Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009288.1 Hibiscus syriacus cultivar Beakdansim tig00112981_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 633898
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 3 of 3
Found at i:422636 original size:33 final size:33
Alignment explanation
Indices: 422594--422708 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
422584 CAAAATCGCA
422594 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
422627 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
422660 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
422693 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
422709 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:424842 original size:92 final size:93
Alignment explanation
Indices: 424402--424869 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
424392 TAGATTGCTT
*
424402 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
424467 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
424495 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
424560 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
424588 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
424653 TTTGTCTTTGTTTTATCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
424681 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
424746 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
424774 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
424838 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
424865 AGTAA
1 AGTAA
424870 TGCAATCCAT
Statistics
Matches: 371, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
91 4 0.01
92 88 0.24
93 279 0.75
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:424957 original size:19 final size:19
Alignment explanation
Indices: 424917--425044 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
424907 TAGTTTACTT
* *
424917 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
424937 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
424956 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
424975 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
424989 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
425008 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
425022 TCGCAACGCGAAACC-AAA
1 TCGCAACGCGAAACCAAAA
425040 TCGCA
1 TCGCA
425045 TTGCGATTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 9 0.10
19 38 0.43
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:424996 original size:33 final size:32
Alignment explanation
Indices: 424953--425044 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
424943 CGCGAAACCA
**
424953 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
424985 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
425018 AAGATCGCAACGCGAAACC-AAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
425045 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
32 10 0.18
33 46 0.82
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:425067 original size:19 final size:19
Alignment explanation
Indices: 425040--425174 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
425030 CGAAACCAAA
*
425040 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
425059 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
425075 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
425092 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
425108 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
425125 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
425144 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
425164 TCGTGTTGCGA
1 TCGCGTTGCGA
425175 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:425081 original size:14 final size:14
Alignment explanation
Indices: 425062--425118 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
425052 TTTCATTTCG
425062 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
425076 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
425093 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
425109 CGTTGCGATT
1 CGTTGCGATT
425119 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:425087 original size:33 final size:33
Alignment explanation
Indices: 425045--425137 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
425035 CCAAATCGCA
*
425045 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
425078 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
425111 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
425138 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:425657 original size:21 final size:21
Alignment explanation
Indices: 425603--425663 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
425593 CTCGAGAGTC
*
425603 CCCTCCCACCGTTCAAGAGGT
1 CCCTCCCACCATTCAAGAGGT
* ** * *
425624 CACTGTCATCATTGAAGAGGT
1 CCCTCCCACCATTCAAGAGGT
425645 CCCTCCCACCATTCAAGAG
1 CCCTCCCACCATTCAAGAG
425664 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (21 bp):
CCCTCCCACCATTCAAGAGGT
Found at i:427084 original size:14 final size:14
Alignment explanation
Indices: 427065--427100 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
427055 ATTGTTTAAT
427065 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
427079 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
427093 TGATTTGT
1 TGATTTGT
427101 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:427223 original size:19 final size:20
Alignment explanation
Indices: 427207--427252 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
427197 AAAAATGACT
427207 ATCGCAATGC-GAAATGAAA
1 ATCGCAATGCGGAAATGAAA
427226 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGGAAATGAAA
427246 ATCGCAA
1 ATCGCAA
427253 CGAGAGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAATGCGGAAATGAAA
Found at i:427314 original size:33 final size:33
Alignment explanation
Indices: 427277--427587 Score: 222
Period size: 33 Copynumber: 8.9 Consensus size: 33
427267 TGCGTTTATA
427277 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* * * *
427310 ATTTCGCATTGCGATT-TTTCATTTCGCA-TTGC
1 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC
* * * *
427342 GATTCTCTCGTTGTGATTTTCATTTCGCATTGCGATTTTC
1 -ATT-TCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
427382 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
427415 ATTTCGCATTACGATTTTCATTTCGCATGCGATTCTCTCGATTTTC
1 ATTTCGCATTGCGA--TTC---T--C-T-CG--T-T-GCGATTTTC
* *
427461 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
427495 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
427527 ATTTCCGCA-TGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
427560 A-TTCGCATTGCGATTCTCTCGTTGCGAT
1 ATTTCGCATTGCGATTCTCTCGTTGCGAT
427588 GTAATTTCCG
Statistics
Matches: 222, Mismatches: 26, Indels: 61
0.72 0.08 0.20
Matches are distributed among these distances:
31 5 0.02
32 52 0.23
33 74 0.33
34 19 0.09
35 8 0.04
36 6 0.03
38 14 0.06
39 4 0.02
40 11 0.05
41 1 0.00
42 3 0.01
44 1 0.00
45 3 0.01
46 12 0.05
47 9 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:427323 original size:19 final size:19
Alignment explanation
Indices: 427299--427574 Score: 189
Period size: 19 Copynumber: 16.4 Consensus size: 19
427289 GATTCTCTCG
427299 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
427318 TTGCGATTTTTCATTTCGCA
1 TTGCGA-TTTTCATTTCGCA
*
427338 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
427352 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
427371 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
427390 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
427404 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
427423 TTACGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
427442 -TGCGA--TTC---T--C-
1 TTGCGATTTTCATTTCGCA
427452 -T-CGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
427470 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
427484 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
427503 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
427517 TTGCGA-TTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
427536 -TGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
427549 TTGGGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
427567 TTGCGATT
1 TTGCGATT
427575 CTCTCGTTGC
Statistics
Matches: 205, Mismatches: 14, Indels: 77
0.69 0.05 0.26
Matches are distributed among these distances:
9 3 0.01
10 1 0.00
11 4 0.02
13 1 0.00
14 39 0.19
15 5 0.02
16 26 0.13
17 22 0.11
18 17 0.08
19 59 0.29
20 28 0.14
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:427403 original size:52 final size:52
Alignment explanation
Indices: 427277--427482 Score: 334
Period size: 52 Copynumber: 4.0 Consensus size: 52
427267 TGCGTTTATA
427277 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA-TTTTC
*
427330 ATTTCGCATTGCGATTCTCTCGTTGTGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
427382 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
427434 ATTTCGCA-TGCGA-T-TCTC--T-CGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
427481 AT
1 AT
427483 GTTGGGATTT
Statistics
Matches: 148, Mismatches: 4, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
46 12 0.08
47 17 0.11
49 4 0.03
50 1 0.01
51 5 0.03
52 63 0.43
53 46 0.31
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:427464 original size:27 final size:28
Alignment explanation
Indices: 427325--427516 Score: 102
Period size: 26 Copynumber: 7.0 Consensus size: 28
427315 GCATTGCGAT
427325 TTTTCATTTCGCATTGCGATTCTCTCG-
1 TTTTCATTTCGCATTGCGATTCTCTCGA
* * * * *
427352 TTGTGATTT-TCATTTCGCA-T-T-GCGA
1 TTTTCATTTCGCATTGCG-ATTCTCTCGA
427377 TTTTCATTTCGCATTGCGATTCTCTCG-
1 TTTTCATTTCGCATTGCGATTCTCTCGA
* * * *
427404 -TTGCGATTT-TCATTTCGCA-T-T-ACGA
1 TTTTC-ATTTCGCATTGCG-ATTCTCTCGA
**
427429 TTTTCATTTCGCATGC-GATTCTCTCGA
1 TTTTCATTTCGCATTGCGATTCTCTCGA
* *
427456 TTTTCATTTCCGCATTGCGATTTTCATGTTGGGA
1 TTTTCATTT-CGCATTGCGA--TTC-T-CT-CGA
427490 TTTTCATTTCGCATTGCGATTCTCTCG
1 TTTTCATTTCGCATTGCGATTCTCTCG
427517 TTGCGATTTC
Statistics
Matches: 119, Mismatches: 25, Indels: 41
0.64 0.14 0.22
Matches are distributed among these distances:
24 5 0.04
25 16 0.13
26 31 0.26
27 26 0.22
28 8 0.07
29 3 0.03
30 1 0.01
31 6 0.05
32 1 0.01
33 11 0.09
34 11 0.09
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (28 bp):
TTTTCATTTCGCATTGCGATTCTCTCGA
Found at i:427587 original size:64 final size:66
Alignment explanation
Indices: 427326--427606 Score: 273
Period size: 64 Copynumber: 4.3 Consensus size: 66
427316 CATTGCGATT
* * * *
