Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 8 of 126
Found at i:1907258 original size:11 final size:10
Alignment explanation
Indices: 1907217--1907258 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
1907207 TAATTATAAT
*
1907217 TTAAAATTTT
1 TTAAAATTTA
1907227 TTAAAATTTA
1 TTAAAATTTA
1907237 TTAAAATTTTA
1 TTAAAA-TTTA
1907248 TATAAAATTTA
1 T-TAAAATTTA
1907259 CACTTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 15 0.52
11 9 0.31
12 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTAAAATTTA
Found at i:1907874 original size:23 final size:23
Alignment explanation
Indices: 1907820--1907876 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1907810 TTTAAAATTA
*
1907820 AATTTAACAATATAAATATAATAT
1 AATTTAA-AATATAAAGATAATAT
** * *
1907844 AAAATAAAATATGAAGATGATAT
1 AATTTAAAATATAAAGATAATAT
1907867 AATTTAAAAT
1 AATTTAAAAT
1907877 TTTAATAATA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (23 bp):
AATTTAAAATATAAAGATAATAT
Found at i:1908005 original size:20 final size:19
Alignment explanation
Indices: 1907959--1908006 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1907949 ATAATATATA
1907959 ATTTTTATA-AAATATTAT
1 ATTTTTATATAAATATTAT
** *
1907977 ATTAATATATAAATTTTAAT
1 ATTTTTATATAAATATT-AT
1907997 ATTTTTATAT
1 ATTTTTATAT
1908007 TATATAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 7 0.30
19 6 0.26
20 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTTATATAAATATTAT
Found at i:1908024 original size:33 final size:33
Alignment explanation
Indices: 1907970--1908033 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1907960 TTTTTATAAA
* * *
1907970 ATATTATATTAATATATAAATT-TTAATATTTTT
1 ATATTATATAAATACACAAATTATT-ATATTTTT
1908003 ATATTATATAAATACACAAATTATTATATTT
1 ATATTATATAAATACACAAATTATTATATTT
1908034 AAAAAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (33 bp):
ATATTATATAAATACACAAATTATTATATTTTT
Found at i:1914780 original size:28 final size:29
Alignment explanation
Indices: 1914726--1914785 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
1914716 ATAATCAAGC
* *
1914726 ATTTAATTAAGTGAAAATAGATTTTAAGA
1 ATTTAATTAAGTGAAAATAAATTTTAAAA
*
1914755 ATTTAATTAGGT-AAAA-AAATATTTAAAA
1 ATTTAATTAAGTGAAAATAAAT-TTTAAAA
1914783 ATT
1 ATT
1914786 CAACTGATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.11
28 13 0.48
29 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (29 bp):
ATTTAATTAAGTGAAAATAAATTTTAAAA
Found at i:1915113 original size:12 final size:12
Alignment explanation
Indices: 1915096--1915121 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1915086 TTCAAATGTA
1915096 AAATTAAAAAAT
1 AAATTAAAAAAT
1915108 AAATTAAAAAAT
1 AAATTAAAAAAT
1915120 AA
1 AA
1915122 GATAATAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATTAAAAAAT
Found at i:1916367 original size:22 final size:22
Alignment explanation
Indices: 1916342--1916384 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1916332 AACTCGCATA
1916342 TATAGAAATTAAAAA-TAAAAAT
1 TATAGAAA-TAAAAATTAAAAAT
* *
1916364 TATATATATAAAAATTAAAAA
1 TATAGAAATAAAAATTAAAAA
1916385 ATAAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
TATAGAAATAAAAATTAAAAAT
Found at i:1916376 original size:15 final size:14
Alignment explanation
Indices: 1916339--1916394 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 14
1916329 TTTAACTCGC
*
1916339 ATATATAGAAATTA
1 ATATATAAAAATTA
*
1916353 A-AAATAAAAATTA
1 ATATATAAAAATTA
1916366 TATATATAAAAATTA
1 -ATATATAAAAATTA
* *
1916381 AAAAAT-AAAATTA
1 ATATATAAAAATTA
1916394 A
1 A
1916395 GTTTAATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
13 18 0.51
14 6 0.17
15 11 0.31
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
ATATATAAAAATTA
Found at i:1917389 original size:15 final size:17
Alignment explanation
Indices: 1917359--1917396 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
1917349 CCAAATTTGA
1917359 TATATGTAGTTTATATT
1 TATATGTAGTTTATATT
1917376 TATATG-AG-TTATATT
1 TATATGTAGTTTATATT
*
1917391 TTTATG
1 TATATG
1917397 GTATTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (17 bp):
TATATGTAGTTTATATT
Found at i:1919257 original size:16 final size:16
Alignment explanation
Indices: 1919236--1919266 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1919226 CCGGGAAGCC
*
1919236 TCTTTTTCTTTTTCTA
1 TCTTTTGCTTTTTCTA
1919252 TCTTTTGCTTTTTCT
1 TCTTTTGCTTTTTCT
1919267 TTTTCTTACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.74
Consensus pattern (16 bp):
TCTTTTGCTTTTTCTA
Found at i:1919265 original size:22 final size:23
Alignment explanation
Indices: 1919237--1919286 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
1919227 CGGGAAGCCT
* *
1919237 CTTTTTCTTTTTC-TATCTTTTG
1 CTTTTTCTTTTTCTTACCTTTTC
1919259 CTTTTTCTTTTTCTTACCTTTTC
1 CTTTTTCTTTTTCTTACCTTTTC
1919282 CTTTT
1 CTTTT
1919287 AGAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.72
Consensus pattern (23 bp):
CTTTTTCTTTTTCTTACCTTTTC
Found at i:1919733 original size:21 final size:21
Alignment explanation
Indices: 1919709--1919762 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1919699 TGATAAAATA
* *
1919709 TTAATTTTTAATTTTAATAAT
1 TTAAATTTAAATTTTAATAAT
*
1919730 TTAAATTTAAATTTTTATAATT
1 TTAAATTTAAATTTTAATAA-T
*
1919752 TTAAATATAAA
1 TTAAATTTAAA
1919763 AAAAATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAATTTAAATTTTAATAAT
Found at i:1919762 original size:22 final size:21
Alignment explanation
Indices: 1919718--1919762 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1919708 ATTAATTTTT
*
1919718 AATTTTAATAATTTAAATTTA
1 AATTTTAATAATTTAAATATA
*
1919739 AATTTTTATAATTTTAAATATA
1 AATTTTAATAA-TTTAAATATA
1919761 AA
1 AA
1919763 AAAAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTTAATAATTTAAATATA
Found at i:1925207 original size:11 final size:10
Alignment explanation
Indices: 1925166--1925207 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
1925156 TAATTATAAT
*
1925166 TTAAAATTTT
1 TTAAAATTTA
1925176 TTAAAATTTA
1 TTAAAATTTA
1925186 TTAAAATTTTA
1 TTAAAA-TTTA
1925197 TATAAAATTTA
1 T-TAAAATTTA
1925208 CACTTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 15 0.52
11 9 0.31
12 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTAAAATTTA
Found at i:1926460 original size:23 final size:22
Alignment explanation
Indices: 1926434--1926487 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 22
1926424 ATTATTTATT
1926434 TAATTTTATATTTATAATAAA-AA
1 TAATTTTATATTTA-AA-AAATAA
1926457 TAATTTTTATATTTAAAAAATAA
1 TAA-TTTTATATTTAAAAAATAA
1926480 T-ATTTTAT
1 TAATTTTAT
1926488 TAATTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.21
22 4 0.14
23 8 0.28
24 11 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATTTTATATTTAAAAAATAA
Found at i:1927345 original size:11 final size:10
Alignment explanation
Indices: 1927304--1927345 Score: 66
Period size: 10 Copynumber: 4.0 Consensus size: 10
1927294 TAATTATAAT
1927304 TTAAAATTTA
1 TTAAAATTTA
1927314 TTAAAATTTA
1 TTAAAATTTA
1927324 TTAAAATTTTA
1 TTAAAA-TTTA
1927335 TATAAAATTTA
1 T-TAAAATTTA
1927346 CACTTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 16 0.53
11 9 0.30
12 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTAAAATTTA
Found at i:1928099 original size:20 final size:19
Alignment explanation
Indices: 1928053--1928100 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1928043 ATAATATATA
1928053 ATTTTTATA-AAATATTAT
1 ATTTTTATATAAATATTAT
** *
1928071 ATTAATATATAAATTTTAAT
1 ATTTTTATATAAATATT-AT
1928091 ATTTTTATAT
1 ATTTTTATAT
1928101 TATATAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 7 0.30
19 6 0.26
20 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTTATATAAATATTAT
Found at i:1928118 original size:33 final size:33
Alignment explanation
Indices: 1928064--1928127 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1928054 TTTTTATAAA
* * *
1928064 ATATTATATTAATATATAAATT-TTAATATTTTT
1 ATATTATATAAATACACAAATTATT-ATATTTTT
1928097 ATATTATATAAATACACAAATTATTATATTT
1 ATATTATATAAATACACAAATTATTATATTT
1928128 AAAAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (33 bp):
ATATTATATAAATACACAAATTATTATATTTTT
Found at i:1929792 original size:8 final size:8
Alignment explanation
Indices: 1929779--1929810 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1929769 CTTTTTTTTT
1929779 TAATTTAA
1 TAATTTAA
1929787 TAATTTAA
1 TAATTTAA
1929795 TAATTT-A
1 TAATTTAA
1929802 T-ATTTAA
1 TAATTTAA
1929809 TA
1 TA
1929811 TATATAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 4 0.18
7 4 0.18
8 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TAATTTAA
Found at i:1934881 original size:28 final size:29
Alignment explanation
Indices: 1934827--1934886 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
1934817 ATAATCAAGC
* *
1934827 ATTTAATTAAGGGAAAATAGATTTTAAGA
1 ATTTAATTAAGGGAAAATAAATTTTAAAA
*
1934856 ATTTAATT-AGGTAAAA-AAATATTTAAAA
1 ATTTAATTAAGGGAAAATAAAT-TTTAAAA
1934884 ATT
1 ATT
1934887 CAACTGATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.11
28 16 0.59
29 8 0.30
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.37
Consensus pattern (29 bp):
ATTTAATTAAGGGAAAATAAATTTTAAAA
Found at i:1936471 original size:22 final size:22
Alignment explanation
Indices: 1936446--1936488 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1936436 AACTCGCATA
1936446 TATAGAAATTAAAAA-TAAAAAT
1 TATAGAAA-TAAAAATTAAAAAT
* *
1936468 TATATATATAAAAATTAAAAA
1 TATAGAAATAAAAATTAAAAA
1936489 ATAAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
TATAGAAATAAAAATTAAAAAT
Found at i:1936480 original size:15 final size:14
Alignment explanation
Indices: 1936443--1936498 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 14
1936433 TTTAACTCGC
*
1936443 ATATATAGAAATTA
1 ATATATAAAAATTA
*
1936457 A-AAATAAAAATTA
1 ATATATAAAAATTA
1936470 TATATATAAAAATTA
1 -ATATATAAAAATTA
* *
1936485 AAAAAT-AAAATTA
1 ATATATAAAAATTA
1936498 A
1 A
1936499 GTTTAATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
13 18 0.51
14 6 0.17
15 11 0.31
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
ATATATAAAAATTA
Found at i:1938588 original size:17 final size:18
Alignment explanation
Indices: 1938554--1938588 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1938544 CATATCGTGT
*
1938554 TTATATTTTATCACTATA
1 TTATATTTTATAACTATA
1938572 TTATATTTTA-AACTATA
1 TTATATTTTATAACTATA
1938589 AAATCTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATATTTTATAACTATA
Found at i:1939379 original size:22 final size:23
Alignment explanation
Indices: 1939349--1939400 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
1939339 GCCGGGAGCC
*
1939349 TCCTTTTTCTTTTTC-TATCTTT
1 TCCTTTTTCTTTTTCTTACCTTT
*
1939371 TGCTTTTTCTTTTTCTTACCTTT
1 TCCTTTTTCTTTTTCTTACCTTT
1939394 TCCTTTT
1 TCCTTTT
1939401 AGAAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.04, C:0.23, G:0.02, T:0.71
Consensus pattern (23 bp):
TCCTTTTTCTTTTTCTTACCTTT
Found at i:1945799 original size:21 final size:22
Alignment explanation
Indices: 1945774--1945820 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
1945764 GAAGCCTACT
* *
1945774 TTTTCTTTTTC-TATCTTTTGC
1 TTTTCTTTTTCTTACCTTTTCC
1945795 TTTTCTTTTTCTTACCTTTTCC
1 TTTTCTTTTTCTTACCTTTTCC
1945817 TTTT
1 TTTT
1945821 AGAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTCTTTTTCTTACCTTTTCC
Found at i:1946270 original size:21 final size:21
Alignment explanation
Indices: 1946246--1946299 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1946236 TGATAAAATA
* *
1946246 TTAATTTTTAATTTTAATAAT
1 TTAAATTTAAATTTTAATAAT
*
1946267 TTAAATTTAAATTTTTATAAT
1 TTAAATTTAAATTTTAATAAT
*
1946288 TTCAAATATAAA
1 TT-AAATTTAAA
1946300 AGGAACTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAAATTTAAATTTTAATAAT
Found at i:1953602 original size:33 final size:34
Alignment explanation
Indices: 1953565--1953630 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
1953555 TATAATATTT
1953565 TTATA-TATATTTAAT-TTTTGATAAAATT-TTAAA
1 TTATATTAT-TTTAATATTTT-ATAAAATTATTAAA
1953598 TTATATTATTTTAATATTTTATAAAATTATTAA
1 TTATATTATTTTAATATTTTATAAAATTATTAA
1953631 TATCGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 19 0.63
34 11 0.37
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (34 bp):
TTATATTATTTTAATATTTTATAAAATTATTAAA
Found at i:1958047 original size:16 final size:17
Alignment explanation
Indices: 1958028--1958065 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1958018 TTTATTAAAA
1958028 TTTTAAATTATTT-TAT
1 TTTTAAATTATTTGTAT
*
1958044 TTTTAAATTTTTTGTAT
1 TTTTAAATTATTTGTAT
1958061 TTTTA
1 TTTTA
1958066 TTTTTTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTAAATTATTTGTAT
Found at i:1958450 original size:17 final size:18
Alignment explanation
Indices: 1958430--1958465 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1958420 TTTAATTTTT
*
1958430 TAATT-TTTTATTATAAA
1 TAATTATTTAATTATAAA
1958447 TAATTATTTAATTATAAA
1 TAATTATTTAATTATAAA
1958465 T
1 T
1958466 TTAATTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTATTTAATTATAAA
Found at i:1958994 original size:35 final size:38
Alignment explanation
Indices: 1958923--1958994 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
1958913 ACTATTATAC
*
1958923 TTAAAAAATTATATTCATTATATTGTTTTTATAATATT
1 TTAAAAAATTATATTCATTATATTGTTTTTAAAATATT
1958961 TTAAAAAATTA-ATGT-ATTAT-TT-TTTTTAAAATAT
1 TTAAAAAATTATAT-TCATTATATTGTTTTTAAAATAT
1958995 CACTTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 11 0.34
36 2 0.06
37 7 0.22
38 12 0.38
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (38 bp):
TTAAAAAATTATATTCATTATATTGTTTTTAAAATATT
Found at i:1960066 original size:19 final size:20
Alignment explanation
Indices: 1960042--1960087 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1960032 TTCGAAAACG
* *
1960042 AATTTTT-AAAAAGTTATAA
1 AATTTTTCAAAAAATCATAA
*
1960061 AATTTTTCAAAAAATCATAC
1 AATTTTTCAAAAAATCATAA
1960081 AATTTTT
1 AATTTTT
1960088 TGAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (20 bp):
AATTTTTCAAAAAATCATAA
Found at i:1963251 original size:15 final size:16
Alignment explanation
Indices: 1963229--1963279 Score: 86
Period size: 15 Copynumber: 3.2 Consensus size: 16
1963219 ACAGCCACCT
1963229 ATATAATTAGGCTTTC
1 ATATAATTAGGCTTTC
1963245 A-ATAATTAGGCTTTC
1 ATATAATTAGGCTTTC
1963260 AATATAATTAGGCTTTC
1 -ATATAATTAGGCTTTC
1963277 ATA
1 ATA
1963280 GTTTTGGCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.42
16 5 0.15
17 14 0.42
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (16 bp):
ATATAATTAGGCTTTC
Found at i:1963268 original size:17 final size:17
Alignment explanation
Indices: 1963229--1963277 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
1963219 ACAGCCACCT
1963229 ATATAATTAGGCTTTC-
1 ATATAATTAGGCTTTCA
1963245 A-ATAATTAGGCTTTCA
1 ATATAATTAGGCTTTCA
1963261 ATATAATTAGGCTTTCA
1 ATATAATTAGGCTTTCA
1963278 TAGTTTTGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 14 0.45
16 2 0.06
17 15 0.48
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
ATATAATTAGGCTTTCA
Found at i:1971918 original size:28 final size:27
Alignment explanation
Indices: 1971859--1971924 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
1971849 AATTAAAATT
1971859 TTTTAATTTTTTAAAAAAATTTTACAC
1 TTTTAATTTTTTAAAAAAATTTTACAC
*
1971886 ATTTAATTTATTTAATAAAATATTTTA-A-
1 TTTTAATTT-TTTAA-AAAA-ATTTTACAC
