Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 2 of 196
Found at i:326195 original size:49 final size:49
Alignment explanation
Indices: 326139--326233 Score: 147
Period size: 49 Copynumber: 1.9 Consensus size: 49
326129 GAAAGGATAT
326139 ATCTTAGAAATAAACG-AGTGCATAAAGAAAAGGTAGCTAAATTGGTTAC
1 ATCTTAGAAATAAACGTA-TGCATAAAGAAAAGGTAGCTAAATTGGTTAC
** *
326188 ATCTTAGAAATAAGTGTATGCATAAAGAAAAGGTGGCTAAATTGGT
1 ATCTTAGAAATAAACGTATGCATAAAGAAAAGGTAGCTAAATTGGT
326234 ATTTCTCTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
49 41 0.98
50 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.26
Consensus pattern (49 bp):
ATCTTAGAAATAAACGTATGCATAAAGAAAAGGTAGCTAAATTGGTTAC
Found at i:326424 original size:52 final size:53
Alignment explanation
Indices: 326321--326427 Score: 164
Period size: 52 Copynumber: 2.0 Consensus size: 53
326311 CAAGAGAGAT
*
326321 ATAGTTTAGATGCTAAGTAAAGTTGAAAAAGAAACAATGCAACTCTTATGCTG
1 ATAGTTTAAATGCTAAGTAAAGTTGAAAAAGAAACAATGCAACTCTTATGCTG
* *
326374 ATAGTTTAAATGCTAAGTAGAGTTG-GAAAG-AACAAATGCAACTCTTATGCTG
1 ATAGTTTAAATGCTAAGTAAAGTTGAAAAAGAAAC-AATGCAACTCTTATGCTG
326426 AT
1 AT
326428 GAATTTCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
51 3 0.06
52 24 0.48
53 23 0.46
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (53 bp):
ATAGTTTAAATGCTAAGTAAAGTTGAAAAAGAAACAATGCAACTCTTATGCTG
Found at i:328488 original size:22 final size:21
Alignment explanation
Indices: 328462--328513 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
328452 CGATTTCTGC
328462 TTCTTCTTCTCATACGTTTCTT
1 TTCTTCTTCTC-TACGTTTCTT
328484 TTCTTCTAT-T-TACGTTTCTT
1 TTCTTCT-TCTCTACGTTTCTT
*
328504 TT-TTTTTCTC
1 TTCTTCTTCTC
328514 CATTTTATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
18 1 0.04
19 4 0.15
20 12 0.46
22 8 0.31
23 1 0.04
ACGTcount: A:0.08, C:0.23, G:0.04, T:0.65
Consensus pattern (21 bp):
TTCTTCTTCTCTACGTTTCTT
Found at i:328489 original size:19 final size:19
Alignment explanation
Indices: 328465--328505 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
328455 TTTCTGCTTC
328465 TTCTTCTCA-TACGTTTCTT
1 TTCTTCT-ATTACGTTTCTT
328484 TTCTTCTATTTACGTTTCTT
1 TTCTTCTA-TTACGTTTCTT
328504 TT
1 TT
328506 TTTTTCTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 1 0.05
19 7 0.35
20 12 0.60
ACGTcount: A:0.10, C:0.22, G:0.05, T:0.63
Consensus pattern (19 bp):
TTCTTCTATTACGTTTCTT
Found at i:329544 original size:78 final size:78
Alignment explanation
Indices: 329423--329566 Score: 207
Period size: 78 Copynumber: 1.8 Consensus size: 78
329413 GTGTTGCTAT
* * *
329423 CTTACCAAAGGAAGCTAAGCCAAATAAGATAGAATCACCATTGCGAATTCAGTCCTCATTAACCC
1 CTTACCAAAGGAAGCTAAGCCAAATAAGATAGAATCACAATTGCAAATTCACTCCTCATTAACCC
329488 CGAGTGCCACTGC
66 CGAGTGCCACTGC
* * * * **
329501 CTTATCAATGGAAGCTAAGCCAATTAAGTTAGAATCACAATTGCAAATTCACTCCTTGTTAACCC
1 CTTACCAAAGGAAGCTAAGCCAAATAAGATAGAATCACAATTGCAAATTCACTCCTCATTAACCC
329566 C
66 C
329567 TTGGCTGATA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
78 57 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (78 bp):
CTTACCAAAGGAAGCTAAGCCAAATAAGATAGAATCACAATTGCAAATTCACTCCTCATTAACCC
CGAGTGCCACTGC
Found at i:333447 original size:49 final size:49
Alignment explanation
Indices: 333390--333493 Score: 181
Period size: 49 Copynumber: 2.1 Consensus size: 49
333380 TCATGTGTTA
* * *
333390 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
333439 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
333488 TAATTT
1 TAATTT
333494 GTTTTTTTCT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:334918 original size:21 final size:21
Alignment explanation
Indices: 334877--334919 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
334867 AATAAAGTAG
*
334877 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
334898 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
334919 A
1 A
334920 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:334981 original size:28 final size:27
Alignment explanation
Indices: 334932--335002 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 27
334922 TTCATATAAG
* *
334932 AATAATTA-TATTTAATTTTATTAAAT
1 AATAATTATTATTAAATTATATTAAAT
* * *
334958 TATATATTTTTATTAAATTATATTTAAT
1 AATA-ATTATTATTAAATTATATTAAAT
334986 AATAATTATT-TTAAATT
1 AATAATTATTATTAAATT
335003 CTGCTAAGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 10 0.28
27 8 0.22
28 18 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
AATAATTATTATTAAATTATATTAAAT
Found at i:335234 original size:6 final size:6
Alignment explanation
Indices: 335223--335287 Score: 130
Period size: 6 Copynumber: 10.8 Consensus size: 6
335213 TAATAAATAA
335223 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
335271 ATATTT ATATTT ATATT
1 ATATTT ATATTT ATATT
335288 ACATAATATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATATTT
Found at i:335403 original size:34 final size:33
Alignment explanation
Indices: 335357--335420 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
335347 AATAAAATGT
335357 AAATATTGTTAAATTATATTCATAATAAATAATA
1 AAATATTGTTAAATTAT-TTCATAATAAATAATA
* *
335391 AAATATAT-TTAAATTATTTTATATTAAATA
1 AAATAT-TGTTAAATTATTTCATAATAAATA
335421 TAATTAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 11 0.41
34 15 0.56
35 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (33 bp):
AAATATTGTTAAATTATTTCATAATAAATAATA
Found at i:335824 original size:14 final size:14
Alignment explanation
Indices: 335790--335821 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
335780 TGAAAAGATG
335790 TAAA-TAAAAATAT
1 TAAATTAAAAATAT
335803 TAAATTAAAAA-AT
1 TAAATTAAAAATAT
335816 TAAATT
1 TAAATT
335822 TAAGTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAATTAAAAATAT
Found at i:335829 original size:18 final size:18
Alignment explanation
Indices: 335808--335859 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
335798 AATATTAAAT
335808 TAAAAAATTAAATTTAAG
1 TAAAAAATTAAATTTAAG
* **
335826 TAAAAATTTAAATTTATT
1 TAAAAAATTAAATTTAAG
*
335844 TAAAATA-TAAATTTAA
1 TAAAAAATTAAATTTAA
335860 TTTGAACTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 8 0.29
18 20 0.71
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TAAAAAATTAAATTTAAG
Found at i:335862 original size:18 final size:18
Alignment explanation
Indices: 335791--335862 Score: 65
Period size: 17 Copynumber: 3.9 Consensus size: 18
335781 GAAAAGATGT
* *
335791 AAATAAAAATATTAAATTA
1 AAATATAAAT-TTAATTTA
* * *
335810 AAAAATTAAATTTAAGTAA
1 AAATA-TAAATTTAATTTA
*
335829 AAATTTAAATTT-ATTTA
1 AAATATAAATTTAATTTA
335846 AAATATAAATTTAATTT
1 AAATATAAATTTAATTT
335863 GAACTTCAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
17 14 0.33
18 11 0.26
19 13 0.31
20 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (18 bp):
AAATATAAATTTAATTTA
Found at i:336718 original size:19 final size:19
Alignment explanation
Indices: 336694--336806 Score: 68
Period size: 19 Copynumber: 5.9 Consensus size: 19
336684 TGCAAACTCT
336694 TTTTTACAATTTTATATAA
1 TTTTTACAATTTTATATAA
** * *
336713 TTTTTACTTTTTTTTGTAA
1 TTTTTACAATTTTATATAA
* * * *
336732 TTTCTATAATTTTTTATACT
1 TTTTTACAATTTTATATA-A
** *
336752 TTTTTGTAATTTTGTA-AA
1 TTTTTACAATTTTATATAA
* * *
336770 ATTTTGCAATTTTATATTA
1 TTTTTACAATTTTATATAA
336789 TTTTTA-ATATTTTATATA
1 TTTTTACA-ATTTTATATA
336807 TTTCTTAAAA
Statistics
Matches: 70, Mismatches: 21, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
18 14 0.20
19 43 0.61
20 13 0.19
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTTACAATTTTATATAA
Found at i:336733 original size:29 final size:28
Alignment explanation
Indices: 336692--336774 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
336682 CATGCAAACT
**
336692 CTTTTTTACAATTTTATATAATTTTTACT-
1 CTTTTTTGTAATTTTATA-AATTTTTA-TA
* *
336721 TTTTTTTGTAATTTCTATAATTTTTTATA
1 CTTTTTTGTAATTT-TATAAATTTTTATA
* *
336750 CTTTTTTGTAATTTTGTAAAATTTT
1 CTTTTTTGTAATTTTATAAATTTTT
336775 GCAATTTTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
28 9 0.20
29 31 0.70
30 4 0.09
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (28 bp):
CTTTTTTGTAATTTTATAAATTTTTATA
Found at i:336754 original size:10 final size:10
Alignment explanation
Indices: 336693--336774 Score: 53
Period size: 10 Copynumber: 8.4 Consensus size: 10
336683 ATGCAAACTC
*
336693 TTTTTTACAA
1 TTTTTTATAA
