Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 123 of 128
Found at i:40644659 original size:3 final size:3
Alignment explanation
Indices: 40644651--40644679 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40644641 CATGAGATTT
40644651 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
40644680 GAGTTGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:40652359 original size:61 final size:60
Alignment explanation
Indices: 40652230--40652383 Score: 155
Period size: 61 Copynumber: 2.5 Consensus size: 60
40652220 GAACAGTTGC
* * **
40652230 CAAGTTTAAGGCCTAACTTGGACCAAAGAAAAAAAATTCAAGTCCCAACGTGGGAACATTTG
1 CAAGTTCAAGGCCTAACTTGGA-CAAA-AAAAAAAATTCAAGCCCCAACGTGGGAACAACTG
*** * *
40652292 CTAAGTTCAAGGCCTAACTTGGACAAAAAAAAGGGTTCAGGCCCCAATGTGGGAACAACTG
1 C-AAGTTCAAGGCCTAACTTGGACAAAAAAAAAAATTCAAGCCCCAACGTGGGAACAACTG
* * * *
40652353 TCAAGTTCATGACTTAATTTGGACAAAAAAA
1 -CAAGTTCAAGGCCTAACTTGGACAAAAAAA
40652384 GTTCAAACCT
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
61 51 0.66
62 6 0.08
63 20 0.26
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (60 bp):
CAAGTTCAAGGCCTAACTTGGACAAAAAAAAAAATTCAAGCCCCAACGTGGGAACAACTG
Found at i:40652681 original size:21 final size:22
Alignment explanation
Indices: 40652649--40652703 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
40652639 TTTTTTTCAC
* *
40652649 TGTTGTTTTGCTGCTATTTTGT
1 TGTTGTTTTGCTGCCATTTTGA
40652671 TGTTG-TTTGCTGCCATTTTGA
1 TGTTGTTTTGCTGCCATTTTGA
*
40652692 TGTTATTTTGCT
1 TGTTGTTTTGCT
40652704 ATTATTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.07, C:0.11, G:0.22, T:0.60
Consensus pattern (22 bp):
TGTTGTTTTGCTGCCATTTTGA
Found at i:40652710 original size:22 final size:22
Alignment explanation
Indices: 40652694--40652782 Score: 79
Period size: 22 Copynumber: 3.9 Consensus size: 22
40652684 CATTTTGATG
*
40652694 TTATTTTGCTATTATTTTATTA
1 TTATTTTACTATTATTTTATTA
* *
40652716 TTATTTTATTATTATTTTTTGGATA
1 TTATTTTACTATTATTTTAT---TA
* * *
40652741 TTATATAACTCTTATTTTATTA
1 TTATTTTACTATTATTTTATTA
*
40652763 TTAATTTTGCTATTATTTTA
1 TT-ATTTTACTATTATTTTA
40652783 GAGGAATTTG
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
22 21 0.41
23 13 0.25
25 17 0.33
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (22 bp):
TTATTTTACTATTATTTTATTA
Found at i:40658077 original size:22 final size:21
Alignment explanation
Indices: 40658030--40658078 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
40658020 AGTTTATACA
40658030 ATTTTAATAAATTTAATATAT
1 ATTTTAATAAATTTAATATAT
* *
40658051 TTTTTAA-AGAATTCTAATATGT
1 ATTTTAATA-AATT-TAATATAT
40658073 ATTTTA
1 ATTTTA
40658079 TTTTAAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 10 0.43
22 12 0.52
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (21 bp):
ATTTTAATAAATTTAATATAT
Found at i:40658160 original size:20 final size:19
Alignment explanation
Indices: 40658096--40658178 Score: 75
Period size: 19 Copynumber: 4.5 Consensus size: 19
40658086 TAGGTTTCAT
40658096 TAATTTTT-TATATTTTTA
1 TAATTTTTATATATTTTTA
* *
40658114 TAATATTTATA-AGTTTATA
1 TAATTTTTATATA-TTTTTA
* *
40658133 TAAATTTTAATATCTTTTTA
1 T-AATTTTTATATATTTTTA
40658153 TAATTTTTA-AT-TTTTTA
1 TAATTTTTATATATTTTTA
*
40658170 TGATTTTTA
1 TAATTTTTA
40658179 GGGGAAAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
17 14 0.26
18 10 0.19
19 15 0.28
20 14 0.26
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (19 bp):
TAATTTTTATATATTTTTA
Found at i:40661420 original size:22 final size:24
Alignment explanation
Indices: 40661378--40661422 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
40661368 ATATAATAGG
*
40661378 AGATAAATTACTTCTATTTATCTA
1 AGATAAATCACTTCTATTTATCTA
40661402 AGATAAATCA-TT-TATTTATCT
1 AGATAAATCACTTCTATTTATCT
40661423 TTATGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 2 0.10
24 9 0.45
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (24 bp):
AGATAAATCACTTCTATTTATCTA
Found at i:40662010 original size:13 final size:13
Alignment explanation
Indices: 40661989--40662017 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40661979 CTTTTCTATT
40661989 TTTATTTTTTTTC
1 TTTATTTTTTTTC
40662002 TTTATTTTTTTTC
1 TTTATTTTTTTTC
40662015 TTT
1 TTT
40662018 CGAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTATTTTTTTTC
Found at i:40662754 original size:15 final size:14
Alignment explanation
Indices: 40662694--40662757 Score: 53
Period size: 15 Copynumber: 4.5 Consensus size: 14
40662684 TTATTATCTT
*
40662694 TTATTATTATGATTA
1 TTATTATCAT-ATTA
40662709 TTATT-TC-TATTA
1 TTATTATCATATTA
*
40662721 TTATTTAT-ATCATTT
1 TTA-TTATCAT-ATTA
40662736 TTATTCATCATATTA
1 TTATT-ATCATATTA
40662751 TTATTAT
1 TTATTAT
40662758 ATGATAGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
12 7 0.17
13 3 0.08
14 7 0.17
15 21 0.52
16 2 0.05
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (14 bp):
TTATTATCATATTA
Found at i:40662956 original size:21 final size:20
Alignment explanation
Indices: 40662936--40663056 Score: 74
Period size: 20 Copynumber: 6.1 Consensus size: 20
40662926 ATGTACATAT
40662936 TATATATATATATATTTATA
1 TATATATATATATATTTATA
* *
40662956 TAT-TCTTTATAT-TTTA-A
1 TATATATATATATATTTATA
*
40662973 AATATATTATATATATTT-TA
1 TATATA-TATATATATTTATA
*
40662993 TATATACTTTATA-ATTCTA-A
1 TATATA-TATATATATT-TATA
* * * *
40663013 CATACATACATGCATATATATA
1 TATATATATAT--ATATTTATA
*
40663035 TATATATATATATATATATA
1 TATATATATATATATTTATA
40663055 TA
1 TA
40663057 ATGTGACTTC
Statistics
Matches: 75, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
17 3 0.04
18 5 0.07
19 19 0.25
20 34 0.45
21 3 0.04
22 11 0.15
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (20 bp):
TATATATATATATATTTATA
Found at i:40662993 original size:11 final size:11
Alignment explanation
Indices: 40662940--40663005 Score: 59
Period size: 11 Copynumber: 6.4 Consensus size: 11
40662930 ACATATTATA
*
40662940 TATATATATAT
1 TATATATATTT
*
40662951 T-TATATATTC
1 TATATATATTT
40662961 T-T-TATATTT
1 TATATATATTT
* *
40662970 TA-AAATATAT
1 TATATATATTT
40662980 TATATATATTT
1 TATATATATTT
*
40662991 TATATATACTT
1 TATATATATTT
40663002 TATA
1 TATA
40663006 ATTCTAACAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 7 0.16
10 16 0.36
11 21 0.48
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TATATATATTT
Found at i:40663033 original size:2 final size:2
Alignment explanation
Indices: 40663026--40663056 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40663016 ACATACATGC
40663026 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40663057 ATGTGACTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40663226 original size:18 final size:17
Alignment explanation
Indices: 40663203--40663238 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
40663193 TTTAATTTTA
*
40663203 TATTTGTTTATTTACTTT
1 TATTTGTTGATTT-CTTT
40663221 TATTTGTTGATTTCTTT
1 TATTTGTTGATTTCTTT
40663238 T
1 T
40663239 CATTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (17 bp):
TATTTGTTGATTTCTTT
Found at i:40665989 original size:21 final size:22
Alignment explanation
Indices: 40665962--40666010 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
40665952 AGTTTATACA
40665962 ATTTTAATA-AATT-TAATATAT
1 ATTTTAA-AGAATTCTAATATAT
*
40665983 TTTTTAAAGAATTCTAATATAT
1 ATTTTAAAGAATTCTAATATAT
40666005 ATTTTA
1 ATTTTA
40666011 TTTTAAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 10 0.42
22 13 0.54
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTTAAAGAATTCTAATATAT
Found at i:40666045 original size:8 final size:9
Alignment explanation
Indices: 40666032--40666110 Score: 63
Period size: 9 Copynumber: 8.7 Consensus size: 9
40666022 TTTCATTAAT
40666032 TTTTTAT-A
1 TTTTTATAA
40666040 TTTTTATAA
1 TTTTTATAA
*
40666049 TATTTATAA
1 TTTTTATAA
*
40666058 GTTTATATAAA
1 -TTTTTAT-AA
* *
40666069 TTTTAATATC
1 TTTTTATA-A
40666079 TTTTTATAA
1 TTTTTATAA
*
40666088 TTTTT-TAT
1 TTTTTATAA
*
40666096 TTTTTATGA
1 TTTTTATAA
40666105 TTTTTA
1 TTTTTA
40666111 AGGGAAAATA
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
8 14 0.25
9 22 0.40
10 17 0.31
11 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:40666092 original size:10 final size:10
Alignment explanation
Indices: 40666028--40666095 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
40666018 TAGGTTTCAT
40666028 TAATTTTTTA
1 TAATTTTTTA
40666038 T-A-TTTTTA
1 TAATTTTTTA
*
40666046 TAA-TATTTA
1 TAATTTTTTA
* *
40666055 TAAGTTTATA
1 TAATTTTTTA
* *
40666065 TAAATTTTAA
1 TAATTTTTTA
40666075 T-ATCTTTTTA
1 TAAT-TTTTTA
40666085 TAATTTTTTA
1 TAATTTTTTA
40666095 T
1 T
40666096 TTTTTATGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
8 7 0.15
9 11 0.24
10 26 0.57
11 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:40668103 original size:2 final size:2
Alignment explanation
Indices: 40668096--40668124 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40668086 ATATTAATGC
40668096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40668125 GCTCTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40669651 original size:18 final size:18
Alignment explanation
Indices: 40669617--40669651 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40669607 ATTTAATCAA
* *
40669617 TTTTAATTTTTATATTTT
1 TTTTAATTTTGAAATTTT
40669635 TTTTAATTTTGAAATTT
1 TTTTAATTTTGAAATTT
40669652 CAATAATAAT
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:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTAATTTTGAAATTTT
Found at i:40672004 original size:27 final size:29
Alignment explanation
Indices: 40671960--40672023 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
40671950 TCTTCCTCAC
** *
40671960 CTTCTTCCTCAGTTGAAG-ACC-CTTCTT
1 CTTCTTCCTCAGAAGAAGCACCTCTTCAT
40671987 CTTCTTCCTCAGAAGAAGTCACCTCTTCAT
1 CTTCTTCCTCAGAAGAAG-CACCTCTTCAT
40672017 CTTCTTC
1 CTTCTTC
40672024 AGATGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 16 0.52
29 3 0.10
30 12 0.39
ACGTcount: A:0.17, C:0.34, G:0.09, T:0.39
Consensus pattern (29 bp):
