Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008914.1 Hibiscus syriacus cultivar Beakdansim tig00112217_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: 1601432
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:433258 original size:12 final size:12
Alignment explanation
Indices: 433233--433281 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
433223 TATACTTAAT
*
433233 TACTTGTATATA
1 TACTTATATATA
*
433245 TACTTATATGTA
1 TACTTATATATA
433257 TA-TATATATATA
1 TACT-TATATATA
*
433269 CACTTATATATA
1 TACTTATATATA
433281 T
1 T
433282 TTACGTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
11 1 0.03
12 28 0.93
13 1 0.03
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (12 bp):
TACTTATATATA
Found at i:433496 original size:32 final size:32
Alignment explanation
Indices: 433455--433559 Score: 201
Period size: 32 Copynumber: 3.3 Consensus size: 32
433445 AGTCTCGTTC
433455 GTTCATTTACGTTTGTGAACGTTCGATAATCT
1 GTTCATTTACGTTTGTGAACGTTCGATAATCT
433487 GTTCATTTACGTTTGTGAACGTTCGATAATCT
1 GTTCATTTACGTTTGTGAACGTTCGATAATCT
*
433519 GTTCATTTACGTTTGTGAACGTTCGATAATCC
1 GTTCATTTACGTTTGTGAACGTTCGATAATCT
433551 GTTCATTTA
1 GTTCATTTA
433560 TGTTCATTTA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (32 bp):
GTTCATTTACGTTTGTGAACGTTCGATAATCT
Found at i:433578 original size:24 final size:24
Alignment explanation
Indices: 433551--433618 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
433541 TCGATAATCC
*
433551 GTTCATTTATGTTCATTTATTTAT
1 GTTCATTTATGTTCGTTTATTTAT
* *
433575 GTTCGTTTATGTTCGTTCATTTAT
1 GTTCATTTATGTTCGTTTATTTAT
*
433599 G-TCTATGTATGTTCGTTTAT
1 GTTC-ATTTATGTTCGTTTAT
433619 ATTCAGCTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 2 0.05
24 35 0.95
ACGTcount: A:0.16, C:0.10, G:0.15, T:0.59
Consensus pattern (24 bp):
GTTCATTTATGTTCGTTTATTTAT
Found at i:433599 original size:14 final size:14
Alignment explanation
Indices: 433550--433600 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
433540 TTCGATAATC
433550 CGTTCATTTATGTT
1 CGTTCATTTATGTT
* *
433564 CATTTATTTATGTT
1 CGTTCATTTATGTT
433578 CG----TTTATGTT
1 CGTTCATTTATGTT
433588 CGTTCATTTATGT
1 CGTTCATTTATGT
433601 CTATGTATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
10 10 0.33
14 20 0.67
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.59
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:433695 original size:16 final size:18
Alignment explanation
Indices: 433670--433706 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
433660 AATCATTAAT
433670 ATTTTAAAACCCAAAT-A
1 ATTTTAAAACCCAAATCA
*
433687 ATTTT-AAACTCAAATCA
1 ATTTTAAAACCCAAATCA
433704 ATT
1 ATT
433707 AAAGAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTTTAAAACCCAAATCA
Found at i:433919 original size:24 final size:23
Alignment explanation
Indices: 433892--433963 Score: 96
Period size: 24 Copynumber: 3.2 Consensus size: 23
433882 ATTGTGTTCA
433892 TTTACATTCGTACGTTTATGTTTG
1 TTTACATTCGT-CGTTTATGTTTG
433916 TTTACA-T--TCGTTTATGTTTG
1 TTTACATTCGTCGTTTATGTTTG
*
433936 TTTACATCCGTTCGTTTATGTTTG
1 TTTACATTCG-TCGTTTATGTTTG
433960 TTTA
1 TTTA
433964 TGTTCGTTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
20 18 0.42
21 1 0.02
23 1 0.02
24 23 0.53
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.57
Consensus pattern (23 bp):
TTTACATTCGTCGTTTATGTTTG
Found at i:433929 original size:20 final size:21
Alignment explanation
Indices: 433904--433963 Score: 86
Period size: 20 Copynumber: 2.8 Consensus size: 21
433894 TACATTCGTA
433904 CGTTTATGTTTGTTTACA-TT
1 CGTTTATGTTTGTTTACACTT
433924 CGTTTATGTTTGTTTACATCCGTT
1 CGTTTATGTTTGTTTACA--C-TT
433948 CGTTTATGTTTGTTTA
1 CGTTTATGTTTGTTTA
433964 TGTTCGTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.50
24 18 0.50
ACGTcount: A:0.13, C:0.12, G:0.17, T:0.58
Consensus pattern (21 bp):
CGTTTATGTTTGTTTACACTT
Found at i:433938 original size:10 final size:10
Alignment explanation
Indices: 433905--433967 Score: 54
Period size: 10 Copynumber: 5.9 Consensus size: 10
433895 ACATTCGTAC
433905 GTTTATGTTT
1 GTTTATGTTT
** *
433915 GTTTACATTC
1 GTTTATGTTT
433925 GTTTATGTTT
1 GTTTATGTTT
*
433935 GTTTACATCCGTTC
1 GTTT--AT--GTTT
433949 GTTTATGTTT
1 GTTTATGTTT
433959 GTTTATGTT
1 GTTTATGTT
433968 CGTTCATTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
10 30 0.73
12 4 0.10
14 7 0.17
ACGTcount: A:0.13, C:0.10, G:0.17, T:0.60
Consensus pattern (10 bp):
GTTTATGTTT
Found at i:433968 original size:20 final size:20
Alignment explanation
Indices: 433904--433971 Score: 82
Period size: 20 Copynumber: 3.2 Consensus size: 20
433894 TACATTCGTA
**
433904 CGTTTATGTTTGTTTACATT
1 CGTTTATGTTTGTTTATGTT
433924 CGTTTATGTTTGTTTACATCCGTT
1 CGTTTATGTTTGTTT--AT--GTT
433948 CGTTTATGTTTGTTTATGTT
1 CGTTTATGTTTGTTTATGTT
433968 CGTT
1 CGTT
433972 CATTTGTGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 22 0.52
22 3 0.07
24 17 0.40
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (20 bp):
CGTTTATGTTTGTTTATGTT
Found at i:433970 original size:44 final size:47
Alignment explanation
Indices: 433864--433987 Score: 146
Period size: 44 Copynumber: 2.7 Consensus size: 47
433854 GTTTGTGCAG
* *
433864 GTTTGTTTATGTTCATTTATTGTGTTCATTTACATTCGTACGTTTAT
1 GTTTGTTTATGTTCGTTTATTGTGTTCATTTACATCCGTACGTTTAT
** * *
433911 GTTTGTTTACATTCGTTTA-TGT-TT-GTTTACATCCGTTCGTTTAT
1 GTTTGTTTATGTTCGTTTATTGTGTTCATTTACATCCGTACGTTTAT
* *
433955 GTTTGTTTATGTTCGTTCATTTGTGTTCGTTTA
1 GTTTGTTTATGTTCGTTTA-TTGTGTTCATTTA
433988 TCATTTAAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
44 33 0.52
45 2 0.03
46 6 0.09
47 18 0.28
48 5 0.08
ACGTcount: A:0.14, C:0.11, G:0.17, T:0.58
Consensus pattern (47 bp):
GTTTGTTTATGTTCGTTTATTGTGTTCATTTACATCCGTACGTTTAT
Found at i:433971 original size:24 final size:23
Alignment explanation
Indices: 433898--433988 Score: 80
Period size: 24 Copynumber: 4.0 Consensus size: 23
433888 TTCATTTACA
*
433898 TTCGTACGTTTATGTTTGTTTA-
1 TTCGTTCGTTTATGTTTGTTTAT
* *
433920 --CATTCGTTTATGTTTGTTTACA
1 TTCGTTCGTTTATGTTTGTTTA-T
*
433942 TCCGTTCGTTTATGTTTGTTTAT
1 TTCGTTCGTTTATGTTTGTTTAT
* * *
433965 GTTCGTTCATTTGTGTTCGTTTAT
1 -TTCGTTCGTTTATGTTTGTTTAT
433989 CATTTAAATG
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
20 18 0.32
24 38 0.68
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.58
Consensus pattern (23 bp):
TTCGTTCGTTTATGTTTGTTTAT
Found at i:436672 original size:18 final size:18
Alignment explanation
Indices: 436651--436689 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
436641 GTTAGCATTG
436651 ATGATCCAGTTACTTTTC
1 ATGATCCAGTTACTTTTC
* * *
436669 ATGATGCTGTTAGTTTTC
1 ATGATCCAGTTACTTTTC
436687 ATG
1 ATG
436690 TTCCCCTTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (18 bp):
ATGATCCAGTTACTTTTC
Found at i:438746 original size:20 final size:21
Alignment explanation
Indices: 438717--438758 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
438707 ACATTTATCG
*
438717 TACATTTATTATATACA-ATA
1 TACATATATTATATACACATA
438737 TACATATATTATATACACATA
1 TACATATATTATATACACATA
438758 T
1 T
438759 TATATATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (21 bp):
TACATATATTATATACACATA
Found at i:438765 original size:15 final size:13
Alignment explanation
Indices: 438734--438764 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
438724 ATTATATACA
*
438734 ATATACATATATT
1 ATATACACATATT
438747 ATATACACATATT
1 ATATACACATATT
438760 ATATA
1 ATATA
438765 TCTATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATACACATATT
Found at i:439347 original size:294 final size:287
Alignment explanation
Indices: 438859--439400 Score: 693
Period size: 294 Copynumber: 1.9 Consensus size: 287
438849 TTAGTCCTTA
* *
438859 AAATTATATTATAATATACAAAACCTAATAAACTTTTGTTCCTCAACTTTTGAAATGAATGCAAT
1 AAATTATATCATAATATACAAAACCTAATAAACTTTTGTTACTCAACTTTTGAAATGAATGCAAT
*
438924 TCAACCCATTTTATATTAATTTCAGCTTCATATTTTATAATTATTTCGAATTAATCCCTATGAGT
66 TCAACCCATTTTATATTAATTTCAACTTCATATTTTATAATTATTTCGAATTAATCCCTATGAGT
438989 TGTTTAATTTATTTAAATCTTAACTTGTAATTTCATATTTGTTCAATTTAGTGCTTAAAATTATA
131 TGTTTAATTTATTTAAATCTTAACTTGTAATTTCATATTTGTTCAATTTAGTGCTTAAAATTATA
* * * *
439054 TTTGTATATGAAATTGATCCATACTTATTTAT-ATTTTTATAATTTACTTCAAAACCAATAAATC
196 TTTGTAT-TAAAATTGACCCATAATTATTTATAATTTTTATAATTTACTACAAAACCAATAAATC
439118 ATATAATAAACTTCATTTCAAACTATAT
260 ATATAATAAACTTCATTTCAAACTATAT
* * * * *
439146 AAATTATATCATAATCTCCAAAACCT-ATAAA-TGTTTGTTTAC-CAACTTTTTAAATGGATTCA
1 AAATTATATCATAATATACAAAACCTAATAAACT-TTTG-TTACTCAACTTTTGAAATGAATGCA
* ** * * *
439208 ATTTAGTCCATTTTTATATTAATTTCAACTT-ATCATTTTATAATTATTTTGATTTGATCCATCA
64 ATTCAACCCA-TTTTATATTAATTTCAACTTCAT-ATTTTATAATTATTTCGAATTAATCC--C-
* * * *
439272 TTCATGCGTGTTGTTTAATTTATTTAAGT-TTCAATTTGTAATTTCATGTTTGTTCAATTTAGT-
124 -T-AT--GAGTTGTTTAATTTATTTAAATCTT-AACTTGTAATTTCATATTTGTTCAATTTAGTG
