Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 208 of 210
Found at i:61621698 original size:2 final size:2
Alignment explanation
Indices: 61621691--61621734 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
61621681 ATAAGAGATG
61621691 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61621733 AT
1 AT
61621735 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61628029 original size:19 final size:19
Alignment explanation
Indices: 61627988--61628030 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
61627978 ATTGAACCGA
*
61627988 ATTTA-AAATATTTTAATT
1 ATTTATAAATATTTTAATG
* *
61628006 TTTTATAAATGTTTTAATG
1 ATTTATAAATATTTTAATG
61628025 ATTTAT
1 ATTTAT
61628031 CTAATCAAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTTATAAATATTTTAATG
Found at i:61635596 original size:13 final size:13
Alignment explanation
Indices: 61635578--61635608 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
61635568 TAAAGATCAT
61635578 ATTTATTGAGGTA
1 ATTTATTGAGGTA
61635591 ATTTATTGAGGTA
1 ATTTATTGAGGTA
61635604 ATTTA
1 ATTTA
61635609 GATCGAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (13 bp):
ATTTATTGAGGTA
Found at i:61637419 original size:16 final size:15
Alignment explanation
Indices: 61637384--61637433 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
61637374 TTTGATAAAT
*
61637384 TAAAAAAATAATTA-
1 TAAAAAAATAAGTAC
*
61637398 TTAAAAAATAAGTAC
1 TAAAAAAATAAGTAC
*
61637413 TGAAAAAATTAAGTAC
1 T-AAAAAAATAAGTAC
61637429 TAAAA
1 TAAAA
61637434 TCAGATTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 12 0.40
15 5 0.17
16 13 0.43
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (15 bp):
TAAAAAAATAAGTAC
Found at i:61639912 original size:2 final size:2
Alignment explanation
Indices: 61639905--61639951 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
61639895 GTGAAATAAG
61639905 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61639947 TA TA T
1 TA TA T
61639952 TCTAAATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61642169 original size:16 final size:17
Alignment explanation
Indices: 61642148--61642181 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
61642138 GTGTAATTTT
*
61642148 ATTTTTATTAA-TTTAA
1 ATTTTTATAAACTTTAA
61642164 ATTTTTATAAACTTTAA
1 ATTTTTATAAACTTTAA
61642181 A
1 A
61642182 GGAGTCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTTATAAACTTTAA
Found at i:61645716 original size:31 final size:31
Alignment explanation
Indices: 61645680--61645745 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
61645670 TTATAAAATG
61645680 GTCATTAAATTATTAGAAAGT-TTTCATTTAA
1 GTCATTAAATTATTAGAAAGTATTT-ATTTAA
* *
61645711 GTCATTGAATTATTCGAAAGTATTTATTTAA
1 GTCATTAAATTATTAGAAAGTATTTATTTAA
61645742 GTCA
1 GTCA
61645746 ATAGGCTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 29 0.91
32 3 0.09
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (31 bp):
GTCATTAAATTATTAGAAAGTATTTATTTAA
Found at i:61646434 original size:27 final size:25
Alignment explanation
Indices: 61646396--61646468 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 25
61646386 ATATTTTTTA
61646396 TTTTTATTTTTAATTTTAAAATAATT
1 TTTTTATTTTTAATTTTAAAAT-ATT
*
61646422 TTTTTATTTTTTATTTTTAAAATATT
1 TTTTTA-TTTTTAATTTTAAAATATT
*
61646448 TTTTTAATGTTT-ATTTTAAAA
1 TTTTT-ATTTTTAATTTTAAAA
61646469 ATGGGCCGGG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.19
26 18 0.43
27 16 0.38
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (25 bp):
TTTTTATTTTTAATTTTAAAATATT
Found at i:61655550 original size:24 final size:26
Alignment explanation
Indices: 61655523--61655571 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
61655513 TTTGCGAGGA
*
61655523 AAAT-GCAACTAAAA-AATTAAAAAT
1 AAATAGCAACAAAAATAATTAAAAAT
61655547 AAATGAGCAACAAAAATAATTAAAA
1 AAAT-AGCAACAAAAATAATTAAAA
61655572 TTTCAATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
26 9 0.43
27 8 0.38
ACGTcount: A:0.67, C:0.08, G:0.06, T:0.18
Consensus pattern (26 bp):
AAATAGCAACAAAAATAATTAAAAAT
Found at i:61656190 original size:24 final size:21
Alignment explanation
Indices: 61656129--61656177 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
61656119 AGTTAGACAA
*
61656129 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
*
61656150 AAAAAGAGAAGTAACTTGGAT
1 AAAAAGAGAAGTAACTTGGAC
61656171 AAAAAGA
1 AAAAAGA
61656178 AACGAAGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.57, C:0.08, G:0.22, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:61662039 original size:21 final size:21
Alignment explanation
Indices: 61662010--61662049 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
61662000 CACATTTTGA
*
61662010 TTGTTTTGTTCCTATGTAACC
1 TTGTCTTGTTCCTATGTAACC
*
61662031 TTGTCTTGTTCCTTTGTAA
1 TTGTCTTGTTCCTATGTAA
61662050 TTTGATAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.17, G:0.15, T:0.55
Consensus pattern (21 bp):
TTGTCTTGTTCCTATGTAACC
Found at i:61672519 original size:112 final size:112
Alignment explanation
Indices: 61672317--61672545 Score: 440
Period size: 112 Copynumber: 2.0 Consensus size: 112
61672307 AATCCATAAA
*
61672317 AACAAGCATTCAGCCTGTCAAAATCAGTATATGGTCACCTAATCAATACCTACTACCACTAATAC
1 AACAGGCATTCAGCCTGTCAAAATCAGTATATGGTCACCTAATCAATACCTACTACCACTAATAC
61672382 ATTGAAACTTGGTAAACCAAGCTTGTACACATAAACAAAGCTGAGTT
66 ATTGAAACTTGGTAAACCAAGCTTGTACACATAAACAAAGCTGAGTT
*
61672429 AACAGGCATTCAGCTTGTCAAAATCAGTATATGGTCACCTAATCAATACCTACTACCACTAATAC
1 AACAGGCATTCAGCCTGTCAAAATCAGTATATGGTCACCTAATCAATACCTACTACCACTAATAC
61672494 ATTGAAACTTGGTAAACCAAGCTTGTACACATAAACAAAGCTGAGTT
66 ATTGAAACTTGGTAAACCAAGCTTGTACACATAAACAAAGCTGAGTT
61672541 AACAG
1 AACAG
61672546 TTCAATCACC
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 115 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (112 bp):
AACAGGCATTCAGCCTGTCAAAATCAGTATATGGTCACCTAATCAATACCTACTACCACTAATAC
ATTGAAACTTGGTAAACCAAGCTTGTACACATAAACAAAGCTGAGTT
Found at i:61675150 original size:31 final size:28
Alignment explanation
Indices: 61675115--61675179 Score: 67
Period size: 30 Copynumber: 2.1 Consensus size: 28
61675105 TTAGTAAAGG
*
61675115 TAAAATTGCATTTTGATCCTTTTAAAAATGA
1 TAAAATTG-A-TTTAAT-CTTTTAAAAATGA
*
61675146 TAAAAAATTGATTTAATCTTTTAAAAATTA
1 T--AAAATTGATTTAATCTTTTAAAAATGA
61675176 TAAA
1 TAAA
61675180 TATATAGACT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
28 3 0.10
30 13 0.43
31 6 0.20
32 1 0.03
33 7 0.23
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (28 bp):
TAAAATTGATTTAATCTTTTAAAAATGA
Found at i:61676094 original size:25 final size:24
Alignment explanation
Indices: 61676046--61676094 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
61676036 AAAAAAATTA
* *
61676046 ATTTATTTTCAATTTTTGGGAAAT
1 ATTTATTTTAAATTTTTAGGAAAT
*
61676070 ATTTATTTTAATATTTTTAGTAAAT
1 ATTTATTTTAA-ATTTTTAGGAAAT
61676095 TTAGTGTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (24 bp):
ATTTATTTTAAATTTTTAGGAAAT
Found at i:61687547 original size:16 final size:16
Alignment explanation
Indices: 61687526--61687561 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
61687516 TGTTTTTATC
* *
61687526 ATTGTACTAACACTCG
1 ATTGTACCAACACTAG
61687542 ATTGTACCAACACTAG
1 ATTGTACCAACACTAG
61687558 ATTG
1 ATTG
61687562 GTTGGAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (16 bp):
ATTGTACCAACACTAG
Found at i:61693184 original size:17 final size:17
Alignment explanation
Indices: 61693158--61693215 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 17
61693148 AAAGTTAGTA
*
61693158 ATTATTTAAATTTAATG
1 ATTATATAAATTTAATG
61693175 ATTATATAAAATATATAATG
1 ATTATAT-AAAT-T-TAATG
*
61693195 ATGTATTATTAATTTAATG
1 AT-TA-TATAAATTTAATG
61693214 AT
1 AT
61693216 ATGAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
17 6 0.18
18 4 0.12
19 8 0.24
20 8 0.24
21 5 0.15
22 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (17 bp):
ATTATATAAATTTAATG
Found at i:61696234 original size:23 final size:22
Alignment explanation
