Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 101 of 199
Found at i:28525060 original size:12 final size:12
Alignment explanation
Indices: 28525026--28525072 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
28525016 TGAGTATAGA
28525026 AATAATGATAAT
1 AATAATGATAAT
** *
28525038 AACCATAATAAT
1 AATAATGATAAT
28525050 AAATAAT-ATAAT
1 -AATAATGATAAT
28525062 AATAATGATAA
1 AATAATGATAA
28525073 ATATTTTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
11 6 0.21
12 18 0.64
13 4 0.14
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (12 bp):
AATAATGATAAT
Found at i:28525060 original size:21 final size:21
Alignment explanation
Indices: 28525036--28525075 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28525026 AATAATGATA
*
28525036 ATAACCATAATAATAAATAAT
1 ATAACAATAATAATAAATAAT
* *
28525057 ATAATAATAATGATAAATA
1 ATAACAATAATAATAAATA
28525076 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (21 bp):
ATAACAATAATAATAAATAAT
Found at i:28530325 original size:10 final size:9
Alignment explanation
Indices: 28530291--28530324 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
28530281 ATATTTATAT
28530291 ATTTTTAATA
1 ATTTTTAA-A
*
28530301 ATTTTTACA
1 ATTTTTAAA
28530310 ATTTTTAAA
1 ATTTTTAAA
28530319 ATTTTT
1 ATTTTT
28530325 TGGTCCAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:28531597 original size:24 final size:23
Alignment explanation
Indices: 28531570--28531614 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
28531560 CAGTTATTTT
*
28531570 AAACATTAATGTATTTCTAGAAGA
1 AAAC-TTAATCTATTTCTAGAAGA
* *
28531594 AAACTTAGTCTATTTTTAGAA
1 AAACTTAATCTATTTCTAGAA
28531615 AAACTCATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (23 bp):
AAACTTAATCTATTTCTAGAAGA
Found at i:28532325 original size:30 final size:30
Alignment explanation
Indices: 28532291--28532353 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
28532281 ACTTATTTTA
*
28532291 TTGTTAATTTTGTTATTATTTTAAAGGTAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
28532321 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
28532351 TTG
1 TTG
28532354 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.02, G:0.16, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:28538393 original size:19 final size:19
Alignment explanation
Indices: 28538357--28538394 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28538347 AATCTAAAAC
* *
28538357 TTACATTTCCTTTCTTTTT
1 TTACAATTCATTTCTTTTT
28538376 TTACAATTCATTT-TTTTT
1 TTACAATTCATTTCTTTTT
28538394 T
1 T
28538395 CCAAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (19 bp):
TTACAATTCATTTCTTTTT
Found at i:28542681 original size:28 final size:27
Alignment explanation
Indices: 28542634--28542768 Score: 91
Period size: 28 Copynumber: 4.9 Consensus size: 27
28542624 ATATACAATC
* *
28542634 TTTTACAATTTCTAAGAATTTTTAATTT
1 TTTTATAATTTTTAA-AATTTTTAATTT
* *
28542662 TTTTATAGTTTTTTAAAA-TTCTAATATAT
1 TTTTATA-ATTTTTAAAATTTTTAAT-T-T
*
28542691 TTTTA-AATTTTTAAAATTAATTATATTT
1 TTTTATAATTTTTAAAATT-TTTA-ATTT
* *
28542719 TTTT-TAATTTTTATAGTTTTGTAA-TT
1 TTTTATAATTTTTAAAATTTT-TAATTT
28542745 TTTTA-AATATTTTAAATATTTTTA
1 TTTTATAAT-TTTTAAA-ATTTTTA
28542769 GGTTTTTTCT
Statistics
Matches: 84, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
26 9 0.11
27 25 0.30
28 33 0.39
29 15 0.18
30 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.61
Consensus pattern (27 bp):
TTTTATAATTTTTAAAATTTTTAATTT
Found at i:28547513 original size:8 final size:8
Alignment explanation
Indices: 28547500--28547524 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28547490 TTTACATACG
28547500 TTTTATTT
1 TTTTATTT
28547508 TTTTATTT
1 TTTTATTT
28547516 TTTTATTT
1 TTTTATTT
28547524 T
1 T
28547525 CCTTATCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:28547602 original size:34 final size:35
Alignment explanation
Indices: 28547561--28547639 Score: 92
Period size: 37 Copynumber: 2.3 Consensus size: 35
28547551 TTATGTTTTA
*
28547561 TAAATATATA-CA-TATACA-TTTCTTTTATGTTG
1 TAAATATATAGAATTATACATTTTCTTTTATGTTG
* *
28547593 TAAATATATAGAATTATACATTTTTTTTTCTATTTTG
1 TAAATATATAGAATTATACA-TTTTCTTT-TATGTTG
28547630 TAAATATATA
1 TAAATATATA
28547640 CCTGTCGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 10 0.26
33 1 0.03
34 6 0.15
36 6 0.15
37 16 0.41
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (35 bp):
TAAATATATAGAATTATACATTTTCTTTTATGTTG
Found at i:28548764 original size:6 final size:6
Alignment explanation
Indices: 28548754--28548808 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
28548744 GTGTATATGT
* * ** *
28548754 ATAATA GTAATA CTAATA ATAATA GCAATA ATAATA ATAAAA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
*
28548802 ATGATA A
1 ATAATA A
28548809 ATATTTAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (6 bp):
ATAATA
Found at i:28548777 original size:18 final size:18
Alignment explanation
Indices: 28548754--28548793 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
28548744 GTGTATATGT
* *
28548754 ATAATAGTAATACTAATA
1 ATAATAGCAATAATAATA
28548772 ATAATAGCAATAATAATA
1 ATAATAGCAATAATAATA
28548790 ATAA
1 ATAA
28548794 AAATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (18 bp):
ATAATAGCAATAATAATA
Found at i:28548785 original size:15 final size:15
Alignment explanation
Indices: 28548767--28548809 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
28548757 ATAGTAATAC
**
28548767 TAATAATAATAGCAA
1 TAATAATAATAAAAA
28548782 TAATAATAATAAAAA
1 TAATAATAATAAAAA
*
28548797 TAATAATGATAAA
1 TAATAATAATAAA
28548810 TATTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (15 bp):
TAATAATAATAAAAA
Found at i:28548792 original size:9 final size:9
Alignment explanation
Indices: 28548754--28548808 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
28548744 GTGTATATGT
*
28548754 ATAATAGTA
1 ATAATAATA
*
28548763 ATACTAATA
1 ATAATAATA
**
28548772 ATAATAGCA
1 ATAATAATA
28548781 ATAATAATA
1 ATAATAATA
*
28548790 ATAAAAATA
1 ATAATAATA
*
28548799 ATAATGATA
1 ATAATAATA
28548808 A
1 A
28548809 ATATTTAAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (9 bp):
ATAATAATA
Found at i:28549248 original size:18 final size:16
Alignment explanation
Indices: 28549219--28549254 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
28549209 TGCCGTTTTT
28549219 AAAAAAAAAGAAAATA
1 AAAAAAAAAGAAAATA
28549235 AAAAAACAACAGAAAATA
1 AAAAAA-AA-AGAAAATA
28549253 AA
1 AA
28549255 GTAAAAGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
18 10 0.56
ACGTcount: A:0.83, C:0.06, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAAAAAAAGAAAATA
Found at i:28550905 original size:89 final size:89
Alignment explanation
Indices: 28550593--28550904 Score: 288
Period size: 89 Copynumber: 3.5 Consensus size: 89
28550583 ATATGTTGTA
** * * *
28550593 TTTGATCTACTTCACGCTGATACATGAAGACAATATCTGTTTTCTTCGATCTGCTTCGCCATCAG
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAG
* *
28550658 TACGGGAAGACAAGATCTGGTATC
66 TATGGGAAGGCAAGATCTGGTATC
* *** * * * * * ** *
28550682 TTTGATCTACTTCACGCCAGTATGGGGAGATAAAATCTG-TATATTCGATCCACTTCGCTACC-G
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAG
* * * **
28550745 ATATAGG-AGGACAGGACCTACTATC
66 -TATGGGAAGG-CAAGATCTGGTATC
** ** * * * *
28550770 TTTGATCTGTTTCACGCCGGTACATGAAAACGAGATCTGCTTTCTTTGATCTGTTTCGCCACCAG
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAG
28550835 TATGGGAAGGCAAGATCTGGTATC
66 TATGGGAAGGCAAGATCTGGTATC
*
28550859 TCTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
28550905 TCAACCTGCT
Statistics
Matches: 166, Mismatches: 52, Indels: 10
0.73 0.23 0.04
Matches are distributed among these distances:
87 3 0.02
88 59 0.36
89 100 0.60
90 4 0.02
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (89 bp):
TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAG
TATGGGAAGGCAAGATCTGGTATC
Found at i:28552355 original size:85 final size:85
Alignment explanation
Indices: 28552212--28552390 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
28552202 GGCCGGCCAT
28552212 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
28552277 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
28552297 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
28552362 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
28552382 GGGCATGGG
1 GAGCATGGG
28552391 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:28553706 original size:47 final size:47
Alignment explanation
Indices: 28553652--28554347 Score: 988
Period size: 47 Copynumber: 14.7 Consensus size: 47
28553642 TATTTGAATA
* *
28553652 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28553699 AATGTGAA-AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAACA-TG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
28553748 AATGTGAA-AGTGTATATATGTGATAAGACCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28553795 AATGTGAAAGTATATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTG-AA-CATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28553844 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28553891 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * * *
28553938 AATGTGAACATGCATATATGAGATAAGGCCGAATGACCAATGTGATT
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28553985 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28554032 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28554079 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
