Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 13 of 26
Found at i:1765436 original size:9 final size:9
Alignment explanation
Indices: 1765422--1765466 Score: 54
Period size: 9 Copynumber: 4.6 Consensus size: 9
1765412 TTGGTGAGAA
1765422 TGTTAGGTG
1 TGTTAGGTG
1765431 TGTTAGGTGAG
1 TGTTAGGT--G
1765442 AATGTTAGGTG
1 --TGTTAGGTG
1765453 TGTTAGGTG
1 TGTTAGGTG
1765462 TGTTA
1 TGTTA
1765467 ACATGTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 22 0.69
11 2 0.06
13 8 0.25
ACGTcount: A:0.18, C:0.00, G:0.40, T:0.42
Consensus pattern (9 bp):
TGTTAGGTG
Found at i:1765442 original size:22 final size:22
Alignment explanation
Indices: 1765414--1765461 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1765404 TGATGTATTT
1765414 GGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTA
1765436 GGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTA
1765458 GGTG
1 GGTG
1765462 TGTTAACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (22 bp):
GGTGAGAATGTTAGGTGTGTTA
Found at i:1770177 original size:34 final size:34
Alignment explanation
Indices: 1770139--1770305 Score: 307
Period size: 34 Copynumber: 4.9 Consensus size: 34
1770129 TCTTTGTTAA
1770139 GATGTATTTGGTGAGAATGTTAGGTGTGTTAGGT
1 GATGTATTTGGTGAGAATGTTAGGTGTGTTAGGT
1770173 GATGTATTTGGTGAGAATGTTAGGTGTGTTAGGT
1 GATGTATTTGGTGAGAATGTTAGGTGTGTTAGGT
*
1770207 GATGTGTTTGGTGAGAATGTTAGGTGTGTTAGGT
1 GATGTATTTGGTGAGAATGTTAGGTGTGTTAGGT
*
1770241 GATGTGTTTGGTGAGAATGTTAGGTGTGTTAGGT
1 GATGTATTTGGTGAGAATGTTAGGTGTGTTAGGT
*
1770275 GATGTATTTTGTGAGAATGTTAGGTGTGTTA
1 GATGTATTTGGTGAGAATGTTAGGTGTGTTA
1770306 ACATGTATAT
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 130 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (34 bp):
GATGTATTTGGTGAGAATGTTAGGTGTGTTAGGT
Found at i:1770194 original size:25 final size:23
Alignment explanation
Indices: 1770164--1770266 Score: 65
Period size: 25 Copynumber: 4.4 Consensus size: 23
1770154 AATGTTAGGT
1770164 GTGTTAGGTGATGTATTTGGTGA
1 GTGTTAGGTGATGTATTTGGTGA
*
1770187 GAATGTTAGGTG-TG--TTAGGTGA
1 G--TGTTAGGTGATGTATTTGGTGA
* *
1770209 TGTGTTTGGTGA-GAATGTTAGGT--
1 -GTGTTAGGTGATGTAT-TT-GGTGA
*
1770232 GTGTTAGGTGATGTGTTTGGTGA
1 GTGTTAGGTGATGTATTTGGTGA
1770255 GAATGTTAGGTG
1 G--TGTTAGGTG
1770267 TGTTAGGTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
21 12 0.20
22 19 0.31
23 6 0.10
24 3 0.05
25 21 0.34
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (23 bp):
GTGTTAGGTGATGTATTTGGTGA
Found at i:1774271 original size:25 final size:25
Alignment explanation
Indices: 1774219--1774297 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 25
1774209 AATTTTTTCA
**
1774219 ATTTTAAATGGATTTTATTAAA-AGT
1 ATTTTAAATATATTTTATTAAATA-T
1774244 ATTTTAAATATATTTTATTAAATAT
1 ATTTTAAATATATTTTATTAAATAT
*
1774269 A--TT---TATATTTTATTAAGTAT
1 ATTTTAAATATATTTTATTAAATAT
1774289 ATTTTAAAT
1 ATTTTAAAT
1774298 CTTAATTCGG
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
20 17 0.38
22 2 0.04
23 2 0.04
25 23 0.51
26 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (25 bp):
ATTTTAAATATATTTTATTAAATAT
Found at i:1774275 original size:20 final size:20
Alignment explanation
Indices: 1774252--1774292 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1774242 GTATTTTAAA
1774252 TATATTTTATTAAATATATT
1 TATATTTTATTAAATATATT
*
1774272 TATATTTTATTAAGTATATT
1 TATATTTTATTAAATATATT
1774292 T
1 T
1774293 TAAATCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TATATTTTATTAAATATATT
Found at i:1775052 original size:18 final size:18
Alignment explanation
Indices: 1775020--1775055 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1775010 TAATGCATAT
*
1775020 TTATAAAATCCATTAAAA
1 TTATAAAATCAATTAAAA
*
1775038 TTATAAAATTAATTAAAA
1 TTATAAAATCAATTAAAA
1775056 ATAAAACATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
TTATAAAATCAATTAAAA
Found at i:1775485 original size:12 final size:12
Alignment explanation
Indices: 1775468--1775492 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1775458 TTTCTTAAAG
1775468 AAGAAAAAAAAA
1 AAGAAAAAAAAA
1775480 AAGAAAAAAAAA
1 AAGAAAAAAAAA
1775492 A
1 A
1775493 CTTTCTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:1778859 original size:18 final size:18
Alignment explanation
Indices: 1778838--1778922 Score: 56
Period size: 16 Copynumber: 4.8 Consensus size: 18
1778828 AAAATATTAA
1778838 ATATATAATTTAAAA-TT
1 ATATATAATTTAAAATTT
* *
1778855 -TATATAATATAAATTATT
1 ATATATAATTTAAAAT-TT
1778873 A-ATAT-A-TTAAAATTT
1 ATATATAATTTAAAATTT
1778888 ATATA-AATATTAAATATTTT
1 ATATATAAT-TTAAA-A-TTT
*
1778908 AAATATAATTATAAA
1 ATATATAATT-TAAA
1778923 TAAAATATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
15 3 0.06
16 21 0.40
17 1 0.02
18 11 0.21
19 1 0.02
20 8 0.15
21 7 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATATAATTTAAAATTT
Found at i:1778924 original size:12 final size:13
Alignment explanation
Indices: 1778887--1778943 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 13
1778877 TATTAAAATT
1778887 TATATAAATATTAAA
1 TATATAAATA--AAA
* *
1778902 TATTTTAAATATAA
1 TA-TATAAATAAAA
1778916 T-TATAAATAAAA
1 TATATAAATAAAA
1778928 TATATAAA-AAAA
1 TATATAAATAAAA
1778940 TATA
1 TATA
1778944 AATTCACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
12 18 0.50
13 6 0.17
14 3 0.08
15 2 0.06
16 7 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATATAAATAAAA
Found at i:1779217 original size:6 final size:5
Alignment explanation
Indices: 1779175--1779219 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
1779165 TTATTTCTCG
1779175 AGAAA A-AAA A-AAA A-AAA AGAAA AGAAA AGAAGA AGAAA GAGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAA-A AGAAA -AGAAA A
1779220 TTAGAGGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 12 0.32
5 15 0.41
6 10 0.27
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:1781355 original size:18 final size:17
Alignment explanation
Indices: 1781332--1781392 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 17
1781322 CCTATCAAAA
1781332 TATTTTTTACAATTTTTT
1 TATTTTTTA-AATTTTTT
1781350 TATTTTTAATAAACTATTCTTT
1 TATTTTT--TAAA-T-TT-TTT
*
1781372 TATTTTTTATAATTATTT
1 TATTTTTTA-AATTTTTT
1781390 TAT
1 TAT
1781393 ACGTTCTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
18 13 0.36
19 3 0.08
20 6 0.17
21 4 0.11
22 10 0.28
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTTTTAAATTTTTT
Found at i:1781877 original size:43 final size:42
Alignment explanation
Indices: 1781780--1781880 Score: 122
Period size: 43 Copynumber: 2.5 Consensus size: 42
1781770 ATTAATAAGA
*
1781780 TATTTTA-GTATTT-ATATAATGTTTTAATAATAAAAAGTGC
1 TATTTTATGTATTTAATATAATGTTTTAATAATAAAAAGTAC
*
1781820 TA-TTTATGTATTTAATATAAAT-TTTTATATAATAAATAA-TAT
1 TATTTTATGTATTTAATAT-AATGTTTTA-ATAATAAA-AAGTAC
1781862 TATTTTATGTATTTAATAT
1 TATTTTATGTATTTAATAT
1781881 TAATATAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
39 4 0.08
40 8 0.15
41 9 0.17
42 14 0.26
43 18 0.34
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (42 bp):
TATTTTATGTATTTAATATAATGTTTTAATAATAAAAAGTAC
Found at i:1781879 original size:22 final size:22
