Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 2 of 311
Found at i:397023 original size:19 final size:19
Alignment explanation
Indices: 397001--397092 Score: 73
Period size: 19 Copynumber: 4.8 Consensus size: 19
396991 CTTCTATATA
397001 TTTTATAATTTTTTACAAT
1 TTTTATAATTTTTTACAAT
***
397020 TTTTATAAAAGTTTACAATT
1 TTTTATAATTTTTTACAA-T
* *
397040 TTTTTTATATTTTTTACTA-
1 TTTTATA-ATTTTTTACAAT
397059 TTTTAT-ATTTTTT-CTAAT
1 TTTTATAATTTTTTAC-AAT
*
397077 TGTTATTAATTTTTTA
1 TTTTA-TAATTTTTTA
397093 ATATTTGAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
16 1 0.02
17 8 0.15
18 4 0.07
19 21 0.38
20 14 0.25
21 7 0.13
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:397025 original size:57 final size:57
Alignment explanation
Indices: 396947--397071 Score: 148
Period size: 57 Copynumber: 2.2 Consensus size: 57
396937 TTACATTTTG
* * *
396947 TATAATTTTCTTACGACTTTATAAAATTTTA-TATTTTTTTTATACTTCTATA-TATTT
1 TATAATTTT-TTACAACTTTATAAAAGTTTACAATTTTTTTTATA-TTCTATACTATTT
* * *
397004 TATAATTTTTTACAATTTTTATAAAAGTTTACAATTTTTTTTATATTTTTTACTATTT
1 TATAATTTTTTACAA-CTTTATAAAAGTTTACAATTTTTTTTATATTCTATACTATTT
397062 TAT-ATTTTTT
1 TATAATTTTTT
397072 CTAATTGTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
56 5 0.08
57 34 0.58
58 20 0.34
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (57 bp):
TATAATTTTTTACAACTTTATAAAAGTTTACAATTTTTTTTATATTCTATACTATTT
Found at i:397064 original size:17 final size:17
Alignment explanation
Indices: 397042--397108 Score: 66
Period size: 17 Copynumber: 3.8 Consensus size: 17
397032 TTACAATTTT
397042 TTTTATATTTTTTACTA
1 TTTTATATTTTTTACTA
397059 TTTTATATTTTTT-CTAA
1 TTTTATATTTTTTACT-A
*
397076 TTGTTATTAATTTTTTAATA
1 TT-TTA-T-ATTTTTTACTA
*
397096 TTTGA-ATTTTTTA
1 TTTTATATTTTTTA
397109 TTAAAATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
16 10 0.23
17 16 0.37
18 3 0.07
19 3 0.07
20 10 0.23
21 1 0.02
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTATATTTTTTACTA
Found at i:397365 original size:92 final size:90
Alignment explanation
Indices: 397168--397395 Score: 230
Period size: 92 Copynumber: 2.5 Consensus size: 90
397158 AATTTTTAAT
* * * *
397168 AAAAA-CAAAGACTTAATTATTTTTTTAAAAAAGATTTGAGGGTCTTTTTTATGCATTTTGAAAG
1 AAAAAGCAAAGGCTTAATTGTTTTTTT-GAAAAGATTTGAGGG-CTTTTTTATGCATTTTAAAAG
*
397232 TTCAATTATCCAATGGAGTGCAAAAAA
64 TTCAAGTATCCAATGGAGTGCAAAAAA
**** *
397259 AAAAAGTGGGGGCTTAATTGCTTTTTTTGAAAAGGTTTGAGGGCTTTGTTTATGCATTTTAAAAG
1 AAAAAGCAAAGGCTTAATTG-TTTTTTTGAAAAGATTTGAGGGCTTT-TTTATGCATTTTAAAAG
*
397324 TTTAAGTA-CCTAAAT-GAGTG-AAAAAA
64 TTCAAGTATCC--AATGGAGTGCAAAAAA
* * *
397350 GAAGAAGCAAAGGCTTAAATGTATTTTTTGAAAAAATTTGAGGGCT
1 -AAAAAGCAAAGGCTTAATTGT-TTTTTTGAAAAGATTTGAGGGCT
397396 AATAATATAA
Statistics
Matches: 111, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
91 18 0.16
92 83 0.75
93 10 0.09
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (90 bp):
AAAAAGCAAAGGCTTAATTGTTTTTTTGAAAAGATTTGAGGGCTTTTTTATGCATTTTAAAAGTT
CAAGTATCCAATGGAGTGCAAAAAA
Found at i:403766 original size:51 final size:53
Alignment explanation
Indices: 403670--403770 Score: 134
Period size: 51 Copynumber: 1.9 Consensus size: 53
403660 TGGTAATAGA
403670 AACAGTAACAGTAACGGTACACAGAATACCTCATCGGAACAAATCCGGAATAAT
1 AACAGTAACAGTAACGGTA-ACAGAATACCTCATCGGAACAAATCCGGAATAAT
* * * **
403724 AACAGTAACAGTAA-GGT-ACGGAGTACCTCTTCGGAATGAATCCGGAA
1 AACAGTAACAGTAACGGTAACAGAATACCTCATCGGAACAAATCCGGAA
403771 CAGTAACAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 25 0.60
53 3 0.07
54 14 0.33
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (53 bp):
AACAGTAACAGTAACGGTAACAGAATACCTCATCGGAACAAATCCGGAATAAT
Found at i:405094 original size:20 final size:21
Alignment explanation
Indices: 405071--405118 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
405061 TATAATTATT
*
405071 TAATTAATAAATATCT-TTTA
1 TAATTAATAAATATCTATTAA
405091 TAATTAATAAATATCTATTAA
1 TAATTAATAAATATCTATTAA
405112 TAATTAA
1 TAATTAA
405119 ATACATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATTAATAAATATCTATTAA
Found at i:409253 original size:16 final size:16
Alignment explanation
Indices: 409232--409270 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
409222 TCATTTATTA
409232 AATAAAA-ATAATTTT
1 AATAAAACATAATTTT
*
409247 AATTAAAACATTATTTT
1 AA-TAAAACATAATTTT
409264 AATAAAA
1 AATAAAA
409271 TGATTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 10 0.48
17 9 0.43
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAAAACATAATTTT
Found at i:411632 original size:22 final size:19
Alignment explanation
Indices: 411587--411636 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 19
411577 TTTGTTTCAT
*
411587 GAAAAATAATTTAGTCAAT
1 GAAAAATAATTTAGTCAAC
*
411606 AAAAAATAACTTATAGGTCAAC
1 GAAAAATAA-TT-TA-GTCAAC
411628 GAAAAATAA
1 GAAAAATAA
411637 ATTCATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 8 0.32
20 2 0.08
21 2 0.08
22 13 0.52
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.24
Consensus pattern (19 bp):
GAAAAATAATTTAGTCAAC
Found at i:411782 original size:19 final size:17
Alignment explanation
Indices: 411752--411794 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
411742 TAATATTACT
*
411752 ATATTAATAATAATTTTAA
1 ATATTAAAAAT-A-TTTAA
*
411771 ATTTTAAAAATATTTAA
1 ATATTAAAAATATTTAA
411788 ATATTAA
1 ATATTAA
411795 GATCAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 11 0.52
18 1 0.05
19 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTAAAAATATTTAA
Found at i:416539 original size:24 final size:22
Alignment explanation
Indices: 416496--416539 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
416486 AGAAAATTGA
**
416496 TTTTTTTTTCAAATTTTTAAGT
1 TTTTTTTTTCAAATGATTAAGT
416518 TTTTTTTTTCAAGAATGATTAA
1 TTTTTTTTTC-A-AATGATTAA
416540 ATATAAATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 1 0.06
24 7 0.39
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTTTTTTTCAAATGATTAAGT
Found at i:423631 original size:27 final size:27
Alignment explanation
Indices: 423583--423687 Score: 108
Period size: 27 Copynumber: 3.9 Consensus size: 27
423573 GCGAGGCTGC
* * *
423583 CAGATATTGTGAC-GAAGTCACCAAATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
423610 CAGATATTGTTGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
423636 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
423663 CAGATAATCGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
423688 GACGCTTCCT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
26 8 0.12
27 56 0.84
28 3 0.04
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:425326 original size:26 final size:26
Alignment explanation
Indices: 425295--425402 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
425285 TGAAATGCCC
425295 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
425321 ATCATGGAACATTTACCT-AACTCATT
1 ATCATGGAACATTTACCTAAAC-CATT
* *
425347 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
*
425373 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
425399 ATCA
1 ATCA
425403 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
25 3 0.04
26 71 0.93
27 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:431347 original size:12 final size:12
Alignment explanation
Indices: 431332--431365 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
431322 TGGGTTTCTA
431332 TGGACCTTACGG
1 TGGACCTTACGG
431344 TGGACCTTACGG
1 TGGACCTTACGG
431356 TGGACCTTAC
1 TGGACCTTAC
431366 AGTGAGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (12 bp):
TGGACCTTACGG