** *
28554126 AATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28554173 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
28554220 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
28554267 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
28554314 GATGTGGAA-GTGTATAAATGTGATAAGTGCCGAA
1 AATGT-GAACATGTATATATGTGATAAG-GCCGAA
28554348 GGGCAATTGT
Statistics
Matches: 603, Mismatches: 38, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
46 1 0.00
47 500 0.83
48 13 0.02
49 88 0.15
50 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (47 bp):
AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:28554218 original size:22 final size:22
Alignment explanation
Indices: 28554191--28554312 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
28554181 CATGTGTATG
28554191 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
28554213 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
28554238 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
28554260 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
28554285 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
28554307 TGTGAT
1 TGTGAT
28554313 GGATGTGGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 21 0.30
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:28567176 original size:3 final size:3
Alignment explanation
Indices: 28567155--28567203 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
28567145 GTGTATATGT
* * ** *
28567155 ATA ATA GTA ATA CTA ATA ATA ATA ATA ATA GCA ATA ATA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28567203 A
1 A
28567204 ATATTTTTAA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:28568483 original size:12 final size:12
Alignment explanation
Indices: 28568455--28568501 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
28568445 GCAAGTTTAC
*
28568455 TTGTATACTATAC
1 TTGTATA-TATAT
28568468 TTGTATATATAT
1 TTGTATATATAT
*
28568480 TTGTAAATAT-T
1 TTGTATATATAT
28568491 TATGTATATAT
1 T-TGTATATAT
28568502 GCTTTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 2 0.07
12 21 0.70
13 7 0.23
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (12 bp):
TTGTATATATAT
Found at i:28569910 original size:19 final size:19
Alignment explanation
Indices: 28569883--28569920 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28569873 TGGGTGTCAA
*
28569883 ATTGGTGTGTTGGTTGGAT
1 ATTGATGTGTTGGTTGGAT
28569902 ATTGATGTGTTGGTTGGAT
1 ATTGATGTGTTGGTTGGAT
28569921 TTGCGTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.47
Consensus pattern (19 bp):
ATTGATGTGTTGGTTGGAT
Found at i:28570894 original size:11 final size:11
Alignment explanation
Indices: 28570878--28570902 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28570868 AAATACAACT
28570878 AAAAATTAAAA
1 AAAAATTAAAA
28570889 AAAAATTAAAA
1 AAAAATTAAAA
28570900 AAA
1 AAA
28570903 TCTAATTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATTAAAA
Found at i:28574976 original size:43 final size:42
Alignment explanation
Indices: 28574929--28575010 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
28574919 AATATTCTTA
* *
28574929 AAATTTTAAAATCTTTATATATTTTTTAGAATTTTTTAAATAT
1 AAATTTTAAAATCTTTATAAATATTTT-GAATTTTTTAAATAT
** *
28574972 AAATTTTGGAATTTTTATAAATATTTTGAATTTTTTAAA
1 AAATTTTAAAATCTTTATAAATATTTTGAATTTTTTAAA
28575011 ATTATTTTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 12 0.35
43 22 0.65
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (42 bp):
AAATTTTAAAATCTTTATAAATATTTTGAATTTTTTAAATAT
Found at i:28574992 original size:18 final size:19
Alignment explanation
Indices: 28574969--28575010 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
28574959 ATTTTTTAAA
28574969 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
28574987 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
28575006 T-TAAA
1 TATAAA
28575011 ATTATTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:28574999 original size:20 final size:18
Alignment explanation
Indices: 28574974--28575029 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 18
28574964 TTAAATATAA
28574974 ATTTTGGAATTTTTATAAAT
1 ATTTT-GAATTTTT-TAAAT
28574994 ATTTTGAATTTTTTAAAATT
1 ATTTTGAATTTTTT-AAA-T
28575014 ATTTTG-ATTTTTTAAA
1 ATTTTGAATTTTTTAAA
28575030 AAGTTTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.12
19 18 0.53
20 12 0.35
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (18 bp):
ATTTTGAATTTTTTAAAT
Found at i:28575038 original size:20 final size:20
Alignment explanation
Indices: 28574952--28575030 Score: 83
Period size: 20 Copynumber: 3.9 Consensus size: 20
28574942 TTTATATATT
*
28574952 TTTTAGAATTTTTTAAATATAAA
1 TTTT-GAATTTTTTAAA-AT-TA
28574975 TTTTGGAA-TTTTTATAAA-TA
1 TTTT-GAATTTTTTA-AAATTA
28574995 TTTTGAATTTTTTAAAATTA
1 TTTTGAATTTTTTAAAATTA
28575015 TTTTG-ATTTTTTAAAA
1 TTTTGAATTTTTTAAAA
28575031 AGTTTTTTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
19 17 0.33
20 18 0.35
22 7 0.14
23 9 0.18
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
TTTTGAATTTTTTAAAATTA
Found at i:28575193 original size:23 final size:23
Alignment explanation
Indices: 28575143--28575196 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
28575133 CTCGACTCGA
*
28575143 AACTCGAATTACTTGTTCGAGTT
1 AACTCGAATAACTTGTTCGAGTT
* *
28575166 GACTCGAATAACTTGATTC-ATTT
1 AACTCGAATAACTTG-TTCGAGTT
28575189 AACTCGAA
1 AACTCGAA
28575197 ATTTGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (23 bp):
AACTCGAATAACTTGTTCGAGTT
Found at i:28577277 original size:25 final size:25
Alignment explanation
Indices: 28577249--28577305 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
28577239 ACCTTAGCGC
28577249 GCTCTCTAATTATTAGCACGA-TAGT
1 GCTCTCTAATTATTAGCAC-ATTAGT
*
28577274 GCTCTCCAATTATTAGCACATTAGT
1 GCTCTCTAATTATTAGCACATTAGT
28577299 GCTCTCT
1 GCTCTCT
28577306 GTTAAATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.03
25 28 0.97
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (25 bp):
GCTCTCTAATTATTAGCACATTAGT
Found at i:28582239 original size:31 final size:31
Alignment explanation
Indices: 28582154--28582240 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
28582144 AGGGTTTAAA
* * *
28582154 GTATCAGGTACTATGTACCGGTGATTATGTT
1 GTATCAAGTACTATGTACCGGTGTTTATATT
* * *
28582185 ATAACAAGTACTTTGTACCGGTGTTTATATT
1 GTATCAAGTACTATGTACCGGTGTTTATATT
*
28582216 GTATCAAGTACTATATACCGGTGTT
1 GTATCAAGTACTATGTACCGGTGTT
28582241 GGATACCTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (31 bp):
GTATCAAGTACTATGTACCGGTGTTTATATT
Found at i:28585402 original size:17 final size:16
Alignment explanation
Indices: 28585377--28585411 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
28585367 CAACTAATTC
28585377 TTTTGATATATATATAT
1 TTTTGATATATA-ATAT
*
28585394 TTTTTATATATAATAT
1 TTTTGATATATAATAT
28585410 TT
1 TT
28585412 ATATGTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTTGATATATAATAT
Found at i:28585776 original size:13 final size:13
Alignment explanation
Indices: 28585758--28585801 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
28585748 AGATAGCGTG
28585758 TTAAAAATATTAA
1 TTAAAAATATTAA
*
28585771 TTAAAAAAATTAA
1 TTAAAAATATTAA
28585784 --AAAAATATTAA
1 TTAAAAATATTAA
*
28585795 ATAAAAA
1 TTAAAAA
28585802 ATACAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 10 0.37
13 17 0.63
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TTAAAAATATTAA
Found at i:28586266 original size:6 final size:6
Alignment explanation
Indices: 28586255--28586281 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28586245 GGCTCAGATT
28586255 CACCTC CACCTC CACCTC CACCTC CAC
1 CACCTC CACCTC CACCTC CACCTC CAC
28586282 GTAACCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.67, G:0.00, T:0.15
Consensus pattern (6 bp):
CACCTC
Found at i:28597647 original size:21 final size:22
Alignment explanation
Indices: 28597621--28597707 Score: 108
Period size: 22 Copynumber: 4.0 Consensus size: 22
28597611 CTATCTAATT
*
28597621 TTTCCTTTCT-AATCCTCTCAA
1 TTTCCTTTCTAAATTCTCTCAA
28597642 TTTCCTTT-TAAAATTCTCTCAA
1 TTTCCTTTCT-AAATTCTCTCAA
28597664 TTTCC-TTCTAAAATTCTCTCAA
1 TTTCCTTTCT-AAATTCTCTCAA
* *
28597686 TTTCCTTCCAAAATTCTCTCAA
1 TTTCCTTTCTAAATTCTCTCAA
28597708 ACTCATATTT
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
20 1 0.02
21 10 0.17
22 46 0.78
23 2 0.03
ACGTcount: A:0.25, C:0.29, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTCCTTTCTAAATTCTCTCAA
Found at i:28597663 original size:22 final size:22
Alignment explanation
Indices: 28597635--28597707 Score: 128
Period size: 22 Copynumber: 3.3 Consensus size: 22
28597625 CTTTCTAATC
*
28597635 CTCTCAATTTCCTTTTAAAATT
1 CTCTCAATTTCCTTCTAAAATT
28597657 CTCTCAATTTCCTTCTAAAATT
1 CTCTCAATTTCCTTCTAAAATT
*
28597679 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCTAAAATT
28597701 CTCTCAA
1 CTCTCAA
28597708 ACTCATATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.44
Consensus pattern (22 bp):
CTCTCAATTTCCTTCTAAAATT
Found at i:28597791 original size:32 final size:31
Alignment explanation
Indices: 28597753--28597818 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 31
28597743 CTCAAATCCA
*
28597753 TTTTTTAAAATAATTATAATTTTTTTTTATAT
1 TTTTTTAAAATAATTATAA-ATTTTTTTATAT
*
28597785 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
