Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002648.1 Hibiscus syriacus cultivar Beakdansim tig00005411_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: 636717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:3965 original size:13 final size:13
Alignment explanation
Indices: 3947--3971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3937 ATTATAATTA
3947 TATTTTTTATATG
1 TATTTTTTATATG
3960 TATTTTTTATAT
1 TATTTTTTATAT
3972 TTTTTATACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TATTTTTTATATG
Found at i:3989 original size:22 final size:22
Alignment explanation
Indices: 3944--3991 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3934 TTTATTATAA
**
3944 TTATATTTTTTATATGTATTTT
1 TTATATTTTTTATATGTAAATT
3966 TTATATTTTTTATACT-TAAATT
1 TTATATTTTTTATA-TGTAAATT
3988 TTAT
1 TTAT
3992 TTCATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTATATTTTTTATATGTAAATT
Found at i:4029 original size:30 final size:32
Alignment explanation
Indices: 3981--4042 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
3971 TTTTTTATAC
* *
3981 TTAAATTTTATTTCATATATA-ATAATATTTT
1 TTAAATTTTATATAATATATATATAATATTTT
*
4012 TTAAA-TTTATATAATATATATATATTATTTT
1 TTAAATTTTATATAATATATATATAATATTTT
4043 AATAGTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (32 bp):
TTAAATTTTATATAATATATATATAATATTTT
Found at i:4204 original size:58 final size:59
Alignment explanation
Indices: 4086--4214 Score: 208
Period size: 58 Copynumber: 2.2 Consensus size: 59
4076 ATTTTATTTT
*
4086 AAATTTTAAATGAGTGGTTGTGGTTAAATCGAAATAATTAAAATATTATCTTAAAATTC
1 AAATGTTAAATGAGTGGTTGTGGTTAAATCGAAATAATTAAAATATTATCTTAAAATTC
* *
4145 AAATGTTAGATGAGTGGTTGTGGTTATATC-ATAATAA-TAAAATATTATCTTAAAATTC
1 AAATGTTAAATGAGTGGTTGTGGTTAAATCGA-AATAATTAAAATATTATCTTAAAATTC
4203 AAATGTTAAATG
1 AAATGTTAAATG
4215 GTTTGTTAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
58 33 0.51
59 32 0.49
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.39
Consensus pattern (59 bp):
AAATGTTAAATGAGTGGTTGTGGTTAAATCGAAATAATTAAAATATTATCTTAAAATTC
Found at i:12418 original size:2 final size:2
Alignment explanation
Indices: 12411--12472 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
12401 ATATTATCAA
12411 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
12453 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
12473 CGTAACCATC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12838 original size:17 final size:16
Alignment explanation
Indices: 12816--12877 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
12806 TAGAATAAAG
12816 TAAATACAAAGTAAAAT
1 TAAATA-AAAGTAAAAT
* *
12833 TAAATAAAAAATTAAA-
1 TAAAT-AAAAGTAAAAT
12849 TAAATAAAAG-AAAAT
1 TAAATAAAAGTAAAAT
12864 ATAAATTAAAAGTA
1 -TAAA-TAAAAGTA
12878 TTAAATTAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
14 3 0.08
15 4 0.11
16 9 0.25
17 18 0.50
18 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (16 bp):
TAAATAAAAGTAAAAT
Found at i:12843 original size:12 final size:12
Alignment explanation
Indices: 12828--12852 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12818 AATACAAAGT
12828 AAAATTAAATAA
1 AAAATTAAATAA
12840 AAAATTAAATAA
1 AAAATTAAATAA
12852 A
1 A
12853 TAAAAGAAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATTAAATAA
Found at i:12867 original size:16 final size:16
Alignment explanation
Indices: 12816--12875 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 16
12806 TAGAATAAAG
12816 TAAATACAAAGTAAAAT-
1 TAAATA-AAAG-AAAATA
12833 TAAATAAAA-AATTAA-A
1 TAAATAAAAGAA--AATA
12849 TAAATAAAAGAAAATA
1 TAAATAAAAGAAAATA
12865 TAAATTAAAAG
1 TAAA-TAAAAG
12876 TATTAAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 2 0.05
15 2 0.05
16 19 0.51
17 14 0.38
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (16 bp):
TAAATAAAAGAAAATA
Found at i:14346 original size:2 final size:2
Alignment explanation
Indices: 14339--14396 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
14329 TTTTAAAAAC
14339 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14381 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
14397 AGTTTTCAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14431 original size:36 final size:35
Alignment explanation
Indices: 14387--14651 Score: 222
Period size: 36 Copynumber: 7.3 Consensus size: 35
14377 TATATATATA
* * *
14387 TATATATATAAGTTTTCAAAATATGTTTTCAAAAC
1 TATATATATATGTTTTCAAAAAATGTTTTAAAAAC
* *
14422 TATATTATATACGTTTTC-AAAAATCGTTTTTTAAAAGC
1 TATA-TATATATGTTTTCAAAAAAT-G--TTTTAAAAAC
* *
14460 TATATATTATATGTTTTTAAAAAAAATCTTTTAAAAAC
1 TATATA-TATATG-TTTT-CAAAAAATGTTTTAAAAAC
*
14498 TATATATGATATGTTTTCAAAACCAA--TTTTAAAAAT
1 TATATAT-ATATGTTTTCAAAA--AATGTTTTAAAAAC
14534 TATATATTATATGTTTTCAAAACAATCGTTTTAAAAA-
1 TATATA-TATATGTTTTCAAAA-AAT-GTTTTAAAAAC
*
14571 -ATATATA-ATGTTCTT-AAAACAT-TTTTAAAAAC
1 TATATATATATGTT-TTCAAAAAATGTTTTAAAAAC
* *
14603 TATATATTATATGTTTTCAAAAAATATTTTCGAAAAC
1 TATATA-TATATGTTTTCAAAAAATGTTTT-AAAAAC
14640 TATACTATATAT
1 TATA-TATATAT
14652 CTTCAAAAAC
Statistics
Matches: 193, Mismatches: 13, Indels: 46
0.77 0.05 0.18
Matches are distributed among these distances:
31 9 0.05
33 7 0.04
34 13 0.07
35 27 0.14
36 55 0.28
37 22 0.11
38 50 0.26
39 4 0.02
41 6 0.03
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (35 bp):
TATATATATATGTTTTCAAAAAATGTTTTAAAAAC
Found at i:16704 original size:23 final size:23
Alignment explanation
Indices: 16666--16731 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
16656 CACCACAGCT
*
16666 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
16689 TGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
16712 CGTAGAAATGCACCGTAGTG
1 CGTAGAAATGCACCGAAGTG
16732 TCATATAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:19615 original size:16 final size:16
Alignment explanation
Indices: 19594--19630 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
19584 AACTTCAAAA
*
19594 TCTTTAATTTCTCTAT
1 TCTTTAATTGCTCTAT
*
19610 TCTTTACTTGCTCTAT
1 TCTTTAATTGCTCTAT
19626 TCTTT
1 TCTTT
19631 TCAAACACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.22, G:0.03, T:0.62
Consensus pattern (16 bp):
TCTTTAATTGCTCTAT
Found at i:31233 original size:24 final size:24
Alignment explanation
Indices: 31203--31322 Score: 152
Period size: 24 Copynumber: 5.0 Consensus size: 24
31193 GGTTAGTTAC
**
31203 AGAAGCTTGTGCTTTTGCAGCCGA
1 AGAAGCTTGTGCTTTTGCAGAAGA
*
31227 AGAAGCTTGTGCTTTTGCAGAATA
1 AGAAGCTTGTGCTTTTGCAGAAGA
* *
31251 TGAAGCTTGTGCTTTTGCAGACGA
1 AGAAGCTTGTGCTTTTGCAGAAGA
* *
31275 TGAAGCTTGTGCTTTTGCAGTAGA
1 AGAAGCTTGTGCTTTTGCAGAAGA
*
31299 TA-AAGCTTGTGCTTTTGTAGAAGA
1 -AGAAGCTTGTGCTTTTGCAGAAGA
31323 TGAGTCTCCT
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (24 bp):
AGAAGCTTGTGCTTTTGCAGAAGA
Found at i:31325 original size:48 final size:48
Alignment explanation
Indices: 31205--31325 Score: 179
Period size: 48 Copynumber: 2.5 Consensus size: 48
31195 TTAGTTACAG
* * * *
31205 AAGCTTGTGCTTTTGCAGCCGAAGAAGCTTGTGCTTTTGCAGAATATG
1 AAGCTTGTGCTTTTGCAGACGATGAAGCTTGTGCTTTTGCAGAAGATA
*
31253 AAGCTTGTGCTTTTGCAGACGATGAAGCTTGTGCTTTTGCAGTAGATA
1 AAGCTTGTGCTTTTGCAGACGATGAAGCTTGTGCTTTTGCAGAAGATA
* *
31301 AAGCTTGTGCTTTTGTAGAAGATGA
1 AAGCTTGTGCTTTTGCAGACGATGA
31326 GTCTCCTTGA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (48 bp):
AAGCTTGTGCTTTTGCAGACGATGAAGCTTGTGCTTTTGCAGAAGATA
Found at i:34029 original size:21 final size:21
Alignment explanation
Indices: 34005--34047 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
33995 AGTTAGTAAG
*
34005 ATAAAAATCAAAATCAAAATA
1 ATAAAAATCAAAATAAAAATA
* *
34026 ATAATAATGAAAATAAAAATA
1 ATAAAAATCAAAATAAAAATA
34047 A
1 A
34048 AAATTCCTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (21 bp):
ATAAAAATCAAAATAAAAATA
Found at i:35121 original size:16 final size:15
Alignment explanation
Indices: 35102--35151 Score: 73
Period size: 16 Copynumber: 3.2 Consensus size: 15
35092 AAATTGAAGT
*
35102 AAAATTAAATAAATGA
1 AAAAATAAATAAAT-A
35118 AAAAATAAATAAATA
1 AAAAATAAATAAATA
35133 AATAAATAAATAAATA
1 AA-AAATAAATAAATA
35149 AAA
1 AAA
35152 GAAAATCTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
15 4 0.12
16 28 0.88
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAAATAAATAAATA
Found at i:35127 original size:4 final size:4
Alignment explanation
Indices: 35107--35150 Score: 72
Period size: 4 Copynumber: 11.0 Consensus size: 4
35097 GAAGTAAAAT
35107 TAAA TAAA TGAAA -AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
35151 AGAAAATCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 3 0.08
4 32 0.84
5 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:36494 original size:12 final size:11
Alignment explanation
Indices: 36455--36496 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
36445 TAAATGAATA
36455 AAATAATA-AT
1 AAATAATATAT
*
36465 AAATAACATTAT
1 AAATAATA-TAT
36477 AAATAATATAT
1 AAATAATATAT
36488 AATATAATA
1 AA-ATAATA
36497 CGTACTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 7 0.26
11 5 0.19
12 15 0.56
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATATAT
Found at i:36610 original size:2 final size:2
Alignment explanation
Indices: 36603--36641 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
36593 TTTTAAAAAC
36603 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
36642 TTGTATGTTT
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:36765 original size:36 final size:37
