Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 71 of 141
Found at i:20552293 original size:33 final size:33
Alignment explanation
Indices: 20552231--20552296 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
20552221 ATATATAGAC
*
20552231 TAAATAAAATAATAAAATATCTTATTAAAATAT
1 TAAATAAAATAATAAAATATATTATTAAAATAT
*
20552264 TAAATAAATAATAATTAAATA-ATTA-TAAAATAT
1 TAAAT-AA-AATAATAAAATATATTATTAAAATAT
20552297 CACCAACATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 13 0.45
34 5 0.17
35 11 0.38
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (33 bp):
TAAATAAAATAATAAAATATATTATTAAAATAT
Found at i:20554520 original size:32 final size:32
Alignment explanation
Indices: 20554450--20554520 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
20554440 GCTTACTAAG
* *
20554450 CTAATCATTAATCACATCTCATCCTCAATGGA
1 CTAATCATTAATCACATCACATCCACAATGGA
* * *
20554482 CCAATCATTAATTATATCACATCCAC-ATGGGA
1 CTAATCATTAATCACATCACATCCACAAT-GGA
20554514 CTAATCA
1 CTAATCA
20554521 ACATGGTACT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 2 0.06
32 30 0.94
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (32 bp):
CTAATCATTAATCACATCACATCCACAATGGA
Found at i:20556804 original size:16 final size:16
Alignment explanation
Indices: 20556783--20556815 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20556773 AAATAAAGTA
*
20556783 AAAGAATAAAAGAAAC
1 AAAGAAGAAAAGAAAC
20556799 AAAGAAGAAAAGAAAC
1 AAAGAAGAAAAGAAAC
20556815 A
1 A
20556816 GAGATTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAGAAAAGAAAC
Found at i:20557532 original size:39 final size:39
Alignment explanation
Indices: 20557470--20557611 Score: 196
Period size: 39 Copynumber: 3.6 Consensus size: 39
20557460 ACATCGTGAT
* **
20557470 CTGAAGCCCGAAGTCTAGTTGAAGCACATAAGTGCTAAA
1 CTGAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAA
* * *
20557509 CTGCAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAA
1 CTGAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAA
20557548 -TGGAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAA
1 CT-GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAA
* *
20557587 CGGAAGCCCAAAGGCTAACTGAAGC
1 CTGAAGCCCGAAGGCTAACTGAAGC
20557612 TTATCAGAGT
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
38 1 0.01
39 93 0.99
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (39 bp):
CTGAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAA
Found at i:20557553 original size:21 final size:21
Alignment explanation
Indices: 20557529--20557593 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 21
20557519 AAGTCTAGCT
20557529 GAAGCACATAAGTGCTAAATG
1 GAAGCACATAAGTGCTAAATG
** *
20557550 GAAGC-CCGAAG-GCTAACT-
1 GAAGCACATAAGTGCTAAATG
*
20557568 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAATG
20557589 GAAGC
1 GAAGC
20557594 CCAAAGGCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 5 0.15
19 10 0.29
20 9 0.26
21 10 0.29
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAATG
Found at i:20565931 original size:51 final size:49
Alignment explanation
Indices: 20565871--20565996 Score: 117
Period size: 51 Copynumber: 2.5 Consensus size: 49
20565861 AAAAATTTGG
* * * *
20565871 AATTTAATGAAATTTTTAAAAATTTTAAAGGTTTAATTAAAATTATAAAA
1 AATTCAATGAAATTTTTAAAAACTTTAAAGG-CTAATAAAAATTATAAAA
* * * * *
20565921 AATTCCAATGAGAAATTTCAAAAACTTTGAAGGCTAATAAAAATTTTAAAG
1 AATT-CAATGA-AATTTTTAAAAACTTTAAAGGCTAATAAAAATTATAAAA
* *
20565972 GATTTAATGAAAATTTTTAAAAACT
1 AATTCAATG-AAATTTTTAAAAACT
20565997 AGTCCTTTTA
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
50 20 0.33
51 23 0.38
52 17 0.28
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.37
Consensus pattern (49 bp):
AATTCAATGAAATTTTTAAAAACTTTAAAGGCTAATAAAAATTATAAAA