Indices: 61696201--61696243 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
61696191 ATTAAATTAA
*
61696201 AAAATAAAAAGAAACGAATAGT
1 AAAATAAAAAGAAAAGAATAGT
61696223 AAAATAATAAAGAAAAGAATA
1 AAAATAA-AAAGAAAAGAATA
61696244 ATTTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (22 bp):
AAAATAAAAAGAAAAGAATAGT
Found at i:61696946 original size:15 final size:16
Alignment explanation
Indices: 61696928--61696965 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
61696918 AAGATATTTT
61696928 AACAAATGAAATTAA-
1 AACAAATGAAATTAAC
61696943 AACAAATGAAATTAAC
1 AACAAATGAAATTAAC
61696959 AACAAAT
1 AACAAAT
61696966 ATGATGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (16 bp):
AACAAATGAAATTAAC
Found at i:61714281 original size:17 final size:18
Alignment explanation
Indices: 61714259--61714293 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
61714249 ATTTGGGCCA
61714259 TGTGGG-CCACACGGGTG
1 TGTGGGCCCACACGGGTG
61714276 TGTGGGCCCACACGGGTG
1 TGTGGGCCCACACGGGTG
61714294 AACATCATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.11, C:0.26, G:0.46, T:0.17
Consensus pattern (18 bp):
TGTGGGCCCACACGGGTG
Found at i:61717674 original size:15 final size:15
Alignment explanation
Indices: 61717656--61717685 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
61717646 AAGATATTTT
61717656 AACAAATGAAATTAA
1 AACAAATGAAATTAA
61717671 AACAAATGAAATTAA
1 AACAAATGAAATTAA
61717686 CATCAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (15 bp):
AACAAATGAAATTAA
Found at i:61721478 original size:7 final size:7
Alignment explanation
Indices: 61721466--61721560 Score: 60
Period size: 7 Copynumber: 14.0 Consensus size: 7
61721456 AACCCTGAAT
61721466 CCTTAAA
1 CCTTAAA
61721473 CCTTAAA
1 CCTTAAA
*
61721480 CC-TGAA
1 CCTTAAA
61721486 CCTTAAA
1 CCTTAAA
61721493 CCTTAAA
1 CCTTAAA
61721500 -CTCTAAA
1 CCT-TAAA
* *
61721507 TCATTGAA
1 -CCTTAAA
61721515 -CTCTAAA
1 CCT-TAAA
61721522 CC-TAAA
1 CCTTAAA
*
61721528 CTTTAAA
1 CCTTAAA
*
61721535 CC-TCAA
1 CCTTAAA
61721541 CAC-TAAA
1 C-CTTAAA
61721548 -CTTAAA
1 CCTTAAA
61721554 CCTTAAA
1 CCTTAAA
61721561 TCTCAAACCG
Statistics
Matches: 68, Mismatches: 10, Indels: 20
0.69 0.10 0.20
Matches are distributed among these distances:
5 1 0.01
6 21 0.31
7 41 0.60
8 4 0.06
9 1 0.01
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.27
Consensus pattern (7 bp):
CCTTAAA
Found at i:61721491 original size:20 final size:21
Alignment explanation
Indices: 61721459--61721500 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
61721449 AACTTACAAC
61721459 CCTGAATCCTTAAACCTTAAA
1 CCTGAATCCTTAAACCTTAAA
61721480 CCTGAA-CCTTAAACCTTAAA
1 CCTGAATCCTTAAACCTTAAA
61721500 C
1 C
61721501 TCTAAATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.38, C:0.31, G:0.05, T:0.26
Consensus pattern (21 bp):
CCTGAATCCTTAAACCTTAAA
Found at i:61721534 original size:13 final size:13
Alignment explanation
Indices: 61721469--61721560 Score: 55
Period size: 13 Copynumber: 6.8 Consensus size: 13
61721459 CCTGAATCCT
61721469 TAAACCTTAAACC
1 TAAACCTTAAACC
*
61721482 TGAACCTTAAACC
1 TAAACCTTAAACC
*
61721495 TTAAA-CTCTAAATCAT
1 -TAAACCT-TAAA-C-C
*
61721511 TGAA-CTCTAAACC
1 TAAACCT-TAAACC
*
61721524 TAAACTTTAAACC
1 TAAACCTTAAACC
* *
61721537 TCAACAC-TAAACT
1 TAAAC-CTTAAACC
61721550 TAAACCTTAAA
1 TAAACCTTAAA
61721561 TCTCAAACCG
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
12 1 0.02
13 40 0.66
14 9 0.15
15 11 0.18
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.27
Consensus pattern (13 bp):
TAAACCTTAAACC
Found at i:61721568 original size:20 final size:18
Alignment explanation
Indices: 61721467--61721560 Score: 64
Period size: 20 Copynumber: 4.7 Consensus size: 18
61721457 ACCCTGAATC
*
61721467 CTTAAACCTTAAACCTGAAC
1 CTTAAACCTTAAA-CT-AAA
61721487 CTTAAACCTTAAACTCTAAA
1 CTTAAACCTTAAA--CTAAA
*
61721507 TCATTGAA-CTCTAAACCTAAA
1 -C-TTAAACCT-TAAA-CTAAA
*
61721528 CTTTAAACCTCAACACTAAA
1 C-TTAAACCTTAA-ACTAAA
61721548 CTTAAACCTTAAA
1 CTTAAACCTTAAA
61721561 TCTCAAACCG
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
18 1 0.02
19 10 0.17
20 28 0.47
21 13 0.22
22 8 0.13
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.28
Consensus pattern (18 bp):
CTTAAACCTTAAACTAAA
Found at i:61721792 original size:18 final size:18
Alignment explanation
Indices: 61721769--61721803 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61721759 TTGTTTATAA
61721769 TTTAAAAAAATTAATTAT
1 TTTAAAAAAATTAATTAT
* *
61721787 TTTAAATAATTTAATTA
1 TTTAAAAAAATTAATTA
61721804 AAGTTAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAAAAAATTAATTAT
Found at i:61722821 original size:2 final size:2
Alignment explanation
Indices: 61722804--61722871 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
61722794 AAATTAAAAT
* *
61722804 TG TG AG TG TC TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
61722846 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
61722872 ATAACACTCT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.01, C:0.01, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:61738273 original size:25 final size:24
Alignment explanation
Indices: 61738245--61738293 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
61738235 AATACACTAA
* *
61738245 ATTTACTAAAAATATTAAAATAAAT
1 ATTTACCAAAAAT-TGAAAATAAAT
*
61738270 ATTTCCCAAAAATTGAAAATAAAT
1 ATTTACCAAAAATTGAAAATAAAT
61738294 TAATTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (24 bp):
ATTTACCAAAAATTGAAAATAAAT
Found at i:61743468 original size:15 final size:15
Alignment explanation
Indices: 61743448--61743480 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
61743438 CAATTCAATC
61743448 TTAAAACCCAACCTT
1 TTAAAACCCAACCTT
61743463 TTAAAACCCAACCTT
1 TTAAAACCCAACCTT
61743478 TTA
1 TTA
61743481 GATGGAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.30
Consensus pattern (15 bp):
TTAAAACCCAACCTT
Found at i:61749409 original size:17 final size:17
Alignment explanation
Indices: 61749389--61749446 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 17
61749379 AAAGTTAGTA
61749389 ATTATTTAAATTTAATG
1 ATTATTTAAATTTAATG
*
61749406 ATTATATAAAATATATAATG
1 ATTAT-TTAAAT-T-TAATG
*
61749426 ATGTATTATTAATTTAATG
1 AT-TATT-TAAATTTAATG
61749445 AT
1 AT
61749447 ATGAAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
17 5 0.15
18 5 0.15
19 8 0.24
20 9 0.27
21 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (17 bp):
ATTATTTAAATTTAATG
Found at i:61750332 original size:7 final size:7
Alignment explanation
Indices: 61750320--61750355 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
61750310 AAAACTAATC
61750320 TTTATTA
1 TTTATTA
*
61750327 TTTATTC
1 TTTATTA
*
61750334 TTTATTC
1 TTTATTA
61750341 TTTATTA
1 TTTATTA
61750348 TTTATTA
1 TTTATTA
61750355 T
1 T
61750356 ATTACACTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:61752295 original size:22 final size:21
Alignment explanation
Indices: 61752268--61752308 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
61752258 ATTAAATTAA
61752268 AAAATAA-AAAGAAACGAATAGT
1 AAAATAATAAA-AAA-GAATAGT
61752290 AAAATAATAAAAAAGAATA
1 AAAATAATAAAAAAGAATA
61752309 ATTTATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 10 0.56
23 3 0.17
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATAATAAAAAAGAATAGT
Found at i:61753005 original size:15 final size:16
Alignment explanation
Indices: 61752987--61753024 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
61752977 AAGATATTTT
61752987 AACAAATGAAATTAA-
1 AACAAATGAAATTAAC
*
61753002 AACAAATGAATTTAAC
1 AACAAATGAAATTAAC
61753018 AACAAAT
1 AACAAAT
61753025 ACGGTGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (16 bp):
AACAAATGAAATTAAC
Found at i:61761880 original size:16 final size:16
Alignment explanation
Indices: 61761859--61761894 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
61761849 AAGATATTTT
61761859 AACAAATGAAATTAAC
1 AACAAATGAAATTAAC
61761875 AACAAATGAAATTAAC
1 AACAAATGAAATTAAC
61761891 AACA
1 AACA
