Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold132
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: 2458301
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 12 of 15
Found at i:1888262 original size:27 final size:25
Alignment explanation
Indices: 1888227--1888280 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 25
1888217 ATTCGATTAA
*
1888227 TAAATAAATTTATATTTTTAATAAAT
1 TAAATAAATTTAAATTTTTAA-AAAT
1888253 TAAACTAAATTTAAATTTTTAAAAAT
1 TAAA-TAAATTTAAATTTTTAAAAAT
1888279 TA
1 TA
1888281 TAAATATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TAAATAAATTTAAATTTTTAAAAAT
Found at i:1888264 original size:21 final size:21
Alignment explanation
Indices: 1888223--1888264 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1888213 TAATATTCGA
* *
1888223 TTAATAAATAAATTTATATTT
1 TTAATAAATAAATCTAAATTT
1888244 TTAATAAATTAAA-CTAAATTT
1 TTAATAAA-TAAATCTAAATTT
1888265 AAATTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATAAATAAATCTAAATTT
Found at i:1889572 original size:18 final size:19
Alignment explanation
Indices: 1889551--1889590 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1889541 TTATTATAAT
1889551 AAAAAAT-AAAATTATTTA
1 AAAAAATAAAAATTATTTA
*
1889569 AAAATATAAAAATTATTTA
1 AAAAAATAAAAATTATTTA
1889588 AAA
1 AAA
1889591 TTTAATTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAAATAAAAATTATTTA
Found at i:1893932 original size:20 final size:21
Alignment explanation
Indices: 1893899--1893939 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1893889 AAACTTAATC
*
1893899 ATCATATATGAATATAAATATA
1 ATCATATA-GAATAAAAATATA
1893921 ATCATATA-AATAAAAATAT
1 ATCATATAGAATAAAAATAT
1893940 TAAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
ATCATATAGAATAAAAATATA
Found at i:1895620 original size:20 final size:23
Alignment explanation
Indices: 1895578--1895622 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
1895568 AAGATTTTTG
1895578 TATTATAAAATTTTAAATATAAT
1 TATTATAAAATTTTAAATATAAT
1895601 TATTAT-AAA-TTTAAAT-TAAT
1 TATTATAAAATTTTAAATATAAT
1895621 TA
1 TA
1895623 ATTTTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 7 0.32
22 3 0.14
23 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTATAAAATTTTAAATATAAT
Found at i:1898234 original size:27 final size:24
Alignment explanation
Indices: 1898179--1898234 Score: 58
Period size: 27 Copynumber: 2.2 Consensus size: 24
1898169 TATTTAAACG
1898179 TAAAAAATTAAATTAAAATCAAAT
1 TAAAAAATTAAATTAAAATCAAAT
* * *
1898203 CAAAAAATTTATAATTTAAAATGATAT
1 TAAAAAA-TTA-AA-TTAAAATCAAAT
1898230 TAAAA
1 TAAAA
1898235 TTATTTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 6 0.24
25 3 0.12
26 2 0.08
27 14 0.56
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (24 bp):
TAAAAAATTAAATTAAAATCAAAT
Found at i:1905943 original size:3 final size:3
Alignment explanation
Indices: 1905935--1905979 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1905925 TTCCTTCCAG
*
1905935 ATA ATA ATA ATA ATA ACA 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
1905980 GACAGCTAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1907175 original size:22 final size:22
Alignment explanation
Indices: 1907133--1907176 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1907123 ATTAATTCTA
*
1907133 ATTAAATATTTTTTTTATAATT
1 ATTAAATATTTATTTTATAATT
1907155 ATTAAATATATTATTTT-TAATT
1 ATTAAATAT-TTATTTTATAATT
1907177 TTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTAAATATTTATTTTATAATT
Found at i:1907723 original size:3 final size:3
Alignment explanation
Indices: 1907715--1907750 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1907705 GTGCATTTTA
*
1907715 AAT AAT AAT AAT AAT AAT AAT AAT AAT CAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1907751 GGTTAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1908101 original size:19 final size:19
Alignment explanation
Indices: 1908066--1908120 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
1908056 AAAATCATTC
1908066 ATTTTTA-AAACATAAATCTA
1 ATTTTTATAAA-ATAAATC-A
*
1908086 ATTTTTTTAAAA-AAATCA
1 ATTTTTATAAAATAAATCA
1908104 ATTTTTATAAAATAAAT
1 ATTTTTATAAAATAAAT
1908121 AAAATCTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 12 0.39
19 9 0.29
20 7 0.23
21 3 0.10
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTTTATAAAATAAATCA
Found at i:1908710 original size:14 final size:14
Alignment explanation
Indices: 1908681--1908719 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1908671 TTAGATCGTC
1908681 TTTATATTAT-TAT
1 TTTATATTATATAT
1908694 TTTATATTATATAT
1 TTTATATTATATAT
*
1908708 TTTTTATTATAT
1 TTTATATTATAT
1908720 TTAAATAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATATTATATAT
Found at i:1909077 original size:18 final size:20
Alignment explanation
Indices: 1909038--1909078 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1909028 TAATAAATAG
*
1909038 TTATCTAAATTAAACTAATT
1 TTATCTAAATTAAACAAATT
1909058 TTATCTAAA-TAAA-AAATT
1 TTATCTAAATTAAACAAATT
1909076 TTA
1 TTA
1909079 AATTTGATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 4 0.20
20 9 0.45
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATCTAAATTAAACAAATT
Found at i:1912410 original size:17 final size:17
Alignment explanation
Indices: 1912388--1912421 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1912378 CAATTAAAAT
1912388 TTTAAATAGATTTTTTA
1 TTTAAATAGATTTTTTA
**
1912405 TTTAAATTTATTTTTTA
1 TTTAAATAGATTTTTTA
1912422 AATTTAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTAAATAGATTTTTTA
Found at i:1912433 original size:14 final size:13
Alignment explanation
Indices: 1912405--1912434 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
1912395 AGATTTTTTA
1912405 TTTAAATTTATTT
1 TTTAAATTTATTT
1912418 TTTAAATTTAATTT
1 TTTAAATTT-ATTT
1912432 TTT
1 TTT
1912435 TAAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTAAATTTATTT
Found at i:1912454 original size:18 final size:19
Alignment explanation
Indices: 1912421--1912457 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
1912411 TTTATTTTTT
1912421 AAATTTAATTTTTTTAAAAA
1 AAATTTAA-TTTTTTAAAAA
1912441 AAATTTAA-TTTTTAAAA
1 AAATTTAATTTTTTAAAA
1912458 TTAAACGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTAATTTTTTAAAAA
Found at i:1915192 original size:22 final size:24
Alignment explanation
Indices: 1915162--1915208 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
1915152 TAAAAATAAA
1915162 AAAAATTATAA-ATATTAAA-ATT
1 AAAAATTATAATATATTAAATATT
* *
1915184 AAAATTTATAATTTATTAAATATT
1 AAAAATTATAATATATTAAATATT
1915208 A
1 A
1915209 TTTTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 7 0.33
24 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAATTATAATATATTAAATATT
Found at i:1915196 original size:13 final size:15
Alignment explanation
Indices: 1915163--1915208 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1915153 AAAAATAAAA
1915163 AAAATTATAAATATT
1 AAAATTATAAATATT
1915178 AAAATTA-AAAT-TT
1 AAAATTATAAATATT
*
1915191 ATAATTTATTAAATATT
1 A-AAATTA-TAAATATT
1915208 A
1 A
1915209 TTTTTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 3 0.12
14 9 0.35
15 7 0.27
16 4 0.15
17 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:1919738 original size:3 final size:3
Alignment explanation
Indices: 1919730--1919756 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1919720 CAAACATATA
1919730 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1919757 CTACTGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1922841 original size:15 final size:15