CTTCTTCCTCAGAAGAAGCACCTCTTCAT
Found at i:40690713 original size:49 final size:50
Alignment explanation
Indices: 40690641--40690737 Score: 133
Period size: 49 Copynumber: 2.0 Consensus size: 50
40690631 ACATGTGAAA
* * * *
40690641 ATGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGT
1 ATGTGATTATGTGACTACATGTAAGACCATAGCTGGACTATGGCATCGGT
* *
40690691 ATGTGA-TATGTGACTACATGTAAGACCATAGTTTGACTATGGCATCG
1 ATGTGATTATGTGACTACATGTAAGACCATAGCTGGACTATGGCATCG
40690738 AGAAAATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
49 35 0.85
50 6 0.15
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (50 bp):
ATGTGATTATGTGACTACATGTAAGACCATAGCTGGACTATGGCATCGGT
Found at i:40701129 original size:16 final size:17
Alignment explanation
Indices: 40701098--40701130 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40701088 GTGTTTAAAA
40701098 TATTTTCTAGAAATTATG
1 TATTTTCTA-AAATTATG
40701116 TATTTTCT-AAATTAT
1 TATTTTCTAAAATTAT
40701131 CCTTACTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (17 bp):
TATTTTCTAAAATTATG
Found at i:40704831 original size:16 final size:17
Alignment explanation
Indices: 40704800--40704832 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40704790 GTGTTTAAAA
40704800 TATTTTCTAGAAATTATG
1 TATTTTCTA-AAATTATG
40704818 TATTTTCT-AAATTAT
1 TATTTTCTAAAATTAT
40704833 CCTTACTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (17 bp):
TATTTTCTAAAATTATG
Found at i:40705727 original size:18 final size:18
Alignment explanation
Indices: 40705706--40705787 Score: 58
Period size: 18 Copynumber: 4.3 Consensus size: 18
40705696 GATATAAACT
40705706 TAAAAAATATAAATATTA
1 TAAAAAATATAAATATTA
* * *
40705724 TAAAAGATGTAAAAATTA
1 TAAAAAATATAAATATTA
* *
40705742 TAATAAATTATATAAT-TAA
1 TAA-AAAATATA-AATATTA
*
40705761 TAAAACATATTTAAAATATTA
1 TAAAA-A-ATAT-AAATATTA
40705782 TAAAAA
1 TAAAAA
40705788 TGTATTAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
18 20 0.43
19 11 0.23
20 8 0.17
21 8 0.17
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (18 bp):
TAAAAAATATAAATATTA
Found at i:40705781 original size:22 final size:22
Alignment explanation
Indices: 40705756--40705809 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
40705746 AAATTATATA
40705756 ATTAATAAAACATAT-TTAAAAT
1 ATTAATAAAA-ATATATTAAAAT
*
40705778 ATT-ATAAAAATGTATTAAAAT
1 ATTAATAAAAATATATTAAAAT
*
40705799 ACTAA-AAAAAT
1 ATTAATAAAAAT
40705810 CATGAACCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 3 0.11
21 21 0.75
22 4 0.14
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
ATTAATAAAAATATATTAAAAT
Found at i:40705784 original size:21 final size:21
Alignment explanation
Indices: 40705716--40705809 Score: 58
Period size: 21 Copynumber: 4.7 Consensus size: 21
40705706 TAAAAAATAT
* *
40705716 AAATATTAT-AAAAGAT-GTA
1 AAATATTATAAAAATATATTA
40705735 AAA-ATTATAATAAAT-TA-TA
1 AAATATTATAA-AAATATATTA
* *
40705754 TAAT-TAATAAAACATAT-TTA
1 AAATATTATAAAA-ATATATTA
*
40705774 AAATATTATAAAAATGTATTA
1 AAATATTATAAAAATATATTA
* *
40705795 AAATACTAAAAAAAT
1 AAATATTATAAAAAT
40705810 CATGAACCAT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
18 7 0.12
19 16 0.28
20 12 0.21
21 23 0.40
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (21 bp):
AAATATTATAAAAATATATTA
Found at i:40735600 original size:11 final size:11
Alignment explanation
Indices: 40735584--40735610 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40735574 CTACATGTAT
40735584 CAAACTAGGAG
1 CAAACTAGGAG
40735595 CAAACTAGGAG
1 CAAACTAGGAG
40735606 CAAAC
1 CAAAC
40735611 CAACTAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.22, G:0.22, T:0.07
Consensus pattern (11 bp):
CAAACTAGGAG
Found at i:40737592 original size:11 final size:11
Alignment explanation
Indices: 40737557--40737584 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
40737547 CCCTATTTAA
40737557 TCTCAATTTGC
1 TCTCAATTTGC
40737568 TCTCAATTTGC
1 TCTCAATTTGC
40737579 TCTCAA
1 TCTCAA
40737585 ATTTCTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (11 bp):
TCTCAATTTGC
Found at i:40737597 original size:11 final size:12
Alignment explanation
Indices: 40737557--40737597 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
40737547 CCCTATTTAA
40737557 TCTC-AATTTGC
1 TCTCAAATTTGC
40737568 TCTC-AATTTGC
1 TCTCAAATTTGC
40737579 TCTCAAATTT-C
1 TCTCAAATTTGC
*
40737590 TCTTAAAT
1 TCTCAAAT
40737598 CCCTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 23 0.82
12 5 0.18
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.46
Consensus pattern (12 bp):
TCTCAAATTTGC
Found at i:40739651 original size:40 final size:40
Alignment explanation
Indices: 40739575--40739652 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
40739565 TTATGTGGCA
* *
40739575 GCAAAACGCGCCCTTGAGGGAGCGATTTATGTCCACGTAG
1 GCAAAACGCGCCCTTCAGGGAGCGATTTATCTCCACGTAG
*
40739615 GCAAAACGCG-CCTTCAGGGACGCG-TTTTTCTACCACGT
1 GCAAAACGCGCCCTTCAGGGA-GCGATTTATCT-CCACGT
40739653 CCCCTGACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 14 0.42
40 19 0.58
ACGTcount: A:0.23, C:0.28, G:0.27, T:0.22
Consensus pattern (40 bp):
GCAAAACGCGCCCTTCAGGGAGCGATTTATCTCCACGTAG
Found at i:40744001 original size:16 final size:16
Alignment explanation
Indices: 40743980--40744010 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40743970 CTATGCATGC
*
40743980 AAAATATAAAAGATAG
1 AAAATACAAAAGATAG
40743996 AAAATACAAAAGATA
1 AAAATACAAAAGATA
40744011 TAATAGTGAA
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:0.71, C:0.03, G:0.10, T:0.16
Consensus pattern (16 bp):
AAAATACAAAAGATAG
Found at i:40745729 original size:23 final size:23
Alignment explanation
Indices: 40745705--40745857 Score: 85
Period size: 23 Copynumber: 6.5 Consensus size: 23
40745695 ACACCAAAAT
*
40745705 TTGGACAGCATAAATACAACAAT
1 TTGGACAGCATAAATACAACAAA
* *
40745728 TTGGGCAGCATATATATACAAC-AG
1 TTGGACAGCATA-A-ATACAACAAA
* *** *
40745752 TTTGAGCAGCATTTTTACACCAAAA
1 TTGGA-CAGCATAAATACAAC-AAA
* *
40745777 CTGGACAGCATATATACAACAAA
1 TTGGACAGCATAAATACAACAAA
* * * *
40745800 TTGGGCAGCATTTAA-GCATCAAAA
1 TTGGACAGCA-TAAATACAAC-AAA
* *
40745824 TTGGACAGCATATATGCAACAAA
1 TTGGACAGCATAAATACAACAAA
*
40745847 TTGGGCAGCAT
1 TTGGACAGCAT
40745858 TTAAGCATTA
Statistics
Matches: 97, Mismatches: 25, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
23 45 0.46
24 35 0.36
25 17 0.18
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (23 bp):
TTGGACAGCATAAATACAACAAA
Found at i:40745794 original size:24 final size:24
Alignment explanation
Indices: 40745699--40745885 Score: 125
Period size: 24 Copynumber: 7.8 Consensus size: 24
40745689 ATTTTCACAC
*
40745699 CAAAATTTGGACAGCATAAATACAA
1 CAAAA-TTGGACAGCATATATACAA
* * *
40745724 C-AATTTGGGCAGCATATATA-TA
1 CAAAATTGGACAGCATATATACAA
* * * * *
40745746 CAACAGTTTGAGCAGCATTTTTACAC
1 CAA-AATTGGA-CAGCATATATACAA
*
40745772 CAAAACTGGACAGCATATATACAA
1 CAAAATTGGACAGCATATATACAA
* * *
40745796 C-AAATTGGGCAGCATTTA-AGCAT
1 CAAAATTGGACAGCATATATA-CAA
*
40745819 CAAAATTGGACAGCATATATGCAA
1 CAAAATTGGACAGCATATATACAA
* * *
40745843 C-AAATTGGGCAGCATTTA-AGCAT
1 CAAAATTGGACAGCATATATA-CAA
*
40745866 TAAAATTGGACAGCATATAT
1 CAAAATTGGACAGCATATAT
40745886 GTAATAAATT
Statistics
Matches: 120, Mismatches: 32, Indels: 20
0.70 0.19 0.12
Matches are distributed among these distances:
22 3 0.03
23 49 0.41
24 51 0.43
25 14 0.12
26 3 0.03
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (24 bp):
CAAAATTGGACAGCATATATACAA
Found at i:40745796 original size:47 final size:47
Alignment explanation
Indices: 40745739--40745965 Score: 294
Period size: 47 Copynumber: 4.8 Consensus size: 47
40745729 TGGGCAGCAT
** * * * *
40745739 ATATATACAACAGTTTGAGCAGCATTTTTA-CACCAAAACTGGACAGC
1 ATATATACAACAAATTGGGCAGCA-TTTAAGCATCAAAATTGGACAGC
40745786 ATATATACAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGC
1 ATATATACAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGC
* *
40745833 ATATATGCAACAAATTGGGCAGCATTTAAGCATTAAAATTGGACAGC
1 ATATATACAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGC
** * * *
40745880 ATATATGTAATAAATTGGGCAGCATTTAAGCATCAAAATAGTACAGC
1 ATATATACAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGC
** *
40745927 ATATATGTAACAAATTGGGAAGCATTTAAGCATCAAAAT
1 ATATATACAACAAATTGGGCAGCATTTAAGCATCAAAAT
40745966 ATGTATATAT
Statistics
Matches: 164, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 4 0.02
47 160 0.98
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (47 bp):
ATATATACAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGC
Found at i:40745804 original size:72 final size:71
Alignment explanation
Indices: 40745646--40745810 Score: 208
Period size: 72 Copynumber: 2.3 Consensus size: 71
40745636 GGACAACTTT
* * * * *
40745646 TATACATCAATTTGGACAGCATTTATATACCAAAGTAGACAGTATTTTCACACCAAAATTTGGAC
1 TATACAACAATTTGGGCAGCATATATATACCAAAGTAGACAGCATTTTCACACCAAAATCTGGAC
40745711 AGCATA
66 AGCATA
* * *
40745717 AATACAACAATTTGGGCAGCATATATATA-CAACAGTTTGAGCAGCATTTTTACACCAAAA-CTG
1 TATACAACAATTTGGGCAGCATATATATACCAA-AG-TAGA-CAGCATTTTCACACCAAAATCTG
40745780 GACAGCATA
63 GACAGCATA
*
40745789 TATACAACAAATTGGGCAGCAT
1 TATACAACAATTTGGGCAGCAT
40745811 TTAAGCATCA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
70 3 0.04
71 27 0.33
72 34 0.42
73 17 0.21
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (71 bp):
TATACAACAATTTGGGCAGCATATATATACCAAAGTAGACAGCATTTTCACACCAAAATCTGGAC
AGCATA
Found at i:40745893 original size:24 final size:24
Alignment explanation
Indices: 40745773--40745933 Score: 116
Period size: 23 Copynumber: 6.8 Consensus size: 24
40745763 TTTTTACACC
* *
40745773 AAAACTGGACAGCATATATACAA-
1 AAAATTGGACAGCATATATGCAAT
* * * *
40745796 CAAATTGGGCAGCATTTAAGC-AT
1 AAAATTGGACAGCATATATGCAAT
40745819 CAAAATTGGACAGCATATATGCAA-
1 -AAAATTGGACAGCATATATGCAAT
* * * * *
40745843 CAAATTGGGCAGCATTTAAGCATT
1 AAAATTGGACAGCATATATGCAAT
*
40745867 AAAATTGGACAGCATATATGTAAT
1 AAAATTGGACAGCATATATGCAAT
* * *
40745891 -AAATTGGGCAGCATTTAAGC-AT
1 AAAATTGGACAGCATATATGCAAT
* *