28597816 TTT
1 TTT
28597819 CATCAATGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 14 0.44
32 18 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
TTTTTTAAAATAATTATAAATTTTTTTATAT
Found at i:28598910 original size:7 final size:7
Alignment explanation
Indices: 28598898--28598922 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28598888 AGTCGATTGA
28598898 TATTTAG
1 TATTTAG
28598905 TATTTAG
1 TATTTAG
28598912 TATTTAG
1 TATTTAG
28598919 TATT
1 TATT
28598923 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:28600190 original size:28 final size:28
Alignment explanation
Indices: 28600151--28600564 Score: 612
Period size: 28 Copynumber: 14.5 Consensus size: 28
28600141 AAAACCCTAA
28600151 CCTAACCTTAACCTAAATTAATTAAAAAC
1 CCTAACC-TAACCTAAATTAATTAAAAAC
* *
28600180 CCTAATCTAACCTAAATTAACTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
28600208 CCTAACCTAACCTAAATTAATTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
28600236 CCTAAACCTAACCTAAAATTAATTAAAAAC
1 CCT-AACCTAACCT-AAATTAATTAAAAAC
*
28600266 CCTAAACCTAACCTAAATTAACTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
* * *
28600295 CATAATCTAACCTAAATTAATTTAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
28600323 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAA-CCTAACCTAAATTAATTAAAAAC
* *
28600352 CCTAATCTAACCTAAATTAACTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
28600380 CCTAACCTAACCTAAATTAATTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
28600408 CCTAAACCTAACCTAAAATTAATTAAAAAC
1 CCT-AACCTAACCT-AAATTAATTAAAAAC
*
28600438 CCTAAACCTAACCTAAATTAACTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
* * *
28600467 CATAATCTAACCTAAATTAATTTAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
28600495 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAA-CCTAACCTAAATTAATTAAAAAC
* * *
28600524 CTTAATCTAACCTAAATTAACTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
28600552 CCTAACCTAACCT
1 CCTAACCTAACCT
28600565 GTAACACCCC
Statistics
Matches: 350, Mismatches: 29, Indels: 13
0.89 0.07 0.03
Matches are distributed among these distances:
28 183 0.52
29 109 0.31
30 58 0.17
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (28 bp):
CCTAACCTAACCTAAATTAATTAAAAAC
Found at i:28600252 original size:57 final size:56
Alignment explanation
Indices: 28600151--28600564 Score: 639
Period size: 57 Copynumber: 7.2 Consensus size: 56
28600141 AAAACCCTAA
*
28600151 CCTAACCTTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAAC
1 CCTAACC-TAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
*
28600208 CCTAACCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAAAATTAATTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAACCCT-AATCTAACCT-AAATTAATTAAAAAC
* * *
28600266 CCTAAACCTAACCTAAATTAACTAAAAACCATAATCTAACCTAAATTAATTTAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
*
28600323 CCTAACCCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAAC
1 CCTAA-CCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
*
28600380 CCTAACCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAAAATTAATTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAACCCT-AATCTAACCT-AAATTAATTAAAAAC
* * *
28600438 CCTAAACCTAACCTAAATTAACTAAAAACCATAATCTAACCTAAATTAATTTAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
* *
28600495 CCTAACCCTAACCTAAATTAATTAAAAACCTTAATCTAACCTAAATTAACTAAAAAC
1 CCTAA-CCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
28600552 CCTAACCTAACCT
1 CCTAACCTAACCT
28600565 GTAACACCCC
Statistics
Matches: 329, Mismatches: 20, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
56 62 0.19
57 163 0.50
58 52 0.16
59 52 0.16
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (56 bp):
CCTAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
Found at i:28600402 original size:172 final size:172
Alignment explanation
Indices: 28600151--28600564 Score: 810
Period size: 172 Copynumber: 2.4 Consensus size: 172
28600141 AAAACCCTAA
*
28600151 CCTAACCTTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACCT
1 CCTAACCCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACCT
28600216 AACCTAAATTAATTAAAAACCCTAAACCTAACCTAAAATTAATTAAAAACCCTAAACCTAACCTA
66 AACCTAAATTAATTAAAAACCCTAAACCTAACCTAAAATTAATTAAAAACCCTAAACCTAACCTA
28600281 AATTAACTAAAAACCATAATCTAACCTAAATTAATTTAAAAC
131 AATTAACTAAAAACCATAATCTAACCTAAATTAATTTAAAAC
28600323 CCTAACCCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACCT
1 CCTAACCCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACCT
28600388 AACCTAAATTAATTAAAAACCCTAAACCTAACCTAAAATTAATTAAAAACCCTAAACCTAACCTA
66 AACCTAAATTAATTAAAAACCCTAAACCTAACCTAAAATTAATTAAAAACCCTAAACCTAACCTA
28600453 AATTAACTAAAAACCATAATCTAACCTAAATTAATTTAAAAC
131 AATTAACTAAAAACCATAATCTAACCTAAATTAATTTAAAAC
*
28600495 CCTAACCCTAACCTAAATTAATTAAAAACCTTAATCTAACCTAAATTAACTAAAAACCCTAACCT
1 CCTAACCCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACCT
28600560 AACCT
66 AACCT
28600565 GTAACACCCC
Statistics
Matches: 240, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 240 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (172 bp):
CCTAACCCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACCT
AACCTAAATTAATTAAAAACCCTAAACCTAACCTAAAATTAATTAAAAACCCTAAACCTAACCTA
AATTAACTAAAAACCATAATCTAACCTAAATTAATTTAAAAC
Found at i:28604235 original size:46 final size:45
Alignment explanation
Indices: 28604077--28604346 Score: 176
Period size: 46 Copynumber: 5.8 Consensus size: 45
28604067 ACATGAGATT
* * *
28604077 TGTATGCCAGTGTAAGACCATGTATGGGACATGGCATCGGCATTGAGGCA
1 TGTA-GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGA-G-A
* * * * * *
28604127 AG-GGCTAGTGTAAGACATGTTTGGGACATGCATCAGCCAC-AGTA
1 TGTAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAG-A
28604171 TG-AGATCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGA
1 TGTAG--CCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGA
* * * * *
28604217 TGTTAGCCAATGTCAGACATGTCTGGGACATGCGTTGG-CTACGGGA
1 TG-TAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGA
* * * * *
28604263 TGT-GCTAGTGTAAGACATGTCTGGGACATGCGTCAGCACGAT-TACA
1 TGTAGCCAGTGTAAGACATGTCTGGGACATGCATCGGC-C--TCGAGA
* *
28604309 TGT-GTCAGTGTAAGACCTGTCTGGGACATGGCATCGGC
1 TGTAGCCAGTGTAAGACATGTCTGGGACAT-GCATCGGC
28604347 ACAGATGGAT
Statistics
Matches: 176, Mismatches: 33, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
44 32 0.18
45 4 0.02
46 104 0.59
47 21 0.12
48 14 0.08
50 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (45 bp):
TGTAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGA
Found at i:28607321 original size:28 final size:28
Alignment explanation
Indices: 28607231--28607495 Score: 386
Period size: 28 Copynumber: 9.3 Consensus size: 28
28607221 GGCTGTTACA
*
28607231 TAACCTAAATTAATTAAAAATCCTAAACC
1 TAACCTAAATTAATTAAAAACCCT-AACC
*
28607260 TAGCCTAAAATTAATTAAAAACCCTAAACC
1 TAACCT-AAATTAATTAAAAACCCT-AACC
* *
28607290 TAACCTAAATTAACTAAAAACCCTAATC
1 TAACCTAAATTAATTAAAAACCCTAACC
*
28607318 TAACCTAAATTAATTTAAAACCCTAACCC
1 TAACCTAAATTAATTAAAAACCCTAA-CC
*
28607347 TAACCTAAATTAATTAAAAACCCTAATC
1 TAACCTAAATTAATTAAAAACCCTAACC
* *
28607375 TAACCTAAATTAACTAAAAACCCTAATC
1 TAACCTAAATTAATTAAAAACCCTAACC
* *
28607403 TAACCTAAATTAATTTAAAACCCTAATC
1 TAACCTAAATTAATTAAAAACCCTAACC
28607431 TAACCTAAATTAATTAAAAACCCTAAACC
1 TAACCTAAATTAATTAAAAACCCT-AACC
*
28607460 TAACCTAAATTAATTAAAAACCCTAAAC
1 TAACCTAAATTAATTAAAAACCCTAACC
28607488 TAACCTAA
1 TAACCTAA
28607496 TTTTTTTTGG
Statistics
Matches: 217, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
28 115 0.53
29 75 0.35
30 27 0.12
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.26
Consensus pattern (28 bp):
TAACCTAAATTAATTAAAAACCCTAACC
Found at i:28607349 original size:57 final size:57
Alignment explanation
Indices: 28607231--28607495 Score: 415
Period size: 57 Copynumber: 4.6 Consensus size: 57
28607221 GGCTGTTACA
* * *
28607231 TAACCTAAATTAATTAAAAATCCTAAACCTAGCCTAAAATTAATTAAAAACCCTAAACC
1 TAACCTAAATTAATTAAAAACCCT-AATCTAACCT-AAATTAATTAAAAACCCTAAACC
* * *
28607290 TAACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTTAAAACCCTAACCC
1 TAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCCTAAACC
* *
28607347 TAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCT-AATC
1 TAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCCTAAACC
*
28607403 TAACCTAAATTAATTTAAAACCCTAATCTAACCTAAATTAATTAAAAACCCTAAACC
1 TAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCCTAAACC
*
28607460 TAACCTAAATTAATTAAAAACCCTAAACTAACCTAA
1 TAACCTAAATTAATTAAAAACCCTAATCTAACCTAA
28607496 TTTTTTTTGG
Statistics
Matches: 189, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
56 52 0.28
57 107 0.57
58 8 0.04
59 22 0.12
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.26
Consensus pattern (57 bp):
TAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCCTAAACC
Found at i:28607399 original size:85 final size:85
Alignment explanation
Indices: 28607231--28607495 Score: 433
Period size: 85 Copynumber: 3.1 Consensus size: 85
28607221 GGCTGTTACA
* * *
28607231 TAACCTAAATTAATTAAAAATCCTAAACCTAGCCTAAAATTAATTAAAAACCCTAAACCTAACCT
1 TAACCTAAATTAATTTAAAACCCT-AACCTAACCT-AAATTAATTAAAAACCCTAAACCTAACCT
28607296 AAATTAACTAAAAACCCTAATC
64 AAATTAACTAAAAACCCTAATC
*
28607318 TAACCTAAATTAATTTAAAACCCTAACCCTAACCTAAATTAATTAAAAACCCT-AATCTAACCTA