*
336703 TTTTATATAA
1 TTTTTTATAA
*
336713 -TTTTTACT-T
1 TTTTTTA-TAA
*
336722 TTTTTTGTAA
1 TTTTTTATAA
*
336732 -TTTCTATAA
1 TTTTTTATAA
*
336741 TTTTTTATAC
1 TTTTTTATAA
*
336751 TTTTTTGTAA
1 TTTTTTATAA
* *
336761 TTTTGTAAAA
1 TTTTTTATAA
336771 TTTT
1 TTTT
336775 GCAATTTTAT
Statistics
Matches: 53, Mismatches: 15, Indels: 8
0.70 0.20 0.11
Matches are distributed among these distances:
9 13 0.25
10 40 0.75
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.66
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:336814 original size:19 final size:19
Alignment explanation
Indices: 336778--336814 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
336768 AAATTTTGCA
336778 ATTTTATATTATTTTTAAT
1 ATTTTATATTATTTTTAAT
336797 ATTTTATA-TATTTCTTAA
1 ATTTTATATTATTT-TTAA
336815 AATTCTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTATATTATTTTTAAT
Found at i:338255 original size:37 final size:34
Alignment explanation
Indices: 338196--338279 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 34
338186 ATGCAACATG
338196 ACATGTTATAAC-AAATTAATACAGTAGCAA-TA
1 ACATGTTATAACAAAATTAATACAGTAGCAATTA
338228 ACATGTTTATAACAAATATATATATACAGTAGCAATTA
1 ACATG-TTATAACAAA-AT-TA-ATACAGTAGCAATTA
*
338266 TCATGCTTATAACA
1 ACATG-TTATAACA
338280 GATCATGACA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
32 5 0.11
33 7 0.16
34 2 0.05
35 2 0.05
36 2 0.05
37 12 0.27
38 14 0.32
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.32
Consensus pattern (34 bp):
ACATGTTATAACAAAATTAATACAGTAGCAATTA
Found at i:340493 original size:97 final size:96
Alignment explanation
Indices: 340361--340560 Score: 247
Period size: 97 Copynumber: 2.1 Consensus size: 96
340351 ACTGGATTGG
* * * * ** * *
340361 GGAGTCGTGGATCTATTACGGAGAGGTTCCAATTGAATATGGTGGAAATATTTAAAGATGTTTTT
1 GGAGTCGTAGATCAATTACGGAGAGGCTCCAATTGAATAGGGAAGAAATATTTAAAGATATTGTT
* * *
340426 GGAACGACGCCTACTGTGGTCGAGTACTGGAT
66 GGAACAACGCCTACTATGG-CAAGTACTGGAT
* ** * *
340458 GGAGTCGTAGATCAATTATGGAGAGGCTCTGATTGAATGGGGAAGAAATATTTAAAGGTATTGTT
1 GGAGTCGTAGATCAATTACGGAGAGGCTCCAATTGAATAGGGAAGAAATATTTAAAGATATTGTT
340523 GGAACAACGCCTACTATGGCAAGTACTGGAT
66 GGAACAACGCCTACTATGGCAAGTACTGGAT
340554 GGAGTCG
1 GGAGTCG
340561 ACGGAGAGGA
Statistics
Matches: 87, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
96 18 0.21
97 69 0.79
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.28
Consensus pattern (96 bp):
GGAGTCGTAGATCAATTACGGAGAGGCTCCAATTGAATAGGGAAGAAATATTTAAAGATATTGTT
GGAACAACGCCTACTATGGCAAGTACTGGAT
Found at i:341518 original size:34 final size:34
Alignment explanation
Indices: 341474--341570 Score: 133
Period size: 34 Copynumber: 2.9 Consensus size: 34
341464 ATACAATATG
*
341474 ACATGCTTATAACATATCAATACTA-TAGCAATTA
1 ACATGCTTATAACAAATCAATAC-AGTAGCAATTA
*
341508 GCATGCTTATAACAAATCAATACAGTAGCAATTA
1 ACATGCTTATAACAAATCAATACAGTAGCAATTA
* * *
341542 ATATGCTTATAACAAATAAATAAAGTAGC
1 ACATGCTTATAACAAATCAATACAGTAGC
341571 TATAGACACC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 1 0.02
34 55 0.98
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.29
Consensus pattern (34 bp):
ACATGCTTATAACAAATCAATACAGTAGCAATTA
Found at i:341746 original size:12 final size:12
Alignment explanation
Indices: 341729--341753 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
341719 TAAGCAAGAT
341729 TGAAAAGTAGTA
1 TGAAAAGTAGTA
341741 TGAAAAGTAGTA
1 TGAAAAGTAGTA
341753 T
1 T
341754 ATATACATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (12 bp):
TGAAAAGTAGTA
Found at i:344465 original size:92 final size:92
Alignment explanation
Indices: 344280--344465 Score: 212
Period size: 92 Copynumber: 2.0 Consensus size: 92
344270 AATATATTGA
* * *
344280 TGGATGAATCATTCGTCTGTGCAGATAAAAGCTACTAATACGTTGTGGATGACCCACTAGTCAAG
1 TGGATGAACCATTCGTCTGTGCAGATAAAAGCTACTAATACGTTGTGGATGAACCACTAGTCAAA
* * * *
344345 TAGATAAACTTCTGACTAAAATATTGG
66 CAGATAAACTACCGACTAAAATAGTGG
* * * * ** * *
344372 TGGATGAACCATTCGTTTGTGTATATAAAAGTTGTTAATACGTTGTGGATGAACCACTGGTTAAA
1 TGGATGAACCATTCGTCTGTGCAGATAAAAGCTACTAATACGTTGTGGATGAACCACTAGTCAAA
*
344437 CAGAT-GACTACCGACTAAAATACGTGG
66 CAGATAAACTACCGACTAAAATA-GTGG
344464 TG
1 TG
344466 AATAAGCCAC
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
91 14 0.18
92 63 0.82
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (92 bp):
TGGATGAACCATTCGTCTGTGCAGATAAAAGCTACTAATACGTTGTGGATGAACCACTAGTCAAA
CAGATAAACTACCGACTAAAATAGTGG
Found at i:347080 original size:14 final size:14
Alignment explanation
Indices: 347061--347090 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
347051 AATTAGCTTG
347061 ACATAGTTAACAAT
1 ACATAGTTAACAAT
347075 ACATAGTTAACAAT
1 ACATAGTTAACAAT
347089 AC
1 AC
347091 CTTGACACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.27
Consensus pattern (14 bp):
ACATAGTTAACAAT
Found at i:364369 original size:21 final size:21
Alignment explanation
Indices: 364315--364369 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
364305 AATTTTCAGT
*
364315 TTTCAATAACTTTTTTTTATAAA
1 TTTCAA-AA-TTTTTTTAATAAA
* **
364338 TTTTATGATTTTTTTAATAAA
1 TTTCAAAATTTTTTTAATAAA
364359 TTTCAAAATTT
1 TTTCAAAATTT
364370 AAAAAAGGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
21 20 0.80
22 1 0.04
23 4 0.16
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTCAAAATTTTTTTAATAAA
Found at i:375965 original size:6 final size:6
Alignment explanation
Indices: 375949--375999 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
375939 AAATTATGAA
*
375949 TAATTT CAATTT TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT
1 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT
375997 TAA
1 TAA
376000 AAATTCAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (6 bp):
TAATTT
Found at i:376621 original size:6 final size:6
Alignment explanation
Indices: 376610--376640 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
376600 TAAAATTTCA
*
376610 GTGAGG GTGAGG GTGAGG GTGAGG GAGAGG G
1 GTGAGG GTGAGG GTGAGG GTGAGG GTGAGG G
376641 GGACGGGGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.68, T:0.13
Consensus pattern (6 bp):
GTGAGG
Found at i:381989 original size:29 final size:28
Alignment explanation
Indices: 381900--381991 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
381890 ATTTGTGTAT
381900 TTTGGTATATTTATGTTTTGAAAATTATG
1 TTTGGTATATTTATGTTTTG-AAATTATG
* * **
381929 TTTGGTATA-TGATGTTTTGTAATGGTG
1 TTTGGTATATTTATGTTTTGAAATTATG
*
381956 CTTTGGTATATTTATGTTTTCAAGATTATG
1 -TTTGGTATATTTATGTTTTGAA-ATTATG
381986 TTTGGT
1 TTTGGT
381992 TGATGGACTT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 5 0.10
28 18 0.35
29 24 0.47
30 4 0.08
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.54
Consensus pattern (28 bp):
TTTGGTATATTTATGTTTTGAAATTATG
Found at i:383848 original size:15 final size:15
Alignment explanation
Indices: 383810--383849 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
383800 GTGGTTGCTG
*
383810 TGAATCCTACAAATC
1 TGAATCCTGCAAATC
* *
383825 TGAATCCTGTAAATT
1 TGAATCCTGCAAATC
383840 TGAATCCTGC
1 TGAATCCTGC
383850 TGAATCGAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (15 bp):
TGAATCCTGCAAATC
Found at i:387223 original size:46 final size:46
Alignment explanation
Indices: 387163--387517 Score: 455
Period size: 46 Copynumber: 8.1 Consensus size: 46
387153 CTTGTCCCTA
*
387163 ATCAGATTAGTGTAGCT-AAGACTACCACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAAG-CTACCACTTATCACTTTGTCACTTG
* *
387209 ATTAGATAAGTGTAGCTAAGGCTACCCACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAAGCTA-CCACTTATCACTTTGTCACTTG
* *
387256 ATCAGATAAGTGTAGCTAAAGTTAACACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
*
387302 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTG
1 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
387348 ATCAGATAA--GT-G-T--AG-T---ACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
* *
387384 ATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTG
1 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
387430 ATCAGATAA--GT-G-T--A--T--CACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
* *
387466 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCTTG
1 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
387512 ATCAGA
1 ATCAGA
387518 AGTACTCAAA
Statistics