427326 TTTCATTT-CGCATTGCGATTCTC-TCGTTGTGATTTTCATTTCGCATTGCGATT-T-TCATTTC
1 TTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
427387 GCA
65 G-A
* **
427390 TTGCGATTCTCTCG--TTGCGATTTTCATTTCGCATTACGATTTTCATTTCGCA-TGCGATTCTC
1 TTTC-ATT-TC-CGCATTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTC
*
427452 TCGAT----
58 TCGTTGCGA
427457 TTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
1 TTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
427522 A
66 A
427523 TTTCATTTCCGCA-TGCGATTTTCATGTTGGGATTTTCA-TTCGCATTGCGATTCTCTCGTTGCG
1 TTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
427586 A
66 A
* * **
427587 TGTAATTTCCGTGTTGCGAT
1 TTTCATTTCCGCATTGCGAT
427607 AGTCAAATGC
Statistics
Matches: 184, Mismatches: 14, Indels: 37
0.78 0.06 0.16
Matches are distributed among these distances:
61 17 0.09
62 14 0.08
63 1 0.01
64 41 0.22
65 36 0.20
66 39 0.21
67 3 0.02
68 2 0.01
69 3 0.02
70 7 0.04
71 18 0.10
72 3 0.02
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (66 bp):
TTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
A
Found at i:430092 original size:24 final size:23
Alignment explanation
Indices: 430052--430097 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
430042 CTGAAACATC
430052 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGTGTATT-ACCAAT
*
430076 ATCAAAGTCCG-GATATTACCAA
1 ATCAAAATCCGTG-TATTACCAA
430098 GACCAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (23 bp):
ATCAAAATCCGTGTATTACCAAT
Found at i:430804 original size:20 final size:20
Alignment explanation
Indices: 430776--431005 Score: 228
Period size: 20 Copynumber: 11.5 Consensus size: 20
430766 AAATTTCAGT
* * *
430776 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
430796 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
430816 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
430836 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
430856 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
430876 GTTACGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
430896 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
430916 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
430936 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
430956 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
430976 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
430996 GTTGCGATTT
1 GTTGCGATTT
431006 TGGAAACTGA
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:434659 original size:157 final size:159
Alignment explanation
Indices: 434354--434670 Score: 586
Period size: 157 Copynumber: 2.0 Consensus size: 159
434344 AATTTAAAAT
*
434354 TATTATAAATTTTAAAATTATTTTTTTTGTTTTTCATTGAAAATGATTTCACCCTCTAAAATTTT
1 TATTATAAATTTT-AAATTATTTTTTGTGTTTTTCATTGAAAATGATTTCACCCTCTAAAATTTT
434419 TTAAATTTAAGCTCGTTCTCCTGAAATTTTAAAAGTTCAAATTTATCCTTTCGATATAAAATCTT
65 TTAAATTTAAGCTCGTTCTCCTGAAATTTTAAAAGTTCAAATTTATCCTTTCGATATAAAATCTT
434484 GTGTCGTTCCCTATATTTCCTGGTCCACTC
130 GTGTCGTTCCCTATATTTCCTGGTCCACTC
434514 TATTATAAATTTT-AA-T-TTTTTTGTGTTTTTCATTGAAAACTGATTTCACCCTCTAAAATTTT
1 TATTATAAATTTTAAATTATTTTTTGTGTTTTTCATTGAAAA-TGATTTCACCCTCTAAAATTTT
434576 TTAAATTTAAGCTCGTTCTCCTGAAATTTTAAAAGTTCAAATTTATCCTTTCGATATAAAATCTT
65 TTAAATTTAAGCTCGTTCTCCTGAAATTTTAAAAGTTCAAATTTATCCTTTCGATATAAAATCTT
434641 GTGTCGTTCCCTATATTTCCTGGTCCACTC
130 GTGTCGTTCCCTATATTTCCTGGTCCACTC
434671 AATTTCAAAC
Statistics
Matches: 155, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
156 22 0.14
157 118 0.76
158 2 0.01
160 13 0.08
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.47
Consensus pattern (159 bp):
TATTATAAATTTTAAATTATTTTTTGTGTTTTTCATTGAAAATGATTTCACCCTCTAAAATTTTT
TAAATTTAAGCTCGTTCTCCTGAAATTTTAAAAGTTCAAATTTATCCTTTCGATATAAAATCTTG
TGTCGTTCCCTATATTTCCTGGTCCACTC
Found at i:436389 original size:38 final size:39
Alignment explanation
Indices: 436294--436392 Score: 98
Period size: 38 Copynumber: 2.6 Consensus size: 39
436284 TTTCACGCGT
*
436294 CTTCAAGCTAAATAT-A-AAGACTCCACGACTACATGACGT
1 CTTCAAG-TAAAT-TGAGAAGACTCCACGACTACATGACGC
* * * *
436333 CTTC-AGGAAAATGAAGAAGAC-CCACGATTGCATGACGC
1 CTTCAAGTAAATTG-AGAAGACTCCACGACTACATGACGC
436371 CTTCAAGTAAATTGAGAAGACT
1 CTTCAAGTAAATTGAGAAGACT
436393 TCAGGAATGC
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
36 1 0.02
37 3 0.06
38 28 0.58
39 16 0.33
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (39 bp):
CTTCAAGTAAATTGAGAAGACTCCACGACTACATGACGC
Found at i:439356 original size:19 final size:19
Alignment explanation
Indices: 439313--439356 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
439303 TTTAAAAATC
439313 AATA-AAAATGCAATAAAA
1 AATATAAAATGCAATAAAA
*
439331 AAT-TAAAATTCAATAAAA
1 AATATAAAATGCAATAAAA
439349 AATATAAA
1 AATATAAA
439357 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (19 bp):
AATATAAAATGCAATAAAA
Found at i:441265 original size:22 final size:22
Alignment explanation
Indices: 441226--441267 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
441216 ACTTCATATA
*
441226 AAATATTTATAAAGTATCAACT
1 AAATATTTACAAAGTATCAACT
441248 AAATATTTACATAA-TATCAA
1 AAATATTTACA-AAGTATCAA
441268 AATACAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATATTTACAAAGTATCAACT
Found at i:445221 original size:24 final size:24
Alignment explanation
Indices: 445193--445242 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
445183 TTCCATGAAA
*
445193 AGTTCATTGCTTTTCTGTTTATCG
1 AGTTCATTGCTTTCCTGTTTATCG
445217 AGTTCATTGCTTTCCTGTTTATCG
1 AGTTCATTGCTTTCCTGTTTATCG
445241 AG
1 AG
445243 CAATAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (24 bp):
AGTTCATTGCTTTCCTGTTTATCG
Found at i:447245 original size:60 final size:62
Alignment explanation
Indices: 447159--447292 Score: 170
Period size: 62 Copynumber: 2.2 Consensus size: 62
447149 AAGATAATAT
* * *
447159 AAAG-TAT-AAATAATCCTCCAACTATA-GG-GTAATATTTTGTTAAGTCACCT-GACTATTA
1 AAAGTTATAAAATGATCATCCAACTATAGGGTGTAATATTTTGTTAAGTC-CCTCAACTATTA
** *
447217 AAAGTTATAAAATGATCATCCAACTATAGGGTGTTTTATTTTGTTGAGTCCCTCAACTATTA
1 AAAGTTATAAAATGATCATCCAACTATAGGGTGTAATATTTTGTTAAGTCCCTCAACTATTA
447279 AAAGTTATAAAATG
1 AAAGTTATAAAATG
447293 GTTACCCGAC
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
58 4 0.06
59 3 0.05
60 17 0.26
61 5 0.08
62 36 0.55
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (62 bp):
AAAGTTATAAAATGATCATCCAACTATAGGGTGTAATATTTTGTTAAGTCCCTCAACTATTA
Found at i:448950 original size:2 final size:2
Alignment explanation
Indices: 448943--449067 Score: 148
Period size: 2 Copynumber: 61.5 Consensus size: 2
448933 ACACGAGAAC
* *
448943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG GA TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* *
448986 T- TCA T- TCA CGA GA -A CTA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA T-A TA T-A -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
449027 TA TA TA TA 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 TA TA TA TA T
449068 GGATATGATT
Statistics
Matches: 110, Mismatches: 5, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.03
2 102 0.93
3 5 0.05
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:449398 original size:22 final size:22
Alignment explanation
Indices: 449373--449442 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
449363 CGCTGAATGT
*
449373 TGAACGATTCAATATTCAACGC
1 TGAACGATTCAACATTCAACGC
*
449395 TGAACAATTCAACATTCAACGC
1 TGAACGATTCAACATTCAACGC
*
449417 TGAACGATTCAACATTCAGCGC
1 TGAACGATTCAACATTCAACGC
449439 TGAA
1 TGAA
449443 TAATTCCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.24
Consensus pattern (22 bp):
TGAACGATTCAACATTCAACGC
Found at i:451566 original size:62 final size:61
Alignment explanation
Indices: 451383--451569 Score: 234
Period size: 60 Copynumber: 3.1 Consensus size: 61
451373 ATTTTATTGC
* * * *
451383 CATTATTTCATCACTATTCCTTGATTTTTTTTATCAGCTTCATGTTTAGTATCTTAATTAT
1 CATTAATTCATCACTATTCTTTGATTTTTTTTATCAGCTACACGTTTAGTATCTTAATTAT
* * * *
451444 TATTAATTCATCACTATT-TCTT-ATTTTTTTTATCAACTAAACGTTTAGTATTTTAATTAT
1 CATTAATTCATCACTATTCT-TTGATTTTTTTTATCAGCTACACGTTTAGTATCTTAATTAT
*** *
451504 CATTAATTCATTTTTATTCTTTGACTTTTTTTTATCAGCTACACGTTTAGTATCTTATTTAT
1 CATTAATTCATCACTATTCTTTGA-TTTTTTTTATCAGCTACACGTTTAGTATCTTAATTAT
451566 CATT
1 CATT
451570 TTTATTCCAT
Statistics
Matches: 106, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
60 49 0.46
61 20 0.19
62 37 0.35
ACGTcount: A:0.25, C:0.14, G:0.05, T:0.55
Consensus pattern (61 bp):
CATTAATTCATCACTATTCTTTGATTTTTTTTATCAGCTACACGTTTAGTATCTTAATTAT
Found at i:457255 original size:16 final size:16
Alignment explanation
Indices: 457236--457270 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
457226 CCATAACCCC
*
457236 TATCATACATATATCA
1 TATCATACATACATCA
*
457252 TATCATGCATACATCA
1 TATCATACATACATCA
457268 TAT
1 TAT
457271 AACAAATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (16 bp):
TATCATACATACATCA
Found at i:457492 original size:23 final size:23
Alignment explanation
Indices: 457466--457529 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
457456 CAGCTCATAT
457466 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
457489 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
457512 AATTGTACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
457530 TATAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:459305 original size:21 final size:21
Alignment explanation
Indices: 459281--459325 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
459271 TGTTGTTCGT
* *
459281 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
459302 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
459323 TTG
1 TTG
459326 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:462250 original size:16 final size:16
Alignment explanation
Indices: 462231--462267 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
462221 CCATAACCCC
*
462231 TATCATACATATATCA
1 TATCATACATACATCA
*
462247 TATCATGCATACATCA
1 TATCATACATACATCA
462263 TATCA
1 TATCA
462268 CAAATCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.35
Consensus pattern (16 bp):
TATCATACATACATCA
Found at i:462491 original size:23 final size:23
Alignment explanation
Indices: 462461--462524 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
462451 CAGCTCATAT
462461 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
462484 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
462507 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
462525 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:464303 original size:21 final size:21