40745913 CAAAATAGTACAGCATATATG
1 -AAAATTGGACAGCATATATG
40745934 TAACAAATTG
Statistics
Matches: 102, Mismatches: 30, Indels: 11
0.71 0.21 0.08
Matches are distributed among these distances:
22 3 0.03
23 49 0.48
24 49 0.48
25 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (24 bp):
AAAATTGGACAGCATATATGCAAT
Found at i:40745950 original size:23 final size:23
Alignment explanation
Indices: 40745783--40745951 Score: 101
Period size: 23 Copynumber: 7.2 Consensus size: 23
40745773 AAAACTGGAC
* *
40745783 AGCATATATACAACAAATTGGGC
1 AGCATATATGCAACAAATTGGGA
* * *
40745806 AGCATTTAAGCATCAAAATT-GGA
1 AGCATATATGCAAC-AAATTGGGA
*
40745829 CAGCATATATGCAACAAATTGGGC
1 -AGCATATATGCAACAAATTGGGA
* *
40745853 AGCATTTAAGCATTA-AAATT-GGA
1 AGCATATATGCA--ACAAATTGGGA
* * *
40745876 CAGCATATATGTAATAAATTGGGC
1 -AGCATATATGCAACAAATTGGGA
* * * * * *
40745900 AGCATTTAAGCATCAAAATAGTA
1 AGCATATATGCAACAAATTGGGA
*
40745923 CAGCATATATGTAACAAATTGGGA
1 -AGCATATATGCAACAAATTGGGA
40745947 AGCAT
1 AGCAT
40745952 TTAAGCATCA
Statistics
Matches: 105, Mismatches: 32, Indels: 18
0.68 0.21 0.12
Matches are distributed among these distances:
22 1 0.01
23 53 0.50
24 50 0.48
25 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (23 bp):
AGCATATATGCAACAAATTGGGA
Found at i:40745979 original size:47 final size:47
Alignment explanation
Indices: 40745772--40745965 Score: 307
Period size: 47 Copynumber: 4.1 Consensus size: 47
40745762 ATTTTTACAC
* **
40745772 CAAAACTGGACAGCATATATACAACAAATTGGGCAGCATTTAAGCAT
1 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCAT
*
40745819 CAAAATTGGACAGCATATATGCAACAAATTGGGCAGCATTTAAGCAT
1 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCAT
* *
40745866 TAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCAT
1 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCAT
* * *
40745913 CAAAATAGTACAGCATATATGTAACAAATTGGGAAGCATTTAAGCAT
1 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCAT
40745960 CAAAAT
1 CAAAAT
40745966 ATGTATATAT
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 137 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.25
Consensus pattern (47 bp):
CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCAT
Found at i:40751204 original size:24 final size:25
Alignment explanation
Indices: 40751150--40751211 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 25
40751140 TCCGCTAAGT
*
40751150 GCTCTATGGAGCTACCCGTTGATTA
1 GCTCTTTGGAGCTACCCGTTGATTA
*
40751175 -CACTTTGGAGCTACCCGTT-A-TA
1 GCTCTTTGGAGCTACCCGTTGATTA
40751197 GGCTCTTTGTGAGCT
1 -GCTCTTTG-GAGCT
40751212 TCTCATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 2 0.06
23 1 0.03
24 23 0.74
25 5 0.16
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (25 bp):
GCTCTTTGGAGCTACCCGTTGATTA
Found at i:40761680 original size:14 final size:14
Alignment explanation
Indices: 40761661--40761687 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40761651 AAGAGAAATT
40761661 TATTTTTGCTTATC
1 TATTTTTGCTTATC
40761675 TATTTTTGCTTAT
1 TATTTTTGCTTAT
40761688 AGATATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.11, G:0.07, T:0.67
Consensus pattern (14 bp):
TATTTTTGCTTATC
Found at i:40763585 original size:19 final size:19
Alignment explanation
Indices: 40763561--40763598 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40763551 TTCCTAATTG
*
40763561 GAATTGTAGATGGCATAAT
1 GAATTGTAGACGGCATAAT
40763580 GAATTGTAGACGGCATAAT
1 GAATTGTAGACGGCATAAT
40763599 AATCCTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.29
Consensus pattern (19 bp):
GAATTGTAGACGGCATAAT
Found at i:40767274 original size:43 final size:42
Alignment explanation
Indices: 40767224--40767358 Score: 150
Period size: 42 Copynumber: 3.2 Consensus size: 42
40767214 TTTGGCACCG
* *
40767224 AAGTGCATTATTAGATAAACCGAAGCAAATATATTGGCACACAT
1 AAGTGCATTATTGGATGAACCGAAGCAAATATATT-G-ACACAT
* *
40767268 -AGTGCA-TATTTGGATGAACTGAAACAAATATATTGACACAT
1 AAGTGCATTA-TTGGATGAACCGAAGCAAATATATTGACACAT
* **
40767309 AAGTGCATCATTGGATGAACCGAAGCAAATATA-CAAGCACAT
1 AAGTGCATTATTGGATGAACCGAAGCAAATATATTGA-CACAT
40767351 AAGTGCAT
1 AAGTGCAT
40767359 CATCAGACAA
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
41 7 0.09
42 43 0.55
43 28 0.36
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (42 bp):
AAGTGCATTATTGGATGAACCGAAGCAAATATATTGACACAT
Found at i:40771371 original size:14 final size:13
Alignment explanation
Indices: 40771352--40771414 Score: 58
Period size: 12 Copynumber: 4.8 Consensus size: 13
40771342 TTAATTTTTT
40771352 TATTTTCAATATAA
1 TATTTT-AATATAA
*
40771366 TATTTTTAT-TAA
1 TATTTTAATATAA
40771378 TATTTTGAATATAAA
1 TATTTT-AATAT-AA
* *
40771393 TAATTTAACATAA
1 TATTTTAATATAA
40771406 -ATTTTAATA
1 TATTTTAATA
40771415 CTACATTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
12 16 0.40
13 6 0.15
14 11 0.28
15 7 0.17
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (13 bp):
TATTTTAATATAA
Found at i:40771754 original size:22 final size:22
Alignment explanation
Indices: 40771724--40771766 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40771714 ATAGCAGAAC
* *
40771724 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
40771746 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
40771767 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:40771912 original size:42 final size:42
Alignment explanation
Indices: 40771838--40772192 Score: 401
Period size: 42 Copynumber: 8.4 Consensus size: 42
40771828 ACGTCACTAA
* *
40771838 CTTTTGCGGCGCTTACATAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCGCTAAAGATCATGTT
*
40771882 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGCT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* *
40771924 CTTTAGCGGCGCTTAGAAAGAAACGCCCCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* * **
40771966 CTTTAGCGGAGCTTATAAAAAAACGTTGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* * *
40772008 CTTTAGCGACGCTTAGGAAAAAATGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* *
40772050 CTTTAGCGGCGCTTTTGTAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGC-TTAGAAAAAAACGCCGCTAAAGATCATGTT
* * * * * ** *
40772093 CTTTAGCGACGATTTGGAAGAAAGCGCTTCTAAA-AGTAATGTT
1 CTTTAGCGGCG-CTTAGAAAAAAACGCCGCTAAAGA-TCATGTT
* **
40772136 CTATAGCGGCGCTTATTAAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGA-TCA-TGTT
40772178 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
40772193 TTTCACAAAC
Statistics
Matches: 264, Mismatches: 43, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
41 1 0.00
42 183 0.69
43 67 0.25
44 13 0.05
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:40772654 original size:21 final size:21
Alignment explanation
Indices: 40772625--40772682 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
40772615 GCTTCTATTG
40772625 CTACTTCTCTCGCTGCGGCCT
1 CTACTTCTCTCGCTGCGGCCT
* **
40772646 CTGCTTCTCTTACTGCGGCCT
1 CTACTTCTCTCGCTGCGGCCT
40772667 CTACTTCTCTCGCTGC
1 CTACTTCTCTCGCTGC
40772683 TTCTCTCGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.05, C:0.41, G:0.17, T:0.36
Consensus pattern (21 bp):
CTACTTCTCTCGCTGCGGCCT
Found at i:40772683 original size:33 final size:32
Alignment explanation
Indices: 40772646--40772740 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 32
40772636 GCTGCGGCCT
*
40772646 CTGCTTCTCTTACTGCGGCCTCTACTTCTCTCG
1 CTGCTTCTCTTGCTGCGGCCTCT-CTTCTCTCG
*
40772679 CTGCTTCTCTCGCTGCGG-C-CTC-TCTCTCG
1 CTGCTTCTCTTGCTGCGGCCTCTCTTCTCTCG
40772708 CTGCTTCT-TTCGCTGCGGCCTCTGCTTCTCTCG
1 CTGCTTCTCTT-GCTGCGGCCTCT-CTTCTCTCG
40772741 TTGTAGCCGC
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
28 1 0.02
29 22 0.41
30 2 0.04
31 4 0.07
32 2 0.04
33 23 0.43
ACGTcount: A:0.02, C:0.41, G:0.19, T:0.38
Consensus pattern (32 bp):
CTGCTTCTCTTGCTGCGGCCTCTCTTCTCTCG
Found at i:40772685 original size:12 final size:12
Alignment explanation
Indices: 40772670--40772723 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 12
40772660 GCGGCCTCTA
40772670 CTTCTCTCGCTG
1 CTTCTCTCGCTG
40772682 CTTCTCTCGCTGCGG
1 CTTCTCTCGCT---G
40772697 CCTCTCTCTCGCTG
1 -CT-TCTCTCGCTG
*
40772711 CTTCTTTCGCTG
1 CTTCTCTCGCTG
40772723 C
1 C
40772724 GGCCTCTGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 21 0.58
13 2 0.06
14 1 0.03
15 1 0.03
16 2 0.06
17 9 0.25
ACGTcount: A:0.00, C:0.43, G:0.19, T:0.39
Consensus pattern (12 bp):
CTTCTCTCGCTG
Found at i:40772704 original size:15 final size:15
Alignment explanation
Indices: 40772684--40772730 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
40772674 TCTCGCTGCT
40772684 TCTCTCGCTGCGGCC
1 TCTCTCGCTGCGGCC
* * *
40772699 TCTCTCTC-GCTGCT
1 TCTCTCGCTGCGGCC
*
40772713 TCTTTCGCTGCGGCC
1 TCTCTCGCTGCGGCC
40772728 TCT
1 TCT
40772731 GCTTCTCTCG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.00, C:0.43, G:0.21, T:0.36
Consensus pattern (15 bp):
TCTCTCGCTGCGGCC
Found at i:40772704 original size:29 final size:29
Alignment explanation
Indices: 40772672--40772730 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
40772662 GGCCTCTACT
40772672 TCTCTCGCTGCTTCTCTCGCTGCGGCCTC
1 TCTCTCGCTGCTTCTCTCGCTGCGGCCTC
*
40772701 TCTCTCGCTGCTTCTTTCGCTGCGGCCTC
1 TCTCTCGCTGCTTCTCTCGCTGCGGCCTC
40772730 T
1 T
40772731 GCTTCTCTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.00, C:0.42, G:0.20, T:0.37
Consensus pattern (29 bp):
TCTCTCGCTGCTTCTCTCGCTGCGGCCTC
Found at i:40772753 original size:21 final size:21
Alignment explanation
Indices: 40772706--40772763 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
40772696 GCCTCTCTCT
* *
40772706 CGCTGCTTCTTTCGCTGCGGC
1 CGCTGCTTCTCTCGCTGCAGC
* * *
40772727 CTCTGCTTCTCTCGTTGTAGC
1 CGCTGCTTCTCTCGCTGCAGC
*
40772748 CGCTGCTTCCCTCGCT
1 CGCTGCTTCTCTCGCT
40772764 ACCGCCTCTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.02, C:0.40, G:0.22, T:0.36
Consensus pattern (21 bp):
CGCTGCTTCTCTCGCTGCAGC
Found at i:40779806 original size:23 final size:24
Alignment explanation
Indices: 40779766--40779826 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
