Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 41 of 204
Found at i:11946921 original size:5 final size:5
Alignment explanation
Indices: 11946911--11946957 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
11946901 ACACATATAC
* * * *
11946911 CATAT CATAT CATAT CATGT CATAT CATGT CATAC CCTAT CATAT CA
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CA
11946958 AAAATTTCAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (5 bp):
CATAT
Found at i:11952634 original size:22 final size:21
Alignment explanation
Indices: 11952609--11952655 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
11952599 AAGGTTATTT
11952609 TATTAATATAAAAAATTTATAA
1 TATTAATAT-AAAAATTTATAA
**
11952631 TATTTTTATAAAAATTTATAA
1 TATTAATATAAAAATTTATAA
11952652 TATT
1 TATT
11952656 TTAATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTAATATAAAAATTTATAA
Found at i:11965746 original size:23 final size:25
Alignment explanation
Indices: 11965703--11965748 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
11965693 AACACAAATT
*
11965703 TTAATTTGTTTATTTTTAAATAATA
1 TTAATTTGTTTATGTTTAAATAATA
11965728 TTAATTT-TTTA-GTTTAAATAA
1 TTAATTTGTTTATGTTTAAATAA
11965749 AAAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
TTAATTTGTTTATGTTTAAATAATA
Found at i:11966683 original size:35 final size:35
Alignment explanation
Indices: 11966633--11966722 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
11966623 AATCGACTCA
*
11966633 AAAAAGGTT-GAGATAGACCAT-TTTATGCCAACCTT
1 AAAAAGGTTAG-GATAGACC-TGTTTAAGCCAACCTT
* *
11966668 AAAAATGTTAGGATAGACCTGTTTAAGGCAACCTT
1 AAAAAGGTTAGGATAGACCTGTTTAAGCCAACCTT
* *
11966703 AAAAAGGTTGGGATAAACCT
1 AAAAAGGTTAGGATAGACCT
11966723 TGTCTGCGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 1 0.02
35 45 0.96
36 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (35 bp):
AAAAAGGTTAGGATAGACCTGTTTAAGCCAACCTT
Found at i:11976040 original size:98 final size:97
Alignment explanation
Indices: 11975871--11976064 Score: 361
Period size: 98 Copynumber: 2.0 Consensus size: 97
11975861 ATGTAAGGCA
11975871 AATGACCAACTTTAAACTAAGACCTCATTCAATGGAGATCCACACAAGCCAATAATAAGATTATA
1 AATGACCAACTTTAAACTAAGACCTCATTCAATGGAGATCCACACAAGCCAATAATAAGATTATA
11975936 TACATGACAAGAAAAAGAATGCACATATTCCAG
66 TACATGACAAGAAAAA-AATGCACATATTCCAG
* *
11975969 AATGACCAACTTTAAACTAAGACCTCATTCAATGGAGATCCGCACAAGCCAATAATAAGATTATG
1 AATGACCAACTTTAAACTAAGACCTCATTCAATGGAGATCCACACAAGCCAATAATAAGATTATA
11976034 TACATGACAAGAAAAAAATGCACATATTCCA
66 TACATGACAAGAAAAAAATGCACATATTCCA
11976065 CATTTGACGA
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
97 15 0.16
98 79 0.84
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (97 bp):
AATGACCAACTTTAAACTAAGACCTCATTCAATGGAGATCCACACAAGCCAATAATAAGATTATA
TACATGACAAGAAAAAAATGCACATATTCCAG
Found at i:11979896 original size:16 final size:17
Alignment explanation
Indices: 11979875--11979913 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
11979865 TGTGCATCAA
11979875 TTTTATTAT-TGACA-AT
1 TTTTATTATGT-ACATAT
11979891 TTTTATTATGTACATAT
1 TTTTATTATGTACATAT
11979908 TTTTAT
1 TTTTAT
11979914 CCTTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (17 bp):
TTTTATTATGTACATAT
Found at i:11982230 original size:16 final size:17
Alignment explanation
Indices: 11982201--11982233 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11982191 ATTTAATGAT
11982201 AAAATTGAAATTTTAAA
1 AAAATTGAAATTTTAAA
*
11982218 AAAATT-AAGTTTTAAA
1 AAAATTGAAATTTTAAA
11982234 TGAGTCATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
AAAATTGAAATTTTAAA
Found at i:11985991 original size:22 final size:22
Alignment explanation
Indices: 11985935--11985992 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
11985925 ATTCGGTTAA
*
11985935 TCAGTCGGTGG-CTGAATTTAGT
1 TCAGTCGGAGGTC-GAATTTAGT
* * *
11985957 TTAGTTGGCGGTCGAATTTAGT
1 TCAGTCGGAGGTCGAATTTAGT
*
11985979 TCGGTCGGAGGTCG
1 TCAGTCGGAGGTCG
11985993 GTTAATGATA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.16, C:0.14, G:0.36, T:0.34
Consensus pattern (22 bp):
TCAGTCGGAGGTCGAATTTAGT
Found at i:11994231 original size:15 final size:15
Alignment explanation
Indices: 11994211--11994243 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11994201 CATAAATTAT
11994211 ATTATTTTCATGTTA
1 ATTATTTTCATGTTA
11994226 ATTATTTTCATGTTA
1 ATTATTTTCATGTTA
11994241 ATT
1 ATT
11994244 TTTATTATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTATTTTCATGTTA
Found at i:11995066 original size:18 final size:18
Alignment explanation
Indices: 11995043--11995082 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
11995033 TTAATTCTAT
11995043 TTAGCTAGGATGATTGTG
1 TTAGCTAGGATGATTGTG
11995061 TTAGCTAGGATGATTGTG
1 TTAGCTAGGATGATTGTG
11995079 TTAG
1 TTAG
11995083 TTTAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.33, T:0.40
Consensus pattern (18 bp):
TTAGCTAGGATGATTGTG
Found at i:12004357 original size:3 final size:3
Alignment explanation
Indices: 12004307--12004341 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
12004297 TTTATAATAC
* *
12004307 TAT TAT TAT TAT TAT TGT TAT TAT TAC TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12004342 ATATAGGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:12004455 original size:20 final size:20
Alignment explanation
Indices: 12004430--12004469 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12004420 TTTGTAATGC
*
12004430 TTTTATCATGTATTATTTTA
1 TTTTATCATGCATTATTTTA
*
12004450 TTTTATTATGCATTATTTTA
1 TTTTATCATGCATTATTTTA
12004470 AATATTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTTATCATGCATTATTTTA
Found at i:12010234 original size:9 final size:9
Alignment explanation
Indices: 12010223--12010289 Score: 71
Period size: 9 Copynumber: 7.4 Consensus size: 9
12010213 TTTTGTTAAA
*
12010223 AATTAACCA
1 AATTAACCG
*
12010232 AATTAACCT
1 AATTAACCG
*
12010241 AATTACCCG
1 AATTAACCG
**
12010250 AATTAACTA
1 AATTAACCG
*
12010259 AATTACCCG
1 AATTAACCG
*
12010268 AATTACCCG
1 AATTAACCG
12010277 AATTAACCG
1 AATTAACCG
12010286 AATT
1 AATT
12010290 GAATCACTAC
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 48 1.00
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:12010256 original size:27 final size:27
Alignment explanation
Indices: 12010223--12010289 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
12010213 TTTTGTTAAA
*
12010223 AATTAACCAAATTAACCTAATTACCCG
1 AATTAACCAAATTAACCGAATTACCCG
* *
12010250 AATTAACTAAATTACCCGAATTACCCG
1 AATTAACCAAATTAACCGAATTACCCG
*
12010277 AATTAACCGAATT
1 AATTAACCAAATT
12010290 GAATCACTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.27
Consensus pattern (27 bp):
AATTAACCAAATTAACCGAATTACCCG
Found at i:12010568 original size:18 final size:18
Alignment explanation
Indices: 12010528--12010568 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
12010518 AATTTTTATT
*
12010528 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGATA
12010546 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGATA
*
12010564 CTTGG
1 ATTGG
12010569 ATTTAGATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.02, G:0.46, T:0.39
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGATA
Found at i:12017986 original size:24 final size:24
Alignment explanation
Indices: 12017957--12018005 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
12017947 TGTATAACAA
12017957 GAAGCTCATAAGAGCC-ATAATCGG
1 GAAGCTCATAAGAGCCAATAA-CGG
*
12017981 GAAGCTCATACGAGCCAATAACGG
1 GAAGCTCATAAGAGCCAATAACGG
12018005 G
1 G
12018006 TTGCTTCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.14
Consensus pattern (24 bp):
GAAGCTCATAAGAGCCAATAACGG
Found at i:12021399 original size:18 final size:18
Alignment explanation
Indices: 12021373--12021416 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
12021363 TCATTTTTAT
*
12021373 TTTTA-TTTTGTTATATA
1 TTTTATTTTTATTATATA
* *
12021390 TTTTATTTTTATTTTCTA
1 TTTTATTTTTATTATATA
12021408 TTTTATTTT
1 TTTTATTTT
12021417 CTTGCATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTATTTTTATTATATA
Found at i:12022422 original size:18 final size:17
Alignment explanation
Indices: 12022395--12022432 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
12022385 CTTAAGCATT
12022395 AAAAAAAT-AATAAAATA
1 AAAAAAATAAAT-AAATA
12022412 AAAATAAATAAATAAATA
1 AAAA-AAATAAATAAATA
12022430 AAA
1 AAA
12022433 TGAAGGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 12 0.63
19 3 0.16
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAAAATAAATAAATA
Found at i:12023781 original size:18 final size:19
Alignment explanation
Indices: 12023758--12023795 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
12023748 TCGAAAACTA
*
12023758 CTTTTCTCAACT-CTATTT
1 CTTTTCACAACTGCTATTT
*
12023776 CTTTTCACAATTGCTATTT
1 CTTTTCACAACTGCTATTT
12023795 C
1 C
12023796 AATTTATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.18, C:0.26, G:0.03, T:0.53
Consensus pattern (19 bp):
CTTTTCACAACTGCTATTT
Found at i:12033621 original size:22 final size:22
Alignment explanation
Indices: 12033565--12033615 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
12033555 GCTTCAGGGG
* * *
12033565 CTATATGTCTTGAGACAAAATC
1 CTATATGTCTCGAAACAAAAGC