Found at i:434678 original size:16 final size:16
Alignment explanation
Indices: 434659--434695 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
434649 TTCGAGTTCG
* *
434659 AATTATTTCAGATTTA
1 AATTATTTCAAATTCA
434675 AATTATTTCAAATTCA
1 AATTATTTCAAATTCA
434691 AATTA
1 AATTA
434696 ATTTTGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (16 bp):
AATTATTTCAAATTCA
Found at i:446452 original size:14 final size:14
Alignment explanation
Indices: 446430--446459 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
446420 TAGACTCGCA
*
446430 GACATACAAGATGC
1 GACACACAAGATGC
446444 GACACACAAGATGC
1 GACACACAAGATGC
446458 GA
1 GA
446460 GCTATCTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
GACACACAAGATGC
Found at i:446495 original size:29 final size:29
Alignment explanation
Indices: 446453--446515 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
446443 CGACACACAA
*
446453 GATGCGAGCTATCTTGACACGCGAATTAC
1 GATGCGAGCTATCTTGACACGCGAACTAC
* * *
446482 GATGTGAGCTATCTTGACATGTGAACTAC
1 GATGCGAGCTATCTTGACACGCGAACTAC
446511 GATGC
1 GATGC
446516 TGTGAACTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (29 bp):
GATGCGAGCTATCTTGACACGCGAACTAC
Found at i:446988 original size:19 final size:19
Alignment explanation
Indices: 446943--447003 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
446933 ATCTAATTAC
446943 AAATATTTAATTATTATATTT
1 AAATATTTAATTA-TA-ATTT
*
446964 AAATATTTAAATATAATTT
1 AAATATTTAATTATAATTT
*
446983 ATATATTCTAATTA-AATTT
1 AAATATT-TAATTATAATTT
447002 AA
1 AA
447004 TAAATAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.46
20 7 0.20
21 12 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATTTAATTATAATTT
Found at i:449214 original size:16 final size:15
Alignment explanation
Indices: 449188--449218 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
449178 ACATTTATTC
449188 AAAATATTAAAAATT
1 AAAATATTAAAAATT
449203 AAAATAATTAAAAATT
1 AAAAT-ATTAAAAATT
449219 TTAGTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATATTAAAAATT
Found at i:451913 original size:29 final size:30
Alignment explanation
Indices: 451872--451928 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
451862 TACAGATAGT
* *
451872 CACCCAACTATAAAAAATTTTCAATTTAGG
1 CACCCAACAATAAAAAATTTCCAATTTAGG
451902 CACCCAA-AATAAAAAATTTCCAATTTA
1 CACCCAACAATAAAAAATTTCCAATTTA
451929 AGTTTCACGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.28
Consensus pattern (30 bp):
CACCCAACAATAAAAAATTTCCAATTTAGG
Found at i:452246 original size:15 final size:16
Alignment explanation
Indices: 452228--452261 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
452218 AAATAGTTTG
*
452228 AAAT-TTAATATTTTA
1 AAATATTAATATTGTA
452243 AAATATTAATATTGTA
1 AAATATTAATATTGTA
452259 AAA
1 AAA
452262 ATCTCCGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AAATATTAATATTGTA
Found at i:457562 original size:24 final size:24
Alignment explanation
Indices: 457534--457580 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
457524 TTCAACTTTA
457534 AGTTAGGTGACAAAACAATCACTT
1 AGTTAGGTGACAAAACAATCACTT
* *
457558 AGTTAGTTGATAAAACAATCACT
1 AGTTAGGTGACAAAACAATCACT
457581 CAGGTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (24 bp):
AGTTAGGTGACAAAACAATCACTT
Found at i:474668 original size:58 final size:60
Alignment explanation
Indices: 474549--474670 Score: 221
Period size: 58 Copynumber: 2.0 Consensus size: 60
474539 TATCTCTCTT
474549 TTTTTAATGGGAAATATTAACCAGACACTGATATTTTAATTTTTAAAAAAGTTAAATATTA
1 TTTTTAATGGGAAATATTAACCAGACACT-ATATTTTAATTTTTAAAAAAGTTAAATATTA
474610 TTTTTAATGGGAAATATTAACCAGACACT-T-TTTTAATTTTTAAAAAAGTTAAATATTA
1 TTTTTAATGGGAAATATTAACCAGACACTATATTTTAATTTTTAAAAAAGTTAAATATTA
474668 TTT
1 TTT
474671 ATTTAATTTC
Statistics
Matches: 61, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
58 31 0.51
59 1 0.02
61 29 0.48
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (60 bp):
TTTTTAATGGGAAATATTAACCAGACACTATATTTTAATTTTTAAAAAAGTTAAATATTA
Found at i:475203 original size:28 final size:28
Alignment explanation
Indices: 475172--475229 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
475162 TAAAATAAAA
* *
475172 AAATTTT-ATTAATATTTTTATAATTTAT
1 AAATTTTAATTAATAATTATA-AATTTAT
475200 AAATTTTAAATTAATAATTATAAATTTAT
1 AAATTTT-AATTAATAATTATAAATTTAT
475229 A
1 A
475230 TTTTATCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 7 0.27
29 8 0.31
30 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AAATTTTAATTAATAATTATAAATTTAT
Found at i:477947 original size:18 final size:18
Alignment explanation
Indices: 477924--478026 Score: 80
Period size: 18 Copynumber: 5.4 Consensus size: 18
477914 ACATTGTGAT
477924 CTGAAGCCCGAAGTCTAA
1 CTGAAGCCCGAAGTCTAA
**
477942 CTGAAGCACATAAGTGCTAAA
1 CTGAAGC-CCGAAGT-CT-AA
* *
477963 CAGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGTCTAA
**
477981 CTGAAGCACATAAGTGCTAAA
1 CTGAAGC-CCGAAGT-CT-AA
* *
478002 CGGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGTCTAA
478020 CTGAAGC
1 CTGAAGC
478027 ACACCAGAGC
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
18 23 0.36
19 13 0.20
20 12 0.19
21 16 0.25
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (18 bp):
CTGAAGCCCGAAGTCTAA
Found at i:477968 original size:21 final size:21
Alignment explanation
Indices: 477944--478008 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
477934 AAGTCTAACT
477944 GAAGCACATAAGTGCTAAACA
1 GAAGCACATAAGTGCTAAACA
** *
477965 GAAGC-CCGAAG-GCT-AACT
1 GAAGCACATAAGTGCTAAACA
*
477983 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACA
478004 GAAGC
1 GAAGC
478009 CCGAAGGCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
20 7 0.20
21 13 0.37
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACA
Found at i:477981 original size:39 final size:39
Alignment explanation
Indices: 477926--478029 Score: 190
Period size: 39 Copynumber: 2.7 Consensus size: 39
477916 ATTGTGATCT
*
477926 GAAGCCCGAAGTCTAACTGAAGCACATAAGTGCTAAACA
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACA
*
477965 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACA
478004 GAAGCCCGAAGGCTAACTGAAGCACA
1 GAAGCCCGAAGGCTAACTGAAGCACA
478030 CCAGAGCTGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.12
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACA
Found at i:479033 original size:18 final size:18
Alignment explanation
Indices: 479010--479054 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
479000 CAATTAACCC
479010 CTCAATTAAGATAATTTT
1 CTCAATTAAGATAATTTT
479028 CTCAATTAAGATAATTTT
1 CTCAATTAAGATAATTTT
479046 CTCAATTAA
1 CTCAATTAA
479055 TACTTTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (18 bp):
CTCAATTAAGATAATTTT
Found at i:481880 original size:29 final size:30
Alignment explanation
Indices: 481833--481921 Score: 108
Period size: 31 Copynumber: 3.0 Consensus size: 30
481823 TTGATTTAAT
* * *
481833 GTGCAATTATACACATG-AATTTTAATTTG
1 GTGCAATTATATACTTGAAACTTTAATTTG
481862 GTGCAATTATATACTTGAAACTTTAATTATG
1 GTGCAATTATATACTTGAAACTTTAATT-TG
* * *
481893 GTTCAAATGTATACTTGAAACTTTAATTT
1 GTGCAATTATATACTTGAAACTTTAATTT
481922 TAATTTAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
29 15 0.29
30 10 0.19
31 27 0.52
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (30 bp):
GTGCAATTATATACTTGAAACTTTAATTTG
Found at i:485558 original size:18 final size:19
Alignment explanation
Indices: 485537--485572 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
485527 TAAAAAATAA
485537 ATAAAT-TTTAGAATTTTC
1 ATAAATATTTAGAATTTTC
485555 ATAAATATTTAGAATTTT