Matches: 270, Mismatches: 17, Indels: 44
0.82 0.05 0.13
Matches are distributed among these distances:
36 56 0.21
38 5 0.02
39 3 0.01
40 5 0.02
42 5 0.02
43 3 0.01
44 5 0.02
46 143 0.53
47 45 0.17
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (46 bp):
ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
Found at i:387369 original size:36 final size:37
Alignment explanation
Indices: 387327--387480 Score: 186
Period size: 36 Copynumber: 4.0 Consensus size: 37
387317 CTAAAGCTAC
*
387327 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGT
*
387364 -ACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTAAAGCT
1 CACTTATCACTTTGTCACTTGATCAGATAA--GT-G-T--AG-T
*
387407 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA-T
1 --CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGT
387445 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
387481 CTAAAGCTAC
Statistics
Matches: 101, Mismatches: 5, Indels: 22
0.79 0.04 0.17
Matches are distributed among these distances:
36 61 0.60
38 3 0.03
39 1 0.01
40 2 0.02
42 3 0.03
43 2 0.02
44 2 0.02
46 27 0.27
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGT
Found at i:387376 original size:82 final size:82
Alignment explanation
Indices: 387281--387517 Score: 440
Period size: 82 Copynumber: 2.9 Consensus size: 82
387271 CTAAAGTTAA
387281 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
387346 TGATCAGATAAGTGTAGT
66 TGATCAGATAAGTGTA-T
*
387364 -ACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
387428 TGATCAGATAAGTGTAT
66 TGATCAGATAAGTGTAT
*
387445 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
387510 TGATCAGA
66 TGATCAGA
387518 AGTACTCAAA
Statistics
Matches: 150, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
81 1 0.01
82 149 0.99
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
TGATCAGATAAGTGTAT
Found at i:387496 original size:128 final size:134
Alignment explanation
Indices: 387163--387515 Score: 423
Period size: 128 Copynumber: 2.7 Consensus size: 134
387153 CTTGTCCCTA
* *
387163 ATCAGATTAGTGTAGCTAAGACTACCACTTATCACTTTGTCACTTGATTAGATAAGTGTAGCTAA
1 ATCAGATAAG-GTAGCT-A-ACTA-CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA
* * *
387228 GGCTACCCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGTTAACACTTATCACTT
62 AGCTA-CCACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTAAAGCTAACACTTATCACTT
387293 TGTCACTTG
126 TGTCACTTG
*
387302 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--
1 ATCAGATAAG-GTAGCT-AA-CTA-CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA
*
387361 AG-T---ACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTT
62 AGCTACCACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTAAAGCTAACACTTATCACTTT
*
387422 GTCTCTTG
127 GTCACTTG
387430 ATCAGATAA-GT-G-T-A-T-CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 ATCAGATAAGGTAGCTAACTACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
* *
387489 ACCACTTATCACTTTATCTCTTGATCA
66 ACCACTTATCACTTTGTCACTTGATCA
387516 GAAGTACTCA
Statistics
Matches: 192, Mismatches: 11, Indels: 33
0.81 0.05 0.14
Matches are distributed among these distances:
118 29 0.15
120 3 0.02
121 1 0.01
122 2 0.01
124 3 0.02
125 2 0.01
126 2 0.01
128 93 0.48
132 1 0.01
133 1 0.01
135 1 0.01
136 1 0.01
137 2 0.01
138 1 0.01
139 50 0.26
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (134 bp):
ATCAGATAAGGTAGCTAACTACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
ACCACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCA
CTTG
Found at i:389547 original size:21 final size:21
Alignment explanation
Indices: 389523--389564 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
389513 CTTTTTGTTC
*
389523 AATTAATTATCGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
**
389544 AATTTCTTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
389565 TACTAACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:389975 original size:45 final size:45
Alignment explanation
Indices: 389924--390066 Score: 236
Period size: 46 Copynumber: 3.2 Consensus size: 45
389914 TTATCTGATC
389924 AAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACA
1 AAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACA
* *
389969 AAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATAAAGTGAGA
1 AAGTGATAAGTGGTAGCC-TAGCTACACTTATCTGATCAAGTGACA
*
390015 AAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATC-AGGGAC-
1 AAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACA
390058 AAGTGATAA
1 AAGTGATAA
390067 ATGATCATAC
Statistics
Matches: 92, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
43 9 0.10
44 4 0.04
45 36 0.39
46 43 0.47
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (45 bp):
AAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACA
Found at i:395471 original size:18 final size:18
Alignment explanation
Indices: 395444--395481 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
395434 TACCTGACAT
395444 ATAAATAATATATATAAAA
1 ATAAATAATATATA-AAAA
395463 ATAAA-AATATATAAAAA
1 ATAAATAATATATAAAAA
395480 AT
1 AT
395482 TAGTTGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 8 0.42
19 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAATAATATATAAAAA
Found at i:397241 original size:14 final size:14
Alignment explanation
Indices: 397219--397265 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
397209 TTGTTACTGA
397219 TTTTGGGTTATTTGG
1 TTTT-GGTTATTTGG
* *
397234 TTTTGGTTA-CTGC
1 TTTTGGTTATTTGG
*
397247 TTTCGGTTATTTGG
1 TTTTGGTTATTTGG
397261 TTTTG
1 TTTTG
397266 CTAGGTTTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
13 10 0.40
14 11 0.44
15 4 0.16
ACGTcount: A:0.06, C:0.06, G:0.28, T:0.60
Consensus pattern (14 bp):
TTTTGGTTATTTGG
Found at i:400329 original size:18 final size:18
Alignment explanation
Indices: 400291--400329 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
400281 ATATTTACGA
* *
400291 TTTTTTATAATTTTAAGT
1 TTTTTTATAATTATAAAT
*
400309 TTTTTTATTATTATAAAT
1 TTTTTTATAATTATAAAT
400327 TTT
1 TTT
400330 ATGTATTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTTTATAATTATAAAT
Found at i:404662 original size:3 final size:3
Alignment explanation
Indices: 404647--404693 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
404637 AAGAGTTTCA
*
404647 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
404694 AGTGTATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:411539 original size:29 final size:29
Alignment explanation
Indices: 411495--411550 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
411485 TAGCTATTTG
* *
411495 AACTAATTAATTACATTGTAAAAATATTA
1 AACTAATTAATAACATTATAAAAATATTA
411524 AACTAATTAATAACATTATAAAAATAT
1 AACTAATTAATAACATTATAAAAATAT
411551 AGAGACCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (29 bp):
AACTAATTAATAACATTATAAAAATATTA
Found at i:430955 original size:15 final size:17
Alignment explanation
Indices: 430935--430974 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
430925 AATCTTTTAA
430935 AAATTATAAAAATA-T-
1 AAATTATAAAAATAGTG
*
430950 AAATTATTAAAATAGTG
1 AAATTATAAAAATAGTG
430967 AAATTATA
1 AAATTATA
430975 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 1 0.05
17 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (17 bp):
AAATTATAAAAATAGTG
Found at i:453131 original size:39 final size:39
Alignment explanation
Indices: 453072--453149 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
453062 ACGTATGTCT
* *
453072 TGATTTTTTGTCAAAAATATATTTGAACACTGAAACAAA
1 TGATCTTTTGTCAAAAATATATATGAACACTGAAACAAA
* *
453111 TGATCTTTTGTCAAAAATATATATGTACATTGAAACAAA
1 TGATCTTTTGTCAAAAATATATATGAACACTGAAACAAA
453150 ATTATAGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (39 bp):
TGATCTTTTGTCAAAAATATATATGAACACTGAAACAAA
Found at i:460909 original size:85 final size:87
Alignment explanation
Indices: 460732--460889 Score: 234
Period size: 85 Copynumber: 1.9 Consensus size: 87
460722 GCGCCGCCAA
* * *
460732 AAACGCCGCTA-AAGACCAGGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGAA
1 AAACGCCGCTATAAGACAAGGACCTTTAGCGGCACTTTTCACACAAACGCCGCTATAGATCAGAA
460796 CCTTTAGCGACACTTTTCCCAC
66 CCTTTAGCGACACTTTTCCCAC
* *
460818 AAACGCCGCTATAA-ATAAGGACCTTTAGTGGCACTTTT-ACACAAACGCCGCTATAGATCA-AG
1 AAACGCCGCTATAAGACAAGGACCTTTAGCGGCACTTTTCACACAAACGCCGCTATAGATCAGA-
