Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 47 of 51
Found at i:11709139 original size:17 final size:19
Alignment explanation
Indices: 11709111--11709159 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
11709101 TATTTTAAAA
11709111 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
11709129 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
11709148 CACCGATGCACT
1 CATCGATGCACT
11709160 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:11712000 original size:37 final size:37
Alignment explanation
Indices: 11711950--11712030 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
11711940 GATAATATAA
*
11711950 AAACAACTGGATCTGACTAAACTGGCACACTTATTAG
1 AAACAATTGGATCTGACTAAACTGGCACACTTATTAG
11711987 AAACAATTGGATCTGACTAAACTGGCACACTTATTAG
1 AAACAATTGGATCTGACTAAACTGGCACACTTATTAG
11712024 AAACAAT
1 AAACAAT
11712031 AAATATCAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.25
Consensus pattern (37 bp):
AAACAATTGGATCTGACTAAACTGGCACACTTATTAG
Found at i:11735912 original size:5 final size:6
Alignment explanation
Indices: 11735896--11735921 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11735886 TTTAAAATTT
11735896 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
11735922 TTTAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:11736438 original size:2 final size:2
Alignment explanation
Indices: 11736431--11736484 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
11736421 TGGTTCTAAA
11736431 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
11736473 AT AT AT AT AT AT
1 AT AT AT AT AT AT
11736485 GGATCAAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11737831 original size:20 final size:21
Alignment explanation
Indices: 11737806--11737862 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
11737796 TGGGGCTTGC
11737806 AAAATAAAAATAATAAA-AAT
1 AAAATAAAAATAATAAATAAT
* * *
11737826 AAAATAAAATTTATAAATAGT
1 AAAATAAAAATAATAAATAAT
11737847 AAAATTAAATAATAAT
1 AAAA-TAAA-AATAAT
11737863 TTTCGTTCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 15 0.52
21 6 0.21
22 4 0.14
23 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAATAAAAATAATAAATAAT
Found at i:11737844 original size:27 final size:27
Alignment explanation
Indices: 11737813--11737864 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
11737803 TGCAAAATAA
11737813 AAATAATAAAAATAAAATAA-AATTTAT
1 AAATAAT-AAAATAAAATAATAATTTAT
* *
11737840 AAATAGTAAAATTAAATAATAATTT
1 AAATAATAAAATAAAATAATAATTT
11737865 TCGTTCGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
AAATAATAAAATAAAATAATAATTTAT
Found at i:11738186 original size:19 final size:19
Alignment explanation
Indices: 11738162--11738218 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
11738152 GGTAAACCCC
11738162 ATTGAAAATTCAAACTCAT
1 ATTGAAAATTCAAACTCAT
* *
11738181 ATTG--AATT--TA--CAC
1 ATTGAAAATTCAAACTCAT
11738194 ATTGAAAATTCAAACTCAT
1 ATTGAAAATTCAAACTCAT
11738213 ATTGAA
1 ATTGAA
11738219 TATAAACACT
Statistics
Matches: 28, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
13 6 0.21
15 5 0.18
17 5 0.18
19 12 0.43
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (19 bp):
ATTGAAAATTCAAACTCAT
Found at i:11741139 original size:57 final size:57
Alignment explanation
Indices: 11741051--11741166 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
11741041 CTTTAAAAGA
11741051 ATCTCCCTACTAAAAAATTAAAACCTTTTAGGTTATTTAACATTTAGGTTAGACATC
1 ATCTCCCTACTAAAAAATTAAAACCTTTTAGGTTATTTAACATTTAGGTTAGACATC
11741108 ATCTCCCTACTAAAAAATTAAAACCTTTTAGGTTATTTAACATTTAGGTTAGACATC
1 ATCTCCCTACTAAAAAATTAAAACCTTTTAGGTTATTTAACATTTAGGTTAGACATC
11741165 AT
1 AT
11741167 ATGTTCTTGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (57 bp):
ATCTCCCTACTAAAAAATTAAAACCTTTTAGGTTATTTAACATTTAGGTTAGACATC
Found at i:11743122 original size:21 final size:20
Alignment explanation
Indices: 11743067--11743143 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 20
11743057 TAAGAATTAT
11743067 ATATATATTCCAAAGGATCAA
1 ATATATATTCCAAA-GATCAA
* * * *
11743088 ATATGTGTTTCAAAGACTCGA
1 ATATATATTCCAAAGA-TCAA
* *
11743109 ATATATATTCCAAAGGATTAT
1 ATATATATTCCAAA-GATCAA
*
11743130 ATATATATCCCAAA
1 ATATATATTCCAAA
11743144 AGACCACGTA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.05
21 39 0.91
22 2 0.05
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.32
Consensus pattern (20 bp):
ATATATATTCCAAAGATCAA
Found at i:11749813 original size:23 final size:24
Alignment explanation
Indices: 11749777--11749822 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
11749767 CAACACAGCT
*
11749777 CGTATAAAATGCACCGAAGTGCCA
1 CGTATAAAATGCACCGAAATGCCA
11749801 CGTAT-AAATGCACCGAAATGCC
1 CGTATAAAATGCACCGAAATGCC
11749823 GCGAAGGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (24 bp):
CGTATAAAATGCACCGAAATGCCA
Found at i:11749912 original size:21 final size:21
Alignment explanation
Indices: 11749888--11749975 Score: 56
Period size: 21 Copynumber: 4.2 Consensus size: 21
11749878 CTCCTTAAGA
11749888 ATCATATATATATTCCAAAGG
1 ATCATATATATATTCCAAAGG
*
11749909 ATCA-A-ATATGTGTCTCAAA-G
1 ATCATATATATAT-TC-CAAAGG
** *
11749929 ACTCGCATATATGTTCCAAAGG
1 A-TCATATATATATTCCAAAGG
* * * *
11749951 ATTATACATATATCCCGAAGG
1 ATCATATATATATTCCAAAGG
11749972 ATCA
1 ATCA
11749976 CGTAGAACCC
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
19 5 0.10
20 5 0.10
21 30 0.59
22 5 0.10
23 6 0.12
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (21 bp):
ATCATATATATATTCCAAAGG
Found at i:11750700 original size:35 final size:35
Alignment explanation
Indices: 11750643--11750709 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
11750633 TCAAAAATGA
*
11750643 TATCGATACTGTCCTAATGGTATCAGTACCCCTAG
1 TATCGATACTGTCCTAATGGTATCAATACCCCTAG
* *
11750678 TATCGATACTTTCCCTTA-GGTATCAATACCCC
1 TATCGATACTGT-CCTAATGGTATCAATACCCC
11750710 ATGAGGATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 24 0.86
36 4 0.14
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.33
Consensus pattern (35 bp):
TATCGATACTGTCCTAATGGTATCAATACCCCTAG
Found at i:11763746 original size:34 final size:34
Alignment explanation
Indices: 11763708--11763781 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
11763698 ACCAATCTAT
11763708 AACAAAAAGAACTATAAACAGCCTACTTACAAAA
1 AACAAAAAGAACTATAAACAGCCTACTTACAAAA
11763742 AACAAAAAGAACTATAAACAGCCTACTTACAAAA
1 AACAAAAAGAACTATAAACAGCCTACTTACAAAA
11763776 AACAAA
1 AACAAA
11763782 GATTGGTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.61, C:0.20, G:0.05, T:0.14
Consensus pattern (34 bp):
AACAAAAAGAACTATAAACAGCCTACTTACAAAA
Found at i:11769038 original size:64 final size:62
Alignment explanation
Indices: 11768986--11769147 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 62
11768976 TGGTGCACTA
*
11768986 AGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAA-ATAGCCTG-GTGCATCGATGCAT
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAT-GCC-GAGTGCATCGATGCAT
* * * *
11769048 GGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCCGAGTGCATCGATGCAT
1 AG--AGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCCGAGTGCATCGATGCAT
* *
11769112 GGAGAATGCATCGGTGCATGAAATGCATTCGATGTT
1 --AGAGTGCATCGATGCATGAAATGCATTCGATGTT
11769148 CAATTAAATC
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 79 0.94
65 2 0.02
66 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (62 bp):
AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCCGAGTGCATCGATGCAT
Found at i:11769138 original size:17 final size:19
Alignment explanation
Indices: 11769099--11769145 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
11769089 ATATTCCGAG
11769099 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
11769118 TGCATCGGTGCAT-GA-AA
1 TGCATCGATGCATGGAGAA
11769135 TGCATTCGATG
1 TGCA-TCGATG
11769146 TTCAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 12 0.48
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:11769166 original size:64 final size:60
Alignment explanation
Indices: 11768990--11769195 Score: 173
Period size: 64 Copynumber: 3.2 Consensus size: 60
11768980 GCACTAAGAG
* * * *
11768990 TGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGGCTTG-
1 TGCATCGATGCATGAAATGCATTCGATG-TTCAAAAAT--CATGGTGCATCGATGCATGG--AGA
* * *
11769054 TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTC-CGAGTGCATCGATGCATGGAGAA
1 TGCATCGATGCATGAAATGCATTCGATG-TTCAAAA-A-TCATG-GTGCATCGATGCATGGAG-A
* *
11769118 TGCATCGGTGCATGAAATGCATTCGATGTTCAATTAAATCATAGGTGCATCGATGCATGGTTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTCAA--AAATCAT-GGTGCATCGATGCATGG--AGA
*
11769183 TGCATCGGTGCAT
1 TGCATCGATGCAT
11769196 CACCTTGAAT
Statistics
Matches: 122, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
62 1 0.01
63 7 0.06
64 94 0.77
65 18 0.15
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (60 bp):
TGCATCGATGCATGAAATGCATTCGATGTTCAAAAATCATGGTGCATCGATGCATGGAGA
Found at i:11775036 original size:21 final size:21
Alignment explanation
Indices: 11775012--11775064 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
11775002 GAGTTTGTTT
*
11775012 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTTCATATTTT-AAAAA
11775033 TCATTTTT-ATATTTTAAAAA
1 TCATTTTTCATATTTTAAAAA
*
11775053 TAATTTTTCATA
1 TCATTTTTCATA
11775065 ATCCGAAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (21 bp):
TCATTTTTCATATTTTAAAAA
Found at i:11777031 original size:18 final size:17
Alignment explanation
Indices: 11776977--11777025 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
11776967 TTGGACTCCT
* *
11776977 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
11776995 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
11777013 AGTGCATTCGATG
1 AGTGCA-TCGATG
11777026 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:11777175 original size:64 final size:62
Alignment explanation
Indices: 11776994--11777155 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 62
11776984 CGGTGCACTA
* *
11776994 AGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCCTGGTGCATTGATGCATGG
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT--CATGGTGCATTGATGCATGG
*** * *
11777058 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATAT-TTCGAGTGCATTGATGCATGG
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAA-ATCAT-G-GTGCATTGATGCATGG
11777122 AGAGTGCATC-AGTGCATGAAATGCATTCGATGTT