1 ATAAATATTTAGAATTTT
485573 TCGTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (19 bp):
ATAAATATTTAGAATTTTC
Found at i:487750 original size:14 final size:14
Alignment explanation
Indices: 487722--487755 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
487712 TCCTATGAAA
487722 ATTAAATATATAAT
1 ATTAAATATATAAT
487736 ATTATAATATA-AAT
1 ATTA-AATATATAAT
487750 ATTAAA
1 ATTAAA
487756 AGAATATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 11 0.58
15 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAAATATATAAT
Found at i:495648 original size:18 final size:16
Alignment explanation
Indices: 495625--495664 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 16
495615 AATTTTCCTG
495625 TAATTTCACAAAATATTA
1 TAATTTCA-AAAAT-TTA
495643 TAATTT-AAAAATTTA
1 TAATTTCAAAAATTTA
495658 TAATTTC
1 TAATTTC
495665 TAATTTCGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 1 0.05
18 6 0.29
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTTCAAAAATTTA
Found at i:496398 original size:2 final size:2
Alignment explanation
Indices: 496391--496419 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
496381 CAGGCATCTA
496391 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
496420 CCTTCTCCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:501998 original size:80 final size:83
Alignment explanation
Indices: 501908--502070 Score: 233
Period size: 80 Copynumber: 2.0 Consensus size: 83
501898 TACTTTTTTA
* * * * *
501908 TCTTTAAATTTTAATGATGTGGCATTATTTTATTGGTTCGT-AAAAA-TAT-TTTTTTAGGATAA
1 TCTTTAAATTTTAATGATGTGGCACTATTTTATTGGTGCATAAAAAACTATACTTTTTAAGATAA
*
501970 TCCTAATAGAATTTATTC
66 TCCGAATAGAATTTATTC
*
501988 TCTTTAAATTTTAATGATGTGGCACTATTTTATTGGTGCATAAAAAACTATACTTTTTAAGATCA
1 TCTTTAAATTTTAATGATGTGGCACTATTTTATTGGTGCATAAAAAACTATACTTTTTAAGATAA
*
502053 TCCGAATATAATTTATTC
66 TCCGAATAGAATTTATTC
502071 CCTATTTAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
80 38 0.53
81 5 0.07
82 3 0.04
83 26 0.36
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.46
Consensus pattern (83 bp):
TCTTTAAATTTTAATGATGTGGCACTATTTTATTGGTGCATAAAAAACTATACTTTTTAAGATAA
TCCGAATAGAATTTATTC
Found at i:503872 original size:4 final size:4
Alignment explanation
Indices: 503863--503894 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
503853 ACAACTAGGA
503863 TGAG TGAG TGAG TGAG TGAG TGAG TGAG TGAG
1 TGAG TGAG TGAG TGAG TGAG TGAG TGAG TGAG
503895 ACAAGGCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
TGAG
Found at i:511624 original size:21 final size:21
Alignment explanation
Indices: 511600--511643 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
511590 TAATTAAAAA
511600 AATGTAATAAATAT-TTTTAAT
1 AATGT-ATAAATATATTTTAAT
* *
511621 AATGTCTACATATATTTTAAT
1 AATGTATAAATATATTTTAAT
511642 AA
1 AA
511644 AATTTACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (21 bp):
AATGTATAAATATATTTTAAT
Found at i:511651 original size:21 final size:20
Alignment explanation
Indices: 511610--511660 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
511600 AATGTAATAA
**
511610 ATATTTTTAATAATGTCTAC
1 ATATTTTTAATAAAATCTAC
*
511630 ATATATTTTAATAAAATTTAC
1 ATAT-TTTTAATAAAATCTAC
511651 ACT-TTTTTAA
1 A-TATTTTTAA
511661 ATGTTTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 10 0.38
21 15 0.58
22 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (20 bp):
ATATTTTTAATAAAATCTAC
Found at i:511847 original size:16 final size:14
Alignment explanation
Indices: 511811--511864 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 14
511801 AAAGATTTAA
511811 AAAAAAAACAAAA-
1 AAAAAAAACAAAAT
511824 AAACAAAAACAAAATT
1 AAA-AAAAACAAAA-T
*
511840 AAAGAAAAATAAAAT
1 AAA-AAAAACAAAAT
511855 GAAAAAAAAC
1 -AAAAAAAAC
511865 TCCAAACTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 3 0.09
14 10 0.29
15 6 0.18
16 15 0.44
ACGTcount: A:0.81, C:0.07, G:0.04, T:0.07
Consensus pattern (14 bp):
AAAAAAAACAAAAT
Found at i:512197 original size:22 final size:22
Alignment explanation
Indices: 512172--512215 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
512162 AAACAACGTA
* *
512172 AAATTAAGGATTAAAAAAAATT
1 AAATGAAGGACTAAAAAAAATT
* *
512194 AAATGAATGACTAAAATAAATT
1 AAATGAAGGACTAAAAAAAATT
512216 TATTTTTATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.27
Consensus pattern (22 bp):
AAATGAAGGACTAAAAAAAATT
Found at i:525342 original size:24 final size:24
Alignment explanation
Indices: 525295--525344 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
525285 TTTGGGTTAG
*
525295 TTGGGTTAGACTTAGTATTCGGGC
1 TTGGGTTAGACTTAATATTCGGGC
* * *
525319 TTGGGTTAGATTTAATGTTTGGGC
1 TTGGGTTAGACTTAATATTCGGGC
525343 TT
1 TT
525345 TTAATTTAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.16, C:0.08, G:0.32, T:0.44
Consensus pattern (24 bp):
TTGGGTTAGACTTAATATTCGGGC
Found at i:525696 original size:14 final size:14
Alignment explanation
Indices: 525673--525702 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
525663 TTGAAAATAT
525673 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
525687 GTTGATTTGGATTG
1 GTTGAATTGGATTG
525701 GT
1 GT
525703 CTCGGTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:535290 original size:21 final size:21
Alignment explanation
Indices: 535249--535332 Score: 72
Period size: 18 Copynumber: 4.3 Consensus size: 21
535239 AGAGGTAACC
*
535249 GAAGAAGATGAAGT--TGT-T
1 GAAGAAGATGAAGTACTTTAT
*
535267 GAAGAAGGTGAAGTACTTTAT
1 GAAGAAGATGAAGTACTTTAT
* * *
535288 GAAGAAAATGATGT--TGTA-
1 GAAGAAGATGAAGTACTTTAT
535306 GAAGAAGATGAAGTACTTTAT
1 GAAGAAGATGAAGTACTTTAT
*
535327 GGAGAA
1 GAAGAA
535333 AATGGTGTTG
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
18 25 0.50
19 3 0.06
20 5 0.10
21 17 0.34
ACGTcount: A:0.42, C:0.02, G:0.30, T:0.26
Consensus pattern (21 bp):
GAAGAAGATGAAGTACTTTAT
Found at i:535342 original size:39 final size:39
Alignment explanation
Indices: 535249--535344 Score: 138
Period size: 39 Copynumber: 2.5 Consensus size: 39
535239 AGAGGTAACC
* * * *
535249 GAAGAAGATGAAGTTGTTGAAGAAGGTGAAGTACTTTAT
1 GAAGAAAATGATGTTGTAGAAGAAGATGAAGTACTTTAT
535288 GAAGAAAATGATGTTGTAGAAGAAGATGAAGTACTTTAT
1 GAAGAAAATGATGTTGTAGAAGAAGATGAAGTACTTTAT
* *
535327 GGAGAAAATGGTGTTGTA
1 GAAGAAAATGATGTTGTA
535345 CAGGATGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.40, C:0.02, G:0.30, T:0.28
Consensus pattern (39 bp):
GAAGAAAATGATGTTGTAGAAGAAGATGAAGTACTTTAT
Found at i:535356 original size:21 final size:21
Alignment explanation
Indices: 535330--535374 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
535320 ACTTTATGGA
* *
535330 GAAAATGGTGTTGTACAGGAT
1 GAAAATGATGTTGTACAAGAT
*
535351 GAAAATGATGTTGTAGAAGAT
1 GAAAATGATGTTGTACAAGAT
535372 GAA
1 GAA
535375 GTACTTTGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.31, T:0.27
Consensus pattern (21 bp):
GAAAATGATGTTGTACAAGAT
Found at i:535454 original size:33 final size:34
Alignment explanation
Indices: 535351--535457 Score: 114
Period size: 33 Copynumber: 3.1 Consensus size: 34
535341 TGTACAGGAT
535351 GAAAATGATGTTGTAGAAGATGAAGTACTTTG-TGAA
1 GAAAATGATGTTGTAGAAGATGAAG-A--TTGATGAA
* *
535387 GAAAATGATATTTTAGAAGAT-ATAGATT-ATGAA
1 GAAAATGATGTTGTAGAAGATGA-AGATTGATGAA
* *
535420 GAAAATGGTGTTGTAGAAGATGAAG-TTGAAGAA
1 GAAAATGATGTTGTAGAAGATGAAGATTGATGAA
535453 GAAAA
1 GAAAA
535458 GTGTTATTGG
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 2 0.03
33 35 0.57
34 1 0.02
35 2 0.03
36 21 0.34
ACGTcount: A:0.45, C:0.01, G:0.26, T:0.28
Consensus pattern (34 bp):
GAAAATGATGTTGTAGAAGATGAAGATTGATGAA