Alignment explanation
Indices: 1781822--1781879 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
1781812 AAAAGTGCTA
1781822 TTTATGTATTTAAT-ATAAATT
1 TTTATGTATTTAATAATAAATT
* * * *
1781843 TTTATATAATAAATAAT-ATTAT
1 TTTATGTATTTAATAATAAAT-T
1781865 TTTATGTATTTAATA
1 TTTATGTATTTAATA
1781880 TTAATATAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (22 bp):
TTTATGTATTTAATAATAAATT
Found at i:1781898 original size:26 final size:26
Alignment explanation
Indices: 1781831--1781912 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 26
1781821 ATTTATGTAT
*
1781831 TTAATATAA-A-TTTT-TATATAATA
1 TTAATATAATATTTTTGTATTTAATA
*
1781854 --AATAATATTATTTTATGTATTTAATA
1 TTAAT-ATAATATTTT-TGTATTTAATA
*
1781880 TTAATATAATATTTTTGTATTAAATA
1 TTAATATAATATTTTTGTATTTAATA
1781906 TTAATAT
1 TTAATAT
1781913 TTGAAATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
21 3 0.06
22 3 0.06
23 1 0.02
24 3 0.06
25 1 0.02
26 25 0.52
27 9 0.19
28 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
TTAATATAATATTTTTGTATTTAATA
Found at i:1782124 original size:21 final size:20
Alignment explanation
Indices: 1782100--1782139 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1782090 TATTAAAAAA
1782100 TTATTTTATATTAATATTTAT
1 TTATTTTATATTAA-ATTTAT
*
1782121 TTATTTTTTATTAAATTTA
1 TTATTTTATATTAAATTTA
1782140 AATAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTTATATTAAATTTAT
Found at i:1782125 original size:47 final size:47
Alignment explanation
Indices: 1782070--1782161 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
1782060 ATTTAAATTA
*
1782070 TTATTTATTTTATTAAAAAATATTAAA-AAAT-TATTTTATATTAATAT
1 TTATTTATTTT-TTAAAAAAT-TTAAATAAATATATATTATATTAATAT
** *
1782117 TTATTTATTTTTTATTAAATTTAAATAAATATATATTATTTTAAT
1 TTATTTATTTTTTAAAAAATTTAAATAAATATATATTATATTAAT
1782162 TAAAAATGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
45 5 0.13
46 11 0.28
47 23 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (47 bp):
TTATTTATTTTTTAAAAAATTTAAATAAATATATATTATATTAATAT
Found at i:1787153 original size:26 final size:23
Alignment explanation
Indices: 1787123--1787174 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 23
1787113 TAAAATCTAA
*
1787123 ATTTTAATATTTACAATCTTTTATTT
1 ATTTTAAGA-TTACAAT-TTTT-TTT
*
1787149 ATTTTCAGATTACAATTTTTTTT
1 ATTTTAAGATTACAATTTTTTTT
1787172 ATT
1 ATT
1787175 AAAAAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.25
24 4 0.17
25 7 0.29
26 7 0.29
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTTTAAGATTACAATTTTTTTT
Found at i:1788104 original size:2 final size:2
Alignment explanation
Indices: 1788043--1788089 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
1788033 CTTTTCAAAT
* * *
1788043 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA CA TA TA CA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1788084 TA TA TA
1 TA TA TA
1788090 AATTAACGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1791173 original size:32 final size:32
Alignment explanation
Indices: 1791119--1791199 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
1791109 CACAAATGTC
*
1791119 TCAAAATCTATATAATACGAATTATTACAATA
1 TCAAAATTTATATAATACGAATTATTACAATA
* * *
1791151 TCAAGATTTATATATTATGAATTATTACAATA
1 TCAAAATTTATATAATACGAATTATTACAATA
*
1791183 TCAAAATTTATAAAATA
1 TCAAAATTTATATAATA
1791200 TAAACTACCT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (32 bp):
TCAAAATTTATATAATACGAATTATTACAATA
Found at i:1791521 original size:12 final size:12
Alignment explanation
Indices: 1791504--1791528 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1791494 TTAAGAGCTC
1791504 TTGCAAATAATT
1 TTGCAAATAATT
1791516 TTGCAAATAATT
1 TTGCAAATAATT
1791528 T
1 T
1791529 AAGTTGTTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTGCAAATAATT
Found at i:1792506 original size:46 final size:46
Alignment explanation
Indices: 1792436--1792524 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
1792426 CCAAAGAATT
* *
1792436 AAATTTTTTATTTATTTTTTAATTAATTTAATTCAATTAAAAATAA
1 AAATTATTTATTTATTTTTAAATTAATTTAATTCAATTAAAAATAA
* *
1792482 AAATTATTTGTTTATTTTTAAATTAATTTAATTTAATTAAAAA
1 AAATTATTTATTTATTTTTAAATTAATTTAATTCAATTAAAAA
1792525 ATTAATAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (46 bp):
AAATTATTTATTTATTTTTAAATTAATTTAATTCAATTAAAAATAA
Found at i:1792776 original size:14 final size:15
Alignment explanation
Indices: 1792744--1792779 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1792734 AAACTTTTAC
*
1792744 TTTAATTAAAAAATT
1 TTTAATTAAAAAATA
1792759 TTTAATTAAAAAA-A
1 TTTAATTAAAAAATA
1792773 TTTAATT
1 TTTAATT
1792780 GATATGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAATTAAAAAATA
Found at i:1793345 original size:17 final size:17
Alignment explanation
Indices: 1793325--1793369 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
1793315 TTAGATTACT
* *
1793325 AAAAATTAAATTTTTTA
1 AAAAAATAAATTTCTTA
*
1793342 AAAAAATATA-TTCTTA
1 AAAAAATAAATTTCTTA
1793358 AAAAAATAAATT
1 AAAAAATAAATT
1793370 AAAAAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAAAATAAATTTCTTA
Found at i:1793371 original size:13 final size:13
Alignment explanation
Indices: 1793355--1793379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1793345 AAATATATTC
1793355 TTAAAAAAATAAA
1 TTAAAAAAATAAA
1793368 TTAAAAAAATAA
1 TTAAAAAAATAA
1793380 TATTGATGAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TTAAAAAAATAAA
Found at i:1794950 original size:3 final size:3
Alignment explanation
Indices: 1794942--1794976 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1794932 TAACAGCTGC
1794942 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1794977 ATGTGATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1795822 original size:21 final size:21
Alignment explanation
Indices: 1795798--1795869 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
1795788 TAATGATTGA
1795798 ATAAATAAATATAAATTATAT
1 ATAAATAAATATAAATTATAT
*
1795819 ATAAA-ATTATATAAA-TATAT
1 ATAAATA-AATATAAATTATAT
*
1795839 A-AAACTAAAT-T-AATTTTAT
1 ATAAA-TAAATATAAATTATAT
1795858 ACTAAAATAAAT
1 A-T-AAATAAAT
1795870 GAATCCTCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
18 2 0.05
19 9 0.22
20 9 0.22
21 18 0.44
22 3 0.07
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAATAAATATAAATTATAT
Found at i:1796252 original size:21 final size:21
Alignment explanation
Indices: 1796210--1796253 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1796200 TAAAATCAAA
*
1796210 TAATAAATAAAAAATTTAATT
1 TAATAAATAAAAAATTAAATT
*
1796231 TAATAAATAAGAAA-TAACATT
1 TAATAAATAAAAAATTAA-ATT
1796252 TA
1 TA
1796254 TTTCTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
TAATAAATAAAAAATTAAATT
Found at i:1796428 original size:2 final size:2
Alignment explanation
Indices: 1796421--1796445 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1796411 TAGTCAAAAT
1796421 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
1796446 TGATTGGTAG
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:1796648 original size:25 final size:25
Alignment explanation
