Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001868.1 Hibiscus syriacus cultivar Beakdansim tig00003783_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: 358561
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:213297 original size:14 final size:14
Alignment explanation
Indices: 213278--213313 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
213268 ATTGTTTAAT
213278 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
213292 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
213306 TGATTTGT
1 TGATTTGT
213314 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:213436 original size:19 final size:19
Alignment explanation
Indices: 213420--213521 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
213410 AAAAATGACT
213420 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
213439 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
213458 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
213472 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
213491 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
213511 ATCGCAATGCG
1 ATCGCAATGCG
213522 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:213580 original size:19 final size:19
Alignment explanation
Indices: 213550--213940 Score: 440
Period size: 19 Copynumber: 22.4 Consensus size: 19
213540 GATTCTCTCG
213550 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
213568 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
213587 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
213601 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
213620 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
213639 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
213658 TTGCGAGTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
213677 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
213691 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
213710 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
213729 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
213743 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
213762 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
213781 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
213795 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
213814 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
213828 TTGCGATTTGCATTTCGCA
1 TTGCGATTTTCATTTCGCA
213847 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
213866 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
213880 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
213900 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
213914 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
213933 TTGCGATT
1 TTGCGATT
213941 GTAATTTCCG
Statistics
Matches: 321, Mismatches: 15, Indels: 73
0.78 0.04 0.18
Matches are distributed among these distances:
14 47 0.15
16 44 0.14
17 42 0.13
18 9 0.03
19 167 0.52
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:213608 original size:33 final size:36
Alignment explanation
Indices: 213550--213940 Score: 388
Period size: 33 Copynumber: 11.2 Consensus size: 36
213540 GATTCTCTCG
213550 TTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTCATTTCG-ATTGCGATTTTCATTTCGCA
213587 TTGCGA-TTC-TTTCG-TTGCGATTTTCATTTCGCA
1 TTGCGATTTCATTTCGATTGCGATTTTCATTTCGCA
213620 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
*
213658 TTGCGAGTTTCATTTCGCATTGCGA--TTC-TGTCG--
1 TTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
213691 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
*
213729 TTGCGA-TTC-TGTCG-TTGCGATTTTCATTTCGCA
1 TTGCGATTTCATTTCGATTGCGATTTTCATTTCGCA
*
213762 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--
1 TTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
*
213795 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--
1 TTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
213828 TTGCGATTTGCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTT-CATTTCG-ATTGCGATTTTCATTTCGCA
*
213866 TTGCGA-TTC-TCTCG-TTGCGATTTTCATTTCCGCA
1 TTGCGATTTCATTTCGATTGCGATTTTCATTT-CGCA
* *
213900 TTGCGATTTTCA--T-G-TTGGGATTTTCATTTCGCG
1 TTGCGA-TTTCATTTCGATTGCGATTTTCATTTCGCA
213933 TTGCGATT
1 TTGCGATT
213941 GTAATTTCCG
Statistics
Matches: 318, Mismatches: 11, Indels: 55
0.83 0.03 0.14
Matches are distributed among these distances:
32 5 0.02
33 152 0.48
34 25 0.08
35 34 0.11
36 33 0.10
37 8 0.03
38 61 0.19
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (36 bp):
TTGCGATTTCATTTCGATTGCGATTTTCATTTCGCA
Found at i:213634 original size:52 final size:55
Alignment explanation
Indices: 213528--213940 Score: 376
Period size: 52 Copynumber: 7.9 Consensus size: 55
213518 TGCGTTTATA
*
213528 ATTTCGCATTGCGA-TTC-TCTCG-TTGCGA-TTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCATTGCGATTTTC
213579 ATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCATTGCGATTTTC
*
213631 ATTTCGCATTGCGATTTTCATTTCGCATTGCGAGTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
*
213686 -TGTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
*
213738 -TGTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
* * *
213790 -TCTCG--TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTGC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
*
213839 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
* *
213891 ATTTCCGCATTGCGATTTTCA--T-G-TTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGA-TTTCATTTCGATTGCGATTTTCATTTCGCATTGCGATT
213941 GTAATTTCCG
Statistics
Matches: 334, Mismatches: 11, Indels: 32
0.89 0.03 0.08
Matches are distributed among these distances:
47 6 0.02
48 5 0.01
49 6 0.02
50 11 0.03
51 32 0.10
52 211 0.63
53 24 0.07
54 7 0.02
55 8 0.02
57 24 0.07
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (55 bp):
ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:216236 original size:12 final size:12
Alignment explanation
Indices: 216219--216243 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
216209 TCTTCGGGGA
216219 CTTTTTCTTCTT
1 CTTTTTCTTCTT
216231 CTTTTTCTTCTT
1 CTTTTTCTTCTT
216243 C
1 C
216244 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:216452 original size:24 final size:24
Alignment explanation
Indices: 216418--216464 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
216408 CTGAAACATC
216418 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
216442 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
216465 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:217175 original size:20 final size:20
Alignment explanation
Indices: 217147--217356 Score: 206
Period size: 20 Copynumber: 10.5 Consensus size: 20
217137 AAATTTCAGT
* * *
217147 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
217167 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* * *
217187 GTTACGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
217207 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
217227 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
217247 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
* *
217267 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
217287 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
217307 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
217327 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
217347 GTTGCGATTT
1 GTTGCGATTT
217357 TGGAAAATCG
Statistics
Matches: 162, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 161 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:217350 original size:60 final size:57
Alignment explanation
Indices: 217206--217477 Score: 161
Period size: 60 Copynumber: 4.5 Consensus size: 57
217196 TACAGATTCT
* * ** * ** *
217206 CGTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGAAACG
1 CGTTGCGATTTTCAGATTCGCGTTGCGATTT-CGGATACGCATTGCGAT-TTTGG-ATCG
* * * * *
217266 CGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCG
1 CGTTGCGATTTTCAGATTCGCGTTGCGATTT-CGGATACGCATTGCGATTT-TG-GATCG
* * * * * *
217326 CGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCAATGCGAATTTGACTATCG
1 CGTTGCGATTTTCAGATTCGCGTTGCGATTTCGG-ATA-CGCATTGCGATTTTG--GATCG
* * * * *
217387 CATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGACACTG-ATTTGCGATTCTGGGGATCG
1 CGTTGCGATTTTC-AGATTCGCGTTGCGATTTCGGATAC-GCA-TTGCGATT-T-TGGATCG
* *
217448 CGTTGCGATTTTTA-TTTCGCGTTGCGATTT
1 CGTTGCGATTTTCAGATTCGCGTTGCGATTT
217478 TGTTGGTCAT
Statistics
Matches: 170, Mismatches: 32, Indels: 21
0.76 0.14 0.09
Matches are distributed among these distances:
59 17 0.10
60 81 0.48
61 51 0.30
62 20 0.12
63 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (57 bp):
CGTTGCGATTTTCAGATTCGCGTTGCGATTTCGGATACGCATTGCGATTTTGGATCG
Found at i:217373 original size:21 final size:20
Alignment explanation
Indices: 217323--217420 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
217313 ATTTATGTGT
* * * *