* *
439335 CTTTAAAATTATATTTTTATTAAAATTGACCCATAATTATTTATAATTTTTGTAATTTACTACAA
184 C-TTAAAATTATATTTGTATTAAAATTGACCCATAATTATTTATAATTTTTATAATTTACTACAA
439400 A
248 A
439401 TCATATACAA
Statistics
Matches: 217, Mismatches: 24, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
285 1 0.00
286 35 0.16
287 68 0.31
289 1 0.00
291 1 0.00
292 2 0.01
293 24 0.11
294 85 0.39
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (287 bp):
AAATTATATCATAATATACAAAACCTAATAAACTTTTGTTACTCAACTTTTGAAATGAATGCAAT
TCAACCCATTTTATATTAATTTCAACTTCATATTTTATAATTATTTCGAATTAATCCCTATGAGT
TGTTTAATTTATTTAAATCTTAACTTGTAATTTCATATTTGTTCAATTTAGTGCTTAAAATTATA
TTTGTATTAAAATTGACCCATAATTATTTATAATTTTTATAATTTACTACAAAACCAATAAATCA
TATAATAAACTTCATTTCAAACTATAT
Found at i:441052 original size:19 final size:19
Alignment explanation
Indices: 441028--441068 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
441018 TGACGATTAT
*
441028 GAATGAAGTAAATTTGAGG
1 GAATGAAGTAAATTAGAGG
441047 GAATGAAGTAAATTAGAGG
1 GAATGAAGTAAATTAGAGG
441066 GAA
1 GAA
441069 GATTACTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.22
Consensus pattern (19 bp):
GAATGAAGTAAATTAGAGG
Found at i:444902 original size:21 final size:21
Alignment explanation
Indices: 444869--444908 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
444859 TAGGAATTTT
444869 TATTTTTATATTATTAAAATA
1 TATTTTTATATTATTAAAATA
444890 TATTCTTTA-ATTATTAAAA
1 TATT-TTTATATTATTAAAA
444909 ATGTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTTTATATTATTAAAATA
Found at i:444948 original size:23 final size:23
Alignment explanation
Indices: 444921--444996 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
444911 GTAAAATTAT
444921 TTTAAAATATAATATTTTAATAA
1 TTTAAAATATAATATTTTAATAA
444944 TTTAAAATATAATA----AATAA
1 TTTAAAATATAATATTTTAATAA
*
444963 -TTATAAATATATTATTTTAATGAA
1 TTTA-AAATATAATATTTTAAT-AA
444987 TTTAAAATAT
1 TTTAAAATAT
444997 TAATTTATTG
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
18 3 0.07
19 14 0.31
23 17 0.38
24 8 0.18
25 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (23 bp):
TTTAAAATATAATATTTTAATAA
Found at i:444951 original size:41 final size:42
Alignment explanation
Indices: 444876--444996 Score: 124
Period size: 41 Copynumber: 2.9 Consensus size: 42
444866 TTTTATTTTT
* * *
444876 ATATTATTAAAATAT-AT-TCTTTAATTATTAAAAATGTAA-AA
1 ATATT-TTAAAATATAATAT-TTTAATAATTTAAAATATAATAA
*
444917 TTATTTTAAAATATAATATTTTAATAATTTAAAATATAATAA
1 ATATTTTAAAATATAATATTTTAATAATTTAAAATATAATAA
* *
444959 ATA-ATTATAAATATATTATTTTAATGAATTTAAAATAT
1 ATATTTTA-AAATATAATATTTTAAT-AATTTAAAATAT
444997 TAATTTATTG
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
40 9 0.13
41 26 0.38
42 21 0.31
43 12 0.18
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (42 bp):
ATATTTTAAAATATAATATTTTAATAATTTAAAATATAATAA
Found at i:445261 original size:30 final size:30
Alignment explanation
Indices: 445227--445299 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
445217 CCACCAAGAA
*
445227 GGATAATGCAATTGGATCCAAGTCAATGAC
1 GGATAATGCAATTGGATCCAAGTCAATAAC
*
445257 GGATAATGCAATTGGATCCAAGTCAATAAT
1 GGATAATGCAATTGGATCCAAGTCAATAAC
445287 GGATAATGCAATT
1 GGATAATGCAATT
445300 TTAACATATC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (30 bp):
GGATAATGCAATTGGATCCAAGTCAATAAC
Found at i:446912 original size:20 final size:21
Alignment explanation
Indices: 446867--446912 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
446857 CAGGACGAGG
446867 TTATCGATATTAAGCCCTTCA
1 TTATCGATATTAAGCCCTTCA
* *
446888 ATATCGATATTAA-CCCTTGA
1 TTATCGATATTAAGCCCTTCA
446908 TTATC
1 TTATC
446913 AATACTCACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (21 bp):
TTATCGATATTAAGCCCTTCA
Found at i:447183 original size:99 final size:99
Alignment explanation
Indices: 447065--447277 Score: 381
Period size: 99 Copynumber: 2.2 Consensus size: 99
447055 ATTTACTCAA
** * *
447065 TATCGATACTCTTATTGAGAGTATCAATATTTTACTTCAGTATTGATACTCCCTTTAGTATCGAT
1 TATCGATACTCCCAGTGAGAGTATCAATATTTTACTTCAGTATTGATACTCCCTTCAGTATCGAT
447130 ACCATTGGAATAATATTGATACTTATTGAACTGG
66 ACCATTGGAATAATATTGATACTTATTGAACTGG
*
447164 TATCGATACTCCCAGTGAGAGTATCGATATTTTACTTCAGTATTGATACTCCCTTCAGTATCGAT
1 TATCGATACTCCCAGTGAGAGTATCAATATTTTACTTCAGTATTGATACTCCCTTCAGTATCGAT
447229 ACCATTGGAATAATATTGATACTTATTGAACTGG
66 ACCATTGGAATAATATTGATACTTATTGAACTGG
447263 TATCGATACTCCCAG
1 TATCGATACTCCCAG
447278 CTCCAAAACA
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 109 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (99 bp):
TATCGATACTCCCAGTGAGAGTATCAATATTTTACTTCAGTATTGATACTCCCTTCAGTATCGAT
ACCATTGGAATAATATTGATACTTATTGAACTGG
Found at i:453946 original size:21 final size:21
Alignment explanation
Indices: 453901--453948 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
453891 GGTGGTAGCG
* **
453901 ATACTCTTAGTTAAAGTATTT
1 ATACTCTTAGGTAAAGTATCA
*
453922 ATACTCTTAGGTAAATTATCA
1 ATACTCTTAGGTAAAGTATCA
453943 ATACTC
1 ATACTC
453949 CTATACTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (21 bp):
ATACTCTTAGGTAAAGTATCA
Found at i:457666 original size:21 final size:21
Alignment explanation
Indices: 457615--457666 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
457605 TGCTTCCGGG
* *
457615 TCTCCATCATCTATATTTGTT
1 TCTCCATCATCTACATTTGCT
* * *
457636 TCTTCTTCATCTACCTTTGCT
1 TCTCCATCATCTACATTTGCT
457657 TCTCCATCAT
1 TCTCCATCAT
457667 TTATCTTAGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.31, G:0.04, T:0.50
Consensus pattern (21 bp):
TCTCCATCATCTACATTTGCT
Found at i:458903 original size:12 final size:11
Alignment explanation
Indices: 458886--458919 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
458876 ATAAACATAA
458886 ATAAATGAGTC
1 ATAAATGAGTC
458897 GATAAATGAGCTC
1 -ATAAATGAG-TC
458910 ATAAATGAGT
1 ATAAATGAGT
458920 TTGTTCATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 18 0.86
13 2 0.10
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (11 bp):
ATAAATGAGTC
Found at i:459986 original size:25 final size:25
Alignment explanation
Indices: 459950--459998 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
459940 CACCAATCGA
*
459950 ATGAATTGATAAAAT-TAATTAAAC
1 ATGAATTCATAAAATATAATTAAAC
*
459974 ATGATATTCATAAAATATATTTAAA
1 ATGA-ATTCATAAAATATAATTAAA
459999 ATAATAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 10 0.48
26 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (25 bp):
ATGAATTCATAAAATATAATTAAAC
Found at i:461522 original size:14 final size:14
Alignment explanation
Indices: 461503--461529 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
461493 ACCGAGTCAC
461503 GCACGAGCACATCT
1 GCACGAGCACATCT
461517 GCACGAGCACATC
1 GCACGAGCACATC
461530 ATCATGCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.37, G:0.22, T:0.11
Consensus pattern (14 bp):
GCACGAGCACATCT
Found at i:466306 original size:14 final size:14
Alignment explanation
Indices: 466287--466313 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
466277 GCCGAGTCAC
466287 GCACGAGCACATCT
1 GCACGAGCACATCT
466301 GCACGAGCACATC
1 GCACGAGCACATC
466314 ATCATGCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.37, G:0.22, T:0.11
Consensus pattern (14 bp):
GCACGAGCACATCT
Found at i:467200 original size:77 final size:82
Alignment explanation
Indices: 467103--467262 Score: 195
Period size: 81 Copynumber: 2.0 Consensus size: 82
467093 TGGTGGGTTA
**
467103 TCTTAATTTTGACAAAATT-A-A-GGATGAGTTATATCTAGGTTAGTGTTCCTTC-CC-CGGAGG
1 TCTTAATTTTGACAAAATTAATAGGGATGAGTTATATCTAGGTTAAAGTTCCTTCTCCACGGAGG
*
467163 ATTCTCAGCACTTTGTT
66 ATTCTCAACACTTTGTT
** * * *
467180 TCTTAATTTTGGTAAGATTAAATAGGGATGAGTTATATCTAGGTTAAAGTTCTTTCTCCATGGAG
1 TCTTAATTTTGACAAAATT-AATAGGGATGAGTTATATCTAGGTTAAAGTTCCTTCTCCACGGAG
*
467245 GATTCTCAACATTTTGTT
65 GATTCTCAACACTTTGTT
467263 AGGATGATTC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
77 16 0.24
79 1 0.01
80 1 0.01
81 28 0.41
82 2 0.03
83 20 0.29
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (82 bp):
TCTTAATTTTGACAAAATTAATAGGGATGAGTTATATCTAGGTTAAAGTTCCTTCTCCACGGAGG
ATTCTCAACACTTTGTT
Found at i:467873 original size:18 final size:18
Alignment explanation
Indices: 467852--467889 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
467842 ATAGAAAATG
467852 ATTAT-AATATTAGATTTT
1 ATTATAAAT-TTAGATTTT
*
467870 ATTATAAATTTAGTTTTT
1 ATTATAAATTTAGATTTT
467888 AT
1 AT
467890 GTAATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
ATTATAAATTTAGATTTT
Found at i:471783 original size:4 final size:4
Alignment explanation
Indices: 471774--471804 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
471764 AAGACCTCAT
471774 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
471805 TCATTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:475772 original size:74 final size:74