1 AGAGTGCATCGA-TGCATGAAATGCATTCGATGTT
11777156 CAATTAAATC
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 79 0.94
65 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (62 bp):
AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATCATGGTGCATTGATGCATGG
Found at i:11778374 original size:29 final size:32
Alignment explanation
Indices: 11778306--11778376 Score: 76
Period size: 34 Copynumber: 2.2 Consensus size: 32
11778296 TTTAAGTAAG
* **
11778306 AATATTATATTATATTTTAAAATTTATTAAAT
1 AATATTATATTATATATTAAAATACATTAAAT
11778338 AGACTATTATATTA-ATATT-AAATACA-TAAAT
1 A-A-TATTATATTATATATTAAAATACATTAAAT
11778369 AATATTAT
1 AATATTAT
11778377 TCAATTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
29 6 0.18
30 1 0.03
31 6 0.18
32 6 0.18
33 5 0.15
34 10 0.29
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (32 bp):
AATATTATATTATATATTAAAATACATTAAAT
Found at i:11778377 original size:27 final size:26
Alignment explanation
Indices: 11778347--11778427 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 26
11778337 TAGACTATTA
11778347 TATTAATATTAAATACATAAATAATAT
1 TATTAATATTAAATA-ATAAATAATAT
* *
11778374 TATTCAAT-TTTAATAATTTAATAATAT
1 TATT-AATATTAAATAA-TAAATAATAT
** *
11778401 TATTTTTATGAAAATAATAAATAATAT
1 TATTAATAT-TAAATAATAAATAATAT
11778428 AAATTTAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
26 2 0.05
27 33 0.77
28 8 0.19
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (26 bp):
TATTAATATTAAATAATAAATAATAT
Found at i:11778497 original size:23 final size:23
Alignment explanation
Indices: 11778467--11778517 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
11778457 TTAAAATAAA
11778467 AATATAATATCA-TATATTATTAT
1 AATATAAT-TCAGTATATTATTAT
*
11778490 AATATAATTGAGTATATTATTAT
1 AATATAATTCAGTATATTATTAT
11778513 AATAT
1 AATAT
11778518 TAAAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (23 bp):
AATATAATTCAGTATATTATTAT
Found at i:11778532 original size:22 final size:22
Alignment explanation
Indices: 11778502--11778553 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
11778492 TATAATTGAG
* *
11778502 TATATTATTATAAT-ATTAAAAA
1 TATAATATTAT-ATCATCAAAAA
11778524 TATAATATTATATCATCAAAAA
1 TATAATATTATATCATCAAAAA
11778546 TATTAATA
1 TA-TAATA
11778554 AATATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.08
22 19 0.73
23 5 0.19
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TATAATATTATATCATCAAAAA
Found at i:11779618 original size:23 final size:23
Alignment explanation
Indices: 11779572--11779619 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
11779562 AACGTATAAT
*
11779572 TATAAATTATTTGAAAATCTATA
1 TATAAATTATTTGAAAATCAATA
*
11779595 TATAATTTATTT-AAAATACAATA
1 TATAAATTATTTGAAAAT-CAATA
11779618 TA
1 TA
11779620 ATTACATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
TATAAATTATTTGAAAATCAATA
Found at i:11782122 original size:17 final size:17
Alignment explanation
Indices: 11782100--11782136 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
11782090 GGTATTGTAG
*
11782100 TAGTACTTTGTGTACTT
1 TAGTACTTTGCGTACTT
11782117 TAGTACTTTGCGTACTT
1 TAGTACTTTGCGTACTT
11782134 TAG
1 TAG
11782137 CACTATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (17 bp):
TAGTACTTTGCGTACTT
Found at i:11782241 original size:21 final size:23
Alignment explanation
Indices: 11782212--11782272 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 23
11782202 TTGCATATTC
11782212 GTAAGAGTACTTTGTGTACT-T-
1 GTAAGAGTACTTTGTGTACTATG
* *
11782233 G-AAGTAGTACATAGTGTACTATG
1 GTAAG-AGTACTTTGTGTACTATG
11782256 GTAAGAGTACTTTGTGT
1 GTAAGAGTACTTTGTGT
11782273 GCAAGGATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 3 0.09
21 14 0.44
22 1 0.03
23 11 0.34
24 3 0.09
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (23 bp):
GTAAGAGTACTTTGTGTACTATG
Found at i:11789297 original size:21 final size:23
Alignment explanation
Indices: 11789268--11789331 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 23
11789258 TTGAATTTTC
11789268 GTAAGAGTACTTTGTGTACT-T-
1 GTAAGAGTACTTTGTGTACTCTA
* *
11789289 G-AAGTAGTACTTAGTTTACTCTA
1 GTAAG-AGTACTTTGTGTACTCTA
11789312 GTAAGAGTACTTTGTGTACT
1 GTAAGAGTACTTTGTGTACT
11789332 ATGACACTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 3 0.09
21 14 0.40
22 1 0.03
23 14 0.40
24 3 0.09
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.41
Consensus pattern (23 bp):
GTAAGAGTACTTTGTGTACTCTA
Found at i:11789887 original size:2 final size:2
Alignment explanation
Indices: 11789880--11789934 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
11789870 TGATGGACTT
* *
11789880 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TG 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
11789922 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
11789935 GTATGTATGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11790880 original size:22 final size:22
Alignment explanation
Indices: 11790853--11790900 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
11790843 TTCAATCCCA
*
11790853 AAAAAAATCTTTAAAATATATT
1 AAAAAAATATTTAAAATATATT
* * *
11790875 AAAAAATTATTTAATATATGTT
1 AAAAAAATATTTAAAATATATT
11790897 AAAA
1 AAAA
11790901 GACATTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAAAATATTTAAAATATATT
Found at i:11790984 original size:13 final size:12
Alignment explanation
Indices: 11790946--11790986 Score: 50
Period size: 10 Copynumber: 3.5 Consensus size: 12
11790936 ATTTATCTAA
11790946 ATTATTTAAATT
1 ATTATTTAAATT
*
11790958 ATT-TTT-AATA
1 ATTATTTAAATT
11790968 ATTATTTAAATT
1 ATTATTTAAATT
11790980 GATTATT
1 -ATTATT
11790987 CCTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
10 6 0.25
11 6 0.25
12 6 0.25
13 6 0.25
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
ATTATTTAAATT
Found at i:11791035 original size:20 final size:20
Alignment explanation
Indices: 11790947--11791042 Score: 61
Period size: 20 Copynumber: 4.5 Consensus size: 20
11790937 TTTATCTAAA
*
11790947 TTATTTAAATTATTTTTAAT
1 TTATTTAAATTATATTTAAT
*
11790967 AATTATTTAAATTGATTATTCCTTAT
1 --TTATTTAAATT-A-TATT--TAAT
* * *
11790993 TT-TTAATAACTAT-TTTAAA
1 TTATTTA-AATTATATTTAAT
11791012 TTATTTAAATTATATTTAAT
1 TTATTTAAATTATATTTAAT
*
11791032 TTATCTAAATT
1 TTATTTAAATT
11791043 TTCCTATTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
19 9 0.16
20 18 0.32
21 2 0.04
22 12 0.21
23 5 0.09
24 8 0.14
26 3 0.05
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (20 bp):
TTATTTAAATTATATTTAAT
Found at i:11796268 original size:32 final size:33
Alignment explanation
Indices: 11796231--11796296 Score: 80
Period size: 35 Copynumber: 2.0 Consensus size: 33
11796221 CTTTTGTATA
* *
11796231 TTTAAGCATTA-TTTTAATGCAGTATAAATATT
1 TTTAAGAATTACTTTTAATACAGTATAAATATT
*
11796263 TTTAAGAATTACGTTTTTCATACAGTATAAATAT
1 TTTAAGAATTAC--TTTTAATACAGTATAAATAT
11796297 GAGGCAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 10 0.36
35 18 0.64
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (33 bp):
TTTAAGAATTACTTTTAATACAGTATAAATATT
Found at i:11799056 original size:17 final size:17
Alignment explanation
Indices: 11799007--11799061 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
11798997 AAGCTCGAGA
*
11799007 CTCGAACTCGATTAAAG
1 CTCGAACTCGATTTAAG
*
11799024 CTC-AA-T---TTTGAG
1 CTCGAACTCGATTTAAG
11799036 CTCGAACTCGATTTAAG
1 CTCGAACTCGATTTAAG
11799053 CTCGAACTC
1 CTCGAACTC
11799062 AAACTCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
12 7 0.23
13 2 0.07
14 1 0.03
15 1 0.03
16 2 0.07
17 17 0.57
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (17 bp):
CTCGAACTCGATTTAAG
Found at i:11801830 original size:14 final size:14
Alignment explanation
Indices: 11801811--11802049 Score: 78
Period size: 14 Copynumber: 16.8 Consensus size: 14
11801801 ATGTGTATAA
11801811 CCTAAACCTTAAAC
1 CCTAAACCTTAAAC
11801825 CCTAAACCTTAAACC
1 CCTAAACCTTAAA-C
** *
11801840 TAACTCTTAATGCATAAAC
1 ---C-C-TAAACCTTAAAC
*
11801859 CCTAAACTTTAAAC
1 CCTAAACCTTAAAC
* *
11801873 TCTAAACCTT-AAT
1 CCTAAACCTTAAAC
*
11801886 CCTATAA-CATAAAC
1 CCTA-AACCTTAAAC
*
11801900 TCTAAATCC-T-AAC
1 CCTAAA-CCTTAAAC
* *
11801913 CCTTAACACATAAAC
1 CCTAAAC-CTTAAAC
*
11801928 CCTAAACCCTAAAC
1 CCTAAACCTTAAAC
* *
11801942 TCTAAACCTTAAAT
1 CCTAAACCTTAAAC
* * *
11801956 CCT-ATCATATAAGC
1 CCTAAACCT-TAAAC
* *
11801970 TCTAAACCCTAAAC
1 CCTAAACCTTAAAC
* * * *
11801984 TCTAGACCGTATA-
1 CCTAAACCTTAAAC
*
11801997 CCTAAACCTT-ATC
1 CCTAAACCTTAAAC
** *
11802010 ATATAAACTTTAAAC
1 -CCTAAACCTTAAAC
* *
11802025 CCTAAACCCTACAC
1 CCTAAACCTTAAAC
11802039 CCTAAACCTTA
1 CCTAAACCTTA
11802050 TCATTAGAAA
Statistics
Matches: 158, Mismatches: 49, Indels: 36
0.65 0.20 0.15
Matches are distributed among these distances:
12 1 0.01
13 27 0.17
14 102 0.65
15 16 0.10
16 1 0.01
18 1 0.01
19 2 0.01
20 8 0.05
ACGTcount: A:0.41, C:0.31, G:0.02, T:0.26
Consensus pattern (14 bp):
CCTAAACCTTAAAC
Found at i:11801933 original size:7 final size:7
Alignment explanation
Indices: 11801811--11801959 Score: 65
Period size: 7 Copynumber: 21.6 Consensus size: 7
11801801 ATGTGTATAA
11801811 CCTAAAC
1 CCTAAAC
*
11801818 CTTAAAC
1 CCTAAAC
11801825 CCTAAAC
1 CCTAAAC
*
11801832 CTTAAA-
1 CCTAAAC
11801838 CCT-AAC
1 CCTAAAC
* **
11801844 TCTTAATG
1 -CCTAAAC
*
11801852 CATAAAC
1 CCTAAAC
11801859 CCTAAAC
1 CCTAAAC
**
11801866 TTTAAAC
1 CCTAAAC
*
11801873 TCTAAA-
1 CCTAAAC
* *
11801879 CCTTAAT
1 CCTAAAC
11801886 CCTATAA-
1 CCTA-AAC
*
11801893 CATAAAC
1 CCTAAAC
* *
11801900 TCTAAAT
1 CCTAAAC
11801907 CCT-AAC
1 CCTAAAC
*
11801913 CCTTAAC
1 CCTAAAC
*
11801920 ACATAAAC
1 -CCTAAAC
11801928 CCTAAAC
1 CCTAAAC
11801935 CCTAAAC
1 CCTAAAC
*
11801942 TCTAAAC
1 CCTAAAC
* *
11801949 CTTAAAT
1 CCTAAAC
11801956 CCTA
1 CCTA
11801960 TCATATAAGC
Statistics
Matches: 103, Mismatches: 31, Indels: 16
0.69 0.21 0.11
Matches are distributed among these distances:
5 2 0.02
6 13 0.13
7 80 0.78
8 8 0.08
ACGTcount: A:0.42, C:0.31, G:0.01, T:0.26
Consensus pattern (7 bp):
CCTAAAC
Found at i:11801942 original size:42 final size:42
Alignment explanation
Indices: 11801895--11801987 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
11801885 TCCTATAACA
11801895 TAAACTCTAAATCC-T-AACCCTTAACACATAAACCCTAAACCC
1 TAAACTCTAAA-CCTTAAACCC-TAACACATAAACCCTAAACCC
* * * * *
11801937 TAAACTCTAAACCTTAAATCCTATCATATAAGCTCTAAACCC
1 TAAACTCTAAACCTTAAACCCTAACACATAAACCCTAAACCC