1 TAACCTAAATTAATTTAAAACCCTAA-CCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTA
28607382 AATTAACTAAAAACCCTAATC
65 AATTAACTAAAAACCCTAATC
*
28607403 TAACCTAAATTAATTTAAAACCCTAATCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAA
1 TAACCTAAATTAATTTAAAACCCTAACCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAA
* *
28607468 ATTAATTAAAAACCCTAAAC
66 ATTAACTAAAAACCCTAATC
28607488 TAACCTAA
1 TAACCTAA
28607496 TTTTTTTTGG
Statistics
Matches: 168, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
84 25 0.15
85 94 0.56
86 20 0.12
87 29 0.17
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.26
Consensus pattern (85 bp):
TAACCTAAATTAATTTAAAACCCTAACCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAA
ATTAACTAAAAACCCTAATC
Found at i:28607532 original size:26 final size:26
Alignment explanation
Indices: 28607497--28607552 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
28607487 CTAACCTAAT
28607497 TTTTTTTGGCTTAATAATTTTACATA
1 TTTTTTTGGCTTAATAATTTTACATA
28607523 TTTTTTTGGCTTAATAATTTTACATA
1 TTTTTTTGGCTTAATAATTTTACATA
28607549 TTTT
1 TTTT
28607553 GAACACTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.61
Consensus pattern (26 bp):
TTTTTTTGGCTTAATAATTTTACATA
Found at i:28607663 original size:10 final size:10
Alignment explanation
Indices: 28607648--28607672 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28607638 TTTTGGCTTA
28607648 ATAATTTTAC
1 ATAATTTTAC
28607658 ATAATTTTAC
1 ATAATTTTAC
28607668 ATAAT
1 ATAAT
28607673 GTTAGATCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:28621448 original size:20 final size:20
Alignment explanation
Indices: 28621423--28621462 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28621413 CGTAAAATGA
*
28621423 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
28621443 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
28621463 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:28622826 original size:12 final size:13
Alignment explanation
Indices: 28622804--28622832 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
28622794 TCCAACACTA
28622804 AAAAACTTTTTTT
1 AAAAACTTTTTTT
28622817 AAAAACTTTTTTT
1 AAAAACTTTTTTT
28622830 AAA
1 AAA
28622833 TATTGGTATA
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:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAAACTTTTTTT
Found at i:28623496 original size:21 final size:22
Alignment explanation
Indices: 28623466--28623514 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
28623456 TAAGATTCAA
*
28623466 TTTT-TTGAAATTTGAG-TTTT
1 TTTTCTTGAAATTTGAGAATTT
28623486 TTTTCTTGAAATTTGAGAATTT
1 TTTTCTTGAAATTTGAGAATTT
28623508 TTTTCTT
1 TTTTCTT
28623515 TTAATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 4 0.15
21 12 0.46
22 10 0.38
ACGTcount: A:0.20, C:0.04, G:0.12, T:0.63
Consensus pattern (22 bp):
TTTTCTTGAAATTTGAGAATTT
Found at i:28623800 original size:49 final size:49
Alignment explanation
Indices: 28623721--28623817 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
28623711 TTATGCTATG
* * * *
28623721 CATTTCTAAACTTGGTTTTCCACTGCCTACACTCTTATCACTATTTATA
1 CATTGCTAAACTTAGTCTTCCACTGCCTACACTCTTACCACTATTTATA
*
28623770 CATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTACCACTATTTAT
1 CATTGCTAAACTTAGTCTTCCACTGCCTACACTCTTACCACTATTTAT
28623818 CCCTTCTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.41
Consensus pattern (49 bp):
CATTGCTAAACTTAGTCTTCCACTGCCTACACTCTTACCACTATTTATA
Found at i:28625142 original size:43 final size:43
Alignment explanation
Indices: 28625093--28625178 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
28625083 TCATATTTGA
*
28625093 TTTCTCATCTCATAATCATTTCTCAT-TTTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTGT-CATTTCAATAT
*
28625136 TTTCTCATCTCATATTCATTTCTCATATTTGTCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTGTCATTTCAATAT
28625179 CAATCACATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 36 0.90
44 4 0.10
ACGTcount: A:0.23, C:0.22, G:0.01, T:0.53
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCATATTTGTCATTTCAATAT
Found at i:28625612 original size:26 final size:27
Alignment explanation
Indices: 28625573--28625624 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
28625563 CTCAGTACAT
* *
28625573 ATATATTCATAATCAATATATTTCATA
1 ATATATTCAAAATCAATACATTTCATA
*
28625600 ATATATT-AAAATCAATCCATTTCAT
1 ATATATTCAAAATCAATACATTTCAT
28625625 TTCAATTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATATTCAAAATCAATACATTTCATA
Found at i:28628273 original size:3 final size:3
Alignment explanation
Indices: 28628267--28628309 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
28628257 ATCATCATCA
28628267 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
28628310 TAAGGAGGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:28637725 original size:21 final size:21
Alignment explanation
Indices: 28637699--28637745 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28637689 ATGATGATGA
* * *
28637699 TGAGATTAGTTACTGTAGTGG
1 TGAGATTAGATACTATAATGG
*
28637720 TGAGATTTGATACTATAATGG
1 TGAGATTAGATACTATAATGG
28637741 TGAGA
1 TGAGA
28637746 ATAAAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.36
Consensus pattern (21 bp):
TGAGATTAGATACTATAATGG
Found at i:28638778 original size:46 final size:44
Alignment explanation
Indices: 28638678--28639039 Score: 353
Period size: 46 Copynumber: 8.6 Consensus size: 44
28638668 TACATATGAT
* *
28638678 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCTA-GCTAC
28638721 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCT-A-GCTAC
* * *
28638767 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCT-A-GCTAC
28638813 CACTTATCACTTTGTCACTTGATCAGAT-A-AGTA--TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCTAGCTAC
* *
28638849 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCT--AGCTAC
*
28638895 CACTTATCACTTTGTCTCTTGATCAGAT-A-AGT-G-TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCTAGCTAC
*
28638931 CACTTATCACTTTTTCACTTGATCAGAT-A-AGT-G-TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCTAGCTAC
* *
28638967 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCT-A-GCTAC
*
28639013 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
28639040 AGTACTCAAA
Statistics
Matches: 279, Mismatches: 17, Indels: 43
0.82 0.05 0.13
Matches are distributed among these distances:
36 88 0.32
37 2 0.01
38 5 0.02
39 1 0.00
40 5 0.02
41 2 0.01
42 5 0.02
43 11 0.04
44 10 0.04
45 21 0.08
46 129 0.46
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (44 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCTAGCTAC
Found at i:28638854 original size:36 final size:36
Alignment explanation
Indices: 28638813--28639003 Score: 247
Period size: 36 Copynumber: 5.0 Consensus size: 36
28638803 CTAAGGCTAA
*
28638813 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
*
28638849 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GT-G-T--AG
*
28638891 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
*
28638931 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
*
28638967 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
28639003 C
1 C
28639004 TAATGCTACC
Statistics
Matches: 138, Mismatches: 7, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
36 99 0.72
38 2 0.01
40 3 0.02
42 3 0.02
43 1 0.01
44 2 0.01
46 28 0.20
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
Found at i:28638904 original size:82 final size:82
Alignment explanation
Indices: 28638767--28638967 Score: 357
Period size: 82 Copynumber: 2.5 Consensus size: 82
28638757 CTAAGGCTAC
* *
28638767 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
28638832 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
* *
28638849 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
*
28638914 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTATAG
28638931 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGC
28638968 ACTTATCACT
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 114 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
TGATCAGATAAGTATAG
Found at i:28638952 original size:118 final size:118
Alignment explanation
Indices: 28638813--28639039 Score: 400
Period size: 118 Copynumber: 1.9 Consensus size: 118
28638803 CTAAGGCTAA
*
28638813 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCACTTATCACTTTCTCACTTGATCAGATA
* *
28638878 AGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
66 AGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
* *
28638931 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCACTTATCACTTTCTCACTTGATCAGATA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCACTTATCACTTTCTCACTTGATCAGATA
*
28638996 AGTGTAGCTAATGCTACCACTTATCACTTTATCACTTGATCAGA
66 AGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGA
28639040 AGTACTCAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 103 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (118 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCACTTATCACTTTCTCACTTGATCAGATA
AGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
Found at i:28639017 original size:82 final size:80
Alignment explanation
Indices: 28638721--28639039 Score: 256
Period size: 82 Copynumber: 3.9 Consensus size: 80
28638711 GCTAGGCTAC
* * *
28638721 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCTAAGGCTACCACTTATCACTTTCTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAA-TGTAGCTAATG-TACCACTTATCACTTTTTCACT