Indices: 1796614--1796668 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
1796604 AAATATAAAA
* * *
1796614 TATTAAAAATTAATATAAATAATTT
1 TATTTAAAATAAATAAAAATAATTT
1796639 TATTTAAAATAAATAAAAATAATTT
1 TATTTAAAATAAATAAAAATAATTT
1796664 TATTT
1 TATTT
1796669 TTCTTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TATTTAAAATAAATAAAAATAATTT
Found at i:1798609 original size:25 final size:25
Alignment explanation
Indices: 1798581--1798630 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1798571 AAAAAATCTG
*
1798581 GGTACTGTCAAAAACAAACATTACC
1 GGTACTATCAAAAACAAACATTACC
1798606 GGTACTATCAAAAACAAACATTACC
1 GGTACTATCAAAAACAAACATTACC
1798631 TGTTGCCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.24, G:0.10, T:0.20
Consensus pattern (25 bp):
GGTACTATCAAAAACAAACATTACC
Found at i:1800670 original size:22 final size:24
Alignment explanation
Indices: 1800629--1800684 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
1800619 ACCTTTTAAA
*
1800629 TTTATCCAAAATAGTAATTT-TT-
1 TTTATCAAAAATAGTAATTTATTG
* * *
1800651 TTTGTCAAAAATGGTGATTTATTG
1 TTTATCAAAAATAGTAATTTATTG
1800675 TTTATCAAAA
1 TTTATCAAAA
1800685 TTAATGACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 16 0.59
23 2 0.07
24 9 0.33
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (24 bp):
TTTATCAAAAATAGTAATTTATTG
Found at i:1802122 original size:16 final size:16
Alignment explanation
Indices: 1802101--1802146 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
1802091 TTTGAAGTGG
1802101 TTTGCTACTATGCTGA
1 TTTGCTACTATGCTGA
1802117 TTTGCTACTATGCTGA
1 TTTGCTACTATGCTGA
1802133 TTTGCTACTATGCT
1 TTTGCTACTATGCT
1802147 ACTATGATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (16 bp):
TTTGCTACTATGCTGA
Found at i:1802146 original size:8 final size:8
Alignment explanation
Indices: 1802103--1802152 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
1802093 TGAAGTGGTT
1802103 TGCTACTA
1 TGCTACTA
*
1802111 TGCTGA-TT
1 TGCT-ACTA
1802119 TGCTACTA
1 TGCTACTA
*
1802127 TGCTGA-TT
1 TGCT-ACTA
1802135 TGCTACTA
1 TGCTACTA
1802143 TGCTACTA
1 TGCTACTA
1802151 TG
1 TG
1802153 ATACAAATCG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
7 2 0.06
8 30 0.88
9 2 0.06
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (8 bp):
TGCTACTA
Found at i:1805693 original size:27 final size:28
Alignment explanation
Indices: 1805663--1805724 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
1805653 AAAGCCACCC
1805663 TTTGTATTTATCAAAAAT-GATGATT-TT
1 TTTGTATTTATCAAAAATAG-TGATTCTT
* *
1805690 TTTGTGTTTGTCAAAAATAGTGATTCTT
1 TTTGTATTTATCAAAAATAGTGATTCTT
1805718 TTT-TATT
1 TTTGTATT
1805725 ACAAAATAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 24 0.80
28 6 0.20
ACGTcount: A:0.27, C:0.05, G:0.13, T:0.55
Consensus pattern (28 bp):
TTTGTATTTATCAAAAATAGTGATTCTT
Found at i:1806292 original size:17 final size:18
Alignment explanation
Indices: 1806267--1806301 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1806257 TAGTCGTGAT
1806267 ATAAAATAAA-ATAAAAA
1 ATAAAATAAATATAAAAA
*
1806284 ATAATATAAATATAAAAA
1 ATAAAATAAATATAAAAA
1806302 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAAATAAATATAAAAA
Found at i:1806329 original size:43 final size:45
Alignment explanation
Indices: 1806276--1806389 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 45
1806266 TATAAAATAA
* *
1806276 AATAAAAAATAATATAAATATAAAAATATTTTAAA-AT-TTATAT
1 AATATAAAATAATATAAATATAAAAATAATTTAAATATATTATAT
1806319 AATATAAAAT-AT-TAATATATTAAAAATAATTTAAATATAATTATAT
1 AATATAAAATAATATAA-ATA-TAAAAATAATTTAAATAT-ATTATAT
*
1806365 AATATAATAAAATATATAAATATAA
1 AATATAA-AATA-ATATAAATATAA
1806390 TATAAATATA
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
41 3 0.05
42 5 0.08
43 23 0.39
44 2 0.03
46 13 0.22
47 2 0.03
48 3 0.05
49 5 0.08
50 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (45 bp):
AATATAAAATAATATAAATATAAAAATAATTTAAATATATTATAT
Found at i:1806366 original size:8 final size:7
Alignment explanation
Indices: 1806314--1806402 Score: 66
Period size: 6 Copynumber: 13.0 Consensus size: 7
1806304 TTTTAAAATT
1806314 TATATAA
1 TATATAA
*
1806321 TATAAAA
1 TATATAA
1806328 TAT-TAA
1 TATATAA
1806334 TATATTAA
1 TATA-TAA
*
1806342 -AAATAA
1 TATATAA
1806348 T-T-TAA
1 TATATAA
1806353 -ATATAA
1 TATATAA
1806359 TTATATAA
1 -TATATAA
1806367 TATAATAAAA
1 TAT-AT--AA
1806377 TATATAA
1 TATATAA
1806384 -ATATAA
1 TATATAA
1806390 TATA-AA
1 TATATAA
1806396 TATATAA
1 TATATAA
1806403 ATTTTTAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 24
0.70 0.04 0.26
Matches are distributed among these distances:
5 4 0.06
6 23 0.35
7 21 0.32
8 11 0.17
9 2 0.03
10 5 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TATATAA
Found at i:1806388 original size:31 final size:30
Alignment explanation
Indices: 1806315--1806404 Score: 55
Period size: 28 Copynumber: 3.1 Consensus size: 30
1806305 TTTAAAATTT
* *
1806315 ATATAATATA-AA-ATATTAATATAT-TAA
1 ATATAATATATAATATAATAAAATATATAA
* * * *
1806342 AAATAATTTA-AATATAATTATATA-ATATA
1 ATATAATATATAATATAATAAAATATATA-A
*
1806371 ATAAAATATATAAATATAATATAAATATATAA
1 ATATAATATAT-AATATAATA-AAATATATAA
1806403 AT
1 AT
1806405 TTTTAAAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
27 10 0.21
28 11 0.23
29 8 0.17
31 8 0.17
32 7 0.15
33 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
ATATAATATATAATATAATAAAATATATAA
Found at i:1806403 original size:8 final size:8
Alignment explanation
Indices: 1806265--1806404 Score: 53
Period size: 8 Copynumber: 17.0 Consensus size: 8
1806255 ATTAGTCGTG
1806265 ATATAAA-
1 ATATAAAT
1806272 ATA-AAAT
1 ATATAAAT
*
1806279 A-AAAAAT
1 ATATAAAT
1806286 AATATAAAT
1 -ATATAAAT
*
1806295 ATAAAAAT
1 ATATAAAT
*
1806303 ATTTTAAAAT
1 A-TAT-AAAT
*
1806313 TTATATAAT
1 ATATA-AAT
1806322 ATA-AAAT
1 ATATAAAT
1806329 AT-T-AAT
1 ATATAAAT
*
1806335 ATATTAAAA
1 ATA-TAAAT
*
1806344 ATAATTTAA-
1 AT-A-TAAAT
*
1806353 ATATAATT
1 ATATAAAT
1806361 ATAT-AAT
1 ATATAAAT
1806368 ATAATAAAAT
1 AT-AT-AAAT
1806378 ATATAAATAT
1 ATAT-AA-AT
1806388 AATATAAAT
1 -ATATAAAT
1806397 ATATAAAT
1 ATATAAAT
1806405 TTTTAAAATA
Statistics
Matches: 103, Mismatches: 12, Indels: 35
0.69 0.08 0.23
Matches are distributed among these distances:
6 9 0.09
7 19 0.18
8 27 0.26
9 26 0.25
10 18 0.17
11 4 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATAAAT
Found at i:1806412 original size:36 final size:36
Alignment explanation
Indices: 1806273--1806414 Score: 124
Period size: 33 Copynumber: 4.2 Consensus size: 36
1806263 TGATATAAAA
* *
1806273 TAAAATA-AAAA-ATAATATAAATATAAAAATATTT
1 TAAAATATAAAATATAATATAAATATATAAATATAT
* *
1806307 TAAAAT-T--TATATAATATAAA-ATATTAATATAT
1 TAAAATATAAAATATAATATAAATATATAAATATAT
** * *
1806339 TAAAA-ATAATTTA-AATATAATTATAT-AATATAA
1 TAAAATATAAAATATAATATAAATATATAAATATAT
*
1806372 TAAAATATATAAATATAATATAAATATATAAAT-TTT
1 TAAAATATA-AAATATAATATAAATATATAAATATAT
1806408 TAAAATA
1 TAAAATA
1806415 AATATATCAT
Statistics
Matches: 86, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
32 16 0.19
33 28 0.33
34 16 0.19
35 3 0.03
36 20 0.23
