Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 83 of 235
Found at i:28816343 original size:3 final size:3
Alignment explanation
Indices: 28816335--28816365 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
28816325 CGTGTTATGA
*
28816335 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
28816366 CAAATAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:28817903 original size:27 final size:27
Alignment explanation
Indices: 28817873--28817933 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
28817863 TTTTGGTTAC
28817873 TTTACCTTATGGGGGTATTTCGATCAT
1 TTTACCTTATGGGGGTATTTCGATCAT
* * *
28817900 TTTACCCTATTGGGGTATTTCGGTCAT
1 TTTACCTTATGGGGGTATTTCGATCAT
28817927 TTTACCT
1 TTTACCT
28817934 ATTTTAGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.46
Consensus pattern (27 bp):
TTTACCTTATGGGGGTATTTCGATCAT
Found at i:28822187 original size:9 final size:9
Alignment explanation
Indices: 28822175--28822217 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
28822165 AAACTAGGGA
28822175 ACAATTTTT
1 ACAATTTTT
28822184 ACAATTTTT
1 ACAATTTTT
28822193 ACAATTTTT
1 ACAATTTTT
28822202 ACAATTTTT
1 ACAATTTTT
*
28822211 GCAATTT
1 ACAATTT
28822218 AGTCCCCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (9 bp):
ACAATTTTT
Found at i:28825726 original size:19 final size:19
Alignment explanation
Indices: 28825699--28825737 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
28825689 TTATTCCAGC
28825699 AACTAAATTAACTAAGATG
1 AACTAAATTAACTAAGATG
*
28825718 AACTCAATTAACTAAGATG
1 AACTAAATTAACTAAGATG
28825737 A
1 A
28825738 GTAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26
Consensus pattern (19 bp):
AACTAAATTAACTAAGATG
Found at i:28830424 original size:42 final size:40
Alignment explanation
Indices: 28830355--28830491 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 40
28830345 TATAAGTTAT
* *
28830355 CGTGTAAGACCTCGTCTAGGACGTTGGCATCGACT-TGTGTTG
1 CGTGTAAGACCT-GTCTGGGACATTGGCATC-A-TATGTGTTG
* * *
28830397 CGTGTAAGACCATATCTGGGACATTGGCATCATATTTGTTT
1 CGTGTAAGACC-TGTCTGGGACATTGGCATCATATGTGTTG
* * *
28830438 TGTGTAAGACCTTGTCTGGGACAGTGGCATCAGTATGTGATTA
1 CGTGTAAGACC-TGTCTGGGACATTGGCATCA-TATGTG-TTG
*
28830481 CATGTAAGACC
1 CGTGTAAGACC
28830492 ACGTCCGGGA
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
40 1 0.01
41 34 0.44
42 31 0.40
43 12 0.15
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (40 bp):
CGTGTAAGACCTGTCTGGGACATTGGCATCATATGTGTTG
Found at i:28830456 original size:41 final size:41
Alignment explanation
Indices: 28830355--28830469 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 41
28830345 TATAAGTTAT
* * *
28830355 CGTGTAAGACCTCGTCTAGGACGTTGGCATCGACTTGTGTTG
1 CGTGTAAGACCTTGTCTGGGACATTGGCATC-ACTTGTGTTG
* * * *
28830397 CGTGTAAGACCATATCTGGGACATTGGCATCA-TATTTGTTT
1 CGTGTAAGACCTTGTCTGGGACATTGGCATCACT-TGTGTTG
* *
28830438 TGTGTAAGACCTTGTCTGGGACAGTGGCATCA
1 CGTGTAAGACCTTGTCTGGGACATTGGCATCA
28830470 GTATGTGATT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
40 1 0.02
41 34 0.56
42 26 0.43
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (41 bp):
CGTGTAAGACCTTGTCTGGGACATTGGCATCACTTGTGTTG
Found at i:28840261 original size:2 final size:2
Alignment explanation
Indices: 28840254--28840289 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
28840244 CATTCCGAAG
* *
28840254 TA TA TA TA TA TA CA TA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28840290 CTTCGGAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:28841771 original size:18 final size:19
Alignment explanation
Indices: 28841748--28841794 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
28841738 TTATAGAAAT
28841748 TAAATAGAAAA-TTAAAAA
1 TAAATAGAAAATTTAAAAA
28841766 TAAATA-AATAATTTAAAAA
1 TAAATAGAA-AATTTAAAAA
*
28841785 -CAATAGAAAA
1 TAAATAGAAAA
28841795 GGGAAATGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.08
18 14 0.56
19 9 0.36
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (19 bp):
TAAATAGAAAATTTAAAAA
Found at i:28842001 original size:27 final size:27
Alignment explanation
Indices: 28841964--28842023 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
28841954 CTAGATGTAT
*
28841964 TTTTTTAGAATTTTAGGAAATTTTTA-A
1 TTTTTTAGAATTTTAGG-AATATTTACA
*
28841991 TTTTTTAGAATTTTATGAATATTTACA
1 TTTTTTAGAATTTTAGGAATATTTACA
28842018 TTTTTT
1 TTTTTT
28842024 CAAAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 7 0.23
27 23 0.77
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (27 bp):
TTTTTTAGAATTTTAGGAATATTTACA
Found at i:28842662 original size:21 final size:21
Alignment explanation
Indices: 28842606--28842648 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
28842596 ATTTAAAAAT
28842606 ATTATAAAATTTAAAATAAATAA
1 ATTATAAAATTT--AATAAATAA
28842629 ATTATAAAATTTAATAAATA
1 ATTATAAAATTTAATAAATA
28842649 CAATATTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATTATAAAATTTAATAAATAA
Found at i:28847609 original size:17 final size:16
Alignment explanation
Indices: 28847587--28847633 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
28847577 TTTTTCAGCT
28847587 TTCTTTTCTTGCTCACA
1 TTCTTTT-TTGCTCACA
*
28847604 TTCTTTTTCGCTCACA
1 TTCTTTTTTGCTCACA
*
28847620 ATCTCTTTTTGCTC
1 TTCT-TTTTTGCTC
28847634 TCTTTCATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.11, C:0.30, G:0.06, T:0.53
Consensus pattern (16 bp):
TTCTTTTTTGCTCACA
Found at i:28847618 original size:16 final size:16
Alignment explanation
Indices: 28847595--28847633 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
28847585 CTTTCTTTTC
28847595 TTGCTCAC-ATTCTTT
1 TTGCTCACAATTCTTT
28847610 TTCGCTCACAATCTCTTT
1 TT-GCTCACAAT-TCTTT
28847628 TTGCTC
1 TTGCTC
28847634 TCTTTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 6 0.29
17 6 0.29
18 7 0.33
ACGTcount: A:0.13, C:0.31, G:0.08, T:0.49
Consensus pattern (16 bp):
TTGCTCACAATTCTTT
Found at i:28847684 original size:18 final size:18
Alignment explanation
Indices: 28847645--28847687 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28847635 CTTTCATTCT
*
28847645 CTTTTTCTTTTTCAATTT
1 CTTTTTCTTTTTCAATTG
28847663 CTTTTTCTTTTTCACA-TG
1 CTTTTTCTTTTTCA-ATTG
28847681 CTTTTTC
1 CTTTTTC
28847688 GATTTCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.67
Consensus pattern (18 bp):
CTTTTTCTTTTTCAATTG
Found at i:28850019 original size:52 final size:51
Alignment explanation
Indices: 28849913--28850084 Score: 192
Period size: 50 Copynumber: 3.4 Consensus size: 51
28849903 ATGATGCTTA
* * * *
28849913 AATGCATGATTTAA-TTAA-GATGCAAAC-TAAATGAACA-AATGAGTTACTT
1 AATGCATGACTTAATTTAATGATGCAAACTTAACT-AACATGA-GAGTTACAT
* *
28849962 AATGCATGACTTAATTTAATGATGCAGACTTAAACTAACATGGGAGTTACAT
1 AATGCATGACTTAATTTAATGATGCAAACTT-AACTAACATGAGAGTTACAT
* *
28850014 AATGCATGTCATAATTT-ATGATGCAAACTTAACTAACATGAGAGTTACAT
1 AATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGAGAGTTACAT
* *
28850064 AATGCATGACTTTATTAAATG
1 AATGCATGACTTAATTTAATG
28850085 CAGAACACAT
Statistics
Matches: 103, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
49 13 0.13
50 36 0.35
51 23 0.22
52 28 0.27
53 3 0.03
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (51 bp):
AATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGAGAGTTACAT
Found at i:28851336 original size:19 final size:19
Alignment explanation
Indices: 28851314--28851395 Score: 60
Period size: 19 Copynumber: 4.3 Consensus size: 19
28851304 AAATAACTTG
28851314 AAATATTATATATTATTTT
1 AAATATTATATATTATTTT
* *
28851333 AAATATCATAAATATCATTTT
1 AAATAT--TATATATTATTTT
** * * * *
28851354 -CGTA-TATAAATAACTTG
1 AAATATTATATATTATTTT
28851371 AAATATTATATATTATTTT
1 AAATATTATATATTATTTT
28851390 AAATAT
1 AAATAT
28851396 CATAAAATAT
Statistics
Matches: 44, Mismatches: 15, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
17 8 0.18
18 2 0.05
19 21 0.48
20 2 0.05
21 11 0.25
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
AAATATTATATATTATTTT
Found at i:28851350 original size:57 final size:57
Alignment explanation
Indices: 28851287--28851401 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
28851277 AAATGTTATT
28851287 ATATCATTTTCATATATAAATAACTTGAAATATTATATATTATTTTAAATATCATAA
1 ATATCATTTTCATATATAAATAACTTGAAATATTATATATTATTTTAAATATCATAA
*
28851344 ATATCATTTTCGTATATAAATAACTTGAAATATTATATATTATTTTAAATATCATAA
1 ATATCATTTTCATATATAAATAACTTGAAATATTATATATTATTTTAAATATCATAA
28851401 A
1 A
28851402 ATATTGTGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (57 bp):
ATATCATTTTCATATATAAATAACTTGAAATATTATATATTATTTTAAATATCATAA
Found at i:28851403 original size:29 final size:28
Alignment explanation
Indices: 28851314--28851406 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 28
28851304 AAATAACTTG
28851314 AAATATTATATATTATTTTAAATATCAT
1 AAATATTATATATTATTTTAAATATCAT
* * * * *
28851342 AAATATCAT-T-TTCGTATATAAATAACTT
1 AAATATTATATATT-AT-TTTAAATATCAT
28851370 GAAATATTATATATTATTTTAAATATCAT
1 -AAATATTATATATTATTTTAAATATCAT
28851399 AAAATATT
1 -AAATATT
28851407 GTGATAACTA
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
26 2 0.04
27 2 0.04
28 17 0.35
29 24 0.49
30 2 0.04
31 2 0.04
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (28 bp):
AAATATTATATATTATTTTAAATATCAT
Found at i:28853281 original size:56 final size:50
Alignment explanation
Indices: 28853195--28853393 Score: 195
Period size: 50 Copynumber: 3.9 Consensus size: 50
28853185 ACATTAGGGG
* **
28853195 ATGAGA-G-CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTAA
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCA--AA
* * *
28853245 GGTTATGAGAGGTCCCACGTAAGATCATGTCCGGGACATGGCGTTGGCACCAAA
1 ----ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCAAA
* * *
28853299 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCAAA
** * * * *
28853349 ATGAGAACTTCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
28853394 GTACAGGAAA
Statistics
Matches: 123, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
50 81 0.66
54 8 0.07
55 1 0.01
56 33 0.27
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCAAA
Found at i:28857499 original size:39 final size:39
Alignment explanation
Indices: 28857446--28857623 Score: 130
Period size: 40 Copynumber: 4.5 Consensus size: 39
28857436 GATATAGCTC
* * * *
28857446 CTCATTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAA
1 CTCATACAA-TGCCTTCGGGACTTAACCCGGATTATA-AAA
*
28857486 CTCATACAATGCCTTCGGGACTTAACCCGGATTTTAAAA
1 CTCATACAATGCCTTCGGGACTTAACCCGGATTATAAAA
** *
28857525 CTCGCACGAATGCCTTCGGGACTTAACCCGGAATTAGT--AT
1 CTCATAC-AATGCCTTCGGGACTTAACCCGG-ATTA-TAAAA
** * *
28857565 CTCGCACAAAGGCCTTCGGGACTTAACCCGGAATTA-ATAA
1 CTCATAC-AATGCCTTCGGGACTTAACCCGG-ATTATAAAA
**
28857605 CTCGCACAAATGCCTTCGG
1 CTCATAC-AATGCCTTCGG
28857624 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.22
40 89 0.75
41 3 0.03