11801979 TAAACTCTA
1 TAAACTCTA
11801988 GACCGTATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 2 0.05
42 38 0.86
43 4 0.09
ACGTcount: A:0.42, C:0.31, G:0.01, T:0.26
Consensus pattern (42 bp):
TAAACTCTAAACCTTAAACCCTAACACATAAACCCTAAACCC
Found at i:11802333 original size:17 final size:17
Alignment explanation
Indices: 11802307--11802358 Score: 95
Period size: 17 Copynumber: 3.1 Consensus size: 17
11802297 TTAAGAACAT
11802307 GAGTCGAGTTCGAGCTC
1 GAGTCGAGTTCGAGCTC
*
11802324 GAGTCAAGTTCGAGCTC
1 GAGTCGAGTTCGAGCTC
11802341 GAGTCGAGTTCGAGCTC
1 GAGTCGAGTTCGAGCTC
11802358 G
1 G
11802359 TGATCTGTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.19, C:0.23, G:0.35, T:0.23
Consensus pattern (17 bp):
GAGTCGAGTTCGAGCTC
Found at i:11813704 original size:41 final size:41
Alignment explanation
Indices: 11813647--11813755 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 41
11813637 AGTTTAGTGT
* * * *
11813647 ATTCACCCTTCGGGATGAATTTTACTTCAGATTAT-CA-GCA
1 ATTCACCATTCGGGATGAATTTCACTTCAGAATATAAATG-A
*
11813687 GATTCACCATTCGGGATGAATTTCACTTTAGAATATAAATGA
1 -ATTCACCATTCGGGATGAATTTCACTTCAGAATATAAATGA
*
11813729 ATTCACCATTCGAGATGAATTTCACTT
1 ATTCACCATTCGGGATGAATTTCACTT
11813756 TGAAATATTA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
41 57 0.95
42 2 0.03
43 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (41 bp):
ATTCACCATTCGGGATGAATTTCACTTCAGAATATAAATGA
Found at i:11813756 original size:41 final size:41
Alignment explanation
Indices: 11813688--11813800 Score: 149
Period size: 41 Copynumber: 2.8 Consensus size: 41
11813678 TTATCAGCAG
*
11813688 ATTCACCATTCGGGATGAATTTCACTTTAGAATATAAATGA
1 ATTCACCATTCGAGATGAATTTCACTTTAGAATATAAATGA
* * *
11813729 ATTCACCATTCGAGATGAATTTCACTTT-GAAATATTAGTGG
1 ATTCACCATTCGAGATGAATTTCACTTTAG-AATATAAATGA
*
11813770 ATTCATCATTTCGAG-TGAATTTCACTTTAGA
1 ATTCACCA-TTCGAGATGAATTTCACTTTAGA
11813801 TTATCAGTGA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
40 1 0.02
41 56 0.88
42 7 0.11
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (41 bp):
ATTCACCATTCGAGATGAATTTCACTTTAGAATATAAATGA
Found at i:11816602 original size:23 final size:22
Alignment explanation
Indices: 11816576--11816631 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
11816566 AAAAATATTG
*
11816576 AAGTTTGAAAGTGAAAATGTTCT
1 AAGTTTGAAA-TAAAAATGTTCT
* * *
11816599 AAGTTTTAAATAAAAATTTTTT
1 AAGTTTGAAATAAAAATGTTCT
*
11816621 AAGTTTTAAAT
1 AAGTTTGAAAT
11816632 TTGTTGATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (22 bp):
AAGTTTGAAATAAAAATGTTCT
Found at i:11816614 original size:22 final size:22
Alignment explanation
Indices: 11816589--11816631 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11816579 TTTGAAAGTG
11816589 AAAATGTTCTAAGTTTTAAATA
1 AAAATGTTCTAAGTTTTAAATA
* *
11816611 AAAATTTTTTAAGTTTTAAAT
1 AAAATGTTCTAAGTTTTAAAT
11816632 TTGTTGATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (22 bp):
AAAATGTTCTAAGTTTTAAATA
Found at i:11817021 original size:28 final size:28
Alignment explanation
Indices: 11816965--11817023 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
11816955 CACTCTTGAA
* *
11816965 TATTTTGAAACATCAAATGCATTTTGTG
1 TATTTTGAAACATCAAATGCAATTAGTG
* *
11816993 TATTTTGAAACATCGAATGTAATTAGTG
1 TATTTTGAAACATCAAATGCAATTAGTG
11817021 TAT
1 TAT
11817024 CGATGCACCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.42
Consensus pattern (28 bp):
TATTTTGAAACATCAAATGCAATTAGTG
Found at i:11820099 original size:15 final size:17
Alignment explanation
Indices: 11820064--11820100 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
11820054 TTTTTGATTT
*
11820064 AATTACATTGTTTTGAA
1 AATTACATTGTTTTCAA
11820081 AATTACA-TG-TTTCAA
1 AATTACATTGTTTTCAA
11820096 AATTA
1 AATTA
11820101 TTTTCAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 2 0.11
17 7 0.37
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (17 bp):
AATTACATTGTTTTCAA
Found at i:11824313 original size:17 final size:18
Alignment explanation
Indices: 11824291--11824328 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
11824281 ATTTTATTTT
*
11824291 TATTTTCATATATAT-TA
1 TATTTTAATATATATATA
11824308 TATTTTAATATATATATA
1 TATTTTAATATATATATA
11824326 TAT
1 TAT
11824329 ATAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTTAATATATATATA
Found at i:11824405 original size:17 final size:17
Alignment explanation
Indices: 11824366--11824405 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
11824356 ATACTTAATT
*
11824366 TTTTTAAAATATTTTTA
1 TTTTTAAAATAATTTTA
**
11824383 AATTTAAAATAATTTTA
1 TTTTTAAAATAATTTTA
11824400 TTTTTA
1 TTTTTA
11824406 TTAAAAATCA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTAAAATAATTTTA
Found at i:11824516 original size:15 final size:16
Alignment explanation
Indices: 11824496--11824538 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
11824486 GTTTACTTCA
*
11824496 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
11824511 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
11824527 GAATGATTCAAA
1 GAATGATTCAAA
11824539 GGCTCTGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.28
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:11824529 original size:16 final size:16
Alignment explanation
Indices: 11824508--11824538 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
11824498 ATGATTAAGC
11824508 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
11824524 GCTGAATGATTCAAA
1 GCTGAATGATTCAAA
11824539 GGCTCTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (16 bp):
GCTGAATGATTCAAAT
Found at i:11828261 original size:13 final size:13
Alignment explanation
Indices: 11828258--11828287 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
11828248 CCGTTGACCC
11828258 GACCCGACCCGTT
1 GACCCGACCCGTT
11828271 GACCCGACCCGTT
1 GACCCGACCCGTT
11828284 GACC
1 GACC
11828288 ATTGACCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:11828266 original size:18 final size:18
Alignment explanation
Indices: 11828245--11828281 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
11828235 CCGACTCGTT
11828245 GACCCGTTGACCCGACCC
1 GACCCGTTGACCCGACCC
11828263 GACCCGTTGACCCGACCC
1 GACCCGTTGACCCGACCC
11828281 G
1 G
11828282 TTGACCATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.49, G:0.24, T:0.11
Consensus pattern (18 bp):
GACCCGTTGACCCGACCC
Found at i:11828300 original size:15 final size:15
Alignment explanation
Indices: 11828276--11828309 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11828266 CCGTTGACCC
*
11828276 GACCCGTTGACCATT
1 GACCCATTGACCATT
*
11828291 GACCCATTGACCGTT
1 GACCCATTGACCATT
11828306 GACC
1 GACC
11828310 GGAGTTGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.24
Consensus pattern (15 bp):
GACCCATTGACCATT
Found at i:11828319 original size:17 final size:17
Alignment explanation
Indices: 11828297--11828336 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
11828287 CATTGACCCA
11828297 TTGACCGTTGACCGGAG
1 TTGACCGTTGACCGGAG
11828314 TTGACCGTTGACCGGAG
1 TTGACCGTTGACCGGAG
11828331 TTGACC
1 TTGACC
11828337 ACTGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.25, G:0.33, T:0.25
Consensus pattern (17 bp):
TTGACCGTTGACCGGAG
Found at i:11829652 original size:18 final size:18
Alignment explanation
Indices: 11829626--11829661 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11829616 AGAATTGTTC
11829626 GAAAGGACTGAAGTAAAT
1 GAAAGGACTGAAGTAAAT
* *
11829644 GAAATGACTGAATTAAAT
1 GAAAGGACTGAAGTAAAT
11829662 AATAAGATCG
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:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (18 bp):
GAAAGGACTGAAGTAAAT
Found at i:11830888 original size:24 final size:24
Alignment explanation
Indices: 11830792--11830892 Score: 71
Period size: 24 Copynumber: 4.2 Consensus size: 24
11830782 GAATATTTTA
* * *
11830792 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTAATCTGAATTATGT
* * * * *
11830816 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTAATCTGAATTATGT
* * * *
11830840 TCTGAT-TCCTAACCCGGATTCTGT
1 TCTGATAT-CTAATCTGAATTATGT
11830864 TCTGATATCTAATCTGAATTATGT
1 TCTGATATCTAATCTGAATTATGT
11830888 T-TGAT
1 TCTGAT
11830893 TTCTGATATC
Statistics
Matches: 58, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
23 5 0.09
24 52 0.90
25 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.46
Consensus pattern (24 bp):
TCTGATATCTAATCTGAATTATGT
Found at i:11832830 original size:15 final size:15
Alignment explanation
Indices: 11832810--11832852 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
11832800 TAATTTGAGG
*
11832810 AATTAAATTTTCATA
1 AATTAAATTTTAATA
*
11832825 AATTAAATTTAAATA
1 AATTAAATTTTAATA
*
11832840 TATTAAATTTTAA
1 AATTAAATTTTAA
11832853 AATAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAAATTTTAATA
Found at i:11836797 original size:15 final size:15
Alignment explanation
Indices: 11836777--11836807 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11836767 TCAAAAAGTT
11836777 CACGTCCGCGATACC
1 CACGTCCGCGATACC
11836792 CACGTCCGCGATACC
1 CACGTCCGCGATACC
11836807 C
1 C
11836808 GACGCGTGAC
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:0.19, C:0.48, G:0.19, T:0.13
Consensus pattern (15 bp):
CACGTCCGCGATACC
Found at i:11839477 original size:30 final size:30
Alignment explanation
Indices: 11839327--11839483 Score: 110
Period size: 30 Copynumber: 5.4 Consensus size: 30
11839317 CATATTCGAT
* * **
11839327 TTAAATGACTTAAATAGCGAAAACATAAAC
1 TTAAAGGACTAAAATAGAAAAAACATAAAC
* * * *
11839357 TTAAAGGGCTAAAATAGAAAACATATAAAT
1 TTAAAGGACTAAAATAGAAAAAACATAAAC
* * * *
11839387 TTAAGGGACTAAAATAGCAAAAATAGAAAC
1 TTAAAGGACTAAAATAGAAAAAACATAAAC
* * *
11839417 TTAAAGGACTAACAT--AACAAA-AT---T
1 TTAAAGGACTAAAATAGAAAAAACATAAAC
* *
11839441 TTAAAGGAATAAAATGGAAAAAACATAAAC
1 TTAAAGGACTAAAATAGAAAAAACATAAAC
*
11839471 TTAAAGGGCTAAA
1 TTAAAGGACTAAA
11839484 CAGTAAAAAT
Statistics
Matches: 95, Mismatches: 26, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
24 13 0.14
26 5 0.05
27 3 0.03
28 4 0.04
30 70 0.74
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGAAAAAACATAAAC
Found at i:11839546 original size:112 final size:114
Alignment explanation
Indices: 11839346--11839550 Score: 274
Period size: 112 Copynumber: 1.8 Consensus size: 114
11839336 TTAAATAGCG
* * * *