Alignment explanation
Indices: 36649--36829 Score: 226
Period size: 38 Copynumber: 4.9 Consensus size: 37
36639 TATTTGTATG
* *
36649 TTTTCAAAACTATAT-TATATACGTTTTCAAAAACCATT
1 TTTTAAAAACTATATAT-TATATGTTTTCAAAAACCA-T
*
36687 TTTTAAAAACTATATATTATATGTTTTCAAAAACCGT
1 TTTTAAAAACTATATATTATATGTTTTCAAAAACCAT
*
36724 CTTTTAAAAACTATATATTATATGTTTTC-AAAATCAT
1 -TTTTAAAAACTATATATTATATGTTTTCAAAAACCAT
**
36761 TTTTAAAAACTATATATTATATGTTTTCAAAAAATAT
1 TTTTAAAAACTATATATTATATGTTTTCAAAAACCAT
* * *
36798 TTTTGAAAAC--TATATTATATATCTTCAAAAAC
1 TTTTAAAAACTATATATTATATGTTTTCAAAAAC
36830 TATATACATT
Statistics
Matches: 129, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
35 19 0.15
36 28 0.22
37 22 0.17
38 59 0.46
39 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATGTTTTCAAAAACCAT
Found at i:36784 original size:74 final size:76
Alignment explanation
Indices: 36649--36818 Score: 240
Period size: 74 Copynumber: 2.3 Consensus size: 76
36639 TATTTGTATG
*
36649 TTTTCAAAACTATATTATATACGTTTTCAAAAACCATTTTTTAAAAACTATATATTATATGTTTT
1 TTTTAAAAACTATATTATATACGTTTTCAAAAACCATTTTTTAAAAACTATATATTATATGTTTT
36714 CAAAAACCGTC
66 CAAAAACCGTC
* *
36725 TTTTAAAAACTATA-TATTATATGTTTTC-AAAATCA-TTTTTAAAAACTATATATTATATGTTT
1 TTTTAAAAACTATATTA-TATACGTTTTCAAAAACCATTTTTTAAAAACTATATATTATATGTTT
***
36787 TCAAAAAATAT-
65 TCAAAAACCGTC
*
36798 TTTTGAAAACTATATTATATA
1 TTTTAAAAACTATATTATATA
36819 TCTTCAAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
73 17 0.20
74 37 0.44
75 8 0.09
76 23 0.27
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.45
Consensus pattern (76 bp):
TTTTAAAAACTATATTATATACGTTTTCAAAAACCATTTTTTAAAAACTATATATTATATGTTTT
CAAAAACCGTC
Found at i:41183 original size:3 final size:3
Alignment explanation
Indices: 41165--41245 Score: 99
Period size: 3 Copynumber: 26.3 Consensus size: 3
41155 TTGTAATATT
* * *
41165 TAA TAAA TAA TAAA TAA TAT TAC TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
41212 TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
41246 TTAAAATAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
3 62 0.91
4 6 0.09
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:41520 original size:76 final size:77
Alignment explanation
Indices: 41391--42693 Score: 2133
Period size: 76 Copynumber: 17.2 Consensus size: 77
41381 TTCTGCCCAG
* *
41391 AGGACTTACAGATGACCCTGAG-GGTTTGAAAACATCAAAAATCTCCCGAAGGCTTTTTGGAAAC
1 AGGACTTACAGATGACCCTGAGAGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
*
41455 ATCATGCACTGT
66 ATCATGCACTGA
* *
41467 AGAACTTACAGATGACCCTGAGAG-TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAAC
1 AGGACTTACAGATGACCCTGAGAGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
41531 ATCATGCACTGA
66 ATCATGCACTGA
*
41543 AGGGCTTACAGATGACCC-GA-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
1 AGGACTTACAGATGACCCTGAGA-GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
41606 CATCATGCACTGA
65 CATCATGCACTGA
*
41619 AGGACTTACAGATGACCC-GA-AGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
1 AGGACTTACAGATGACCCTGAGA-GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
41682 CATCATGCACTGA
65 CATCATGCACTGA
* *
41695 AGGGCTTATAGATGACCC-GA-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
1 AGGACTTACAGATGACCCTGAGA-GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
41758 CATCATGCACTGA
65 CATCATGCACTGA
*
41771 AGGGCTTACAGATGACCC-GA-AGGCTTTGAAAACATCAAAAAGCT-CCGAAGGC-TTTTGGAAA
1 AGGACTTACAGATGACCCTGAGA-GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
41832 CATCATGCACTGA
65 CATCATGCACTGA
41845 AGGACTTACAGATGACCC-GA-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
1 AGGACTTACAGATGACCCTGAGA-GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
41908 CATCATGCACTGA
65 CATCATGCACTGA
* *
41921 AGGGCTTACAGATGACCC-GA-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
1 AGGACTTACAGATGACCCTGAGA-GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
41984 CATCATGCACTGA
65 CATCATGCACTGA
*
41997 AGGACTTACAGATGACCCTAAG-GCTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAAC
1 AGGACTTACAGATGACCCTGAGAGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
42060 ATCATGCACTGA
66 ATCATGCACTGA
*
42072 AGGACTTACAGATGACCC-GA-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGAAA
1 AGGACTTACAGATGACCCTGAGA-GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
42135 CATCATGCACTGA
65 CATCATGCACTGA
42148 AGGACTTACAGATGACCCTGAG-GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
1 AGGACTTACAGATGACCCTGAGAGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
42212 ATCATGCACTGA
66 ATCATGCACTGA
*
42224 AGGACTTACAGATGACCCTGAG-GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAAC
1 AGGACTTACAGATGACCCTGAGAGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
42288 ATCATGCACTGA
66 ATCATGCACTGA
*
42300 AGGACTTACAGATGACCCTAAG-GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
1 AGGACTTACAGATGACCCTGAGAGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
42364 ATCATGCACTGA
66 ATCATGCACTGA
*
42376 AGGACTTACAGATGACCC-GA-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGACTTTTTGGAAA
1 AGGACTTACAGATGACCCTGAGA-GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
*
42439 CATCATGCACTAA
65 CATCATGCACTGA
*
42452 AGGACTTACAGATGACCCTGAG-GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAAC
1 AGGACTTACAGATGACCCTGAGAGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
42516 ATCATGCACTGA
66 ATCATGCACTGA
*
42528 AGGACTTACAGATGACCCTAAG-GCTTTTG-AAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
1 AGGACTTACAGATGACCCTGAGAGC-TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
42591 CATCATGCACTGA
65 CATCATGCACTGA
*
42604 AGGACTTACAGATGACCCTAAG-GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
1 AGGACTTACAGATGACCCTGAGAGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
42668 ATCATGCACTGA
66 ATCATGCACTGA
42680 AGGACTTACAGATG
1 AGGACTTACAGATG
42694 TGGAAAATAG
Statistics
Matches: 1176, Mismatches: 33, Indels: 36
0.94 0.03 0.03
Matches are distributed among these distances:
74 67 0.06
75 94 0.08
76 1005 0.85
77 10 0.01
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (77 bp):
AGGACTTACAGATGACCCTGAGAGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
ATCATGCACTGA
Found at i:43391 original size:22 final size:22
Alignment explanation
Indices: 43366--43423 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
43356 TTCCATAAAG
43366 CTTTCATCTTTGAAAAGAGAAT
1 CTTTCATCTTTGAAAAGAGAAT
*
43388 CTTTCATCTTTAAAAAGAGAAT
1 CTTTCATCTTTGAAAAGAGAAT
*
43410 CTATCATCTTTGAA
1 CTTTCATCTTTGAA
43424 GAGTGTAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
CTTTCATCTTTGAAAAGAGAAT
Found at i:46359 original size:114 final size:115
Alignment explanation
Indices: 46074--46391 Score: 498
Period size: 115 Copynumber: 2.8 Consensus size: 115
46064 GATCATGCAG
* * * * * * *
46074 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
* * *
46139 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAAA
66 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAAA
46189 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
46254 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATG-G-ACAAA
66 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCA-AAA
* *
46303 TTCATCTTTTAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAATTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
46368 ACACTTCCAGAAGATGCTA-TGAGC
66 ACACTTCCAGAAGATGCTATTGAGC
46392 ACATTCATCT
Statistics
Matches: 190, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
113 6 0.03
114 86 0.45
115 98 0.52
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAAA
Found at i:46460 original size:93 final size:93
Alignment explanation
Indices: 46302--46759 Score: 740
Period size: 93 Copynumber: 4.9 Consensus size: 93
46292 CCATGGACAA
** * * * *
46302 ATTCATCTTTTAAATCCAATGATTGATT-T-TGGAGTTCATACCAAATCAGATCAGATAATTCAA
1 ATTCATCTTCCAAATTCAATGATTGATTCTGTGG-TTTCATACCAAACCAGATCAGATAACTCAA
46365 AGAACACTTCCAGAAGATGCTATGAGCAC
65 AGAACACTTCCAGAAGATGCTATGAGCAC
* * *
46394 ATTCATCTTCCAAATTCATTGATTGATTCTGTGGTTTCATACCAAATCAGATCAGATAATTCAAA
1 ATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAA
46459 GAACACTTCCAGAAGATGCTATGAGCAC
66 GAACACTTCCAGAAGATGCTATGAGCAC
* *
46487 ATTCATCTTCCAAATTCAATGATTAATTTTGTGGTTTCATACCAAACCAGATCAGATAACTCAAA
1 ATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAA
*
46552 GAACACTTCCAAAAGATGCTATGAGCAC
66 GAACACTTCCAGAAGATGCTATGAGCAC
*
46580 ATTCATCTTCCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAA
1 ATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAA
*
46645 GAACACTTCCAAAAGATGCTATGAGCAC
66 GAACACTTCCAGAAGATGCTATGAGCAC
* *
46673 ATTCATCTTCCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATTAGATAACTCAAA
1 ATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAA
*
46738 GAACATTTCCAGAAGATGCTAT
66 GAACACTTCCAGAAGATGCTAT
46760 TGGGTCTTCT
Statistics
Matches: 347, Mismatches: 17, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
92 24 0.07
93 320 0.92
94 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (93 bp):
ATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATGAGCAC
Found at i:48911 original size:2 final size:2
Alignment explanation
Indices: 48904--48991 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
48894 ACAACAAAGG
