Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 6 of 175
Found at i:1755999 original size:78 final size:77
Alignment explanation
Indices: 1755917--1756059 Score: 225
Period size: 78 Copynumber: 1.8 Consensus size: 77
1755907 ACCAGTTTCC
* * **
1755917 AATTTT-AATATGTTAAAAAAATGTTGAGTATAACTGATTTTAAATTTTTAATATACTTAATATA
1 AATTTTGAATATATTAAAAAAAT-TTAAGTATAACCAATTTTAAATTTTTAATATA-TTAATATA
1755981 TTAAAATATATTAA
64 TTAAAATATATTAA
1755995 AATTTTGAATATATTAAAAAAATTTAAGTATAACCAATTTTAAATTTTTAATATATTAATATATT
1 AATTTTGAATATATTAAAAAAATTTAAGTATAACCAATTTTAAATTTTTAATATATTAATATATT
1756060 TTTTAATAGG
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
77 10 0.17
78 35 0.58
79 15 0.25
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (77 bp):
AATTTTGAATATATTAAAAAAATTTAAGTATAACCAATTTTAAATTTTTAATATATTAATATATT
AAAATATATTAA
Found at i:1766233 original size:28 final size:29
Alignment explanation
Indices: 1766193--1766255 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
1766183 AAAAACATAG
* *
1766193 AAAAATTACGTTAAAAGAAA-AT-AAAGAA
1 AAAAATAAAGTTAAAA-AAATATAAAAGAA
1766221 AAAAATAAAGTTAAAAAAATATAAAAGAA
1 AAAAATAAAGTTAAAAAAATATAAAAGAA
1766250 AAAAAT
1 AAAAAT
1766256 TAAATTACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 3 0.10
28 16 0.52
29 12 0.39
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (29 bp):
AAAAATAAAGTTAAAAAAATATAAAAGAA
Found at i:1768371 original size:16 final size:16
Alignment explanation
Indices: 1768350--1768401 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
1768340 TTTGGTTCGC
*
1768350 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
1768366 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1768382 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1768398 TGTA
1 TGTA
1768402 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:1768466 original size:44 final size:45
Alignment explanation
Indices: 1768382--1768472 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1768372 GGATTAGAGG
* * *
1768382 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
1768427 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
1768471 TG
1 TG
1768473 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:1768654 original size:16 final size:16
Alignment explanation
Indices: 1768617--1768671 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
1768607 TTAATCATAT
*
1768617 TTAAACATA-ATTATAA
1 TTAAA-ATATATTTTAA
1768633 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
1768648 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
1768666 -TAAAAT
1 TTAAAAT
1768672 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:1768664 original size:18 final size:18
Alignment explanation
Indices: 1768623--1768671 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
1768613 ATATTTAAAC
1768623 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
1768641 AT--TTTAATTAAAATAT
1 ATAATTTAATTAAAATAT
1768657 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
1768672 TCTTAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 6 0.21
18 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:1768730 original size:61 final size:61
Alignment explanation
Indices: 1768665--1768849 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
1768655 ATATAATTTA
1768665 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATTATAATATATGATACT
1 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATTATAATATATGATACT
* * * * * * *
1768726 ATAAAA-TATAAATTAA-C-ATAATTATTAAAT--ATATTA-T--AATTAAAATATATAAT-TT
1 ATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAAT-TTACTCAAATTATAATATATGATACT
*
1768781 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATTATAATATATGATACT
1768843 ATAAAAT
1 ATAAAAT
1768850 ATAAATTAAC
Statistics
Matches: 96, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
55 1 0.01
56 23 0.24
57 13 0.14
58 8 0.08
59 8 0.08
60 13 0.14
61 29 0.30
62 1 0.01
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (61 bp):
ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATTATAATATATGATACT
Found at i:1768766 original size:117 final size:119
Alignment explanation
Indices: 1768669--1768918 Score: 468
Period size: 117 Copynumber: 2.1 Consensus size: 119
1768659 AATTTAATAA
*
1768669 AATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATTATAATATATGATACTATAAAATA
1 AATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATA
1768734 TAAATTAACAT-A-ATTATTAAATATATTATAATTAAAATATATAATTTAATAA
66 TAAATTAACATAATATTATTAAATATATTATAATTAAAATATATAATTTAATAA
1768786 AATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATA
1 AATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATA
1768851 TAAATTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAA
66 TAAATTAACATAA-TATTATTAAATATATTATAATTAAAATATATAATTTAATAA
1768906 AATTCTTAATAAT
1 AATTCTTAATAAT
1768919 TAGCAGAAAT
Statistics
Matches: 129, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
117 75 0.58
118 1 0.01
120 53 0.41
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (119 bp):
AATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATA
TAAATTAACATAATATTATTAAATATATTATAATTAAAATATATAATTTAATAA
Found at i:1768902 original size:14 final size:15
Alignment explanation
Indices: 1768853--1768904 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1768843 ATAAAATATA
1768853 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
1768868 TATTAAATATATTAT
1 AATTAAATATATTAT
1768883 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
1768896 AATTTAATA
1 AATTAAATA
1768905 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:1769048 original size:16 final size:16
Alignment explanation
Indices: 1769011--1769052 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1769001 TTAATCATAT
*
1769011 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
1769027 TT-AAATATATTATAA
1 TTAAAATATATTATAA
1769042 TTAAAATATAT
1 TTAAAATATAT
1769053 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:1769059 original size:14 final size:15
Alignment explanation
Indices: 1769020--1769061 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1769010 TTTAAACATA
*
1769020 ATTATTATTAAATAT
1 ATTATAATTAAATAT
1769035 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
1769049 A-TATAATTTAATA
1 ATTATAATTAAATA
1769062 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:1769507 original size:13 final size:13
Alignment explanation
Indices: 1769489--1769513 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1769479 GCCTTAACAA
1769489 GAGCAGCACTCAT
1 GAGCAGCACTCAT
1769502 GAGCAGCACTCA
1 GAGCAGCACTCA
1769514 AAACAGATTT
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:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (13 bp):
GAGCAGCACTCAT
Found at i:1772699 original size:13 final size:13
Alignment explanation
Indices: 1772681--1772712 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1772671 TATCATTCAT
1772681 AATATAAATATAA
1 AATATAAATATAA
1772694 AATATAAATATAA
1 AATATAAATATAA
*
1772707 GATATA
1 AATATA
1772713 GTTTTTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
AATATAAATATAA
Found at i:1773231 original size:3 final size:3
Alignment explanation
Indices: 1773223--1773264 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1773213 CCTGTATAAT
1773223 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1773265 GTTCGTCTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:1778309 original size:21 final size:21
Alignment explanation
Indices: 1778283--1778324 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1778273 TATTTTTTAC
1778283 ATTATAAA-AAATTTAAAAATA
1 ATTATAAATAAA-TTAAAAATA
1778304 ATTATAAATTAAATTAAAAAT
1 ATTATAAA-TAAATTAAAAAT
1778325 TTAGTTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 8 0.42
23 3 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTATAAATAAATTAAAAATA
Found at i:1780074 original size:2 final size:2
Alignment explanation
Indices: 1780063--1780093 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1780053 GTTTTCTTCA
1780063 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1780094 TATAATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:1780513 original size:3 final size:3
Alignment explanation
Indices: 1780507--1780545 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
1780497 GCTAGTGCCG
* *
1780507 CCA CCA CCA CCA CCA CCA CCA CCC CCA CCA CCA CAA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
1780546 GTTATAATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:1784943 original size:7 final size:7
Alignment explanation
Indices: 1784931--1784960 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1784921 TCTAAATTTT
1784931 TTTAAAA
1 TTTAAAA
1784938 TTTAAAA
1 TTTAAAA
1784945 TTTAAAA
1 TTTAAAA
1784952 TTTAAAA
1 TTTAAAA
1784959 TT
1 TT
1784961 ATAATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TTTAAAA
Found at i:1787339 original size:15 final size:16
Alignment explanation
Indices: 1787319--1787357 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1787309 AACTAGCTTG
1787319 AATTAATATT-TAAAA
1 AATTAATATTATAAAA
1787334 AATTAAT-TTATAAAA
1 AATTAATATTATAAAA
*
1787349 TATTAATAT
1 AATTAATAT
1787358 ATTATGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.86
16 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTAATATTATAAAA
Found at i:1787418 original size:3 final size:3
Alignment explanation
Indices: 1787410--1787439 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1787400 TTTTTAAAAT
1787410 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1787440 GATTTATGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1792081 original size:15 final size:14
Alignment explanation
Indices: 1792052--1792090 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
1792042 AAAAGTTGTG
1792052 CTAAACCCTAAATC
1 CTAAACCCTAAATC
*
1792066 CTAAACTCTAAAATC
1 CTAAACCCT-AAATC
1792081 CTAAACCCTA
1 CTAAACCCTA
1792091 TATCTTTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (14 bp):