42 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
CTCATACAATGCCTTCGGGACTTAACCCGGATTATAAAA
Found at i:28857607 original size:80 final size:80
Alignment explanation
Indices: 28857491--28857676 Score: 229
Period size: 80 Copynumber: 2.3 Consensus size: 80
28857481 AGTAACTCAT
* * *
28857491 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
28857555 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
28857570 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
28857634 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
28857651 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
28857677 CAGCATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
79 11 0.12
80 72 0.77
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:28857636 original size:40 final size:40
Alignment explanation
Indices: 28857493--28857676 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
28857483 TAACTCATAC
* *
28857493 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
28857533 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
28857573 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
28857613 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
28857654 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28857677 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 105 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:28865727 original size:18 final size:18
Alignment explanation
Indices: 28865704--28865759 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
28865694 GTTTAGAAAT
28865704 TAAATAATTGAAACAGCA
1 TAAATAATTGAAACAGCA
*
28865722 T--A-AA-T-AAACAG-T
1 TAAATAATTGAAACAGCA
28865734 TAAATAAATTGAAACAGCA
1 TAAAT-AATTGAAACAGCA
28865753 TAAATAA
1 TAAATAA
28865760 ACAGTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
12 1 0.03
13 6 0.21
14 2 0.07
15 2 0.07
16 3 0.10
17 1 0.03
18 9 0.31
19 5 0.17
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.23
Consensus pattern (18 bp):
TAAATAATTGAAACAGCA
Found at i:28865747 original size:31 final size:31
Alignment explanation
Indices: 28865703--28865775 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
28865693 TGTTTAGAAA
28865703 TTAAAT-AATTGAAACAGCATAAATAAACAG
1 TTAAATAAATTGAAACAGCATAAATAAACAG
28865733 TTAAATAAATTGAAACAGCATAAATAAACAG
1 TTAAATAAATTGAAACAGCATAAATAAACAG
28865764 TTAAATAAATTG
1 TTAAATAAATTG
28865776 GAAATAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 6 0.14
31 36 0.86
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (31 bp):
TTAAATAAATTGAAACAGCATAAATAAACAG
Found at i:28865789 original size:16 final size:16
Alignment explanation
Indices: 28865765--28865801 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
28865755 AATAAACAGT
28865765 TAAATAAATT-GGAAA
1 TAAATAAATTGGGAAA
28865780 TAAATGAAATTGGGAAA
1 TAAAT-AAATTGGGAAA
28865797 TAAAT
1 TAAAT
28865802 TTTGATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 5 0.25
17 10 0.50
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.27
Consensus pattern (16 bp):
TAAATAAATTGGGAAA
Found at i:28867200 original size:17 final size:16
Alignment explanation
Indices: 28867167--28867204 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
28867157 AATAAACAAT
28867167 TAAA-TAAATTGGAAA
1 TAAATTAAATTGGAAA
28867182 TAAATTAAATTGCGAAA
1 TAAATTAAATTG-GAAA
28867199 TAAATT
1 TAAATT
28867205 CAGATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.19
16 7 0.33
17 10 0.48
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.32
Consensus pattern (16 bp):
TAAATTAAATTGGAAA
Found at i:28870913 original size:20 final size:20
Alignment explanation
Indices: 28870884--28870937 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
28870874 TACAGGTTTT
* *
28870884 CACTTCGGTGCCTCTATTTG
1 CACTTTGGTGCCTCTATCTG
*
28870904 CACTTTGGTGCCTCTGTCTG
1 CACTTTGGTGCCTCTATCTG
28870924 CACTTTGGTGCCTC
1 CACTTTGGTGCCTC
28870938 CGTTATGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.07, C:0.31, G:0.22, T:0.39
Consensus pattern (20 bp):
CACTTTGGTGCCTCTATCTG
Found at i:28874908 original size:12 final size:12
Alignment explanation
Indices: 28874891--28874917 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28874881 GGCCGAAATT
28874891 AGCAAGGGGGGA
1 AGCAAGGGGGGA
28874903 AGCAAGGGGGGA
1 AGCAAGGGGGGA
28874915 AGC
1 AGC
28874918 CATAGTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.11, G:0.56, T:0.00
Consensus pattern (12 bp):
AGCAAGGGGGGA
Found at i:28875336 original size:50 final size:50
Alignment explanation
Indices: 28875233--28875473 Score: 252
Period size: 50 Copynumber: 4.7 Consensus size: 50
28875223 GGGAATAAGA
* *
28875233 TCCCATGTAAGACCATGTTTGGGACATGGCATTGGC-CTCATTGAGATTATGAGATG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC-C---GAG---ATGAGAGG
* *
28875289 TCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* *
28875339 TCCCATGTAACACCATGTCTGGGACATGGCTTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * **
28875389 TCCTC-CGTAAGACCATGTCTGGGATATGGCATGGGCACCGATATGAGAAC
1 TCC-CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * *
28875439 TCTCATGTAAGACCATATCTGGGATATGACATTGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG
28875474 TAGTACAGAA
Statistics
Matches: 162, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
49 1 0.01
50 122 0.75
51 1 0.01
53 3 0.02
56 34 0.21
57 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:28882518 original size:50 final size:50
Alignment explanation
Indices: 28882415--28882657 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
28882405 GGGAATAAGA
* * *
28882415 TCCCATGTAAGACCATGCCTGGGACATGGCATTGGCATCATTGAGATTATGAGATG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
*
28882471 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
28882521 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * **
28882571 TCCCCCGTAAGACCATATCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * *
28882621 TCTCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28882658 GTACAAAAAA
Statistics
Matches: 169, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
50 130 0.77
53 3 0.02
55 1 0.01
56 35 0.21
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:28882922 original size:4 final size:4
Alignment explanation
Indices: 28882906--28882944 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
28882896 ATGAGTTATT
* * *
28882906 TAAG TAAG CAAG TAAG TAAG CAAG TAAG TGAG TAAG TAA
1 TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAA
28882945 AGAAGCGAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.49, C:0.05, G:0.26, T:0.21
Consensus pattern (4 bp):
TAAG
Found at i:28882923 original size:12 final size:12
Alignment explanation
Indices: 28882906--28882944 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
28882896 ATGAGTTATT
28882906 TAAGTAAGCAAG
1 TAAGTAAGCAAG
28882918 TAAGTAAGCAAG
1 TAAGTAAGCAAG
* *
28882930 TAAGTGAGTAAG
1 TAAGTAAGCAAG
28882942 TAA
1 TAA
28882945 AGAAGCGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.26, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:28888950 original size:16 final size:17
Alignment explanation
Indices: 28888929--28888962 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28888919 GGTCAAGCAA
28888929 ATCAAA-ACAAGATTTG
1 ATCAAATACAAGATTTG
*
28888945 ATCAAATACAAGTTTTG
1 ATCAAATACAAGATTTG
28888962 A
1 A
28888963 GGATGAATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
ATCAAATACAAGATTTG
Found at i:28890241 original size:17 final size:18
Alignment explanation
Indices: 28890204--28890244 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
28890194 CGAAAAAGTG
**
28890204 AAAAATAGAAAAATATGA
1 AAAAATAGAAAAATAAAA
28890222 AAAAATA-AAAAATAAAA
1 AAAAATAGAAAAATAAAA
28890239 AAAAAT
1 AAAAAT
28890245 TTGGGTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAATAGAAAAATAAAA
Found at i:28893960 original size:17 final size:17
Alignment explanation
Indices: 28893935--28893973 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28893925 TTCTGTTCTT
* *
28893935 TTCCTATTTGTTGCTGC
1 TTCCGATTTGCTGCTGC
28893952 TTCCGATTTGCTGCTGC
1 TTCCGATTTGCTGCTGC
28893969 TTCCG
1 TTCCG
28893974 TGTGTTATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.28, G:0.21, T:0.46
Consensus pattern (17 bp):
TTCCGATTTGCTGCTGC
Found at i:28894820 original size:44 final size:44
Alignment explanation
Indices: 28894714--28895399 Score: 344
Period size: 44 Copynumber: 15.6 Consensus size: 44
28894704 TTCGGTCTAT
* * * * *
28894714 TCCACTGTAATTTCAGGGAGATAAGA-CC-TGAT-GTGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGATCCTTTATCTTAATCTGC
* *
28894755 TCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATCTTAATCTGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATCTTAATCTGC
* * *
28894799 TCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTATCTT-AATCTGC
* * *
28894843 TCCACTGTAATCTCAGGGAGATAAGATTTCTGGATTCAATCTGGTGCGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGA-TCCT---TT--ATCT--T--AATCTGC
* * * *
28894897 TCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATCTTAATCTGC
* * *
28894941 TCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTATCTT-AATCTGC
* * * *
28894985 TCCGA-TGTAATCTCAAGGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTAC
1 TCC-ACTGTAATCTCAGGGAGATAAGA--TC---CTT-TATCT--T--AATCTGC
* * * *
28895039 TCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATCTTAATCTGC
* * *
28895083 TCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTATCTT-AATCTGC
** * *
28895127 TCTGCTGTAATCTCAGGGAGATAAGATGC--GATC-T-A-CT-C
1 TCCACTGTAATCTCAGGGAGATAAGATCCTTTATCTTAATCTGC
* *
28895165 T--ACTGTAA-CTTCAGAGAGATAAGATCCTTTATCTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATCTTAATCTGC
* * *
28895207 TCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTATCTT-AATCTGC
** * *
28895251 TCTGCTGTAATCTCAGGGAGATAAGATGC--GATC-T-A-CT-C
1 TCCACTGTAATCTCAGGGAGATAAGATCCTTTATCTTAATCTGC
* *
28895289 T--ACTGTAA-CTTCAGAGAGATAAGATCCTTTATCTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATCTTAATCTGC
* * * *
28895331 TCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAGTCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTATCTT-AATCTGC
*
28895375 TCCACTATAATCTCAGGGAGATAAG
1 TCCACTGTAATCTCAGGGAGATAAG
28895400 CTTTCTGGCT
Statistics
Matches: 493, Mismatches: 86, Indels: 129
0.70 0.12 0.18
Matches are distributed among these distances:
35 2 0.00
36 42 0.09
38 10 0.02
39 6 0.01
40 4 0.01
41 24 0.05
42 13 0.03
43 30 0.06
44 268 0.54
45 7 0.01
46 3 0.01
47 1 0.00
48 6 0.01
49 5 0.01
50 2 0.00
51 7 0.01
52 2 0.00
53 8 0.02
54 53 0.11
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
TCCACTGTAATCTCAGGGAGATAAGATCCTTTATCTTAATCTGC
Found at i:28894922 original size:142 final size:142
Alignment explanation
Indices: 28894741--28895153 Score: 738