Alignment explanation
Indices: 464279--464319 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
464269 TGTTGTTCGT
* *
464279 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
464300 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
464320 TTTGCCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:471649 original size:22 final size:22
Alignment explanation
Indices: 471596--471649 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
471586 CTTCGAGACA
*
471596 ATTCTATGTGGTCATTTGGGAC
1 ATTCTATGTGGTCATTTAGGAC
*
471618 A-TATATGTGGTCATTTAGGAC
1 ATTCTATGTGGTCATTTAGGAC
471639 ATTCTATGTGG
1 ATTCTATGTGG
471650 CACTTCGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (22 bp):
ATTCTATGTGGTCATTTAGGAC
Found at i:471677 original size:24 final size:24
Alignment explanation
Indices: 471640--471689 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
471630 ATTTAGGACA
* *
471640 TTCTATGTGGCACTTCGGTGCATT
1 TTCTATGCGACACTTCGGTGCATT
*
471664 TTCTATGCGACACTTCGGTGTATT
1 TTCTATGCGACACTTCGGTGCATT
471688 TT
1 TT
471690 ATACGAGCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.44
Consensus pattern (24 bp):
TTCTATGCGACACTTCGGTGCATT
Found at i:475593 original size:20 final size:20
Alignment explanation
Indices: 475568--475880 Score: 247
Period size: 20 Copynumber: 15.4 Consensus size: 20
475558 ATTTTGCCAG
** *
475568 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
**
475588 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* *
475608 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* ** *
475627 CTATCGCAACTAGTATCCGTAAA
1 -AATCGCAACGCGAATCCGT--A
* *
475650 AATCACAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
475670 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
475691 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
475711 AATCGCAACGCGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
475731 AATCGCAACGCG-ATTCGGA
1 AATCGCAACGCGAATCCGTA
* * *
475750 ATATCGCAACGAGAATACGTT
1 A-ATCGCAACGCGAATCCGTA
* *
475771 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
475791 AATCGCAACGAGAATACGTAA
1 AATCGCAACGCGAATCCGT-A
* **
475812 AATCGCAACGAGAATTTGTA
1 AATCGCAACGCGAATCCGTA
*
475832 AATCGCAACGAGAATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
475852 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGTA
475872 AATCGCAAC
1 AATCGCAAC
475881 ACTGAAATTT
Statistics
Matches: 239, Mismatches: 42, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
19 7 0.03
20 175 0.73
21 41 0.17
22 15 0.06
23 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:475815 original size:101 final size:100
Alignment explanation
Indices: 475690--475879 Score: 249
Period size: 101 Copynumber: 1.9 Consensus size: 100
475680 ACAATACGTA
* * * * * *
475690 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACGTAAATCGCAACGCG-ATTCGGAATAT
1 AAATCGCAACGAGAATACGTAAATCGCAACGAGAATACGTAAATCGCAACGAGAATCCGGAA-AT
*
475754 CGCAACGAGAATAC-GTTAATCGCAATGCGTATCCGT
65 CGCAACGAGAAT-CTGTAAATCGCAATGCGTATCCGT
** *
475790 AAATCGCAACGAGAATACGTAAAATCGCAACGAGAATTTGTAAATCGCAACGAGAATCCGTAAAT
1 AAATCGCAACGAGAATACGT-AAATCGCAACGAGAATACGTAAATCGCAACGAGAATCCGGAAAT
475855 CGCAACGAGAATCTGTAAATCGCAA
65 CGCAACGAGAATCTGTAAATCGCAA
475880 CACTGAAATT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
100 18 0.23
101 53 0.69
102 6 0.08
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (100 bp):
AAATCGCAACGAGAATACGTAAATCGCAACGAGAATACGTAAATCGCAACGAGAATCCGGAAATC
GCAACGAGAATCTGTAAATCGCAATGCGTATCCGT
Found at i:475833 original size:121 final size:122
Alignment explanation
Indices: 475568--475861 Score: 392
Period size: 121 Copynumber: 2.4 Consensus size: 122
475558 ATTTTGCCAG
* * ** * *
475568 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCGATTCTGACTATCG
1 AATCGCAACGCGAATATGTAAATCGCAACGCGAATACGTAAATCGCAACGCGATTCGGAATATCG
* * *
475633 CAACTAGTATCCGTAAAAATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAA
66 CAACGAGAATACGT-AAAATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAA
* **
475691 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACGTAAATCGCAACGCGATTCGGAATATCG
1 AATCGCAACGCGAATATGTAAATCGCAACGCGAATACGTAAATCGCAACGCGATTCGGAATATCG
* * * *
475756 CAACGAGAATACGT-TAATCGCAATGCGTATCCGTAAATCGCAACGAGAATACGTAA
66 CAACGAGAATACGTAAAATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAA
* * * *
475812 AATCGCAACGAGAATTTGTAAATCGCAACGAGAATCCGTAAATCGCAACG
1 AATCGCAACGCGAATATGTAAATCGCAACGCGAATACGTAAATCGCAACG
475862 AGAATCTGTA
Statistics
Matches: 149, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
121 82 0.55
123 67 0.45
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (122 bp):
AATCGCAACGCGAATATGTAAATCGCAACGCGAATACGTAAATCGCAACGCGATTCGGAATATCG
CAACGAGAATACGTAAAATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAA
Found at i:476742 original size:24 final size:24
Alignment explanation
Indices: 476684--476730 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
476674 AGTCAGTATT
*
476684 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
476708 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
476731 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:479239 original size:20 final size:20
Alignment explanation
Indices: 479210--479263 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
479200 GACATTCATT
479210 TGACTATCGCAACA-CTGAAA
1 TGACTATCGCAACATCT-AAA
* *
479230 TGACTTTCGCAATCATCTTAA
1 TGACTATCGCAA-CATCTAAA
479251 TGACTATCGCAAC
1 TGACTATCGCAAC
479264 GCGAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.41
21 15 0.52
22 2 0.07
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (20 bp):
TGACTATCGCAACATCTAAA
Found at i:479317 original size:33 final size:33
Alignment explanation
Indices: 479256--479456 Score: 224
Period size: 33 Copynumber: 5.8 Consensus size: 33
479246 CTTAATGACT
* * *
479256 ATCGCAACGCGAAAATTACAATCGCAACGAGAGA
1 ATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
*
479290 ATCGCAATGCGAAATGAAAATCGCAACGTA-AAA
1 ATCGCAATGCGAAATGAAAATCGCAACG-AGAGA
** * *
479323 ATTACAACGCGAATATGAATATCGCAACGCAGAAATGA
1 ATCGCAATGCGAA-ATGAAAATCGCAACG-AG--A-GA
479361 CTATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 --ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
479396 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
479429 ATCGCAATGCGAAATTAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
479457 CGAATTTAGT
Statistics
Matches: 143, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
33 86 0.60
34 26 0.18
35 2 0.01
36 1 0.01
37 1 0.01
38 3 0.02
39 14 0.10
40 10 0.07
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:479352 original size:20 final size:19
Alignment explanation
Indices: 479290--479423 Score: 90
Period size: 19 Copynumber: 7.5 Consensus size: 19
479280 CAACGAGAGA
* *
479290 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAT
*
479309 ATCGCAACG-TAAA--AAT
1 ATCGCAACGCGAAATGAAT
*
479325 -T-ACAACGCGAATATGAAT
1 ATCGCAACGCGAA-ATGAAT
*
479343 ATCGCAACGCAGAAATGACT
1 ATCGCAACGC-GAAATGAAT
* *
479363 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAT
*
479382 ATCGCAA--CGAGA-G-A-
1 ATCGCAACGCGAAATGAAT
* *
479396 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAT
479415 ATCGCAACG
1 ATCGCAACG
479424 AGGGAATCGC
Statistics
Matches: 90, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
14 12 0.13
15 4 0.04
16 8 0.09
17 5 0.06
18 7 0.08
19 31 0.34
20 20 0.22
21 3 0.03
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAT
Found at i:479380 original size:73 final size:66
Alignment explanation
Indices: 479260--479456 Score: 216
Period size: 73 Copynumber: 2.9 Consensus size: 66
479250 ATGACTATCG
* * *
479260 CAACGCGAAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGTA-AAAA
1 CAACGCG-AAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACG-AGAAAA
*
479324 TTA
64 TCA
* *
479327 CAACGCGAATATGAATATCGCAACGCAGAAATGACTATCGCAATGCGAAATGAAAATCGCAACGA
1 CAACGCGAA-ATGAAAATCGCAACG-AG---GGA--ATCGCAATGCGAAATGAAAATCGCAACGA
* *
479392 GAGAATCG
59 GAAAATCA
* *
479400 CAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATTAAAATCGCAACG
1 CAACGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACG
479457 CGAATTTAGT
Statistics
Matches: 111, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
66 29 0.26
67 19 0.17
68 4 0.04
71 4 0.04
72 15 0.14
73 40 0.36
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.15
Consensus pattern (66 bp):
CAACGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATC
A
Found at i:479441 original size:106 final size:106
Alignment explanation
Indices: 479249--479457 Score: 296
Period size: 106 Copynumber: 2.0 Consensus size: 106
479239 CAATCATCTT
* *
479249 AATGACTATCGCAACGCGAAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
* *
479314 AACGTAAAAATTACAACGCGAATATGAATATCGCAACGCAGA
66 AACGTAAAAATCACAACGCGAA-ATGAAAATCGCAACGCAGA
*
479356 AATGACTATCGCAATGCG-AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
** * * *
479420 AACG-AGGGAATCGCAATGCGAAATTAAAATCGCAACGC
66 AACGTA-AAAATCACAACGCGAAATGAAAATCGCAACGC
479458 GAATTTAGTT
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
105 15 0.16
106 59 0.65
107 17 0.19
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (106 bp):
AATGACTATCGCAACGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
AACGTAAAAATCACAACGCGAAATGAAAATCGCAACGCAGA
Found at i:479510 original size:33 final size:33
Alignment explanation
Indices: 479466--479534 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
479456 GCGAATTTAG
* * *
479466 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCATTGCGATTTTCA
**
479499 TTTCGCATTGCGATTCTCTTGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCATTGCGATTTTCA
479532 TTT
1 TTT
479535 TTGCCTTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.51
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCATTGCGATTTTCA
Found at i:479652 original size:14 final size:14
Alignment explanation
Indices: 479633--479669 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
479623 CATCAATTAA
479633 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
479647 ACAAATCATCTTTT
1 ACAAATCAACTTTT
479661 ACAAATCAA
1 ACAAATCAA
479670 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:481108 original size:42 final size:42
Alignment explanation
Indices: 481062--481145 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
481052 TGATGACAGT
* *
481062 GGCCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTAAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * * *
481104 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTAAACGATAGGAGGGGACTCTCGAGGAATGATAGG
481146 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTAAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:482019 original size:20 final size:20
Alignment explanation
Indices: 481991--482087 Score: 88
Period size: 20 Copynumber: 4.7 Consensus size: 20
481981 TGAAAATAAA
481991 ATACGCGTTGCGATTTACGG
1 ATACGCGTTGCGATTTACGG
* * *
482011 ATACACGTTGTGATTTTACGT
1 ATACGCGTTGCGA-TTTACGG
*
482032 AT-TGTCGTTGCGATTTACGG
1 ATACG-CGTTGCGATTTACGG
* *
482052 ATACGCGTTACGATTTTTACGA
1 ATACGCGTTGCGA--TTTACGG
*
482074 ATACTCGTTGCGAT
1 ATACGCGTTGCGAT
482088 AGTCAGAATC
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
20 27 0.45
21 16 0.27
22 17 0.28
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
ATACGCGTTGCGATTTACGG
Found at i:482053 original size:41 final size:42
Alignment explanation
Indices: 481990--482087 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 42
481980 TTGAAAATAA
* **
481990 AATACGCGTTGCGATTTACGGATACACGTTGTGA-TTTTACG
1 AATACTCGTTGCGATTTACGGATACACGTTACGATTTTTACG
* ** *
482031 TATTGTCGTTGCGATTTACGGATACGCGTTACGATTTTTACG
1 AATACTCGTTGCGATTTACGGATACACGTTACGATTTTTACG
482073 AATACTCGTTGCGAT
1 AATACTCGTTGCGAT
482088 AGTCAGAATC
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
41 27 0.59
42 19 0.41
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (42 bp):
AATACTCGTTGCGATTTACGGATACACGTTACGATTTTTACG
Found at i:482077 original size:22 final size:22
Alignment explanation
Indices: 482045--482087 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
482035 GTCGTTGCGA
*
482045 TTTACGGATACGCGTTACGATT
1 TTTACGAATACGCGTTACGATT
* *
482067 TTTACGAATACTCGTTGCGAT
1 TTTACGAATACGCGTTACGAT
482088 AGTCAGAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (22 bp):
TTTACGAATACGCGTTACGATT
Found at i:482119 original size:20 final size:20
Alignment explanation
Indices: 482096--482148 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
482086 ATAGTCAGAA
*
482096 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
482116 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
482136 TCGCGTTGCGATT
1 TCGCGTTGCGATT
482149 CTGGCAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:485622 original size:59 final size:59
Alignment explanation
Indices: 485502--485633 Score: 146
Period size: 59 Copynumber: 2.2 Consensus size: 59
485492 TTAATTGACT
* * *
485502 ATTTTATAACTTTTAATAGTCAATTGACTCAACAAAACAATGTCATATAATTGAGAGATC
1 ATTTTGTAACTTTTAATAGTCAA-TGACTCAAAAAAACAATGTCATATAATCGAGAGATC
* *
485562 ATTTTGTAACTTTTAATAGTCAGA-GACTCAATAAAAAACAAT-T-TTATAATCGAGGGATC
1 ATTTTGTAACTTTTAATAGTCA-ATGACTC-A-AAAAAACAATGTCATATAATCGAGAGATC
485621 ATTTGTGT-ACTTT
1 ATTT-TGTAACTTT
485634 ACCCTAATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
59 27 0.43
60 26 0.41
61 10 0.16
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTCAATGACTCAAAAAAACAATGTCATATAATCGAGAGATC
Found at i:489502 original size:17 final size:18
Alignment explanation
Indices: 489470--489503 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
489460 GTTGAGCTGG
*
489470 CTGTTAGGATTGGTTATT
1 CTGTTAAGATTGGTTATT
489488 CTGTTAAGA-TGGTTAT
1 CTGTTAAGATTGGTTAT
489504 GAGCTACTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.06, G:0.26, T:0.47
Consensus pattern (18 bp):
CTGTTAAGATTGGTTATT
Found at i:494217 original size:13 final size:13
Alignment explanation
Indices: 494199--494224 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
494189 CGATGGGTTT
494199 TTAAATAAATAAA
1 TTAAATAAATAAA
494212 TTAAATAAATAAA
1 TTAAATAAATAAA
494225 GGCTAAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAATAAATAAA
Found at i:495543 original size:33 final size:32
Alignment explanation
Indices: 495497--495561 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
495487 TTAAGTCATG
* *
495497 TAAGGAAAATGTCTCAATTGAGACAAATTTTT
1 TAAGGAAAATGTCTCAAGTGAGACAAAGTTTT
*
495529 TAAGTGAAAATGTCTCAAGTGAGATAAAGTTTT
1 TAAG-GAAAATGTCTCAAGTGAGACAAAGTTTT
495562 ATTTAGAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (32 bp):
TAAGGAAAATGTCTCAAGTGAGACAAAGTTTT
Found at i:495695 original size:71 final size:71
Alignment explanation
Indices: 495534--496125 Score: 609
Period size: 71 Copynumber: 8.5 Consensus size: 71
495524 TTTTTTAAGT
* * * * * ** *
495534 GAAAATGTCTCAAGTGAGAT-AAAGTTTTATTT-AGAGAGAAATTGTCTTGAGTGTGATGAAAAT
1 GAAAATATCTCAAGTGAGATGAAA-TTTTGTTTCA-AGAGAAACTGTCTCGAGTGAGACAAAAAA
495597 TTTCCAAGG
64 TTT-CAAGG
* * *
495606 GAAAATATCTCATGTGAGATGAAATTTTGTTTCAAGAGAAATTGTTTCGAGTGAGACAAAAAATT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACAAAAAATT
495671 TCAAGG
66 TCAAGG
* * * * *
495677 GAAAATATCTCAAGTGAGACGAAGTTTTATTTCAAGAGAAACTGTCTCGA--GAGAC--GAATTT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACAAAAAATT
495738 TCAAGG
66 TCAAGG
* * * * * * *
495744 GAAAATATTTCAACTAAGATAAAATTTTGTTTCGAGAGAAACTGTCTTGAGTGAGACAAAAATTT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACAAAAAATT
495809 TCAAGG
66 TCAAGG
* * * * **
495815 GAAAATATCTCAAGTGAGATGAAATTTTGTTACGAGAGAAACTGTCTCGACTAAGATGAAAAATT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACAAAAAATT
495880 TCACA-G
66 TCA-AGG
* ** * * **
495886 GAAAATACCTCAAGTGAGATGAAATTTTGTTTTGAGAGAAACTATCTTGAGTGAGATGAAAAATT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACAAAAAATT
495951 TCACA-G
66 TCA-AGG
* * ** *
495957 GAAAGTATCTCAAGTGAGATGAAAATTTGTTTTTAGAGAAACTGTCTCGAGTGAGA-TAAAAA-T
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACAAAAAATT
*
496020 T-AAAG
66 TCAAGG
* * *
496025 GAAAATATCTCAAGTGAGATGAAATTTTATTT-AGAGAGAAAC--TCTCGAGTGAGACAGAAATT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCA-AGAGAAACTGTCTCGAGTGAGACAAAAAAT
*
496087 TTTAAGG
65 TTCAAGG
*
496094 GAAAATATCTCAAGTGAGATGATATTTTGTTT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTT
496126 GTGAGGAAAA
Statistics
Matches: 446, Mismatches: 62, Indels: 27
0.83 0.12 0.05
Matches are distributed among these distances:
66 12 0.03
67 55 0.12
68 41 0.09
69 45 0.10
70 5 0.01
71 232 0.52
72 52 0.12
73 4 0.01
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (71 bp):
GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACAAAAAATT
TCAAGG
Found at i:495712 original size:37 final size:36
Alignment explanation
Indices: 495501--496214 Score: 107
Period size: 37 Copynumber: 20.3 Consensus size: 36
495491 GTCATGTAAG
* * * *
495501 GAAAATGTCTCAATTGAGAC-AAATTT-TTT-AAGT
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
* **
495534 GAAAATGTCTCAAGTGAGATAAAGTTTTATTT-AGAGA
1 GAAAATATCTCAAGTGAGACGAA-TTTTATTTCA-AGA
* * ** * * ** * *
495571 GAAATTGTCTTGAGTGTGATGAAAATT-TTCCAAGG
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
* * *
495606 GAAAATATCTCATGTGAGATGAAATTTTGTTTCAAGA
1 GAAAATATCTCAAGTGAGACG-AATTTTATTTCAAGA
* * * * *** *
495643 GAAATTGTTTCGAGTGAGAC-AA-AAAATTTCAAGG
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
495677 GAAAATATCTCAAGTGAGACGAAGTTTTATTTCAAGA
1 GAAAATATCTCAAGTGAGACGAA-TTTTATTTCAAGA
* * * *
495714 GAAACTGTCTC--GAGAGACGAA---T-TTTCAAGG
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
* * * ** * *
495744 GAAAATATTTCAACTAAGATAAAATTTTGTTTCGAGA
1 GAAAATATCTCAAGTGAGA-CGAATTTTATTTCAAGA
* * ** *** *
495781 GAAACTGTCTTGAGTGAGAC-AAAAAT-TTTCAAGG
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
* * * *
495815 GAAAATATCTCAAGTGAGATGAAATTTTGTTACGAGA
1 GAAAATATCTCAAGTGAGACG-AATTTTATTTCAAGA
* * * * * * **
495852 GAAACTGTCTCGACTAAGATGAA--AAATTTCACAG-
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCA-AGA
* * * **
495886 GAAAATACCTCAAGTGAGATGAAATTTTGTTTTGAGA
1 GAAAATATCTCAAGTGAGACG-AATTTTATTTCAAGA
* ** * **
495923 GAAACTATCTTGAGTGAGATGAA--AAATTTCACAG-
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCA-AGA
* * * * **
495957 GAAAGTATCTCAAGTGAGATGAAAATTTGTTTTTAGA
1 GAAAATATCTCAAGTGAGACG-AATTTTATTTCAAGA
* * * * * * *
495994 GAAACTGTCTCGAGTGAGA-TAA---AAATTAAAG-
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
*
496025 GAAAATATCTCAAGTGAGATGAAATTTTATTT--AGA
1 GAAAATATCTCAAGTGAGACG-AATTTTATTTCAAGA
* * * *
496060 GAGAAA-CTCTCGAGTGAGACAGAA-ATT-TTT-AAGG
1 GA-AAATATCTCAAGTGAGAC-GAATTTTATTTCAAGA
* * **
496094 GAAAATATCTCAAGTGAGATGATATTTTGTTT-GTGA
1 GAAAATATCTCAAGTGAGACGA-ATTTTATTTCAAGA
** * *
496130 GGAAAATTATCTCAAGTGAGATAAAAAATTTGTTTCAAGA
1 -GAAAA-TATCTCAAGTGAG--ACGAATTTTATTTCAAGA
* *
496170 -AAAACTGTCTCGAGTGAGACGAATTTT-TTT-AAG-
1 GAAAA-TATCTCAAGTGAGACGAATTTTATTTCAAGA
496203 GAAAACTATCTC
1 GAAAA-TATCTC
496215 TAGTAAGATA
Statistics
Matches: 475, Mismatches: 157, Indels: 97
0.65 0.22 0.13
Matches are distributed among these distances:
30 15 0.03
31 17 0.04
32 7 0.01
33 30 0.06
34 118 0.25
35 68 0.14
36 40 0.08
37 140 0.29
38 28 0.06
39 8 0.02
40 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.31
Consensus pattern (36 bp):
GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
Found at i:495926 original size:209 final size:210
Alignment explanation
Indices: 495534--496134 Score: 650
Period size: 209 Copynumber: 2.9 Consensus size: 210
495524 TTTTTTAAGT
* * * * * * * *
495534 GAAAATGTCTCAAGTGAGATAAAGTTTTATTTAGAGAGAAATTGTCTTGAGTGTGATGAAAATTT
1 GAAAATATCTCAACTAAGATAAAATTTTGTTTAGAGAGAAACTGTCTTGAGTGAGATAAAAATTT
* * * * *
495599 TCCAAGGGAAAATATCTCATGTGAGATGAAATTTTGTTTCAAGAGAAATTGTTTCGAGTGAGACA
66 T-CAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTACGAGAGAAACTGTCTCGAGTGAGA-A
* * * ** *
495664 AAAAATTTCAAGGGAAAATATCTCAAGTGAGACGAAGTTTTATTTCAAGAGAAACTGTCTCGA-G
129 AAAAATTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTTGAGAGAAACTATCTCGAGG
*
495728 AGACG-AATTTTCA-AGG
194 AGACGAAAATTTCACA-G
* * *
495744 GAAAATATTTCAACTAAGATAAAATTTTGTTTCGAGAGAAACTGTCTTGAGTGAGACAAAAATTT
1 GAAAATATCTCAACTAAGATAAAATTTTGTTTAGAGAGAAACTGTCTTGAGTGAGATAAAAATTT
* * *
495809 TCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTACGAGAGAAACTGTCTCGACTAAGATGA
66 TCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTACGAGAGAAACTGTCTCGAGTGAGA-AA
* *
495874 AAAATTTCACA-GGAAAATACCTCAAGTGAGATGAAATTTTGTTTTGAGAGAAACTATCTTGAGT
130 AAAATTTCA-AGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTTGAGAGAAACTATCTCGAG-
*
495938 GAGATGAAAAATTTCACAG
193 GAGACG-AAAATTTCACAG
* * * ** *
495957 GAAAGTATCTCAAGTGAGATGAAAA-TTTGTTTTTAGAGAAACTGTCTCGAGTGAGATAAAAA--
1 GAAAATATCTCAACTAAGAT-AAAATTTTGTTTAGAGAGAAACTGTCTTGAGTGAGATAAAAATT
* *
496019 TT-AAAGGAAAATATCTCAAGTGAGATGAAATTTTATTTA-GAGAGAAAC--TCTCGAGTGAGAC
65 TTCAAGGGAAAATATCTCAAGTGAGATGAAATTTT-GTTACGAGAGAAACTGTCTCGAGTGAGA-
* * * *