48904 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
48946 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
48988 AT AT
1 AT AT
48992 TAAAGGATAA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59206 original size:3 final size:3
Alignment explanation
Indices: 59188--59274 Score: 93
Period size: 3 Copynumber: 28.3 Consensus size: 3
59178 TTGTAATATT
* * * * *
59188 TAA TAAA TAA TAAA TAA TAT TAC TAT TAT TAT TAA TAA TAA TAA TAA
1 TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
59235 TAA TAA TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
59275 TTAAAATGAA
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
3 68 0.92
4 6 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:61556 original size:14 final size:14
Alignment explanation
Indices: 61537--61572 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
61527 CTTCGAGTAT
61537 CAGTACCGTTAGAA
1 CAGTACCGTTAGAA
*
61551 CAGTACCATTAGAA
1 CAGTACCGTTAGAA
61565 CAGTACCG
1 CAGTACCG
61573 ATACTTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (14 bp):
CAGTACCGTTAGAA
Found at i:61668 original size:20 final size:20
Alignment explanation
Indices: 61604--61668 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
61594 TGAAGTTATT
61604 AAGGGTAGTATCGATACCTGTTG
1 AAGGGTAGTATCGATACC---TG
* *
61627 AAGAG--GTATCGATA-TTG
1 AAGGGTAGTATCGATACCTG
61644 TAAGGGTAGTATCGATACCTG
1 -AAGGGTAGTATCGATACCTG
61665 AAGG
1 AAGG
61669 ATGGCATTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
17 2 0.06
18 4 0.12
20 13 0.38
21 11 0.32
23 4 0.12
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.28
Consensus pattern (20 bp):
AAGGGTAGTATCGATACCTG
Found at i:62149 original size:21 final size:21
Alignment explanation
Indices: 62132--62184 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
62122 ATATGAATAT
62132 GGAAATGTGAAATTTGAATCA
1 GGAAATGTGAAATTTGAATCA
* *
62153 GTAAATGTGAATTTTGAATCA
1 GGAAATGTGAAATTTGAATCA
62174 GTG-AATGTGAA
1 G-GAAATGTGAA
62185 CAGACCCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.32
Consensus pattern (21 bp):
GGAAATGTGAAATTTGAATCA
Found at i:62372 original size:21 final size:21
Alignment explanation
Indices: 62319--62366 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
62309 TCGAGGGTCT
* *
62319 TATGTGGTCATT-GAGACAAA
1 TATGTGGTCCTTCGGGACAAA
62339 TATGTGGTCCTTCGGGACAAA
1 TATGTGGTCCTTCGGGACAAA
62360 TATGTGG
1 TATGTGG
62367 CACTTCAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.31
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAA
Found at i:62380 original size:21 final size:21
Alignment explanation
Indices: 62335--62429 Score: 65
Period size: 21 Copynumber: 4.5 Consensus size: 21
62325 GTCATTGAGA
*
62335 CAAATATGTGGTCCTTC-GGG
1 CAAATATGTGGTCCTTCAGTG
62355 ACAAATATGTGG-CACTTCAGTG
1 -CAAATATGTGGTC-CTTCAGTG
*
62377 CAAACCTATATGGTCCTTCAG-G
1 CAAA--TATGTGGTCCTTCAGTG
* *
62399 AAAATTATGTGG-CACTTCGGTG
1 CAAA-TATGTGGTC-CTTCAGTG
62421 CAAAT-TGTG
1 CAAATATGTG
62430 AGTTGTGGTG
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
20 6 0.10
21 31 0.52
22 10 0.17
23 12 0.20
24 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (21 bp):
CAAATATGTGGTCCTTCAGTG
Found at i:63724 original size:13 final size:13
Alignment explanation
Indices: 63706--63741 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
63696 TCATAACCCG
63706 ACCCGACCCGTTT
1 ACCCGACCCGTTT
63719 ACCCGACCCGTTT
1 ACCCGACCCGTTT
63732 ACCCGACCCG
1 ACCCGACCCG
63742 ACCTGTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:63755 original size:13 final size:13
Alignment explanation
Indices: 63739--63763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63729 TTTACCCGAC
63739 CCGACCTGTTGAT
1 CCGACCTGTTGAT
63752 CCGACCTGTTGA
1 CCGACCTGTTGA
63764 CCGTTGACCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.24, T:0.28
Consensus pattern (13 bp):
CCGACCTGTTGAT
Found at i:63755 original size:18 final size:18
Alignment explanation
Indices: 63719--63757 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
63709 CGACCCGTTT
*
63719 ACCCGACCCGTTTACCCG
1 ACCCGACCCGTTGACCCG
* *
63737 ACCCGACCTGTTGATCCG
1 ACCCGACCCGTTGACCCG
63755 ACC
1 ACC
63758 TGTTGACCGT
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:0.18, C:0.46, G:0.18, T:0.18
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:65117 original size:18 final size:18
Alignment explanation
Indices: 65091--65131 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
65081 TCGAAATGAC
* *
65091 TGAAGTAAATGATAAGAT
1 TGAATTAAATAATAAGAT
65109 TGAATTAAATAATAAGAT
1 TGAATTAAATAATAAGAT
*
65127 CGAAT
1 TGAAT
65132 GGCAGGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAATTAAATAATAAGAT
Found at i:66307 original size:23 final size:24
Alignment explanation
Indices: 66269--66349 Score: 119
Period size: 24 Copynumber: 3.4 Consensus size: 24
66259 AATTATGTTA
*
66269 TGATACCTGACCTGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
*
66293 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
* *
66316 TGATACATGACCTGGATTCTGATA
1 TGATACTTGACCTGGATTCTGATC
66340 TGATACTTGA
1 TGATACTTGA
66350 TTTGAATTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
23 21 0.42
24 29 0.58
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGATACTTGACCTGGATTCTGATC
Found at i:68495 original size:31 final size:31
Alignment explanation
Indices: 68457--68523 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
68447 ACCGATCATA
* *
68457 ACCCGACCCGA-CTCGTTTACCCGATCCGTTG
1 ACCCGACCCGACCT-GTTGACCCGACCCGTTG
*
68488 ACCCGACCCGACCTGTTGATCCGACCCGTTG
1 ACCCGACCCGACCTGTTGACCCGACCCGTTG
68519 ACCCG
1 ACCCG
68524 TTGACCGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.16, C:0.43, G:0.21, T:0.19
Consensus pattern (31 bp):
ACCCGACCCGACCTGTTGACCCGACCCGTTG
Found at i:68496 original size:18 final size:18
Alignment explanation
Indices: 68475--68515 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
68465 CGACTCGTTT
68475 ACCCGATCC-GTTGACCCG
1 ACCCGA-CCTGTTGACCCG
*
68493 ACCCGACCTGTTGATCCG
1 ACCCGACCTGTTGACCCG
68511 ACCCG
1 ACCCG
68516 TTGACCCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.17, C:0.44, G:0.22, T:0.17
Consensus pattern (18 bp):
ACCCGACCTGTTGACCCG
Found at i:68523 original size:8 final size:8
Alignment explanation
Indices: 68510--68571 Score: 74
Period size: 8 Copynumber: 7.5 Consensus size: 8
68500 CTGTTGATCC
68510 GACCCGTT
1 GACCCGTT
68518 GACCCGTT
1 GACCCGTT
68526 GA-CCGTT
1 GACCCGTT
68533 GACCCGTT
1 GACCCGTT
68541 GA-CCGTT
1 GACCCGTT
68548 GACCGGCGTT
1 GACC--CGTT
68558 GACCACTGTT
1 GACC-C-GTT
68568 GACC
1 GACC
68572 AAAACTTTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
7 14 0.29
8 18 0.38
9 1 0.02
10 15 0.31
ACGTcount: A:0.15, C:0.34, G:0.27, T:0.24
Consensus pattern (8 bp):
GACCCGTT
Found at i:68533 original size:7 final size:7
Alignment explanation
Indices: 68513--68552 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
68503 TTGATCCGAC
68513 CCGTTGA
1 CCGTTGA
68520 CCCGTTGA
1 -CCGTTGA
68528 CCGTTGA
1 CCGTTGA
68535 CCCGTTGA
1 -CCGTTGA
68543 CCGTTGA
1 CCGTTGA
68550 CCG
1 CCG
68553 GCGTTGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.12, C:0.35, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:68533 original size:15 final size:15
Alignment explanation
Indices: 68513--68561 Score: 80
Period size: 15 Copynumber: 3.1 Consensus size: 15
68503 TTGATCCGAC
68513 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
68528 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
68543 CCGTTGACCGGCGTTGA
1 CCGTTGACC--CGTTGA
68560 CC
1 CC
68562 ACTGTTGACC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 24 0.75
17 8 0.25
ACGTcount: A:0.12, C:0.35, G:0.29, T:0.24
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:69889 original size:18 final size:18
Alignment explanation
Indices: 69863--69898 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
69853 TTGAAAGGAC
*
69863 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
69881 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
69899 CGGATGGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:70665 original size:13 final size:13
Alignment explanation
Indices: 70646--70677 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
70636 CTATTTTTTT
70646 CCAAAAAAAAAAG
1 CCAAAAAAAAAAG
*
70659 GCAAAAAAAAAAG
1 CCAAAAAAAAAAG
70672 CCAAAA
1 CCAAAA
70678 TTTCAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.75, C:0.16, G:0.09, T:0.00
Consensus pattern (13 bp):
CCAAAAAAAAAAG
Found at i:73289 original size:9 final size:9
Alignment explanation
Indices: 73275--73301 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
73265 TAATAACTCG
73275 GATATTTCT
1 GATATTTCT
73284 GATATTTCT
1 GATATTTCT
73293 GATATTTCT
1 GATATTTCT
73302 ACCCATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
GATATTTCT
Found at i:79413 original size:11 final size:11
Alignment explanation
Indices: 79397--79459 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
79387 GTATTATAGA
79397 ATTTTTAATAT
1 ATTTTTAATAT
79408 ATTTTTAA-A-
1 ATTTTTAATAT
79417 ATTTTATAAT-T
1 ATTTT-TAATAT
** * *
79428 ATTAATAGTGT
1 ATTTTTAATAT
*
79439 ATTTTTAATTT
1 ATTTTTAATAT
79450 ATTTTTAATA
1 ATTTTTAATA
79460 ATGTATTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
9 5 0.12
10 7 0.17
11 28 0.70
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:79461 original size:14 final size:14
Alignment explanation