217323 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
217343 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
217364 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
217384 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
217405 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
217421 GACACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:217415 original size:41 final size:41
Alignment explanation
Indices: 217323--217479 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
217313 ATTTATGTGT
* * *
217323 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
217364 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
217405 TCGCGTTGCGATTTTGGACACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
217445 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
217480 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:217747 original size:23 final size:22
Alignment explanation
Indices: 217712--217754 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
217702 TTAATTATTT
217712 AAAAAATTAAATAAAAAATACC
1 AAAAAATTAAATAAAAAATACC
*
217734 AAAAACATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
217755 GTTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATACC
Found at i:226026 original size:17 final size:17
Alignment explanation
Indices: 226004--226038 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
225994 GACTAGGTAG
226004 GTCGCCATGCAATCCAT
1 GTCGCCATGCAATCCAT
*
226021 GTCGCCATGCAGTCCAT
1 GTCGCCATGCAATCCAT
226038 G
1 G
226039 CTTGGCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.34, G:0.23, T:0.23
Consensus pattern (17 bp):
GTCGCCATGCAATCCAT
Found at i:226075 original size:27 final size:27
Alignment explanation
Indices: 226037--226089 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
226027 ATGCAGTCCA
226037 TGCTTGGCAAATGCCTGAACAATGTTC
1 TGCTTGGCAAATGCCTGAACAATGTTC
*
226064 TGCTTGGCAAATGCCTGGACAATGTT
1 TGCTTGGCAAATGCCTGAACAATGTT
226090 GATGGTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (27 bp):
TGCTTGGCAAATGCCTGAACAATGTTC
Found at i:226337 original size:17 final size:17
Alignment explanation
Indices: 226315--226349 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
226305 ATTTGCCAAG
226315 CATGGATTGCATGGCGA
1 CATGGATTGCATGGCGA
226332 CATGGATTGCATGGCGA
1 CATGGATTGCATGGCGA
226349 C
1 C
226350 CTACCTAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (17 bp):
CATGGATTGCATGGCGA
Found at i:226396 original size:29 final size:30
Alignment explanation
Indices: 226339--226413 Score: 125
Period size: 29 Copynumber: 2.5 Consensus size: 30
226329 CGACATGGAT
226339 TGCATGGCGACCTACCTAGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
**
226369 TGCATGGCGACCT-GGTAGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
226398 TGCATGGCGACCTACC
1 TGCATGGCGACCTACC
226414 CCCAGGGACG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.13, C:0.29, G:0.37, T:0.20
Consensus pattern (30 bp):
TGCATGGCGACCTACCTAGGTCGCTGGGCG
Found at i:234442 original size:22 final size:22
Alignment explanation
Indices: 234417--234465 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
234407 ATATATTTAT
234417 TAATATTTATAATAATATAATA
1 TAATATTTATAATAATATAATA
* * *
234439 TAATATTTTTTATATTATAATA
1 TAATATTTATAATAATATAATA
*
234461 AAATA
1 TAATA
234466 ATCAATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAATATTTATAATAATATAATA
Found at i:234636 original size:19 final size:20
Alignment explanation
Indices: 234608--234646 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
234598 CAATAAAATT
234608 ATAAAAAAA-TATTTTAATA
1 ATAAAAAAATTATTTTAATA
*
234627 ATAAATAAATTATTTTAATA
1 ATAAAAAAATTATTTTAATA
234647 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAAAAAATTATTTTAATA
Found at i:236445 original size:15 final size:15
Alignment explanation
Indices: 236425--236464 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
236415 ATTAATTTAT
*
236425 TTTCTGCTTTTTACA
1 TTTCTGCTTTTTAAA
**
236440 TTTCTGCCCTTTAAA
1 TTTCTGCTTTTTAAA
236455 TTTCTGCTTT
1 TTTCTGCTTT
236465 CTAGCATTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.12, C:0.23, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTCTGCTTTTTAAA
Found at i:238506 original size:10 final size:10
Alignment explanation
Indices: 238477--238545 Score: 81
Period size: 10 Copynumber: 7.1 Consensus size: 10
238467 GCTGCTGGAA
238477 AACCGGTTTG
1 AACCGGTTTG
*
238487 -ACCAGTTTTG
1 AACC-GGTTTG
238497 AACCGGTTTG
1 AACCGGTTTG
*
238507 -ACCGGTTCG
1 AACCGGTTTG
238516 AACCGGTTTG
1 AACCGGTTTG
*
238526 -ACCGGTCTG
1 AACCGGTTTG
238535 AACCGGTTTG
1 AACCGGTTTG
238545 A
1 A
238546 CCCGACCCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
9 19 0.39
10 27 0.55
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:238520 original size:19 final size:19
Alignment explanation
Indices: 238477--238547 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
238467 GCTGCTGGAA
* *
238477 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
238497 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
238516 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
238535 AACCGGTTTGACC
1 AACCGGTTTGACC
238548 CGACCCGACT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
18 2 0.04
19 33 0.69
20 13 0.27
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:238569 original size:22 final size:21
Alignment explanation
Indices: 238544--238603 Score: 74
Period size: 17 Copynumber: 3.0 Consensus size: 21
238534 GAACCGGTTT
238544 GACCCGACCCGACTGTTGACCC
1 GACCCGACCCGAC-GTTGACCC
238566 GACCCGA--C--CGTTGACCC
1 GACCCGACCCGACGTTGACCC
238583 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGA-CGTTGACC
238604 GTGACCGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 15 0.45
18 1 0.03
19 1 0.03
20 1 0.03
22 15 0.45
ACGTcount: A:0.18, C:0.47, G:0.23, T:0.12
Consensus pattern (21 bp):
GACCCGACCCGACGTTGACCC
Found at i:238603 original size:17 final size:17
Alignment explanation
Indices: 238542--238591 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
238532 CTGAACCGGT
*
238542 TTGACCCGACCCGACTG
1 TTGACCCGACCCGACCG
238559 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
238576 TTGACCCGACCCGACC
1 TTGACCCGACCCGACC
238592 CGACCGTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.18, C:0.46, G:0.22, T:0.14
Consensus pattern (17 bp):
TTGACCCGACCCGACCG
Found at i:238610 original size:6 final size:7
Alignment explanation
Indices: 238593--238622 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
238583 GACCCGACCC
238593 GACCGTT
1 GACCGTT
238600 GACCG-T
1 GACCGTT
238606 GACCGTT
1 GACCGTT
238613 GACCGTT
1 GACCGTT
238620 GAC
1 GAC
238623 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:238611 original size:13 final size:13
Alignment explanation
Indices: 238593--238618 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
238583 GACCCGACCC
238593 GACCGTTGACCGT
1 GACCGTTGACCGT
238606 GACCGTTGACCGT
1 GACCGTTGACCGT
238619 TGACTTTCTT
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:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:240240 original size:95 final size:95
Alignment explanation
Indices: 240077--240260 Score: 341
Period size: 95 Copynumber: 1.9 Consensus size: 95
240067 ACATTGTTTG
240077 AATAACGGTTTCGGAAAAATGTCTTAAAGAATCATAATGTGATCCACTAGACTTAGTCAAAACGC
1 AATAACGGTTTCGGAAAAATGTCTTAAAGAATCATAATGTGATCCACTAGACTTAGTCAAAACGC
*
240142 ATAGGCCTGGTCTAGGGGGTGACATTTATA
66 ATAGGCCGGGTCTAGGGGGTGACATTTATA
*
240172 AATAACGGTTTCGGAAAAATGTCTTAAAGAATCATAATGTGATCCACTAGACTTAGTCAAAATGC
1 AATAACGGTTTCGGAAAAATGTCTTAAAGAATCATAATGTGATCCACTAGACTTAGTCAAAACGC
*
240237 ATAGGCCGGGTTTAGGGGGTGACA
66 ATAGGCCGGGTCTAGGGGGTGACA
240261 CAACACCCCT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 86 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (95 bp):
AATAACGGTTTCGGAAAAATGTCTTAAAGAATCATAATGTGATCCACTAGACTTAGTCAAAACGC
ATAGGCCGGGTCTAGGGGGTGACATTTATA
Found at i:243478 original size:16 final size:16
Alignment explanation
Indices: 243457--243490 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
243447 TTACTATTCA
*
243457 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
243473 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
243489 CG
1 CG
243491 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:247535 original size:25 final size:22
Alignment explanation
Indices: 247507--247553 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 22
247497 TTAAAATGTA
247507 TTGCGAGAGTTTGAAAAACGTGTTG
1 TTGCGAGAG--TGAAAAA-GTGTTG
*
247532 TTGCGATAGTGAAAAAGTGTTG
1 TTGCGAGAGTGAAAAAGTGTTG
247554 CGATAGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 7 0.33
25 8 0.38
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (22 bp):
TTGCGAGAGTGAAAAAGTGTTG
Found at i:247566 original size:19 final size:20
Alignment explanation
Indices: 247479--247567 Score: 92
Period size: 19 Copynumber: 4.3 Consensus size: 20
247469 CGCGATTTTA