Found at i:20570393 original size:5 final size:5
Alignment explanation
Indices: 20570383--20570410 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
20570373 GTTCATCGTT
20570383 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
20570411 GAATCACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:20570925 original size:16 final size:17
Alignment explanation
Indices: 20570904--20570943 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
20570894 TTTTATGAAC
20570904 TTTTTATTTCTTT-AGA
1 TTTTTATTTCTTTAAGA
* *
20570920 TTTTTATTTTTTTAATA
1 TTTTTATTTCTTTAAGA
20570937 TTTTTAT
1 TTTTTAT
20570944 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTTTATTTCTTTAAGA
Found at i:20579260 original size:26 final size:26
Alignment explanation
Indices: 20579230--20579284 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
20579220 CGAATTTTGA
20579230 AAATTAAAAAATAAAGAGTAAATTCT
1 AAATTAAAAAATAAAGAGTAAATTCT
*
20579256 AAATTGAAAAATAAAGAGTAAATTCT
1 AAATTAAAAAATAAAGAGTAAATTCT
20579282 AAA
1 AAA
20579285 AGTATAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.62, C:0.04, G:0.09, T:0.25
Consensus pattern (26 bp):
AAATTAAAAAATAAAGAGTAAATTCT
Found at i:20584599 original size:21 final size:21
Alignment explanation
Indices: 20584573--20584616 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20584563 AGCTCTTTTA
20584573 TCCCTTTAACTACTTAATTTC
1 TCCCTTTAACTACTTAATTTC
20584594 TCCCTTTAACTACTTAATTTC
1 TCCCTTTAACTACTTAATTTC
20584615 TC
1 TC
20584617 TTGTGTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.48
Consensus pattern (21 bp):
TCCCTTTAACTACTTAATTTC
Found at i:20585128 original size:43 final size:43
Alignment explanation
Indices: 20585067--20585153 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
20585057 AATAAGGTTG
20585067 ATTGTATTATTCGATGGTTCTAGTGGAGACATGATCAAAACCA
1 ATTGTATTATTCGATGGTTCTAGTGGAGACATGATCAAAACCA
20585110 ATTGTATTATTCGATGGTTCTAGTGGAGACATGATCAAAACCA
1 ATTGTATTATTCGATGGTTCTAGTGGAGACATGATCAAAACCA
20585153 A
1 A
20585154 AGGAAACTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (43 bp):
ATTGTATTATTCGATGGTTCTAGTGGAGACATGATCAAAACCA
Found at i:20587791 original size:15 final size:15
Alignment explanation
Indices: 20587767--20587798 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20587757 TATGCATGTA
*
20587767 AAATATAAAAGACAT
1 AAATACAAAAGACAT
20587782 AAATACAAAAGACAT
1 AAATACAAAAGACAT
20587797 AA
1 AA
20587799 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:20588795 original size:16 final size:16
Alignment explanation
Indices: 20588774--20588809 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
20588764 AATCCCTAAC
* *
20588774 AATCTTCAAGTCCCTA
1 AATCTTCAAATACCTA
20588790 AATCTTCAAATACCTA
1 AATCTTCAAATACCTA
20588806 AATC
1 AATC
20588810 GATAGCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.03, T:0.31
Consensus pattern (16 bp):
AATCTTCAAATACCTA
Found at i:20589188 original size:117 final size:117
Alignment explanation
Indices: 20588978--20589188 Score: 269
Period size: 117 Copynumber: 1.8 Consensus size: 117
20588968 TTTGATTAGT
* * *
20588978 TGGTTATTTGTGATTAACTATTGCAATTTGAGTGCGAAAATGTAAGGTTTATTTTGTCGATTTTT
1 TGGTTAATTGTGATTAACTATTGCAATTTCAGTGCGAAAATGTAAGGTTTATTTTGTCGATTTGT
* ** * *
20589043 GATGCGATGGTGATCCTAATGTTATTGATAAAACTGTTGTAAAAATTGTAGA
66 GATGAGACAGTGATCCCAATGATATTGATAAAACTGTTGTAAAAATTGTAGA
* * * * * *
20589095 TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCTAGAATGTAGGGTTTGTTTTGTCGATTTGT
1 TGGTTAATTGTGATTAACTATTGCAATTTCAGTGCGAAAATGTAAGGTTTATTTTGTCGATTTGT
* * *
20589160 GATGAGACAGTGGTCCCGATGATGTTGAT
66 GATGAGACAGTGATCCCAATGATATTGAT
20589189 TTCTATTACC
Statistics
Matches: 77, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
117 77 1.00