61761895 GATACGGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.64, C:0.14, G:0.06, T:0.17
Consensus pattern (16 bp):
AACAAATGAAATTAAC
Found at i:61769437 original size:18 final size:18
Alignment explanation
Indices: 61769414--61769448 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
61769404 ATATTTTTTA
*
61769414 AATTCAGATATCAAAATG
1 AATTCAGATACCAAAATG
61769432 AATTCAGATACCAAAAT
1 AATTCAGATACCAAAAT
61769449 AAACCTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (18 bp):
AATTCAGATACCAAAATG
Found at i:61772345 original size:3 final size:3
Alignment explanation
Indices: 61772337--61772362 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61772327 CTCCTAATAT
61772337 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
61772363 TTACAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:61774801 original size:57 final size:58
Alignment explanation
Indices: 61774704--61774814 Score: 197
Period size: 57 Copynumber: 1.9 Consensus size: 58
61774694 TTGGTATTCT
61774704 TCTTGTCCATTTTATAATTTATATTCGAGATTTATAGTTATTCCTCTCAACAATGTTG
1 TCTTGTCCATTTTATAATTTATATTCGAGATTTATAGTTATTCCTCTCAACAATGTTG
* *
61774762 TCTT-TCCGTTTTATAATTTATATTCGAGATTTGTAGTTATTCCTCTCAACAAT
1 TCTTGTCCATTTTATAATTTATATTCGAGATTTATAGTTATTCCTCTCAACAAT
61774815 ACTGTCTTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
57 47 0.92
58 4 0.08
ACGTcount: A:0.25, C:0.16, G:0.10, T:0.49
Consensus pattern (58 bp):
TCTTGTCCATTTTATAATTTATATTCGAGATTTATAGTTATTCCTCTCAACAATGTTG
Found at i:61783336 original size:9 final size:8
Alignment explanation
Indices: 61783314--61783338 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
61783304 TAAGTTGTAT
61783314 TTAAAAAA
1 TTAAAAAA
61783322 TTAAAAAA
1 TTAAAAAA
61783330 TTAAAAAA
1 TTAAAAAA
61783338 T
1 T
61783339 ATATAAGACA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
TTAAAAAA
Found at i:61785556 original size:7 final size:7
Alignment explanation
Indices: 61785544--61785568 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
61785534 GGGGTCAAAA
61785544 TTAAATT
1 TTAAATT
61785551 TTAAATT
1 TTAAATT
61785558 TTAAATT
1 TTAAATT
61785565 TTAA
1 TTAA
61785569 TAGCTTATAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:61791285 original size:35 final size:35
Alignment explanation
Indices: 61791239--61791309 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
61791229 ATCAATTGGG
61791239 ATTTACCAACATATGATAAAACCTTAACTACCAAC
1 ATTTACCAACATATGATAAAACCTTAACTACCAAC
61791274 ATTTACCAACATATGATAAAACCTTAACTACCAAC
1 ATTTACCAACATATGATAAAACCTTAACTACCAAC
61791309 A
1 A
61791310 ATGTATCCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.46, C:0.25, G:0.03, T:0.25
Consensus pattern (35 bp):
ATTTACCAACATATGATAAAACCTTAACTACCAAC
Found at i:61795166 original size:36 final size:36
Alignment explanation
Indices: 61795126--61795233 Score: 189
Period size: 36 Copynumber: 3.0 Consensus size: 36
61795116 GATGTAAAAA
61795126 ATGGTACTACAAATGAAGTGGTTTCATCTGATGTTG
1 ATGGTACTACAAATGAAGTGGTTTCATCTGATGTTG
* *
61795162 ATGGTACAACAAATGAAGTGATTTCATCTGATGTTG
1 ATGGTACTACAAATGAAGTGGTTTCATCTGATGTTG
*
61795198 ATGGTACTACGAATGAAGTGGTTTCATCTGATGTTG
1 ATGGTACTACAAATGAAGTGGTTTCATCTGATGTTG
61795234 GTGGGGGTAA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (36 bp):
ATGGTACTACAAATGAAGTGGTTTCATCTGATGTTG
Found at i:61795444 original size:285 final size:285
Alignment explanation
Indices: 61794929--61795450 Score: 805
Period size: 285 Copynumber: 1.8 Consensus size: 285
61794919 CTACAAACAC
*
61794929 AGTGGTTGCATCTGATGTTGGTGGGGGTAATAAGATGACTTCAGACTCAAGAACCATGCCTTTTG
1 AGTGGTTGCATCTGATGTTGGTGGGGGTAATAAGATGACTTCAGACTCAAGAACCATGCCTGTTG
* * *
61794994 GGACTGATGATTCGAGTACAGAGAAACAGGAATCTCAAGGATGCTCTGGTTATGATTCTCAAAAG
66 AGACTGATGATTCGAGTACAGAGAAACAGGAATCTCAAGGATGCTCTAGCTATGATTCTCAAAAG
* ** *
61795059 GATTCTTTTGATAATATTTCTGTGGGAAGTGAAGAGTCGCCTGCTAAAGAACCTCAAGATGTAAA
131 GATTCTTTTGATAATATTTCTGTGAGAAGTGAAGAGTCGCAGGCTAAAGAACCTCAAGATATAAA
* * *
61795124 AAATGGTACTACAAATGAAGTGGTTTCATCTGATGTTGATGGTACAACAAATGAAGTGATTTCAT
196 AAATGATAATACAAATGAAGTGGTTTCACCTGATGTTGATGGTACAACAAATGAAGTGATTTCAT
61795189 CTGATGTTGATGGTACTACGAATGA
261 CTGATGTTGATGGTACTACGAATGA
* * **
61795214 AGTGGTTTCATCTGATGTTGGTGGGGGTAATAGGATGACTTCAGACATC-AGAACTGTGCCTGTT
1 AGTGGTTGCATCTGATGTTGGTGGGGGTAATAAGATGACTTCAGAC-TCAAGAACCATGCCTGTT
*
61795278 GAGACTGATGACTT-GAGTACAGAGAAACAGGAATCTCAAGGATGCTCTAGCTATGATTCTCCAA
65 GAGACTGATGA-TTCGAGTACAGAGAAACAGGAATCTCAAGGATGCTCTAGCTATGATTCTCAAA
* * * *
61795342 AGGATTCTTTTGATACTATTTCTGTGAGAAGTGAAGAGTTGCAGGCTAAGGAACCTCAGGATATA
129 AGGATTCTTTTGATAATATTTCTGTGAGAAGTGAAGAGTCGCAGGCTAAAGAACCTCAAGATATA
* * *
61795407 AAAGATGATAATACGAATGATGTGGTTTCACCTGATGTTGATGG
194 AAAAATGATAATACAAATGAAGTGGTTTCACCTGATGTTGATGG
61795451 GGGTAATAGG
Statistics
Matches: 212, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
285 208 0.98
286 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (285 bp):
AGTGGTTGCATCTGATGTTGGTGGGGGTAATAAGATGACTTCAGACTCAAGAACCATGCCTGTTG
AGACTGATGATTCGAGTACAGAGAAACAGGAATCTCAAGGATGCTCTAGCTATGATTCTCAAAAG
GATTCTTTTGATAATATTTCTGTGAGAAGTGAAGAGTCGCAGGCTAAAGAACCTCAAGATATAAA
AAATGATAATACAAATGAAGTGGTTTCACCTGATGTTGATGGTACAACAAATGAAGTGATTTCAT
CTGATGTTGATGGTACTACGAATGA
Found at i:61797391 original size:14 final size:13
Alignment explanation
Indices: 61797374--61797399 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61797364 TTTGTTTTTA
61797374 TTTTTTTTTCACC
1 TTTTTTTTTCACC
61797387 TTTTTTTTTCACC
1 TTTTTTTTTCACC
61797400 AATTCCTTTT
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:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTTTCACC
Found at i:61813158 original size:16 final size:18
Alignment explanation
Indices: 61813139--61813175 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
61813129 TTTTTTGTGT
61813139 TATAAAT-T-ACATAATA
1 TATAAATATAACATAATA
*
61813155 TATAAATATAATATAATA
1 TATAAATATAACATAATA
61813173 TAT
1 TAT
61813176 CAGAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAAATATAACATAATA
Found at i:61816093 original size:30 final size:33
Alignment explanation
Indices: 61816025--61816102 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
61816015 AATTTTACAT
61816025 GTTTAATTGAATTTTTATTAAAAAAATTAAAGG
1 GTTTAATTGAATTTTTATTAAAAAAATTAAAGG
* *
61816058 GTTTAATTAAATTTTTATT-AAAAAA-TAGA-G
1 GTTTAATTGAATTTTTATTAAAAAAATTAAAGG
61816088 GTTTAA-TGAATTTTT
1 GTTTAATTGAATTTTT
61816103 CAAAAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 8 0.19
30 7 0.17
31 3 0.07
32 6 0.14
33 18 0.43
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (33 bp):
GTTTAATTGAATTTTTATTAAAAAAATTAAAGG
Found at i:61823440 original size:30 final size:31
Alignment explanation
Indices: 61823381--61823450 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
61823371 ATTAATAGAT
*
61823381 AATATTATAATTTTTAATATTATTAAATATA
1 AATATTATAATTTTTAATATTAATAAATATA
61823412 AATATT-TAATTATTT-ATATTAA-ATAATATA
1 AATATTATAATT-TTTAATATTAATA-AATATA
61823442 AGATATTAT
1 A-ATATTAT
61823451 TAATATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
29 1 0.03
30 18 0.53
31 14 0.41
32 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (31 bp):
AATATTATAATTTTTAATATTAATAAATATA
Found at i:61823585 original size:15 final size:15
Alignment explanation
Indices: 61823561--61823593 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
61823551 TATTTATATT
*
61823561 AATATTTTAATAATA
1 AATATATTAATAATA
61823576 AATATATTAATAATA
1 AATATATTAATAATA
61823591 AAT
1 AAT
61823594 GTTTTATACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:61830149 original size:18 final size:19
Alignment explanation
Indices: 61830112--61830152 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
61830102 TGGGAGACAG
61830112 AAATGCCAGAAATAAAAAT
1 AAATGCCAGAAATAAAAAT
* *
61830131 AAATGCCTGGAAT-AAAAT
1 AAATGCCAGAAATAAAAAT
61830149 AAAT
1 AAAT
61830153 TGAGGTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.20
Consensus pattern (19 bp):
AAATGCCAGAAATAAAAAT