*
12033587 CTATTTGTCTCGAAACAAAAGC
1 CTATATGTCTCGAAACAAAAGC
12033609 CTATATG
1 CTATATG
12033616 CATCGAGACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (22 bp):
CTATATGTCTCGAAACAAAAGC
Found at i:12036393 original size:17 final size:16
Alignment explanation
Indices: 12036368--12036406 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
12036358 TAATAATGTC
12036368 AATAAAATAAAATAAT
1 AATAAAATAAAATAAT
*
12036384 AATAATAATAAATTAAT
1 AATAA-AATAAAATAAT
*
12036401 ATTAAA
1 AATAAA
12036407 CTAATTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAAAATAAAATAAT
Found at i:12036393 original size:22 final size:22
Alignment explanation
Indices: 12036350--12036395 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12036340 ATATGTAACC
* *
12036350 AAATATAATAATAATGTCAATA
1 AAATAAAATAATAATATCAATA
12036372 AAATAAAATAATAATAAT-AATA
1 AAATAAAATAATAAT-ATCAATA
12036394 AA
1 AA
12036396 TTAATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (22 bp):
AAATAAAATAATAATATCAATA
Found at i:12036400 original size:11 final size:11
Alignment explanation
Indices: 12036368--12036419 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
12036358 TAATAATGTC
12036368 AATAAAATAA-
1 AATAAAATAAT
12036378 AATAATAATAAT
1 AATAA-AATAAT
*
12036390 AATAAATTAAT
1 AATAAAATAAT
* *
12036401 ATTAAACTAATT
1 AATAAAATAA-T
12036413 AATAAAA
1 AATAAAA
12036420 CAATGGGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 5 0.15
11 18 0.53
12 11 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:12039505 original size:34 final size:34
Alignment explanation
Indices: 12039444--12039576 Score: 149
Period size: 34 Copynumber: 3.9 Consensus size: 34
12039434 CTTGCATACT
* * * * *
12039444 ACCTAGGATCCGCATGACATATTGGCTCGCATAA
1 ACCTAGGGTTCGCATAACATATAGGCTCGCATAG
* * *
12039478 ACCTAGGGTTTGCATAATATGTAGGCTCGCATAG
1 ACCTAGGGTTCGCATAACATATAGGCTCGCATAG
* *
12039512 ACTTAGGGTTCGCATAACATATAGGCTCACATAG
1 ACCTAGGGTTCGCATAACATATAGGCTCGCATAG
* **
12039546 ACCTAGGGTTCACATGGCATATAGGCTCGCA
1 ACCTAGGGTTCGCATAACATATAGGCTCGCA
12039577 CAGGTAGGGC
Statistics
Matches: 81, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 81 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (34 bp):
ACCTAGGGTTCGCATAACATATAGGCTCGCATAG
Found at i:12039767 original size:14 final size:14
Alignment explanation
Indices: 12039748--12039812 Score: 87
Period size: 14 Copynumber: 4.6 Consensus size: 14
12039738 GATTTTTAAC
*
12039748 TCGCATGTATTGAT
1 TCGCATATATTGAT
*
12039762 TCGCATATATTGAC
1 TCGCATATATTGAT
*
12039776 TCACATATATTGAT
1 TCGCATATATTGAT
12039790 TCGCATATATTGACT
1 TCGCATATATTGA-T
12039805 T-GCATATA
1 TCGCATATA
12039813 CAATAGTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
14 43 0.96
15 2 0.04
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (14 bp):
TCGCATATATTGAT
Found at i:12039810 original size:28 final size:28
Alignment explanation
Indices: 12039746--12039812 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
12039736 GTGATTTTTA
*
12039746 ACTCGCATGTATTGATTCGCATATATTG
1 ACTCGCATATATTGATTCGCATATATTG
*
12039774 ACTCACATATATTGATTCGCATATATTG
1 ACTCGCATATATTGATTCGCATATATTG
*
12039802 ACTTGCATATA
1 ACTCGCATATA
12039813 CAATAGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (28 bp):
ACTCGCATATATTGATTCGCATATATTG
Found at i:12041364 original size:19 final size:19
Alignment explanation
Indices: 12041324--12041410 Score: 81
Period size: 19 Copynumber: 4.6 Consensus size: 19
12041314 CTATTCTAGA
*
12041324 ATTATAAAAAT-ATAAAAA
1 ATTATAAAAATAATAAAAT
*
12041342 ATTATAAAAATAATTAAAT
1 ATTATAAAAATAATAAAAT
*
12041361 ATTATAAAAATTATTAGAAAT
1 ATTATAAAAA-TAATA-AAAT
* *
12041382 -TAATTAAAAACAATAAAAT
1 ATTA-TAAAAATAATAAAAT
12041401 -TTATAAAAAT
1 ATTATAAAAAT
12041411 TTTATATTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
18 17 0.30
19 21 0.38
20 8 0.14
21 10 0.18
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (19 bp):
ATTATAAAAATAATAAAAT
Found at i:12041412 original size:10 final size:9
Alignment explanation
Indices: 12041323--12041411 Score: 72
Period size: 9 Copynumber: 9.4 Consensus size: 9
12041313 TCTATTCTAG
12041323 AATTATAAA
1 AATTATAAA
12041332 AA-TATAAAA
1 AATTAT-AAA
12041341 AATTATAAA
1 AATTATAAA
*
12041350 AATAATTAAA
1 AATTA-TAAA
*
12041360 TATTATAAA
1 AATTATAAA
*
12041369 AATTATTAGA
1 AATTA-TAAA
12041379 AATTAATTAAA
1 AATT-A-TAAA
**
12041390 AACAATAAA
1 AATTATAAA
*
12041399 ATTTATAAA
1 AATTATAAA
12041408 AATT
1 AATT
12041412 TTATATTTAT
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
8 3 0.05
9 35 0.56
10 18 0.29
11 7 0.11
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (9 bp):
AATTATAAA
Found at i:12043127 original size:15 final size:15
Alignment explanation
Indices: 12043107--12043147 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
12043097 TTTTTAACCC
*
12043107 TAAACCCTAAAATCA
1 TAAACCTTAAAATCA
*
12043122 TAAACCTTAAAATCC
1 TAAACCTTAAAATCA
12043137 TAAACCTTAAA
1 TAAACCTTAAA
12043148 CCCTAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAACCTTAAAATCA
Found at i:12043158 original size:15 final size:15
Alignment explanation
Indices: 12043102--12043154 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
12043092 TTTAATTTTT
*
12043102 AACCCTAAACCCTAA
1 AACCCTAAACCTTAA
* *
12043117 AATCATAAACCTTAA
1 AACCCTAAACCTTAA
*
12043132 AATCCTAAACCTT-A
1 AACCCTAAACCTTAA
12043146 AACCCTAAA
1 AACCCTAAA
12043155 ACCTAGAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
14 9 0.27
15 24 0.73
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCTAAACCTTAA
Found at i:12048826 original size:17 final size:19
Alignment explanation
Indices: 12048806--12048850 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
12048796 TATCTTAAAC
12048806 TATATTTATT-AAAA-ATA
1 TATATTTATTGAAAAGATA
*
12048823 TATATTAATTGAAAATGATA
1 TATATTTATTGAAAA-GATA
12048843 TATATTTA
1 TATATTTA
12048851 GCATAAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 9 0.39
18 4 0.17
20 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
TATATTTATTGAAAAGATA
Found at i:12049684 original size:26 final size:25
Alignment explanation
Indices: 12049635--12049693 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
12049625 TACGTGTTTA
*
12049635 TTTTTAAAATTTATTAAATAATATC
1 TTTTTAAAATTTATTAAAAAATATC
*
12049660 TTTTTATAAATTT-TTAAAAATATATA
1 TTTTTA-AAATTTATTAAAAA-ATATC
12049686 TTTGTTAA
1 TTT-TTAA
12049694 TTAAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 12 0.41
26 14 0.48
27 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
TTTTTAAAATTTATTAAAAAATATC
Found at i:12051830 original size:15 final size:15
Alignment explanation
Indices: 12051810--12051839 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12051800 ACTATTAATA
12051810 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
12051825 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
12051840 TACCATACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:12054057 original size:28 final size:28
Alignment explanation
Indices: 12053990--12054063 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
12053980 TTCAGGTTCT
* * * *
12053990 GTTTCAAGTTTCGATTTTTGAATTTTGG
1 GTTTCAAATTTTGAGTTTTGAATTATGG
* *
12054018 ATTTCAAATTTTGAGTTTTGAGTTATGG
1 GTTTCAAATTTTGAGTTTTGAATTATGG
*
12054046 GTTTCAAATTTTGGGTTT
1 GTTTCAAATTTTGAGTTT
12054064 GATATTTTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.20, C:0.05, G:0.22, T:0.53
Consensus pattern (28 bp):
GTTTCAAATTTTGAGTTTTGAATTATGG
Found at i:12054071 original size:14 final size:14
Alignment explanation
Indices: 12054010--12054063 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
12054000 TCGATTTTTG
*
12054010 AATTTTGGATTTCA
1 AATTTTGGGTTTCA
* **
12054024 AATTTTGAGTTTTG
1 AATTTTGGGTTTCA
* *
12054038 AGTTATGGGTTTCA
1 AATTTTGGGTTTCA
12054052 AATTTTGGGTTT
1 AATTTTGGGTTT
12054064 GATATTTTTG
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.52
Consensus pattern (14 bp):
AATTTTGGGTTTCA
Found at i:12058940 original size:22 final size:24
Alignment explanation
Indices: 12058896--12058940 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
12058886 ATAAACAACG
* *
12058896 AAATGTAAAATATCAAATGAATAT
1 AAATGTAAAACATCAAATCAATAT
12058920 AAATG-AAAACAT-AAATCAATA
1 AAATGTAAAACATCAAATCAATA
12058941 AGCAAATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (24 bp):
AAATGTAAAACATCAAATCAATAT
Found at i:12059128 original size:51 final size:52
Alignment explanation
Indices: 12059066--12059172 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 52
12059056 TTATAAAACT
* * *
12059066 TATATATATATAAAATACA-TAATGCATTTATGAAAACAATGAAA-ATATAAA
1 TATATACATATAAAATACATTAATGCATTTA-CAAAAAAATGAAATATATAAA
* * *
12059117 TATATACATATAAAATATATTCATGCATTTACAAAAAAATGAAATATATAAG
1 TATATACATATAAAATACATTAATGCATTTACAAAAAAATGAAATATATAAA
12059169 TATA
1 TATA
12059173 ATATAAAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
51 28 0.58
52 20 0.42
ACGTcount: A:0.55, C:0.07, G:0.06, T:0.33
Consensus pattern (52 bp):
TATATACATATAAAATACATTAATGCATTTACAAAAAAATGAAATATATAAA
Found at i:12059385 original size:27 final size:29
Alignment explanation
Indices: 12059355--12059411 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