460880 ACCTTTAGCG
65 ACCTTTAGCG
460890 GCGCTTTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
84 1 0.02
85 31 0.48
86 31 0.48
87 2 0.03
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (87 bp):
AAACGCCGCTATAAGACAAGGACCTTTAGCGGCACTTTTCACACAAACGCCGCTATAGATCAGAA
CCTTTAGCGACACTTTTCCCAC
Found at i:460917 original size:43 final size:43
Alignment explanation
Indices: 460732--460956 Score: 222
Period size: 43 Copynumber: 5.3 Consensus size: 43
460722 GCGCCGCCAA
* * * *
460732 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * *
460775 AAACGCCGCTATAGATC-AGAACCTTTAGCGACACTTTTCCCAC
1 AAACGCCGCTATAGATCAAG-ACCTTTAGCGGCGCTTTTTCCAC
* * * *
460818 AAACGCCGCTATAAAT-AAGGACCTTTAGTGGCAC-TTTTACAC
1 AAACGCCGCTATAGATCAA-GACCTTTAGCGGCGCTTTTTCCAC
** *
460860 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTTTAT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * * * * * *
460903 AAACGCCACTATAGATCATGACTTTTAGCGACGTTTTTTTCGC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
460946 AAACGCCGCTA
1 AAACGCCGCTA
460957 AAAGTGCCAT
Statistics
Matches: 152, Mismatches: 25, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
42 35 0.23
43 116 0.76
44 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
Found at i:468755 original size:21 final size:21
Alignment explanation
Indices: 468731--468771 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
468721 AACCCTAAAT
468731 CCCTAACTCTTAACCCCTAAC
1 CCCTAACTCTTAACCCCTAAC
*
468752 CCCTAACTCTTAATCCCTAA
1 CCCTAACTCTTAACCCCTAA
468772 ACCTTAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.44, G:0.00, T:0.27
Consensus pattern (21 bp):
CCCTAACTCTTAACCCCTAAC
Found at i:469008 original size:23 final size:24
Alignment explanation
Indices: 468969--469022 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
468959 TACATGAAAT
*
468969 TATTTAATATATAAATTAAAAAAA
1 TATTTAATAAATAAATTAAAAAAA
468993 TATTTAA-AAATAAATT-AAAAAA
1 TATTTAATAAATAAATTAAAAAAA
*
469015 TAATTAAT
1 TATTTAAT
469023 CTAAACCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 12 0.44
23 8 0.30
24 7 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TATTTAATAAATAAATTAAAAAAA
Found at i:469129 original size:14 final size:15
Alignment explanation
Indices: 469112--469145 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
469102 AACCCTTAAA
469112 CCATAATCCCT-AAT
1 CCATAATCCCTCAAT
*
469126 CCATAATCCTTCAAT
1 CCATAATCCCTCAAT
469141 CCATA
1 CCATA
469146 CTCCATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (15 bp):
CCATAATCCCTCAAT
Found at i:469425 original size:41 final size:41
Alignment explanation
Indices: 469379--469494 Score: 146
Period size: 41 Copynumber: 2.8 Consensus size: 41
469369 TAAAATGTTT
469379 TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCCCCTA-CCA
1 TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCCCC-AGCCA
* * * *
469420 TTAGCGGCGC-TTATCCAAAAACGCCACTAAAGACCCAGGCA
1 TTAGCGGCGCTTTAT-AAAAAACGCCGCTAAAGCCCCAGCCA
* *
469461 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAGCC
1 TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCC
469495 ACGAAATGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
40 5 0.08
41 56 0.88
42 3 0.05
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (41 bp):
TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCCCCAGCCA
Found at i:469574 original size:39 final size:39
Alignment explanation
Indices: 469530--469608 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
469520 TGGGCTAAGG
* * *
469530 TTTTTTGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCATTTTTTT-AAAAACGCCACTAATGCTCA
469570 TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
1 TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
469609 ATCTTTAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 19 0.53
40 17 0.47
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (39 bp):
TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
Found at i:469580 original size:40 final size:40
Alignment explanation
Indices: 469530--469667 Score: 136
Period size: 40 Copynumber: 3.5 Consensus size: 40
469520 TGGGCTAAGG
*
469530 TTTTTTGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCA
* *
469570 TTTTTAGCGGCATTTTTTT-AAAAACGCCACTAATGCTCAA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTC-A
* * * *** * *
469610 TCTTTAGTGGCGATTTCCAG-AAAGCGCCGCTAATGCTTAA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCGCTAATGC-TCA
*
469650 TTTTTACCGGCGTTTTTT
1 TTTTTAGCGGCGTTTTTT
469668 GTCCAAACGC
Statistics
Matches: 76, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
39 18 0.24
40 57 0.75
41 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCA
Found at i:473816 original size:4 final size:4
Alignment explanation
Indices: 473807--473832 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
473797 ACTTCCACTT
473807 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
473833 ATCGTCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:489375 original size:22 final size:22
Alignment explanation
Indices: 489349--489398 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
489339 GACTCACATA
489349 CTTTTCTTCT-AATCCGCAATAT
1 CTTTTCTTCTAAATCCGCAA-AT
**
489371 CTTTT-TTCTAAATCTTCAAAT
1 CTTTTCTTCTAAATCCGCAAAT
489392 CTTTTCT
1 CTTTTCT
489399 GACTGACATC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.52
Consensus pattern (22 bp):
CTTTTCTTCTAAATCCGCAAAT
Found at i:498378 original size:16 final size:16
Alignment explanation
Indices: 498357--498392 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
498347 TAACTCAGGA
498357 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
498373 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
498389 GCTG
1 GCTG
498393 TGATTTCTTA
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:0.22, C:0.19, G:0.39, T:0.19
Consensus pattern (16 bp):
GCTGCAGGAGTACATG
Found at i:499258 original size:18 final size:17
Alignment explanation
Indices: 499230--499264 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
499220 ATTATTAAGA
*
499230 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
499247 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
499265 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:499288 original size:146 final size:142
Alignment explanation
Indices: 499210--499485 Score: 345
Period size: 146 Copynumber: 1.9 Consensus size: 142
499200 AAATTCATAT
* *
499210 AAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAA
1 AAGAATACTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAA
* * *
499275 TTATGTTTAAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAAA
66 TTATGTTTAAATATGATTTAA-TATTAATTATT--TA-TAATAATCTTATTAAAATTCAAATAAA
499340 TAATTTACCAAAACAA
127 TAATTTACCAAAACAA
**** *
499356 ATTTCTGCTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAA
1 AAGAATACTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAA
* * * *
499421 TTATGTTTAAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAA
66 TTATGTTTAAATATGATTTAA-TATTAATTATT--T-AT-AATAATCTTATTAAAATTCAAATAA
499486 CAATAACAAT
Statistics
Matches: 120, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
146 94 0.78
147 26 0.22
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (142 bp):
AAGAATACTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAA
TTATGTTTAAATATGATTTAATATTAATTATTTATAATAATCTTATTAAAATTCAAATAAATAAT
TTACCAAAACAA
Found at i:499404 original size:18 final size:17
Alignment explanation
Indices: 499376--499410 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
499366 ATTATTAAGA
*
499376 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
499393 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
499411 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:499621 original size:44 final size:45
Alignment explanation
Indices: 499572--499666 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
499562 TTACACCTCT
* * *
499572 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
** *
499616 ATTACATTCAACCAAACAGTTGATTTGCTATTACACATCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
499661 ATTACA
1 ATTACA
499667 CCTCTAATCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
Found at i:499666 original size:16 final size:16
Alignment explanation
Indices: 499647--499698 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