247479 AAAAATGTGTTGCGATAGT-
1 AAAAATGTGTTGCGATAGTG
* * *
247498 TAAAATGTATTGCGAGAGTTTG
1 AAAAATGTGTTGCGATAG--TG
247520 AAAAACGTGTTGTTGCGATAGTG
1 AAAAA--TG-TGTTGCGATAGTG
247543 AAAAA-GTGTTGCGATAGTG
1 AAAAATGTGTTGCGATAGTG
247562 AAAAAT
1 AAAAAT
247568 CCAAAATAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
19 33 0.58
20 1 0.02
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.04
25 9 0.16
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.30
Consensus pattern (20 bp):
AAAAATGTGTTGCGATAGTG
Found at i:247981 original size:21 final size:21
Alignment explanation
Indices: 247931--247981 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
247921 TTCTTAAGAA
247931 ATCGCAACGTAAACTTGGACT
1 ATCGCAACGTAAACTTGGACT
*
247952 ATTGCAACGTAAACTTGGACT
1 ATCGCAACGTAAACTTGGACT
*
247973 ATCGTAACG
1 ATCGCAACG
247982 AATTTAGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (21 bp):
ATCGCAACGTAAACTTGGACT
Found at i:248032 original size:20 final size:20
Alignment explanation
Indices: 248007--248097 Score: 137
Period size: 20 Copynumber: 4.5 Consensus size: 20
247997 AAATTTGGAA
*
248007 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
248027 AATCGCGTTGCAATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
248047 AATCGCGTTGTGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
248067 AATCGCGTTGCGATAGTTAG
1 AATCGCGTTGCGATAGTCAG
*
248087 AATCGCATTGC
1 AATCGCGTTGC
248098 AATTTACATA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:264091 original size:20 final size:21
Alignment explanation
Indices: 264041--264091 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
264031 TGTTTTTTTC
*
264041 TTTTTAAAATATATATATAAT
1 TTTTTAAAATTTATATATAAT
*
264062 TTTTT-TAATTTATATA-AAT
1 TTTTTAAAATTTATATATAAT
264081 TTTTTAAAATT
1 TTTTTAAAATT
264092 ATGAGATTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 8 0.31
20 13 0.50
21 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTAAAATTTATATATAAT
Found at i:269972 original size:31 final size:31
Alignment explanation
Indices: 269927--270035 Score: 137
Period size: 31 Copynumber: 3.5 Consensus size: 31
269917 GGGTCGAGGG
* * *
269927 TTTACTTATATTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTA
* *
269958 TTTACCTGTGTTCTTCGGGATATATGGACTA
1 TTTACCTATGTTCTTCGGGACATATGGACTA
* *
269989 TTTACCTATGTTCTTCTGGACATATGGATTA
1 TTTACCTATGTTCTTCGGGACATATGGACTA
* *
270020 ATTACCTAGGTTCTTC
1 TTTACCTATGTTCTTC
270036 AGAATCTATG
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.43
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTA
Found at i:270025 original size:62 final size:62
Alignment explanation
Indices: 269927--270049 Score: 149
Period size: 62 Copynumber: 2.0 Consensus size: 62
269917 GGGTCGAGGG
* ** * *
269927 TTTACTTATATTCTTCGGGACATATGGACTGTTTACCT-GTGTTCTTCGGGATATATGGACTA
1 TTTACCTATATTCTTCGGGACATATGGACTAATTACCTAG-GTTCTTCAGAATATATGGACTA
* * * *
269989 TTTACCTATGTTCTTCTGGACATATGGATTAATTACCTAGGTTCTTCAGAATCTATGGACT
1 TTTACCTATATTCTTCGGGACATATGGACTAATTACCTAGGTTCTTCAGAATATATGGACT
270050 GGTCCTTCGG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
62 50 0.98
63 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (62 bp):
TTTACCTATATTCTTCGGGACATATGGACTAATTACCTAGGTTCTTCAGAATATATGGACTA
Found at i:270046 original size:31 final size:31
Alignment explanation
Indices: 269937--270049 Score: 86
Period size: 31 Copynumber: 3.6 Consensus size: 31
269927 TTTACTTATA
* * **
269937 TTCTTCGGGACATATGGACTGTTTACCT-GTG
1 TTCTTCAGAACATATGGACTAATTACCTAG-G
* * * * *
269968 TTCTTCGGGATATATGGACTATTTACCTATG
1 TTCTTCAGAACATATGGACTAATTACCTAGG
* * *
269999 TTCTTCTGGACATATGGATTAATTACCTAGG
1 TTCTTCAGAACATATGGACTAATTACCTAGG
270030 TTCTTCAGAATC-TATGGACT
1 TTCTTCAGAA-CATATGGACT
270050 GGTCCTTCGG
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
31 68 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (31 bp):
TTCTTCAGAACATATGGACTAATTACCTAGG
Found at i:271882 original size:172 final size:171
Alignment explanation
Indices: 271597--271939 Score: 490
Period size: 172 Copynumber: 2.0 Consensus size: 171
271587 ATCCAATAAA
** *
271597 AAAAGCCTTAAAACTCATATTAGAACATGCACTAACCGACAACCACCTCATATCCCAAAAAAAGA
1 AAAAGCCTTAAAACTCATATTAGAACACACAATAACCGACAACCACCTCATATCCCAAAAAAAGA
* * * *
271662 CAACACGCGATACCCTACAAGACAAAGCACCATCTCCGACAATCTCCATATTTCCCATAACGATG
66 CAACACGCGAGACCCTACAAGACAAAGAACCATCTCCAACAATCTCCATATTTCCCAGAACGATG
*
271727 CTAGCCCGAGTGC-CTATACACCCAATCTATCAAAACAGCCT
131 CTAGCCCGAGTGCTC-ATAAACCCAATCTATCAAAACAGCCT
* * * *
271768 AAAAGCCTTAAAACTCATATTAGAACACACAATCACCCGACAACCGCCTCATATCCCACAAAAGG
1 AAAAGCCTTAAAACTCATATTAGAACACACAAT-AACCGACAACCACCTCATATCCCAAAAAAAG
** * * *
271833 ACAGTATGCGAGACCCTACAAGACAGAGAACCATCTCTAACAATCTCCATATTTCCCAGAACGAT
65 ACAACACGCGAGACCCTACAAGACAAAGAACCATCTCCAACAATCTCCATATTTCCCAGAACGAT
* *
271898 GCTAGCCCGAGTGCTCATAAACCCAATCTTTCAAAACTGCCT
130 GCTAGCCCGAGTGCTCATAAACCCAATCTATCAAAACAGCCT
271940 GTCGAAACTG
Statistics
Matches: 151, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
171 30 0.20
172 120 0.79
173 1 0.01
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.19
Consensus pattern (171 bp):
AAAAGCCTTAAAACTCATATTAGAACACACAATAACCGACAACCACCTCATATCCCAAAAAAAGA
CAACACGCGAGACCCTACAAGACAAAGAACCATCTCCAACAATCTCCATATTTCCCAGAACGATG
CTAGCCCGAGTGCTCATAAACCCAATCTATCAAAACAGCCT
Found at i:274068 original size:20 final size:20
Alignment explanation
Indices: 273996--274344 Score: 418
Period size: 20 Copynumber: 17.4 Consensus size: 20
273986 GATTTTCCAT
* ** *
273996 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
274016 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
274036 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
274056 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
274076 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
274096 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
274116 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
274136 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
274156 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
274176 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
274196 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
274216 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
274236 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
274256 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
274276 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
274296 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
274316 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
274336 AATCACAAC
1 AATCGCAAC
274345 ACTGAAATTT
Statistics
Matches: 285, Mismatches: 36, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
19 3 0.01
20 279 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:275065 original size:24 final size:24
Alignment explanation
Indices: 275026--275072 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
275016 AAATTTGGTC
275026 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
275050 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
275073 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:277574 original size:19 final size:19
Alignment explanation
Indices: 277552--277856 Score: 358
Period size: 19 Copynumber: 17.4 Consensus size: 19
277542 CGGAAAATAC
*
277552 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
277571 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
277585 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
277605 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
277619 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
277638 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
277656 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
277670 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
277689 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
277708 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
277722 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
277741 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
277760 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
277779 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
277797 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
277811 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
277830 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
277849 AATCGCAA
1 AATCGCAA
277857 CGAGATAATC
Statistics
Matches: 249, Mismatches: 10, Indels: 54
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.00
14 47 0.19
15 2 0.01
16 22 0.09
17 7 0.03
18 21 0.08
19 136 0.55
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:277624 original size:14 final size:15
Alignment explanation
Indices: 277605--277682 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 15
277595 CGGAAATGAA
277605 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
*