Alignment explanation
Indices: 475660--476164 Score: 562
Period size: 74 Copynumber: 6.8 Consensus size: 74
475650 TAATGTTCTC
* * * * * * * *
475660 ATGAATACAGTAATGTGATTCATGGATATCATCACTCCTTGGGGATTGTTCTCATGAGAGGTGAA
1 ATGAATGCGGTAATGTGATTCATGCATATCCTTACTCCTTGGGGAGTGTCCTCATAAGAGGTGAA
* *
475725 AATGTCTGA
66 AAAGTCTAA
* * * *
475734 ATGAATGCAGTAATGCGATTCATGCATATCCTTGCTCCTTGGGGAGTGTCCTCATAAGAGGTGTA
1 ATGAATGCGGTAATGTGATTCATGCATATCCTTACTCCTTGGGGAGTGTCCTCATAAGAGGTGAA
* *
475799 AAAGACTGA
66 AAAGTCTAA
* * * *
475808 ATGAATGCGGTAATGTGATTCATGTATATACTTAATCCTTGGGAAGTGTCCTCATAAGAGGTGAA
1 ATGAATGCGGTAATGTGATTCATGCATATCCTTACTCCTTGGGGAGTGTCCTCATAAGAGGTGAA
475873 AAAGT-TAAA
66 AAAGTCT-AA
* * ***
475882 ATGAATGTGGTAATGTGATTCATACATATCCTTACTCCTTATAGAGTGTCCTCATAAGAGGTGAA
1 ATGAATGCGGTAATGTGATTCATGCATATCCTTACTCCTTGGGGAGTGTCCTCATAAGAGGTGAA
475947 AAAGTCTAA
66 AAAGTCTAA
* ** * *
475956 ATGAATACGGTAATGTGATTCATGCATATTTTTACTCCATGGGGAGTGTCCTCATAAGAAGTGAA
1 ATGAATGCGGTAATGTGATTCATGCATATCCTTACTCCTTGGGGAGTGTCCTCATAAGAGGTGAA
* * *
476021 ACAGCCTGA
66 AAAGTCTAA
* * * *
476030 ATGAATGCGGTAATGTGATTTATGCATATACTTACTCCTTGGGGAGTATCCTCATAAGTGGTGAA
1 ATGAATGCGGTAATGTGATTCATGCATATCCTTACTCCTTGGGGAGTGTCCTCATAAGAGGTGAA
*
476095 AAAGTGTAA
66 AAAGTCTAA
* ** ** * * * * *
476104 ATAAATGCAATAATGCAATTCATGTATATCCTTACTCCTTTGGGAATATCCTCATGAGAGG
1 ATGAATGCGGTAATGTGATTCATGCATATCCTTACTCCTTGGGGAGTGTCCTCATAAGAGG
476165 AAAAACAAAG
Statistics
Matches: 361, Mismatches: 68, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
73 1 0.00
74 359 0.99
75 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (74 bp):
ATGAATGCGGTAATGTGATTCATGCATATCCTTACTCCTTGGGGAGTGTCCTCATAAGAGGTGAA
AAAGTCTAA
Found at i:479574 original size:19 final size:19
Alignment explanation
Indices: 479523--479575 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
479513 TATTGATCGA
*
479523 TGATCGTTGACTTTTTCAT
1 TGATCGTTGACATTTTCAT
* * *
479542 TGACCGTTAACATTTTCGT
1 TGATCGTTGACATTTTCAT
*
479561 TGATCGTTGTCATTT
1 TGATCGTTGACATTT
479576 CCATAGGCCG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (19 bp):
TGATCGTTGACATTTTCAT
Found at i:479845 original size:29 final size:29
Alignment explanation
Indices: 479796--479918 Score: 120
Period size: 29 Copynumber: 4.2 Consensus size: 29
479786 CAGATTCTAA
* * * * *
479796 ATGGGATTATATTCTCGTCCTGATTATGC
1 ATGGGATTATATCCCCATCATGATTCTGC
* * *
479825 ATGGGATTATATCCCCATCCTGATTTTGA
1 ATGGGATTATATCCCCATCATGATTCTGC
* * * *
479854 ATGTGATTGTATCGCCATCATGATTCTAC
1 ATGGGATTATATCCCCATCATGATTCTGC
* *
479883 ATGGGATTGTATCCCCATCATGATTCTTC
1 ATGGGATTATATCCCCATCATGATTCTGC
479912 ATGGGAT
1 ATGGGAT
479919 CATCTATAGA
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 79 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (29 bp):
ATGGGATTATATCCCCATCATGATTCTGC
Found at i:482270 original size:2 final size:2
Alignment explanation
Indices: 482263--482290 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
482253 AGGAAAATTG
482263 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
482291 AACTAAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:487305 original size:20 final size:20
Alignment explanation
Indices: 487280--487317 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
487270 TACTGAGTTT
487280 GTATATAAAT-AATTTTTTGA
1 GTATAT-AATGAATTTTTTGA
487300 GTATATAATGAATTTTTT
1 GTATATAATGAATTTTTT
487318 TACACTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (20 bp):
GTATATAATGAATTTTTTGA
Found at i:488557 original size:47 final size:46
Alignment explanation
Indices: 488415--488638 Score: 348
Period size: 47 Copynumber: 4.9 Consensus size: 46
488405 GATGGACTTG
*
488415 TTTTTATTTATTTTGTTTCTTAA-TGTTT-TTATTTAATTATGGAC
1 TTTTTATTTATTTTGTTTCTTAATTTTTTATTATTTAATTATGGAC
*
488459 TTTTTTATTTATTTTGTTTCTTAA-TGTTT-TTATTTAATTATGGAC
1 -TTTTTATTTATTTTGTTTCTTAATTTTTTATTATTTAATTATGGAC
*
488504 TTTTTATTTATTTTGTTTCTTAATTTTTTTATTATTTAATTATGGAA
1 TTTTTATTTATTTTGTTTCTTAA-TTTTTTATTATTTAATTATGGAC
*
488551 TTTTTATTTATTTTATTTCTTAATGTTTTTATTATTTAATTATGGAC
1 TTTTTATTTATTTTGTTTCTTAAT-TTTTTATTATTTAATTATGGAC
488598 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATT
1 TTTTTATTTATTTTGTTTCTTAAT-TTTTTATTATTTAATT
488639 GTTTGAATTA
Statistics
Matches: 170, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
44 23 0.14
45 44 0.26
46 5 0.03
47 98 0.58
ACGTcount: A:0.21, C:0.04, G:0.07, T:0.68
Consensus pattern (46 bp):
TTTTTATTTATTTTGTTTCTTAATTTTTTATTATTTAATTATGGAC
Found at i:488662 original size:94 final size:91
Alignment explanation
Indices: 488415--488680 Score: 294
Period size: 94 Copynumber: 2.9 Consensus size: 91
488405 GATGGACTTG
* * * ** * *
488415 TTTTTATTTATTTTGTTTCTTAATG--TTT-TTATTTAATTATGGACTTTTTTATTTATTTTGTT
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATGGA-ATTATAACGTATTGTATT
488477 TCTTAATGTTTTTATTTAATTATGGAC
65 TCTTAATGTTTTTATTTAATTATGGAC
* * * ** *
488504 TTTTTATTTATTTTGTTTCTTAATTTTTTTATTATTTAATTATGGAATTTTTATTTATTTTATTT
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATGGAATTATAACGTATTGTATTT
488569 CTTAATGTTTTTATTATTTAATTATGGAC
66 CTTAATG--TTT-TTATTTAATTATGGAC
* *
488598 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTGTTTGAATTATAACGT-TTGTA--
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATT-ATGGAATTATAACGTATTGTATT
*
488660 T-TTAATGTTTCTATTTAATTA
65 TCTTAATGTTTTTATTTAATTA
488681 CTTTTATTGT
Statistics
Matches: 158, Mismatches: 12, Indels: 15
0.85 0.06 0.08
Matches are distributed among these distances:
88 10 0.06
89 27 0.17
91 33 0.21
92 16 0.10
93 3 0.02
94 60 0.38
95 9 0.06
ACGTcount: A:0.23, C:0.04, G:0.08, T:0.66
Consensus pattern (91 bp):
TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATGGAATTATAACGTATTGTATTT
CTTAATGTTTTTATTTAATTATGGAC
Found at i:488674 original size:13 final size:13
Alignment explanation
Indices: 488630--488678 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
488620 ATGTTTTTAT
488630 TATTTAATTGTTTG
1 TATTTAA-TGTTTG
* *
488644 AATTATAACGTTTG
1 TATT-TAATGTTTG
*
488658 TATTTAATGTTTC
1 TATTTAATGTTTG
488671 TATTTAAT
1 TATTTAAT
488679 TACTTTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 15 0.52
14 11 0.38
15 3 0.10
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (13 bp):
TATTTAATGTTTG
Found at i:488691 original size:23 final size:23
Alignment explanation
Indices: 488660--488725 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
488650 AACGTTTGTA
*
488660 TTTAATGTTTCTATTTAATTACT
1 TTTAATGTTTTTATTTAATTACT
* * *
488683 TTTATTGTTTTTA-TTATTTAGT
1 TTTAATGTTTTTATTTAATTACT
488705 TTGTAATGTTTTTATTTAATT
1 TT-TAATGTTTTTATTTAATT
488726 TTCACTTGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
22 9 0.26
23 21 0.60
24 5 0.14
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (23 bp):
TTTAATGTTTTTATTTAATTACT
Found at i:494184 original size:43 final size:43
Alignment explanation
Indices: 494126--494222 Score: 178
Period size: 43 Copynumber: 2.3 Consensus size: 43
494116 AATCCCTCCA
*
494126 ACCAA-ACACCATAATGTGTAGGTTTCCCAGAACCATACACCC
1 ACCAACACACCATAATGTGTAGGTTCCCCAGAACCATACACCC
494168 ACCAACACACCATAATGTGTAGGTTCCCCAGAACCATACACCC
1 ACCAACACACCATAATGTGTAGGTTCCCCAGAACCATACACCC
494211 ACCAACACACCA
1 ACCAACACACCA
494223 AGTAAGGCCC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 5 0.09
43 48 0.91
ACGTcount: A:0.37, C:0.37, G:0.10, T:0.15
Consensus pattern (43 bp):
ACCAACACACCATAATGTGTAGGTTCCCCAGAACCATACACCC
Found at i:494350 original size:24 final size:24
Alignment explanation
Indices: 494337--494455 Score: 193
Period size: 24 Copynumber: 5.0 Consensus size: 24
494327 AAACATAATT
*
494337 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
* *
494361 CAGGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
494385 CAAGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
494409 CATGTCAAATATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
494433 CATGTCAAGTATCATATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
494456 TCAAATCCAA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 87 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:497019 original size:18 final size:18
Alignment explanation
Indices: 496996--497052 Score: 114
Period size: 18 Copynumber: 3.2 Consensus size: 18
496986 GCCGGTCAAC
496996 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
497014 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
497032 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
497050 GGT
1 GGT
497053 TATGATCGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.11, C:0.21, G:0.51, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:499229 original size:43 final size:43
Alignment explanation
Indices: 499181--499269 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
499171 CTCCAATCGA
*
499181 ACACCATAATGTGTAGGTTTCCCAGAACCATACACCCACCAAC