28638786 TGATCAGATAAGTGTAGCTAAGG
64 TGATCAGATAA--GT-G-T-A-G
28638809 CTAACACTTATCACTTTGTCACTTGATCAGATAA-GTA--T-A-G---CACTTATCACTTTTTCA
1 ----CACTTATCACTTTGTCACTTGATCAGATAATGTAGCTAATGTACCACTTATCACTTTTTCA
28638866 CTTGATCAGATAAGTGTAGCTAAAG
62 CTTGATCAGATAA--GT-G-T--AG
*
28638891 CTACCACTTATCACTTTGTCTCTTGATCAGATAA-GT-G-T-A-G---CACTTATCACTTTTTCA
1 ----CACTTATCACTTTGTCACTTGATCAGATAATGTAGCTAATGTACCACTTATCACTTTTTCA
28638948 CTTGATCAGATAAGTGTAG
62 CTTGATCAGATAAGTGTAG
* *
28638967 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTATCACT
1 CACTTATCACTTTGTCACTTGATCAGATAA-TGTAGCTAATG-TACCACTTATCACTTTTTCACT
28639032 TGATCAGA
64 TGATCAGA
28639040 AGTACTCAAA
Statistics
Matches: 209, Mismatches: 6, Indels: 34
0.84 0.02 0.14
Matches are distributed among these distances:
72 28 0.13
74 2 0.01
75 1 0.00
76 3 0.01
77 1 0.00
78 2 0.01
79 1 0.00
80 2 0.01
82 131 0.63
83 2 0.01
86 1 0.00
87 1 0.00
88 1 0.00
90 3 0.01
92 30 0.14
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (80 bp):
CACTTATCACTTTGTCACTTGATCAGATAATGTAGCTAATGTACCACTTATCACTTTTTCACTTG
ATCAGATAAGTGTAG
Found at i:28642411 original size:14 final size:14
Alignment explanation
Indices: 28642392--28642430 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
28642382 TTGTTTCACT
28642392 GAAAATGACTTTCG
1 GAAAATGACTTTCG
* *
28642406 GAAAATGATTTTTG
1 GAAAATGACTTTCG
28642420 GAAAATGACTT
1 GAAAATGACTT
28642431 ACTTTTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (14 bp):
GAAAATGACTTTCG
Found at i:28643188 original size:23 final size:25
Alignment explanation
Indices: 28643160--28643217 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
28643150 TTGAACATCA
28643160 ATAATTT-G-AGTTTTAAATATGTC
1 ATAATTTAGCAGTTTTAAATATGTC
*
28643183 ATAATTTAAGCATTTTTAAATATGTC
1 ATAATTT-AGCAGTTTTAAATATGTC
*
28643209 CTAAGTTTA
1 ATAA-TTTA
28643218 TTAATTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 7 0.24
25 1 0.03
26 18 0.62
27 3 0.10
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (25 bp):
ATAATTTAGCAGTTTTAAATATGTC
Found at i:28644824 original size:15 final size:15
Alignment explanation
Indices: 28644804--28644855 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
28644794 ACTACAAAAC
28644804 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
28644819 ATTTATAATTATAATAAAT
1 ATTTATTA-T-TAAT--AT
*
28644838 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
28644853 ATT
1 ATT
28644856 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:28644841 original size:19 final size:19
Alignment explanation
Indices: 28644817--28644853 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28644807 TATTATTAAT
*
28644817 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
28644836 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
28644854 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:28644966 original size:20 final size:20
Alignment explanation
Indices: 28644937--28644974 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28644927 AATAAAATTG
*
28644937 AAATATTAAATAATTTATTA
1 AAATAATAAATAATTTATTA
*
28644957 AAATAATAAATTATTTAT
1 AAATAATAAATAATTTAT
28644975 ATGATTAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATAATAAATAATTTATTA
Found at i:28649591 original size:7 final size:7
Alignment explanation
Indices: 28649579--28649661 Score: 94
Period size: 7 Copynumber: 11.9 Consensus size: 7
28649569 AAAAAAATAT
28649579 TTGAGAA
1 TTGAGAA
28649586 TTGAGAA
1 TTGAGAA
*
28649593 TTAAGAA
1 TTGAGAA
28649600 TTGAGAA
1 TTGAGAA
*
28649607 TTGAAAA
1 TTGAGAA
28649614 TTGAGAA
1 TTGAGAA
* *
28649621 TCGAGGA
1 TTGAGAA
*
28649628 TTAAGAA
1 TTGAGAA
28649635 TTGAGAA
1 TTGAGAA
**
28649642 TTGATTA
1 TTGAGAA
*
28649649 TTGAGTA
1 TTGAGAA
28649656 TTGAGA
1 TTGAGA
28649662 TAAAAAGAAT
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 62 1.00
ACGTcount: A:0.42, C:0.01, G:0.25, T:0.31
Consensus pattern (7 bp):
TTGAGAA
Found at i:28650181 original size:65 final size:65
Alignment explanation
Indices: 28650099--28650285 Score: 241
Period size: 65 Copynumber: 2.9 Consensus size: 65
28650089 TATAAGATAA
* * * * * *
28650099 ATAATTTGTGTATTTATATTTGGTATTTAGATATCTTATTGAATTATAATCATATTTATTTTAAT
1 ATAATTTGTATATTTATAATTGGTATTTAAATATTTTATTGAATTATAATAATATTTATCTTAAT
* * *
28650164 ATAATTTGTATATTTATAACTAGTATTTAAATATTTTATTAAATTATAATAATATTTATCTTAAT
1 ATAATTTGTATATTTATAATTGGTATTTAAATATTTTATTGAATTATAATAATATTTATCTTAAT
* * ** *
28650229 ATAATTTTTAGATTTATAATTGACATTAAAATATTTTATTGAATTATAATAA-ATTTA
1 ATAATTTGTATATTTATAATTGGTATTTAAATATTTTATTGAATTATAATAATATTTA
28650286 AAAAATTTGT
Statistics
Matches: 105, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
64 5 0.05
65 100 0.95
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (65 bp):
ATAATTTGTATATTTATAATTGGTATTTAAATATTTTATTGAATTATAATAATATTTATCTTAAT
Found at i:28653960 original size:162 final size:157
Alignment explanation
Indices: 28653719--28654041 Score: 430
Period size: 162 Copynumber: 2.0 Consensus size: 157
28653709 CAGAAATTGA
* *
28653719 TTACAATGCTTCTTTTTTTTTGTACAAAATTTGTTCATTCATTTTTTTTGTATTTCATTTGTATT
1 TTACAATGCTTCTTTTTTTTTGTACAAAATCTATTCATTCATTTTTTTTGTATTTCATTTGTATT
* * * * *
28653784 TTTAAATATCTACTAACATTCATATAGTGGAAAATTTGCTATTTTAAGTGTTACATCAAATACAA
66 TGTAAACATCTACTAACATTCATATAGTGGAAAAATAGCTACTTTAAGTGTTACATCAAATACAA
*
28653849 ATTACAATTTCTCTGGCGATTGAACTT
131 ATTACAATTTCTCTGGCGATTGAACAT
* *
28653876 TTACAATGCTTATTTTTTTTCTTGTGCAAAATCTATTCATTCATTTTTTTTTTGGTATTTCATTT
1 TTACAATGCTT-CTTTTTTT-TTGTACAAAATCTATTCATTCA--TTTTTTTT-GTATTTCATTT
* * * * * *
28653941 GTATTTGTCACCGTCTACTAACATTCATATAGTGGAAAAATAGCTACTTTAAGTTTTACGTCAAG
61 GTATTTGTAAACATCTACTAACATTCATATAGTGGAAAAATAGCTACTTTAAGTGTTACATCAAA
* * *
28654006 TACCAATTACAATTTCTTTGGTGATTGAACAT
126 TACAAATTACAATTTCTCTGGCGATTGAACAT
28654038 TTAC
1 TTAC
28654042 CATTTTTACT
Statistics
Matches: 142, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
157 11 0.08
158 7 0.05
159 19 0.13
161 8 0.06
162 97 0.68
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (157 bp):
TTACAATGCTTCTTTTTTTTTGTACAAAATCTATTCATTCATTTTTTTTGTATTTCATTTGTATT
TGTAAACATCTACTAACATTCATATAGTGGAAAAATAGCTACTTTAAGTGTTACATCAAATACAA
ATTACAATTTCTCTGGCGATTGAACAT
Found at i:28656558 original size:20 final size:19
Alignment explanation
Indices: 28656497--28656562 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 19
28656487 ATTTTAGAAA
*
28656497 TTTTTTAAAATTTTAACTT
1 TTTTTTAAAATTTTAAATT
* *
28656516 TCTTTATATATATTTTTAGAATT
1 T-TTT-T-TAAAATTTTA-AATT
28656539 TTTTTTAAAATTTTACAATT
1 TTTTTTAAAATTTTA-AATT
28656559 TTTT
1 TTTT
28656563 AAAAATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 19 0.51
21 2 0.05
22 11 0.30
23 4 0.11
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTTAAAATTTTAAATT
Found at i:28656575 original size:28 final size:27
Alignment explanation
Indices: 28656544--28656616 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
28656534 GAATTTTTTT
28656544 TAAAATTTTACAATTTTTTAAAAATATA
1 TAAAATTTTA-AATTTTTTAAAAATATA
* * *
28656572 TAAAATTTAAAATTTTTTATAAATATT
1 TAAAATTTTAAATTTTTTAAAAATATA
**
28656599 TTGAATTTTAAATTTTTT
1 TAAAATTTTAAATTTTTT
28656617 TTTGGTAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 30 0.77
28 9 0.23
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (27 bp):
TAAAATTTTAAATTTTTTAAAAATATA
Found at i:28659820 original size:36 final size:35
Alignment explanation
Indices: 28659780--28659851 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
28659770 AATGAGGCAG
* *
28659780 TCCAAAATGTGTTCTCAAACTACGGAATCTTAACAT
1 TCCAAAATCTATTCTCAAACTACGGAATCTT-ACAT
*
28659816 TCCAAAATCTATTCTCAAATTACGGAATCTTACAT
1 TCCAAAATCTATTCTCAAACTACGGAATCTTACAT
28659851 T
1 T
28659852 GGAGGATCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 5 0.15
36 28 0.85
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.33
Consensus pattern (35 bp):
TCCAAAATCTATTCTCAAACTACGGAATCTTACAT
Found at i:28662248 original size:32 final size:31
Alignment explanation
Indices: 28662203--28662298 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
28662193 CTTAGATAAT
28662203 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
28662234 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
28662266 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
28662297 TT
1 TT
28662299 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:28662656 original size:4 final size:4
Alignment explanation
Indices: 28662602--28662640 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
28662592 ATCTATCCTT
28662602 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
28662641 ACTAATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:28664195 original size:32 final size:31
Alignment explanation
Indices: 28664150--28664245 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
28664140 CTTAGATAAT
28664150 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
28664181 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
28664213 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
28664244 TT
1 TT
28664246 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:28666130 original size:32 final size:31
Alignment explanation
Indices: 28666085--28666180 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
28666075 CTTAGATAAT
