Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 34 of 204
Found at i:12315716 original size:21 final size:20
Alignment explanation
Indices: 12315674--12315780 Score: 81
Period size: 21 Copynumber: 5.2 Consensus size: 20
12315664 ACATCATAAC
*
12315674 CAGAAGCCCA-AAGGCTACA
1 CAGAAGCCCATAAGGCTAAA
*
12315693 CAGAAGCACATAAGTGCTAAA
1 CAGAAGCCCATAAG-GCTAAA
* * *
12315714 CAGAAACCCATAAGGGTTGAA
1 CAGAAGCCCATAA-GGCTAAA
* * *
12315735 CGGAAGCTCATAAGAGCTGAA
1 CAGAAGCCCATAAG-GCTAAA
* *
12315756 CGGAAGCCCATAAAGGTTAAA
1 CAGAAGCCCAT-AAGGCTAAA
12315777 CAGA
1 CAGA
12315781 GCTCAAAAGA
Statistics
Matches: 69, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
19 9 0.13
20 4 0.06
21 52 0.75
22 4 0.06
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.12
Consensus pattern (20 bp):
CAGAAGCCCATAAGGCTAAA
Found at i:12315791 original size:41 final size:42
Alignment explanation
Indices: 12315692--12315906 Score: 184
Period size: 42 Copynumber: 5.1 Consensus size: 42
12315682 CAAAGGCTAC
* * * * * *
12315692 ACAGAAGCACATAAGTGCTAAACAGAAACCCATAAGGGTTGA
1 ACAGAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAA
* * * *
12315734 ACGGAAGCTCATAAGAGCTGAACGGAAGCCCATAAAGGTTAA
1 ACAGAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAA
* * * *
12315776 ACAG-AGCTCAAAAGAGTTTAACGAAAACCTATAAGGGTTAA
1 ACAGAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAA
* * * * *
12315817 ACAGAAGCTCAATAGAGCTGAACGGAAACTCATATGAGTTGA
1 ACAGAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAA
* * * *
12315859 ACAGAAGCTCGAAAA-AACTGAACGAAAACTCATATA-AGTTAA
1 ACAGAAGCTC-AAAAGAGCTGAACGGAAACCCATA-AGGGTTAA
12315901 ACAGAA
1 ACAGAA
12315907 TCTCGTGAGA
Statistics
Matches: 140, Mismatches: 30, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
41 34 0.24
42 103 0.74
43 3 0.02
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (42 bp):
ACAGAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAA
Found at i:12315862 original size:83 final size:84
Alignment explanation
Indices: 12315717--12315924 Score: 203
Period size: 83 Copynumber: 2.5 Consensus size: 84
12315707 TGCTAAACAG
* * * *
12315717 AAACCCATAAGGGTTGAACGGAAGCTCATAAGAGCTGAACGGAAGCCCATAAAGGTTAAACAG-A
1 AAACCTATAAGGGTTAAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAAGGTTAAACAGAA
** *
12315781 GCTC-AAAAGAGTTTAACGA
66 GCTCGAAAA-AACTGAACGA
* * *
12315800 AAACCTATAAGGGTTAAACAGAAGCTCA-ATAGAGCTGAACGGAAACTCAT-ATGAGTTGAACAG
1 AAACCTATAAGGGTTAAACAGAAGCTCATA-AGAGCTGAACGGAAACCCATAAAG-GTTAAACAG
12315863 AAGCTCGAAAAAACTGAACGA
64 AAGCTCGAAAAAACTGAACGA
* * * *
12315884 AAACTCATATAA--GTTAAACAGAATCTCGTGAGAGCTAAACG
1 AAAC-C-TATAAGGGTTAAACAGAAGCTCATAAGAGCTGAACG
12315925 AAAAGTAAAC
Statistics
Matches: 104, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
82 3 0.03
83 51 0.49
84 40 0.38
85 5 0.05
86 5 0.05
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (84 bp):
AAACCTATAAGGGTTAAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAAGGTTAAACAGAA
GCTCGAAAAAACTGAACGA
Found at i:12315925 original size:42 final size:41
Alignment explanation
Indices: 12315737--12315928 Score: 131
Period size: 42 Copynumber: 4.6 Consensus size: 41
12315727 GGGTTGAACG
* * * *
12315737 GAAGCTCATAAGAGCTGAACGGAAGCCCATA-AAGGTTAAACA
1 GAAGCTCGT-AGAGCTGAACGAAAACTCATATAA-GTTAAACA
** * *
12315779 G-AGCTCAAAAGAGTTTAACGAAAAC-C-TATAAGGGTTAAACA
1 GAAGCTC-GTAGAGCTGAACGAAAACTCATATAA--GTTAAACA
* * * *
12315820 GAAGCTCAATAGAGCTGAACGGAAACTCATATGAGTTGAACA
1 GAAGCTC-GTAGAGCTGAACGAAAACTCATATAAGTTAAACA
* * *
12315862 GAAGCTCGAAAAAACTGAACGAAAACTCATATAAGTTAAACA
1 GAAGCTCG-TAGAGCTGAACGAAAACTCATATAAGTTAAACA
* *
12315904 GAATCTCGTGAGAGCTAAACGAAAA
1 GAAGCTCGT-AGAGCTGAACGAAAA
12315929 GTAAACACGA
Statistics
Matches: 119, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 27 0.23
42 82 0.69
43 1 0.01
44 4 0.03
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (41 bp):
GAAGCTCGTAGAGCTGAACGAAAACTCATATAAGTTAAACA
Found at i:12318243 original size:9 final size:9
Alignment explanation
Indices: 12318225--12318353 Score: 52
Period size: 9 Copynumber: 14.1 Consensus size: 9
12318215 TTCCATATTT
12318225 AAAATCTATA
1 AAAAT-TATA
12318235 AAAATTAT-
1 AAAATTATA
*
12318243 AAAATTAACA
1 AAAATT-ATA
12318253 AAAATATATA
1 AAAAT-TATA
* * * *
12318263 GAATTTTTT
1 AAAATTATA
*
12318272 ATAATTATA
1 AAAATTATA
*
12318281 AAAAATATTA
1 AAAATTA-TA
*
12318291 TATAA-TATA
1 -AAAATTATA
12318300 AAAATTATA
1 AAAATTATA
12318309 AAAA-TAT-
1 AAAATTATA
* *
12318316 AAACTTTTA
1 AAAATTATA
*
12318325 AAAA-AATA
1 AAAATTATA
*
12318333 TAAGATATATA
1 -AAAAT-TATA
12318344 AAAATTATA
1 AAAATTATA
12318353 A
1 A
12318354 TTTAATCATC
Statistics
Matches: 85, Mismatches: 23, Indels: 23
0.65 0.18 0.18
Matches are distributed among these distances:
7 3 0.04
8 16 0.19
9 36 0.42
10 23 0.27
11 7 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAATTATA
Found at i:12318308 original size:16 final size:18
Alignment explanation
Indices: 12318282--12318353 Score: 69
Period size: 17 Copynumber: 4.1 Consensus size: 18
12318272 ATAATTATAA
*
12318282 AAAATATTAT-ATAATAT
1 AAAATATTATAAAAATAT
12318299 AAAA-ATTATAAAAATAT
1 AAAATATTATAAAAATAT
* * *
12318316 AAACTTTTAAAAAAATAT
1 AAAATATTATAAAAATAT
*
12318334 AAGATA-TATAAAAATTAT
1 AAAATATTATAAAAA-TAT
12318352 AA
1 AA
12318354 TTTAATCATC
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
16 5 0.11
17 20 0.45
18 19 0.43
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (18 bp):
AAAATATTATAAAAATAT
Found at i:12318557 original size:38 final size:37
Alignment explanation
Indices: 12318515--12318625 Score: 141
Period size: 38 Copynumber: 2.9 Consensus size: 37
12318505 CCTACTAAGA
* *
12318515 ACATGATAAGCATGTCTACTGTTAATGATGAATTGAGT
1 ACATGTTAA-CATGTCTACTGTTAATGATGAATTGAAT
*
12318553 ACATGTTTAACATGTCTACTGTTAATGATGATTTGAAT
1 ACATG-TTAACATGTCTACTGTTAATGATGAATTGAAT
* * *
12318591 ACATGTTAAACATGTCTGCTGCTAATGTTGAATTG
1 ACATGTT-AACATGTCTACTGTTAATGATGAATTG
12318626 TTCTATTACA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
37 2 0.03
38 59 0.92
39 3 0.05
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.38
Consensus pattern (37 bp):
ACATGTTAACATGTCTACTGTTAATGATGAATTGAAT
Found at i:12318744 original size:43 final size:44
Alignment explanation
Indices: 12318687--12318850 Score: 185
Period size: 44 Copynumber: 3.8 Consensus size: 44
12318677 AGATTGGTAG
* *
12318687 TTTATCTGCAAA-TTTGTTATGCATCCACAACCCAGT-GAAAGTT
1 TTTATCTGCAAATTTTGTTGTGCATCCACAGCCCAGTGGAAA-TT
* * * *
12318730 TTTATCTACAAATTTTGTTGTGTATCCACAGCCAAGTGGCAATT
1 TTTATCTGCAAATTTTGTTGTGCATCCACAGCCCAGTGGAAATT
* *
12318774 TTTATCTGCAAATTTTGTTGTGCATCCGCAGCCCAG-GGACCA-T
1 TTTATCTGCAAATTTTGTTGTGCATCCACAGCCCAGTGGA-AATT
* *
12318817 TTTATCTGTAAA-TATGTTGTGCATCCACAGCCCA
1 TTTATCTGCAAATTTTGTTGTGCATCCACAGCCCA
12318851 TCGATAATTT
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
42 20 0.19
43 25 0.24
44 55 0.53
45 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.35
Consensus pattern (44 bp):
TTTATCTGCAAATTTTGTTGTGCATCCACAGCCCAGTGGAAATT
Found at i:12320139 original size:10 final size:9
Alignment explanation
Indices: 12320079--12320254 Score: 64
Period size: 9 Copynumber: 19.3 Consensus size: 9
12320069 AGAAAACTTT
12320079 TAAAAATTA
1 TAAAAATTA
*
12320088 TAAAAGTTAA
1 TAAAAATT-A
*
12320098 CTATCAAA-TA
1 -TA-AAAATTA
12320108 TAAAAA--A
1 TAAAAATTA
12320115 TAGAAAATTA
1 TA-AAAATTA
12320125 TTAAAAATCTA
1 -TAAAAAT-TA
12320136 T-AAAATTA
1 TAAAAATTA
12320144 T-AAAATTA
1 TAAAAATTA
*
12320152 AAATAAATATA
1 TAA-AAAT-TA
* * *
12320163 TAGAATTTT
1 TAAAAATTA
* *
12320172 TTATAATTA
1 TAAAAATTA
12320181 TAAAAATTA
1 TAAAAATTA
*
12320190 TTATATAA-TA
1 -TA-AAAATTA
12320200 TAAAAATTA
1 TAAAAATTA
12320209 TAAAAA-TA
1 TAAAAATTA
* * *
12320217 -GAAACTTT
1 TAAAAATTA
*
12320225 TAAAAAATA
1 TAAAAATTA
*
12320234 T-AAGATATA
1 TAAAAAT-TA
12320243 TAAAAATTA
1 TAAAAATTA
12320252 TAA
1 TAA
12320255 TTTAATCATC
Statistics
Matches: 121, Mismatches: 28, Indels: 36
0.65 0.15 0.19
Matches are distributed among these distances:
7 6 0.05
8 26 0.21
9 50 0.41
10 24 0.20
11 13 0.11
12 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:12320158 original size:47 final size:47
Alignment explanation
Indices: 12320061--12320167 Score: 121
Period size: 47 Copynumber: 2.3 Consensus size: 47
12320051 TTTAAAATTT
**
12320061 TAAAATATAGAAAACTTTTAAAAATTATAAAAGTTAACTATCAAATA
1 TAAAATATAGAAAACTTTTAAAAATTATAAAAGTTAAAAATCAAATA
* *
12320108 TAAAAAATAGAAAA-TTATTAAAAATCTATAAAA-TTATAAAATTAAA-A
1 TAAAATATAGAAAACTT-TTAAAAAT-TATAAAAGTTA-AAAATCAAATA
12320155 TAAATATATAGAA
1 TAAA-ATATAGAA
12320168 TTTTTTATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
46 2 0.04
47 29 0.57
48 20 0.39
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (47 bp):
TAAAATATAGAAAACTTTTAAAAATTATAAAAGTTAAAAATCAAATA
Found at i:12320159 original size:27 final size:27
Alignment explanation
Indices: 12320081--12320169 Score: 74
Period size: 27 Copynumber: 3.2 Consensus size: 27
12320071 AAAACTTTTA
*
12320081 AAAATTATAAAAGTTAACTATCAAATATA-
1 AAAATTATAAAA-TTAA-AAT-AAATATAT
* * * *
12320110 AAAAATAGAAAATTATTAA-AAATCTAT
1 AAAATTATAAAATTA-AAATAAATATAT
12320137 AAAATTATAAAATTAAAATAAATATAT
1 AAAATTATAAAATTAAAATAAATATAT
*
12320164 AGAATT
1 AAAATT
12320170 TTTTATAATT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
26 8 0.17
27 25 0.53
28 4 0.09
29 10 0.21
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (27 bp):
AAAATTATAAAATTAAAATAAATATAT
Found at i:12320676 original size:30 final size:29
Alignment explanation
Indices: 12320632--12320696 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
12320622 TATATAATAA
12320632 ATTT-TAATATTTTTAA-AAGTTTTCTATATT
1 ATTTATAATATTTTTAATAA-TTTT-T-TATT
12320662 ATTTATAA-ATTTTTAATAATTTTTTATT
1 ATTTATAATATTTTTAATAATTTTTTATT
12320690 -TTTATAA
1 ATTTATAA
12320697 GCTTCTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
27 7 0.21
28 4 0.12
29 1 0.03
30 16 0.48
31 5 0.15
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (29 bp):
ATTTATAATATTTTTAATAATTTTTTATT
Found at i:12320727 original size:46 final size:47
Alignment explanation
Indices: 12320639--12320730 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 47
12320629 TAAATTTTAA
*
12320639 TATTTTTAAAAGTTTTCTATATTATTTATAAATTTTTAATAATTTTT
1 TATTTTTAAAAGTCTTCTATATTATTTATAAATTTTTAATAATTTTT
* *
12320686 TATTTTTATAAG-CTTCTATATT-TTTA-AATATCTTTTTATAATTTT
1 TATTTTTAAAAGTCTTCTATATTATTTATAA-AT-TTTTAATAATTTT
12320731 AATAATTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
44 2 0.05
45 6 0.15
46 21 0.52
47 11 0.28
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (47 bp):
TATTTTTAAAAGTCTTCTATATTATTTATAAATTTTTAATAATTTTT
Found at i:12321309 original size:28 final size:28
Alignment explanation
Indices: 12321271--12321346 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
12321261 TTTTTTATTA
*
12321271 AATATTA-AAAAATATGAAAATTGAT-AT
1 AATATTATAAAAATAT-AAAATAGATGAT
12321298 AA-ACTTATAAAAATTATAAAATAGATGAT
1 AATA-TTATAAAAA-TATAAAATAGATGAT
12321327 AATATTATAAAAATA-AAAAT
1 AATATTATAAAAATATAAAAT
12321347 TCTAATAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
26 1 0.02
27 10 0.23
28 15 0.35
29 16 0.37
30 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (28 bp):
AATATTATAAAAATATAAAATAGATGAT
Found at i:12321367 original size:21 final size:19
Alignment explanation
Indices: 12321341--12321393 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
12321331 TTATAAAAAT
* *
12321341 AAAAATTCTAATAAATTACAA
1 AAAAATTATAA-AAAATA-AA
12321362 AAAAATTATAAAAAATAAA
1 AAAAATTATAAAAAATAAA
12321381 AAAATATT-TAAAA
1 AAAA-ATTATAAAA
12321394 TTTTATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 8 0.28
21 10 0.34
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATTATAAAAAATAAA
Found at i:12321420 original size:19 final size:21
Alignment explanation
Indices: 12321380--12321426 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
12321370 TAAAAAATAA
12321380 AAAAATATTTAAAATTTTATAT
1 AAAAATATTTAAAA-TTTATAT
12321402 AAAAATA-TTAAAA-TTATAT
1 AAAAATATTTAAAATTTATAT
12321421 AAAAAT
1 AAAAAT
12321427 CATAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.48
21 6 0.24
22 7 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAATATTTAAAATTTATAT
Found at i:12321424 original size:31 final size:29
Alignment explanation
Indices: 12321367--12321424 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
12321357 TACAAAAAAA
*
12321367 TTATAAAAAATAAAAAAATATTTAAAATT
1 TTATAAAAAATAAAAAAATATATAAAATT
* *
12321396 TTATATAAAAATATTAAAATTATATAAAA
1 TTATA-AAAAATA-AAAAAATATATAAAA
12321425 ATCATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.21