496080 AGAAATTTTTAAGGGAAAATATCTCAAGTGAGATGATATTTTGTTTGTGAG-GAAA
128 AAAAAATTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTT-TGAGAGAAA
496135 ATTATCTCAA
Statistics
Matches: 332, Mismatches: 49, Indels: 22
0.82 0.12 0.05
Matches are distributed among these distances:
207 1 0.00
208 52 0.16
209 111 0.33
210 96 0.29
211 10 0.03
213 57 0.17
214 5 0.02
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (210 bp):
GAAAATATCTCAACTAAGATAAAATTTTGTTTAGAGAGAAACTGTCTTGAGTGAGATAAAAATTT
TCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTACGAGAGAAACTGTCTCGAGTGAGAAAA
AAATTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTTGAGAGAAACTATCTCGAGGAG
ACGAAAATTTCACAG
Found at i:496159 original size:280 final size:279
Alignment explanation
Indices: 495515--496160 Score: 734
Period size: 280 Copynumber: 2.3 Consensus size: 279
495505 ATGTCTCAAT
* * * *
495515 TGAGACAAATTTTTTAAGTGAAAATGTCTCAAGTGAGAT-AAAGTTTTATTTAGAGAGAAATTGT
1 TGAGACAAAATTTTTAAGGGAAAATATCTCAAGTGAGATGAAA-TTTTGTTTAGAGAGAAATTGT
* * * * *
495579 CTTGAGTGTGATGAAAATTTTCCAAGGGAAAATATCTCATGTGAGATGAAATTTTGTTTCAAGAG
65 CTCGAGTGAGATGAAAAATTTCCAAGGGAAAATACCTCAAGTGAGATGAAATTTTGTTTCAAGAG
* * **
495644 AAATTGTTTCGAGTGAGACAAAAAATTTCAAGGGAAAATATCTCAAGTGAGACGAAGTTTTATTT
130 AAACTATTTCGAGTGAGACAAAAAATTTCAAGGGAAAATATCTCAAGTGAGACGAAAATTTATTT
* ** * * *
495709 CAAGAGAAACTGTCTCGAGAGACGAATTTTCAAGGGAAAATATTTCAACTAAGATAAAATTTTGT
195 CAAGAGAAACTGTCTCGAGAGACAAAAATTCAAAGGAAAATATCTCAACTAAGATAAAATTTTAT
* *
495774 TTCGAGAGAAACTGTCTTGAG
260 TTAGAGAGAAAC-GTCTCGAG
* *
495795 TGAGACAAAAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTG-TTACGAGAGAAACTG
1 TGAGAC-AAAATTTTTAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTA-GAGAGAAATTG
* * **
495859 TCTCGACTAAGATGAAAAATTT-CACA-GGAAAATACCTCAAGTGAGATGAAATTTTGTTTTGAG
64 TCTCGAGTGAGATGAAAAATTTCCA-AGGGAAAATACCTCAAGTGAGATGAAATTTTGTTTCAAG
** * *
495922 AGAAACTATCTT-GAGTGAGATGAAAAATTTCACA-GGAAAGTATCTCAAGTGAGATGAAAATTT
128 AGAAACTAT-TTCGAGTGAGACAAAAAATTTCA-AGGGAAAATATCTCAAGTGAGACGAAAATTT
* ** * * * *
495985 GTTTTTAGAGAAACTGTCTCGAGTGAGATAAAAATT-AAAGGAAAATATCTCAAGTGAGATGAAA
191 ATTTCAAGAGAAACTGTCTCGA--GAGACAAAAATTCAAAGGAAAATATCTCAACTAAGATAAAA
496049 TTTTATTTAGAGAGAAAC-TCTCGAG
254 TTTTATTTAGAGAGAAACGTCTCGAG
* *
496074 TGAGACAGAAATTTTTAAGGGAAAATATCTCAAGTGAGATGATATTTTGTTT-GTGAGGAAAATT
1 TGAGACA-AAATTTTTAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTAGAGA-G-AAATT
* * *
496138 ATCTCAAGTGAGATAAAAAATTT
63 GTCTCGAGTGAGATGAAAAATTT
496161 GTTTCAAGAA
Statistics
Matches: 307, Mismatches: 47, Indels: 24
0.81 0.12 0.06
Matches are distributed among these distances:
278 4 0.01
279 52 0.17
280 137 0.45
281 103 0.34
282 11 0.04
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (279 bp):
TGAGACAAAATTTTTAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTAGAGAGAAATTGTC
TCGAGTGAGATGAAAAATTTCCAAGGGAAAATACCTCAAGTGAGATGAAATTTTGTTTCAAGAGA
AACTATTTCGAGTGAGACAAAAAATTTCAAGGGAAAATATCTCAAGTGAGACGAAAATTTATTTC
AAGAGAAACTGTCTCGAGAGACAAAAATTCAAAGGAAAATATCTCAACTAAGATAAAATTTTATT
TAGAGAGAAACGTCTCGAG
Found at i:496213 original size:110 final size:106
Alignment explanation
Indices: 496023--496223 Score: 255
Period size: 110 Copynumber: 1.9 Consensus size: 106
496013 TAAAAATTAA
* * *
496023 AGGAAAATATCTCAAGTGAGATGAAATTTTATTTAGAGAGAAACTCTCGAGTGAGACAGAAATTT
1 AGGAAAATATCTCAAGTGAGATAAAAATTTATTTAGAGAAAAACTCTCGAGTGAGACAGAAATTT
*
496088 TTAAGGGAAAATATCTCAAGTGAGATGATATTTTGTTTGTG
66 TTAAGGGAAAATATCTCAAGTAAGATGATATTTTGTTTGTG
*
496129 AGGAAAATTATCTCAAGTGAGATAAAAAATTTGTTTCA-AGAAAAACTGTCTCGAGTGAGAC-GA
1 AGGAAAA-TATCTCAAGTGAGAT-AAAAATTTATTT-AGAGAAAAAC--TCTCGAGTGAGACAGA
* *
496192 ATTTTTTTAA-GGAAAACTATCTCTAGTAAGAT
61 A-ATTTTTAAGGGAAAA-TATCTCAAGTAAGAT
496224 AAGCTTTGTA
Statistics
Matches: 81, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
106 7 0.09
107 15 0.19
108 16 0.20
109 10 0.12
110 33 0.41
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.31
Consensus pattern (106 bp):
AGGAAAATATCTCAAGTGAGATAAAAATTTATTTAGAGAAAAACTCTCGAGTGAGACAGAAATTT
TTAAGGGAAAATATCTCAAGTAAGATGATATTTTGTTTGTG
Found at i:505012 original size:21 final size:21
Alignment explanation
Indices: 504988--505038 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
504978 CCTTCATTAT
504988 CACCACCATGATCATCATAAC
1 CACCACCATGATCATCATAAC
505009 CACCACCATGATCATCATAAC
1 CACCACCATGATCATCATAAC
505030 CACCACCAT
1 CACCACCAT
505039 CATTGTCGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.41, G:0.04, T:0.18
Consensus pattern (21 bp):
CACCACCATGATCATCATAAC
Found at i:511301 original size:22 final size:22
Alignment explanation
Indices: 511270--511374 Score: 106
Period size: 23 Copynumber: 4.7 Consensus size: 22
511260 TTGGTGCAGA
* *
511270 GGGAATCGATACCCCCTTGAAT
1 GGGAACCGATACCCCCTTGAAG
* *
511292 GGGAACCGATTACCCCTTTGAAT
1 GGGAACCGA-TACCCCCTTGAAG
* *
511315 GGGAAACGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
511338 GGGAACCGATTACCCCCTT--AG
1 GGGAACCGA-TACCCCCTTGAAG
*
511359 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
511375 ACGGGTTCTG
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
20 7 0.10
21 10 0.14
22 13 0.18
23 35 0.49
24 6 0.08
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.21
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:511312 original size:23 final size:23
Alignment explanation
Indices: 511270--511353 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
511260 TTGGTGCAGA
* *
511270 GGGAATCGA-TACCCCCTTGAAT
1 GGGAACCGATTACCCCTTTGAAT
511292 GGGAACCGATTACCCCTTTGAAT
1 GGGAACCGATTACCCCTTTGAAT
* * *
511315 GGGAAACGATTCCCCCTTTGAAG
1 GGGAACCGATTACCCCTTTGAAT
511338 GGGAACCGATTACCCC
1 GGGAACCGATTACCCC
511354 CTTAGGGGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 8 0.15
23 46 0.85
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (23 bp):
GGGAACCGATTACCCCTTTGAAT
Found at i:514644 original size:22 final size:22
Alignment explanation
Indices: 514619--514665 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
514609 GATATGAAAA
514619 AATTTCAA-TTTAAAATTAA-ATT
1 AATTT-AATTTTAAAA-TAATATT
514641 AATTTAATTTTAAAATAATATT
1 AATTTAATTTTAAAATAATATT
514663 AAT
1 AAT
514666 AGTAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTTAATTTTAAAATAATATT
Found at i:514674 original size:22 final size:21
Alignment explanation
Indices: 514625--514684 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
514615 AAAAAATTTC
*
514625 AATTTAAAATTAAATTAATTT
1 AATTTAAAATTAAATTAATGT
514646 AATTTTAAAA-TAATATTAATAGT
1 AA-TTTAAAATTAA-ATTAAT-GT
514669 AATTTAATTAATTAAA
1 AATTTAA--AATTAAA
514685 ATTTAAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
21 5 0.16
22 18 0.56
23 3 0.09
24 3 0.09
25 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AATTTAAAATTAAATTAATGT
Found at i:515012 original size:232 final size:226
Alignment explanation
Indices: 514603--515269 Score: 1062
Period size: 232 Copynumber: 2.9 Consensus size: 226
514593 AATTACGTCA
* * *
514603 ATTTTAGATATGAAAAAATTTCAATTTAAAATTAAATTAATTTAATTTTAAAATAATATTAATAG
1 ATTTTAGATATG-AAAAATTTCAATTTAAATTTAAATTAATTTAATTTTAAAATAATGTTAATAA
*
514668 TAATTTAATTAATTAAAATTTAAGTAACTAACTTTAAACATAACTATTACGATATTAGTAATGAT
65 TAATTTAATTAATTCAAATTTAAGTAACTAACTTTAAACATAACTATTACGATATTAGTAATGAT
*
514733 ATATATTTATAATCCAGTTTTAAAAATTAAATTAGAACAATTCATCTATGTAATTTTATATTT-A
130 ATATATTTATAATCCAGTTTTAAGAATTAAATTAGAACAATTCATCTATGTAATTTTATATTTCA
514797 GATAATTTAAAGTTTATTGCGACTTTGCGGTGTTGCAT
195 GATAATTTAAAGTTTATTGCG-----GCGGTG-TGCAT
*
514835 ATATTTAGATATGAAAAATTTTCAATTTAAATTTAAATTAATTTAATTTTAAAAT-ATGTCAATA
1 AT-TTTAGATATGAAAAA-TTTCAATTTAAATTTAAATTAATTTAATTTTAAAATAATGTTAATA
514899 ATAATTTAATTAATTCAAATTTAAGTAACTAACTTTAAACATAACTATTACGATATTAGTAATGA
64 ATAATTTAATTAATTCAAATTTAAGTAACTAACTTTAAACATAACTATTACGATATTAGTAATGA
514964 TATATATTTATAATCCAGTTTTAAGAATTAAATTAGAACAATTCATCTATGTAATTTTATATTTC
129 TATATATTTATAATCCAGTTTTAAGAATTAAATTAGAACAATTCATCTATGTAATTTTATATTTC
* * *
515029 AGATAATTTAAAGTTTGTTGCGGCGTTGTGTAT
194 AGATAATTTAAAGTTTATTGCGGCGGTGTGCAT
515062 ATTTTAGATATG--AAATTT---TTT-AATTTAAATTAATTTAATTTTAAAATAATGTTAATAAA
1 ATTTTAGATATGAAAAATTTCAATTTAAATTTAAATTAATTTAATTTTAAAATAATGTTAAT-AA
*
515121 TAATTTAATTAATTCAAATTTAAGTAACTAACTTTAAACATAACTATTACGATATTTGTAATGAT
65 TAATTTAATTAATTCAAATTTAAGTAACTAACTTTAAACATAACTATTACGATATTAGTAATG--
*
515186 ATATATATTTATAATCCAGTTTTAAGAATTAAATTAGAACAATTCATATATGTAATTTTATATTT
128 ATATATATTTATAATCCAGTTTTAAGAATTAAATTAGAACAATTCATCTATGTAATTTTATATTT
*
515251 CAAATAATTTAAAGTTTAT
193 CAGATAATTTAAAGTTTAT
515270 AACGCAATAT
Statistics
Matches: 414, Mismatches: 14, Indels: 23
0.92 0.03 0.05
Matches are distributed among these distances:
219 26 0.06
220 10 0.02
221 64 0.15
223 84 0.20
224 3 0.01
226 10 0.02
227 6 0.01
228 5 0.01
232 140 0.34
233 66 0.16
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (226 bp):
ATTTTAGATATGAAAAATTTCAATTTAAATTTAAATTAATTTAATTTTAAAATAATGTTAATAAT
AATTTAATTAATTCAAATTTAAGTAACTAACTTTAAACATAACTATTACGATATTAGTAATGATA
TATATTTATAATCCAGTTTTAAGAATTAAATTAGAACAATTCATCTATGTAATTTTATATTTCAG
ATAATTTAAAGTTTATTGCGGCGGTGTGCAT
Found at i:515106 original size:16 final size:16
Alignment explanation
Indices: 515080--515117 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
515070 TATGAAATTT
*
515080 TTTAA-TTTAAATTAA
1 TTTAATTTTAAAATAA
515095 TTTAATTTTAAAATAA
1 TTTAATTTTAAAATAA
515111 TGTTAAT
1 T-TTAAT
515118 AAATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 10 0.50
17 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAATTTTAAAATAA
Found at i:523569 original size:23 final size:24
Alignment explanation
Indices: 523515--523580 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 24
523505 AGGTAAGGTT
* *
523515 TATTTTCTCCTTTTTTTTTTGTTTC
1 TATTCTCTCC-TTTTTTTTTGTCTC
* *
523540 GAATCTCTCCTTTTTTTTT-TCTC
1 TATTCTCTCCTTTTTTTTTGTCTC
523563 TATTCTCT-CTTTTTTTTT
1 TATTCTCTCCTTTTTTTTT
523581 AAAACCAACC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
22 10 0.29
23 9 0.26
24 9 0.26
25 7 0.20
ACGTcount: A:0.06, C:0.20, G:0.03, T:0.71
Consensus pattern (24 bp):
TATTCTCTCCTTTTTTTTTGTCTC
Found at i:524097 original size:3 final size:3
Alignment explanation
Indices: 524076--524143 Score: 61
Period size: 3 Copynumber: 22.3 Consensus size: 3
524066 ATGTAAAAAT
* *
524076 ATA ATA TTA ATA A-A ATA ATA AT- ATA A-A TATA AAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
524119 ATAA ATA TATAA ATA ATA ATA ATA A
1 AT-A ATA -AT-A ATA ATA ATA ATA A
524144 AAAAGACCCG
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
2 5 0.09
3 40 0.74
4 8 0.15
