Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006443.1 Hibiscus syriacus cultivar Beakdansim tig00015564_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 132563
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:389 original size:9 final size:9
Alignment explanation
Indices: 375--511 Score: 88
Period size: 9 Copynumber: 15.2 Consensus size: 9
365 TATTGAACCC
375 TTATTTTTT
1 TTATTTTTT
*
384 TTATTTCTT
1 TTATTTTTT
*
393 TCATTTTTT
1 TTATTTTTT
*
402 TCATTTTCTT
1 TTATTTT-TT
*
412 TCA-TTTTT
1 TTATTTTTT
*
420 TCA-TTTTT
1 TTATTTTTT
428 TTATTTTTT
1 TTATTTTTT
*
437 TCATTTCATTT
1 TTATTT--TTT
*
448 TT-TTTCATT
1 TTATTT-TTT
*
457 TCATTTTTT
1 TTATTTTTT
*
466 TCA-TTTTT
1 TTATTTTTT
474 TTA-TTTTT
1 TTATTTTTT
482 TTATTTTTT
1 TTATTTTTT
491 TT-TTTTCATT
1 TTATTTT--TT
*
501 TTCTTTTTT
1 TTATTTTTT
510 TT
1 TT
512 TTCAGGCGAA
Statistics
Matches: 108, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
8 31 0.29
9 54 0.50
10 15 0.14
11 8 0.07
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (9 bp):
TTATTTTTT
Found at i:426 original size:7 final size:8
Alignment explanation
Indices: 379--502 Score: 91
Period size: 8 Copynumber: 15.5 Consensus size: 8
369 GAACCCTTAT
*
379 TTTTTTTA
1 TTTTTTCA
387 TTTCTTTCA
1 TTT-TTTCA
396 TTTTTTTCA
1 -TTTTTTCA
405 TTTTCTTTCA
1 -TTT-TTTCA
415 TTTTTTCA
1 TTTTTTCA
*
423 TTTTTTTA
1 TTTTTTCA
431 TTTTTTTCA
1 -TTTTTTCA
440 ---TTTCA
1 TTTTTTCA
445 TTTTTT--
1 TTTTTTCA
*
451 TTCATTTCA
1 TT-TTTTCA
460 TTTTTTTCA
1 -TTTTTTCA
*
469 TTTTTTTA
1 TTTTTTCA
*
477 TTTTTTTA
1 TTTTTTCA
485 TTTTTT--
1 TTTTTTCA
491 TTTTTTCA
1 TTTTTTCA
499 TTTT
1 TTTT
503 CTTTTTTTTT
Statistics
Matches: 97, Mismatches: 6, Indels: 26
0.75 0.05 0.20
Matches are distributed among these distances:
5 5 0.05
6 8 0.08
7 3 0.03
8 43 0.44
9 28 0.29
10 10 0.10
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCA
Found at i:446 original size:30 final size:29
Alignment explanation
Indices: 405--513 Score: 104
Period size: 29 Copynumber: 3.9 Consensus size: 29
395 ATTTTTTTCA
405 TTTTC-TTTCATTTTTTCATTTTTTTATTT
1 TTTTCATTTCATTTTTT-ATTTTTTTATTT
* *
434 TTTTCATTTCATTTTTT-TTCATTTCATTT
1 TTTTCATTTCATTTTTTATT-TTTTTATTT
463 TTTTCA--T--TTTTTTATTTTTTTATTT
1 TTTTCATTTCATTTTTTATTTTTTTATTT
** *
488 TTTTTTTTTCATTTTCTTTTTTTTTT
1 TTTTCATTTCATTTT-TTATTTTTTT
514 CAGGCGAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
25 17 0.26
26 2 0.03
27 2 0.03
28 2 0.03
29 22 0.34
30 20 0.31
ACGTcount: A:0.10, C:0.09, G:0.00, T:0.81
Consensus pattern (29 bp):
TTTTCATTTCATTTTTTATTTTTTTATTT
Found at i:447 original size:14 final size:14
Alignment explanation
Indices: 430--510 Score: 76
Period size: 14 Copynumber: 5.6 Consensus size: 14
420 TCATTTTTTT
430 ATTTTTTTCATTTC
1 ATTTTTTTCATTTC
444 ATTTTTTTTCATTTC
1 A-TTTTTTTCATTTC
*
459 ATTTTTTTCATTTTTTT
1 ATTTTTTTCA---TTTC
*
476 ATTTTTTT-ATTTT
1 ATTTTTTTCATTTC
*
489 TTTTTTTTCATTTTC
1 ATTTTTTTCA-TTTC
504 -TTTTTTT
1 ATTTTTTT
511 TTTCAGGCGA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
13 11 0.19
14 18 0.31
15 17 0.29
16 1 0.02
17 11 0.19
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (14 bp):
ATTTTTTTCATTTC
Found at i:473 original size:54 final size:53
Alignment explanation
Indices: 375--510 Score: 186
Period size: 54 Copynumber: 2.5 Consensus size: 53
365 TATTGAACCC
*
375 TTATTTTTTTTATTTC-TTTCATTTTTTTCATTTTCTTTCATTTTTTCATTTTT
1 TTATTTTTTTTATTTCATTT-TTTTTTTTCATTTTCTTTCATTTTTTCATTTTT
* *
428 TTATTTTTTTCATTTCATTTTTTTTCATTTCATTTT-TTTCATTTTTTTATTTTT
1 TTATTTTTTTTATTTCATTTTTTTT--TTTCATTTTCTTTCATTTTTTCATTTTT
*
482 TTATTTTTTTTTTTTCATTTTCTTTTTTT
1 TTATTTTTTTTATTTCATTTT-TTTTTTT
511 TTTCAGGCGA
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
53 22 0.30
54 39 0.53
55 13 0.18
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (53 bp):
TTATTTTTTTTATTTCATTTTTTTTTTTCATTTTCTTTCATTTTTTCATTTTT
Found at i:493 original size:44 final size:44
Alignment explanation
Indices: 379--511 Score: 171
Period size: 44 Copynumber: 3.0 Consensus size: 44
369 GAACCCTTAT
* *
379 TTTTTTTATTTCTTTCATTTTTTTCATTTTC-TTTCA-TTTTTTCA
1 TTTTTTTATTT-TTTTATTTTTTT-TTTTTCATTTCATTTTTTTCA
*
423 TTTTTTTATTTTTTTCATTTCATTTTTTTTCATTTCATTTTTTTCA
1 TTTTTTTATTTTTTT-ATTT-TTTTTTTTTCATTTCATTTTTTTCA
*
469 TTTTTTTATTTTTTTATTTTTTTTTTTTCATTTTCTTTTTTTT
1 TTTTTTTATTTTTTTATTTTTTTTTTTTCA-TTTCATTTTTTT
512 TTCAGGCGAA
Statistics
Matches: 79, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
43 3 0.04
44 30 0.38
45 23 0.29
46 23 0.29
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.80
Consensus pattern (44 bp):
TTTTTTTATTTTTTTATTTTTTTTTTTTCATTTCATTTTTTTCA
Found at i:511 original size:15 final size:15
Alignment explanation
Indices: 391--511 Score: 113
Period size: 15 Copynumber: 7.8 Consensus size: 15
381 TTTTTATTTC
*
391 TTTCATTTTTTTCAT
1 TTTCTTTTTTTTCAT
406 TTTCTTTCATTTTTTCATT
1 TTTC-TT--TTTTTTCA-T
*
425 TTTTTATTTTTTTCA-
1 TTTCT-TTTTTTTCAT
440 TTTCATTTTTTTTCA-
1 TTTC-TTTTTTTTCAT
*
455 TTTCATTTTTTTCAT
1 TTTCTTTTTTTTCAT
* *
470 TTTTTTATTTTTTTAT
1 TTTCTT-TTTTTTCAT
486 TTT-TTTTTTTTCAT
1 TTTCTTTTTTTTCAT
500 TTTCTTTTTTTT
1 TTTCTTTTTTTT
512 TTCAGGCGAA
Statistics
Matches: 89, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
14 20 0.22
15 34 0.38
16 13 0.15
17 8 0.09
18 9 0.10
19 5 0.06
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTTTTTTTCAT
Found at i:511 original size:45 final size:47
Alignment explanation
Indices: 378--511 Score: 172
Period size: 46 Copynumber: 2.9 Consensus size: 47
368 TGAACCCTTA
*
378 TTTTT-TTTATTTC-TTTCA-TTTTTTTCATTTTCTTTCATTTTTTCATT
1 TTTTTATTTTTTTCATTTCATTTTTTTTCATTTTC-TT--TTTTTTCATT
*
425 TTTTTATTTTTTTCATTTCATTTTTTTTCA-TTTCATTTTTTTCATT
1 TTTTTATTTTTTTCATTTCATTTTTTTTCATTTTCTTTTTTTTCATT
*
471 TTTTTATTTTTTT-ATTT-TTTTTTTTTCATTTTCTTTTTTTT
1 TTTTTATTTTTTTCATTTCATTTTTTTTCATTTTCTTTTTTTT
512 TTCAGGCGAA
Statistics
Matches: 79, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
44 10 0.13
45 15 0.19
46 23 0.29
47 5 0.06
48 8 0.10
49 9 0.11
50 9 0.11
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (47 bp):
TTTTTATTTTTTTCATTTCATTTTTTTTCATTTTCTTTTTTTTCATT