40779756 ATATGAATTT
*
40779766 TAAA-AAATTAATAAAATTTAAGG
1 TAAATAAATTAATAAAATTCAAGG
*
40779789 TAAATAAATT-ATATAATTCAAGG
1 TAAATAAATTAATAAAATTCAAGG
40779812 TAAATAAAATTAATA
1 TAAAT-AAATTAATA
40779827 TCGGAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 20 0.61
24 10 0.30
25 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (24 bp):
TAAATAAATTAATAAAATTCAAGG
Found at i:40781308 original size:34 final size:34
Alignment explanation
Indices: 40781270--40781381 Score: 197
Period size: 34 Copynumber: 3.3 Consensus size: 34
40781260 TTCTTCCAGC
*
40781270 ATGCAAAATCTAAATGCAAAATCATTTTTTACGG
1 ATGCAAAATCTAAATGCAAAATCAATTTTTACGG
40781304 ATGCAAAATCTAAATGCAAAATCAATTTTTACGG
1 ATGCAAAATCTAAATGCAAAATCAATTTTTACGG
*
40781338 ATGCAAAATCTAAATGCAAAATCAATTTTTACAG
1 ATGCAAAATCTAAATGCAAAATCAATTTTTACGG
*
40781372 ATGGAAAATC
1 ATGCAAAATC
40781382 ATTTTTTACG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 75 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (34 bp):
ATGCAAAATCTAAATGCAAAATCAATTTTTACGG
Found at i:40782219 original size:73 final size:72
Alignment explanation
Indices: 40782136--40782370 Score: 179
Period size: 74 Copynumber: 3.2 Consensus size: 72
40782126 ATCAAGGACA
* *
40782136 AAACGGCACCGTTATAAGATAACATTAAACATTGTTGCGGCGCTTTAGCTAAAGCGCCACTAATA
1 AAACGACACCGTTATAAGATAACATTAAACATT-TTGTGGCGCTTTAGCTAAAGCGCCACTAATA
40782201 AAAAAAGG
65 AAAAAAGG
* * * *** ** * * * *
40782209 AAACGACACCGTTTCCTCAGCTCGTGATT-TGCGAATTTGTGGCGTTTTTA--TAATGTGCCACT
1 AAACGACACCG-TT-ATAAGAT-AACATTAAAC-ATTTTGTGGCG-CTTTAGCTAAAGCGCCACT
* **
40782271 AAAAGAAAACAACA
61 AATA-AAAA-AAGG
* *
40782285 AAACGGCACCGTTATAAGATAACATTAAACATTTTTGTGGCGCTTTAGCTAAAGCGCCACTACTA
1 AAACGACACCGTTATAAGATAACATTAAACA-TTTTGTGGCGCTTTAGCTAAAGCGCCACTAATA
*
40782350 AAAATAGG
65 AAAAAAGG
*
40782358 AAACGACGCCGTT
1 AAACGACACCGTT
40782371 TCCTCAGCTC
Statistics
Matches: 114, Mismatches: 37, Indels: 22
0.66 0.21 0.13
Matches are distributed among these distances:
73 30 0.26
74 33 0.29
75 30 0.26
76 21 0.18
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (72 bp):
AAACGACACCGTTATAAGATAACATTAAACATTTTGTGGCGCTTTAGCTAAAGCGCCACTAATAA
AAAAAGG
Found at i:40782473 original size:147 final size:147
Alignment explanation
Indices: 40782133--40782473 Score: 415
Period size: 149 Copynumber: 2.3 Consensus size: 147
40782123 AATATCAAGG
* *
40782133 ACAAAACGGCACCGTTATAAGATAACATTAAAC-ATTGTTGC-GGCGCTTTAGCTAAAGCGCCAC
1 ACAAAACGGCACCGTTAT-ACATAACATTAAACAAAT-TT-CTGGCGCTTTAGCTAAAGCGCCAC
** * *
40782196 TAATAAAAAAAGGAAACGACACCGTTTCCTCAGCTCGTGATTTGCGAATTTGTGGCGTTTTTATA
63 TAATAAAAAAAGGAAACGACACCGTTTCCTCAGCTCGTGA-TAACAAATTTGTGGCGTTTTTAAA
*
40782261 ATGTGCCACTAAAAGAAAACA
127 ATGCGCCACTAAAAGAAAACA
* ** *
40782282 ACAAAACGGCACCGTTATAAGATAACATTAAACATTTTTGTGGCGCTTTAGCTAAAGCGCCACTA
1 ACAAAACGGCACCGTTAT-ACATAACATTAAACAAATTTCTGGCGCTTTAGCTAAAGCGCCACTA
* * *
40782347 CTAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGT-A-AACAATATTTGTGGCGTTTTTAAAAT
65 ATAAAAAAAGGAAACGACACCGTTTCCTCAGCTCGTGATAACAA-ATTTGTGGCGTTTTTAAAAT
40782410 GCGCCACTAAAAGAAAACA
129 GCGCCACTAAAAGAAAACA
* *
40782429 ACAAAACGGCACCGTCT-T-CATTACAGTTAAAGGAAATTTCTGGCG
1 ACAAAACGGCACCGT-TATACATAACA-TTAAA-CAAATTTCTGGCG
40782474 TTTCTTCATA
Statistics
Matches: 170, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
145 5 0.03
146 7 0.04
147 62 0.36
148 2 0.01
149 92 0.54
150 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (147 bp):
ACAAAACGGCACCGTTATACATAACATTAAACAAATTTCTGGCGCTTTAGCTAAAGCGCCACTAA
TAAAAAAAGGAAACGACACCGTTTCCTCAGCTCGTGATAACAAATTTGTGGCGTTTTTAAAATGC
GCCACTAAAAGAAAACA
Found at i:40782602 original size:115 final size:115
Alignment explanation
Indices: 40782396--40782635 Score: 399
Period size: 115 Copynumber: 2.1 Consensus size: 115
40782386 CAATATTTGT
* *
40782396 GGCGTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCATTACAGTTAAAG
1 GGCGTTTTTTAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCATCACAGTTAAAG
* *
40782461 GAAATTTCTGGCGTTTCTTCATAAAACGCCGGTAATATATCACTTTTAGC
66 GAAATTTCTGGCGTTTCTTCACAAAACGCCGGTAATATATCACCTTTAGC
**
40782511 GGCGTTTTTTAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAGTTAAAG
1 GGCGTTTTTTAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCATCACAGTTAAAG
* *
40782576 GAAATTTGTGGCGTTTCTTCACAAAACGCCGGTAATATATGACCTTTAGC
66 GAAATTTCTGGCGTTTCTTCACAAAACGCCGGTAATATATCACCTTTAGC
*
40782626 GACGTTTTTT
1 GGCGTTTTTT
40782636 CTGAAGCGCC
Statistics
Matches: 116, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
115 116 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (115 bp):
GGCGTTTTTTAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCATCACAGTTAAAG
GAAATTTCTGGCGTTTCTTCACAAAACGCCGGTAATATATCACCTTTAGC
Found at i:40782833 original size:25 final size:23
Alignment explanation
Indices: 40782791--40782840 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
40782781 TTACATCAAT
40782791 ATATTTTTATATTGAATAAATATAA
1 ATATTTTTATATTGAAT--ATATAA
*
40782816 ATATTTTTGTA-TGCAATATATAA
1 ATATTTTTATATTG-AATATATAA
40782839 AT
1 AT
40782841 GAAAAATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 13 0.57
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (23 bp):
ATATTTTTATATTGAATATATAA
Found at i:40783138 original size:14 final size:13
Alignment explanation
Indices: 40783092--40783172 Score: 58
Period size: 14 Copynumber: 5.8 Consensus size: 13
40783082 ATATATACCA
40783092 TAAACCTTAAA-TC
1 TAAACC-TAAACTC
*
40783105 TTAAATCCTAAACCC
1 -TAAA-CCTAAACTC
*
40783120 CAAACCTAAAACTC
1 TAAACCT-AAACTC
*
40783134 TAAACTCTAAACTG
1 TAAAC-CTAAACTC
40783148 TAAACCCTAAAC-C
1 TAAA-CCTAAACTC
40783161 ATAAACCTAAAC
1 -TAAACCTAAAC
40783173 CATATTTTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
13 10 0.18
14 39 0.71
15 6 0.11
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.22
Consensus pattern (13 bp):
TAAACCTAAACTC
Found at i:40783145 original size:21 final size:20
Alignment explanation
Indices: 40783092--40783171 Score: 54
Period size: 21 Copynumber: 3.8 Consensus size: 20
40783082 ATATATACCA
* * *
40783092 TAAACCTTAAATCTTAAATCC
1 TAAACC-TAAACCTAAAACCC
* *
40783113 TAAACCCCAAACCTAAAACTC
1 TAAA-CCTAAACCTAAAACCC
*
40783134 TAAACTCTAAA-CTGTAAACCC
1 TAAAC-CTAAACCT-AAAACCC
40783155 TAAACCATAAACCTAAA
1 TAAACC-TAAACCTAAA
40783172 CCATATTTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
20 4 0.09
21 37 0.82
22 4 0.09
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.23
Consensus pattern (20 bp):
TAAACCTAAACCTAAAACCC
Found at i:40784262 original size:72 final size:70
Alignment explanation
Indices: 40784169--40784366 Score: 206
Period size: 72 Copynumber: 2.8 Consensus size: 70
40784159 AAAGCTTGGA
* *
40784169 AAACGACACCGTTTGGCTTAGGTTTTTTAGCGGCGCTTTTCCAAAAACGCCGCTAAAT-CCCAAA
1 AAACGGCACCGTTTGTCTTAGG-TTTTTAGCGGCGCTTTT-CAAAAACGCCGCTAAATCCCCAAA
*
40784233 AACTACCG
64 AACT-CAG
*** * *
40784241 AAACGGCACCGTTTGTCTTAGGAAAATTAGTGGCGCTTGATT-AAAAACGTCGCTAAATCCCCAA
1 AAACGGCACCGTTTGTCTTAGG-TTTTTAGCGGCGCTT--TTCAAAAACGCCGCTAAATCCCCAA
40784305 AAACTCAG
63 AAACTCAG
* *
40784313 AAACGGCATCGTTTGTCTTTGGTTTTT-GCGGCGC-TTTCAGTAAAACGCCGCTAA
1 AAACGGCACCGTTTGTCTTAGGTTTTTAGCGGCGCTTTTCA--AAAACGCCGCTAA
40784367 TGATCTAACT
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
67 2 0.02
68 1 0.01
69 1 0.01
70 18 0.17
71 2 0.02
72 68 0.65
73 10 0.10
74 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (70 bp):
AAACGGCACCGTTTGTCTTAGGTTTTTAGCGGCGCTTTTCAAAAACGCCGCTAAATCCCCAAAAA
CTCAG
Found at i:40785165 original size:29 final size:30
Alignment explanation
Indices: 40785133--40785190 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
40785123 ATTAAATGTA
40785133 TAATGTTATACAT-AAATTTTGATTTTATG
1 TAATGTTATACATGAAATTTTGATTTTATG
* * * *
40785162 TAATTTTATATATGAATTTTTTATTTTAT
1 TAATGTTATACATGAAATTTTGATTTTAT
40785191 TCAATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (30 bp):
TAATGTTATACATGAAATTTTGATTTTATG
Found at i:40786101 original size:15 final size:14
Alignment explanation
Indices: 40786073--40786099 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40786063 TGTCTTGTGT
40786073 TTTTTTAATATTTA
1 TTTTTTAATATTTA
40786087 TTTTTTAATATTT
1 TTTTTTAATATTT
40786100 TACTAACCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:40789823 original size:27 final size:27
Alignment explanation
Indices: 40789793--40789844 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
40789783 TGATGTTTCG
*
40789793 AGACACTAACATAAATTGACTTAAACC
1 AGACACTAACATAAAATGACTTAAACC
*
40789820 AGACTCTAACATAAAATGACTTAAA
1 AGACACTAACATAAAATGACTTAAA
40789845 ATAAACATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (27 bp):
AGACACTAACATAAAATGACTTAAACC
Found at i:40792391 original size:21 final size:22
Alignment explanation
Indices: 40792365--40792411 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
40792355 CCTTTGTGTG
40792365 AATTTATCA-AAAATAAATCAA
1 AATTTATCATAAAATAAATCAA
* * *
40792386 AATTTATTATAAAATTAATTAA
1 AATTTATCATAAAATAAATCAA
40792408 AATT
1 AATT
40792412 CAACATGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTTATCATAAAATAAATCAA
Found at i:40792861 original size:270 final size:271
Alignment explanation
Indices: 40792371--40792913 Score: 1054
Period size: 270 Copynumber: 2.0 Consensus size: 271
40792361 TGTGAATTTA
40792371 TCAAAAATAAATCAAAATTTATTATAAAATTAATTAAAATTCAACATGTTAATAATTTAAGTACA
1 TCAAAAATAAATCAAAATTTATTATAAAATTAATTAAAATTCAACATGTTAATAATTTAAGTACA
40792436 ATTTAATTATTTTATAATTATTATATATATTTTTTGACAAGAATTATACCGAAACTGCATGAATT
66 ATTTAATTATTTTATAATTATTATATATATTTTTTGACAAGAATTATACCGAAACTGCATGAATT
40792501 TGAGTTAAAAAGGAAATAAAAAGTGTATATATTTTCGTGTTTCCAATAACATGCATAAAGCGTTG
131 TGAGTTAAAAAGGAAATAAAAAGTGTATATATTTTCGTGTTTCCAATAACATGCATAAAGCGTTG
40792566 AATCAAATATAACATACGTAAAGTGATAATTATAACACGCATAAAGCTCTAAATATAACACACAC
196 AATCAAATATAACATACGTAAAGTGATAATTATAACACGCATAAAGCTCTAAATATAACACACAC
40792631 ATCGTTAAATC
261 ATCGTTAAATC
*
40792642 TCAAAAAT-AATCAAAATTTGA-TATAAAATTAATTAAAATTCAACATGTTCATAATTTAAGTAC