5 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:524124 original size:21 final size:21
Alignment explanation
Indices: 524087--524144 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
524077 TAATATTAAT
524087 AAAATAATAAT-ATAAATATA
1 AAAATAATAATAATAAATATA
524107 AAAATAATAATAATAAATATA
1 AAAATAATAATAATAAATATA
*
524128 TAAATAATAATAATAAA
1 AAAATAATAATAATAAA
524145 AAAGACCCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 11 0.31
21 25 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAATAATAATAATAAATATA
Found at i:524405 original size:47 final size:45
Alignment explanation
Indices: 524340--524717 Score: 211
Period size: 40 Copynumber: 8.7 Consensus size: 45
524330 TCTAAAGGTG
524340 ACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGAGTTC-TGGCCATCT-AAGGTGATA
* * * * ** *
524387 ACACAGTTCCTACGTGATGAGGACG-GCTGGTTATCTAAGG-G-TG
1 ACACGGCTCCTACGTGATGAAGA-GTTCTGGCCATCTAAGGTGATA
* * * *
524430 ACACGGCTCCTACGTGATGAGGAGATCTGG---TC--AGCTGATG
1 ACACGGCTCCTACGTGATGAAGAGTTCTGGCCATCTAAGGTGATA
* *
524470 ACACGGCTCATGCGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGAGTTC-TGGCCATCT-AAGGTGATA
* * * ** * * * *
524517 ACACGGTTCCTACGTAATGAGGAAATATGGTCGTCT-AGG-G-TG
1 ACACGGCTCCTACGTGATGAAGAGTTCTGGCCATCTAAGGTGATA
* * * * *
524559 ACACTGCTCATACGTGATGAAGAGATCTGG---TC---GGGGAATG
1 ACACGGCTCCTACGTGATGAAGAGTTCTGGCCATCTAAGGTG-ATA
*
524599 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGAGTTCTGGCCATCT-AAGGTGATA
* * * ** * *
524645 ACACGGTTCCTACGTGATGAGGA-TGGCTGGTTATCTATGGT--TG
1 ACACGGCTCCTACGTGATGAAGAGT-TCTGGCCATCTAAGGTGATA
* *
524688 ACACGGCTCATACGTGATGAAGAGATCTGG
1 ACACGGCTCCTACGTGATGAAGAGTTCTGG
524718 TCTGGGGATG
Statistics
Matches: 256, Mismatches: 52, Indels: 50
0.72 0.15 0.14
Matches are distributed among these distances:
37 2 0.01
38 3 0.01
39 3 0.01
40 57 0.22
41 3 0.01
42 25 0.10
43 54 0.21
44 6 0.02
45 9 0.04
46 44 0.17
47 49 0.19
48 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (45 bp):
ACACGGCTCCTACGTGATGAAGAGTTCTGGCCATCTAAGGTGATA
Found at i:524621 original size:129 final size:129
Alignment explanation
Indices: 524338--524747 Score: 590
Period size: 129 Copynumber: 3.2 Consensus size: 129
524328 CGTCTAAAGG
* *
524338 TGACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACAGTTCCTACGTG
1 TGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
* * * **
524403 ATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCTGA
66 ATGAGGAAGGCTGGTTATCT-AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGGA
* *
524468 TGACACGGCTCATGCGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTA
1 TGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
*** ** *
524533 ATGAGGAAATATGGTCGTCTAGGGTGACACTGCTCATACGTGATGAAGAGATCTGGTC-GGGGAA
66 ATGAGGAAGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGG-A
524597 TGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
1 TGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
* * *
524661 ATGAGGATGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGA
66 ATGAGGAAGGCTGGTTATCTA-GGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGGA
* * *
524726 TGACACGGTTCCTACATGATGA
1 TGACACGGCTCATACGTGATGA
524748 GGACGGCTGG
Statistics
Matches: 249, Mismatches: 28, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
128 51 0.20
129 119 0.48
130 79 0.32
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (129 bp):
TGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
ATGAGGAAGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGGA
Found at i:524869 original size:31 final size:28
Alignment explanation
Indices: 524796--524872 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 28
524786 AAACCAAATT
524796 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
524824 AAAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
524852 AAAGATAATGTGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
524873 CAACTGTCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 29 0.69
29 2 0.05
30 3 0.07
31 8 0.19
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.26
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:525063 original size:66 final size:63
Alignment explanation
Indices: 524874--525056 Score: 170
Period size: 66 Copynumber: 2.8 Consensus size: 63
524864 TTTCAAAAGC
** * *
524874 AACTGTCTCGAAAGAGACAAAATTCGTTTCAAATGAAAC-AACTCAAAAGATGACGTTTAAAGGG
1 AACTGTCTC-AAAGAGACAAAATTCGTTTCAAGGGAAACGATCTC-AAAGATGATGTTTAAAGGG
* * * * * * * * * *
524938 AATTGTCTCAAGCGAGATAAAATTTGTTTTTAAGGGAAACGTTCTCAAATATCGGTGTTTCATGG
1 AACTGTCTCAA-AGAGACAAAATTCG-TTTCAAGGGAAACGATCTCAAAGAT-GATGTTTAAAGG
525003 G
63 G
525004 AAACTGTCTCAAATGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATG
1 -AACTGTCTCAAA-GAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATG
525057 TTTGTTTTGT
Statistics
Matches: 92, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
63 2 0.02
64 19 0.21
65 16 0.17
66 34 0.37
67 21 0.23
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (63 bp):
AACTGTCTCAAAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGATGTTTAAAGGG
Found at i:525810 original size:67 final size:67
Alignment explanation
Indices: 525705--526137 Score: 768
Period size: 67 Copynumber: 6.5 Consensus size: 67
525695 TCATTTTAAG
* * *
525705 AGAAACAGATTCAAAGA--TTT-TTTCAAAAGAAATTATCTTAAGAGAGGCAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
525767 AA
66 AA
525769 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
525834 AA
66 AA
525836 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA-TTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
525900 -A
66 AA
*
525901 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
525966 AA
66 AA
525968 AGAAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTC
1 AG-AAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTC
526033 CAA
65 CAA
*
526036 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
526101 AA
66 AA
*
526103 AGAAACAAACTTAAAGATTTTTGTTTCAAAAGAAA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
526138 CAATCTCAAA
Statistics
Matches: 356, Mismatches: 7, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
64 15 0.04
65 55 0.15
66 21 0.06
67 199 0.56
68 66 0.19
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:526067 original size:200 final size:201
Alignment explanation
Indices: 525705--526137 Score: 768
Period size: 200 Copynumber: 2.2 Consensus size: 201
525695 TCATTTTAAG
* * * *
525705 AGAAACAGATTCAAAGA--TTT-TTTCAAAAGAAATTATCTTAAGAGAGGCAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCC
525767 AAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTT
66 AAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTT
*
525832 CCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA-TTTGT
131 CCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGT
525896 TTCC-A
196 TTCCAA
525901 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCC
525966 AAAGAAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTT
66 AAAG-AAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTT
526031 TCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTG
130 TCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTG
526096 TTTCCAA
195 TTTCCAA
*
526103 AGAAACAAACTTAAAGATTTTTGTTTCAAAAGAAA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
526138 CAATCTCAAA
Statistics
Matches: 225, Mismatches: 6, Indels: 6
0.95 0.03 0.03
Matches are distributed among these distances:
196 15 0.07
198 3 0.01
199 44 0.20
200 119 0.53
201 9 0.04
202 35 0.16
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (201 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCC
AAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTT
CCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGT
TTCCAA
Found at i:526287 original size:57 final size:56
Alignment explanation
Indices: 526204--526341 Score: 174
Period size: 57 Copynumber: 2.4 Consensus size: 56
526194 AAGTAAATAG
* *
526204 ACTCAAAGA-TTTTTTCAAACGAAAC-AACTCACAGATTTTTATTCCAA-AGGAACAA
1 ACTCAAAGATTTTTTTCAAAAGAAACAAACTCAAAGATTTTT-TT-CAAGAGGAACAA
* *
526259 ACTCCAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAAGAAACAAACTCAAAGATTTTTTTCAAGAGGAACAA
*
526316 ACTCAAAGATTTTTCCTCAAAAGAAA
1 ACTCAAAGATTTTT-TTCAAAAGAAA
526342 TTGTCTTTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
55 8 0.11
56 7 0.10
57 42 0.59
58 14 0.20
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (56 bp):
ACTCAAAGATTTTTTTCAAAAGAAACAAACTCAAAGATTTTTTTCAAGAGGAACAA
Found at i:526329 original size:28 final size:28
Alignment explanation
Indices: 526204--526329 Score: 161
Period size: 29 Copynumber: 4.5 Consensus size: 28
526194 AAGTAAATAG
*
526204 ACTCAAAGA-TTTT-TTCAAACGAA-ACA
1 ACTCAAAGATTTTTATTCAAAGGAACA-A
*
526230 ACTCACAGATTTTTATTCCAAAGGAACAA
1 ACTCAAAGATTTTTATT-CAAAGGAACAA
*
526259 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTC-AAAGGAACAA
526288 ACTCAAAGATTTTT-TTCAAGAGGAACAA
1 ACTCAAAGATTTTTATTCAA-AGGAACAA
526316 ACTCAAAGATTTTT
1 ACTCAAAGATTTTT
526330 CCTCAAAAGA
Statistics
Matches: 89, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
26 8 0.09
27 6 0.07
28 28 0.31
29 46 0.52
30 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.29
Consensus pattern (28 bp):
ACTCAAAGATTTTTATTCAAAGGAACAA
Found at i:526665 original size:36 final size:36
Alignment explanation
Indices: 526581--526684 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
526571 GAGAAAATGA
* * *
526581 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
526615 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
526651 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
526685 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:526712 original size:36 final size:36
Alignment explanation
Indices: 526582--526700 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
526572 AGAAAATGAT
* * * *
526582 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
526616 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
526652 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
526687 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
526701 TCAACTTTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 19 0.28
35 12 0.17
36 38 0.55
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:526831 original size:105 final size:100
Alignment explanation
Indices: 526652--526883 Score: 263
Period size: 105 Copynumber: 2.3 Consensus size: 100
526642 TAGAGAAATT
*
526652 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
* *
526716 GTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