11839346 AAAACATAAACTTAAAGGGCTAAAATAGAAAACATATAAATTTAAGGGACTAAAATAGCAAAAAT
1 AAAACATAAACTTAAAGGGCTAAAACAGAAAACATAGAAAGTTAAGGGACTAAAATAGCAAAAAC
* *
11839411 AGAAACTTAAAGGACTAACATAACAAAATTTTAAAGGAATAAAATGGAA
66 AGAAACTTAAAAGACTAAAATAACAAAATTTTAAAGGAATAAAATGGAA
* *
11839460 AAAACATAAACTTAAAGGGCT-AAACAGTAAAA-ATCGAAAGTTAA-GGATCT-AAATAGCAAAT
1 AAAACATAAACTTAAAGGGCTAAAACAG-AAAACATAGAAAGTTAAGGGA-CTAAAATAGCAAAA
* *
11839521 ACAGACATTTAAAAGACTAAAATAACAAAA
64 ACAGAAACTTAAAAGACTAAAATAACAAAA
11839551 ACAAAAATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
112 38 0.48
113 16 0.20
114 25 0.32
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.20
Consensus pattern (114 bp):
AAAACATAAACTTAAAGGGCTAAAACAGAAAACATAGAAAGTTAAGGGACTAAAATAGCAAAAAC
AGAAACTTAAAAGACTAAAATAACAAAATTTTAAAGGAATAAAATGGAA
Found at i:11846603 original size:3 final size:3
Alignment explanation
Indices: 11846595--11846635 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
11846585 ATGTAAATGA
11846595 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AATT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
11846636 TTATTTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:11846982 original size:43 final size:44
Alignment explanation
Indices: 11846935--11847122 Score: 122
Period size: 43 Copynumber: 4.3 Consensus size: 44
11846925 AACACGATTC
11846935 CTACGTGATGAGGACGACTGATTATCTAGGAG-TGACACGGCTT
1 CTACGTGATGAGGACGACTGATTATCTAGGAGATGACACGGCTT
* * * * * * *
11846978 CTACGTGATAAGGAGGTCTG---GTC-GGGGGATGACACGGTTT
1 CTACGTGATGAGGACGACTGATTATCTAGGAGATGACACGGCTT
* * *
11847018 CTACGTGATGAGGACGACAAGCCATCT-T-TAGGGATGATAACACGGTTT
1 CTACGTGATGAGGACGAC-TG--AT-TATCTA-GGA-GATGACACGGCTT
* * * *
11847066 CTACGTGATGAGGACGTCTGGTTATCTAGG-GGTGACACGGCTC
1 CTACGTGATGAGGACGACTGATTATCTAGGAGATGACACGGCTT
* *
11847109 CTATGTTATGAGGA
1 CTACGTGATGAGGA
11847123 GGTCTGGTCG
Statistics
Matches: 109, Mismatches: 23, Indels: 26
0.69 0.15 0.16
Matches are distributed among these distances:
39 3 0.03
40 27 0.25
41 1 0.01
43 38 0.35
44 1 0.01
45 4 0.04
46 3 0.03
47 3 0.03
48 29 0.27
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (44 bp):
CTACGTGATGAGGACGACTGATTATCTAGGAGATGACACGGCTT
Found at i:11847080 original size:131 final size:131
Alignment explanation
Indices: 11846908--11847183 Score: 390
Period size: 131 Copynumber: 2.1 Consensus size: 131
11846898 GACATCTTAT
*
11846908 CCATCTTTAGGGAGGATAACACGATTCCTACGTGATGAGGACGACTGATTATCTAGGAGTGACAC
1 CCATCTTTAGGGATGATAACACGATTCCTACGTGATGAGGACGACTGATTATCTAGGAGTGACAC
* ** * *
11846973 GGCTTCTACGTGATAAGGAGGTCTGGTCGGGGGATGACACGGTTTCTACGTGATGAGGACGACAA
66 GGCTCCTACGTGATAAGGAGGTCTGGTCGGGAAATGACACGGTTCCTACGCGATGAGGACGACAA
11847038 G
131 G
* * * * *
11847039 CCATCTTTAGGGATGATAACACGGTTTCTACGTGATGAGGACGTCTGGTTATCTAGGGGTGACAC
1 CCATCTTTAGGGATGATAACACGATTCCTACGTGATGAGGACGACTGATTATCTAGGAGTGACAC
* * * * * **
11847104 GGCTCCTATGTTATGAGGAGGTCTGGTCGGGAAATGACATGGTTCCTACGCGATGAGGACGTCTG
66 GGCTCCTACGTGATAAGGAGGTCTGGTCGGGAAATGACACGGTTCCTACGCGATGAGGACGACAA
11847169 G
131 G
11847170 CCATCTTTAGGGAT
1 CCATCTTTAGGGAT
11847184 AATGTTTCAA
Statistics
Matches: 127, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
131 127 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (131 bp):
CCATCTTTAGGGATGATAACACGATTCCTACGTGATGAGGACGACTGATTATCTAGGAGTGACAC
GGCTCCTACGTGATAAGGAGGTCTGGTCGGGAAATGACACGGTTCCTACGCGATGAGGACGACAA
G
Found at i:11847375 original size:32 final size:32
Alignment explanation
Indices: 11847315--11847375 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
11847305 GAGACAAAAC
* * *
11847315 TTTGTTTCAAAGGAAACGATCTCGAAGATGGA
1 TTTGTTTCAAAGAAAAAGATCTCAAAGATGGA
11847347 TTTGTTTCAAGAGAAAAAGA-CTCAAAGAT
1 TTTGTTTCAA-AGAAAAAGATCTCAAAGAT
11847376 TTTTGTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 18 0.72
33 7 0.28
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.28
Consensus pattern (32 bp):
TTTGTTTCAAAGAAAAAGATCTCAAAGATGGA
Found at i:11849936 original size:3 final size:3
Alignment explanation
Indices: 11849928--11849963 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
11849918 ATGTAAATGA
11849928 AAT AAT AAT AAT AAT AAT AATT AAT AAT AATT AAT A
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA-T AAT A
11849964 TTATTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 25 0.81
4 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:11849954 original size:10 final size:10
Alignment explanation
Indices: 11849930--11849963 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
11849920 GTAAATGAAA
11849930 TAATAATAA-
1 TAATAATAAT
11849939 TAATAATAAT
1 TAATAATAAT
11849949 TAATAATAAT
1 TAATAATAAT
11849959 TAATA
1 TAATA
11849964 TTATTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAATAATAAT
Found at i:11850320 original size:25 final size:25
Alignment explanation
Indices: 11850283--11850332 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
11850273 ATGTCTTTAT
11850283 TTGTATTTTTA-TTTTTAAAAATTA
1 TTGTATTTTTATTTTTTAAAAATTA
*
11850307 TTGTGTTTTCTATTTTTTAAAAATTA
1 TTGTATTTT-TATTTTTTAAAAATTA
11850333 AAAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.35
25 2 0.09
26 13 0.57
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (25 bp):
TTGTATTTTTATTTTTTAAAAATTA
Found at i:11850446 original size:2 final size:2
Alignment explanation
Indices: 11850439--11850472 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
11850429 ATAAAAATTA
11850439 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
11850473 TCGAACCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11858326 original size:21 final size:21
Alignment explanation
Indices: 11858279--11858319 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11858269 GTTATTAGTT
* *
11858279 GTTAGTGGCTCGATTGACTCA
1 GTTAATGGCTCGATTAACTCA
11858300 GTTAATGGCTCGATTAACTC
1 GTTAATGGCTCGATTAACTC
11858320 GATTAATAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (21 bp):
GTTAATGGCTCGATTAACTCA
Found at i:11858490 original size:19 final size:19
Alignment explanation
Indices: 11858418--11858482 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
11858408 AGTTAGATCA
11858418 ATTCAGACCGTTCCAATCG
1 ATTCAGACCGTTCCAATCG
*
11858437 ATTCAGACCGTTCTAATCG
1 ATTCAGACCGTTCCAATCG
11858456 ATTCAGACCGTTCCAATCG
1 ATTCAGACCGTTCCAATCG
11858475 ATTCAGAC
1 ATTCAGAC
11858483 TGGCCCAACC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (19 bp):
ATTCAGACCGTTCCAATCG
Found at i:11858495 original size:19 final size:19
Alignment explanation
Indices: 11858418--11858497 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 19
11858408 AGTTAGATCA
** *
11858418 ATTCAGACCGTTCCAATCG
1 ATTCAGACCGGCCCAACCG
** * *
11858437 ATTCAGACCGTTCTAATCG
1 ATTCAGACCGGCCCAACCG
** *
11858456 ATTCAGACCGTTCCAATCG
1 ATTCAGACCGGCCCAACCG
*
11858475 ATTCAGACTGGCCCAACCG
1 ATTCAGACCGGCCCAACCG
11858494 ATTC
1 ATTC
11858498 TAAAAGACTC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 55 1.00
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.26
Consensus pattern (19 bp):
ATTCAGACCGGCCCAACCG
Found at i:11858496 original size:38 final size:38
Alignment explanation
Indices: 11858418--11858497 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
11858408 AGTTAGATCA
** * *
11858418 ATTCAGACCGTTCCAATCGATTCAGACCGTTCTAATCG
1 ATTCAGACCGTTCCAATCGATTCAGACCGGCCCAACCG
*
11858456 ATTCAGACCGTTCCAATCGATTCAGACTGGCCCAACCG
1 ATTCAGACCGTTCCAATCGATTCAGACCGGCCCAACCG
11858494 ATTC
1 ATTC
11858498 TAAAAGACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.26
Consensus pattern (38 bp):
ATTCAGACCGTTCCAATCGATTCAGACCGGCCCAACCG
Found at i:11861608 original size:33 final size:33
Alignment explanation
Indices: 11861564--11861651 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 33
11861554 ATGGTTTGGT
* * **
11861564 CATATGGATTAGCATTTGGTTGTGCAAGTTGAC
1 CATATGAATTAGCATTTGGCTGCACAAGTTGAC
* *
11861597 CAGT-TGTATTAGCATTTGGCTGCACAGGTTGAC
1 CA-TATGAATTAGCATTTGGCTGCACAAGTTGAC
*
11861630 CATATGAATTAGCATTTAGCTG
1 CATATGAATTAGCATTTGGCTG
11861652 TGAGGGTTGG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
32 1 0.02
33 44 0.96
34 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (33 bp):
CATATGAATTAGCATTTGGCTGCACAAGTTGAC
Found at i:11863849 original size:31 final size:30
Alignment explanation
Indices: 11863811--11863881 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 30
11863801 AGAGGTTAGG
11863811 CCCAAAATTACCTAAAAGT-TA-CAAAATGACC
1 CCCAAAATTA--T-AAAGTCTATCAAAATGACC
**
11863842 CCCAAAATTATAAAGTCTATCAATTTGACC
1 CCCAAAATTATAAAGTCTATCAAAATGACC
11863872 CCCAAAATTA
1 CCCAAAATTA
11863882 AAACAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 5 0.14
29 3 0.08
30 18 0.50
31 10 0.28
ACGTcount: A:0.45, C:0.25, G:0.06, T:0.24
Consensus pattern (30 bp):
CCCAAAATTATAAAGTCTATCAAAATGACC
Found at i:11865027 original size:15 final size:16
Alignment explanation
Indices: 11865007--11865041 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
11864997 ACTATTTTCG
11865007 TACTAT-CCCTGCCAT
1 TACTATACCCTGCCAT
11865022 TACTATACCCTGCCAT
1 TACTATACCCTGCCAT
11865038 TACT
1 TACT
11865042 CTTTAAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.23, C:0.37, G:0.06, T:0.34
Consensus pattern (16 bp):
TACTATACCCTGCCAT
Found at i:11867198 original size:2 final size:2
Alignment explanation
Indices: 11867191--11867215 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11867181 TATTCGCTCA
11867191 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11867216 AATCTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11869400 original size:14 final size:14
Alignment explanation
Indices: 11869381--11869414 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
11869371 AAGGCCAAAG
11869381 TGACCTTTAGTAGT
1 TGACCTTTAGTAGT
11869395 TGACCTTTAGTAGT
1 TGACCTTTAGTAGT
*
11869409 CGACCT
1 TGACCT
11869415 AAAGGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (14 bp):
TGACCTTTAGTAGT
Found at i:11872367 original size:14 final size:14
Alignment explanation
Indices: 11872344--11872423 Score: 81
Period size: 14 Copynumber: 5.4 Consensus size: 14
11872334 TTATCCGGGA
*
11872344 TATAAATATTATAT
1 TATAATTATTATAT
11872358 TATAATTATTACTAT
1 TATAATTATTA-TAT
11872373 TAT-ATTATTATAT
1 TATAATTATTATAT
*
11872386 TAATATTATTATTGTTAT
1 T-ATA--ATTATT-ATAT
*
11872404 TATAACTATTATAT
1 TATAATTATTATAT
11872418 TATAAT
1 TATAAT