CTAAACCCTAAATC
Found at i:1798194 original size:17 final size:17
Alignment explanation
Indices: 1798171--1798216 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1798161 AAGGATAAGG
*
1798171 AAAGAAATAAAGAAAGA
1 AAAGAAAGAAAGAAAGA
* *
1798188 GAAGAAAGAAAGAGAGA
1 AAAGAAAGAAAGAAAGA
1798205 AAAGAACAGAAA
1 AAAGAA-AGAAA
1798217 AAGAGAGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.72, C:0.02, G:0.24, T:0.02
Consensus pattern (17 bp):
AAAGAAAGAAAGAAAGA
Found at i:1798210 original size:13 final size:13
Alignment explanation
Indices: 1798170--1798206 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1798160 CAAGGATAAG
*
1798170 GAAAGA-AATAAA
1 GAAAGAGAAGAAA
1798182 GAAAGAGAAGAAA
1 GAAAGAGAAGAAA
1798195 GAAAGAG-AGAAA
1 GAAAGAGAAGAAA
1798207 AGAACAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (13 bp):
GAAAGAGAAGAAA
Found at i:1798221 original size:18 final size:17
Alignment explanation
Indices: 1798171--1798222 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
1798161 AAGGATAAGG
*
1798171 AAAGAAATAAAGAA-AGA
1 AAAGAAAGAAA-AAGAGA
* *
1798188 GAAGAAAGAAAGAGAGA
1 AAAGAAAGAAAAAGAGA
1798205 AAAGAACAGAAAAAGAGA
1 AAAGAA-AGAAAAAGAGA
1798223 GTAAAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 1 0.04
17 17 0.61
18 10 0.36
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (17 bp):
AAAGAAAGAAAAAGAGA
Found at i:1800378 original size:28 final size:29
Alignment explanation
Indices: 1800341--1800443 Score: 153
Period size: 26 Copynumber: 3.7 Consensus size: 29
1800331 AATAATAAAA
1800341 ATTTACCAAAATAT-TACAACTTTTTTTT
1 ATTTACCAAAATATATACAACTTTTTTTT
*
1800369 ATTTATCAAAATAT-TACAACTATTTTTTT
1 ATTTACCAAAATATATACAACT-TTTTTTT
1800398 ATTTACCAAAATATATA-AAC--TTTTTT
1 ATTTACCAAAATATATACAACTTTTTTTT
1800424 ATTTACCAAAATATATACAA
1 ATTTACCAAAATATATACAA
1800444 AAAAAACAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 7
0.89 0.03 0.09
Matches are distributed among these distances:
26 23 0.33
27 2 0.03
28 20 0.29
29 23 0.33
30 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTTACCAAAATATATACAACTTTTTTTT
Found at i:1800553 original size:27 final size:27
Alignment explanation
Indices: 1800514--1800589 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 27
1800504 TACTGGTCAC
**
1800514 GCCAATGGTATTGGCGGCACCAAAGGT
1 GCCAATGCCATTGGCGGCACCAAAGGT
*
1800541 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAAAGGT
*
1800568 GCCAATGCCATTGGTGGCACCA
1 GCCAATGCCATTGGCGGCACCA
1800590 CTCGTATTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.24, C:0.28, G:0.30, T:0.18
Consensus pattern (27 bp):
GCCAATGCCATTGGCGGCACCAAAGGT
Found at i:1800751 original size:19 final size:21
Alignment explanation
Indices: 1800713--1800751 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1800703 AATAATTGAT
*
1800713 TATATTATTGTTATTATTTTG
1 TATATTATTGTTAATATTTTG
1800734 TATATT-TTG-TAATATTTT
1 TATATTATTGTTAATATTTT
1800752 TTGTTGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TATATTATTGTTAATATTTTG
Found at i:1801102 original size:12 final size:12
Alignment explanation
Indices: 1801085--1801115 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1801075 ATAATTTTAG
1801085 TGTGTATTATTT
1 TGTGTATTATTT
1801097 TGTGTATTATTT
1 TGTGTATTATTT
*
1801109 TGAGTAT
1 TGTGTAT
1801116 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:1807499 original size:37 final size:38
Alignment explanation
Indices: 1807458--1807573 Score: 146
Period size: 40 Copynumber: 3.0 Consensus size: 38
1807448 CTTCCCTCTT
*
1807458 CTTCTTT-TTTTTTTCTCTTCTCCTTTCCCTTTCTTTC
1 CTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
*
1807495 CTTCTTTCTTTCTTTTTTCTTCT-CTTCTCCTTTTCTTCTTC
1 CTTCTTTCTTT-TTTTCTCTTCTCCTT-TCCTTTTC-T-TTC
* *
1807536 TTTCTTTCCTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1807574 TTTCCTCTCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
37 7 0.10
38 9 0.13
39 18 0.26
40 19 0.28
41 15 0.22
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (38 bp):
CTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
Found at i:1807503 original size:4 final size:4
Alignment explanation
Indices: 1807486--1807595 Score: 68
Period size: 4 Copynumber: 26.2 Consensus size: 4
1807476 TCTCCTTTCC
*
1807486 CTTT CTTT CCTT CTTT CTTT CTTT -TTT CTTCT CTTCT CCTTT -TCTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT-T CTT-T -CTTT CT-TT
*
1807532 C-TT CTTT CTTT CCTTT -TTT CTCTT C-TC CTTT CCTTTT CTTT CTTT
1 CTTT CTTT CTTT -CTTT CTTT CT-TT CTTT CTTT -C-TTT CTTT CTTT
*
1807577 CCTCTC CTTT CTTT CTTT C
1 -CT-TT CTTT CTTT CTTT C
1807596 CCTCCTTCTG
Statistics
Matches: 86, Mismatches: 6, Indels: 28
0.72 0.05 0.23
Matches are distributed among these distances:
3 12 0.14
4 47 0.55
5 20 0.23
6 7 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:1807533 original size:34 final size:35
Alignment explanation
Indices: 1807490--1807577 Score: 112
Period size: 34 Copynumber: 2.6 Consensus size: 35
1807480 CTTTCCCTTT
*
1807490 CTTTCCTTCTTTCTTTCTTT-TTTCTTCTCTTCTC
1 CTTTTCTTCTTTCTTTCTTTCTTTCTTCTCTTCTC
*
1807524 CTTTTCTTC-TTCTTTCTTTCCTTTTTTCTCTTCTC
1 CTTTTCTTCTTTCTTTCTTT-CTTTCTTCTCTTCTC
*
1807559 C-TTTCCT-TTTCTTTCTTTC
1 CTTTTCTTCTTTCTTTCTTTC
1807578 CTCTCCTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
33 11 0.23
34 23 0.48
35 14 0.29
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (35 bp):
CTTTTCTTCTTTCTTTCTTTCTTTCTTCTCTTCTC
Found at i:1807543 original size:49 final size:45
Alignment explanation
Indices: 1807457--1807594 Score: 132
Period size: 44 Copynumber: 3.2 Consensus size: 45
1807447 TCTTCCCTCT
*
1807457 TCTTCTTTTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTC
1 TCTTC-TTTTTTCTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTC
* *
1807503 T-TTCTTTTTTCTTCTCTTCTCCTTT-TC-TTC-TTCTTTCTTTC
1 TCTTCTTTTTTCTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTC
* *
1807544 -CTT-TTTTCTCTTCTCCTT-TCCTTT-TCTTTCTTTCCTCTCCTTTC
1 TCTTCTTTTTTCTTCT-CTTCTCCTTTCCCTTTCTTTCCT-T-CTTTC
1807588 T-TTCTTT
1 TCTTCTTT
1807595 CCCTCCTTCT
Statistics
Matches: 79, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
40 18 0.23
41 18 0.23
42 7 0.09
43 2 0.03
44 27 0.34
45 6 0.08
46 1 0.01
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (45 bp):
TCTTCTTTTTTCTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTC
Found at i:1807553 original size:30 final size:32
Alignment explanation
Indices: 1807489--1807579 Score: 87
Period size: 35 Copynumber: 2.7 Consensus size: 32
1807479 CCTTTCCCTT
*
1807489 TCTTTCCTTCTTTCTTTCTTT--TTTCTTCTCTTC
1 TCTTTCC-T-TTTCTTTCTTTCCTTTTTTCTC-TC
*
1807522 TCCTTTTCTTCTTCTTTCTTTCCTTTTTTCTCTTC
1 T-CTTTCCTT-TTCTTTCTTTCCTTTTTTCTC-TC
1807557 TCCTTTCCTTTTCTTTCTTTCCT
1 T-CTTTCCTTTTCTTTCTTTCCT
1807580 CTCCTTTCTT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
32 1 0.02
33 12 0.24
34 18 0.35
35 20 0.39
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (32 bp):
TCTTTCCTTTTCTTTCTTTCCTTTTTTCTCTC
Found at i:1807568 original size:19 final size:19
Alignment explanation
Indices: 1807453--1807586 Score: 82
Period size: 19 Copynumber: 6.9 Consensus size: 19
1807443 CCTTTCTTCC
* **
1807453 CTCTTCTTCTTTTTTTTTT
1 CTCTTCTCCTTTCCTTTTT
1807472 CTCTTCTCCTTTCCCTTTCTT
1 CTCTTCTCCTTT-CCTTT-TT
*
1807493 -TCCTTCTTTCTTT-CTTTTT
1 CT-CTTC-TCCTTTCCTTTTT
1807512 -TCTTCT-CTTCTCC-TTTT
1 CTCTTCTCCTT-TCCTTTTT
*
1807529 CTTCTTCTTTCTTTCCTTTTTT
1 C-TCTTC-TCCTTTCC-TTTTT
1807551 CTCTTCTCCTTTCCTTTTCT
1 CTCTTCTCCTTTCCTTTT-T
* *
1807571 TTCTT-TCCTCTCCTTT
1 CTCTTCTCCTTTCCTTT
1807587 CTTTCTTTCC
Statistics
Matches: 95, Mismatches: 7, Indels: 26
0.74 0.05 0.20
Matches are distributed among these distances:
16 3 0.03
17 6 0.06
18 5 0.05
19 33 0.35
20 24 0.25
21 14 0.15
22 10 0.11
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (19 bp):
CTCTTCTCCTTTCCTTTTT
Found at i:1807578 original size:34 final size:36
Alignment explanation
Indices: 1807455--1807579 Score: 134
Period size: 37 Copynumber: 3.5 Consensus size: 36
1807445 TTTCTTCCCT
*
1807455 CTTCTTCTTT-TTT-TTTTCTCTTCTCCTT-TCCCTTTC
1 CTTCTTCTTTCTTTCCTTT-TCTTCT-CTTCT-CCTTTC
* * *
1807491 TTTCCTTCTTTCTTTCTTTTTTCTTCTCTTCTCCTTTT
1 CTT-CTTCTTTCTTTC-CTTTTCTTCTCTTCTCCTTTC
1807529 CTTCTTCTTTCTTTCCTTTT-TTCTCTTCTCCTTTC
1 CTTCTTCTTTCTTTCCTTTTCTTCTCTTCTCCTTTC
1807564 CTT-TTCTTTCTTTCCT
1 CTTCTTCTTTCTTTCCT
1807580 CTCCTTTCTT
Statistics
Matches: 79, Mismatches: 5, Indels: 12
0.82 0.05 0.12
Matches are distributed among these distances:
34 13 0.16
35 17 0.22
36 6 0.08
37 19 0.24
38 13 0.16
39 7 0.09
40 4 0.05
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (36 bp):
CTTCTTCTTTCTTTCCTTTTCTTCTCTTCTCCTTTC
Found at i:1807711 original size:27 final size:27
Alignment explanation
Indices: 1807637--1807703 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
1807627 TAACACCAAC
1807637 TGGTGCCGCCAATGGTATTGGCACCAT
1 TGGTGCCGCCAATGGTATTGGCACCAT
* * *
1807664 TGGTGCCGCCAATGGTTTTGGTACCTT
1 TGGTGCCGCCAATGGTATTGGCACCAT
1807691 TGGTGCCGCCAAT
1 TGGTGCCGCCAAT
1807704 ACCATTGGCG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.15, C:0.25, G:0.30, T:0.30
Consensus pattern (27 bp):
TGGTGCCGCCAATGGTATTGGCACCAT
Found at i:1807805 original size:27 final size:28
Alignment explanation
Indices: 1807767--1807840 Score: 125
Period size: 27 Copynumber: 2.7 Consensus size: 28
1807757 TTTTTGTTTT
1807767 TTTATATATTTTGGTAAAT-AAAAAAAG
1 TTTATATATTTTGGTAAATAAAAAAAAG
1807794 TTTATATATTTTGGTAAATAAAAAAAAG
1 TTTATATATTTTGGTAAATAAAAAAAAG
1807822 -TTATAATATTTTGGTAAAT
1 TTTAT-ATATTTTGGTAAAT
1807841 TTTTATTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
27 23 0.51
28 22 0.49
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (28 bp):
TTTATATATTTTGGTAAATAAAAAAAAG
Found at i:1807830 original size:28 final size:27
Alignment explanation
Indices: 1807768--1807840 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 27