1971914 TTTTAATTTTT
1 TTTTAATTTTT
1971925 AATTTTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 10 0.29
28 13 0.38
29 5 0.15
30 6 0.18
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTTAATTTTTTAAAAAAATTTTACAC
Found at i:1971970 original size:22 final size:22
Alignment explanation
Indices: 1971945--1971990 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1971935 CATTTTAATA
1971945 AAAAATTTT-ACAAACTTCACTT
1 AAAAATTTTGA-AAACTTCACTT
* *
1971967 AAAAGTTTTGAAAACTTCATTT
1 AAAAATTTTGAAAACTTCACTT
1971989 AA
1 AA
1971991 GTTTTCTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (22 bp):
AAAAATTTTGAAAACTTCACTT
Found at i:1973275 original size:12 final size:12
Alignment explanation
Indices: 1973260--1973285 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1973250 TATTAATTAT
1973260 ATAAAATTTTTA
1 ATAAAATTTTTA
1973272 ATAAAATTTTTA
1 ATAAAATTTTTA
1973284 AT
1 AT
1973286 TATATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATAAAATTTTTA
Found at i:1973305 original size:16 final size:15
Alignment explanation
Indices: 1973280--1973309 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1973270 TAATAAAATT
1973280 TTTAATTATATTATA
1 TTTAATTATATTATA
1973295 TTTATATTATATTAT
1 TTTA-ATTATATTAT
1973310 CGTATCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAATTATATTATA
Found at i:1975220 original size:10 final size:10
Alignment explanation
Indices: 1975207--1975247 Score: 73
Period size: 10 Copynumber: 4.1 Consensus size: 10
1975197 TTTTATATTA
1975207 ATTTAAATAT
1 ATTTAAATAT
1975217 ATTTAAATAT
1 ATTTAAATAT
1975227 ATTTAAATAT
1 ATTTAAATAT
*
1975237 ATCTAAATAT
1 ATTTAAATAT
1975247 A
1 A
1975248 AAATAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (10 bp):
ATTTAAATAT
Found at i:1976694 original size:53 final size:53
Alignment explanation
Indices: 1976632--1976744 Score: 203
Period size: 51 Copynumber: 2.2 Consensus size: 53
1976622 ATCCCAACTA
1976632 CTTAAACATATATATATATATATATGTAAAGTTTATTAAGCTTAACAAAATAT
1 CTTAAACATATATATATATATATATGTAAAGTTTATTAAGCTTAACAAAATAT
*
1976685 CTTAAAC--ATATATATATATATATGTAACGTTTATTAAGCTTAACAAAATAT
1 CTTAAACATATATATATATATATATGTAAAGTTTATTAAGCTTAACAAAATAT
1976736 CTTAAACAT
1 CTTAAACAT
1976745 TATTTGTGCA
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
51 50 0.88
53 7 0.12
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (53 bp):
CTTAAACATATATATATATATATATGTAAAGTTTATTAAGCTTAACAAAATAT
Found at i:1977627 original size:2 final size:2
Alignment explanation
Indices: 1977622--1977659 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1977612 AAAAAAAATG
* *
1977622 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1977660 AAAAGAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1978911 original size:16 final size:17
Alignment explanation
Indices: 1978882--1978913 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1978872 AAATATTCAT
1978882 TAAATATGAATATAAAA
1 TAAATATGAATATAAAA
1978899 TAAATAT-AATATAAA
1 TAAATATGAATATAAA
1978914 CATCTAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
TAAATATGAATATAAAA
Found at i:1979412 original size:21 final size:21
Alignment explanation
Indices: 1979388--1979430 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1979378 ATAATAAAAG
*
1979388 TAAAATTTATTATTATAATAA
1 TAAAATTAATTATTATAATAA
1979409 TAAAATTAATTATTATAATAA
1 TAAAATTAATTATTATAATAA
1979430 T
1 T
1979431 GAGATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAATTAATTATTATAATAA
Found at i:1979443 original size:24 final size:22
Alignment explanation
Indices: 1979375--1979444 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 22
1979365 GATATTAAAA
1979375 ATAATAATAA-AAGTAAAATTTATT
1 ATAATAATAATAA--AAAA-TTATT
*
1979399 ATTATAATAATAAAATTAATTATT
1 ATAATAATAATAAAA--AATTATT
1979423 ATAATAATGAGATAAAAAATTA
1 ATAATAAT-A-ATAAAAAATTA
1979445 ACAATAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
23 2 0.05
24 26 0.67
25 5 0.13
26 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
ATAATAATAATAAAAAATTATT
Found at i:1979688 original size:50 final size:50
Alignment explanation
Indices: 1979594--1979696 Score: 127
Period size: 50 Copynumber: 2.1 Consensus size: 50
1979584 ATTAATAAAT
* * * ** *
1979594 AATTAAAAATTATTAAAATTATTTTATGTCAAGTAATATTTTTATTAATA
1 AATTAAAAAATACTAAAATTATTTTATATCAAACAATATCTTTATTAATA
*
1979644 AATTAAAAAATACTAAAATTATTTTTATATCAAACAATA-CTTTATTATTA
1 AATTAAAAAATACTAAAATTA-TTTTATATCAAACAATATCTTTATTAATA
1979694 AAT
1 AAT
1979697 ATTTAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 31 0.69
51 14 0.31
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.45
Consensus pattern (50 bp):
AATTAAAAAATACTAAAATTATTTTATATCAAACAATATCTTTATTAATA
Found at i:1980722 original size:33 final size:33
Alignment explanation
Indices: 1980685--1980757 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
1980675 TTAGTATTTT
1980685 TATTAGTATACTATA-ATATTATTATATATATTA
1 TATTA-TATACTATAGATATTATTATATATATTA
*
1980718 TATTATATACTATAGTTATTATTATATATATTA
1 TATTATATACTATAGATATTATTATATATATTA
1980751 TATTATA
1 TATTATA
1980758 CATTACATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 9 0.24
33 29 0.76
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (33 bp):
TATTATATACTATAGATATTATTATATATATTA
Found at i:1980749 original size:45 final size:45
Alignment explanation
Indices: 1980696--1980791 Score: 76
Period size: 45 Copynumber: 2.1 Consensus size: 45
1980686 ATTAGTATAC
* * *
1980696 TATA-ATATTAT-TATATATATTATATTATATACTATAGTTATTAT-T
1 TATATATATTATAT-TATACATTACATTATATACTATAGCTA-T-TAT
*
1980741 ATAT--ATATTATATTATACATTACATTATATATTATAGCTATTAT
1 -TATATATATTATATTATACATTACATTATATACTATAGCTATTAT
1980785 TACTATA
1 TA-TATA
1980792 ATTTTACGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
43 3 0.07
44 3 0.07
45 30 0.73
46 5 0.12
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (45 bp):
TATATATATTATATTATACATTACATTATATACTATAGCTATTAT
Found at i:1980757 original size:12 final size:12
Alignment explanation
Indices: 1980700--1980776 Score: 74
Period size: 12 Copynumber: 6.7 Consensus size: 12
1980690 GTATACTATA
1980700 ATATTAT-TATAT
1 ATATTATAT-TAT
1980712 ATATTATATTAT
1 ATATTATATTAT
*
1980724 ATACTATAGTTAT
1 ATATTATA-TTAT
1980737 -TA-T-TA-TAT
1 ATATTATATTAT
1980745 ATATTATATTAT
1 ATATTATATTAT
* *
1980757 ACATTACATTAT
1 ATATTATATTAT
1980769 ATATTATA
1 ATATTATA
1980777 GCTATTATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
8 3 0.06
9 2 0.04
10 3 0.06
11 3 0.06
12 38 0.70
13 5 0.09
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (12 bp):
ATATTATATTAT
Found at i:1980776 original size:5 final size:5
Alignment explanation
Indices: 1980704--1980757 Score: 58
Period size: 5 Copynumber: 10.4 Consensus size: 5
1980694 ACTATAATAT
1980704 TATTA TA-TA TATTA TATTA TATACTA TAGTTA TTATTA TA-TA TATTA
1 TATTA TATTA TATTA TATTA TAT--TA TA-TTA -TATTA TATTA TATTA
1980751 TATTA TA
1 TATTA TA
1980758 CATTACATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
4 8 0.19
5 23 0.53
6 5 0.12
7 6 0.14
8 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (5 bp):
TATTA
Found at i:1980784 original size:33 final size:33
Alignment explanation
Indices: 1980701--1980776 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
1980691 TATACTATAA
* *
1980701 TATTATTATATATATTATATTATATACTATAGT
1 TATTATTATATATATTATATTATACACTACAGT
*
1980734 TATTATTATATATATTATATTATACATTACA-T
1 TATTATTATATATATTATATTATACACTACAGT
1980766 TATATATTATA
1 TAT-TATTATA
1980777 GCTATTATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
32 4 0.10
33 35 0.90
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (33 bp):
TATTATTATATATATTATATTATACACTACAGT