28666085 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
28666116 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
* *
28666148 TTGAAAGAGTTTTATTAGGATTCAATTATTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
28666179 TT
1 TT
28666181 GTAATTTGCC
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 32 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:28668065 original size:32 final size:31
Alignment explanation
Indices: 28668020--28668115 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
28668010 CTTAGATAAT
28668020 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
28668051 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
28668083 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
28668114 TT
1 TT
28668116 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:28670004 original size:32 final size:31
Alignment explanation
Indices: 28669959--28670054 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
28669949 CTTAGATAAT
28669959 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
28669990 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
28670022 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
28670053 TT
1 TT
28670055 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:28672571 original size:26 final size:26
Alignment explanation
Indices: 28672542--28672731 Score: 117
Period size: 26 Copynumber: 7.5 Consensus size: 26
28672532 ATCCTCTCTC
28672542 GAGCCATATAA-CAGGAAGCTCACAAA
1 GAGCCAT-TAATCAGGAAGCTCACAAA
*
28672568 GAGCCATTAATCGGGAAGCTCACAAA
1 GAGCCATTAATCAGGAAGCTCACAAA
* * * *
28672594 AAGTC-TT--TCAGGAAGCTTATC--C
1 GAGCCATTAATCAGGAAGCTCA-CAAA
* * * *
28672616 GGGCTATATAAT-GGGAAGCTCACACA
1 GAGCCAT-TAATCAGGAAGCTCACAAA
* * *
28672642 GAGCCA-TAATCAGAAAGTTCACATA
1 GAGCCATTAATCAGGAAGCTCACAAA
* ** *
28672667 GAACTTTTAATCAAGAAGCTCACAAA
1 GAGCCATTAATCAGGAAGCTCACAAA
* * * *
28672693 GAGCCTTTAAACGGGAAGCTCACGAA
1 GAGCCATTAATCAGGAAGCTCACAAA
28672719 GAGCCATTAATCA
1 GAGCCATTAATCA
28672732 AGAGCTCCAG
Statistics
Matches: 119, Mismatches: 35, Indels: 20
0.68 0.20 0.11
Matches are distributed among these distances:
22 1 0.01
23 11 0.09
24 7 0.06
25 26 0.22
26 74 0.62
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAGCTCACAAA
Found at i:28672853 original size:65 final size:65
Alignment explanation
Indices: 28672784--28672943 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 65
28672774 ATATCAGGAT
* * * * *
28672784 GCTCACAAAGAGCTGCGTTTGAGTCTGCAACATATGTAGGATCACAGCCGATCATAAAACAAGAC
1 GCTCACAAAGAGCTGCGTTTCAGTCCGCAACATATGCAAGATCACAACCGATCATAAAACAAGAC
* * * * ** *
28672849 GCTCACAAAGAGCTACGTTTCTGTCCGCAATATATGCAAGATTACAACCGATCATTTAACAGGAC
1 GCTCACAAAGAGCTGCGTTTCAGTCCGCAACATATGCAAGATCACAACCGATCATAAAACAAGAC
*
28672914 GCTCACAAAGAGCTGCG-GT-AGTCCGCAACA
1 GCTCACAAAGAGCTGCGTTTCAGTCCGCAACA
28672944 CATACAGGAT
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
63 9 0.11
64 1 0.01
65 69 0.87
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (65 bp):
GCTCACAAAGAGCTGCGTTTCAGTCCGCAACATATGCAAGATCACAACCGATCATAAAACAAGAC
Found at i:28676654 original size:59 final size:59
Alignment explanation
Indices: 28676591--28676760 Score: 306
Period size: 59 Copynumber: 2.9 Consensus size: 59
28676581 TCAAGTTTGT
*
28676591 TTTACTAATCAAATGTTAGATTTTGTTA-ATACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACA-ACAATTAATACAATTAATAATTTGATAAA
28676650 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
28676709 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
28676761 AATAATTTGA
Statistics
Matches: 108, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
59 107 0.99
60 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:28678512 original size:6 final size:6
Alignment explanation
Indices: 28678501--28678530 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
28678491 GAATTTTTTT
28678501 TCACTA TCACTA TCACTA TCACTA TCACTA
1 TCACTA TCACTA TCACTA TCACTA TCACTA
28678531 CTATCAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
TCACTA
Found at i:28691319 original size:22 final size:21
Alignment explanation
Indices: 28691294--28691352 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
28691284 TAGATTATGA
*
28691294 TTTTTTGAAATTTTTCATGATTT
1 TTTTTTG-AATTTTTAATG-TTT
*
28691317 TTTTTTGGATTTTTAATGTTT
1 TTTTTTGAATTTTTAATGTTT
28691338 TTTTTT-AATTTTTAA
1 TTTTTTGAATTTTTAA
28691353 GTAAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.24
21 9 0.27
22 9 0.27
23 7 0.21
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.69
Consensus pattern (21 bp):
TTTTTTGAATTTTTAATGTTT
Found at i:28691338 original size:20 final size:20
Alignment explanation
Indices: 28691294--28691352 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
28691284 TAGATTATGA
*
28691294 TTTTTTGAAATTTTTCATGATTT
1 TTTTTTG-AATTTTTAATG--TT
*
28691317 TTTTTTGGATTTTTAATGTT
1 TTTTTTGAATTTTTAATGTT
*
28691337 TTTTTTTAATTTTTAA
1 TTTTTTGAATTTTTAA
28691353 GTAAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 16 0.50
22 9 0.28
23 7 0.22
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.69
Consensus pattern (20 bp):
TTTTTTGAATTTTTAATGTT
Found at i:28695359 original size:22 final size:22
Alignment explanation
Indices: 28695334--28695376 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28695324 TGTAATAATA
* *
28695334 ATATTTTAATTTTAGAATATAT
1 ATATATTAATTTTAAAATATAT
*
28695356 ATATATTAGTTTTAAAATATA
1 ATATATTAATTTTAAAATATA
28695377 ATTACATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
ATATATTAATTTTAAAATATAT
Found at i:28700964 original size:4 final size:4
Alignment explanation
Indices: 28700957--28701001 Score: 81
Period size: 4 Copynumber: 11.2 Consensus size: 4
28700947 CCTACCTACC
*
28700957 TACA TACA TACA TACA TACT TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T
28701002 GTATATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (4 bp):
TACA
Found at i:28701183 original size:48 final size:48
Alignment explanation
Indices: 28701112--28701203 Score: 184
Period size: 48 Copynumber: 1.9 Consensus size: 48
28701102 GTTAGCTGCG
28701112 GCAGTATATTGGATATTATTATAGAATGAGAGAGCAAACAGACATGCA
1 GCAGTATATTGGATATTATTATAGAATGAGAGAGCAAACAGACATGCA
28701160 GCAGTATATTGGATATTATTATAGAATGAGAGAGCAAACAGACA
1 GCAGTATATTGGATATTATTATAGAATGAGAGAGCAAACAGACA
28701204 GTTTGAAGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (48 bp):
GCAGTATATTGGATATTATTATAGAATGAGAGAGCAAACAGACATGCA
Found at i:28711327 original size:34 final size:33
Alignment explanation
Indices: 28711283--28711347 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
28711273 TTTTTTTGAG
*
28711283 TTAAATTTGGCCATCAAATCTTTTTTTAAAAAAA
1 TTAAAATTGGCCAT-AAATCTTTTTTTAAAAAAA
* * *
28711317 TTAAAATTGGCTATTAATCTTTTTTTTAAAA
1 TTAAAATTGGCCATAAATCTTTTTTTAAAAA
28711348 GAGTTGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 15 0.56
34 12 0.44
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.46
Consensus pattern (33 bp):
TTAAAATTGGCCATAAATCTTTTTTTAAAAAAA
Found at i:28720851 original size:16 final size:16
Alignment explanation
Indices: 28720830--28720862 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28720820 TTAAATTAAA
*
28720830 TTTAATTAATTAATTT
1 TTTAATTAAATAATTT
28720846 TTTAATTAAATAATTT
1 TTTAATTAAATAATTT
28720862 T
1 T
28720863 CTCAACTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAATTAAATAATTT
Found at i:28721739 original size:17 final size:17
Alignment explanation
Indices: 28721717--28721751 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
28721707 CAATCATCCA
*
28721717 CTTAGGATTAATGTATG
1 CTTAGGATTAAGGTATG
28721734 CTTAGGATTAAGGTATG
1 CTTAGGATTAAGGTATG
28721751 C
1 C
28721752 CACACTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.37
Consensus pattern (17 bp):
CTTAGGATTAAGGTATG
Found at i:28724460 original size:239 final size:239
Alignment explanation
Indices: 28724041--28724729 Score: 1143
Period size: 239 Copynumber: 2.9 Consensus size: 239
28724031 TAAACCTATG
* * **
28724041 ATGATTATAATATTTGCCACTCCTAGCTAAGAATCTCCTTTCAGTCTCATCCTAGACTAAAAGAT
1 ATGATTATAATGTTTGTCACTTTTAGCTAAGAATCTCCTTTCAGTCTCATCCTAGACTAAAAGAT
*
28724106 GCCACCTAGGTTCTCCTCTCGGTCTCACCTAGGCATATAAATCTTCTCTTGGTTTCACTATTCGA
66 GCCACCTAGGTTCTCCTCTCGGTCTCACCTAGGCATATAGATCTTCTCTTGGTTTCACTATTCGA
28724171 CACAAGTGTATCAAATTCCTATACGATAGAGTCTCCTCTTAGTCTCATCTATCTAAATCTTCCAT
131 CACAAGTGTATCAAATTCCTATACGATAGAGTCTCCTCTTAGTCTCATCTATCTAAATCTTCCAT
28724236 TAGAGGCGTCAATTCTAGTATAATATGCAATTTAATACACTTGA
196 TAGAGGCGTCAATTCTAGTATAATATGCAATTTAATACACTTGA
28724280 ATGATTATAATGTTTGTCACTTTTAGCTAAGAATCTCCTTTCAGTCTCATCCTAGACTAAAAGAT
1 ATGATTATAATGTTTGTCACTTTTAGCTAAGAATCTCCTTTCAGTCTCATCCTAGACTAAAAGAT
28724345 GCCACCTAGGTTCTCCTCTCGGTCTCACCTAGGCATATAGATCTTCTCTTGGTTTCACTATTCGA
66 GCCACCTAGGTTCTCCTCTCGGTCTCACCTAGGCATATAGATCTTCTCTTGGTTTCACTATTCGA
28724410 CACAAGTGTATCAAATTCCTATACGATAGAGTCTCCTCTTAGTCTCATCTATCTAAATCTTCCAT
131 CACAAGTGTATCAAATTCCTATACGATAGAGTCTCCTCTTAGTCTCATCTATCTAAATCTTCCAT
* *
28724475 TAAAAGCGTCAATTCTAGTATAATATGCAATTTAATACACTTGA
196 TAGAGGCGTCAATTCTAGTATAATATGCAATTTAATACACTTGA
* *
28724519 ATGATTATAATGGTTGTCACTTTTAGCTAATAATCTCCTTTC-GATCTCATCCTAGACTAAAAGA
1 ATGATTATAATGTTTGTCACTTTTAGCTAAGAATCTCCTTTCAG-TCTCATCCTAGACTAAAAGA
* * * * *
28724583 TGCTTA-CTAGGTTCT-CTCTCGATCTCACCT-GGACATATAGATCTCCTCTTGATCTCACTATT
65 TGC-CACCTAGGTTCTCCTCTCGGTCTCACCTAGG-CATATAGATCTTCTCTTGGTTTCACTATT