1807758 TTTTGTTTTT
1807768 TTAT-ATATTTTGGTAAATAAAAAAAG
1 TTATAATATTTTGGTAAATAAAAAAAG
1807794 TT-TATATATTTTGGTAAATAAAAAAAAG
1 TTATA-ATATTTTGGTAAAT-AAAAAAAG
1807822 TTATAATATTTTGGTAAAT
1 TTATAATATTTTGGTAAAT
1807841 TTTTATTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
25 1 0.02
26 2 0.05
27 14 0.33
28 24 0.56
29 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (27 bp):
TTATAATATTTTGGTAAATAAAAAAAG
Found at i:1810844 original size:18 final size:16
Alignment explanation
Indices: 1810823--1810861 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1810813 AATAATGGAA
1810823 ATATATAAAAACATGT
1 ATATATAAAAACATGT
**
1810839 ATATATAAAAGTATGT
1 ATATATAAAAACATGT
1810855 ATATATA
1 ATATATA
1810862 TAAATTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:1812973 original size:88 final size:88
Alignment explanation
Indices: 1812883--1813748 Score: 1190
Period size: 88 Copynumber: 9.8 Consensus size: 88
1812873 TCTTCGATCT
* * * *
1812883 GCTCCA-CTACAACCGAG-GAAGGTAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAATGCAAGA
1 GCTCCATC-ACAACCGAGAG-AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAGA
* ** * ** *
1812946 AGGCAAGAGCTGCTATCTTTGACCT
64 AGGCAAGATCTTTTGTCTTCAACCA
* * * * * ** *
1812971 GCTCCA-CTAAAACCGAGAGAGGTAAGGCTTGTATCTTCGACCTGCTTCGTTGTCAATGTAGGAA
1 GCTCCATC-ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAGAA
*
1813035 GACAAGATCTTTTGTCTTCAACCA
65 GGCAAGATCTTTTGTCTTCAACCA
* * * *
1813059 GCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCACTGCAGGAAG
1 GCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAGAAG
1813124 GCAAGATCTTTTGTCTTCAACCA
66 GCAAGATCTTTTGTCTTCAACCA
* *
1813147 GCTCCATCACAATCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTTAATAC-AGAAA
1 GCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAG-AA
*
1813211 GGCAAGATCTTTTGTCTTTAACCA
65 GGCAAGATCTTTTGTCTTCAACCA
1813235 GCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATAC-AGAAA
1 GCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAG-AA
1813299 GGCAAGATCTTTTGTCTTCAACCA
65 GGCAAGATCTTTTGTCTTCAACCA
* * *
1813323 GCTCCATCACAATCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTATCAATAC-AGAAA
1 GCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAG-AA
*
1813387 TGCAAGATCTTTTGTCTTCAACCA
65 GGCAAGATCTTTTGTCTTCAACCA
* * *
1813411 GCTCCATCACAACTGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGAAG
1 GCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAGAAG
1813476 GCAAGATCTTTTGTCTTCAACCA
66 GCAAGATCTTTTGTCTTCAACCA
* * * *
1813499 ACTCCATCACAACCGAGAGAGACAAGGTTTGTGTCTTCGACCTACTTCGCTATCAATAC-AGAAA
1 GCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAG-AA
*
1813563 GGCAAGATATTTTGTCTTCAACCA
65 GGCAAGATCTTTTGTCTTCAACCA
* * **
1813587 GCTCTATCACAATCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGGAAATAC-AGAAA
1 GCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAG-AA
1813651 GGCAAGATCTTTTGTCTTCAACCA
65 GGCAAGATCTTTTGTCTTCAACCA
* * *
1813675 GCTCCATCACAATCGAGAGAGGCAAGGTTTGTGTCTTCGACCTACTTCGCTGTCAATACAGGAAG
1 GCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAGAAG
1813740 GCAAGATCT
66 GCAAGATCT
1813749 GCAACTTCAT
Statistics
Matches: 704, Mismatches: 68, Indels: 12
0.90 0.09 0.02
Matches are distributed among these distances:
87 2 0.00
88 698 0.99
89 4 0.01
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (88 bp):
GCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAGAAG
GCAAGATCTTTTGTCTTCAACCA
Found at i:1815005 original size:16 final size:17
Alignment explanation
Indices: 1814979--1815014 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1814969 AGCCTCTCCA
1814979 TTTTTACTTTTTCATTT
1 TTTTTACTTTTTCATTT
1814996 TTTTTA-TTTTTCATTT
1 TTTTTACTTTTTCATTT
1815012 TTT
1 TTT
1815015 CTTTCATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTACTTTTTCATTT
Found at i:1815874 original size:1 final size:1
Alignment explanation
Indices: 1815868--1815931 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
1815858 ACCTCTCCTC
* * * * * * * *
1815868 TTTTTTTTCTTTCTTTTTTTTTTGTTTTTTGTTTTTGTTTTTGTTTTTGTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1815932 AATCTGAACT
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:1815895 original size:6 final size:6
Alignment explanation
Indices: 1815881--1815928 Score: 71
Period size: 6 Copynumber: 7.8 Consensus size: 6
1815871 TTTTTCTTTC
1815881 TTTTT- TTTTTG TTTTTTG TTTTTG TTTTTG TTTTTG TTTTTTG TTTTT
1 TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG -TTTTTG TTTTT
1815929 TTTAATCTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.12
6 23 0.57
7 12 0.30
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:1815897 original size:7 final size:7
Alignment explanation
Indices: 1815870--1815929 Score: 72
Period size: 7 Copynumber: 8.9 Consensus size: 7
1815860 CTCTCCTCTT
*
1815870 TTTTTTC
1 TTTTTTG
*
1815877 TTTCTTTT
1 TTT-TTTG
1815885 TTTTTTG
1 TTTTTTG
1815892 TTTTTTG
1 TTTTTTG
1815899 -TTTTTG
1 TTTTTTG
1815905 -TTTTTG
1 TTTTTTG
1815911 -TTTTTG
1 TTTTTTG
1815917 TTTTTTG
1 TTTTTTG
1815924 TTTTTT
1 TTTTTT
1815930 TTAATCTGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
6 18 0.37
7 25 0.51
8 6 0.12
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (7 bp):
TTTTTTG
Found at i:1815902 original size:12 final size:11
Alignment explanation
Indices: 1815868--1815931 Score: 67
Period size: 12 Copynumber: 5.5 Consensus size: 11
1815858 ACCTCTCCTC
*
1815868 TTTTTTTTCTT
1 TTTTTTTTGTT
1815879 TCTTTTTTT-TT
1 T-TTTTTTTGTT
*
1815890 TGTTTTTTGTT
1 TTTTTTTTGTT
1815901 TTTGTTTTTGTTT
1 TTT-TTTTTG-TT
1815914 TTGTTTTTTGTT
1 TT-TTTTTTGTT
1815926 TTTTTT
1 TTTTTT
1815932 AATCTGAACT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
10 6 0.13
11 12 0.26
12 17 0.37
13 10 0.22
14 1 0.02
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:1820737 original size:18 final size:16
Alignment explanation
Indices: 1820716--1820754 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1820706 AATAATGGAA
1820716 ATATATAAAAACATGT
1 ATATATAAAAACATGT
**
1820732 ATATATAAAAGTATGT
1 ATATATAAAAACATGT
1820748 ATATATA
1 ATATATA
1820755 TAAATTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:1823037 original size:5 final size:5
Alignment explanation
Indices: 1823003--1823070 Score: 70
Period size: 5 Copynumber: 13.4 Consensus size: 5
1822993 TTATGTTATG
*
1823003 TATAT TAT-T T-TAT TATAT AATATAA TATAT TATAT T-TAT TATAT TATAT
1 TATAT TATAT TATAT TATAT --TATAT TATAT TATAT TATAT TATAT TATAT
1823052 TATAT TATTAT ATATAT TA
1 TATAT TA-TAT -TATAT TA
1823071 AATAAAGTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
3 1 0.02
4 8 0.15
5 33 0.61
6 6 0.11
7 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:1824014 original size:19 final size:19
Alignment explanation
Indices: 1823986--1824022 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1823976 GTAATAACAT
*
1823986 TTGAAATTATGTGTGAATA
1 TTGAAATTATATGTGAATA
*
1824005 TTGAATTTATATGTGAAT
1 TTGAAATTATATGTGAAT
1824023 TGATATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGAAATTATATGTGAATA
Found at i:1826419 original size:130 final size:130
Alignment explanation
Indices: 1826253--1826539 Score: 389
Period size: 130 Copynumber: 2.2 Consensus size: 130
1826243 TAAAAATGAC
* * *
1826253 AGTTGCGATCGTAAATCAGCGAACCTTAATAATATCAGCTGTGATCGTAAATCAATGGGCTGTTT
1 AGTTGTGATCGTAAATCAGCGAACCTTAATAATATCAGCTGTGATCGTAAATCAACGAGCTGTTT
*
1826318 GGACTAGCCATAGTAAATCAGCTAACTCAGAGAAG-ATTGTTCATGATAGTAAATCAATGAACTT
66 GGACTAGCCATAGTAAATCAACTAACTCAGA-AAGTATTGTTCATGATAGTAAATCAATGAACTT
1826382 A
130 A
* ** * * * *
1826383 AGTTGTGATTGTAAATCAGC-AAGCCTTAATGGTATCAGTTGTGATTGTAAATCGACGAGTTGTT
1 AGTTGTGATCGTAAATCAGCGAA-CCTTAATAATATCAGCTGTGATCGTAAATCAACGAGCTGTT
* *
1826447 TGGAGTAGCGATAGTAAATCAACTAACTCAGAAAGTATTGTTCATGATAGTAAATCAATGAACTT
65 TGGACTAGCCATAGTAAATCAACTAACTCAGAAAGTATTGTTCATGATAGTAAATCAATGAACTT
1826512 A
130 A
* * **
1826513 GGTTGTGATCATAAATCAATGAACCTT
1 AGTTGTGATCGTAAATCAGCGAACCTT
1826540 TGTGATCATA
Statistics
Matches: 136, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
129 5 0.04
130 129 0.95
131 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.31
Consensus pattern (130 bp):
AGTTGTGATCGTAAATCAGCGAACCTTAATAATATCAGCTGTGATCGTAAATCAACGAGCTGTTT
GGACTAGCCATAGTAAATCAACTAACTCAGAAAGTATTGTTCATGATAGTAAATCAATGAACTTA
Found at i:1826547 original size:24 final size:24
Alignment explanation
Indices: 1826497--1826563 Score: 98
Period size: 24 Copynumber: 2.7 Consensus size: 24
1826487 TTCATGATAG
*
1826497 TAAATCAATGAACTTAGGTTGTGATCA
1 TAAATCAATGAACCT---TTGTGATCA
1826524 TAAATCAATGAACCTTTGTGATCA
1 TAAATCAATGAACCTTTGTGATCA
1826548 TAAATCAATGAACCTT
1 TAAATCAATGAACCTT
1826564 AATAATATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
24 25 0.64
27 14 0.36
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (24 bp):
TAAATCAATGAACCTTTGTGATCA
Found at i:1826665 original size:154 final size:154
Alignment explanation
Indices: 1826406--1826693 Score: 461
Period size: 154 Copynumber: 1.9 Consensus size: 154
1826396 AATCAGCAAG
** * * * * * *
1826406 CCTTAATGGTATCAGTTGTGATTGTAAATCGACGAGTTGTTTGGAGTAGCGATAGTAAATCAACT
1 CCTTAATAATATCAGCTGTGATCGTAAATCAACAAGTTGTTTGGAATAGAGATAGTAAATCAACT
1826471 AACTCAGAAAGTATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCATAAATCAATGAA
66 AACTCAGAAAGTATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCATAAATCAATGAA
1826536 CCTTTGTGATCATAAATCAATGAA
131 CCTTTGTGATCATAAATCAATGAA
*
1826560 CCTTAATAATATCAGCTGTGATCGTAAATCAACAAGTTTTTTGGAATAGAGATAGTAAATCAACT
1 CCTTAATAATATCAGCTGTGATCGTAAATCAACAAGTTGTTTGGAATAGAGATAGTAAATCAACT
* *
1826625 AACTCAGAGAAG-ATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCATAAATTAGTGA
66 AACTCAGA-AAGTATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCATAAATCAATGA
1826689 ACCTT
130 ACCTT
1826694 AATAATATCA
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
154 119 0.98