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.42
Consensus pattern (117 bp):
TGGTTAATTGTGATTAACTATTGCAATTTCAGTGCGAAAATGTAAGGTTTATTTTGTCGATTTGT
GATGAGACAGTGATCCCAATGATATTGATAAAACTGTTGTAAAAATTGTAGA
Found at i:20589875 original size:33 final size:34
Alignment explanation
Indices: 20589828--20589940 Score: 97
Period size: 33 Copynumber: 3.4 Consensus size: 34
20589818 GGGTGGAAGT
* * **
20589828 TGATGGGGAGGGTGATGATA-AAGGGGTAGAATC
1 TGATGAGGAAGGTGATGATAGAAAAGGTAGAATC
* *
20589861 TGATGATGAAGGTGAT-TTAGAAAAGGTAGAATC
1 TGATGAGGAAGGTGATGATAGAAAAGGTAGAATC
* * * *
20589894 TGGTGAGGAAGGTGATG-TAGGAAAGGTACAAGC
1 TGATGAGGAAGGTGATGATAGAAAAGGTAGAATC
* *
20589927 TGATGGGGAGGGTG
1 TGATGAGGAAGGTG
20589941 TGTCTGCTAC
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
32 2 0.03
33 62 0.97
ACGTcount: A:0.32, C:0.04, G:0.42, T:0.22
Consensus pattern (34 bp):
TGATGAGGAAGGTGATGATAGAAAAGGTAGAATC
Found at i:20590129 original size:51 final size:51
Alignment explanation
Indices: 20590053--20590201 Score: 208
Period size: 51 Copynumber: 2.9 Consensus size: 51
20590043 CTGGTAATGG
*
20590053 ATATGCTAGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTGATGA
1 ATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTGATGA
* * * *
20590104 ATATGTTGGTGATTTTGCAACATCAGATAGAGTGAATAATGTTGCGGATGA
1 ATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTGATGA
* * * * *
20590155 ATATGCTGATGACTTTGCAACATCAAATGGACTAGATAATGTTGCTG
1 ATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTG
20590202 CTACACGTAG
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 84 1.00
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.33
Consensus pattern (51 bp):
ATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGCTGATGA
Found at i:20593000 original size:22 final size:22
Alignment explanation
Indices: 20592974--20593018 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
20592964 TCATATGCTT
*
20592974 TTGTAAAGTACACTTATCGAAA
1 TTGTAAAGTACACTTATCCAAA
*
20592996 TTGTAAAGTACATTTATCCAAA
1 TTGTAAAGTACACTTATCCAAA
20593018 T
1 T
20593019 CATATGCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (22 bp):
TTGTAAAGTACACTTATCCAAA
Found at i:20595830 original size:39 final size:39
Alignment explanation
Indices: 20595772--20595928 Score: 142
Period size: 39 Copynumber: 4.0 Consensus size: 39
20595762 TTCAGTGATG
**
20595772 TATATCCGGACTTAGGGT-CCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAAGTCCCGCAGGCT-TGTGCTGGAAT
* * *
20595811 TATATCCGGACTTAAGGT-CCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAAGTCCCGCAGGCT-TGTGCTGGAAT
* * * *
20595850 TATGTCCGGGC-TAAAGTCCCGCAGGCTTCGAGCTGGTAT
1 TATATCCGGACTTAAAGTCCCGCAGGCTT-GTGCTGGAAT
** *
20595889 TATA-CCGGGTTTAAATTCCCGCAGGCTTGTGCTGGTAAT
1 TATATCCGGACTTAAAGTCCCGCAGGCTTGTGCTGG-AAT
20595928 T
1 T
20595929 GGTTTCAAGT
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
38 16 0.16
39 83 0.84
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAAAGTCCCGCAGGCTTGTGCTGGAAT
Found at i:20598221 original size:64 final size:64
Alignment explanation
Indices: 20598115--20598242 Score: 202
Period size: 64 Copynumber: 2.0 Consensus size: 64
20598105 TATTCTGAGA
* * *
20598115 GCACATTTTTGAGCCACATATCATACAGCAGGATTACCAGTCCAAGCTAAATCCTGCCTGTAAC
1 GCACATTCTCGAGCCACATATCATACAACAGGATTACCAGTCCAAGCTAAATCCTGCCTGTAAC
* * *
20598179 GCACATTCTCGAGCCACATATCATACAACAGGATTACTAGTCCAGGCTAAATCCTGTCTGTAAC
1 GCACATTCTCGAGCCACATATCATACAACAGGATTACCAGTCCAAGCTAAATCCTGCCTGTAAC
20598243 ATATGCTCTA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (64 bp):
GCACATTCTCGAGCCACATATCATACAACAGGATTACCAGTCCAAGCTAAATCCTGCCTGTAAC
Found at i:20599987 original size:21 final size:21
Alignment explanation
Indices: 20599963--20600003 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20599953 TATATATACT