1 TCAAAAATAAATCAAAATTT-ATTATAAAATTAATTAAAATTCAACATGTTAATAATTTAAGTAC
40792705 AATTTAATTATTTTATAATTATTATATATATTTTTTGACAAGAATTATACCGAAACTGCATGAAT
65 AATTTAATTATTTTATAATTATTATATATATTTTTTGACAAGAATTATACCGAAACTGCATGAAT
40792770 TTGAGTTAAAAAGGAAATAAAAAGTGTATATATTTTCGTGTTTCCAATAACATGCATAAAGCGTT
130 TTGAGTTAAAAAGGAAATAAAAAGTGTATATATTTTCGTGTTTCCAATAACATGCATAAAGCGTT
40792835 GAATCAAATATAACATACGTAAAGTGATAATTATAACACGCATAAAGCTCTAAATATAACACACA
195 GAATCAAATATAACATACGTAAAGTGATAATTATAACACGCATAAAGCTCTAAATATAACACACA
40792900 CATCGTTAAATC
260 CATCGTTAAATC
40792912 TC
1 TC
40792914 CCACCTATAA
Statistics
Matches: 270, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
270 261 0.97
271 9 0.03
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (271 bp):
TCAAAAATAAATCAAAATTTATTATAAAATTAATTAAAATTCAACATGTTAATAATTTAAGTACA
ATTTAATTATTTTATAATTATTATATATATTTTTTGACAAGAATTATACCGAAACTGCATGAATT
TGAGTTAAAAAGGAAATAAAAAGTGTATATATTTTCGTGTTTCCAATAACATGCATAAAGCGTTG
AATCAAATATAACATACGTAAAGTGATAATTATAACACGCATAAAGCTCTAAATATAACACACAC
ATCGTTAAATC
Found at i:40800404 original size:9 final size:10
Alignment explanation
Indices: 40800390--40800432 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
40800380 ATTAATATCC
40800390 AAAT-AAGTA
1 AAATAAAGTA
*
40800399 AAATAAAATA
1 AAATAAAGTA
40800409 AAATAAAGTAA
1 AAATAAAGT-A
40800420 TAAATAAAGTA
1 -AAATAAAGTA
40800431 AA
1 AA
40800433 GAAAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 4 0.14
10 14 0.48
11 2 0.07
12 9 0.31
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (10 bp):
AAATAAAGTA
Found at i:40800426 original size:17 final size:17
Alignment explanation
Indices: 40800403--40800461 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
40800393 TAAGTAAAAT
40800403 AAAATAAAATAAAGTAA
1 AAAATAAAATAAAGTAA
* * *
40800420 TAAATAAAGTAAAGAAA
1 AAAATAAAATAAAGTAA
*
40800437 AAAATAAAA-AAAATAA
1 AAAATAAAATAAAGTAA
40800453 AAAATAAAA
1 AAAATAAAA
40800462 ATTGGGTTGC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
16 14 0.40
17 21 0.60
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (17 bp):
AAAATAAAATAAAGTAA
Found at i:40800461 original size:12 final size:12
Alignment explanation
Indices: 40800398--40800461 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
40800388 CCAAATAAGT
40800398 AAAATAAAAT--
1 AAAATAAAATAA
*
40800408 AAAATAAAGTAA
1 AAAATAAAATAA
* *
40800420 TAAATAAAGTAA
1 AAAATAAAATAA
40800432 AGAAA-AAAAT--
1 A-AAATAAAATAA
40800442 AAAA-AAAATAA
1 AAAATAAAATAA
40800453 AAAATAAAA
1 AAAATAAAA
40800462 ATTGGGTTGC
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
9 8 0.18
10 10 0.23
11 4 0.09
12 19 0.43
13 3 0.07
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:40806599 original size:308 final size:309
Alignment explanation
Indices: 40806041--40806663 Score: 1230
Period size: 308 Copynumber: 2.0 Consensus size: 309
40806031 CTTTAATTAC
40806041 ATATTTCCAGTCGGTCCCTCCTTTAGCTTGCTAAAACTAGAAATTAATTGTATGTAGAACCAAAT
1 ATATTTCCAGTCGGTCCCTCCTTTAGCTTGCTAAAACTAGAAATTAATTGTATGTAGAACCAAAT
40806106 GAAAAAAAATGAATAGAAATGATGAAGCTAGAGAATTGGGTCGTGTTAAAAAAATGAATGTGTTT
66 GAAAAAAAATGAATAGAAATGATGAAGCTAGAGAATTGGGTCGTGTTAAAAAAATGAATGTGTTT
40806171 TCTCACTATAAAAATTACTTGAGAATTAATTTAAGGTTTTCAAATTATTATTTAATTAATTATAA
131 TCTCACTATAAAAATTACTTGAGAATTAATTTAAGGTTTTCAAATTATTATTTAATTAATTATAA
40806236 TTAAATAACTGAAATTCAAAAATGGAATTAAATTAATTAGCCATCATGAATTCGTTGAAAATGGA
196 TTAAATAACTGAAATTCAAAAATGGAATTAAATTAATTAGCCATCATGAATTCGTTGAAAATGGA
40806301 AATTAAATATATTTCCTCATAGATTTTTTTATC-AAAAAATTACTAATA
261 AATTAAATATATTTCCTCATAGATTTTTTTATCAAAAAAATTACTAATA
40806349 ATATTTCCAGTCGGTCCCTCCTTTAGCTTGCTAAAACTAGAAATTAATTGTATGTAGAACCAAAT
1 ATATTTCCAGTCGGTCCCTCCTTTAGCTTGCTAAAACTAGAAATTAATTGTATGTAGAACCAAAT
40806414 GAAAAAAAATGAATAGAAATGATGAAGCTAGAGAATTGGGTCGTGTTAAAAAAATGAATGTGTTT
66 GAAAAAAAATGAATAGAAATGATGAAGCTAGAGAATTGGGTCGTGTTAAAAAAATGAATGTGTTT
40806479 TCTCACTATAAAAATTACTTGAGAATTAATTTAAGGTTTTCAAATTATTATTTAATTAATTATAA
131 TCTCACTATAAAAATTACTTGAGAATTAATTTAAGGTTTTCAAATTATTATTTAATTAATTATAA
40806544 TTAAATAACTGAAATTCAAAAATGGAATTAAATTAATTAGCCATCATGAATTCGTTGAAAATGGA
196 TTAAATAACTGAAATTCAAAAATGGAATTAAATTAATTAGCCATCATGAATTCGTTGAAAATGGA
40806609 AATTAAATATATTTCCTCATAGATTTTTTTATCAAAAAAATTACTAATA
261 AATTAAATATATTTCCTCATAGATTTTTTTATCAAAAAAATTACTAATA
*
40806658 AAATTT
1 ATATTT
40806664 GAATTGAATT
Statistics
Matches: 313, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
308 293 0.94
309 20 0.06
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (309 bp):
ATATTTCCAGTCGGTCCCTCCTTTAGCTTGCTAAAACTAGAAATTAATTGTATGTAGAACCAAAT
GAAAAAAAATGAATAGAAATGATGAAGCTAGAGAATTGGGTCGTGTTAAAAAAATGAATGTGTTT
TCTCACTATAAAAATTACTTGAGAATTAATTTAAGGTTTTCAAATTATTATTTAATTAATTATAA
TTAAATAACTGAAATTCAAAAATGGAATTAAATTAATTAGCCATCATGAATTCGTTGAAAATGGA
AATTAAATATATTTCCTCATAGATTTTTTTATCAAAAAAATTACTAATA
Found at i:40811392 original size:14 final size:14
Alignment explanation
Indices: 40811373--40811402 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40811363 CTGACCCGTG
*
40811373 TGGCCCACACGGCT
1 TGGCCCACAAGGCT
40811387 TGGCCCACAAGGCT
1 TGGCCCACAAGGCT
40811401 TG
1 TG
40811403 TGGCTCAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.37, G:0.30, T:0.17
Consensus pattern (14 bp):
TGGCCCACAAGGCT
Found at i:40816515 original size:87 final size:88
Alignment explanation
Indices: 40816408--40816593 Score: 286
Period size: 87 Copynumber: 2.1 Consensus size: 88
40816398 ATCCACTCTT
* *
40816408 CTGC-ACTTCAAATAGATATGACTTGTAACTGCAATCTTCTTCGCAACAACTTCAAGGGGAAGAG
1 CTGCAACTTCAGATAGATATGACTTGTAACTGCAATCTTCTTCGCAACAACTTCAAGGGGAAAAG
40816472 ATTTGTGGTTTTAGCCTACT-CA
66 ATTTGTGGTTTTAGCCTACTCCA
* * * *
40816494 CTGCAACTTCAGATAGATATGACTTGTAACTTCAATCTTCTTCGTAACAACTTTAGGGGGAAAAG
1 CTGCAACTTCAGATAGATATGACTTGTAACTGCAATCTTCTTCGCAACAACTTCAAGGGGAAAAG
* *
40816559 ATTTGTGGTTTTAGTCTGCTCCA
66 ATTTGTGGTTTTAGCCTACTCCA
40816582 CTGCAACTTCAG
1 CTGCAACTTCAG
40816594 GGAGATTAGA
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
86 4 0.04
87 72 0.80
88 14 0.16
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (88 bp):
CTGCAACTTCAGATAGATATGACTTGTAACTGCAATCTTCTTCGCAACAACTTCAAGGGGAAAAG
ATTTGTGGTTTTAGCCTACTCCA
Found at i:40816971 original size:131 final size:132
Alignment explanation
Indices: 40816718--40817201 Score: 783
Period size: 132 Copynumber: 3.7 Consensus size: 132
40816708 TTACTTCCCT
* * ** * *
40816718 ACTACCTTGGGAAGATAAGATTCACCATCTTTTATCTGCTCCAATACTGCTTAAGGAGACA-AGA
1 ACTATCTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGA-A
* * * **
40816782 TCTGCAATCTTCAACTTACTCCACTGCTGCTCAGGGAGATATAACTAATGGCTTAAATCTGCTTC
65 TCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTC
40816847 TCC
130 TCC
40816850 ACTATCTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
1 ACTATCTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
40816915 -TGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
*
40816979 CT
131 CC
* *
40816981 ACTATCTTGAGAAGATAAGATTCACTATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAAAT
1 ACTATCTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
* *
40817046 CTGCAATTTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTACTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
40817111 CC
131 CC
*
40817113 ACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
1 ACTATCTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
*
40817178 TTGCAATCTTCAACCTACTCCACT
66 CTGCAATCTTCAACCTACTCCACT
40817202 GTCAGTACAA
Statistics
Matches: 328, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
131 123 0.38
132 204 0.62
133 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (132 bp):
ACTATCTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
CC
Found at i:40817199 original size:44 final size:44
Alignment explanation
Indices: 40816888--40817201 Score: 150
Period size: 44 Copynumber: 7.2 Consensus size: 44
40816878 CTTCGATCTG
*
40816888 CTCCACTACTGCTTAGGGAGACAGAA-TTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAGAATTTGCAATCTTCAACCTA
* * * * *
40816931 CTCCACTACTGCTTAGGGAGATAGGA-CT--AATGGCTTAAATCTG
1 CTCCACTACTGCTTAGGGAGATAGAATTTGCAAT--CTTCAACCTA
* * * * ** * * * *
40816974 CTTCTCTACTATCTT-GAGAAGATA-AGATTCACTATCTTCGATCTG
1 CTCCACTACT-GCTTAG-GGAGATAGA-ATTTGCAATCTTCAACCTA
* * * *
40817019 CTCCACTACTGCTTAGGGAGACAAAATCTGCAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAGAATTTGCAATCTTCAACCTA
* * * *
40817063 CTCCACTACTGCTTAGGGAGATAGGA-CT--AATGGCTTAAATCTACTT
1 CTCCACTACTGCTTAGGGAGATAGAATTTGCAAT--CTTCAA-C--CTA
** * * * *
40817109 CTCCACTA-T-CTT-GGGAAGATA-AGATTCACCATCTTCGATCTG
1 CTCCACTACTGCTTAGGG-AGATAGA-ATTTGCAATCTTCAACCTA
*
40817151 CTCCACTACTGCTTAGGGAGACAGAATTTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAGAATTTGCAATCTTCAACCTA
40817195 CTCCACT
1 CTCCACT
40817202 GTCAGTACAA
Statistics
Matches: 197, Mismatches: 50, Indels: 47
0.67 0.17 0.16
Matches are distributed among these distances:
41 6 0.03
42 10 0.05
43 51 0.26
44 89 0.45
45 27 0.14
46 10 0.05
47 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAGAATTTGCAATCTTCAACCTA
Found at i:40818083 original size:89 final size:89
Alignment explanation
Indices: 40817195--40818070 Score: 1115
Period size: 89 Copynumber: 9.8 Consensus size: 89
40817185 CTTCAACCTA
* * * * *** * * * *
40817195 CTCCACTGTCAGTACAAGAAGGCAAGGCCGGTGTTTTCGATCCAATTCACTGTCGGTATAGGAAG
1 CTCCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAG
40817260 GCAAGATCTGCTATCTTCAGTCTG
66 GCAAGATCTGCTATCTTCAGTCTG
* * * * * * * * *
40817284 CTCTGCCGTCTGTAAAGGAATGCAAGGCTGGTGTCTTTGATCTGTTTCGCCGTCAGTATAAGAAG
1 CTCCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAG
* * *
40817349 GCAAGATCTACTATTTTTAGTCTG
66 GCAAGATCTGCTATCTTCAGTCTG
* * ** ** * * * *
40817373 CTCCGTTGTTAGTACAAAAAGGCAAAACTGGTGTCTTTGATCTGCTTCGCTGTCAGTATAGGAAA
1 CTCCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAG
* *
40817438 ACAAGATCTACTATCTTCAGTCTG
66 GCAAGATCTGCTATCTTCAGTCTG