155 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (154 bp):
CCTTAATAATATCAGCTGTGATCGTAAATCAACAAGTTGTTTGGAATAGAGATAGTAAATCAACT
AACTCAGAAAGTATTGTTCATGATAGTAAATCAATGAACTTAGGTTGTGATCATAAATCAATGAA
CCTTTGTGATCATAAATCAATGAA
Found at i:1826774 original size:284 final size:281
Alignment explanation
Indices: 1826259--1826979 Score: 892
Period size: 284 Copynumber: 2.6 Consensus size: 281
1826249 TGACAGTTGC
* ** * * * *
1826259 GATCGTAAATCAGCGAACCTTAATAATATCAGCTGTGATCGTAAATCAATGGGCTGTTTGGACTA
1 GATCATAAATCAATGAACCTTAATAATATCAGCTGTGATCGTAAATCAACGAGTTGTTTGGAATA
* *
1826324 GCCATAGTAAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAAGTTGT
66 GCGATAGTAAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTTGT
* * * * ** * * * *
1826389 GATTGTAAATCAGCAAGCCTTAATGGTATCAGTTGTGATTGTAAATCGACGAGTTGTTTGGAGTA
131 GATCGTAAATTAGTAAACCTTAATAATATCAATTGTGATTGTAAATCGACGAGCTATTTGGAATA
* *
1826454 GCGATAGTAAATCAACTAACTCAGAAAGTATTGTTCATGATAGTAAATCAATGAACTTAGGTTGT
196 GAGATAGTAAATCAACTAACTCAGAAAGTATTGTTCATGATAGTAAATCAATGAACTTAGGTTCT
1826519 GATCATAAATCAATGAACCTTTGT
261 GATCATAAATCAATGAA-C-TT-T
* *
1826543 GATCATAAATCAATGAACCTTAATAATATCAGCTGTGATCGTAAATCAACAAGTTTTTTGGAATA
1 GATCATAAATCAATGAACCTTAATAATATCAGCTGTGATCGTAAATCAACGAGTTGTTTGGAATA
* *
1826608 GAGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTTGT
66 GCGATAGTAAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTTGT
* * * **
1826673 GATCATAAATTAGTGAACCTTAATAATATCAATTGTGATCGTAAATCGGTGAGCTATTTGGAATA
131 GATCGTAAATTAGTAAACCTTAATAATATCAATTGTGATTGTAAATCGACGAGCTATTTGGAATA
* *
1826738 GAGATAGTAAATCAACTAACTCAGAGCAG-ATTGTTCATGATAGTAAATCAATTAACTTAGGTTC
196 GAGATAGTAAATCAACTAACTCAGA-AAGTATTGTTCATGATAGTAAATCAATGAACTTAGGTTC
1826802 TGATCATAAATCAATGAACTTT
260 TGATCATAAATCAATGAACTTT
*** *
1826824 -A--AT-AAT--AT----C------AT-T----TGTGATCGTAAATTGGCGAGTTGTTTGGAGTA
1 GATCATAAATCAATGAACCTTAATAATATCAGCTGTGATCGTAAATCAACGAGTTGTTTGGAATA
*
1826868 GCGATAGTAAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAAATTAGGTTGT
66 GCGATAGTAAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTTGT
* * *
1826933 GACCGTAAATTAGTAAACCTTAATAATATCAACTCTGATTGTAAATC
131 GATCGTAAATTAGTAAACCTTAATAATATCAATTGTGATTGTAAATC
1826980 AGCAAGTTGT
Statistics
Matches: 389, Mismatches: 47, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
260 129 0.33
264 1 0.00
265 2 0.01
271 1 0.00
275 2 0.01
277 3 0.01
278 2 0.01
280 1 0.00
281 1 0.00
282 2 0.01
283 1 0.00
284 242 0.62
285 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (281 bp):
GATCATAAATCAATGAACCTTAATAATATCAGCTGTGATCGTAAATCAACGAGTTGTTTGGAATA
GCGATAGTAAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAATGAACTTAGGTTGT
GATCGTAAATTAGTAAACCTTAATAATATCAATTGTGATTGTAAATCGACGAGCTATTTGGAATA
GAGATAGTAAATCAACTAACTCAGAAAGTATTGTTCATGATAGTAAATCAATGAACTTAGGTTCT
GATCATAAATCAATGAACTTT
Found at i:1826988 original size:130 final size:130
Alignment explanation
Indices: 1826524--1826991 Score: 627
Period size: 130 Copynumber: 3.6 Consensus size: 130
1826514 GTTGTGATCA
* * * *
1826524 TAAATCAATGAACCT---TTGTGATCATAAATCAATGAACCTTAATAATATCAGCTGTGATCGTA
1 TAAATCAATGAACTTAGGTTGTGATCATAAATTAGTGAACCTTAATAATATCAACTGTGATCGTA
* *
1826586 AATCAACAAGTTTTTTGGAATAGAGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAG
66 AATCAGCAAGTTGTTTGGAATAGAGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAG
*
1826651 TAAATCAATGAACTTAGGTTGTGATCATAAATTAGTGAACCTTAATAATATCAATTGTGATCGTA
1 TAAATCAATGAACTTAGGTTGTGATCATAAATTAGTGAACCTTAATAATATCAACTGTGATCGTA
* ** * * *
1826716 AATCGGTGAGCTATTTGGAATAGAGATAGTAAATCAACTAACTCAGAGCAGATTGTTCATGATAG
66 AATCAGCAAGTTGTTTGGAATAGAGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAG
* * * * * **
1826781 TAAATCAATTAACTTAGGTTCTGATCATAAATCAATGAACTTTAATAATATCATTTGTGATCGTA
1 TAAATCAATGAACTTAGGTTGTGATCATAAATTAGTGAACCTTAATAATATCAACTGTGATCGTA
** * * * *
1826846 AATTGGCGAGTTGTTTGGAGTAGCGATAGTAAATCAGCTAACTCAGAGAAGATTGTTCATGATAG
66 AATCAGCAAGTTGTTTGGAATAGAGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAG
* * * * * *
1826911 TAAATCAATGAAATTAGGTTGTGACCGTAAATTAGTAAACCTTAATAATATCAACTCTGATTGTA
1 TAAATCAATGAACTTAGGTTGTGATCATAAATTAGTGAACCTTAATAATATCAACTGTGATCGTA
1826976 AATCAGCAAGTTGTTT
66 AATCAGCAAGTTGTTT
1826992 CATATATGTT
Statistics
Matches: 296, Mismatches: 42, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
127 14 0.05
130 282 0.95
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (130 bp):
TAAATCAATGAACTTAGGTTGTGATCATAAATTAGTGAACCTTAATAATATCAACTGTGATCGTA
AATCAGCAAGTTGTTTGGAATAGAGATAGTAAATCAACTAACTCAGAGAAGATTGTTCATGATAG
Found at i:1833557 original size:26 final size:27
Alignment explanation
Indices: 1833506--1833557 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
1833496 TCTGTTAAGA
*
1833506 ATTTGGGGGCTCAAAACGAAATTTTAT
1 ATTTGGGGGCTCAAAACGAAACTTTAT
*
1833533 ATTTTGGGG-TCAAAA-GATAACTTTA
1 ATTTGGGGGCTCAAAACGA-AACTTTA
1833558 CCGTTATACC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 2 0.09
26 12 0.55
27 8 0.36
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.35
Consensus pattern (27 bp):
ATTTGGGGGCTCAAAACGAAACTTTAT
Found at i:1834961 original size:3 final size:3
Alignment explanation
Indices: 1834953--1834981 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1834943 ACAGGGAAGT
1834953 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1834982 TATGTTTGAG
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:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1836995 original size:15 final size:16
Alignment explanation
Indices: 1836975--1837006 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1836965 CCTCAATCGA
1836975 TAAATTT-AATAATTT
1 TAAATTTAAATAATTT
1836990 TAAATTTAAATAATTT
1 TAAATTTAAATAATTT
1837006 T
1 T
1837007 CCATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATTTAAATAATTT
Found at i:1838620 original size:21 final size:21
Alignment explanation
Indices: 1838586--1838626 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1838576 CACGTCAACA
*
1838586 AAATATAATAAATTCATTTTTT
1 AAATATAAAAAATT-ATTTTTT
1838608 AAATA-AAAAAATTATTTTT
1 AAATATAAAAAATTATTTTT
1838627 ATTGGAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATAAAAAATTATTTTTT
Found at i:1838715 original size:14 final size:14
Alignment explanation
Indices: 1838677--1838724 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 14
1838667 CTTTCAAAGC
1838677 TTAATTTCTTTTAAAA
1 TTAATTT-TTTT-AAA
1838693 TTTATATTTTTTTAAA
1 -TTA-ATTTTTTTAAA
1838709 TTAATTTTTTTAAA
1 TTAATTTTTTTAAA
1838723 TT
1 TT
1838725 TCATATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 13 0.43
15 3 0.10
16 3 0.10
17 7 0.23
18 4 0.13
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TTAATTTTTTTAAA
Found at i:1838733 original size:15 final size:15
Alignment explanation
Indices: 1838685--1838741 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
1838675 GCTTAATTTC
* *
1838685 TTTTAAAATTTATATT
1 TTTTTAAATTTA-ATA
*
1838701 TTTTTAAA-TTAATT
1 TTTTTAAATTTAATA
*
1838715 TTTTTAAATTTCATA
1 TTTTTAAATTTAATA
*
1838730 TTTTAAAATTTA
1 TTTTTAAATTTA
1838742 TAAAAAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 11 0.31
15 17 0.49
16 7 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTTAAATTTAATA
Found at i:1841018 original size:139 final size:140
Alignment explanation
Indices: 1840863--1841139 Score: 448
Period size: 139 Copynumber: 2.0 Consensus size: 140
1840853 GGAAGAGAGG
* * * *
1840863 TTAAACCAAAATAGAAACTCAGCAGAGAAGAGGGAAGAAATTTTAGTAGCAATTGAATGGAAAAA
1 TTAAACCAAAACAGAAACTCACCACAGAAGAGGGAAGAAATTTTAGTAGCAATCGAATGGAAAAA
* * *
1840928 ATGCAAAAAAAA-AAGAAGGAAGAATTTTGCAATAACAAAGGAACTAATGTGAAAAGAAAGATAG
66 ATGCAAAAAAAATAAAAAGGAAGAATTTTGCAATAACAAAGGAAATAATGTCAAAAGAAAGATAG
1840992 TGGGATGTGA
131 TGGGATGTGA
* * *
1841002 TTAAACCAAAACAGAAACTCACCACAGAAGAGGGAGGAAATTTTAGTAGTAATCGAATGGAAAAT
1 TTAAACCAAAACAGAAACTCACCACAGAAGAGGGAAGAAATTTTAGTAGCAATCGAATGGAAAAA
*
1841067 TTGCAAAAAAAATAAAAAGGAAGAATTTTGCAATAACAAAGGAAATAATGTCAAAAGAAAGATAG
66 ATGCAAAAAAAATAAAAAGGAAGAATTTTGCAATAACAAAGGAAATAATGTCAAAAGAAAGATAG
1841132 TGGGATGT
131 TGGGATGT
1841140 AGACTGCAGT
Statistics
Matches: 126, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
139 69 0.55
140 57 0.45
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.19
Consensus pattern (140 bp):
TTAAACCAAAACAGAAACTCACCACAGAAGAGGGAAGAAATTTTAGTAGCAATCGAATGGAAAAA
ATGCAAAAAAAATAAAAAGGAAGAATTTTGCAATAACAAAGGAAATAATGTCAAAAGAAAGATAG
TGGGATGTGA
Found at i:1842690 original size:14 final size:14
Alignment explanation
Indices: 1842650--1842692 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1842640 TTTTAATCTT
1842650 ATAAAAAATATTAAA
1 ATAAAAAATATT-AA
* * *
1842665 ATATAAATTATTAG
1 ATAAAAAATATTAA
1842679 ATAAAAAATATTAA
1 ATAAAAAATATTAA
1842693 TTTCAACACT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
ATAAAAAATATTAA
Found at i:1850720 original size:41 final size:40
Alignment explanation
Indices: 1850657--1850733 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 40
1850647 GTTGAATGCA
* * *
1850657 ATAAATCATTCAAAGCACTAAAATGAATAATTAATTCAAT
1 ATAAATCATTAAAAGCACTAAAATAAACAATTAATTCAAT
* *
1850697 ATAATATCATTAAAAGTATTAAAATAAACAATTAATT
1 ATAA-ATCATTAAAAGCACTAAAATAAACAATTAATT
1850734 TAACTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 4 0.13
41 27 0.87
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (40 bp):
ATAAATCATTAAAAGCACTAAAATAAACAATTAATTCAAT
Found at i:1866422 original size:18 final size:18
Alignment explanation
Indices: 1866381--1866422 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1866371 TATAAAAATA
1866381 TCAAAATTTATA-TTTTT
1 TCAAAATTTATATTTTTT
* *
1866398 TAAAAAATTATAATTTTTT
1 TCAAAATTTAT-ATTTTTT
1866417 TCAAAA
1 TCAAAA
1866423 AAAATATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 9 0.45
18 1 0.05
19 10 0.50
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
TCAAAATTTATATTTTTT
Found at i:1866448 original size:12 final size:11