Found at i:5543 original size:24 final size:24
Alignment explanation
Indices: 5511--5565 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
5501 GTGAAGTGGC
* *
5511 CTACCTCATCCATATCTTTCTTAA
1 CTACCTCATCCACATCTTCCTTAA
5535 CTACCTCATCCACATCTTCCTTAA
1 CTACCTCATCCACATCTTCCTTAA
*
5559 CAACCTC
1 CTACCTC
5566 TGAACTCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.40, G:0.00, T:0.35
Consensus pattern (24 bp):
CTACCTCATCCACATCTTCCTTAA
Found at i:12134 original size:20 final size:20
Alignment explanation
Indices: 12106--12162 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
12096 TTGGTTTACT
*
12106 GAATGAAAGATTACCAGTAG
1 GAATAAAAGATTACCAGTAG
*
12126 GAATAAAAGATTACCAGTAT
1 GAATAAAAGATTACCAGTAG
12146 GAATAAAAGATTACCAG
1 GAATAAAAGATTACCAG
12163 GGAATAGGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (20 bp):
GAATAAAAGATTACCAGTAG
Found at i:13666 original size:33 final size:33
Alignment explanation
Indices: 13624--13686 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
13614 TCCACACATT
*
13624 TTAGTGGAGCAATAAGTGGAAATGAGTTGTTAC
1 TTAGTGGAGCAATAAGTGAAAATGAGTTGTTAC
*
13657 TTAGTGGAGCAGTAAGTGAAAATGAGTTGT
1 TTAGTGGAGCAATAAGTGAAAATGAGTTGT
13687 CTACAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.33, C:0.05, G:0.32, T:0.30
Consensus pattern (33 bp):
TTAGTGGAGCAATAAGTGAAAATGAGTTGTTAC
Found at i:14923 original size:19 final size:19
Alignment explanation
Indices: 14886--14924 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
14876 TATTAATTTT
*
14886 ATTTTATTTTAATACTTAA
1 ATTTTATTTTAATAATTAA
**
14905 ATTTTATTTTTTTAATTAA
1 ATTTTATTTTAATAATTAA
14924 A
1 A
14925 CTTAACGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTATTTTAATAATTAA
Found at i:15929 original size:43 final size:43
Alignment explanation
Indices: 15880--15964 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
15870 TCAAGAATAT
*
15880 TTTTAATATCTCAGTATGATGTATTTGT-GAATTGTTGCTTTGG
1 TTTTAATATCTCAGTATGATGTATTTGTAG-ATTGTTACTTTGG
* * *
15923 TTTTAATATGTTAGTTTGATGTATTTGTAGATTGTTACTTTG
1 TTTTAATATCTCAGTATGATGTATTTGTAGATTGTTACTTTG
15965 AAGTTTAGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 36 0.97
44 1 0.03
ACGTcount: A:0.21, C:0.05, G:0.20, T:0.54
Consensus pattern (43 bp):
TTTTAATATCTCAGTATGATGTATTTGTAGATTGTTACTTTGG
Found at i:16343 original size:10 final size:10
Alignment explanation
Indices: 16328--16375 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
16318 ATTAGTATAA
16328 TTATTAATAT
1 TTATTAATAT
*
16338 TTATTACTAT
1 TTATTAATAT
16348 TTA-T-ATAT
1 TTATTAATAT
*
16356 TT-TT-ATAA
1 TTATTAATAT
16364 TTATTAATAT
1 TTATTAATAT
16374 TT
1 TT
16376 GATTTATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
8 11 0.35
9 3 0.10
10 17 0.55
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATTAATAT
Found at i:16367 original size:16 final size:18
Alignment explanation
Indices: 16323--16375 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
16313 CACCTATTAG
16323 TATAATTATTAATATTTAT
1 TATAATTA-TAATATTTAT
*
16342 TACTATTTAT-ATATTT-T
1 TA-TAATTATAATATTTAT
16359 TATAATTATTAATATTT
1 TATAATTA-TAATATTT
16376 GATTTATTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 5 0.17
17 4 0.14
18 12 0.41
19 3 0.10
20 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TATAATTATAATATTTAT
Found at i:18517 original size:19 final size:20
Alignment explanation
Indices: 18475--18517 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18465 AAATTATTAA
*
18475 TAAAAAATACATAAAATATC
1 TAAAAAATACATAAAAAATC
* *
18495 TAAAATATA-ATAAAAAATT
1 TAAAAAATACATAAAAAATC
18514 TAAA
1 TAAA
18518 TAAAAAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAAAATACATAAAAAATC
Found at i:18887 original size:7 final size:7
Alignment explanation
Indices: 18875--18916 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
18865 AGAACTATAG
18875 ATTTTTT
1 ATTTTTT
18882 ATTTTTT
1 ATTTTTT
18889 ATTTTTT
1 ATTTTTT
18896 ATTTTTT
1 ATTTTTT
18903 ATTTTTT
1 ATTTTTT
18910 ATTTTTT
1 ATTTTTT
18917 CAATGATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
ATTTTTT
Found at i:19766 original size:21 final size:21
Alignment explanation
Indices: 19737--19780 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
19727 TAAGGGATAG
*
19737 GAACATCGATTATCGCAACGC
1 GAACATCGACTATCGCAACGC
* * *
19758 GAACTTCGACTATTGCAATGC
1 GAACATCGACTATCGCAACGC
19779 GA
1 GA
19781 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
GAACATCGACTATCGCAACGC
Found at i:19819 original size:21 final size:19
Alignment explanation
Indices: 19790--20083 Score: 133
Period size: 21 Copynumber: 14.2 Consensus size: 19
19780 ATTTTTTAAA
19790 TTCGTTGCGATAGTTCAAG
1 TTCGTTGCGATAGTTCAAG
19809 TTCGTGTTGCGATAG-TCTAAG
1 TTC--GTTGCGATAGTTC-AAG
19830 TTCGTTGCGATAG-TCGAAG
1 TTCGTTGCGATAGTTC-AAG
*
19849 TTCGAGTTGCGATTTA-TTCTAAA
1 TTC--GTTGCGA--TAGTTC-AAG
* *
19872 TTCGTTGCAATTTA-TTCCAAA
1 TTCGTTGCGA--TAGTT-CAAG
*
19893 TTCGTTGCGATAGTCCAAG
1 TTCGTTGCGATAGTTCAAG
19912 TTTGCGTTGCGATTTA-TTCCAAG
1 -TT-CGTTGCGA--TAGTT-CAAG
*
19935 TTCGTTGTGATAG-TCGAAG
1 TTCGTTGCGATAGTTC-AAG
*
19954 TTCGCGTTGCTATTTA-TTCCAAG
1 TT--CGTTGCGA--TAGTT-CAAG
19977 TTCGTTGCGATAGTAT-AAG
1 TTCGTTGCGATAGT-TCAAG
19996 TTCGCGTTGCGATTTA-TTCTAAG
1 TT--CGTTGCGA--TAGTTC-AAG
*
20019 TTCGTTGCGATAGTACAAG
1 TTCGTTGCGATAGTTCAAG
20038 TTCGCGTTGCGATTTA-TTCCAAG
1 TT--CGTTGCGA--TAGTT-CAAG
20061 TTCGTTGCGATAG-TCGAAG
1 TTCGTTGCGATAGTTC-AAG
20080 TTCG
1 TTCG
20084 CGTCCAAGTA
Statistics
Matches: 222, Mismatches: 14, Indels: 78
0.71 0.04 0.25
Matches are distributed among these distances:
18 2 0.01
19 58 0.26
20 8 0.04
21 109 0.49
22 6 0.03
23 38 0.17
24 1 0.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (19 bp):
TTCGTTGCGATAGTTCAAG
Found at i:20081 original size:42 final size:42
Alignment explanation
Indices: 19874--20086 Score: 329
Period size: 42 Copynumber: 5.1 Consensus size: 42
19864 ATTCTAAATT
* * * *
19874 CGTTGCAATTTATTCCAAATTCGTTGCGATAGTCCAAGTTTG
1 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
*
19916 CGTTGCGATTTATTCCAAGTTCGTTGTGATAGTCGAAGTTCG
1 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