11872424 AAAAATAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
13 4 0.07
14 27 0.49
15 11 0.20
17 9 0.16
18 4 0.07
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (14 bp):
TATAATTATTATAT
Found at i:11872421 original size:37 final size:39
Alignment explanation
Indices: 11872343--11872443 Score: 114
Period size: 40 Copynumber: 2.6 Consensus size: 39
11872333 TTTATCCGGG
*
11872343 ATATAAATATTATATTATAATTATTACTATTATATTATT
1 ATATAAATATTATATTATAATTATAACTATTATATTATT
* * * *
11872382 ATATTAATATTATTATTGTTATTATAACTATTATATTATA
1 ATATAAATATTA-TATTATAATTATAACTATTATATTATT
* * *
11872422 ATAAAAATAATA-ATTATTATTA
1 ATATAAATATTATATTATAATTA
11872444 ATATTAGTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
38 9 0.17
39 11 0.21
40 32 0.62
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (39 bp):
ATATAAATATTATATTATAATTATAACTATTATATTATT
Found at i:11872440 original size:3 final size:3
Alignment explanation
Indices: 11872350--11872420 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
11872340 GGGATATAAA
* * *
11872350 TAT TA- TAT TAT AAT TAT TAC TAT TA- TAT TAT TA- TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
11872395 TAT TGT TAT TAT AAC TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
11872421 AATAAAAATA
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
2 8 0.15
3 44 0.85
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:11872685 original size:21 final size:22
Alignment explanation
Indices: 11872636--11872685 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
11872626 ACCAAGCTGT
11872636 TGCCCATGCTCCACTAGACCCCA
1 TGCCC-TGCTCCACTAGACCCCA
*
11872659 TACCCTGCTCCAC-A-ACGCCCA
1 TGCCCTGCTCCACTAGAC-CCCA
11872680 TGCCCT
1 TGCCCT
11872686 AAAAAAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.08
21 10 0.42
22 8 0.33
23 4 0.17
ACGTcount: A:0.20, C:0.50, G:0.12, T:0.18
Consensus pattern (22 bp):
TGCCCTGCTCCACTAGACCCCA
Found at i:11876403 original size:55 final size:55
Alignment explanation
Indices: 11876245--11876404 Score: 212
Period size: 55 Copynumber: 2.9 Consensus size: 55
11876235 TCAAATGATT
* *
11876245 CATGAAGAAAGACATTCGATGAATGAAGAAGTTTGAAATTGATTAAAGACCGATA
1 CATGAAGAAAGACATCCGATGAATGAAGAAGTTTGAAATTGATTGAAGACCGATA
* * * * * *
11876300 CATGAAGAAAGACATCCGATGAATGAAGAAATTTAAAACTAATTGAAGATCGATC
1 CATGAAGAAAGACATCCGATGAATGAAGAAGTTTGAAATTGATTGAAGACCGATA
* * * *
11876355 CATTAAGAAAGACATCCAATGAATGAAGAAGTTTGAAGTTGATCGAAGAC
1 CATGAAGAAAGACATCCGATGAATGAAGAAGTTTGAAATTGATTGAAGAC
11876405 TTCTTTCAAA
Statistics
Matches: 88, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 88 1.00
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.23
Consensus pattern (55 bp):
CATGAAGAAAGACATCCGATGAATGAAGAAGTTTGAAATTGATTGAAGACCGATA
Found at i:11881071 original size:10 final size:9
Alignment explanation
Indices: 11881057--11881104 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 9
11881047 AAGAAAAGAA
11881057 AAAAAATGG
1 AAAAAATGG
11881066 AAAAAATGG
1 AAAAAATGG
11881075 AAAAAATGG
1 AAAAAATGG
*
11881084 GAAAAA-GG
1 AAAAAATGG
11881092 -AAAAA-GG
1 AAAAAATGG
11881099 AAAAAA
1 AAAAAA
11881105 AAAAAGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
7 7 0.19
8 7 0.19
9 23 0.62
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (9 bp):
AAAAAATGG
Found at i:11881103 original size:1 final size:1
Alignment explanation
Indices: 11881099--11881189 Score: 92
Period size: 1 Copynumber: 91.0 Consensus size: 1
11881089 AGGAAAAAGG
* * * * * *
11881099 AAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAGAAAAAATAAAAGAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
11881164 AAAAGAAAAAAGAAAGAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
11881190 GCAGGTCTAA
Statistics
Matches: 70, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.02
Consensus pattern (1 bp):
A
Found at i:11881105 original size:9 final size:9
Alignment explanation
Indices: 11881050--11881174 Score: 59
Period size: 9 Copynumber: 14.3 Consensus size: 9
11881040 CTTGAAGAAG
*
11881050 AAAAGAAAA
1 AAAAGGAAA
11881059 AAAATGGAAA
1 AAAA-GGAAA
*
11881069 AAATGGAAA
1 AAAAGGAAA
* *
11881078 AAATGG-GA
1 AAAAGGAAA
11881086 AAAAGGAAA
1 AAAAGGAAA
*
11881095 AAGGAA-AAAA
1 AA--AAGGAAA
*
11881105 AAAAAGAAA
1 AAAAGGAAA
11881114 AAAA--AAA
1 AAAAGGAAA
**
11881121 AAAAAAAAA
1 AAAAGGAAA
*
11881130 AAAAGAAAA
1 AAAAGGAAA
*
11881139 AAAAAGAAA
1 AAAAGGAAA
11881148 AAATA--AAA
1 AAA-AGGAAA
*
11881156 GAAA-GAAA
1 AAAAGGAAA
11881164 AAAA-GAAA
1 AAAAGGAAA
11881172 AAA
1 AAA
11881175 GAAAGAAAAT
Statistics
Matches: 95, Mismatches: 12, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
7 8 0.08
8 26 0.27
9 46 0.48
10 13 0.14
11 2 0.02
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.03
Consensus pattern (9 bp):
AAAAGGAAA
Found at i:11881107 original size:19 final size:18
Alignment explanation
Indices: 11881085--11881183 Score: 96
Period size: 18 Copynumber: 5.6 Consensus size: 18
11881075 AAAAAATGGG
*
11881085 AAAAAGGAAAAAGGAAAAA
1 AAAAAAGAAAAA-GAAAAA
*
11881104 AAAAAAGAAAAAAAAAAA
1 AAAAAAGAAAAAGAAAAA
*
11881122 AAAAAAAAAAAAGAAAAA
1 AAAAAAGAAAAAGAAAAA
* * *
11881140 AAAAGA-AAAAATAAAAG
1 AAAAAAGAAAAAGAAAAA
*
11881157 AAAGAA-AAAAAG-AAAA
1 AAAAAAGAAAAAGAAAAA
*
11881173 AAGAAAGAAAA
1 AAAAAAGAAAA
11881184 TAAAAAGCAG
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
16 7 0.11
17 22 0.33
18 26 0.39
19 11 0.17
ACGTcount: A:0.87, C:0.00, G:0.12, T:0.01
Consensus pattern (18 bp):
AAAAAAGAAAAAGAAAAA
Found at i:11881113 original size:12 final size:12
Alignment explanation
Indices: 11881092--11881189 Score: 121
Period size: 12 Copynumber: 8.3 Consensus size: 12
11881082 GGGAAAAAGG
*
11881092 AAAAAGGAAAAA
1 AAAAAAGAAAAA
11881104 AAAAAAGAAAAA
1 AAAAAAGAAAAA
11881116 AAAAAA-AAAAA
1 AAAAAAGAAAAA
*
11881127 AAAAAA-AGAAA
1 AAAAAAGAAAAA
11881138 AAAAAAGAAAAA
1 AAAAAAGAAAAA
* *
11881150 ATAAAAGAAAGA
1 AAAAAAGAAAAA
11881162 AAAAAAG-AAAA
1 AAAAAAGAAAAA
*
11881173 AAGAAAGAAAATA
1 AAAAAAGAAAA-A
11881186 AAAA
1 AAAA
11881190 GCAGGTCTAA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
11 30 0.41
12 40 0.54
13 4 0.05
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:11881116 original size:7 final size:7
Alignment explanation
Indices: 11881085--11881178 Score: 86
Period size: 7 Copynumber: 13.3 Consensus size: 7
11881075 AAAAAATGGG
*
11881085 AAAAAGG
1 AAAAAGA
*
11881092 AAAAAGG
1 AAAAAGA
11881099 AAAAA-A
1 AAAAAGA
11881105 AAAAAGA
1 AAAAAGA
11881112 AAAAA-A
1 AAAAAGA
11881118 AAAAA-A
1 AAAAAGA
*
11881124 AAAAAAA
1 AAAAAGA
*
11881131 AAAGAAAA
1 AAA-AAGA
11881139 AAAAAGA
1 AAAAAGA
*
11881146 AAAAATAA
1 AAAAA-GA
11881154 AAGAAAGAA
1 AA-AAAG-A
11881163 AAAAAGA
1 AAAAAGA
11881170 AAAAAGA
1 AAAAAGA
11881177 AA
1 AA
11881179 GAAAATAAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
6 17 0.22
7 40 0.52
8 14 0.18
9 6 0.08
ACGTcount: A:0.87, C:0.00, G:0.12, T:0.01
Consensus pattern (7 bp):
AAAAAGA
Found at i:11881119 original size:24 final size:23
Alignment explanation
Indices: 11881092--11881190 Score: 121
Period size: 23 Copynumber: 4.3 Consensus size: 23
11881082 GGGAAAAAGG
*
11881092 AAAAAGGAAAAAAAAAAAGAAAA
1 AAAAAAGAAAAAAAAAAAGAAAA
*
11881115 AAAAAA-AAAAAAAAAAAAAGAAA
1 AAAAAAGAAAAAAAAAAAGA-AAA
*
11881138 AAAAAAGAAAAAATAAAAGAAAGA
1 AAAAAAGAAAAAAAAAAAGAAA-A
*
11881162 AAAAAAG-AAAAAAGAAAGAAAA
1 AAAAAAGAAAAAAAAAAAGAAAA
*
11881184 TAAAAAG
1 AAAAAAG
11881191 CAGGTCTAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
22 19 0.29
23 28 0.42
24 19 0.29
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (23 bp):
AAAAAAGAAAAAAAAAAAGAAAA
Found at i:11881123 original size:34 final size:34
Alignment explanation
Indices: 11881085--11881189 Score: 124
Period size: 34 Copynumber: 3.1 Consensus size: 34
11881075 AAAAAATGGG
* *
11881085 AAAAAGGAAAAAGGAAAAAAAAAAAGAAAAAAAA
1 AAAAAGAAAAAAAGAAAAAAAAAAAGAAAAAAAA
*
11881119 AAAAA-AAAAAAAAAAGAAAAAAAAAGAAAAAATAA
1 AAAAAGAAAAAAAGAA-AAAAAAAAAGAAAAAA-AA
* *
11881154 AAGAAAGAAAAAAAG-AAAAAAGAAAGAAAATAAA
1 AA-AAAGAAAAAAAGAAAAAAAAAAAGAAAAAAAA
11881188 AA
1 AA
11881190 GCAGGTCTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
33 7 0.11
34 25 0.41
35 18 0.30
36 4 0.07
37 7 0.11
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (34 bp):
AAAAAGAAAAAAAGAAAAAAAAAAAGAAAAAAAA
Found at i:11881202 original size:46 final size:46
Alignment explanation
Indices: 11881092--11881190 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 46
11881082 GGGAAAAAGG
* *
11881092 AAAAAGGAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAGAAA
1 AAAAAAGAAAAAATAAAAGAAAAAAAAAAAAAAAAAAAAAAAGAAA
* * *
11881138 AAAAAAGAAAAAATAAAAG-AAAGAAAAAAAGAAAAAAGAAAGAAA
1 AAAAAAGAAAAAATAAAAGAAAAAAAAAAAAAAAAAAAAAAAGAAA
11881183 ATAAAAAG
1 A-AAAAAG
11881191 CAGGTCTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 24 0.51
46 23 0.49
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (46 bp):
AAAAAAGAAAAAATAAAAGAAAAAAAAAAAAAAAAAAAAAAAGAAA
Found at i:11882536 original size:55 final size:55
Alignment explanation
Indices: 11882476--11883128 Score: 818
Period size: 55 Copynumber: 11.9 Consensus size: 55
11882466 GTGAAGCAAA
* * *
11882476 AGAAGATTGTTCAAGTTCTACACTCCCAT-AAGCAAGAGGGAGCGAACCCGTTGGT
1 AGAAGATTGTTCGAGTTCTATACTCCC-TGAAGCAAGAGGGAGCGAACCCGTTGGC
* *
11882531 AGAAGATTGTTCGAGTT-TCATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTGGA
1 AGAAGATTGTTCGAGTTCT-ATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
* * * * * **
11882586 AGAATATTGTTCAAATTCTACACTCCCTGAAGCAATA-GGAGCG-ACCCTGTTAAC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCC-GTTGGC
* * * * * * * *
11882640 -GAAAGATTATTCGAGTTATATACGCCTTGAAGAAAAAGGGAGTGAACCCGTCGGC
1 AG-AAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
* * * * *
11882695 AGAAGATTGTTCGAGCTCTACACTCCCTGAAGCAAGAGGGAGGGAACCCGTCGAC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
* * *
11882750 AGAAGATTGTTCGAGTTCTACACTCCCTGAAGCAAGAGGGAGCGAACCTGTTGGT
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
* *
11882805 AGAAGATTGTTCGAGTT-TCATACTCCCTGAAGCAAGAGGGAGAGAA-CCATTGGC
1 AGAAGATTGTTCGAGTTCT-ATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
* * * *
11882859 AGAAGATTGTTCGAGTT-TCATACTCCCTAAAGAAAGAGGAAGCGAACCCGTTGGT
1 AGAAGATTGTTCGAGTTCT-ATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
* *