277619 AATCGCAATGCGAAATGAA
1 AATCGCAA-GCG--A-GAG
*
277638 AATCGCAATGCGAAATG
1 AATCGCAA-GCGAGA-G
277655 AAATCGCAA-CGAGAG
1 -AATCGCAAGCGAGAG
277670 AATCGCAATGCGA
1 AATCGCAA-GCGA
277683 AATGAAAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
14 16 0.31
15 1 0.02
16 10 0.20
17 1 0.02
18 9 0.18
19 14 0.27
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (15 bp):
AATCGCAAGCGAGAG
Found at i:277671 original size:51 final size:52
Alignment explanation
Indices: 277580--277856 Score: 370
Period size: 51 Copynumber: 5.2 Consensus size: 52
277570 AAATCCCAAC
277580 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
277633 ATGAAAATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
277684 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
277736 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
277793 ATG-AAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
277844 ATGAAAATCGCAA
1 ATGAAAATCGCAA
277857 CGAGATAATC
Statistics
Matches: 212, Mismatches: 5, Indels: 15
0.91 0.02 0.06
Matches are distributed among these distances:
51 87 0.41
52 74 0.35
53 17 0.08
54 7 0.03
56 10 0.05
57 17 0.08
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:277802 original size:141 final size:137
Alignment explanation
Indices: 277552--277894 Score: 514
Period size: 141 Copynumber: 2.5 Consensus size: 137
277542 CGGAAAATAC
* * *
277552 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CG
1 AATCGCAATGCGAAATGAAAATCGCAAC--GAAAATCGCAATGC-GAAATTAAAATCGCAATGCG
* *
277615 -AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAAT
63 AAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAAT
277679 GCGAAATGAA
128 GCGAAATGAA
277689 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTAAAATCGCAATGCG-
277754 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAA
63 AA-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAA
277819 TGCGAAATGAA
127 TGCGAAATGAA
*
277830 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATAAA-CGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTA-AAATCGCAATGCG
277894 A
63 A
277895 TTTTCATTTC
Statistics
Matches: 190, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
135 2 0.01
136 16 0.08
137 37 0.19
138 2 0.01
140 2 0.01
141 128 0.67
142 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (137 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAATCGCAATGCGAAATTAAAATCGCAATGCGAAG
AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCG
AAATGAA
Found at i:277894 original size:52 final size:51
Alignment explanation
Indices: 277619--277878 Score: 243
Period size: 52 Copynumber: 4.9 Consensus size: 51
277609 GCAACGAGAG
*
277619 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATG-AAATCGCAA--CGAAA-G-AATCGCAATGCGAAATGAA
*
277670 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATG-AAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
*
277722 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAA-TGAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
277779 AATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
* *
277830 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATG-AAATCGCAACGAAAGAATCGCAATGCGAAAT
277879 TATAAACGCA
Statistics
Matches: 194, Mismatches: 5, Indels: 19
0.89 0.02 0.09
Matches are distributed among these distances:
51 72 0.37
52 83 0.43
53 2 0.01
54 11 0.06
55 1 0.01
56 10 0.05
57 15 0.08
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (51 bp):
AATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:277994 original size:19 final size:19
Alignment explanation
Indices: 277885--277986 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
277875 AAATTATAAA
277885 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
277904 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
277924 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
277940 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
277957 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
277976 CGCATTGCGAT
1 CGCATTGCGAT
277987 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:278112 original size:14 final size:14
Alignment explanation
Indices: 278093--278129 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
278083 CATCAATTAC
278093 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
278107 ACAAATCATCTTTT
1 ACAAATCAACTTTT
278121 ACAAATCAA
1 ACAAATCAA
278130 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:280122 original size:14 final size:14
Alignment explanation
Indices: 280103--280159 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
280093 GCGAAATGAA
*
280103 AATCGCAACGACAG
1 AATCGCAACGAAAG
280117 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
280134 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
280150 AATCGCAACG
1 AATCGCAACG
280160 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:280130 original size:33 final size:33
Alignment explanation
Indices: 280084--280176 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
280074 GCGAAACCAA
*
280084 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
280117 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
280150 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
280177 TGCGATTTTG
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:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:280141 original size:19 final size:19
Alignment explanation
Indices: 280047--280181 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
280037 TAGTTTACTT
* *
280047 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
280067 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
280086 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
280105 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
280119 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
280138 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
280152 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
280171 TCGCAATGCGA
1 TCGCAACGCGA
280182 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:280212 original size:20 final size:19
Alignment explanation
Indices: 280177--280220 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
280167 AAAATCGCAA
*
280177 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTAGTTTCGCGT
*
280196 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-AGTTTCGCGT
280216 TGCGA
1 TGCGA
280221 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.11, C:0.14, G:0.30, T:0.45
Consensus pattern (19 bp):
TGCGATTTTAGTTTCGCGT
Found at i:280404 original size:93 final size:93
Alignment explanation
Indices: 280264--280921 Score: 1300
Period size: 93 Copynumber: 7.1 Consensus size: 93
280254 TTGAATGGAT
280264 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
280329 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
280357 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
280422 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
280450 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
280515 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
280543 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
280608 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
280636 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
280701 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
280729 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
280793 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
280821 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
*
280886 GTTTAGCAGAATTGGCAGCAACCGAATA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
280914 AATTTACT
1 AATTTACT
280922 AAGCAATCTA
Statistics
Matches: 563, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
92 92 0.16
93 471 0.84
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACA
Found at i:282642 original size:14 final size:14
Alignment explanation
Indices: 282623--282712 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
282613 TTGAAATGAA
282623 AATCGCAACGAGAG
1 AATCGCAACGAGAG
282637 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
282654 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
282670 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
282689 AATCGCAACGAGAG
1 AATCGCAACGAGAG
282703 AATCGCAACG
1 AATCGCAACG
282713 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:282660 original size:33 final size:33
Alignment explanation
Indices: 282615--282729 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
282605 TCTTTTGGTT
282615 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
282648 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
282681 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
282714 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
282730 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:282661 original size:19 final size:18
Alignment explanation