Alignment explanation
Indices: 1866427--1866456 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
1866417 TCAAAAAAAA
1866427 TATAAAAAATT
1 TATAAAAAATT
1866438 TATAAAGAAATT
1 TATAAA-AAATT
1866450 TATAAAA
1 TATAAAA
1866457 TTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
TATAAAAAATT
Found at i:1880681 original size:41 final size:40
Alignment explanation
Indices: 1880633--1880709 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 40
1880623 ATTAAAGTTA
* * *
1880633 AATTAATTGTTTATTTTAATACTTTTAATGATGTTATACTG
1 AATTAATTATTCATTTTAATACTTTGAATGAT-TTATACTG
* *
1880674 AATTAATTATTCATTTTAGTGCTTTGAATGATTTAT
1 AATTAATTATTCATTTTAATACTTTGAATGATTTAT
1880710 TGCATTCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 4 0.13
41 27 0.87
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.53
Consensus pattern (40 bp):
AATTAATTATTCATTTTAATACTTTGAATGATTTATACTG
Found at i:1884305 original size:20 final size:20
Alignment explanation
Indices: 1884280--1884325 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1884270 ACTGTTAGTA
*
1884280 GTTTTGGGACTTTATTATTG
1 GTTTTGGGACTTTATTAATG
1884300 GTTTTGGGACTTTATTAATG
1 GTTTTGGGACTTTATTAATG
1884320 GTTTTG
1 GTTTTG
1884326 AGCTCTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.04, G:0.26, T:0.54
Consensus pattern (20 bp):
GTTTTGGGACTTTATTAATG
Found at i:1887039 original size:31 final size:31
Alignment explanation
Indices: 1886996--1887054 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1886986 AATAACCCAA
*
1886996 TGACTTAAATAAAAACTTTCGAATAGTTTAG
1 TGACATAAATAAAAACTTTCGAATAGTTTAG
** *
1887027 TGACATAAATAAAATTTTTTGAATAGTT
1 TGACATAAATAAAAACTTTCGAATAGTT
1887055 CACTGATCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (31 bp):
TGACATAAATAAAAACTTTCGAATAGTTTAG
Found at i:1889952 original size:34 final size:35
Alignment explanation
Indices: 1889897--1889963 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1889887 CAAACACCAG
*
1889897 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
1889932 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
1889964 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1893200 original size:42 final size:42
Alignment explanation
Indices: 1893113--1893272 Score: 207
Period size: 42 Copynumber: 3.8 Consensus size: 42
1893103 GTTTACAAAC
* *
1893113 AAAAACGCCGCTAAAGAACAAGTTCTTTAGCGGCACTTAGAA
1 AAAAACGCCGCTAAAGAACAGGTTCTTTAGCGGCGCTTAGAA
* * *
1893155 AAAAA-GCCGCTAAAGAACAGGGTCTTTAGCAGCGCTAAGAA
1 AAAAACGCCGCTAAAGAACAGGTTCTTTAGCGGCGCTTAGAA
* *
1893196 AAAAACGCCGCTAAAG-ACCGTATTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACAG-GTTCTTTAGCGGCGCTTAGAA
* * *
1893238 GAAAACGCCGCTAAAGAACATGATCTTTAGCGGCG
1 AAAAACGCCGCTAAAGAACAGGTTCTTTAGCGGCG
1893273 TTTTTTTCTA
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
41 39 0.39
42 59 0.59
43 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.18
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACAGGTTCTTTAGCGGCGCTTAGAA
Found at i:1893210 original size:83 final size:84
Alignment explanation
Indices: 1893113--1893268 Score: 235
Period size: 83 Copynumber: 1.9 Consensus size: 84
1893103 GTTTACAAAC
1893113 AAAAACGCCGCTAAAGAAC-AAGTTCTTTAGCGGCACTTAGAA-AAAAAGCCGCTAAAGAACAGG
1 AAAAACGCCGCTAAAGAACGAA-TTCTTTAGCGGCACTTAGAAGAAAAAGCCGCTAAAGAACAGG
*
1893176 GTCTTTAGCAGCGCTAAGAA
65 ATCTTTAGCAGCGCTAAGAA
* * * * *
1893196 AAAAACGCCGCTAAAGACCGTATTCTTTAGCGGCGCTTAGAAGAAAACGCCGCTAAAGAACATGA
1 AAAAACGCCGCTAAAGAACGAATTCTTTAGCGGCACTTAGAAGAAAAAGCCGCTAAAGAACAGGA
1893261 TCTTTAGC
66 TCTTTAGC
1893269 GGCGTTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
83 37 0.57
84 28 0.43
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (84 bp):
AAAAACGCCGCTAAAGAACGAATTCTTTAGCGGCACTTAGAAGAAAAAGCCGCTAAAGAACAGGA
TCTTTAGCAGCGCTAAGAA
Found at i:1893294 original size:42 final size:42
Alignment explanation
Indices: 1893243--1893521 Score: 445
Period size: 42 Copynumber: 6.7 Consensus size: 42
1893233 TAGAAGAAAA
*
1893243 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* * * *
1893285 CGCCTCTAAAGAACATGTTCTTTAACGGCGTTTATTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
1893327 CGCCGCTAAAGAACAGGGTCTTTAGCGGCG-TTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* *
1893368 CGCCGCTAAAGAACACGGTCTTTAGCAGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
1893410 CGCCGCTAAAAAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
1893452 CGCCGCTAAAGAACACGGTCTTTAGCGGCG-TTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
1893493 CGCCGCTAAAGAACATGTTCTTTAGCGGC
1 CGCCGCTAAAGAACATGGTCTTTAGCGGC
1893522 ACTTTTATAC
Statistics
Matches: 218, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
41 76 0.35
42 142 0.65
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:1893295 original size:84 final size:83
Alignment explanation
Indices: 1893201--1893521 Score: 389
Period size: 83 Copynumber: 3.8 Consensus size: 83
1893191 AAGAAAAAAA
* ***** * *
1893201 CGCCGCTAAAGACCGTATTCTTTAGCGGCGCTTAGAAGAAAACGCCGCTAAAGAACATGATCTTT
1 CGCCGCTAAAGACCGT-TTCTTTAGCGGCGTTTATTTCTAAGCGCCGCTAAAGAACATGGTCTTT
1893266 AGCGGCGTTTTTTTCTAAG
65 AGCGGCGTTTTTTTCTAAG
* * * * *
1893285 CGCCTCTAAAGAACATGTTCTTTAACGGCGTTTATTTCTAAGCGCCGCTAAAGAACAGGGTCTTT
1 CGCCGCTAAAGACCGT-TTCTTTAGCGGCGTTTATTTCTAAGCGCCGCTAAAGAACATGGTCTTT
1893350 AGCGGCG-TTTTTTCTAAG
65 AGCGGCGTTTTTTTCTAAG
* * * *
1893368 CGCCGCTAAAGAACACG-GTCTTTAGCAGCGTTTTTTTCTAAGCGCCGCTAAAAAACATGGTCTT
1 CGCCGCTAAAG-AC-CGTTTCTTTAGCGGCGTTTATTTCTAAGCGCCGCTAAAGAACATGGTCTT
1893432 TAGCGGCGTTTTTTTCTAAG
64 TAGCGGCGTTTTTTTCTAAG
* *
1893452 CGCCGCTAAAGAACACG-GTCTTTAGCGGCGTTT-TTTCTAAGCGCCGCTAAAGAACATGTTCTT
1 CGCCGCTAAAG-AC-CGTTTCTTTAGCGGCGTTTATTTCTAAGCGCCGCTAAAGAACATGGTCTT
1893515 TAGCGGC
64 TAGCGGC
1893522 ACTTTTATAC
Statistics
Matches: 208, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
83 105 0.50
84 102 0.49
85 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (83 bp):
CGCCGCTAAAGACCGTTTCTTTAGCGGCGTTTATTTCTAAGCGCCGCTAAAGAACATGGTCTTTA
GCGGCGTTTTTTTCTAAG
Found at i:1893377 original size:125 final size:125
Alignment explanation
Indices: 1893243--1893521 Score: 468
Period size: 125 Copynumber: 2.2 Consensus size: 125
1893233 TAGAAGAAAA
* * *
1893243 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCTCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAAAACATGGTCTTT
*
1893308 AACGGCGTTTATTTCTAAGCGCCGCTAAAGAACAGGGTCTTTAGCGGCGTTTTTTCTAAG
66 AACGGCGTTTATTTCTAAGCGCCGCTAAAGAACACGGTCTTTAGCGGCGTTTTTTCTAAG
* * *
1893368 CGCCGCTAAAGAACACGGTCTTTAGCAGCGTTTTTTTCTAAGCGCCGCTAAAAAACATGGTCTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAAAACATGGTCTTT
* *
1893433 AGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACACGGTCTTTAGCGGCGTTTTTTCTAAG
66 AACGGCGTTTATTTCTAAGCGCCGCTAAAGAACACGGTCTTTAGCGGCGTTTTTTCTAAG
*
1893493 CGCCGCTAAAGAACATGTTCTTTAGCGGC
1 CGCCGCTAAAGAACATGATCTTTAGCGGC
1893522 ACTTTTATAC
Statistics
Matches: 142, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 142 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (125 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAAAACATGGTCTTT
AACGGCGTTTATTTCTAAGCGCCGCTAAAGAACACGGTCTTTAGCGGCGTTTTTTCTAAG
Found at i:1893399 original size:83 final size:83
Alignment explanation
Indices: 1893243--1893521 Score: 452
Period size: 83 Copynumber: 3.3 Consensus size: 83
1893233 TAGAAGAAAA
* * * *
1893243 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCTCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACACGGTCTTT
*
1893308 AACGGCGTTTATTTCTAAG
66 AGCGGCGTTT-TTTCTAAG
*
1893327 CGCCGCTAAAGAACAGGGTCTTTAGCGGCG-TTTTTTCTAAGCGCCGCTAAAGAACACGGTCTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACACGGTCTTT
*
1893391 AGCAGCGTTTTTTTCTAAG
66 AGCGGCG-TTTTTTCTAAG
*
1893410 CGCCGCTAAAAAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACACGGTCTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACACGGTCTTT
1893475 AGCGGCGTTTTTTCTAAG
66 AGCGGCGTTTTTTCTAAG
*
1893493 CGCCGCTAAAGAACATGTTCTTTAGCGGC
1 CGCCGCTAAAGAACATGGTCTTTAGCGGC
1893522 ACTTTTATAC
Statistics
Matches: 181, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
83 110 0.61
84 71 0.39
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (83 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACACGGTCTTT
AGCGGCGTTTTTTCTAAG
Found at i:1893881 original size:21 final size:21
Alignment explanation
Indices: 1893857--1893897 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1893847 TCTGCTTCTC
*
1893857 TCGCTGCAGCCTCCGCTTCCG
1 TCGCTGCAGCCGCCGCTTCCG
*
1893878 TCGCTGCAGCCGCTGCTTCC
1 TCGCTGCAGCCGCCGCTTCC
1893898 CTTGCTTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.46, G:0.24, T:0.24
Consensus pattern (21 bp):
TCGCTGCAGCCGCCGCTTCCG
Found at i:1897581 original size:114 final size:113
Alignment explanation
Indices: 1897380--1897808 Score: 308
Period size: 114 Copynumber: 3.8 Consensus size: 113
1897370 TAAATTATTT
*
1897380 TAAATCCCTAAGCATTAGCGGCGCTTTTCTAAAAACGCCGCTAAATCCCTGAAAGCATAGAAAAC
1 TAAATCCCTAAGCATTAGCGGCGCTTCTCTAAAAACGCCGCTAAATCCCTGAAAGCATAGAAAAC
* *
1897445 GACGACGTTGGGCTTAGTTTTTTTTGTGGCGCTACTCCAAAAACGCTAC
66 GACGACGTTGGACTTAG-GTTTTTTGTGGCGCTACTCCAAAAACGCTAC
* * * * * *
1897494 TAAATCCCTGAGCATTAGCGGCGCTTCTCTAGAAATGCTGCTAAAT-TCTCGAAAAG-GTCAG-A
1 TAAATCCCTAAGCATTAGCGGCGCTTCTCTAAAAACGCCGCTAAATCCCT-G-AAAGCAT-AGAA
* * ** *** **
1897556 AACG-CTGTCGTTGTACTTAGGTTTTTTGTGGCGCTTTTTTGAAAACGCCGC
63 AACGAC-GACGTTGGACTTAGGTTTTTTGTGGCGCTACTCCAAAAACGCTAC
* * * * *
1897607 TAAAGCCCTAAGAATTAGCGGCGCTTAAT-TAAAAACGCCACT-AATCACTCGAAAGC-TCAGAA
1 TAAATCCCTAAGCATTAGCGGCGCTT-CTCTAAAAACGCCGCTAAATCCCT-GAAAGCAT-AG-A
* * * * * *
1897669 AAACGGCGTCGTTGGGA-TTAGGCTTTTTGCGGCGCT-TTCTCAAAAACGCTGC
62 AAACGACGACGTT-GGACTTAGGTTTTTTGTGGCGCTACTC-CAAAAACGCTAC
* * * * * *
1897721 TAAATCCCTGAGCATTAACGGCGCTT-TATTAGAAACGCCGCTAAAT-CCTCGAAAGC-TCGGCA
1 TAAATCCCTAAGCATTAGCGGCGCTTCT-CTAAAAACGCCGCTAAATCCCT-GAAAGCAT-AGAA
*