12059345 ATAATAAAGT
12059355 ATGTTT-ATA-ATATGTATATATATTAAA
1 ATGTTTAATATATATGTATATATATTAAA
12059382 ATGTTTAAAATATATATGTATATATATTAA
1 ATGTTT--AATATATATGTATATATATTAA
12059412 CATGCATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 6 0.23
30 3 0.12
31 17 0.65
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (29 bp):
ATGTTTAATATATATGTATATATATTAAA
Found at i:12059447 original size:3 final size:3
Alignment explanation
Indices: 12059439--12059500 Score: 99
Period size: 3 Copynumber: 20.3 Consensus size: 3
12059429 ATATGTAGAT
12059439 ATA ATA ATA ATA TATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12059484 ATAA ATA ATA ATA ATA A
1 AT-A ATA ATA ATA ATA A
12059501 CAAAATTAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.04
3 48 0.86
4 6 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12059963 original size:23 final size:22
Alignment explanation
Indices: 12059935--12059979 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
12059925 AAATTAAATA
12059935 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
*
12059958 TCTAAGATTACATATCATATCT
1 TCTAAGATTACAAATCATATCT
12059980 AAGATTGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:12059996 original size:21 final size:19
Alignment explanation
Indices: 12059958--12060032 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
12059948 AATCATATCT
*
12059958 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
12059977 TCTAAGATTGCATGTATCATA
1 TCTAAGATTGCA--TATCATA
12059998 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
12060017 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
12060033 CTCGAAGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 34 0.64
21 19 0.36
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:12060859 original size:44 final size:43
Alignment explanation
Indices: 12060805--12061180 Score: 370
Period size: 44 Copynumber: 8.7 Consensus size: 43
12060795 GCTATTCTCC
* * * *
12060805 ACCTACTCCACTGTTGCTCAGGGAGATAGGGTTCACGATCTTCA
1 ACCTATTCCACTGCTGC-CAGGGAGATAGGATTCACAATCTTCA
* *
12060849 ACCTATTCCACTGCTGACCATGGAGATAGGA-CCTACAATCTTCA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTC-ACAATCTTCA
* * * * *
12060893 ATCTATTCCACTGCTGCCCAGGGCGCTAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
* * * *
12060937 ACCTATTTCACTGCTGACCAGGGAGATAAGATTTACAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
* * **
12060981 ACTTATTCCACTACTGTTTAGGGAGATAGGATT--C--T-TT-A
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
* * * * *
12061019 ATCTATTCCACTACTGTCCAGGGATATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
* *
12061063 ACCTATTCCACTACTGACCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
*
12061107 ACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGATTCACAATCTTCA
12061151 ACCTATTCCACTGCTGACCAGGGAGATAGG
1 ACCTATTCCACTGCTG-CCAGGGAGATAGG
12061181 GCTGGGGTCA
Statistics
Matches: 277, Mismatches: 46, Indels: 18
0.81 0.13 0.05
Matches are distributed among these distances:
38 28 0.10
39 2 0.01
40 2 0.01
42 2 0.01
43 3 0.01
44 238 0.86
45 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (43 bp):
ACCTATTCCACTGCTGCCAGGGAGATAGGATTCACAATCTTCA
Found at i:12061069 original size:126 final size:126
Alignment explanation
Indices: 12060823--12061140 Score: 393
Period size: 126 Copynumber: 2.5 Consensus size: 126
12060813 CACTGTTGCT
* * * * * * *
12060823 CAGGGAGATAGGGTTCACGATCTTCAACCTATTCCACTGCTGACCATGGAGATAGGACCTACAAT
1 CAGGGAGATAAGATTCACAATCTTTAACCTATTCCACTACTGTCCAGGGAGATAGGA--T----T
* * * * *
12060888 CTTCAATCTATTCCACTGCTGCCCAGGGCGCTAGAATTCTCAATCTTCAACCTATTTCACTGCTG
60 CTTCAATCTATTCCACTACTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTACTG
12060953 AC
125 AC
* * ** *
12060955 CAGGGAGATAAGATTTACAATCTTTAACTTATTCCACTACTGTTTAGGGAGATAGGATTCTTTAA
1 CAGGGAGATAAGATTCACAATCTTTAACCTATTCCACTACTGTCCAGGGAGATAGGATTCTTCAA
* *
12061020 TCTATTCCACTACTGTCCAGGGATATAGAATTCTCAATCTTCAACCTATTCCACTACTGAC
66 TCTATTCCACTACTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTACTGAC
* *
12061081 CAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAGGGAGATAGGATTC
1 CAGGGAGATAAGATTCACAATCTTTAACCTATTCCACTACTGTCCAGGGAGATAGGATTC
12061141 ACAATCTTTA
Statistics
Matches: 161, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
126 114 0.71
130 1 0.01
132 46 0.29
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (126 bp):
CAGGGAGATAAGATTCACAATCTTTAACCTATTCCACTACTGTCCAGGGAGATAGGATTCTTCAA
TCTATTCCACTACTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTACTGAC
Found at i:12061294 original size:43 final size:43
Alignment explanation
Indices: 12061241--12061382 Score: 108
Period size: 44 Copynumber: 3.3 Consensus size: 43
12061231 TATTTTTAAC
*
12061241 CTGCTCCGCTGCAACCCAGGGAGACAAGGCTGGTGTCTTCGAT
1 CTGCTTCGCTGCAACCCAGGGAGACAAGGCTGGTGTCTTCGAT
***** * * * * * *
12061284 CTGCTTCGCTGTCGGTGTAGGAAGACAAGATCTGCTATTTTC-AG
1 CTGCTTCGCTG-CAACCCAGGGAGACAAG-GCTGGTGTCTTCGAT
*
12061328 CATGC-TCTGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGAT
1 C-TGCTTC-GCTGCAACCCAGGGAGACAAGGCTGGTGTCTTCGAT
*
12061372 CTGTTTCGCTG
1 CTGCTTCGCTG
12061383 TCGGTGCAAG
Statistics
Matches: 68, Mismatches: 25, Indels: 12
0.65 0.24 0.11
Matches are distributed among these distances:
43 24 0.35
44 29 0.43
45 15 0.22
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.27
Consensus pattern (43 bp):
CTGCTTCGCTGCAACCCAGGGAGACAAGGCTGGTGTCTTCGAT
Found at i:12061442 original size:44 final size:44
Alignment explanation
Indices: 12061394--12061530 Score: 125
Period size: 44 Copynumber: 3.1 Consensus size: 44
12061384 CGGTGCAAGA
12061394 AGGCAAGATCTGCTATTTTTAGCCTGCTCCGTTGCAACCCAGGG
1 AGGCAAGATCTGCTATTTTTAGCCTGCTCCGTTGCAACCCAGGG
* * * * ** * **** *
12061438 AGGCAAG-GCTGGTGACTTTGA-TTTGCTTCGTTGTCGGTACAGGA
1 AGGCAAGATCTGCT-ATTTTTAGCCTGCTCCGTTG-CAACCCAGGG
*
12061482 AGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAACCCAGGG
1 AGGCAAGATCTGCTATTTTTAGCCTGCTCCGTTGCAACCCAGGG
12061526 AGGCA
1 AGGCA
12061531 GGGCTGGTGT
Statistics
Matches: 64, Mismatches: 25, Indels: 8
0.66 0.26 0.08
Matches are distributed among these distances:
43 13 0.20
44 39 0.61
45 12 0.19
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.27
Consensus pattern (44 bp):
AGGCAAGATCTGCTATTTTTAGCCTGCTCCGTTGCAACCCAGGG
Found at i:12061714 original size:88 final size:88
Alignment explanation
Indices: 12061180--12061757 Score: 787
Period size: 88 Copynumber: 6.6 Consensus size: 88
12061170 AGGGAGATAG
* * * * * * * *
12061180 GGCTGGGGTCATCAATCTGCTTCGCTGTCGGTGTAGGAAGGTAAGATATACTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
*
12061245 TCCGCTGCAACCCAGGGAGACAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * *
12061268 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAAGACAAGATCTGCTATTTTCAGCATGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
*
12061333 TCTGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* *
12061356 GGCTGGTGTCTTCGATCTGTTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
*
12061421 TCCGTTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * * *
12061444 GGCTGGTGACTTTGATTTGCTTCGTTGTCGGTACAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
*
12061509 TCCGCTGCAACCCAGGGAGGCAG
66 TCCGCTGCAACCCAGGGAGGCAA
* * * *
12061532 GGCTGGTGTCTTTGATCTGCTTCGCTATAGGTGCAGGAAGGCAAGATCTGCTATTTTTAGTCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
*
12061597 TTCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * ** * * *
12061620 GACTGGTGACTTCGATCTGCTTCGCTGTCGGTGCAAAAATGTAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
12061685 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * ** *
12061708 GGCTGGTGTCTTTGATTTGCTTCGCTGCCAATACAGGAAGGCAAGATCTG
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
12061758 TTATCTTCAC
Statistics
Matches: 428, Mismatches: 62, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 428 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.28
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
TCCGCTGCAACCCAGGGAGGCAA
Found at i:12068272 original size:3 final size:3
Alignment explanation
Indices: 12068264--12068322 Score: 54
Period size: 3 Copynumber: 20.0 Consensus size: 3
12068254 ATATGTAGAT
*
12068264 ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA AAA ATA A-A ATTA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
12068309 A-A ATTA ATA A-A ATA
1 ATA A-TA ATA ATA ATA
12068323 GACTAAAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
2 8 0.17
3 32 0.68
4 7 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12068307 original size:18 final size:21
Alignment explanation
Indices: 12068262--12068322 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 21
12068252 ATATATGTAG
*
12068262 ATATAATAATAATAATATATA
1 ATATAATAATAATAATATAAA
12068283 ATATAATAATAA-AA-ATAAA
1 ATATAATAATAATAATATAAA
*
12068302 AT-TAATAA-AATTA-ATAAA
1 ATATAATAATAATAATATAAA
12068320 ATA
1 ATA
12068323 GACTAAAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
17 2 0.06
18 14 0.39
19 6 0.17
20 2 0.06
21 12 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATAATAATAATAATATAAA
Found at i:12068566 original size:19 final size:21
Alignment explanation
Indices: 12068528--12068566 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
12068518 CCTTTTTTAA
*
12068528 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
12068549 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
12068567 AGAAAACAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:12068770 original size:23 final size:22
Alignment explanation
Indices: 12068727--12068784 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
12068717 AAAGGGTATC
* *
12068727 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
12068748 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
12068771 TACATATCATATCT
1 TACAAATCATATCT
12068785 AAGATTGCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:12070181 original size:20 final size:21
Alignment explanation
Indices: 12070141--12070181 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
12070131 ATTAGAATTT
*
12070141 AATAGTATTACTAATACATAA
1 AATAATATTACTAATACATAA
*
12070162 AATAATATTA-TAATATATAA
1 AATAATATTACTAATACATAA
12070182 CTATTACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
AATAATATTACTAATACATAA
Found at i:12070193 original size:30 final size:30
Alignment explanation
Indices: 12070140--12070217 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 30
12070130 TATTAGAATT
* *
12070140 TAATAGTATTACTAATACATAAAATAATATT-A
1 TAATA-TATAACTATTACAT-AAA-AATATTAA
12070172 TAATATATAACTATTAC-TAAAAATATTAA
1 TAATATATAACTATTACATAAAAATATTAA
12070201 TACATATATAACTATTA
1 TA-ATATATAACTATTA
12070218 TTATTATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 6 0.14
29 6 0.14
30 15 0.36
31 10 0.24
32 5 0.12
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.38
Consensus pattern (30 bp):
TAATATATAACTATTACATAAAAATATTAA
Found at i:12070621 original size:234 final size:232
Alignment explanation
Indices: 12070214--12070773 Score: 634
Period size: 234 Copynumber: 2.4 Consensus size: 232
12070204 ATATATAACT
* *
12070214 ATTATTATTATATT---GATTATAAT-AAAGATATAGTATTACATGATA-T-TAATGTTTAATCA
1 ATTATTATTATATTACATATTATAATAAAAGATATAATATTACATGATATTATAATGTTTAATCA
12070273 TTGATGCATATATATATAAACTATTAATA--TATTACATGATATGATATAACATTATATAATAAT
66 TTGATGCATA-A-ATATAAACTATTAATATTTATTACATGATATGATATAACATTATATAATAAT
* * *
12070336 GTAGGAAGTCTAACATTCAAATGTACGAAAAATATAGAGACTTAGAGCATATTTCAACTAGTATA
129 GTAGGAAGACTAACATTCAAATGTACGAAAAATATAGAGACTTAAAGCATATTTCAACCAGTATA
*
12070401 ATA-ATAAACAACAATATATAATAAT-ATT-TATGTATA
194 ATATATAAACAACAATATATAATAATAATTATATATATA
12070437 ATTATTATTATATTACATATTATAATAAAAGATATAATATTACATGATATTATAATGTTTAATCA
1 ATTATTATTATATTACATATTATAATAAAAGATATAATATTACATGATATTATAATGTTTAATCA
* * *
12070502 TTGATGCACAAATATAAACTATTAATATTTTATAAACTATATGATATGATATATCATTATATAAT
66 TTGATGCATAAATATAAACTATTAATA-TTTAT----TACATGATATGATATAACATTATATAAT
* *
12070567 -ATAGTAGGATA-ACTAACTTTCAAATGTACGAAAAATATAGGGAAC-TAAAGCATATTTCAACC
126 AAT-GTAGGA-AGACTAACATTCAAATGTACGAAAAATATAGAG-ACTTAAAGCATATTTCAACC
* *
12070629 AGTATAATATATAAACAATAATATATGATAATAATTAATATATATA
188 AGTATAATATATAAACAACAATATATAATAATAATT-ATATATATA
* * ** *
12070675 ATGTGTTACTAT-TATATCATAGAATAACATAAAA-AT-T-ATATTACATGATATTATAACGTTT
1 AT-TATTATTATAT-TA-CATATTAT-A-ATAAAAGATATAATATTACATGATATTATAATGTTT
* * ** *
12070736 AATTATTAATGTGTATATATAAACTATTAATATATTAT
61 AATCATTGATGCATAAATATAAACTATTAATAT-TTAT
12070774 GTACTACTCT
Statistics
Matches: 287, Mismatches: 24, Indels: 36
0.83 0.07 0.10
Matches are distributed among these distances:
223 14 0.05
226 8 0.03
227 37 0.13
228 2 0.01
229 22 0.08
230 3 0.01
233 2 0.01
234 84 0.29
235 23 0.08
236 3 0.01
238 11 0.04
239 62 0.22
240 7 0.02
241 3 0.01
242 6 0.02
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (232 bp):
ATTATTATTATATTACATATTATAATAAAAGATATAATATTACATGATATTATAATGTTTAATCA
TTGATGCATAAATATAAACTATTAATATTTATTACATGATATGATATAACATTATATAATAATGT
AGGAAGACTAACATTCAAATGTACGAAAAATATAGAGACTTAAAGCATATTTCAACCAGTATAAT
ATATAAACAACAATATATAATAATAATTATATATATA
Found at i:12070972 original size:13 final size:15
Alignment explanation
Indices: 12070952--12070993 Score: 61
Period size: 13 Copynumber: 2.9 Consensus size: 15
12070942 CTCGTAATAT
12070952 ATAAAATATTATT-A
1 ATAAAATATTATTCA
12070966 A-AAAATATTATCTCA
1 ATAAAATATTAT-TCA
12070981 ATAAAATATTATT
1 ATAAAATATTATT
12070994 TTTATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.40
14 2 0.08
15 3 0.12
16 10 0.40
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAAATATTATTCA
Found at i:12071473 original size:18 final size:18
Alignment explanation
Indices: 12071447--12071482 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12071437 CATATAATAT
*
12071447 CATAGAATAATAAATTTA
1 CATACAATAATAAATTTA
*
12071465 CATACAATAATCAATTTA
1 CATACAATAATAAATTTA
12071483 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (18 bp):
CATACAATAATAAATTTA
Found at i:12077535 original size:14 final size:13
Alignment explanation
Indices: 12077516--12077549 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
12077506 TGAATATACC
12077516 ATGAAAAATGAAAA
1 ATGAAAAATG-AAA
12077530 ATGAAAAATGAAA
1 ATGAAAAATGAAA
12077543 ATGAAAA
1 ATGAAAA
12077550 TGTTCTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:12077551 original size:6 final size:7
Alignment explanation
Indices: 12077516--12077549 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
12077506 TGAATATACC
12077516 ATGAAAA
1 ATGAAAA
12077523 ATGAAAA
1 ATGAAAA
12077530 ATGAAAA
1 ATGAAAA
12077537 ATG-AAA
1 ATGAAAA
12077543 ATGAAAA
1 ATGAAAA
12077550 TGTTCTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:12079721 original size:24 final size:24
Alignment explanation
Indices: 12079688--12079741 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
12079678 GTATCTTGAA
* *
12079688 CTTTGCAATCGGAAGACTTCTAGT
1 CTTTGAAATCGAAAGACTTCTAGT
*
12079712 CTTTGAAATCGAAAGACTTTTAGT
1 CTTTGAAATCGAAAGACTTCTAGT
12079736 CTTTGA
1 CTTTGA
12079742 CTTGTGCACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (24 bp):
CTTTGAAATCGAAAGACTTCTAGT
Found at i:12083464 original size:7 final size:7
Alignment explanation
Indices: 12083452--12083497 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
12083442 ACTTCTGATC
12083452 AGTGACA
1 AGTGACA
12083459 AGTGACA
1 AGTGACA
12083466 AGTGACA
1 AGTGACA
12083473 AGTGACA
1 AGTGACA
12083480 AGTGACA
1 AGTGACA
*
12083487 AGTGATA
1 AGTGACA
12083494 AGTG
1 AGTG
12083498 TTAGCTTTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.41, C:0.11, G:0.30, T:0.17
Consensus pattern (7 bp):
AGTGACA
Found at i:12083554 original size:51 final size:51
Alignment explanation
Indices: 12083473--12083596 Score: 230
Period size: 51 Copynumber: 2.4 Consensus size: 51
12083463 ACAAGTGACA
* *
12083473 AGTGACAAGTGACAAGTGATAAGTGTTAGCTTTAGCTACACTTATTTGATC
1 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
12083524 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
12083575 AGTGACAAGTGACAAGTGATAA
1 AGTGACAAGTGACAAGTGATAA
12083597 ATGTGATCTG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 71 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (51 bp):
AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:12093951 original size:23 final size:23
Alignment explanation
Indices: 12093925--12094069 Score: 191
Period size: 23 Copynumber: 6.2 Consensus size: 23
12093915 ATTGGGTATA
* *
12093925 TATATATGCTATCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
12093948 TATAAATGCTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
*
12093971 TATAAATGCTGCCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* * *
12093994 TATATATGCTGTCCAATTTGATA
1 TATAAATGCTGTCCAATTTGGTG
*
12094017 TATATATATGCTGTCCAATTGGGTG
1 TATA-A-ATGCTGTCCAATTTGGTG
* *
12094042 TATAAATGCTGTCCGATTTGATG
1 TATAAATGCTGTCCAATTTGGTG
12094065 TATAA
1 TATAA
12094070 GAGATATCCA
Statistics
Matches: 106, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
23 86 0.81
24 1 0.01
25 19 0.18
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (23 bp):
TATAAATGCTGTCCAATTTGGTG
Found at i:12094080 original size:71 final size:69
Alignment explanation
Indices: 12093925--12094080 Score: 179
Period size: 71 Copynumber: 2.2 Consensus size: 69
12093915 ATTGGGTATA
* * * * *
12093925 TATATATGCTATCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGCCCAATTT
1 TATATAAGATATCCAATTTGATATATAAATGCTGTCCAATTGGGTGTATAAATGCTGCCCAATTT
*
12093990 GGTG
66 GATG
* * * * *
12093994 TATATATGCTGTCCAATTTGATATATATATATGCTGTCCAATTGGGTGTATAAATGCTGTCCGAT
1 TATATAAGATATCCAATTTGATATATA-A-ATGCTGTCCAATTGGGTGTATAAATGCTGCCCAAT
12094059 TTGATG
64 TTGATG
12094065 TATA-AGAGATATCCAA
1 TATATA-AGATATCCAA
12094081 ATAGGGTAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
69 24 0.32
70 2 0.03
71 48 0.65
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.38
Consensus pattern (69 bp):
TATATAAGATATCCAATTTGATATATAAATGCTGTCCAATTGGGTGTATAAATGCTGCCCAATTT
GATG
Found at i:12098812 original size:21 final size:22
Alignment explanation
Indices: 12098786--12098835 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
12098776 TTTCAAAAAC
12098786 TGAATTTC-TAT-CAGTGTTTT
1 TGAATTTCGTATGCAGTGTTTT
*
12098806 TGAAATTCGTATGCAGTGTTTT