Found at i:1980786 original size:24 final size:24
Alignment explanation
Indices: 1980713--1980787 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
1980703 TTATTATATA
* *
1980713 TATTATATTATATACTATAGTTAT
1 TATTACATTATATATTATAGTTAT
1980737 TATT--A-TATATATTATA-TTAT
1 TATTACATTATATATTATAGTTAT
* *
1980757 ACATTACATTATATATTATAGCTAT
1 -TATTACATTATATATTATAGTTAT
1980782 TATTAC
1 TATTAC
1980788 TATAATTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 4 0.10
21 13 0.31
22 1 0.02
23 1 0.02
24 20 0.48
25 3 0.07
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.52
Consensus pattern (24 bp):
TATTACATTATATATTATAGTTAT
Found at i:1981194 original size:22 final size:21
Alignment explanation
Indices: 1981156--1981197 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1981146 AACAAAAAGA
* *
1981156 AACAAAAAAATTTCTTTTTTT
1 AACAAAAAAAATCCTTTTTTT
1981177 AACAAAAAGAAATCCTTTTTT
1 AACAAAAA-AAATCCTTTTTT
1981198 GTAAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (21 bp):
AACAAAAAAAATCCTTTTTTT
Found at i:1984494 original size:40 final size:40
Alignment explanation
Indices: 1984450--1984529 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
1984440 TGTTTCCCCC
1984450 ATTGTTGTTTACTCTTTAACTACCTGTATATATGAACATG
1 ATTGTTGTTTACTCTTTAACTACCTGTATATATGAACATG
*
1984490 ATTGTTGTTTCCTCTTTAACTACCTGTATATATGAACATG
1 ATTGTTGTTTACTCTTTAACTACCTGTATATATGAACATG
1984530 CTTCAAGGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.45
Consensus pattern (40 bp):
ATTGTTGTTTACTCTTTAACTACCTGTATATATGAACATG
Found at i:1984775 original size:39 final size:39
Alignment explanation
Indices: 1984732--1984806 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
1984722 CTTCAGGACT
1984732 CTAAATTCTAAAACCTTATGTTTAGATCCCAAATGACGC
1 CTAAATTCTAAAACCTTATGTTTAGATCCCAAATGACGC
*
1984771 CTAAATTCTAAAACCTTATGTTTAGATCCCACATGA
1 CTAAATTCTAAAACCTTATGTTTAGATCCCAAATGA
1984807 TGCCACTAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (39 bp):
CTAAATTCTAAAACCTTATGTTTAGATCCCAAATGACGC
Found at i:1991034 original size:2 final size:2
Alignment explanation
Indices: 1991029--1991060 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1991019 TTTGGTAATC
1991029 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
1991061 TGAGGGTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1996278 original size:2 final size:2
Alignment explanation
Indices: 1996271--1996306 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1996261 CATGACTGAC
*
1996271 AT AT AT AT AT AT AT AT AT AT AC 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
1996307 TTCAAGTTAT
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:2000157 original size:22 final size:21
Alignment explanation
Indices: 2000119--2000160 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2000109 AACAAAAAGA
* *
2000119 AACAAAAAAATTTCTTTTTTT
1 AACAAAAAAAATCCTTTTTTT
2000140 AACAAAAAGAAATCCTTTTTT
1 AACAAAAA-AAATCCTTTTTT
2000161 ATAAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (21 bp):
AACAAAAAAAATCCTTTTTTT
Found at i:2002275 original size:65 final size:65
Alignment explanation
Indices: 2002171--2002303 Score: 248
Period size: 65 Copynumber: 2.0 Consensus size: 65
2002161 GCAACACACC
* *
2002171 ATTGCACCGTAATTGCTCGGAAAAGCTGCTTAGTTGCAATGGAAGGTGTTAAAATCCTCGTGGTA
1 ATTGCACCATAACTGCTCGGAAAAGCTGCTTAGTTGCAATGGAAGGTGTTAAAATCCTCGTGGTA
2002236 ATTGCACCATAACTGCTCGGAAAAGCTGCTTAGTTGCAATGGAAGGTGTTAAAATCCTCGTGGTA
1 ATTGCACCATAACTGCTCGGAAAAGCTGCTTAGTTGCAATGGAAGGTGTTAAAATCCTCGTGGTA
2002301 ATT
1 ATT
2002304 TCCCTGTTGG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (65 bp):
ATTGCACCATAACTGCTCGGAAAAGCTGCTTAGTTGCAATGGAAGGTGTTAAAATCCTCGTGGTA
Found at i:2003503 original size:40 final size:40
Alignment explanation
Indices: 2003459--2003578 Score: 222
Period size: 40 Copynumber: 3.0 Consensus size: 40
2003449 TGTTTCCGCC
*
2003459 ATTGTTGTTTCCTCTTTAACTACTTGTATATATGAACATG
1 ATTGTTGTTTCCTCTTTAACTACCTGTATATATGAACATG
*
2003499 ATTGTTGTTTCCTCTTTAATTACCTGTATATATGAACATG
1 ATTGTTGTTTCCTCTTTAACTACCTGTATATATGAACATG
2003539 ATTGTTGTTTCCTCTTTAACTACCTGTATATATGAACATG
1 ATTGTTGTTTCCTCTTTAACTACCTGTATATATGAACATG
2003579 CTTCAAGGAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (40 bp):
ATTGTTGTTTCCTCTTTAACTACCTGTATATATGAACATG
Found at i:2028213 original size:10 final size:10
Alignment explanation
Indices: 2028198--2028239 Score: 57
Period size: 10 Copynumber: 3.9 Consensus size: 10
2028188 AATCTCTGGC
2028198 GAGAGAGAAA
1 GAGAGAGAAA
2028208 GAGAGAGGAAA
1 GAGAGA-GAAA
2028219 GAGAGAGAAA
1 GAGAGAGAAA
2028229 CTGAGAGAGAA
1 --GAGAGAGAA
2028240 TATATAGCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.34
11 10 0.34
12 9 0.31
ACGTcount: A:0.55, C:0.02, G:0.40, T:0.02
Consensus pattern (10 bp):
GAGAGAGAAA
Found at i:2028671 original size:27 final size:27
Alignment explanation
Indices: 2028641--2028716 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
2028631 ATATTTAAAA
*
2028641 TATTATTATATTAATTAAT-ATAATATT
1 TATTATTATATTAATTAATAAAAAT-TT
*
2028668 TATT-TTAAATATAATTAACTAAAAATTT
1 TATTATTATAT-TAATTAA-TAAAAATTT
* *
2028696 TAATATCATATTAATTAATAA
1 TATTATTATATTAATTAATAA
2028717 TTAATAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
26 5 0.12
27 14 0.35
28 13 0.32
29 8 0.20
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (27 bp):
TATTATTATATTAATTAATAAAAATTT
Found at i:2028719 original size:7 final size:7
Alignment explanation
Indices: 2028707--2028736 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
2028697 AATATCATAT
2028707 TAATTAA
1 TAATTAA
2028714 TAATTAA
1 TAATTAA
2028721 TAATTAA
1 TAATTAA
2028728 TAACTTAA
1 TAA-TTAA
2028736 T
1 T
2028737 TATCATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (7 bp):
TAATTAA
Found at i:2030247 original size:24 final size:26
Alignment explanation
Indices: 2030218--2030281 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 26
2030208 TATATGTAAA
2030218 TATAAATAAAAAGATAAAACTTTATT
1 TATAAATAAAAAGATAAAACTTTATT
* *
2030244 TAAATACAATAAAAATATAAAATTTTA-T
1 T--ATA-AATAAAAAGATAAAACTTTATT
2030272 T-TAAATAAAA
1 TATAAATAAAA
2030282 TTAAATCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
24 7 0.21
25 2 0.06
26 1 0.03
28 5 0.15
29 18 0.55
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (26 bp):
TATAAATAAAAAGATAAAACTTTATT
Found at i:2030257 original size:29 final size:29
Alignment explanation
Indices: 2030222--2030278 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
2030212 TGTAAATATA
2030222 AATAAAAAGATAAAACTTTATTTAAATAC
1 AATAAAAAGATAAAACTTTATTTAAATAC
* *
2030251 AATAAAAATATAAAATTTTATTTAAATA
1 AATAAAAAGATAAAACTTTATTTAAATA
2030279 AAATTAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (29 bp):
AATAAAAAGATAAAACTTTATTTAAATAC
Found at i:2031086 original size:19 final size:19
Alignment explanation
Indices: 2031062--2031101 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2031052 TAGATTGTTC
*
2031062 AGTTTCTTAGATCAAAATA
1 AGTTTCTCAGATCAAAATA
2031081 AGTTTCTCAGATCAAAATA
1 AGTTTCTCAGATCAAAATA
2031100 AG
1 AG
2031102 ATGTATCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (19 bp):
AGTTTCTCAGATCAAAATA
Found at i:2034048 original size:18 final size:21
Alignment explanation
Indices: 2034016--2034057 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 21
2034006 TTTTAAATTT
2034016 TTTTTTTTGAGAATATATA-A
1 TTTTTTTTGAGAATATATATA
2034036 TTTTTTTT-A-AATATATATA
1 TTTTTTTTGAGAATATATATA
2034055 TTT
1 TTT
2034058 AATTATAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTTTTTTGAGAATATATATA
Found at i:2034375 original size:24 final size:24
Alignment explanation