1897783 AACGACGTCGTTCGGA-TTAGGTTTTT
63 AACGACGACGTT-GGACTTAGGTTTTT
1897809 GCGGCACTTT
Statistics
Matches: 254, Mismatches: 46, Indels: 31
0.77 0.14 0.09
Matches are distributed among these distances:
112 12 0.05
113 88 0.35
114 142 0.56
115 12 0.05
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.27
Consensus pattern (113 bp):
TAAATCCCTAAGCATTAGCGGCGCTTCTCTAAAAACGCCGCTAAATCCCTGAAAGCATAGAAAAC
GACGACGTTGGACTTAGGTTTTTTGTGGCGCTACTCCAAAAACGCTAC
Found at i:1897658 original size:113 final size:110
Alignment explanation
Indices: 1897534--1897835 Score: 313
Period size: 114 Copynumber: 2.7 Consensus size: 110
1897524 AGAAATGCTG
* * * *
1897534 CTAAATTCTCGAAAAGGTCAG-AAACGCTGTCGTT-GTACTTAGGTTTTTTGTGGCGCTTTTTTG
1 CTAAATCCTCG-AAAGCTCAGAAAACGC-GTCGTTCGGA-TTAGG-TTTTTGCGGCGCTTTTTT-
*
1897597 AAAACGCCGCTAAAGCCCTAAGAATTAGCGGCGCTTAATTAAAAACGCCA
61 AAAACGCCGCTAAAGCCCTAAGAATTAACGGCGCTTAATTAAAAACGCCA
* **
1897647 CT-AATCACTCGAAAGCTCAGAAAAACGGCGTCGTTGGGATTAGGCTTTTTGCGGCGCTTTCTCA
1 CTAAATC-CTCGAAAGCTCAG-AAAAC-GCGTCGTTCGGATTAGG-TTTTTGCGGCGCTTT-TTT
* * * * * * *
1897711 AAAACGCTGCTAAATCCCTGAGCATTAACGGCGCTTTATTAGAAACGCCG
61 AAAACGCCGCTAAAGCCCTAAGAATTAACGGCGCTTAATTAAAAACGCCA
* * *
1897761 CTAAATCCTCGAAAGCTCGGCAAACGACGTCGTTCGGATTAGGTTTTTGCGGCACTTTTTATAAA
1 CTAAATCCTCGAAAGCTCAGAAAACG-CGTCGTTCGGATTAGGTTTTTGCGGCGCTTTTT-TAAA
1897826 ACGCCGCTAA
64 ACGCCGCTAA
1897836 TTCTTATTCT
Statistics
Matches: 158, Mismatches: 22, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
111 1 0.01
112 38 0.24
113 25 0.16
114 85 0.54
115 9 0.06
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (110 bp):
CTAAATCCTCGAAAGCTCAGAAAACGCGTCGTTCGGATTAGGTTTTTGCGGCGCTTTTTTAAAAC
GCCGCTAAAGCCCTAAGAATTAACGGCGCTTAATTAAAAACGCCA
Found at i:1897805 original size:227 final size:226
Alignment explanation
Indices: 1897380--1897835 Score: 536
Period size: 227 Copynumber: 2.0 Consensus size: 226
1897370 TAAATTATTT
* * * * *
1897380 TAAATCCCTAAGCATTAGCGGCGCTTTTCTAAAAACGCCGCTAAATCCCTGAAAGCATAGAAAAC
1 TAAAGCCCTAAGAATTAGCGGCGCTTATCTAAAAACGCCACTAAATCACTGAAAGCATAGAAAAC
* ** *
1897445 GACGACGTTGGGCTTAGTTTTTTTTGTGGCGCTACTCCAAAAACGCTACTAAATCCCTGAGCATT
66 GACGACGTTGGGATTAGTGCTTTTTGCGGCGCTACTCCAAAAACGCTACTAAATCCCTGAGCATT
* * * * * *
1897510 AGCGGCGCTTCTCTAGAAATGCTGCTAAATTCTCGAAAAGGTCAGAAACGCTGTCGTTGTACTTA
131 AACGGCGCTTCTCTAGAAACGCCGCTAAATCCTCGAAAAGCTCAGAAACGCTGTCGTTGGACTTA
* *
1897575 GGTTTTTTGTGGCGCTTTTT-TGAAAACGCCGC
196 GG-TTTTTGCGGCACTTTTTAT-AAAACGCCGC
1897607 TAAAGCCCTAAGAATTAGCGGCGCTTAAT-TAAAAACGCCACT-AATCACTCGAAAGC-TCAGAA
1 TAAAGCCCTAAGAATTAGCGGCGCTT-ATCTAAAAACGCCACTAAATCACT-GAAAGCAT-AG-A
* * * *
1897669 AAACGGCGTCGTTGGGATTAG-GCTTTTTGCGGCGCT-TTCTCAAAAACGCTGCTAAATCCCTGA
62 AAACGACGACGTTGGGATTAGTGCTTTTTGCGGCGCTACTC-CAAAAACGCTACTAAATCCCTGA
* *
1897732 GCATTAACGGCGCTT-TATTAGAAACGCCGCTAAATCCTCG-AAAGCTCGGCAAACGAC-GTCGT
126 GCATTAACGGCGCTTCT-CTAGAAACGCCGCTAAATCCTCGAAAAGCTCAG-AAACG-CTGTCGT
1897794 TCGGA-TTAGGTTTTTGCGGCACTTTTTATAAAACGCCGC
188 T-GGACTTAGGTTTTTGCGGCACTTTTTATAAAACGCCGC
1897833 TAA
1 TAA
1897836 TTCTTATTCT
Statistics
Matches: 196, Mismatches: 23, Indels: 21
0.82 0.10 0.09
Matches are distributed among these distances:
226 45 0.23
227 128 0.65
228 23 0.12
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.27
Consensus pattern (226 bp):
TAAAGCCCTAAGAATTAGCGGCGCTTATCTAAAAACGCCACTAAATCACTGAAAGCATAGAAAAC
GACGACGTTGGGATTAGTGCTTTTTGCGGCGCTACTCCAAAAACGCTACTAAATCCCTGAGCATT
AACGGCGCTTCTCTAGAAACGCCGCTAAATCCTCGAAAAGCTCAGAAACGCTGTCGTTGGACTTA
GGTTTTTGCGGCACTTTTTATAAAACGCCGC
Found at i:1906552 original size:30 final size:30
Alignment explanation
Indices: 1906516--1906575 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1906506 GGTGAGCTGA
1906516 GTGGCACTCAGCAGTGCTCACAGTAAACTG
1 GTGGCACTCAGCAGTGCTCACAGTAAACTG
1906546 GTGGCACTCAGCAGTGCTCACAGTAAACTG
1 GTGGCACTCAGCAGTGCTCACAGTAAACTG
1906576 TCACTGAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (30 bp):
GTGGCACTCAGCAGTGCTCACAGTAAACTG
Found at i:1907355 original size:16 final size:16
Alignment explanation
Indices: 1907336--1907384 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1907326 GTTAGAAATG
1907336 TGAAGAGACTTGAATA
1 TGAAGAGACTTGAATA
*
1907352 TGAAGAG--TTAGTAATG
1 TGAAGAGACTT-G-AATA
1907368 TGAAGAGACTTGAATA
1 TGAAGAGACTTGAATA
1907384 T
1 T
1907385 AAAAAGTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 2 0.07
15 1 0.04
16 21 0.78
17 1 0.04
18 2 0.07
ACGTcount: A:0.41, C:0.04, G:0.27, T:0.29
Consensus pattern (16 bp):
TGAAGAGACTTGAATA
Found at i:1907368 original size:32 final size:32
Alignment explanation
Indices: 1907320--1907393 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
1907310 AAATAAATTT
1907320 TGAAAAGTTAGAAATGTGAAGAGACTTGAATA
1 TGAAAAGTTAGAAATGTGAAGAGACTTGAATA
* *
1907352 TGAAGAGTTAGTAATGTGAAGAGACTTGAATA
1 TGAAAAGTTAGAAATGTGAAGAGACTTGAATA
*
1907384 TAAAAAGTTA
1 TGAAAAGTTA
1907394 CACACATGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.27
Consensus pattern (32 bp):
TGAAAAGTTAGAAATGTGAAGAGACTTGAATA
Found at i:1907487 original size:38 final size:38
Alignment explanation
Indices: 1907403--1907491 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 38
1907393 ACACACATGC
*
1907403 ATGAATAATCACAACTCCTATAGCATTTAAGTTATGTAA
1 ATGAATAGTCACAACTCCTATAGCATTTAAG-TATGTAA
*
1907442 ATGAATAGTCACAACTCCTATAGCATTTAGAG-ATGTAG
1 ATGAATAGTCACAACTCCTATAGCATTTA-AGTATGTAA
1907480 ATGAATAGTCAC
1 ATGAATAGTCAC
1907492 TTACAATTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
38 17 0.36
39 28 0.60
40 2 0.04
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (38 bp):
ATGAATAGTCACAACTCCTATAGCATTTAAGTATGTAA
Found at i:1911825 original size:19 final size:19
Alignment explanation
Indices: 1911794--1911852 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
1911784 TATTTTATGG
1911794 TACTATTACTTGTTTATTAT
1 TACTATTA-TTGTTTATTAT
*
1911814 TACTATTATTGTATATTAT
1 TACTATTATTGTTTATTAT
* * *
1911833 TACTAATATTATTCATTAT
1 TACTATTATTGTTTATTAT
1911852 T
1 T
1911853 TTCATGTACA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 26 0.76
20 8 0.24
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (19 bp):
TACTATTATTGTTTATTAT
Found at i:1915855 original size:20 final size:20
Alignment explanation
Indices: 1915830--1915869 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1915820 TTCACCCCAT
1915830 GCATCGCATCATATGCATTA
1 GCATCGCATCATATGCATTA
1915850 GCATCGCATCATATGCATTA
1 GCATCGCATCATATGCATTA
1915870 AAGACCTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (20 bp):
GCATCGCATCATATGCATTA
Found at i:1924049 original size:50 final size:50
Alignment explanation
Indices: 1923976--1924532 Score: 294
Period size: 50 Copynumber: 11.1 Consensus size: 50
1923966 GCAGCGGAAC
* ** * *
1923976 AGATTGAAGCTACGACGATGGATCTAGTTTTCCGGATATTGCAATTTAAA
1 AGATTGAAGCTACAACGGCGGATCTAGTTTCCCGGATATTGCAATTGAAA
* * ** * * *** *
1924026 AGATTGAAGCCACAACGGCGGATCT--TACTCCCTTAACAGTGCAGCGGAAC
1 AGATTGAAGCTACAACGGCGGATCTAGT-TTCCC-GGATATTGCAATTGAAA
* * *
1924076 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCGGATATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGGATCTAGTTTCCCGGATATTGCAATTGAAA
* * ** * * * *
1924126 AGATTGAAGCCACAACGGCGGATCT--TACTCCCTTAGCAGTGCAGTGGAATA
1 AGATTGAAGCTACAACGGCGGATCTAGT-TTCCCGGA-TATTGCAATTGAA-A
* * * *
1924177 A-ATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTTAAA
1 AGATTGAAGCTACAACGGCGGATCTAGTTTCCCGGATATTGCAATTGAAA
* * * * * *** *
1924226 AGATTGAAGCCACAACGGCAGATCTTA-CTTCCTTAGCA-A-TGCAGCGGAAC
1 AGATTGAAGCTACAACGGCGGATC-TAGTTTCC--CGGATATTGCAATTGAAA
* * *
1924276 GGATTGAAGCTACGACGGCGGATCTAGTTTCCCGGATATTGCAATTTAAA
1 AGATTGAAGCTACAACGGCGGATCTAGTTTCCCGGATATTGCAATTGAAA
* * *** * * *** *
1924326 AGATTGAAGCCACAACGGCGGATCTTA-CTT-CTTTAGCAGTGCAGCAGAAC
1 AGATTGAAGCTACAACGGCGGATC-TAGTTTCCCGGA-TATTGCAATTGAAA
* * *
1924376 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCGGATATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGGATCTAGTTTCCCGGATATTGCAATTGAAA
* * * * * * *
1924426 AGATTGAAGCTACAACAGCGGATCTTA-CTTCCC-TAGCAGTGCAATGGAAC
1 AGATTGAAGCTACAACGGCGGATC-TAGTTTCCCGGA-TATTGCAATTGAAA
* * * * *
1924476 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTGCAGTTGAACA
1 AGATTGAAGCTACAACGGCGGATCTAGTTTCCCGGATATTGCAATTGAA-A
1924527 A-ATTGA
1 AGATTGA
1924533 GGATTACAGA
Statistics
Matches: 364, Mismatches: 118, Indels: 50
0.68 0.22 0.09
Matches are distributed among these distances:
48 4 0.01
49 18 0.05
50 318 0.87
51 21 0.06
52 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCGGATCTAGTTTCCCGGATATTGCAATTGAAA
Found at i:1924100 original size:100 final size:100
Alignment explanation
Indices: 1923922--1924518 Score: 926
Period size: 100 Copynumber: 6.0 Consensus size: 100
1923912 TTGAAAAGTA
* *
1923922 AAAAGATTAAAGCCACAACGGCGGATCTTACTTCCTTAGCAAGTGCAGCGGAACAGATTGAAGCT
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTCCCTTAGC-AGTGCAGCGGAACAGATTGAAGCT
** * *
1923987 ACGACGATGGATCTAGTTTTCCGGATATTGCAATTT
65 ACGACGGCGGATCTGGTTTCCCGGATATTGCAATTT
*
1924023 AAAAGATTGAAGCCACAACGGCGGATCTTACTCCCTTAACAGTGCAGCGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTCCCTTAGCAGTGCAGCGGAACAGATTGAAGCTA
*
1924088 CGACGGCGGATCTGGTTTCCCGGATATTGCAATTA
66 CGACGGCGGATCTGGTTTCCCGGATATTGCAATTT
* * *
1924123 AAAAGATTGAAGCCACAACGGCGGATCTTACTCCCTTAGCAGTGCAGTGGAATAAATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTCCCTTAGCAGTGCAGCGGAACAGATTGAAGCTA
*
1924188 CGACGGCGGATCTGGTTTCCCTGATATTGCAATTT
66 CGACGGCGGATCTGGTTTCCCGGATATTGCAATTT
* * * *
1924223 AAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAATGCAGCGGAACGGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTCCCTTAGCAGTGCAGCGGAACAGATTGAAGCTA
*
1924288 CGACGGCGGATCTAGTTTCCCGGATATTGCAATTT
66 CGACGGCGGATCTGGTTTCCCGGATATTGCAATTT
* * *
1924323 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCTTTAGCAGTGCAGCAGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTCCCTTAGCAGTGCAGCGGAACAGATTGAAGCTA