Indices: 79429--79471 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
79419 TTTATAATTA
*
79429 TTAATAGTGTATTT
1 TTAATAATGTATTT
79443 TTAAT--T-TATTT
1 TTAATAATGTATTT
79454 TTAATAATGTATTT
1 TTAATAATGTATTT
79468 TTAA
1 TTAA
79472 AAAATCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 10 0.38
12 1 0.04
13 1 0.04
14 14 0.54
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (14 bp):
TTAATAATGTATTT
Found at i:82057 original size:46 final size:46
Alignment explanation
Indices: 82004--82096 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
81994 ACAAAGAGAA
*
82004 TGATTAAATAACTCAGAGAAAGTTGTGTCAATAAT-ATTTTCACAAC
1 TGATTAAATAACTCAGAGAAAGTTGTGCCAATAATAATTTT-ACAAC
82050 TGATTAAATAACTCAGAGAAAGTTGTGCCAATAATAATTTTACAAC
1 TGATTAAATAACTCAGAGAAAGTTGTGCCAATAATAATTTTACAAC
82096 T
1 T
82097 CAAAGAATGG
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 40 0.89
47 5 0.11
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (46 bp):
TGATTAAATAACTCAGAGAAAGTTGTGCCAATAATAATTTTACAAC
Found at i:84496 original size:2 final size:2
Alignment explanation
Indices: 84485--84539 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
84475 AATAATTTTG
84485 AT AT -T 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
84526 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
84540 TATTTTTCTA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:87265 original size:18 final size:18
Alignment explanation
Indices: 87242--87277 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
87232 AAGTGGTTGG
87242 TGGATACTAGGAAAGTGA
1 TGGATACTAGGAAAGTGA
87260 TGGATACTAGGAAAGTGA
1 TGGATACTAGGAAAGTGA
87278 ACACTTATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.22
Consensus pattern (18 bp):
TGGATACTAGGAAAGTGA
Found at i:88281 original size:24 final size:24
Alignment explanation
Indices: 88236--88281 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
88226 TTTAGTCCAT
*
88236 TTTTATATTAATATCAGCTTCACA
1 TTTTATATTAATATCAACTTCACA
*
88260 TTTTATAATTAAT-TCAATTTCA
1 TTTTAT-ATTAATATCAACTTCA
88282 TCCCTCATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTATATTAATATCAACTTCACA
Found at i:88397 original size:30 final size:30
Alignment explanation
Indices: 88356--88413 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
88346 TTTGGTACTT
*
88356 TATATACATATATAAACTATAAATTATAAG
1 TATATACATATATAAACTATAAAATATAAG
* * *
88386 TATATATATATATATAGTATAAAATATA
1 TATATACATATATAAACTATAAAATATA
88414 TAATATAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (30 bp):
TATATACATATATAAACTATAAAATATAAG
Found at i:88416 original size:32 final size:29
Alignment explanation
Indices: 88356--88420 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
88346 TTTGGTACTT
88356 TATATACATATATAAACTATAAATTATAA
1 TATATACATATATAAACTATAAATTATAA
* * *
88385 GTATATATATATATATAGTATAAAATATATAA
1 -TATATACATATATAAACTAT-AAAT-TATAA
88417 TATA
1 TATA
88421 AAGTATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 17 0.57
31 8 0.27
32 5 0.17
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (29 bp):
TATATACATATATAAACTATAAATTATAA
Found at i:88432 original size:8 final size:7
Alignment explanation
Indices: 88366--88507 Score: 55
Period size: 8 Copynumber: 19.6 Consensus size: 7
88356 TATATACATA
*
88366 TATAAAC
1 TATAAAG
*
88373 TATAAAT
1 TATAAAG
88380 TAT-AAG
1 TATAAAG
88386 TATATATA-
1 TATA-A-AG
88394 TATATATAG
1 TATA-A-AG
*
88403 TATAAAA
1 TATAAAG
88410 TATATAA-
1 TATA-AAG
88417 TATAAAG
1 TATAAAG
88424 TATTAAAG
1 TA-TAAAG
88432 TATATAA-
1 TATA-AAG
88439 TATAAAG
1 TATAAAG
88446 TAATAAAG
1 T-ATAAAG
* **
88454 TGT-TTG
1 TATAAAG
*
88460 GATATAAG
1 TATA-AAG
88468 TATTAAAG
1 TA-TAAAG
*
88476 TATATAAA
1 TATA-AAG
88484 TAT-AAG
1 TATAAAG
88490 TATTAAA-
1 TA-TAAAG
88497 TATAAAG
1 TATAAAG
88504 TATA
1 TATA
88508 TTAATTATCA
Statistics
Matches: 105, Mismatches: 13, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
6 19 0.18
7 37 0.35
8 42 0.40
9 7 0.07
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (7 bp):
TATAAAG
Found at i:88498 original size:13 final size:15
Alignment explanation
Indices: 88373--88508 Score: 83
Period size: 14 Copynumber: 9.2 Consensus size: 15
88363 ATATATAAAC
88373 TATAAAT-TATAAGTA
1 TATAAATATA-AAGTA
*
88388 TATATATATATATAGTA
1 TATA-A-ATATAAAGTA
88405 TA-AAATATATAA-TA
1 TATAAATATA-AAGTA
*
88419 TA-AAGTATTAAAGTA
1 TATAAATA-TAAAGTA
88434 TAT-AATATAAAGTA
1 TATAAATATAAAGTA
* ** *
88448 -ATAAAGTGT-TTGGA
1 TATAAA-TATAAAGTA
*
88462 TATAAGTATTAAAGTA
1 TATAAATA-TAAAGTA
88478 TATAAATAT-AAGTA
1 TATAAATATAAAGTA
88492 T-TAAATATAAAGTA
1 TATAAATATAAAGTA
88506 TAT
1 TAT
88509 TAATTATCAT
Statistics
Matches: 93, Mismatches: 14, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
13 9 0.10
14 39 0.42
15 24 0.26
16 11 0.12
17 8 0.09
18 2 0.02
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (15 bp):
TATAAATATAAAGTA
Found at i:88508 original size:22 final size:23
Alignment explanation
Indices: 88378--88508 Score: 123
Period size: 22 Copynumber: 5.8 Consensus size: 23
88368 TAAACTATAA
88378 ATTATAAGTATATATATATATATAGT
1 ATTA-AAGTATATA-ATATATA-AGT
*
88404 A-TAAAATATATAATATA-AAGT
1 ATTAAAGTATATAATATATAAGT
88425 ATTAAAGTATATAATATA-AAGT
1 ATTAAAGTATATAATATATAAGT
* * ***
88447 AATAAAGTGT-TTGGATATAAGT
1 ATTAAAGTATATAATATATAAGT
88469 ATTAAAGTATATAA-ATATAAGT
1 ATTAAAGTATATAATATATAAGT
88491 ATTAAA-TATA-AAGTATAT
1 ATTAAAGTATATAA-TATAT
88509 TAATTATCAT
Statistics
Matches: 89, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
20 2 0.02
21 12 0.13
22 58 0.65
23 6 0.07
24 8 0.09
25 2 0.02
26 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (23 bp):
ATTAAAGTATATAATATATAAGT
Found at i:88524 original size:28 final size:28
Alignment explanation
Indices: 88471--88528 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
88461 ATATAAGTAT
*
88471 TAAAGTATATAAATATAAGTATTAAATA
1 TAAAGTATATAAATATAAGTAATAAATA
* *
88499 TAAAGTATATTAATTATCA-TAATAAATA
1 TAAAGTATA-TAAATATAAGTAATAAATA
88527 TA
1 TA
88529 TTTTTATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (28 bp):
TAAAGTATATAAATATAAGTAATAAATA
Found at i:88850 original size:11 final size:11
Alignment explanation
Indices: 88836--88876 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
88826 TCAATTCGGG
*
88836 CTCAAGTCATT
1 CTCAGGTCATT
*
88847 CTCAGGTCCTT
1 CTCAGGTCATT
88858 CTCAGGTCATT
1 CTCAGGTCATT
88869 CTCAGGTC
1 CTCAGGTC
88877 GGGTGTAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.34
Consensus pattern (11 bp):
CTCAGGTCATT
Found at i:91963 original size:18 final size:18
Alignment explanation
Indices: 91937--91971 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
91927 TCGAAAGGAC
*
91937 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
91955 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
91972 CCGGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:93131 original size:24 final size:24
Alignment explanation
Indices: 93104--93219 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
93094 TTCGATTTGA
93104 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
93128 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
93152 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* * *
93176 ATTCTGATCTGTTACTTAACCT-G
1 ATTCTGATCTGATACTTGACATGG
* *
93199 ATTTCTTATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
93220 CTGATTTCGC
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:98386 original size:18 final size:18
Alignment explanation
Indices: 98336--98379 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
98326 TACCAACTTT
* * *
98336 AATATCATATAAATTTAA
1 AATATAATAAAAATATAA
*
98354 ACTATAATAAAAATATAA
1 AATATAATAAAAATATAA
98372 AATATAAT
1 AATATAAT
98380 TATAATAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
AATATAATAAAAATATAA
Found at i:103316 original size:6 final size:6
Alignment explanation
Indices: 103305--103396 Score: 125
Period size: 6 Copynumber: 15.5 Consensus size: 6
103295 GACACGTATT
103305 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCAACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-ACG ACCACG
* * * *
103354 ACCACG ACCCCG ACCCCG ACCACA ACCCCG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
103397 CGAGACGAGA
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
5 10 0.12
6 64 0.80
7 6 0.08
ACGTcount: A:0.30, C:0.54, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:103908 original size:6 final size:6
Alignment explanation
Indices: 103897--103921 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
103887 TCGTCTCGTC
103897 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
103922 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:104112 original size:21 final size:21
Alignment explanation
Indices: 104019--104112 Score: 77
Period size: 21 Copynumber: 4.5 Consensus size: 21
104009 TTTTGGACTA
*
104019 TCGCAATGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* * *
104040 TCGCATTACGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
104060 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
*
104081 TCACATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
104102 TCGCGTTGCGA
1 TCGCATTGCGA
104113 ATCTGGAAAC
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
20 16 0.29
21 39 0.70
22 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:105258 original size:2 final size:2
Alignment explanation