Alignment explanation
Indices: 1922821--1922866 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1922811 AATTTTAAAT
1922821 TTAATTTTTATTTTA
1 TTAATTTTTATTTTA
* *
1922836 TTAATTATTATTATTT
1 TTAATTTTTATT-TTA
*
1922852 TTAATATTTATTTTA
1 TTAATTTTTATTTTA
1922867 CATTAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTAATTTTTATTTTA
Found at i:1922862 original size:19 final size:18
Alignment explanation
Indices: 1922812--1922863 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
1922802 TTAATTTTAA
*
1922812 ATTTTAA-ATTTAATTTTT
1 ATTTTAATATTT-ATTATT
* *
1922830 ATTTTATTAATTATTATT
1 ATTTTAATATTTATTATT
1922848 ATTTTTAATATTTATT
1 A-TTTTAATATTTATT
1922864 TTACATTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTAATATTTATTATT
Found at i:1924742 original size:32 final size:30
Alignment explanation
Indices: 1924692--1924758 Score: 73
Period size: 32 Copynumber: 2.2 Consensus size: 30
1924682 TAAGTATTTC
1924692 ATAATATGAATAATATGATTCATACTTTTATA
1 ATAATATGAATAATATGA-T-ATACTTTTATA
* *
1924724 ATAATATGAAT-TTGATGATATATTTTTATA
1 ATAATATGAATAAT-ATGATATACTTTTATA
*
1924754 TTAAT
1 ATAAT
1924759 TATGTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 14 0.45
31 2 0.06
32 15 0.48
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (30 bp):
ATAATATGAATAATATGATATACTTTTATA
Found at i:1927466 original size:21 final size:21
Alignment explanation
Indices: 1927433--1927505 Score: 57
Period size: 22 Copynumber: 3.6 Consensus size: 21
1927423 AATAATCTTT
1927433 TAAT-ATTTAAAATTTTTTAAA
1 TAATAATTT-AAATTTTTTAAA
*
1927454 TAATAATTTAAA-TTTATAAA
1 TAATAATTTAAATTTTTTAAA
*
1927474 T--TAAATTAAATTTTTATATAA
1 TAATAATTTAAATTTTT-TA-AA
*
1927495 -AAAAATTTAAA
1 TAATAATTTAAA
1927506 ATATTTTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
18 8 0.20
19 3 0.07
20 10 0.24
21 9 0.22
22 11 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATAATTTAAATTTTTTAAA
Found at i:1928529 original size:21 final size:21
Alignment explanation
Indices: 1928505--1928571 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 21
1928495 ATCATATGTG
* *
1928505 ATTTTTTATTATTTTTTATAT
1 ATTTTTTATTATATTTAATAT
1928526 A-TTTTTA-TATATTTAATAT
1 ATTTTTTATTATATTTAATAT
1928545 -TTATTTTATTATATTATAATTAT
1 ATT-TTTTATTATATT-TAA-TAT
1928568 ATTT
1 ATTT
1928572 ATATTTGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 11 0.29
20 11 0.29
21 7 0.18
22 3 0.08
23 4 0.11
24 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTTTTATTATATTTAATAT
Found at i:1928531 original size:12 final size:11
Alignment explanation
Indices: 1928505--1928558 Score: 58
Period size: 10 Copynumber: 5.0 Consensus size: 11
1928495 ATCATATGTG
1928505 ATTTTTTAT-T
1 ATTTTTTATAT
1928515 ATTTTTTATAT
1 ATTTTTTATAT
1928526 A-TTTTTATAT
1 ATTTTTTATAT
** *
1928536 ATTTAATATTT
1 ATTTTTTATAT
1928547 ATTTTATTATAT
1 ATTTT-TTATAT
1928559 TATAATTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 19 0.54
11 12 0.34
12 4 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTTTTTATAT
Found at i:1932458 original size:59 final size:63
Alignment explanation
Indices: 1932382--1932581 Score: 173
Period size: 68 Copynumber: 3.2 Consensus size: 63
1932372 AAGATGTGTG
*
1932382 TATATATATAAAATAAA-TAATT-AAAAATTATTAAAA-TTATA-TTATATTAAATAATAATA
1 TATAAATATAAAATAAATTAATTGAAAAATTATTAAAATTTATATTTATATTAAATAATAATA
* * * *
1932441 TATAAATATAAATTAAATTTATTTGTATAATTATTAAAATTTATATTTATATTAAATAAT-ATA
1 TATAAATATAAAATAAA-TTAATTGAAAAATTATTAAAATTTATATTTATATTAAATAATAATA
* * * * *
1932504 -ATAAGTTATCAAATTAATATTATGTTTGATAATAATAATTAAAATTTATTTTTATATTAAA-AA
1 TATAA-ATAT-AAAATAA-ATTA--ATTGA-AA-AATTATTAAAATTTATATTTATATTAAATAA
1932567 TAAT-
59 TAATA
1932571 TAGTAAATATA
1 TA-TAAATATA
1932582 GATACATTAA
Statistics
Matches: 115, Mismatches: 11, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
59 15 0.13
61 4 0.03
62 16 0.14
63 11 0.10
64 24 0.21
65 1 0.01
66 4 0.03
67 5 0.04
68 32 0.28
69 3 0.03
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.45
Consensus pattern (63 bp):
TATAAATATAAAATAAATTAATTGAAAAATTATTAAAATTTATATTTATATTAAATAATAATA
Found at i:1932494 original size:21 final size:21
Alignment explanation
Indices: 1932408--1932494 Score: 58
Period size: 22 Copynumber: 4.2 Consensus size: 21
1932398 ATAATTAAAA
1932408 ATTATTAAAA-TTATA-TTAT
1 ATTATTAAAATTTATATTTAT
* * **
1932427 ATTAAATAATAATATATAAATAT
1 ATT-ATTAA-AATTTATATTTAT
*
1932450 A-AATT-AAATTTAT-TTGTAT
1 ATTATTAAAATTTATATT-TAT
1932469 AATTATTAAAATTTATATTTAT
1 -ATTATTAAAATTTATATTTAT
1932491 ATTA
1 ATTA
1932495 AATAATATAA
Statistics
Matches: 50, Mismatches: 9, Indels: 16
0.67 0.12 0.21
Matches are distributed among these distances:
19 12 0.24
20 6 0.12
21 11 0.22
22 15 0.30
23 6 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
ATTATTAAAATTTATATTTAT
Found at i:1932558 original size:68 final size:63
Alignment explanation
Indices: 1932411--1932581 Score: 181
Period size: 68 Copynumber: 2.7 Consensus size: 63
1932401 ATTAAAAATT
* *
1932411 ATTAAAA-TTA-TATTATATTAAATAATAATATATAAATATAAATTAAATTTATTTGTATAATT
1 ATTAAAATTTATTTTTATATTAAATAAT-ATATATAAATATAAATTAAATTTATTTGTATAATA
* * *
1932473 ATTAAAATTTATATTTATATTAAATAATATA-ATAAGTTATCAAATTAATATTATGTTTGATAAT
1 ATTAAAATTTATTTTTATATTAAATAATATATATAA-ATAT-AAATTAA-ATT-TATTTG-T-AT
1932537 AATA
60 AATA
1932541 ATTAAAATTTATTTTTATATTAAA-AATA-ATTAGTAAATATA
1 ATTAAAATTTATTTTTATATTAAATAATATA-TA-TAAATATA
1932582 GATACATTAA
Statistics
Matches: 91, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
62 11 0.12
63 9 0.10
64 21 0.23
65 3 0.03
66 6 0.07
67 6 0.07
68 32 0.35
69 3 0.03
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (63 bp):
ATTAAAATTTATTTTTATATTAAATAATATATATAAATATAAATTAAATTTATTTGTATAATA
Found at i:1932569 original size:31 final size:31
Alignment explanation
Indices: 1932467--1932570 Score: 75
Period size: 34 Copynumber: 3.2 Consensus size: 31
1932457 ATTTATTTGT
* *
1932467 ATAATTATTAAAATTTATATTTATATTAAATAA
1 ATAATAATTAAAATTTATTTTTATATT-AA-AA
* * * * *
1932500 TATAATAAGTTATCAAA-TTAATATTATGTTTGATA
1 -ATAATAA-TTA--AAATTTATTTTTAT-ATTAAAA
1932535 ATAATAATTAAAATTTATTTTTATATTAAAA
1 ATAATAATTAAAATTTATTTTTATATTAAAA
1932566 ATAAT
1 ATAAT
1932571 TAGTAAATAT
Statistics
Matches: 53, Mismatches: 12, Indels: 13
0.68 0.15 0.17
Matches are distributed among these distances:
31 12 0.23
32 8 0.15
33 3 0.06
34 13 0.25
35 4 0.08
36 8 0.15
37 5 0.09
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (31 bp):
ATAATAATTAAAATTTATTTTTATATTAAAA
Found at i:1933352 original size:37 final size:36
Alignment explanation
Indices: 1933311--1933382 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 36
1933301 TTACACAATA
*
1933311 ATTATTTCATCCTTAACAATGATTTATTAATTTTTTT
1 ATTATTTCATCATTAACAATGATTTATT-ATTTTTTT
* * *
1933348 ATTATTTTATCATTGATAATGATTTATTATTTTTT
1 ATTATTTCATCATTAACAATGATTTATTATTTTTT
1933383 GATAAAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 7 0.23
37 24 0.77
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (36 bp):
ATTATTTCATCATTAACAATGATTTATTATTTTTTT
Found at i:1933957 original size:3 final size:3
Alignment explanation
Indices: 1933949--1933976 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1933939 AAAAAGTGAA
1933949 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1933977 GCTTATTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1938393 original size:26 final size:27
Alignment explanation
Indices: 1938345--1938397 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
1938335 CTTTTTAAGA
1938345 AAATATTAATCAATATTTAGTAATACC