Period size: 142 Copynumber: 2.9 Consensus size: 142
28894731 GAGATAAGAC
* * *
28894741 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATCTTAATCTGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
28894806 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATT
28894871 TCTGGATTCAAT
131 TCTGGATTCAAT
*
28894883 CTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
*
28894948 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGA-TGTAATCTCAAGGAGATAAGAT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCC-ACTGTAATCTCAGGGAGATAAGAT
*
28895012 TTCTGGCTTCAAT
130 TTCTGGATTCAAT
28895025 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
**
28895090 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGAT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGAT
28895154 GCGATCTACT
Statistics
Matches: 259, Mismatches: 10, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
142 258 1.00
143 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATT
TCTGGATTCAAT
Found at i:28895181 original size:124 final size:124
Alignment explanation
Indices: 28895027--28895399 Score: 701
Period size: 124 Copynumber: 3.0 Consensus size: 124
28895017 GCTTCAATCT
*
28895027 GATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTA
1 GATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATCTTAATCCGCTCCACTGTA
28895092 ATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAA
66 ATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAA
28895151 GATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATCTTAATCCGCTCCACTGTA
1 GATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATCTTAATCCGCTCCACTGTA
28895216 ATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAA
66 ATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAA
28895275 GATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATCTTAATCCGCTCCACTGTA
1 GATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATCTTAATCCGCTCCACTGTA
* ** *
28895340 ATCTCAGGGAGATAGGATTACTAGCTTCAGTCTGCTCCACTATAATCTCAGGGAGATAA
66 ATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAA
28895399 G
1 G
28895400 CTTTCTGGCT
Statistics
Matches: 244, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 244 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (124 bp):
GATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATCTTAATCCGCTCCACTGTA
ATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAA
Found at i:28895184 original size:36 final size:36
Alignment explanation
Indices: 28895121--28895313 Score: 102
Period size: 36 Copynumber: 4.9 Consensus size: 36
28895111 ACTAGCTTCA
* * *
28895121 ATCTGCTCTGCTGTAATCTCAGGGAGATAAGATGCG
1 ATCTACTCTACTGTAATCTCAGAGAGATAAGATGCG
* *
28895157 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTT
1 ATCTACTCTACTGTAATC-TCAGAGAGATAAGATGC--G
* * * *
28895195 ATCTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCA
1 ATC-T-A----CTCTACTGTAATCTCA--GAG--A-GA-TA--AGATGCG
* * *
28895245 ATCTGCTCTGCTGTAATCTCAGGGAGATAAGATGCG
1 ATCTACTCTACTGTAATCTCAGAGAGATAAGATGCG
28895281 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGAT
1 ATCTACTCTACTGTAATC-TCAGAGAGATAAGAT
28895314 CCTTTATCTT
Statistics
Matches: 119, Mismatches: 19, Indels: 38
0.68 0.11 0.22
Matches are distributed among these distances:
35 2 0.02
36 61 0.51
38 5 0.04
39 3 0.03
40 2 0.02
42 2 0.02
44 27 0.23
45 1 0.01
46 3 0.03
48 1 0.01
49 3 0.03
50 5 0.04
52 4 0.03
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (36 bp):
ATCTACTCTACTGTAATCTCAGAGAGATAAGATGCG
Found at i:28895411 original size:44 final size:44
Alignment explanation
Indices: 28895324--28895424 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 44
28895314 CCTTTATCTT
* * *
28895324 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTATAATCTCAGGGAGATAAGATTACTAGCTTC
* * * *
28895368 AGTCTGCTCCACTATAATCTCAGGGAGATAAGCTTTCTGGCTTC
1 AATCTGCTCCACTATAATCTCAGGGAGATAAGATTACTAGCTTC
28895412 AATCTGCTCCACT
1 AATCTGCTCCACT
28895425 GTTGCTTAGG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTATAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:28904017 original size:19 final size:19
Alignment explanation
Indices: 28903991--28904036 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
28903981 TTAATAATCT
* *
28903991 TGAATGCATATG-ATGACA
1 TGAATGCAGATGCATGAAA
28904009 TGTAATGCAGATGCATGAAA
1 TG-AATGCAGATGCATGAAA
28904029 TGAATGCA
1 TGAATGCA
28904037 AAAAGGAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 7 0.29
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (19 bp):
TGAATGCAGATGCATGAAA
Found at i:28916355 original size:12 final size:14
Alignment explanation
Indices: 28916330--28916358 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28916320 AAGAAATATC
28916330 ATATATAAAGAAAA
1 ATATATAAAGAAAA
28916344 ATATATAAA-AAAA
1 ATATATAAAGAAAA
28916357 AT
1 AT
28916359 TAGTTGGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (14 bp):
ATATATAAAGAAAA
Found at i:28918121 original size:28 final size:30
Alignment explanation
Indices: 28918086--28918146 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
28918076 AAATAAAATA
*
28918086 ATCCCTTT-TAAAAAAAAAA-TTGTCAATC
1 ATCCCTTTAAAAAAAAAAAACTTGTCAATC
28918114 ATCCCTTTCAAAAAAAAAAAACTTGTCAATC
1 ATCCCTTT-AAAAAAAAAAAACTTGTCAATC
28918145 AT
1 AT
28918147 GTTTCATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 8 0.28
30 10 0.34
31 11 0.38
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.30
Consensus pattern (30 bp):
ATCCCTTTAAAAAAAAAAAACTTGTCAATC
Found at i:28921136 original size:21 final size:21
Alignment explanation
Indices: 28921095--28921137 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
28921085 ACACTTGATG
**
28921095 AAGATAAGAAGCAAACTTACA
1 AAGATAAGAAGCAAAAATACA
28921116 AAGATCAAGAA-CAAAAATACA
1 AAGAT-AAGAAGCAAAAATACA
28921137 A
1 A
28921138 TCATTTCACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.63, C:0.14, G:0.12, T:0.12
Consensus pattern (21 bp):
AAGATAAGAAGCAAAAATACA
Found at i:28921361 original size:20 final size:20
Alignment explanation
Indices: 28921338--28921378 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28921328 ATGTTTTCCG
28921338 GAAAATGATTTACTTTTCTA
1 GAAAATGATTTACTTTTCTA
28921358 GAAAATGATTTACTTTTCTA
1 GAAAATGATTTACTTTTCTA
28921378 G
1 G
28921379 TGTTTGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (20 bp):
GAAAATGATTTACTTTTCTA
Found at i:28922778 original size:35 final size:36
Alignment explanation
Indices: 28922732--28922800 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
28922722 TTTCAATCAT
28922732 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
28922767 TTCAATATCCAACAAGCTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
28922801 TCTAACAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:28924796 original size:37 final size:36
Alignment explanation
Indices: 28924741--28924822 Score: 139
Period size: 37 Copynumber: 2.3 Consensus size: 36
28924731 TATTTAACAT
28924741 ATTATTTAT-AAAAAATATACATTAACAGAAATTTG
1 ATTATTTATAAAAAAATATACATTAACAGAAATTTG
28924776 ATTATTTATAGAAAAAATATACATTAACAGAAATTTG
1 ATTATTTATA-AAAAAATATACATTAACAGAAATTTG
*
28924813 ATTATATATA
1 ATTATTTATA
28924823 TGAGTTAGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
35 9 0.20
37 35 0.80
ACGTcount: A:0.51, C:0.05, G:0.06, T:0.38
Consensus pattern (36 bp):
ATTATTTATAAAAAAATATACATTAACAGAAATTTG
Found at i:28925711 original size:10 final size:10
Alignment explanation
Indices: 28925696--28925721 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28925686 TCATTAAGTG
28925696 CTAACAAATA
1 CTAACAAATA
28925706 CTAACAAATA
1 CTAACAAATA
28925716 CTAACA
1 CTAACA
28925722 GATCAATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (10 bp):
CTAACAAATA
Found at i:28929309 original size:40 final size:40
Alignment explanation
Indices: 28929232--28929361 Score: 215
Period size: 41 Copynumber: 3.2 Consensus size: 40
28929222 AACCTTTCTG
28929232 GGCTTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
1 GGCTTTTAGCGGCGTTTTTGA-AAAGCGCCGCTAATGCTCA
* *
28929273 GGCTTCTAGCGGCGTTTTTGAAAAGCACCGCTAATGCTCA
1 GGCTTTTAGCGGCGTTTTTGAAAAGCGCCGCTAATGCTCA
*
28929313 GGCTTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
1 GGCTTTTAGCGGCGTTTTTG-AAAAGCGCCGCTAATGCTCA
28929354 GGCTTTTA
1 GGCTTTTA
28929362 ATTAAAATTC
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 36 0.43
41 47 0.57
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.31
Consensus pattern (40 bp):
GGCTTTTAGCGGCGTTTTTGAAAAGCGCCGCTAATGCTCA
Found at i:28929435 original size:33 final size:33
Alignment explanation
Indices: 28929361--28929423 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
28929351 TCAGGCTTTT
*
28929361 AATTAAAATTCAATTTATTTTTAACATTAATTA
1 AATTAAAATTCAATTTATTTTTAACATGAATTA
*
28929394 AATAAAAATTCAATTTATTTTTAACA-GAAT
1 AATTAAAATTCAATTTATTTTTAACATGAAT
28929424 ATTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (33 bp):
AATTAAAATTCAATTTATTTTTAACATGAATTA
Found at i:28932491 original size:18 final size:18
Alignment explanation
Indices: 28932468--28932504 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28932458 TTTCTAATCC
28932468 ATTCTTTATAAGAAGGAT
1 ATTCTTTATAAGAAGGAT
28932486 ATTCTTTATAAGAAGGAT
1 ATTCTTTATAAGAAGGAT
28932504 A
1 A
28932505 AACATATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (18 bp):
ATTCTTTATAAGAAGGAT
Found at i:28933471 original size:43 final size:43
Alignment explanation
Indices: 28933418--28933706 Score: 341
Period size: 43 Copynumber: 6.7 Consensus size: 43
28933408 AGATTATGTT
* ** *
28933418 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTC
* * * *
28933461 TTTAGGGGCGTTTGTGAGAAAAGCGCCGCTATAGATCGTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTC
* * * *
28933504 TTTAGTGGCGTTTGTGGGAAAAGCACCGTTAAAGATCGTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTC
*
28933547 TTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTC
* *
28933590 TTTAGCGGCG-TTGTGGAAAAAGCGTCGCTAAAGGTCAG-GGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-GTGGTC
** * *
28933632 TTTAGCAACGTTTGTGGAAAAAGCGCTGCTAAAGGTCAG-GGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-GTGGTC
* * *
28933675 TTTAGCGGTGTTTATGGAAAAAGCGCCGCTAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAA
28933707 CGTCGCTAAA
Statistics
Matches: 217, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
42 35 0.16
43 182 0.84
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTC
Found at i:28933647 original size:128 final size:129
Alignment explanation
Indices: 28933418--28933706 Score: 343
Period size: 128 Copynumber: 2.2 Consensus size: 129
28933408 AGATTATGTT
* ** * *
28933418 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGTCGTGGTCTTTAGGGGCGTTTGTGAGAAAA
1 TTTAGCGGCGTTTATGGAAAAAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGAGAAAA
* *** * *
28933483 GCGCCGCTATAGATCGTGGTCTTTAGTGGCGTTTGTGGGAAAAGCACCGTTAAAGATC-GTGGTC
66 GCGCCGCTAAAGATCGTGGTCTTTAGCAACGTTTGTGGAAAAAGCACCGCTAAAGATCAG-GGTC
* * *
28933547 TTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCGTGGTCTTTAGCGGCG-TTGTG-GAAAA
1 TTTAGCGGCGTTTATGGAAAAAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGAG-AAA
* * * * *
28933610 AGCGTCGCTAAAGGTCAG-GGTCTTTAGCAACGTTTGTGGAAAAAGCGCTGCTAAAGGTCAGGGT
65 AGCGCCGCTAAAGATC-GTGGTCTTTAGCAACGTTTGTGGAAAAAGCACCGCTAAAGATCAGGGT
28933674 C
129 C
*
28933675 TTTAGCGGTGTTTATGGAAAAAGCGCCGCTAA
1 TTTAGCGGCGTTTATGGAAAAAGCGCCGCTAA
28933707 CGTCGCTAAA
Statistics
Matches: 136, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
127 1 0.01
128 86 0.63
129 49 0.36
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (129 bp):
TTTAGCGGCGTTTATGGAAAAAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGAGAAAA
GCGCCGCTAAAGATCGTGGTCTTTAGCAACGTTTGTGGAAAAAGCACCGCTAAAGATCAGGGTC
Found at i:28935480 original size:15 final size:15
Alignment explanation
Indices: 28935456--28935507 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
28935446 CAATAATAGC
28935456 AATAATAGTAATAAT
1 AATAATAGTAATAAT
*
28935471 AATGAA-AGTAGTAAT
1 AAT-AATAGTAATAAT
*
28935486 AATAATATTAATAAT
1 AATAATAGTAATAAT
*
28935501 AAAAATA
1 AATAATA
28935508 AATAAAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.06
15 27 0.87
16 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (15 bp):
AATAATAGTAATAAT
Found at i:28936440 original size:15 final size:15
Alignment explanation
Indices: 28936420--28936449 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28936410 TTCGGGCTAG
*
28936420 TGGTATTGGGCTGAA
1 TGGTATTGGACTGAA
28936435 TGGTATTGGACTGAA
1 TGGTATTGGACTGAA
28936450 GTCTGTATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.37, T:0.33
Consensus pattern (15 bp):
TGGTATTGGACTGAA
Found at i:28937242 original size:26 final size:26
Alignment explanation
Indices: 28937212--28937266 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
28937202 CCTCAAAAAA
*
28937212 TTCAGACAACCCTAAAAACCAAGGAC
1 TTCAGACAACCCCAAAAACCAAGGAC
*
28937238 TTCAGACAACCCCAAAAACCAATGAC
1 TTCAGACAACCCCAAAAACCAAGGAC
28937264 TTC
1 TTC
28937267 TTTTGGTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.33, G:0.09, T:0.15
Consensus pattern (26 bp):
TTCAGACAACCCCAAAAACCAAGGAC
Found at i:28940848 original size:49 final size:50
Alignment explanation
Indices: 28940744--28940930 Score: 191
Period size: 49 Copynumber: 3.8 Consensus size: 50
28940734 TCATTGAGAT
* * *
28940744 TATGAGAGGTCCCATGTAAGACCGTGTCTGGGACATGGCGTTGGCACCGA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
* **
28940794 GATGAGAGGTCCCCCGTAAGACCATGT-TGGGACATGGCATGGGCACCGA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
** * * * *
28940843 TATGAGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA--GTA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCG-A
* * ** *
28940892 TAAGAAACATCCCATGTAAGACCATGTATGGGACATGGC
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
28940931 TTTGGCATGT
Statistics
Matches: 112, Mismatches: 23, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
48 1 0.01
49 73 0.65
50 38 0.34
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.21
Consensus pattern (50 bp):
TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
Found at i:28948314 original size:30 final size:30
Alignment explanation
Indices: 28948257--28948318 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
28948247 GCTTTTTGAA
** * *
28948257 AATATTTACAAAAAGAGGTATCTAATTTTT
1 AATATTTACAAAAAGAGCAACCAAATTTTT
28948287 AATATTTACAAAAAGAGCAACCAAATTTTT
1 AATATTTACAAAAAGAGCAACCAAATTTTT
28948317 AA
1 AA
28948319 AAATAATTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGCAACCAAATTTTT
Found at i:28951547 original size:23 final size:23
Alignment explanation
Indices: 28951521--28951665 Score: 175
Period size: 23 Copynumber: 6.3 Consensus size: 23
28951511 GTAAGTGCCA
28951521 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
28951544 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * * *
28951567 CACTGAAATGCAGCCGTATCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
28951590 CACTGAAATGCAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
28951613 CACTGATATGTAGCCGTAGTTAC
1 CACTGATATGTAGCCGAAGCTAC
*
28951636 CACTGA-ATTGTACCCGAAGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
*
28951659 CATTGAT
1 CACTGAT
28951666 CAATAACACT
Statistics
Matches: 106, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
22 1 0.01
23 105 0.99
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:28951659 original size:69 final size:69
Alignment explanation
Indices: 28951521--28951660 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 69
28951511 GTAAGTGCCA
* * * * *
28951521 CACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAAATGCAGCCGTAT
1 CACTGAAATGCAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAAATGCACCCGAAG
28951586 CTAC
66 CTAC
* * *
28951590 CACTGAAATGCAGCCGAAGCTACCACTGATATGTAGCCGTAGTTACCACTGAATTGTACCCGAAG
1 CACTGAAATGCAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAAATGCACCCGAAG
28951655 CTAC
66 CTAC
28951659 CA
1 CA
28951661 TTGATCAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (69 bp):
CACTGAAATGCAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAAATGCACCCGAAG
CTAC
Found at i:28951917 original size:18 final size:17
Alignment explanation
Indices: 28951891--28951929 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
28951881 ATTTTCCTTC
28951891 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
28951908 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
28951926 CACA
1 CACA
28951930 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:28960777 original size:9 final size:9
Alignment explanation
Indices: 28960763--28960794 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
28960753 CAACGCTTTT
28960763 TTGCATTCA
1 TTGCATTCA
28960772 TTGCATTCA
1 TTGCATTCA
28960781 TTGCATTCA
1 TTGCATTCA
28960790 -TGCAT
1 TTGCAT
28960795 CGGCATTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (9 bp):
TTGCATTCA
Found at i:28967795 original size:15 final size:15
Alignment explanation
Indices: 28967760--28967789 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28967750 AGTGTTAATG
*
28967760 GAATCTATTGGTTGT
1 GAATCTACTGGTTGT
28967775 GAATCTACTGGTTGT
1 GAATCTACTGGTTGT
28967790 ATATCTTACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
GAATCTACTGGTTGT
Found at i:28975604 original size:16 final size:17
Alignment explanation
Indices: 28975570--28975605 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
28975560 ATAATAGCGA
28975570 AAACATAAATAGATAAG
1 AAACATAAATAGATAAG
28975587 AAACATAAATAG-TAAG
1 AAACATAAATAGATAAG
28975603 AAA
1 AAA
28975606 ATATATATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.67, C:0.06, G:0.11, T:0.17
Consensus pattern (17 bp):
AAACATAAATAGATAAG
Found at i:28975615 original size:17 final size:16
Alignment explanation
Indices: 28975577--28975633 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 16
28975567 CGAAAACATA
28975577 AATAGATAAGAAACATA-
1 AATAG-TAAGAAA-ATAT
28975594 AATAGTAAGAAAATAT
1 AATAGTAAGAAAATAT
*
28975610 ATATAG-ATGAAAATAT
1 A-ATAGTAAGAAAATAT
28975626 AATAGTAA
1 AATAGTAA
28975634 TAATAATACG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
15 7 0.20
16 19 0.54
17 9 0.26
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.25
Consensus pattern (16 bp):
AATAGTAAGAAAATAT
Found at i:28975717 original size:3 final size:3
Alignment explanation
Indices: 28975709--28976089 Score: 172
Period size: 3 Copynumber: 125.7 Consensus size: 3
28975699 TGATAGTGAC
* * * * * * *
28975709 AAT AAT AAT AAT AAT AAT -AT TAT TAT TAT TAT TAT ATT GAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * * * * * *
28975757 AA- AAGG AAT AAA AAT AAT AGT AAT AAA AAT ATT AAC AAT AGT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
28975802 AAT AAC GAT AAT -AT AAAT ACT AAT ATAT ACAT GAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT A-AT A-AT -AAT AAT AAT AAT AAT
* * * *
28975850 AGT AAT AAT AAT AAT AAC AAT AAT AAT AAC AAT ACATT AAT ATAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT A-AT AAT
* * * * * *
28975898 AAT -AT CAAT AAT ATT AGT AAGT AA- AAA AAGGG AAT AAT AAT AGT AGT
1 AAT AAT -AAT AAT AAT AAT AA-T AAT AAT AA--T AAT AAT AAT AAT AAT
* * * * *
28975945 AAT AAT AAT AAC AAT AGT AAG AAT AAT AAT GAT AAT -AT AAC AA- ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * **
28975992 AGT AAT -AT AAT CAAT AA- AAT -AT AAT AGT AAT AAA AAT AAT GCT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** * *
28976035 AAC GGT AAT AAT AAT AAT AAT GAT AGT AAT -AT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28976082 AAT AAT AA
1 AAT AAT AA
28976090 GTAAAATGAT
Statistics
Matches: 284, Mismatches: 69, Indels: 50
0.70 0.17 0.12
Matches are distributed among these distances:
2 21 0.07
3 231 0.81
4 27 0.10
5 5 0.02
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28977556 original size:16 final size:17
Alignment explanation
Indices: 28977522--28977557 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
28977512 ATAATAGCGA
28977522 AAACATAAATAGATAAG
1 AAACATAAATAGATAAG
28977539 AAACATAAATAG-TAAG
1 AAACATAAATAGATAAG
28977555 AAA
1 AAA
28977558 ATATATATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.67, C:0.06, G:0.11, T:0.17
Consensus pattern (17 bp):
AAACATAAATAGATAAG
Found at i:28977567 original size:17 final size:16
Alignment explanation
Indices: 28977529--28977585 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 16
28977519 CGAAAACATA
28977529 AATAGATAAGAAACATA-
1 AATAG-TAAGAAA-ATAT
28977546 AATAGTAAGAAAATAT
1 AATAGTAAGAAAATAT
*
28977562 ATATAG-ATGAAAATAT
1 A-ATAGTAAGAAAATAT
28977578 AATAGTAA
1 AATAGTAA
28977586 TAATAATACG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
15 7 0.20
16 19 0.54
17 9 0.26
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.25
Consensus pattern (16 bp):
AATAGTAAGAAAATAT
Found at i:28977669 original size:3 final size:3
Alignment explanation
Indices: 28977661--28978041 Score: 172
Period size: 3 Copynumber: 125.7 Consensus size: 3
28977651 TGATAGTGAC
* * * * * * *
28977661 AAT AAT AAT AAT AAT AAT -AT TAT TAT TAT TAT TAT ATT GAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * * * * * *
28977709 AA- AAGG AAT AAA AAT AAT AGT AAT AAA AAT ATT AAC AAT AGT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
28977754 AAT AAC GAT AAT -AT AAAT ACT AAT ATAT ACAT GAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT A-AT A-AT -AAT AAT AAT AAT AAT
* * * *
28977802 AGT AAT AAT AAT AAT AAC AAT AAT AAT AAC AAT ACATT AAT ATAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT A-AT AAT