Found at i:540751 original size:11 final size:11
Alignment explanation
Indices: 540727--540766 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
540717 TGAGTTTATT
*
540727 TTATATTTTACA
1 TTAT-TTTTGCA
540739 TTATTTTTGCA
1 TTATTTTTGCA
540750 TTATTTTTGCA
1 TTATTTTTGCA
540761 TATATT
1 T-TATT
540767 AAAAATATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.62
Consensus pattern (11 bp):
TTATTTTTGCA
Found at i:542203 original size:30 final size:32
Alignment explanation
Indices: 542159--542221 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
542149 TAGTAAAGGT
*
542159 AAAATTGTACTTTAA-CCTCCTAAAATTGATAA
1 AAAATTGTACTTTAATCCTCCAAAAATT-ATAA
*
542191 AAAATTG-A-TTTAATCCTTCAAAAATTATAA
1 AAAATTGTACTTTAATCCTCCAAAAATTATAA
542221 A
1 A
542222 GATATAGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 10 0.36
31 11 0.39
32 7 0.25
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.35
Consensus pattern (32 bp):
AAAATTGTACTTTAATCCTCCAAAAATTATAA
Found at i:546043 original size:13 final size:13
Alignment explanation
Indices: 546025--546061 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
546015 TAATTTTTTT
546025 AAATTTAATAATC
1 AAATTTAATAATC
546038 AAATTTAATAATC
1 AAATTTAATAATC
546051 AAATTTAATAA
1 AAATTTAATAA
546062 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTTAATAATC
Found at i:546076 original size:21 final size:21
Alignment explanation
Indices: 546024--546087 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 21
546014 TTAATTTTTT
*
546024 TAAATTTAATAATCAAATTTAATAA
1 TAAATTTAATAA--AAA--TAAAAA
546049 TCAAATTTAATAAAAATAAAAA
1 T-AAATTTAATAAAAATAAAAA
*
546071 TAAATTTGATAAAAATA
1 TAAATTTAATAAAAATA
546088 TAAACTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 15 0.42
22 6 0.17
24 3 0.08
25 1 0.03
26 11 0.31
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAATTTAATAAAAATAAAAA
Found at i:553654 original size:16 final size:16
Alignment explanation
Indices: 553633--553664 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
553623 GTTTTAGGAG
553633 TTGTAGAATACAAGAA
1 TTGTAGAATACAAGAA
553649 TTGTAGAATACAAGAA
1 TTGTAGAATACAAGAA
553665 ATTCATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (16 bp):
TTGTAGAATACAAGAA
Found at i:563814 original size:14 final size:14
Alignment explanation
Indices: 563791--563826 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
563781 AACATATCAA
* *
563791 TTAAATATAATTTT
1 TTAAAAATAAATTT
563805 TTAAAAATAAATTT
1 TTAAAAATAAATTT
563819 TTAAAAAT
1 TTAAAAAT
563827 TTTGAAGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAAAAATAAATTT
Found at i:566521 original size:20 final size:20
Alignment explanation
Indices: 566496--566533 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
566486 AATGACAAAA
*
566496 CAGTCACTTAACTTTCAATT
1 CAGTCACTCAACTTTCAATT
566516 CAGTCACTCAACTTTCAA
1 CAGTCACTCAACTTTCAA
566534 AAAATAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (20 bp):
CAGTCACTCAACTTTCAATT
Found at i:572380 original size:21 final size:20
Alignment explanation
Indices: 572356--572399 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
572346 ATACGTAATA
572356 ATAGGAATAAAAAGTATATAC
1 ATAGGAATAAAAA-TATATAC
* * *
572377 ATAGTATTAAAAATATGTAC
1 ATAGGAATAAAAATATATAC
572397 ATA
1 ATA
572400 ATATAGCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.30
Consensus pattern (20 bp):
ATAGGAATAAAAATATATAC
Found at i:572448 original size:27 final size:25
Alignment explanation
Indices: 572319--572496 Score: 112
Period size: 25 Copynumber: 7.4 Consensus size: 25
572309 ACGATATATG
*
572319 AATATATGCAT-ATAT-GTATT-AA
1 AATATATACATAATATAGTATTAAA
* * *
572341 AATATATACGTAATAATAGGAATAAA
1 AATATATACATAAT-ATAGTATTAAA
572367 AAGTATATAC-----ATAGTATTAAA
1 AA-TATATACATAATATAGTATTAAA
* **
572388 AATATGTACATAATATAGCGTTAAA
1 AATATATACATAATATAGTATTAAA
*
572413 AATACATACATAATATAGTTATTAAAA
1 AATATATACATAATATAG-TATT-AAA
* *
572440 AATATATACATAAGATAATATGT-AA
1 AATATATACATAATATAGTAT-TAAA
* *
572465 AA-A-A-A-GTAATATAGTATTAGA
1 AATATATACATAATATAGTATTAAA
572486 AATATATACAT
1 AATATATACAT
572497 GACATATATG
Statistics
Matches: 117, Mismatches: 21, Indels: 33
0.68 0.12 0.19
Matches are distributed among these distances:
20 7 0.06
21 23 0.20
22 11 0.09
23 4 0.03
24 4 0.03
25 33 0.28
26 9 0.08
27 26 0.22
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (25 bp):
AATATATACATAATATAGTATTAAA
Found at i:572688 original size:23 final size:23
Alignment explanation
Indices: 572629--572676 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
572619 ATGATACTAC
*
572629 ATAAATATATACATATATATTAAAA
1 ATAAATACATA-ATA-ATATTAAAA
572654 ATAAATACATAATAATATTAAAA
1 ATAAATACATAATAATATTAAAA
572677 GTATGTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.41
24 3 0.14
25 10 0.45
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAATACATAATAATATTAAAA
Found at i:572927 original size:13 final size:13
Alignment explanation
Indices: 572909--572989 Score: 60
Period size: 13 Copynumber: 6.2 Consensus size: 13
572899 GATATTAAAA
572909 ATATATACATAAT
1 ATATATACATAAT
*
572922 ATATATATATAAAT
1 ATATATACAT-AAT
* *
572936 ATAATGTTA-AAAAT
1 AT-AT-ATACATAAT
572950 ATATATACATAAT
1 ATATATACATAAT
* *
572963 ATATAT--GTAAA
1 ATATATACATAAT
*
572974 ATGTATACATAAT
1 ATATATACATAAT
572987 ATA
1 ATA
572990 GTTATTAAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
11 8 0.16
12 2 0.04
13 26 0.51
14 10 0.20
15 3 0.06
16 2 0.04
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (13 bp):
ATATATACATAAT
Found at i:572950 original size:28 final size:27
Alignment explanation
Indices: 572919--573043 Score: 81
Period size: 25 Copynumber: 4.9 Consensus size: 27
572909 ATATATACAT
*
572919 AATATATATATATAA-ATATAATGTTAAA
1 AATATATATACATAATATAT-ATG-TAAA
572947 AATATATATACATAATATATATGT--A
1 AATATATATACATAATATATATGTAAA
*
572972 AA-ATGTATACATAATATAGTTAT-TAAA
1 AATATATATACATAATATA--TATGTAAA
* **
572999 AA-ATATATGC--AATATATA-GTATT
1 AATATATATACATAATATATATGTAAA
* *
573022 AAGA-ATATACACAATATATATG
1 AATATATATACATAATATATATG
573044 GCATTAAAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 22
0.73 0.06 0.20
Matches are distributed among these distances:
23 11 0.14
24 16 0.20
25 18 0.22
26 4 0.05
27 10 0.12
28 17 0.21
29 4 0.05
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (27 bp):
AATATATATACATAATATATATGTAAA
Found at i:572973 original size:27 final size:26
Alignment explanation
Indices: 572922--573043 Score: 80
Period size: 24 Copynumber: 4.8 Consensus size: 26
572912 TATACATAAT
*
572922 ATATATATATAA-ATATAATGTTAAAAA
1 ATATATACATAATATAT-ATG-TAAAAA
572949 TATATATACATAATATATATGT--AAA
1 -ATATATACATAATATATATGTAAAAA
*
572974 ATGTATACATAATATAGTTAT-TAAAAA
1 ATATATACATAATATA--TATGTAAAAA
* * *
573001 ATATATGC--AATATATA-GTATTAAG
1 ATATATACATAATATATATGTA-AAAA
*
573025 A-ATATACACAATATATATG
1 ATATATACATAATATATATG
573044 GCATTAAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 22
0.73 0.07 0.21
Matches are distributed among these distances:
23 9 0.12
24 18 0.23
25 18 0.23
26 4 0.05
27 10 0.13
28 14 0.18
29 4 0.05
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (26 bp):
ATATATACATAATATATATGTAAAAA
Found at i:573181 original size:12 final size:12
Alignment explanation
Indices: 573164--573190 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
573154 ATATTAAAAA
573164 TATTAATAATAC
1 TATTAATAATAC
573176 TATTAATAATAC
1 TATTAATAATAC
573188 TAT
1 TAT
573191 ATATATATAA
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:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (12 bp):