30 7 0.29
31 12 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
TTATAAAAAATAAAAAAATATATAAAATT
Found at i:12321432 original size:19 final size:19
Alignment explanation
Indices: 12321396--12321453 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
12321386 ATTTAAAATT
12321396 TTATATAAAAAT-ATTAAAA
1 TTATATAAAAATCA-TAAAA
12321415 TTATATAAAAATCATAAAA
1 TTATATAAAAATCATAAAA
* * *
12321434 ATATTTTAAAAAACATAAAA
1 TTA-TATAAAAATCATAAAA
12321454 ACTTGATCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TTATATAAAAATCATAAAA
Found at i:12321434 original size:20 final size:20
Alignment explanation
Indices: 12321396--12321454 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
12321386 ATTTAAAATT
*
12321396 TTATATAAAAAT-ATTAAAA
1 TTATATAAAAATCATAAAAA
12321415 TTATATAAAAATCATAAAAA
1 TTATATAAAAATCATAAAAA
* *
12321435 -TATTTTAAAAAACATAAAAA
1 TTA-TATAAAAATCATAAAAA
12321455 CTTGATCTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 14 0.40
20 21 0.60
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
TTATATAAAAATCATAAAAA
Found at i:12321812 original size:27 final size:27
Alignment explanation
Indices: 12321728--12321812 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
12321718 AAATACATTT
* *
12321728 TTTTTTTATTTTA-AATATTT-TAAATAA
1 TTTTTATATTTCATAATATTTAT-AAT-A
* *
12321755 TTTTTATTAATTTCAT-A-ATTTATTATT
1 TTTTTA-T-ATTTCATAATATTTATAATA
12321782 TTTTTATATTTCATAATATTTATAATA
1 TTTTTATATTTCATAATATTTATAATA
12321809 TTTT
1 TTTT
12321813 ATGATTTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 7 0.15
26 2 0.04
27 23 0.50
28 7 0.15
29 7 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTTATATTTCATAATATTTATAATA
Found at i:12321867 original size:9 final size:9
Alignment explanation
Indices: 12321751--12321869 Score: 50
Period size: 9 Copynumber: 13.0 Consensus size: 9
12321741 AATATTTTAA
12321751 ATAATTTTT
1 ATAATTTTT
*
12321760 ATTAA-TTTC
1 A-TAATTTTT
12321769 ATAATTTATT
1 ATAATTT-TT
*
12321779 AT-TTTTTT
1 ATAATTTTT
*
12321787 AT-A-TTTC
1 ATAATTTTT
*
12321794 ATAATATTT
1 ATAATTTTT
12321803 ATAATATTTT
1 ATAAT-TTTT
*
12321813 ATGATTTTTTT
1 AT-A-ATTTTT
* *
12321824 ATAACTTTA
1 ATAATTTTT
**
12321833 ATAAGTTTAC
1 ATAA-TTTTT
*
12321843 ATCAATTTTA
1 AT-AATTTTT
12321853 AT-ATTTTT
1 ATAATTTTT
12321861 ATAATTTTT
1 ATAATTTTT
12321870 TCTGATTCTT
Statistics
Matches: 81, Mismatches: 18, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
7 5 0.06
8 15 0.19
9 30 0.37
10 21 0.26
11 9 0.11
12 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:12325972 original size:19 final size:20
Alignment explanation
Indices: 12325937--12325977 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
12325927 GCTTATGATT
*
12325937 AATTAATTAAAGTTTAATTA
1 AATTAATTAAAGATTAATTA
12325957 AATTAATT-AAGATTAATTA
1 AATTAATTAAAGATTAATTA
12325976 AA
1 AA
12325978 AATTAAACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
AATTAATTAAAGATTAATTA
Found at i:12325973 original size:10 final size:10
Alignment explanation
Indices: 12325938--12325976 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
12325928 CTTATGATTA
12325938 ATTAATTAAAG
1 ATTAATT-AAG
*
12325949 TTTAATTAA-
1 ATTAATTAAG
12325958 ATTAATTAAG
1 ATTAATTAAG
12325968 ATTAATTAA
1 ATTAATTAA
12325977 AAATTAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.32
10 11 0.44
11 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (10 bp):
ATTAATTAAG
Found at i:12327269 original size:24 final size:23
Alignment explanation
Indices: 12327242--12327322 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
12327232 TAATATTTTA
*
12327242 TTATTTTAAATTTATCATGTATGT
1 TTATTTAAAATTTATCATGTAT-T
* *
12327266 TTATTTCAAATTTATTATGTATT
1 TTATTTAAAATTTATCATGTATT
* * *
12327289 ATAATTAAAATTTGTCATGTATT
1 TTATTTAAAATTTATCATGTATT
12327312 TT-TTTAAAATT
1 TTATTTAAAATT
12327323 CAATATAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
22 8 0.17
23 20 0.42
24 20 0.42
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (23 bp):
TTATTTAAAATTTATCATGTATT
Found at i:12329797 original size:3 final size:3
Alignment explanation
Indices: 12329789--12329831 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
12329779 ATATGTAGGT
* *
12329789 ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA AAA ATA CTA ATA A
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12329832 CAAAATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12331636 original size:36 final size:36
Alignment explanation
Indices: 12331589--12331779 Score: 238
Period size: 36 Copynumber: 5.0 Consensus size: 36
12331579 GCTAAGCTAC
*
12331589 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
12331625 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
12331661 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
* * * *
12331703 CTACCACTTATCACTTTGTCTCTTGACCAGATAAGTGTAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
12331743 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
12331779 C
1 C
12331780 TAAAGCTACC
Statistics
Matches: 137, Mismatches: 8, Indels: 20
0.83 0.05 0.12
Matches are distributed among these distances:
36 99 0.72
38 3 0.02
40 3 0.02
42 3 0.02
44 2 0.01
46 27 0.20
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:12331712 original size:46 final size:46
Alignment explanation
Indices: 12331661--12331815 Score: 195
Period size: 46 Copynumber: 3.6 Consensus size: 46
12331651 ATAAGTATAG
12331661 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* * *
12331707 CACTTATCACTTTGTCTCTTGACCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
12331743 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
12331789 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
12331816 AGTACTCAAA
Statistics
Matches: 91, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
36 27 0.30
38 2 0.02
39 1 0.01
40 3 0.03
42 3 0.03
43 1 0.01
44 2 0.02
46 52 0.57
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:12331719 original size:82 final size:82
Alignment explanation
Indices: 12331625--12331815 Score: 337
Period size: 82 Copynumber: 2.3 Consensus size: 82
12331615 ATAAGTATAG
* *
12331625 CACTTATCACTTTTTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTATCTCTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
12331690 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
* * *
12331707 CACTTATCACTTTGTCTCTTGACCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTATCTCTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
12331772 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
12331789 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTATCTCTTGATCAGA
12331816 AGTACTCAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 103 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (82 bp):
CACTTATCACTTTATCTCTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
AGTGTAGCTAAAGCTAC
Found at i:12331720 original size:118 final size:115
Alignment explanation
Indices: 12331546--12331779 Score: 396
Period size: 118 Copynumber: 2.0 Consensus size: 115
12331536 TACTTATGAT
12331546 CACTTATCATTTTTCCCTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGA
1 CACTTATCATTTTTCCCTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGA
*
12331611 TCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
66 CCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
* *
12331661 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCA-TTTTTC-CCTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACT
* *
12331726 TGACCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
63 TGACCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
12331779 C
1 C
12331780 TAAAGCTACC
Statistics
Matches: 111, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
115 9 0.08
116 6 0.05
117 20 0.18
118 76 0.68
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (115 bp):
CACTTATCATTTTTCCCTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGA
CCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:12333145 original size:21 final size:21
Alignment explanation
Indices: 12333119--12333228 Score: 163
Period size: 21 Copynumber: 5.3 Consensus size: 21
12333109 AATTCAGTGG
12333119 TGTATATATCATATCTAAGAT
1 TGTATATATCATATCTAAGAT
12333140 TGTATATATCATATCTAAGAT
1 TGTATATATCATATCTAAGAT
*
12333161 TGCATATATCATATCTAAGAT
1 TGTATATATCATATCTAAGAT
*
12333182 TGCT-TATATTATATCTAAGAT
1 TG-TATATATCATATCTAAGAT
*
12333203 TG--CATATCATATCTAAGAT
1 TGTATATATCATATCTAAGAT
12333222 TGTATAT
1 TGTATAT
12333229 CCTCAAAAAT
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
19 17 0.21
21 63 0.79
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (21 bp):
TGTATATATCATATCTAAGAT
Found at i:12333942 original size:20 final size:20
Alignment explanation
Indices: 12333902--12333940 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
12333892 TATGGTTAAT
*
12333902 TAATTAAAGTTTAATTAAAA
1 TAATTAAAGATTAATTAAAA
12333922 TAATT-AAGATTAATTAAAA
1 TAATTAAAGATTAATTAAAA
12333941 ATTAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TAATTAAAGATTAATTAAAA
Found at i:12337910 original size:2 final size:2
Alignment explanation
Indices: 12337898--12337930 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
12337888 TTCATACATA
12337898 AT AT GAT 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
12337931 TGTAACACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12340334 original size:41 final size:41
Alignment explanation
Indices: 12340289--12340389 Score: 148
Period size: 41 Copynumber: 2.5 Consensus size: 41
12340279 GATAGTGATT
*
12340289 CAGGCTTTGTGCCAGTGTATTGATTTAGACTTTATGCCAAG
1 CAGGCTTTGTGCCGGTGTATTGATTTAGACTTTATGCCAAG
* ** * *
12340330 CAGGCTTTGTGTCGGTGTATTGATTTAGGTTTTGTGCCTAG
1 CAGGCTTTGTGCCGGTGTATTGATTTAGACTTTATGCCAAG
12340371 CAGGCTTTGTGCCGGTGTA
1 CAGGCTTTGTGCCGGTGTA
12340390 ATGAATCAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.16, C:0.16, G:0.30, T:0.39
Consensus pattern (41 bp):
CAGGCTTTGTGCCGGTGTATTGATTTAGACTTTATGCCAAG
Found at i:12340412 original size:41 final size:41
Alignment explanation
Indices: 12340328--12340418 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
12340318 CTTTATGCCA
* * * * ** *
12340328 AGCAGGCTTTGTGTCGGTGTATTGATTTAGGTTTTGTGCCT
1 AGCAGGCTTTGTGCCGGTGTAATGAATCAGGCCTTGAGCCT
*
12340369 AGCAGGCTTTGTGCCGGTGTAATGAATCAGGCCTTGAGTCT
1 AGCAGGCTTTGTGCCGGTGTAATGAATCAGGCCTTGAGCCT
12340410 AGCAGGCTT
1 AGCAGGCTT
12340419 CGTTCTGGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.35
Consensus pattern (41 bp):
AGCAGGCTTTGTGCCGGTGTAATGAATCAGGCCTTGAGCCT
Found at i:12354302 original size:30 final size:29
Alignment explanation
Indices: 12354246--12354303 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
12354236 GTAAATATTT
* * * *
12354246 AAAATTTGAGGGGTTAAAGTGTAAATATG
1 AAAATTTGAAGGATCAAAGTGCAAATATG
12354275 AAAATTTGAAGGATCAATAGTGCAAATAT
1 AAAATTTGAAGGATCAA-AGTGCAAATAT
12354304 TTTAAGGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.29
Consensus pattern (29 bp):
AAAATTTGAAGGATCAAAGTGCAAATATG
Found at i:12354576 original size:22 final size:26
Alignment explanation
Indices: 12354535--12354590 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 26
12354525 ATATTAGTTT
12354535 ATAATATTTTGATTTGATTTT-TTTA
1 ATAATATTTTGATTTGATTTTATTTA
12354560 ATAATATTTT-A-TT-ATTTTATTTA
1 ATAATATTTTGATTTGATTTTATTTA
*
12354583 GT-ATATTT
1 ATAATATTT
12354591 ATATGTGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 11 0.38
23 7 0.24
24 1 0.03
25 10 0.34
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (26 bp):
ATAATATTTTGATTTGATTTTATTTA
Found at i:12356815 original size:17 final size:17
Alignment explanation
Indices: 12356795--12356829 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12356785 AAAATTTTTT
12356795 AATTTTTTAATTGTATA
1 AATTTTTTAATTGTATA
* *
12356812 AATTTTTTCATTTTATA
1 AATTTTTTAATTGTATA
12356829 A
1 A
12356830 TTTAGGAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (17 bp):
AATTTTTTAATTGTATA
Found at i:12358325 original size:31 final size:31
Alignment explanation
Indices: 12358290--12358370 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
12358280 TTTGGAACAT
* *
12358290 GACTAAAATT-TCAAATTTTGAAAATTATAAG
1 GACTAAAATTGACAAA-TTTGAAAAGTATAAG
*
12358321 GACTAAAATTGACCAATTTGAAAAGTATAAG
1 GACTAAAATTGACAAATTTGAAAAGTATAAG
* *
12358352 AACTAAAATCGATCAAATT
1 GACTAAAATTGA-CAAATT
12358371 AAAGTACATG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 34 0.81
32 8 0.19
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (31 bp):
GACTAAAATTGACAAATTTGAAAAGTATAAG
Found at i:12359235 original size:18 final size:18
Alignment explanation