Indices: 105251--105288 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
105241 GTCATATACA
105251 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
105289 TTTATATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:105397 original size:25 final size:25
Alignment explanation
Indices: 105364--105421 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
105354 ATGTCATTAT
* *
105364 CCACGTCACCTGTCACTGTGGACTG
1 CCACATCACATGTCACTGTGGACTG
105389 CCACATCACATGTCACTGTGGACTG
1 CCACATCACATGTCACTGTGGACTG
*
105414 TCACATCA
1 CCACATCA
105422 TCACTATAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.24
Consensus pattern (25 bp):
CCACATCACATGTCACTGTGGACTG
Found at i:106024 original size:14 final size:14
Alignment explanation
Indices: 105957--106040 Score: 60
Period size: 14 Copynumber: 5.6 Consensus size: 14
105947 TTTATGTCCG
* *
105957 TTTATGTTTGTTCA
1 TTTATGTTCGTTTA
105971 TTTATGTTCGTTTA
1 TTTATGTTCGTTTA
*
105985 TTTATGTCCGTGTATA
1 TTTATGTTCGT-T-TA
106001 TTCGTTTATGTTCGTTTA
1 ----TTTATGTTCGTTTA
** *
106019 TTTATGTTAATTCA
1 TTTATGTTCGTTTA
106033 TTTATGTT
1 TTTATGTT
106041 TTTGTAAGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
14 41 0.72
15 1 0.02
16 2 0.04
18 2 0.04
19 1 0.02
20 10 0.18
ACGTcount: A:0.17, C:0.08, G:0.14, T:0.61
Consensus pattern (14 bp):
TTTATGTTCGTTTA
Found at i:106138 original size:16 final size:18
Alignment explanation
Indices: 106113--106149 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
106103 AATCATTAAT
106113 ATTTTAAAACCCAAAT-A
1 ATTTTAAAACCCAAATCA
*
106130 ATTTT-AAACTCAAATCA
1 ATTTTAAAACCCAAATCA
106147 ATT
1 ATT
106150 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:106272 original size:28 final size:28
Alignment explanation
Indices: 106198--106257 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
106188 ATTTTAACTC
* *
106198 TGAAATTGTAAGTTGTATTAATGAATAA
1 TGAAGTTGTAAGTTATATTAATGAATAA
106226 TGAAGTTGTAAGTTATATTAATGAATAA
1 TGAAGTTGTAAGTTATATTAATGAATAA
106254 TGAA
1 TGAA
106258 TTTTATGTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.38
Consensus pattern (28 bp):
TGAAGTTGTAAGTTATATTAATGAATAA
Found at i:106407 original size:23 final size:23
Alignment explanation
Indices: 106342--106420 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
106332 CTCTTTTATA
* * *
106342 TTCATTTATTGTGTTCATTTGCA
1 TTCATTTATTGTATTCATTTACG
*
106365 TTCATTCGT-TTATATTCATTTACG
1 TTCATT--TATTGTATTCATTTACG
*
106389 TTCATTTATTGTATTCATTTATG
1 TTCATTTATTGTATTCATTTACG
*
106412 TTCGTTTAT
1 TTCATTTAT
106421 GTTTGTTTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
22 1 0.02
23 27 0.59
24 17 0.37
25 1 0.02
ACGTcount: A:0.19, C:0.13, G:0.10, T:0.58
Consensus pattern (23 bp):
TTCATTTATTGTATTCATTTACG
Found at i:111386 original size:19 final size:19
Alignment explanation
Indices: 111358--111394 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
111348 TCATATTTAT
* *
111358 ATATATAAATTATAATATA
1 ATATAAAAATAATAATATA
111377 ATATAAAAATAATAATAT
1 ATATAAAAATAATAATAT
111395 TATAATTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATAAAAATAATAATATA
Found at i:111388 original size:16 final size:18
Alignment explanation
Indices: 111355--111398 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
111345 GCATCATATT
*
111355 TATATATATAAATTATAA
1 TATATATATAAATAATAA
*
111373 TATAATATAAAAATAATAA
1 TAT-ATATATAAATAATAA
111392 TAT-TATA
1 TATATATA
111399 ATTTTGAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 3 0.13
19 16 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATATATATAAATAATAA
Found at i:111951 original size:5 final size:6
Alignment explanation
Indices: 111924--111950 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
111914 AAATTTAAAA
111924 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
111951 AAATTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:121485 original size:43 final size:43
Alignment explanation
Indices: 121430--121782 Score: 555
Period size: 43 Copynumber: 8.2 Consensus size: 43
121420 TGTGAACAAA
* *
121430 AAACGCCACAATAGGTCGAGATCTATAGCGGCGTTTTTAGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
121473 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
121516 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
* *
121559 AAACGCCTCAATAGGTCGAGATCTATAGCGCCGTTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
*
121602 AAACGCCTCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
* *
121645 AAACGCCGCAATAGGTCGAGATCTATAGCGACGTTTTTGGAAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
* * *
121688 AAACGCCGCAATATGTCGAGATTTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
* * * **
121731 AAACGCCACAAAAGGT-TAGATCTATAGCGGCGTTTTTTGATAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCG-TTTTTGGGAC
121774 AAACGCCGC
1 AAACGCCGC
121783 TAATGACCGT
Statistics
Matches: 290, Mismatches: 19, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
42 14 0.05
43 276 0.95
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
Found at i:122500 original size:42 final size:42
Alignment explanation
Indices: 122452--122740 Score: 276
Period size: 42 Copynumber: 7.0 Consensus size: 42
122442 CTAGAGTTCG
*
122452 TGTAATTAGCGGCGTTTGTGTATAAAACGCCACTAAAGAACA
1 TGTAATTAGCGGCGTTTGTGTATAAAACGCCACTAAAGTACA
*
122494 TGTAATTAGCGGCGTTTTTGCT-TAAAACGCCACTAAAGTACGA
1 TGTAATTAGCGGCGTTTGTG-TATAAAACGCCACTAAAGTAC-A
**
122537 CCT--TTAGCGGCG-TT-TGTATAAAATCGCCACTAAAGTACA
1 TGTAATTAGCGGCGTTTGTGTATAAAA-CGCCACTAAAGTACA
* * * * * * * * *
122576 -GTATTTATCAGCATTTATATA-AAAACGCCACTATAGTGCG
1 TGTAATTAGCGGCGTTTGTGTATAAAACGCCACTAAAGTACA
** *
122616 TGTAATTAGCGGCGTTTGTGCGTAAAACGCCACTAAAGAACA
1 TGTAATTAGCGGCGTTTGTGTATAAAACGCCACTAAAGTACA
122658 TGTAATTAGCGGCGTTTGTGCT-TAAAACGCCACTAAAGTACGA
1 TGTAATTAGCGGCGTTTGTG-TATAAAACGCCACTAAAGTAC-A
** * *
122701 CCT--TTAGCGGCGTTTGTATA-AAAATGCCACTAAAGTACA
1 TGTAATTAGCGGCGTTTGTGTATAAAACGCCACTAAAGTACA
122740 T
1 T
122741 TATTTTCCGG
Statistics
Matches: 203, Mismatches: 31, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
38 2 0.01
39 9 0.04
40 52 0.26
41 42 0.21
42 93 0.46
43 5 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (42 bp):
TGTAATTAGCGGCGTTTGTGTATAAAACGCCACTAAAGTACA
Found at i:122623 original size:122 final size:122
Alignment explanation
Indices: 122475--122698 Score: 308
Period size: 122 Copynumber: 1.8 Consensus size: 122
122465 GTTTGTGTAT
* * *
122475 AAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTTTGCTTAAAACGCCACTAAAGTACGACCT
1 AAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTGTGCGTAAAACGCCACTAAAGAAC-ACCT
122540 -TTAGCGGCGTTTGT-ATAAAATCGCCACTAAAGTACAGTATTTATCAGCATTTATATA
65 ATTAGCGGCGTTTGTCATAAAA-CGCCACTAAAGTACAGTATTTATCAGCATTTATATA
* ** * **
122597 AAAACGCCACTATAGTGCGTGTAATTAGCGGCGTTTGTGCGTAAAACGCCACTAAAGAACATGTA
1 AAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTGTGCGTAAAACGCCACTAAAGAACACCT-
*
122662 ATTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTAC
65 ATTAGCGGCGTTTGT-CATAAAACGCCACTAAAGTAC
122699 GACCTTTAGC
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
121 2 0.02
122 53 0.60
123 14 0.16
124 14 0.16
125 5 0.06
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (122 bp):
AAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTGTGCGTAAAACGCCACTAAAGAACACCTA
TTAGCGGCGTTTGTCATAAAACGCCACTAAAGTACAGTATTTATCAGCATTTATATA
Found at i:122670 original size:164 final size:164
Alignment explanation
Indices: 122399--122745 Score: 579
Period size: 164 Copynumber: 2.1 Consensus size: 164
122389 GAGTATTTAT
* * * * *
122399 CCACTAAAGTATAGTATTTCTCGGCATTTATATAAAAATGCAACTAGAGTTCGTGTAATTAGCGG
1 CCACTAAAGTACAGTATTTATCAGCATTTATATAAAAACGCAACTAGAGTGCGTGTAATTAGCGG
* *
122464 CGTTTGTGTATAAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTTTGCTTAAAACGCCACTA
66 CGTTTGTGCATAAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTGTGCTTAAAACGCCACTA
122529 AAGTACGACCTTTAGCGGCGTTTGTAT-AAAATCG
131 AAGTACGACCTTTAGCGGCGTTTGTATAAAAAT-G
* *
122563 CCACTAAAGTACAGTATTTATCAGCATTTATATAAAAACGCCACTATAGTGCGTGTAATTAGCGG
1 CCACTAAAGTACAGTATTTATCAGCATTTATATAAAAACGCAACTAGAGTGCGTGTAATTAGCGG
*
122628 CGTTTGTGCGTAAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTGTGCTTAAAACGCCACTA
66 CGTTTGTGCATAAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTGTGCTTAAAACGCCACTA
122693 AAGTACGACCTTTAGCGGCGTTTGTATAAAAATG
131 AAGTACGACCTTTAGCGGCGTTTGTATAAAAATG
*
122727 CCACTAAAGTACATTATTT
1 CCACTAAAGTACAGTATTT
122746 TCCGGCGTTT
Statistics
Matches: 171, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
164 166 0.97
165 5 0.03
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (164 bp):
CCACTAAAGTACAGTATTTATCAGCATTTATATAAAAACGCAACTAGAGTGCGTGTAATTAGCGG
CGTTTGTGCATAAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTGTGCTTAAAACGCCACTA
AAGTACGACCTTTAGCGGCGTTTGTATAAAAATG
Found at i:128911 original size:32 final size:31
Alignment explanation
Indices: 128858--128919 Score: 97
Period size: 32 Copynumber: 2.0 Consensus size: 31
128848 AACACGTGAA
*
128858 AATTTCATTTTTATTTCAATTTTATAAATTC
1 AATTTCACTTTTATTTCAATTTTATAAATTC
*
128889 AATTGTCACTTTTATTTTAATTTTATAAATT
1 AATT-TCACTTTTATTTCAATTTTATAAATT
128920 TGTATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (31 bp):
AATTTCACTTTTATTTCAATTTTATAAATTC
Found at i:130701 original size:65 final size:64
Alignment explanation
Indices: 130628--130749 Score: 158