1 ACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACCAAC
499224 ACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACCAAC
1 ACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACCAAC
499267 ACA
1 ACA
499270 TCAAGTAAGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.36, C:0.36, G:0.11, T:0.17
Consensus pattern (43 bp):
ACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACCAAC
Found at i:499503 original size:24 final size:24
Alignment explanation
Indices: 499388--499506 Score: 175
Period size: 24 Copynumber: 5.0 Consensus size: 24
499378 AAACATAATT
*
499388 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
*
499412 CAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
* * *
499436 CAAGTCAAGTATCAGATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
*
499460 CATGTCAAATATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
499484 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
499507 TCAAATCGAA
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:499522 original size:72 final size:71
Alignment explanation
Indices: 499388--499529 Score: 196
Period size: 72 Copynumber: 2.0 Consensus size: 71
499378 AAACATAATT
* * * *
499388 CATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAGTCAAGTATCAGAT
1 CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAAGAATCAGAT
499453 CAAAATC
66 -AAAATC
* * *
499460 CATGTCAAATATCATATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATCGAA-AATCAGA
1 CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATC-AAGAATCAGA
499524 TAAAAT
65 TAAAAT
499530 ATTCATGTGG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
71 5 0.08
72 55 0.89
73 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (71 bp):
CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAAGAATCAGAT
AAAATC
Found at i:502051 original size:7 final size:7
Alignment explanation
Indices: 502039--502077 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
502029 TGGTCAACGC
502039 CGGTCAA
1 CGGTCAA
502046 CGGTCAA
1 CGGTCAA
502053 CGGTCAA
1 CGGTCAA
502060 CGGGTCAA
1 C-GGTCAA
*
502068 TGGTCAA
1 CGGTCAA
502075 CGG
1 CGG
502078 GTCGGTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:502067 original size:15 final size:15
Alignment explanation
Indices: 502039--502080 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
502029 TGGTCAACGC
502039 CGGTCAAC-GGTCAA
1 CGGTCAACGGGTCAA
502053 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
*
502068 TGGTCAACGGGTC
1 CGGTCAACGGGTC
502081 GGTTCAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.24, C:0.26, G:0.33, T:0.17
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:502072 original size:22 final size:23
Alignment explanation
Indices: 502030--502077 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
502020 GGTCAATAGT
502030 GGTCAACGCCGGTCAACGGTCAAC
1 GGTCAACG-CGGTCAACGGTCAAC
*
502054 GGTCAACG-GGTCAATGGTCAAC
1 GGTCAACGCGGTCAACGGTCAAC
502076 GG
1 GG
502078 GTCGGTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.65
24 8 0.35
ACGTcount: A:0.25, C:0.27, G:0.33, T:0.15
Consensus pattern (23 bp):
GGTCAACGCGGTCAACGGTCAAC
Found at i:502112 original size:31 final size:31
Alignment explanation
Indices: 502069--502133 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
502059 ACGGGTCAAT
* * * * *
502069 GGTCAACGGGTCGGTTCAATGGGTCGGGTTG
1 GGTCAACAGGTCGGGTAAACGGGTCGGGTCG
502100 GGTCAACAGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACAGGTCGGGTAAACGGGTCGGGTCG
502131 GGT
1 GGT
502134 TATGACCGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.17, G:0.46, T:0.22
Consensus pattern (31 bp):
GGTCAACAGGTCGGGTAAACGGGTCGGGTCG
Found at i:516763 original size:15 final size:15
Alignment explanation
Indices: 516743--516788 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
516733 GTGGAGCTGG
516743 AAAAAAGAAAAGAAA
1 AAAAAAGAAAAGAAA
*
516758 AAAAAAGCAAA-AAA
1 AAAAAAGAAAAGAAA
*
516772 AAAGAAGAAGAAGAAA
1 AAAAAAGAA-AAGAAA
516788 A
1 A
516789 TTGAGAGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 10 0.38
15 12 0.46
16 4 0.15
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAGAAA
Found at i:516769 original size:11 final size:10
Alignment explanation
Indices: 516744--516777 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
516734 TGGAGCTGGA
516744 AAAAAGAAAAG
1 AAAAA-AAAAG
516755 AAAAAAAAAG
1 AAAAAAAAAG
516765 CAAAAAAAAAG
1 -AAAAAAAAAG
516776 AA
1 AA
516778 GAAGAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:516788 original size:16 final size:15
Alignment explanation
Indices: 516743--516807 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 15
516733 GTGGAGCTGG
516743 AAAA-AAGAAAAGAA
1 AAAAGAAGAAAAGAA
* *
516757 AAAAAAAGCAAA-AA
1 AAAAGAAGAAAAGAA
516771 AAAAGAAGAAGAAGAA
1 AAAAGAAGAA-AAGAA
** *
516787 AATTGAGAGAGAAGAA
1 AAAAGA-AGAAAAGAA
516803 AAAAG
1 AAAAG
516808 GTGACCAGGA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
14 14 0.36
15 8 0.21
16 14 0.36
17 3 0.08
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.03
Consensus pattern (15 bp):
AAAAGAAGAAAAGAA
Found at i:525885 original size:36 final size:36
Alignment explanation
Indices: 525828--525940 Score: 113
Period size: 36 Copynumber: 3.1 Consensus size: 36
525818 TTCAGTTAAG
* * * *
525828 ATTTTATCTCGCTTGAGATTGTTTTTCTTAAAACAT
1 ATTTCATCTCACTTAAGATTGTTTTTCTTAAAACAA
* *
525864 ATTTCATCTCA-TTAGATATTGTTTTTCTCAAAGA-AA
1 ATTTCATCTCACTTA-AGATTGTTTTTCTTAAA-ACAA
* * *
525900 ATTTTATCTTACTTAAGATTGTTTTTCTTAAAACAC
1 ATTTCATCTCACTTAAGATTGTTTTTCTTAAAACAA
525936 ATTTC
1 ATTTC
525941 GTCTTCCATG
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
35 3 0.05
36 54 0.89
37 4 0.07
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (36 bp):
ATTTCATCTCACTTAAGATTGTTTTTCTTAAAACAA
Found at i:526586 original size:116 final size:116
Alignment explanation
Indices: 526380--526596 Score: 281
Period size: 116 Copynumber: 1.9 Consensus size: 116
526370 CTAATGGAAG
* *
526380 AGTTCACAATGAGAAGAACTCCTTCGATGAGAGAGAAGAAGTTCCTAATAAGAAGAACTTGTTCA
1 AGTTCACAATGAGAAGAACTCCTCCGATGAGAGAGAAGAAGTTCCTAATAAGAAGAACTTATTCA
* ** *
526445 ATATTGGTTTGTCCATAACAGAAGGAGATGAATCAATGTTTATAGTGAAAT
66 ATATTGGCTCATCAATAACAGAAGGAGATGAATCAATGTTTATAGTGAAAT
* * * * *
526496 AGTTCATAATTAGAAGAACTCCTCCGATGAGGGAGAAGAAGTTGCTAATGAGAAGAACTTATTCA
1 AGTTCACAATGAGAAGAACTCCTCCGATGAGAGAGAAGAAGTTCCTAATAAGAAGAACTTATTCA
* * * * * *
526561 ATCTTTGCTCATCAATCACATAAGGAGTTGGATCAA
66 ATATTGGCTCATCAATAACAGAAGGAGATGAATCAA
526597 CATCATTGTG
Statistics
Matches: 84, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
116 84 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (116 bp):
AGTTCACAATGAGAAGAACTCCTCCGATGAGAGAGAAGAAGTTCCTAATAAGAAGAACTTATTCA
ATATTGGCTCATCAATAACAGAAGGAGATGAATCAATGTTTATAGTGAAAT
Found at i:526754 original size:15 final size:15
Alignment explanation
Indices: 526734--526764 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
526724 CATTCCCAAT
526734 AGAGAGTTCGTAATG
1 AGAGAGTTCGTAATG
526749 AGAGAGTTCGTAATG
1 AGAGAGTTCGTAATG
526764 A
1 A
526765 AAGAACTCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (15 bp):
AGAGAGTTCGTAATG
Found at i:542522 original size:2 final size:2
Alignment explanation
Indices: 542515--542544 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
542505 ATTCTCTTAC
*
542515 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
542545 CTTCCTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:546360 original size:299 final size:294
Alignment explanation
Indices: 545809--546372 Score: 728
Period size: 299 Copynumber: 1.9 Consensus size: 294
545799 TTATTAAAAT
* *
545809 TGAAATCATAATTTAAGAATCAAGTTCAACTATACCATTCTAATGAAATAATATGCAAAAACTGG
1 TGAAATCATAACTTAAGAATCAAGTTCAACTATACCATTCTAATGAAATAATATGC-AAAACCGG
* * * * *
545874 AGCTTGATGGAATTGATTCATAACACAACACAGAAACTTCATGTCTTAGGAGCCTAACAGAAAAC
65 AGCTTGATGGAATTGATTCACAACACAACACACAAAATTCATGTCCTAAGAGCCTAACAGAAAAC
* * * *
545939 AGATTCGTGACAGATAAAACAGAAAGTTCTAGTACCAGACCTCCTATGTTCTCAACAAATGTCGG
130 AGATTCATGACAGAAAAAACAGAAAGTTCTAATACCAGACCTCCTATGTTCTCAACAAACGTCGG
* * * * * * *
546004 TTCAAGCCACAAATCATCTCCGGCAAAAGGTGCTTTTCTATACTGCGGTTCTTTTTCACGGACAC
195 TTCAAACCACAAATCACCTCC-GAAAAAGGTACTTCTCTATACTGCAGTTCTTTTTCACGGAAAC
546069 TCAAACCAAGTTCAACTATACCATTCTAATGATTAA
259 TCAAACCAAGTTCAACTATACCATTCTAATGATTAA
546105 TGAAATCATAACTTAAGAATCAAGTTCAACTATACCAATT-TAATGAAATAATATGC-AAACCGG
1 TGAAATCATAACTTAAGAATCAAGTTCAACTATACC-ATTCTAATGAAATAATATGCAAAACCGG
* * *
546168 AGCTTGATGGAATTGATTCACAACGCAAGACACAAAATTCATGTCCTAAGAGCCTAA-ATGAGAA
65 AGCTTGATGGAATTGATTCACAACACAACACACAAAATTCATGTCCTAAGAGCCTAACA-GAAAA
* *
546232 CAGATTCATGA-A-AAAAATACAGTAAGTTCTAATATCAATCTCAGACCTCCTATGTTCTCACCA
129 CAGATTCATGACAGAAAAA-ACAGAAAGTTCT-A-AT--A-C-CAGACCTCCTATGTTCTCAACA
* *