1 AAATATTAATCAATATTTAGTAATACC
1938372 AAATATTAATC-ATATTTAGTAATACC
1 AAATATTAATCAATATTTAGTAATACC
1938398 GATAAAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (27 bp):
AAATATTAATCAATATTTAGTAATACC
Found at i:1938512 original size:28 final size:28
Alignment explanation
Indices: 1938442--1938512 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 28
1938432 TTATTTATTT
1938442 TATA-TTTAATAAAAATAAAATATTAAA
1 TATATTTTAATAAAAATAAAATATTAAA
** *
1938469 TATATTTTTTTAAAAA-ATAATAATTAAA
1 TATATTTTAATAAAAATAAAAT-ATTAAA
*
1938497 TA-ATTCTTAATCAAAA
1 TATATT-TTAATAAAAA
1938513 GAGTAAAGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
27 11 0.31
28 24 0.69
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (28 bp):
TATATTTTAATAAAAATAAAATATTAAA
Found at i:1941874 original size:16 final size:16
Alignment explanation
Indices: 1941836--1941882 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1941826 TTTGTTTGAT
*
1941836 ATTTAAA-AATTATAA
1 ATTTAAATATTTATAA
*
1941851 ATACTAAATATTTATAA
1 AT-TTAAATATTTATAA
*
1941868 ATTTAAATATATATA
1 ATTTAAATATTTATA
1941883 TATATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 2 0.08
16 15 0.58
17 9 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTTAAATATTTATAA
Found at i:1941936 original size:2 final size:2
Alignment explanation
Indices: 1941874--1941921 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1941864 ATAAATTTAA
1941874 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1941916 AT AT AT
1 AT AT AT
1941922 GCAATGGAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1944134 original size:2 final size:2
Alignment explanation
Indices: 1944093--1944119 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1944083 GAAAAGAAGA
1944093 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1944120 CATGCATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1944169 original size:26 final size:26
Alignment explanation
Indices: 1944103--1944171 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
1944093 ATATATATAT
* *
1944103 ATATATATATATATATACATGCATAC
1 ATATATATATATATATACATACACAC
*
1944129 ATATATGA-ATGTATATACGA-ACACAC
1 ATATAT-ATATATATATAC-ATACACAC
1944155 ATATATATATATATATA
1 ATATATATATATATATA
1944172 TATGCACTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 1 0.03
26 33 0.92
27 2 0.06
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (26 bp):
ATATATATATATATATACATACACAC
Found at i:1947295 original size:14 final size:15
Alignment explanation
Indices: 1947251--1947307 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 15
1947241 GCTCGTTTAA
1947251 TATATTTTATTATTAAT
1 TATATTTTATTATT--T
*
1947268 TAATAATATTATTA-TT
1 T-AT-ATTTTATTATTT
1947284 TATATTTTATTATTT
1 TATATTTTATTATTT
1947299 TATATTTTA
1 TATATTTTA
1947308 AGCAAATAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 8 0.23
15 13 0.37
16 2 0.06
17 1 0.03
18 3 0.09
19 8 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATTTTATTATTT
Found at i:1948868 original size:22 final size:21
Alignment explanation
Indices: 1948843--1948883 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1948833 TATTTTTAAA
1948843 TCAATAAAAAACCACTAAAAAC
1 TCAATAAAAAACCA-TAAAAAC
*
1948865 TCAATAAAAAATCATAAAA
1 TCAATAAAAAACCATAAAA
1948884 TTGATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (21 bp):
TCAATAAAAAACCATAAAAAC
Found at i:1949047 original size:20 final size:20
Alignment explanation
Indices: 1949024--1949088 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
1949014 ATTTAATACT
1949024 TATTTACTATTTAAATTATA
1 TATTTACTATTTAAATTATA
* * *
1949044 TATTAACTATTAAAATTACA
1 TATTTACTATTTAAATTATA
* * *
1949064 TATTTAATTTTTAAATTATT
1 TATTTACTATTTAAATTATA
1949084 TATTT
1 TATTT
1949089 CAATTCAATT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTACTATTTAAATTATA
Found at i:1951558 original size:141 final size:141
Alignment explanation
Indices: 1951304--1951565 Score: 443
Period size: 141 Copynumber: 1.9 Consensus size: 141
1951294 GTTTTGAATT
* * *
1951304 TTGGCTATGTTTTGGACCATGCCATTGGGCATAAATACAATGGTACTGTATGCTAGCATTTACGT
1 TTGGCTATGTTCTGGACCATGCCATTGGGCATAAATACAATGGTACTATATGCTAGCATGTACGT
**
1951369 ATCCTTTCTGAGGTTACATTATGAATATGGACCTTGCCACTAGGGTGAAAATGGTCATAGTTTAG
66 ATCCTTTCTGAGGTTACATTATGAATATAAACCTTGCCACTAGGGTGAAAATGGTCATAGTTTAG
1951434 TGTTATTTGAC
131 TGTTATTTGAC
* * * *
1951445 TTGGCTATGTTCTGGACCTTGCTATTGGGGATAAATACAATGGTACTATATGTTAGCATGTACGT
1 TTGGCTATGTTCTGGACCATGCCATTGGGCATAAATACAATGGTACTATATGCTAGCATGTACGT
1951510 ATCCTTTCTGAGGTTACATTATGAATATAAACCTTGCCACTAGGGTGAAAATGGTC
66 ATCCTTTCTGAGGTTACATTATGAATATAAACCTTGCCACTAGGGTGAAAATGGTC
1951566 GTAGCCTAAT
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
141 112 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (141 bp):
TTGGCTATGTTCTGGACCATGCCATTGGGCATAAATACAATGGTACTATATGCTAGCATGTACGT
ATCCTTTCTGAGGTTACATTATGAATATAAACCTTGCCACTAGGGTGAAAATGGTCATAGTTTAG
TGTTATTTGAC
Found at i:1960572 original size:22 final size:22
Alignment explanation
Indices: 1960545--1960601 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
1960535 TATGTAATTT
1960545 AAAATATTTAATTT-ATATATTA
1 AAAATATTTAATTTAATATA-TA
*
1960567 AAAATATAATTATTTTAATATATA
1 AAAATAT--TTAATTTAATATATA
*
1960591 AATATATTTAA
1 AAAATATTTAA
1960602 AAATATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 10 0.34
24 14 0.48
25 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAATATTTAATTTAATATATA
Found at i:1960600 original size:17 final size:17
Alignment explanation
Indices: 1960559--1960603 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
1960549 TATTTAATTT
*
1960559 ATATATTAAAAATATAA
1 ATATATTTAAAATATAA
* *
1960576 TTAT-TTTAATATATAA
1 ATATATTTAAAATATAA
1960592 ATATATTTAAAA
1 ATATATTTAAAA
1960604 ATATTTAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATATTTAAAATATAA
Found at i:1963152 original size:13 final size:12
Alignment explanation
Indices: 1963132--1963165 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1963122 TATATATTTT
1963132 ATTTATTTTTAA
1 ATTTATTTTTAA
1963144 ATTTAATTTTTAA
1 ATTT-ATTTTTAA
*
1963157 ATATATTTT
1 ATTTATTTT
1963166 AAAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTATTTTTAA
Found at i:1965347 original size:23 final size:23
Alignment explanation
Indices: 1965321--1965364 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1965311 TTTGGAAGGC
* *
1965321 AAAAAAGATTAAAAATAAAAATT
1 AAAAAAAATAAAAAATAAAAATT
1965344 AAAAAAAATAAAAAATAAAAA
1 AAAAAAAATAAAAAATAAAAA
1965365 AAATCACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAAAAAATAAAAAATAAAAATT
Found at i:1965351 original size:17 final size:16
Alignment explanation
Indices: 1965331--1965368 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1965321 AAAAAAGATT
*
1965331 AAAAATAAAAATTAAA
1 AAAAATAAAAAATAAA
1965347 AAAAATAAAAAATAAA
1 AAAAATAAAAAATAAA
1965363 AAAAAT
1 AAAAAT
1965369 CACATTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATAAAAAATAAA
Found at i:1965483 original size:21 final size:20
Alignment explanation
Indices: 1965457--1965506 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1965447 CAATAATTTA
1965457 TATCGATACAAACAGTAAATG
1 TATCGATACAAACAGT-AATG
**
1965478 TATCGATAC-ATTAGTAATG
1 TATCGATACAAACAGTAATG
1965497 TATCGATACA
1 TATCGATACA
1965507 GTATATCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 13 0.50
20 4 0.15
21 9 0.35
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
TATCGATACAAACAGTAATG
Found at i:1967996 original size:51 final size:51
Alignment explanation
Indices: 1967941--1968084 Score: 175