*
1924388 CGACGGCGGATCTGGTTTCCCGGATATTGCAATTA
66 CGACGGCGGATCTGGTTTCCCGGATATTGCAATTT
* * **
1924423 AAAAGATTGAAGCTACAACAGCGGATCTTACTTCCC-TAGCAGTGCAATGGAACAGATTGAAGCT
1 AAAAGATTGAAGCCACAACGGCGGATCTTAC-TCCCTTAGCAGTGCAGCGGAACAGATTGAAGCT
* *
1924487 ACGACGGCGGATCTGGTTTCCCCGACATTGCA
65 ACGACGGCGGATCTGGTTTCCCGGATATTGCA
1924519 GTTGAACAAA
Statistics
Matches: 456, Mismatches: 39, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
100 417 0.91
101 39 0.09
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTCCCTTAGCAGTGCAGCGGAACAGATTGAAGCTA
CGACGGCGGATCTGGTTTCCCGGATATTGCAATTT
Found at i:1925586 original size:15 final size:14
Alignment explanation
Indices: 1925558--1925584 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1925548 TGAATCGTTT
1925558 TTTTTATTTTTTTC
1 TTTTTATTTTTTTC
1925572 TTTTTATTTTTTT
1 TTTTTATTTTTTT
1925585 TCATCTATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTATTTTTTTC
Found at i:1926219 original size:19 final size:19
Alignment explanation
Indices: 1926188--1926246 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
1926178 TATTTTATGG
1926188 TACTATTACTTGTTTATTAT
1 TACTATTA-TTGTTTATTAT
*
1926208 TACTATTATTGTATATTAT
1 TACTATTATTGTTTATTAT
* * *
1926227 TACTAATATTATTCATTAT
1 TACTATTATTGTTTATTAT
1926246 T
1 T
1926247 TTCATGTACA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 26 0.76
20 8 0.24
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (19 bp):
TACTATTATTGTTTATTAT
Found at i:1928707 original size:38 final size:38
Alignment explanation
Indices: 1928664--1928751 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 38
1928654 ACACACATGC
* *
1928664 ATGAATAGTCAC-ACTTCTATAGCATTTAAGTTATGTAA
1 ATGAATAGTCACAACTCCTATAGCATTT-AGTGATGTAA
*
1928702 ATGAATAGTCACAACTCCTATAGCATTTAGTGATGTAG
1 ATGAATAGTCACAACTCCTATAGCATTTAGTGATGTAA
1928740 ATGAATAGTCAC
1 ATGAATAGTCAC
1928752 TTACAACTCC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 32 0.70
39 14 0.30
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (38 bp):
ATGAATAGTCACAACTCCTATAGCATTTAGTGATGTAA
Found at i:1934234 original size:16 final size:16
Alignment explanation
Indices: 1934213--1934244 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1934203 TAATGTGTTT
1934213 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
1934229 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
1934245 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:1934426 original size:45 final size:45
Alignment explanation
Indices: 1934358--1934588 Score: 246
Period size: 45 Copynumber: 4.9 Consensus size: 45
1934348 AAGAGGTGGA
** * *
1934358 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCATTTGAC
* *
1934403 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCATTTGAC
1934448 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCAT-G--G-A----A-GAA--A-TTGAGGAAGCATTTGAC
* * *
1934505 CAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCATTTGAC
* * *
1934550 CAACATCATGCATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCA
1934589 CCATGGCCGA
Statistics
Matches: 158, Mismatches: 16, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
45 108 0.68
46 1 0.01
48 4 0.03
49 2 0.01
53 2 0.01
54 4 0.03
56 1 0.01
57 36 0.23
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCATTTGAC
Found at i:1934483 original size:12 final size:12
Alignment explanation
Indices: 1934468--1934503 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1934458 CATAATTCAT
*
1934468 GGAAGAATTTGA
1 GGAAGCATTTGA
1934480 GGAAGCATTTGA
1 GGAAGCATTTGA
1934492 GGAAGCATTTGA
1 GGAAGCATTTGA
1934504 CCAACATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (12 bp):
GGAAGCATTTGA
Found at i:1934495 original size:57 final size:57
Alignment explanation
Indices: 1934423--1934547 Score: 214
Period size: 57 Copynumber: 2.2 Consensus size: 57
1934413 CATAATTCAT
* * * *
1934423 GGAAGAATTTGAGGAAGCATTTGGCCAACATCATGCATAATTCATGGAAGAATTTGA
1 GGAAGCATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAA
1934480 GGAAGCATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAA
1 GGAAGCATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAA
1934537 GGAAGCATTTG
1 GGAAGCATTTG
1934548 GCCAACATCA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (57 bp):
GGAAGCATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAA
Found at i:1934547 original size:102 final size:102
Alignment explanation
Indices: 1934389--1934588 Score: 346
Period size: 102 Copynumber: 2.0 Consensus size: 102
1934379 GAACAAATTA
* *
1934389 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGCCAACAT
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGCCAACAT
* * *
1934454 CATGCATAATTCATGGAAGAATTTGAGGAAGCATTTG
66 CATGCATAATTCAAGGAACAAATTGAGGAAGCATTTG
1934491 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGCCAACAT
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGCCAACAT
*
1934556 CATGCATAATTTAAGGAACAAATTGAGGAAGCA
66 CATGCATAATTCAAGGAACAAATTGAGGAAGCA
1934589 CCATGGCCGA
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (102 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGCCAACAT
CATGCATAATTCAAGGAACAAATTGAGGAAGCATTTG
Found at i:1935290 original size:66 final size:67
Alignment explanation
Indices: 1935209--1935339 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 67
1935199 ATGGTTTTGT
*
1935209 AAAAAAAAAAATTTGCCTACGGTCTAGGCGCGGACTAAAAGAACGTGAAAGATCCGTA-AAAAAA
1 AAAAAAAAAAATTTGCCTACGGTCTAGGCGCGGACGAAAAGAACGTGAAAGATCCGTATAAAAAA
1935273 TC
66 TC
*
1935275 AAAAAAAAAATTTTGCCTACGGTCTAGGCGCGGACGAAAAGAACGTGAAAGATCCGTATAAAAAA
1 AAAAAAAAAAATTTGCCTACGGTCTAGGCGCGGACGAAAAGAACGTGAAAGATCCGTATAAAAAA
1935340 AGAGTCTGGA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
66 56 0.90
67 6 0.10
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.17
Consensus pattern (67 bp):
AAAAAAAAAAATTTGCCTACGGTCTAGGCGCGGACGAAAAGAACGTGAAAGATCCGTATAAAAAA
TC
Found at i:1938253 original size:16 final size:16
Alignment explanation
Indices: 1938232--1938263 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1938222 TAATGTGTTT
1938232 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
1938248 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
1938264 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:1938445 original size:45 final size:45
Alignment explanation
Indices: 1938377--1938607 Score: 246
Period size: 45 Copynumber: 4.9 Consensus size: 45
1938367 AAGAGGTGGA
** * *
1938377 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCATTTGAC
* *
1938422 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCATTTGAC
1938467 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCAT-G--G-A----A-GAA--A-TTGAGGAAGCATTTGAC
* * *
1938524 CAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCATTTGAC
* * *
1938569 CAACATCATGCATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCA
1938608 CCATGGCCGA
Statistics
Matches: 158, Mismatches: 16, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
45 108 0.68
46 1 0.01
48 4 0.03
49 2 0.01
53 2 0.01
54 4 0.03
56 1 0.01
57 36 0.23
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCATTTGAC
Found at i:1938502 original size:12 final size:12
Alignment explanation
Indices: 1938487--1938522 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1938477 CATAATTCAT
*
1938487 GGAAGAATTTGA
1 GGAAGCATTTGA
1938499 GGAAGCATTTGA
1 GGAAGCATTTGA
1938511 GGAAGCATTTGA
1 GGAAGCATTTGA
1938523 CCAACATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (12 bp):
GGAAGCATTTGA
Found at i:1938514 original size:57 final size:57
Alignment explanation
Indices: 1938442--1938566 Score: 214
Period size: 57 Copynumber: 2.2 Consensus size: 57
1938432 CATAATTCAT
* * * *
1938442 GGAAGAATTTGAGGAAGCATTTGGCCAACATCATGCATAATTCATGGAAGAATTTGA
1 GGAAGCATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAA
1938499 GGAAGCATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAA
1 GGAAGCATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAA
1938556 GGAAGCATTTG
1 GGAAGCATTTG
1938567 GCCAACATCA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (57 bp):
GGAAGCATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAA
Found at i:1938566 original size:102 final size:102
Alignment explanation
Indices: 1938408--1938607 Score: 346
Period size: 102 Copynumber: 2.0 Consensus size: 102
1938398 GAACAAATTA
* *
1938408 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGCCAACAT
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGCCAACAT
* * *
1938473 CATGCATAATTCATGGAAGAATTTGAGGAAGCATTTG
66 CATGCATAATTCAAGGAACAAATTGAGGAAGCATTTG
1938510 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGCCAACAT
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGCCAACAT
*
1938575 CATGCATAATTTAAGGAACAAATTGAGGAAGCA
66 CATGCATAATTCAAGGAACAAATTGAGGAAGCA
1938608 CCATGGCCGA
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (102 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGCCAACAT
CATGCATAATTCAAGGAACAAATTGAGGAAGCATTTG
Found at i:1939309 original size:66 final size:67
Alignment explanation
Indices: 1939228--1939358 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 67
1939218 ATGGTTTTGT
*
1939228 AAAAAAAAAAATTTGCCTACGGTCTAGGCGCGGACTAAAAGAACGTGAAAGATCCGTA-AAAAAA
1 AAAAAAAAAAATTTGCCTACGGTCTAGGCGCGGACGAAAAGAACGTGAAAGATCCGTATAAAAAA
1939292 TC
66 TC
*
1939294 AAAAAAAAAATTTTGCCTACGGTCTAGGCGCGGACGAAAAGAACGTGAAAGATCCGTATAAAAAA
1 AAAAAAAAAAATTTGCCTACGGTCTAGGCGCGGACGAAAAGAACGTGAAAGATCCGTATAAAAAA
1939359 AGAGTCTGGA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
66 56 0.90
67 6 0.10
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.17
Consensus pattern (67 bp):
AAAAAAAAAAATTTGCCTACGGTCTAGGCGCGGACGAAAAGAACGTGAAAGATCCGTATAAAAAA
TC
Found at i:1942268 original size:16 final size:16
Alignment explanation
Indices: 1942247--1942278 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1942237 TAATGTGTTT