Indices: 2034328--2034376 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2034318 TTTTTGAAAA
*
2034328 TTTTTTTAAAAAAATTTATATAAT
1 TTTTTTTAAAAAAATATATATAAT
* * *
2034352 TTTTTTTAAATATATATATTTAAT
1 TTTTTTTAAAAAAATATATATAAT
2034376 T
1 T
2034377 ATAAATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTTTTTAAAAAAATATATATAAT
Found at i:2034442 original size:307 final size:300
Alignment explanation
Indices: 2033870--2034450 Score: 738
Period size: 307 Copynumber: 1.9 Consensus size: 300
2033860 AAATCAAACA
* * *
2033870 GATGTAAACTGATTTAGAAATTTTTAAGAATGGAGGAGCGAGGAATTTTTAAGATCAAACAGAAA
1 GATGTAAACTGATTTAGAAACTTTTAAGAATGGAGGAGCAAGGAATTTTTAAGACCAAACAGAAA
***
2033935 ATCTATATCTGAGAATTTTTTCGAATTATGCAAAATAGATTTTCAAGAATCGTTTTTTAAAATTC
66 ATCTATATCTGAGAATTTTTTCGAATTATGCAAAATAGATTTTCAAGAATCGTTTACGAAAATTC
* * *** *
2034000 GTGTATTTTTAAATTTTTTTTTTTGAGAATATATAATTTTTTTTAAATATATATATTTAATTATA
131 ATGTATTTTTAAATATTTTTTTAAAAAAATATATAATTTTTTTTAAATATATATATTTAATTATA
* * *
2034065 AACTTTTAACAATAAAAAAATTAGAATATTTAACATTTGGGTCATTAAAACATGTCATCAATAGA
196 AACTTTTAACAATAAAAAAATTAAAATATTTAACATTTGGATCATTAAAAAATG--ATC---A-A
2034130 TTAATAAATTTGATAGTTAGGATTGACGTTGAAAGGTAGGCCAAATT
255 TTAATAAA-TTGATAGTTAGGATTGACGTTGAAAGGTAGGCCAAATT
* * *
2034177 GATGTAAACTGATTTAGGAACTTTTAAGAGTGGAGGAGCAAGGAATTTTTAAGACCAAACGGAAA
1 GATGTAAACTGATTTAGAAACTTTTAAGAATGGAGGAGCAAGGAATTTTTAAGACCAAACAGAAA
* * * *
2034242 ATCTATATCTGAGAATTTTTTTGAATTATGCAAAATGGATTTTCGAGAGTCAGCACTATTCACGA
66 ATCTATATCTGAGAATTTTTTCGAATTATGCAAAATAGATTTTCAAGAATC-G---T-TT-ACGA
2034307 AAATTCATGTATTTTTGAAA-ATTTTTTTAAAAAAATTTATATAATTTTTTTTAAATATATATAT
125 AAATTCATGTATTTTT-AAATATTTTTTTAAAAAAA--TATATAATTTTTTTTAAATATATATAT
* * * * *
2034371 TTAATTATAAATTTTTTATAATAAAAAAATTAAAATCTTTAA-TTTTAGGATCATTAAAAAATG-
187 TTAATTATAAACTTTTAACAATAAAAAAATTAAAATATTTAACATTT-GGATCATTAAAAAATGA
2034434 TC-ATTAATAAATTGATA
251 TCAATTAATAAATTGATA
2034451 AATTTAATAG
Statistics
Matches: 237, Mismatches: 27, Indels: 21
0.83 0.09 0.07
Matches are distributed among these distances:
306 6 0.03
307 115 0.49
308 1 0.00
311 1 0.00
312 4 0.02
313 26 0.11
314 6 0.03
315 78 0.33
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (300 bp):
GATGTAAACTGATTTAGAAACTTTTAAGAATGGAGGAGCAAGGAATTTTTAAGACCAAACAGAAA
ATCTATATCTGAGAATTTTTTCGAATTATGCAAAATAGATTTTCAAGAATCGTTTACGAAAATTC
ATGTATTTTTAAATATTTTTTTAAAAAAATATATAATTTTTTTTAAATATATATATTTAATTATA
AACTTTTAACAATAAAAAAATTAAAATATTTAACATTTGGATCATTAAAAAATGATCAATTAATA
AATTGATAGTTAGGATTGACGTTGAAAGGTAGGCCAAATT
Found at i:2034576 original size:2 final size:2
Alignment explanation
Indices: 2034569--2034593 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2034559 AATATACATG
2034569 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 T
2034594 GAGTAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2044694 original size:2 final size:2
Alignment explanation
Indices: 2044687--2044721 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2044677 CCCTCACTCC
2044687 AT AT AT AT 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 AT AT AT AT A
2044722 ATGGTCCTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2046474 original size:40 final size:41
Alignment explanation
Indices: 2046419--2046512 Score: 149
Period size: 40 Copynumber: 2.3 Consensus size: 41
2046409 TTACAAAACA
2046419 TGCCGGCTTTGCCAATTGTCTATGATTATTGGAATCT-CAT
1 TGCCGGCTTTGCCAATTGTCTATGATTATTGGAATCTCCAT
*
2046459 TGCCGGCTTTGCCAATTTTCTATGATTATTGGAATCTCCAT
1 TGCCGGCTTTGCCAATTGTCTATGATTATTGGAATCTCCAT
2046500 T-CCGGGC-TTGCCA
1 TGCC-GGCTTTGCCA
2046513 TTTCCTTATG
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
40 44 0.86
41 7 0.14
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.38
Consensus pattern (41 bp):
TGCCGGCTTTGCCAATTGTCTATGATTATTGGAATCTCCAT
Found at i:2051447 original size:40 final size:40
Alignment explanation
Indices: 2051392--2051472 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
2051382 AGATTAGGCC
*
2051392 AGCAGGGGATGTAAGCAAGTTATCGGATGCCTTTAGTTTA
1 AGCAGGGGATGTAAGCAAGTTATCGGATGCCTGTAGTTTA
* *
2051432 AGCAGGGGATTTAAGCAAGTTATTGGATGCCTGTAGTTTA
1 AGCAGGGGATGTAAGCAAGTTATCGGATGCCTGTAGTTTA
2051472 A
1 A
2051473 TCTTACTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.31
Consensus pattern (40 bp):
AGCAGGGGATGTAAGCAAGTTATCGGATGCCTGTAGTTTA
Found at i:2054179 original size:13 final size:13
Alignment explanation
Indices: 2054161--2054188 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2054151 TCTTTCCATT
2054161 TCATGAATCTTTG
1 TCATGAATCTTTG
2054174 TCATGAATCTTTG
1 TCATGAATCTTTG
2054187 TC
1 TC
2054189 TTTCAGTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.46
Consensus pattern (13 bp):
TCATGAATCTTTG
Found at i:2056590 original size:2 final size:2
Alignment explanation
Indices: 2056583--2056630 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2056573 TGGCTCCATT
2056583 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
2056625 TA TA TA
1 TA TA TA
2056631 AATGGTCCTG
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):
TA
Found at i:2065297 original size:2 final size:2
Alignment explanation
Indices: 2065292--2065318 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2065282 ACAAAAAAAT
2065292 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 T
2065319 TCAGCATCCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2066416 original size:243 final size:237
Alignment explanation
Indices: 2065864--2066461 Score: 634
Period size: 243 Copynumber: 2.5 Consensus size: 237
2065854 AAAAAAAAGC
* * * * * **
2065864 CTTAAATAATACCATTCAATATTTTAGATTGTATTATTTAA-GACCT-TTTTTTACTAAAAATTT
1 CTTAAATAATACCCTTAAATTTTTTAGATCGTATTATTTAATG---TGTTTTTGACTAAAAATAC
* *
2065927 CTTAAATAATCAATTTCATTACTTATAAGATTTAAGAGATAAAATATAAAAAATTAGAGTAGTTC
63 CTTAAATAATCAATTTCATTACTTATAAGATTTAAGAGATAAAATATAAAAAATTAGAATAGCTC
* ** * *
2065992 AGTAGGTTAGAGTATATGGCTATTAATTATAATCATTGGTTCAACATTCCATTCTAACACTTTAA
128 AGTAGGTTAGAGTATATAGCTATTAACCATAATCATAGATTCAACATTCCATTCTAACACTTTAA
* * *
2066057 TGTTTTTTTTTTAAGGAGATTATTTATGATATTTTTTGTCAAAATAT
193 TG--TTTTTTTTAAGGAGATTATTTATAATATTTTTGGTAAAAATAT
* * *
2066104 CTTAAATAATACCCTTAAATTTTTTAGATTGTATTATTTAATGTGTTTTTTACTAAAAATACATT
1 CTTAAATAATACCCTTAAATTTTTTAGATCGTATTATTTAATGTGTTTTTGACTAAAAATACCTT
* * *
2066169 AAATAATCCATTTCATTACTTATAAGATTCAAGAGATAAAATATAAAAAATTTTTGAAATAGCTC
66 AAATAATCAATTTCATTACTTATAAGATTTAAGAGATAAAATATAAAAAA--TTAG-AATAGCTC
* * * * * * *
2066234 ATTCGGTTCA-AGTATATAGCTATTAACCATAAGGTTATAGATTCGACTCATT-C-TTTTAGCAT
128 AGTAGGTT-AGAGTATATAGCTATTAACCATAA--TCATAGATTC-A-ACATTCCATTCTAACAC
*
2066296 TTTAATG-TTTTTTTAAGGAGATTATTTA-AATTATTTTTGGTAAAAAATGT
188 TTTAATGTTTTTTTTAAGGAGATTATTTATAA-TATTTTTGGT-AAAAATAT
* ** * * * *
2066346 CTTATATAATATCTTTTAATTTTTTTGGATCGTATTATTTTATGTGTTTTTGATTAAAAATACCT
1 CTTAAATAATA-CCCTTAAATTTTTTAGATCGTATTATTTAATGTGTTTTTGACTAAAAATACCT
** *
2066411 TAAATAATTTATTTTATTACTTATAAGATTTAAGAGATAAAATATAAAAAA
65 TAAATAATCAATTTCATTACTTATAAGATTTAAGAGATAAAATATAAAAAA
2066462 ATCGAAGTAG
Statistics
Matches: 304, Mismatches: 41, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
238 1 0.00
239 65 0.21
240 39 0.13
241 34 0.11
242 47 0.15
243 92 0.30
244 20 0.07
245 2 0.01
246 4 0.01
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (237 bp):
CTTAAATAATACCCTTAAATTTTTTAGATCGTATTATTTAATGTGTTTTTGACTAAAAATACCTT
AAATAATCAATTTCATTACTTATAAGATTTAAGAGATAAAATATAAAAAATTAGAATAGCTCAGT
AGGTTAGAGTATATAGCTATTAACCATAATCATAGATTCAACATTCCATTCTAACACTTTAATGT
TTTTTTTAAGGAGATTATTTATAATATTTTTGGTAAAAATAT
Found at i:2066575 original size:23 final size:22
Alignment explanation
Indices: 2066540--2066591 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