64 GTGAAACAAATTCAAAATTTGGATCTC-AAGGAAAAAG
* *
526754 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTGTTT
* * * *
526818 -TTAGTGAATCAAATTCAAAATTTGTATCTCAAGGAAAAAT
61 AAT-GTGAAACAAATTCAAAATTTGGATCTCAAGGAAAAAG
* *
526858 GTCTCAAGCGAGACGCAATTTCTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
526884 AAAATTCTCA
Statistics
Matches: 112, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 37 0.33
105 47 0.42
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (100 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAGGAAAAAG
Found at i:527037 original size:13 final size:14
Alignment explanation
Indices: 527012--527042 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
527002 CGCCACTTTA
527012 TTTATTATATTTTT
1 TTTATTATATTTTT
527026 TTTATT-TATTTTT
1 TTTATTATATTTTT
527039 TTTA
1 TTTA
527043 AAAGAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTATATTTTT
Found at i:527375 original size:4 final size:4
Alignment explanation
Indices: 527366--527431 Score: 118
Period size: 4 Copynumber: 17.0 Consensus size: 4
527356 TTTATGTATC
527366 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
527412 ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT
527432 TCTCGATCTA
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
4 58 0.97
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:528642 original size:17 final size:17
Alignment explanation
Indices: 528600--528650 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
528590 ACTTTCTGTT
*
528600 CTTTT-TTTTCACTTTG
1 CTTTTCTTTTCTCTTTG
528616 --TTTC-TTTCTCTTTG
1 CTTTTCTTTTCTCTTTG
*
528630 CTTTTCTTTTCTCTTCG
1 CTTTTCTTTTCTCTTTG
528647 CTTT
1 CTTT
528651 AATATGATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 12 0.41
16 4 0.14
17 13 0.45
ACGTcount: A:0.02, C:0.24, G:0.06, T:0.69
Consensus pattern (17 bp):
CTTTTCTTTTCTCTTTG
Found at i:531763 original size:31 final size:32
Alignment explanation
Indices: 531707--531768 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
531697 TGACAAAATG
531707 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
531739 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
531769 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:534747 original size:22 final size:22
Alignment explanation
Indices: 534695--534759 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
534685 AGGTAAGGTT
* *
534695 TATTTTCTCCTTTTTTTTTGTTTC
1 TATTCTCTCC-TTTTTTTT-TCTC
* *
534719 GAATCTCTCCTTTTTTTTTCTC
1 TATTCTCTCCTTTTTTTTTCTC
*
534741 TATTCTCTCTTTTTTTTTT
1 TATTCTCTCCTTTTTTTTT
534760 AAACCAACCG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 19 0.56
23 8 0.24
24 7 0.21
ACGTcount: A:0.06, C:0.20, G:0.03, T:0.71
Consensus pattern (22 bp):
TATTCTCTCCTTTTTTTTTCTC
Found at i:535274 original size:3 final size:3
Alignment explanation
Indices: 535253--535320 Score: 61
Period size: 3 Copynumber: 22.3 Consensus size: 3
535243 ATGTAAAAAT
* *
535253 ATA ATA TTA ATA A-A ATA ATA AT- ATA A-A TATA AAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
535296 ATAA ATA TATAA ATA ATA ATA ATA A
1 AT-A ATA -AT-A ATA ATA ATA ATA A
535321 AAAAGACCCG
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
2 5 0.09
3 40 0.74
4 8 0.15
5 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:535301 original size:21 final size:21
Alignment explanation
Indices: 535264--535321 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
535254 TAATATTAAT
535264 AAAATAATAAT-ATAAATATA
1 AAAATAATAATAATAAATATA
535284 AAAATAATAATAATAAATATA
1 AAAATAATAATAATAAATATA
*
535305 TAAATAATAATAATAAA
1 AAAATAATAATAATAAA
535322 AAAGACCCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 11 0.31
21 25 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAATAATAATAATAAATATA
Found at i:541881 original size:2 final size:2
Alignment explanation
Indices: 541874--541934 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
541864 TTATGAAAAC
541874 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
541916 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
541935 CAAAAGTTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:545633 original size:81 final size:82
Alignment explanation
Indices: 545378--545802 Score: 270
Period size: 81 Copynumber: 5.2 Consensus size: 82
545368 TTCAGAAAAC
* * * ** * * *
545378 AAACGTCACTATTTATCTGGCTATCGCGGCCTTTTTTTACATAAACACCACTAAAGTACGCGTTT
1 AAACGCCACTATATATATGGCTATAACGG-CATTTTTTACATAAACGCCACTAAAGTACGCATTT
* * ** * *
545443 TCAGTGGCGTTTCCCCAA
65 TTAGCGGTATTTTCACAA
* * * * * * * *
545461 AAATG-CACTATATATCA-GGCTATCACGACATTTTTAACATAAACGCCGCTAAAGCACGCGTAC
1 AAACGCCACTATATAT-ATGGCTATAACGGCATTTTTTACATAAACGCCACTAAAGTACGCAT-T
* *
545524 TTTAGTGGTATTTACACAA
64 TTTAGCGGTATTTTCACAA
* * * *
545543 AAACACCACTATATATATGGCTATAATGGC-TTTTTTACATAAACACCACTAAAGTATGCATTTT
1 AAACGCCACTATATATATGGCTATAACGGCATTTTTTACATAAACGCCACTAAAGTACGCATTTT
*
545607 TAGCGGTATTTTCACAT
66 TAGCGGTATTTTCACAA
** * * * ** * **
545624 AAACGCCACTATATATCCGGCTATAGCAGCGTCGTTTACATAAACGTCACTAAAGTGTGCA-TTT
1 AAACGCCACTATATATATGGCTATAACGGCATTTTTTACATAAACGCCACTAAAGTACGCATTTT
*
545688 TAGCGG-AGTTTTCACAT
66 TAGCGGTA-TTTTCACAA
* * * ** * **
545705 AAATGCCACTATACATCTATCTATAGCGGTGTTTTTTACATAAACGCCACTAAAGTA--CATGTT
1 AAACGCCACTATATATATGGCTATAACGGCATTTTTTACATAAACGCCACTAAAGTACGCAT-TT
* * * **
545768 TCTAGCTGCACTTTCTTAA
65 T-TAGCGGTATTTTCACAA
545787 AAACGCCACTATATAT
1 AAACGCCACTATATAT
545803 TAGGATATCG
Statistics
Matches: 272, Mismatches: 60, Indels: 21
0.77 0.17 0.06
Matches are distributed among these distances:
79 2 0.01
80 1 0.00
81 135 0.50
82 110 0.40
83 24 0.09
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (82 bp):
AAACGCCACTATATATATGGCTATAACGGCATTTTTTACATAAACGCCACTAAAGTACGCATTTT
TAGCGGTATTTTCACAA
Found at i:555287 original size:107 final size:107
Alignment explanation
Indices: 555112--555315 Score: 318
Period size: 107 Copynumber: 1.9 Consensus size: 107
555102 AATATAATTA
* * *
555112 TATATATACAATAAAGCTGAGCTATTCCTATAAAGCAATTGGTTAAAAGCCCTGACTTTATGGAT
1 TATATATACAATAAAGCTGAGCTATTCCTATAAAGAAACTAGTTAAAAGCCCTGACTTTATGGAT
*
555177 AGATTCCTTCAGCTAGCCAAACAAAGGCAAATAATATATATG
66 AGATTCCTTCAGCTAGCCAAACAAAGGAAAATAATATATATG
* * ** * *
555219 TATATATACAATAAAGTTGAGTTATTTTTCTAAAGAAACTAGTTAAGAGCCCTGACTTTATGGAT
1 TATATATACAATAAAGCTGAGCTATTCCTATAAAGAAACTAGTTAAAAGCCCTGACTTTATGGAT
555284 AGATTCCTTCAGCTAGCCAAACAAAGGAAAAT
66 AGATTCCTTCAGCTAGCCAAACAAAGGAAAAT
555316 TAAATTAAAT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
107 87 1.00
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (107 bp):
TATATATACAATAAAGCTGAGCTATTCCTATAAAGAAACTAGTTAAAAGCCCTGACTTTATGGAT
AGATTCCTTCAGCTAGCCAAACAAAGGAAAATAATATATATG
Found at i:556123 original size:17 final size:18
Alignment explanation
Indices: 556077--556124 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
556067 TCACAAGATG
*
556077 AAGACTCAAC-AAGGATA
1 AAGACTCAACAAAGGACA
556094 AAGACTCAACAAAGG-CA
1 AAGACTCAACAAAGGACA
556111 AAGACTCAACAAAG
1 AAGACTCAACAAAG
556125 AGAATGAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 25 0.86
18 4 0.14
ACGTcount: A:0.54, C:0.21, G:0.17, T:0.08
Consensus pattern (18 bp):
AAGACTCAACAAAGGACA
Found at i:558725 original size:14 final size:14
Alignment explanation
Indices: 558686--558726 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
558676 AATATTTTAA
558686 AATA-ATTAA-AAT
1 AATATATTAATAAT
*
558698 AATATAATTTATAAT
1 AATAT-ATTAATAAT
558713 AATATATTAATAAT
1 AATATATTAATAAT
558727 TATTTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
14 12 0.50
15 8 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATATTAATAAT
Found at i:558767 original size:30 final size:29
Alignment explanation
Indices: 558740--558805 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
558730 TTATTATATT
558740 TTAAAAAGTTAAATTAACATATTTTATAATA
1 TTAAAAA-TTAAA-TAACATATTTTATAATA
* *
558771 TTAATAATTAAATAATATATTTTAATAATA
1 TTAAAAATTAAATAACATATTTT-ATAATA
558801 -TAAAA
1 TTAAAA
558806 TAAAATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 14 0.45
30 11 0.35
31 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (29 bp):
TTAAAAATTAAATAACATATTTTATAATA
Found at i:560809 original size:16 final size:16
Alignment explanation
Indices: 560788--560818 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
560778 CCGGATAAAT
560788 TTATTAATTTAGAGAG
1 TTATTAATTTAGAGAG
560804 TTATTAATTTAGAGA
1 TTATTAATTTAGAGA
560819 TAAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (16 bp):
TTATTAATTTAGAGAG
Found at i:561186 original size:17 final size:17
Alignment explanation
Indices: 561152--561203 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
561142 GCCGGAAAAA
*
561152 TTTATTATTTTAGAGAG
1 TTTATTAATTTAGAGAG
**
561169 TTTATTAATTTATCGAG
1 TTTATTAATTTAGAGAG
*
561186 --TATTAATTTAAAGAG
1 TTTATTAATTTAGAGAG
561201 TTT
1 TTT
561204 CTGCTGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (17 bp):
TTTATTAATTTAGAGAG
Found at i:562759 original size:29 final size:29
Alignment explanation
Indices: 562706--562762 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
562696 TTTCATCTTA
*
562706 CTGAAATTTTATAAATTTAAATTCGTCTC
1 CTGAAATTTTATAAATTCAAATTCGTCTC
*
562735 CTGAAATTTTA-AAAGTTCAAGTTCGTCT
1 CTGAAATTTTATAAA-TTCAAATTCGTCT
562763 TATAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (29 bp):
CTGAAATTTTATAAATTCAAATTCGTCTC
Found at i:566400 original size:14 final size:14
Alignment explanation
Indices: 566381--566417 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
566371 ACATGAATTG
566381 GACTGTTGACCGTT
1 GACTGTTGACCGTT
566395 GACTGTTGACCGTT
1 GACTGTTGACCGTT
566409 GACT-TTGAC
1 GACTGTTGAC
566418 TATGACCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (14 bp):
GACTGTTGACCGTT
Found at i:570283 original size:28 final size:28
Alignment explanation
Indices: 570200--570274 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
570190 TGCATTTTTA
* * *
570200 ATTCTGCATGGGATTATATCTCTTTCTG
1 ATTCTACATGGGATTATATCTCATCCTG
** *
570228 ATTCTATGTGAGATTATATCTCATCCTG
1 ATTCTACATGGGATTATATCTCATCCTG
570256 ATTCTACATGGGATTATAT
1 ATTCTACATGGGATTATAT
570275 TTCGCCCTGT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (28 bp):
ATTCTACATGGGATTATATCTCATCCTG
Found at i:571498 original size:14 final size:15
Alignment explanation
Indices: 571470--571498 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
571460 AATCCCCTCT
571470 ATTGAGGAGTACTGA
1 ATTGAGGAGTACTGA
571485 ATTGAGGA-TACTGA
1 ATTGAGGAGTACTGA
571499 GCATCTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.07, G:0.31, T:0.28