1942247 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
1942263 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
1942279 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:1942460 original size:45 final size:45
Alignment explanation
Indices: 1942392--1942622 Score: 246
Period size: 45 Copynumber: 4.9 Consensus size: 45
1942382 AAGAGGTGGA
** * *
1942392 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCATTTGAC
* *
1942437 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCATTTGAC
1942482 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCAT-G--G-A----A-GAA--A-TTGAGGAAGCATTTGAC
* * *
1942539 CAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCATTTGAC
* * *
1942584 CAACATCATGCATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCA
1942623 CCATGGCCGA
Statistics
Matches: 158, Mismatches: 16, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
45 108 0.68
46 1 0.01
48 4 0.03
49 2 0.01
53 2 0.01
54 4 0.03
56 1 0.01
57 36 0.23
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAAATTGAGGAAGCATTTGAC
Found at i:1942517 original size:12 final size:12
Alignment explanation
Indices: 1942502--1942537 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1942492 CATAATTCAT
*
1942502 GGAAGAATTTGA
1 GGAAGCATTTGA
1942514 GGAAGCATTTGA
1 GGAAGCATTTGA
1942526 GGAAGCATTTGA
1 GGAAGCATTTGA
1942538 CCAACATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (12 bp):
GGAAGCATTTGA
Found at i:1942529 original size:57 final size:57
Alignment explanation
Indices: 1942457--1942581 Score: 214
Period size: 57 Copynumber: 2.2 Consensus size: 57
1942447 CATAATTCAT
* * * *
1942457 GGAAGAATTTGAGGAAGCATTTGGCCAACATCATGCATAATTCATGGAAGAATTTGA
1 GGAAGCATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAA
1942514 GGAAGCATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAA
1 GGAAGCATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAA
1942571 GGAAGCATTTG
1 GGAAGCATTTG
1942582 GCCAACATCA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (57 bp):
GGAAGCATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAA
Found at i:1942581 original size:102 final size:102
Alignment explanation
Indices: 1942423--1942622 Score: 346
Period size: 102 Copynumber: 2.0 Consensus size: 102
1942413 GAACAAATTA
* *
1942423 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGCCAACAT
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGCCAACAT
* * *
1942488 CATGCATAATTCATGGAAGAATTTGAGGAAGCATTTG
66 CATGCATAATTCAAGGAACAAATTGAGGAAGCATTTG
1942525 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGCCAACAT
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGCCAACAT
*
1942590 CATGCATAATTTAAGGAACAAATTGAGGAAGCA
66 CATGCATAATTCAAGGAACAAATTGAGGAAGCA
1942623 CCATGGCCGA
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (102 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAACTTAAGGAAGCATTTGGCCAACAT
CATGCATAATTCAAGGAACAAATTGAGGAAGCATTTG
Found at i:1944822 original size:24 final size:24
Alignment explanation
Indices: 1944795--1944846 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1944785 TTAGTAAGTC
* *
1944795 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1944819 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1944843 AAAT
1 AAAT
1944847 GTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1960251 original size:22 final size:23
Alignment explanation
Indices: 1960192--1960251 Score: 59
Period size: 25 Copynumber: 2.6 Consensus size: 23
1960182 AATTTAAATT
* *
1960192 TTAAAATTCAAAAAATAGAATGA
1 TTAAACTTCAAATAATAGAATGA
* *
1960215 TTAAATTCTTAAAATAATAGTAT-A
1 TTAAA--CTTCAAATAATAGAATGA
1960239 TTAAACTTCAAAT
1 TTAAACTTCAAAT
1960252 TTATAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
22 7 0.23
23 5 0.17
24 6 0.20
25 12 0.40
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (23 bp):
TTAAACTTCAAATAATAGAATGA
Found at i:1962616 original size:47 final size:47
Alignment explanation
Indices: 1962556--1962648 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
1962546 ATTGCACACT
*
1962556 TGCATACATAAAGTACACATAGCATGGTAATCAAGCACTTATTACGC
1 TGCAAACATAAAGTACACATAGCATGGTAATCAAGCACTTATTACGC
1962603 TGCAAACATAAAGTACACATAGCATGGTAATCAAGCACTTATTACG
1 TGCAAACATAAAGTACACATAGCATGGTAATCAAGCACTTATTACG
1962649 AAACTTTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (47 bp):
TGCAAACATAAAGTACACATAGCATGGTAATCAAGCACTTATTACGC
Found at i:1964929 original size:2 final size:2
Alignment explanation
Indices: 1964922--1964986 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1964912 ATTCCATTAA
1964922 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1964964 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
1964987 GTATATATAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1968924 original size:22 final size:22
Alignment explanation
Indices: 1968899--1968943 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1968889 ATAGATGGAG
1968899 TTTAATAAAGTTTTAAAAACCT
1 TTTAATAAAGTTTTAAAAACCT
*
1968921 TTTAATAAGGTTTTAAAAACCT
1 TTTAATAAAGTTTTAAAAACCT
1968943 T
1 T
1968944 ATTCTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (22 bp):
TTTAATAAAGTTTTAAAAACCT
Found at i:1969081 original size:27 final size:27
Alignment explanation
Indices: 1969050--1969104 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1969040 CTTAATCCTA
1969050 ACAAAATTTGATTCTTCTTTTAACTCC
1 ACAAAATTTGATTCTTCTTTTAACTCC
1969077 ACAAAATTTGATTCTTCTTTTAACTCC
1 ACAAAATTTGATTCTTCTTTTAACTCC
1969104 A
1 A
1969105 ATGGTGTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.44
Consensus pattern (27 bp):
ACAAAATTTGATTCTTCTTTTAACTCC
Found at i:1969501 original size:74 final size:74
Alignment explanation
Indices: 1969378--1969602 Score: 396
Period size: 74 Copynumber: 3.0 Consensus size: 74
1969368 GTTTTTTTTT
* *
1969378 TTTTACTTTTCACAGGTTTCTAATTTTGCAAACAAAAGTTGACCCTTCAATGATATTTTTATACA
1 TTTTACTTTTTACAGGTTTTTAA--TTGCAAACAAAAGTTGACCCTTCAATGATATTTTTATACA
1969443 ATTTGAAGTTG
64 ATTTGAAGTTG
*
1969454 TTTTACTTTTTACAGGTTTTTAATTGCAAACAAAAGTTGACCCTTCAATGATATTTTTATACGAT
1 TTTTACTTTTTACAGGTTTTTAATTGCAAACAAAAGTTGACCCTTCAATGATATTTTTATACAAT
1969519 TTGAAGTTG
66 TTGAAGTTG
*
1969528 TTCTACTTTTTACAGGTTTTTAATTGCAAACAAAAGTTGACCCTTCAATGATATTTTTATACAAT
1 TTTTACTTTTTACAGGTTTTTAATTGCAAACAAAAGTTGACCCTTCAATGATATTTTTATACAAT
1969593 TTGAAGTTG
66 TTGAAGTTG
1969602 T
1 T
1969603 ATGGAGTGGG
Statistics
Matches: 144, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
74 123 0.85
76 21 0.15
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.44
Consensus pattern (74 bp):
TTTTACTTTTTACAGGTTTTTAATTGCAAACAAAAGTTGACCCTTCAATGATATTTTTATACAAT
TTGAAGTTG
Found at i:1970213 original size:18 final size:16
Alignment explanation
Indices: 1970190--1970229 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
1970180 GTTCAACTAA
1970190 TTTTTATTTGTTAAATAT
1 TTTTTATTT-TTAAA-AT
*
1970208 TTTTTATTTTTATAAT
1 TTTTTATTTTTAAAAT
1970224 TTTTTA
1 TTTTTA
1970230 ATAATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 4 0.19
18 9 0.43
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTATTTTTAAAAT
Found at i:1980713 original size:22 final size:22
Alignment explanation
Indices: 1980663--1980713 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1980653 AAATTTTTCA
* * *
1980663 TGCTGTTGTTTTGTTGCTATCT
1 TGCTGTTGTTTTGCTACCATCT
* *
1980685 TGTTGTTGTTTTGCTACCATTT
1 TGCTGTTGTTTTGCTACCATCT
1980707 TGCTGTT
1 TGCTGTT
1980714 ATATTTGTAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.06, C:0.14, G:0.22, T:0.59
Consensus pattern (22 bp):
TGCTGTTGTTTTGCTACCATCT
Found at i:1988551 original size:41 final size:42
Alignment explanation
Indices: 1988504--1988584 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 42
1988494 CTTTTTACAT
* *
1988504 CAATTTTTTTATTAAGAATTATAAATT-AATTATAATTATCA
1 CAATTTTTTAACTAAGAATTATAAATTAAATTATAATTATCA
* *
1988545 CAATTTTTTAACTAATAATTCTAAATTAAATTATAATTAT
1 CAATTTTTTAACTAAGAATTATAAATTAAATTATAATTAT
1988585 TTTTAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 23 0.66
42 12 0.34
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.48
Consensus pattern (42 bp):
CAATTTTTTAACTAAGAATTATAAATTAAATTATAATTATCA
Found at i:1999335 original size:24 final size:24
Alignment explanation
Indices: 1999304--1999363 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
1999294 TAAAACAAAC
1999304 TTAACCCAAAACCCAACTACCCAA
1 TTAACCCAAAACCCAACTACCCAA
* * *
1999328 TTAACCCACCAGCCCAACTACCCAT
1 TTAACCCA-AAACCCAACTACCCAA
1999353 TTACACCCAAA
1 TTA-ACCCAAA
1999364 CCTGAAGCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 8 0.27
25 17 0.57
26 5 0.17
ACGTcount: A:0.40, C:0.43, G:0.02, T:0.15
Consensus pattern (24 bp):
TTAACCCAAAACCCAACTACCCAA
Found at i:2004452 original size:22 final size:23
Alignment explanation
Indices: 2004410--2004452 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2004400 TTATTTTAGT
* *
2004410 ATTTATAATTTTTTTATAATTAA
1 ATTTATAATTTTATTAAAATTAA
2004433 ATTTA-AATTTTATTAAAATT
1 ATTTATAATTTTATTAAAATT
2004453 TGATGCTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTATAATTTTATTAAAATTAA
Found at i:2011780 original size:20 final size:20
Alignment explanation
Indices: 2011746--2011787 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2011736 AACTATTTAA
** *
2011746 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
2011766 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
2011786 AT
1 AT
2011788 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:2015754 original size:24 final size:23
Alignment explanation
Indices: 2015727--2015796 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
2015717 TTATTAACAT
*
2015727 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* * *
2015751 TGTTCATGAACATATTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
2015774 TGTTTGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
2015797 GTTAAATGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Done.