TATTAATAATAC
Found at i:573240 original size:29 final size:29
Alignment explanation
Indices: 573189--573244 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
573179 TAATAATACT
*
573189 ATATATATATAATATTGAAAATATTAAAC
1 ATATATATATAATAATGAAAATATTAAAC
*
573218 ATATATATATACATAAT-ATAATATTAA
1 ATATATATATA-ATAATGAAAATATTAA
573245 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (29 bp):
ATATATATATAATAATGAAAATATTAAAC
Found at i:573383 original size:22 final size:22
Alignment explanation
Indices: 573230--573405 Score: 71
Period size: 22 Copynumber: 7.8 Consensus size: 22
573220 ATATATATAC
* *
573230 ATAAT-ATAATATTAAGAAAA-
1 ATAATAATAATAATAATAAAAT
*
573250 ATAATAATAACAA-AA-AAAACT
1 ATAATAATAATAATAATAAAA-T
* *
573271 ATTAATAATACTATATAATATATAT
1 A-TAATAATAATA-ATAATA-AAAT
* * *
573296 ACATATAAGTATTAAGTAAAAATAAT
1 ATA-ATAA-TAATAA-TAATAA-AAT
**
573322 ACTAATGCTAATAAATAAT-AAAT
1 A-TAATAATAAT-AATAATAAAAT
*
573345 ATAATAATAATAGTAATAAAAT
1 ATAATAATAATAATAATAAAAT
*
573367 ATAATAGTATACATAATATTAAAAT
1 ATAATA--ATA-ATAATAATAAAAT
573392 -TAA-AATAA-AATAAT
1 ATAATAATAATAATAAT
573406 GAGAAAAAGT
Statistics
Matches: 118, Mismatches: 20, Indels: 37
0.67 0.11 0.21
Matches are distributed among these distances:
19 9 0.08
20 8 0.07
21 14 0.12
22 27 0.23
23 6 0.05
24 10 0.08
25 26 0.22
26 17 0.14
27 1 0.01
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (22 bp):
ATAATAATAATAATAATAAAAT
Found at i:599287 original size:19 final size:17
Alignment explanation
Indices: 599263--599334 Score: 54
Period size: 19 Copynumber: 3.8 Consensus size: 17
599253 CTTCATACTA
599263 ATATTTTTCCTGAATTTTT
1 ATATTTTT--TGAATTTTT
*
599282 ATATTTTTTGAATTTTGA
1 ATATTTTTTGAATTTT-T
599300 ATATTATTTTTGAATATTTTT
1 ATA-T-TTTTTG-A-ATTTTT
* *
599321 ATAATTTTTAAATT
1 ATATTTTTTGAATT
599335 ATCTATTGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
17 11 0.25
18 4 0.09
19 14 0.32
20 6 0.14
21 4 0.09
22 5 0.11
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (17 bp):
ATATTTTTTGAATTTTT
Found at i:603696 original size:29 final size:29
Alignment explanation
Indices: 603663--603720 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
603653 CAAATAGAGT
603663 AACTA-AATTCATAAAATTAAAAGTATAAG
1 AACTACAATTCA-AAAATTAAAAGTATAAG
* * *
603692 AACTACATTTCAAAAGTTCAAAGTATAAG
1 AACTACAATTCAAAAATTAAAAGTATAAG
603721 GACCAGATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.53, C:0.10, G:0.09, T:0.28
Consensus pattern (29 bp):
AACTACAATTCAAAAATTAAAAGTATAAG
Found at i:610903 original size:21 final size:21
Alignment explanation
Indices: 610872--610919 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
610862 CTTAACATTT
610872 AATTAATTTTTAAAAATTTAAA
1 AATT-ATTTTTAAAAATTTAAA
**
610894 AATTATTTTTAAATTTTTAAA
1 AATTATTTTTAAAAATTTAAA
610915 AATTA
1 AATTA
610920 ATTAAATACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTATTTTTAAAAATTTAAA
Found at i:611462 original size:21 final size:21
Alignment explanation
Indices: 611433--611485 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
611423 TCGTCATCTA
*
611433 TTTAGTTTTTTAAAA-ATTAAT
1 TTTA-TTTTTTAAAACAATAAT
*
611454 TTTATTTTTAAAAACAATAAT
1 TTTATTTTTTAAAACAATAAT
611475 TTTAATTTTTT
1 TTT-ATTTTTT
611486 TTAGTAGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.33
21 12 0.44
22 6 0.22
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTATTTTTTAAAACAATAAT
Found at i:620142 original size:4 final size:4
Alignment explanation
Indices: 620133--620179 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
620123 GGTATTAAAC
620133 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
620180 AAGAAAAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:621217 original size:19 final size:18
Alignment explanation
Indices: 621195--621248 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
621185 AAAAATATAA
621195 ATTTTAAAATTATTAATTT
1 ATTTTAAAATTA-TAATTT
* *
621214 ATTTAAAAAATTATATTTT
1 ATTT-TAAAATTATAATTT
*
621233 ATTTT-TAATTATAATT
1 ATTTTAAAATTATAATT
621249 AAAAATAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 9 0.31
19 13 0.45
20 7 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAAAATTATAATTT
Found at i:622634 original size:23 final size:23
Alignment explanation
Indices: 622552--622638 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
622542 CCTGATCAGT
*
622552 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
622574 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
622594 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
622617 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
622639 TCAGTAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:624123 original size:16 final size:17
Alignment explanation
Indices: 624088--624123 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
624078 CCTAATTCTC
624088 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
624104 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
624119 CCTTC
1 CCTTC
624124 CCCTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:630694 original size:25 final size:25
Alignment explanation
Indices: 630666--630718 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
630656 ACCAATGAAG
* *
630666 ATTATAAATTTTACATATTAAAAAA
1 ATTATAAATTCTACATAATAAAAAA
*
630691 ATTATAAATTCTACATAATAATAAA
1 ATTATAAATTCTACATAATAAAAAA
630716 ATT
1 ATT
630719 TATTATTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTATAAATTCTACATAATAAAAAA
Found at i:637119 original size:27 final size:26
Alignment explanation
Indices: 637071--637131 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
637061 GTTAAGATAC
*
637071 TATATAAAAAATTCAATAATTAAAAAA
1 TATATAAAAAATTAAATAATT-AAAAA
*
637098 TATATAAAATTATTAAAT-ATTAAAAA
1 TATATAAAA-AATTAAATAATTAAAAA
637124 TAATATAA
1 T-ATATAA
637132 TATAATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 6 0.20
27 18 0.60
28 6 0.20
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
TATATAAAAAATTAAATAATTAAAAA
Found at i:637146 original size:32 final size:34
Alignment explanation
Indices: 637099--637164 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 34
637089 ATTAAAAAAT
*
637099 ATATAAAATTATT-AAATA-TTAAAAATAATATA
1 ATATAAAATTATTAAAAAATTTAAAAATAATATA
* *
637131 ATATAATATTTTTAAAAAAATTTAAAAATAATAT
1 ATATAAAATTATT-AAAAAATTTAAAAATAATAT
637165 GGGCGGGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 11 0.39
34 4 0.14
35 13 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
ATATAAAATTATTAAAAAATTTAAAAATAATATA
Found at i:647780 original size:38 final size:39
Alignment explanation
Indices: 647738--647813 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
647728 TTTATAAATT
* *
647738 TTAAAGGA-TTAAATC-AAATTTTTATCATTTTTAGAGAG
1 TTAAAGGATTTAAATCAAAAATTTTCT-ATTTTTAGAGAG
* *
647776 TTAAAGTATTTAAATGAAAAATTTTCTATTTTTAGAGA
1 TTAAAGGATTTAAATCAAAAATTTTCTATTTTTAGAGA
647814 CAGAGGCCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 7 0.22
39 17 0.53
40 8 0.25
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (39 bp):
TTAAAGGATTTAAATCAAAAATTTTCTATTTTTAGAGAG
Found at i:652153 original size:34 final size:34
Alignment explanation
Indices: 652110--652177 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
652100 AGTGGACTTA
652110 GCTTTTTATGCCCTTAAATAGATTAATTCTATTT
1 GCTTTTTATGCCCTTAAATAGATTAATTCTATTT
652144 GCTTTTTATGCCCTTAAATAGATTAATTCTATTT
1 GCTTTTTATGCCCTTAAATAGATTAATTCTATTT
652178 ACTTATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (34 bp):
GCTTTTTATGCCCTTAAATAGATTAATTCTATTT