* **
19958 CGTTGCTATTTATTCCAAGTTCGTTGCGATAGTATAAGTTCG
1 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
*
20000 CGTTGCGATTTATTCTAAGTTCGTTGCGATAGTAC-AAGTTCG
1 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGT-CGAAGTTCG
20042 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
20084 CGT
1 CGT
20087 CCAAGTATTG
Statistics
Matches: 156, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
41 1 0.01
42 155 0.99
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (42 bp):
CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
Found at i:20978 original size:19 final size:19
Alignment explanation
Indices: 20954--20995 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
20944 AATCGCAACG
20954 CGAACTTCGACTATCGCAA
1 CGAACTTCGACTATCGCAA
*
20973 CGAACTTGGACTATCGCAA
1 CGAACTTCGACTATCGCAA
20992 CGAA
1 CGAA
20996 TTTGCAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (19 bp):
CGAACTTCGACTATCGCAA
Found at i:21008 original size:18 final size:19
Alignment explanation
Indices: 20944--21009 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
20934 ATTTGGAATA
20944 AATCGCAACGCGAACTT-CGAC
1 AATCGCAA--CGAACTTGC-AC
* *
20965 TATCGCAACGAACTTGGAC
1 AATCGCAACGAACTTGCAC
* *
20984 TATCGCAACGAATTTGCA-
1 AATCGCAACGAACTTGCAC
21002 AATCGCAA
1 AATCGCAA
21010 TGCGATAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 7 0.18
19 25 0.64
21 7 0.18
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (19 bp):
AATCGCAACGAACTTGCAC
Found at i:24122 original size:3 final size:3
Alignment explanation
Indices: 24114--24154 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
24104 ACTAAAGACA
24114 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
24155 CTTAGCCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:27792 original size:29 final size:29
Alignment explanation
Indices: 27706--27798 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
27696 ATTTATTCTC
* * *
27706 AAACTTTTAAATATTCTAATTTCATCGTC
1 AAACTTTTGAATATTCTAATTTCATCTTT
* * * * *
27735 AAA-TTATGACTCTTATTTTAAATTAATCTTT
1 AAACTTTTGA---ATATTCTAATTTCATCTTT
*
27766 AAACTTTTGAATATTCTAATTTCATCTCT
1 AAACTTTTGAATATTCTAATTTCATCTTT
27795 AAAC
1 AAAC
27799 AATGACTCTC
Statistics
Matches: 46, Mismatches: 14, Indels: 8
0.68 0.21 0.12
Matches are distributed among these distances:
28 4 0.09
29 21 0.46
31 16 0.35
32 5 0.11
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.46
Consensus pattern (29 bp):
AAACTTTTGAATATTCTAATTTCATCTTT
Found at i:28161 original size:60 final size:60
Alignment explanation
Indices: 28031--28161 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 60
28021 ACTAATGGAG
* * * ** ** *
28031 AATGAAGGTCATAGTTTAGGGATGAAATTGAAATGTTTAAAAGTTTGAGGATTAATTTAG
1 AATGAGGGTCAGAGTTTAGGGATAAAATTGAAACATTTAAAAGTTTGAGGACCAATTTAA
* *
28091 AATG-GTGGTCAGAGTTTAGGGATAAAATTGGAGCATTTAAAAGTTT-AGGGACCAATTTAA
1 AATGAG-GGTCAGAGTTTAGGGATAAAATTGAAACATTTAAAAGTTTGA-GGACCAATTTAA
28151 AATGAGGGTCA
1 AATGAGGGTCA
28162 TATTTTGAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
59 1 0.02
60 56 0.97
61 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (60 bp):
AATGAGGGTCAGAGTTTAGGGATAAAATTGAAACATTTAAAAGTTTGAGGACCAATTTAA
Found at i:32856 original size:25 final size:25
Alignment explanation
Indices: 32828--32894 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
32818 ACTAATGCAC
32828 TTTGGTTGAAGAAACATTCGACAGA
1 TTTGGTTGAAGAAACATTCGACAGA
32853 TTTGGTTGAAGAAACATTCGACAGA
1 TTTGGTTGAAGAAACATTCGACAGA
*
32878 TTTGATTGAAGAAACAT
1 TTTGGTTGAAGAAACAT
32895 GCTTACCTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.30
Consensus pattern (25 bp):
TTTGGTTGAAGAAACATTCGACAGA
Found at i:40580 original size:60 final size:59
Alignment explanation
Indices: 40499--40657 Score: 173
Period size: 59 Copynumber: 2.7 Consensus size: 59
40489 CACATGTCCT
* * *
40499 CAAAGTATGATCC-TCATTTTAAATTGGTCCCTAAACTTTTAA-ATGTTTCAATTCCATCCC
1 CAAACTATGA-CCTTCATTTTAAATTGGTCCCTAAACTTTTAACA--ATTCAATTCCAGCCC
* * * *
40559 TAAACTATGA-CTATCATTTTAAATTAGT-CCTCAAATTTTTAACAATTCAATTTCAGCCC
1 CAAACTATGACCT-TCATTTTAAATTGGTCCCT-AAACTTTTAACAATTCAATTCCAGCCC
*
40618 CAAACTATGACCTTCATTCTAAATTGGTCCCTAAACTTTT
1 CAAACTATGACCTTCATTTTAAATTGGTCCCTAAACTTTT
40658 TGAACATTCT
Statistics
Matches: 82, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
58 1 0.01
59 44 0.54
60 36 0.44
61 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (59 bp):
CAAACTATGACCTTCATTTTAAATTGGTCCCTAAACTTTTAACAATTCAATTCCAGCCC
Found at i:40635 original size:59 final size:60
Alignment explanation
Indices: 40512--40674 Score: 156
Period size: 59 Copynumber: 2.7 Consensus size: 60
40502 AGTATGATCC
* * * ** * * *
40512 TCATTTTAAATTGGTCCCTAAAC-TTTTAAATGTTTCAATTCCATCCCTAAACTATGACTA
1 TCATTCTAAATTAGTCCCTAAACTTTTTGAA-CATTCAATTTCAGCCCCAAACTATGACTA
*
40572 TCATTTTAAATTAGT-CCTCAAA-TTTTT-AACAATTCAATTTCAGCCCCAAACTATGACCT-
1 TCATTCTAAATTAGTCCCT-AAACTTTTTGAAC-ATTCAATTTCAGCCCCAAACTATGA-CTA
*
40631 TCATTCTAAATTGGTCCCTAAACTTTTTGAACATTCTAATTTCA
1 TCATTCTAAATTAGTCCCTAAACTTTTTGAACATTC-AATTTCA
40675 TCTCAAACTA
Statistics
Matches: 87, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
59 42 0.48
60 35 0.40
61 10 0.11
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCCTAAACTTTTTGAACATTCAATTTCAGCCCCAAACTATGACTA
Found at i:40960 original size:61 final size:61
Alignment explanation
Indices: 40875--41000 Score: 159
Period size: 61 Copynumber: 2.1 Consensus size: 61
40865 TCATATTTTA
* * *
40875 GGGATGAAATTAGAATGCTTAAAAGTTTAAGGA-CACATTTAGAAT-AAGAATCATAGTTTGG
1 GGGATGAAATTAGAATGATTAAAAGTTTAAAGACCA-ATTTAAAATGAAG-ATCATAGTTTGG
* *
40936 GGGATGAAATTAGAAT-ATTCAAAAGTTTAAAGACCAATTTAAAATGAAGGTTATAGTTTGG
1 GGGATGAAATTAGAATGATT-AAAAGTTTAAAGACCAATTTAAAATGAAGATCATAGTTTGG
40997 GGGA
1 GGGA
41001 CATAATATGC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
60 2 0.04
61 50 0.88
62 5 0.09
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (61 bp):
GGGATGAAATTAGAATGATTAAAAGTTTAAAGACCAATTTAAAATGAAGATCATAGTTTGG
Found at i:46097 original size:23 final size:21
Alignment explanation