* ** * *
40817462 CTTCGCTGTCAGTACAGGAAGGCAAAACTGGTGTCTTCGATCTGCTTCTCTGTCAGTACAGGAAG
1 CTCCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAG
*
40817527 GCAAGATCTGCTATCTTCAGTCTA
66 GCAAGATCTGCTATCTTCAGTCTG
* *
40817551 CTCCGCTGTCGGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCCGTCAGTACAAGAAG
1 CTCCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAG
* *
40817616 GCAAGATCTTCTATCTTCAGCCTG
66 GCAAGATCTGCTATCTTCAGTCTG
* * * * *
40817640 CTCCGCTGTCAGTACAGGAATGCAAGACTGGTGTCTTCGATCTGCTTCGCTGTCAATATAGGAAG
1 CTCCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAG
*
40817705 GCAAGATCTGTTATCTTCAGTCTG
66 GCAAGATCTGCTATCTTCAGTCTG
* * * ** * *
40817729 CTTCACTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCTCTATTAGTACATGAAG
1 CTCCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAG
*
40817794 GTAAGATCTGCTATCTTCAGTCTG
66 GCAAGATCTGCTATCTTCAGTCTG
* * * *
40817818 CTCCGCTGTCAGTATAGGAAGGCAAGGCTAGTGTCTTCAATCTGCTTCGCCATCAGTACAGGAAG
1 CTCCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAG
40817883 GCAAGATCTGCTATCTTCAGTCTG
66 GCAAGATCTGCTATCTTCAGTCTG
* *
40817907 CTCCGCTGTCAGTACAGGAAGGCAAGGCTAGTGTCTTCGATCTGCTTCACCGTCAGTACAGGAAG
1 CTCCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAG
*
40817972 GCAATATCTGCTATCTTCAGTCTG
66 GCAAGATCTGCTATCTTCAGTCTG
* * *
40817996 CTCCGCTGTCAGTACACGAAGGCAAGGCTGATGTCTTC-ATTCTGCTTTGCCGTCAGTACAGGAA
1 CTCCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGA-TCTGCTTCGCCGTCAGTACAGGAA
40818060 GGCAAGATCTG
65 GGCAAGATCTG
40818071 TTGTTTTTAG
Statistics
Matches: 683, Mismatches: 103, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
88 1 0.00
89 682 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.29
Consensus pattern (89 bp):
CTCCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAG
GCAAGATCTGCTATCTTCAGTCTG
Found at i:40818505 original size:182 final size:182
Alignment explanation
Indices: 40818198--40818551 Score: 674
Period size: 182 Copynumber: 1.9 Consensus size: 182
40818188 ATATTACCTG
40818198 CAAAATCCATTTTATGGACCTATTTATGCCTAGTGTTTAGGATGTCATGATTAGAATGAATCAAA
1 CAAAATCCATTTTATGGACCTATTTATGCCTAGTGTTTAGGATGTCATGATTAGAATGAATCAAA
40818263 TAATCCTAACTAGATGTGTATGTATGATATTTGTAGAATGTCATGAGAATGATCCCTTTTTAATG
66 TAATCCTAACTAGATGTGTATGTATGATATTTGTAGAATGTCATGAGAATGATCCCTTTTTAATG
40818328 CTTAGGTTATCATTACTC-AAGTTTCATCAAGGTTCTATCACTAATGCTTTCT
131 CTTAGGTTATCATTACTCAAAGTTT-ATCAAGGTTCTATCACTAATGCTTTCT
40818380 CAAAATCCATTTTATGGACCTATTTATGCCTAGTGTTTAGGATGTCATGATTAGAATGAATCAAA
1 CAAAATCCATTTTATGGACCTATTTATGCCTAGTGTTTAGGATGTCATGATTAGAATGAATCAAA
40818445 TAATCCTAACTAGATGTGTATGTATGATATTTGTAGAATGTCATGAGAATGATCCCTTTTTAATG
66 TAATCCTAACTAGATGTGTATGTATGATATTTGTAGAATGTCATGAGAATGATCCCTTTTTAATG
* *
40818510 CTTAGGTTATCATTACTCAAAGTTTATTAAGGTTTTATCACT
131 CTTAGGTTATCATTACTCAAAGTTTATCAAGGTTCTATCACT
40818552 GACGTGCTAC
Statistics
Matches: 169, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
182 163 0.96
183 6 0.04
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (182 bp):
CAAAATCCATTTTATGGACCTATTTATGCCTAGTGTTTAGGATGTCATGATTAGAATGAATCAAA
TAATCCTAACTAGATGTGTATGTATGATATTTGTAGAATGTCATGAGAATGATCCCTTTTTAATG
CTTAGGTTATCATTACTCAAAGTTTATCAAGGTTCTATCACTAATGCTTTCT
Found at i:40819604 original size:11 final size:11
Alignment explanation
Indices: 40819578--40819665 Score: 81
Period size: 11 Copynumber: 7.8 Consensus size: 11
40819568 TGGCCTCTCA
40819578 TTTTCTTTTACT
1 TTTTCTTTT-CT
40819590 TTTTCTTTTTCT
1 TTTTC-TTTTCT
*
40819602 TTTCCTTTTCT
1 TTTTCTTTTCT
40819613 TTTTCTTTTCT
1 TTTTCTTTTCT
*
40819624 TCTTCTTCTTTCT
1 TTTTC-T-TTTCT
*
40819637 TTTT-TCTTCT
1 TTTTCTTTTCT
* *
40819647 ATTTC-CTTCT
1 TTTTCTTTTCT
40819657 TTTTCTTTT
1 TTTTCTTTT
40819666 TTCTCTCTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
10 16 0.25
11 23 0.37
12 12 0.19
13 12 0.19
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:40819643 original size:17 final size:17
Alignment explanation
Indices: 40819578--40819666 Score: 94
Period size: 17 Copynumber: 5.2 Consensus size: 17
40819568 TGGCCTCTCA
*
40819578 TTTTCTTTTACTTTTTCT
1 TTTTCTTTT-CTTCTTCT
40819596 TTTTCTTTTCCTT-TTCT
1 TTTTCTTTT-CTTCTTCT
40819613 TTTTCTTTTCTTCTTCT
1 TTTTCTTTTCTTCTTCT
40819630 TCTTTCTTTT-TTCTTCT
1 T-TTTCTTTTCTTCTTCT
* * *
40819647 ATTTC-CTTCTTTTTCT
1 TTTTCTTTTCTTCTTCT
40819663 TTTT
1 TTTT
40819667 TCTCTCTTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
15 2 0.03
16 16 0.25
17 25 0.40
18 20 0.32
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCTTTTCTTCTTCT
Found at i:40819666 original size:6 final size:6
Alignment explanation
Indices: 40819578--40819640 Score: 76
Period size: 6 Copynumber: 10.7 Consensus size: 6
40819568 TGGCCTCTCA
* *
40819578 TTTTCT TTTACT TTTTCT TTTTC- TTTTCC TTTTCT TTTTC- TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
*
40819624 TCTTCT TCTTTCT TTTT
1 TTTTCT T-TTTCT TTTT
40819641 TCTTCTATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
5 10 0.20
6 34 0.69
7 5 0.10
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:40822543 original size:19 final size:20
Alignment explanation
Indices: 40822514--40822565 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
40822504 CACTTTGTGA
* *
40822514 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
40822533 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
40822553 AAATG-AATGCAAA
1 AAATGTAATGCAAA
40822566 AAGAGACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:40824399 original size:12 final size:13
Alignment explanation
Indices: 40824375--40824399 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40824365 ATATTGCCTT
40824375 ATTTAGAAAAAAA
1 ATTTAGAAAAAAA
40824388 ATTTAGAAAAAA
1 ATTTAGAAAAAA
40824400 TCATCATCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
ATTTAGAAAAAAA
Found at i:40826610 original size:27 final size:28
Alignment explanation
Indices: 40826551--40826604 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
40826541 AAAATAATTA
*
40826551 AAATTAAATATGTTAATAATTTAAGTGC
1 AAATTAAATATGTTAATAATTAAAGTGC
* *
40826579 AAATTAATTAT-TTTATAATTAAAGTG
1 AAATTAAATATGTTAATAATTAAAGTG
40826605 TGAATTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (28 bp):
AAATTAAATATGTTAATAATTAAAGTGC
Found at i:40828649 original size:13 final size:13
Alignment explanation
Indices: 40828620--40828674 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
40828610 ACTTTTAAAT
40828620 AAAT-AATTAAT-
1 AAATCAATTAATC
*
40828631 AGAATCAATTGATC
1 A-AATCAATTAATC
40828645 AAATCAATTAAT-
1 AAATCAATTAATC
*
40828657 AAATTCAATTCATC
1 AAA-TCAATTAATC
40828671 AAAT
1 AAAT
40828675 TAAATACTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 1 0.03
12 6 0.17
13 25 0.69
14 4 0.11
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.33
Consensus pattern (13 bp):
AAATCAATTAATC
Found at i:40828655 original size:26 final size:24
Alignment explanation
Indices: 40828620--40828705 Score: 77
Period size: 26 Copynumber: 3.5 Consensus size: 24
40828610 ACTTTTAAAT
40828620 AAAT-AATTAATAGAATCAATTGATC
1 AAATCAATTAATA-AATCAATT-ATC
40828645 AAATCAATTAATAAATTCAATTCATC
1 AAATCAATTAATAAA-TCAATT-ATC
* * * *
40828671 AAATTAAATACTACAATCAAATATC
1 AAATCAATTAATA-AATCAATTATC
40828696 -AATCAATTAA
1 AAATCAATTAA
40828706 AAAAAAATCT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
24 7 0.14
25 9 0.18
26 32 0.64
27 2 0.04
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.31
Consensus pattern (24 bp):
AAATCAATTAATAAATCAATTATC
Found at i:40831165 original size:7 final size:7
Alignment explanation
Indices: 40831153--40831194 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
40831143 TTTTTGAAAA
40831153 TATTTTT
1 TATTTTT
40831160 TA-TTTT
1 TATTTTT
40831166 TA-TTTT
1 TATTTTT
*
40831172 TACTTTT
1 TATTTTT
40831179 TATTTTT
1 TATTTTT
40831186 TATTTTT
1 TATTTTT
40831193 TA
1 TA
40831195 GAAATAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
6 12 0.36
7 21 0.64
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (7 bp):
TATTTTT
Found at i:40831169 original size:13 final size:13
Alignment explanation
Indices: 40831153--40831192 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
40831143 TTTTTGAAAA
40831153 TATTTTTTATTTT
1 TATTTTTTATTTT
40831166 TA-TTTTTACTTTT
1 TATTTTTTA-TTTT
40831179 TATTTTTTATTTT
1 TATTTTTTATTTT
40831192 T
1 T
40831193 TAGAAATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.24
13 13 0.52
14 6 0.24
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:40831171 original size:5 final size:6
Alignment explanation
Indices: 40831156--40831192 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
40831146 TTGAAAATAT
40831156 TTTTTA TTTTTA TTTTTA CTTTTTA TTTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA -TTTTTA -TTTTTA TTTTT
40831193 TAGAAATAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 17 0.59
7 12 0.41
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:40833098 original size:14 final size:14
Alignment explanation
Indices: 40833081--40833114 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
40833071 ACCTTTGAAT
*
40833081 CCAAACTTGTAACC
1 CCAAACTCGTAACC
40833095 CCAAACTCGTAACC
1 CCAAACTCGTAACC
40833109 CCAAAC
1 CCAAAC
40833115 AAAAACCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.38, C:0.41, G:0.06, T:0.15
Consensus pattern (14 bp):
CCAAACTCGTAACC
Found at i:40835473 original size:28 final size:28
Alignment explanation
Indices: 40835435--40835489 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
40835425 GAATATGTAT
*
40835435 AAATAACGAGCGAAAGATGAACAAATAA
1 AAATAACGAGCGAAAAATGAACAAATAA
* *
40835463 AAATAATGAGCGAAAAATGTACAAATA
1 AAATAACGAGCGAAAAATGAACAAATA
40835490 TGAACATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.60, C:0.09, G:0.16, T:0.15
Consensus pattern (28 bp):
AAATAACGAGCGAAAAATGAACAAATAA
Found at i:40841987 original size:23 final size:24
Alignment explanation
Indices: 40841943--40841989 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
40841933 TCAATATAGG
