATTTTTTTATTTTTATATAT
1 ATTTTTTCAAAAA-TATTTTTGTATTGTTATATAT
277523 ATTTTTT
1 ATTTTTT
277530 AGATTTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 6 0.18
32 4 0.12
33 17 0.50
34 1 0.03
35 6 0.18
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (34 bp):
ATTTTTTCAAAAATATTTTTGTATTGTTATATAT
Done.