546295 AACGTTGGTTCAAACCACAAATCACCTTC-AAAGAAGAGTACTTCTCTATACTAG-AGTTCTTTT
187 AACGTCGGTTCAAACCACAAATCACCTCCGAAA-AAG-GTACTTCTCTATACT-GCAGTTCTTTT
546358 TCACGGAAACTCAAA
249 TCACGGAAACTCAAA
546373 ACAATTTTCA
Statistics
Matches: 231, Mismatches: 25, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
292 4 0.02
293 13 0.06
294 71 0.31
295 1 0.00
296 51 0.22
297 6 0.03
298 4 0.02
299 80 0.35
300 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (294 bp):
TGAAATCATAACTTAAGAATCAAGTTCAACTATACCATTCTAATGAAATAATATGCAAAACCGGA
GCTTGATGGAATTGATTCACAACACAACACACAAAATTCATGTCCTAAGAGCCTAACAGAAAACA
GATTCATGACAGAAAAAACAGAAAGTTCTAATACCAGACCTCCTATGTTCTCAACAAACGTCGGT
TCAAACCACAAATCACCTCCGAAAAAGGTACTTCTCTATACTGCAGTTCTTTTTCACGGAAACTC
AAACCAAGTTCAACTATACCATTCTAATGATTAA
Found at i:546901 original size:3 final size:3
Alignment explanation
Indices: 546893--546957 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
546883 TTAATTTTAA
546893 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
546941 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
546958 AAGATTGAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:548737 original size:29 final size:30
Alignment explanation
Indices: 548694--548781 Score: 135
Period size: 29 Copynumber: 2.9 Consensus size: 30
548684 CTCACCTAAC
548694 TAAATTGATGTAAGCAATGACATCA-TTACT
1 TAAA-TGATGTAAGCAATGACATCATTTACT
548724 TAAATGATGTAAGCAATGACAT-ATTTACT
1 TAAATGATGTAAGCAATGACATCATTTACT
*
548753 TAAATGATGTAAGCAATTACATCAATTTA
1 TAAATGATGTAAGCAATGACATC-ATTTA
548782 GTTTGGGTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
28 1 0.02
29 44 0.81
30 4 0.07
31 5 0.09
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (30 bp):
TAAATGATGTAAGCAATGACATCATTTACT
Found at i:552152 original size:15 final size:15
Alignment explanation
Indices: 552132--552161 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
552122 CTTTCTCATA
552132 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
552147 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
552162 CCAACCTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.53
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:553468 original size:29 final size:30
Alignment explanation
Indices: 553425--553512 Score: 144
Period size: 29 Copynumber: 2.9 Consensus size: 30
553415 CTCACCTAAC
553425 TAAATTGATGTAAGCAATGACATCA-TTACT
1 TAAA-TGATGTAAGCAATGACATCATTTACT
553455 TAAATGATGTAAGCAATGACAT-ATTTACT
1 TAAATGATGTAAGCAATGACATCATTTACT
553484 TAAATGATGTAAGCAATGACATCAATTTA
1 TAAATGATGTAAGCAATGACATC-ATTTA
553513 GTTTGGATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
28 1 0.02
29 45 0.82
30 4 0.07
31 5 0.09
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (30 bp):
TAAATGATGTAAGCAATGACATCATTTACT
Found at i:554933 original size:2 final size:2
Alignment explanation
Indices: 554926--554972 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
554916 ATCATATACG
554926 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
554968 CAT AT
1 -AT AT
554973 TTTTCATTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:560102 original size:20 final size:20
Alignment explanation
Indices: 560059--560103 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
560049 TCAAGCATTT
*
560059 AATTAATAAATAAGATTAAG
1 AATTAATAAATAAGACTAAG
*
560079 AATTAATTAAATAATACTAA-
1 AATTAA-TAAATAAGACTAAG
560099 AATTA
1 AATTA
560104 TTATGTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
AATTAATAAATAAGACTAAG
Found at i:560241 original size:12 final size:12
Alignment explanation
Indices: 560224--560250 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
560214 AAAACTTAAA
560224 AAATAATAATAT
1 AAATAATAATAT
560236 AAATAATAATAT
1 AAATAATAATAT
560248 AAA
1 AAA
560251 AATTTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATAATAATAT
Found at i:560721 original size:13 final size:13
Alignment explanation
Indices: 560703--560747 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
560693 GGTAATCTCT
560703 GCCCCGATTACCC
1 GCCCCGATTACCC
560716 GCCCCGATTACCC
1 GCCCCGATTACCC
560729 G-CCCGA-TACCC
1 GCCCCGATTACCC
*
560740 GACCCGAT
1 GCCCCGAT
560748 AAATATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.20
12 10 0.33
13 14 0.47
ACGTcount: A:0.18, C:0.51, G:0.18, T:0.13
Consensus pattern (13 bp):
GCCCCGATTACCC
Found at i:560771 original size:2 final size:2
Alignment explanation
Indices: 560764--560859 Score: 60
Period size: 2 Copynumber: 51.0 Consensus size: 2
560754 TAAAAATAAT
* *
560764 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA AA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
560803 TA -A TT TA AA TA -A AA AA TA TA TA TT TA TA TA TT TA -A TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
560842 AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
560860 CTCGGCCCGA
Statistics
Matches: 71, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
1 6 0.08
2 65 0.92
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:561639 original size:43 final size:45
Alignment explanation
Indices: 561582--561704 Score: 155
Period size: 43 Copynumber: 2.8 Consensus size: 45
561572 GATATGAATA
561582 TATTAATATTTTAAAATAATTAAAATAATATATTTTATAAT-TATT
1 TATT-ATATTTTAAAATAATTAAAATAATATATTTTATAATATATT
* * *
561627 TATTATA-TTTAAAATAGTTAAATTAATAT-TTTTATAATATGTT
1 TATTATATTTTAAAATAATTAAAATAATATATTTTATAATATATT
* * *
561670 TTTTAAATTTTTAAATAATT-AAATAATATATTTTA
1 TATTATATTTTAAAATAATTAAAATAATATATTTTA
561705 GGGTTAATTA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
42 9 0.13
43 36 0.54
44 18 0.27
45 4 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (45 bp):
TATTATATTTTAAAATAATTAAAATAATATATTTTATAATATATT
Found at i:568299 original size:58 final size:57
Alignment explanation
Indices: 568174--568329 Score: 201
Period size: 58 Copynumber: 2.8 Consensus size: 57
568164 ACCATAACTT
* *
568174 GGTGTCAGTCCTCGATTGAAGCACAGAGGTGCTCAATCA---TCTTAGCTACACAGA
1 GGTGTCAGTTCTCGATTGAAGCACAGAGGTGCTCAATCATTTTCTTAACTACACAGA
* ** * * *
568228 GGTGTCAGCTCTCGGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGA
1 GGTGTCAGTTCTCGATTGAAGCACAGAGGTGCTCAATCA-TTTTCTTAACTACACAGA
568286 GGTGTCAGTTCTCGATTGAAGCACAGAGGTGCTCAATCACTTTT
1 GGTGTCAGTTCTCGATTGAAGCACAGAGGTGCTCAATCA-TTTT
568330 GGTTATGACC
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 34 0.40
58 51 0.60
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (57 bp):
GGTGTCAGTTCTCGATTGAAGCACAGAGGTGCTCAATCATTTTCTTAACTACACAGA
Found at i:568310 original size:27 final size:27
Alignment explanation
Indices: 568174--568316 Score: 80
Period size: 27 Copynumber: 5.1 Consensus size: 27
568164 ACCATAACTT
*
568174 GGTGTCAGTCCTCGATTGAAGCACAGA
1 GGTGTCAGTTCTCGATTGAAGCACAGA
* *
568201 GGTGCTCA-ATCATC--TTAGCTA-CACAGA
1 GGTG-TCAGTTC-TCGATT-G-AAGCACAGA
* **
568228 GGTGTCAGCTCTCGGCTGAAGCACAGA
1 GGTGTCAGTTCTCGATTGAAGCACAGA
*** *
568255 GGTGCTCAG-TCATTTTTTTTAACTGCACAGA
1 GGTG-TCAGTTC--TCGATTGAA--GCACAGA
568286 GGTGTCAGTTCTCGATTGAAGCACAGA
1 GGTGTCAGTTCTCGATTGAAGCACAGA
568313 GGTG
1 GGTG
568317 CTCAATCACT
Statistics
Matches: 87, Mismatches: 15, Indels: 28
0.67 0.12 0.22
Matches are distributed among these distances:
26 8 0.09
27 42 0.48
28 11 0.13
29 9 0.10
30 4 0.05
31 13 0.15
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (27 bp):
GGTGTCAGTTCTCGATTGAAGCACAGA
Found at i:570765 original size:3 final size:3
Alignment explanation
Indices: 570759--570799 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
570749 TGTATTATTT
* *
570759 ATA ATA ATA ATA ATA AT- ATT ATT ATA AT- ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
570800 ATACGTAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:576770 original size:21 final size:22
Alignment explanation
Indices: 576746--576789 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
576736 ATAATTTTTA
576746 AGTTTTA-ATAATTAAAAAAAT
1 AGTTTTACATAATTAAAAAAAT
* *
576767 AGTTTTACATAATTTAACAAAT
1 AGTTTTACATAATTAAAAAAAT
576789 A
1 A
576790 ATTATATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (22 bp):
AGTTTTACATAATTAAAAAAAT
Found at i:582737 original size:17 final size:17
Alignment explanation
Indices: 582715--582756 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
582705 AAAATCGTTT
*
582715 AAATATTTATTTTAAAA
1 AAATATTTAGTTTAAAA
*
582732 AAATATATAGTTTAAAA
1 AAATATTTAGTTTAAAA
*
582749 AATTATTT
1 AAATATTT
582757 TTTAATTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
AAATATTTAGTTTAAAA
Found at i:589749 original size:6 final size:6
Alignment explanation
Indices: 589730--589786 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
589720 GAGCCGCATT
* *
589730 CATCCC CATGCC CATCCC CATCCC CATCCC CATCTC CATCCC CATCCC
1 CATCCC CATCCC CATCCC CATCCC CATCCC CATCCC CATCCC CATCCC
*
589778 CATCTC CAT
1 CATCCC CAT
589787 GAATCATGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.18, C:0.60, G:0.02, T:0.21