Indices: 12359189--12359236 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
12359179 TAGAAAAATG
*
12359189 AAATAAAAAT-AATTTAT
1 AAATAAAAATAAATGTAT
12359206 AAATAAATAATAAATGTAT
1 AAATAAA-AATAAATGTAT
*
12359225 AATTAAAAATAA
1 AAATAAAAATAA
12359237 TTATATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 8 0.30
19 12 0.44
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATAAAAATAAATGTAT
Found at i:12359244 original size:15 final size:16
Alignment explanation
Indices: 12359192--12359245 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 16
12359182 AAAAATGAAA
*
12359192 TAAAAATAATTTATAAA
1 TAAAAATAA-TTATAAT
12359209 TAAATAATAAATGTATAAT
1 TAAA-AAT-AAT-TATAAT
12359228 TAAAAATAATTAT-AT
1 TAAAAATAATTATAAT
12359243 TAA
1 TAA
12359246 TATTAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 5 0.15
16 3 0.09
17 7 0.21
18 7 0.21
19 11 0.33
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
TAAAAATAATTATAAT
Found at i:12359687 original size:16 final size:15
Alignment explanation
Indices: 12359653--12359691 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
12359643 TTAGCTTAGG
*
12359653 TTTTTATTTTTTTTC
1 TTTTTATTTCTTTTC
12359668 -TTTTATCTTCTTTTC
1 TTTTTAT-TTCTTTTC
12359683 TTTTTATTT
1 TTTTTATTT
12359692 TTTGTAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 6 0.29
15 9 0.43
16 6 0.29
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATTTCTTTTC
Found at i:12360400 original size:24 final size:24
Alignment explanation
Indices: 12360373--12360418 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
12360363 AATCAACTTG
12360373 ATAAACACATTTACCAATTTGACA
1 ATAAACACATTTACCAATTTGACA
*
12360397 ATAATCACATTTACCAATTTGA
1 ATAAACACATTTACCAATTTGA
12360419 TAATCTCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (24 bp):
ATAAACACATTTACCAATTTGACA
Found at i:12360423 original size:21 final size:21
Alignment explanation
Indices: 12360370--12360423 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 21
12360360 TGTAATCAAC
*
12360370 TTGATAAACACATTTACCAAT
1 TTGATAATCACATTTACCAAT
12360391 TTGACAATAATCACATTTACCAAT
1 TTG---ATAATCACATTTACCAAT
12360415 TTGATAATC
1 TTGATAATC
12360424 TCTTGGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 9 0.31
24 20 0.69
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.35
Consensus pattern (21 bp):
TTGATAATCACATTTACCAAT
Found at i:12369330 original size:26 final size:27
Alignment explanation
Indices: 12369301--12369354 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
12369291 CCCATTTTTT
* *
12369301 AATAAACATTAAAAAAT-TATTTTAAA
1 AATAAAAAATAAAAAATATATTTTAAA
12369327 AATAAAAAATAAAAAATATATTTTAAA
1 AATAAAAAATAAAAAATATATTTTAAA
12369354 A
1 A
12369355 GTATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (27 bp):
AATAAAAAATAAAAAATATATTTTAAA
Found at i:12373157 original size:4 final size:4
Alignment explanation
Indices: 12373148--12373172 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12373138 ATTAATCAAA
12373148 ACGT ACGT ACGT ACGT ACGT ACGT A
1 ACGT ACGT ACGT ACGT ACGT ACGT A
12373173 TGTATGTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (4 bp):
ACGT
Found at i:12373177 original size:4 final size:4
Alignment explanation
Indices: 12373170--12373222 Score: 90
Period size: 4 Copynumber: 13.5 Consensus size: 4
12373160 ACGTACGTAC
*
12373170 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAC GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12373218 -TAT GT
1 GTAT GT
12373223 GGTTTTACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 3 0.07
4 43 0.93
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:12378034 original size:21 final size:22
Alignment explanation
Indices: 12378005--12378047 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
12377995 TTATCTTTTC
*
12378005 TAAAGTTAAAAGTCAAAACTAT
1 TAAAGTTAAAAGGCAAAACTAT
12378027 TAAA-TTAAAAGGCAAAACTAT
1 TAAAGTTAAAAGGCAAAACTAT
12378048 GTCGTTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (22 bp):
TAAAGTTAAAAGGCAAAACTAT
Found at i:12378820 original size:21 final size:22
Alignment explanation
Indices: 12378791--12378833 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
12378781 TTATCTTTTC
*
12378791 TAAAGTTAAAAGTCAAAACTAT
1 TAAAGTTAAAAGGCAAAACTAT
12378813 TAAA-TTAAAAGGCAAAACTAT
1 TAAAGTTAAAAGGCAAAACTAT
12378834 GTCGTTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (22 bp):
TAAAGTTAAAAGGCAAAACTAT
Found at i:12378970 original size:786 final size:785
Alignment explanation
Indices: 12377436--12379003 Score: 3019
Period size: 785 Copynumber: 2.0 Consensus size: 785
12377426 GGCTTAATTT
12377436 TTTTATTTATTAAATGTAATATTTTTTTTAAATCCTCTCAAATTTTTTGTGAGCCTTCGGACTTA
1 TTTTATTTATTAAATGTAATATTTTTTTTAAATCCTCTCAAATTTTTTGTGAGCCTTCGGACTTA
*
12377501 AGCGACTAGCCTACCCCATAAACAAGTATATGATAAAGTAGTTTGCATAGTAACACCCTAAATTA
66 AGCGACTAACCTACCCCATAAACAAGTATATGATAAAGTAGTTTGCATAGTAACACCCTAAATTA
*
12377566 ATTATTGAATCATCGATCACATGTACCATAAACCTAAATGAACTACTCATTAGTCGACTTACTGC
131 ATTATTGAATCATCAATCACATGTACCATAAACCTAAATGAACTACTCATTAGTCGACTTACTGC
* *
12377631 CATGTCAGATAAGCGACTGTTAAGTAGTCGGTTTTAGGCTTTTAATGGTGAAATGTTGGGACCTT
196 CATGTCAGATAAGCGACTATTAAGTAGTCGGTTTTAGGCTTTTAATGGTGAAATGTTGGGACCGT
12377696 AAAATCGACCAGCCAATATCTATTTTAAGTTTAATGTAACAGTATTGGCTCAATCAATACTAGTG
261 AAAATCGACCAGCCAATATCTATTTTAAGTTTAATGTAACAGTATTGGCTCAATCAATACTAGTG
**
12377761 GGTCTAAAAAAATAACTTTAAGCGGCAGAGTAAAATTCGATTTGATTTTAAAAAGTTGATAAAAA
326 GGTCTAAAAAAATAACTTTAAGCGGCAGAGTAAAATTCGATTTGATTCAAAAAAGTTGATAAAAA
12377826 TTTTAAATTTTAAATTAAATAGTTTAAGGTATTTGAGTTAATTGAATTATTCGGATCAACTCGAA
391 TTTTAAATTTTAAATTAAATAGTTTAAGGTATTTGAGTTAATTGAATTATTCGGATCAACTCGAA
12377891 TAAAAAATCAATTTTTTTAGTTTAACTCGAATATAAATTACACAATTTGAGTTATTCGAAAATTT
456 TAAAAAATCAATTTTTTTAGTTTAACTCGAATATAAATTACACAATTTGAGTTATTCGAAAATTT
12377956 GAATAAGAAAATATAAAATTACGTCGTTTTCATAAATATTTATCTTTTCTAAAGTTAAAAGTCAA
521 GAATAAGAAAATATAAAATTACGTCGTTTTCATAAATATTTATCTTTTCTAAAGTTAAAAGTCAA
*
12378021 AACTATTAAATTAAAAGGCAAAACTATGTCGTTTTGATAAATGTTTACTCGTTAGCGTTACTTAT
586 AACTATTAAATTAAAAGGCAAAACTATGTCGTTTTGATAAATGTTTACCCGTTAGCGTTACTTAT
12378086 GTAGTTAAATAATTTTGTATTTCATCTACTAGTTAAATAATCAGTCTATGTAAACACAACATTGA
651 GTAGTTAAATAATTTTGTATTTCATCTACTAGTTAAATAATCAGTCTATGTAAACACAACATTGA
12378151 GTATAAATAATATGATTCGTTAACTAAACTCGACTTGACTTGAAATTTTTCGACTCAATTCGAAA
716 GTATAAATAATATGATTCGTTAACTAAACTCGACTTGACTTGAAATTTTTCGACTCAATTCGAAA
12378216 AAAAA
781 AAAAA
12378221 TTTTATTTATTAAATGTAATATTTTTTTTAAATCCTCTCAAATTTTTTGTGAGCCTTCGGACTTA
1 TTTTATTTATTAAATGTAATATTTTTTTTAAATCCTCTCAAATTTTTTGTGAGCCTTCGGACTTA
12378286 AGCGACTAACCTACCCCATAAACAAGTATATGATAAAGTAGTTTGCATAGTAACACCCTAAATTA
66 AGCGACTAACCTACCCCATAAACAAGTATATGATAAAGTAGTTTGCATAGTAACACCCTAAATTA
*
12378351 ATTATTGAATCATCAATCACATGTACCATAAACCTAAATGGACTACTCATTAGTCGACTTACTGC
131 ATTATTGAATCATCAATCACATGTACCATAAACCTAAATGAACTACTCATTAGTCGACTTACTGC
12378416 CATGTCAGATAAGCGACTATTAAGTAGTCGGTTTTAGGCTTTTAATGGTGAAATGTTGGGACCGT
196 CATGTCAGATAAGCGACTATTAAGTAGTCGGTTTTAGGCTTTTAATGGTGAAATGTTGGGACCGT
*
12378481 AAAATCGACCAGCCAATATCTATTTTAAGTTTAATGTAACAGTATTGGCTCAATCAATACTGGTG
261 AAAATCGACCAGCCAATATCTATTTTAAGTTTAATGTAACAGTATTGGCTCAATCAATACTAGTG
12378546 GGTCTAAAAAAATAACTTTAAGCGGCAGAGTAAAATTCGATTTGATTCAAAAAAGTTGATAAAAA
326 GGTCTAAAAAAATAACTTTAAGCGGCAGAGTAAAATTCGATTTGATTCAAAAAAGTTGATAAAAA
12378611 TTTTAAATTTTAAATTAAATAGTTTAAGGTATTTGAGTTAATTGAATTATTCGGATCAACTCGAA
391 TTTTAAATTTTAAATTAAATAGTTTAAGGTATTTGAGTTAATTGAATTATTCGGATCAACTCGAA
12378676 TAAAAAAATCAATTTTTTTAGTTTAACTCGAATATAAATTACACAATTTGAGTTATTCGAAAATT
456 T-AAAAAATCAATTTTTTTAGTTTAACTCGAATATAAATTACACAATTTGAGTTATTCGAAAATT
*
12378741 TGAATAAGAAAATATAAAATTACGTCGTTTTGATAAATATTTATCTTTTCTAAAGTTAAAAGTCA
520 TGAATAAGAAAATATAAAATTACGTCGTTTTCATAAATATTTATCTTTTCTAAAGTTAAAAGTCA
12378806 AAACTATTAAATTAAAAGGCAAAACTATGTCGTTTTGATAAATGTTTACCCGTTAGCGTTACTTA
585 AAACTATTAAATTAAAAGGCAAAACTATGTCGTTTTGATAAATGTTTACCCGTTAGCGTTACTTA
*
12378871 TGTAGTTAAATAATTTTGTATTTCATCTACTAGTTAAATAATCAGTCTATGTAAATACAACATTG
650 TGTAGTTAAATAATTTTGTATTTCATCTACTAGTTAAATAATCAGTCTATGTAAACACAACATTG
*
12378936 AGTATAAATAATATGATTCGTTAACTCAACTCGACTTGACTTGAAATTTTTCGACTCAATTCGAA
715 AGTATAAATAATATGATTCGTTAACTAAACTCGACTTGACTTGAAATTTTTCGACTCAATTCGAA
12379001 AAA
780 AAA
12379004 TTTTCAAATT
Statistics
Matches: 770, Mismatches: 12, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
785 448 0.58
786 322 0.42
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (785 bp):
TTTTATTTATTAAATGTAATATTTTTTTTAAATCCTCTCAAATTTTTTGTGAGCCTTCGGACTTA
AGCGACTAACCTACCCCATAAACAAGTATATGATAAAGTAGTTTGCATAGTAACACCCTAAATTA
ATTATTGAATCATCAATCACATGTACCATAAACCTAAATGAACTACTCATTAGTCGACTTACTGC
CATGTCAGATAAGCGACTATTAAGTAGTCGGTTTTAGGCTTTTAATGGTGAAATGTTGGGACCGT
AAAATCGACCAGCCAATATCTATTTTAAGTTTAATGTAACAGTATTGGCTCAATCAATACTAGTG
GGTCTAAAAAAATAACTTTAAGCGGCAGAGTAAAATTCGATTTGATTCAAAAAAGTTGATAAAAA
TTTTAAATTTTAAATTAAATAGTTTAAGGTATTTGAGTTAATTGAATTATTCGGATCAACTCGAA
TAAAAAATCAATTTTTTTAGTTTAACTCGAATATAAATTACACAATTTGAGTTATTCGAAAATTT
GAATAAGAAAATATAAAATTACGTCGTTTTCATAAATATTTATCTTTTCTAAAGTTAAAAGTCAA
AACTATTAAATTAAAAGGCAAAACTATGTCGTTTTGATAAATGTTTACCCGTTAGCGTTACTTAT
GTAGTTAAATAATTTTGTATTTCATCTACTAGTTAAATAATCAGTCTATGTAAACACAACATTGA
GTATAAATAATATGATTCGTTAACTAAACTCGACTTGACTTGAAATTTTTCGACTCAATTCGAAA
AAAAA
Found at i:12379320 original size:5 final size:5
Alignment explanation
Indices: 12379310--12379338 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12379300 GAAATAAAAA
12379310 ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTA
12379339 AGGGCCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:12382224 original size:29 final size:30
Alignment explanation
Indices: 12382186--12382242 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
12382176 AATATTTAAA
*
12382186 AATTATATAAAAAT-ATA-TTAATCAAATTT
1 AATTAAATAAAAATAATATTTAAT-AAATTT
12382215 AATTAAATAAAAATAATATTTAATAAAT
1 AATTAAATAAAAATAATATTTAATAAAT
12382243 GAAACAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 13 0.52
30 7 0.28
31 5 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (30 bp):
AATTAAATAAAAATAATATTTAATAAATTT
Found at i:12391612 original size:16 final size:16
Alignment explanation
Indices: 12391590--12391646 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
12391580 TTTTATTAAA
*
12391590 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
*
12391606 GTTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
12391622 ATCAAAATTAATTGTT
1 ATTAAAATTAATTGTT
12391638 ATTAAAATT
1 ATTAAAATT
12391647 GTATCAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:12391613 original size:22 final size:23
Alignment explanation
Indices: 12391566--12391616 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
12391556 CCCGTTTTCT
* *
12391566 AATTAAAATTATATTTTTATTAA
1 AATTAAAACTATATTGTTATTAA
*
12391589 AATTAAAACTA-ATTGTTGTTAA
1 AATTAAAACTATATTGTTATTAA
12391611 AATTAA
1 AATTAA
12391617 TTGTTATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (23 bp):
AATTAAAACTATATTGTTATTAA
Found at i:12391789 original size:86 final size:90
Alignment explanation
Indices: 12391691--12391867 Score: 263
Period size: 93 Copynumber: 2.0 Consensus size: 90
12391681 TTTGTAAAAT
*
12391691 CTAACATTTTGTTAGT-AAA-ATT-A-TTAATTGTATTAATTGTTACTAAAATTATCAAATTATA
1 CTAACATTTTGTTAGTAAAATATTAATTTAATTGTATTAATTGTTACTAAAATTACCAAATTATA
*
12391752 TCAAATTATTAATTATTAATTGTTA
66 TCAAATTATTAATTACTAATTGTTA
*
12391777 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTACCAAATT
1 CTAACATTTTGTTAGTAAAA-TATTAA-T-TTAATTGTATTAATTGTTACTAAAATTACCAAATT
*
12391842 ATATCAAATTATTAATTGCTAATTGT
63 ATATCAAATTATTAATTACTAATTGT
12391868 ATTAATTGTT
Statistics
Matches: 80, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
86 16 0.20
87 3 0.04
89 3 0.04
90 1 0.01
93 57 0.71
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (90 bp):
CTAACATTTTGTTAGTAAAATATTAATTTAATTGTATTAATTGTTACTAAAATTACCAAATTATA
TCAAATTATTAATTACTAATTGTTA
Found at i:12391809 original size:19 final size:19
Alignment explanation
Indices: 12391785--12391834 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 19
12391775 TACTAACATT
12391785 TTGTTAGTAAAATTATTAA
1 TTGTTAGTAAAATTATTAA
*
12391804 TTG-T--T-AATTGTATTAA
1 TTGTTAGTAAAAT-TATTAA
12391820 TTGTTAGTAAAATTA
1 TTGTTAGTAAAATTA
12391835 CCAAATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
15 3 0.12
16 10 0.42
17 1 0.04
18 1 0.04
19 6 0.25
20 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (19 bp):
TTGTTAGTAAAATTATTAA
Found at i:12391957 original size:21 final size:22
Alignment explanation
Indices: 12391916--12391958 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12391906 AAACTTAAAA