Found at i:61835851 original size:21 final size:21
Alignment explanation
Indices: 61835814--61835853 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61835804 ACACAATTAG
*
61835814 ATATTATAATTTTTAAAAATA
1 ATATTATAATTTATAAAAATA
61835835 ATATTAATAA-TTATAAAAA
1 ATATT-ATAATTTATAAAAA
61835854 AATCAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATTATAATTTATAAAAATA
Found at i:61835853 original size:22 final size:21
Alignment explanation
Indices: 61835814--61835854 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
61835804 ACACAATTAG
* *
61835814 ATATTATAATTTTTAAAAATA
1 ATATTATAATTATAAAAAATA
61835835 ATATTAATAATTATAAAAAA
1 ATATT-ATAATTATAAAAAA
61835855 ATCAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATTATAATTATAAAAAATA
Found at i:61838031 original size:16 final size:17
Alignment explanation
Indices: 61838010--61838041 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
61838000 TAATAATAAT
61838010 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
61838026 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
61838042 GCTTACCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:61838787 original size:21 final size:22
Alignment explanation
Indices: 61838753--61838793 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
61838743 TATTAGTTAA
61838753 TAATAATAACAATATATAATAT
1 TAATAATAACAATATATAATAT
* *
61838775 TAAT-ATAATAATATTTAAT
1 TAATAATAACAATATATAAT
61838794 TCACAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATAATAACAATATATAATAT
Found at i:61838955 original size:30 final size:27
Alignment explanation
Indices: 61838919--61838983 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
61838909 TTTCCTATAA
*
61838919 TATAATATCTTAACTTTAATTAATATAATT
1 TATAATATCTTAA--TTAAATAATAT-ATT
* *
61838949 TATAATATTTTAATTAAATAATATTTT
1 TATAATATCTTAATTAAATAATATATT
61838976 TATAATAT
1 TATAATAT
61838984 AATTCAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.31
28 10 0.31
30 12 0.38
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
TATAATATCTTAATTAAATAATATATT
Found at i:61838985 original size:16 final size:17
Alignment explanation
Indices: 61838949--61838986 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
61838939 TAATATAATT
61838949 TATAATATTTTAATTAA
1 TATAATATTTTAATTAA
*
61838966 -ATAATATTTTTA-TAA
1 TATAATATTTTAATTAA
61838981 TATAAT
1 TATAAT
61838987 TCAAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATAATATTTTAATTAA
Found at i:61844005 original size:12 final size:12
Alignment explanation
Indices: 61843988--61844015 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
61843978 AATTGAATCT
61843988 AAGGCCATGGTG
1 AAGGCCATGGTG
61844000 AAGGCCATGGTG
1 AAGGCCATGGTG
61844012 AAGG
1 AAGG
61844016 GGAAGGTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.43, T:0.14
Consensus pattern (12 bp):
AAGGCCATGGTG
Found at i:61845710 original size:42 final size:42
Alignment explanation
Indices: 61845663--61845742 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
61845653 AAAACACATC
*
61845663 ATCAATAAATTTGTAAATAATT-AGTTAAATTCTATTATGAGT
1 ATCAATAAATTAGTAAATAATTGA-TTAAATTCTATTATGAGT
61845705 ATCAATAAATTAGTAAATAATTGATTAAATTCTATTAT
1 ATCAATAAATTAGTAAATAATTGATTAAATTCTATTAT
61845743 TATTATTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (42 bp):
ATCAATAAATTAGTAAATAATTGATTAAATTCTATTATGAGT
Found at i:61846852 original size:22 final size:23
Alignment explanation
Indices: 61846827--61846870 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
61846817 ATACTAAGGA
61846827 TCGAAATTTAA-TTATAATTTTT
1 TCGAAATTTAATTTATAATTTTT
**
61846849 TCGAGTTTTAATTTATAATTTT
1 TCGAAATTTAATTTATAATTTT
61846871 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.57
Consensus pattern (23 bp):
TCGAAATTTAATTTATAATTTTT
Found at i:61867445 original size:7 final size:7
Alignment explanation
Indices: 61867435--61867484 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
61867425 AATCAAATAT
61867435 TAAAAGC
1 TAAAAGC
61867442 TAAAAGC
1 TAAAAGC
61867449 TAAAAGC
1 TAAAAGC
61867456 TAAAAGC
1 TAAAAGC
61867463 TAAAAGC
1 TAAAAGC
61867470 TAAAAGC
1 TAAAAGC
61867477 TAAAAGC
1 TAAAAGC
61867484 T
1 T
61867485 TATTTGAGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.16
Consensus pattern (7 bp):
TAAAAGC
Found at i:61877154 original size:31 final size:33
Alignment explanation
Indices: 61877095--61877168 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 33
61877085 ATATATTTAA
* * *
61877095 AGGTATTTAAACTTTACAATTTATACCT-ATTT
1 AGGTATCTAAACTTGACAATTTAAACCTAATTT
61877127 -GGTATCTAAACTTGA-AACTTTAAACCTAATTT
1 AGGTATCTAAACTTGACAA-TTTAAACCTAATTT
*
61877159 AGGTGTCTAA
1 AGGTATCTAA
61877169 TTAATATGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 2 0.06
31 21 0.60
32 4 0.11
33 8 0.23
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (33 bp):
AGGTATCTAAACTTGACAATTTAAACCTAATTT
Found at i:61878136 original size:33 final size:33
Alignment explanation
Indices: 61878064--61878136 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
61878054 ACCAGAACAA
*
61878064 CCTA-CAGATGCAACAGCACAAGTTATTCAAGC
1 CCTAGCAGACGCAACAGCACAAGTTATTCAAGC
* * *
61878096 CCCAGCAGACGCAACAGGAGAAGTTATTCAAAG-
1 CCTAGCAGACGCAACAGCACAAGTTATTC-AAGC
61878129 CCTAGCAG
1 CCTAGCAG
61878137 TCCTGCCGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 3 0.09
33 28 0.82
34 3 0.09
ACGTcount: A:0.37, C:0.27, G:0.21, T:0.15
Consensus pattern (33 bp):
CCTAGCAGACGCAACAGCACAAGTTATTCAAGC
Found at i:61892192 original size:2 final size:2
Alignment explanation
Indices: 61892187--61892236 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
61892177 TGTAATATCT
61892187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61892229 TA TA TA TA
1 TA TA TA TA
61892237 ACCTTATTGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61901753 original size:37 final size:37
Alignment explanation
Indices: 61901712--61901859 Score: 260
Period size: 37 Copynumber: 4.0 Consensus size: 37
61901702 TAGTTTTAGC
61901712 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
61901749 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
*
61901786 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGC
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
** *
61901823 TACACTTATCTGATCAAGTGATAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
61901860 AGCTTCAGCT
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 106 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (37 bp):
TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
Found at i:61901930 original size:45 final size:46
Alignment explanation
Indices: 61901821--61901944 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
61901811 GTGATAAGTG
*
61901821 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCCTCA
*
61901867 GCTACACTTATCTGATCAAGTGGTAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCCTCA
*
61901912 GCTACACTTATCTGATCAAG-GA-CAAGTGATAAG
1 GCTACACTTATCTGATCAAGTGATAAAGTGATAAG
61901945 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 1 0.01
45 21 0.28
46 42 0.57
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCCTCA
Found at i:61905246 original size:42 final size:42
Alignment explanation
Indices: 61905199--61905294 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
61905189 TTGGTATCGT
* * * *
61905199 ACACTTAGTGTCTGTTATTCGACATCGTCATTTT-CGTTTCGC
1 ACACTTAGTGTCCGCTATTCAACATCATCATTTTAC-TTTCGC
*
61905241 ACACTTAGTGCCCGCTATTCAACATCATCATTTTACTTTCGC
1 ACACTTAGTGTCCGCTATTCAACATCATCATTTTACTTTCGC
61905283 ACACTTAGTGTC
1 ACACTTAGTGTC
61905295 ATTCGTATAG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 46 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.39
Consensus pattern (42 bp):
ACACTTAGTGTCCGCTATTCAACATCATCATTTTACTTTCGC
Found at i:61918728 original size:23 final size:22
Alignment explanation
Indices: 61918685--61918728 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
61918675 TTCTAAGTCG
61918685 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