Period size: 51 Copynumber: 2.8 Consensus size: 51
1967931 CCCAGGTTCC
* * * *
1967941 ATTTCCAAAACATCAATTTTTCTTCATCGAGGATACTCCAACTCCGATTTT
1 ATTTCCAAAACACCAATTTTCCATAATCGAGGATACTCCAACTCCGATTTT
* * *
1967992 ATTTCTAAAACACCCATTTTCCATAATCGGGGATACTCCAACTCCGATTTT
1 ATTTCCAAAACACCAATTTTCCATAATCGAGGATACTCCAACTCCGATTTT
* *
1968043 ATTTCCAAAACACCGACTTTT-CACAATCG-GAGATACTCCAAC
1 ATTTCCAAAACACC-AATTTTCCATAATCGAG-GATACTCCAAC
1968085 CCCGTTATTT
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
50 1 0.01
51 75 0.94
52 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (51 bp):
ATTTCCAAAACACCAATTTTCCATAATCGAGGATACTCCAACTCCGATTTT
Found at i:1968111 original size:79 final size:79
Alignment explanation
Indices: 1968020--1968502 Score: 644
Period size: 79 Copynumber: 6.2 Consensus size: 79
1968010 TTCCATAATC
* * * * * ** *
1968020 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCGACTTTTCACAATCGGAGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCTTAATCGGGGATACTCCAAC
1968085 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
*
1968099 GGGGACACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTC---ATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCTTAATCGGGGATACTCCAAC
1968161 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
** * * * *
1968175 AAGGATACCCCACCCCCGACTTTATTTCTAAAATATCAATTTTTCTTAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCTTAATCGGGGATACTCCAAC
1968240 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
* *
1968254 GGGGACACTCCAACTCCGATTTTATTTCTAAAACATCAA-TTTT-TT-ATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCTTAATCGGGGATACTCCAAC
1968316 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
* ** *
1968330 GGGGATAC-CCCACCCCGGCTTTATTTCTAAAATATCAATTTTTCTTAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCTTAATCGGGGATACTCCAAC
*
1968394 CCCATTA-TTTCTGA
66 CCCGTTATTTTC-GA
* * * * *
1968408 AGGAATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCATAATC-GGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCTTAATCGGGGATACTCCAAC
1968472 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
1968486 -GGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1968503 TTATTATCTC
Statistics
Matches: 356, Mismatches: 39, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
75 25 0.07
76 110 0.31
77 23 0.06
78 56 0.16
79 142 0.40
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCTTAATCGGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:1968432 original size:154 final size:153
Alignment explanation
Indices: 1968067--1968502 Score: 671
Period size: 155 Copynumber: 2.8 Consensus size: 153
1968057 GACTTTTCAC
* *
1968067 AATCGGAGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGATTTTATTTCTAAAA
1 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCTCGATTTTATTTCTAAAA
* *
1968132 CATCAATTTTTCATCGGGGATACTCCAACCCCGTTATTTTCGAAAGGATACCCCACCCCCGACTT
66 CATCAATTTTTTATCGGGGATACTCCAACCCCGTTATTTTCG-AGGGATACCCCA-CCCCGACTT
1968197 TATTTCTAAAATATCAATTTTTCTT
129 TATTTCTAAAATATCAATTTTTCTT
1968222 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAA-CTCCGATTTTATTTCTAAA
1 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCT-CGATTTTATTTCTAAA
*
1968286 ACATCAATTTTTTATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACCCCACCCCGGCTT
65 ACATCAATTTTTTATCGGGGATACTCCAACCCCGTTATTTTCGA-GGGATACCCCACCCCGACTT
1968351 TATTTCTAAAATATCAATTTTTCTT
129 TATTTCTAAAATATCAATTTTTCTT
* * * * *
1968376 AATCGGGGATACTCCAACCCCATTA-TTTCTGAAGGAATACTCCAACCTCGGTTTTATTTCTAAA
1 AATCGGGGATACTCCAACCCCGTTATTTTC-GAGGGGACACTCCAACCTCGATTTTATTTCTAAA
*
1968440 ACATCAATTTTTCATAATC-GGGATACTCCAACCCCGTTATTTTCGAGGGATACTCCAACCCCG
65 ACATCAATTTTT--T-ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGATAC-CCCACCCCG
1968503 TTATTATCTC
Statistics
Matches: 262, Mismatches: 11, Indels: 15
0.91 0.04 0.05
Matches are distributed among these distances:
153 4 0.02
154 98 0.37
155 121 0.46
156 36 0.14
157 3 0.01
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (153 bp):
AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCTCGATTTTATTTCTAAAA
CATCAATTTTTTATCGGGGATACTCCAACCCCGTTATTTTCGAGGGATACCCCACCCCGACTTTA
TTTCTAAAATATCAATTTTTCTT
Found at i:1970179 original size:2 final size:2
Alignment explanation
Indices: 1970172--1970204 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1970162 AAAAGATGAC
*
1970172 TA TA TA TA TA TA TA TA TA TA TA CA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1970205 AAAGAAGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1970251 original size:2 final size:2
Alignment explanation
Indices: 1970244--1970276 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1970234 CCAACATGTG
*
1970244 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1970277 GTGTATATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1971196 original size:20 final size:20
Alignment explanation
Indices: 1971150--1971196 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
1971140 CACATCATTT
*
1971150 AATAGATTTATTTTTAAAATA
1 AATA-ATTTATTTTTAAAAAA
*
1971171 ATTAATTTA-TTTTAAATAAA
1 AATAATTTATTTTTAAA-AAA
1971191 AATAAT
1 AATAAT
1971197 ATAATATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 7 0.32
20 12 0.55
21 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAATTTATTTTTAAAAAA
Found at i:1971954 original size:14 final size:14
Alignment explanation
Indices: 1971935--1971967 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1971925 AAAAAAAAAC
1971935 ATTTAATACATTAT
1 ATTTAATACATTAT
1971949 ATTTAATACATTAT
1 ATTTAATACATTAT
*
1971963 TTTTA
1 ATTTA
1971968 TAATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTAATACATTAT
Found at i:1974559 original size:13 final size:12
Alignment explanation
Indices: 1974539--1974568 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1974529 TTCCTTTTCC
1974539 TTTTTTTTTTGT
1 TTTTTTTTTTGT
1974551 TTTTGTTTTTTGT
1 TTTT-TTTTTTGT
1974564 TTTTT
1 TTTTT
1974569 CTTTCCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (12 bp):
TTTTTTTTTTGT
Found at i:1978845 original size:26 final size:26
Alignment explanation
Indices: 1978771--1978849 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 26
1978761 TATTAAAAAT
* *
1978771 ATTAAAAATTAATTTTTATATTAATATAT
1 ATTAAAAA-T-ATTTTTAT-TAAATATAA
* *
1978800 A-TATATATATTTTATAATTAAATATAA
1 ATTAAAAATATTTT-T-ATTAAATATAA
1978827 ATTAAAAATATTTTTATTAAATA
1 ATTAAAAATATTTTTATTAAATA
1978850 AGTAATGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
26 13 0.32
27 11 0.27
28 16 0.39
29 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTAAAAATATTTTTATTAAATATAA
Found at i:1980048 original size:2 final size:2
Alignment explanation
Indices: 1980041--1980081 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1980031 AAAAGATGAC
*
1980041 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA T- 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
1980082 AAAGAGGACT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1981850 original size:38 final size:39
Alignment explanation
Indices: 1981807--1981891 Score: 113
Period size: 38 Copynumber: 2.2 Consensus size: 39
1981797 TTTAATACAT
* *
1981807 TATATTTAA-TATATTATTTTTATGATTTTAAAAAGTAA
1 TATATTTAATTATATTATTTTTATGAATTTAAAAAATAA
*
1981845 TATA-TTAATTATATTATTTTTATTAATTTAAAAAATAA
1 TATATTTAATTATATTATTTTTATGAATTTAAAAAATAA
1981883 -ATTATTTAA
1 TA-TATTTAA
1981892 AAAATAACTG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 5 0.12
38 32 0.78
39 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (39 bp):