Indices: 282622--282734 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
282612 GTTGAAATGA
282622 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
282637 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
282654 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
282670 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
282687 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
282703 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
282720 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
282735 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:282765 original size:14 final size:14
Alignment explanation
Indices: 282746--282800 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
282736 TTTGGTTTCG
282746 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
282760 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
282779 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
282793 CGTTGCGA
1 CGTTGCGA
282801 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:282778 original size:33 final size:33
Alignment explanation
Indices: 282730--282800 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
282720 AAAATCGCAA
**
282730 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
282763 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
282796 TGCGA
1 TGCGA
282801 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:282808 original size:33 final size:33
Alignment explanation
Indices: 282741--282822 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
282731 GCGATTTTGG
***
282741 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
282774 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
282807 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
282823 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:282827 original size:20 final size:20
Alignment explanation
Indices: 282753--282841 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
282743 TCGCGTTGCG
282753 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
282773 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
282786 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
282806 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
282826 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
282842 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:282963 original size:33 final size:33
Alignment explanation
Indices: 282921--282991 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
282911 AATACTAACT
*
282921 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
282954 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
282987 TGAAA
1 TGAAA
282992 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:283223 original size:22 final size:22
Alignment explanation
Indices: 283171--283225 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
283161 TGGTTGTGAG
**
283171 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
283193 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
283215 GGATTTCTTCG
1 GGATTTCTTCG
283226 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:283396 original size:20 final size:20
Alignment explanation
Indices: 283371--283563 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
283361 CTTTAAATAT
283371 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
283391 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
283413 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
283432 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* * **
283452 CACATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
283472 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
283492 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
283512 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
283532 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
283552 CGCGTTGCGATT
1 CGCGTTGCGATT
283564 ATGGAAAATC
Statistics
Matches: 144, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:283558 original size:60 final size:60
Alignment explanation
Indices: 283371--283563 Score: 242
Period size: 60 Copynumber: 3.2 Consensus size: 60
283361 CTTTAAATAT
**
283371 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * * *** *
283432 CGCGTTGCGATATACGGATACACATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
283492 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
283552 CGCGTTGCGATT
1 CGCGTTGCGATT
283564 ATGGAAAATC
Statistics
Matches: 109, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 82 0.75
61 27 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:283644 original size:20 final size:20
Alignment explanation
Indices: 283619--283671 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
283609 AAGAATCGCG
*
283619 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
283639 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
283659 TTGCGATTCTGGA
1 TTGCGATTCTGGA
283672 GATCGCGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:283899 original size:22 final size:22
Alignment explanation
Indices: 283874--283915 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
283864 ACGTATTTTA
283874 TTTAGAATTTAAAGA-TTAAGAC
1 TTTA-AATTTAAAGAGTTAAGAC
*
283896 TTTAAATTTTAAGAGTTAAG
1 TTTAAATTTAAAGAGTTAAG
283916 GTCTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.40
Consensus pattern (22 bp):
TTTAAATTTAAAGAGTTAAGAC
Found at i:287915 original size:31 final size:31
Alignment explanation
Indices: 287879--287937 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
287869 AACTTAAAAG
* *
287879 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
287910 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
287938 CCATACAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:287988 original size:22 final size:22
Alignment explanation
Indices: 287962--288004 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
287952 TAATAAATTA
287962 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
287984 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
288005 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:288010 original size:18 final size:18
Alignment explanation
Indices: 287988--288039 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
287978 CCATATTTTA
287988 AAATAAATCAATTCATAC
1 AAATAAATCAATTCATAC
* *
288006 TAATAAAT-TATT--TA-
1 AAATAAATCAATTCATAC
288020 AAATAAATCAATTCATAC
1 AAATAAATCAATTCATAC
288038 AA
1 AA
288040 CTACAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 7 0.27
15 5 0.19
17 5 0.19
18 9 0.35
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAATCAATTCATAC
Found at i:288013 original size:22 final size:22
Alignment explanation
Indices: 287964--288012 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
287954 ATAAATTATT
**
287964 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
287986 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
288009 TAAA
1 TAAA
288013 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:288057 original size:80 final size:78
Alignment explanation
Indices: 287966--288348 Score: 320
Period size: 80 Copynumber: 4.8 Consensus size: 78
287956 AAATTATTTA
*
287966 AAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
*
288031 TTCATACAACTACAAT
66 TCCATA-AA-TA-AAT
288047 -AATAAATCAATCCATATTTTAAAATAAATC-ATCCATACTAATAAATTATTTAAAATAAATCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
**
288110 TCCATATTTTAAAAT
66 TCCATA-AAT-AAAT
* * *
288125 AAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTACAA-TA-TT-AAA
1 AAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAA-TA-AATTATTTAAAA
* **
288186 TCAATCCATAT-TTTAAAATAAAT
58 TAAAT-CA-ATCCAT-AAATAAAT
* * ** ** *
288209 CAGTCCATACTAATAAAT-TATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAAT
1 AAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
* **
288273 CAATCCAT-ATTTTAT
63 CAATCCATAAATAAAT
*
288288 -AATAAATCAATCCAT-TTTTCATAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 AAATAAATCAATCCATATTTT-AAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
288349 TATTTTAAAC
Statistics
Matches: 248, Mismatches: 32, Indels: 49
0.75 0.10 0.15
Matches are distributed among these distances:
75 3 0.01
76 45 0.18
77 1 0.00
78 8 0.03
79 53 0.21
80 60 0.24
81 9 0.04
82 7 0.03
83 1 0.00
84 20 0.08
85 22 0.09
86 17 0.07
87 2 0.01
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (78 bp):
AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
TCCATAAATAAAT
Found at i:288091 original size:22 final size:22
Alignment explanation
Indices: 288018--288091 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 22
288008 ATAAATTATT
* *
288018 TAAAATAAATCAATTCATACAA
1 TAAAATAAATCAATCCATATAA
**
288040 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
288066 TAAAATAAATC-ATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
288088 TAAA
1 TAAA
288092 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
21 7 0.17
22 13 0.32
23 3 0.07