* * * * *
28724645 CGACACAAGTGTATGAAAGTCCTACACGATATAGTCTCCTCTCAGTCTCATCTATCTAAATCTTC
128 CGACACAAGTGTATCAAATTCCTATACGATAGAGTCTCCTCTTAGTCTCATCTATCTAAATCTTC
*
28724710 CACTAGAGGCGTCAATTCTA
193 CATTAGAGGCGTCAATTCTA
28724730 TTATTGTTGG
Statistics
Matches: 425, Mismatches: 22, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
237 2 0.00
238 118 0.28
239 304 0.72
240 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (239 bp):
ATGATTATAATGTTTGTCACTTTTAGCTAAGAATCTCCTTTCAGTCTCATCCTAGACTAAAAGAT
GCCACCTAGGTTCTCCTCTCGGTCTCACCTAGGCATATAGATCTTCTCTTGGTTTCACTATTCGA
CACAAGTGTATCAAATTCCTATACGATAGAGTCTCCTCTTAGTCTCATCTATCTAAATCTTCCAT
TAGAGGCGTCAATTCTAGTATAATATGCAATTTAATACACTTGA
Found at i:28726551 original size:12 final size:12
Alignment explanation
Indices: 28726536--28726561 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28726526 AAAAGAAAAG
28726536 AAAACCTAAACT
1 AAAACCTAAACT
28726548 AAAACCTAAACT
1 AAAACCTAAACT
28726560 AA
1 AA
28726562 GAGCTATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAACCTAAACT
Found at i:28735194 original size:16 final size:15
Alignment explanation
Indices: 28735175--28735208 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
28735165 AAAATAAAAT
28735175 AAAATATTAATATTTA
1 AAAATATTAATA-TTA
28735191 AAAATATTAATATTA
1 AAAATATTAATATTA
28735206 AAA
1 AAA
28735209 TATAGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATTAATATTA
Found at i:28735225 original size:8 final size:8
Alignment explanation
Indices: 28735174--28735228 Score: 53
Period size: 8 Copynumber: 6.9 Consensus size: 8
28735164 TAAAATAAAA
28735174 TAAAATAT
1 TAAAATAT
*
28735182 TAATAT-T
1 TAAAATAT
28735189 TAAAAATAT
1 T-AAAATAT
28735198 T--AATAT
1 TAAAATAT
28735204 TAAAATAT
1 TAAAATAT
28735212 AGTAAAATAT
1 --TAAAATAT
28735222 TAAAATA
1 TAAAATA
28735229 AAATTGTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
6 6 0.15
7 2 0.05
8 21 0.54
9 2 0.05
10 8 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (8 bp):
TAAAATAT
Found at i:28735288 original size:26 final size:25
Alignment explanation
Indices: 28735245--28735295 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
28735235 TTATACTTTT
28735245 TAATTTTATTTTATATTAAAATATA
1 TAATTTTATTTTATATTAAAATATA
*
28735270 TAATTTTATATTTATATTAATATATA
1 TAATTTTAT-TTTATATTAAAATATA
28735296 AATATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TAATTTTATTTTATATTAAAATATA
Found at i:28739706 original size:24 final size:24
Alignment explanation
Indices: 28739635--28739706 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
28739625 TATAACAGAA
* *
28739635 AGCTCACAAAGAGC-CTATAACGGAT
1 AGCTC-CAAAGAGCAAT-TAACGGGT
* *
28739660 AGCTCCAAATAGTAATTAACGGGT
1 AGCTCCAAAGAGCAATTAACGGGT
*
28739684 AGCTCCGAAGAGCAATTAACGGG
1 AGCTCCAAAGAGCAATTAACGGG
28739707 AAGCATCGGA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
24 33 0.85
25 6 0.15
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.18
Consensus pattern (24 bp):
AGCTCCAAAGAGCAATTAACGGGT
Found at i:28739812 original size:26 final size:26
Alignment explanation
Indices: 28739753--28739813 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
28739743 AGCACTAAAG
* *
28739753 GGAAGCTCACAAAGAGCCTTTAATCG
1 GGAAGCTCACAAAGAGCCTATAATCC
*
28739779 GGAAGCTCACGAAGAGCCATATAA-CC
1 GGAAGCTCACAAAGAGCC-TATAATCC
*
28739805 GGACGCTCA
1 GGAAGCTCA
28739814 TAAGAGCTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCTATAATCC
Found at i:28743426 original size:27 final size:27
Alignment explanation
Indices: 28743388--28743445 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
28743378 CTATATATAG
**
28743388 AGTCTGCTGGGATAGTAAACATTAGGT
1 AGTCTGCTGGGATAGTAAACACGAGGT
*
28743415 AGTCTGCTGGGATATTAAACACGAGGT
1 AGTCTGCTGGGATAGTAAACACGAGGT
28743442 AGTC
1 AGTC
28743446 CGTTAGGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (27 bp):
AGTCTGCTGGGATAGTAAACACGAGGT
Found at i:28748774 original size:23 final size:23
Alignment explanation
Indices: 28748748--28748797 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
28748738 GCTCGATTTG
*
28748748 TTTAGCATTTGCGAACATGTTCA
1 TTTAGCATTCGCGAACATGTTCA
* *
28748771 TTTAGCATTCGTGAACATGTTCG
1 TTTAGCATTCGCGAACATGTTCA
28748794 TTTA
1 TTTA
28748798 ATGCTCGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (23 bp):
TTTAGCATTCGCGAACATGTTCA
Found at i:28749203 original size:3 final size:3
Alignment explanation
Indices: 28749195--28749224 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
28749185 TTGTTTGATC
28749195 TAT TAT TAT TAT TAT TAT TAT TAAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA
28749225 AAGAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:28753636 original size:4 final size:4
Alignment explanation
Indices: 28753620--28753650 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
28753610 AAGTTTTATT
28753620 TTTA TTT- TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
28753651 CTTAGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:28759420 original size:38 final size:39
Alignment explanation
Indices: 28759368--28759449 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
28759358 ATTTGTCGGC
* *
28759368 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTAATTAGGCACTTTATGTGCCGAATACTGTTACTG
* * *
28759406 TTACTAATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTAATTAGGCACTTTATGTGCCGAATACTGTTACTG
28759445 TTACT
1 TTACT
28759450 GTTACCGACC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
38 13 0.34
39 25 0.66
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (39 bp):
TTACTAATTAGGCACTTTATGTGCCGAATACTGTTACTG
Found at i:28759464 original size:45 final size:45
Alignment explanation
Indices: 28759395--28759589 Score: 273
Period size: 45 Copynumber: 4.3 Consensus size: 45
28759385 ATGTGCCGAC
** *
28759395 TACTGTTACTGTTACTAATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
*
28759440 TACTGTTACTGTTACCGACCCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
28759485 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
* * * * * * *
28759530 TACCGCTACCGTTACAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
* *
28759575 TACTGCTACCGTTAC
1 TACTGTTACTGTTAC
28759590 TGATTACTGT
Statistics
Matches: 137, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 137 1.00
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (45 bp):
TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
Found at i:28761067 original size:17 final size:19
Alignment explanation
Indices: 28761031--28761071 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
28761021 ACTTCCCGAA
*
28761031 AAAAAATTACATATATTTT
1 AAAAAATTACATATAATTT
28761050 AAAAAA-TACAT-TAATTT
1 AAAAAATTACATATAATTT
28761067 AAAAA
1 AAAAA
28761072 TAATAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 5 0.24
19 6 0.29
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAAATTACATATAATTT
Found at i:28777653 original size:19 final size:19
Alignment explanation
Indices: 28777629--28777670 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28777619 TGCAGCTTTT
28777629 TTTTTTACTATTCTTGCTA
1 TTTTTTACTATTCTTGCTA
* * *
28777648 TTTTTTTCTTTTTTTGCTA
1 TTTTTTACTATTCTTGCTA
28777667 TTTT
1 TTTT
28777671 CTTGTTGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTTTACTATTCTTGCTA
Found at i:28777681 original size:19 final size:19
Alignment explanation
Indices: 28777642--28777681 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28777632 TTTACTATTC
* *
28777642 TTGCTATTTTTTTCTTTTT
1 TTGCTATTTTCTTCTTGTT
*
28777661 TTGCTATTTTCTTGTTGTT
1 TTGCTATTTTCTTCTTGTT
28777680 TT
1 TT
28777682 TTTCACCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.10, G:0.10, T:0.75
Consensus pattern (19 bp):
TTGCTATTTTCTTCTTGTT
Found at i:28786266 original size:25 final size:25
Alignment explanation
Indices: 28786229--28786312 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
28786219 TACCGATTGC
* * * *
28786229 AGCTCATAAGAGCTTATCGATTCGT
1 AGCTCGTATGAGCTTACCGATTCAT
* *
28786254 AGCTCGTATGAGCTTACCGATTTAC
1 AGCTCGTATGAGCTTACCGATTCAT
*
28786279 AGCTCGTGA-GAGCATACCGATTCAT
1 AGCTCGT-ATGAGCTTACCGATTCAT
28786304 AGCTCGTAT
1 AGCTCGTAT
28786313 CTGTAAACTA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
24 1 0.02
25 46 0.96
26 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATTCAT
Found at i:28786300 original size:50 final size:49
Alignment explanation
Indices: 28786218--28786312 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 49
28786208 TCATTAAGGA
* * * *
28786218 TTACCGATTGCAGCTCATAAGAGCTTATCGATTCGTAGCTCGTATGAGC
1 TTACCGATTACAGCTCATAAGAGCATACCGATTCATAGCTCGTATGAGC
* *
28786267 TTACCGATTTACAGCTCGTGAGAGCATACCGATTCATAGCTCGTAT
1 TTACCGA-TTACAGCTCATAAGAGCATACCGATTCATAGCTCGTAT
28786313 CTGTAAACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 7 0.18
50 32 0.82
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (49 bp):
TTACCGATTACAGCTCATAAGAGCATACCGATTCATAGCTCGTATGAGC
Found at i:28787390 original size:15 final size:16
Alignment explanation
Indices: 28787370--28787399 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28787360 TGGTGCCTTA
28787370 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
28787385 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
28787400 GGCATATGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:28790704 original size:15 final size:15