11882914 AGAAGATTGTTCGAGTTTTATACTCCCTGAAGCAAGAGGGAGCGAACCTGTTGGC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
*
11882969 AGAAGATTGTTCGATTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
* * *
11883024 AGAAGAATGTTCAAGTTTTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
* *
11883079 AGAAGATTGTTTGAGTTCTATACTCCTTGAAGCAAGAGGGAGCGAACCCG
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCG
11883129 CTAGTCGAAG
Statistics
Matches: 516, Mismatches: 71, Indels: 22
0.85 0.12 0.04
Matches are distributed among these distances:
53 5 0.01
54 84 0.16
55 420 0.81
56 7 0.01
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (55 bp):
AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGC
Found at i:11882874 original size:219 final size:217
Alignment explanation
Indices: 11882476--11883128 Score: 837
Period size: 219 Copynumber: 3.0 Consensus size: 217
11882466 GTGAAGCAAA
* *
11882476 AGAAGATTGTTCAAGTTCTACACTCCCAT-AAGCAAGAGGGAGCGAACCCGTTGGTAGAAGATTG
1 AGAAGATTGTTCGAGTTCTACACTCCC-TGAAGCAAGAGGGAGCGAACCCGTTGGCAGAAGATTG
* * **
11882540 TTCGAGTT-TCATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTGGAAGAATATTGTTCAAATTC
65 TTCGAGTTCT-ATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGAAGAAGATTGTTCAGTTTC
* * * ** * *
11882604 TACACTCCCTGAAGCAATA-GGAGCGACCCTGTTAAC-GAAAGATTATTCGAGTTATATACGCCT
129 -ATACTCCCTGAAGCAAGAGGGAGCGAACC-GTTGGCAG-AAGATTGTTCGAGTT-TATACTCCT
* *
11882667 TGAAGAAAAAGGGAGTGAACCCGTCGGC
190 TGAAGAAAGAGGGAGCGAACCCGTCGGC
* * * *
11882695 AGAAGATTGTTCGAGCTCTACACTCCCTGAAGCAAGAGGGAGGGAACCCGTCGACAGAAGATTGT
1 AGAAGATTGTTCGAGTTCTACACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGCAGAAGATTGT
* * *
11882760 TCGAGTTCTACACTCCCTGAAGCAAGAGGGAGCGAACCTGTTGGTAGAAGATTGTTCGAGTTTCA
66 TCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGAAGAAGATTGTTC-AGTTTCA
* * * *
11882825 TACTCCCTGAAGCAAGAGGGAGAGAACCATTGGCAGAAGATTGTTCGAGTTTCATACTCCCTAAA
130 TACTCCCTGAAGCAAGAGGGAGCGAACCGTTGGCAGAAGATTGTTCGAGTTT-ATACTCCTTGAA
* * *
11882890 GAAAGAGGAAGCGAACCCGTTGGT
194 GAAAGAGGGAGCGAACCCGTCGGC
* * *
11882914 AGAAGATTGTTCGAGTTTTATACTCCCTGAAGCAAGAGGGAGCGAACCTGTTGGCAGAAGATTGT
1 AGAAGATTGTTCGAGTTCTACACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGCAGAAGATTGT
* * * *
11882979 TCGATTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGCAGAAGAATGTTCAAGTTTTA
66 TCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGAAGAAGATTGTTC-AGTTTCA
*
11883044 TACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGCAGAAGATTGTTTGAGTTCTATACTCCTTGA
130 TACTCCCTGAAGCAAGAGGGAGCGAA-CCGTTGGCAGAAGATTGTTCGAGTT-TATACTCCTTGA
*
11883109 AGCAAGAGGGAGCGAACCCG
193 AGAAAGAGGGAGCGAACCCG
11883129 CTAGTCGAAG
Statistics
Matches: 376, Mismatches: 50, Indels: 15
0.85 0.11 0.03
Matches are distributed among these distances:
218 2 0.01
219 309 0.82
220 64 0.17
221 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (217 bp):
AGAAGATTGTTCGAGTTCTACACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGCAGAAGATTGT
TCGAGTTCTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGAAGAAGATTGTTCAGTTTCAT
ACTCCCTGAAGCAAGAGGGAGCGAACCGTTGGCAGAAGATTGTTCGAGTTTATACTCCTTGAAGA
AAGAGGGAGCGAACCCGTCGGC
Found at i:11882972 original size:274 final size:273
Alignment explanation
Indices: 11882476--11883126 Score: 873
Period size: 274 Copynumber: 2.4 Consensus size: 273
11882466 GTGAAGCAAA
11882476 AGAAGATTGTTCAAGTTCTACACTCCCAT-AAGCAAGAGGGAGCGAACCCGTTGGTAGAAGATTG
1 AGAAGATTGTTCAAGTTCTACACTCCC-TGAAGCAAGAGGGAGCGAACCCGTTGGTAGAAGATTG
* * *
11882540 TTCGAGTTTCATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTGGAAGAATATTGTTCAAATTCT
65 TTCGAGTTTCATACTCCCTGAAGCAAGAGGGAGCGAA-CCATTGGAAGAAGATTGTTCAAATTCT
* * * *
11882605 ACACTCCCTGAAGCAATAGGAGCGACCCTGTTAACGAAAGATTATTCGAGTTATATACGCCTTGA
129 ACACTCCCTAAAGAAAGAGGAGCGACCCTGTTAACGAAAGATTATTCGAGTTATATACGCCCTGA
*
11882670 AGAAAAAGGGAGTGAACCCGTCGGCAGAAGATTGTTCGAGCTCTACACTCCCTGAAGCAAGAGGG
194 AGAAAAAGGGAGCGAACCCGTCGGCAGAAGATTGTTCGAGCTCTACACTCCCTGAAGCAAGAGGG
*
11882735 AGGGAACCCGTCGAC
259 AGCGAACCCGTCGAC
* *
11882750 AGAAGATTGTTCGAGTTCTACACTCCCTGAAGCAAGAGGGAGCGAACCTGTTGGTAGAAGATTGT
1 AGAAGATTGTTCAAGTTCTACACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGTAGAAGATTGT
* * * *
11882815 TCGAGTTTCATACTCCCTGAAGCAAGAGGGAGAGAACCATTGGCAGAAGATTGTTCGAGTT-TCA
66 TCGAGTTTCATACTCCCTGAAGCAAGAGGGAGCGAACCATTGGAAGAAGATTGTTCAAATTCT-A
* * * * *
11882879 TACTCCCTAAAGAAAGAGGAAGCGAACCC-GTT--GGTAGAAGATTGTTCGAGTTTTATACTCCC
130 CACTCCCTAAAGAAAGAGG-AGCG-ACCCTGTTAACG-A-AAGATTATTCGAGTTATATACGCCC
* * * * ** *
11882941 TGAAGCAAGAGGGAGCGAACCTGTTGGCAGAAGATTGTTCGATTTCTATACTCCCTGAAGCAAGA
191 TGAAGAAAAAGGGAGCGAACCCGTCGGCAGAAGATTGTTCGAGCTCTACACTCCCTGAAGCAAGA
* *
11883006 GGGAGCGAACCCGTTGGC
256 GGGAGCGAACCCGTCGAC
* * * *
11883024 AGAAGAATGTTCAAGTTTTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGCAGAAGATTGT
1 AGAAGATTGTTCAAGTTCTACACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGTAGAAGATTGT
* *
11883089 TTGAG-TTCTATACTCCTTGAAGCAAGAGGGAGCGAACC
66 TCGAGTTTC-ATACTCCCTGAAGCAAGAGGGAGCGAACC
11883127 CGCTAGTCGA
Statistics
Matches: 332, Mismatches: 38, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
272 2 0.01
273 41 0.12
274 285 0.86
275 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.23
Consensus pattern (273 bp):
AGAAGATTGTTCAAGTTCTACACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGTAGAAGATTGT
TCGAGTTTCATACTCCCTGAAGCAAGAGGGAGCGAACCATTGGAAGAAGATTGTTCAAATTCTAC
ACTCCCTAAAGAAAGAGGAGCGACCCTGTTAACGAAAGATTATTCGAGTTATATACGCCCTGAAG
AAAAAGGGAGCGAACCCGTCGGCAGAAGATTGTTCGAGCTCTACACTCCCTGAAGCAAGAGGGAG
CGAACCCGTCGAC
Found at i:11883314 original size:14 final size:14
Alignment explanation
Indices: 11883295--11883398 Score: 102
Period size: 14 Copynumber: 7.2 Consensus size: 14
11883285 TTTGTCCTGG
*
11883295 TTATAAATATTATA
1 TTATAATTATTATA
11883309 TTATAATTATTACTA
1 TTATAATTATTA-TA
11883324 TTAT-ATTATTATA
1 TTATAATTATTATA
* *
11883337 TTATTATTATTGTTA
1 TTATAATTATT-ATA
*
11883352 TTATAACTATTATA
1 TTATAATTATTATA
*
11883366 TTATAATAATTATTA
1 TTATAATTATTA-TA
* *
11883381 GTATTATTATTAATA
1 TTATAATTATT-ATA
11883396 TTA
1 TTA
11883399 GTTATATTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 9
0.79 0.12 0.10
Matches are distributed among these distances:
13 6 0.08
14 36 0.49
15 31 0.42
16 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (14 bp):
TTATAATTATTATA
Found at i:11883333 original size:3 final size:3
Alignment explanation
Indices: 11883302--11883412 Score: 88
Period size: 3 Copynumber: 38.3 Consensus size: 3
11883292 TGGTTATAAA
* *
11883302 TAT TA- TAT TAT AAT TAT TAC TAT TA- TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
11883347 TGT TAT TAT AAC TAT TA- TAT TAT AAT AAT TAT TAG TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
11883394 TAT TAGT TA- TAT TTT TAT T
1 TAT TA-T TAT TAT TAT TAT T
11883413 TCTTGCAGGC
Statistics
Matches: 84, Mismatches: 18, Indels: 12
0.74 0.16 0.11
Matches are distributed among these distances:
2 10 0.12
3 71 0.85
4 3 0.04
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:11886835 original size:20 final size:20
Alignment explanation
Indices: 11886812--11886881 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
11886802 TTTTTATTGA
11886812 TAAATAGTTATAAAATGATT
1 TAAATAGTTATAAAATGATT
*
11886832 TAAATAGTTAT-AAATTATT
1 TAAATAGTTATAAAATGATT
* * *
11886851 AAATTATATTTCTAAAATGATT
1 TAA--ATAGTTATAAAATGATT
11886873 TAAATAGTT
1 TAAATAGTT
11886882 TTTGGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 9 0.22
20 16 0.40
21 6 0.15
22 9 0.22
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (20 bp):
TAAATAGTTATAAAATGATT
Found at i:11894566 original size:18 final size:18
Alignment explanation
Indices: 11894543--11894577 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11894533 TTATATTTAT
11894543 TATTATTAATAATAATAG
1 TATTATTAATAATAATAG
*
11894561 TATTATTATTAATAATA
1 TATTATTAATAATAATA
11894578 TTGGTTGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
TATTATTAATAATAATAG
Found at i:11899445 original size:27 final size:27
Alignment explanation
Indices: 11899409--11899586 Score: 275
Period size: 27 Copynumber: 6.6 Consensus size: 27
11899399 GGATCAACAT
*
11899409 TTTTGCATCTGCATTTGCATCTTTGCA
1 TTTTGCATCTGCATTTACATCTTTGCA
* *
11899436 TTTTTCATCTGCATTTACATCTTTGTA
1 TTTTGCATCTGCATTTACATCTTTGCA
*
11899463 TTTTGCATATGCATTTACATCTTTGCA
1 TTTTGCATCTGCATTTACATCTTTGCA
* *
11899490 TTTTGCATCTGTATTTACATATTTGCA
1 TTTTGCATCTGCATTTACATCTTTGCA
* *
11899517 TTTTACATCTGCATTTACATCTTTACA
1 TTTTGCATCTGCATTTACATCTTTGCA
11899544 TTTTGCATCTGCATTTACATCTTTGCA
1 TTTTGCATCTGCATTTACATCTTTGCA
*
11899571 TTTTGCATTTGCATTT
1 TTTTGCATCTGCATTT
11899587 CATTTTTAAA
Statistics
Matches: 135, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 135 1.00
ACGTcount: A:0.20, C:0.19, G:0.10, T:0.51
Consensus pattern (27 bp):
TTTTGCATCTGCATTTACATCTTTGCA
Found at i:11900807 original size:13 final size:12
Alignment explanation
Indices: 11900788--11900849 Score: 72
Period size: 12 Copynumber: 5.0 Consensus size: 12
11900778 AAGCAAGGAT
11900788 AATAAAGAAAAA
1 AATAAAGAAAAA
*
11900800 ATATAAAGCAAAA
1 A-ATAAAGAAAAA
*
11900813 AACAAAGAAAAA
1 AATAAAGAAAAA
11900825 AA-AGAAGAAAAA
1 AATA-AAGAAAAA
11900837 AAGTAAAGAAAAA
1 AA-TAAAGAAAAA
11900850 GGAACGAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
11 1 0.02
12 22 0.51
13 19 0.44
14 1 0.02
ACGTcount: A:0.79, C:0.03, G:0.11, T:0.06
Consensus pattern (12 bp):
AATAAAGAAAAA
Found at i:11900819 original size:25 final size:25
Alignment explanation
Indices: 11900769--11900825 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
11900759 AAAATGAAAA
* *
11900769 AAAAAATTAAAGCAAGGATAATAAAG
1 AAAAAATTAAAGCAA-GAAAACAAAG
11900795 AAAAAATATAAAGCAA-AAAACAAAG
1 AAAAAAT-TAAAGCAAGAAAACAAAG
11900820 AAAAAA
1 AAAAAA
11900826 AAGAAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 13 0.46
26 7 0.25
27 8 0.29
ACGTcount: A:0.74, C:0.05, G:0.11, T:0.11
Consensus pattern (25 bp):
AAAAAATTAAAGCAAGAAAACAAAG
Found at i:11900848 original size:12 final size:11
Alignment explanation
Indices: 11900788--11900849 Score: 52
Period size: 13 Copynumber: 5.1 Consensus size: 11
11900778 AAGCAAGGAT
11900788 AATAAAGAAAAA
1 AATAAAG-AAAA
11900800 ATATAAAGCAAAA
1 A-ATAAAG-AAAA
*
11900813 AACAAAGAAAA
1 AATAAAGAAAA
*