* *
12391916 TAAAACTAAAACTAGTATATTT
1 TAAAAATAAAAATAGTATATTT
12391938 TAAAAATAAAAATA-TATATTT
1 TAAAAATAAAAATAGTATATTT
12391959 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
TAAAAATAAAAATAGTATATTT
Found at i:12399795 original size:14 final size:14
Alignment explanation
Indices: 12399778--12399839 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 14
12399768 TGTGTATACT
12399778 TATTTATATATATA
1 TATTTATATATATA
12399792 TA-TT-T-T-TATA
1 TATTTATATATATA
* * *
12399802 TATTAAAATATGTA
1 TATTTATATATATA
12399816 TATTTATATATATA
1 TATTTATATATATA
*
12399830 CA-TTATATAT
1 TATTTATATAT
12399840 TTTATCTTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
10 6 0.16
11 2 0.05
12 1 0.03
13 11 0.30
14 17 0.46
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (14 bp):
TATTTATATATATA
Found at i:12399805 original size:24 final size:24
Alignment explanation
Indices: 12399785--12399844 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
12399775 ACTTATTTAT
*
12399785 ATATATATATTTTTATATATTAAA
1 ATATATATATTTATATATATTAAA
* *
12399809 ATATGTATATTTATATATA-TACA
1 ATATATATATTTATATATATTAAA
*
12399832 TTATATAT-TTTAT
1 ATATATATATTTAT
12399845 CTTACCTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 5 0.16
23 9 0.29
24 17 0.55
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
ATATATATATTTATATATATTAAA
Found at i:12399843 original size:22 final size:23
Alignment explanation
Indices: 12399787--12399844 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
12399777 TTATTTATAT
12399787 ATATATATTTT-TATATATTAAA
1 ATATATATTTTATATATATTAAA
* *
12399809 ATATGTATATTTATATATA-TACA
1 ATATATAT-TTTATATATATTAAA
*
12399832 TTATATATTTTAT
1 ATATATATTTTAT
12399845 CTTACCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 12 0.40
23 12 0.40
24 6 0.20
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
ATATATATTTTATATATATTAAA
Found at i:12400406 original size:108 final size:109
Alignment explanation
Indices: 12400126--12400536 Score: 632
Period size: 109 Copynumber: 3.8 Consensus size: 109
12400116 AAGGAAAATA
*
12400126 TTTC-AAATTAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
1 TTTCAAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
*
12400190 CGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
66 CGATTTCACGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
* *
12400234 TTTCAAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTAGGTTT
1 TTTCAAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
* * *
12400299 CGACTTCACGTTCCACCAAAT-GACTTAATATCCTTTTCAAAAA-T
66 CGATTTCACGTTCGACCAAATAG-CTAAATATCCTTTT-AAAAACT
*
12400343 TTTC-AAAATAAGTCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
1 TTTCAAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
* *
12400407 CGATTTCTCGTTCGACCAAATAGCTAAATATCTTTTTAAAAACT
66 CGATTTCACGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
* * * *
12400451 TTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGCTGGGTTT
1 TTTCAAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
**
12400516 CGATTTCACGTTTAACCAAAT
66 CGATTTCACGTTCGACCAAAT
12400537 TGCCAAATTT
Statistics
Matches: 274, Mismatches: 23, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
107 5 0.02
108 97 0.35
109 167 0.61
110 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (109 bp):
TTTCAAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
CGATTTCACGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
Found at i:12400501 original size:217 final size:218
Alignment explanation
Indices: 12400120--12400536 Score: 737
Period size: 217 Copynumber: 1.9 Consensus size: 218
12400110 AAAAAAAAGG
*
12400120 AAAATATTTCAAATTAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
1 AAAATATTTCAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
12400185 GGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGCA
66 GGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGCA
* *
12400250 ATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTAGGTTTCGACTTCACGTTCCAC
131 ATATTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTACTAGGTTTCGACTTCACGTTCAAC
12400315 CAAATGACTTAATATCCTTTTCA
196 CAAATGACTTAATATCCTTTTCA
*
12400338 AAAAT-TTTCAAAATAAGTCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
1 AAAATATTTCAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
*
12400402 GGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCTTTTTAAAAACTTTTCAAAAATAAGGCA
66 GGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGCA
* * * * *
12400467 ATGTTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGCTGGGTTTCGATTTCACGTTTAAC
131 ATATTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTACTAGGTTTCGACTTCACGTTCAAC
12400532 CAAAT
196 CAAAT
12400537 TGCCAAATTT
Statistics
Matches: 189, Mismatches: 10, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
217 184 0.97
218 5 0.03
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (218 bp):
AAAATATTTCAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
GGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGCA
ATATTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTACTAGGTTTCGACTTCACGTTCAAC
CAAATGACTTAATATCCTTTTCA
Found at i:12404214 original size:8 final size:8
Alignment explanation
Indices: 12404193--12404258 Score: 60
Period size: 8 Copynumber: 7.8 Consensus size: 8
12404183 TCAGACTCAA
12404193 AAAAAAAT
1 AAAAAAAT
**
12404201 TCAAAAAT
1 AAAAAAAT
12404209 AAAAAAAATT
1 -AAAAAAA-T
12404219 AAAAAAAAT
1 -AAAAAAAT
12404228 CAAAAAAAT
1 -AAAAAAAT
*
12404237 TAAAAAAT
1 AAAAAAAT
*
12404245 CAAAAAAT
1 AAAAAAAT
12404253 AAAAAA
1 AAAAAA
12404259 TCAAAGTCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
8 25 0.52
9 14 0.29
10 9 0.19
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAAAAAT
Found at i:12404216 original size:10 final size:9
Alignment explanation
Indices: 12404203--12404258 Score: 62
Period size: 9 Copynumber: 6.3 Consensus size: 9
12404193 AAAAAAATTC
12404203 AAAAATAAA
1 AAAAATAAA
12404212 AAAAATTAAA
1 AAAAA-TAAA
*
12404222 AAAAATCAA
1 AAAAATAAA
*
12404231 AAAAAT-TA
1 AAAAATAAA
*
12404239 AAAAAT-CA
1 AAAAATAAA
12404247 AAAAATAAA
1 AAAAATAAA
12404256 AAA
1 AAA
12404259 TCAAAGTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 14 0.34
9 18 0.44
10 9 0.22
ACGTcount: A:0.82, C:0.04, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAATAAA
Found at i:12404233 original size:27 final size:27
Alignment explanation
Indices: 12404192--12404251 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
12404182 TTCAGACTCA
*
12404192 AAAAAAAATTC-AAAAATAAAAAAAATT
1 AAAAAAAATTCAAAAAAT-AAAAAAATC
*
12404219 AAAAAAAA-TCAAAAAAATTAAAAAATC
1 AAAAAAAATTC-AAAAAATAAAAAAATC
12404246 AAAAAA
1 AAAAAA
12404252 TAAAAAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 2 0.07
27 21 0.72
28 6 0.21
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (27 bp):
AAAAAAAATTCAAAAAATAAAAAAATC
Found at i:12404255 original size:15 final size:16
Alignment explanation
Indices: 12404194--12404263 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 16
12404184 CAGACTCAAA
* *
12404194 AAAAAATTCAAAAATAA
1 AAAAAATTAAAAAAT-C
12404211 AAAAAATTAAAAAAAATC
1 AAAAAATT--AAAAAATC
12404229 AAAAAAATTAAAAAATC
1 -AAAAAATTAAAAAATC
12404246 AAAAAA-TAAAAAATC
1 AAAAAATTAAAAAATC
12404261 AAA
1 AAA
12404264 GTCAAAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
15 12 0.25
16 6 0.12
17 16 0.33
19 14 0.29
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAATTAAAAAATC
Found at i:12404297 original size:14 final size:13
Alignment explanation
Indices: 12404278--12404308 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
12404268 AAAATAGGGG
12404278 AAAAAGAAAGAAGA
1 AAAAAGAAA-AAGA
12404292 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
12404305 AAAA
1 AAAA
12404309 GGAGAGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:12406807 original size:85 final size:87
Alignment explanation
Indices: 12406617--12406808 Score: 194
Period size: 85 Copynumber: 2.2 Consensus size: 87
12406607 TGTCAGATCT
* *
12406617 TATCTCCCTGAGATTACAGCAGAGCAGATCGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTG
1 TATCTCCCTGAGATTACAGCAGAGAAGATCGAAGCTAG-AATCCTATCTCCCTGAGATTACAGCG
** * *
12406682 GAGTGGATTAAAATAAAGGATCT
65 GAGCAGATTAAAATAAAGAATCC
* * * * * *
12406705 TATCTCTCTGA-AGTTACAGCAGAGAAGATCGTATC-AG-GTCTTATCTCCCTGAGATTATAGCG
1 TATCTCCCTGAGA-TTACAGCAGAGAAGATCGAAGCTAGAATCCTATCTCCCTGAGATTACAGCG
* * *
12406767 GAGCAGATTGAAGT-TAGTAATCC
65 GAGCAGATTAAAATAAAG-AATCC
12406790 TATCTCCCTGAGATTACAG
1 TATCTCCCTGAGATTACAG
12406809 TGGAGCGGAT
Statistics
Matches: 85, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
84 2 0.02
85 50 0.59
86 1 0.01
87 3 0.04
88 29 0.34
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (87 bp):
TATCTCCCTGAGATTACAGCAGAGAAGATCGAAGCTAGAATCCTATCTCCCTGAGATTACAGCGG
AGCAGATTAAAATAAAGAATCC
Found at i:12406814 original size:44 final size:43
Alignment explanation
Indices: 12406617--12406819 Score: 151
Period size: 44 Copynumber: 4.7 Consensus size: 43
12406607 TGTCAGATCT
* * *
12406617 TATCTCCCTGAGATTACAGCAGAGCAGATCGAAGCTAGTAATCC
1 TATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAG-AATCC
* ** * * * * *
12406661 TATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCT
1 TATCTCCCTGAGATTACAGCGGAGCAGATTGAAGT-TAGAATCC
* * * * * * * *
12406705 TATCTCTCTGA-AGTTACAGCAGAGAAGATCGTA-TCAG-GTCT
1 TATCTCCCTGAGA-TTACAGCGGAGCAGATTGAAGTTAGAATCC
*
12406746 TATCTCCCTGAGATTATAGCGGAGCAGATTGAAGTTAGTAATCC
1 TATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAG-AATCC
* *
12406790 TATCTCCCTGAGATTACAGTGGAGCGGATT
1 TATCTCCCTGAGATTACAGCGGAGCAGATT
12406820 AAAACAAAGG
Statistics
Matches: 120, Mismatches: 33, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
41 28 0.23
42 6 0.05
43 2 0.02
44 82 0.68
45 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (43 bp):
TATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGAATCC
Found at i:12406838 original size:44 final size:43
Alignment explanation
Indices: 12406612--12406852 Score: 148
Period size: 44 Copynumber: 5.6 Consensus size: 43
12406602 AAGAATGTCA
* ** * *
12406612 GATCTTATCTCCCTGAGATTACAGCAGAGCAGATCGAAGCTAG
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAACAAG
* * * ** *
12406655 TAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAG
1 -GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAA-CAAG
* * * *** *
12406700 GATCTTATCTCTCTGA-AGTTACAGCAGAGAAGATCGTATC-AG
1 GATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTAAAACAAG
* * ***
12406742 G-TCTTATCTCCCTGAGATTATAGCGGAGCAGATTGAAGTTAG
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAACAAG
* * * *
12406784 TAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAAAG
1 -GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAC-AAG
*
12406829 GATCTTATCTCTCTGA-AGTTACAG
1 GATCTTATCTCCCTGAGA-TTACAG
12406853 TAGAGTAGAT
Statistics
Matches: 146, Mismatches: 43, Indels: 16
0.71 0.21 0.08
Matches are distributed among these distances:
41 28 0.19
42 6 0.04
43 2 0.01
44 106 0.73
45 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAACAAG
Found at i:12406844 original size:129 final size:129
Alignment explanation
Indices: 12406609--12406926 Score: 465
Period size: 129 Copynumber: 2.5 Consensus size: 129
12406599 TTGAAGAATG
* * *
12406609 TCAGATCTTATCTCCCTGAGATTACAGCAGAGCAGATCGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * *
12406674 TTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCGTA
66 TTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCGCA
* *
12406738 TCAGGTCTTATCTCCCTGAGATTATAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
12406803 TTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA
66 TTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCGCA
* * * * * * * * *
12406867 TCAGGTTTTACCTCCCTGTGGTTACAGTGGAGAACATTGAAGCCAGTAATTCTATCTCCC
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCC
12406927 CGACGTTGCG
Statistics
Matches: 168, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
129 168 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (129 bp):
TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCGCA
Found at i:12408602 original size:2 final size:2
Alignment explanation
Indices: 12408585--12408628 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
12408575 ATGTTGTTAT
*
12408585 TA TA TA -A TA GA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12408625 TA TA
1 TA TA
12408629 CATGTATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12408759 original size:14 final size:14
Alignment explanation
Indices: 12408742--12408803 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 14