61918708 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
61918729 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:61919015 original size:49 final size:49
Alignment explanation
Indices: 61918825--61919016 Score: 190
Period size: 51 Copynumber: 3.8 Consensus size: 49
61918815 ATGTTTGGTT
* * * *
61918825 CACATAGTAGCTTGCACATAGTACTACACATGTGGCCATTACCA-TCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCA-T--CATTCCGGTA
** * * *
61918876 CATGTAGCAGCCTGCACATAGTACTACACACGTGATCAAAACTATT-CGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-C-CATC-ATTCCGGTA
* * * * *
61918927 CGCATAGTAGCCTACACATAGTACTACACATGCGCCCATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCATTCCGGTA
61918976 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCA
61919017 CTTTCACTTT
Statistics
Matches: 112, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
48 3 0.03
49 43 0.38
50 2 0.02
51 61 0.54
52 2 0.02
53 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (49 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCATTCCGGTA
Found at i:61919044 original size:100 final size:101
Alignment explanation
Indices: 61918825--61919013 Score: 247
Period size: 100 Copynumber: 1.9 Consensus size: 101
61918815 ATGTTTGGTT
* * * * **
61918825 CACATAGTAGCTTGCACATAGTACTACACATGTGGCCATTACCATCCGATACATGTAGCAGCCTG
1 CACATAGTAGCCTACACATAGTACTACACATGCGCCCATTA-CATCCGATACACATAGCAGCCTG
* *
61918890 CACATAGTACTACACACGTGATCAAAACTATTCGGTA
65 CACATAGTACTACACACGTGACCAAAACTATTCCGTA
* * *
61918927 CGCATAGTAGCCTACACATAGTACTACACATGCGCCCA-T-CATTCCGGTACACATAGTAGCCTG
1 CACATAGTAGCCTACACATAGTACTACACATGCGCCCATTACA-TCCGATACACATAGCAGCCTG
61918990 CACATAGTACTACACACGTGACCA
65 CACATAGTACTACACACGTGACCA
61919014 TCACTTTCAC
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
99 2 0.03
100 40 0.53
101 1 0.01
102 33 0.43
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (101 bp):
CACATAGTAGCCTACACATAGTACTACACATGCGCCCATTACATCCGATACACATAGCAGCCTGC
ACATAGTACTACACACGTGACCAAAACTATTCCGTA
Found at i:61929653 original size:12 final size:12
Alignment explanation
Indices: 61929621--61929654 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
61929611 GGTGCAATTA
61929621 CTTGAGAAAGTG
1 CTTGAGAAAGTG
* *
61929633 CTAGTGAAAGTG
1 CTTGAGAAAGTG
61929645 CTTGAGAAAG
1 CTTGAGAAAG
61929655 ACGTTCATTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.24
Consensus pattern (12 bp):
CTTGAGAAAGTG
Found at i:61933100 original size:18 final size:18
Alignment explanation
Indices: 61933077--61933117 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
61933067 TTTTTTATAA
61933077 TTTTTTGCTATTATTCTC
1 TTTTTTGCTATTATTCTC
* *
61933095 TTTTTTGCTGTTATTCTG
1 TTTTTTGCTATTATTCTC
61933113 TTTTT
1 TTTTT
61933118 CTCTTGCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.07, C:0.12, G:0.10, T:0.71
Consensus pattern (18 bp):
TTTTTTGCTATTATTCTC
Found at i:61934064 original size:13 final size:13
Alignment explanation
Indices: 61934046--61934072 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
61934036 CTCATATTCA
61934046 AAAGTAAACACTC
1 AAAGTAAACACTC
61934059 AAAGTAAACACTC
1 AAAGTAAACACTC
61934072 A
1 A
61934073 GCTGAATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (13 bp):
AAAGTAAACACTC
Found at i:61935276 original size:17 final size:17
Alignment explanation
Indices: 61935242--61935276 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
61935232 CATGATTTAA
61935242 TTATTAAATTATATTTT
1 TTATTAAATTATATTTT
*
61935259 TTATTCAAATTTTATTTT
1 TTATT-AAATTATATTTT
61935277 GCTCTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTAAATTATATTTT
Found at i:61938153 original size:15 final size:16
Alignment explanation
Indices: 61938125--61938166 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
61938115 TAGAAGTAAA
**
61938125 ATAAATTATTATATTT
1 ATAAATTAAAATATTT
61938141 A-AAATTAAAATATTT
1 ATAAATTAAAATATTT
*
61938156 ATAACTTAAAA
1 ATAAATTAAAA
61938167 ACTTCAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAATTAAAATATTT
Found at i:61939289 original size:20 final size:21
Alignment explanation
Indices: 61939264--61939307 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
61939254 CTTATTTTTA
61939264 TTTTTATTTTT-AAA-ATATTT
1 TTTTTATTTTTGAAACA-ATTT
61939284 TTTTTATTTTTGAAACAATTT
1 TTTTTATTTTTGAAACAATTT
61939305 TTT
1 TTT
61939308 AATGTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.50
21 10 0.45
22 1 0.05
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTTATTTTTGAAACAATTT
Found at i:61939294 original size:21 final size:20
Alignment explanation
Indices: 61939264--61939307 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
61939254 CTTATTTTTA
*
61939264 TTTTTATTTTTAAA-ATATTT
1 TTTTTATTTTGAAACA-ATTT
61939284 TTTTTATTTTTGAAACAATTT
1 TTTTTA-TTTTGAAACAATTT
61939305 TTT
1 TTT
61939308 AATGTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 14 0.67
22 1 0.05
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTTATTTTGAAACAATTT
Found at i:61950137 original size:23 final size:23
Alignment explanation
Indices: 61950097--61950144 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
61950087 AATTCAAAGT
* * *
61950097 AAATAATATGCAACGCAAAATAA
1 AAATAACATACAAAGCAAAATAA
*
61950120 AAATAACATACAAAGCAAATTAA
1 AAATAACATACAAAGCAAAATAA
61950143 AA
1 AA
61950145 TAAATAACCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.17
Consensus pattern (23 bp):
AAATAACATACAAAGCAAAATAA
Found at i:61952315 original size:24 final size:24
Alignment explanation
Indices: 61952288--61952337 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
61952278 TTTCTAGAAG
*
61952288 TTTAATAGTTATTAGTATAATATA
1 TTTAATAGTTATTAGCATAATATA
* * *
61952312 TTTAGTATTTATTAGCATAATTTA
1 TTTAATAGTTATTAGCATAATATA
61952336 TT
1 TT
61952338 GTACTTATAA
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:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (24 bp):
TTTAATAGTTATTAGCATAATATA
Found at i:61967240 original size:30 final size:32
Alignment explanation
Indices: 61967197--61967262 Score: 91
Period size: 30 Copynumber: 2.1 Consensus size: 32
61967187 CCCCGCAAGG
***
61967197 ATTTAGTCGAATTTAATTTTTGTACTTTTTAA
1 ATTTAGTCGAATTTAATCCCTGTACTTTTTAA
61967229 ATTTA-TC-AATTTAATCCCTGTACTTTTTAA
1 ATTTAGTCGAATTTAATCCCTGTACTTTTTAA
61967259 ATTT
1 ATTT
61967263 TGAAATTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 24 0.77
31 2 0.06
32 5 0.16
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.55
Consensus pattern (32 bp):
ATTTAGTCGAATTTAATCCCTGTACTTTTTAA
Found at i:61967270 original size:30 final size:31
Alignment explanation
Indices: 61967217--61967275 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
61967207 ATTTAATTTT
*
61967217 TGTACTTTTTAAATTTATCAATTT-AATCCC
1 TGTACTTTTTAAATTTATAAATTTCAATCCC
61967247 TGTACTTTTTAAATTT-TGAAATTTCAATC
1 TGTACTTTTTAAATTTAT-AAATTTCAATC
61967276 TTGACTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 1 0.04
30 21 0.81
31 4 0.15
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.51
Consensus pattern (31 bp):
TGTACTTTTTAAATTTATAAATTTCAATCCC
Found at i:61971133 original size:18 final size:18
Alignment explanation
Indices: 61971110--61971145 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
61971100 ACCTTGACGG
61971110 CGGACCGCTGTTCGAACC
1 CGGACCGCTGTTCGAACC
61971128 CGGACCGCTGTTCGAACC
1 CGGACCGCTGTTCGAACC
61971146 GGCTCGAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.39, G:0.28, T:0.17
Consensus pattern (18 bp):
CGGACCGCTGTTCGAACC
Found at i:61973628 original size:82 final size:81
Alignment explanation
Indices: 61973470--61973626 Score: 255
Period size: 82 Copynumber: 1.9 Consensus size: 81
61973460 TAATTCTATC
* * *
61973470 CTTTATATATTTTTCTCAATTTTTATTAAATAACTTTAAATTTGAAATTTGAAACTCACAAAGAA
1 CTTTATATATTTTTCTCAAATATTATTAAATAACTTTAAATTTGAAATTTGAAACCCACAAAGAA
61973535 TATTTCTTTTTCCATA
66 TATTTCTTTTTCCATA
61973551 CTTTATATACATTTTT-TCAAATATTATTAAATAACTTTAAATTTGAAATTTGAAACCCAC-AAG
1 CTTTATAT--ATTTTTCTCAAATATTATTAAATAACTTTAAATTTGAAATTTGAAACCCACAAAG