TATATTTAATTATATTATTTTTATGAATTTAAAAAATAA
Found at i:1981924 original size:12 final size:12
Alignment explanation
Indices: 1981907--1981933 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1981897 AACTGCTTAT
1981907 AAATATTTTCAA
1 AAATATTTTCAA
1981919 AAATATTTTCAA
1 AAATATTTTCAA
1981931 AAA
1 AAA
1981934 GACCAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATATTTTCAA
Found at i:1984404 original size:13 final size:14
Alignment explanation
Indices: 1984386--1984432 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
1984376 GTACCATCTC
1984386 TTTTTCTTT-TTTT
1 TTTTTCTTTGTTTT
1984399 TTTTTCTTTGTTTT
1 TTTTTCTTTGTTTT
* *
1984413 TTGTT-TTTGCTTT
1 TTTTTCTTTGTTTT
*
1984426 TCTTTCT
1 TTTTTCT
1984433 ATTTGTTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 19 0.68
14 9 0.32
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (14 bp):
TTTTTCTTTGTTTT
Found at i:1984412 original size:12 final size:13
Alignment explanation
Indices: 1984386--1984440 Score: 51
Period size: 13 Copynumber: 4.1 Consensus size: 13
1984376 GTACCATCTC
*
1984386 TTTTTCTTTTTTT
1 TTTTTCTTTTGTT
1984399 TTTTTC-TTTGTT
1 TTTTTCTTTTGTT
1984411 TTTTGT-TTTTGCTT
1 TTTT-TCTTTTG-TT
1984425 TTCTTTCTATTTGTT
1 TT-TTTCT-TTTGTT
1984440 T
1 T
1984441 GAATGTGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 9 0.26
13 11 0.31
14 5 0.14
15 6 0.17
16 4 0.11
ACGTcount: A:0.02, C:0.09, G:0.07, T:0.82
Consensus pattern (13 bp):
TTTTTCTTTTGTT
Found at i:1984419 original size:18 final size:17
Alignment explanation
Indices: 1984392--1984425 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1984382 TCTCTTTTTC
*
1984392 TTTTTTTTTTTTCTTTG
1 TTTTTTTTTTTGCTTTG
1984409 TTTTTTGTTTTTGCTTT
1 TTTTTT-TTTTTGCTTT
1984426 TCTTTCTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (17 bp):
TTTTTTTTTTTGCTTTG
Found at i:1989689 original size:2 final size:2
Alignment explanation
Indices: 1989665--1989713 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
1989655 CCTAAAATTT
* *
1989665 TA TA TA -A TA TA CA TGA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
1989707 TA TA TA T
1 TA TA TA T
1989714 TCCAGTATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1991526 original size:2 final size:2
Alignment explanation
Indices: 1991519--1991563 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1991509 ATTCTGGCTT
1991519 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1991561 TA T
1 TA T
1991564 CAAACTCTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1992687 original size:13 final size:12
Alignment explanation
Indices: 1992669--1992706 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1992659 TATTTTATTT
1992669 ATTTTTAAATTAA
1 ATTTTTAAA-TAA
*
1992682 ATTTTTAAATAT
1 ATTTTTAAATAA
1992694 ATTTTTAAA-AA
1 ATTTTTAAATAA
1992705 AT
1 AT
1992707 ATATGTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 3 0.13
12 11 0.48
13 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTTTTAAATAA
Found at i:1992697 original size:12 final size:13
Alignment explanation
Indices: 1992668--1992702 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1992658 ATATTTTATT
1992668 TATTTTTAAATTA
1 TATTTTTAAATTA
*
1992681 AATTTTTAAA-TA
1 TATTTTTAAATTA
1992693 TATTTTTAAA
1 TATTTTTAAA
1992703 AAATATATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTTTTAAATTA
Found at i:1993834 original size:38 final size:35
Alignment explanation
Indices: 1993791--1993860 Score: 88
Period size: 34 Copynumber: 1.9 Consensus size: 35
1993781 AATAGATAAT
1993791 TTAAATGTTAAAAATATAATTTTAATAATAA-ATAAGTA
1 TTAAATG-TAAAAA-AT-A-TTTAATAATAATATAAGTA
*
1993829 TTAAATGTAATAAATATTTAATAATAATATAA
1 TTAAATGTAAAAAATATTTAATAATAATATAA
1993861 ATTTGATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 11 0.37
35 5 0.17
36 2 0.07
37 5 0.17
38 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (35 bp):
TTAAATGTAAAAAATATTTAATAATAATATAAGTA
Found at i:1993856 original size:17 final size:17
Alignment explanation
Indices: 1993811--1993857 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1993801 AAAATATAAT
*
1993811 TTTAATAATAAATAAGTA
1 TTTAATAAT-AATAAATA
* *
1993829 TTAAAT-GTAATAAATA
1 TTTAATAATAATAAATA
1993845 TTTAATAATAATA
1 TTTAATAATAATA
1993858 TAAATTTGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
16 12 0.52
17 6 0.26
18 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (17 bp):
TTTAATAATAATAAATA
Found at i:1994513 original size:21 final size:21
Alignment explanation
Indices: 1994479--1994540 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
1994469 TTTATTAGAA
*
1994479 TAAAATGAGAATTTAATTAGTTT
1 TAAAATTA-AATTTAATTA-TTT
*
1994502 T-AAATTATATTTAATTATTT
1 TAAAATTAAATTTAATTATTT
1994522 TAAAATTAAATTTTAATTA
1 TAAAATTAAA-TTTAATTA
1994541 AAGTAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 4 0.12
21 16 0.47
22 13 0.38
23 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TAAAATTAAATTTAATTATTT
Found at i:1995669 original size:13 final size:13
Alignment explanation
Indices: 1995651--1995681 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1995641 TTTTTCTTAA
1995651 AATATTTATATTC
1 AATATTTATATTC
*
1995664 AATATTTATATTT
1 AATATTTATATTC
1995677 AATAT
1 AATAT
1995682 ATATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (13 bp):
AATATTTATATTC
Found at i:1995708 original size:14 final size:13
Alignment explanation
Indices: 1995674--1995708 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
1995664 AATATTTATA
1995674 TTTAATAT-ATAT
1 TTTAATATAATAT
1995686 TTTAATATAATAT
1 TTTAATATAATAT
1995699 TTTAAATATA
1 TTT-AATATA
1995709 TAAAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.38
13 7 0.33
14 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAATATAATAT
Found at i:1998221 original size:8 final size:8
Alignment explanation
Indices: 1998208--1998262 Score: 92
Period size: 8 Copynumber: 6.9 Consensus size: 8
1998198 AACATGTGTT
*
1998208 TATATATA
1 TATATATG
1998216 TATATATG
1 TATATATG
1998224 TATATATG
1 TATATATG
*
1998232 TATATATA
1 TATATATG
1998240 TATATATG
1 TATATATG
1998248 TATATATG
1 TATATATG
1998256 TATATAT
1 TATATAT
1998263 CTATTTGTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 44 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (8 bp):
TATATATG
Found at i:1998240 original size:24 final size:24
Alignment explanation
Indices: 1998208--1998262 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
1998198 AACATGTGTT
1998208 TATATATATATATATGTATATATG
1 TATATATATATATATGTATATATG
1998232 TATATATATATATATGTATATATG
1 TATATATATATATATGTATATATG
1998256 TATATAT
1 TATATAT
1998263 CTATTTGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (24 bp):
TATATATATATATATGTATATATG
Found at i:2003055 original size:22 final size:22
Alignment explanation
Indices: 2003027--2003070 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2003017 CTAATTCTAT
2003027 CACATATACAATTGGATCTTTG
1 CACATATACAATTGGATCTTTG
*
2003049 CACATATACAATTGGATTTTTG
1 CACATATACAATTGGATCTTTG
2003071 TTATGGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (22 bp):
CACATATACAATTGGATCTTTG
Found at i:2003297 original size:74 final size:74
Alignment explanation
Indices: 2003196--2003345 Score: 264
Period size: 74 Copynumber: 2.0 Consensus size: 74
2003186 AGCCAATGAG
* *
2003196 ATTTTAGATTGACATTTCAAAGCATGGGCCATGTTTATTTTGTCTCAGATACATGTGCCATTTTC
1 ATTTAAGATTGACATTTCAAAGCATGGGCCATGTTTATTTTGTCTCAGATACATGTGACATTTTC
2003261 TTACCCAAC
66 TTACCCAAC
* *
2003270 ATTTAAGATTGACATTTCAAAGTATGGGCCATGTTTATTTTGTCTTAGATACATGTGACATTTTC