12408732 TGTGTATACT
12408742 TATTTATATATATA
1 TATTTATATATATA
12408756 TA-TT-T-T-TATA
1 TATTTATATATATA
* * *
12408766 TATTAAAATATGTA
1 TATTTATATATATA
12408780 TATTTATATATATA
1 TATTTATATATATA
*
12408794 CA-TTATATAT
1 TATTTATATAT
12408804 TTTATCTTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
10 6 0.16
11 2 0.05
12 1 0.03
13 11 0.30
14 17 0.46
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (14 bp):
TATTTATATATATA
Found at i:12408769 original size:24 final size:24
Alignment explanation
Indices: 12408749--12408808 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
12408739 ACTTATTTAT
*
12408749 ATATATATATTTTTATATATTAAA
1 ATATATATATTTATATATATTAAA
* *
12408773 ATATGTATATTTATATATA-TACA
1 ATATATATATTTATATATATTAAA
*
12408796 TTATATAT-TTTAT
1 ATATATATATTTAT
12408809 CTTACCTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 5 0.16
23 9 0.29
24 17 0.55
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
ATATATATATTTATATATATTAAA
Found at i:12408807 original size:22 final size:23
Alignment explanation
Indices: 12408751--12408808 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
12408741 TTATTTATAT
12408751 ATATATATTTT-TATATATTAAA
1 ATATATATTTTATATATATTAAA
* *
12408773 ATATGTATATTTATATATA-TACA
1 ATATATAT-TTTATATATATTAAA
*
12408796 TTATATATTTTAT
1 ATATATATTTTAT
12408809 CTTACCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 12 0.40
23 12 0.40
24 6 0.20
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
ATATATATTTTATATATATTAAA
Found at i:12409373 original size:108 final size:109
Alignment explanation
Indices: 12409090--12409516 Score: 628
Period size: 109 Copynumber: 3.9 Consensus size: 109
12409080 AAGGAAAATA
* *
12409090 TTTC-AAATTAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
1 TTTCAAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
* *
12409154 TGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
66 CGATTTCACGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
* * *
12409198 TTTCAAAAATAAGGCAATGTTTTGAGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGCTT
1 TTTCAAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
* * *
12409263 CGACTTCACGTTCCACCAAAT-GACTTAATATCCTTTTCAAAAA-T
66 CGATTTCACGTTCGACCAAATAG-CTAAATATCCTTTT-AAAAACT
12409307 TTTC-AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
1 TTTCAAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
*
12409371 CGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
66 CGATTTCACGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
* * * *
12409415 TTTCAAAAATAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGCTGGGTTT
1 TTTCAAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
** * * *
12409480 CGATTTCACGTTTAACCAAATTGCCAAATTTCCTTTT
66 CGATTTCACGTTCGACCAAATAGCTAAATATCCTTTT
12409517 GAATTTTAAT
Statistics
Matches: 286, Mismatches: 27, Indels: 11
0.88 0.08 0.03
Matches are distributed among these distances:
107 5 0.02
108 98 0.34
109 178 0.62
110 5 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (109 bp):
TTTCAAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
CGATTTCACGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
Found at i:12409465 original size:217 final size:218
Alignment explanation
Indices: 12409084--12409500 Score: 737
Period size: 217 Copynumber: 1.9 Consensus size: 218
12409074 AAAAAAAAGG
*
12409084 AAAATATTTCAAATTAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
1 AAAATATTTCAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
*
12409149 GGTTTTGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGCA
66 GGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGCA
* *
12409214 ATGTTTTGAGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGCTTCGACTTCACGTTCCAC
131 ATGTTTTGAGTTTGGAAATTCGAGAAACGTGCCCTAAGGTACTGGGCTTCGACTTCACGTTCAAC
12409279 CAAATGACTTAATATCCTTTTCA
196 CAAATGACTTAATATCCTTTTCA
*
12409302 AAAAT-TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
1 AAAATATTTCAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
12409366 GGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGCA
66 GGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGCA
* * * * *
12409431 ATGTTTTGTGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGCTGGGTTTCGATTTCACGTTTAAC
131 ATGTTTTGAGTTTGGAAATTCGAGAAACGTGCCCTAAGGTACTGGGCTTCGACTTCACGTTCAAC
12409496 CAAAT
196 CAAAT
12409501 TGCCAAATTT
Statistics
Matches: 189, Mismatches: 10, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
217 184 0.97
218 5 0.03
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (218 bp):
AAAATATTTCAAAATAAGGCAATATTTAGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
GGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAGGCA
ATGTTTTGAGTTTGGAAATTCGAGAAACGTGCCCTAAGGTACTGGGCTTCGACTTCACGTTCAAC
CAAATGACTTAATATCCTTTTCA
Found at i:12414411 original size:19 final size:19
Alignment explanation
Indices: 12414389--12414426 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12414379 TCATTTTTAT
* *
12414389 TCAATTGTACACTTTTAAA
1 TCAATTATACACGTTTAAA
12414408 TCAATTATACACGTTTAAA
1 TCAATTATACACGTTTAAA
12414427 AGCATAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (19 bp):
TCAATTATACACGTTTAAA
Found at i:12414759 original size:15 final size:14
Alignment explanation
Indices: 12414731--12414757 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12414721 CGTGTCTCTT
12414731 TTTTTAAATATTTA
1 TTTTTAAATATTTA
12414745 TTTTTAAATATTT
1 TTTTTAAATATTT
12414758 TACTATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTAAATATTTA
Found at i:12416420 original size:34 final size:35
Alignment explanation
Indices: 12416359--12416424 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
12416349 ATAATTAATT
12416359 AAATTAATAATATATTATATAAATTATTTATACTA
1 AAATTAATAATATATTATATAAATTATTTATACTA
12416394 AAATTAACGTAAT-TATTAT-T-AATTATTTATA
1 AAATTAA--TAATATATTATATAAATTATTTATA
12416425 TTTGGTAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
34 11 0.38
35 8 0.28
36 6 0.21
37 4 0.14
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (35 bp):
AAATTAATAATATATTATATAAATTATTTATACTA
Found at i:12417301 original size:3 final size:3
Alignment explanation
Indices: 12417293--12417326 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
12417283 ACCGCACTAA
12417293 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
12417327 TATTCCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:12425260 original size:109 final size:109
Alignment explanation
Indices: 12425082--12425600 Score: 797
Period size: 109 Copynumber: 4.8 Consensus size: 109
12425072 ATATTTGGCA
* * *
12425082 ATTTGGTTAAACGAGAAAAATCGACACCCAACACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
*
12425147 CAAAACATTGTCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
*
12425191 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
*
12425256 CAAAACATAT-TCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
66 CAAAACAT-TGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
* * * *
12425300 ATTTGGTTAAAAGAGAAAAATAGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAATG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
* * *
12425365 CAAAACATTGCCTTATTTTAAAAATTTTACAAGGATATTAAGCT
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
*
12425409 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACATTAGGGCATGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
** * * *
12425474 CAAAACATTGCCTTATTTTGGAATTTTTAGAAGGATATTTAGCT
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
* * *
12425518 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTCCTCGAATTTCCAAATG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
* * *
12425583 CTAAATATTGCCTCATTT
66 CAAAACATTGCCTTATTT
12425601 AGAAAAATTT
Statistics
Matches: 380, Mismatches: 28, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
108 1 0.00
109 378 0.99
110 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (109 bp):
ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
Found at i:12425732 original size:4 final size:4
Alignment explanation
Indices: 12425723--12425762 Score: 71
Period size: 4 Copynumber: 9.8 Consensus size: 4
12425713 ATACCATAGC
12425723 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAACT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAA
12425763 GCATAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 31 0.89
5 4 0.11
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:12425809 original size:38 final size:36
Alignment explanation
Indices: 12425741--12425823 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 36
12425731 AAATAAATAA
12425741 ATAAATAAATAAATAAACTAAAGCATAAAAATGGACAT
1 ATAAATAAATAAATAAACTAAAGCATAAAAA-GGA-AT
* *
12425779 ATAAATAAATACATAAA-TGAA-CATAAAAAAAGGAAT
1 ATAAATAAATAAATAAACTAAAGCAT--AAAAAGGAAT
*
12425815 ATAGATAAA
1 ATAAATAAA
12425824 AATTATAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 13 0.32
37 6 0.15
38 21 0.52
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.20
Consensus pattern (36 bp):
ATAAATAAATAAATAAACTAAAGCATAAAAAGGAAT
Found at i:12426137 original size:2 final size:2
Alignment explanation
Indices: 12426084--12426119 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
12426074 AAAATTATTA
*
12426084 AT AT AT AT AT AC 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
12426120 GAGTATGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12426302 original size:3 final size:3
Alignment explanation
Indices: 12426288--12426411 Score: 135
Period size: 3 Copynumber: 41.7 Consensus size: 3
12426278 AAATGGAAAC
* * * * *
12426288 ATA ATG ATA ATA ATA ATA TTA ATA TTA ATA ACA ATA ATA ATA A-A GATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* *
12426336 ATG ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
12426384 ATA ATA ATG ATA ACA TTA A-A ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12426412 GTTAACAATA
Statistics
Matches: 100, Mismatches: 18, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
2 3 0.03
3 97 0.97
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12427191 original size:19 final size:19
Alignment explanation
Indices: 12427169--12427207 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12427159 AATAAATACT
*
12427169 AAAGAAACTGAAAAATAAA
1 AAAGAAACAGAAAAATAAA
*
12427188 AAAGAAACAGAGAAATAAA
1 AAAGAAACAGAAAAATAAA
12427207 A
1 A
12427208 GTTGAAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (19 bp):
AAAGAAACAGAAAAATAAA
Found at i:12428361 original size:44 final size:44
Alignment explanation
Indices: 12428293--12428963 Score: 434
Period size: 44 Copynumber: 15.5 Consensus size: 44
12428283 ACTGAATGCG
*
12428293 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* * * * * * *
12428337 ATCCGCTCCATTGTAACTTTAGAGAGATAGGAT-TGAT-TTCTTTC
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTG-TGGT-TTTA
* * * * * *
12428381 GTTTGCTCCACTGCAACTTCAGGGAGATAAGA-C--TGGATGTG
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* *
12428422 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGGGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* * * * *
12428466 ATCCGCTCCTCTGCAACTTCAGAGAGATAGGAT-TGAT-TTCTTTC
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTG-TGGT-TTTA
* * * * * *
12428510 GTCTGCTTCACTGCAACTTTAGAGAGATAAGA-CTGT--ATGTG
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* *
12428551 ATTTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* * * * * * *
12428595 ATCCGCTCCACTACAACTTTAGGGAGATAGGAT-TGAT-TTCTTTT
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTG-TGGT-TTTA
* * * *
12428639 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-C--TGGATGTG
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* * * *
12428680 ACCTACTCTACTGCAACTTCAGAGAGATAAGATATGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* * * *
12428724 AT-TCGCTCCACTGCAACTTCAGGGAGATAGGAT-TGAT-TTCTTTT
1 ATCT-GCTCCACTGCAACTTCAGAGAGATAAGATCTG-TGGT-TTTA
* * * * * *
12428768 GTTTGCTCCACTGCAACTTCAGGGAGATAAGA-CTGT--ATATG
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* * *
12428809 ATCTGCTCTACTACAACTTCAGAGAGATGAGATCTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* * * * *
12428853 ATCTGCTCCACTGCAACTTCAGGGAGATAGGAT-TATCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGT-GGTTTTA
* * * * ** **
12428897 ATTTACTCCACTGCAACCTT-AGGGAGATAAGATTTGTCATCTTCG
1 ATCTGCTCCACTGCAA-CTTCAGAGAGATAAGATCTGTGGT-TTTA
*
12428942 ATCTGCCCCACTGCAACTTCAG
1 ATCTGCTCCACTGCAACTTCAG
12428964 GGGGTTAAGA
Statistics
Matches: 477, Mismatches: 117, Indels: 65
0.72 0.18 0.10
Matches are distributed among these distances:
41 119 0.25