61973614 AATATTTCTTTTT
64 AATATTTCTTTTT
61973627 TCTTTTATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
81 24 0.34
82 41 0.58
83 6 0.08
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (81 bp):
CTTTATATATTTTTCTCAAATATTATTAAATAACTTTAAATTTGAAATTTGAAACCCACAAAGAA
TATTTCTTTTTCCATA
Found at i:61975084 original size:8 final size:8
Alignment explanation
Indices: 61975071--61975095 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
61975061 TATTAATTCA
61975071 TTTAAAAT
1 TTTAAAAT
61975079 TTTAAAAT
1 TTTAAAAT
61975087 TTTAAAAT
1 TTTAAAAT
61975095 T
1 T
61975096 AAAGCTCGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAAAT
Found at i:61977772 original size:5 final size:5
Alignment explanation
Indices: 61977764--61977792 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
61977754 ATGAACTGAA
61977764 TCGAT TCGAT TCGAT TCGAT TCGAT TCGA
1 TCGAT TCGAT TCGAT TCGAT TCGAT TCGA
61977793 AAATGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (5 bp):
TCGAT
Found at i:61978376 original size:20 final size:20
Alignment explanation
Indices: 61978351--61978390 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61978341 CGTAAAATGA
*
61978351 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
61978371 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
61978391 GGAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:61978380 original size:34 final size:35
Alignment explanation
Indices: 61978336--61978402 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
61978326 CAGTAAAATA
*
61978336 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
61978370 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
61978403 TTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:61998004 original size:20 final size:20
Alignment explanation
Indices: 61997966--61998004 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
61997956 ATTCAAAGCC
*
61997966 TGAATCTTGAACCCTAACCT
1 TGAATCTTGAACCCGAACCT
* *
61997986 TGAATTTTGAACTCGAACC
1 TGAATCTTGAACCCGAACC
61998005 CTAAACTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (20 bp):
TGAATCTTGAACCCGAACCT
Found at i:62010228 original size:15 final size:15
Alignment explanation
Indices: 62010210--62010240 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
62010200 AAGTGTGGCG
62010210 ATGATAAATATCGAC
1 ATGATAAATATCGAC
62010225 ATGATAAATATCGAC
1 ATGATAAATATCGAC
62010240 A
1 A
62010241 CCTTGGGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (15 bp):
ATGATAAATATCGAC
Found at i:62013318 original size:16 final size:15
Alignment explanation
Indices: 62013284--62013326 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
62013274 AAAAGAATGG
62013284 AAAATAAAAGAAAAA
1 AAAATAAAAGAAAAA
* *
62013299 AAAATTAAAAGAACAT
1 AAAA-TAAAAGAAAAA
*
62013315 AAAAGAAAAGAA
1 AAAATAAAAGAA
62013327 TTAAATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.79, C:0.02, G:0.09, T:0.09
Consensus pattern (15 bp):
AAAATAAAAGAAAAA
Found at i:62014916 original size:28 final size:28
Alignment explanation
Indices: 62014876--62014933 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
62014866 ATAAAATTTA
62014876 TTAAGCATTGTCATAACCTTCATACTTT
1 TTAAGCATTGTCATAACCTTCATACTTT
62014904 TTAAGCATTGTCATAACCTTCATACTTT
1 TTAAGCATTGTCATAACCTTCATACTTT
62014932 TT
1 TT
62014934 TTTTTTTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (28 bp):
TTAAGCATTGTCATAACCTTCATACTTT
Found at i:62019623 original size:16 final size:16
Alignment explanation
Indices: 62019602--62019647 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
62019592 AAATAAGGGT
62019602 TGTAATGGAATAAAAA
1 TGTAATGGAATAAAAA
* *
62019618 TGTAATGGAATACAAT
1 TGTAATGGAATAAAAA
62019634 TGTAATGGAATAAA
1 TGTAATGGAATAAA
62019648 GCTGTAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAAAAA
Found at i:62019977 original size:23 final size:21
Alignment explanation
Indices: 62019936--62020002 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 21
62019926 TAATTATATG
*
62019936 AATTAATAAAAATTATAATAAAT
1 AATTAAT-ACAATT-TAATAAAT
62019959 AATTTAAT-CATATTTTAATATAAT
1 AA-TTAATACA-A-TTTAATA-AAT
*
62019983 TATTAATACAATTTAATAAA
1 AATTAATACAATTTAATAAA
62020003 AGAATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
21 2 0.05
22 8 0.22
23 14 0.38
24 13 0.35
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTAATACAATTTAATAAAT
Found at i:62022888 original size:15 final size:15
Alignment explanation
Indices: 62022839--62022889 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
62022829 TTGCCTTAGG
62022839 TTACGTTTTAGTCAT
1 TTACGTTTTAGTCAT
* **
62022854 TTATG-TTT-GAAAT
1 TTACGTTTTAGTCAT
62022867 GTTACGTTTTAGTCAT
1 -TTACGTTTTAGTCAT
62022883 TTACGTT
1 TTACGTT
62022890 ATCATGTTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 3 0.11
14 7 0.26
15 14 0.52
16 3 0.11
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.53
Consensus pattern (15 bp):
TTACGTTTTAGTCAT
Found at i:62023789 original size:98 final size:98
Alignment explanation
Indices: 62023620--62023814 Score: 338
Period size: 98 Copynumber: 2.0 Consensus size: 98
62023610 ATACAATAAA
* *
62023620 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATC
62023685 CCTTTAGAATC-CTAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCTC-AAACTCGGAATATTTCCTTT
* *
62023718 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATC
62023783 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
62023815 CATGATTTTT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
98 91 0.99
99 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATC
CCTTTAGAATCTCAAACTCGGAATATTTCCTTT
Found at i:62024572 original size:3 final size:3
Alignment explanation
Indices: 62024564--62024589 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
62024554 AATAGTACTA
62024564 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
62024590 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:62024594 original size:3 final size:3
Alignment explanation
Indices: 62024588--62024641 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
62024578 CAACAACAAC
*
62024588 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
62024636 AAT AAT
1 AAT AAT
62024642 GAGAAAATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:62026303 original size:132 final size:132
Alignment explanation
Indices: 62026066--62026845 Score: 1303
Period size: 132 Copynumber: 5.9 Consensus size: 132
62026056 CTGCAACTTC
* * *
62026066 AGGGAGATAAGA-CTTGTCAAT-TTCAGTCTATTCCACTGTTACCCAGGGAAGTAGAATTACTAG
1 AGGGAGATAAGATC-TG-AAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAG
*
62026129 CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACT
64 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACT
62026194 GCTT
129 GCTT
* * *
62026198 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACCGTTGCCTAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
*
62026263 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
62026328 TT
131 TT
62026330 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
* * ** *
62026395 TCAATGTACTCCATTGTAATCACAATGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
62026460 TT
131 TT
* *
62026462 AGGGAGATAAGATCTGAAATCTTTAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
62026527 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
62026592 TT
131 TT
*
62026594 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGAAAGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
* ** * *
62026659 TCAATGTACTCCATTGTAACCACAATGAGGTAAAATCCGTCATCTTTGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
62026724 TT
131 TT
* *
62026726 AGGGAGATAAGATCTGAAATCTTTAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
* *
62026791 TCAATGTACTCCAATGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCT
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
62026846 TCGCTGTCAA
Statistics
Matches: 607, Mismatches: 39, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