499637 GATTTGCTAT
* * *
499647 TACACATCTATTCCAT
1 TACACCTCTAATCCAA
499663 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
499679 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
499695 TACA
1 TACA
499699 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:500060 original size:12 final size:12
Alignment explanation
Indices: 500030--500062 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
500020 CAAGCACATC
*
500030 TCTAAAAATTTT
1 TCTAGAAATTTT
500042 TCT-GAAATTTT
1 TCTAGAAATTTT
500053 TCTAGAAATT
1 TCTAGAAATT
500063 CTAATAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (12 bp):
TCTAGAAATTTT
Found at i:502099 original size:17 final size:17
Alignment explanation
Indices: 502069--502113 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
502059 CTGATATAAT
* *
502069 AAATATATTTATTTTTA
1 AAATATTTTTAATTTTA
502086 AAAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
502102 AAATATTTTTAA
1 AAATATTTTTAA
502114 AATACTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:504114 original size:28 final size:28
Alignment explanation
Indices: 504094--504165 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
504084 ATTATTAAAA
504094 AATAAATTTTAATAATTTATTGTTTAAT
1 AATAAATTTTAATAATTTATTGTTTAAT
*
504122 ATTAAATTTTAATAATTTATTGTTTAAT
1 AATAAATTTTAATAATTTATTGTTTAAT
*
504150 AATAAATGTTAA-AATT
1 AATAAATTTTAATAATT
504166 CATGTTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 4 0.10
28 37 0.90
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (28 bp):
AATAAATTTTAATAATTTATTGTTTAAT
Found at i:504121 original size:15 final size:15
Alignment explanation
Indices: 504101--504152 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
504091 AAAAATAAAT
504101 TTTAATAATTTATTG
1 TTTAATAATTTATTG
* *
504116 TTTAAT-ATTAAAT-
1 TTTAATAATTTATTG
504129 TTTAATAATTTATTG
1 TTTAATAATTTATTG
504144 TTTAATAAT
1 TTTAATAAT
504153 AAATGTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 6 0.19
14 10 0.32
15 15 0.48
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (15 bp):
TTTAATAATTTATTG
Found at i:504172 original size:12 final size:12
Alignment explanation
Indices: 504155--504179 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
504145 TTAATAATAA
504155 ATGTTAAAATTC
1 ATGTTAAAATTC
504167 ATGTTAAAATTC
1 ATGTTAAAATTC
504179 A
1 A
504180 AGCCATAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTAAAATTC
Found at i:509633 original size:23 final size:23
Alignment explanation
Indices: 509588--509633 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
509578 TGTTAAAATT
* *
509588 GTATCGTGAAAATTGTATTTTTA
1 GTATCGTGAAAATTATATATTTA
509611 GTATCGTGAAAA-TATATAATTTA
1 GTATCGTGAAAATTATAT-ATTTA
509634 ATTCCGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.43
Consensus pattern (23 bp):
GTATCGTGAAAATTATATATTTA
Found at i:515195 original size:13 final size:13
Alignment explanation
Indices: 515177--515203 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
515167 AGCTATCCCA
515177 AACTCTCATGCTT
1 AACTCTCATGCTT
515190 AACTCTCATGCTT
1 AACTCTCATGCTT
515203 A
1 A
515204 TAACATGCTT
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:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (13 bp):
AACTCTCATGCTT
Found at i:518506 original size:20 final size:17
Alignment explanation
Indices: 518472--518526 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 17
518462 ATATAAAAAA
518472 TAAATTTTAAAAAATTAT
1 TAAATTTTAAAAAATT-T
518490 TAAATTTTAATAAAAATTT
1 TAAATTTT-A-AAAAATTT
518509 TCAAATTTATTAAAAAAT
1 T-AAA-TT-TTAAAAAAT
518527 AGAATATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 8 0.25
19 3 0.09
20 16 0.50
21 3 0.09
22 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTTAAAAAATTT
Found at i:518524 original size:19 final size:20
Alignment explanation
Indices: 518472--518516 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
518462 ATATAAAAAA
518472 TAAATTTT-A-AAAAATTAT
1 TAAATTTTAATAAAAATTAT
518490 TAAATTTTAATAAAAATT-T
1 TAAATTTTAATAAAAATTAT
518509 TCAAATTT
1 T-AAATTT
518517 ATTAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
19 3 0.12
20 13 0.54
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATTTTAATAAAAATTAT
Found at i:518765 original size:10 final size:9
Alignment explanation
Indices: 518748--518832 Score: 54
Period size: 8 Copynumber: 9.6 Consensus size: 9
518738 ACTTTATAAA
518748 ATTTTATAT
1 ATTTTATAT
*
518757 -TTCTATAT
1 ATTTTATAT
518765 ATTTTATA-
1 ATTTTATAT
518773 ATTTTATACT
1 ATTTTATA-T
*
518783 ATTTTAATAAA
1 ATTTT-AT-AT
* * *
518794 AGTTTACAA
1 ATTTTATAT
518803 ATTTTATAT
1 ATTTTATAT
518812 -TTTTATGAT
1 ATTTTAT-AT
518821 -TTTTATAT
1 ATTTTATAT
518829 -TTTT
1 ATTTT
518833 TTAACTGTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
8 27 0.44
9 22 0.35
10 6 0.10
11 6 0.10
12 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (9 bp):
ATTTTATAT
Found at i:518770 original size:17 final size:18
Alignment explanation
Indices: 518748--518788 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
518738 ACTTTATAAA
518748 ATTTTAT-ATTTCTATA-T
1 ATTTTATAATTT-TATACT
518765 ATTTTATAATTTTATACT
1 ATTTTATAATTTTATACT
518783 ATTTTA
1 ATTTTA
518789 ATAAAAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTATAATTTTATACT
Found at i:518793 original size:46 final size:44
Alignment explanation
Indices: 518692--518831 Score: 117
Period size: 46 Copynumber: 3.1 Consensus size: 44
518682 TTTTATAAAT
* * * *
518692 TATTTTATGAAA-TTTATATTTCTTTACATTGTATAATTTTCTTAC
1 TATTTTATAAAATTTTATATTTCTATATATTTTATAA-TTT-TTAC
* *
518737 GACTTTATAAAATTTTATATTTCTATATATTTTATAATTTTATAC
1 TATTTTATAAAATTTTATATTTCTATATATTTTATAATTTT-TAC
* * *
518782 TATTTTAATAAAAGTTTACAAATTT-TATAT-TTTTATGATTTTTA-
1 TATTTT-ATAAAA-TTT-TATATTTCTATATATTTTATAATTTTTAC
518826 TATTTT
1 TATTTT
518832 TTTAACTGTT
Statistics
Matches: 79, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
44 7 0.09
45 21 0.27
46 38 0.48
47 8 0.10
48 5 0.06
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.58
Consensus pattern (44 bp):
TATTTTATAAAATTTTATATTTCTATATATTTTATAATTTTTAC
Found at i:519148 original size:92 final size:95
Alignment explanation
Indices: 518956--519160 Score: 255
Period size: 92 Copynumber: 2.2 Consensus size: 95
518946 ATTTCTTTTT
*
518956 CTTTTTTTTTGAAAAAGTTTGAAGGTCTTTTTTTATGCATTTTGAAAGTTCAAGTACCTAAATGA
1 CTTTTTTTTTGAAAAAGTTTGAAGGTCTTTTTTTATGCATTTTGAAAGTTCAAGTACCAAAATGA
* * * * * *
519021 GTGCAAAAAAAGAGAGTAGGGGTTTAATTG
66 GTGCAAAAAAAGAAAGCAGAGGCTTAAATA
*
519051 C-TTTTTTTT-AAAAAGTTTG-A-GTGCTTTTTTTATGCATTTTGAAAGTTTAAGTACCAAAATG
1 CTTTTTTTTTGAAAAAGTTTGAAGGT-CTTTTTTTATGCATTTTGAAAGTTCAAGTACCAAAATG
519112 AGTG-AAAAAAA-AAAGCAGAGGCTTAAATA
65 AGTGCAAAAAAAGAAAGCAGAGGCTTAAATA
* *
519141 C--ATTTTTTGAAAAAATTTGA
1 CTTTTTTTTTGAAAAAGTTTGA
519161 GGGCTTCTTA
Statistics
Matches: 97, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
89 6 0.06
90 22 0.23
91 9 0.09
92 41 0.42
93 10 0.10
94 8 0.08
95 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (95 bp):
CTTTTTTTTTGAAAAAGTTTGAAGGTCTTTTTTTATGCATTTTGAAAGTTCAAGTACCAAAATGA
GTGCAAAAAAAGAAAGCAGAGGCTTAAATA
Found at i:520276 original size:3 final size:3
Alignment explanation
Indices: 520268--520305 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
520258 AATTAAGGAA
520268 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
520306 GATTTCCATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:532474 original size:18 final size:18
Alignment explanation
Indices: 532448--532482 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
532438 CCTAATATTG
*
532448 TTATATTAATAATATTTT
1 TTATATTAAAAATATTTT
*
532466 TTATTTTAAAAATATTT
1 TTATATTAAAAATATTT
532483 AAAATATTAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATTAAAAATATTTT
Found at i:532695 original size:15 final size:15
Alignment explanation
Indices: 532677--532713 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
532667 TATTTATATT
532677 AATAATTTAATAATA
1 AATAATTTAATAATA
532692 AAT-ATATTAATAATA
1 AATAAT-TTAATAATA
532707 AA-AATTT
1 AATAATTT
532714 TAGTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATAATTTAATAATA
Found at i:532720 original size:15 final size:15
Alignment explanation
Indices: 532682--532721 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