42 9 0.02
43 17 0.04
44 308 0.65
45 24 0.05
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
Found at i:12428389 original size:129 final size:129
Alignment explanation
Indices: 12428175--12428886 Score: 1046
Period size: 129 Copynumber: 5.5 Consensus size: 129
12428165 TATGCTATAT
* * ** ** * * *
12428175 TGCAACTCCAGATAGATAAGATCCATCATTTTAATCCACTTCACTGCAACTTCAGGAAGATAGGA
1 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
* * * * *
12428240 TTAATTTTTTTCGTCTGCTCCACTGCAACTTCTGGGAGATAAGACTGAATGCGATCTGCTCTAC
66 TTGATTTCTTTCGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTAC
* * * *
12428304 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCATTGTAACTTTAGAGAGATAGGA
1 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
*
12428369 TTGATTTCTTTCGTTTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTAC
66 TTGATTTCTTTCGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTAC
* * *
12428433 TGCAACTTCAGAGAGATAAGATCTGGGGTTTTAATCCGCTCCTCTGCAACTTCAGAGAGATAGGA
1 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
* * * * *
12428498 TTGATTTCTTTCGTCTGCTTCACTGCAACTTTAGAGAGATAAGACTGTATGTGATTTGCTCTAC
66 TTGATTTCTTTCGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTAC
* *
12428562 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTACAACTTTAGGGAGATAGGA
1 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
** * *
12428627 TTGATTTCTTTTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGACCTACTCTAC
66 TTGATTTCTTTCGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTAC
* *
12428691 TGCAACTTCAGAGAGATAAGATATGTGGTTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGA
1 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
* * * *
12428756 TTGATTTCTTTTGTTTGCTCCACTGCAACTTCAGGGAGATAAGACTGTATATGATCTGCTCTAC
66 TTGATTTCTTTCGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTAC
* * *
12428820 TACAACTTCAGAGAGATGAGATCTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGA
1 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
12428885 TT
66 TT
12428887 ATCGGCTTCA
Statistics
Matches: 524, Mismatches: 59, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
129 524 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (129 bp):
TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
TTGATTTCTTTCGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTAC
Found at i:12429016 original size:218 final size:217
Alignment explanation
Indices: 12428776--12429193 Score: 554
Period size: 218 Copynumber: 1.9 Consensus size: 217
12428766 TTGTTTGCTC
* ** *
12428776 CACTGCAACTTCAGGGAGATAAGA-CTGTATATGATCTGCTCTACTACAACTTCAGAGAGATGAG
1 CACTGCAACTTCAGGGAGATAAGACCTG-ATACGATCCACTCTACTACAACTTCAGAGAGATAAG
* ** * ** * *
12428840 ATCT-GTGGTTTTAATCTGCTCCA-CTGCAACTTCAGGGAGATAGGATTATCGGCTTCAATTTAC
65 ATCTACT-ACTTCAATCCACT-CATCTGCAACTTCAGGGAAATAGGATTATCGGCTTCAATCTAC
* * * *
12428903 TCCACTGCAACCTTAGGGAGATAAGATTTGTCATCTTCGATCTGCCCCACTGCAACTTCAGGGGG
128 TCCACTGCAACCTCAGGGAGATAAGATTTGT-ACCTTCAATCTGCCCCACTGCAACTTCAAGGGG
*
12428968 TTAAGACTTGATTACTCAGTCTGTTT
192 ATAAGACTTGATTACTCAGTCTGTTT
* * *
12428994 CACTGCAACTTTAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGA
1 CACTGCAACTTCAGGGAGATAAGACCTGATACGATCCACTCTACTACAACTTCAGAGAGATAAGA
* *
12429059 TCTACTACTTCAATCCACTCATCTGCAACTTCAGGGAAATAGGATTATCTGCTTCAATCTGCTCC
66 TCTACTACTTCAATCCACTCATCTGCAACTTCAGGGAAATAGGATTATCGGCTTCAATCTACTCC
* * *
12429124 ACTGCAACCTCAGGGAGATAAGATTTGTACCTTCAATTTGTCCCACTGCATCTTCAAGGGGATAA
131 ACTGCAACCTCAGGGAGATAAGATTTGTACCTTCAATCTGCCCCACTGCAACTTCAAGGGGATAA
12429189 GACTT
196 GACTT
12429194 TGGTTCTTCG
Statistics
Matches: 172, Mismatches: 25, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
217 37 0.22
218 131 0.76
219 4 0.02
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (217 bp):
CACTGCAACTTCAGGGAGATAAGACCTGATACGATCCACTCTACTACAACTTCAGAGAGATAAGA
TCTACTACTTCAATCCACTCATCTGCAACTTCAGGGAAATAGGATTATCGGCTTCAATCTACTCC
ACTGCAACCTCAGGGAGATAAGATTTGTACCTTCAATCTGCCCCACTGCAACTTCAAGGGGATAA
GACTTGATTACTCAGTCTGTTT
Found at i:12429158 original size:44 final size:43
Alignment explanation
Indices: 12428253--12429241 Score: 364
Period size: 44 Copynumber: 22.9 Consensus size: 43
12428243 ATTTTTTTCG
* * * * *
12428253 TCTGCTCCACTGCAACTTCTGGGAGATAAGA-CTG-AATGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTTCAA
* * * ** *
12428294 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-ACTTCAA
* * * * * * * *
12428338 TCCGCTCCATTGTAACTTTAGAGAGATAGGA-TTGATTTCTTTC-G
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG--TAC-TTCAA
* * * *
12428382 TTTGCTCCACTGCAACTTCAGGGAGATAAGA-CTGGA-TGT-GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACT-TCAA
* * * *** *
12428423 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGGGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TTGTACTTCAA
* * * * * *
12428467 TCCGCTCCTCTGCAACTTCAGAGAGATAGGA-TTGATTTCTTTC-G
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG--TAC-TTCAA
* * * * *
12428511 TCTGCTTCACTGCAACTTTAGAGAGATAAGA-CTGTA-TGT-GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACT-TCAA
* * * * ** *
12428552 TTTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-ACTTCAA
* * * * * **
12428596 TCCGCTCCACTACAACTTTAGGGAGATAGGA-TTGATTTCTTTTA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG--TACTTCAA
* * *
12428640 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTGGA-TGT-GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACT-TCAA
* * * * * ** *
12428681 CCTACTCTACTGCAACTTCAGAGAGATAAGATATGTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-ACTTCAA
* * ***
12428725 T-TCGCTCCACTGCAACTTCAGGGAGATAGGA-TTGATTTCTTTTG
1 TCT-GCTCCACTGCAACTTCAGGGAGATAAGATTTG--TACTTCAA
* * *
12428769 TTTGCTCCACTGCAACTTCAGGGAGATAAGA-CTGTA-TAT-GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACT-TCAA
* * * * * ** *
12428810 TCTGCTCTACTACAACTTCAGAGAGATGAGATCTGTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-ACTTCAA
* *
12428854 TCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCG-GCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-T-GTACTTCAA
* * *
12428898 TTTACTCCACTGCAACCTT-AGGGAGATAAGATTTGTCATCTTCGA
1 TCTGCTCCACTGCAA-CTTCAGGGAGATAAGATTTGT-A-CTTCAA
* * * * *
12428943 TCTGCCCCACTGCAACTTCAGGGGGTTAAGACTTGATTAC-TCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG--TACTTCAA
* * * ** * *
12428987 TCTGTTTCACTGCAACTTTAGGGAGATAAGACCTG-A-TGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTTCAA
** * * **
12429028 TCCACTCTACTGCAACTTCAGAGAGATAAGATCTACTACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TTGTACTTCAA
** * * * *
12429072 TCCACT-CATCTGCAACTTCAGGGAAATAGGATTATCTGCTTCAA
1 TCTGCTCCA-CTGCAACTTCAGGGAGATAAGATT-TGTACTTCAA
*
12429116 TCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGTACCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTA-CTTCAA
* * * *
12429160 TTTG-TCCCACTGCATCTTCAAGGG-GATAAGACTTTGGTTCTTCGA
1 TCTGCT-CCACTGCAACTTC-AGGGAGATAAGA-TTT-GTACTTCAA
** * *
12429205 TCCACTCCACTGTAA-TATCAGGGAGATAGGATTTGTA
1 TCTGCTCCACTGCAACT-TCAGGGAGATAAGATTTGTA
12429242 ACTCGAAACT
Statistics
Matches: 708, Mismatches: 179, Indels: 120
0.70 0.18 0.12
Matches are distributed among these distances:
40 2 0.00
41 167 0.24
42 20 0.03
43 22 0.03
44 418 0.59
45 73 0.10
46 5 0.01
47 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTTCAA
Found at i:12429420 original size:125 final size:125
Alignment explanation
Indices: 12429274--12429511 Score: 318
Period size: 125 Copynumber: 1.9 Consensus size: 125
12429264 GATTCGCCAT
* * * * *
12429274 TGTGGCTTTAATCTTTTTAACTGCAATGTCG-GAGAAGCAAAATTCTCCAATTTGGCTTTAATCT
1 TGTGGCTTTAATATTTTTAACTACAATGTAGAG-GAAGCAAAATTCACCAATGTGGCTTTAATCT
* * * * *
12429338 GTTCCACTGCATCGCTTG-GGGAGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
65 GTTCCACTGCACCGCCTGAGAG-GTAAGATTCACTGCTGTAGCTTTAATCAAGATTCACCGA
* * * *
12429399 TGTGGCTTTAATATTTTTAACTATAATGTAGAGGAAGCAAGATTCACCGATGTGGTTTTAATCTG
1 TGTGGCTTTAATATTTTTAACTACAATGTAGAGGAAGCAAAATTCACCAATGTGGCTTTAATCTG
12429464 TTCCACTGCACCGCCTGAGAGGTAAGATTCACTGCTGTAGCTTTAATC
66 TTCCACTGCACCGCCTGAGAGGTAAGATTCACTGCTGTAGCTTTAATC
12429512 TTTTTAATCT
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
125 94 0.97
126 3 0.03
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (125 bp):
TGTGGCTTTAATATTTTTAACTACAATGTAGAGGAAGCAAAATTCACCAATGTGGCTTTAATCTG
TTCCACTGCACCGCCTGAGAGGTAAGATTCACTGCTGTAGCTTTAATCAAGATTCACCGA
Found at i:12429491 original size:50 final size:50
Alignment explanation
Indices: 12429387--12429866 Score: 347
Period size: 50 Copynumber: 9.6 Consensus size: 50
12429377 AGCTTTAATC
* * ** * * *
12429387 AAGATTCACCGATGTGGCTTTAATATTTTTAACTATAATG--TAGAGGAAGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAACGCCT-GA-GAGGT
* * * ** *
12429437 AAGATTCACCGATGTGGTTTTAATCTGTTCCACTGCACCGCCTGAGAGGT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAACGCCTGAGAGGT
* * * * * * * *
12429487 AAGATTCACTGCTGTAGCTTTAATCTTTTTAATCT-CAATGTCAGGGAGGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAA-CTGCAACGCCTGAGAGGT
* * * * *
12429537 AAGATTCACCGTTGTGGCTTTAATCTTTTTTACTGCACCGCATGGGAGAT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAACGCCTGAGAGGT
* * * * * * * * *
12429587 AAGATTCGCTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGAGAGGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAACGCCTGAGAGGT
* * *
12429637 AAGATTCACCGTTGTGGCTTTAATCTTTTT-ACTGCACCGCCTGGGAGAT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAACGCCTGAGAGGT
* * * * * * ** *
12429686 AAGATTCGCTGATGTAGCTTTAATCTTTTTAACTGCAATGTCAAAGAGGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAACGCCTGAGAGGT
* ** *
12429736 AAGATTCACCGTTGTGGCTTTAATCTATTCCACTGCATCGCCTGAGAGGT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAACGCCTGAGAGGT
** * * * * *** * *
12429786 AAGATTTGCTGATGTAGCTTTAATCTTTTTAACCGCAATTTCAGAGAGGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAACGCCTGAGAGGT
12429836 AAGATTCACCGTTGTGGCTTTAATCTTTTTA
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTA
12429867 CTACACCGCC
Statistics
Matches: 319, Mismatches: 106, Indels: 10
0.73 0.24 0.02
Matches are distributed among these distances:
49 39 0.12
50 275 0.86
51 4 0.01
52 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (50 bp):
AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAACGCCTGAGAGGT
Found at i:12429560 original size:100 final size:98
Alignment explanation
Indices: 12429387--12429887 Score: 653
Period size: 100 Copynumber: 5.0 Consensus size: 98
12429377 AGCTTTAATC
* * * * * * *
12429387 AAGATTCACCGATGTGGCTTTAATATTTTTAACTATAATGT-AGAGGAAGCAAGATTCACCGATG
1 AAGATTCGCTGATGTAGCTTTAATCTTTTTAACT-CAATGTCAGA-GAGGCAAGATTCACCGTTG
* ** *
12429451 TGGTTTTAATCTGTTCCACTGCACCGCCTGAGAGGT
64 TGGCTTTAATCT-TTTTACTGCACCGCCTGGGAGGT
* * *
12429487 AAGATTCACTGCTGTAGCTTTAATCTTTTTAATCTCAATGTCAGGGAGGCAAGATTCACCGTTGT
1 AAGATTCGCTGATGTAGCTTTAATCTTTTTAA-CTCAATGTCAGAGAGGCAAGATTCACCGTTGT
* *
12429552 GGCTTTAATCTTTTTTACTGCACCGCATGGGAGAT
65 GGCTTTAATC-TTTTTACTGCACCGCCTGGGAGGT
* *
12429587 AAGATTCGCTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCACCGTTGT
1 AAGATTCGCTGATGTAGCTTTAATCTTTTTAA-CTCAATGTCAGAGAGGCAAGATTCACCGTTGT
*
12429652 GGCTTTAATCTTTTTACTGCACCGCCTGGGAGAT
65 GGCTTTAATCTTTTTACTGCACCGCCTGGGAGGT
*
12429686 AAGATTCGCTGATGTAGCTTTAATCTTTTTAACTGCAATGTCAAAGAGGCAAGATTCACCGTTGT
1 AAGATTCGCTGATGTAGCTTTAATCTTTTTAACT-CAATGTCAGAGAGGCAAGATTCACCGTTGT
** * *
12429751 GGCTTTAATCTATTCCACTGCATCGCCTGAGAGGT
65 GGCTTTAATCT-TTTTACTGCACCGCCTGGGAGGT
* * *
12429786 AAGATTTGCTGATGTAGCTTTAATCTTTTTAACCGCAATTTCAGAGAGGCAAGATTCACCGTTGT
1 AAGATTCGCTGATGTAGCTTTAATCTTTTTAA-CTCAATGTCAGAGAGGCAAGATTCACCGTTGT
* *
12429851 GGCTTTAATCTTTTTACTACACCGCCTGGGAAGT
65 GGCTTTAATCTTTTTACTGCACCGCCTGGGAGGT
12429885 AAG
1 AAG
12429888 GCTTTATTTT
Statistics
Matches: 358, Mismatches: 37, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
98 1 0.00
99 114 0.32
100 237 0.66
101 6 0.02
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (98 bp):
AAGATTCGCTGATGTAGCTTTAATCTTTTTAACTCAATGTCAGAGAGGCAAGATTCACCGTTGTG
GCTTTAATCTTTTTACTGCACCGCCTGGGAGGT
Found at i:12429728 original size:199 final size:199
Alignment explanation
Indices: 12429387--12429881 Score: 688
Period size: 199 Copynumber: 2.5 Consensus size: 199
12429377 AGCTTTAATC
* * * * *** * *
12429387 AAGATTCACCGATGTGGCTTTAATATTTTTAACTATAATGT-AGAGGAAGCAAGATTCACCGATG
1 AAGATTCGCTGATGTAGCTTTAATCTTTTTAACCGCAATGTCAGA-GAGGCAAGATTCACCGTTG
* ** * * *
12429451 TGGTTTTAATCTGTTCCACTGCACCGCCTGAGAGGTAAGATTCACTGCTGTAGCTTTAATCTTTT
65 TGGCTTTAATCT-TTTTACTGCACCGCCTGGGAGATAAGATTCACTGATGTAGCTTTAATCTTTT