* * * * * *
28977850 AAT -AT CAAT AAT ATT AGT AAGT AA- AAA AAGGG AAT AAT AAT AGT AGT
1 AAT AAT -AAT AAT AAT AAT AA-T AAT AAT AA--T AAT AAT AAT AAT AAT
* * * * *
28977897 AAT AAT AAT AAC AAT AGT AAG AAT AAT AAT GAT AAT -AT AAC AA- ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * **
28977944 AGT AAT -AT AAT CAAT AA- AAT -AT AAT AGT AAT AAA AAT AAT GCT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** * *
28977987 AAC GGT AAT AAT AAT AAT AAT GAT AGT AAT -AT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28978034 AAT AAT AA
1 AAT AAT AA
28978042 GTAAAATGAT
Statistics
Matches: 284, Mismatches: 69, Indels: 50
0.70 0.17 0.12
Matches are distributed among these distances:
2 21 0.07
3 231 0.81
4 27 0.10
5 5 0.02
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28987337 original size:24 final size:24
Alignment explanation
Indices: 28987287--28987340 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
28987277 AATCGAATTT
*
28987287 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
28987311 GCACACATAGTGCCATAG-CACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
28987335 GCACAC
1 GCACAC
28987341 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 6 0.22
26 2 0.07
ACGTcount: A:0.30, C:0.39, G:0.17, T:0.15
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Found at i:28988915 original size:469 final size:470
Alignment explanation
Indices: 28987991--28988927 Score: 1813
Period size: 469 Copynumber: 2.0 Consensus size: 470
28987981 CGAATATACC
28987991 AAATTAAATTTAACCTTACTTATGTAATTACCTATAAGTTATTATACATCAAATTTCATACATTT
1 AAATTAAATTTAACCTTACTTATGTAATTACCTATAAGTTATTATACATCAAATTTCATACATTT
28988056 AACCTTTTAATGCCTATTAACCATTCTTTTGATCTTAACCTAAAATGACAACTCCCATACTCAAC
66 AACCTTTTAATGCCTATTAACCATTCTTTTGATCTTAACCTAAAATGACAACTCCCATACTCAAC
*
28988121 ATTTCAACCGAATTATCTCTATCACCCGAACTAAAATTCGCACCTTAACTTCATACATTTTTTTT
131 ATTTCAACCGAATTATCCCTATCACCCGAACTAAAATTCGCACCTTAACTTCATACATTTTTTTT
* *
28988186 TTAACTTTCATAATTCATTCGGCCCCATCAAAGGACCCCTTTAACATACAAGGAAAATAATCATA
196 ATAACTTTCATAATTCATTCGGCCCCATCAAAGGACCCATTTAACATACAAGGAAAATAATCATA
28988251 GAGAAAGAAATTAACATTCTAATTAGACTCAATGTAACCGAATGTACCAAGTGCTACTAACCTAC
261 GAGAAAGAAATTAACATTCTAATTAGACTCAATGTAACCGAATGTACCAAGTGCTACTAACCTAC
* *
28988316 TTATTCAAAAATCTTCATTCCATACTATCATCCCCCTTTTATCCCATACAACATGAAAATGACCT
326 TTAATCAAAAATCTTCATTCCATACTATCATCCCCCTTTTATCACATACAACATGAAAATGACCT
28988381 CCAATGTTAACACTTAGATTCACGGCATGATGCCCAAACCACCATAAAAGCTCCAACTTTCTTAA
391 CCAATGTTAACACTTAGATTCACGGCATGATGCCCAAACCACCATAAAAGCTCCAACTTTCTTAA
28988446 CATTACCAAGAGTCA
456 CATTACCAAGAGTCA
28988461 AAATTAAATTTAACCTTACTTATGTAATTACCTATAAGTTATTATACATCAAATTTCATACATTT
1 AAATTAAATTTAACCTTACTTATGTAATTACCTATAAGTTATTATACATCAAATTTCATACATTT
28988526 AACCTTTTAATGCCTATTAACCATTCTTTTGATCTTAACCTAAAATGACAACTCCCATACTCAAC
66 AACCTTTTAATGCCTATTAACCATTCTTTTGATCTTAACCTAAAATGACAACTCCCATACTCAAC
28988591 ATTTCAACCGAATTATCCCTATCACCCGAACTAAAATTCGCACCTTAACTTCATACATTTTTTTT
131 ATTTCAACCGAATTATCCCTATCACCCGAACTAAAATTCGCACCTTAACTTCATACATTTTTTTT
*
28988656 ATGACTTTCATAATTCATTCGGCCCCATCAAAGGA-CCATTTAACATACAAGGAAAATAATCATA
196 ATAACTTTCATAATTCATTCGGCCCCATCAAAGGACCCATTTAACATACAAGGAAAATAATCATA
28988720 GAGAAAGAAATTAACATTCTAATTAGACTCAATGTAACCGAATGTACCAAGTGCTACTAACCTAC
261 GAGAAAGAAATTAACATTCTAATTAGACTCAATGTAACCGAATGTACCAAGTGCTACTAACCTAC
28988785 TTAATCAAAAATCTTCATTCCATACTATCATCCCCCTTTTATCACATACAACATGAAAATGACCT
326 TTAATCAAAAATCTTCATTCCATACTATCATCCCCCTTTTATCACATACAACATGAAAATGACCT
28988850 CCAATGTTAACACTTAGATTCACGGCATGATGCCCAAACCACCATAAAAGCTCCAACTTTCTTAA
391 CCAATGTTAACACTTAGATTCACGGCATGATGCCCAAACCACCATAAAAGCTCCAACTTTCTTAA
28988915 CATTACCAAGAGT
456 CATTACCAAGAGT
28988928 GCATCCAATT
Statistics
Matches: 461, Mismatches: 6, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
469 234 0.51
470 227 0.49
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (470 bp):
AAATTAAATTTAACCTTACTTATGTAATTACCTATAAGTTATTATACATCAAATTTCATACATTT
AACCTTTTAATGCCTATTAACCATTCTTTTGATCTTAACCTAAAATGACAACTCCCATACTCAAC
ATTTCAACCGAATTATCCCTATCACCCGAACTAAAATTCGCACCTTAACTTCATACATTTTTTTT
ATAACTTTCATAATTCATTCGGCCCCATCAAAGGACCCATTTAACATACAAGGAAAATAATCATA
GAGAAAGAAATTAACATTCTAATTAGACTCAATGTAACCGAATGTACCAAGTGCTACTAACCTAC
TTAATCAAAAATCTTCATTCCATACTATCATCCCCCTTTTATCACATACAACATGAAAATGACCT
CCAATGTTAACACTTAGATTCACGGCATGATGCCCAAACCACCATAAAAGCTCCAACTTTCTTAA
CATTACCAAGAGTCA
Found at i:29009251 original size:55 final size:56
Alignment explanation
Indices: 29009166--29009287 Score: 228
Period size: 55 Copynumber: 2.2 Consensus size: 56
29009156 TCACAAAAAG
29009166 GGGGGGATTTTGATGTTTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTAA
1 GGGGGGATTTTGATGTTTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTAA
*
29009222 GGGGGGATTTTGATG-TTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTTA
1 GGGGGGATTTTGATGTTTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTAA
29009277 GGGGGGATTTT
1 GGGGGGATTTT
29009288 TTGATATTTC
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
55 50 0.77
56 15 0.23
ACGTcount: A:0.21, C:0.03, G:0.33, T:0.43
Consensus pattern (56 bp):
GGGGGGATTTTGATGTTTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTAA
Found at i:29018747 original size:46 final size:46
Alignment explanation
Indices: 29018685--29019004 Score: 196
Period size: 46 Copynumber: 7.1 Consensus size: 46
29018675 ATAACTCTAT
*
29018685 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTAC
* * * ** * *
29018731 CTTCCTGTATTTGGCAG-CGAAGCAGATCAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATTGCAGATCTTAC
* * * * ** * * *
29018777 CTCCCTG-A-CT-ACAGTGGAGTACATTGAAG-CCG-ATAACTCTAT
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCT-TAC
*
29018819 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTAC
* * * ** * *
29018865 CTTCCTGTATTTGGCAG-CGAAGCAGATCAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATTGCAGATCTTAC
* * * * ** * * *
29018911 CTCCCTG-A-CT-ACAGTGGAGTACATTGAAG-CCG-ATAACTCTAT
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCT-TAC
* *
29018953 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTACAGATCTTAT
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTAC
29018999 CTCCCT
1 CTCCCT
29019005 AAGCAATAGT
Statistics
Matches: 193, Mismatches: 65, Indels: 32
0.67 0.22 0.11
Matches are distributed among these distances:
41 6 0.03
42 20 0.10
43 20 0.10
44 8 0.04
45 40 0.21
46 91 0.47
47 8 0.04
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (46 bp):
CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTAC
Found at i:29018888 original size:134 final size:134
Alignment explanation
Indices: 29018648--29019091 Score: 689
Period size: 134 Copynumber: 3.3 Consensus size: 134
29018638 NNNNNNNNNN
29018648 TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATT
1 TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATT
29018713 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
66 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
29018778 TCCC
131 TCCC
29018782 TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATT
1 TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATT
29018847 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
66 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
29018912 TCCC
131 TCCC
29018916 TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATT
1 TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATT
* ** * * * * * * * * *
29018981 GAAGATTACAGATCTTATCTCCCTAAGCA-AT---AGTGGAGCAGGTCGAAGACGGCGGATTTTA
66 GAAGATTGCAGATCTTGCCTTCCT--GTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTA
29019042 CCTCCC
129 CCTCCC
* * * **
29019048 TGATTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTG
1 TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTG
29019092 GGCAACAGTG
Statistics
Matches: 291, Mismatches: 17, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
132 69 0.24
134 219 0.75
135 1 0.00
136 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (134 bp):
TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATT
GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
TCCC
Found at i:29019047 original size:44 final size:44
Alignment explanation
Indices: 29018999--29019178 Score: 114
Period size: 44 Copynumber: 4.1 Consensus size: 44
29018989 CAGATCTTAT
* *
29018999 CTCCCTAAGCAATAGTGGAGCAGGTCGAAGACGGCGGATTTTAC
1 CTCCCTAAGCAACAGTGGAGCAGATCGAAGACGGCGGATTTTAC
* ** * * * * * * *
29019043 CTCCCTGA-TTACAGTGGAGTACATTGAAG-CTG-GTAGTTCTAT
1 CTCCCTAAGCAACAGTGGAGCAGATCGAAGACGGCGGA-TTTTAC
** ** *** * * *
29019085 CTCCCTGGGCAACAGTGGAATAGATCGAAGATTACAGATCTTAT
1 CTCCCTAAGCAACAGTGGAGCAGATCGAAGACGGCGGATTTTAC
* *
29019129 CTCCCTAAGCAATAGTGGAGCAGGTCGAAGACGGCGGATTTTAC
1 CTCCCTAAGCAACAGTGGAGCAGATCGAAGACGGCGGATTTTAC
29019173 CTCCCT
1 CTCCCT
29019179 GATTACAGTG
Statistics
Matches: 96, Mismatches: 36, Indels: 8
0.69 0.26 0.06
Matches are distributed among these distances:
41 2 0.02
42 13 0.14
43 30 0.31
44 50 0.52
45 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (44 bp):
CTCCCTAAGCAACAGTGGAGCAGATCGAAGACGGCGGATTTTAC
Found at i:29019100 original size:43 final size:43
Alignment explanation
Indices: 29019053--29019244 Score: 120
Period size: 43 Copynumber: 4.4 Consensus size: 43
29019043 CTCCCTGATT
* * *
29019053 ACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGGGCA
1 ACAGTGGAGTACATCGAAGCTGGCAGTTCTATCTCCCTGGACA
* * * ** * *
29019096 ACAGTGGAATAGATCGAAGATTACAGATCTTATCTCCCT-AAGCA
1 ACAGTGGAGTACATCGAAGCTGGCAGTTC-TATCTCCCTGGA-CA
* * ** * * * **
29019140 ATAGTGGAGCAGGTCGAAGAC-GGCGGATTTTACCTCCCT-GATT
1 ACAGTGGAGTACATCGAAG-CTGGCAG-TTCTATCTCCCTGGACA
* *
29019183 ACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGGACA
1 ACAGTGGAGTACATCGAAGCTGGCAGTTCTATCTCCCTGGACA
* *
29019226 ACAGTGGAATAGATCGAAG
1 ACAGTGGAGTACATCGAAG
29019245 AAAACAACAT
Statistics
Matches: 105, Mismatches: 38, Indels: 12
0.68 0.25 0.08
Matches are distributed among these distances:
42 11 0.10
43 56 0.53
44 37 0.35
45 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (43 bp):
ACAGTGGAGTACATCGAAGCTGGCAGTTCTATCTCCCTGGACA
Found at i:29019151 original size:130 final size:130
Alignment explanation
Indices: 29018751--29019245 Score: 571
Period size: 130 Copynumber: 3.8 Consensus size: 130
29018741 TTGGCAGCGA
* * * * * * * **
29018751 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTC
1 AGCAGGTCGAAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTC
* *** * * ** * * *
29018816 TATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCT--GTATTTGG
66 TATCTCCCTGGA--CAACAGTGGAATAGATCGAAGATTACAGATCTTATCTCCCTAAGCA-AT--
* *
29018879 CAGCGA
126 -AGTGG
* * * * * * * **
29018885 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTC
1 AGCAGGTCGAAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTC
* *** *
29018950 TATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGT
66 TATCTCCCTGGA--CAACAGTGGAATAGATCGAAGATTACAGATCTTATCTCCCTAAGCAATAGT
29019015 GG
129 GG
29019017 AGCAGGTCGAAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTC
1 AGCAGGTCGAAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTC
*
29019082 TATCTCCCTGGGCAACAGTGGAATAGATCGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGG
66 TATCTCCCTGGACAACAGTGGAATAGATCGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGG
29019147 AGCAGGTCGAAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTC
1 AGCAGGTCGAAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTC
29019212 TATCTCCCTGGACAACAGTGGAATAGATCGAAGA
66 TATCTCCCTGGACAACAGTGGAATAGATCGAAGA
29019246 AAACAACATT
Statistics
Matches: 335, Mismatches: 24, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
130 147 0.44
132 69 0.21
134 116 0.35
135 1 0.00
136 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (130 bp):
AGCAGGTCGAAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTC
TATCTCCCTGGACAACAGTGGAATAGATCGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGG
Found at i:29022109 original size:42 final size:43
Alignment explanation
Indices: 29022005--29022122 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 43
29021995 GTACGTATCA
* * * *
29022005 ATGCCATACCCCAGATATGGTCTTACATGAAAT-ATCATATCG
1 ATGCCATATCCCAGATATGGTCTTATACGAAATCATCATACCG
* * * * *
29022047 ACGCTATGTCCCTGACATGGTCTTATACGAAATCA-CATACCG
1 ATGCCATATCCCAGATATGGTCTTATACGAAATCATCATACCG
*
29022089 ATGCCATATCCCAGATATGGTCTTATACGGAATC
1 ATGCCATATCCCAGATATGGTCTTATACGAAATC
29022123 TCGGTAGTAC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 59 0.98
43 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGCCATATCCCAGATATGGTCTTATACGAAATCATCATACCG
Found at i:29026470 original size:68 final size:67
Alignment explanation
Indices: 29026398--29026547 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
29026388 CATCATGTGT
* * * *
29026398 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
29026460 ATGTAG
62 ATGTAG
** * *
29026466 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
29026531 AG
66 AG
29026533 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
29026548 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:29026503 original size:64 final size:64
Alignment explanation
Indices: 29026422--29026601 Score: 186
Period size: 67 Copynumber: 2.8 Consensus size: 64
29026412 AGACATTATG
* *
29026422 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
29026486 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
29026551 AA
63 AA
* * * *
29026553 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGA
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGA
29026602 AAGCCGAACT
Statistics
Matches: 94, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 15 0.16
64 21 0.22
65 8 0.09
66 16 0.17
67 31 0.33
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:29028941 original size:20 final size:20
Alignment explanation
Indices: 29028908--29028948 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
29028898 AGCTCAATAC
29028908 ATAAGCTAGATGAATGGACA
1 ATAAGCTAGATGAATGGACA
* *
29028928 ATAAGTTAGCTGAATGGACA
1 ATAAGCTAGATGAATGGACA
29028948 A
1 A
29028949 CTTGTGTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (20 bp):
ATAAGCTAGATGAATGGACA
Found at i:29029495 original size:40 final size:39
Alignment explanation
Indices: 29029440--29029517 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
29029430 TTAACTCAAC
* *
29029440 CAGCTAATTAAGTTGTAATGAGCTAAGACATACTTAAATT
1 CAGCTAATTAAGTTGTAATAAGCTAAGACA-AATTAAATT
29029480 CAGCTAATTAAGTTGTAATAAGCTAAGACAAATTAAAT
1 CAGCTAATTAAGTTGTAATAAGCTAAGACAAATTAAAT
29029518 AGCTGTACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 7 0.19
40 29 0.81
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (39 bp):
CAGCTAATTAAGTTGTAATAAGCTAAGACAAATTAAATT
Found at i:29029584 original size:47 final size:47
Alignment explanation
Indices: 29029503--29029659 Score: 224
Period size: 47 Copynumber: 3.3 Consensus size: 47
29029493 TGTAATAAGC
* * * *
29029503 TAAGACAAATTAAATAGCTGTACTAACTAAAACATATTAAATTAACT
1 TAAGACAAATTAAATAGCTGAACTAATTAGAACATATTAAATAAACT
* *
29029550 TAGGACATATTAAATAGCTGAACTAATTAGAACATATTAAATAAACT
1 TAAGACAAATTAAATAGCTGAACTAATTAGAACATATTAAATAAACT
* * *
29029597 TAAGACAAATTAAATTGCTGAACTAATCAGAACACATTAAATAAACT
1 TAAGACAAATTAAATAGCTGAACTAATTAGAACATATTAAATAAACT
*
29029644 TAAGACAAATCAAATA
1 TAAGACAAATTAAATA
29029660 CTTAAGCTAA
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 97 1.00
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (47 bp):
TAAGACAAATTAAATAGCTGAACTAATTAGAACATATTAAATAAACT
Found at i:29032689 original size:49 final size:49
Alignment explanation
Indices: 29032617--29032747 Score: 172
Period size: 49 Copynumber: 2.7 Consensus size: 49
29032607 TGTTGTTTGT
* * *
29032617 TAGTGTAAGACTTGTCTGGGACATGGCATCGACATCGATAGATGAGAGC
1 TAGTGTAAGACCTGTCTGAGACATGGCATCGACATCGATAGATGAAAGC
* * * * *
29032666 TAGTGTAAGACCTGCCTGTGACATGGCATCGACCTCGATATATGAAAGT
1 TAGTGTAAGACCTGTCTGAGACATGGCATCGACATCGATAGATGAAAGC
* *
29032715 TAGTGTAAGACCTGTCTGAGACTTTGCATCGAC
1 TAGTGTAAGACCTGTCTGAGACATGGCATCGAC
29032748 TTTAATGTGC
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 71 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (49 bp):
TAGTGTAAGACCTGTCTGAGACATGGCATCGACATCGATAGATGAAAGC
Found at i:29042748 original size:43 final size:43
Alignment explanation
Indices: 29042667--29042752 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
29042657 AAATCATATA
**
29042667 ATGCCAATGTCCCAGATGTGGTCTTACATGTAGCCACATATCG
1 ATGCCAATGTCCCAGATGTGGTCTTACATGTAAACACATATCG
*
29042710 ATGCCACTGTCCCAGATAG-GGTCTTAC-TCGTAAACACATATCG
1 ATGCCAATGTCCCAGAT-GTGGTCTTACAT-GTAAACACATATCG
29042753 GAATCACACA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 1 0.03
43 36 0.95
44 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGATGTGGTCTTACATGTAAACACATATCG
Found at i:29051032 original size:10 final size:10
Alignment explanation
Indices: 29051019--29051064 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
29051009 AGCTCACTTG
29051019 AGCTCGTTTT
1 AGCTCGTTTT
*
29051029 AGCTCGTTTG
1 AGCTCGTTTT
*
29051039 AGCTCGAATTT
1 AGCTCG-TTTT
*
29051050 AGCTCGTTTC
1 AGCTCGTTTT
29051060 AGCTC
1 AGCTC
29051065 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:29051052 original size:21 final size:20
Alignment explanation
Indices: 29051016--29051064 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
29051006 ATCAGCTCAC
*
29051016 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
29051036 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
29051057 TTCAGCTC
1 TTGAGCTC
29051065 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:29051307 original size:13 final size:13
Alignment explanation
Indices: 29051289--29051317 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29051279 AATAGTTGTG
29051289 TGTTATTTAATTA
1 TGTTATTTAATTA
29051302 TGTTATTTAATTA
1 TGTTATTTAATTA
29051315 TGT
1 TGT
29051318 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:29062795 original size:46 final size:46
Alignment explanation
Indices: 29062745--29062920 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
29062735 TGGTTGAGCA
29062745 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
29062791 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
29062836 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
29062884 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29062921 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:29062901 original size:93 final size:93
Alignment explanation
Indices: 29062742--29062913 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
29062732 GGATGGTTGA
* *
29062742 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
29062807 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
29062835 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
29062900 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
29062914 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:29071728 original size:40 final size:39
Alignment explanation
Indices: 29071639--29071736 Score: 115
Period size: 40 Copynumber: 2.5 Consensus size: 39
29071629 CTAAGTCGGT
* *
29071639 ACCGCACACTTAGTGCCCTCTATAGCCGAAGCTATGCCA
1 ACCGCACACTTAGTGCCATCTATAGCCGAAGCTATGCAA
* * * **
29071678 ACTCGTACACTTAGTGCCATTTGTAGCCGAAGCTATATTAA
1 AC-CGCACACTTAGTGCCATCTATAGCCGAAGCTAT-GCAA
29071719 ACCGCACACTTAGTGCCA
1 ACCGCACACTTAGTGCCA
29071737 ATCATAGTCG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.04
40 44 0.90
41 3 0.06
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (39 bp):
ACCGCACACTTAGTGCCATCTATAGCCGAAGCTATGCAA
Found at i:29073656 original size:46 final size:46
Alignment explanation
Indices: 29073587--29073715 Score: 163
Period size: 46 Copynumber: 2.8 Consensus size: 46
29073577 GGTGGTAGGT
*
29073587 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAT-CATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCA-ATACACGA
* * * *
29073633 GTGCTAGTGTAAGACATGTCTGGGATATGCATCGG-CATTGAGACGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAAT-ACACGA
* *
29073679 GAGCTAGTGTCATACATGTCTGGGACATGCATCGGCC
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC
29073716 TCGGGATATA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
44 1 0.01
45 2 0.03
46 67 0.94
47 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAATACACGA
Found at i:29074507 original size:21 final size:21
Alignment explanation
Indices: 29074460--29074500 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
29074450 GGCTAATATT
**
29074460 AAAATTTTTTTTATGAATGCA
1 AAAATTTTTTCCATGAATGCA
29074481 AGAAATTTTTTCCATGAATG
1 A-AAATTTTTTCCATGAATG
29074501 TGAAAATGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.06
22 16 0.94
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (21 bp):
AAAATTTTTTCCATGAATGCA
Found at i:29075131 original size:21 final size:20
Alignment explanation
Indices: 29075101--29075140 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
29075091 GTCATGATGG
29075101 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCGTGTT-CCCTT
*
29075122 CCACATGGGCGTGTTCCCT
1 CCACACGGGCGTGTTCCCT
29075141 GCTTCAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.10, C:0.38, G:0.28, T:0.25
Consensus pattern (20 bp):
CCACACGGGCGTGTTCCCTT
Found at i:29076692 original size:21 final size:22
Alignment explanation
Indices: 29076666--29076723 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
29076656 CAGCTTGTCT
29076666 GAGCTTACTATT-AACTCGATA-
1 GAGCTTACTATTCAACTCG-TAC
*
29076687 GAGCTTACCATTTCAACTCGTAC
1 GAGCTTACTA-TTCAACTCGTAC
*
29076710 GAACTTACTATTCA