11900824 AAAAGAAGAAAAA
1 AATA-AAG-AAAA
11900837 AAGTAAAGAAAA
1 AA-TAAAGAAAA
11900849 A
1 A
11900850 GGAACGAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
11 7 0.17
12 14 0.33
13 20 0.48
14 1 0.02
ACGTcount: A:0.79, C:0.03, G:0.11, T:0.06
Consensus pattern (11 bp):
AATAAAGAAAA
Found at i:11901620 original size:28 final size:28
Alignment explanation
Indices: 11901531--11901609 Score: 131
Period size: 28 Copynumber: 2.8 Consensus size: 28
11901521 TAACCAAAAA
11901531 TAACCTGAAACACATTACCTTCCCAAAT
1 TAACCTGAAACACATTACCTTCCCAAAT
* *
11901559 TAACCTGAAACGCATTACCTCCCCAAAT
1 TAACCTGAAACACATTACCTTCCCAAAT
*
11901587 TAACCTGAAACACGTTACCTTCC
1 TAACCTGAAACACATTACCTTCC
11901610 TAAGTCAACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.35, C:0.34, G:0.06, T:0.24
Consensus pattern (28 bp):
TAACCTGAAACACATTACCTTCCCAAAT
Found at i:11902937 original size:20 final size:21
Alignment explanation
Indices: 11902912--11902972 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
11902902 TTCTTGATTT
11902912 GTAAGTCCTCCGGGCCATCA-
1 GTAAGTCCTCCGGGCCATCAC
* * *
11902932 GTAAGTCTTCCGAG-CATGATGC
1 GTAAGTCCTCCGGGCCATCA--C
11902954 GTAAGTCCTCCGGGCCATC
1 GTAAGTCCTCCGGGCCATC
11902973 CATAAGACCT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.13
20 12 0.39
22 12 0.39
23 3 0.10
ACGTcount: A:0.20, C:0.31, G:0.26, T:0.23
Consensus pattern (21 bp):
GTAAGTCCTCCGGGCCATCAC
Found at i:11903201 original size:20 final size:21
Alignment explanation
Indices: 11903175--11903236 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
11903165 TTTCTTGATT
11903175 TGTAAGTCCTCCGGGCCATCA
1 TGTAAGTCCTCCGGGCCATCA
* * *
11903196 -GTAAGTCTTCCGAG-CATGA
1 TGTAAGTCCTCCGGGCCATCA
11903215 TGTGTAAGTCCTCCGGGCCATC
1 --TGTAAGTCCTCCGGGCCATC
11903237 CATAAGACCT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
19 4 0.13
20 12 0.39
22 12 0.39
23 3 0.10
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (21 bp):
TGTAAGTCCTCCGGGCCATCA
Found at i:11903354 original size:132 final size:132
Alignment explanation
Indices: 11902857--11903904 Score: 1794
Period size: 132 Copynumber: 7.9 Consensus size: 132
11902847 ACCCAAATAA
* * *
11902857 CAGGATGTTTTCAAATGATATTTTAGAAACTAACCCTTCGGGCGTTTCTTGATTTGTAAGTCCTC
1 CAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTC
11902922 CGGGCCATCAGTAAGTCTTCCGAGCATGATGCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAG
66 CGGGCCATCAGTAAGTCTTCCGAGCATGATGCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAG
11902987 TG
131 TG
* *
11902989 CAGGATGTTTTCAAATGAGATTTTAGAAACTAATCCTT-TGGGGTTTCTTGATTTGTAAGTCCTC
1 CAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTC
* *
11903053 CAGGCCATCAGTAAGTCTTCCGAGCATGATGCGTAAGTCCTCTGGGCCATCCATAAGACCTTCAG
66 CGGGCCATCAGTAAGTCTTCCGAGCATGATGCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAG
11903118 TG
131 TG
11903120 CAGGATGTTTTCAAATGAGATTTTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCT
1 CAGGATGTTTTCAAATGAGATTTT-AGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCT
*
11903185 CCGGGCCATCAGTAAGTCTTCCGAGCATGATGTGTAAGTCCTCCGGGCCATCCATAAGACCTTCA
65 CCGGGCCATCAGTAAGTCTTCCGAGCATGATGCGTAAGTCCTCCGGGCCATCCATAAGACCTTCA
11903250 GTG
130 GTG
* * * * *
11903253 CAGGATGTTTTCAAATGATATTTTAAAAACTAACCCTTCAGGCGTTTCTTGATTTGTAAGTCCTC
1 CAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTC
*
11903318 CGAGCCATCAGTAAGTCTTCCGAGCATGATGCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAG
66 CGGGCCATCAGTAAGTCTTCCGAGCATGATGCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAG
11903383 TG
131 TG
*
11903385 CAGGATATTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTC
1 CAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTC
* * *
11903450 TGGGCCATCAGTAAGTCTTCCGAGCATGATGTGTAAGTCCTCCGGGACATCCATAAGACCTTCAG
66 CGGGCCATCAGTAAGTCTTCCGAGCATGATGCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAG
11903515 TG
131 TG
* *
11903517 CAAGATGTTTTCAAATGAGATTTTAAGAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCT
1 CAGGATGTTTTCAAATGAGATTTT-AGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCT
* *
11903582 CCGGACCATCAGTAAGTCTTCCGAGCATGATGTGTAAGTCCTCCGGGCCATCCATAAGACCTTCA
65 CCGGGCCATCAGTAAGTCTTCCGAGCATGATGCGTAAGTCCTCCGGGCCATCCATAAGACCTTCA
11903647 GTG
130 GTG
*
11903650 CAGGATGTTTTCAAATGATATTTTAGAAACTAAGCCTTC-GGGGTTTCTTGATTTGTAAGTCCTC
1 CAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTC
* *
11903714 CGGGCCATCAGTAAGTCTTCCAAGCATGATGTGTAAGTCCTCCGGGCCATCCATAAGACCTTCAG
66 CGGGCCATCAGTAAGTCTTCCGAGCATGATGCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAG
11903779 TG
131 TG
* * *
11903781 CATGATGTTTTCAAATGAGATTTTAGAAACTAAGACTTCGGGGGTTTCTTGATTTGTAAGTCCTT
1 CAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTC
* *
11903846 CGGGCCATCAGTAAGTCTTCCGAGCATGATGCGTAAGTCCTCTGGGCCATCCCTAAGAC
66 CGGGCCATCAGTAAGTCTTCCGAGCATGATGCGTAAGTCCTCCGGGCCATCCATAAGAC
11903905 ATTGGGCAGA
Statistics
Matches: 865, Mismatches: 47, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
131 238 0.28
132 389 0.45
133 238 0.28
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (132 bp):
CAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTC
CGGGCCATCAGTAAGTCTTCCGAGCATGATGCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAG
TG
Found at i:11904156 original size:3 final size:3
Alignment explanation
Indices: 11904141--11904189 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
11904131 AATATTATAC
* * *
11904141 TTA TTA -TA ATA TTA TTA -TA TTA TTA TTA TTA ATA TTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11904187 TTA
1 TTA
11904190 ATAATAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:11910358 original size:21 final size:21
Alignment explanation
Indices: 11910333--11910395 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
11910323 AATGGGATGA
*
11910333 GTGCCACAACAATGATGTTGT
1 GTGCCACAACAATGATGTTGC
*
11910354 GTGCCACAAAAATGATGTTGC
1 GTGCCACAACAATGATGTTGC
* * *
11910375 ATGCCACAGCAATGATATTGC
1 GTGCCACAACAATGATGTTGC
11910396 TACTAGCAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (21 bp):
GTGCCACAACAATGATGTTGC
Found at i:11920446 original size:37 final size:36
Alignment explanation
Indices: 11920403--11920930 Score: 324
Period size: 36 Copynumber: 14.2 Consensus size: 36
11920393 TTTTAAATCA
* *
11920403 ATAATATATAATTTTAAAAATCTGTTTTTAAAAATAT
1 ATAATATATAATTTTAAAAA-CTATTTTTAAAAACAT
** *
11920440 AT-A-ATATGGTTTTGAAAA-TATGTTTTAAAAACAT
1 ATAATATATAATTTTAAAAACTAT-TTTTAAAAACAT
* * * *
11920474 ATATTATATAGTTTTAAAAA-TAATTTTTGAAAACGT
1 ATAATATATAATTTTAAAAACT-ATTTTTAAAAACAT
* *
11920510 ATAATATATTATTTTAAAAA-TAATTTTTAAAAATAT
1 ATAATATATAATTTTAAAAACT-ATTTTTAAAAACAT
* * ** * * *
11920546 ATATTATATAATTTCAAAAA--A--AATGAATATAT
1 ATAATATATAATTTTAAAAACTATTTTTAAAAACAT
* * * * *
11920578 ATATTATATAATTTTGAAAAACAATATTTGAAAACCT
1 ATAATATATAATTTT-AAAAACTATTTTTAAAAACAT
* * *
11920615 ATAATATATAGTTTTAAAAACAATTTTTGAAAACAT
1 ATAATATATAATTTTAAAAACTATTTTTAAAAACAT
* * * *
11920651 ATATTATATAATTTCAAAAACAATTTTTGAAAACAT
1 ATAATATATAATTTTAAAAACTATTTTTAAAAACAT
* * * *
11920687 ATATATATTATATAGCTTTGAAAAACAATTTTTGAAAACGT
1 ATA-ATA-TATA-A--TTTTAAAAACTATTTTTAAAAACAT
**
11920728 ATAATATATAATTTTTTTTAAAAA-TATTTTTAAAAATGT
1 ATAATATATAA----TTTTAAAAACTATTTTTAAAAACAT
* **
11920767 ATAATATATAATATTTAAAAATATATATTTTTAAAAATGT
1 ATAATATATAAT-TTT-AAAA-A-CTATTTTTAAAAACAT
*
11920807 ATAATATATAGTTTTTAAAAAAC-ATTTTTTAAAAACCAT
1 ATAATATATA-ATTTT-AAAAACTA-TTTTTAAAAA-CAT
* *
11920846 ATAATATATAGTTTTTAAAAAATACTTTTT-AAAACAT
1 ATAATATATA-ATTTTAAAAACTA-TTTTTAAAAACAT
* **
11920883 ATAATATATAATTTTTTAAAAACATATTTTTGAAAATGT
1 ATAATATATAA--TTTTAAAAAC-TATTTTTAAAAACAT
11920922 ATAATATAT
1 ATAATATAT
11920931 TTTTTTTAGA
Statistics
Matches: 407, Mismatches: 55, Indels: 56
0.79 0.11 0.11
Matches are distributed among these distances:
32 21 0.05
33 7 0.02
34 14 0.03
35 14 0.03
36 130 0.32
37 43 0.11
38 39 0.10
39 68 0.17
40 44 0.11
41 27 0.07
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.43
Consensus pattern (36 bp):
ATAATATATAATTTTAAAAACTATTTTTAAAAACAT
Found at i:11920618 original size:105 final size:109
Alignment explanation
Indices: 11920472--11920896 Score: 386
Period size: 105 Copynumber: 3.8 Consensus size: 109
11920462 TTTTAAAAAC
*
11920472 ATATATTATATAGTTTT-AAAAATAATTTTTGAAAACGTATAATATATTATTTTAAAAATAATTT
1 ATATATTATATAGTTTTGAAAAACAATTTTTGAAAACGTATAATATATTATTTTAAAAATAATTT
11920536 TTAAAAATATATATTATATAATTTCAAAAA-AA-ATG-A-ATAT
66 TTAAAAATATATATTATATAATTTCAAAAACAATATGAACATAT
* * * *
11920576 ATATATTATATAATTTTGAAAAACAATATTTGAAAACCTATAATATA-TAGTTTTAAAAACAATT
1 ATATATTATATAGTTTTGAAAAACAATTTTTGAAAACGTATAATATATTA-TTTTAAAAATAATT
* * *
11920640 TTTGAAAACATATATTATATAATTTCAAAAACAATTTTTGAAAACATAT
65 TTTAAAAATATATATTATATAATTTCAAAAACAA--TATG--AACATAT
* *
11920689 ATATATTATATAGCTTTGAAAAACAATTTTTGAAAACGTATAATATATAATTTTTTTTAAAAAT-
1 ATATATTATATAGTTTTGAAAAACAATTTTTGAAAACGTAT-A-ATAT-A-TTATTTTAAAAATA
* * * * * *
11920753 ATTTTTAAAAATGTATAATATATAATATTTAAAAATATATATTTTTAA-AAAT
62 ATTTTTAAAAATATATATTATATAAT-TTCAAAAACA-ATA---TGAACATAT
* * * * * *
11920805 GTATAATATATAGTTTTTAAAAAACATTTTTTAAAAACCATATAATATA-TAGTTTTTAAAAAAT
1 ATATATTATATAG-TTTTGAAAAACAATTTTTGAAAA-CGTATAATATATTA--TTTT-AAAAAT
*
11920869 ACTTTTTAAAACATATA-A-TATATAATTT
61 AATTTTTAAAA-ATATATATTATATAATTT
11920897 TTTAAAAACA
Statistics
Matches: 261, Mismatches: 33, Indels: 43
0.77 0.10 0.13
Matches are distributed among these distances:
104 18 0.07
105 68 0.26
106 2 0.01
109 2 0.01
112 1 0.00
113 42 0.16
114 1 0.00
115 11 0.04
116 56 0.21
117 49 0.19
118 10 0.04
119 1 0.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (109 bp):
ATATATTATATAGTTTTGAAAAACAATTTTTGAAAACGTATAATATATTATTTTAAAAATAATTT
TTAAAAATATATATTATATAATTTCAAAAACAATATGAACATAT
Found at i:11920758 original size:39 final size:37
Alignment explanation
Indices: 11920577--11920952 Score: 253
Period size: 39 Copynumber: 9.8 Consensus size: 37
11920567 AATGAATATA
* * * * * *
11920577 TATATTATATAATTTTGAAAAACA-ATATTTGAAAACC
1 TATAATATATATTTTTTAAAAA-ATATTTTTAAAAACG
* * *
11920614 TATAATATATA-GTTTTAAAAACA-ATTTTTGAAAACA
1 TATAATATATATTTTTTAAAAA-ATATTTTTAAAAACG
* * * * *
11920650 TATATTATATA-ATTTCAAAAACA-ATTTTTGAAAACA
1 TATAATATATATTTTTTAAAAA-ATATTTTTAAAAACG
* * *
11920686 TATATATATTATATAGCTTTGAAAAACA-ATTTTTGAAAACG