1 ATTTAAGATTGACATTTCAAAGCATGGGCCATGTTTATTTTGTCTCAGATACATGTGACATTTTC
2003335 TTACCCAAC
66 TTACCCAAC
2003344 AT
1 AT
2003346 AAAAGAGTAA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (74 bp):
ATTTAAGATTGACATTTCAAAGCATGGGCCATGTTTATTTTGTCTCAGATACATGTGACATTTTC
TTACCCAAC
Found at i:2004142 original size:20 final size:20
Alignment explanation
Indices: 2004092--2004141 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
2004082 ATCTAAACTA
*
2004092 TAATGTAAAATAATTTAATAG
1 TAAT-TAAAATAATTTAAAAG
*
2004113 TAATTAAAATAATTTTAAAAT
1 TAATTAAAATAA-TTTAAAAG
2004134 TAATTAAA
1 TAATTAAA
2004142 TTTTCATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (20 bp):
TAATTAAAATAATTTAAAAG
Found at i:2005042 original size:22 final size:21
Alignment explanation
Indices: 2004985--2005049 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 21
2004975 AAAGTGATAT
2004985 TAAAAA-AATATTT-AATTAA
1 TAAAAATAATATTTAAATTAA
* *
2005004 T-AAATTATTTATTTTAAATTAA
1 TAAAAATA-ATA-TTTAAATTAA
2005026 TAAAAATAATATATTAAATATAA
1 TAAAAATAATAT-TTAAAT-TAA
2005049 T
1 T
2005050 TTTTTAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 2 0.06
21 4 0.11
22 15 0.43
23 9 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAAAATAATATTTAAATTAA
Found at i:2010276 original size:22 final size:24
Alignment explanation
Indices: 2010229--2010281 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
2010219 ATGAAATTTG
*
2010229 ATCT-AATATATATGTACATTTCTA
1 ATCTAAAT-TATAAGTACATTTCTA
*
2010253 AT-TAAATTATAAGTA-ATTTTTA
1 ATCTAAATTATAAGTACATTTCTA
2010275 ATCTAAA
1 ATCTAAA
2010282 ATGATGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 8 0.32
23 12 0.48
24 5 0.20
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (24 bp):
ATCTAAATTATAAGTACATTTCTA
Found at i:2026263 original size:2 final size:2
Alignment explanation
Indices: 2026256--2026288 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2026246 ATTCTGGCTT
2026256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2026289 CAAACTCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2027980 original size:3 final size:3
Alignment explanation
Indices: 2027972--2027997 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2027962 TTTGAGGAAT
2027972 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2027998 TTTAGTAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2028554 original size:40 final size:41
Alignment explanation
Indices: 2028501--2028577 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 41
2028491 TTAATTAATT
2028501 ATATTAAAATAAATAATTTAAA-A-AATAAATATGTAATTTTA
1 ATATTAAAATAAAT-A-TTAAATATAATAAATATGTAATTTTA
*
2028542 ATATT-AAATAAATATTAAATATAATAAATATTTAAT
1 ATATTAAAATAAATATTAAATATAATAAATATGTAAT
2028578 AATAATATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
38 5 0.15
39 2 0.06
40 21 0.64
41 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (41 bp):
ATATTAAAATAAATATTAAATATAATAAATATGTAATTTTA
Found at i:2028559 original size:17 final size:16
Alignment explanation
Indices: 2028539--2028594 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 16
2028529 ATATGTAATT
2028539 TTAATATTAAATAAATA
1 TTAATA-TAAATAAATA
2028556 TTAA-ATATAATAAATA
1 TTAATATA-AATAAATA
2028572 TTTAATAATAATATAAAT-
1 -TTAAT-ATAA-ATAAATA
2028590 TTAAT
1 TTAAT
2028595 TAAGTAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
15 2 0.06
16 9 0.26
17 13 0.38
18 1 0.03
19 9 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAATATAAATAAATA
Found at i:2028569 original size:16 final size:17
Alignment explanation
Indices: 2028548--2028584 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
2028538 TTTAATATTA
2028548 AATAAATATTAAAT-AT
1 AATAAATATTAAATAAT
*
2028564 AATAAATATTTAATAAT
1 AATAAATATTAAATAAT
2028581 AATA
1 AATA
2028585 TAAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAATATTAAATAAT
Found at i:2028584 original size:40 final size:40
Alignment explanation
Indices: 2028491--2028589 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 40
2028481 ATTGATTAAA
*
2028491 TTAATTAATTATATTAAAATAAATAATTTAAAAAATAAATAT
1 TTAA-TAATAATATT-AAATAAATAATTTAAAAAATAAATAT
* **
2028533 GTAATTTTAATATTAAATAAAT-A-TTAAATATAATAAATAT
1 TTAATAATAATATTAAATAAATAATTTAAA-A-AATAAATAT
2028573 TTAATAATAATA-TAAAT
1 TTAATAATAATATTAAAT
2028590 TTAATTAAGT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
38 5 0.10
39 7 0.15
40 26 0.54
41 7 0.15
42 3 0.06
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (40 bp):
TTAATAATAATATTAAATAAATAATTTAAAAAATAAATAT
Found at i:2029130 original size:13 final size:13
Alignment explanation
Indices: 2029107--2029157 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
2029097 TTTTTTATTT
*
2029107 AAATAAATTAAAA
1 AAATTAATTAAAA
*
2029120 AAATT-ATTTAAA
1 AAATTAATTAAAA
* * *
2029132 AAAGTAGTGAAAA
1 AAATTAATTAAAA
2029145 AAATTAATTAAAA
1 AAATTAATTAAAA
2029158 TTAATTTTAA
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (13 bp):
AAATTAATTAAAA
Found at i:2030614 original size:16 final size:16
Alignment explanation
Indices: 2030593--2030634 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2030583 TCTATTTAGA
*
2030593 TATATTTAAATTATTT
1 TATATTTAAATTACTT
2030609 TATATTTAAATTACTT
1 TATATTTAAATTACTT
*
2030625 TAAATTTAAA
1 TATATTTAAA
2030635 AATGTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATTTAAATTACTT
Found at i:2031120 original size:2 final size:2
Alignment explanation
Indices: 2031113--2031153 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2031103 TTTGCATTGC
*
2031113 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2031154 AAGAGAGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2031752 original size:2 final size:2
Alignment explanation
Indices: 2031745--2031828 Score: 93
Period size: 2 Copynumber: 43.0 Consensus size: 2
2031735 CTATTGAAGT
* * * *
2031745 TA TA TA TA TT TA TA TA TA TA TA TA GA -A AA GA -A GT- 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
*
2031785 TA TA TA TA TA TA TA TA TA TA TA TA TT 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
2031827 TA
1 TA
2031829 CACACACACC
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
1 3 0.04
2 69 0.96
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2032196 original size:139 final size:136
Alignment explanation
Indices: 2032031--2032285 Score: 474
Period size: 139 Copynumber: 1.9 Consensus size: 136
2032021 TGAAGTTCAG
2032031 AAAAAAAAAAAAAAAAAAAGAAAAGGTTTTAGTAGCTAAAGTCATAATCAAATGACGAATAATTT
1 AAAAAAAAAAAAAAAAAAAGAAAAGGTTTTAGTAGCTAAAGTCATAATCAAATGACGAATAATTT
2032096 TTTCAATCTTCTCATTGAATAAAGTAAAAAAGAATAAAAAAAATAAAGAAAAGGTTTTAGTACCT
66 TTTCAATCTTCTCATTGAATAAAGTAAAAAAGAATAAAAAAAATAAAGAAAAGGTTTTAGTACCT
2032161 ACAGTA
131 ACAGTA
*
2032167 AAAAATAAAAAGAAAAAGAAAAGAAAAGGTTTTAGTAGCTAAAGTCATAATCAAATGACGTATAA
1 AAAAA-AAAAA-AAAAA-AAAAGAAAAGGTTTTAGTAGCTAAAGTCATAATCAAATGACGAATAA
2032232 TTTTTTCAATCTTCTCATTGAATAAAGTAAAAAAGAATAAAAAAAATAAAGAAA
63 TTTTTTCAATCTTCTCATTGAATAAAGTAAAAAAGAATAAAAAAAATAAAGAAA
2032286 GAACTAAGCT
Statistics
Matches: 115, Mismatches: 1, Indels: 3
0.97 0.01 0.03
Matches are distributed among these distances:
136 5 0.04
137 5 0.04
138 5 0.04
139 100 0.87
ACGTcount: A:0.56, C:0.07, G:0.12, T:0.25
Consensus pattern (136 bp):
AAAAAAAAAAAAAAAAAAAGAAAAGGTTTTAGTAGCTAAAGTCATAATCAAATGACGAATAATTT
TTTCAATCTTCTCATTGAATAAAGTAAAAAAGAATAAAAAAAATAAAGAAAAGGTTTTAGTACCT
ACAGTA
Found at i:2032615 original size:15 final size:16
Alignment explanation
Indices: 2032584--2032616 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2032574 AATATTAATG