Consensus pattern (6 bp):
CATCCC
Found at i:589753 original size:18 final size:18
Alignment explanation
Indices: 589730--589786 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
589720 GAGCCGCATT
* *
589730 CATCCCCATGCCCATCCC
1 CATCCCCATCCCCATCTC
589748 CATCCCCATCCCCATCTC
1 CATCCCCATCCCCATCTC
589766 CATCCCCATCCCCATCTC
1 CATCCCCATCCCCATCTC
589784 CAT
1 CAT
589787 GAATCATGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.18, C:0.60, G:0.02, T:0.21
Consensus pattern (18 bp):
CATCCCCATCCCCATCTC
Found at i:591659 original size:21 final size:22
Alignment explanation
Indices: 591635--591675 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
591625 ACATGACATG
*
591635 GAGTATCGGTAC-TCCTTTAAT
1 GAGTATCAGTACTTCCTTTAAT
*
591656 GAGTATTAGTACTTCCTTTA
1 GAGTATCAGTACTTCCTTTA
591676 TAATATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (22 bp):
GAGTATCAGTACTTCCTTTAAT
Found at i:591787 original size:18 final size:18
Alignment explanation
Indices: 591764--591811 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
591754 TGTGTAAAGT
591764 AGTATCGATACCCCTTTG
1 AGTATCGATACCCCTTTG
591782 AGTATCGATACCCCTTTG
1 AGTATCGATACCCCTTTG
591800 AGTATCGATACC
1 AGTATCGATACC
591812 TATTTTACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (18 bp):
AGTATCGATACCCCTTTG
Found at i:593503 original size:2 final size:2
Alignment explanation
Indices: 593498--593544 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
593488 TTTCATTTAA
593498 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
593540 A- AT AT
1 AT AT AT
593545 TATGTTAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:593503 original size:24 final size:25
Alignment explanation
Indices: 593444--593503 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
593434 TATTGACTTA
593444 TTAAATATATTTTATTATTAATTAAT
1 TTAAATATATTTTATTATT-ATTAAT
* * *
593470 TTAAAAATATTTTTTTATT-TTCAT
1 TTAAATATATTTTATTATTATTAAT
593494 TTAAATATAT
1 TTAAATATAT
593504 ATATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 13 0.43
26 17 0.57
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TTAAATATATTTTATTATTATTAAT
Found at i:600087 original size:24 final size:24
Alignment explanation
Indices: 600042--600087 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
600032 TATCTGATTT
* * *
600042 ATGACTTGAATTATGTTTTGATAC
1 ATGACCTGAATTATATTATGATAC
*
600066 ATGACCTGAATTCTATTATGAT
1 ATGACCTGAATTATATTATGAT
600088 TTCTGATCTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (24 bp):
ATGACCTGAATTATATTATGATAC
Found at i:600102 original size:24 final size:24
Alignment explanation
Indices: 600071--600142 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
600061 GATACATGAC
*
600071 CTGAATTCTATTATGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* * *
600095 CT-AGATTCTGTTCTGATATCTGTT
1 CTGA-ATTCTGTTATGATTTCTGAT
*
600119 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
600143 ATCTCTGTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 1 0.03
24 37 0.95
25 1 0.03
ACGTcount: A:0.19, C:0.14, G:0.15, T:0.51
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:604871 original size:24 final size:24
Alignment explanation
Indices: 604812--604876 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 24
604802 GATACATTAC
* * *
604812 CTAAATTCTGTTCTGATTTCTGAT
1 CTAAATTCTATTCTGATATATGAT
** * *
604836 CTGGATTATATTCTGATATATGTT
1 CTAAATTCTATTCTGATATATGAT
*
604860 CTAAATTCTATTTTGAT
1 CTAAATTCTATTCTGAT
604877 TTCTGATATC
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (24 bp):
CTAAATTCTATTCTGATATATGAT
Found at i:608126 original size:113 final size:114
Alignment explanation
Indices: 607994--608248 Score: 317
Period size: 112 Copynumber: 2.3 Consensus size: 114
607984 ATATTCTTAG
* * * ** *
607994 GAAAATAAAATCAACGATTTATTTATTTTTATAAACAT-AAA-CATTTGAGATTCT-AAAATATA
1 GAAAATAAATTTAAAGATTTATTTATTTTTATAAA-ATAAAATCATTCAAGATTCTCAAAA-AAA
** *
608056 AACTCAATGATTTATTTCCTTTCATAAAAT-AGAATCATTCAAAATTCTCAA
64 AACTCAACAATTTATTTCCTTTCACAAAATAAG-ATCATTCAAAATTCTCAA
*
608107 GAAAATAAATTTAAAGATTTATTTA--TTTATAAAATAAAATCATTCAATATTCTCAAAAAAAAA
1 GAAAATAAATTTAAAGATTTATTTATTTTTATAAAATAAAATCATTCAAGATTCTCAAAAAAAAA
*
608170 TTCAACAATTTATTTCCTTTCACAAAATAAGATCATTCAAAATTCTCAA
66 CTCAACAATTTATTTCCTTTCACAAAATAAGATCATTCAAAATTCTCAA
*
608219 GAAAATAAATTTAATA-ATTTATTTCTTTTT
1 GAAAATAAATTTAA-AGATTTATTTATTTTT
608249 TAGGAAAATA
Statistics
Matches: 123, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
110 2 0.02
111 11 0.09
112 78 0.63
113 29 0.24
114 3 0.02
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.38
Consensus pattern (114 bp):
GAAAATAAATTTAAAGATTTATTTATTTTTATAAAATAAAATCATTCAAGATTCTCAAAAAAAAA
CTCAACAATTTATTTCCTTTCACAAAATAAGATCATTCAAAATTCTCAA
Found at i:608127 original size:58 final size:57
Alignment explanation
Indices: 608065--608243 Score: 242
Period size: 56 Copynumber: 3.2 Consensus size: 57
608055 AAACTCAATG
608065 ATTTATTTCCTTTCATAAAATAGAATCATTCAAAATTCTCAAGAAAATAAATTTAA-A
1 ATTTATTTCCTTTCATAAAATA-AATCATTCAAAATTCTCAAGAAAATAAATTTAACA
* * *
608122 GATTTATTT-ATTT-ATAAAATAAAATCATTCAATATTCTCAA-AAAA-AAATTCAACA
1 -ATTTATTTCCTTTCATAAAAT-AAATCATTCAAAATTCTCAAGAAAATAAATTTAACA
* *
608177 ATTTATTTCCTTTCACAAAATAAGATCATTCAAAATTCTCAAGAAAATAAATTTAATA
1 ATTTATTTCCTTTCATAAAATAA-ATCATTCAAAATTCTCAAGAAAATAAATTTAACA
608235 ATTTATTTC
1 ATTTATTTC
608244 TTTTTTAGGA
Statistics
Matches: 106, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
54 15 0.14
55 10 0.09
56 48 0.45
57 8 0.08
58 25 0.24
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (57 bp):
ATTTATTTCCTTTCATAAAATAAATCATTCAAAATTCTCAAGAAAATAAATTTAACA
Found at i:608148 original size:56 final size:56
Alignment explanation
Indices: 607940--608242 Score: 230
Period size: 56 Copynumber: 5.4 Consensus size: 56
607930 TAATTTATAA
* * * * * *
607940 AAAATAAATTTAATAATTTATTT-TTTA-AATAATAAGATCGTAT-AATATTCTTAGG
1 AAAATAAATTCAATAATTTATTTATTTATAA-AATAAAATCAT-TCAAAATTCTCAAG
* ** ** *
607995 AAAATAAAATCAACGATTTATTTATTTTTATAAACAT-AAA-CATTTGAGATTCT-AA-
1 AAAATAAATTCAATAATTTATTTA--TTTATAAA-ATAAAATCATTCAAAATTCTCAAG
* * * * *
608050 AATATAAACTCAATGATTTATTTCCTTTCATAAAATAGAATCATTCAAAATTCTCAAG
1 AAAATAAATTCAATAATTTATTT-ATTT-ATAAAATAAAATCATTCAAAATTCTCAAG
* *
608108 AAAATAAATTTAA-AGATTTATTTATTTATAAAATAAAATCATTCAATATTCTCAA-
1 AAAATAAATTCAATA-ATTTATTTATTTATAAAATAAAATCATTCAAAATTCTCAAG
* * * *
608163 AAAA-AAATTCAACAATTTATTTCCTTTCACAAAATAAGATCATTCAAAATTCTCAAG
1 AAAATAAATTCAATAATTTATTT-ATTT-ATAAAATAAAATCATTCAAAATTCTCAAG
*
608220 AAAATAAATTTAATAATTTATTT
1 AAAATAAATTCAATAATTTATTT
608243 CTTTTTTAGG
Statistics
Matches: 199, Mismatches: 31, Indels: 33
0.76 0.12 0.13
Matches are distributed among these distances:
54 20 0.10
55 54 0.27
56 63 0.32
57 17 0.09
58 41 0.21
59 4 0.02
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (56 bp):
AAAATAAATTCAATAATTTATTTATTTATAAAATAAAATCATTCAAAATTCTCAAG
Found at i:608264 original size:56 final size:54
Alignment explanation
Indices: 608092--608265 Score: 142
Period size: 56 Copynumber: 3.1 Consensus size: 54
608082 AAATAGAATC
* *
608092 ATTCAAAATTCTCAAGAAAATAAATTTAAAGATTTATTTATTTATAA-AATAA-AA
1 ATTCAAAATTCTCAAGAAAATAAATTTAAA-ATTTATTTCTTTTTAACAA-AATAA
* * * *
608146 TCATTCAATATTCTCAA-AAAA-AAATTCAACAATTTATTTC-CTTTCACAAAATAAGA
1 --ATTCAAAATTCTCAAGAAAATAAATTTAA-AATTTATTTCTTTTTAACAAAAT-A-A
**
608202 TCATTCAAAATTCTCAAGAAAATAAATTTAATAATTTATTTCTTTTTTAGGAAAATAA
1 --ATTCAAAATTCTCAAGAAAATAAATTTAA-AATTTATTTC-TTTTTAACAAAATAA
608260 ATTCAA
1 ATTCAA
608266 TACAAAATAC
Statistics
Matches: 96, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
53 5 0.05
54 17 0.18
55 6 0.06
56 37 0.39
57 4 0.04
58 18 0.19
59 1 0.01
60 8 0.08
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.37
Consensus pattern (54 bp):
ATTCAAAATTCTCAAGAAAATAAATTTAAAATTTATTTCTTTTTAACAAAATAA
Found at i:610846 original size:28 final size:27
Alignment explanation
Indices: 610815--610886 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 27
610805 AATTAATCAT
*
610815 TAATTAAAATTTAATTTTAATAGAATTA
1 TAATTAAAATTTAATTTTAATA-AAATA
* * * *
610843 TAATTTAAATATATTTTTATTAAAATA
1 TAATTAAAATTTAATTTTAATAAAATA
610870 TAA-TAATTAATTTAATT
1 TAATTAA--AATTTAATT
610887 GATTCAATTT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
26 2 0.06
27 7 0.21
28 25 0.74
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (27 bp):
TAATTAAAATTTAATTTTAATAAAATA
Found at i:611508 original size:2 final size:2
Alignment explanation
Indices: 611501--611528 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
611491 GATTTTAGAC
611501 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
611529 TTAATAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:613233 original size:9 final size:9
Alignment explanation