1 GAGCTTACTATTCA
29076724 TCAACTCAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 9 0.29
22 8 0.26
23 14 0.45
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (22 bp):
GAGCTTACTATTCAACTCGTAC
Found at i:29082355 original size:27 final size:27
Alignment explanation
Indices: 29082325--29082377 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
29082315 TATTCTACCA
*
29082325 TACAGGGGTATTACGGTCATTTTACAC
1 TACAAGGGTATTACGGTCATTTTACAC
* *
29082352 TACAAGGGTATTTCGGTTATTTTACA
1 TACAAGGGTATTACGGTCATTTTACA
29082378 AATCGAGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (27 bp):
TACAAGGGTATTACGGTCATTTTACAC
Found at i:29085934 original size:5 final size:5
Alignment explanation
Indices: 29085924--29085949 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29085914 GCCTTTTTGA
29085924 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
29085950 TAAAAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:29091102 original size:27 final size:27
Alignment explanation
Indices: 29091072--29091132 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
29091062 GGGCATAATC
29091072 ATCATTCTACCA-TACAAGGGTATTGCG
1 ATCATT-TACCACTACAAGGGTATTGCG
** *
29091099 ATCATTTTTCACTACAAGGGTATTTCG
1 ATCATTTACCACTACAAGGGTATTGCG
*
29091126 ATGATTT
1 ATCATTT
29091133 TACAAACCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (27 bp):
ATCATTTACCACTACAAGGGTATTGCG
Found at i:29097517 original size:24 final size:24
Alignment explanation
Indices: 29097490--29097547 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
29097480 AGCTCCCGTT
*
29097490 ATATGGCTCTTTGTGAGCTTCCTG
1 ATATGGCTCTTTGTGAACTTCCTG
*
29097514 ATATGGTTCTTTGTGAACTTCCTG
1 ATATGGCTCTTTGTGAACTTCCTG
29097538 ACTATGGCTC
1 A-TATGGCTC
29097548 GTATGAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 23 0.77
25 7 0.23
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (24 bp):
ATATGGCTCTTTGTGAACTTCCTG
Found at i:29099768 original size:44 final size:42
Alignment explanation
Indices: 29099711--29099809 Score: 110
Period size: 44 Copynumber: 2.3 Consensus size: 42
29099701 TTCGATATGC
* * *
29099711 AATTTCATGTAAGACCACATCTAGGACGTTGGCATCG-ATTT
1 AATTTCGTGTAAGACCACATCTAGGACATCGGCATCGTATTT
** *
29099752 GAGATTTACGTGTAAGACCATGTCTGGGACATCGGCATCGTATTT
1 -A-ATTT-CGTGTAAGACCACATCTAGGACATCGGCATCGTATTT
29099797 AATTTCGTGTAAG
1 AATTTCGTGTAAG
29099810 GCCTTGTCTG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
42 9 0.19
43 8 0.17
44 27 0.56
45 4 0.08
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (42 bp):
AATTTCGTGTAAGACCACATCTAGGACATCGGCATCGTATTT
Found at i:29099818 original size:42 final size:44
Alignment explanation
Indices: 29099718--29099865 Score: 117
Period size: 42 Copynumber: 3.4 Consensus size: 44
29099708 TGCAATTTCA
** * * *
29099718 TGTAAGACCACATCTAGGACGTTGGCATCGATTTGAGATTTACG
1 TGTAAGACCATGTCTGGGACATCGGCATCGATTTGAGATTTACG
29099762 TGTAAGACCATGTCTGGGACATCGGCATCGTATTT-A-ATTT-CG
1 TGTAAGACCATGTCTGGGACATCGGCATCG-ATTTGAGATTTACG
* * * * * * *
29099804 TGTAAGGCCTTGTCTGGGATAGT-GGCATTGATATGTGA-TTACA
1 TGTAAGACCATGTCTGGGACA-TCGGCATCGATTTGAGATTTACG
**
29099847 TGTAAGACCACATCTGGGA
1 TGTAAGACCATGTCTGGGA
29099866 TGTTGGCATT
Statistics
Matches: 83, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
41 3 0.04
42 28 0.34
43 22 0.27
44 26 0.31
45 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACATCGGCATCGATTTGAGATTTACG
Found at i:29107378 original size:44 final size:44
Alignment explanation
Indices: 29107328--29107482 Score: 169
Period size: 43 Copynumber: 3.6 Consensus size: 44
29107318 TGAAATTTCA
29107328 TGTAAGACCACGTCTGGGACATTGGCATC-AATTTGAGATTTACG
1 TGTAAGACCACGTCTGGGACATTGGCATCGAATTT-AGATTTACG
* * *
29107372 TGTAAGACCATGTCTGGGACATCGGCATCGTATTTA-ATTT-CG
1 TGTAAGACCACGTCTGGGACATTGGCATCGAATTTAGATTTACG
* *
29107414 TGTAAGACC-CTGTCTGGGACAGTGGCATCGATATTT-GA-TTACA
1 TGTAAGACCAC-GTCTGGGACATTGGCATCGA-ATTTAGATTTACG
* * *
29107457 TGTAAGACCAGGTCTAGGACGTTGGC
1 TGTAAGACCACGTCTGGGACATTGGC
29107483 GTTGTATGAG
Statistics
Matches: 93, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
42 30 0.32
43 31 0.33
44 28 0.30
45 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGAATTTAGATTTACG
Found at i:29107429 original size:42 final size:41
Alignment explanation
Indices: 29107321--29107465 Score: 150
Period size: 42 Copynumber: 3.4 Consensus size: 41
29107311 TCCGATATGA
*
29107321 AATTTCATGTAAGACCAC-GTCTGGGACATTGGCATC-AATTT
1 AATTTCATGTAAGACC-CTGTCTGGGACA-TGGCATCGTATTT
* *
29107362 GAGATTTACGTGTAAGACCATGTCTGGGACATCGGCATCGTATTT
1 -A-ATTT-CATGTAAGACCCTGTCTGGGACAT-GGCATCGTATTT
*
29107407 AATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATTT
1 AATTTCATGTAAGACCCTGTCTGGGACA-TGGCATCG-TATTT
* *
29107450 GATTACATGTAAGACC
1 AATTTCATGTAAGACC
29107466 AGGTCTAGGA
Statistics
Matches: 89, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
42 30 0.34
43 28 0.31
44 27 0.30
45 4 0.04
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (41 bp):
AATTTCATGTAAGACCCTGTCTGGGACATGGCATCGTATTT
Found at i:29109351 original size:46 final size:46
Alignment explanation
Indices: 29109216--29109389 Score: 158
Period size: 46 Copynumber: 3.7 Consensus size: 46
29109206 GTTATTGTGA
* * ** *
29109216 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCAC-ATTATAAGA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGA-GACGAGT
* * * * *
29109262 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGAGACGAGT
1 GCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCTCGAGACGAGT
*
29109310 GCTAGTGTAAGACATGT-TTGGAACATGCATCGGCCTCGAGACGTAAGT
1 GCTAGTGTAAGACATGTCTAGG-ACATGCATCGGCCTCGAGACG--AGT
*
29109358 -C-AGTGTAAGATATGTCTAGGACATGCATCGGC
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGC
29109390 TATGAGATGT
Statistics
Matches: 104, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
46 53 0.51
47 26 0.25
48 24 0.23
49 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGACGAGT
Found at i:29109432 original size:46 final size:45
Alignment explanation
Indices: 29109219--29109434 Score: 120
Period size: 46 Copynumber: 4.7 Consensus size: 45
29109209 ATTGTGAGCT
* * * * *
29109219 AGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATAAG-AGC-C
1 AGTGTAAGACATGTCTGGGACAGGCATCGG-C-TATGAGAAGTA-CTC
* *
29109265 AGTGTAAGACCATGTCTGGGACATGGCATCAGC-ATTGAGACGAGTGCT-
1 AGTGTAAGA-CATGTCTGGGACA-GGCATCGGCTA-TGAGA--AGTACTC
* * * * * *
29109313 AGTGTAAGACATGTTTGGAACATGCATCGGCCT-CGAGACGTAAGTC
1 AGTGTAAGACATGTCTGGGACAGGCATCGG-CTATGAGAAGT-ACTC
* * * *
29109359 AGTGTAAGATATGTCTAGGACATGCATCGGCTATGAGATGT-CTC
1 AGTGTAAGACATGTCTGGGACAGGCATCGGCTATGAGAAGTACTC
*
29109403 AGTGTAAGACCATGTTTGGGACACGGCATCGG
1 AGTGTAAGA-CATGTCTGGGACA-GGCATCGG
29109435 AACAGATATG
Statistics
Matches: 131, Mismatches: 25, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
44 13 0.10
45 14 0.11
46 61 0.47
47 25 0.19
48 18 0.14
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACAGGCATCGGCTATGAGAAGTACTC
Found at i:29112411 original size:27 final size:27
Alignment explanation
Indices: 29112381--29112558 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29112371 ATATTGAGTC
* * * *
29112381 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29112408 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29112435 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29112463 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29112490 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29112517 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29112544 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29112559 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29112520 original size:82 final size:81
Alignment explanation
Indices: 29112402--29112557 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29112392 TGCTATATAA
* *
29112402 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29112467 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29112484 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29112548 CACTTAGTGC
65 CACTTAGTGC
29112558 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:29120600 original size:27 final size:27
Alignment explanation
Indices: 29120570--29120747 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29120560 ATATTGAGTC
* * * *
29120570 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29120597 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29120624 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29120652 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29120679 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29120706 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29120733 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29120748 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29120709 original size:82 final size:81
Alignment explanation
Indices: 29120591--29120746 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29120581 TGCTATATAA
* *
29120591 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29120656 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29120673 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29120737 CACTTAGTGC
65 CACTTAGTGC
29120747 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:29151262 original size:44 final size:44
Alignment explanation
Indices: 29151214--29151303 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
29151204 GAGCAAGATA
* * * *
29151214 AAGCTACAAAACTTATATCCCTGAAATTGTAGTGGATCAGATTG
1 AAGCTACAAAACATATACCCCTGAAATTGCAGTGGATCAGAATG
** * *
29151258 AAGCTACAATTCATATACCCCTGAAGTTGCAGTGGGTCAGAATG
1 AAGCTACAAAACATATACCCCTGAAATTGCAGTGGATCAGAATG
29151302 AA
1 AA
29151304 ACTATGAGGG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (44 bp):
AAGCTACAAAACATATACCCCTGAAATTGCAGTGGATCAGAATG
Found at i:29151330 original size:94 final size:94
Alignment explanation
Indices: 29151220--29151760 Score: 541
Period size: 94 Copynumber: 5.8 Consensus size: 94
29151210 GATAAAGCTA
* * * * *
29151220 CAAAACTTATATCCCTGAAATTGTAGTGGATCAGATTGAAGCTACAATTCATATACCCCTGAAGT
1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT
* **
29151285 TGCAGTGGGTCAGAATGAAACTATGAGGG
66 TGCAGTGGGTCAGAATGAAACTACGATAG
* ** * *
29151314 TAAATCTTATCTCCCTGATGTTGCAGTGGAGCAAGA-TGAAGCTACAAATCTTATACCCCTAAAG
1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGC-AGATTGAAGCTACAAATCTTATACCCCTGAAG
* ** *
29151378 TTACAGTGGGTTGGAATAAAACTACGATAG
65 TTGCAGTGGGTCAGAATGAAACTACGATAG
** * *
29151408 CAAATCTTATCTCCCT-AAAGTTGTAGTAAAGTAAGA-TGAAGCTACAAATCCTATACCCCTGAA
1 CAAATCTTATCTCCCTGAAA-TTGTAGTGGAG-CAGATTGAAGCTACAAATCTTATACCCCTGAA
* * * * *
29151471 GTTGTAGTGAGTCAGATTGAATCTACCATAG
64 GTTGCAGTGGGTCAGAATGAAACTACGATAG
* * *
29151502 CAAATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCTTATCCCCCTGAAGT
1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT
* ** * * *
29151567 TGCAGTAGGTTGGATTGAATCTACTATAG
66 TGCAGTGGGTCAGAATGAAACTACGATAG
* ** **
29151596 CAAATCTTATCTCCCTGAAATTGTAGTAGAGCAGATTGAAATTACAAATCTTATACATCTGAAGT
1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT
** **
29151661 TGCAGTGGGTCA-AATTGATTCTAATATAG
66 TGCAGTGGGTCAGAA-TGAAACTACGATAG
* * * * * * * * *
29151690 CAAACCTTATCTCCTTGAAGTTGCAATGGAGCAAATTAAACCTACAAATCTTATACCCTTGAAGT
1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT
29151755 TGCAGT
66 TGCAGT
29151761 AGATTAGATG
Statistics
Matches: 366, Mismatches: 75, Indels: 12
0.81 0.17 0.03
Matches are distributed among these distances:
93 5 0.01
94 356 0.97
95 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (94 bp):
CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT
TGCAGTGGGTCAGAATGAAACTACGATAG
Found at i:29151385 original size:44 final size:43
Alignment explanation
Indices: 29151315--29151572 Score: 103
Period size: 44 Copynumber: 5.6 Consensus size: 43
29151305 CTATGAGGGT
* *
29151315 AAATCTTAT-CTCCCTGATGTTGCAGTGGAGCAAGATGAAGCTAC
1 AAATCTTATAC-CCCTAAAGTTGCAGTGGAGC-AGATGAAGCTAC
* ** * *
29151359 AAATCTTATACCCCTAAAGTTACAGTGG-GTTGGAATAAAACTACGATAGC
1 AAATCTTATACCCCTAAAGTTGCAGTGGAG-CAG-AT--GA--A-GCTA-C
* ** *
29151409 AAATCTTAT-CTCCCTAAAGTTGTAGTAAAGTAAGATGAAGCTAC
1 AAATCTTATAC-CCCTAAAGTTGCAGTGGAG-CAGATGAAGCTAC
* * * *
29151453 AAATCCTATACCCCTGAAGTTGTAGT-GAGTCAGATTGAATCTACCATAGC
1 AAATCTTATACCCCTAAAGTTGCAGTGGAG-CAGA-TG-A---AGC-TA-C
* * *
29151503 AAATCTTAT-CTCCTTGAAGTTGTAGTGGAGCAGATTGAAGCTAC
1 AAATCTTATAC-CCCTAAAGTTGCAGTGGAGCAGA-TGAAGCTAC
* *
29151547 AAATCTTATCCCCCTGAAGTTGCAGT
1 AAATCTTATACCCCTAAAGTTGCAGT
29151573 AGGTTGGATT
Statistics
Matches: 167, Mismatches: 25, Indels: 44
0.71 0.11 0.19
Matches are distributed among these distances:
43 8 0.05
44 73 0.44
45 9 0.05
46 4 0.02
48 4 0.02
49 8 0.05
50 55 0.33
51 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (43 bp):
AAATCTTATACCCCTAAAGTTGCAGTGGAGCAGATGAAGCTAC
Found at i:29151386 original size:138 final size:138
Alignment explanation
Indices: 29151133--29151386 Score: 341
Period size: 138 Copynumber: 1.8 Consensus size: 138
29151123 AAACAAATCC
* * * * * * *
29151133 TATACCCTTGAAGTTGCAGTGGGTCGGATTGAACCTACTATGGCGAATCTTATCTCCTTGAAGTT
1 TATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACTAGGGCAAATCTTATCTCCCTGAAGTT
* * **
29151198 TCAGTGGAGCAAGATAAAGCTACAAAACTTATATCCCTGAAATTGTAGTGGATCAGATTGAAGCT
66 GCAGTGGAGCAAGATAAAGCTACAAAACTTATACCCCTGAAATTACAGTGGATCAGATTGAAGCT
29151263 ACAATTCA
131 ACAATTCA
* *
29151271 TATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTA-TGAGGGTAAATCTTATCTCCCTGATGT
1 TATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACT-AGGGCAAATCTTATCTCCCTGAAGT
* *
29151335 TGCAGTGGAGCAAGATGAAGCTACAAATCTTATACCCCT-AAAGTTACAGTGG
65 TGCAGTGGAGCAAGATAAAGCTACAAAACTTATACCCCTGAAA-TTACAGTGG
29151387 GTTGGAATAA
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
137 4 0.04
138 95 0.96
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (138 bp):
TATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACTAGGGCAAATCTTATCTCCCTGAAGTT
GCAGTGGAGCAAGATAAAGCTACAAAACTTATACCCCTGAAATTACAGTGGATCAGATTGAAGCT
ACAATTCA
Found at i:29151509 original size:188 final size:189
Alignment explanation
Indices: 29151220--29151762 Score: 619
Period size: 188 Copynumber: 2.9 Consensus size: 189
29151210 GATAAAGCTA
* * ** ** *
29151220 CAAAACTTATATCCCTGAAATTGTAGTGGATCAGATTGAAGCTACAATTCATATACCCCTGAAGT
1 CAAATCTTATCTCCCTGAAATTGTAGTAAAGAAGATTGAAGCTACAAATCATATACCCCTGAAGT
* * ** ** * * *
29151285 TGCAGTGGGTCAGAATGAAACTATGAGGGTAAATCTTATCTCCCTGATGTTGCAGTGGAGCAAGA
66 TGCAGTGGGTCAGATTGAATCTAACATAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGA
*
29151350 -TGAAGCTACAAATCTTATACCCCTAAAGTTACAGTGGGTTGGAATAAAACTACGATAG
131 TTGAAGCTACAAATCTTATACCCCTAAAGTTACAGTAGGTTGGAATAAAACTACGATAG
*
29151408 CAAATCTTATCTCCCT-AAAGTTGTAGTAAAGTAAGA-TGAAGCTACAAATCCTATACCCCTGAA
1 CAAATCTTATCTCCCTGAAA-TTGTAGTAAAG-AAGATTGAAGCTACAAATCATATACCCCTGAA
* * * *
29151471 GTTGTAGTGAGTCAGATTGAATCTACCATAGCAAATCTTATCTCCTTGAAGTTGTAGTGGAGC-A
64 GTTGCAGTGGGTCAGATTGAATCTAACATAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAA
* * * * * * *
29151535 GATTGAAGCTACAAATCTTATCCCCCTGAAGTTGCAGTAGGTTGGATTGAATCTACTATAG
129 GATTGAAGCTACAAATCTTATACCCCTAAAGTTACAGTAGGTTGGAATAAAACTACGATAG
* * ** * **
29151596 CAAATCTTATCTCCCTGAAATTGTAGTAGAGCAGATTGAAATTACAAATCTTATACATCTGAAGT
1 CAAATCTTATCTCCCTGAAATTGTAGTAAAGAAGATTGAAGCTACAAATCATATACCCCTGAAGT
* * * * *
29151661 TGCAGTGGGTCAAATTGATTCTAATATAGCAAACCTTATCTCCTTGAAGTTGCAATGGAGCAA-A
66 TGCAGTGGGTCAGATTGAATCTAACATAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGA
* * * * *
29151725 TTAAACCTACAAATCTTATACCCTTGAAGTTGCAGTAG
131 TTGAAGCTACAAATCTTATACCCCTAAAGTTACAGTAG
29151763 ATTAGATGCA
Statistics
Matches: 301, Mismatches: 48, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
187 9 0.03
188 285 0.95
189 7 0.02
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (189 bp):
CAAATCTTATCTCCCTGAAATTGTAGTAAAGAAGATTGAAGCTACAAATCATATACCCCTGAAGT
TGCAGTGGGTCAGATTGAATCTAACATAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGA
TTGAAGCTACAAATCTTATACCCCTAAAGTTACAGTAGGTTGGAATAAAACTACGATAG
Found at i:29151527 original size:50 final size:50
Alignment explanation
Indices: 29151464--29151635 Score: 182
Period size: 50 Copynumber: 3.6 Consensus size: 50
29151454 AATCCTATAC
29151464 CCCTGAAGTTGTAGTGAGTCAGATTGAATCTACCATAGCAAATCTTATCT
1 CCCTGAAGTTGTAGTGAGTCAGATTGAATCTACCATAGCAAATCTTATCT
* * *
29151514 CCTTGAAGTTGTAGTGGAG-CAGATTG-A---AGC-TA-CAAATCTTATCC
1 CCCTGAAGTTGTAGT-GAGTCAGATTGAATCTACCATAGCAAATCTTATCT
* ** *
29151558 CCCTGAAGTTGCAGT-AGGTTGGATTGAATCTACTATAGCAAATCTTATCT
1 CCCTGAAGTTGTAGTGA-GTCAGATTGAATCTACCATAGCAAATCTTATCT
*
29151608 CCCTGAAATTGTAGTAGAG-CAGATTGAA
1 CCCTGAAGTTGTAGT-GAGTCAGATTGAA
29151636 ATTACAAATC
Statistics
Matches: 97, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 29 0.30
45 3 0.03
46 2 0.02
48 1 0.01
49 3 0.03
50 52 0.54
51 4 0.04
52 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (50 bp):
CCCTGAAGTTGTAGTGAGTCAGATTGAATCTACCATAGCAAATCTTATCT
Found at i:29151747 original size:282 final size:282
Alignment explanation
Indices: 29151220--29151756 Score: 605
Period size: 282 Copynumber: 1.9 Consensus size: 282
29151210 GATAAAGCTA
* *
29151220 CAAAACTTATATCCCTGAAATTGTAGTGGATCAGATTGAAGCTACAATTCATATACCCCTGAAGT
1 CAAAACTTATATCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCATATACCCCTGAAGT
* * * ** *
29151285 TGCAGTGGGTCAGAATGAAACTATGAGGGTAAATCTTATCTCCCTGATGTTGCAGTGGAGCAAGA
66 TGCAGTAGGTCAGAATGAAACTATGAGAGCAAATCTTATCTCCCTGAAATTGCAGTAGAGCAAGA
* * ** * *
29151350 TGAAGCTACAAATCTTATACCCCTAAAGTTACAGTGGGTTGGAATAAAACTACGATAGCAAATCT
131 TGAAACTACAAATCTTATACACCTAAAGTTACAGTGGGTTCAAATAAAACTAAGATAGCAAACCT
* * * * *
29151415 TATCTCCCTAAAGTTGTAGTAAAGTAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTG
196 TATCTCCCTAAAGTTGCAATAAAGCAAGATAAACCTACAAATCCTATACCCCTGAAGTTGTAGTG
29151480 AGTCAGATTGAATCTACCATAG
261 AGTCAGATTGAATCTACCATAG
* * * * * *
29151502 CAAATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCTTATCCCCCTGAAGT
1 CAAAACTTATATCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCATATACCCCTGAAGT
** * * * *
29151567 TGCAGTAGGTTGGATTGAATCTACT-ATAGCAAATCTTATCTCCCTGAAATTGTAGTAGAGC-AG
66 TGCAGTAGGTCAGAATGAAACTA-TGAGAGCAAATCTTATCTCCCTGAAATTGCAGTAGAGCAAG
* * * * * ** *
29151630 ATTGAAATTACAAATCTTATACATCTGAAGTTGCAGTGGG-TCAAATTGATTCTAATATAGCAAA
130 A-TGAAACTACAAATCTTATACACCTAAAGTTACAGTGGGTTCAAA-TAAAACTAAGATAGCAAA
* * ** * *
29151694 CCTTATCTCCTTGAAGTTGCAATGGAGCAA-ATTAAACCTACAAATCTTATACCCTTGAAGTTG
193 CCTTATCTCCCTAAAGTTGCAATAAAGCAAGA-TAAACCTACAAATCCTATACCCCTGAAGTTG
29151757 CAGTAGATTA
Statistics
Matches: 206, Mismatches: 45, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
281 7 0.03
282 198 0.96
283 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (282 bp):
CAAAACTTATATCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCATATACCCCTGAAGT
TGCAGTAGGTCAGAATGAAACTATGAGAGCAAATCTTATCTCCCTGAAATTGCAGTAGAGCAAGA
TGAAACTACAAATCTTATACACCTAAAGTTACAGTGGGTTCAAATAAAACTAAGATAGCAAACCT
TATCTCCCTAAAGTTGCAATAAAGCAAGATAAACCTACAAATCCTATACCCCTGAAGTTGTAGTG
AGTCAGATTGAATCTACCATAG
Found at i:29154222 original size:40 final size:40
Alignment explanation
Indices: 29154142--29154360 Score: 345
Period size: 40 Copynumber: 5.5 Consensus size: 40
29154132 TTCGGATGAC
*
29154142 ATCCGGGCTAAGTCCCGAAGGCA-TGGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
29154181 ATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
29154221 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
29154261 ATTCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
* *
29154301 ATCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTAT
*
29154341 ATCC-GGCTAAATCCCGAAGG
1 ATCCGGGCTAAGTCCCGAAGG
29154361 TACTTGGGTT
Statistics
Matches: 168, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
39 38 0.23
40 128 0.76
41 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
Found at i:29158742 original size:14 final size:14
Alignment explanation
Indices: 29158723--29158749 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29158713 AATTTTTATA
29158723 AAAAATTATTTTCT
1 AAAAATTATTTTCT
29158737 AAAAATTATTTTC
1 AAAAATTATTTTC
29158750 AATAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAAATTATTTTCT
Found at i:29158756 original size:15 final size:14
Alignment explanation
Indices: 29158722--29158756 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
29158712 CAATTTTTAT
29158722 AAAAAATTATTTTC
1 AAAAAATTATTTTC
*
29158736 TAAAAATTATTTTC
1 AAAAAATTATTTTC
29158750 AATAAAA
1 AA-AAAA
29158757 CAATCACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAAATTATTTTC
Found at i:29165789 original size:48 final size:48
Alignment explanation
Indices: 29165734--29165829 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
29165724 ATAATGGAAA
*
29165734 GAGTGGGGTTGGTTTGTTGTTGTGGTGGTGGTGTTTATTATTCAGTTT
1 GAGTGGGGTTGGTTTGTTGTGGTGGTGGTGGTGTTTATTATTCAGTTT
29165782 GAGTGGGGTTGGTTTGTTGTGGTGGTGGTGGTGTTTATTATTCAGTTT
1 GAGTGGGGTTGGTTTGTTGTGGTGGTGGTGGTGTTTATTATTCAGTTT
29165830 CTTTGCGCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.08, C:0.02, G:0.41, T:0.49
Consensus pattern (48 bp):
GAGTGGGGTTGGTTTGTTGTGGTGGTGGTGGTGTTTATTATTCAGTTT
Found at i:29167970 original size:14 final size:14
Alignment explanation
Indices: 29167951--29167986 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
29167941 GCTTTGAATG
29167951 CCAAAATTTATGAA
1 CCAAAATTTATGAA
29167965 CCAAAATTTATGAA
1 CCAAAATTTATGAA
29167979 CCAAAATT
1 CCAAAATT
29167987 CAAACGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (14 bp):
CCAAAATTTATGAA
Done.