Consensus pattern (15 bp):
ATTGAGGAGTACTGA
Found at i:577351 original size:20 final size:20
Alignment explanation
Indices: 577313--577351 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
577303 TTGCTCAAAA
**
577313 GATTGATCACTTAGCAAAGG
1 GATTGATCACTTAAAAAAGG
*
577333 GATTGATCCCTTAAAAAAG
1 GATTGATCACTTAAAAAAG
577352 ATCAATTGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (20 bp):
GATTGATCACTTAAAAAAGG
Found at i:579465 original size:15 final size:16
Alignment explanation
Indices: 579437--579471 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
579427 GCTTTCAAAA
*
579437 TTGAAAAATTAAAATT
1 TTGAAAAATGAAAATT
579453 TTGAAAAA-GAAAATT
1 TTGAAAAATGAAAATT
579468 TTGA
1 TTGA
579472 TTAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.34
Consensus pattern (16 bp):
TTGAAAAATGAAAATT
Found at i:589840 original size:24 final size:21
Alignment explanation
Indices: 589806--589848 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
589796 TGCACAAGAT
*
589806 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
589828 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
589849 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:598709 original size:6 final size:6
Alignment explanation
Indices: 598698--598723 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
598688 AGGAGGGTAG
598698 TTCTCT TTCTCT TTCTCT TTCTCT TT
1 TTCTCT TTCTCT TTCTCT TTCTCT TT
598724 GGTGTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTCTCT
Found at i:600382 original size:385 final size:384
Alignment explanation
Indices: 599625--600399 Score: 1381
Period size: 385 Copynumber: 2.0 Consensus size: 384
599615 AGGATTGGTT
*
599625 TATAATAAAAACTTGAACAATGAAATACAAAAGATCTAATCGCACCCAAAAAAATTGTAACTTAG
1 TATAATAAAAACTTGAACAATGAAATACAAAAGATCTAATCGCACCCAAAAAAATTGTAACTCAG
599690 AGTTGAGCGACGTGAAAAAACTATCCATGAACACAAATCAAGTATCCAAATCCAATTCAAAGGAC
66 AGTTGAGCGACGTGAAAAAACTATCCATGAACACAAATCAAGTATCCAAATCCAATTCAAAGGAC
* *
599755 CAAAGTAGGGAAGATCATCATGATAACATATAAGTGTCATCTAGATCAATCGTGACAATGTCGAA
131 CAAAGTAGGGAAGATCAACATGATAACATATAAGTGTCATCTAGATCAATCGTGACAATATCGAA
*
599820 CCAACCCTAAAATGATAAATGAAAAAAGTAACGGCAAAACGACCTAAAACATGCCAAAAAAACAA
196 CCAACCCTAAAATGATAAATGAAAAAAATAACGGCAAAACGACCTAAAACATGCCAAAAAAACAA
* **
599885 GAAAAAATATGTCATAAAGATAGATGAAAATGTTTTATAAAGATAAACTTACTGAAAATTAAAAA
261 GAAAAAATATGTCATAAAGATAGATGAAAACGTGATATAAAGATAAACTTACTGAAAATTAAAAA
*
599950 CAATAGAAAAATAAAGATGCGATATAAAAATAAAAGGATACTAAAAGTTACTGACAATA
326 CAATAGAAAAATAAAGATGCGATATAAAAATAAAAGGATAATAAAAGTTACTGACAATA
*
600009 TATAATAAAAACTTGAACAATGAAATA-AAAAGATCTAATCGCACCGAAAAAAATTGTAACTCAG
1 TATAATAAAAACTTGAACAATGAAATACAAAAGATCTAATCGCACCCAAAAAAATTGTAACTCAG
* *
600073 AGTTGAGCGACGTGAAAAAACTATCCATGAACACAAATCAAGTATCCAAATCCAATTCAAATGAT
66 AGTTGAGCGACGTGAAAAAACTATCCATGAACACAAATCAAGTATCCAAATCCAATTCAAAGGAC
* *
600138 CAAAGTATGGAAGATCAACATGTTAACATATAAGTGTCATCTAGATCAATCGTGACAATATCGAA
131 CAAAGTAGGGAAGATCAACATGATAACATATAAGTGTCATCTAGATCAATCGTGACAATATCGAA
*
600203 CCAACCCTCAAAAATGATAAATGAAAAAAATAACGGCAAAACGACCTAAAACGTGCCAAAAAAAC
196 CCAACCCT--AAAATGATAAATGAAAAAAATAACGGCAAAACGACCTAAAACATGCCAAAAAAAC
*
600268 AAGAAAAAATATGTCATAAAGATAGATGAAAACGTGATATAAAGATAAATTTACTGAAAATTAAA
259 AAGAAAAAATATGTCATAAAGATAGATGAAAACGTGATATAAAGATAAACTTACTGAAAATTAAA
*
600333 AACAATAGAAAAATAAAGATGCGATATAAAAATAAAAGGATAATAAAAGTTACTGACAGTA
324 AACAATAGAAAAATAAAGATGCGATATAAAAATAAAAGGATAATAAAAGTTACTGACAATA
600394 TATAAT
1 TATAAT
600400 TAACATCAAG
Statistics
Matches: 373, Mismatches: 16, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
383 167 0.45
384 27 0.07
385 179 0.48
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.21
Consensus pattern (384 bp):
TATAATAAAAACTTGAACAATGAAATACAAAAGATCTAATCGCACCCAAAAAAATTGTAACTCAG
AGTTGAGCGACGTGAAAAAACTATCCATGAACACAAATCAAGTATCCAAATCCAATTCAAAGGAC
CAAAGTAGGGAAGATCAACATGATAACATATAAGTGTCATCTAGATCAATCGTGACAATATCGAA
CCAACCCTAAAATGATAAATGAAAAAAATAACGGCAAAACGACCTAAAACATGCCAAAAAAACAA
GAAAAAATATGTCATAAAGATAGATGAAAACGTGATATAAAGATAAACTTACTGAAAATTAAAAA
CAATAGAAAAATAAAGATGCGATATAAAAATAAAAGGATAATAAAAGTTACTGACAATA
Found at i:603163 original size:151 final size:151
Alignment explanation
Indices: 602702--603169 Score: 758
Period size: 151 Copynumber: 3.1 Consensus size: 151
602692 TTTAGTAGTT
*
602702 AAAAAATGTTATTTTACACGAATCAAGTAGCCTCTGTGATAAGGATTCGAGTTTGAGCACCATAG
1 AAAAAATGTAATTTTACACGAATCAAGTAGCCTCTGTGATAAGGATTCGAGTTTGAGCACCATAG
* * * * *
602767 ATG-TCAAGTGTGTGACCATTCAATATCAAAAGGGTTGAGAGTTATCTTTGAACAGATATTACAT
66 ATGCT-AAGAGTGTGATCATTCATTATCAAAAGGGTTGAGAGTTATCTTTGAACAGATACTACCT
602831 TGTACATTCCCCTAATTAATAA
130 TGTACATTCCCCTAATTAATAA
* *
602853 AAAGAACGTAATTTTACACGAATCAAGTAGCCTCTGTGATAAGGATTCGAGTTTGAGCACCATAG
1 AAAAAATGTAATTTTACACGAATCAAGTAGCCTCTGTGATAAGGATTCGAGTTTGAGCACCATAG
* *
602918 ATGCCATGAGTGTGATCATTCATTATCAAAAGGGTTGAGAGTTATCTTTGAACAGATACTACCTT
66 ATGCTAAGAGTGTGATCATTCATTATCAAAAGGGTTGAGAGTTATCTTTGAACAGATACTACCTT
602983 GTACATTCCCCTAATTAATAA
131 GTACATTCCCCTAATTAATAA
* *
603004 AAAGAATGTAATTTTACACGAATCAAGTAGCCTCTATGATAAGGATTCGAGTTTGAGCACCATAG
1 AAAAAATGTAATTTTACACGAATCAAGTAGCCTCTGTGATAAGGATTCGAGTTTGAGCACCATAG
* * * *
603069 ATGCTAGGAGTGTGATCATTCATTATCAAAAGGGTTGAGAGTTATCTTGGAAGAGATACTACCTC
66 ATGCTAAGAGTGTGATCATTCATTATCAAAAGGGTTGAGAGTTATCTTTGAACAGATACTACCTT
*
603134 GTACATACCCCTAATTAATAA
131 GTACATTCCCCTAATTAATAA
*
603155 AAAAAATGTTATTTT
1 AAAAAATGTAATTTT
603170 TCTAGAGATA
Statistics
Matches: 296, Mismatches: 20, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
151 296 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (151 bp):
AAAAAATGTAATTTTACACGAATCAAGTAGCCTCTGTGATAAGGATTCGAGTTTGAGCACCATAG
ATGCTAAGAGTGTGATCATTCATTATCAAAAGGGTTGAGAGTTATCTTTGAACAGATACTACCTT
GTACATTCCCCTAATTAATAA
Found at i:603755 original size:17 final size:18
Alignment explanation
Indices: 603729--603762 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
603719 AAAAATTATT
603729 TTATTATTTAT-TTTAAA
1 TTATTATTTATATTTAAA
*
603746 TTATTTTTTATATTTAA
1 TTATTATTTATATTTAA
603763 TAATAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTATTTATATTTAAA
Found at i:612497 original size:23 final size:21
Alignment explanation
Indices: 612444--612506 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
612434 TTTTGGTGCA
*
612444 GAGGGAATCGATTCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
612465 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
612486 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
612507 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:612514 original size:21 final size:21
Alignment explanation
Indices: 612446--612526 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
612436 TTGGTGCAGA
* *
612446 GGGAATCGATTCCCCCC-CTG
1 GGGAACCGATTCCCCCCACAG
*
612466 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
612490 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
612511 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
612527 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 1 0.02
21 31 0.63
23 16 0.33
24 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:616553 original size:3 final size:3
Alignment explanation
Indices: 616545--616603 Score: 109
Period size: 3 Copynumber: 19.3 Consensus size: 3
616535 TGGTCTCCAC
616545 ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
616591 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
616604 AATCTCAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:618692 original size:15 final size:14
Alignment explanation
Indices: 618671--618717 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 14
618661 AATTTGAAAT
618671 TTAGAGTAATTAAA
1 TTAGAGTAATTAAA
618685 TTAGGAGTAATTTAAAAA
1 TTA-GAGTAA-TT--AAA
618703 TTA-AGTAATTAAA
1 TTAGAGTAATTAAA
618716 TT
1 TT
618718 TTAAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 5 0.17
14 3 0.10
15 8 0.28
16 7 0.24
18 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (14 bp):
TTAGAGTAATTAAA
Found at i:619699 original size:20 final size:19
Alignment explanation
Indices: 619656--619699 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
619646 AAATTAAATT
*
619656 TAAAATTATACCCAAACCC
1 TAAATTTATACCCAAACCC
* *
619675 AAAATTTATACCATAAACCC
1 TAAATTTATACC-CAAACCC
619695 TAAAT
1 TAAAT
619700 CACAAATCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (19 bp):
TAAATTTATACCCAAACCC
Found at i:622623 original size:3 final size:3
Alignment explanation
Indices: 622615--622648 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
622605 GATTTAAAGT
622615 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
622649 TTTAATGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:624433 original size:20 final size:20
Alignment explanation
Indices: 624403--624452 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
624393 ATTTTTTTAA
624403 AATTAAATATTTATATCC-AAC
1 AATT-AATATTTAT-TCCAAAC
624424 AATTAATATTTATTCCAAAC
1 AATTAATATTTATTCCAAAC
*
624444 AAATAATAT
1 AATTAATAT
624453 AATATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 3 0.11
20 20 0.74
21 4 0.15
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTAATATTTATTCCAAAC
Found at i:626488 original size:48 final size:48
Alignment explanation
Indices: 626401--626498 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 48
626391 AACTTGATTT
* * * * **
626401 GATAAATATTCGATTCGATTGAACTTGATTTGAGTTCGAACTCGACTC
1 GATAAATACTCGATTCAATTGAACTTGACTCGAACTCGAACTCGACTC
* *
626449 GATAAATACTCGATTCAATTGGACTTGACTCGAACTCGAACTCTACTC
1 GATAAATACTCGATTCAATTGAACTTGACTCGAACTCGAACTCGACTC
626497 GA
1 GA
626499 GTTCTTAACG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (48 bp):
GATAAATACTCGATTCAATTGAACTTGACTCGAACTCGAACTCGACTC
Found at i:627567 original size:28 final size:29
Alignment explanation
Indices: 627515--627569 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
627505 TATCACATAT
* * *
627515 TAGATAAAATTTTATAGTTTTATAGTAAA
1 TAGATAAAATTATATACTATTATAGTAAA
627544 TAGATAAAA-TATATACTATTATAGTA
1 TAGATAAAATTATATACTATTATAGTA
627570 TTATAAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (29 bp):
TAGATAAAATTATATACTATTATAGTAAA
Found at i:627720 original size:16 final size:17
Alignment explanation
Indices: 627693--627728 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
627683 GATATGAGAA
627693 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
627710 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
627726 AAA
1 AAA
627729 ATAACGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Done.