Found at i:658893 original size:18 final size:17
Alignment explanation
Indices: 658872--658910 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
658862 ATTTGATCTT
658872 AAATATTAAAAAATTACA
1 AAATATTAAAAAATTA-A
* *
658890 AAATTTTTAAAAATTAA
1 AAATATTAAAAAATTAA
658907 AAAT
1 AAAT
658911 TATCATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATTAAAAAATTAA
Found at i:666521 original size:20 final size:19
Alignment explanation
Indices: 666470--666527 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
666460 GTTGCAAATC
666470 AAAGGTATCGATATTTATCA
1 AAAGGTAT-GATATTTATCA
** *
666490 ATTGGTACTGATAGTTTATGA
1 AAAGGTA-TGATA-TTTATCA
*
666511 AAAGGTATGATACTTAT
1 AAAGGTATGATATTTAT
666528 ATAAATATGG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 4 0.13
20 14 0.47
21 12 0.40
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (19 bp):
AAAGGTATGATATTTATCA
Found at i:668865 original size:5 final size:5
Alignment explanation
Indices: 668855--668880 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
668845 AATATCATCT
668855 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
668881 ACTTTACTTT
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:669806 original size:3 final size:3
Alignment explanation
Indices: 669798--669826 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
669788 TTGCAAATCT
669798 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
669827 TAATCTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:673947 original size:16 final size:16
Alignment explanation
Indices: 673926--673957 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
673916 TTCATCATAG
673926 CATAGATACATTTATA
1 CATAGATACATTTATA
*
673942 CATAGATTCATTTATA
1 CATAGATACATTTATA
673958 TTAAAACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (16 bp):
CATAGATACATTTATA
Found at i:677810 original size:22 final size:22
Alignment explanation
Indices: 677770--677811 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
677760 AGGGAACTAA
677770 GATAAAATTATAAAATTTTGAG
1 GATAAAATTATAAAATTTTGAG
*
677792 GATACAAATTA-AAATTTTTG
1 GATA-AAATTATAAAATTTTG
677812 TTTTGAAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (22 bp):
GATAAAATTATAAAATTTTGAG
Found at i:693485 original size:9 final size:9
Alignment explanation
Indices: 693471--693520 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
693461 ATAAATATAA
693471 AATTAACCG
1 AATTAACCG
*
693480 AATTAATCG
1 AATTAACCG
* *
693489 AATTACCCT
1 AATTAACCG
693498 AATTAACCG
1 AATTAACCG
*
693507 AATTAACTG
1 AATTAACCG
693516 AATTA
1 AATTA
693521 TTTGTATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTAACCG
Found at i:693552 original size:14 final size:14
Alignment explanation
Indices: 693544--693570 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
693534 ATATTTTTTT
693544 ATTTTTATTTTTAG
1 ATTTTTATTTTTAG
693558 ATTTTTATTTTTA
1 ATTTTTATTTTTA
693571 TTTATTAAAT
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:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (14 bp):
ATTTTTATTTTTAG
Found at i:693554 original size:5 final size:6
Alignment explanation
Indices: 693539--693573 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
693529 AAATTATATT
693539 TTTTTA TTTTTA TTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTT--A TTTTTA TTTTTA TTT
693574 ATTAAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 21 0.78
8 6 0.22
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:697893 original size:19 final size:20
Alignment explanation
Indices: 697858--697899 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
697848 CTATTCCACC
697858 TTAAAAATAATTAAATTATT
1 TTAAAAATAATTAAATTATT
* *
697878 TTAAAAAT-ATTGAATTTTT
1 TTAAAAATAATTAAATTATT
697897 TTA
1 TTA
697900 TATTTAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTAAAAATAATTAAATTATT
Found at i:699778 original size:69 final size:69
Alignment explanation
Indices: 699698--699832 Score: 198
Period size: 69 Copynumber: 2.0 Consensus size: 69
699688 CTCTGGTTAA
* *
699698 AACAGCAGAGTTGTTCGCACACTAACATTTGACTTTTCTATCGATAGACTGATGCATCAAAAACT
1 AACAGCAGAGTTGTTCGCACACTAACATTTGACTTGTCTATCGATAGACTGATACATCAAAAACT
699763 AAAC
66 AAAC
* ** * * *
699767 AACATCAGAGTTGTTTTCACACTAGCATTTGACTTGTCTATCTATAGATTGATACATCAAAAACT
1 AACAGCAGAGTTGTTCGCACACTAACATTTGACTTGTCTATCGATAGACTGATACATCAAAAACT
699832 A
66 A
699833 TTACTTTTGC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (69 bp):
AACAGCAGAGTTGTTCGCACACTAACATTTGACTTGTCTATCGATAGACTGATACATCAAAAACT
AAAC
Found at i:705991 original size:13 final size:14
Alignment explanation
Indices: 705975--706016 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
705965 TTTCAATTTT
705975 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
705988 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
706003 ATTTTAAATAATAT
1 ATTTT-AATAATAT
706017 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:706001 original size:16 final size:16
Alignment explanation
Indices: 705979--706015 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
705969 AATTTTATTT
705979 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
705996 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
706011 TAATA
1 TAATA
706016 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:708030 original size:26 final size:26
Alignment explanation
Indices: 707995--708059 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
707985 TAAAAATAAT
707995 TAAAAA-TATAAAATATAAAAAAACA
1 TAAAAATTATAAAATATAAAAAAACA
* * **
708020 -AAAATATTATAATATATATAAAATTA
1 TAAAA-ATTATAAAATATAAAAAAACA
708046 TAAAAATTATAAAA
1 TAAAAATTATAAAA
708060 AAAACTTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 4 0.12
25 1 0.03
26 23 0.72
27 4 0.12
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (26 bp):
TAAAAATTATAAAATATAAAAAAACA
Found at i:708071 original size:22 final size:21
Alignment explanation
Indices: 708039--708081 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
708029 TAATATATAT
*
708039 AAAATTATAAAAATTATAAAA
1 AAAATTATAAAAACTATAAAA
*
708060 AAAACTTATAAATACTATAAAA
1 AAAA-TTATAAAAACTATAAAA
708082 TATGAAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATTATAAAAACTATAAAA
Found at i:710584 original size:48 final size:48
Alignment explanation
Indices: 710471--710588 Score: 119
Period size: 48 Copynumber: 2.4 Consensus size: 48
710461 CTACCATCAA
* * ** * *
710471 ATCTCTAAGAATATAAAATCATATCTTCTAAGTTTACCTATCTTATCTAAG
1 ATCTCTAAGATTAT-AAA--ATATCTTATAAAATTACATATCATATCTAAG
* * **
710522 ATATGTAATCTTATAAAATATCTTATAAAATTACATATCATATCTAAG
1 ATCTCTAAGATTATAAAATATCTTATAAAATTACATATCATATCTAAG
710570 ATCTCTAAGATTATAAAAT
1 ATCTCTAAGATTATAAAAT
710589 CATATCTTTC
Statistics
Matches: 53, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
48 41 0.77
50 3 0.06
51 9 0.17
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (48 bp):
ATCTCTAAGATTATAAAATATCTTATAAAATTACATATCATATCTAAG
Found at i:714078 original size:13 final size:13
Alignment explanation
Indices: 714060--714085 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
714050 AAAAAAGCAC
714060 TTCATTGGTCATT
1 TTCATTGGTCATT
714073 TTCATTGGTCATT
1 TTCATTGGTCATT
714086 GGTCAGCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
TTCATTGGTCATT
Found at i:714449 original size:51 final size:51
Alignment explanation
Indices: 714387--714511 Score: 151
Period size: 51 Copynumber: 2.5 Consensus size: 51
714377 AATTAAATCC
* * * *
714387 CTAAGAATATAAAATCATATCTTTTAAGATTACCTATCTTATCTAAGATAT
1 CTAAGATTATAAAATCATATCTTATAAGATTACATATCATATCTAAGATAT