*
2032584 TTAATATTAAAATATT
1 TTAATATTAAAAAATT
2032600 TTAATA-TAAAAAATT
1 TTAATATTAAAAAATT
2032615 TT
1 TT
2032617 TAGATTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAATATTAAAAAATT
Found at i:2035857 original size:25 final size:25
Alignment explanation
Indices: 2035795--2035864 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
2035785 AATAAAAATT
*
2035795 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
2035819 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
2035844 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
2035865 CAAAGGAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:2035910 original size:27 final size:27
Alignment explanation
Indices: 2035849--2035919 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
2035839 AAACAAGCCT
* *
2035849 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
2035877 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
2035904 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
2035920 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:2035922 original size:24 final size:24
Alignment explanation
Indices: 2035797--2035922 Score: 92
Period size: 24 Copynumber: 4.9 Consensus size: 24
2035787 TAAAAATTAG
* *
2035797 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAACAA-ATAA
* * *
2035821 CCACCAATTTTGACAAATAAACAA
1 CCACCATTTTTGACAAACAAATAA
* * *
2035845 GCCTCCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGAC-AA-ACAAA--TAA
2035874 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
2035901 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
2035923 GGGTGGCTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.01
24 24 0.29
25 13 0.15
26 4 0.05
27 20 0.24
28 17 0.20
29 5 0.06
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:2040451 original size:25 final size:25
Alignment explanation
Indices: 2040389--2040458 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
2040379 AATAAAAATT
*
2040389 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
2040413 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
2040438 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
2040459 CAAAGGAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:2040504 original size:27 final size:27
Alignment explanation
Indices: 2040443--2040513 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
2040433 AAACAAGCCT
* *
2040443 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
2040471 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
2040498 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
2040514 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:2040516 original size:24 final size:24
Alignment explanation
Indices: 2040391--2040516 Score: 92
Period size: 24 Copynumber: 4.9 Consensus size: 24
2040381 TAAAAATTAG
* *
2040391 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAACAA-ATAA
* * *
2040415 CCACCAATTTTGACAAATAAACAA
1 CCACCATTTTTGACAAACAAATAA
* * *
2040439 GCCTCCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGAC-AA-ACAAA--TAA
2040468 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
2040495 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
2040517 GGGTGGCTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.01
24 24 0.29
25 13 0.15
26 4 0.05
27 20 0.24
28 17 0.20
29 5 0.06
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:2044973 original size:10 final size:10
Alignment explanation
Indices: 2044954--2045005 Score: 56
Period size: 9 Copynumber: 5.4 Consensus size: 10
2044944 TGAAAAAAAT
2044954 AAAAAT-AAA
1 AAAAATGAAA
*
2044963 AAAAAGGAAA
1 AAAAATGAAA
*
2044973 AAGAATTG-AA
1 AA-AAATGAAA
2044983 AAAAATGAAA
1 AAAAATGAAA
2044993 AAAAA-GAAA
1 AAAAATGAAA
2045002 AAAA
1 AAAA
2045006 TTATTTAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 17 0.47
10 16 0.44
11 3 0.08
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.08
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:2046661 original size:11 final size:11
Alignment explanation
Indices: 2046647--2046692 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
2046637 TTCATCAGTA
*
2046647 ATTTTTATTTT
1 ATTTTTAGTTT
2046658 ATTTTTAGTTT
1 ATTTTTAGTTT
*
2046669 A--TTTATTTT
1 ATTTTTAGTTT
2046678 ATTTTTAGTTT
1 ATTTTTAGTTT
2046689 ATTT
1 ATTT
2046693 GAATTGATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 8 0.27
11 22 0.73
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (11 bp):
ATTTTTAGTTT
Found at i:2046675 original size:20 final size:20
Alignment explanation
Indices: 2046650--2046692 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2046640 ATCAGTAATT
2046650 TTTATTTTATTTTTAGTTTA
1 TTTATTTTATTTTTAGTTTA
2046670 TTTATTTTATTTTTAGTTTA
1 TTTATTTTATTTTTAGTTTA
2046690 TTT
1 TTT
2046693 GAATTGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTATTTTATTTTTAGTTTA
Found at i:2049664 original size:32 final size:32
Alignment explanation
Indices: 2049618--2049687 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
2049608 AGCTACAATT
* * *
2049618 CAAATTTGAGTTAGACTTAATCATTGTTGAAC
1 CAAATTCGAATTAGACTTAATCATTGTTAAAC
* *
2049650 CAAATTCGAATTAGATTTGATCATTGTTAAAC
1 CAAATTCGAATTAGACTTAATCATTGTTAAAC
2049682 CAAATT
1 CAAATT
2049688 TAAATATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (32 bp):
CAAATTCGAATTAGACTTAATCATTGTTAAAC
Found at i:2050969 original size:3 final size:3
Alignment explanation
Indices: 2050961--2050987 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2050951 AAACATTAAA
2050961 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2050988 CTAGAAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2052724 original size:9 final size:9
Alignment explanation
Indices: 2052710--2052749 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
2052700 AGTTAATTGA
2052710 TTTTTGAAT
1 TTTTTGAAT
2052719 TTTTTGAAT
1 TTTTTGAAT
*
2052728 TTTTTTAAT
1 TTTTTGAAT
2052737 TTAATTTGAAT
1 TT--TTTGAAT
2052748 TT
1 TT
2052750 CATGCTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (9 bp):
TTTTTGAAT
Found at i:2053307 original size:43 final size:43
Alignment explanation
Indices: 2053249--2053334 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
2053239 TGATTTTATG
2053249 AATTAATAAAATTATTAT-TTTATTAAAATTTTAAATAAAATAA
1 AATTAATAAAATTATTATATTT-TTAAAATTTTAAATAAAATAA
* *
2053292 AATTAA-AAATATTATTATATTTTTATAATTTTTAATAAAATAA
1 AATTAATAAA-ATTATTATATTTTTAAAATTTTAAATAAAATAA
2053335 TTTTAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
42 3 0.08
43 33 0.85
44 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (43 bp):
AATTAATAAAATTATTATATTTTTAAAATTTTAAATAAAATAA
Found at i:2053341 original size:43 final size:42
Alignment explanation
Indices: 2053249--2053348 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 42
2053239 TGATTTTATG
2053249 AATTAATAAAATTATTATTTTATTAAAATTTTAAATAAAATAA
1 AATTAA-AAAATTATTATTTTATTAAAATTTTAAATAAAATAA
* *
2053292 AATTAAAAATATTATTATATTT-TTATAATTTTTAATAAAATAA
1 AATTAAAAA-ATTATTAT-TTTATTAAAATTTTAAATAAAATAA
**
2053335 TTTTAAAATAATTA
1 AATTAAAA-AATTA
2053349 AAATTAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
42 3 0.06
43 43 0.86
44 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (42 bp):
AATTAAAAAATTATTATTTTATTAAAATTTTAAATAAAATAA
Found at i:2053450 original size:19 final size:19
Alignment explanation
Indices: 2053404--2053454 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
2053394 CACCTACTTT
2053404 TTTTAAAAAAATTTTATAA
1 TTTTAAAAAAATTTTATAA
**
2053423 ACTTAAAAAAATTTTAT-A
1 TTTTAAAAAAATTTTATAA