2066530 TTAGGGTTTA
*
2066540 TTTTTGGAGATTACTTATAAGATT
1 TTTTTGGAGATTA-TT-TAAGATG
*
2066564 TTTTTTGA-ATTATTTAAGATG
1 TTTTTGGAGATTATTTAAGATG
2066585 TTTTTGG
1 TTTTTGG
2066592 TTAGAAAACG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 12 0.48
22 2 0.08
23 4 0.16
24 7 0.28
ACGTcount: A:0.25, C:0.02, G:0.17, T:0.56
Consensus pattern (22 bp):
TTTTTGGAGATTATTTAAGATG
Found at i:2067217 original size:3 final size:3
Alignment explanation
Indices: 2067193--2067231 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2067183 TTTAATTCAC
* * *
2067193 ATT ATT CTT GTT ATT TTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2067232 TTCACCAGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:2070635 original size:31 final size:30
Alignment explanation
Indices: 2070574--2070636 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
2070564 ATGGTAATAA
* *
2070574 TTATTTAAATAAAAATTTATGTCTACTCAT
1 TTATTTAAATAAAAATTTATGTATAATCAT
*
2070604 TTATTATAAAT-AAAATTTTTAGTATAATCAT
1 TTATT-TAAATAAAAATTTAT-GTATAATCAT
2070635 TT
1 TT
2070637 TTACTATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.49
Consensus pattern (30 bp):
TTATTTAAATAAAAATTTATGTATAATCAT
Found at i:2071961 original size:154 final size:154
Alignment explanation
Indices: 2071681--2071988 Score: 589
Period size: 154 Copynumber: 2.0 Consensus size: 154
2071671 AGAATATGGA
2071681 AAGCTTGAGTTTACTAAACAAAGCTGATTTTGAGGGTGTTTATATTTGACATCATATTTATTGAT
1 AAGCTTGAGTTTACTAAACAAAGCTGATTTTGAGGGTGTTTATATTTGACATCATATTTATTGAT
*
2071746 GTATACTCTCATATTGAGTTAAAATATAAAAATTTTAAAATTTTTATGAAATGTAAATATTAAAA
66 GTATACTCTCATATTGAGTTAAAATATAAAAATTTTAAAATTTTTATGAAATGGAAATATTAAAA
2071811 TATAGAATATTCATTAGTTATCTT
131 TATAGAATATTCATTAGTTATCTT
2071835 AAGCTTGAGTTTACTAAACAAAGCTGATTTTGAGGGTGTTTATATTTGACATCATATTTATTGAT
1 AAGCTTGAGTTTACTAAACAAAGCTGATTTTGAGGGTGTTTATATTTGACATCATATTTATTGAT
* *
2071900 GTATACTTTCATATTTAGTTAAAATATAAAAATTTTAAAATTTTTATGAAATGGAAATATTAAAA
66 GTATACTCTCATATTGAGTTAAAATATAAAAATTTTAAAATTTTTATGAAATGGAAATATTAAAA
2071965 TATAGAATATTCATTAGTTATCTT
131 TATAGAATATTCATTAGTTATCTT
2071989 TTACTAATGA
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
154 151 1.00
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (154 bp):
AAGCTTGAGTTTACTAAACAAAGCTGATTTTGAGGGTGTTTATATTTGACATCATATTTATTGAT
GTATACTCTCATATTGAGTTAAAATATAAAAATTTTAAAATTTTTATGAAATGGAAATATTAAAA
TATAGAATATTCATTAGTTATCTT
Found at i:2073825 original size:2 final size:2
Alignment explanation
Indices: 2073818--2073850 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2073808 ATGTATACTT
*
2073818 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2073851 GTATGTTCAG
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:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:2075412 original size:2 final size:2
Alignment explanation
Indices: 2075405--2075440 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2075395 GATCAATCTG
2075405 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2075441 TTGCCAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2075429 original size:17 final size:17
Alignment explanation
Indices: 2075407--2075441 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2075397 TCAATCTGTA
2075407 TATATATATATATATAT
1 TATATATATATATATAT
2075424 TATATATATATATATAT
1 TATATATATATATATAT
2075441 T
1 T
2075442 TGCCAATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:2078369 original size:34 final size:34
Alignment explanation
Indices: 2078326--2078390 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
2078316 TAATCCATGA
* * *
2078326 TACTTTGATAGTGGATGCTCAAAGCGCACAATGG
1 TACTTTGATAATAGATGCTCAAAGCACACAATGG
*
2078360 TACTTTGATAATAGATGCTCGAAGCACACAA
1 TACTTTGATAATAGATGCTCAAAGCACACAA
2078391 CCAGAGACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (34 bp):
TACTTTGATAATAGATGCTCAAAGCACACAATGG
Found at i:2090178 original size:11 final size:11
Alignment explanation
Indices: 2090164--2090215 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
2090154 ATAAGATATG
*
2090164 AATAAATTTAA
1 AATAAATATAA
* *
2090175 AATACATGTTAA
1 AATAAAT-ATAA
2090187 ATATAAATATAA
1 A-ATAAATATAA
2090199 AATAAATATAA
1 AATAAATATAA
*
2090210 TATAAA
1 AATAAA
2090216 AATATAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 21 0.60
12 9 0.26
13 5 0.14
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAAATATAA
Found at i:2090193 original size:6 final size:6
Alignment explanation
Indices: 2090184--2090223 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
2090174 AAATACATGT
*
2090184 TAAATA TAAATA TAAA-A TAAATA TAATATA AAAATA TAAA
1 TAAATA TAAATA TAAATA TAAATA TAA-ATA TAAATA TAAA
2090224 GATAGAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 20 0.67
7 5 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
TAAATA
Found at i:2090219 original size:17 final size:17
Alignment explanation
Indices: 2090184--2090216 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2090174 AAATACATGT
2090184 TAAATATAAATATAAAA
1 TAAATATAAATATAAAA
2090201 TAAATAT-AATATAAAA
1 TAAATATAAATATAAAA
2090217 ATATAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAATATAAATATAAAA
Found at i:2090800 original size:16 final size:17
Alignment explanation
Indices: 2090768--2090801 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2090758 TCTTTGATGG
2090768 ATAATTAATTAACAATA
1 ATAATTAATTAACAATA
*
2090785 ATAATT-ATTAAGAATA
1 ATAATTAATTAACAATA
2090801 A
1 A
2090802 ATTATGCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (17 bp):
ATAATTAATTAACAATA
Found at i:2100138 original size:2 final size:2
Alignment explanation
Indices: 2100131--2100161 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2100121 ATTAAGTGAG
2100131 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2100162 TAAGAGATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2126635 original size:14 final size:13
Alignment explanation
Indices: 2126618--2126652 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2126608 TGATATAAAA
2126618 AATATTAATATTTT
1 AATATTAATA-TTT
*
2126632 AATAATAATATTT
1 AATATTAATATTT
2126645 AATATTAA
1 AATATTAA
2126653 AATATTATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATATTAATATTT
Found at i:2126656 original size:21 final size:20
Alignment explanation
Indices: 2126618--2126676 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
2126608 TGATATAAAA
**
2126618 AATATTAATATTTTAATAAT
1 AATATTAATATTAAAATAAT
2126638 AATATTTAATATTAAAAT-AT
1 AATA-TTAATATTAAAATAAT
* *
2126658 TATGTTAATA-TAAAA-AAT
1 AATATTAATATTAAAATAAT
2126676 A
1 A
2126677 TTTAAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 7 0.22
19 6 0.19
20 8 0.25
21 11 0.34
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AATATTAATATTAAAATAAT
Found at i:2126665 original size:19 final size:18
Alignment explanation
Indices: 2126630--2126681 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
2126620 TATTAATATT
*
2126630 TTAATAATAATATTTAATA
1 TTAA-AATATTATTTAATA
2126649 TTAAAATATTATGTTAATA
1 TTAAAATATTAT-TTAATA
*
2126668 -TAAAA-AATATTTAA
1 TTAAAATATTATTTAA
2126682 AAATAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 4 0.13
17 4 0.13
18 12 0.40
19 10 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTAAAATATTATTTAATA
Found at i:2126753 original size:22 final size:22
Alignment explanation
Indices: 2126711--2126768 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
2126701 TTTATATTAT
*
2126711 TTTATTAATAA--ATTATAATA
1 TTTATTAATAATTATAATAATA
2126731 TTTATTAATAATTATAATAATA
1 TTTATTAATAATTATAATAATA
*
2126753 TTAATTAATATATTAT
1 TTTATTAATA-ATTAT
2126769 TTATTAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 11 0.33