25 3 0.07
26 15 0.37
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:288102 original size:133 final size:134
Alignment explanation
Indices: 287952--288249 Score: 553
Period size: 133 Copynumber: 2.2 Consensus size: 134
287942 ACAACCACAA
*
287952 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
288017 TTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCA-TCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAGTCC
288081 ATAC
131 ATAC
288085 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
288150 TTAAAATAAATCAATCCATACAACTACAATATTAAATCAATCCATATTTTAAAATAAATCAGTCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAGTCC
288215 ATAC
131 ATAC
*
288219 TAATAAATTATTTAAAATAAATCAATTCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
288250 CTAATAAATT
Statistics
Matches: 160, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
133 123 0.77
134 37 0.23
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (134 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAGTCC
ATAC
Found at i:288113 original size:32 final size:32
Alignment explanation
Indices: 288064--288170 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 32
288054 CAATCCATAT
288064 TTTAAAATAAATC-ATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
288095 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
288117 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
288149 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
288171 AACTACAATA
Statistics
Matches: 65, Mismatches: 0, Indels: 21
0.76 0.00 0.24
Matches are distributed among these distances:
22 16 0.25
23 2 0.03
24 1 0.02
26 3 0.05
28 3 0.05
30 1 0.02
31 15 0.23
32 24 0.37
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:288121 original size:22 final size:22
Alignment explanation
Indices: 288095--288137 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
288085 TAATAAATTA
288095 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
288117 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
288138 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:288146 original size:22 final size:22
Alignment explanation
Indices: 288097--288145 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
288087 ATAAATTATT
**
288097 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
288119 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
288142 TAAA
1 TAAA
288146 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:288159 original size:54 final size:54
Alignment explanation
Indices: 288047--288302 Score: 277
Period size: 54 Copynumber: 4.7 Consensus size: 54
288037 CAACTACAAT
288047 AATAAATCAATCCATATTTTAAAATAAATC-ATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
288100 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*** ** * ** *
288154 AATAAATCAATCCATACAACTACAATATTAAATCAATCCATA-TTTTAAAATAAAT-C
1 AATAAATCAATCCATA-TTTTA-AA-A-TAAATCAATCCATACTAATAAATTATTTAA
* ** ** *
288210 AGTCCATACTAATAAAT-TATTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
288266 AATAAATCAATCCATATTTTATAATAAATCAATCCAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCAT
288303 TTTTCATAAT
Statistics
Matches: 161, Mismatches: 31, Indels: 21
0.76 0.15 0.10
Matches are distributed among these distances:
53 30 0.19
54 75 0.47
55 13 0.08
56 12 0.07
57 12 0.07
58 19 0.12
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:288207 original size:22 final size:23
Alignment explanation
Indices: 288148--288218 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 23
288138 CTAATAAATT
288148 ATTTAAAATAAATCAATCCATAC
1 ATTTAAAATAAATCAATCCATAC
**
288171 AACTACAATATTAAATCAATCCATA-
1 ATTTA-AA-A-TAAATCAATCCATAC
* *
288196 TTTTAAAATAAATCAGTCCATAC
1 ATTTAAAATAAATCAATCCATAC
288219 TAATAAATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
22 13 0.34
23 4 0.11
24 4 0.11
25 3 0.08
26 14 0.37
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.31
Consensus pattern (23 bp):
ATTTAAAATAAATCAATCCATAC
Found at i:288236 original size:32 final size:32
Alignment explanation
Indices: 288197--288281 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
288187 CAATCCATAT
*
288197 TTTAAAATAAATCAGTCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
288229 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
288261 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
288282 TTTTATAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:288237 original size:112 final size:108
Alignment explanation
Indices: 287967--288348 Score: 355
Period size: 108 Copynumber: 3.6 Consensus size: 108
287957 AATTATTTAA
*
287967 AATAAATCAATCCATATTTT-AAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCCAT-TTTTCAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
* * **
288031 TTCATAC-AACTACA--A--T--AATAAATCAATCCATATTTTAA-
65 TCCATACTAA-TAAATTATTTAAAATAAATCAATCCATA-TACAAT
* * * ** * * *
288069 AATAAATC-ATCCA---TAC-TAATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 AATAAATCAATCCATTTTTCAAAATAAATCAATCCATACT-AATAAAT---TA-TTTAAAATAAA
288128 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
61 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---A-TACAAT
* *
288180 ATTAAATCAATCCATATTTT-AAAATAAATCAGTCCATACTAATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCCAT-TTTTCAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
* ***
288244 TTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAT
65 TCCATACTAATAAATTATTTAAAATAAATCAATCCATATACAAT
*
288288 AATAAATCAATCCATTTTTCATAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 AATAAATCAATCCATTTTTCAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
288349 TATTTTAAAC
Statistics
Matches: 226, Mismatches: 29, Indels: 44
0.76 0.10 0.15
Matches are distributed among these distances:
96 6 0.03
97 14 0.06
100 2 0.01
101 29 0.13
102 10 0.04
103 1 0.00
105 1 0.00
107 19 0.08
108 56 0.25
109 1 0.00
110 4 0.02
111 7 0.03
112 56 0.25
113 2 0.01
116 14 0.06
117 4 0.02
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (108 bp):
AATAAATCAATCCATTTTTCAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACTAATAAATTATTTAAAATAAATCAATCCATATACAAT
Found at i:288239 original size:14 final size:14
Alignment explanation
Indices: 288220--288272 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
288210 AGTCCATACT
288220 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
288234 AATAAATCAATTCATACT
1 AATAAAT-TATT--TA-A
288252 AATAAATTATTTAA
1 AATAAATTATTTAA
288266 AATAAAT
1 AATAAAT
288273 CAATCCATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 5 0.16
17 5 0.16
18 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:288291 original size:22 final size:22
Alignment explanation
Indices: 288261--288325 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
288251 TAATAAATTA
*
288261 TTTAAAATAAATCAATCCATAT
1 TTTATAATAAATCAATCCATAT
288283 TTTATAATAAATCAATCCAT-T
1 TTTATAATAAATCAATCCATAT
288304 TTTCATAATAAATCAATCCATA
1 TTT-ATAATAAATCAATCCATA
288326 CTAATAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 4 0.10
22 36 0.90
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTATAATAAATCAATCCATAT
Found at i:288357 original size:15 final size:15
Alignment explanation
Indices: 288328--288419 Score: 113
Period size: 15 Copynumber: 6.5 Consensus size: 15
288318 AATCCATACT
288328 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
288342 AATAAATTATTTT--
1 AATAAATTATTTTAA
* *
288355 AA-ACA-TATTTTAT
1 AATAAATTATTTTAA
288368 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
288383 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
288398 AATAAATTATTTTTA
1 AATAAATTATTTTAA
288413 AATAAAT
1 AATAAAT
288420 AACCTTATTA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
11 6 0.09
12 2 0.03
13 4 0.06
14 11 0.16
15 44 0.66
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:288396 original size:30 final size:30
Alignment explanation
Indices: 288328--288441 Score: 125
Period size: 30 Copynumber: 4.0 Consensus size: 30
288318 AATCCATACT
*
288328 AATAAATTA-TTTAAAATAAATTATTTT--
1 AATAAATTATTTTATAATAAATTATTTTAA
*
288355 AA-ACA-TATTTTATAATAAATTATTTTAA
1 AATAAATTATTTTATAATAAATTATTTTAA
*
288383 AATAAATTATTTTATAATAAATTATTTTTA
1 AATAAATTATTTTATAATAAATTATTTTAA
* **
288413 AATAAATAACCTTAT--TAAATTATTTTAA
1 AATAAATTATTTTATAATAAATTATTTTAA
288441 A
1 A
288442 TTATAACCAT
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
25 2 0.03
26 19 0.26
27 2 0.03
28 15 0.20
29 2 0.03
30 34 0.46
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
AATAAATTATTTTATAATAAATTATTTTAA
Found at i:288415 original size:41 final size:40
Alignment explanation
Indices: 288327--288405 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 40
288317 CAATCCATAC
*
288327 TAATAAATTATTTAAAATAAATTATTTTAAACATATTTTA
1 TAATAAATTATTTAAAATAAATTATTTTAAACAAATTTTA
*
288367 TAATAAATTATTTTAAAATAAATTATTTTATAATAAATT
1 TAATAAATTA-TTTAAAATAAATTATTTTA-AACAAATT