Period size: 64 Copynumber: 1.9 Consensus size: 64
130618 GAACTGGTGT
* * * *
130628 TGACTTGAACCTGATTTGGACCTGGAAAT-TG-TGGATCCGAACCCGACCTGCATCCGACCTGAG
1 TGACTTGAACCTGAATTGAACC-GAAAATATGAT--ATCCGAACCCGAACTGCATCCGACCTGAG
130691 AA
63 AA
*
130693 TGACTTGAATCTGAATTGAACCGAAAATATGATATCCGAACCCGAACTGCATCCGAC
1 TGACTTGAACCTGAATTGAACCGAAAATATGATATCCGAACCCGAACTGCATCCGAC
130750 TGATATGAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
64 28 0.56
65 21 0.42
66 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (64 bp):
TGACTTGAACCTGAATTGAACCGAAAATATGATATCCGAACCCGAACTGCATCCGACCTGAGAA
Found at i:130867 original size:16 final size:16
Alignment explanation
Indices: 130800--130870 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
130790 TGTATTACCC
130800 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
130816 GACATGTTTTCAACCT
1 GACCTGTTTTCAACCT
* * *
130832 GACTTGTTTTTAACAT
1 GACCTGTTTTCAACCT
*
130848 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
130864 GACCTGT
1 GACCTGT
130871 AAATGATCCG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:131150 original size:23 final size:24
Alignment explanation
Indices: 131116--131165 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
131106 ATGCAAAGGA
131116 AAATTAATATAGTCTAATTTATAT
1 AAATTAATATAGTCTAATTTATAT
*
131140 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTCTAATTTATAT
131163 AAA
1 AAA
131166 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
AAATTAATATAGTCTAATTTATAT
Found at i:131264 original size:22 final size:24
Alignment explanation
Indices: 131225--131279 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
131215 GGTTTACATT
*
131225 AATAATATAATAATTTTGGCAATA
1 AATAATATAATAATTTTGACAATA
* *
131249 AATAATA-ATTAA-TTTGATAATA
1 AATAATATAATAATTTTGACAATA
131271 AATGAATAT
1 AAT-AATAT
131280 TAGTATAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 11 0.42
23 8 0.31
24 7 0.27
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (24 bp):
AATAATATAATAATTTTGACAATA
Found at i:131643 original size:39 final size:40
Alignment explanation
Indices: 131612--131690 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
131602 AAATTTGGCG
131612 CCAACTT-CC-CAAAATTTTCT-A-TTCCCTCTAAATTTC
1 CCAACTTCCCTCAAAATTTTCTAATTTCCCTCTAAATTTC
* *
131648 CCAATTTCCCTCTAAATTTTCTAATTTCCCTCTAAA-TTC
1 CCAACTTCCCTCAAAATTTTCTAATTTCCCTCTAAATTTC
131687 CCAA
1 CCAA
131691 ATAAAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
36 6 0.16
37 2 0.05
38 10 0.27
39 8 0.22
40 11 0.30
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.39
Consensus pattern (40 bp):
CCAACTTCCCTCAAAATTTTCTAATTTCCCTCTAAATTTC
Found at i:131658 original size:20 final size:20
Alignment explanation
Indices: 131633--131690 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
131623 AAATTTTCTA
131633 TTCCCTCTAAATTTCCCAAT
1 TTCCCTCTAAATTTCCCAAT
* *
131653 TTCCCTCTAAATTTTCTAAT
1 TTCCCTCTAAATTTCCCAAT
131673 TTCCCTCTAAA-TTCCCAA
1 TTCCCTCTAAATTTCCCAA
131691 ATAAAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 5 0.15
20 29 0.85
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (20 bp):
TTCCCTCTAAATTTCCCAAT
Found at i:131665 original size:12 final size:12
Alignment explanation
Indices: 131633--131685 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
131623 AAATTTTCTA
131633 TTCCCTCTAAAT
1 TTCCCTCTAAAT
131645 TT-CC-C--AAT
1 TTCCCTCTAAAT
131653 TTCCCTCTAAAT
1 TTCCCTCTAAAT
131665 TT---TCT-AAT
1 TTCCCTCTAAAT
131673 TTCCCTCTAAAT
1 TTCCCTCTAAAT
131685 T
1 T
131686 CCCAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 16
0.67 0.00 0.33
Matches are distributed among these distances:
8 10 0.30
9 5 0.15
10 2 0.06
11 5 0.15
12 11 0.33
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (12 bp):
TTCCCTCTAAAT
Found at i:131687 original size:11 final size:11
Alignment explanation
Indices: 131632--131688 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
131622 AAAATTTTCT
131632 ATTCCCTCTAA
1 ATTCCCTCTAA
*
131643 ATTTCC-C-AA
1 ATTCCCTCTAA
*
131652 TTTCCCTCTAA
1 ATTCCCTCTAA
*
131663 ATT--TTCTAA
1 ATTCCCTCTAA
*
131672 TTTCCCTCTAA
1 ATTCCCTCTAA
131683 ATTCCC
1 ATTCCC
131689 AAATAAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
9 13 0.38
10 2 0.06
11 19 0.56
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTCCCTCTAA
Found at i:131765 original size:2 final size:2
Alignment explanation
Indices: 131758--131806 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
131748 ACTTTGAATA
131758 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
131800 AT AT AT A
1 AT AT AT A
131807 ATTAAACATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:132257 original size:2 final size:2
Alignment explanation
Indices: 132250--132284 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
132240 TATGTTTAAT
132250 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 T
132285 TATTCAAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:132418 original size:19 final size:20
Alignment explanation
Indices: 132396--132437 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
132386 AGAATATAGA
*
132396 GAAATTG-GGAATTTAGAGG
1 GAAATTGAGAAATTTAGAGG
132415 GAAATTGAGAAATTTAGAGG
1 GAAATTGAGAAATTTAGAGG
132435 GAA
1 GAA
132438 TAGAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.24
Consensus pattern (20 bp):
GAAATTGAGAAATTTAGAGG
Found at i:132441 original size:46 final size:46
Alignment explanation
Indices: 132352--132453 Score: 120
Period size: 46 Copynumber: 2.2 Consensus size: 46
132342 TTTTGATTTT
*
132352 AATTGGGAATTTAGAGGAAAATTAGGAAAATTTGAGAATATAGAGA
1 AATTGGGAATTTAGAGGAAAATTAGGAAAATTTGAGAATATAGAAA
* *
132398 AATTGGGAATTTAGAGGGAAATT--GAGAAATTTAGAGGGA-ATAGAAA
1 AATTGGGAATTTAGAGGAAAATTAGGA-AAATTT-GA-GAATATAGAAA
132444 AATTTGGGAA
1 AA-TTGGGAA
132454 GTTGGCGCCA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
44 2 0.04
45 6 0.12
46 32 0.65
47 9 0.18
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.25
Consensus pattern (46 bp):
AATTGGGAATTTAGAGGAAAATTAGGAAAATTTGAGAATATAGAAA
Found at i:132448 original size:19 final size:20
Alignment explanation
Indices: 132405--132448 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
132395 AGAAATTGGG
* *
132405 AATTTAGAGGGAAATTGAGA
1 AATTTAGAGGGAAATAGAAA
132425 AATTTAGAGGG-AATAGAAA
1 AATTTAGAGGGAAATAGAAA
132444 AATTT
1 AATTT
132449 GGGAAGTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (20 bp):
AATTTAGAGGGAAATAGAAA
Found at i:132677 original size:7 final size:7
Alignment explanation
Indices: 132666--132777 Score: 68
Period size: 7 Copynumber: 16.0 Consensus size: 7
132656 TATAGTTTAT
132666 ATAAACC
1 ATAAACC
*
132673 TTAAACC
1 ATAAACC
* *
132680 CTAAATC
1 ATAAACC
132687 ATAAACC
1 ATAAACC
*
132694 TTAAATCC
1 ATAAA-CC
*
132702 -TAAACT
1 ATAAACC
*
132708 TTAAACC
1 ATAAACC
* **
132715 CTAAATA
1 ATAAACC
*
132722 ATAAACT
1 ATAAACC
132729 ATAAACC
1 ATAAACC
*
132736 CTAAACC
1 ATAAACC
*
132743 CTAAA-C
1 ATAAACC
132749 ACTAAATCC
1 A-TAAA-CC
132758 -TAAACC
1 ATAAACC
132764 ATAAACC
1 ATAAACC
132771 ATAAACC
1 ATAAACC
132778 CTAATGTATG
Statistics
Matches: 82, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
6 4 0.05
7 75 0.91
8 2 0.02
9 1 0.01
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (7 bp):
ATAAACC
Found at i:132691 original size:14 final size:14
Alignment explanation
Indices: 132667--132781 Score: 86
Period size: 14 Copynumber: 8.2 Consensus size: 14
132657 ATAGTTTATA
*
132667 TAAACCTTAAACCC
1 TAAACCCTAAACCC
* * *
132681 TAAATCATAAACCT
1 TAAACCCTAAACCC
* **
132695 TAAATCCTAAACTT
1 TAAACCCTAAACCC
***
132709 TAAACCCTAAATAA
1 TAAACCCTAAACCC
**
132723 TAAACTATAAACCC
1 TAAACCCTAAACCC
*
132737 TAAACCCTAAACAC
1 TAAACCCTAAACCC
* *
132751 TAAATCCTAAACCA
1 TAAACCCTAAACCC
*
132765 TAAACCATAAACCC
1 TAAACCCTAAACCC
132779 TAA
1 TAA
132782 TGTATGTATA
Statistics
Matches: 78, Mismatches: 23, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 78 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAACCC
Found at i:132692 original size:21 final size:20
Alignment explanation
Indices: 132666--132781 Score: 106
Period size: 21 Copynumber: 5.5 Consensus size: 20
132656 TATAGTTTAT
*
132666 ATAAACCTTAAACCCTAAATC
1 ATAAACCCTAAACCCTAAA-C
* *
132687 ATAAACCTTAAATCCTAAAC
1 ATAAACCCTAAACCCTAAAC
* ***
132707 TTTAAACCCTAAATAATAAAC
1 -ATAAACCCTAAACCCTAAAC
132728 TATAAACCCTAAACCCTAAAC
1 -ATAAACCCTAAACCCTAAAC
* *
132749 ACTAAATCCTAAACCATAAACC
1 A-TAAACCCTAAACCCTAAA-C
132771 ATAAACCCTAA
1 ATAAACCCTAA
132782 TGTATGTATA
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.03
21 76 0.95
22 2 0.03
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (20 bp):
ATAAACCCTAAACCCTAAAC
Found at i:132778 original size:35 final size:35
Alignment explanation
Indices: 132666--132781 Score: 135
Period size: 35 Copynumber: 3.3 Consensus size: 35
132656 TATAGTTTAT
* *
132666 ATAAACCTTAAACCCTAAATCATAAACCTTAAATCC
1 ATAAACCCTAAACCCTAAATCATAAACCATAAA-CC
** * *
132702 -TAAACTTTAAACCCTAAATAATAAACTATAAACC
1 ATAAACCCTAAACCCTAAATCATAAACCATAAACC
* * *
132736 CTAAACCCTAAACACTAAATCCTAAACCATAAACC
1 ATAAACCCTAAACCCTAAATCATAAACCATAAACC
132771 ATAAACCCTAA
1 ATAAACCCTAA
132782 TGTATGTATA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 2 0.03
35 66 0.97
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (35 bp):
ATAAACCCTAAACCCTAAATCATAAACCATAAACC
Found at i:132811 original size:2 final size:2