Indices: 613219--613248 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
613209 TATAACCTAA
613219 TAAAAAAAT
1 TAAAAAAAT
*
613228 TAAAAAATT
1 TAAAAAAAT
613237 TAAAAAAAT
1 TAAAAAAAT
613246 TAA
1 TAA
613249 TAATATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:613454 original size:24 final size:24
Alignment explanation
Indices: 613427--613473 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
613417 AATATCGAAT
613427 GAACTA-TTAAAGCAAATATAGGAA
1 GAACTACTT-AAGCAAATATAGGAA
*
613451 GAACTACTTAAGTAAATATAGGA
1 GAACTACTTAAGCAAATATAGGA
613474 GGAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (24 bp):
GAACTACTTAAGCAAATATAGGAA
Found at i:613932 original size:20 final size:20
Alignment explanation
Indices: 613907--613976 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
613897 TGTACAGTGT
613907 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * *
613927 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
613947 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
613968 CGTTGCGAT
1 CGTTGCGAT
613977 AGTTTATACT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 4 0.10
20 20 0.51
21 11 0.28
22 4 0.10
ACGTcount: A:0.13, C:0.23, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:613992 original size:46 final size:41
Alignment explanation
Indices: 613843--614005 Score: 256
Period size: 41 Copynumber: 3.9 Consensus size: 41
613833 TAGTTGAAAA
*
613843 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATCTT-CATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
*
613883 TCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
613924 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
613965 TCGCGTTGCGATAGTTTATACTACAGTGTCGTTGCGATTTT
1 TCGCGTTGCGATAG----T-CTACAGTGTCGTTGCGATTTT
614006 GTTTCTTAAG
Statistics
Matches: 114, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
40 34 0.30
41 58 0.51
45 1 0.01
46 21 0.18
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
Found at i:615200 original size:21 final size:21
Alignment explanation
Indices: 615144--615221 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
615134 TTTTTAATTT
*
615144 ACTGTACACTATCGCAACGAGA
1 ACTGTACACTATCGCAACGA-C
* **
615166 AATG-A-AAAATCGCAACGAC
1 ACTGTACACTATCGCAACGAC
*
615185 ATTGTACACTATCGCAACGAC
1 ACTGTACACTATCGCAACGAC
*
615206 ACTGTAGACTATCGCA
1 ACTGTACACTATCGCA
615222 GCGCGAAATG
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.07
20 12 0.27
21 27 0.60
22 3 0.07
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (21 bp):
ACTGTACACTATCGCAACGAC
Found at i:615244 original size:36 final size:37
Alignment explanation
Indices: 615197--615298 Score: 152
Period size: 36 Copynumber: 2.7 Consensus size: 37
615187 TGTACACTAT
615197 CGCAACGACACTGTAGACTATCGCAGCGCGAAATG-C
1 CGCAACGACACTGTAGACTATCGCAGCGCGAAATGAC
*
615233 CGCAACGACACTGTAGACTATCGCAGCGCGAAATGAAAAAT
1 CGCAACGACACTGTAGACTATCGCAGCGCGAAATG----AC
615274 CGCAACGACACTGTAGACTATCGCA
1 CGCAACGACACTGTAGACTATCGCA
615299 ACACGAAAAG
Statistics
Matches: 60, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
36 35 0.58
41 25 0.42
ACGTcount: A:0.34, C:0.28, G:0.23, T:0.15
Consensus pattern (37 bp):
CGCAACGACACTGTAGACTATCGCAGCGCGAAATGAC
Found at i:615290 original size:41 final size:41
Alignment explanation
Indices: 615233--615321 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
615223 CGCGAAATGC
* * *
615233 CGCAACGACACTGTAGACTATCGCAGCGCGAAATGAAAAAT
1 CGCAACGACACTGTAGACTATCGCAACACGAAAAGAAAAAT
*
615274 CGCAACGACACTGTAGACTATCGCAACACGAAAAGGAAAAT
1 CGCAACGACACTGTAGACTATCGCAACACGAAAAGAAAAAT
615315 CGCAACG
1 CGCAACG
615322 CGATTTTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.12
Consensus pattern (41 bp):
CGCAACGACACTGTAGACTATCGCAACACGAAAAGAAAAAT
Found at i:615298 original size:21 final size:21
Alignment explanation
Indices: 615174--615300 Score: 83
Period size: 21 Copynumber: 6.4 Consensus size: 21
615164 GAAATGAAAA
* *
615174 ATCGCAACGACATTGTACACT
1 ATCGCAACGACACTGTAGACT
615195 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* *
615216 ATCGC-A-G-CGC-G-A-AAT
1 ATCGCAACGACACTGTAGACT
**
615231 GCCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* * **
615252 ATCGCAGCG-CGAAATG-A-AAA
1 ATCGCAACGAC--ACTGTAGACT
615272 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
615293 ATCGCAAC
1 ATCGCAAC
615301 ACGAAAAGGA
Statistics
Matches: 77, Mismatches: 18, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
15 5 0.06
16 2 0.03
17 2 0.03
18 4 0.05
19 5 0.06
20 13 0.17
21 43 0.56
22 3 0.04
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:615335 original size:41 final size:41
Alignment explanation
Indices: 615249--615389 Score: 173
Period size: 41 Copynumber: 3.4 Consensus size: 41
615239 GACACTGTAG
* * *
615249 ACTATCGCAGCGCGAAAT-GAAAAATCGCAACGAC-ACTGT-A
1 ACTATCGCAACGCGAAATAG-AAAATCGCAACG-CGATTTTCA
*
615289 GACTATCGCAACACGAAA-AGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATA-GAAAATCGCAACGCGATTTTCA
*
615331 ACTATCGCAACGCGAAATAGAAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCA
615372 ACTATCGCAACGCGAAAT
1 ACTATCGCAACGCGAAAT
615390 GCAGCGCGAA
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
40 1 0.01
41 85 0.96
42 3 0.03
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCA
Found at i:615339 original size:21 final size:21
Alignment explanation
Indices: 615313--615386 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
615303 GAAAAGGAAA
615313 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
615334 ATCGCAACGCGAAATAGAA-A
1 ATCGCAACGCGATTTTCAACT
*
615354 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
615375 ATCGCAACGCGA
1 ATCGCAACGCGA
615387 AATGCAGCGC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:615424 original size:20 final size:20
Alignment explanation
Indices: 615401--615446 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
615391 CAGCGCGAAT
* *
615401 TTGCGATACTGGAGATCGCG
1 TTGCGATACTAGAGATCGCA
*
615421 TTGCGA-ATTAGAGATCGCA
1 TTGCGATACTAGAGATCGCA
615440 TTGCGAT
1 TTGCGAT
615447 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TTGCGATACTAGAGATCGCA
Found at i:615845 original size:22 final size:22
Alignment explanation
Indices: 615802--615846 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
615792 AAATGTAGTC
*
615802 TTTTTTTTTATTTTGATCATTA
1 TTTTTTTTTATTTTGATAATTA
*
615824 TTTTTTTTATATTTT-TTAATTA
1 TTTTTTTT-TATTTTGATAATTA
615846 T
1 T
615847 ATCATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTTTTTTATTTTGATAATTA
Found at i:615868 original size:21 final size:22
Alignment explanation
Indices: 615829--615869 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
615819 CATTATTTTT
* *
615829 TTTATATTTTTTAATTATATCA
1 TTTATATTATTTAAATATATCA
615851 TTTA-ATTATTTAAATATAT
1 TTTATATTATTTAAATATAT
615870 TTAATTAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTATATTATTTAAATATATCA
Found at i:627915 original size:31 final size:31
Alignment explanation
Indices: 627828--627954 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
627818 ATAGTCGAGG
627828 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
627859 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
* *
627891 GTATACATATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
627922 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
627953 GT
1 GT
627955 TGCCAAGGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 52 0.66
32 27 0.34
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:627996 original size:30 final size:30
Alignment explanation
Indices: 627942--628013 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
627932 GTTCTTCGGA
* * * *
627942 ACCTATGGACAGTTGCCAAGGATCTTTTTG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
*
627972 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
628002 ACCTCTGGATAG
1 ACCTCTGGATAG
628014 GTCCTTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATCTTTATG
Found at i:632770 original size:31 final size:31
Alignment explanation
Indices: 632683--632778 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
632673 AGAGTCGAGG
* *
632683 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACATATGTTCTAAGGAACATATGGACA
* * ***
632714 GAATAACTTATG-TCTTTCGAGACATATGGACA
1 GTAT-ACATATGTTCTAAGGA-ACATATGGACA
632746 GTATACATATGTTCTAAGGAACATATGGACA
1 GTATACATATGTTCTAAGGAACATATGGACA
632777 GT
1 GT
632779 TTACCTAGGT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
31 27 0.52
32 25 0.48
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (31 bp):
GTATACATATGTTCTAAGGAACATATGGACA
Found at i:632791 original size:31 final size:31
Alignment explanation
Indices: 632735--632810 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
632725 GTCTTTCGAG
* *
632735 ACATATGGACAGTATACATATGTTCTAAGGA
1 ACATATGGACAGTTTACATAGGTTCTAAGGA