131 3 0.00
132 603 0.99
133 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (132 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TT
Found at i:62026378 original size:44 final size:44
Alignment explanation
Indices: 62026129--62026640 Score: 127
Period size: 44 Copynumber: 11.6 Consensus size: 44
62026119 GAATTACTAG
* ** * * * **
62026129 CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCACTATTGCC-CAGGGAGATAAGATCTGAAAT
* * * **
62026174 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAAT
1 CTTCAATCTACTCCACTATTGCCCAGGGAGATAAGATCTGAAAT
* ** * *
62026218 CTTCAATCTATTCCACCGTTGCCTAGGGA-AGT-AGAATTACTG---G
1 CTTCAATCTACTCCACTATTGCCCAGGGAGA-TAAG-A-T-CTGAAAT
* ** * * * **
62026261 CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCACTATTGCC-CAGGGAGATAAGATCTGAAAT
* * * **
62026306 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAAT
1 CTTCAATCTACTCCACTATTGCCCAGGGAGATAAGATCTGAAAT
* * * *
62026350 CTTCAATCTATTCCACTGTTGCCCAGGGA-AGT-AGAAT-T-ACTAG
1 CTTCAATCTACTCCACTATTGCCCAGGGAGA-TAAG-ATCTGA-AAT
* * * * ** * * * **
62026393 CTTCAATGTACTCCATTGTAAT-CACAATGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCA--CTATTGCCCAGGGAGATAAGATCTGAAAT
** * * **
62026438 CTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAAT
1 CTTCAATCTACTCCACTATTGCCCAGGGAGATAAGATCTGAAAT
* * * *
62026482 CTTTAATCTATTCCACTGTTGCCCAGGGA-AGT-AGAATTACTG---G
1 CTTCAATCTACTCCACTATTGCCCAGGGAGA-TAAG-A-T-CTGAAAT
* * ** * * * **
62026525 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCACTATTGCC-CAGGGAGATAAGATCTGAAAT
* * * **
62026570 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAAT
1 CTTCAATCTACTCCACTATTGCCCAGGGAGATAAGATCTGAAAT
* *
62026614 CTTCAATCTATTCCACTGTTGCCCAGG
1 CTTCAATCTACTCCACTATTGCCCAGG
62026641 AAAGTAGAAT
Statistics
Matches: 316, Mismatches: 121, Indels: 61
0.63 0.24 0.12
Matches are distributed among these distances:
42 5 0.02
43 64 0.20
44 175 0.55
45 66 0.21
46 6 0.02
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (44 bp):
CTTCAATCTACTCCACTATTGCCCAGGGAGATAAGATCTGAAAT
Found at i:62028224 original size:9 final size:9
Alignment explanation
Indices: 62028210--62028278 Score: 79
Period size: 9 Copynumber: 7.8 Consensus size: 9
62028200 TTCACTTTTA
62028210 TTTTTTTGT
1 TTTTTTTGT
62028219 TTTTTTT-T
1 TTTTTTTGT
62028227 GTTTTTTTGT
1 -TTTTTTTGT
62028237 TTTTTTTG-
1 TTTTTTTGT
62028245 TTTTTTTGT
1 TTTTTTTGT
* *
62028254 TATTGTTGT
1 TTTTTTTGT
* *
62028263 TGTTGTTGT
1 TTTTTTTGT
62028272 TTTTTTT
1 TTTTTTT
62028279 TTTGAATCTG
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
8 9 0.17
9 42 0.81
10 1 0.02
ACGTcount: A:0.01, C:0.00, G:0.14, T:0.84
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:62028226 original size:18 final size:18
Alignment explanation
Indices: 62028205--62028279 Score: 91
Period size: 17 Copynumber: 4.2 Consensus size: 18
62028195 TTTCTTTCAC
*
62028205 TTTTATTTTTTTGTTTTT
1 TTTTGTTTTTTTGTTTTT
62028223 TTTTGTTTTTTTG-TTTT
1 TTTTGTTTTTTTGTTTTT
*
62028240 TTTTGTTTTTTTG-TTAT
1 TTTTGTTTTTTTGTTTTT
* *
62028257 TGTTGTTGTTGTTGTTTTT
1 TTTTGTT-TTTTTGTTTTT
62028276 TTTT
1 TTTT
62028280 TTGAATCTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
17 26 0.53
18 17 0.35
19 6 0.12
ACGTcount: A:0.03, C:0.00, G:0.13, T:0.84
Consensus pattern (18 bp):
TTTTGTTTTTTTGTTTTT
Found at i:62032590 original size:98 final size:98
Alignment explanation
Indices: 62032421--62032615 Score: 338
Period size: 98 Copynumber: 2.0 Consensus size: 98
62032411 ATACAATAAA
* *
62032421 ACTTTAAAAGAATATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
62032486 CCTTTAGAATC-CTAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCTC-AAACTCGGAATATTTCCTTT
* *
62032519 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
62032584 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
62032616 CATGATTTTT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
98 91 0.99
99 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCTCAAACTCGGAATATTTCCTTT
Found at i:62039013 original size:3 final size:3
Alignment explanation
Indices: 62039007--62039062 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
62038997 CAACAACAAC
*
62039007 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
62039055 AAT AAT AA
1 AAT AAT AA
62039063 GAAAATAACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:62041651 original size:24 final size:24
Alignment explanation
Indices: 62041624--62041669 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
62041614 AGTTAATTAA
62041624 TGACGAGTTATAGTATAAACATAG
1 TGACGAGTTATAGTATAAACATAG
62041648 TGACGAGTTATAGTATAAACAT
1 TGACGAGTTATAGTATAAACAT
62041670 GCATGAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (24 bp):
TGACGAGTTATAGTATAAACATAG
Found at i:62043873 original size:8 final size:8
Alignment explanation
Indices: 62043860--62043915 Score: 78
Period size: 8 Copynumber: 7.1 Consensus size: 8
62043850 TTATAATTAT
62043860 TATTATAA
1 TATTATAA
62043868 TATTATAA
1 TATTATAA
* * *
62043876 TGTAAT-T
1 TATTATAA
62043883 TATTATAA
1 TATTATAA
62043891 TATTATAA
1 TATTATAA
62043899 TATTATAA
1 TATTATAA
62043907 TATTATAA
1 TATTATAA
62043915 T
1 T
62043916 GTAATTTAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
7 4 0.10
8 37 0.90
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (8 bp):
TATTATAA
Found at i:62046473 original size:5 final size:5
Alignment explanation
Indices: 62046463--62046487 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
62046453 CAAACGCCAC
62046463 CAAAA CAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA
62046488 GCACTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:62046890 original size:13 final size:13
Alignment explanation
Indices: 62046872--62047039 Score: 90
Period size: 13 Copynumber: 13.6 Consensus size: 13
62046862 TAACTTTTAT
62046872 AAGTTAATATTAA
1 AAGTTAATATTAA
62046885 AAGTTAATATTAA
1 AAGTTAATATTAA
*
62046898 AA---AAT-TTAG
1 AAGTTAATATTAA
* * *
62046907 AATTTAACTTTTAT
1 AAGTTAA-TATTAA
62046921 AAGTTAATATTAA
1 AAGTTAATATTAA
* *
62046934 AAGGTAATATTCA
1 AAGTTAATATTAA
*
62046947 AA---AAT-TTAG
1 AAGTTAATATTAA
* * *
62046956 AATTTAACTTTTAT
1 AAGTTAA-TATTAA
62046970 AAGTTAATATTAA
1 AAGTTAATATTAA
*
62046983 AAGTTAATATTCA
1 AAGTTAATATTAA
*
62046996 AA---AAT-TTAG
1 AAGTTAATATTAA
* * *
62047005 AATTTAACTTTTAT
1 AAGTTAA-TATTAA
62047019 AAGTTAATATTAA
1 AAGTTAATATTAA
62047032 AAGTTAAT
1 AAGTTAAT
62047040 TAGGGTTCAA
Statistics
Matches: 120, Mismatches: 20, Indels: 30
0.71 0.12 0.18
Matches are distributed among these distances:
9 13 0.11
10 9 0.08
12 6 0.05
13 65 0.54
14 27 0.22
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (13 bp):
AAGTTAATATTAA
Found at i:62046913 original size:49 final size:49
Alignment explanation
Indices: 62046840--62047039 Score: 364
Period size: 49 Copynumber: 4.1 Consensus size: 49
62046830 NNNNNNNNNN
62046840 AATATTCAAAAAATTTAGAATTTAACTTTTATAAGTTAATATTAAAAGTT
1 AATATT-AAAAAATTTAGAATTTAACTTTTATAAGTTAATATTAAAAGTT
*
62046890 AATATTAAAAAATTTAGAATTTAACTTTTATAAGTTAATATTAAAAGGT
1 AATATTAAAAAATTTAGAATTTAACTTTTATAAGTTAATATTAAAAGTT
*
62046939 AATATTCAAAAATTTAGAATTTAACTTTTATAAGTTAATATTAAAAGTT
1 AATATTAAAAAATTTAGAATTTAACTTTTATAAGTTAATATTAAAAGTT
*
62046988 AATATTCAAAAATTTAGAATTTAACTTTTATAAGTTAATATTAAAAGTT
1 AATATTAAAAAATTTAGAATTTAACTTTTATAAGTTAATATTAAAAGTT
62047037 AAT
1 AAT
62047040 TAGGGTTCAA
Statistics
Matches: 147, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
49 141 0.96
50 6 0.04
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.42
Consensus pattern (49 bp):
AATATTAAAAAATTTAGAATTTAACTTTTATAAGTTAATATTAAAAGTT
Found at i:62047487 original size:22 final size:23
Alignment explanation
Indices: 62047444--62047488 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
62047434 TTTAATTCAA
**
62047444 AATATTGAATAATTAATTAAATT
1 AATATTGAATAATTAACAAAATT
*
62047467 AATATTG-CTAATTAACAAAATT
1 AATATTGAATAATTAACAAAATT
62047489 GAATGTGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (23 bp):