2053441 TTTTATAAAAAATT
1 TTTTA-AAAAAATT
2053455 ATTTTTTTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTTAAAAAAATTTTATAA
Found at i:2054029 original size:13 final size:13
Alignment explanation
Indices: 2054011--2054035 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2054001 TTCTTCTTTT
2054011 AAATATTTATATA
1 AAATATTTATATA
2054024 AAATATTTATAT
1 AAATATTTATAT
2054036 TTAACATGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATATTTATATA
Found at i:2054244 original size:22 final size:25
Alignment explanation
Indices: 2054210--2054255 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
2054200 AATTTTAAAA
2054210 ATAAATATAAATAATA-TTAATTTT
1 ATAAATATAAATAATATTTAATTTT
2054234 ATAAA-AT-AATAATATTTAATTT
1 ATAAATATAAATAATATTTAATTT
2054256 ATCGATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 9 0.43
24 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATAAATATAAATAATATTTAATTTT
Found at i:2055161 original size:17 final size:17
Alignment explanation
Indices: 2055149--2055182 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
2055139 TAATTATATA
2055149 AATTTTAATATTAAAAT
1 AATTTTAATATTAAAAT
2055166 AATTTTAATATTTAAAA
1 AATTTTAATA-TTAAAA
2055183 ATATATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTTAATATTAAAAT
Found at i:2055428 original size:40 final size:40
Alignment explanation
Indices: 2055373--2055448 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
2055363 ATAGTTGATT
2055373 TGGCATGGAATACACGTAATTGAACACATGTGGTACGATA
1 TGGCATGGAATACACGTAATTGAACACATGTGGTACGATA
*
2055413 TGGCATGGAATACACGTACTTGAACACATGTGGTAC
1 TGGCATGGAATACACGTAATTGAACACATGTGGTAC
2055449 ATAAATTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (40 bp):
TGGCATGGAATACACGTAATTGAACACATGTGGTACGATA
Found at i:2055922 original size:18 final size:18
Alignment explanation
Indices: 2055895--2055942 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
2055885 CATCCACTCA
*
2055895 TTTA-AATTATGTTTATG
1 TTTATAATTATATTTATG
2055912 TTTATAATTATATTTATG
1 TTTATAATTATATTTATG
2055930 TTT-TAATTATATT
1 TTTATAATTATATT
2055943 ATATTTATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (18 bp):
TTTATAATTATATTTATG
Found at i:2055958 original size:20 final size:22
Alignment explanation
Indices: 2055913--2055959 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2055903 ATGTTTATGT
*
2055913 TTATAATTATATTTATGTTTTAA
1 TTATAATTATATTTA-GTTGTAA
2055936 TTAT-ATTATATTTA-TTGTAA
1 TTATAATTATATTTAGTTGTAA
2055956 TTAT
1 TTAT
2055960 TAATATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
22 10 0.43
23 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
TTATAATTATATTTAGTTGTAA
Found at i:2055988 original size:27 final size:26
Alignment explanation
Indices: 2055958--2056040 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 26
2055948 TATTGTAATT
*
2055958 ATTAATATAAAAATATTAATATAGATA
1 ATTAA-ATAAAAATATAAATATAGATA
*
2055985 ATTAAAATATAAAATATAAATATTGATA
1 ATT-AAATA-AAAATATAAATATAGATA
* *
2056013 ATTAAATAAAATTA-AAAT-TAGAAA
1 ATTAAATAAAAATATAAATATAGATA
2056037 ATTA
1 ATTA
2056041 TGAATATAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
24 8 0.16
25 4 0.08
26 5 0.10
27 11 0.22
28 21 0.43
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (26 bp):
ATTAAATAAAAATATAAATATAGATA
Found at i:2056006 original size:28 final size:29
Alignment explanation
Indices: 2055961--2056018 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
2055951 TGTAATTATT
*
2055961 AATATAAAAATATTAATATAGATAATTAA
1 AATATAAAAATATAAATATAGATAATTAA
*
2055990 AATAT-AAAATATAAATATTGATAATTAA
1 AATATAAAAATATAAATATAGATAATTAA
2056018 A
1 A
2056019 TAAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
AATATAAAAATATAAATATAGATAATTAA
Found at i:2056039 original size:24 final size:25
Alignment explanation
Indices: 2055993--2056040 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
2055983 TAATTAAAAT
*
2055993 ATAAAATATAAATATTGATAATTAA
1 ATAAAATATAAATATTGAAAATTAA
2056018 ATAAAAT-TAAA-ATTAGAAAATTA
1 ATAAAATATAAATATT-GAAAATTA
2056041 TGAATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 11 0.52
25 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (25 bp):
ATAAAATATAAATATTGAAAATTAA
Found at i:2056055 original size:38 final size:39
Alignment explanation
Indices: 2055969--2056057 Score: 94
Period size: 38 Copynumber: 2.3 Consensus size: 39
2055959 TTAATATAAA
*
2055969 AATATTAATATAGATAATTAAAATATAAAATATAAATATT
1 AATATTAA-ATAGATAATTAAAATAGAAAATATAAATATT
* *
2056009 GATAATTAAATA-A-AATTAAAATTAGAAAATTATGAATA-T
1 AAT-ATTAAATAGATAATTAAAA-TAGAAAA-TATAAATATT
2056048 AATATTAAAT
1 AATATTAAAT
2056058 TATTATCACT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
38 15 0.36
39 10 0.24
40 12 0.29
41 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (39 bp):
AATATTAAATAGATAATTAAAATAGAAAATATAAATATT
Found at i:2058228 original size:10 final size:11
Alignment explanation
Indices: 2058203--2058231 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2058193 CGTTGAATCA
2058203 ATAAAAATTAG
1 ATAAAAATTAG
2058214 ATAAAAATTAG
1 ATAAAAATTAG
2058225 -TAAAAAT
1 ATAAAAAT
2058232 CAATTTGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (11 bp):
ATAAAAATTAG
Found at i:2059258 original size:24 final size:25
Alignment explanation
Indices: 2059225--2059273 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2059215 AATTTGATTT
2059225 AAATTATTA-TTTAATAATAAAATA
1 AAATTATTATTTTAATAATAAAATA
* *
2059249 AAATTTTTATTTTAATTATAAAATA
1 AAATTATTATTTTAATAATAAAATA
2059274 TATAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATTATTATTTTAATAATAAAATA
Found at i:2059703 original size:50 final size:50
Alignment explanation
Indices: 2059644--2059742 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
2059634 ATCGTTGCCC
2059644 ACAATTTCAATTGATATTAACACTTAATTAAAAATTCAAAATAATTCCCA
1 ACAATTTCAATTGATATTAACACTTAATTAAAAATTCAAAATAATTCCCA
2059694 ACAATTTCAATTGATATTAACACTTAATTAAAAATTCAAAATAATTCCC
1 ACAATTTCAATTGATATTAACACTTAATTAAAAATTCAAAATAATTCCC
2059743 TGAAAGAGAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.34
Consensus pattern (50 bp):
ACAATTTCAATTGATATTAACACTTAATTAAAAATTCAAAATAATTCCCA
Found at i:2059857 original size:35 final size:34
Alignment explanation
Indices: 2059772--2059876 Score: 97
Period size: 35 Copynumber: 3.0 Consensus size: 34
2059762 GATTTATCTA
* * **
2059772 TTTTATTTATATATAATTTTTTTAATATAAAT-T
1 TTTTATTTAAATTTAATTTTAATAATATAAATAT
*
2059805 GATTTAATTTAAA-TTAATATTTAATAATATAAATAT
1 --TTTTATTTAAATTTAAT-TTTAATAATATAAATAT
* *
2059841 TTTTATTTAAATTTAATTATAAAATATATAAATAT
1 TTTTATTTAAATTTAATTTTAATA-ATATAAATAT
2059876 T
1 T
2059877 AATATAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
34 19 0.33
35 38 0.66
36 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (34 bp):
TTTTATTTAAATTTAATTTTAATAATATAAATAT
Found at i:2059882 original size:21 final size:21
Alignment explanation
Indices: 2059848--2059887 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2059838 TATTTTTATT
2059848 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
2059869 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
2059888 AATTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:2062174 original size:15 final size:14
Alignment explanation
Indices: 2062154--2062183 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2062144 TTTTTTTTTT
2062154 AAATTTTATAAAAAA
1 AAATTTTA-AAAAAA
2062169 AAATTTTAAAAAAA
1 AAATTTTAAAAAAA
2062183 A
1 A
2062184 TCATGAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATTTTAAAAAAA
Done.