532672 ATATTAATAA
*
532682 TTTAATAATAAATAT
1 TTTAATAATAAAAAT
*
532697 ATTAATAATAAAAAT
1 TTTAATAATAAAAAT
*
532712 TTTAGTAATA
1 TTTAATAATA
532722 TAAAGGTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TTTAATAATAAAAAT
Found at i:535578 original size:6 final size:6
Alignment explanation
Indices: 535567--535594 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
535557 AAAAGATTCA
535567 GTGAAG GTGAAG GTGAAG GTGAAG GTGA
1 GTGAAG GTGAAG GTGAAG GTGAAG GTGA
535595 GAGAAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.50, T:0.18
Consensus pattern (6 bp):
GTGAAG
Found at i:536371 original size:23 final size:25
Alignment explanation
Indices: 536343--536390 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
536333 AATTTGATAA
536343 TTTTTT-TCATATTGA-CTCCTAAAT
1 TTTTTTATCATATTGATC-CCTAAAT
536367 TTTTTTATCATATTGATCCCTAAA
1 TTTTTTATCATATTGATCCCTAAA
536391 GTTGACATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
25 15 0.68
26 1 0.05
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTTTTATCATATTGATCCCTAAAT
Found at i:536547 original size:20 final size:21
Alignment explanation
Indices: 536524--536577 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 21
536514 TAATCATTTT
536524 TTAAAAAATTTAAAAAA-AAC
1 TTAAAAAATTTAAAAAAGAAC
*
536544 TT-AAAAA-TTAAAAAAGAAG
1 TTAAAAAATTTAAAAAAGAAC
* *
536563 GTAAAAAATATAAAA
1 TTAAAAAATTTAAAA
536578 GTATATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 8 0.29
19 8 0.29
20 7 0.25
21 5 0.18
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (21 bp):
TTAAAAAATTTAAAAAAGAAC
Found at i:536567 original size:19 final size:19
Alignment explanation
Indices: 536527--536569 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
536517 TCATTTTTTA
*
536527 AAAAATTTAAAAAAAACTT
1 AAAAATTTAAAAAAAACGT
*
536546 AAAAA-TTAAAAAAGAAGGT
1 AAAAATTTAAAAAA-AACGT
536565 AAAAA
1 AAAAA
536570 ATATAAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (19 bp):
AAAAATTTAAAAAAAACGT
Found at i:536661 original size:21 final size:22
Alignment explanation
Indices: 536620--536661 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
536610 AATTGAAAAT
*
536620 AAATAAATTAAATATGTTTAAA
1 AAATAAATTAAATATGGTTAAA
*
536642 AAATAAA-TAAATTTGGTTAA
1 AAATAAATTAAATATGGTTAA
536662 CTTTTTAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (22 bp):
AAATAAATTAAATATGGTTAAA
Found at i:537298 original size:35 final size:35
Alignment explanation
Indices: 537259--537330 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
537249 TATATTAAGC
537259 ATTAAAAAAACTAATGGTGTTCACCATAGAAACCG
1 ATTAAAAAAACTAATGGTGTTCACCATAGAAACCG
537294 ATTAAAAAAACTAATGGTGTTCACCATAGAAACCG
1 ATTAAAAAAACTAATGGTGTTCACCATAGAAACCG
537329 AT
1 AT
537331 ATGCGTAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.24
Consensus pattern (35 bp):
ATTAAAAAAACTAATGGTGTTCACCATAGAAACCG
Found at i:545764 original size:16 final size:15
Alignment explanation
Indices: 545743--545774 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
545733 TAATATTATT
545743 TAATATTAAATATAAA
1 TAATATTAAAT-TAAA
545759 TAATATTAAATTAAA
1 TAATATTAAATTAAA
545774 T
1 T
545775 TTAATACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATATTAAATTAAA
Found at i:545780 original size:26 final size:26
Alignment explanation
Indices: 545730--545780 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
545720 AACTATTCAA
*
545730 AAATAATATTATTTAATATTAAATAT
1 AAATAATATTAATTAATATTAAATAT
*
545756 AAATAATATTAAATTAA-ATTTAATA
1 AAATAATATT-AATTAATATTAAATA
545781 CTTATCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AAATAATATTAATTAATATTAAATAT
Found at i:545957 original size:26 final size:26
Alignment explanation
Indices: 545892--545959 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 26
545882 AATAAGATTT
*
545892 AATATTAAATTTAATCTAATATTTATA
1 AATATT-AATTTAATTTAATATTTATA
545919 AATATT-ATATTAATTTAATA-TTA-A
1 AATATTAAT-TTAATTTAATATTTATA
545943 AATGATTAAGTTTAATT
1 AAT-ATTAA-TTTAATT
545960 ATAGTTGAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
24 4 0.11
25 8 0.22
26 17 0.47
27 7 0.19
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (26 bp):
AATATTAATTTAATTTAATATTTATA
Found at i:549708 original size:24 final size:25
Alignment explanation
Indices: 549659--549708 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
549649 GTTATAACTT
549659 TTTTTTATTTACCAAAAAATATATAA
1 TTTTTTATTTACC-AAAAATATATAA
549685 TTTTTTATTTACC-AAAATATATAA
1 TTTTTTATTTACCAAAAATATATAA
549709 AAAAACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 11 0.46
26 13 0.54
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTTTTATTTACCAAAAATATATAA
Found at i:549857 original size:18 final size:18
Alignment explanation
Indices: 549834--549988 Score: 63
Period size: 18 Copynumber: 8.3 Consensus size: 18
549824 AAGGAGAGGG
549834 GAAGAAGAAGAAAGAAAA
1 GAAGAAGAAGAAAGAAAA
*
549852 GAAGAAAGAAAAAGAAGGAAAA
1 GAAG-AAG---AAGAAAGAAAA
* *
549874 GGAAAGGAGAGGAAAG-AAA
1 -G-AAGAAGAAGAAAGAAAA
*
549893 GAAAAAGAAGGAAAGAAAA
1 GAAGAAGAA-GAAAGAAAA
** *
549912 GGAAAGGGGAGGAAAG-AAA
1 -G-AAGAAGAAGAAAGAAAA
* *
549931 GAAAAATAAGGAAAGAAAA
1 GAAGAAGAA-GAAAGAAAA
549950 GAA-AATG-AGAAGAGAAAA
1 GAAGAA-GAAGAA-AGAAAA
549968 -AA-AA-AAGAAAGAAGAA
1 GAAGAAGAAGAAAGAA-AA
549984 GAAGA
1 GAAGA
549989 GGGAAGGAAG
Statistics
Matches: 102, Mismatches: 17, Indels: 36
0.66 0.11 0.23
Matches are distributed among these distances:
15 4 0.04
16 6 0.06
17 17 0.17
18 26 0.25
19 18 0.18
20 11 0.11
21 4 0.04
22 10 0.10
23 3 0.03
24 3 0.03
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.01
Consensus pattern (18 bp):
GAAGAAGAAGAAAGAAAA
Found at i:549866 original size:10 final size:10
Alignment explanation
Indices: 549835--549986 Score: 55
Period size: 10 Copynumber: 15.1 Consensus size: 10
549825 AGGAGAGGGG
*
549835 AAGAAGAAGA
1 AAGAAAAAGA
549845 AAGAAAAGAAGA
1 AAG-AAA-AAGA
549857 AAGAAAAAGA
1 AAGAAAAAGA
* *
549867 AGGAAAAGGA
1 AAGAAAAAGA
549877 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
549891 AAGAAAAAGA
1 AAGAAAAAGA
* *
549901 AGGAAAGA-A
1 AAGAAAAAGA
* * *
549910 AAGGAAAGGG
1 AAGAAAAAGA
* *
549920 GAG-GAAAGA
1 AAGAAAAAGA
*
549929 AAGAAAAATA
1 AAGAAAAAGA
* *
549939 AGGAAAGA-A
1 AAGAAAAAGA
*
549948 AAGAAAATGA
1 AAGAAAAAGA
*
549958 GAAG-AGAA-A
1 -AAGAAAAAGA
549967 AA-AAAAAGA
1 AAGAAAAAGA
*
549976 AAGAAGAAGA
1 AAGAAAAAGA
549986 A
1 A
549987 GAGGGAAGGA
Statistics
Matches: 101, Mismatches: 28, Indels: 26
0.65 0.18 0.17
Matches are distributed among these distances:
8 5 0.05
9 20 0.20
10 49 0.49
11 10 0.10
12 9 0.09
13 2 0.02
14 6 0.06
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:549868 original size:28 final size:29
Alignment explanation
Indices: 549834--549988 Score: 87
Period size: 28 Copynumber: 5.4 Consensus size: 29
549824 AAGGAGAGGG
549834 GAAGAAGAAGAAAGAAAAGAAGAAAGAAA
1 GAAGAAGAAGAAAGAAAAGAAGAAAGAAA
* *
549863 -AAGAAGGAA-AAGGAAAGGAGAGGAAAGAAA
1 GAAGAA-GAAGAAAGAAA--AGAAGAAAGAAA
* *
549893 GAAAAAGAAGGAAAGAAAAG--GAAAG--G
1 GAAGAAGAA-GAAAGAAAAGAAGAAAGAAA
* * *
549919 GGAGGA-AAGAAAGAAAAATAAGGAAAGAAAA
1 GAAGAAGAAGAAAG-AAAAGAA-GAAAG-AAA
*
549950 GAA-AATG-AGAAGAGAAAA-AAAAAAGAAA
1 GAAGAA-GAAGAA-AGAAAAGAAGAAAGAAA
549978 GAAGAAGAAGA
1 GAAGAAGAAGA
549989 GGGAAGGAAG
Statistics
Matches: 95, Mismatches: 13, Indels: 36
0.66 0.09 0.25
Matches are distributed among these distances:
24 5 0.05
25 6 0.06
26 3 0.03
28 28 0.29
29 12 0.13
30 19 0.20
31 14 0.15
32 8 0.08
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.01
Consensus pattern (29 bp):
GAAGAAGAAGAAAGAAAAGAAGAAAGAAA
Found at i:549911 original size:38 final size:38
Alignment explanation
Indices: 549853--550011 Score: 161
Period size: 38 Copynumber: 4.3 Consensus size: 38
549843 GAAAGAAAAG
549853 AAGAAAGAAAAAGAA-G---GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
*
549887 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
* * * *
549925 AAGAAAGAAAAATAAGGAAAGAAAAGAAAATGAGAAGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
* * *
549963 GAA-AAA-AAAAAGAAAGAAGAAGAAGAGGGAAGGA-AGGA
1 -AAGAAAGAAAAAG-AAGGA-AAGAAAAGGAAAGGAGAGGA
*
550001 AAAAAAGAAAA
1 AAGAAAGAAAA
550012 TAAGGTAATT
Statistics
Matches: 103, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
34 15 0.15
35 1 0.01
37 7 0.07
38 63 0.61