* ** * * * *
714438 GTAATCTTATAAAATAATATATTATAAGATTACATATCATATCTAAGGTCT
1 CTAAGATTATAAAATCATATCTTATAAGATTACATATCATATCTAAGATAT
714489 CTAAGATTATAAAATCATATCTT
1 CTAAGATTATAAAATCATATCTT
714512 CCAAAATCAT
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (51 bp):
CTAAGATTATAAAATCATATCTTATAAGATTACATATCATATCTAAGATAT
Found at i:726853 original size:21 final size:21
Alignment explanation
Indices: 726829--726870 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
726819 ACTATATATG
726829 CTTTTTAATAGATTATTAATT
1 CTTTTTAATAGATTATTAATT
726850 CTTTTTAATAGATTATTAATT
1 CTTTTTAATAGATTATTAATT
726871 AGCACCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
CTTTTTAATAGATTATTAATT
Found at i:729659 original size:22 final size:22
Alignment explanation
Indices: 729625--729667 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
729615 GTTGGTCTTG
*
729625 AGACCTAGTCTCGAGACATAAA
1 AGACCTAGCCTCGAGACATAAA
* *
729647 AGACCTTGCCTCGATACATAA
1 AGACCTAGCCTCGAGACATAA
729668 CATGTAATGT
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:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (22 bp):
AGACCTAGCCTCGAGACATAAA
Found at i:730605 original size:20 final size:20
Alignment explanation
Indices: 730573--730610 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
730563 TGTTTCACAT
730573 TCATATAACTAATATTTATA
1 TCATATAACTAATATTTATA
*
730593 TCAT-TAACATAATTTTTA
1 TCATATAAC-TAATATTTA
730611 ACTTAATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TCATATAACTAATATTTATA
Found at i:731121 original size:18 final size:18
Alignment explanation
Indices: 731098--731138 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
731088 TACTTTTCTC
731098 TTTCTA-TCACAATTCCAA
1 TTTCTATTCACAATT-CAA
*
731116 TTTCTATTCATAATTCAA
1 TTTCTATTCACAATTCAA
731134 TTTCT
1 TTTCT
731139 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTCTATTCACAATTCAA
Found at i:734518 original size:21 final size:19
Alignment explanation
Indices: 734486--734526 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
734476 AAAAATTCAT
734486 TAATCACATAATTCAAACA
1 TAATCACATAATTCAAACA
*
734505 TAATCTACAATAATTTAAACA
1 TAATC-AC-ATAATTCAAACA
734526 T
1 T
734527 GAATACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (19 bp):
TAATCACATAATTCAAACA
Found at i:738167 original size:17 final size:17
Alignment explanation
Indices: 738146--738203 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
738136 TTTAGAATGT
*
738146 AAATAAAATAATAATAA
1 AAATAAAATAAAAATAA
*
738163 TAATAAAATAAAAATAA
1 AAATAAAATAAAAATAA
**
738180 AAATAGACTTTAAAAATAA
1 AAATA-A-AATAAAAATAA
738199 AAATA
1 AAATA
738204 GACTTTTGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 19 0.56
18 1 0.03
19 14 0.41
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAAAATAA
Found at i:738195 original size:19 final size:19
Alignment explanation
Indices: 738171--738209 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
738161 AATAATAAAA
738171 TAAAAATAAAAATAGACTT
1 TAAAAATAAAAATAGACTT
738190 TAAAAATAAAAATAGACTT
1 TAAAAATAAAAATAGACTT
738209 T
1 T
738210 TGGCCTAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (19 bp):
TAAAAATAAAAATAGACTT
Found at i:738806 original size:22 final size:23
Alignment explanation
Indices: 738778--738820 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
738768 TACTATAATG
738778 TGAACAT-TAAAAAATATTAAGA
1 TGAACATATAAAAAATATTAAGA
* *
738800 TGAACATATATAAAATTTTAA
1 TGAACATATAAAAAATATTAA
738821 TAAATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (23 bp):
TGAACATATAAAAAATATTAAGA
Found at i:738975 original size:14 final size:14
Alignment explanation
Indices: 738958--738985 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
738948 AAACTCAGGA
738958 TTAAAAATATATAT
1 TTAAAAATATATAT
738972 TTAAAAATATATAT
1 TTAAAAATATATAT
738986 AGAGAGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATATATAT
Found at i:750661 original size:24 final size:24
Alignment explanation
Indices: 750634--750685 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
750624 TTAGTAAGTC
*
750634 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
750658 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
750682 AAAT
1 AAAT
750686 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:759968 original size:15 final size:15
Alignment explanation
Indices: 759922--759970 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
759912 TTTGTATAAA
*
759922 AAATT-ATTTAATAT
1 AAATTAATTAAATAT
*
759936 -AATTAAAATAAATAT
1 AAATT-AATTAAATAT
759951 AAATTAATTAAATAT
1 AAATTAATTAAATAT
759966 AAATT
1 AAATT
759971 TTTAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 4 0.14
15 21 0.72
16 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTAATTAAATAT
Found at i:766953 original size:13 final size:12
Alignment explanation
Indices: 766934--766976 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
766924 ATGATTTTAA
766934 TTTTTTTAAAAT
1 TTTTTTTAAAAT
*
766946 TATTTTTTATCAAT
1 T-TTTTTTA-AAAT
766960 TTTTTTTAAAGAT
1 TTTTTTTAAA-AT
766973 TTTT
1 TTTT
766977 AAAGTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 2 0.08
13 20 0.77
14 4 0.15
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTTTTAAAAT
Found at i:772053 original size:122 final size:123
Alignment explanation
Indices: 771882--772126 Score: 440
Period size: 122 Copynumber: 2.0 Consensus size: 123
771872 AGAGTAAAGC
*
771882 ATAATTGACTAGTCTTTCAGCCAATGATTGGCTCTCCACGAGTTCATCAACCTGATTA-GTGTTT
1 ATAATTGACTAGTCTTTCAGCCAATAATTGGCTCTCCACGAGTTCATCAACCTGATTAGGT-TTT
*
771946 TTCTTAATTTGTTTCAGCT-GCTAGGACGTGGAAAGATGTTAGTTCAAAGTTCCTAATG
65 TTCTTAATTTGTTTCAGCTGGCTAGGACGTGGAAAGATGTTACTTCAAAGTTCCTAATG
*
772004 ATAATTGACTAGTCTTTCAGCCAATAATTGGCTCTCCACTAGTTCATCAACCTGATTAGGTTTTT
1 ATAATTGACTAGTCTTTCAGCCAATAATTGGCTCTCCACGAGTTCATCAACCTGATTAGGTTTTT
772069 TCTTAATTTGTTTCAGCTGGCTAGGACGTGGAAAGATGTTACTTCAAAGTTCCTAATG
66 TCTTAATTTGTTTCAGCTGGCTAGGACGTGGAAAGATGTTACTTCAAAGTTCCTAATG
772127 TTCTTACATA
Statistics
Matches: 118, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
122 78 0.66
123 40 0.34
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (123 bp):
ATAATTGACTAGTCTTTCAGCCAATAATTGGCTCTCCACGAGTTCATCAACCTGATTAGGTTTTT
TCTTAATTTGTTTCAGCTGGCTAGGACGTGGAAAGATGTTACTTCAAAGTTCCTAATG
Found at i:774629 original size:45 final size:45
Alignment explanation
Indices: 774578--774707 Score: 179
Period size: 45 Copynumber: 2.9 Consensus size: 45
774568 TAAACCACTG
* *
774578 AGTGGTTTATCCACACTGTATTAGCAACTTTTATTTGCAATAATA
1 AGTGGTTTATCCACACCGTATTAGCAACTTTTATTTGCAACAATA
*
774623 AGTGGTTTATCCACACCGTATTAGCAACTTTTATTTGCAACAATG
1 AGTGGTTTATCCACACCGTATTAGCAACTTTTATTTGCAACAATA
* * * * * *
774668 AGTGATCTATCCACACCATACTAGCAACTTTAATCTGCAA
1 AGTGGTTTATCCACACCGTATTAGCAACTTTTATTTGCAA
774708 ATATGTTGTG
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35
Consensus pattern (45 bp):
AGTGGTTTATCCACACCGTATTAGCAACTTTTATTTGCAACAATA
Found at i:775684 original size:20 final size:20
Alignment explanation
Indices: 775659--775708 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
775649 TGGCTTTAAA
775659 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
775679 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
775696 GTGGTAGTGGATT
1 TTGGTAGTGGATT
775709 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:780322 original size:20 final size:20
Alignment explanation
Indices: 780297--780346 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
780287 TGGCTTTAAA