AATATTGAATAATTAACAAAATT
Found at i:62050258 original size:15 final size:16
Alignment explanation
Indices: 62050234--62050276 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
62050224 AAAATATAAT
62050234 TAATCT-AATTAATCC
1 TAATCTAAATTAATCC
**
62050249 TAAT-TAAATTAATTT
1 TAATCTAAATTAATCC
62050264 TAATCTAAATTAA
1 TAATCTAAATTAA
62050277 CAACTTTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 15 0.62
16 8 0.33
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATCTAAATTAATCC
Found at i:62050868 original size:33 final size:33
Alignment explanation
Indices: 62050831--62050900 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
62050821 GATTATATAA
*
62050831 AAAAATTAAAT-AAATAAAATTTAAAAAAATATT
1 AAAAATTAAATGAAA-AAAATATAAAAAAATATT
* * *
62050864 AAAAATTAAATGAAAATAATATAATAAAATTTT
1 AAAAATTAAATGAAAAAAATATAAAAAAATATT
62050897 AAAA
1 AAAA
62050901 TAATATGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (33 bp):
AAAAATTAAATGAAAAAAATATAAAAAAATATT
Found at i:62056642 original size:15 final size:15
Alignment explanation
Indices: 62056596--62056656 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
62056586 TTTTAAATTT
* *
62056596 TTTTATATTATTTAAA
1 TTTTATATT-TTTTAC
* **
62056612 TTTAATATTTAATAC
1 TTTTATATTTTTTAC
62056627 TTTTATATTTTTTAC
1 TTTTATATTTTTTAC
*
62056642 TTATTAAATTTTTTA
1 TT-TTATATTTTTTA
62056657 TATAGTTATC
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
15 16 0.46
16 19 0.54
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTATATTTTTTAC
Found at i:62063123 original size:22 final size:24
Alignment explanation
Indices: 62063082--62063125 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
62063072 GGACCCAGAA
62063082 TTAAATTGTATATTTTTACAATAG
1 TTAAATTGTATATTTTTACAATAG
62063106 TTAAATTGTA-A-TTTTACAAT
1 TTAAATTGTATATTTTTACAAT
62063126 TTTAGTAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
24 10 0.50
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (24 bp):
TTAAATTGTATATTTTTACAATAG
Found at i:62065385 original size:2 final size:2
Alignment explanation
Indices: 62065373--62065404 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
62065363 ATTCTTCCCC
*
62065373 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62065405 CTCCTTCCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:62076470 original size:9 final size:8
Alignment explanation
Indices: 62076445--62076478 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
62076435 TTTGTATGTC
62076445 AAATTAAA
1 AAATTAAA
62076453 AAATTAAA
1 AAATTAAA
62076461 AAATTAAA
1 AAATTAAA
*
62076469 AAATTTAA
1 AAATTAAA
62076477 AA
1 AA
62076479 CGTTGAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AAATTAAA
Found at i:62083482 original size:20 final size:21
Alignment explanation
Indices: 62083441--62083483 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
62083431 AATAGACATG
*
62083441 CATATTTTTTAAAAATTGATT
1 CATATATTTTAAAAATTGATT
*
62083462 CATATATTTTAAATA-TGATT
1 CATATATTTTAAAAATTGATT
62083482 CA
1 CA
62083484 CATTAGACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49
Consensus pattern (21 bp):
CATATATTTTAAAAATTGATT
Found at i:62085650 original size:43 final size:43
Alignment explanation
Indices: 62085509--62085650 Score: 106
Period size: 43 Copynumber: 3.3 Consensus size: 43
62085499 TGCAACTGAC
** *
62085509 TGTGGATGCACAACATGTTAGCAAGTAAGAGCTGTCAATAGGT
1 TGTGGATGCACAACATGTTAATAGGTAAGAGCTGTCAATAGGT
** *** * * * ** ** *
62085552 TGTGGATGCACAGTAAAATAATGTAGATAAAATCTCCCACGA-AT
1 TGTGGATGCACAACATGTTAA--TAGGTAAGAGCTGTCAATAGGT
*
62085596 TGTAGATGCACAACATGTTAATAGGTAAGAGCTGTCAATAGGT
1 TGTGGATGCACAACATGTTAATAGGTAAGAGCTGTCAATAGGT
62085639 TGTGGATGCACA
1 TGTGGATGCACA
62085651 TCATATTTGC
Statistics
Matches: 65, Mismatches: 31, Indels: 6
0.64 0.30 0.06
Matches are distributed among these distances:
42 12 0.18
43 27 0.42
44 16 0.25
45 10 0.15
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (43 bp):
TGTGGATGCACAACATGTTAATAGGTAAGAGCTGTCAATAGGT
Found at i:62085912 original size:35 final size:33
Alignment explanation
Indices: 62085852--62085947 Score: 102
Period size: 35 Copynumber: 2.8 Consensus size: 33
62085842 CATTAATGCA
* * *
62085852 CTTATAACAGATCAATACAGTAGCAAATAGTATG
1 CTTATAACA-ATCAATACAATAGCAAATAATACG
* *
62085886 CTTTATAACATATCAATACAAAAGCAATTAATACG
1 C-TTATAACA-ATCAATACAATAGCAAATAATACG
*
62085921 CTTATAACAATTCAATATAATAGCAAA
1 CTTATAACAA-TCAATACAATAGCAAA
62085948 AGACATGCTT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
33 1 0.02
34 22 0.43
35 28 0.55
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (33 bp):
CTTATAACAATCAATACAATAGCAAATAATACG
Found at i:62085956 original size:69 final size:70
Alignment explanation
Indices: 62085807--62085957 Score: 159
Period size: 69 Copynumber: 2.2 Consensus size: 70
62085797 TATTCAATGC
**** *
62085807 AATATGACATGC-TTATAACATATCAATATGGTAGTCATTAATGCACTTATAACAGATCAATACA
1 AATA-GACATGCTTTATAACATATCAATACAAAAGTCATTAATACACTTATAACAGATCAATACA
*
62085871 GTAGCA
65 ATAGCA
* * *
62085877 AATAG-TATGCTTTATAACATATCAATACAAAAG-CAATTAATACGCTTATAACA-ATTCAATAT
1 AATAGACATGCTTTATAACATATCAATACAAAAGTC-ATTAATACACTTATAACAGA-TCAATAC
62085939 AATAGCA
64 AATAGCA
62085946 AA-AGACATGCTT
1 AATAGACATGCTT
62085958 ATTATGTGTT
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
68 8 0.12
69 55 0.82
70 4 0.06
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (70 bp):
AATAGACATGCTTTATAACATATCAATACAAAAGTCATTAATACACTTATAACAGATCAATACAA
TAGCA
Found at i:62086779 original size:29 final size:30
Alignment explanation
Indices: 62086708--62086789 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
62086698 TAAATCTCAA
*
62086708 AATTATACAC--GAACTTTGATTTAATGTGT
1 AATTATACACATGAACTTTGATTT-AGGTGT
* *
62086737 AATT-TGATATATGAACTTTGATTT-GGTGT
1 AATTAT-ACACATGAACTTTGATTTAGGTGT
62086766 AATTATACACATGAAACTTTGATT
1 AATTATACACATG-AACTTTGATT
62086790 ACGATTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
28 1 0.02
29 19 0.44
30 11 0.26
31 12 0.28
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.43
Consensus pattern (30 bp):
AATTATACACATGAACTTTGATTTAGGTGT
Found at i:62087517 original size:25 final size:28
Alignment explanation
Indices: 62087461--62087517 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
62087451 CGGGGAAATT
62087461 GGCCCATTCCGGTAAATAATAAAATACCG
1 GGCCCATTCCGGTAAATAATAAAATA-CG
* *
62087490 GGCCTATTTCGGT-AATAA-AAAATA-G
1 GGCCCATTCCGGTAAATAATAAAATACG
62087515 GGC
1 GGC
62087518 TTTTATGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 4 0.15
27 6 0.23
28 5 0.19
29 11 0.42
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (28 bp):
GGCCCATTCCGGTAAATAATAAAATACG
Found at i:62091626 original size:16 final size:16
Alignment explanation
Indices: 62091601--62091631 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62091591 GTTTTGATTA
62091601 TATGTATATGTATATG
1 TATGTATATGTATATG
*
62091617 TATGTGTATGTATAT
1 TATGTATATGTATAT
62091632 AATTGTTAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (16 bp):
TATGTATATGTATATG
Found at i:62097787 original size:6 final size:6
Alignment explanation
Indices: 62097755--62097790 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
62097745 GTTCCGTAAC
* *
62097755 ACCCCA ACACCA ACACCA ACCCCA ACCCCA ACCCCA
1 ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA
62097791 TCCAACATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.39, C:0.61, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCCA
Found at i:62103561 original size:14 final size:12
Alignment explanation
Indices: 62103542--62103587 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
62103532 CAATATGTAA
62103542 ATGTGTGTTTAAGT
1 ATGTGTGTTT--GT
62103556 ATGTGTGTTTGT
1 ATGTGTGTTTGT
*
62103568 ATGTGTGTGTGT
1 ATGTGTGTTTGT
*
62103580 GTGTGTGT
1 ATGTGTGT
62103588 GTGGCCCCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 20 0.67
14 10 0.33
ACGTcount: A:0.11, C:0.00, G:0.37, T:0.52
Consensus pattern (12 bp):
ATGTGTGTTTGT
Done.