39 17 0.17
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (38 bp):
AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
Found at i:549970 original size:72 final size:72
Alignment explanation
Indices: 549853--550006 Score: 165
Period size: 72 Copynumber: 2.2 Consensus size: 72
549843 GAAAGAAAAG
* * * *
549853 AAGAAAGAAAAAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAA-AAGGAA-
1 AAGAAAGAAAAAGAAGGAAAAGAAAAGAAAAGGAAAGAAAGAAAAA-AAAGAAAGAAGAA-GAAG
*
549916 AGGGGAGGA
64 AGGGAAGGA
* *
549925 AAGAAAGAAAAATAAGG-AAAGAAAAGAAAATGAGAAGAGAA-AAAAAAAAGAAAGAAGAAGAAG
1 AAGAAAGAAAAAGAAGGAAAAGAAAAGAAAAGGA-AAGA-AAGAAAAAAAAGAAAGAAGAAGAAG
549988 AGGGAAGGA
64 AGGGAAGGA
*
549997 AGGAAA-AAAA
1 AAGAAAGAAAA
550007 GAAAATAAGG
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
71 28 0.40
72 40 0.57
73 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (72 bp):
AAGAAAGAAAAAGAAGGAAAAGAAAAGAAAAGGAAAGAAAGAAAAAAAAGAAAGAAGAAGAAGAG
GGAAGGA
Found at i:550723 original size:19 final size:19
Alignment explanation
Indices: 550675--550726 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
550665 AAAAAATATA
** *
550675 TAATATTTTGGTATTTTTT
1 TAATATTTTATTATTTTTG
550694 TAATATTTTATTATTTTTG
1 TAATATTTTATTATTTTTG
*
550713 TAATGTTTTATTAT
1 TAATATTTTATTAT
550727 GGGTTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
TAATATTTTATTATTTTTG
Found at i:550813 original size:27 final size:28
Alignment explanation
Indices: 550763--550831 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
550753 AAATAAAAAA
*
550763 TTACTAAAATAT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAAC-TTTTTTTAT
550791 TTACCAAAATATATATAA-TTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
550818 TTACCAAAATATAT
1 TTACCAAAATATAT
550832 CAAAAAAAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 23 0.59
28 11 0.28
29 5 0.13
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.51
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:550853 original size:16 final size:16
Alignment explanation
Indices: 550832--550863 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
550822 CAAAATATAT
*
550832 CAAAAAAAGTAAAAAA
1 CAAAAAAAATAAAAAA
550848 CAAAAAAAATAAAAAA
1 CAAAAAAAATAAAAAA
550864 AGGAAAAAAA
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:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (16 bp):
CAAAAAAAATAAAAAA
Found at i:552195 original size:17 final size:17
Alignment explanation
Indices: 552173--552209 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
552163 ATGGGGTAAG
552173 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
552190 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
552207 ATG
1 ATG
552210 ACATCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:553213 original size:15 final size:14
Alignment explanation
Indices: 553173--553201 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
553163 TTTTTGTATC
553173 AATTTAATTATTCT
1 AATTTAATTATTCT
553187 AATTTAATTATTCT
1 AATTTAATTATTCT
553201 A
1 A
553202 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:555607 original size:18 final size:18
Alignment explanation
Indices: 555581--555618 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
555571 ATCCCAATGA
* *
555581 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
555599 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
555617 TC
1 TC
555619 ACCACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:555625 original size:18 final size:18
Alignment explanation
Indices: 555584--555625 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
555574 CCAATGATCG
* *
555584 CCACCACCTTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
555602 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
555620 CCACCA
1 CCACCA
555626 ACCATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:556294 original size:39 final size:38
Alignment explanation
Indices: 556243--556319 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 38
556233 AATAACTAAC
* *
556243 ACTAATAATATTAATAATTTTA-TATACAAAATAATACTA
1 ACTAATAATATTAATAA-CTAACTATA-AAAATAATACTA
556282 ACTAA-AATTATTAATAACTAACTATAAAAATAATACTA
1 ACTAATAA-TATTAATAACTAACTATAAAAATAATACTA
556320 GTTTTTTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 16 0.47
39 18 0.53
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (38 bp):
ACTAATAATATTAATAACTAACTATAAAAATAATACTA
Found at i:556694 original size:27 final size:27
Alignment explanation
Indices: 556653--556758 Score: 86
Period size: 27 Copynumber: 3.9 Consensus size: 27
556643 AACACGAGTA
* ** **
556653 GTGCCGCCAATCTGGTTGGCAGGACTG
1 GTGCCGCCAACCTGGTTCCCACCACTG
*
556680 GTGCCGCCAACCTGGTTCCCTCCACTG
1 GTGCCGCCAACCTGGTTCCCACCACTG
* *****
556707 GTGCCGCCAACCTGCTTCCCTTGTTTG
1 GTGCCGCCAACCTGGTTCCCACCACTG
* *
556734 GTGCCGCCAACCTGCTTCCCTCCAC
1 GTGCCGCCAACCTGGTTCCCACCAC
556759 CCAGGGAGTT
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.11, C:0.40, G:0.25, T:0.25
Consensus pattern (27 bp):
GTGCCGCCAACCTGGTTCCCACCACTG
Found at i:556846 original size:24 final size:25
Alignment explanation
Indices: 556818--556867 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
556808 TTTTGTTTTT
*
556818 TTATATA-TTTTGGTAAATAAAAAA
1 TTATATATTTTTGATAAATAAAAAA
556842 TTATATATTTTTTGATAAATAAAAAA
1 TTATATA-TTTTTGATAAATAAAAAA
556868 AAGTTATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
26 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (25 bp):
TTATATATTTTTGATAAATAAAAAA
Found at i:560005 original size:97 final size:97
Alignment explanation
Indices: 559839--560033 Score: 390
Period size: 97 Copynumber: 2.0 Consensus size: 97
559829 CTGGTCTTCT
559839 TGGGGTCTTACGATGGCCTACTCCAATCACATCTGAGGGAGTAATTTTTTTCATTGGCTAACATC
1 TGGGGTCTTACGATGGCCTACTCCAATCACATCTGAGGGAGTAATTTTTTTCATTGGCTAACATC
559904 TGGTTGTTGAGAGGGGCAGTCTACATCATCGA
66 TGGTTGTTGAGAGGGGCAGTCTACATCATCGA
559936 TGGGGTCTTACGATGGCCTACTCCAATCACATCTGAGGGAGTAATTTTTTTCATTGGCTAACATC
1 TGGGGTCTTACGATGGCCTACTCCAATCACATCTGAGGGAGTAATTTTTTTCATTGGCTAACATC
560001 TGGTTGTTGAGAGGGGCAGTCTACATCATCGA
66 TGGTTGTTGAGAGGGGCAGTCTACATCATCGA
560033 T
1 T
560034 TGAATACATG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (97 bp):
TGGGGTCTTACGATGGCCTACTCCAATCACATCTGAGGGAGTAATTTTTTTCATTGGCTAACATC
TGGTTGTTGAGAGGGGCAGTCTACATCATCGA
Found at i:563389 original size:14 final size:14
Alignment explanation
Indices: 563370--563447 Score: 50
Period size: 14 Copynumber: 5.1 Consensus size: 14
563360 TTGATTCCCA
563370 GTAAAATATTTTCT
1 GTAAAATATTTTCT
563384 GTAAAATGA-TTTCT
1 GTAAAAT-ATTTTCT
*
563398 GGAAAATGTTTTACTTTTCT
1 GTAAAA-----TA-TTTTCT
*
563418 GTAAAATGATTTACT
1 GTAAAAT-ATTTTCT
*
563433 GGAAAATATTTTCT
1 GTAAAATATTTTCT
563447 G
1 G
563448 GTGTTTGATT
Statistics
Matches: 50, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
14 24 0.48
15 13 0.26
16 1 0.02
18 1 0.02
19 1 0.02
20 10 0.20
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (14 bp):
GTAAAATATTTTCT
Found at i:563416 original size:34 final size:35
Alignment explanation
Indices: 563378--563444 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
563368 CAGTAAAATA
*
563378 TTTTCTGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTTAC
563412 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
563445 CTGGTGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (35 bp):
TTTTCTGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:563418 original size:20 final size:20
Alignment explanation
Indices: 563393--563432 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
563383 TGTAAAATGA
*
563393 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
563413 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
563433 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:567965 original size:43 final size:43
Alignment explanation
Indices: 567904--567989 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
567894 ACGCATGTCG
*
567904 TTAGTGAAACTCCCATGGCGAAACCTAGGGTTGAAGAGGTCAC
1 TTAGTGAAACTCCCATGGCGAAACCTAGCGTTGAAGAGGTCAC
567947 TTAGTGAAACTCCCATGGCGAAACCTAGCGTTGAAGAGGTCAC
1 TTAGTGAAACTCCCATGGCGAAACCTAGCGTTGAAGAGGTCAC
567990 GTGGGAGTCG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (43 bp):
TTAGTGAAACTCCCATGGCGAAACCTAGCGTTGAAGAGGTCAC
Found at i:569998 original size:21 final size:22