288406 ATTTTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 10 0.29
41 19 0.54
42 6 0.17
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (40 bp):
TAATAAATTATTTAAAATAAATTATTTTAAACAAATTTTA
Found at i:288454 original size:26 final size:28
Alignment explanation
Indices: 288400--288454 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
288390 TATTTTATAA
*
288400 TAAATTATTTTTAAATAAATAACCTTAT
1 TAAATTATTTTTAAATAAATAACCATAT
*
288428 TAAATTA-TTTTAAAT-TATAACCATAT
1 TAAATTATTTTTAAATAAATAACCATAT
288454 T
1 T
288455 TTATAATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.40
27 8 0.32
28 7 0.28
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (28 bp):
TAAATTATTTTTAAATAAATAACCATAT
Found at i:288924 original size:22 final size:22
Alignment explanation
Indices: 288883--288925 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
288873 ATGTCTTAGG
* * *
288883 AATTATCTTTTGCATTAATGAC
1 AATTATCTATTGAATAAATGAC
288905 AATTATCTATTGAATAAATGA
1 AATTATCTATTGAATAAATGA
288926 TGATTAGAAA
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:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (22 bp):
AATTATCTATTGAATAAATGAC
Found at i:289332 original size:40 final size:40
Alignment explanation
Indices: 289269--289349 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
289259 AAATGAGAGT
*
289269 AGATTTTTGCAGGCTTAACATTTATTGTATAGGAAATATC
1 AGATTTTTACAGGCTTAACATTTATTGTATAGGAAATATC
* * * *
289309 AGATTTTTACGGGTTTAATATTTATTGTTTAGGAAATATC
1 AGATTTTTACAGGCTTAACATTTATTGTATAGGAAATATC
289349 A
1 A
289350 ATTACTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.43
Consensus pattern (40 bp):
AGATTTTTACAGGCTTAACATTTATTGTATAGGAAATATC
Found at i:289464 original size:18 final size:19
Alignment explanation
Indices: 289441--289478 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
289431 TTAAAATCAT
289441 TTAATA-ATTTTAATTTTA
1 TTAATACATTTTAATTTTA
*
289459 TTAATACTTTTTAATTTTA
1 TTAATACATTTTAATTTTA
289478 T
1 T
289479 GACTCTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TTAATACATTTTAATTTTA
Found at i:293650 original size:75 final size:75
Alignment explanation
Indices: 293547--293742 Score: 229
Period size: 75 Copynumber: 2.6 Consensus size: 75
293537 GACCGTTGAA
* * *
293547 CAGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTAT-GGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
**
293611 ACAAAAATGTT
65 ACAAAAACATT
* * * *
293622 TAGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAA
* *
293687 CCAAACCATT
66 CAAAAACATT
* *
293697 CAGGGGGGAATCGG-T--TCCTATGGGGGGAATCAGTTCCCTCTGAGCA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGG-ATCGGTTCCCTCCGAGCA
293743 ATCTGTAATT
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
72 11 0.11
73 16 0.15
74 1 0.01
75 75 0.72
76 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.22
Consensus pattern (75 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAA
CAAAAACATT
Found at i:294374 original size:17 final size:17
Alignment explanation
Indices: 294352--294395 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
294342 TTCATAAATC
294352 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
294369 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
294386 -AAATATCCAA
1 CAAA-ATCCAA
294396 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:294387 original size:9 final size:8
Alignment explanation
Indices: 294347--294397 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
294337 CACCATTCAT
294347 AAATCC-A
1 AAATCCAA
294354 AAATCCAA
1 AAATCCAA
*
294362 CAATCCACA
1 AAATCCA-A
294371 AAAT-CAA
1 AAATCCAA
294378 ACAATCCAA
1 A-AATCCAA
294387 AATATCCAA
1 AA-ATCCAA
294396 AA
1 AA
294398 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:296407 original size:20 final size:21
Alignment explanation
Indices: 296361--296421 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
296351 TTCCCCTGTG
296361 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
296384 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
296404 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
296422 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:302267 original size:75 final size:76
Alignment explanation
Indices: 302167--302363 Score: 254
Period size: 75 Copynumber: 2.6 Consensus size: 76
302157 CCGTTGAACA
* * *
302167 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
1 GGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
** *
302231 AAAATGTTTAG
66 AAAACATTCAG
* * * * *
302242 GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCTAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
*
302306 AAACCATTCAG
66 AAAACATTCAG
*
302317 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCTCCTATGGGGGGG-ATCGGTTCCCTCCGAGCA
302364 ATCTGTAATT
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
75 82 0.79
76 6 0.06
77 16 0.15
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.23
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
AAAACATTCAG
Found at i:302268 original size:21 final size:22
Alignment explanation
Indices: 302242--302283 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
302232 AAATGTTTAG
302242 GGGGGAATCGGTT-CCTCCTAT
1 GGGGGAATCGGTTCCCTCCTAT
302263 GGGGGAATCGGTTCCCTCCTA
1 GGGGGAATCGGTTCCCTCCTA
302284 GCATTCTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.14, C:0.26, G:0.33, T:0.26
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTCCTAT
Found at i:303297 original size:14 final size:15
Alignment explanation
Indices: 303266--303302 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
303256 ATAATTTAGT
*
303266 TAAAAT-TTTAAAGC
1 TAAAATATTTAAAGA
303280 TAAAATATTTAAA-A
1 TAAAATATTTAAAGA
303294 TAAAATATT
1 TAAAATATT
303303 AATTATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (15 bp):
TAAAATATTTAAAGA
Found at i:303336 original size:14 final size:15
Alignment explanation
Indices: 303301--303338 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
303291 AAATAAAATA
*
303301 TTAATTATATTATTT
1 TTAATAATATTATTT
*
303316 TTTATAATATT-TTT
1 TTAATAATATTATTT
303330 TTAATAATA
1 TTAATAATA
303339 ATTAGATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTAATAATATTATTT
Found at i:303987 original size:60 final size:60
Alignment explanation
Indices: 303906--304048 Score: 157
Period size: 60 Copynumber: 2.4 Consensus size: 60
303896 ACTTTTAAAT
* * * **
303906 ATTTCAATTTCATCTCTAAACTATGAC-TATCATTCTAAATTAGTCATTAAAATTTCT-AAC
1 ATTTCAATTTCATCCCCAAACTATGACAT-TCATTCTAAAGT-GTCACCAAAATTTCTGAAC
* * * *
303966 ATTTCAATTTCATCCCCAAACTATGGCATTCATTCTAAAGTGTCCCCAAACTTTTTGAAC
1 ATTTCAATTTCATCCCCAAACTATGACATTCATTCTAAAGTGTCACCAAAATTTCTGAAC
*
304026 ATTCCAATTTCAT-CCCAAACTAT
1 ATTTCAATTTCATCCCCAAACTAT
304049 ATGTATATAC
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
59 20 0.28
60 50 0.70
61 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.38
Consensus pattern (60 bp):
ATTTCAATTTCATCCCCAAACTATGACATTCATTCTAAAGTGTCACCAAAATTTCTGAAC
Found at i:304323 original size:60 final size:60
Alignment explanation
Indices: 304187--304323 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
304177 AAGAAATTGA
** ** *
304187 AATATTCAAAAGTTTGGGGACTAATTTAGAAATAGGGTCATGGTTTAGGGATGCAATTAG
1 AATATTCAAAAGTTTAAGGACTAATTTAGAAATAAAGTCATAGTTTAGGGATGCAATTAG
* *
304247 AATGTTCAAATA-TTTAAGGATTAATTTAG-AATGAAAGTCATAGTTTAGGGAT-CAAATTAG
1 AATATTCAAA-AGTTTAAGGACTAATTTAGAAAT-AAAGTCATAGTTTAGGGATGC-AATTAG
304307 AATATTCAAAAGTTTAA
1 AATATTCAAAAGTTTAA
304324 AGAACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
59 5 0.08
60 59 0.91
61 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (60 bp):
AATATTCAAAAGTTTAAGGACTAATTTAGAAATAAAGTCATAGTTTAGGGATGCAATTAG
Found at i:304333 original size:60 final size:60
Alignment explanation
Indices: 304223--304340 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
304213 TAGAAATAGG
* * * ** *
304223 GTCATGGTTTAGGGATGCAATTAGAATGTTCAAATATTTAAGGATTAATTTAGAATGAAA
1 GTCATAGTTTAGGGATGCAATTAGAATATTCAAATATTTAAAGAACAATTTAAAATGAAA
304283 GTCATAGTTTAGGGAT-CAAATTAGAATATTCAAA-AGTTTAAAGAACAATTTAAAATGA
1 GTCATAGTTTAGGGATGC-AATTAGAATATTCAAATA-TTTAAAGAACAATTTAAAATGA
304341 GATTTATAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.04
60 48 0.96
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (60 bp):
GTCATAGTTTAGGGATGCAATTAGAATATTCAAATATTTAAAGAACAATTTAAAATGAAA
Found at i:305594 original size:21 final size:21
Alignment explanation
Indices: 305568--305607 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
305558 CATAAAGAAG
305568 GATCTCCATTTGTCAGATAAT
1 GATCTCCATTTGTCAGATAAT
305589 GATCTCCATTTGTCAGATA
1 GATCTCCATTTGTCAGATA
305608 TAGTGCGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (21 bp):
GATCTCCATTTGTCAGATAAT
Found at i:311007 original size:23 final size:23
Alignment explanation
Indices: 310981--311058 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
310971 CACCACAGCT