** * **
12429516 TAATCTCAATGTCAGGGAGGCAAGATTCACCGTTGTGGCTTTAATCTTTTTTACTGCACCGCATG
129 TAATCTCAATGTCAAAGAGGCAAGATTCACCGTTGTGGCTTTAATCTATTCCACTGCACCGCATG
*
12429581 GGAGAT
194 AGAGAT
*
12429587 AAGATTCGCTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCACCGTTGT
1 AAGATTCGCTGATGTAGCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCACCGTTGT
*
12429652 GGCTTTAATCTTTTTACTGCACCGCCTGGGAGATAAGATTCGCTGATGTAGCTTTAATCTTTTTA
66 GGCTTTAATCTTTTTACTGCACCGCCTGGGAGATAAGATTCACTGATGTAGCTTTAATCTTTTTA
* *
12429717 A-CTGCAATGTCAAAGAGGCAAGATTCACCGTTGTGGCTTTAATCTATTCCACTGCATCGCCTGA
131 ATCT-CAATGTCAAAGAGGCAAGATTCACCGTTGTGGCTTTAATCTATTCCACTGCACCGCATGA
*
12429781 GAGGT
195 GAGAT
* *
12429786 AAGATTTGCTGATGTAGCTTTAATCTTTTTAACCGCAATTTCAGAGAGGCAAGATTCACCGTTGT
1 AAGATTCGCTGATGTAGCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCACCGTTGT
*
12429851 GGCTTTAATCTTTTTACTACACCGCCTGGGA
66 GGCTTTAATCTTTTTACTGCACCGCCTGGGA
12429882 AGTAAGGCTT
Statistics
Matches: 263, Mismatches: 30, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
198 2 0.01
199 197 0.75
200 61 0.23
201 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (199 bp):
AAGATTCGCTGATGTAGCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCACCGTTGT
GGCTTTAATCTTTTTACTGCACCGCCTGGGAGATAAGATTCACTGATGTAGCTTTAATCTTTTTA
ATCTCAATGTCAAAGAGGCAAGATTCACCGTTGTGGCTTTAATCTATTCCACTGCACCGCATGAG
AGAT
Found at i:12430103 original size:12 final size:13
Alignment explanation
Indices: 12430082--12430110 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12430072 AGAATTTTTA
12430082 TTTTATTTTATTT
1 TTTTATTTTATTT
12430095 TTTTA-TTTATTT
1 TTTTATTTTATTT
12430107 TTTT
1 TTTT
12430111 TAAAAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:12430103 original size:17 final size:17
Alignment explanation
Indices: 12430076--12430111 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
12430066 GAATGCAGAA
12430076 TTTTTATTTTATTTTATT
1 TTTTTATTTTATTTT-TT
12430094 TTTTTA-TTTATTTTTT
1 TTTTTATTTTATTTTTT
12430110 TT
1 TT
12430112 AAAAATGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 8 0.44
18 6 0.33
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTATTTTATTTTTT
Found at i:12432143 original size:47 final size:48
Alignment explanation
Indices: 12432092--12432189 Score: 121
Period size: 47 Copynumber: 2.1 Consensus size: 48
12432082 TCTTTTTTCA
12432092 TTCTTCTTTCT-TTTTCTCATTTT-TATTTTGATATTGA-TTTTGATTTT
1 TTCTTCTTTCTCTTTT-T-ATTTTGTATTTTGATATTGATTTTTGATTTT
* * * *
12432139 TTCTTCTTTCTCTTTTTTTTTTGTTTTTTTATTTTGATTTTTGATTTT
1 TTCTTCTTTCTCTTTTTATTTTGTATTTTGATATTGATTTTTGATTTT
12432187 TTC
1 TTC
12432190 ATTTTCATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
46 4 0.09
47 23 0.52
48 17 0.39
ACGTcount: A:0.09, C:0.10, G:0.06, T:0.74
Consensus pattern (48 bp):
TTCTTCTTTCTCTTTTTATTTTGTATTTTGATATTGATTTTTGATTTT
Found at i:12432173 original size:13 final size:13
Alignment explanation
Indices: 12432111--12432186 Score: 55
Period size: 13 Copynumber: 5.8 Consensus size: 13
12432101 CTTTTTCTCA
12432111 TTTTTATTTTGA-
1 TTTTTATTTTGAT
* *
12432123 TATTGATTTTGAT
1 TTTTTATTTTGAT
* **
12432136 TTTTTCTTCTTTCT
1 TTTTTATT-TTGAT
* *
12432150 CTTTTTTTTTTGTT
1 -TTTTTATTTTGAT
12432164 TTTTTATTTTGAT
1 TTTTTATTTTGAT
*
12432177 TTTTGATTTT
1 TTTTTATTTT
12432187 TTCATTTTCA
Statistics
Matches: 48, Mismatches: 13, Indels: 5
0.73 0.20 0.08
Matches are distributed among these distances:
12 10 0.21
13 25 0.52
14 6 0.12
15 7 0.15
ACGTcount: A:0.11, C:0.05, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTTATTTTGAT
Found at i:12432202 original size:20 final size:21
Alignment explanation
Indices: 12432156--12432200 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
12432146 TTCTCTTTTT
* *
12432156 TTTTTG-TTTTTTTATTTTGA
1 TTTTTGATTTTTTCATTTTCA
12432176 TTTTTGATTTTTTCATTTTCA
1 TTTTTGATTTTTTCATTTTCA
12432197 TTTT
1 TTTT
12432201 GACTTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.11, C:0.04, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTGATTTTTTCATTTTCA
Found at i:12435827 original size:109 final size:109
Alignment explanation
Indices: 12435590--12436215 Score: 959
Period size: 109 Copynumber: 5.8 Consensus size: 109
12435580 ATATTTGGCA
* * *
12435590 ATTTGGTTAAACGAGAAAAATCGACACTCAGCAGCTTAGGGCATGTTTTCTCAAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
*
12435655 CAAAA-ATTGTCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
12435698 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
*
12435763 CAAAACATTGTCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
* *
12435807 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAATG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
*
12435872 CAAAACATT-CCTTATTTTAAAATTTTTAAAAGGATATTAAGAC
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
* *
12435915 ATTTGGTTGAACGAGAAAAATTGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
* ** * * *
12435980 CAAAATATTGCCTTATTTTGGAATTTTTAGAAGGATATTTAGCT
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
* *
12436024 ATTTGGTTGAACGAGAAAAATCGACACCTAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
** * * **
12436089 CAAAACATTGCCTTATTTTGGAATTTTTAGAAGGATATTTAGAT
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
* * * *
12436133 ATTTGGTTGAACGAGAAAAATCGACACCCAACACCTTAGGGCACGTTTCCTCAAATTTCCAAATG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
* * *
12436198 CTAAATATTGCCTCATTT
66 CAAAACATTGCCTTATTT
12436216 AGAAAAATTT
Statistics
Matches: 487, Mismatches: 29, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
108 170 0.35
109 317 0.65
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (109 bp):
ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACG
CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
Found at i:12435952 original size:217 final size:218
Alignment explanation
Indices: 12435590--12436215 Score: 977
Period size: 217 Copynumber: 2.9 Consensus size: 218
12435580 ATATTTGGCA
* * * *
12435590 ATTTGGTTAAACGAGAAAAATCGACACTCAGCAGCTTAGGGCATGTTTTCTCAAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
* *
12435655 CAAAA-ATTGTCTTATTTTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAAT
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGACATTTGGTTGAACGAGAAAAAT
*
12435719 CGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATTGTCTTATTTTAA
131 CGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATTGCCTTATTTTAA
12435784 AATTTTTAAAAGGATATTAAGCC
196 AATTTTTAAAAGGATATTAAGCC
*
12435807 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAATG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
12435872 CAAAACATT-CCTTATTTTAAAATTTTTAAAAGGATATTAAGACATTTGGTTGAACGAGAAAAAT
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGACATTTGGTTGAACGAGAAAAAT
* * * **
12435936 TGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGG
131 CGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATTGCCTTATTTTAA
* * *
12436001 AATTTTTAGAAGGATATTTAGCT
196 AATTTTTAAAAGGATATTAAGCC
*
12436024 ATTTGGTTGAACGAGAAAAATCGACACCTAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
** * * *
12436089 CAAAACATTGCCTTATTTTGGAATTTTTAGAAGGATATTTAGATATTTGGTTGAACGAGAAAAAT
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGACATTTGGTTGAACGAGAAAAAT
* * * * * * *
12436154 CGACACCCAACACCTTAGGGCACGTTTCCTCAAATTTCCAAATGCTAAATATTGCCTCATTT
131 CGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATTGCCTTATTT
12436216 AGAAAAATTT
Statistics
Matches: 376, Mismatches: 31, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
217 269 0.72
218 107 0.28
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (218 bp):
ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGACATTTGGTTGAACGAGAAAAAT
CGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATTGCCTTATTTTAA
AATTTTTAAAAGGATATTAAGCC
Found at i:12436888 original size:3 final size:3
Alignment explanation
Indices: 12436874--12437009 Score: 123
Period size: 3 Copynumber: 45.7 Consensus size: 3
12436864 AAATGGAAAC
* * * * *
12436874 ATA ATG ATA ATA ATA ATA TTA ATA TTA ATA ACA ATA ATA ATA A-A GATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * *
12436922 ATG ATA ATG ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
12436970 ATA ATA ATG ATG ATG ATA ATG ATA ACA TTA A-A ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12437010 GTTAACAATA
Statistics
Matches: 110, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
2 3 0.03
3 107 0.97
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12439447 original size:25 final size:25
Alignment explanation
Indices: 12439410--12439490 Score: 101
Period size: 25 Copynumber: 3.2 Consensus size: 25
12439400 CGGACACACC
* *
12439410 ACAGCTCGTATGAGCTTCTCGTTTT
1 ACAGCTCGCATGAGCTTCCCGTTTT
* *
12439435 ACAGCTCGCATGAGCTTCCCATTAT
1 ACAGCTCGCATGAGCTTCCCGTTTT
*
12439460 ACAGCTCGGATGAGCTTCCCGTTATT
1 ACAGCTCGCATGAGCTTCCCGTT-TT
12439486 -CAGCT
1 ACAGCT
12439491 TGGAAGAGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 47 0.98
26 1 0.02
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (25 bp):
ACAGCTCGCATGAGCTTCCCGTTTT
Found at i:12439515 original size:24 final size:25
Alignment explanation
Indices: 12439450--12439518 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
12439440 TCGCATGAGC
* * * *
12439450 TTCCCATTATACAGCTCGGATGAGC
1 TTCCCGTTATACAGCTTGGAAGAGA
*
12439475 TTCCCGTTATTCAGCTTGGAAGAGA
1 TTCCCGTTATACAGCTTGGAAGAGA
*
12439500 TTTCCGTT-TACAGCTTGGA
1 TTCCCGTTATACAGCTTGGA
12439519 GGAGCATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 10 0.27
25 27 0.73
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (25 bp):
TTCCCGTTATACAGCTTGGAAGAGA
Found at i:12445348 original size:16 final size:17
Alignment explanation
Indices: 12445327--12445374 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
12445317 ATTTTTTTTA
*
12445327 AAAAATATAATACAT-C
1 AAAAATATAATAAATAC
12445343 AAAAATACTAA-AAATAC
1 AAAAATA-TAATAAATAC
12445360 AAAAATA-AATAAATA
1 AAAAATATAATAAATA
12445375 TATATATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 2 0.07
16 15 0.54
17 11 0.39
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATATAATAAATAC
Found at i:12449858 original size:18 final size:16
Alignment explanation
Indices: 12449799--12449859 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
12449789 TAATTTATCA
12449799 ATTATATTAATAATTTT
1 ATTAT-TTAATAATTTT
**
12449816 ACAGATTT-ATAATTTT
1 A-TTATTTAATAATTTT
*
12449832 ATTAATTAATAATATTGT
1 ATTATTTAATAAT-TT-T
12449850 ATTATTTAAT
1 ATTATTTAAT
12449860 TACTTCTGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
15 3 0.09
16 14 0.41
17 5 0.15
18 12 0.35
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTATTTAATAATTTT
Found at i:12478137 original size:37 final size:37
Alignment explanation
Indices: 12478081--12478151 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
12478071 TTTCACATTT
**
12478081 TGTAAAGAAAAAATGAAGATGAACAATAACGATTCTC
1 TGTAAAGAAAAAACAAAGATGAACAATAACGATTCTC
*
12478118 TGTAAAGAAAAGACAAAGATGAACAATAACGATT
1 TGTAAAGAAAAAACAAAGATGAACAATAACGATT
12478152 TTCTACAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.54, C:0.10, G:0.17, T:0.20
Consensus pattern (37 bp):
TGTAAAGAAAAAACAAAGATGAACAATAACGATTCTC
Found at i:12480086 original size:25 final size:27
Alignment explanation
Indices: 12480067--12480121 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
12480057 TCGATATATA
12480067 GCTC-TTCA-GAGCTTCCCGATTAAAG
1 GCTCTTTCATGAGCTTCCCGATTAAAG
* *
12480092 GCTCTTTCATGGGCTTCCCGATTAATG
1 GCTCTTTCATGAGCTTCCCGATTAAAG
12480119 GCT
1 GCT
12480122 TTCCAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 4 0.15
26 4 0.15
27 18 0.69
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (27 bp):
GCTCTTTCATGAGCTTCCCGATTAAAG
Found at i:12482283 original size:24 final size:24
Alignment explanation
Indices: 12482237--12482284 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
12482227 ACCCTGCTTT
* *
12482237 TATTAAAAATATAAAATATTATAA
1 TATTAAAAATATAAAAAAATATAA
12482261 TATTAAAAAT-TAGAAAAAATATAA
1 TATTAAAAATATA-AAAAAATATAA
12482285 AAATCGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
TATTAAAAATATAAAAAAATATAA
Found at i:12482757 original size:91 final size:90
Alignment explanation
Indices: 12482656--12482861 Score: 211
Period size: 90 Copynumber: 2.3 Consensus size: 90
12482646 TTTAATAAGA
* **** * *
12482656 GCAGGTGCTTAATTGTTTGTTTTTTTTTAAGTTTTGAGGATATTTTTGATGCATTTTGAAAGATC
1 GCAGGGGCTTAATTGTTT-TTTTTGAAGAAG-TTTGAGGACATTTTTGATACATTTTGAAAGATC
12482721 AAGT-ATCCAATTAAGTG-AAAAAAAAG
64 AAGTGAT-CAATTAAGTGAAAAAAAAAG
* * *
12482747 GCAGGGGCTTAATTGCTTTTTTTTGAAGAAGTTTGAGGGCCTTTTTGATACATTTTGAAAGCTCA