22 17 0.52
23 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTATTAATAATTATAATAATA
Found at i:2126826 original size:25 final size:23
Alignment explanation
Indices: 2126762--2126859 Score: 89
Period size: 23 Copynumber: 4.5 Consensus size: 23
2126752 ATTAATTAAT
* * *
2126762 ATATTATTTATTAATATAGTGTC
1 ATATTATTTATTAATATATTATA
* * * * *
2126785 TTAATATTGAATAAT-TAATATA
1 ATATTATTTATTAATATATTATA
2126807 ATATT-TTTATTAATATATTATA
1 ATATTATTTATTAATATATTATA
2126829 ATATTATTTATTAATATA--AT-
1 ATATTATTTATTAATATATTATA
2126849 ATATTATTTAT
1 ATATTATTTAT
2126860 GAGTAAAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
20 11 0.18
21 9 0.15
22 18 0.30
23 23 0.38
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (23 bp):
ATATTATTTATTAATATATTATA
Found at i:2126873 original size:23 final size:20
Alignment explanation
Indices: 2126807--2126873 Score: 55
Period size: 23 Copynumber: 3.1 Consensus size: 20
2126797 AATTAATATA
2126807 ATATT-TTTATTAATATATTAT
1 ATATTATTTATTAA-A-ATTAT
* *
2126828 AATATTATTTATTAATATAAT
1 -ATATTATTTATTAAAATTAT
2126849 ATATTATTTATGAGTAAAATTAT
1 ATATTATTTAT---TAAAATTAT
2126872 AT
1 AT
2126874 TCAAAAGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 11 0.30
21 4 0.11
22 5 0.14
23 17 0.46
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
ATATTATTTATTAAAATTAT
Found at i:2126874 original size:82 final size:80
Alignment explanation
Indices: 2126724--2126900 Score: 175
Period size: 82 Copynumber: 2.2 Consensus size: 80
2126714 ATTAATAAAT
* ***
2126724 TATAATA-TTTATTAATAATTATAATAATATTAATTAATATATTATTTATTAATATAGTGTCTTA
1 TATAATATTTTATTAATAATTATAATAATATTAATTAATATAATATTTATT-ATATAGTAAATTA
* *
2126788 ATATTGAATA-ATTAA
65 ATATTCAAAAGATTAA
* *
2126803 TATAATATTTTTATTAATATATTATAATATTATTTATTAATATAATATATTATT-TATGAGTAAA
1 TATAATA-TTTTATTAATA-ATTATAATAATATTAATTAATATAATAT-TTATTATAT-AGT-AA
2126867 ATT-ATATTCAAAAGTATTAA
61 ATTAATATTCAAAAG-ATTAA
2126887 TA-AATAATTTTATT
1 TATAAT-ATTTTATT
2126901 TATTGAAACA
Statistics
Matches: 81, Mismatches: 8, Indels: 14
0.79 0.08 0.14
Matches are distributed among these distances:
79 7 0.09
81 13 0.16
82 36 0.44
83 17 0.21
84 8 0.10
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.50
Consensus pattern (80 bp):
TATAATATTTTATTAATAATTATAATAATATTAATTAATATAATATTTATTATATAGTAAATTAA
TATTCAAAAGATTAA
Found at i:2127070 original size:14 final size:14
Alignment explanation
Indices: 2127047--2127078 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2127037 TTTCACCTAC
*
2127047 AATTATTTAATTAT
1 AATTAATTAATTAT
2127061 AATTAATTAATTAT
1 AATTAATTAATTAT
2127075 AATT
1 AATT
2127079 TATATTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTAATTAATTAT
Found at i:2127433 original size:22 final size:22
Alignment explanation
Indices: 2127407--2127448 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2127397 TATTTTTTTG
*
2127407 ATTTTTATTAAAATTATATATA
1 ATTTTTACTAAAATTATATATA
*
2127429 ATTTTTACTAAAATTTTATA
1 ATTTTTACTAAAATTATATA
2127449 CTATCATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTTACTAAAATTATATATA
Found at i:2128923 original size:1 final size:1
Alignment explanation
Indices: 2128917--2128946 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
2128907 AGATCAAGGC
2128917 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2128947 AGGAATCAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2129504 original size:25 final size:25
Alignment explanation
Indices: 2129476--2129535 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
2129466 TCATTTTGCC
*
2129476 ACTTCAGAATAT-TTCTCATCCTCTG
1 ACTTCAGAATATGTTCTCATCCT-TA
*
2129501 ACTTCAGAAT-TGTTGTCATCCTTA
1 ACTTCAGAATATGTTCTCATCCTTA
*
2129525 ACTTCACAATA
1 ACTTCAGAATA
2129536 CCCAGATCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 11 0.37
25 19 0.63
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (25 bp):
ACTTCAGAATATGTTCTCATCCTTA
Found at i:2141339 original size:8 final size:8
Alignment explanation
Indices: 2141326--2141352 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
2141316 GACAAGGTTT
2141326 TTTTTTTA
1 TTTTTTTA
2141334 TTTTTTTA
1 TTTTTTTA
2141342 TTTTTTTA
1 TTTTTTTA
2141350 TTT
1 TTT
2141353 CAAGTTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2142477 original size:27 final size:27
Alignment explanation
Indices: 2142440--2142500 Score: 104
Period size: 27 Copynumber: 2.2 Consensus size: 27
2142430 AATTTTGAAT
2142440 CTTATCTCTCAATTAAGTTATTACTTAA
1 CTTAT-TCTCAATTAAGTTATTACTTAA
*
2142468 TTTATTCTCAATTAAGTTATTACTTAA
1 CTTATTCTCAATTAAGTTATTACTTAA
2142495 CTTATT
1 CTTATT
2142501 TGATCTACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (27 bp):
CTTATTCTCAATTAAGTTATTACTTAA
Found at i:2148806 original size:2 final size:2
Alignment explanation
Indices: 2148799--2148824 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2148789 CTGCTTGTTA
2148799 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
2148825 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2148829 original size:2 final size:2
Alignment explanation
Indices: 2148824--2148852 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2148814 TATATATATA
2148824 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2148853 ATTTGTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2152492 original size:2 final size:2
Alignment explanation
Indices: 2152485--2152509 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2152475 TTCCAAACTG
2152485 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
2152510 ACACACACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2152514 original size:2 final size:2
Alignment explanation
Indices: 2152509--2152544 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2152499 CTCTCTCTCT
2152509 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2152545 GATGCATTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2155036 original size:2 final size:2
Alignment explanation
Indices: 2154993--2155020 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2154983 AAAACAAGAA
2154993 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
2155021 TGTTAAACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2156066 original size:2 final size:2
Alignment explanation
Indices: 2156059--2156084 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2156049 TGCTTATTGA
2156059 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
2156085 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2163080 original size:24 final size:25
Alignment explanation
Indices: 2163044--2163090 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
2163034 TAATAATTTT
2163044 ATTAATATAAAT-ATATAAATATAAA
1 ATTAATATAAATAATA-AAATATAAA
2163069 ATTAAT-TAAATAATAAAATATA
1 ATTAATATAAATAATAAAATATA
2163091 TATTTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATTAATATAAATAATAAAATATAAA
Found at i:2173805 original size:18 final size:16
Alignment explanation
Indices: 2173752--2173838 Score: 66
Period size: 14 Copynumber: 5.8 Consensus size: 16
2173742 AAAATAAAAC
2173752 TATTAAT-TATTT-TT
1 TATTAATATATTTATT
*
2173766 TATTACT-TA-TTATT
1 TATTAATATATTTATT
2173780 ATATT-ATA-ATTTTATT
1 -TATTAATATA-TTTATT
2173796 TATTAATATA-TTA--
1 TATTAATATATTTATT
2173809 TATTAATAGTATATTATT
1 TATTAATA-TAT-TTATT
2173827 TATTAATATATT
1 TATTAATATATT
2173839 GTTATAATAT
Statistics
Matches: 59, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
13 10 0.17
14 14 0.24
15 11 0.19
16 12 0.20
17 4 0.07
18 8 0.14
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (16 bp):
TATTAATATATTTATT
Found at i:2173808 original size:31 final size:31
Alignment explanation
Indices: 2173755--2173844 Score: 87