*
310981 CATATAATTACACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
311004 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
311027 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
311050 TATAATAAT
1 CAT-ATAAT
311059 GTCCATAAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
23 42 0.91
24 4 0.09
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:311236 original size:103 final size:103
Alignment explanation
Indices: 311065--311282 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
311055 TAATGTCCAT
* *
311065 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
311130 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
*
311168 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
311233 GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
311271 AAGGACCACATA
1 AAGGACCACATA
311283 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
Found at i:316584 original size:26 final size:26
Alignment explanation
Indices: 316555--316605 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
316545 CGAATCTCAA
316555 AAAAAACTCAGCGAGAGATGGGCCAC
1 AAAAAACTCAGCGAGAGATGGGCCAC
*
316581 AAAAAATTCAGCGAGAGATGGGCCA
1 AAAAAACTCAGCGAGAGATGGGCCA
316606 AACAGGAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.20, G:0.27, T:0.10
Consensus pattern (26 bp):
AAAAAACTCAGCGAGAGATGGGCCAC
Found at i:317720 original size:17 final size:17
Alignment explanation
Indices: 317700--317737 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
317690 AGAGAAACAT
317700 GAGTGAATACTATGTCA
1 GAGTGAATACTATGTCA
*
317717 GAGTGAATGCTATGTCA
1 GAGTGAATACTATGTCA
317734 GAGT
1 GAGT
317738 TCATACCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.29
Consensus pattern (17 bp):
GAGTGAATACTATGTCA
Found at i:318095 original size:13 final size:13
Alignment explanation
Indices: 318077--318102 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
318067 TATTACATGC
318077 GTTGCATAAGTGT
1 GTTGCATAAGTGT
318090 GTTGCATAAGTGT
1 GTTGCATAAGTGT
318103 TTATTTTTAA
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:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (13 bp):
GTTGCATAAGTGT
Found at i:319269 original size:15 final size:16
Alignment explanation
Indices: 319236--319269 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
319226 AAGGAACAAC
*
319236 TTTATTATTTTCTTAA
1 TTTATAATTTTCTTAA
319252 TTTATAATTTTC-TAA
1 TTTATAATTTTCTTAA
319267 TTT
1 TTT
319270 TTAAGAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATAATTTTCTTAA
Found at i:320921 original size:18 final size:20
Alignment explanation
Indices: 320895--320932 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
320885 ATAAGTGATC
320895 ATGTGTTTC-ATTT-TTAAT
1 ATGTGTTTCAATTTCTTAAT
*
320913 ATGTTTTTCAATTTCTTAAT
1 ATGTGTTTCAATTTCTTAAT
320933 CAATACACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.61
Consensus pattern (20 bp):
ATGTGTTTCAATTTCTTAAT
Found at i:324727 original size:2 final size:2
Alignment explanation
Indices: 324634--324708 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
324624 GTGGTAAGAA
324634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
324676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
324709 ATTTTTAAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:329638 original size:15 final size:15
Alignment explanation
Indices: 329620--329653 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
329610 CAGTGTAATC
*
329620 AAAAGAAGCAAAGAG
1 AAAAGAAGAAAAGAG
*
329635 AAAAGAGGAAAAGAG
1 AAAAGAAGAAAAGAG
329650 AAAA
1 AAAA
329654 TCCAAGACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAAAGAG
Found at i:333648 original size:2 final size:2
Alignment explanation
Indices: 333641--333679 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
333631 TTTTAACTTT
333641 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 T
333680 GAGAGATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:336597 original size:21 final size:21
Alignment explanation
Indices: 336571--336672 Score: 57
Period size: 23 Copynumber: 4.8 Consensus size: 21
336561 TCGTTGCGAT
336571 TTTAGACTATCGCAACACGAA
1 TTTAGACTATCGCAACACGAA
* *
336592 TTTAGAATAAATCGCAACGCGAA
1 TTTAGACT--ATCGCAACACGAA
* *
336615 CTTCGACTAT--CATA-ACGAA
1 TTTAGACTATCGCA-ACACGAA
* * *
336634 TTTGGAATAAATCGCAACGCGAA
1 TTTAGACT--ATCGCAACACGAA
* *
336657 CTTCGACTATCGCAAC
1 TTTAGACTATCGCAAC
336673 GAACTTGGAA
Statistics
Matches: 60, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
19 11 0.18
20 1 0.02
21 19 0.32
22 1 0.02
23 28 0.47
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.24
Consensus pattern (21 bp):
TTTAGACTATCGCAACACGAA
Found at i:336673 original size:21 final size:21
Alignment explanation
Indices: 336575--336719 Score: 100
Period size: 21 Copynumber: 6.8 Consensus size: 21
336565 TGCGATTTTA
* * *
336575 GACTATCGCAACACGAATTTA
1 GACTATCGCAACGCGAACTTC
*
336596 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
** * *
336619 GACTATCATAA--CGAATTTG
1 GACTATCGCAACGCGAACTTC
*
336638 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
*
336661 GACTATCGCAA--CGAACTTG
1 GACTATCGCAACGCGAACTTC
*
336680 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
*
336703 GACTATCGCAATGCGAA
1 GACTATCGCAACGCGAA
336720 TATGTAAATC
Statistics
Matches: 94, Mismatches: 20, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
19 19 0.20
21 39 0.41
23 36 0.38
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTTC
Found at i:336710 original size:42 final size:42
Alignment explanation
Indices: 336575--336713 Score: 224
Period size: 42 Copynumber: 3.3 Consensus size: 42
336565 TGCGATTTTA
*
336575 GACTATCGCAACACGAATTTAGAATAAATCGCAACGCGAACTTC
1 GACTATCGC-A-ACGAATTTGGAATAAATCGCAACGCGAACTTC
**
336619 GACTATCATAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
336661 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
336703 GACTATCGCAA
1 GACTATCGCAA
336714 TGCGAATATG
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
42 81 0.91
43 1 0.01
44 7 0.08
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:336732 original size:20 final size:20
Alignment explanation
Indices: 336707--336754 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
336697 AACTTCGACT
336707 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
336727 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
336747 ATCGCAAT
1 ATCGCAAT
336755 ACGATAGTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:337197 original size:14 final size:15
Alignment explanation
Indices: 337178--337216 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
337168 CTGATCCTCA
337178 TTGTTTTATTTTAT-
1 TTGTTTTATTTTATG
337192 TTGTTTT-TGTTTATG
1 TTGTTTTAT-TTTATG
337207 TTGTTTTATT
1 TTGTTTTATT
337217 ATTTCTTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 12 0.55
15 8 0.36
16 1 0.05
ACGTcount: A:0.10, C:0.00, G:0.13, T:0.77
Consensus pattern (15 bp):
TTGTTTTATTTTATG
Found at i:345437 original size:2 final size:2
Alignment explanation
Indices: 345430--345454 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
345420 TACTATTCAC
345430 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 T
345455 CATTTAGACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:346416 original size:29 final size:29
Alignment explanation
Indices: 346374--346448 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
346364 CCATGCCCCA
**
346374 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
346403 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
346432 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
346449 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:346454 original size:29 final size:29
Alignment explanation
Indices: 346375--346462 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
346365 CATGCCCCAT
* * ****
346375 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
346404 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
346433 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
346462 A
1 A
346463 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:346714 original size:29 final size:29
Alignment explanation
Indices: 346679--346765 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
346669 GTTGGCTGGT
*
346679 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
346708 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
346737 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
346766 CCCGGTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:355967 original size:15 final size:15
Alignment explanation
Indices: 355955--355985 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
355945 TTAATAACCT
355955 GAAAAAAAATAACAA
1 GAAAAAAAATAACAA
*
355970 GAAAAAAAAAAACAA
1 GAAAAAAAATAACAA
355985 G
1 G
355986 TGGTGGATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.81, C:0.06, G:0.10, T:0.03
Consensus pattern (15 bp):
GAAAAAAAATAACAA
Done.