37 3 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (36 bp):
TAAAATATAAAATATAATATAAATATATAAATATAT
Found at i:1806415 original size:21 final size:19
Alignment explanation
Indices: 1806265--1806421 Score: 77
Period size: 19 Copynumber: 7.9 Consensus size: 19
1806255 ATTAGTCGTG
1806265 ATATAAAATAAA-ATA-AA
1 ATATAAAATAAATATATAA
* * *
1806282 AAATAATATAAATATAAAA
1 ATATAAAATAAATATATAA
*** *
1806301 ATATTTTA-AAATTTATATA
1 ATATAAAATAAATATATA-A
1806320 ATATAAAATATTAATATATTAA
1 ATATAAAATA--AATATA-TAA
* ** *
1806342 AAATAATTTAAATATAATTAT
1 ATATAAAATAAATAT-A-TAA
*
1806363 ATAATATAATAAAATATATAA
1 AT-ATAAAAT-AAATATATAA
*
1806384 ATATAATATAAATATATAA
1 ATATAAAATAAATATATAA
*
1806403 ATTTTTAAAATAAATATAT
1 A--TATAAAATAAATATAT
1806422 CATTGCTGTC
Statistics
Matches: 104, Mismatches: 24, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
17 10 0.10
18 10 0.10
19 24 0.23
20 11 0.11
21 23 0.22
22 18 0.17
23 8 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATAAAATAAATATATAA
Found at i:1807766 original size:16 final size:17
Alignment explanation
Indices: 1807724--1807767 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1807714 ACTTATTTTT
*
1807724 AAAATTTTTTCAATTTC
1 AAAATTTTTTGAATTTC
**
1807741 AAAACATTTTGAA-TTC
1 AAAATTTTTTGAATTTC
1807757 AAAATTTTTTG
1 AAAATTTTTTG
1807768 TTAGAACTCG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.48
Consensus pattern (17 bp):
AAAATTTTTTGAATTTC
Found at i:1808079 original size:22 final size:23
Alignment explanation
Indices: 1808039--1808083 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1808029 AGATATTCAT
*
1808039 ATTATTTTTCGTATCATATTTTA
1 ATTATTTTTCATATCATATTTTA
*
1808062 ATTATTTTT-ATATTATATTTTA
1 ATTATTTTTCATATCATATTTTA
1808084 TGTCGTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTATTTTTCATATCATATTTTA
Found at i:1808689 original size:3 final size:3
Alignment explanation
Indices: 1808681--1808717 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1808671 AAACAAACCT
1808681 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1808718 AAGATGTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1809057 original size:7 final size:7
Alignment explanation
Indices: 1809045--1809069 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1809035 TATCTTTATC
1809045 TAATAAA
1 TAATAAA
1809052 TAATAAA
1 TAATAAA
1809059 TAATAAA
1 TAATAAA
1809066 TAAT
1 TAAT
1809070 TTGTTAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TAATAAA
Found at i:1809427 original size:2 final size:2
Alignment explanation
Indices: 1809422--1809448 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1809412 TTTTTGTGTG
1809422 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
1809449 GTTTTTGTTG
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:1809593 original size:2 final size:2
Alignment explanation
Indices: 1809586--1809633 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1809576 AAAAAGGAAT
1809586 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1809628 GA GA GA
1 GA GA GA
1809634 ATTGAACTTG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1811069 original size:2 final size:2
Alignment explanation
Indices: 1811057--1811095 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1811047 ATGCATTAAT
1811057 TA TA T- 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
1811096 AAACTTTAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1812330 original size:14 final size:14
Alignment explanation
Indices: 1812313--1812340 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1812303 AAGTTTTAAT
1812313 TTTTTAAATATATA
1 TTTTTAAATATATA
1812327 TTTTTAAATATATA
1 TTTTTAAATATATA
1812341 AATGAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTTAAATATATA
Found at i:1813124 original size:21 final size:21
Alignment explanation
Indices: 1813098--1813176 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 21
1813088 AGATAAAAAT
*
1813098 AAATATGATAAAAAATAATTA
1 AAATATAATAAAAAATAATTA
*
1813119 AAATATAATATTAAATATAA-TA
1 AAATATAATA--AAAAATAATTA
1813141 AAA-ATACAT-AAAAAT-ATTA
1 AAATATA-ATAAAAAATAATTA
**
1813160 AAAT-TAATTTAAAATAA
1 AAATATAATAAAAAATAA
1813177 AATATTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.06
19 17 0.36
20 1 0.02
21 12 0.26
22 7 0.15
23 7 0.15
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (21 bp):
AAATATAATAAAAAATAATTA
Found at i:1813126 original size:11 final size:11
Alignment explanation
Indices: 1813106--1813175 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 11
1813096 ATAAATATGA
*
1813106 TAAAAAATAAT
1 TAAAATATAAT
1813117 TAAAATATAAT
1 TAAAATATAAT
*
1813128 ATTAAATATAA-
1 -TAAAATATAAT
1813139 TAAAA-ATACA-
1 TAAAATATA-AT
1813149 TAAAA-AT-AT
1 TAAAATATAAT
1813158 TAAAAT-TAATT
1 TAAAATATAA-T
1813169 TAAAATA
1 TAAAATA
1813176 AAATATTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
8 1 0.02
9 9 0.18
10 13 0.27
11 17 0.35
12 9 0.18
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAATATAAT
Found at i:1813142 original size:33 final size:34
Alignment explanation
Indices: 1813091--1813166 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
1813081 TAATTTTAGA
* * *
1813091 TAAAAATAAATATGATAAAAAATA-ATTAAAATA-
1 TAAAATTAAATATAAT-AAAAATACATAAAAATAT
*
1813124 TAATATTAAATATAATAAAAATACATAAAAATAT
1 TAAAATTAAATATAATAAAAATACATAAAAATAT
1813158 TAAAATTAA
1 TAAAATTAA
1813167 TTTAAAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 7 0.19
33 21 0.58
34 8 0.22
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (34 bp):
TAAAATTAAATATAATAAAAATACATAAAAATAT
Found at i:1814441 original size:18 final size:19
Alignment explanation
Indices: 1814407--1814442 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1814397 AAAATCATCT
1814407 AATTTTAAAATAATTTATA
1 AATTTTAAAATAATTTATA
*
1814426 AATTTTTAAA-AATTTAT
1 AATTTTAAAATAATTTAT
1814443 TGCATTCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTTTAAAATAATTTATA
Found at i:1816559 original size:5 final size:5
Alignment explanation
Indices: 1816545--1816596 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
1816535 TTTAAAATTT
* * *
1816545 TTAT- TTATA TTATA TATAAA TTATTT TTATA TTATA TTATA TTATT TTATA
1 TTATA TTATA TTATA T-TATA TTA-TA TTATA TTATA TTATA TTATA TTATA
1816596 T
1 T
1816597 ACTATATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
4 4 0.10
5 28 0.72
6 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:1816573 original size:22 final size:21
Alignment explanation
Indices: 1816539--1816620 Score: 85
Period size: 22 Copynumber: 3.8 Consensus size: 21
1816529 ATAAATTTTA
*
1816539 AAATTTTTATTTATATTATATAT
1 AAATTATT-TTTATATTATAT-T
1816562 AAATTATTTTTATATTATATT
1 AAATTATTTTTATATTATATT
* *
1816583 ATATTATTTTATATACTATATTT
1 AAATTATTTT-TATATTATA-TT
*
1816606 TAATT-TTTTTATATT
1 AAATTATTTTTATATT
1816621 TAGAGACAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 15 0.29
22 24 0.47
23 12 0.24
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (21 bp):
AAATTATTTTTATATTATATT
Found at i:1818913 original size:13 final size:14
Alignment explanation
Indices: 1818889--1818919 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1818879 ATAAAATAAT