Indices: 46058--46110 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
46048 ATTTTTTGGT
* *
46058 ATTTTATTTTATTTATTTATTGA
1 ATTTT-TTATATTTATTT-TTAA
46081 ATATTTTTATATTTATTTTTAA
1 AT-TTTTTATATTTATTTTTAA
46103 ATTTTTTA
1 ATTTTTTA
46111 AAAATCGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 6 0.22
22 5 0.19
23 13 0.48
24 3 0.11
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
ATTTTTTATATTTATTTTTAA
Found at i:47724 original size:50 final size:49
Alignment explanation
Indices: 47599--47724 Score: 135
Period size: 50 Copynumber: 2.5 Consensus size: 49
47589 TTAGGAGGAA
* * * *
47599 AGCGCGCCCCCTGCACCGCGCTATATGCTGATTTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTG-ACCGCGATATACGCTGATCTGGCGCCACGTGAGTAT
* * * *
47649 AGCACGCCCCCTGCCCTGCGATATACGGTGATCTGGTGCCACGTGAGTAT
1 AGCGCGCCCCCTGACC-GCGATATACGCTGATCTGGCGCCACGTGAGTAT
* *
47699 AGCGCGACCCCTGATCCGCGTTATAC
1 AGCGCGCCCCCTGA-CCGCGATATAC
47725 CTGGATATCC
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
49 2 0.03
50 58 0.94
51 2 0.03
ACGTcount: A:0.17, C:0.34, G:0.28, T:0.21
Consensus pattern (49 bp):
AGCGCGCCCCCTGACCGCGATATACGCTGATCTGGCGCCACGTGAGTAT
Found at i:47887 original size:12 final size:10
Alignment explanation
Indices: 47846--47886 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
47836 TTTATCACAC
47846 CAAATTCTCT
1 CAAATTCTCT
47856 CAAATTCTCT
1 CAAATTCTCT
47866 -AAATTTCTCT
1 CAAA-TTCTCT
*
47876 CAAATACTCT
1 CAAATTCTCT
47886 C
1 C
47887 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:48204 original size:111 final size:111
Alignment explanation
Indices: 48010--48231 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
48000 TGGAAATCAT
*
48010 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
48075 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
*
48121 ATATCTCGACACTTTGCTGATACGGTAACATTTTATCGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
48186 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
48232 TTTTTGTAAT
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:50116 original size:6 final size:6
Alignment explanation
Indices: 50101--50148 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
50091 ACTTGCTCAG
* *
50101 GACGAC GACGAT GACGAT GACGAT GGTAACGAC GACGAT GACGAT GAC
1 GACGAT GACGAT GACGAT GACGAT -G--ACGAT GACGAT GACGAT GAC
50149 AACGAGGAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
6 30 0.83
7 1 0.03
8 1 0.03
9 4 0.11
ACGTcount: A:0.33, C:0.21, G:0.33, T:0.12
Consensus pattern (6 bp):
GACGAT
Found at i:50152 original size:21 final size:21
Alignment explanation
Indices: 50108--50153 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
50098 CAGGACGACG
* **
50108 ACGATGACGATGACGATGGTA
1 ACGACGACGATGACGATGACA
50129 ACGACGACGATGACGATGACA
1 ACGACGACGATGACGATGACA
50150 ACGA
1 ACGA
50154 GGAGTCAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.13
Consensus pattern (21 bp):
ACGACGACGATGACGATGACA
Found at i:54355 original size:22 final size:21
Alignment explanation
Indices: 54330--54374 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
54320 TTATATTAAC
54330 AAATTAATAAAATTATTTTTTA
1 AAATT-ATAAAATTATTTTTTA
*
54352 AAATTTTAAAATTATTTTTTA
1 AAATTATAAAATTATTTTTTA
54373 AA
1 AA
54375 TGAGAAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATTATAAAATTATTTTTTA
Found at i:57495 original size:20 final size:21
Alignment explanation
Indices: 57470--57562 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
57460 TTTTCCCAAT
*
57470 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
57490 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
57511 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
57531 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
57552 TCGCAATGCGA
1 TCGCAATGCGA
57563 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:57515 original size:41 final size:41
Alignment explanation
Indices: 57470--57562 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
57460 TTTTCCCAAT
57470 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
57511 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
57552 TCGCAATGCGA
1 TCGCAATGCGA
57563 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:57575 original size:41 final size:41
Alignment explanation
Indices: 57489--57623 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
57479 GAATAAGTAA
* *
57489 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
57530 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
57571 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
57612 TTCGCAACGCGA
1 ATCGCAACGCGA
57624 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:57576 original size:20 final size:20
Alignment explanation
Indices: 57551--57645 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
57541 AATTGGGAAA
*
57551 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
57571 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
57592 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
57612 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
57632 TTCGCAACGCGATA
1 ATCGCAACGCGATA
57646 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:57861 original size:22 final size:22
Alignment explanation
Indices: 57833--57876 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
57823 CACTCTCTCA
57833 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
57855 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
57877 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:58165 original size:20 final size:20
Alignment explanation
Indices: 58140--58177 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
58130 CGATTCTCTC
58140 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
58160 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
58178 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:60510 original size:33 final size:33
Alignment explanation
Indices: 60468--60594 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
60458 GGAAATTACT
60468 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
60501 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