780297 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
780317 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
780334 GTGGTAGTGGATT
1 TTGGTAGTGGATT
780347 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:784993 original size:24 final size:24
Alignment explanation
Indices: 784954--785024 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
784944 ATGTTATCTG
784954 AAAAAGG-TATCTAATGAAAAGGTC
1 AAAAAGGATATC-AATGAAAAGGTC
*
784978 GAAAAGGATATCAATGAAAAGGTC
1 AAAAAGGATATCAATGAAAAGGTC
* *
785002 AAAAAGAATAGCAATGAAAAGGT
1 AAAAAGGATATCAATGAAAAGGT
785025 TGGTTTCTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 38 0.90
25 4 0.10
ACGTcount: A:0.54, C:0.07, G:0.23, T:0.17
Consensus pattern (24 bp):
AAAAAGGATATCAATGAAAAGGTC
Found at i:786402 original size:55 final size:55
Alignment explanation
Indices: 786293--786404 Score: 152
Period size: 55 Copynumber: 2.0 Consensus size: 55
786283 ATCGAATGCA
* * * * * *
786293 CACACGGTTTGACACATGACCTATGACGCGGCAGTGTGGCCCTATTTCGAATACT
1 CACACGGGTGGACACACGACCTACGACACGGCAGTGTGGCCCTATTTCAAATACT
* *
786348 CACACGGGTGGACACACGACCTACGACACGGCCGTGTGGCCTTATTTCAAATACT
1 CACACGGGTGGACACACGACCTACGACACGGCAGTGTGGCCCTATTTCAAATACT
786403 CA
1 CA
786405 TGCGAATGGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.22
Consensus pattern (55 bp):
CACACGGGTGGACACACGACCTACGACACGGCAGTGTGGCCCTATTTCAAATACT
Found at i:787119 original size:48 final size:48
Alignment explanation
Indices: 787045--787248 Score: 196
Period size: 48 Copynumber: 4.2 Consensus size: 48
787035 AAGCTGCTAG
* * * * * *
787045 TACGTTGTGGATGAACTACTGGTCGTGTAGATAAAATTCCAACTAAGA
1 TACGTTTTGGATGAACCATTGGTCGTGCAGATAAACTTCCGACTAAGA
* * *
787093 TATGTTTTGGACGAACCATTGGTCGTGCAGATTAACTAT-CGACTAAGA
1 TACGTTTTGGATGAACCATTGGTCGTGCAGATAAACT-TCCGACTAAGA
* * * * *
787141 TACGTTTTGGATGAACAACTAGTCGTGCAGATAAACTCCCGACTAAAA
1 TACGTTTTGGATGAACCATTGGTCGTGCAGATAAACTTCCGACTAAGA
* ** * *
787189 TACATTTTGGATGAACCATTGGTCCAGCAAATAAACTGT-CGACTAAAA
1 TACGTTTTGGATGAACCATTGGTCGTGCAGATAAACT-TCCGACTAAGA
*
787237 TACGTTGTGGAT
1 TACGTTTTGGAT
787249 AAATAATGTG
Statistics
Matches: 126, Mismatches: 27, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
48 125 0.99
49 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (48 bp):
TACGTTTTGGATGAACCATTGGTCGTGCAGATAAACTTCCGACTAAGA
Found at i:787209 original size:96 final size:96
Alignment explanation
Indices: 787045--787248 Score: 255
Period size: 96 Copynumber: 2.1 Consensus size: 96
787035 AAGCTGCTAG
* * * * * **
787045 TACGTTGTGGATGAACTACTGGTCGTGTAGATAAAATTCCAACTAAGATATGTTTTGGACGAACC
1 TACGTTGTGGATGAACAACTAGTCGTGCAGATAAAATCCCAACTAAAATACATTTTGGACGAACC
** * * *
787110 ATTGGTCGTGCAGATTAACTATCGACTAAGA
66 ATTGGTCCAGCAAATAAACTATCGACTAAAA
* * * *
787141 TACGTTTTGGATGAACAACTAGTCGTGCAGATAAACTCCCGACTAAAATACATTTTGGATGAACC
1 TACGTTGTGGATGAACAACTAGTCGTGCAGATAAAATCCCAACTAAAATACATTTTGGACGAACC
*
787206 ATTGGTCCAGCAAATAAACTGTCGACTAAAA
66 ATTGGTCCAGCAAATAAACTATCGACTAAAA
787237 TACGTTGTGGAT
1 TACGTTGTGGAT
787249 AAATAATGTG
Statistics
Matches: 90, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
96 90 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (96 bp):
TACGTTGTGGATGAACAACTAGTCGTGCAGATAAAATCCCAACTAAAATACATTTTGGACGAACC
ATTGGTCCAGCAAATAAACTATCGACTAAAA
Found at i:788661 original size:53 final size:53
Alignment explanation
Indices: 788580--788730 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
788570 CTTACACGGT
* *
788580 TCACATATCATACCGAAGCCATATCCCAGACATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAGACATGGTCTTATACGGAATCACATTA
*
788635 TCACATTATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGAC-ATGGTCTTATACGGAATCACATTA
** * *
788688 TCACATTGCACCGATGCCATAGCCCAGATATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGACATGGTCTTATACGG
788731 GCACACTTAT
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
52 1 0.01
53 79 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGACATGGTCTTATACGGAATCACATTA
Found at i:793349 original size:17 final size:18
Alignment explanation
Indices: 793315--793358 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
793305 TTTTAGATAA
793315 AAATATTAAATATGAAAAAT
1 AAAT-TTAAATA-GAAAAAT
*
793335 AAATTTAAATA-AAAATT
1 AAATTTAAATAGAAAAAT
793352 AAATTTA
1 AAATTTA
793359 TTTAAAATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 12 0.52
19 7 0.30
20 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AAATTTAAATAGAAAAAT
Found at i:793945 original size:43 final size:43
Alignment explanation
Indices: 793884--793970 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
793874 TTAAATTAAA
*
793884 GATCAAATTAGTTTTTCTGTTAAAAATTTCATCCATTTTTACT
1 GATCAAATTAGTTTTTCTGTTAAAAATTCCATCCATTTTTACT
*
793927 GATCAAATTAGTTTTTCTGTTAAAAATTCCATTCATTTTTACT
1 GATCAAATTAGTTTTTCTGTTAAAAATTCCATCCATTTTTACT
793970 G
1 G
793971 TTAAGTGCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (43 bp):
GATCAAATTAGTTTTTCTGTTAAAAATTCCATCCATTTTTACT
Found at i:795037 original size:19 final size:20
Alignment explanation
Indices: 795002--795039 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
794992 ATAAAATAAC
*
795002 ATATAATTATATTTTAAAAA
1 ATATAATTATATATTAAAAA
795022 ATATAA-TATATATTAAAA
1 ATATAATTATATATTAAAA
795040 TTAAAATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATAATTATATATTAAAAA
Found at i:795067 original size:22 final size:23
Alignment explanation
Indices: 795018--795067 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
795008 TTATATTTTA
795018 AAAAATATAATATATATTAAAAT
1 AAAAATATAATATATATTAAAAT
* * * *
795041 TAAAATCTATTAT-TATTAATAT
1 AAAAATATAATATATATTAAAAT
795063 AAAAA
1 AAAAA
795068 AAATTTTGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAAATATAATATATATTAAAAT
Found at i:795727 original size:3 final size:3
Alignment explanation
Indices: 795719--795762 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
795709 CATGACTCTG
* * *
795719 CAT CAT CAT CAT CAT CAC CAC CAC CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
795763 CGGTTAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (3 bp):
CAT
Found at i:797285 original size:17 final size:16
Alignment explanation
Indices: 797249--797300 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
797239 AAAAATGATA
797249 TTTTCTATCCTTTTAT
1 TTTTCTATCCTTTTAT
797265 TTTTCTA-CTCTTTTAAT
1 TTTTCTATC-CTTTT-AT
**
797282 TTTT-TATTTTTTTAT
1 TTTTCTATCCTTTTAT
797297 TTTT
1 TTTT
797301 TTAATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 7 0.23
16 18 0.58
17 6 0.19
ACGTcount: A:0.13, C:0.12, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTCTATCCTTTTAT
Found at i:797286 original size:24 final size:24
Alignment explanation
Indices: 797259--797310 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
797249 TTTTCTATCC
797259 TTTTATTTTTCTACTCTTTTAATT
1 TTTTATTTTTCTACTCTTTTAATT
* * *
797283 TTTTATTTTTTTATTTTTTTAATT
1 TTTTATTTTTCTACTCTTTTAATT
797307 TTTT
1 TTTT
797311 TATTCTACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTATTTTTCTACTCTTTTAATT
Found at i:797292 original size:8 final size:8
Alignment explanation
Indices: 797259--797314 Score: 67
Period size: 8 Copynumber: 6.9 Consensus size: 8
797249 TTTTCTATCC
797259 TTTTATTT
1 TTTTATTT
* * *
797267 TTCTACTC
1 TTTTATTT
*
797275 TTTTAATT
1 TTTTATTT
797283 TTTTATTT
1 TTTTATTT
797291 TTTTATTT
1 TTTTATTT
797299 TTTTAATTT
1 TTTT-ATTT
797308 TTTTATT
1 TTTTATT
797315 CTACCAAGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
8 32 0.80
9 8 0.20
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTATTT
Done.