Alignment explanation
Indices: 132799--132882 Score: 141
Period size: 2 Copynumber: 41.0 Consensus size: 2
132789 ATAAACTATG
*
132799 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
132843 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
132883 AACTATAAAG
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
2 75 0.96
3 3 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:132811 original size:20 final size:18
Alignment explanation
Indices: 132788--132882 Score: 127
Period size: 18 Copynumber: 5.1 Consensus size: 18
132778 CTAATGTATG
*
132788 TATAAACTATGTATAGTATA
1 TATAAA-TATATATA-TATA
132808 TATAAACTATATATATATA
1 TATAAA-TATATATATATA
*
132827 TATATATATATATATATA
1 TATAAATATATATATATA
*
132845 TATATATATATATATATA
1 TATAAATATATATATATA
*
132863 TATATATATATATATATA
1 TATAAATATATATATATA
132881 TA
1 TA
132883 AACTATAAAG
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
18 50 0.68
19 9 0.12
20 14 0.19
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
TATAAATATATATATATA
Found at i:133052 original size:18 final size:18
Alignment explanation
Indices: 133029--133128 Score: 62
Period size: 18 Copynumber: 5.4 Consensus size: 18
133019 AACATATAAC
133029 TATATATTTTATAGTTTA
1 TATATATTTTATAGTTTA
* *
133047 TATATA-TATATACTTATA
1 TATATATTTTATAGTT-TA
**
133065 TAAATAATATTTTATAAATTA
1 T--AT-ATATTTTATAGTTTA
133086 TATACT-TTTTATAGTTTA
1 TATA-TATTTTATAGTTTA
* *
133104 TACACT-TTTAATAGTTTA
1 TATA-TATTTTATAGTTTA
*
133122 TACATAT
1 TATATAT
133129 ATAGTTTTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
17 8 0.12
18 41 0.62
19 3 0.05
20 2 0.03
21 6 0.09
22 6 0.09
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (18 bp):
TATATATTTTATAGTTTA
Found at i:133063 original size:16 final size:16
Alignment explanation
Indices: 133044--133092 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
133034 ATTTTATAGT
*
133044 TTATATATATATATAC
1 TTATATAAATATATAC
133060 TTATATAAATA-ATA-
1 TTATATAAATATATAC
*
133074 TTTTATAAATTATATAC
1 TTATATAAA-TATATAC
133091 TT
1 TT
133093 TTTATAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 8 0.29
15 5 0.18
16 13 0.46
17 2 0.07
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATATAAATATATAC
Found at i:133139 original size:16 final size:15
Alignment explanation
Indices: 133095--133143 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 15
133085 ATATACTTTT
*
133095 TATAGTTTATACACTTT
1 TATAGTTTATACA--TA
133112 TAATAGTTTATACATA
1 T-ATAGTTTATACATA
133128 TATAGTTTTATACATA
1 TATAG-TTTATACATA
133144 GTTTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.14
16 12 0.41
17 1 0.03
18 12 0.41
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (15 bp):
TATAGTTTATACATA
Found at i:133187 original size:23 final size:22
Alignment explanation
Indices: 133125--133187 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 22
133115 TAGTTTATAC
* *
133125 ATATATAGTTTTATACATAGTTT
1 ATATATAGTTATA-ACATAATTT
133148 ATATATAGTTCACATAACATAATTT
1 ATATATAGTT---ATAACATAATTT
133173 ATATATAGCTTATAA
1 ATATATAG-TTATAA
133188 TTATATAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 14 0.41
25 16 0.47
26 4 0.12
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.44
Consensus pattern (22 bp):
ATATATAGTTATAACATAATTT
Found at i:133193 original size:17 final size:16
Alignment explanation
Indices: 133172--133332 Score: 91
Period size: 18 Copynumber: 9.5 Consensus size: 16
133162 TAACATAATT
*
133172 TATATATAGCTTATAA
1 TATATATAGTTTATAA
133188 T-TATATAGTTTATAA
1 TATATATAGTTTATAA
133203 TATAATATAGTTTATAA
1 TAT-ATATAGTTTATAA
133220 TTTTATATACATAGTTTATATA
1 ---TATAT--ATAGTTTATA-A
* **
133242 TATTCACATA-AATATAA
1 TA-T-ATATAGTTTATAA
*
133259 TTTATATATAATTTATAA
1 --TATATATAGTTTATAA
133277 TAATTATATAGTTTATAA
1 T-A-TATATAGTTTATAA
133295 TATACATATAGTTTAT-A
1 TAT--ATATAGTTTATAA
*
133312 TATA-AT--TTTATAT
1 TATATATAGTTTATAA
133325 TATATATA
1 TATATATA
133333 TATTATATTG
Statistics
Matches: 116, Mismatches: 9, Indels: 41
0.70 0.05 0.25
Matches are distributed among these distances:
12 5 0.04
13 4 0.03
14 4 0.03
15 15 0.13
16 4 0.03
17 24 0.21
18 35 0.30
19 9 0.08
20 4 0.03
21 11 0.09
22 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (16 bp):
TATATATAGTTTATAA
Found at i:133194 original size:15 final size:15
Alignment explanation
Indices: 133174--133226 Score: 70
Period size: 15 Copynumber: 3.4 Consensus size: 15
133164 ACATAATTTA
*
133174 TATATAGCTTATAAT
1 TATATAGTTTATAAT
133189 TATATAGTTTATAAT
1 TATATAGTTTATAAT
133204 ATAATATAGTTTATAAT
1 -T-ATATAGTTTATAAT
*
133221 TTTATA
1 TATATA
133227 TACATAGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 18 0.53
16 2 0.06
17 14 0.41
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATAAT
Found at i:133242 original size:89 final size:93
Alignment explanation
Indices: 133136--133311 Score: 281
Period size: 89 Copynumber: 1.9 Consensus size: 93
133126 TATATAGTTT
133136 TATACATAGTTTATATATAGTTCACAT-AACATAATTTATATAT-AGCT-T-ATAATTATATAGT
1 TATACATAGTTTATATATA-TTCACATAAACATAATTTATATATAAGCTATAATAATTATATAGT
133197 TTATAATATA-ATATAGTTTATAATTTTA
65 TTATAATATACATATAGTTTATAATTTTA
* **
133225 TATACATAGTTTATATATATTCACATAAATATAATTTATATATAATTTATAATAATTATATAGTT
1 TATACATAGTTTATATATATTCACATAAACATAATTTATATATAAGCTATAATAATTATATAGTT
133290 TATAATATACATATAGTTTATA
66 TATAATATACATATAGTTTATA
133312 TATAATTTTA
Statistics
Matches: 79, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
88 7 0.09
89 34 0.43
90 2 0.03
91 1 0.01
92 23 0.29
93 12 0.15
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (93 bp):
TATACATAGTTTATATATATTCACATAAACATAATTTATATATAAGCTATAATAATTATATAGTT
TATAATATACATATAGTTTATAATTTTA
Found at i:133269 original size:11 final size:11
Alignment explanation
Indices: 133253--133335 Score: 71
Period size: 11 Copynumber: 7.4 Consensus size: 11
133243 ATTCACATAA
133253 ATATAATTTAT
1 ATATAATTTAT
133264 ATATAATTTAT
1 ATATAATTTAT
133275 A-ATAATTATAT
1 ATATAATT-TAT
* *
133286 AGTTTATAATATAC
1 A---TATAATTTAT
*
133300 ATATAGTTTAT
1 ATATAATTTAT
133311 ATATAATTT-T
1 ATATAATTTAT
* *
133321 ATATTATATAT
1 ATATAATTTAT
133332 ATAT
1 ATAT
133336 TATATTGTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
10 14 0.24
11 36 0.62
14 3 0.05
15 5 0.09
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (11 bp):
ATATAATTTAT
Found at i:133310 original size:47 final size:46
Alignment explanation
Indices: 133184--133330 Score: 148
Period size: 47 Copynumber: 3.2 Consensus size: 46
133174 TATATAGCTT
*
133184 ATAATTATATAGTTTATAATATAATATAGTTTATA-AT-TTTATATA
1 ATAATTATATAGTTTATAATATAATATAGTTTATATATAATT-TATA
* * *
133229 CATAGTTTATATA-TATTCA-CATA-AATATAATTTATATATAATTTATA
1 -ATA-ATTATATAGT-TT-ATAATATAATATAGTTTATATATAATTTATA
133276 ATAATTATATAGTTTATAATATACATATAGTTTATATATAATTT-T-
1 ATAATTATATAGTTTATAATATA-ATATAGTTTATATATAATTTATA
133321 AT-ATTATATA
1 ATAATTATATA
133331 TATATTATAT
Statistics
Matches: 85, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
44 9 0.11
45 14 0.16
46 22 0.26
47 37 0.44
48 3 0.04
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (46 bp):
ATAATTATATAGTTTATAATATAATATAGTTTATATATAATTTATA
Found at i:137933 original size:13 final size:12
Alignment explanation
Indices: 137911--137943 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
137901 AGTTCTCCTA
137911 TCTT-TTTTTTT
1 TCTTGTTTTTTT
137922 TCTTCGTTTTTTT
1 TCTT-GTTTTTTT
137935 TCTTGTTTT
1 TCTTGTTTT
137944 GGATCACCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 5 0.25
13 11 0.55
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (12 bp):
TCTTGTTTTTTT
Found at i:139323 original size:2 final size:2
Alignment explanation
Indices: 139307--139381 Score: 134
Period size: 2 Copynumber: 37.5 Consensus size: 2
139297 TTTCAAAACC
139307 TA TA TGA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
139349 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
139382 TCTGGACAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.01
2 68 0.96
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:140556 original size:3 final size:3
Alignment explanation
Indices: 140550--140577 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
140540 TTAAAAAAAT
140550 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
140578 AAAATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:141100 original size:106 final size:106
Alignment explanation
Indices: 140928--142267 Score: 2267
Period size: 106 Copynumber: 12.7 Consensus size: 106
140918 TCCTTTGCTA
* * *
140928 TGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
* *
140993 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTTGCTG
66 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
141034 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
141099 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
66 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
141140 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
* * *
141205 AAGTTAAACTTGCGTTGTCTGGTGTCTAATATCCTTCGTTG
66 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* * *
141246 TGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCAGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
* *
141311 AAGTTGAACTTGCGTTGTATGGAGTCCAATATCATTCGTTG
66 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* * *
141352 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGATAACCAGCAGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