Alignment explanation
Indices: 28790682--28790718 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
28790672 ATGAAGATTT
28790682 AAAA-AAAAAAAGA-
1 AAAAGAAAAAAAGAG
28790695 AAAATGAAAAAAAGAG
1 AAAA-GAAAAAAAGAG
28790711 AAAAGAAA
1 AAAAGAAA
28790719 TGATAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.19
15 13 0.62
16 4 0.19
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAAGAAAAAAAGAG
Found at i:28799306 original size:11 final size:13
Alignment explanation
Indices: 28799292--28799325 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
28799282 AATTTTACGA
28799292 AAAAATTTCG-T-
1 AAAAATTTCGTTC
28799303 AAAAATTTCGTTC
1 AAAAATTTCGTTC
28799316 AAAAATTTCG
1 AAAAATTTCG
28799326 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:28800566 original size:33 final size:33
Alignment explanation
Indices: 28800497--28800656 Score: 107
Period size: 33 Copynumber: 4.7 Consensus size: 33
28800487 ATGTGAAGGG
*
28800497 GGTTGCTAAGTGCTGATTCCCC---TGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
28800524 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* ** * *
28800557 GGTTGCTAAGTGTTGAACCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG---GT
* *
28800599 GGTTGCTAAGTGTTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
28800632 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
28800657 TAACGGTTAA
Statistics
Matches: 104, Mismatches: 13, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
27 22 0.21
30 2 0.02
32 2 0.02
33 36 0.35
34 10 0.10
36 2 0.02
37 2 0.02
38 2 0.02
39 2 0.02
41 5 0.05
42 19 0.18
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:28800566 original size:102 final size:102
Alignment explanation
Indices: 28800390--28800620 Score: 363
Period size: 102 Copynumber: 2.3 Consensus size: 102
28800380 ATTGAATATA
* *
28800390 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
**
28800455 GATTACTAAGTGCTGATTCCACCGTATCTTAAATGTG
66 GATTACTAAGTGCTGAACCCACCGTATCTTAAATGTG
**
28800492 AAGGGGGTTGCTAAGTGCTGATTCCCCTGAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
28800557 GGTTGCTAAGTGTTGAACCCACCGTATCTTAAATGTG
66 GATTACTAAGTGCTGAACCCACCGTATCTTAAATGTG
* *
28800594 AAAGGGGTTGCTAAGTGTTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
28800621 GACTCATTGG
Statistics
Matches: 118, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 118 1.00
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
GATTACTAAGTGCTGAACCCACCGTATCTTAAATGTG
Found at i:28803802 original size:21 final size:22
Alignment explanation
Indices: 28803763--28803805 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
28803753 AATAAACATC
28803763 ATAAATTAATTCAAATAAATAA
1 ATAAATTAATTCAAATAAATAA
* *
28803785 ATAAATT-TTTCAATTAAATAA
1 ATAAATTAATTCAAATAAATAA
28803806 GTTTCTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAAATTAATTCAAATAAATAA
Found at i:28807204 original size:45 final size:45
Alignment explanation
Indices: 28807133--28807344 Score: 225
Period size: 45 Copynumber: 4.7 Consensus size: 45
28807123 TTTTCAAGGA
* * * * * *
28807133 TGCCATAGCGTCTTTCAGCCACGGTCTTATTAATTTCCGACAT-G
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGATATAG
28807177 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCC-AGTATAG
1 -TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGA-TATAG
* ** *
28807223 TGTCATAGTGTCTTTCAACTATGGTAGTATTCATTTCCGGTATAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGATATAG
* *
28807268 TGCCATAGTGTCTTTCAATTATGGTCTTATTCATTT-CTAGTATAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGA-TATAG
* * *
28807313 TGTCACCA-TATCTTTCAACTATGGTCTTATTC
1 TGCCA-TAGTGTCTTTCAACTATGGTCTTATTC
28807345 GTTTTTCAAG
Statistics
Matches: 142, Mismatches: 20, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
44 2 0.01
45 138 0.97
46 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (45 bp):
TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGATATAG
Found at i:28807214 original size:21 final size:21
Alignment explanation
Indices: 28807190--28807259 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
28807180 CCATAGTGTC
*
28807190 TTTCAACTATGGTCTTATTCA
1 TTTCAACTATGGTCATATTCA
* *
28807211 TTTCCAGTATAGTGTCATAGTGTC-
1 TTTCAACTAT-G-GTCATA-T-TCA
28807235 TTTCAACTATGGT-AGTATTCA
1 TTTCAACTATGGTCA-TATTCA
28807256 TTTC
1 TTTC
28807260 CGGTATAGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
20 2 0.05
21 14 0.37
22 5 0.13
23 6 0.16
24 9 0.24
25 2 0.05
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (21 bp):
TTTCAACTATGGTCATATTCA
Found at i:28807344 original size:90 final size:90
Alignment explanation
Indices: 28807155--28807344 Score: 267
Period size: 90 Copynumber: 2.1 Consensus size: 90
28807145 TTTCAGCCAC
*
28807155 GGTCTTATTAATTTCCGACATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGTA
1 GGTCTTATTCATTTCCGACATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGTA
* *
28807220 TAGTGTCATAGTGTCTTTCAACTAT
66 TAGTGTCACAGTATCTTTCAACTAT
** ** * *
28807245 GGTAGTATTCATTTCCGGTAT-AGTGCCATAGTGTCTTTCAATTATGGTCTTATTCATTTCTAGT
1 GGTCTTATTCATTTCCGACATGA-TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGT
28807309 ATAGTGTCACCA-TATCTTTCAACTAT
65 ATAGTGTCA-CAGTATCTTTCAACTAT
28807335 GGTCTTATTC
1 GGTCTTATTC
28807345 GTTTTTCAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
89 1 0.01
90 85 0.98
91 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (90 bp):
GGTCTTATTCATTTCCGACATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGTA
TAGTGTCACAGTATCTTTCAACTAT
Found at i:28809493 original size:45 final size:45
Alignment explanation
Indices: 28809443--28809530 Score: 176
Period size: 45 Copynumber: 2.0 Consensus size: 45
28809433 CATATTCAAG
28809443 TATGTAATTATAAACACCAATCTCACAACAACATATTACTAAAAT
1 TATGTAATTATAAACACCAATCTCACAACAACATATTACTAAAAT
28809488 TATGTAATTATAAACACCAATCTCACAACAACATATTACTAAA
1 TATGTAATTATAAACACCAATCTCACAACAACATATTACTAAA
28809531 CTTACATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.28
Consensus pattern (45 bp):
TATGTAATTATAAACACCAATCTCACAACAACATATTACTAAAAT
Found at i:28810289 original size:73 final size:73
Alignment explanation
Indices: 28810186--28810369 Score: 228
Period size: 73 Copynumber: 2.5 Consensus size: 73
28810176 CGAGCTGTAG
* * *
28810186 ATATAATCGTGGCAGGCTACCCCT-TCGGGCTAAACCTTTATATAAATACATCAATTGCTCA-TC
1 ATATAATCGTGTCAGGTTACCCATCT-GGGCTAAACCTTTATATAAATACATCAATTGCTCATTC
* *
28810249 TGAGCTGACC
65 -GAACTGAAC
* * * * *
28810259 ATATAATCGTATCAGGTTACCCGTCTGGGCTAAACCTTTATATGAATACATCAGTTGCTCGTTCG
1 ATATAATCGTGTCAGGTTACCCATCTGGGCTAAACCTTTATATAAATACATCAATTGCTCATTCG
28810324 AACTGAAC
66 AACTGAAC
* *
28810332 ATATAATTGTGTCAGGTTACCTATCTGGGCTAAACCTT
1 ATATAATCGTGTCAGGTTACCCATCTGGGCTAAACCTT
28810370 AATGTAGACA
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
73 93 0.97
74 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (73 bp):
ATATAATCGTGTCAGGTTACCCATCTGGGCTAAACCTTTATATAAATACATCAATTGCTCATTCG
AACTGAAC
Found at i:28813400 original size:16 final size:16
Alignment explanation
Indices: 28813379--28813415 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
28813369 TTGGTTCGCT
*
28813379 GTAATGGAATAGGGGC
1 GTAATGGAATAGAGGC
28813395 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
28813411 GTAAT
1 GTAAT
28813416 AGGTAATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.38, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:28813693 original size:18 final size:17
Alignment explanation
Indices: 28813649--28813782 Score: 102
Period size: 17 Copynumber: 8.0 Consensus size: 17
28813639 TTATTATTAA
28813649 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28813666 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
28813683 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
* * *
28813701 -CATAATAT-ATAATACT
1 ATATAATTTAATAA-AAT
* *
28813717 ATAAAATATAACTTAAAAT
1 ATATAATTTAA--TAAAAT
*
28813736 A-ATAA-TT-AT-TAA-
1 ATATAATTTAATAAAAT
*
28813748 ATATAATTTAACAAAAAT
1 ATATAATTTAA-TAAAAT
28813766 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28813783 TCTTAGTGTT
Statistics
Matches: 91, Mismatches: 14, Indels: 24
0.71 0.11 0.19
Matches are distributed among these distances:
12 1 0.01
13 6 0.07
14 3 0.03
15 4 0.04
16 7 0.08
17 37 0.41
18 27 0.30
19 3 0.03
20 3 0.03
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28813783 original size:28 final size:30
Alignment explanation
Indices: 28813704--28813783 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 30
28813694 CTAAAATCAT
* * *
28813704 AATATATAATACT-ATAAAATATAACTTAA
1 AATATATAATATTAATAAAATTTAACTAAA
*
28813733 AATA-ATAATTATTAAATATAATTTAAC-AAA
1 AATATATAA-TATT-AATAAAATTTAACTAAA
28813763 AATATATAAT-TTAATAAAATT
1 AATATATAATATTAATAAAATT
28813784 CTTAGTGTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
28 12 0.29
29 9 0.21
30 7 0.17
31 14 0.33
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (30 bp):
AATATATAATATTAATAAAATTTAACTAAA
Found at i:28813855 original size:21 final size:21
Alignment explanation
Indices: 28813812--28813855 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28813802 TATATGAATT
*
28813812 TACTAAAATCATAATATATAA
1 TACTAAAATCATAATATAAAA
*
28813833 TACTATAAAT-ATAATTTAAAA
1 TACTA-AAATCATAATATAAAA
28813854 TA
1 TA
28813856 ATTATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (21 bp):
TACTAAAATCATAATATAAAA
Done.