1818889 ATATATTTTTTAAA
1 ATATATTTTTTAAA
*
1818903 ATATATTTTTAAAA
1 ATATATTTTTTAAA
1818917 ATA
1 ATA
1818920 ATATAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATATTTTTTAAA
Found at i:1819164 original size:20 final size:20
Alignment explanation
Indices: 1819139--1819236 Score: 66
Period size: 18 Copynumber: 5.1 Consensus size: 20
1819129 AATTTTAGAC
1819139 ATATAAATAATTAAAATATA
1 ATATAAATAATTAAAATATA
1819159 ATAT-AA-AA-TAAAA-ATA
1 ATATAAATAATTAAAATATA
*
1819175 ATAAAAAT-ATTATAAA-AT-
1 ATATAAATAATTA-AAATATA
* *
1819193 ATATAAATATATCAAAATTTA
1 ATATAAATA-ATTAAAATATA
* * *
1819214 TATAAAAATATTTTAAATATA
1 -ATATAAATAATTAAAATATA
1819235 AT
1 AT
1819237 TTTAACGTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
16 6 0.10
17 8 0.13
18 11 0.18
19 10 0.17
20 10 0.17
21 7 0.12
22 8 0.13
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATAAATAATTAAAATATA
Found at i:1819169 original size:25 final size:25
Alignment explanation
Indices: 1819141--1819203 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
1819131 TTTTAGACAT
1819141 ATAAATAAT-TAAAATATAATATAAA
1 ATAAATAATATAAAA-ATAATATAAA
*
1819166 ATAAA-AATAATAAAAATATTATAAA
1 ATAAATAAT-ATAAAAATAATATAAA
*
1819191 ATATATAAATATA
1 ATAAAT-AATATA
1819204 TCAAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
24 3 0.09
25 18 0.56
26 8 0.25
27 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (25 bp):
ATAAATAATATAAAAATAATATAAA
Found at i:1819173 original size:27 final size:29
Alignment explanation
Indices: 1819139--1819224 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
1819129 AATTTTAGAC
1819139 ATATAAATAATTAAAATATAATATAAAAT
1 ATATAAATAATTAAAATATAATATAAAAT
*
1819168 A-A-AAATAA-TAAAA-ATATTATAAAAT
1 ATATAAATAATTAAAATATAATATAAAAT
* *
1819193 ATATAAATATATCAAAAT-TTATATAAAA-
1 ATATAAATA-ATTAAAATATAATATAAAAT
1819221 ATAT
1 ATAT
1819225 TTTAAATATA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
25 12 0.25
26 6 0.12
27 11 0.23
28 6 0.12
29 13 0.27
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
ATATAAATAATTAAAATATAATATAAAAT
Found at i:1819175 original size:16 final size:16
Alignment explanation
Indices: 1819150--1819183 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1819140 TATAAATAAT
1819150 TAAAATATAATATAAAA
1 TAAAATATAATA-AAAA
1819167 TAAAA-ATAATAAAAA
1 TAAAATATAATAAAAA
1819182 TA
1 TA
1819184 TTATAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAATATAATAAAAA
Found at i:1819693 original size:28 final size:29
Alignment explanation
Indices: 1819660--1819722 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
1819650 ATTTTTTATT
1819660 TATTATTTTTAAAAATTTATATT-TAATA
1 TATTATTTTTAAAAATTTATATTCTAATA
**
1819688 TATTATTTTTATTAATTTATATTCGTAATA
1 TATTATTTTTAAAAATTTATATTC-TAATA
1819718 TATTA
1 TATTA
1819723 ATTATATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 21 0.68
30 10 0.32
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (29 bp):
TATTATTTTTAAAAATTTATATTCTAATA
Found at i:1824407 original size:3 final size:3
Alignment explanation
Indices: 1824401--1824432 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1824391 CAACAAAAAG
1824401 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1824433 AACAGCAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1825243 original size:2 final size:2
Alignment explanation
Indices: 1825236--1825265 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1825226 AAGTCATCAA
*
1825236 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1825266 GACTGATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1825573 original size:27 final size:26
Alignment explanation
Indices: 1825537--1825588 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
1825527 ACAAGTTCAA
* *
1825537 TTCACGAGTTCGGTTTAAGAGATTTGG
1 TTCACAAGTTCAGTTTAAGAG-TTTGG
*
1825564 TTCACAAGTTCAGTTTATGAGTTTG
1 TTCACAAGTTCAGTTTAAGAGTTTG
1825589 ATTTGGAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.40
Consensus pattern (26 bp):
TTCACAAGTTCAGTTTAAGAGTTTGG
Found at i:1825672 original size:14 final size:14
Alignment explanation
Indices: 1825655--1825688 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1825645 TAAAATATCA
1825655 AATTTAAAAAATTT
1 AATTTAAAAAATTT
* *
1825669 AATTTAAAGAGTTT
1 AATTTAAAAAATTT
1825683 AATTTA
1 AATTTA
1825689 CATATTCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (14 bp):
AATTTAAAAAATTT
Found at i:1826915 original size:3 final size:3
Alignment explanation
Indices: 1826909--1826948 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1826899 TAAAATTAAA
*
1826909 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1826949 GTGCTACGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1831078 original size:2 final size:2
Alignment explanation
Indices: 1831073--1831105 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1831063 TCTCTCTCTC
*
1831073 TA TA TA TA TA TA TT 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
1831106 GATCAAGAAA
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:1835193 original size:21 final size:20
Alignment explanation
Indices: 1835144--1835205 Score: 90
Period size: 19 Copynumber: 3.0 Consensus size: 20
1835134 AATTAATTTT
1835144 AAATTATAAAT-TTATAAAA
1 AAATTATAAATATTATAAAA
1835163 AAATTATAAATATTATAAAA
1 AAATTATAAATATTATAAAA
*
1835183 TAATATATAAATATATATAAAA
1 AAAT-TATAAATAT-TATAAAA
1835205 A
1 A
1835206 TTAGTATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 11 0.29
20 11 0.29
21 9 0.24
22 7 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATTATAAATATTATAAAA
Found at i:1835299 original size:23 final size:24
Alignment explanation
Indices: 1835273--1835322 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
1835263 TTATTTTATT
* *
1835273 TAAATTTAATAAAAA-TAAAATAA
1 TAAATGTAAAAAAAATTAAAATAA
*
1835296 TAAATGTAAAAAAAATTTAAATAA
1 TAAATGTAAAAAAAATTAAAATAA
1835320 TAA
1 TAA
1835323 TTAAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
TAAATGTAAAAAAAATTAAAATAA
Found at i:1835759 original size:17 final size:17
Alignment explanation
Indices: 1835714--1835761 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1835704 AAAAATTAAA
1835714 ATAA-AATATAAATATTT
1 ATAATAATATAAA-ATTT
* *
1835731 -TAATATTTTAAAATTT
1 ATAATAATATAAAATTT
1835747 ATAATAATATAAAAT
1 ATAATAATATAAAAT
1835762 ACTTTAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATAATATAAAATTT
Found at i:1835818 original size:25 final size:23
Alignment explanation
Indices: 1835790--1835847 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
1835780 ATATGATAAA
*
1835790 ATATATGAATATG-ATATATATAT
1 ATATATGAAT-TGAATATAGATAT
1835813 ATATATACGAATTGAATATAGATAT
1 ATATAT--GAATTGAATATAGATAT
1835838 A-A-ATGAATTG
1 ATATATGAATTG
1835848 GACTGAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 6 0.19
23 8 0.26
24 3 0.10
25 14 0.45
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (23 bp):
ATATATGAATTGAATATAGATAT
Found at i:1835831 original size:21 final size:21
Alignment explanation
Indices: 1835807--1835847 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1835797 AATATGATAT