60533 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
60567 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
60595 CGAGCGATAG
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:60575 original size:66 final size:66
Alignment explanation
Indices: 60469--60595 Score: 245
Period size: 66 Copynumber: 1.9 Consensus size: 66
60459 GAAATTACTA
60469 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
60534 T
66 T
*
60535 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGC
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGC
60596 GAGCGATAGT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
T
Found at i:62154 original size:21 final size:21
Alignment explanation
Indices: 62088--62154 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
62078 GTGAATCGGG
*
62088 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
62108 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
62130 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
62151 CTCT
1 CTCT
62155 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:62173 original size:42 final size:41
Alignment explanation
Indices: 62088--62210 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
62078 GTGAATCGGG
* * * * *
62088 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
62130 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
62172 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
62211 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:64291 original size:33 final size:33
Alignment explanation
Indices: 64234--64332 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
64224 ACGAGATAAT
*
64234 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
64268 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
64301 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
64333 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:64326 original size:19 final size:19
Alignment explanation
Indices: 64209--64393 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
64199 TCTTTTGGTT
*
64209 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
64228 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
64248 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
64266 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
64282 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
64300 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
64315 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
64335 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
64354 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
64373 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
64392 GA
1 GA
64394 TTTTGGTTTC
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.45
20 45 0.33
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:64347 original size:39 final size:38
Alignment explanation
Indices: 64304--64393 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
64294 GCGACCAGAC
64304 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
64343 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
64381 AATCGCAATGCGA
1 AATCGCAACGCGA
64394 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:64422 original size:19 final size:19
Alignment explanation
Indices: 64389--64455 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
64379 AAAATCGCAA
**
64389 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
64408 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
64427 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
64447 TGCGATTTT
1 TGCGATTTT
64456 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:64999 original size:20 final size:20
Alignment explanation
Indices: 64974--65025 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
64964 CGCTATGTAA
*
64974 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
64994 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
65014 ATCTCGTTGCGA
1 ATCGCGTTGCGA
65026 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:65086 original size:41 final size:41
Alignment explanation
Indices: 64995--65129 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
64985 AAAGTCAGTA
* * * ** *
64995 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCCAAT
*
65035 ATCGCATTGCGATAGTAAGTATCACATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCCAAT
* ** *
65077 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCACATTGCGATTTTCCCAAT
65118 TCGCGTTGCGAT
1 TCGCGTTGCGAT
65130 TTACTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCACATTGCGATTTTCCCAAT
Found at i:65087 original size:21 final size:21
Alignment explanation
Indices: 65061--65131 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
65051 AAGTATCACA
65061 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** *
65082 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCCAATTCGCG
65102 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
65123 TTGCGATTT
1 TTGCGATTT
65132 ACTTATTCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:65100 original size:20 final size:20
Alignment explanation
Indices: 65075--65148 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
65065 GATTTTCCCA
*
65075 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
65095 ATTCGCATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
65116 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
65136 ATTCGCATTGCGA
1 ATTCGCATTGCGA
65149 ATTAGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:65130 original size:41 final size:41
Alignment explanation
Indices: 65059--65148 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
65049 GTAAGTATCA
65059 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
65100 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
65141 CATTGCGA
1 CATTGCGA
65149 ATTAGGAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
Found at i:67466 original size:24 final size:24
Alignment explanation
Indices: 67439--67494 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
67429 CGTTCATTTA
*
67439 CGTTTGTGAACGTTCGGTTATGTT
1 CGTTTATGAACGTTCGGTTATGTT