1 GCAGGGGCTTAATTG-TTTTTTTTGAAGAAGTTTGAGGACATTTTTGATACATTTTGAAAGATCA
* *
12482812 ATTGATCAATTGAGTGCAAAAAAAAAAG
65 AGTGATCAATTAAGTG--AAAAAAAAAG
* *
12482840 G-AGAGGCTTAATTATTTTTTTT
1 GCAGGGGCTTAATTGTTTTTTTT
12482862 ATTATTATTT
Statistics
Matches: 96, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
90 40 0.42
91 32 0.33
92 14 0.15
93 10 0.10
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (90 bp):
GCAGGGGCTTAATTGTTTTTTTTGAAGAAGTTTGAGGACATTTTTGATACATTTTGAAAGATCAA
GTGATCAATTAAGTGAAAAAAAAAG
Found at i:12485101 original size:17 final size:17
Alignment explanation
Indices: 12485070--12485110 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
12485060 ATTATTAATT
12485070 TCATTATACAATATT-A
1 TCATTATACAATATTGA
*
12485086 TCATTATATTAATATTGA
1 TCATTATA-CAATATTGA
12485104 T-ATTATA
1 TCATTATA
12485111 ATCAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 12 0.55
18 2 0.09
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (17 bp):
TCATTATACAATATTGA
Found at i:12485216 original size:2 final size:2
Alignment explanation
Indices: 12485203--12485242 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
12485193 ATTTTAAAAC
* * *
12485203 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AC AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12485243 TTTATAATCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:12488895 original size:7 final size:8
Alignment explanation
Indices: 12488875--12488914 Score: 62
Period size: 8 Copynumber: 4.8 Consensus size: 8
12488865 TTAGACTCAA
12488875 AAAAAATTC
1 AAAAAA-TC
12488884 AAAAAATC
1 AAAAAATC
12488892 AAAAAATC
1 AAAAAATC
12488900 AAAAAAATC
1 -AAAAAATC
12488909 AAAAAA
1 AAAAAA
12488915 ATTAAAGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 16 0.53
9 14 0.47
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAATC
Found at i:12488897 original size:17 final size:17
Alignment explanation
Indices: 12488875--12488914 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
12488865 TTAGACTCAA
12488875 AAAAAATTC-AAAAAATC
1 AAAAAA-TCAAAAAAATC
12488892 AAAAAATCAAAAAAATC
1 AAAAAATCAAAAAAATC
12488909 AAAAAA
1 AAAAAA
12488915 ATTAAAGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAATCAAAAAAATC
Found at i:12488915 original size:9 final size:9
Alignment explanation
Indices: 12488874--12488916 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
12488864 TTTAGACTCA
12488874 AAAAAAATTC
1 AAAAAAA-TC
12488884 -AAAAAATC
1 AAAAAAATC
12488892 -AAAAAATC
1 AAAAAAATC
12488900 AAAAAAATC
1 AAAAAAATC
12488909 AAAAAAAT
1 AAAAAAAT
12488917 TAAAGTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 10 0.31
9 22 0.69
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAAAATC
Found at i:12489777 original size:6 final size:7
Alignment explanation
Indices: 12489760--12489804 Score: 65
Period size: 7 Copynumber: 6.3 Consensus size: 7
12489750 TTTAAGTCAA
12489760 AAAAATG
1 AAAAATG
12489767 AAAAATG
1 AAAAATG
12489774 AAAAATG
1 AAAAATG
12489781 AAAAAATG
1 -AAAAATG
12489789 AAAAA-G
1 AAAAATG
12489795 TAAAAATG
1 -AAAAATG
12489803 AA
1 AA
12489805 GAAGCCAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 1 0.03
7 26 0.74
8 8 0.23
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:12489787 original size:22 final size:22
Alignment explanation
Indices: 12489759--12489804 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
12489749 CTTTAAGTCA
12489759 AAAAAATGAAAAA-TGAAAAATG
1 AAAAAATGAAAAAGT-AAAAATG
12489781 AAAAAATGAAAAAGTAAAAATG
1 AAAAAATGAAAAAGTAAAAATG
12489803 AA
1 AA
12489805 GAAGCCAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (22 bp):
AAAAAATGAAAAAGTAAAAATG
Found at i:12491243 original size:100 final size:100
Alignment explanation
Indices: 12491057--12492030 Score: 1002
Period size: 100 Copynumber: 9.9 Consensus size: 100
12491047 AAACCATAGT
* * * * * *
12491057 TTGCAATTTAAAAAGATTAAAGCTACAACGGCGAATCTTATTTCCCAGGCGATGCAGCGGAACAG
1 TTGCAA-TTCAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCAGGCGATGCAGTGGAACAG
* **
12491122 ATTGAAGCTACGACGGCGAATCTTGCTTCCCCGACA
65 ATTGAAGCTACGACAGCGAATCTCACTTCCCCGACA
* * * * *
12491158 TTACAATTTAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCAAGCGATACAGCGGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCAGGCGATGCAGTGGAACAGA
* ** *
12491223 TTGAAGATACGATGGTGAATCTCACTTCCCCGACA
66 TTGAAGCTACGACAGCGAATCTCACTTCCCCGACA
* * * *
12491258 TTACAATTCAAAAGATTGAAGCCACAAC-AGCGAATCCTATTTCCCAGGCGATGCAGCGGAACAG
1 TTGCAATTCAAAAGATTGAAGCCACAACGA-CGAATCTTACTTCCCAGGCGATGCAGTGGAACAG
*
12491322 ATTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
65 ATTGAAGCTACGACAGCGAATCTCACTTCCCCGACA
* **
12491358 TTGTAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGTGGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCAGGCGATGCAGTGGAACAGA
**
12491423 TTGAAGCTACGACAGCGAATCTCACTTCCTTGACA
66 TTGAAGCTACGACAGCGAATCTCACTTCCCCGACA
* * * *
12491458 TTGCAATTCAAAAGATTGAAGTCACTAC-AGTGAATCTTACTTCCCAGGCGATGCAGTGGAATAG
1 TTGCAATTCAAAAGATTGAAGCCACAACGA-CGAATCTTACTTCCCAGGCGATGCAGTGGAACAG
* *
12491522 ATTGAAGCTACGGCAGCGAATCTCACTTCCCTGACA
65 ATTGAAGCTACGACAGCGAATCTCACTTCCCCGACA
* * *
12491558 TTACAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTT-CCAGGCGATGCAGCGGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCAGGCGATGCAGTGGAACAGA
** *
12491622 TTGAAGCTACGACAGTAAATCTCACTTTCCCGACA
66 TTGAAGCTACGACAGCGAATCTCACTTCCCCGACA
* * ** *
12491657 TTGTAATTCAAAAGATTGAAGCCATAACGGTGAATCTTACTT-CCA-G-GTTGCAGTGGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCAGGCGATGCAGTGGAACAGA
* * **
12491719 TTGAAGCTACAACAGCGGATCTTGCTTCCCCG---
66 TTGAAGCTACGACAGCGAATCTCACTTCCCCGACA
* * * * * * * *
12491751 --GCAGTTAAAAAGATTGAAGCTACAAC-AGCGGATCTTACTTTCCTA-GCGTTGTAGTGGAATA
1 TTGCAATTCAAAAGATTGAAGCCACAACGA-CGAATCTTAC-TTCCCAGGCGATGCAGTGGAACA
* * * *
12491812 GATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
64 GATTGAAGCTACGACAGCGAATCTCACTTCCCCGACA
* * * *
12491849 TTGCAATTAAAAAGATTGAAGCTACAAC-AGCGAATCTTACTTTCCTA-GCGTTGCAGTGGAACA
1 TTGCAATTCAAAAGATTGAAGCCACAACGA-CGAATCTTAC-TTCCCAGGCGATGCAGTGGAACA
* * * **
12491912 GATTAAAGCTACAACAGCGGATCTTGCTTCCCCG---
64 GATTGAAGCTACGACAGCGAATCTCACTTCCCCGACA
* * * * * * *
12491946 --GCAGTTAAAAAGATTGAAGCTACAAC-AGCGGATCTTACTTTCCTA-GTGTTGCAGTGGAACA
1 TTGCAATTCAAAAGATTGAAGCCACAACGA-CGAATCTTAC-TTCCCAGGCGATGCAGTGGAACA
* *
12492007 GATTGAAGCTACAACAGCGGATCT
64 GATTGAAGCTACGACAGCGAATCT
12492031 TGTTTCCCCG
Statistics
Matches: 773, Mismatches: 87, Indels: 32
0.87 0.10 0.04
Matches are distributed among these distances:
92 29 0.04
93 2 0.00
94 3 0.00
95 125 0.16
97 39 0.05
98 1 0.00
99 92 0.12
100 477 0.62
101 5 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (100 bp):
TTGCAATTCAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCAGGCGATGCAGTGGAACAGA
TTGAAGCTACGACAGCGAATCTCACTTCCCCGACA
Found at i:12492187 original size:50 final size:50
Alignment explanation
Indices: 12491067--12492244 Score: 638
Period size: 50 Copynumber: 24.0 Consensus size: 50
12491057 TTGCAATTTA
* * * * * *
12491067 AAAAGATTAAAGCTACAACGGCGAATCTTATTTCCCAGGCGA-TGCAGCGG
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGAC-ATTGCAGTGG
* * * * * * * **
12491117 AACAGATTGAAGCTACGACGGCGAATCTTGCTTCCCCGACATTACAATTT
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTGG
* * * *
12491167 AAAAGATTGAAGCCACAAC-GACGAATCTTACTTCCC-AAGCGA-TACAGCGG
1 AAAAGATTGAAGCTACAACAG-CGAATCTTACTTCCCTGA-C-ATTGCAGTGG
* * * ** * * * * * **
12491217 AACAGATTGAAGATACGATGGTGAATCTCACTTCCCCGACATTACAATTC
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTGG
* * * * * *
12491267 AAAAGATTGAAGCCACAACAGCGAATCCTATTTCCCAGGCGA-TGCAGCGG
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGAC-ATTGCAGTGG
* * * * * * * **
12491317 AACAGATTGAAGCTACGACGGCGAATCTCACTTCCCCGACATTGTAATTC
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTGG
* * * * *
12491367 AAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGA-TGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGAC-ATTGCAGTGG
* * * * * **
12491417 AACAGATTGAAGCTACGACAGCGAATCTCACTTCCTTGACATTGCAATTC
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTGG
* * * *
12491467 AAAAGATTGAAG-TCACTACAGTGAATCTTACTTCCCAGGCGA-TGCAGTGG
1 AAAAGATTGAAGCT-ACAACAGCGAATCTTACTTCCCTGAC-ATTGCAGTGG
* ** * * * **
12491517 AATAGATTGAAGCTACGGCAGCGAATCTCACTTCCCTGACATTACAATTC
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTGG
* * * * *
12491567 AAAAGATTGAAGCCACAACGGCGAATCTTACTT-CCAGGCGA-TGCAGCGG
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGAC-ATTGCAGTGG
* * ** * * * **
12491616 AACAGATTGAAGCTACGACAGTAAATCTCACTTTCCC-GACATTGTAATTC
1 AAAAGATTGAAGCTACAACAGCGAATCTTAC-TTCCCTGACATTGCAGTGG
* * * * **
12491666 AAAAGATTGAAGCCATAACGGTGAATCTTACTT-CC--AGGTTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTGG
* * * * **
12491713 AACAGATTGAAGCTACAACAGCGGATCTTGCTTCCC---C--GGCAGTTA
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTGG
* * * *
12491758 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGCGTTGTAGTGG
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGA-CATTGCAGTGG
* * * **
12491808 AATAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTA
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTGG
* *
12491858 AAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCT-AGCGTTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGA-CATTGCAGTGG
* * * * * **
12491908 AACAGATTAAAGCTACAACAGCGGATCTTGCTTCCC---C--GGCAGTTA
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTGG
* * **
12491953 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGTGTTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGA-CATTGCAGTGG
* * ** * **
12492003 AACAGATTGAAGCTACAACAGCGGATCTTGTTTCCC---C--GGCAGTTA
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTGG
* ** * **
12492048 AAAAGATTGAAGCTACAACAGCGGATCTTGTTTCCC---C--GGCAGTTA
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTGG
* * *
12492093 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGTATTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGA-CATTGCAGTGG
* * * *
12492143 AACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAAT-T
1 AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTGG
* * * *
12492192 ATAAAGATTGATGCTACAACAGC-AGATCTTA-TCCCCCTGGCGTTGCAGTGG
1 A-AAAGATTGAAGCTACAACAGCGA-ATCTTACT-TCCCTGACATTGCAGTGG
12492243 AA
1 AA
12492245 CAGAATAAAA
Statistics
Matches: 862, Mismatches: 224, Indels: 84
0.74 0.19 0.07
Matches are distributed among these distances:
45 157 0.18
47 33 0.04
48 5 0.01
49 45 0.05
50 610 0.71
51 12 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (50 bp):
AAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTGG
Found at i:12492238 original size:100 final size:95
Alignment explanation
Indices: 12491761--12492248 Score: 230
Period size: 95 Copynumber: 5.0 Consensus size: 95
12491751 GCAGTTAAAA
* * * ** *
12491761 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGTAGTGGAATAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTAC-TTCC--CCG--GCAATTAAAAAGATTGAAGCTACAA
* * * ** *
12491826 CAGCGGATCTTACTTCCCT-GACATTGCAATTAAAA
61 CAGCAGATCTTACTCCCCTAG-CATTGCAGTGGAAC
* * * ** * *
12491861 AGATTGAAGCTACAACAGCGAATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTAAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTAC-TTCC--CCG--GCAATTAAAAAGATTGAAGCTACAA
* * ** *
12491926 CAGCGGATCTTGCTTCCCC--G----GCAGTTAAAA
61 CAGCAGATCTTAC-TCCCCTAGCATTGCAGTGGAAC
** * ** *
12491956 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTAC-TTCC--CCG--GCAATTAAAAAGATTGAAGCTACAA
* ** ** *
12492021 CAGCGGATCTTGTTTCCCC--G----GCAGTTAAAA
61 CAGCAGATCTT-ACTCCCCTAGCATTGCAGTGGAAC
** * *
12492051 AGATTGAAGCTACAACAGCGGATCTTGTTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAGCG
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCCGGCAATTAAAAAGATTGAAGCTACAACAGCA
** *
12492116 GATCTTACTTTCCTAGTATTGCAGTGGAAC
66 GATCTTACTCCCCTAGCATTGCAGTGGAAC
* * *
12492146 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTATAAAGATTGATGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCC---C--GGCAATTAAAAAGATTGAAGCTACAA
* *
12492211 CAGCAGATCTTA-TCCCCCTGGCGTTGCAGTGGAAC
61 CAGCAGATCTTACT-CCCCTAGCATTGCAGTGGAAC
12492246 AGA
1 AGA
12492249 ATAAAACCAT
Statistics
Matches: 336, Mismatches: 38, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
89 3 0.01
90 33 0.10
91 1 0.00
92 1 0.00
94 4 0.01
95 162 0.48
98 1 0.00
99 1 0.00
100 126 0.38
101 4 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (95 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTCCCCGGCAATTAAAAAGATTGAAGCTACAACAGCA
GATCTTACTCCCCTAGCATTGCAGTGGAAC
Done.