* *
1835807 ATATATATATATACGAATTGA
1 ATATAGATATAAACGAATTGA
*
1835828 ATATAGATATAAATGAATTG
1 ATATAGATATAAACGAATTG
1835848 GACTGAATGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATAGATATAAACGAATTGA
Found at i:1838217 original size:18 final size:17
Alignment explanation
Indices: 1838183--1838215 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1838173 ATAAAAATAT
1838183 AATTTTTTAAATATTTA
1 AATTTTTTAAATATTTA
1838200 AATTTCTTTAAA-ATTT
1 AATTT-TTTAAATATTT
1838216 TATGAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTTTTTAAATATTTA
Found at i:1839317 original size:2 final size:2
Alignment explanation
Indices: 1839312--1839348 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1839302 AAAAACTCTT
1839312 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1839349 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1839353 original size:2 final size:2
Alignment explanation
Indices: 1839348--1839384 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1839338 TATATATATA
*
1839348 TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1839385 TATGATCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1840627 original size:2 final size:2
Alignment explanation
Indices: 1840622--1840651 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1840612 AAACTTTTTA
1840622 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
1840652 GTCCATTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1841753 original size:3 final size:3
Alignment explanation
Indices: 1841745--1841773 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1841735 CTAATAGTCA
1841745 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1841774 AAGATATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1842973 original size:3 final size:3
Alignment explanation
Indices: 1842960--1843005 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
1842950 AAAGTAGCCT
*
1842960 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1843006 ATGATTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1843208 original size:19 final size:21
Alignment explanation
Indices: 1843181--1843222 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1843171 TTATTTATAA
1843181 TAATAAATT-AAAATTATATT
1 TAATAAATTAAAAATTATATT
*
1843201 TAAT-AATTAAAAATTTTATT
1 TAATAAATTAAAAATTATATT
1843221 TA
1 TA
1843223 TCATTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATAAATTAAAAATTATATT
Found at i:1856396 original size:8 final size:8
Alignment explanation
Indices: 1856375--1856403 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1856365 AATATATTAA
1856375 AAAATAAT
1 AAAATAAT
1856383 -AAATAAT
1 AAAATAAT
1856390 AAAATAAT
1 AAAATAAT
1856398 AAAATA
1 AAAATA
1856404 TTAACATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATAAT
Found at i:1856715 original size:15 final size:15
Alignment explanation
Indices: 1856697--1856747 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
1856687 AATTATTAAA
1856697 AAATTTATATAATAT
1 AAATTTATATAATAT
*
1856712 AAATTATTAATATATTA-
1 AAA-T-TT-ATATAATAT
1856729 AAATTTATATGAATAT
1 AAATTTATAT-AATAT
1856745 AAA
1 AAA
1856748 ATAATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 8 0.28
16 5 0.17
17 5 0.17
18 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
AAATTTATATAATAT
Found at i:1856747 original size:17 final size:16
Alignment explanation
Indices: 1856696--1856749 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
1856686 TAATTATTAA
1856696 AAAATTTATATAATAT
1 AAAATTTATATAATAT
*
1856712 AAATTATTA-AT-ATATT
1 AAAAT-TTATATAATA-T
1856728 AAAATTTATATGAATAT
1 AAAATTTATAT-AATAT
1856745 AAAAT
1 AAAAT
1856750 AATTTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 6 0.19
16 13 0.42
17 9 0.29
18 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AAAATTTATATAATAT
Found at i:1856767 original size:22 final size:22
Alignment explanation
Indices: 1856754--1856805 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 22
1856744 TAAAATAATT
1856754 TAAATATAATTATAATAAAATA
1 TAAATATAATTATAATAAAATA
*
1856776 TAAATATAAATATGATATAAATATA
1 TAAATATAATTAT-A-ATAAA-ATA
1856801 TAAAT
1 TAAAT
1856806 TATCGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 12 0.46
23 1 0.04
24 5 0.19
25 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TAAATATAATTATAATAAAATA
Found at i:1856780 original size:6 final size:6
Alignment explanation
Indices: 1856735--1856800 Score: 61
Period size: 6 Copynumber: 11.8 Consensus size: 6
1856725 ATTAAAATTT
* * *
1856735 ATATGA ATATAA A-AT-A ATTTAA ATATAA TTAT-A ATA-AA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
*
1856779 ATATAA ATAT-G ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATA
1856801 TAAATTATCG
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
4 2 0.04
5 14 0.29
6 32 0.67
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:1856793 original size:11 final size:11
Alignment explanation
Indices: 1856756--1856800 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1856746 AAATAATTTA
*
1856756 AATATAATTAT
1 AATATAAATAT
1856767 AATA-AAATAT
1 AATATAAATAT
1856777 AAATATAAATAT
1 -AATATAAATAT
*
1856789 GATATAAATAT
1 AATATAAATAT
1856800 A
1 A
1856801 TAAATTATCG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 5 0.17
11 18 0.62
12 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
AATATAAATAT
Found at i:1857757 original size:4 final size:4
Alignment explanation
Indices: 1857750--1857803 Score: 51
Period size: 4 Copynumber: 14.2 Consensus size: 4
1857740 TCGGCAGGAG
* * *
1857750 AGAA AGAA AGAA AGAA AG-A ACAA A-AA AGAA AAAA AGAA AG-G AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
*
1857795 AAAA AGAA A
1 AGAA AGAA A
1857804 AATATTTGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
3 7 0.17
4 33 0.82
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1857780 original size:22 final size:23
Alignment explanation
Indices: 1857752--1857805 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
1857742 GGCAGGAGAG
*
1857752 AAAGAAAGAAAGAAA-GA-ACAAA
1 AAAGAAAAAAAGAAAGGAGA-AAA
1857774 AAAGAAAAAAAGAAAGGAGAAAA
1 AAAGAAAAAAAGAAAGGAGAAAA
1857797 AAAGAAAAA
1 AAAGAAAAA
1857806 TATTTGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 14 0.48
23 14 0.48
24 1 0.03
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (23 bp):
AAAGAAAAAAAGAAAGGAGAAAA
Found at i:1858652 original size:58 final size:59
Alignment explanation
Indices: 1858543--1858655 Score: 149
Period size: 58 Copynumber: 1.9 Consensus size: 59
1858533 TGTCATATTC
* *
1858543 GTATCATATCTCCATTCATGACATATTTTACATAATTTTTCTTAATAATTTAATTTAAT
1 GTATCATATCTCAATTCATGACATATTTTACATAATTTTTCGTAATAATTTAATTTAAT
* * * *
1858602 GTATCATATCTCAATTCGTGATAT-TTTTTCATAATTTATT-GTAATGATTTAATT
1 GTATCATATCTCAATTCATGACATATTTTACATAATTT-TTCGTAATAATTTAATT
1858656 AAAAAAATTG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 24 0.51
59 23 0.49
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (59 bp):
GTATCATATCTCAATTCATGACATATTTTACATAATTTTTCGTAATAATTTAATTTAAT
Found at i:1858801 original size:11 final size:11