**
67463 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTTATGAACGTTCGGTTATGTT
67487 CGTTTATG
1 CGTTTATG
67495 TTCATTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.11, C:0.12, G:0.27, T:0.50
Consensus pattern (24 bp):
CGTTTATGAACGTTCGGTTATGTT
Found at i:67477 original size:14 final size:14
Alignment explanation
Indices: 67449--67490 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
67439 CGTTTGTGAA
67449 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
67463 CG-T---TTATGTT
1 CGTTCGGTTATGTT
67473 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
67487 CGTT
1 CGTT
67491 TATGTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.07, C:0.14, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:67495 original size:24 final size:24
Alignment explanation
Indices: 67449--67497 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
67439 CGTTTGTGAA
67449 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
67473 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
67497 C
1 C
67498 ATTCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.14, G:0.24, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:67507 original size:24 final size:24
Alignment explanation
Indices: 67455--67510 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
67445 TGAACGTTCG
* *
67455 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
67479 GTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
67503 TTTATGTT
1 GTTATGTT
67511 TAACCCAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.11, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:68439 original size:16 final size:16
Alignment explanation
Indices: 68414--68470 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
68404 CCAACGTTTA
* *
68414 TGTTCGTTTATGATCG
1 TGTTCATTTATGTTCG
68430 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
68446 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
68462 T-TT-ATTTAT
1 TGTTCATTTAT
68471 TAAATGAACG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
14 5 0.14
15 2 0.05
16 30 0.81
ACGTcount: A:0.12, C:0.11, G:0.19, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:68552 original size:16 final size:16
Alignment explanation
Indices: 68531--68563 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
68521 AAAAAAAATT
68531 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
68547 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
68563 T
1 T
68564 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:69954 original size:39 final size:39
Alignment explanation
Indices: 69907--70006 Score: 121
Period size: 39 Copynumber: 2.6 Consensus size: 39
69897 ACATAGCATA
* *
69907 AGGA-CATGCGGTAAGGACTTACCCTGAGCACAAAGCTG
1 AGGAGCATGCGGTAAGGACTTACCCTGAGAACAAAGCCG
* *
69945 AGGAGCATGCAGTAAGGAATTACCCTGAGAACAAAGCCG
1 AGGAGCATGCGGTAAGGACTTACCCTGAGAACAAAGCCG
* * * *
69984 AAGAGCTTACGGTAAGAACTTAC
1 AGGAGCATGCGGTAAGGACTTAC
70007 AAGTCATAGA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
38 4 0.08
39 47 0.92
ACGTcount: A:0.36, C:0.21, G:0.27, T:0.16
Consensus pattern (39 bp):
AGGAGCATGCGGTAAGGACTTACCCTGAGAACAAAGCCG
Found at i:70427 original size:3 final size:3
Alignment explanation
Indices: 70419--70443 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
70409 ATCGGAATTC
70419 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
70444 CCCTATGTAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:70779 original size:18 final size:18
Alignment explanation
Indices: 70756--70791 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
70746 ATCAACGCCA
70756 GCCAACGGTCAACGGTTG
1 GCCAACGGTCAACGGTTG
70774 GCCAACGGTCAACGGTTG
1 GCCAACGGTCAACGGTTG
70792 ATCAATGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.33, T:0.17
Consensus pattern (18 bp):
GCCAACGGTCAACGGTTG
Found at i:70801 original size:18 final size:18
Alignment explanation
Indices: 70757--70808 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
70747 TCAACGCCAG
*
70757 CCAACGGTCAACGGTTGG
1 CCAACGGTCAACGGTTGA
70775 CCAACGGTCAACGGTTGA
1 CCAACGGTCAACGGTTGA
* * *
70793 TCAATGGTCAATGGTT
1 CCAACGGTCAACGGTT
70809 CAGTTCGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (18 bp):
CCAACGGTCAACGGTTGA
Found at i:76828 original size:39 final size:39
Alignment explanation
Indices: 76744--76839 Score: 111
Period size: 39 Copynumber: 2.5 Consensus size: 39
76734 GGCATAAGGA
* * * * *
76744 CCTGTGGTAAGGACTTACCCTGAGCACAAAATTGAGGAG
1 CCTGCGGTAAAGACTTACCCTAAGCACAAAATCGAGAAG
* * * *
76783 CATGCGGTAAAGACTTACCTTAAGCATAAAGTCGAGAAG
1 CCTGCGGTAAAGACTTACCCTAAGCACAAAATCGAGAAG
76822 CCTGCGGTAAAGACTTAC
1 CCTGCGGTAAAGACTTAC
76840 AAGTCATAGA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (39 bp):
CCTGCGGTAAAGACTTACCCTAAGCACAAAATCGAGAAG
Found at i:77260 original size:3 final size:3
Alignment explanation
Indices: 77252--77276 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
77242 ATCAGAATCC
77252 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
77277 CCATATTTAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:79208 original size:25 final size:25
Alignment explanation
Indices: 79180--79242 Score: 126
Period size: 25 Copynumber: 2.5 Consensus size: 25
79170 AATCATAGTC
79180 CAGTAAATCTCATTAAATTATACTG
1 CAGTAAATCTCATTAAATTATACTG
79205 CAGTAAATCTCATTAAATTATACTG
1 CAGTAAATCTCATTAAATTATACTG
79230 CAGTAAATCTCAT
1 CAGTAAATCTCAT
79243 AAAAGAGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (25 bp):
CAGTAAATCTCATTAAATTATACTG
Found at i:79369 original size:63 final size:63
Alignment explanation
Indices: 79263--79386 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
79253 TCCTAAGGGA
* * **
79263 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCATATGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCATAAAGCCTACCTAAGAAC
* * *
79326 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGTAAAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCATAAAGCCTACCTAAGA
79387 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCATAAAGCCTACCTAAGAAC
Found at i:80323 original size:29 final size:29