* *
40841943 TTTTTTCACTCACTGCAGTACCTA
1 TTTTTTCACTCACTGAAATACCTA
*
40841967 TTTTTTC-CTCACTTAAATACCTA
1 TTTTTTCACTCACTGAAATACCTA
40841990 AACTATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.23, C:0.28, G:0.04, T:0.45
Consensus pattern (24 bp):
TTTTTTCACTCACTGAAATACCTA
Found at i:40842395 original size:86 final size:86
Alignment explanation
Indices: 40842288--40842450 Score: 317
Period size: 86 Copynumber: 1.9 Consensus size: 86
40842278 ATTAAATTAG
*
40842288 TTTTCTATAATAGTGTATATTGCCTAAAATTTTAAGTAAAACTATAATTATTTCATACAAGCAAA
1 TTTTATATAATAGTGTATATTGCCTAAAATTTTAAGTAAAACTATAATTATTTCATACAAGCAAA
40842353 CCTACTGATTATTGCCTAAAA
66 CCTACTGATTATTGCCTAAAA
40842374 TTTTATATAATAGTGTATATTGCCTAAAATTTTAAGTAAAACTATAATTATTTCATACAAGCAAA
1 TTTTATATAATAGTGTATATTGCCTAAAATTTTAAGTAAAACTATAATTATTTCATACAAGCAAA
40842439 CCTACTGATTAT
66 CCTACTGATTAT
40842451 AATTTATTAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (86 bp):
TTTTATATAATAGTGTATATTGCCTAAAATTTTAAGTAAAACTATAATTATTTCATACAAGCAAA
CCTACTGATTATTGCCTAAAA
Found at i:40846456 original size:109 final size:109
Alignment explanation
Indices: 40846265--40846480 Score: 432
Period size: 109 Copynumber: 2.0 Consensus size: 109
40846255 TAGAATGTAA
40846265 AATTTACAAGAATTAAGATTGGTATACTGTATAAATACAAATTGGGACATGTTTGGAGGACAAAG
1 AATTTACAAGAATTAAGATTGGTATACTGTATAAATACAAATTGGGACATGTTTGGAGGACAAAG
40846330 AGCCTTACCTCCTCTGCACGTAATGTCCAATATTGATCATTTGT
66 AGCCTTACCTCCTCTGCACGTAATGTCCAATATTGATCATTTGT
40846374 AATTTACAAGAATTAAGATTGGTATACTGTATAAATACAAATTGGGACATGTTTGGAGGACAAAG
1 AATTTACAAGAATTAAGATTGGTATACTGTATAAATACAAATTGGGACATGTTTGGAGGACAAAG
40846439 AGCCTTACCTCCTCTGCACGTAATGTCCAATATTGATCATTT
66 AGCCTTACCTCCTCTGCACGTAATGTCCAATATTGATCATTT
40846481 ATGTTCTCTA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 107 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (109 bp):
AATTTACAAGAATTAAGATTGGTATACTGTATAAATACAAATTGGGACATGTTTGGAGGACAAAG
AGCCTTACCTCCTCTGCACGTAATGTCCAATATTGATCATTTGT
Found at i:40854853 original size:32 final size:32
Alignment explanation
Indices: 40854812--40854875 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
40854802 TAGAACAGCT
40854812 TCAAGGAGGGGCATAAAGTTTAAGACCACACC
1 TCAAGGAGGGGCATAAAGTTTAAGACCACACC
40854844 TCAAGGAGGGGCATAAAGTTTAAGACCACACC
1 TCAAGGAGGGGCATAAAGTTTAAGACCACACC
40854876 CCTTCTGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.16
Consensus pattern (32 bp):
TCAAGGAGGGGCATAAAGTTTAAGACCACACC
Found at i:40862970 original size:20 final size:20
Alignment explanation
Indices: 40862945--40862988 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
40862935 ACTCAGGGGG
*
40862945 ACTTCTACCAATACAAGTCC
1 ACTTCTACCAATACAAGCCC
* *
40862965 ACTTCTATCGATACAAGCCC
1 ACTTCTACCAATACAAGCCC
40862985 ACTT
1 ACTT
40862989 TTAACCATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.34, G:0.07, T:0.27
Consensus pattern (20 bp):
ACTTCTACCAATACAAGCCC
Found at i:40862998 original size:20 final size:20
Alignment explanation
Indices: 40862945--40862999 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
40862935 ACTCAGGGGG
*
40862945 ACTTCT-ACCAATACAAGTCC
1 ACTTCTAACC-ATACAAGCCC
* *
40862965 ACTTCTATCGATACAAGCCC
1 ACTTCTAACCATACAAGCCC
*
40862985 ACTTTTAACCATACA
1 ACTTCTAACCATACA
40863000 TTTTGTGAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.27
Consensus pattern (20 bp):
ACTTCTAACCATACAAGCCC
Found at i:40870388 original size:40 final size:39
Alignment explanation
Indices: 40870327--40870408 Score: 155
Period size: 40 Copynumber: 2.1 Consensus size: 39
40870317 AATTTAATAC
40870327 TTATCTTGATAATATTTTATTAATTTAATATTAAAGTGA
1 TTATCTTGATAATATTTTATTAATTTAATATTAAAGTGA
40870366 TTATCTTGATAAATATTTTATTAATTTAATATTAAAGTGA
1 TTATCTTGAT-AATATTTTATTAATTTAATATTAAAGTGA
40870406 TTA
1 TTA
40870409 AGTTTAATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 10 0.24
40 32 0.76
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (39 bp):
TTATCTTGATAATATTTTATTAATTTAATATTAAAGTGA
Found at i:40874965 original size:17 final size:17
Alignment explanation
Indices: 40874939--40874979 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
40874929 TATTAGACTC
*
40874939 CCAATGTCATAATTTTT
1 CCAATTTCATAATTTTT
40874956 CCAATTTCATAATTTTT
1 CCAATTTCATAATTTTT
40874973 CCAATTT
1 CCAATTT
40874980 AGATCTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.49
Consensus pattern (17 bp):
CCAATTTCATAATTTTT
Found at i:40879962 original size:20 final size:20
Alignment explanation
Indices: 40879937--40879977 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40879927 TTAATGGTAC
40879937 ATAATGTAAGAATCAAGATA
1 ATAATGTAAGAATCAAGATA
40879957 ATAATGTAAGAATCAAGATA
1 ATAATGTAAGAATCAAGATA
40879977 A
1 A
40879978 CATAGTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.24
Consensus pattern (20 bp):
ATAATGTAAGAATCAAGATA
Found at i:40882607 original size:21 final size:21
Alignment explanation
Indices: 40882564--40882613 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
40882554 TTAACTTTTT
40882564 AAAAA-TTCAAATATTATAATA
1 AAAAATTTCAAATA-TATAATA
40882585 AAAAATTTCAAATA-ATAATTA
1 AAAAATTTCAAATATATAA-TA
*
40882606 AAATATTT
1 AAAAATTT
40882614 TTAACTTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.15
21 14 0.54
22 8 0.31
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAATTTCAAATATATAATA
Found at i:40887093 original size:58 final size:61
Alignment explanation
Indices: 40887017--40887129 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 61
40887007 ACCACTTTAA
**
40887017 TATTAAATTAATAAAATAC-T-TA-ACAAGATAAATATTTGATTAAATTTAATATTATATC
1 TATTAAATTAATAAAATACTTATATACAAGATAAATATTAAATTAAATTTAATATTATATC
* * *
40887075 TATTAAATTACTAGAATACTTATATACAAGATAAATATTAAATTAATTTTAATAT
1 TATTAAATTAATAAAATACTTATATACAAGATAAATATTAAATTAAATTTAATAT
40887130 GAAAATTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
58 17 0.36
59 1 0.02
60 2 0.04
61 27 0.57
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (61 bp):
TATTAAATTAATAAAATACTTATATACAAGATAAATATTAAATTAAATTTAATATTATATC
Found at i:40887140 original size:61 final size:58
Alignment explanation
Indices: 40887017--40887148 Score: 149
Period size: 61 Copynumber: 2.2 Consensus size: 58
40887007 ACCACTTTAA
** * *
40887017 TATTAAATTAATAAAATACTTAACAAGATAAATATTTGATTAAATTTAATATTATATC
1 TATTAAATTAATAAAATACTTAACAAGATAAATATTAAATTAAATTTAATATAAAATC
* * *
40887075 TATTAAATTACTAGAATACTTATATACAAGATAAATATTAAATTAATTTTAATATGAAAAT-
1 TATTAAATTAATAAAATAC-T-TA-ACAAGATAAATATTAAATTAAATTTAATAT-AAAATC
*
40887136 TATTAAAATAATA
1 TATTAAATTAATA
40887149 TTATTTTTGG
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 17 0.28
59 1 0.02
60 2 0.03
61 38 0.62
62 3 0.05
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.40
Consensus pattern (58 bp):
TATTAAATTAATAAAATACTTAACAAGATAAATATTAAATTAAATTTAATATAAAATC
Found at i:40887598 original size:19 final size:19
Alignment explanation
Indices: 40887565--40887604 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
40887555 TCCAAATTAT
*
40887565 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
40887584 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
40887603 AT
1 AT
40887605 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:40888522 original size:21 final size:22
Alignment explanation
Indices: 40888478--40888536 Score: 93
Period size: 21 Copynumber: 2.7 Consensus size: 22
40888468 ATTCTTAGAG
40888478 AAATGACTTAATTTTAGAAAAA
1 AAATGACTTAATTTTAGAAAAA
**
40888500 AAATGACTTAATTTT-TTAAAA
1 AAATGACTTAATTTTAGAAAAA
40888521 AAATGACTTAATTTTA
1 AAATGACTTAATTTTA
40888537 TTTTTGATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 19 0.56
22 15 0.44
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (22 bp):
AAATGACTTAATTTTAGAAAAA
Found at i:40894324 original size:1 final size:1
Alignment explanation
Indices: 40894318--40894363 Score: 74
Period size: 1 Copynumber: 46.0 Consensus size: 1
40894308 ACACTAGAGT
**
40894318 AAAAAAAAAAAAAAAAAAAAAAATTAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
40894364 CTTAAAACAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.96, C:0.00, G:0.00, T:0.04
Consensus pattern (1 bp):
A
Found at i:40894349 original size:22 final size:22
Alignment explanation
Indices: 40894321--40894362 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
40894311 CTAGAGTAAA
40894321 AAAAAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAAAAATT
40894343 AAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAA
40894363 ACTTAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.95, C:0.00, G:0.00, T:0.05
Consensus pattern (22 bp):
AAAAAAAAAAAAAAAAAAAATT
Found at i:40894349 original size:23 final size:24
Alignment explanation
Indices: 40894319--40894405 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
40894309 CACTAGAGTA
*
40894319 AAAAAAAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAAAAAACTT
40894343 AAAAAAAAAAAAAAAAAAAAACTT
1 AAAAAAAAAAAAAAAAAAAAACTT
* * ** *
40894367 AAAACATAAATTAAAAGAAAACTT
1 AAAAAAAAAAAAAAAAAAAAACTT
* *
40894391 ACATAAAAAAAAAAA
1 AAAAAAAAAAAAAAA
40894406 CTTAAAATAA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.83, C:0.05, G:0.01, T:0.11
Consensus pattern (24 bp):
AAAAAAAAAAAAAAAAAAAAACTT
Found at i:40894412 original size:12 final size:12
Alignment explanation
Indices: 40894319--40894402 Score: 71
Period size: 12 Copynumber: 6.8 Consensus size: 12
40894309 CACTAGAGTA
**
40894319 AAAAAAAAAAAA
1 AAAAAAAAAATT
40894331 AAAAAAAAAATT
1 AAAAAAAAAATT
*
40894343 AAAAAAAAAA-A
1 AAAAAAAAAATT
40894354 AAAAAAAAAACTT
1 AAAAAAAAAA-TT
* *
40894367 AAAACATAAATT
1 AAAAAAAAAATT
* *
40894379 AAAAGAAAACTT
1 AAAAAAAAAATT
40894391 ACATAAAAAAAA
1 A-A-AAAAAAAA
40894403 AAACTTAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
11 10 0.18
12 32 0.56
13 9 0.16
14 6 0.11
ACGTcount: A:0.82, C:0.05, G:0.01, T:0.12
Consensus pattern (12 bp):
AAAAAAAAAATT
Found at i:40898068 original size:47 final size:48
Alignment explanation