Alignment explanation
Indices: 1858785--1858830 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
1858775 TTGTCAAGAG
1858785 AAAAAGAAAAA
1 AAAAAGAAAAA
* *
1858796 AAAAAGATAGA
1 AAAAAGAAAAA
* *
1858807 AAAAAGGAGAA
1 AAAAAGAAAAA
1858818 AAAAAGAAAAA
1 AAAAAGAAAAA
1858829 AA
1 AA
1858831 TTATGTATTC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:1858817 original size:10 final size:8
Alignment explanation
Indices: 1858780--1858830 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
1858770 TATTTTTGTC
*
1858780 AAGAGAAA
1 AAGAAAAA
1858788 AAGAAAAA
1 AAGAAAAA
*
1858796 AA-AAAGA
1 AAGAAAAA
*
1858803 TAGAAAAA
1 AAGAAAAA
1858811 AGGAGAAAAA
1 A--AGAAAAA
1858821 AAGAAAAA
1 AAGAAAAA
1858829 AA
1 AA
1858831 TTATGTATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 5 0.14
8 22 0.63
10 8 0.23
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (8 bp):
AAGAAAAA
Found at i:1859879 original size:16 final size:17
Alignment explanation
Indices: 1859852--1859892 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1859842 ATTTTTAAAT
1859852 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
1859867 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
1859884 AAATTTTAT
1 AAATTTTAT
1859893 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:1860075 original size:30 final size:29
Alignment explanation
Indices: 1860027--1860083 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
1860017 CTTCAAAAAT
* *
1860027 TATTTAATTATTATTATTTTTTTAAAATTA
1 TATTTAATCATTATTA-TTTATTAAAATTA
1860057 TATTTAATACATTA-TATTTATTAAAAT
1 TATTTAAT-CATTATTATTTATTAAAAT
1860084 AAAAAGTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.42
30 10 0.42
31 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
TATTTAATCATTATTATTTATTAAAATTA
Found at i:1860711 original size:26 final size:27
Alignment explanation
Indices: 1860656--1860711 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1860646 AAAATCTTTT
*
1860656 ATTTTATAATAATTAAAATAATTATCA
1 ATTTTATAATAATTAAAATAATTATAA
1860683 ATTTTA-AATAAATT-AAATAAATT-TAA
1 ATTTTATAAT-AATTAAAAT-AATTATAA
1860709 ATT
1 ATT
1860712 AAAATATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
ATTTTATAATAATTAAAATAATTATAA
Found at i:1861091 original size:22 final size:23
Alignment explanation
Indices: 1861066--1861109 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
1861056 TAAATATAAT
*
1861066 AAAAATATAAAAATTT-ATTTTA
1 AAAAACATAAAAATTTAATTTTA
* *
1861088 AAAAGCATAATAATTTAATTTT
1 AAAAACATAAAAATTTAATTTT
1861110 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
AAAAACATAAAAATTTAATTTTA
Found at i:1862080 original size:12 final size:12
Alignment explanation
Indices: 1862065--1862103 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1862055 GATATAAAAT
1862065 AAATATAATTTA
1 AAATATAATTTA
1862077 AAATATAA-TTA
1 AAATATAATTTA
*
1862088 AAATATAATATA
1 AAATATAATTTA
1862100 AAAT
1 AAAT
1862104 TTGATATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATATAATTTA
Found at i:1865104 original size:32 final size:31
Alignment explanation
Indices: 1865068--1865127 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
1865058 TTTATTCTAA
*
1865068 TCATAT-TTAAGATATTTTATATTTATAAACTT
1 TCATATATTAAGA-ATTTTAT-TATATAAACTT
*
1865100 TCATATATTAATAATTTTATTATATAAA
1 TCATATATTAAGAATTTTATTATATAAA
1865128 TTTTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 7 0.28
32 13 0.52
33 5 0.20
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (31 bp):
TCATATATTAAGAATTTTATTATATAAACTT
Found at i:1869516 original size:15 final size:15
Alignment explanation
Indices: 1869492--1869541 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1869482 AGAAAATATA
* * *
1869492 AAATTATTAAAGATT
1 AAATTTTTAAAAAAT
1869507 AAATTTTTAAAAAAT
1 AAATTTTTAAAAAAT
*
1869522 ATATTTTTAAAAAAT
1 AAATTTTTAAAAAAT
1869537 AAATT
1 AAATT
1869542 AAAAAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
AAATTTTTAAAAAAT
Found at i:1870435 original size:15 final size:14
Alignment explanation
Indices: 1870395--1870436 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1870385 AATTCGTATA
1870395 TTTATATTATATTT
1 TTTATATTATATTT
**
1870409 GATATATT-TATTT
1 TTTATATTATATTT
1870422 TTTATAATTATATTT
1 TTTAT-ATTATATTT
1870437 AAGATATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 8 0.36
14 9 0.41
15 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTATATTATATTT
Found at i:1870435 original size:28 final size:29
Alignment explanation
Indices: 1870395--1870452 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
1870385 AATTCGTATA
1870395 TTTATATTATATTT-GATATATT-TATTT
1 TTTATATTATATTTAGATATATTATATTT
1870422 TTTATAATTATATTTAAGATATATTATATTT
1 TTTAT-ATTATATTT-AGATATATTATATTT
1870453 ATAAATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 5 0.19
28 9 0.33
30 8 0.30
31 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (29 bp):
TTTATATTATATTTAGATATATTATATTT
Found at i:1870453 original size:28 final size:27
Alignment explanation
Indices: 1870391--1870456 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
1870381 TAATAATTCG
1870391 TATATTTAT-ATTATATTTGATATATT
1 TATATTTATAATTATATTTGATATATT
*
1870417 TATTTTTTATAATTATATTTAAGATATA-T
1 TA-TATTTATAATTATATTT--GATATATT
1870446 TATATTTATAA
1 TATATTTATAA
1870457 ATTTTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 2 0.06
27 6 0.18
28 17 0.50
29 3 0.09
30 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (27 bp):
TATATTTATAATTATATTTGATATATT
Found at i:1873409 original size:2 final size:2
Alignment explanation
Indices: 1873404--1873447 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1873394 AATTTGTGTG
1873404 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
1873446 TA
1 TA
1873448 GTAAAAAAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1874110 original size:13 final size:14
Alignment explanation
Indices: 1874092--1874121 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1874082 ATTTTCAAAT
1874092 AAAAATT-AAATTA
1 AAAAATTAAAATTA
1874105 AAAAATTAAAATTA
1 AAAAATTAAAATTA
1874119 AAA
1 AAA
1874122 CTCAAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAATTAAAATTA
Found at i:1874351 original size:18 final size:18
Alignment explanation
Indices: 1874324--1874364 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1874314 TAAAGCTTGG
1874324 AAAA-TAAGCT-GAATTAA
1 AAAATTAAGCTCG-ATTAA
*
1874341 AAAATTAAGCTCGTTTAA
1 AAAATTAAGCTCGATTAA
1874359 AAAATT
1 AAAATT
1874365 GGTCGAGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 16 0.76
19 1 0.05
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (18 bp):
AAAATTAAGCTCGATTAA
Found at i:1875224 original size:19 final size:19
Alignment explanation
Indices: 1875200--1875237 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1875190 AATTTGATTT
1875200 AAATTATTATTTATATAAA
1 AAATTATTATTTATATAAA
* *
1875219 AAATTATTTTTTATTTAAA
1 AAATTATTATTTATATAAA
1875238 TATAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATTATTATTTATATAAA
Found at i:1875878 original size:20 final size:19
Alignment explanation