Alignment explanation
Indices: 80262--80395 Score: 214
Period size: 29 Copynumber: 4.6 Consensus size: 29
80252 CATATTCGAA
*
80262 AATTCCCAAAATGTAACCTTTTTACAAAAT
1 AATTCCCAAAATGTCACCTTTTT-CAAAAT
* *
80292 AATTCCCAGAATGTCACCTTTTTTAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
80321 AATTCCCAAAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
80350 AATTCCCAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
80379 AATTCCTAAAATGTCAC
1 AATTCCCAAAATGTCAC
80396 TAGGTCGGGT
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
29 75 0.78
30 21 0.22
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:80420 original size:17 final size:18
Alignment explanation
Indices: 80398--80442 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
80388 AATGTCACTA
80398 GGTCGGGTCGGGTCAAC-
1 GGTCGGGTCGGGTCAACG
*
80415 GGTCGGGTC-GGTGAACG
1 GGTCGGGTCGGGTCAACG
80432 GGTCGGGTCGG
1 GGTCGGGTCGG
80443 TTCAGACCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 6 0.24
17 18 0.72
18 1 0.04
ACGTcount: A:0.09, C:0.20, G:0.53, T:0.18
Consensus pattern (18 bp):
GGTCGGGTCGGGTCAACG
Found at i:87699 original size:29 final size:29
Alignment explanation
Indices: 87664--87796 Score: 203
Period size: 29 Copynumber: 4.6 Consensus size: 29
87654 CACATTCAAA
87664 AATTCCCAAAATGTCACATTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* *
87693 AATTCCCAGAATGTCACTTTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
*
87722 AATTCCCAAAATGTCATATTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* * *
87751 AATTCCCAGAATGTTACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
*
87780 AATTCCTAAAATGTCAC
1 AATTCCCAAAATGTCAC
87797 TAGGTCGGGT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 92 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.36
Consensus pattern (29 bp):
AATTCCCAAAATGTCACATTTTTCAAAAT
Found at i:87734 original size:58 final size:58
Alignment explanation
Indices: 87664--87796 Score: 230
Period size: 58 Copynumber: 2.3 Consensus size: 58
87654 CACATTCAAA
*
87664 AATTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATGTCACTTTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATGTCACCTTTTTCAAAAT
* *
87722 AATTCCCAAAATGTCATATTTTTCAAAATAATTCCCAGAATGTTACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATGTCACCTTTTTCAAAAT
*
87780 AATTCCTAAAATGTCAC
1 AATTCCCAAAATGTCAC
87797 TAGGTCGGGT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 70 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.36
Consensus pattern (58 bp):
AATTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATGTCACCTTTTTCAAAAT
Found at i:87827 original size:22 final size:22
Alignment explanation
Indices: 87799--87848 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
87789 AATGTCACTA
87799 GGTCGGGTCGGGTCAAC-AGTCG
1 GGTCGGGTC-GGTCAACGAGTCG
*
87821 GGTCGGGTCGGTCAACGGGTCG
1 GGTCGGGTCGGTCAACGAGTCG
87843 GGTCGG
1 GGTCGG
87849 TTCAGACTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.10, C:0.22, G:0.50, T:0.18
Consensus pattern (22 bp):
GGTCGGGTCGGTCAACGAGTCG
Found at i:89431 original size:2 final size:2
Alignment explanation
Indices: 89375--89416 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
89365 AATTTAACAA
89375 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89416 A
1 A
89417 ATCAATATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90026 original size:52 final size:54
Alignment explanation
Indices: 89970--90072 Score: 147
Period size: 53 Copynumber: 1.9 Consensus size: 54
89960 CAAAAAATTT
*
89970 GCTACAATG-AAAAGGTGTGATTACAAACCGTCTTAACTATTCAC-AAAAATGA
1 GCTACAATGTAAAAGGTGGGATTACAAACCGTCTTAACTATTCACTAAAAATGA
* * * *
90022 GCTACAATGTAAACGTTGGGATTACAACCCGTCTTCACTATTCACTAAAAA
1 GCTACAATGTAAAAGGTGGGATTACAAACCGTCTTAACTATTCACTAAAAA
90073 ATAATTAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 9 0.20
53 30 0.68
54 5 0.11
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (54 bp):
GCTACAATGTAAAAGGTGGGATTACAAACCGTCTTAACTATTCACTAAAAATGA
Found at i:94478 original size:38 final size:38
Alignment explanation
Indices: 94409--94483 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
94399 TACATATTTT
* *
94409 AGAAAACCATATAAAACACATACATATCAAAATATCAC
1 AGAAAACCATATAAAACACATACAGAACAAAATATCAC
* ** *
94447 AGAAAACCTTATAAAACATTTACGGAACAAAATATCA
1 AGAAAACCATATAAAACACATACAGAACAAAATATCA
94484 GTAATACGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.56, C:0.19, G:0.05, T:0.20
Consensus pattern (38 bp):
AGAAAACCATATAAAACACATACAGAACAAAATATCAC
Found at i:98285 original size:23 final size:21
Alignment explanation
Indices: 98234--98312 Score: 90
Period size: 22 Copynumber: 3.7 Consensus size: 21
98224 GACCCCGTGA
98234 GGGGTATCGATTCCC-TCAAG
1 GGGGTATCGATTCCCTTCAAG
98254 GAGGG-ATCGATTCCCATTCAAAG
1 G-GGGTATCGATTCCC-TTC-AAG
* *
98277 GGGGAATCGGTTCCCCTTCAAG
1 GGGGTATCGATT-CCCTTCAAG
98299 GGGGTATCGATTCC
1 GGGGTATCGATTCC
98313 TCCTGCACTA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
20 11 0.22
21 5 0.10
22 18 0.36
23 13 0.26
24 3 0.06
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (21 bp):
GGGGTATCGATTCCCTTCAAG
Found at i:105307 original size:18 final size:20
Alignment explanation
Indices: 105284--105320 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
105274 GACTTTTTGG
105284 TCAAC-GGTC-GGTCAACGA
1 TCAACGGGTCAGGTCAACGA
105302 TCAACGGGTCAGGTCAACG
1 TCAACGGGTCAGGTCAACG
105321 GGTCGGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (20 bp):
TCAACGGGTCAGGTCAACGA
Found at i:105320 original size:13 final size:13
Alignment explanation
Indices: 105302--105338 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
105292 CGGTCAACGA
105302 TCAACGGGTCAGG
1 TCAACGGGTCAGG
*
105315 TCAACGGGTCGGG
1 TCAACGGGTCAGG
105328 TCAACGGGTCA
1 TCAACGGGTCA
105339 AACCGGTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.22, C:0.24, G:0.38, T:0.16
Consensus pattern (13 bp):
TCAACGGGTCAGG
Found at i:117238 original size:251 final size:257
Alignment explanation
Indices: 116768--117275 Score: 773
Period size: 251 Copynumber: 2.0 Consensus size: 257
116758 TATAACATGC