Period size: 31 Copynumber: 2.9 Consensus size: 31
2173745 ATAAAACTAT
* * *
2173755 TAATTATTTTTTATTACT-TATTATTATATTA
1 TAATT-TTATTTATTAATATATTATTATATAA
2173786 TAATTTTATTTATTAATATATTA-TAT-TAA
1 TAATTTTATTTATTAATATATTATTATATAA
* *
2173815 TAGTATATTATTTATTAATATATTGTTATA
1 TA--ATTTTATTTATTAATATATTATTATA
2173845 ATATTTATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
29 4 0.08
30 13 0.27
31 29 0.59
32 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (31 bp):
TAATTTTATTTATTAATATATTATTATATAA
Found at i:2173809 original size:15 final size:15
Alignment explanation
Indices: 2173752--2173944 Score: 95
Period size: 15 Copynumber: 13.0 Consensus size: 15
2173742 AAAATAAAAC
*
2173752 TATTAAT-TATTTTT
1 TATTAATATATTATT
*
2173766 TATTACT-TATTATT
1 TATTAATATATTATT
*
2173780 ATATT-ATAATTTTATT
1 -TATTAAT-ATATTATT
2173796 TATTAATATATTATAT
1 TATTAATATATTAT-T
* *
2173812 TAATAGTATATTATT
1 TATTAATATATTATT
*
2173827 TATTAATATATT-GT
1 TATTAATATATTATT
2173841 TA-TAATAT-TTATT
1 TATTAATATATTATT
* *
2173854 AACTAATATAATAATATT
1 TATTAATAT-AT--TATT
*
2173872 AATTAATATA--ATGT
1 TATTAATATATTAT-T
*
2173886 T-CTAATAT-TTAATAT
1 TATTAATATATT-AT-T
*
2173901 TATATAATA-A-AATT
1 TAT-TAATATATTATT
*
2173915 AATTAATATATTATT
1 TATTAATATATTATT
*
2173930 TATTAATATAATATT
1 TATTAATATATTATT
2173945 ATTTATGAAT
Statistics
Matches: 137, Mismatches: 22, Indels: 39
0.69 0.11 0.20
Matches are distributed among these distances:
12 2 0.01
13 21 0.15
14 27 0.20
15 47 0.34
16 22 0.16
17 6 0.04
18 12 0.09
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTAATATATTATT
Found at i:2173837 original size:54 final size:57
Alignment explanation
Indices: 2173766--2173874 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 57
2173756 AATTATTTTT
* * * *
2173766 TATTACTTATTATTATA-TTATAAT-TTTATTTATTAATAT-ATTATATTAATAGTA
1 TATTACTTATTAATATATTTATAATATTTATTAACTAATATAATAATATTAATAGTA
*
2173820 TATTATTTATTAATATATTGTTATAATATTTATTAACTAATATAATAATATTAAT
1 TATTACTTATTAATATA-T-TTATAATATTTATTAACTAATATAATAATATTAAT
2173875 TAATATAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
54 15 0.33
57 7 0.16
58 13 0.29
59 10 0.22
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (57 bp):
TATTACTTATTAATATATTTATAATATTTATTAACTAATATAATAATATTAATAGTA
Found at i:2173879 original size:45 final size:43
Alignment explanation
Indices: 2173823--2173926 Score: 136
Period size: 45 Copynumber: 2.4 Consensus size: 43
2173813 AATAGTATAT
* *
2173823 TATTTATTAATATATTGTTATAATATTTATTAACTAATATAATAA
1 TATTAATTAATATATTGTTATAATATTTAAT-A-TAATATAATAA
* * *
2173868 TATTAATTAATATAATGTTCTAATATTTAATATTATATAATAA
1 TATTAATTAATATATTGTTATAATATTTAATATAATATAATAA
*
2173911 AATTAATTAATATATT
1 TATTAATTAATATATT
2173927 ATTTATTAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
43 24 0.46
44 1 0.02
45 27 0.52
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (43 bp):
TATTAATTAATATATTGTTATAATATTTAATATAATATAATAA
Found at i:2173891 original size:23 final size:23
Alignment explanation
Indices: 2173818--2173924 Score: 78
Period size: 23 Copynumber: 4.8 Consensus size: 23
2173808 ATATTAATAG
* * *
2173818 TATATTATTTATTAATATATTGT
1 TATAATATTAATTAATATAATGT
* * *
2173841 TATAATATTTATTAA-CTAATAT
1 TATAATATTAATTAATATAATGT
*
2173863 AATAATATTAATTAATATAATGT
1 TATAATATTAATTAATATAATGT
* * *
2173886 TCTAATA-T--TTAATATTATAT
1 TATAATATTAATTAATATAATGT
* *
2173906 AATAAAATTAATTAATATA
1 TATAATATTAATTAATATA
2173925 TTATTTATTA
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
20 14 0.22
21 1 0.02
22 18 0.28
23 31 0.48
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TATAATATTAATTAATATAATGT
Found at i:2173920 original size:43 final size:45
Alignment explanation
Indices: 2173828--2173924 Score: 135
Period size: 43 Copynumber: 2.2 Consensus size: 45
2173818 TATATTATTT
* * *
2173828 ATTAATATATTGTTATAATATTTATTAACTAATATAATAATATTA
1 ATTAATATAATGTTATAATATTTAATAACTAATATAATAAAATTA
* *
2173873 ATTAATATAATGTTCTAATATTTAAT-A-TTATATAATAAAATTA
1 ATTAATATAATGTTATAATATTTAATAACTAATATAATAAAATTA
2173916 ATTAATATA
1 ATTAATATA
2173925 TTATTTATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 23 0.49
44 1 0.02
45 23 0.49
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (45 bp):
ATTAATATAATGTTATAATATTTAATAACTAATATAATAAAATTA
Found at i:2173937 original size:45 final size:45
Alignment explanation
Indices: 2173791--2173961 Score: 126
Period size: 45 Copynumber: 3.8 Consensus size: 45
2173781 TATTATAATT
** *
2173791 TTATTTATTAATATATT-ATATTA-ATAGTATATTATTTATTAATATA
1 TTATTTATTAATAT-TTAATATTATATA--ATAAAATTAATTAATATA
* * * *
2173837 TT-GTTA-TAATATTTATTAACTAATATAATAATATTAATTAATATA
1 TTATTTATTAATATTTAAT-A-TTATATAATAAAATTAATTAATATA
*
2173882 --ATGTT-CTAATATTTAATATTATATAATAAAATTAATTAATATA
1 TTAT-TTATTAATATTTAATATTATATAATAAAATTAATTAATATA
2173925 TTATTTATTAATA--TAATATTATTTATGAATAAAATTA
1 TTATTTATTAATATTTAATATTA--TAT-AATAAAATTA
2173962 TACTAAAAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
43 33 0.32
44 10 0.10
45 42 0.41
46 14 0.14
47 3 0.03
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (45 bp):
TTATTTATTAATATTTAATATTATATAATAAAATTAATTAATATA
Found at i:2173942 original size:43 final size:43
Alignment explanation
Indices: 2173859--2173961 Score: 118
Period size: 43 Copynumber: 2.3 Consensus size: 43
2173849 TTATTAACTA
* * *
2173859 ATATAATAATATTAATTAATATAATGTTCTAATATTTAATATT
1 ATATAATAAAATTAATTAATATAATATTCTAATATATAATATT
* *
2173902 ATATAATAAAATTAATTAATATATTATT-TATTAATATAATATT
1 ATATAATAAAATTAATTAATATAATATTCTAAT-ATATAATATT
2173945 ATTTATGAATAAAATTA
1 A--TAT-AATAAAATTA
2173962 TACTAAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
42 3 0.06
43 35 0.69
45 3 0.06
46 10 0.20
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (43 bp):
ATATAATAAAATTAATTAATATAATATTCTAATATATAATATT
Found at i:2173950 original size:18 final size:18
Alignment explanation
Indices: 2173784--2173947 Score: 73
Period size: 18 Copynumber: 8.7 Consensus size: 18
2173774 ATTATTATAT
* *
2173784 TATAATTTTATTTATTAA
1 TATAATATTATTAATTAA
* *
2173802 TATATTA-TATTAA-TAG
1 TATAATATTATTAATTAA
* *
2173818 TATATTATTTATTAATATATTGT
1 TATAATA-TTATTAAT-TA---A
*
2173841 TATAATATTTATTAACTAA
1 TATAATA-TTATTAATTAA
*
2173860 TATAATAATATTAATTAA
1 TATAATATTATTAATTAA
* * *
2173878 TATAATGTTCTAATATTTAA
1 TATAAT-AT-TATTAATTAA
* * *
2173898 TATTATATAATAAAATTAA
1 TATAATATTAT-TAATTAA
*
2173917 T-TAATATATTATTTATTAA
1 TAT-A-ATATTATTAATTAA
2173936 TATAATATTATT
1 TATAATATTATT
2173948 TATGAATAAA
Statistics
Matches: 109, Mismatches: 24, Indels: 26
0.69 0.15 0.16
Matches are distributed among these distances:
16 9 0.08
17 5 0.05
18 36 0.33
19 21 0.19
20 22 0.20
22 2 0.02
23 14 0.13
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (18 bp):
TATAATATTATTAATTAA
Found at i:2174120 original size:22 final size:22
Alignment explanation
Indices: 2174063--2174130 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
2174053 ACTTTATTTT
*
2174063 TTATTTTTTAATAATTAATAAA
1 TTATTTTTTATTAATTAATAAA
*
2174085 TTATTTTTCATTAATTAATAAA
1 TTATTTTTTATTAATTAATAAA
* * *
2174107 TTATTTTTTGTTAATCAATTAA
1 TTATTTTTTATTAATTAATAAA
2174129 TT
1 TT
2174131 TTTATCAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (22 bp):
TTATTTTTTATTAATTAATAAA
Found at i:2175005 original size:17 final size:17
Alignment explanation
Indices: 2174979--2175021 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
2174969 TTTTTTTATC
2174979 ATATTA-ATTTAAAATT
1 ATATTATATTTAAAATT
2174995 ATATTATATTTAAAATT
1 ATATTATATTTAAAATT
*
2175012 GTATTATATT
1 ATATTATATT
2175022 GCTTTGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATATTATATTTAAAATT
Done.