*
141417 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTG
66 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* *
141458 TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
*
141523 AAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTG
66 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* * *
141564 TGAAGTTGAAATTGGCTATGAAATTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
*
141629 AAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTG
66 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* *
141670 TGAAGTTGAAATTGGCTCTGAAATTTAGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
*
141735 AAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTG
66 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* * *
141776 TGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGAGAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
141840 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
66 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
141881 TGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
141945 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
66 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* * *
141986 TGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATATTTGTTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
* *
142050 AAGTTGAACTTGCGTTGTCTGGAGTACAATACCCTTCGTTG
66 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* *
142091 TGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
142155 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
66 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* *
142196 TGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
142260 AAGTTGAA
66 AAGTTGAA
142268 ATTGGCTTTT
Statistics
Matches: 1175, Mismatches: 59, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
105 444 0.38
106 731 0.62
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (106 bp):
TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
Found at i:145893 original size:2 final size:2
Alignment explanation
Indices: 145877--145938 Score: 108
Period size: 2 Copynumber: 31.0 Consensus size: 2
145867 TTTCAAAACC
145877 TA TA TGA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
145919 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
145939 ATTCTGGACA
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 55 0.95
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:147115 original size:3 final size:3
Alignment explanation
Indices: 147109--147142 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
147099 TTAAAAAAAT
147109 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
147143 ATAAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:148079 original size:2 final size:2
Alignment explanation
Indices: 148067--148111 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
148057 ATATTACAGA
148067 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
148106 AT AT AT
1 AT AT AT
148112 GAATTATCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:155250 original size:106 final size:106
Alignment explanation
Indices: 155017--157032 Score: 3027
Period size: 106 Copynumber: 19.3 Consensus size: 106
155007 CTCGAGAGTA
* * * * * * *
155017 AATTTCAACTTCTCAACGAAGGATCTT-GAATCCAAGACAACACAAGCTCAACTTCATGATGAAG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG
* * *
155081 GGGCGGCTGATTGTCAACAAAC-ATTTCTCAATTTCAGAGCC
65 GGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
* *
155122 AATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
155187 GACCGCTGGTTGTCAATAAACAATTTCTCGATTTCAGAGTC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
155228 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
155293 GACCGCTGGTTGTCAACAAAC-ATTTCTCGATTTCAGAGTC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
155333 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
155398 GACTGCTGGTTGTCAACAAAC-ATTTCTCGA-TTCAGAGTC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
155437 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
155502 GACCGCTGGTTGTCAACAAAC-ATTTCTCGATTTCAGAGTC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
*
155542 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
155607 GACCGCTGGTTGTCAACAAAC-ATTTCTCGATTTCAGAGTC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
*
155647 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
155712 GACCACTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
* *
155752 AATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
155817 GACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
* *
155858 AATTTCAACTTCGCCACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
155923 GACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
* * * *
155963 AATTTCGACTTTACAACGAAGGATATTGGACTCCAGAAAACGCAAGTTCAACTTCCCGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
156028 GACTGCTGGTTGTCAATAAAC-ATTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
*
156068 AATTTCGACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
156133 GACCGCTGGTTGTCAATAAACAA-----C---TTC----CC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
*
156162 AATTTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
156227 GACCGCTGGTTGTCAACAAATAATCTC-CTAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTC-AATTTCAGAGCC
* *
156268 AATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
156333 GACCGCTGGTTGTCAACAAATAATTTC-CTAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTC-AATTTCAGAGCC
*
156374 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
156439 GACCGCTGGTTGTCAACAAATAATTTC-CTAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTC-AATTTCAGAGCC
*
156480 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
156545 GACCGCTGGTTGTCAACAAATAATTTC-CTAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTC-AATTTCAGAGCC
* * *
156586 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAAAACGCAAGTTCAACTTCATGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
156651 GACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
* *
156692 AATTTCAACTTCACAGCGAAGGATATTGTACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * *
156757 GACCGTTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
* *
156798 AATTTCAACTTCATAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
156863 GACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
* * * * * * *
156904 AATTTCGACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAATTTCACGACGAAG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG
* * * *
156968 GGGCGGCTGATTGTCAAC-AA-AA-TT-TC-A-TTCAGAGTC
65 GGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
* *
157004 AATTTCAATTTCACAGCGAAGGATATTGG
1 AATTTCAACTTCACAACGAAGGATATTGG
157033 CCTCGAAACA
Statistics
Matches: 1802, Mismatches: 90, Indels: 43
0.93 0.05 0.02
Matches are distributed among these distances:
94 86 0.05
98 4 0.00
100 33 0.02
101 2 0.00
102 4 0.00
103 2 0.00
104 105 0.06
105 676 0.38
106 889 0.49
107 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (106 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCC
Found at i:159179 original size:21 final size:20
Alignment explanation
Indices: 159154--159202 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
159144 GTTGTTATTT
159154 TGTTTTTTCCACTTTTTCTCA
1 TGTTTTTTCCACTTTTT-TCA
** *
159175 TGTTTTTTCTTCTTTTTTTA
1 TGTTTTTTCCACTTTTTTCA
159195 TGTTTTTT
1 TGTTTTTT
159203 TTTCTTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.73
Consensus pattern (20 bp):
TGTTTTTTCCACTTTTTTCA
Found at i:159190 original size:20 final size:20
Alignment explanation
Indices: 159167--159211 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
159157 TTTTTCCACT
159167 TTTTCTCATGTTTTTTCTTC
1 TTTTCTCATGTTTTTTCTTC
* * *
159187 TTTTTTTATGTTTTTTTTTC
1 TTTTCTCATGTTTTTTCTTC
159207 TTTTC
1 TTTTC
159212 AAACTGCTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTCTCATGTTTTTTCTTC
Found at i:164577 original size:12 final size:11
Alignment explanation
Indices: 164558--164591 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
164548 TTAGTATGTT
164558 TAAAAATAAAA
1 TAAAAATAAAA
*
164569 CTTAAAATAAAA
1 -TAAAAATAAAA
164581 TAAAAATAAAA
1 TAAAAATAAAA
164592 ACTTGAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:167326 original size:59 final size:58
Alignment explanation
Indices: 167263--167392 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 58
167253 GGGTGACCAT
* * *
167263 TTTGTTACTTTTAATAGTCGAGGGACTCAATAAAGCAACACTCTATAGTCG-GAGGACTA
1 TTTGTTACTTTTAATAGTCGAGAGACTCAATAAA-CAACACACTATAGTCGAG-GGACAA
* * *
167322 TTTGTTAACTTTTAATAGTCGAGAGACTTAATAAATAATACACTATAGTCGAGGGACAA
1 TTTGTT-ACTTTTAATAGTCGAGAGACTCAATAAACAACACACTATAGTCGAGGGACAA
167381 TTTGTATACTTT
1 TTTGT-TACTTT
167393 ACCCTTAACA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
59 34 0.55
60 28 0.45
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (58 bp):
TTTGTTACTTTTAATAGTCGAGAGACTCAATAAACAACACACTATAGTCGAGGGACAA
Found at i:168104 original size:23 final size:23
Alignment explanation
Indices: 168076--168120 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
168066 AGTTTTATAT
168076 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
168099 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
168121 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Done.