1 TGAATTTCGTATGCAGTGTTTT
12098828 TGAATTTC
1 TGAATTTC
12098836 AGGTCGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 7 0.27
21 3 0.12
22 16 0.62
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.50
Consensus pattern (22 bp):
TGAATTTCGTATGCAGTGTTTT
Found at i:12100512 original size:56 final size:51
Alignment explanation
Indices: 12100295--12100542 Score: 227
Period size: 50 Copynumber: 4.8 Consensus size: 51
12100285 TGATAATAAC
* ** * * *
12100295 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGT-TTCTTAT-A
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCCATCTCA
* * ** * *
12100344 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATTTCT-CATATCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCCATCTCA
* * * *
12100394 GTGCCCATGCTATGTCCGAGACATGGTCTTACGA-GGGACCTC-CCATCTCA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCCATCTCA
* *
12100444 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--CATCTC-A
* *
12100498 TGATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCTCT
1 --ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
12100543 TTACCCAAAT
Statistics
Matches: 163, Mismatches: 25, Indels: 15
0.80 0.12 0.07
Matches are distributed among these distances:
49 42 0.26
50 73 0.45
51 2 0.01
53 5 0.03
54 1 0.01
56 40 0.25
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (51 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCCATCTCA
Found at i:12101999 original size:13 final size:13
Alignment explanation
Indices: 12101981--12102005 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12101971 GAATTAATAT
12101981 GTGTGAAAATTTC
1 GTGTGAAAATTTC
12101994 GTGTGAAAATTT
1 GTGTGAAAATTT
12102006 TATTTTTTGT
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:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:12103175 original size:43 final size:42
Alignment explanation
Indices: 12103112--12103237 Score: 139
Period size: 43 Copynumber: 2.9 Consensus size: 42
12103102 AAGATTCCGT
12103112 TATGTGTTATCGTGTAAGACCACGTCTGGGACGTTGGCATCAAC
1 TATGTGTTA-CGTGTAAGACCACGTCTGGGACGTTGGCATC-AC
** **
12103156 T-TGTGTTTACGTGTAAGACCTTGTCTGGGACAG-TGGCATCGT
1 TATGTG-TTACGTGTAAGACCACGTCTGGGAC-GTTGGCATCAC
* *
12103198 TATGTGATTACATGTAAGACCACGTCTGGAACGTTGGCAT
1 TATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCAT
12103238 TGTACGATAT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
42 2 0.03
43 62 0.90
44 5 0.07
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (42 bp):
TATGTGTTACGTGTAAGACCACGTCTGGGACGTTGGCATCAC
Found at i:12105124 original size:50 final size:50
Alignment explanation
Indices: 12104952--12105192 Score: 288
Period size: 50 Copynumber: 4.8 Consensus size: 50
12104942 TATCGATGAA
* * *
12104952 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGGATCGCTAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAA-ACTTGAT
* * * * * * * * *
12105003 CACATGTGCAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGTA-AAAC-TTGAT
*
12105054 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGTAAAACTTGAT
*
12105104 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGTAAAACTTGAT
* *
12105154 CATGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCG
12105193 AATGATAAAA
Statistics
Matches: 162, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 90 0.56
51 70 0.43
52 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGTAAAACTTGAT
Found at i:12107162 original size:23 final size:24
Alignment explanation
Indices: 12107136--12107253 Score: 107
Period size: 23 Copynumber: 5.0 Consensus size: 24
12107126 GGGTATATAT
*
12107136 ATACTGTCCAATTTGGTGTAT-CA
1 ATACTGTCCAATTTGGTGTATAAA
*
12107159 ATACTATCCAATTTGGTGTATAAA
1 ATACTGTCCAATTTGGTGTATAAA
* *
12107183 ATGCTGTCCAATTTGGTGTAT-AT
1 ATACTGTCCAATTTGGTGTATAAA
* * *
12107206 ATGA-TGTCTAATTTGGTATATATAT
1 AT-ACTGTCCAATTTGGTGTATA-AA
* * *
12107231 ATGCTGTCCGATTTGATGTATAA
1 ATACTGTCCAATTTGGTGTATAA
12107254 GAGCTGTCTG
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
23 38 0.49
24 21 0.27
25 18 0.23
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.42
Consensus pattern (24 bp):
ATACTGTCCAATTTGGTGTATAAA
Found at i:12107198 original size:47 final size:48
Alignment explanation
Indices: 12107129--12107252 Score: 137
Period size: 47 Copynumber: 2.6 Consensus size: 48
12107119 ATTGATTGGG
* * *
12107129 TATATATATACTGTCCAATTTGGTGTATCA-AT-ACTATCCAATTTGGTG
1 TATATAAATGCTGTCCAATTTGGTGTAT-ATATGA-TATCCAATTTGGTA
* *
12107177 TATA-AAATGCTGTCCAATTTGGTGTATATATGATGTCTAATTTGGTA
1 TATATAAATGCTGTCCAATTTGGTGTATATATGATATCCAATTTGGTA
* * *
12107224 TATATATATGCTGTCCGATTTGATGTATA
1 TATATAAATGCTGTCCAATTTGGTGTATA
12107253 AGAGCTGTCT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
46 1 0.02
47 38 0.58
48 26 0.40
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (48 bp):
TATATAAATGCTGTCCAATTTGGTGTATATATGATATCCAATTTGGTA
Found at i:12107259 original size:23 final size:23
Alignment explanation
Indices: 12107233--12107285 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
12107223 ATATATATAT
12107233 GCTGTCCGATTTGATGTATAAGA
1 GCTGTCCGATTTGATGTATAAGA
*
12107256 GCTGTCTGATTTGATGTATAAGA
1 GCTGTCCGATTTGATGTATAAGA
*
12107279 GTTGTCC
1 GCTGTCC
12107286 AAATAGGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (23 bp):
GCTGTCCGATTTGATGTATAAGA
Found at i:12113940 original size:42 final size:41
Alignment explanation
Indices: 12113888--12114069 Score: 143
Period size: 42 Copynumber: 4.4 Consensus size: 41
12113878 AGCTGGCATG
**
12113888 TAAGTGCATCATCGGTTGTAGCGAAGCAAATATATTGGCACA
1 TAAGTGCATCATCGGACGTA-CGAAGCAAATATATTGGCACA
* ** * * * *
12113930 TGAGTGCATCATCAAATCG-ACGAAGCAATTATACTAGTACA
1 TAAGTGCATCATCGGA-CGTACGAAGCAAATATATTGGCACA
* * *** **
12113971 TTAGTACATCATCGGATAAACTGAAGCAAATATACTT-GCATG
1 TAAGTGCATCATCGGACGTAC-GAAGCAAATATA-TTGGCACA
* *
12114013 TAAGTGCATCATCGAACGTACCGAAGCAAATATATTGTCACA
1 TAAGTGCATCATCGGACGTA-CGAAGCAAATATATTGGCACA
12114055 TAAGTGCATCATCGG
1 TAAGTGCATCATCGG
12114070 CTAAACCAAA
Statistics
Matches: 104, Mismatches: 30, Indels: 12
0.71 0.21 0.08
Matches are distributed among these distances:
41 33 0.32
42 68 0.65
43 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (41 bp):
TAAGTGCATCATCGGACGTACGAAGCAAATATATTGGCACA
Found at i:12115978 original size:11 final size:11
Alignment explanation
Indices: 12115964--12116020 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
12115954 ATTGAATTAA
*
12115964 TAAAATACTAT
1 TAAAATAATAT
12115975 TAAAATAAGTAT
1 TAAAATAA-TAT
*
12115987 TAAATTTAATAT
1 TAAA-ATAATAT
*
12115999 T-AAAT-TTAT
1 TAAAATAATAT
12116008 TAAAATAATAT
1 TAAAATAATAT
12116019 TA
1 TA
12116021 TTTTTGAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
9 4 0.11
10 5 0.14
11 14 0.38
12 11 0.30
13 3 0.08
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TAAAATAATAT
Found at i:12121737 original size:17 final size:17
Alignment explanation
Indices: 12121715--12121750 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
12121705 CGATTGCATG
12121715 TTTCTATTGCTGTTTAT
1 TTTCTATTGCTGTTTAT
12121732 TTTCTATTGCTGTTTAT
1 TTTCTATTGCTGTTTAT
12121749 TT
1 TT
12121751 CCCTTTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTCTATTGCTGTTTAT
Found at i:12122212 original size:32 final size:34
Alignment explanation
Indices: 12122149--12122212 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
12122139 TCTAATAATT
* *
12122149 TCACTATTATAAAACTATTTTCCTTAAAAGAATG
1 TCACTATTATAAAACCATTCTCCTTAAAAGAATG
12122183 TCAC-ATTATAAAACCATTCT-CTTAAAAGAA
1 TCACTATTATAAAACCATTCTCCTTAAAAGAA
12122213 AATCGAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 10 0.36
33 14 0.50
34 4 0.14
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (34 bp):
TCACTATTATAAAACCATTCTCCTTAAAAGAATG
Found at i:12123132 original size:23 final size:23
Alignment explanation
Indices: 12123106--12123161 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
12123096 TTGATTTGTT
12123106 CTGGAAATTGTTATGATTGTCTG
1 CTGGAAATTGTTATGATTGTCTG
*
12123129 CTGGAAATTGTTTTGATTGTCTG
1 CTGGAAATTGTTATGATTGTCTG
12123152 CTGGAAATTG
1 CTGGAAATTG
12123162 AATTTGTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.09, G:0.27, T:0.43
Consensus pattern (23 bp):
CTGGAAATTGTTATGATTGTCTG
Found at i:12123342 original size:59 final size:59
Alignment explanation
Indices: 12123250--12123367 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
12123240 AAATGGATAT
12123250 GCTAGTGACGAAAACGAGTTACTTGCAGGACATGTTCATTATTTGTGTTCTTAGATACA
1 GCTAGTGACGAAAACGAGTTACTTGCAGGACATGTTCATTATTTGTGTTCTTAGATACA
12123309 GCTAGTGACGAAAACGAGTTACTTGCAGGACATGTTCATTATTTGTGTTCTTAGATACA
1 GCTAGTGACGAAAACGAGTTACTTGCAGGACATGTTCATTATTTGTGTTCTTAGATACA
12123368 TGATATACAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (59 bp):
GCTAGTGACGAAAACGAGTTACTTGCAGGACATGTTCATTATTTGTGTTCTTAGATACA
Found at i:12124526 original size:95 final size:96
Alignment explanation
Indices: 12124407--12124588 Score: 330
Period size: 95 Copynumber: 1.9 Consensus size: 96
12124397 AAATAATTAC
12124407 ATCAATAATTAAAATAAGGACTTTAATATTTCATTAAAATAAGGACTAATCAATAATTAAAATAA
1 ATCAATAATTAAAATAAGGACTTTAATATTTCATTAAAATAAGGACTAATCAATAATTAAAATAA