Indices: 40897995--40898093 Score: 130
Period size: 47 Copynumber: 2.1 Consensus size: 48
40897985 TCTTATATCA
* **
40897995 CACACCGAAGCCATAGCCCAGCTATGGTCTTACACGGGAA-CACATAT
1 CACACCGAAGCCATAGCCCAGATATGGTCTTACACGAAAATCACATAT
* *
40898042 CACACC-AATGCCATATCCTAGATATGGTCTTACACGAAAATCACATAT
1 CACACCGAA-GCCATAGCCCAGATATGGTCTTACACGAAAATCACATAT
40898090 CACA
1 CACA
40898094 TCACTTGTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 2 0.04
47 32 0.71
48 11 0.24
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.20
Consensus pattern (48 bp):
CACACCGAAGCCATAGCCCAGATATGGTCTTACACGAAAATCACATAT
Found at i:40898158 original size:44 final size:44
Alignment explanation
Indices: 40898095--40898249 Score: 247
Period size: 44 Copynumber: 3.5 Consensus size: 44
40898085 CATATCACAT
* * * *
40898095 CACTTGTCATTTGTCACTGATAAGATAAGTGTAACTAAAGTTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTAC
40898139 CACTTATCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTAC
* *
40898183 CACTTATCACTTGTCACTGATCAGATAGGTGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTAC
*
40898227 CACTTATCACTTGTTACTGATCA
1 CACTTATCACTTGTCACTGATCA
40898250 AAAGTACTCA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 104 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (44 bp):
CACTTATCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTAC
Found at i:40901497 original size:20 final size:20
Alignment explanation
Indices: 40901468--40901506 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
40901458 ACACATAACC
40901468 TTTTTATTAAGAAAAAAAAGG
1 TTTTTATTAA-AAAAAAAAGG
40901489 TTTTT-TTAAAAAAAAAAG
1 TTTTTATTAAAAAAAAAAG
40901507 TAAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (20 bp):
TTTTTATTAAAAAAAAAAGG
Found at i:40905159 original size:17 final size:18
Alignment explanation
Indices: 40905133--40905171 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
40905123 CTTTGGGTGG
* *
40905133 GCTCACAACTT-ATATGA
1 GCTCAAAACTTCAAATGA
40905150 GCTCAAAACTTCAAATGA
1 GCTCAAAACTTCAAATGA
40905168 GCTC
1 GCTC
40905172 GCACATGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (18 bp):
GCTCAAAACTTCAAATGA
Found at i:40921157 original size:513 final size:513
Alignment explanation
Indices: 40920190--40921216 Score: 2054
Period size: 513 Copynumber: 2.0 Consensus size: 513
40920180 CTTGCAATGT
40920190 TGACATAGTGCATCTGGTCTAAACCAACATTTTTCTTCTGGATGACTAGGCCTTTTGCAGTGCTT
1 TGACATAGTGCATCTGGTCTAAACCAACATTTTTCTTCTGGATGACTAGGCCTTTTGCAGTGCTT
40920255 GTAGAGTTGGTCAGCTCTCCTTGCAGCATCAGGCTTAGGCCTGTTTTTCCACACCTTTTTGCCTT
66 GTAGAGTTGGTCAGCTCTCCTTGCAGCATCAGGCTTAGGCCTGTTTTTCCACACCTTTTTGCCTT
40920320 TGTAGGCATTAGTGCTCGAGGCTTCTCTGGCTTTGGCTTGAAAAGCACCTTCTTGATGGTCTTCA
131 TGTAGGCATTAGTGCTCGAGGCTTCTCTGGCTTTGGCTTGAAAAGCACCTTCTTGATGGTCTTCA
40920385 ATTCTGCTAGCTCTTCTTTGCTCCTAAGCATAGAATGTGTTGATTAGCTCATTCAAAGAGATGCT
196 ATTCTGCTAGCTCTTCTTTGCTCCTAAGCATAGAATGTGTTGATTAGCTCATTCAAAGAGATGCT
40920450 AGCTAGGTCTCTTGAATCCTCTAAAGAGGATATCTTTGCCTCATGCCTCTCAAGTAAGGTAGAGA
261 AGCTAGGTCTCTTGAATCCTCTAAAGAGGATATCTTTGCCTCATGCCTCTCAAGTAAGGTAGAGA
40920515 AGACTTTCTCCACTATTCTTACTTCATCAAACTGCTCACCAAGGAGCCTTATGCTGTTGACCACA
326 AGACTTTCTCCACTATTCTTACTTCATCAAACTGCTCACCAAGGAGCCTTATGCTGTTGACCACA
40920580 GCCATGATCCTATCTGCATACTGCTTCACAGTTTCTTCTTCTCTCATTTTTAAGTTTTCAAAGTC
391 GCCATGATCCTATCTGCATACTGCTTCACAGTTTCTTCTTCTCTCATTTTTAAGTTTTCAAAGTC
40920645 TCTTCTTAAGTTCAACAGCTGCTGCTTCCTTGTCCTCTCTGTGCCTTGAAACTCCTCC
456 TCTTCTTAAGTTCAACAGCTGCTGCTTCCTTGTCCTCTCTGTGCCTTGAAACTCCTCC
40920703 TGACATAGTGCATCTGGTCTAAACCAACATTTTTCTTCTGGATGACTAGGCCTTTTGCAGTGCTT
1 TGACATAGTGCATCTGGTCTAAACCAACATTTTTCTTCTGGATGACTAGGCCTTTTGCAGTGCTT
40920768 GTAGAGTTGGTCAGCTCTCCTTGCAGCATCAGGCTTAGGCCTGTTTTTCCACACCTTTTTGCCTT
66 GTAGAGTTGGTCAGCTCTCCTTGCAGCATCAGGCTTAGGCCTGTTTTTCCACACCTTTTTGCCTT
40920833 TGTAGGCATTAGTGCTCGAGGCTTCTCTGGCTTTGGCTTGAAAAGCACCTTCTTGATGGTCTTCA
131 TGTAGGCATTAGTGCTCGAGGCTTCTCTGGCTTTGGCTTGAAAAGCACCTTCTTGATGGTCTTCA
40920898 ATTCTGCTAGCTCTTCTTTGCTCCTAAGCATAGAATGTGTTGATTAGCTCATTCAAAGAGATGCT
196 ATTCTGCTAGCTCTTCTTTGCTCCTAAGCATAGAATGTGTTGATTAGCTCATTCAAAGAGATGCT
40920963 AGCTAGGTCTCTTGAATCCTCTAAAGAGGATATCTTTGCCTCATGCCTCTCAAGTAAGGTAGAGA
261 AGCTAGGTCTCTTGAATCCTCTAAAGAGGATATCTTTGCCTCATGCCTCTCAAGTAAGGTAGAGA
40921028 AGACTTTCTCCACTATTCTTACTTCATCAAACTGCTCACCAAGGAGCCTTATGCTGTTGACCACA
326 AGACTTTCTCCACTATTCTTACTTCATCAAACTGCTCACCAAGGAGCCTTATGCTGTTGACCACA
40921093 GCCATGATCCTATCTGCATACTGCTTCACAGTTTCTTCTTCTCTCATTTTTAAGTTTTCAAAGTC
391 GCCATGATCCTATCTGCATACTGCTTCACAGTTTCTTCTTCTCTCATTTTTAAGTTTTCAAAGTC
40921158 TCTTCTTAAGTTCAACAGCTGCTGCTTCCTTGTCCTCTCTGTGCCTTGAAACTCCTCC
456 TCTTCTTAAGTTCAACAGCTGCTGCTTCCTTGTCCTCTCTGTGCCTTGAAACTCCTCC
40921216 T
1 T
40921217 TGAGCTTGTC
Statistics
Matches: 514, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
513 514 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (513 bp):
TGACATAGTGCATCTGGTCTAAACCAACATTTTTCTTCTGGATGACTAGGCCTTTTGCAGTGCTT
GTAGAGTTGGTCAGCTCTCCTTGCAGCATCAGGCTTAGGCCTGTTTTTCCACACCTTTTTGCCTT
TGTAGGCATTAGTGCTCGAGGCTTCTCTGGCTTTGGCTTGAAAAGCACCTTCTTGATGGTCTTCA
ATTCTGCTAGCTCTTCTTTGCTCCTAAGCATAGAATGTGTTGATTAGCTCATTCAAAGAGATGCT
AGCTAGGTCTCTTGAATCCTCTAAAGAGGATATCTTTGCCTCATGCCTCTCAAGTAAGGTAGAGA
AGACTTTCTCCACTATTCTTACTTCATCAAACTGCTCACCAAGGAGCCTTATGCTGTTGACCACA
GCCATGATCCTATCTGCATACTGCTTCACAGTTTCTTCTTCTCTCATTTTTAAGTTTTCAAAGTC
TCTTCTTAAGTTCAACAGCTGCTGCTTCCTTGTCCTCTCTGTGCCTTGAAACTCCTCC
Found at i:40923524 original size:23 final size:22
Alignment explanation
Indices: 40923494--40923536 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
40923484 AATGCAAAGC
40923494 TAAAAAAACA-AATTTAAAAATTA
1 TAAAAAAA-ATAA-TTAAAAATTA
40923517 TAAAAAAAATAATTAAAAAT
1 TAAAAAAAATAATTAAAAAT
40923537 GACTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
TAAAAAAAATAATTAAAAATTA
Found at i:40923818 original size:61 final size:60
Alignment explanation
Indices: 40923753--40923891 Score: 172
Period size: 60 Copynumber: 2.3 Consensus size: 60
40923743 ATCCTAAATA
* * ** *
40923753 TAAAATATTCAACAAATTTAGCCATCAATGTTTACAAAATTTGTCATTTTAGTT-TGAATTC
1 TAAAA-ATTCAATAAATTTAACCATCAACATTTACAAAATTTGTCAATTTAGTTCT-AATTC
* * *
40923814 TAAAAAATCAATAAATTTAACCTTCAACATTTACAAAGTTTGTCAATTTAGTTCTAATTC
1 TAAAAATTCAATAAATTTAACCATCAACATTTACAAAATTTGTCAATTTAGTTCTAATTC
40923874 TAAAAAATTCAATAAATT
1 T-AAAAATTCAATAAATT
40923892 AATTTTTGGT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
60 46 0.69
61 21 0.31
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (60 bp):
TAAAAATTCAATAAATTTAACCATCAACATTTACAAAATTTGTCAATTTAGTTCTAATTC
Found at i:40925648 original size:3 final size:3
Alignment explanation
Indices: 40925640--40925684 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
40925630 CCAAAAATGA
40925640 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
40925685 CTTGCTACCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GTG
Found at i:40930661 original size:27 final size:27
Alignment explanation
Indices: 40930630--40930687 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
40930620 GCCACTTATA
40930630 TAGAACTACACTTCTTTTATTTTATTT
1 TAGAACTACACTTCTTTTATTTTATTT
40930657 TAGAACTACACTTCTTTTATTTTATTT
1 TAGAACTACACTTCTTTTATTTTATTT
40930684 TAGA
1 TAGA
40930688 GTAAGATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.28, C:0.14, G:0.05, T:0.53
Consensus pattern (27 bp):
TAGAACTACACTTCTTTTATTTTATTT
Found at i:40935283 original size:49 final size:50
Alignment explanation
Indices: 40935223--40935322 Score: 193
Period size: 49 Copynumber: 2.0 Consensus size: 50
40935213 TTCATCTATT
40935223 TGATATTGATTAGAATAAGGTGTTTCAATCTTACTACACTCCCA-TAGAA
1 TGATATTGATTAGAATAAGGTGTTTCAATCTTACTACACTCCCATTAGAA
40935272 TGATATTGATTAGAATAAGGTGTTTCAATCTTACTACACTCCCATTAGAA
1 TGATATTGATTAGAATAAGGTGTTTCAATCTTACTACACTCCCATTAGAA
40935322 T
1 T
40935323 ATGATTTTAC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 44 0.88
50 6 0.12
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (50 bp):
TGATATTGATTAGAATAAGGTGTTTCAATCTTACTACACTCCCATTAGAA
Found at i:40937724 original size:3 final size:3
Alignment explanation
Indices: 40937716--40937753 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
40937706 GGAGCTCTCC
40937716 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40937754 ATTTTAGGTT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:40938033 original size:17 final size:17
Alignment explanation
Indices: 40938011--40938043 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40938001 TTTGTCATTG
40938011 TTATC-ATTGCTATTATA
1 TTATCAATTGC-ATTATA
40938028 TTATCAATTGCATTAT
1 TTATCAATTGCATTAT
40938044 CATGAGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (17 bp):
TTATCAATTGCATTATA
Found at i:40941611 original size:14 final size:15
Alignment explanation
Indices: 40941592--40941631 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
40941582 TTAGTTGTGC
40941592 TCTTCTTCTTC-ATT
1 TCTTCTTCTTCAATT
*
40941606 TCTTCTTTTTCAATT
1 TCTTCTTCTTCAATT
*
40941621 CCTTCTTCTTC
1 TCTTCTTCTTC
40941632 TGTCTCGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.62
Consensus pattern (15 bp):
TCTTCTTCTTCAATT
Found at i:40946801 original size:3 final size:3
Alignment explanation
Indices: 40946774--40946823 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
40946764 ATTACTACCC
*
40946774 TAA TAC TAA T-A TAAA TAA TAA -AA TAA TAA TAAA TAA -AA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
40946818 TAA TAA
1 TAA TAA
40946824 CAAGGATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 6 0.15
3 29 0.73
4 5 0.12
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:40946802 original size:15 final size:14
Alignment explanation
Indices: 40946787--40946823 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
40946777 TACTAATATA
40946787 AATAATAAAATAAT
1 AATAATAAAATAAT
40946801 AATAAATAAAATAAT
1 AAT-AATAAAATAAT
40946816 AATAATAA
1 AATAATAA
40946824 CAAGGATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAATAAAATAAT
Done.