Alignment explanation
Indices: 569957--569998 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
569947 TAAATATTAG
*
569957 ATTAAATTTAATATTAAATTTT
1 ATTAAATTTAATATGAAATTTT
569979 ATTAAA-TTAATA-GAATATTT
1 ATTAAATTTAATATGAA-ATTT
569999 ATCTACAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 10 0.56
22 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAAATTTAATATGAAATTTT
Found at i:581742 original size:19 final size:20
Alignment explanation
Indices: 581702--581748 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
581692 GTATGTAATG
* *
581702 AAATTT-ATAACATATTTGA
1 AAATTTAATAACATAATTAA
581721 AAATTTAATAA-ATAATTAA
1 AAATTTAATAACATAATTAA
581740 AAATATTAA
1 AAAT-TTAA
581749 AATTACTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
AAATTTAATAACATAATTAA
Found at i:581894 original size:16 final size:15
Alignment explanation
Indices: 581868--581898 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
581858 AAATTTATTC
581868 AAAATATTAAAAATT
1 AAAATATTAAAAATT
581883 AAAATAATTAAAAATT
1 AAAAT-ATTAAAAATT
581899 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:582811 original size:13 final size:13
Alignment explanation
Indices: 582793--582818 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
582783 AGAAGTGTAA
582793 AATTTACATTCAT
1 AATTTACATTCAT
582806 AATTTACATTCAT
1 AATTTACATTCAT
582819 CTATGAAGAA
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:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTACATTCAT
Found at i:584740 original size:19 final size:19
Alignment explanation
Indices: 584716--584774 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
584706 TATGTGTTAT
584716 TTTTAAACACAAATATGAG
1 TTTTAAACACAAATATGAG
*
584735 TTTTAAATAC--AT-T-A-
1 TTTTAAACACAAATATGAG
*
584749 TTTCAAACACAAATATGAG
1 TTTTAAACACAAATATGAG
584768 TTTTAAA
1 TTTTAAA
584775 TACATTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 8 0.26
15 1 0.03
16 3 0.10
17 3 0.10
18 1 0.03
19 15 0.48
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (19 bp):
TTTTAAACACAAATATGAG
Found at i:584758 original size:33 final size:33
Alignment explanation
Indices: 584720--584785 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
584710 TGTTATTTTT
584720 AAACACAAATATGAGTTTTAAATACATTATTTC
1 AAACACAAATATGAGTTTTAAATACATTATTTC
584753 AAACACAAATATGAGTTTTAAATACATTATTTC
1 AAACACAAATATGAGTTTTAAATACATTATTTC
584786 CTCAAGCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (33 bp):
AAACACAAATATGAGTTTTAAATACATTATTTC
Found at i:594642 original size:58 final size:55
Alignment explanation
Indices: 594465--594649 Score: 155
Period size: 58 Copynumber: 3.2 Consensus size: 55
594455 TAAATTTACT
*
594465 ATTAAATTTAATTTAATTATTATATTAAT-AGTACTTTATTAATTTAATATTAAAGTG
1 ATTAAATTTAATTTAATT-TTAT-TTGATAAGTA-TTTATTAATTTAATATTAAAGTG
* * *
594522 ATT--ATCTTAATATTAATTTTAATTAAGATAAATATTCTATTAATTTAATAAATTTAA-T-
1 ATTAAAT-TTAAT-TTAATTTT-ATT-TGATAAGTATT-TATTAATTTAAT--ATTAAAGTG
* *
594580 ATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTGAATATTAAAGTG
1 ATTAAATTTAATTTAAT-TTTAT-TTGATAAGTATT-TATTAATTTAATATTAAAGTG
*
594638 ATTAAGTTTAAT
1 ATTAAATTTAAT
594650 AATAGTTGAA
Statistics
Matches: 103, Mismatches: 11, Indels: 27
0.73 0.08 0.19
Matches are distributed among these distances:
55 2 0.02
56 13 0.13
57 16 0.16
58 55 0.53
59 10 0.10
60 7 0.07
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (55 bp):
ATTAAATTTAATTTAATTTTATTTGATAAGTATTTATTAATTTAATATTAAAGTG
Found at i:600061 original size:30 final size:30
Alignment explanation
Indices: 600020--600079 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
600010 AGTAATTTGT
* *
600020 AAAGGGTTTTAGTTAAGCTACAAAAACTAG
1 AAAGGGCTTTAGTTAAGCCACAAAAACTAG
*
600050 AAAGGGCTTTAGTTTAGCCACAAAAACTAG
1 AAAGGGCTTTAGTTAAGCCACAAAAACTAG
600080 GGGAAATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (30 bp):
AAAGGGCTTTAGTTAAGCCACAAAAACTAG
Found at i:601125 original size:20 final size:19
Alignment explanation
Indices: 601102--601154 Score: 52
Period size: 22 Copynumber: 2.6 Consensus size: 19
601092 TATCTCTCAA
*
601102 CAAAAATTATAAAAATAATT
1 CAAAAATTATAAAAA-AATC
601122 CAAAATATTTAATAAAAAAATC
1 CAAAA-A-TT-ATAAAAAAATC
*
601144 CAAAATTTATA
1 CAAAAATTATA
601155 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 3 0.11
20 7 0.25
21 1 0.04
22 10 0.36
23 7 0.25
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (19 bp):
CAAAAATTATAAAAAAATC
Found at i:612899 original size:24 final size:23
Alignment explanation
Indices: 612863--612908 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
612853 AAATGAGTCT
* *
612863 TGAACTTGATAATTGTTCTCAATC
1 TGAACTAGATAATTATT-TCAATC
*
612887 TGAACTAGGTAATTATTTCAAT
1 TGAACTAGATAATTATTTCAAT
612909 ATTCTTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (23 bp):
TGAACTAGATAATTATTTCAATC
Found at i:627307 original size:12 final size:13
Alignment explanation
Indices: 627240--627319 Score: 58
Period size: 14 Copynumber: 5.9 Consensus size: 13
627230 ATATACACAT
*
627240 TAAAAATATAAATA
1 TAAAAATA-AATTA
*
627254 TGAAAATAAATATA
1 TAAAAATAAAT-TA
627268 TAAAAAATAAA--A
1 T-AAAAATAAATTA
*
627280 AAAGACATATAAATTA
1 TAA-A-A-ATAAATTA
627296 TAAAAA-AAATTA
1 TAAAAATAAATTA
627308 TAAAAATAAATT
1 TAAAAATAAATT
627320 TTGTTTATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 17
0.71 0.07 0.23
Matches are distributed among these distances:
11 2 0.04
12 14 0.26
13 9 0.17
14 16 0.30
15 9 0.17
16 3 0.06
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (13 bp):
TAAAAATAAATTA
Found at i:627314 original size:21 final size:20
Alignment explanation
Indices: 627249--627315 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
627239 TTAAAAATAT
*
627249 AAATATGAAAATAAATATATAA
1 AAATAT-AAAAAAAAT-TATAA
*
627271 AAA-ATAAAAAAAGA-CATATA
1 AAATATAAAAAAA-ATTATA-A
*
627291 AATTATAAAAAAAATTATAA
1 AAATATAAAAAAAATTATAA
627311 AAATA
1 AAATA
627316 AATTTTGTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
19 3 0.08
20 15 0.42
21 15 0.42
22 3 0.08
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (20 bp):
AAATATAAAAAAAATTATAA
Found at i:627649 original size:88 final size:88
Alignment explanation
Indices: 627545--627721 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
627535 GTTTTTATGA
627545 TTTTGTAAATGAAATATTTTGTTTGAAATTAAGTTACAGTTGATAAACATAAATTTGAAATTATT
1 TTTTGTAAATGAAATATTTTGTTTGAAATTAAGTTACAGTTGATAAACATAAATTTGAAATTATT
627610 TTTTTATACAATAAATATTTAAC
66 TTTTTATACAATAAATATTTAAC
627633 TTTTGTAAATGAAATATTTTGTTTGAAATTAAGTTACAGTTGATAAACATAAATTTGAAATTATT
1 TTTTGTAAATGAAATATTTTGTTTGAAATTAAGTTACAGTTGATAAACATAAATTTGAAATTATT
627698 TTTTTATACAATAAATATTTAAC
66 TTTTTATACAATAAATATTTAAC
627721 T
1 T
627722 CTGTTACAAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.46
Consensus pattern (88 bp):
TTTTGTAAATGAAATATTTTGTTTGAAATTAAGTTACAGTTGATAAACATAAATTTGAAATTATT
TTTTTATACAATAAATATTTAAC
Found at i:643029 original size:45 final size:45
Alignment explanation
Indices: 642975--643060 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 45
642965 CAAATCGGAT
*
642975 ACATGTGGTCAAGCCACTAT-ATTGCA-ACCAAGCTGCCAGAACAA
1 ACATGTGGTCAAGCCACCATAATTGCAGA-CAAGCTGCCAGAACAA
643019 ACATAGTGGTCAAGCCACCATAATTGCAGACAAGCTGCCAGA
1 ACAT-GTGGTCAAGCCACCATAATTGCAGACAAGCTGCCAGA
643061 CAGAATTGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
44 4 0.11
45 15 0.39
46 18 0.47
47 1 0.03
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (45 bp):
ACATGTGGTCAAGCCACCATAATTGCAGACAAGCTGCCAGAACAA
Found at i:668726 original size:24 final size:24
Alignment explanation
Indices: 668698--668750 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
668688 ATTAGTAATT
* *
668698 TAAATAAACTATGCTAATAAATGC
1 TAAATAAACTATACTAATAAATAC
* *
668722 TAAATATATTATACTAATAAATAC
1 TAAATAAACTATACTAATAAATAC
668746 TAAAT
1 TAAAT
668751 TTTCTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (24 bp):
TAAATAAACTATACTAATAAATAC
Found at i:671587 original size:7 final size:7
Alignment explanation
Indices: 671574--671607 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
671564 GATTCTGACG
671574 AATGGCC
1 AATGGCC
*
671581 TATGGCC
1 AATGGCC
*
671588 TATGGCC
1 AATGGCC
671595 AATGGCC
1 AATGGCC
671602 AATGGC
1 AATGGC
671608 AGTGGGAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (7 bp):
AATGGCC
Done.