* **
632766 ACATATGGACAGTTTACCTAGGTTCTTCGGA
1 ACATATGGACAGTTTACATAGGTTCTAAGGA
* *
632797 ACCTATAGACAGTT
1 ACATATGGACAGTT
632811 GCCAAGGATC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (31 bp):
ACATATGGACAGTTTACATAGGTTCTAAGGA
Found at i:637981 original size:96 final size:96
Alignment explanation
Indices: 637817--638018 Score: 404
Period size: 96 Copynumber: 2.1 Consensus size: 96
637807 TAGTGAGCTT
637817 AATTTGTAAACACCTACCTTTAGATGTTTTCTTGTTTACACATATTTAACCTTTTGTAAAAGGGG
1 AATTTGTAAACACCTACCTTTAGATGTTTTCTTGTTTACACATATTTAACCTTTTGTAAAAGGGG
637882 GTGATTCTAATTTAGCTATTGAAAACTAAGG
66 GTGATTCTAATTTAGCTATTGAAAACTAAGG
637913 AATTTGTAAACACCTACCTTTAGATGTTTTCTTGTTTACACATATTTAACCTTTTGTAAAAGGGG
1 AATTTGTAAACACCTACCTTTAGATGTTTTCTTGTTTACACATATTTAACCTTTTGTAAAAGGGG
637978 GTGATTCTAATTTAGCTATTGAAAACTAAGG
66 GTGATTCTAATTTAGCTATTGAAAACTAAGG
638009 AATTTGTAAA
1 AATTTGTAAA
638019 GATAACTTTT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 106 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (96 bp):
AATTTGTAAACACCTACCTTTAGATGTTTTCTTGTTTACACATATTTAACCTTTTGTAAAAGGGG
GTGATTCTAATTTAGCTATTGAAAACTAAGG
Found at i:642983 original size:43 final size:43
Alignment explanation
Indices: 642907--643001 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
642897 AATACGATTA
* * ** * * **
642907 AAAATGTTATAAAAATTATAATATTTTTTATTGGGTATAATTT
1 AAAATATTATAAAAATTATAACATTTTCGATTGGATACAATCG
*
642950 AAAATATTATAAAATTTATAACATTTTCGATTGGATACAATCG
1 AAAATATTATAAAAATTATAACATTTTCGATTGGATACAATCG
642993 AAAATATTA
1 AAAATATTA
643002 ATTTTTTATT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (43 bp):
AAAATATTATAAAAATTATAACATTTTCGATTGGATACAATCG
Found at i:643625 original size:31 final size:29
Alignment explanation
Indices: 643563--643640 Score: 79
Period size: 31 Copynumber: 2.7 Consensus size: 29
643553 ATTTTTTATC
* * *
643563 TAAATATTTAAA-ATATTTTTTGTCATAA
1 TAAATACTTAAAGTTATTTTTTGTCAAAA
*
643591 TAAATGCTTAAAGTTATTATTTTGATCAAAA
1 TAAATACTTAAAGTTATT-TTTTG-TCAAAA
*
643622 TAAATATTTAAAG-TATTTT
1 TAAATACTTAAAGTTATTTT
643641 GTTCTATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
28 10 0.24
29 6 0.15
30 9 0.22
31 16 0.39
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (29 bp):
TAAATACTTAAAGTTATTTTTTGTCAAAA
Found at i:647154 original size:12 final size:12
Alignment explanation
Indices: 647137--647169 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
647127 TTGAATAGAA
647137 ATAAATTTAATT
1 ATAAATTTAATT
647149 ATAAATTTAAATT
1 ATAAATTT-AATT
647162 -TAAATTTA
1 ATAAATTTA
647170 GGACTAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 15 0.75
13 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATAAATTTAATT
Found at i:647686 original size:12 final size:12
Alignment explanation
Indices: 647669--647698 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
647659 CAATTAATAT
*
647669 TTTAATGGTTAA
1 TTTAATGGTCAA
647681 TTTAATGGTCAA
1 TTTAATGGTCAA
647693 TTTAAT
1 TTTAAT
647699 CCATAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (12 bp):
TTTAATGGTCAA
Found at i:648159 original size:28 final size:28
Alignment explanation
Indices: 648127--648190 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
648117 TTTTTTACTA
*
648127 CAATTATTTG-CAAATTCTTTATTCTCAT
1 CAATTATTTGACAAATT-TATATTCTCAT
* * *
648155 CAATTGTTTGACTACTTTATATTCTCAT
1 CAATTATTTGACAAATTTATATTCTCAT
648183 CAA-TATTT
1 CAATTATTT
648191 TACCCTCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 4 0.13
28 22 0.73
29 4 0.13
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (28 bp):
CAATTATTTGACAAATTTATATTCTCAT
Found at i:649561 original size:29 final size:28
Alignment explanation
Indices: 649389--649563 Score: 151
Period size: 29 Copynumber: 6.2 Consensus size: 28
649379 GATCGGGTGG
* *
649389 TATTTTAGTAATTATTTGGAAAATGGTGG
1 TATTTTAGTAATTATTTTGAAAAT-GTGA
* * *
649418 TATTCTGGTAATTATTTTGAAAAATGTGC
1 TATTTTAGTAATTATTTTG-AAAATGTGA
* * *
649447 TATTTTTGT-ATTTTTTTTAAAA--TGA
1 TATTTTAGTAATTATTTTGAAAATGTGA
* * *
649472 TAATTTAGTAATT-TTTTAAAGAAAGTGA
1 TATTTTAGTAATTATTTTGAA-AATGTGA
*
649500 TATTTTAGTAATTATTTTAAAAATTGTGA
1 TATTTTAGTAATTATTTTGAAAA-TGTGA
* *
649529 TATTTTGGTAATTATTTTGAAAATGATGT
1 TATTTTAGTAATTATTTTGAAAATG-TGA
649558 TATTTT
1 TATTTT
649564 CGTTAAATGG
Statistics
Matches: 121, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
25 15 0.12
26 5 0.04
27 4 0.03
28 26 0.21
29 66 0.55
30 5 0.04
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.51
Consensus pattern (28 bp):
TATTTTAGTAATTATTTTGAAAATGTGA
Found at i:650448 original size:42 final size:42
Alignment explanation
Indices: 650389--650554 Score: 260
Period size: 42 Copynumber: 4.0 Consensus size: 42
650379 GAAGTATTAT
* *
650389 CAGGTCCCTTTGCTGTGTACAAAAGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCC
650431 CAGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCC
* *
650473 CAGGTCCCTTTGCTGTGTGCAAAGGTAAACCTTATAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCC
* * * *
650515 CAGGTCCCTTCGCTGTGTGCGAGGGTAAGCCTTATAGTTT
1 CAGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTT
650555 TCCTAGGCTC
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 116 1.00
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (42 bp):
CAGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCC
Found at i:651655 original size:23 final size:23
Alignment explanation
Indices: 651609--651655 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
651599 TCGACATGTC
* *
651609 TAATTTAATTTCTAATTAGAATT
1 TAATTTAATATCTAATTAAAATT
651632 TAATTTAATATCTAA-TAAATATT
1 TAATTTAATATCTAATTAAA-ATT
651655 T
1 T
651656 TTATCAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
TAATTTAATATCTAATTAAAATT
Found at i:655655 original size:32 final size:32
Alignment explanation
Indices: 655614--655675 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
655604 GGGTATCGGG
* *
655614 TACCCGATTACCGGGTACTCGTAAAATCCGAA
1 TACCCGATTACCGGATACCCGTAAAATCCGAA
* *
655646 TACCCGATTATCGGATACCCGTAACATCCG
1 TACCCGATTACCGGATACCCGTAAAATCCG
655676 GATCGGGACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (32 bp):
TACCCGATTACCGGATACCCGTAAAATCCGAA
Found at i:655754 original size:16 final size:15
Alignment explanation
Indices: 655716--655755 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
655706 CCGAAAGTTC
*
655716 CGGGTACCCGAAAAT
1 CGGGTACCCAAAAAT
*
655731 CGGATACCCAAAAATT
1 CGGGTACCCAAAAA-T
655747 CGGGTACCC
1 CGGGTACCC
655756 GGATTTGCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.15
Consensus pattern (15 bp):
CGGGTACCCAAAAAT
Found at i:658011 original size:85 final size:84
Alignment explanation
Indices: 657893--658070 Score: 241
Period size: 85 Copynumber: 2.1 Consensus size: 84
657883 TTCTTTGAGT
*
657893 GTCATTGAAGCCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
1 GTCATTGAAGCCCCCGTCATAAATT-AGATGACACACATTTGTGCGTCATAAATTTATGACACAC
* *
657958 ACGTATGACTTACATTGCGC
65 ACATATGACTTACATTGCAC
* * * *
657978 GTCATTGAAGCCCCTGTCATAAATCT-GTTTGACATACATTTGTGTGTCATAAATTTATGACACA
1 GTCATTGAAGCCCCCGTCATAAAT-TAG-ATGACACACATTTGTGCGTCATAAATTTATGACACA
* *
658042 CATATATGACTTACATTGCAT
64 CACATATGACTTACATTGCAC
658063 GTCATTGA
1 GTCATTGA
658071 TGCACACGTC
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
84 1 0.01
85 80 0.98
86 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (84 bp):
GTCATTGAAGCCCCCGTCATAAATTAGATGACACACATTTGTGCGTCATAAATTTATGACACACA
CATATGACTTACATTGCAC
Found at i:658135 original size:2 final size:2
Alignment explanation
Indices: 658128--658187 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
658118 TATTTCGGAA
658128 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
658170 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
658188 GTAGATTGAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:659606 original size:12 final size:12
Alignment explanation
Indices: 659589--659616 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
659579 TATTAATAAT
659589 CAAATGAAAAAA
1 CAAATGAAAAAA
659601 CAAATGAAAAAA
1 CAAATGAAAAAA
659613 CAAA
1 CAAA
659617 CCCGTGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.75, C:0.11, G:0.07, T:0.07
Consensus pattern (12 bp):
CAAATGAAAAAA
Found at i:662136 original size:23 final size:22
Alignment explanation
Indices: 662109--662183 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
662099 TGATATATGA
662109 ATATGCAATACGTGATACATGTG
1 ATATG-AATACGTGATACATGTG
* ** *
662132 ATATG-ATATGAAATGACATATG
1 ATATGAATACGTGAT-ACATGTG
662154 AATATGTAATACGTGATACATGTG
1 -ATATG-AATACGTGATACATGTG
662178 ATATGA
1 ATATGA
662184 TATGAAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 6 0.15
22 7 0.17
23 15 0.38
24 6 0.15
25 6 0.15
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (22 bp):
ATATGAATACGTGATACATGTG
Done.