12124472 GGACTTTAATATTTTATTAAAATAAGGACTA
66 GGACTTTAATATTTTATTAAAATAAGGACTA
* * *
12124503 ATCAATAATTAAAAT-AGGACTTTAATATTTTATTAAAATAAGGACTAATTAATATTTAAAATAA
1 ATCAATAATTAAAATAAGGACTTTAATATTTCATTAAAATAAGGACTAATCAATAATTAAAATAA
12124567 GGACTTTAATATTTTATTAAAA
66 GGACTTTAATATTTTATTAAAA
12124589 ATCAAGAAAT
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
95 68 0.82
96 15 0.18
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (96 bp):
ATCAATAATTAAAATAAGGACTTTAATATTTCATTAAAATAAGGACTAATCAATAATTAAAATAA
GGACTTTAATATTTTATTAAAATAAGGACTA
Found at i:12124540 original size:47 final size:48
Alignment explanation
Indices: 12124407--12124588 Score: 330
Period size: 48 Copynumber: 3.8 Consensus size: 48
12124397 AAATAATTAC
*
12124407 ATCAATAATTAAAATAAGGACTTTAATATTTCATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
12124455 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
12124503 ATCAATAATTAAAAT-AGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
* *
12124550 ATTAATATTTAAAATAAGGACTTTAATATTTTATTAAAA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAA
12124589 ATCAAGAAAT
Statistics
Matches: 130, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
47 45 0.35
48 85 0.65
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (48 bp):
ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
Found at i:12127912 original size:92 final size:91
Alignment explanation
Indices: 12127755--12127963 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
12127745 TTGATTTTAG
* * *
12127755 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
12127820 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
12127847 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
12127911 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
12127939 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
12127964 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:12127926 original size:24 final size:25
Alignment explanation
Indices: 12127891--12127938 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
12127881 TTATGAAATT
12127891 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
12127915 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
12127939 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:12128117 original size:120 final size:120
Alignment explanation
Indices: 12127979--12128271 Score: 470
Period size: 120 Copynumber: 2.4 Consensus size: 120
12127969 AATTATTTTA
* * *
12127979 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-AT
*
12128041 TTTATAGTATCATATATTA-GCATGTT-AGTAAATTCATATAAGAATATTAATTATTAAG
63 TTTACAGTATCATATATTATG-AT-TTGAGTAAATTCATATAAGAATATTAATTATTAAG
12128099 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
12128164 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
12128219 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
12128272 TAAATATGAT
Statistics
Matches: 164, Mismatches: 4, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
119 8 0.05
120 153 0.93
121 3 0.02
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:12128139 original size:15 final size:15
Alignment explanation
Indices: 12128104--12128155 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
12128094 TTAAGAATTT
*
12128104 TATTAAATTAT-ATA
1 TATTTAATTATAATA
12128118 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
12128132 TATTTAATAATAAT-
1 TATTTAATTATAATA
12128146 TATGTTAATT
1 TAT-TTAATT
12128156 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:12128254 original size:16 final size:16
Alignment explanation
Indices: 12128233--12128274 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12128223 TTATTAAATT
*
12128233 ATATATTTTAATTATA
1 ATATATTTTAATAATA
12128249 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
12128264 AT-TATGTTTAA
1 ATATAT-TTTAA
12128275 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:12128259 original size:15 final size:15
Alignment explanation
Indices: 12128224--12128265 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12128214 TTAAGAATTT
*
12128224 TATTAAATTAT-ATA
1 TATTTAATTATAATA
12128238 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
12128252 TATTTAATAATAAT
1 TATTTAATTATAAT
12128266 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:12128386 original size:157 final size:154
Alignment explanation
Indices: 12128208--12128521 Score: 538
Period size: 157 Copynumber: 2.0 Consensus size: 154
12128198 ATAAGAATAT
*
12128208 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
12128273 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAAT---AA
* *
12128338 TAATAATTTATCAAAACAAATTTCTGC
128 TAATAATTTACCAAAACAAATTTATGC
12128365 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
12128430 AAATATGATTAAAATATTTATTATTGATAATAATTATCTTATTAAAATTTAAATAACAATAATAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAATAA
*
12128495 TCATTTACCAAAACAAATTTATGC
131 TAATTTACCAAAACAAATTTATGC
12128519 TAA
1 TAA
12128522 GGGTATTCTA
Statistics
Matches: 150, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
154 29 0.19
157 121 0.81
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (154 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAATAA
TAATTTACCAAAACAAATTTATGC
Found at i:12128405 original size:18 final size:17
Alignment explanation
Indices: 12128377--12128411 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12128367 ATTATTAAGA
*
12128377 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12128394 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12128412 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12128665 original size:16 final size:16
Alignment explanation
Indices: 12128644--12128679 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
12128634 GATTTGCTAT
12128644 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12128660 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12128676 TACA
1 TACA
12128680 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:12130998 original size:28 final size:28
Alignment explanation
Indices: 12130966--12131022 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
12130956 TTAATAATAA
12130966 AGTCTTAAGAATAATATGATTATTCTTG
1 AGTCTTAAGAATAATATGATTATTCTTG
12130994 AGTCTTAAGAATAATATGATTATTCTTG
1 AGTCTTAAGAATAATATGATTATTCTTG
12131022 A
1 A
12131023 AAGTCCTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (28 bp):
AGTCTTAAGAATAATATGATTATTCTTG
Found at i:12133626 original size:49 final size:50
Alignment explanation
Indices: 12133550--12133782 Score: 249
Period size: 49 Copynumber: 4.7 Consensus size: 50
12133540 AATATGTGAG
*
12133550 CCATGTAAGACCATGTCTGGGATATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
**
12133600 TTATGTAAGACC-TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
* * * * **
12133649 CCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
* * * * * * **
12133699 CCATGTAAGACCATATCTGAGATATGGCATTGGCA--GTACA-GAAAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCG-AGATG-AGAGGTC
* *
12133748 CCACGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
12133783 TGTTATTATC
Statistics
Matches: 155, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
48 2 0.01
49 81 0.52
50 72 0.46
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
Found at i:12134010 original size:20 final size:20
Alignment explanation
Indices: 12133985--12134027 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
12133975 TGAGTTATTT
*
12133985 AAGTAAGCA-AGTAAGTAAAG
1 AAGTAAG-AGAGTAAGAAAAG
12134005 AAGTAAGAGAGTAAGAAAAG
1 AAGTAAGAGAGTAAGAAAAG
12134025 AAG
1 AAG
12134028 AAGTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.58, C:0.02, G:0.28, T:0.12
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGAAAAG
Found at i:12143236 original size:17 final size:19
Alignment explanation
Indices: 12143208--12143244 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
12143198 AAAATTCGAA
12143208 TTTATTTCCCAAT-TTAAT
1 TTTATTTCCCAATATTAAT
12143226 TTTATTT-CCAATATTAAT
1 TTTATTTCCCAATATTAAT
12143244 T
1 T
12143245 AATTGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATTTCCCAATATTAAT
Found at i:12153104 original size:3 final size:3
Alignment explanation
Indices: 12153096--12153123 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12153086 ACGCCTTGTC
12153096 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12153124 TTCTTTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12157651 original size:23 final size:24
Alignment explanation
Indices: 12157625--12157669 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
12157615 ATATCCCCAC
*
12157625 ATGGAGTGTAG-GGTTGGATGGAG
1 ATGGAGTGTAGAGGCTGGATGGAG
*
12157648 ATGGTGTGTAGAGGCTGGATGG
1 ATGGAGTGTAGAGGCTGGATGG
12157670 GTAGGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.20, C:0.02, G:0.51, T:0.27
Consensus pattern (24 bp):
ATGGAGTGTAGAGGCTGGATGGAG
Found at i:12157786 original size:34 final size:34
Alignment explanation
Indices: 12157743--12157820 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
12157733 GCATTTTTGA
* *
12157743 CACTGTACTGAGATGGGCTAAGGCCCAA-ACTGT
1 CACTGTACTGAAAAGGGCTAAGGCCCAAGACTGT
*
12157776 CACTGATACTGAAAAGGGCTTAGGCCCAAGACTGTT