1 TATA-ATA-TATAT--TTTTTAAAAA-ATATTTTTAAAAACG
* *
11920727 TATAATATATAATTTTTTTTAAAAATATTTTTAAAAATG
1 TATAATATAT-A-TTTTTTAAAAAATATTTTTAAAAACG
* * *
11920766 TATAATATATAATATTTAAAAATATATATTTTTAAAAATG
1 TATAATATAT-ATTTTTTAAAA-A-ATATTTTTAAAAACG
* * *
11920806 TATAATATATAGTTTTTAAAAAACATTTTTTAAAAACCA
1 TATAATATATATTTTTTAAAAAATA-TTTTTAAAAA-CG
* *
11920845 TATAATATATAGTTTTTAAAAAATACTTTTT-AAAACA
1 TATAATATATATTTTTTAAAAAATA-TTTTTAAAAACG
* *
11920882 TATAATATATAATTTTTTAAAAACATATTTTTGAAAATG
1 TATAATATAT-ATTTTTTAAAAA-ATATTTTTAAAAACG
*
11920921 TATAATATATTTTTTTTAGAAAAATGATTTTT
1 TATAATATATATTTTTTA-AAAAAT-ATTTTT
11920953 TTATTTTGAA
Statistics
Matches: 290, Mismatches: 32, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
36 58 0.20
37 26 0.09
38 52 0.18
39 98 0.34
40 29 0.10
41 27 0.09
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (37 bp):
TATAATATATATTTTTTAAAAAATATTTTTAAAAACG
Found at i:11920802 original size:15 final size:17
Alignment explanation
Indices: 11920769--11920813 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
11920759 AAAAATGTAT
11920769 AATATATAATATTTAAA
1 AATATATAATATTTAAA
*
11920786 AATATAT-ATTTTTAAA
1 AATATATAATATTTAAA
*
11920802 AATGTATAATAT
1 AATATATAATAT
11920814 ATAGTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATATATAATATTTAAA
Found at i:11921029 original size:13 final size:12
Alignment explanation
Indices: 11920979--11921029 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
11920969 TTATCGGTTA
*
11920979 TTTTATGTATTT
1 TTTTATTTATTT
*
11920991 ATTTATTTATTT
1 TTTTATTTATTT
*
11921003 TGTTTTTTTA-TT
1 T-TTTATTTATTT
11921015 TTTTATTTCATTT
1 TTTTATTT-ATTT
11921028 TT
1 TT
11921030 AGGTCCATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 6 0.19
12 14 0.45
13 11 0.35
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTATTTATTT
Found at i:11921709 original size:21 final size:21
Alignment explanation
Indices: 11921685--11921725 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
11921675 TGTGTTTCGG
11921685 GTATTTAGGCTTCAGTTTTGA
1 GTATTTAGGCTTCAGTTTTGA
11921706 GTATTTAGGCTTCAGTTTTG
1 GTATTTAGGCTTCAGTTTTG
11921726 GGTAGGCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.10, G:0.24, T:0.49
Consensus pattern (21 bp):
GTATTTAGGCTTCAGTTTTGA
Found at i:11921930 original size:14 final size:14
Alignment explanation
Indices: 11921911--11921946 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
11921901 CGTTCGATTA
*
11921911 TATGTTTGTCCATT
1 TATGTTCGTCCATT
*
11921925 TATGTTCGTTCATT
1 TATGTTCGTCCATT
11921939 TATGTTCG
1 TATGTTCG
11921947 AACATATTGC
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:0.14, C:0.14, G:0.17, T:0.56
Consensus pattern (14 bp):
TATGTTCGTCCATT
Found at i:11922270 original size:27 final size:23
Alignment explanation
Indices: 11922210--11922254 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
11922200 GTGTTTGTGT
*
11922210 TGTTCATTTATTGTGTTCGTTTA
1 TGTTCATTTATTATGTTCGTTTA
11922233 TGTTCATTTATTATGTTCGTTT
1 TGTTCATTTATTATGTTCGTTT
11922255 GTTTGAGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.09, G:0.16, T:0.62
Consensus pattern (23 bp):
TGTTCATTTATTATGTTCGTTTA
Found at i:11922354 original size:16 final size:16
Alignment explanation
Indices: 11922333--11922365 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11922323 ACAAAAAAAT
*
11922333 TGTTCGTTTATGTTCG
1 TGTTCGTATATGTTCG
11922349 TGTTCGTATATGTTCG
1 TGTTCGTATATGTTCG
11922365 T
1 T
11922366 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.24, T:0.55
Consensus pattern (16 bp):
TGTTCGTATATGTTCG
Found at i:11923606 original size:16 final size:18
Alignment explanation
Indices: 11923575--11923612 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
11923565 ATTTTTAAGT
11923575 TAAGAAACGAAAG-TTTA
1 TAAGAAACGAAAGTTTTA
11923592 TAAGAAACG-AAGTTTTA
1 TAAGAAACGAAAGTTTTA
11923609 TAAG
1 TAAG
11923613 GTTTTGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.26
Consensus pattern (18 bp):
TAAGAAACGAAAGTTTTA
Found at i:11923691 original size:4 final size:4
Alignment explanation
Indices: 11923684--11925647 Score: 3410
Period size: 4 Copynumber: 500.5 Consensus size: 4
11923674 CGCATATATA
11923684 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11923732 TATG TATG TATG TATG -ATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11923779 TATG TATG TATTG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TA-TG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11923828 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11923876 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11923924 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11923972 TATG TTATG TATG TA-G TATG TATG TATG TATG TATG --TG TATG TATG
1 TATG -TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
11924018 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAGG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924066 TATG TATG TA-G TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924113 TATG TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
11924160 TATG TATG TATG TATT TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924208 TATG TATG TATG TATG TATG TATG TATG T-TG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924255 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924303 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
11924349 TATG TATG TATG TATG TATG TATG TCTG TATG TATG TA-- TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924395 TATG TA-G TATG TATG TATG TATG TATG TATG TA-- TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924440 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924488 TATG TA-G TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924535 TATG TA-G TATG TATG TATG -ATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924581 -ATG TATG TATG TATG TATG T-TG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924627 TATG T-TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924674 TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924720 -ATG TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924765 TAGTG TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATG TATG
1 TA-TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
11924813 TATG TATG TATG TATG TATG TATG TATTG TATG TATG TAGG TATG TATG
1 TATG TATG TATG TATG TATG TATG TA-TG TATG TATG TATG TATG TATG
11924862 TA-G TATG TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11924908 TATG TATG TATG TATG TATG T-TG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
11924955 TATG TATG TAGG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11925003 TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11925050 TATG TATG TATG TATG TATG TATG TATG TGATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG T-ATG TATG TATG TATG TATG
*
11925099 TATG TATG TCTG TATG TATG TATG TATG --TG TATG TATG TAGTG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-TG TATG
*
11925146 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TCTG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11925194 TA-G TATG TATG TATG --TG TATG TATG TATG TATG TATCTG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA--TG TATG TATG
11925241 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11925289 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
11925337 TATG TAGTA TATG TATG TATG TATG T-TG TATG TATG TATG TATG TATG
1 TATG TA-TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
11925385 TATG TCTG TATG TATG TATG GATG TATG TATG TATG TATG -ATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11925432 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG -ATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
11925479 TATG TATG TATG TATG TA-- TATG TATG TATG TATG TCTG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11925525 TATG TA-- TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
11925569 TATG TATG TA-- TATG TATG TCTG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11925615 TATG TATG TATG TATG TATG TATG TATG -ATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TA
11925648 CATGTGTGTA
Statistics
Matches: 1880, Mismatches: 24, Indels: 112
0.93 0.01 0.06
Matches are distributed among these distances:
2 24 0.01
3 69 0.04
4 1756 0.93
5 27 0.01
6 4 0.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:11925798 original size:16 final size:15
Alignment explanation
Indices: 11925769--11925819 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
11925759 CGTTCATTTA
11925769 ATAAAT-AAACGAAC
1 ATAAATGAAACGAAC
11925783 ATAAATGAATACGAAC
1 ATAAATGAA-ACGAAC
*
11925799 ATAAACGAACACGAAC
1 ATAAATGAA-ACGAAC
11925815 ATAAA
1 ATAAA
11925820 CGAACAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.18
15 2 0.06
16 25 0.76
ACGTcount: A:0.61, C:0.16, G:0.10, T:0.14
Consensus pattern (15 bp):
ATAAATGAAACGAAC
Found at i:11925820 original size:16 final size:16
Alignment explanation
Indices: 11925777--11925825 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
11925767 TAATAAATAA
* *
11925777 ACGAACATAAATGAAT
1 ACGAACATAAACGAAC
11925793 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
11925809 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
11925825 A
1 A
11925826 ATTTTTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:11925911 original size:24 final size:24
Alignment explanation
Indices: 11925879--11925971 Score: 116
Period size: 24 Copynumber: 3.9 Consensus size: 24
11925869 CATTTAAATG
*
11925879 ATAAACGAACACAAACAAACGAAC
1 ATAAACGAACACAAACAAACAAAC
11925903 ATAAACGAACACAAACAAACAAAC
1 ATAAACGAACACAAACAAACAAAC
* * *
11925927 ATAAACGAACATAAAGAAACATA-
1 ATAAACGAACACAAACAAACAAAC
* * *
11925950 ATAAATGAACATAAACGAACAA
1 ATAAACGAACACAAACAAACAA
11925972 CACAAACACA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
23 18 0.30
24 43 0.70
ACGTcount: A:0.65, C:0.19, G:0.08, T:0.09
Consensus pattern (24 bp):
ATAAACGAACACAAACAAACAAAC
Found at i:11926251 original size:14 final size:16
Alignment explanation
Indices: 11926232--11926263 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
11926222 GCCATCTGTT
11926232 CGAACATA-AAT-GAA
1 CGAACATATAATCGAA
11926246 CGAACATATAATCGAA
1 CGAACATATAATCGAA
11926262 CG
1 CG
11926264 TTCACGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (16 bp):
CGAACATATAATCGAA
Done.