Indices: 1875840--1875887 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1875830 TTATTTATTT
1875840 AAATTTAATTAAAATATAA
1 AAATTTAATTAAAATATAA
1875859 AAATATTAATATAAAA-ATAA
1 AAAT-TTAAT-TAAAATATAA
*
1875879 AATTTTAAT
1 AAATTTAAT
1875888 CTAATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 9 0.35
20 12 0.46
21 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTAATTAAAATATAA
Found at i:1877338 original size:3 final size:3
Alignment explanation
Indices: 1877330--1877354 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1877320 AAAACATTTA
1877330 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1877355 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1883194 original size:30 final size:30
Alignment explanation
Indices: 1883158--1883216 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
1883148 TTGGAGCTGA
*
1883158 AGCTGGAGCTGAGAGCTGTAACAGAATTGG
1 AGCTGGAGCTGAGAGCTGTAACAAAATTGG
*
1883188 AGCTGGAGCTGGGAGCTGTAACAAAATTG
1 AGCTGGAGCTGAGAGCTGTAACAAAATTG
1883217 AAACCAGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.14, G:0.36, T:0.20
Consensus pattern (30 bp):
AGCTGGAGCTGAGAGCTGTAACAAAATTGG
Found at i:1888401 original size:30 final size:30
Alignment explanation
Indices: 1888366--1888427 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
1888356 CATTTGGAGC
* *
1888366 TGGAGCTGGAGCTGGGAGCTGTAACAGAAT
1 TGGAGCTGAAGCTGGGAACTGTAACAGAAT
1888396 TGGAGCTGAAGCTGGGAACTGTAACAGAAT
1 TGGAGCTGAAGCTGGGAACTGTAACAGAAT
1888426 TG
1 TG
1888428 AAGCCAGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.13, G:0.37, T:0.21
Consensus pattern (30 bp):
TGGAGCTGAAGCTGGGAACTGTAACAGAAT
Found at i:1890667 original size:18 final size:18
Alignment explanation
Indices: 1890586--1890674 Score: 67
Period size: 18 Copynumber: 4.9 Consensus size: 18
1890576 CATTAACCAT
1890586 AGGTGCTTCATTAACTGTG-
1 AGGTGCTTCATT-ACT-TGA
* * *
1890605 -GGTGCTTTAATACTTGC
1 AGGTGCTTCATTACTTGA
* * *
1890622 GGGTACTTCTTTACTTGA
1 AGGTGCTTCATTACTTGA
1890640 AGGTGCTTCATTACTTGA
1 AGGTGCTTCATTACTTGA
*
1890658 AGG-GATTTCATTACTTG
1 AGGTG-CTTCATTACTTG
1890675 TAGGACGAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
16 2 0.04
17 4 0.07
18 50 0.89
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (18 bp):
AGGTGCTTCATTACTTGA
Found at i:1891274 original size:2 final size:2
Alignment explanation
Indices: 1891267--1891292 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1891257 ACAGTTTTCT
1891267 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
1891293 AATTCCACCA
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):
TA
Found at i:1892381 original size:21 final size:21
Alignment explanation
Indices: 1892357--1892402 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1892347 ACTGTTCTCG
1892357 TTCTTACTCTT-CTTATTCTTC
1 TTCTTACTCTTCCTT-TTCTTC
**
1892378 TTCTTTTTCTTCCTTTTCTTC
1 TTCTTACTCTTCCTTTTCTTC
1892399 TTCT
1 TTCT
1892403 CCGAAGTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.67
Consensus pattern (21 bp):
TTCTTACTCTTCCTTTTCTTC
Found at i:1892477 original size:29 final size:30
Alignment explanation
Indices: 1892443--1892520 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
1892433 CCTCCTCTCT
*
1892443 CTTCCTCT-TCTTTTTCTTCTTCT-TTTCAA
1 CTTCCTCTCTC-TTTTCTTCTTCTACTTCAA
*
1892472 CTTCCTCACTCTTTTCTTCTTCTACTTCAA
1 CTTCCTCTCTCTTTTCTTCTTCTACTTCAA
*
1892502 CATCCTCTCTCTTTTCTTC
1 CTTCCTCTCTCTTTTCTTC
1892521 AGTTTCCTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 19 0.44
30 24 0.56
ACGTcount: A:0.09, C:0.36, G:0.00, T:0.55
Consensus pattern (30 bp):
CTTCCTCTCTCTTTTCTTCTTCTACTTCAA
Found at i:1895203 original size:2 final size:2
Alignment explanation
Indices: 1895196--1895227 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1895186 TGATAACCAA
1895196 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
1895228 TAAAAGAGGT
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:1896573 original size:2 final size:2
Alignment explanation
Indices: 1896566--1896612 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
1896556 AGATTAGGTG
1896566 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA -A 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
1896606 TA -A TA TA
1 TA TA TA TA
1896613 AAAGAAAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1902096 original size:28 final size:27
Alignment explanation
Indices: 1902033--1902093 Score: 92
Period size: 24 Copynumber: 2.4 Consensus size: 27
1902023 ATTTTATTAT
1902033 TTTTAAAATAATTTATATTTAAATAAA
1 TTTTAAAATAATTTATATTTAAATAAA
*
1902060 TTTT--AATAATTTATA-TTATATAAA
1 TTTTAAAATAATTTATATTTAAATAAA
1902084 TTTTAAAATA
1 TTTTAAAATA
1902094 TAAATATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 12 0.39
25 11 0.35
26 4 0.13
27 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TTTTAAAATAATTTATATTTAAATAAA
Found at i:1902106 original size:28 final size:27
Alignment explanation
Indices: 1902019--1902108 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 27
1902009 TATCGAATTT
* *
1902019 ATATATTT-TATTATTTTTAAAATA-A
1 ATATATTTATATAAATTTTAAAATATA
* *
1902044 TTTATATTTAAATAAATTTTAATAAT-T-
1 -ATATATTTATATAAATTTTAA-AATATA
1902071 -TATA-TTATATAAATTTTAAAATATAA
1 ATATATTTATATAAATTTTAAAATAT-A
1902097 ATATATTTATAT
1 ATATATTTATAT
1902109 CATATTATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
23 3 0.06
24 15 0.29
25 4 0.08
26 7 0.14
27 13 0.25
28 9 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATATATTTATATAAATTTTAAAATATA
Found at i:1902132 original size:24 final size:23
Alignment explanation
Indices: 1902097--1902147 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
1902087 TAAAATATAA
* *
1902097 ATATATTTATATCATATTATATC
1 ATATATTAATATCATATAATATC
**
1902120 ATATATTAAATATTTTATAATATC
1 ATATATT-AATATCATATAATATC
1902144 ATAT
1 ATAT
1902148 TCATTTAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATATTAATATCATATAATATC
Found at i:1902307 original size:21 final size:21
Alignment explanation
Indices: 1902265--1902307 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1902255 GATTATGAAT
*
1902265 ATTTTTTTAATTATTGTTAAA
1 ATTTTTTTAATTATTGTAAAA
*
1902286 ATTTTTTTATTTTATT-TAAAA
1 ATTTTTTTA-ATTATTGTAAAA
1902307 A
1 A
1902308 ATTAATGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTTTTTTAATTATTGTAAAA
Found at i:1902596 original size:34 final size:32
Alignment explanation
Indices: 1902537--1902651 Score: 116
Period size: 34 Copynumber: 3.6 Consensus size: 32
1902527 ATGAATACAA
*
1902537 TAATTTTAAATATA-ATA-TAA-TAAATATAT
1 TAATTTAAAATATATATATTAATTAAATATAT
1902566 TAATTTAAAATATATATATTAATTTAAA-ATAT
1 TAATTTAAAATATATATATTAA-TTAAATATAT
* *
1902598 T-ATTTAATATTATAATTATATTAATTAATTATAT
1 TAATTTAA-AATAT-A-TATATTAATTAAATATAT
1902632 TAA-TTAAAATATTATATATT
1 TAATTTAAAATA-TATATATT
1902652 TACTTCAAAG
Statistics
Matches: 72, Mismatches: 4, Indels: 17
0.77 0.04 0.18
Matches are distributed among these distances:
29 13 0.18
30 3 0.04
31 9 0.12
32 15 0.21
33 13 0.18
34 18 0.25
35 1 0.01
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
TAATTTAAAATATATATATTAATTAAATATAT
Done.