1 CACTG-TACTGAAAAGGGCTAAGGCCCAAGACTG-T
12157812 CAACTGTAC
1 C-ACTGTAC
12157821 ACTATGAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 5 0.13
34 20 0.53
35 4 0.11
36 5 0.13
37 4 0.11
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (34 bp):
CACTGTACTGAAAAGGGCTAAGGCCCAAGACTGT
Found at i:12160040 original size:15 final size:15
Alignment explanation
Indices: 12160020--12160060 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
12160010 ATGGTATATA
12160020 TATTTTTAAATTTTT
1 TATTTTTAAATTTTT
*
12160035 TATTTTAAAATTTTT
1 TATTTTTAAATTTTT
*
12160050 TTTATTTTAAA
1 TAT-TTTTAAA
12160061 AAATGAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTAAATTTTT
Found at i:12166615 original size:72 final size:72
Alignment explanation
Indices: 12166498--12166645 Score: 215
Period size: 72 Copynumber: 2.1 Consensus size: 72
12166488 CGTTTATTAT
* *
12166498 GGCCTGACAAATGGTCGTGTCCTTATCGTTGGGTATTTTACACGTCACACACACAACCTCAGGCT
1 GGCCTGACAAATAGTCGTGTCCTTATCATTGGGTATTTTACACGTCACACACACAACCTCAGGCT
12166563 GTTACAC
66 GTTACAC
* * ** ** *
12166570 GGCCTGACACATAGTCGTGTCCTTATCATTGGGTATTTTGCACGTCGTACACACGGCCTTAGGCT
1 GGCCTGACAAATAGTCGTGTCCTTATCATTGGGTATTTTACACGTCACACACACAACCTCAGGCT
12166635 GTTACAC
66 GTTACAC
12166642 GGCC
1 GGCC
12166646 GTGTACCCCC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (72 bp):
GGCCTGACAAATAGTCGTGTCCTTATCATTGGGTATTTTACACGTCACACACACAACCTCAGGCT
GTTACAC
Found at i:12171543 original size:13 final size:14
Alignment explanation
Indices: 12171509--12171542 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
12171499 ATTTGAAATT
*
12171509 TTAAAAATATATTA
1 TTAAAAAGATATTA
12171523 TTAAAAAGATATTA
1 TTAAAAAGATATTA
12171537 TTAAAA
1 TTAAAA
12171543 GGTTTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TTAAAAAGATATTA
Found at i:12171863 original size:29 final size:28
Alignment explanation
Indices: 12171830--12171892 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 28
12171820 TTTATAATTT
*
12171830 TATTTTTATGATTTTTATAAAATTTTATA
1 TATTTTTATGATTTTTAT-AAATTTTAAA
*
12171859 TATTTTTATTATTTTTATAAATTTTAAA
1 TATTTTTATGATTTTTATAAATTTTAAA
12171887 TATTTT
1 TATTTT
12171893 ATTAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (28 bp):
TATTTTTATGATTTTTATAAATTTTAAA
Found at i:12171883 original size:9 final size:9
Alignment explanation
Indices: 12171818--12171923 Score: 51
Period size: 9 Copynumber: 11.8 Consensus size: 9
12171808 TTTTTGATGC
12171818 ATTTTAT-A
1 ATTTTATAA
12171826 ATTTTAT--
1 ATTTTATAA
*
12171833 -TTTTATGA
1 ATTTTATAA
*
12171841 TTTTTATAAA
1 ATTTTAT-AA
12171851 ATTTTATATA
1 ATTTTATA-A
* *
12171861 TTTTTATTA
1 ATTTTATAA
*
12171870 TTTTTATAA
1 ATTTTATAA
12171879 ATTTTA-AA
1 ATTTTATAA
12171887 TATTTTATTAAA
1 -ATTTTA-T-AA
*
12171899 ATTTAATAA
1 ATTTTATAA
* *
12171908 CTTTAATAA
1 ATTTTATAA
*
12171917 CTTTTAT
1 ATTTTAT
12171924 TGATTTTTAT
Statistics
Matches: 80, Mismatches: 9, Indels: 17
0.75 0.08 0.16
Matches are distributed among these distances:
6 6 0.08
8 9 0.11
9 43 0.54
10 15 0.19
11 5 0.06
12 2 0.03
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (9 bp):
ATTTTATAA
Found at i:12171890 original size:19 final size:19
Alignment explanation
Indices: 12171830--12171892 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
12171820 TTTATAATTT
* *
12171830 TATTTTTATGATTTTTATAA
1 TATTTTTATAAATTTTA-AA
* * * *
12171850 -AATTTTATATATTTTTAT
1 TATTTTTATAAATTTTAAA
12171868 TATTTTTATAAATTTTAAA
1 TATTTTTATAAATTTTAAA
12171887 TATTTT
1 TATTTT
12171893 ATTAAAATTT
Statistics
Matches: 32, Mismatches: 10, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
18 1 0.03
19 31 0.97
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTTTTATAAATTTTAAA
Found at i:12171903 original size:28 final size:29
Alignment explanation
Indices: 12171843--12171903 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
12171833 TTTTATGATT
* **
12171843 TTTATAAAATTTTATATATTTTTATTATT
1 TTTATAAAATTTTAAATATTTTTATTAAA
12171872 TTTAT-AAATTTTAAATA-TTTTATTAAAA
1 TTTATAAAATTTTAAATATTTTTATT-AAA
12171900 TTTA
1 TTTA
12171904 ATAACTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.25
28 16 0.57
29 5 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTATAAAATTTTAAATATTTTTATTAAA
Found at i:12171946 original size:9 final size:9
Alignment explanation
Indices: 12171831--12171947 Score: 69
Period size: 9 Copynumber: 12.7 Consensus size: 9
12171821 TTATAATTTT
*
12171831 ATTTTTATG
1 ATTTTTATA
12171840 ATTTTTATAA
1 ATTTTTAT-A
*
12171850 AATTTTATA
1 ATTTTTATA
*
12171859 TATTTTTATT
1 -ATTTTTATA
12171869 ATTTTTATA
1 ATTTTTATA
*
12171878 AATTTTA-A
1 ATTTTTATA
12171886 ATATTTTATTAA
1 AT-TTTTA-T-A
* *
12171898 AATTTAATA
1 ATTTTTATA
* *
12171907 ACTTTAATA
1 ATTTTTATA
* *
12171916 ACTTTTATTG
1 ATTTTTA-TA
12171926 ATTTTTAT-
1 ATTTTTATA
12171934 -TTTTTATA
1 ATTTTTATA
12171942 ATTTTT
1 ATTTTT
12171948 TGCCACATGT
Statistics
Matches: 86, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
7 7 0.08
8 2 0.02
9 49 0.57
10 22 0.26
11 4 0.05
12 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (9 bp):
ATTTTTATA
Found at i:12172241 original size:88 final size:90
Alignment explanation
Indices: 12172052--12172278 Score: 253
Period size: 88 Copynumber: 2.6 Consensus size: 90
12172042 ATTAAATGGT
** * * * *
12172052 CTTTTTGATGTATTTTGACAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGAAATGGATTAATT
1 CTTTTTGATACATTTTGAAAGTTCAAGTACCCAACTAAGTGCAAAAAAAAAGAAAGGGATTAATT
* * * **
12172117 GCTTTTTTTGAAAAAGTTTGTGGGC
66 GCATTTTGTAAAAAAGTTTGAAGGC
* * *
12172142 CTTTTTGATACATTTTGAAAGTTCAAGTGCCCAACTAAGTGC-AAAAAAAAG-TAGGGCTTAATT
1 CTTTTTGATACATTTTGAAAGTTCAAGTACCCAACTAAGTGCAAAAAAAAAGAAAGGGATTAATT
12172205 GCATTTTGTAAAAAAGTTTGAAGGC
66 GCATTTTGTAAAAAAGTTTGAAGGC
* * * * * *
12172230 CTTTTTTATACATTTTGAAGGTTTAAGTACCGAATTGAGTG-AAAAAAAA
1 CTTTTTGATACATTTTGAAAGTTCAAGTACCCAACTAAGTGCAAAAAAAA
12172279 TAGATTTAAA
Statistics
Matches: 115, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
88 70 0.61
89 9 0.08
90 36 0.31
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.35
Consensus pattern (90 bp):
CTTTTTGATACATTTTGAAAGTTCAAGTACCCAACTAAGTGCAAAAAAAAAGAAAGGGATTAATT
GCATTTTGTAAAAAAGTTTGAAGGC
Found at i:12184632 original size:13 final size:13
Alignment explanation
Indices: 12184614--12184639 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12184604 ATTAAAAGTG
12184614 CAAAAAGAAAATT
1 CAAAAAGAAAATT
12184627 CAAAAAGAAAATT
1 CAAAAAGAAAATT
12184640 AACGAGTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
CAAAAAGAAAATT
Found at i:12184920 original size:18 final size:18
Alignment explanation
Indices: 12184894--12184928 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12184884 ATGATATGCC
*
12184894 AAACTATTTTCATGCTTG
1 AAACCATTTTCATGCTTG
*
12184912 AAACCATTTTGATGCTT
1 AAACCATTTTCATGCTT
12184929 ACCATTCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (18 bp):
AAACCATTTTCATGCTTG
Found at i:12190372 original size:79 final size:79
Alignment explanation
Indices: 12190261--12190484 Score: 292
Period size: 79 Copynumber: 2.8 Consensus size: 79
12190251 GCTACTCGTT
* * *
12190261 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
12190326 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
*
12190341 CAAATGCCTTCGGGCTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
12190404 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * * *
12190419 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
12190483 GA
64 GA
12190485 CATCATTCAA
Statistics
Matches: 127, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
78 36 0.28
79 57 0.45
80 34 0.27
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:12190378 original size:39 final size:40
Alignment explanation
Indices: 12190261--12190484 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
12190251 GCTACTCGTT
* *
12190261 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
12190301 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
12190341 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
12190380 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
12190419 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
12190460 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12190485 CATCATTCAA
Statistics
Matches: 166, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 74 0.45
40 77 0.46
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:12198213 original size:22 final size:21
Alignment explanation
Indices: 12198177--12198217 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
12198167 TGGGATCTCA
12198177 TGAAATTATAGAAAAATACCTT
1 TGAAATTATAG-AAAATACCTT
**
12198199 TGAAATTATTTAAAATACC
1 TGAAATTATAGAAAATACC
12198218 CCAAATTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (21 bp):
TGAAATTATAGAAAATACCTT
Found at i:12206018 original size:40 final size:40
Alignment explanation
Indices: 12205973--12206236 Score: 228
Period size: 40 Copynumber: 6.6 Consensus size: 40
12205963 GTAGATGTAG
* * *
12205973 AACAGGGGCACACATGTGAATTCAGGGGTACCAAAGTATA
1 AACAGGGGCACATATGTGCATTCAGGGGTACCAAAGTACA
* ** * * * *
12206013 AACAGGGGCACGTATGTGCATTTTGAGGGTA-CTATGAACT
1 AACAGGGGCACATATGTGCATTCAG-GGGTACCAAAGTACA