* *
116768 AAAATTTTTGTACATAAATATTAATATTCATCAACAATCAAATTAACTATAATAGATAATTTAAA
1 AAAATTTTTCTACATAAATATTAATATTCATCAACAATCAAATTAACTATAATAAATAATTTAAA
116833 AATTTAAAAAAATTAATGATATAATATTACTTAATTAAAAATTAAAATATACACATACTTACAAA
66 AATTTAAAAAAA-TAAT-ATATAATATTACTTAATTAAAAATTAAAATATACACATACTTACAAA
* * *
116898 TATTTTCTCCTTCTTATTCCTTCTTCTTCTTGTTCTTCTTTTACAATTTTTTATTATTCTCAAAT
129 TATTTTCTCCTTCTTATTCCTTCTTCTCCTTCTTCTTCTTTTACAATTTTTTATTATTCTCAAAC
*
116963 TACATGCATAATATTACAATTATATTAATATTTCTCAACAATCAAACTAACTATATAATATAGT
194 TACATGCATAATATTACAATTATATTAACATTTCTCAACAATCAAACTAACTATATAATATAGT
*
117027 AAAATTTTTCTACATAAATATTAATATTCATCAATAATCAAATTAACTATAATAAATAATTTAAA
1 AAAATTTTTCTACATAAATATTAATATTCATCAACAATCAAATTAACTATAATAAATAATTTAAA
* **
117092 AA-TT-AAAAAA-AAT-TA-AA-ATTTCTTAATTAAAAATTAAAATATACATC-TACTTATTAAT
66 AATTTAAAAAAATAATATATAATATTACTTAATTAAAAATTAAAATATACA-CATACTTACAAAT
* * *
117150 ATTTTCTCCTTCTTCTTTCTTTTTCTCCTTCTT-TTCTTTTACAATTTTTTCATTATTCTCAAAC
130 ATTTTCTCCTTCTTATTCCTTCTTCTCCTTCTTCTTCTTTTACAATTTTTT-ATTATTCTCAAAC
* *
117214 TACATGCATAATTTTA-ATATTATATTAACATTTCTCAACAATCAAACTAGCTATATAATATA
194 TACATGCATAATATTACA-ATTATATTAACATTTCTCAACAATCAAACTAACTATATAATATA
117276 TCATTTAAAA
Statistics
Matches: 231, Mismatches: 15, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
250 18 0.08
251 133 0.58
252 3 0.01
253 2 0.01
255 3 0.01
257 6 0.03
258 2 0.01
259 64 0.28
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.43
Consensus pattern (257 bp):
AAAATTTTTCTACATAAATATTAATATTCATCAACAATCAAATTAACTATAATAAATAATTTAAA
AATTTAAAAAAATAATATATAATATTACTTAATTAAAAATTAAAATATACACATACTTACAAATA
TTTTCTCCTTCTTATTCCTTCTTCTCCTTCTTCTTCTTTTACAATTTTTTATTATTCTCAAACTA
CATGCATAATATTACAATTATATTAACATTTCTCAACAATCAAACTAACTATATAATATAGT
Found at i:119325 original size:47 final size:48
Alignment explanation
Indices: 119274--119458 Score: 146
Period size: 47 Copynumber: 3.8 Consensus size: 48
119264 GACTCTGGAC
* *
119274 CTCATCT-AATGTCTAGTGTATATTCCTGATGCTATGTGACCCCATGT
1 CTCATCTGAATGTCGAGTGTACATTCCTGATGCTATGTGACCCCATGT
* * * * *
119321 CTCAT-TCG-ATGTCGGGTGTACGTTTCTGATGTTGTGTGACCCCAAT-T
1 CTCATCT-GAATGTCGAGTGTACATTCCTGATGCTATGTGACCCC-ATGT
*
119368 CTCATCTGAGGATGGATGTCGAGTGTACATTCCTGATGCTATGTGACCCCATGC
1 CTCATCT---GA---ATGTCGAGTGTACATTCCTGATGCTATGTGACCCCATGT
** * *
119422 CTCGCCTGATTG-CTGAGTGTACATTCCTGATGTTATG
1 CTCATCTGAATGTC-GAGTGTACATTCCTGATGCTATG
119459 CCCAAACCTC
Statistics
Matches: 108, Mismatches: 18, Indels: 23
0.72 0.12 0.15
Matches are distributed among these distances:
46 1 0.01
47 40 0.37
48 27 0.25
50 1 0.01
51 2 0.02
53 2 0.02
54 35 0.32
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (48 bp):
CTCATCTGAATGTCGAGTGTACATTCCTGATGCTATGTGACCCCATGT
Found at i:119865 original size:31 final size:31
Alignment explanation
Indices: 119731--119858 Score: 168
Period size: 31 Copynumber: 4.1 Consensus size: 31
119721 TCATGGATGA
*
119731 GTAGGTGAATGATAACATGCTTAAGCAGCGT
1 GTAGGTGAATGATAACATGCTTAAGTAGCGT
*
119762 GTAGGTGAATGATAACATGCTTGAA-TAGTGT
1 GTAGGTGAATGATAACATGCTT-AAGTAGCGT
* * **
119793 GTAGGTAAATGATAAAATGCTTAAGTAATGT
1 GTAGGTGAATGATAACATGCTTAAGTAGCGT
* *
119824 GTATGTGAATGATAACATGCTTGAGTAGCGT
1 GTAGGTGAATGATAACATGCTTAAGTAGCGT
119855 GTAG
1 GTAG
119859 ACGAATGTTG
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
30 2 0.02
31 79 0.95
32 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (31 bp):
GTAGGTGAATGATAACATGCTTAAGTAGCGT
Found at i:120455 original size:23 final size:22
Alignment explanation
Indices: 120396--120456 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 22
120386 ACAAATATAT
120396 CAAACTAACATATTAC-A-ACA
1 CAAACTAACATATTACAATACA
* *
120416 -AAAATAACA-ATCCACAATACA
1 CAAACTAACATAT-TACAATACA
120437 CCAAACTAACATATTACAAT
1 -CAAACTAACATATTACAAT
120457 CATCCCTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
18 2 0.06
19 10 0.32
20 1 0.03
21 3 0.10
23 13 0.42
24 2 0.06
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.20
Consensus pattern (22 bp):
CAAACTAACATATTACAATACA
Found at i:121547 original size:2 final size:2
Alignment explanation
Indices: 121540--121569 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
121530 CTAATAAGAC
121540 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
121570 TTCTTTTTAA
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:123954 original size:17 final size:17
Alignment explanation
Indices: 123932--123965 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
123922 GACATTTTTC
123932 ATGACACGTGTCACAAA
1 ATGACACGTGTCACAAA
*
123949 ATGACACGTGTCCCAAA
1 ATGACACGTGTCACAAA
123966 TTTTATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (17 bp):
ATGACACGTGTCACAAA
Found at i:126025 original size:60 final size:60
Alignment explanation
Indices: 125931--126083 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 60
125921 GATGACTCTG
* ** * * * *
125931 GGGATGAAAAT-GAAATATTCAAAAGTTTGGGGACTGATTTAGAAA-GAGGGTCATAGTTTA
1 GGGATGAAATTAG-AATATTCAAAAGTTTAAGGACTAATTTA-AAATGAGAGTCACAATTTA
* * *
125991 TGGATGAAATTAGAATGTTCAAAATTTTAAGGACTAATTTAAAATGAGAGTCACAATTTA
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCACAATTTA
**
126051 GGGATGGCATTAGAATATTCAAAAGTTTAAGGA
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGA
126084 TCAATATAAG
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
59 3 0.04
60 72 0.95
61 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.30
Consensus pattern (60 bp):
GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCACAATTTA
Found at i:131597 original size:28 final size:29
Alignment explanation
Indices: 131553--131626 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
131543 ATATTGCGAT
* * *
131553 TTTCCCGATATATCACCGGTGA-AATATA
1 TTTCCCGATCTAACACCGGTCATAATATA
*
131581 TTTCCCGATCTAACACCGGTCATATTATA
1 TTTCCCGATCTAACACCGGTCATAATATA
131610 TTTCCCGATCTAACACC
1 TTTCCCGATCTAACACC
131627 CTTAGCAGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 19 0.46
29 22 0.54
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.32
Consensus pattern (29 bp):
TTTCCCGATCTAACACCGGTCATAATATA
Done.