* * * * * **
12206053 AACAAGAGCACGTGTGTGCATTCTGGTCTACCAAAGTACA
1 AACAGGGGCACATATGTGCATTCAGGGGTACCAAAGTACA
* * * * *
12206093 AACAGGGGCGCGTATGTGCATTTAGGGGTACCGAAGTACG
1 AACAGGGGCACATATGTGCATTCAGGGGTACCAAAGTACA
* *
12206133 AATAGGGGCACATATGTGCATTCAGGGGTACCGAAGTACA
1 AACAGGGGCACATATGTGCATTCAGGGGTACCAAAGTACA
*
12206173 AACAGGGGCACGA-ATGTGCATTCAGGGGTATCGAAA-TACA
1 AACAGGGGCAC-ATATGTGCATTCAGGGGTA-CCAAAGTACA
* * *
12206213 AATAGGGGCACACATGTGCGTTCA
1 AACAGGGGCACATATGTGCATTCA
12206237 AGTACATTTT
Statistics
Matches: 179, Mismatches: 40, Indels: 10
0.78 0.17 0.04
Matches are distributed among these distances:
39 4 0.02
40 166 0.93
41 9 0.05
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.21
Consensus pattern (40 bp):
AACAGGGGCACATATGTGCATTCAGGGGTACCAAAGTACA
Found at i:12206151 original size:80 final size:79
Alignment explanation
Indices: 12205976--12206236 Score: 279
Period size: 80 Copynumber: 3.3 Consensus size: 79
12205966 GATGTAGAAC
* * *
12205976 AGGGGCACACATGTGAATTCAGGGGTACCAAAGTATAAACAGGGGCACGTATGTGCATTTTGAGG
1 AGGGGCACACATGTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCATTTAG-GG
* * * * *
12206041 GTACTATGAACTAAC
65 GTACGAAGTACAAAT
* * *** * ** *
12206056 AAGAGCACGTGTGTGCATTCTGGTCTACCAAAGTACAAACAGGGGCGCGTATGTGCATTTAGGGG
1 AGGGGCACACATGTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCATTTAGGGG
*
12206121 TACCGAAGTACGAAT
66 TA-CGAAGTACAAAT
* * * *
12206136 AGGGGCACATATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGAATGTGCATTCAGGGG
1 AGGGGCACACATGTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCATTTAGGGG
*
12206201 TATCGAAATACAAAT
66 TA-CGAAGTACAAAT
*
12206216 AGGGGCACACATGTGCGTTCA
1 AGGGGCACACATGTGCATTCA
12206237 AGTACATTTT
Statistics
Matches: 147, Mismatches: 33, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
79 5 0.03
80 142 0.97
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.21
Consensus pattern (79 bp):
AGGGGCACACATGTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCATTTAGGGG
TACGAAGTACAAAT
Found at i:12206159 original size:20 final size:19
Alignment explanation
Indices: 12206136--12206200 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
12206126 AAGTACGAAT
12206136 AGGGGCACATATGTGCATTC
1 AGGGGCACA-ATGTGCATTC
* * **
12206156 AGGGGTACCGAA-GTACAAAC
1 AGGGGCA-C-AATGTGCATTC
12206176 AGGGGCACGAATGTGCATTC
1 AGGGGCAC-AATGTGCATTC
12206196 AGGGG
1 AGGGG
12206201 TATCGAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 4 0.12
20 27 0.79
21 2 0.06
22 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.35, T:0.17
Consensus pattern (19 bp):
AGGGGCACAATGTGCATTC
Found at i:12206230 original size:120 final size:120
Alignment explanation
Indices: 12205973--12206236 Score: 262
Period size: 120 Copynumber: 2.2 Consensus size: 120
12205963 GTAGATGTAG
* * * **
12205973 AACAGGGGCACACATGTGAATTCAGGGGTACCAAAGTATAAACAGGGGCACGTATGTGCATTTTG
1 AACAGGGGCACACATGTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACATATGTGCATTCAG
* * * ** * *
12206038 AGGGTACTATGAACTAACAAGAGCACGTGTGTGCATTCTGGTCTACCAAAGTACA
66 AGGGTACGAAGAACAAACAAGAGCACGAATGTGCATTCAGGGCTACCAAAGTACA
* ** * * * *
12206093 AACAGGGGCGCGTATGTGCATTTAGGGGTACCGAAGTACGAATAGGGGCACATATGTGCATTCAG
1 AACAGGGGCACACATGTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACATATGTGCATTCAG
* * * * *
12206158 -GGGTACCGAAGTACAAACAGGGGCACGAATGTGCATTCAGGGGTATCGAAA-TACA
66 AGGGTA-CGAAGAACAAACAAGAGCACGAATGTGCATTCAGGGCTA-CCAAAGTACA
* *
12206213 AATAGGGGCACACATGTGCGTTCA
1 AACAGGGGCACACATGTGCATTCA
12206237 AGTACATTTT
Statistics
Matches: 112, Mismatches: 30, Indels: 4
0.77 0.21 0.03
Matches are distributed among these distances:
119 5 0.04
120 103 0.92
121 4 0.04
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.21
Consensus pattern (120 bp):
AACAGGGGCACACATGTGCATTCAGGGGTACCAAAGTACAAACAGGGGCACATATGTGCATTCAG
AGGGTACGAAGAACAAACAAGAGCACGAATGTGCATTCAGGGCTACCAAAGTACA
Found at i:12206691 original size:15 final size:14
Alignment explanation
Indices: 12206675--12206710 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
12206665 GATACCTTAT
12206675 TTTAATTTTATTTA
1 TTTAATTTTATTTA
*
12206689 TTTATGTTTTATTTA
1 TTTA-ATTTTATTTA
12206704 TTTAATT
1 TTTAATT
12206711 ACAAGTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTAATTTTATTTA
Found at i:12210851 original size:91 final size:91
Alignment explanation
Indices: 12210687--12210855 Score: 302
Period size: 91 Copynumber: 1.9 Consensus size: 91
12210677 TGACTTACTA
* *
12210687 GACTAAAAATAAATCAGATTGGACCCAAGAAGAATAGATCTTGAATCTGTTTATGGATTTATTTA
1 GACTAAAAATAAATCAGATTGGACCCAAGAAGAATAGATCTTGAATCCGTTTATGGATTTATTCA
12210752 CTTATGACGTTCAGAGTGTGATATTG
66 CTTATGACGTTCAGAGTGTGATATTG
*
12210778 GACTAACAATAAATCAGATTGGACCCAAGAAGAATAGATCTTGAATCCGTTTATGGATTTATTCA
1 GACTAAAAATAAATCAGATTGGACCCAAGAAGAATAGATCTTGAATCCGTTTATGGATTTATTCA
*
12210843 CTTGTGACGTTCA
66 CTTATGACGTTCA
12210856 AAATGTGACA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 74 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (91 bp):
GACTAAAAATAAATCAGATTGGACCCAAGAAGAATAGATCTTGAATCCGTTTATGGATTTATTCA
CTTATGACGTTCAGAGTGTGATATTG
Found at i:12214735 original size:7 final size:7
Alignment explanation
Indices: 12214723--12214817 Score: 172
Period size: 7 Copynumber: 13.6 Consensus size: 7
12214713 GTATGTAAAC
12214723 ATATAAT
1 ATATAAT
12214730 ATATAAT
1 ATATAAT
12214737 ATATAAT
1 ATATAAT
12214744 ATATAAT
1 ATATAAT
12214751 ATATAAT
1 ATATAAT
12214758 ATATAAT
1 ATATAAT
*
12214765 ATATAGT
1 ATATAAT
12214772 ATATAAT
1 ATATAAT
12214779 ATATAAT
1 ATATAAT
12214786 ATATAAT
1 ATATAAT
12214793 ATATAAT
1 ATATAAT
*
12214800 ATATAGT
1 ATATAAT
12214807 ATATAAT
1 ATATAAT
12214814 ATAT
1 ATAT
12214818 GATAAAAACA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 84 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (7 bp):
ATATAAT
Found at i:12224902 original size:43 final size:44
Alignment explanation
Indices: 12224854--12224971 Score: 150
Period size: 44 Copynumber: 2.7 Consensus size: 44
12224844 AATCTGCCTA
*
12224854 AAAAAGAGAAGAAGATAATCTTGGGTTGTTG-AAAACAGAA-TTT
1 AAAAAGAG-AGAAGATAATCTTGGGTTGTTGAAAAAAAGAATTTT
* **
12224897 AAAAAGAGGAGAAGATAATCCTAAGTTGTTGAAAAAAAGAATTTT
1 AAAAAGA-GAGAAGATAATCTTGGGTTGTTGAAAAAAAGAATTTT
* *
12224942 AAAAAAAGAGAAGATAAACTTGGGTTGTTG
1 AAAAAGAGAGAAGATAATCTTGGGTTGTTG
12224972 GATTTTCCCT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
43 26 0.41
44 28 0.44
45 9 0.14
ACGTcount: A:0.48, C:0.04, G:0.23, T:0.25
Consensus pattern (44 bp):
AAAAAGAGAGAAGATAATCTTGGGTTGTTGAAAAAAAGAATTTT
Found at i:12224939 original size:44 final size:44
Alignment explanation
Indices: 12224854--12224958 Score: 133
Period size: 43 Copynumber: 2.4 Consensus size: 44
12224844 AATCTGCCTA
* * ** *
12224854 AAAAAGAGAAGAAGATAATCTTGGGTTGTTGAAAACAGAA-TTT
1 AAAAAGAGGAGAAGATAATCCTAAGTTGTTGAAAAAAGAATTTT
12224897 AAAAAGAGGAGAAGATAATCCTAAGTTGTTGAAAAAAAGAATTTT
1 AAAAAGAGGAGAAGATAATCCTAAGTTGTTG-AAAAAAGAATTTT
*
12224942 AAAAA-AAGAGAAGATAA
1 AAAAAGAGGAGAAGATAA
12224959 ACTTGGGTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
43 27 0.50
44 19 0.35
45 8 0.15
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.22
Consensus pattern (44 bp):
AAAAAGAGGAGAAGATAATCCTAAGTTGTTGAAAAAAGAATTTT
Found at i:12231481 original size:9 final size:9
Alignment explanation
Indices: 12231467--12231491 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12231457 CATTTCAAAA
12231467 TCATTCAAT
1 TCATTCAAT
12231476 TCATTCAAT
1 TCATTCAAT
12231485 TCATTCA
1 TCATTCA
12231492 TCCATTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (9 bp):
TCATTCAAT
Found at i:12245595 original size:22 final size:22
Alignment explanation
Indices: 12245478--12245588 Score: 93
Period size: 22 Copynumber: 5.0 Consensus size: 22
12245468 ACTCTGCATA
12245478 ACATGCGAGCCTATATGTTAGT
1 ACATGCGAGCCTATATGTTAGT
* * *
12245500 -CTATACGAGCTTATACGTTAGT
1 AC-ATGCGAGCCTATATGTTAGT
* *** *
12245522 ACATGCAAGCCTATCCATTA-C
1 ACATGCGAGCCTATATGTTAGT
*
12245543 ATCAT-CTGAACCTATATGTTAGT
1 A-CATGC-GAGCCTATATGTTAGT
12245566 ACATGCGAGCCTATATGTTAGT
1 ACATGCGAGCCTATATGTTAGT
12245588 A
1 A
12245589 TGTGCGAACC
Statistics
Matches: 67, Mismatches: 16, Indels: 12
0.71 0.17 0.13
Matches are distributed among these distances:
21 3 0.04
22 61 0.91
23 3 0.04
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (22 bp):
ACATGCGAGCCTATATGTTAGT
Found at i:12245598 original size:44 final size:43
Alignment explanation
Indices: 12245478--12245598 Score: 109
Period size: 44 Copynumber: 2.7 Consensus size: 43
12245468 ACTCTGCATA
* * *
12245478 ACATGCGAGCCTATATGTTAGTCTATACGAGCTTATACGTTAGT
1 ACATGCGAGCCTATATGTTAGTATAT-CGAACCTATACGTTAGT
* *** * *
12245522 ACATGCAAGCCTATCCATTA-CATCATCTGAACCTATATGTTAGT
1 ACATGCGAGCCTATATGTTAGTAT-ATC-GAACCTATACGTTAGT
*
12245566 ACATGCGAGCCTATATGTTAGTATGTGCGAACC
1 ACATGCGAGCCTATATGTTAGTATAT-CGAACC
12245599 CCTAAGGTAA
Statistics
Matches: 58, Mismatches: 15, Indels: 8
0.72 0.19 0.10
Matches are distributed among these distances:
43 2 0.03
44 53 0.91
45 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (43 bp):
ACATGCGAGCCTATATGTTAGTATATCGAACCTATACGTTAGT
Done.