20599963 AAATAAAAT-AATAATATTTAA
1 AAATAAAATCAA-AATATTTAA
*
20599984 AAATCAAATCAAAATATTTA
1 AAATAAAATCAAAATATTTA
20600004 TAAACTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATAAAATCAAAATATTTAA
Found at i:20604026 original size:48 final size:46
Alignment explanation
Indices: 20603919--20604130 Score: 187
Period size: 46 Copynumber: 4.5 Consensus size: 46
20603909 TATGTGTGAT
* *** *
20603919 AGTGTAAGAAATGTCTGGGACATGCATCAATCAC-AG-TATAAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATAT-A-AGCC
**
20603965 AGTGTAAGACATGTCTGGGACATGCATTAGCCTCGAGATATTTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATA--TAAGCC
* * * * * *
20604013 AGTGTGAGACATGTCTGAGACATGCATCGGCATTGAGACGA-AAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGA-TATAAGCC
* *
20604059 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGCGATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATAT--AAGCC
* *
20604107 AGTGTAAGACCTATCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
20604131 GCGTTAGCTT
Statistics
Matches: 137, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
45 1 0.01
46 66 0.48
47 2 0.01
48 65 0.47
49 2 0.01
50 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATAAGCC
Found at i:20605421 original size:20 final size:21
Alignment explanation
Indices: 20605382--20605421 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20605372 GTTATAATGA
*
20605382 CCACACGGGCGTGTTGCCCTT
1 CCACACGAGCGTGTTGCCCTT
20605403 CCACACGAGCGTG-TGCCCT
1 CCACACGAGCGTGTTGCCCT
20605422 GTTACAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.12, C:0.40, G:0.28, T:0.20
Consensus pattern (21 bp):
CCACACGAGCGTGTTGCCCTT
Found at i:20608508 original size:48 final size:48
Alignment explanation
Indices: 20608387--20608618 Score: 217
Period size: 48 Copynumber: 4.9 Consensus size: 48
20608377 CATGGTAAGG
* * * *
20608387 TGCCAATGCCATATCCGAGATATGGTCTTACATGGGATCACATAT--A
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCTCATATCGA
* * *
20608433 T-CGAA-GCCGATAG-CCTAG-CTATGGTCTTACACGATG-TCTCATATCGA
1 TGCCAATGCC-AT-GTCCTAGAC-ATGGTCTTACATG-GGATCTCATATCGA
* *
20608480 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCACATAACGA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCTCATATCGA
* * *
20608528 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCACATCGA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCTCATATCGA
* * * * * *
20608576 TGCCGATGTCATATCCTAGATATGGTCTTATACGGGATCTCAT
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCTCAT
20608619 CAAACCAATG
Statistics
Matches: 149, Mismatches: 26, Indels: 20
0.76 0.13 0.10
Matches are distributed among these distances:
44 3 0.02
45 28 0.19
46 2 0.01
47 4 0.03
48 108 0.72
49 4 0.03
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (48 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCTCATATCGA
Found at i:20616414 original size:13 final size:13
Alignment explanation
Indices: 20616396--20616422 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20616386 TTTCCAGCAA
20616396 TTATGAATTTATT
1 TTATGAATTTATT
20616409 TTATGAATTTATT
1 TTATGAATTTATT
20616422 T
1 T
20616423 AATGTTGATC
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:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:20616662 original size:50 final size:50
Alignment explanation
Indices: 20616522--20616663 Score: 230
Period size: 50 Copynumber: 2.8 Consensus size: 50
20616512 ATTTGGGTAA
* *
20616522 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGAACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
20616572 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
20616622 AGAGGTCCCCCGTAAGACCATGTCTGGAACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
20616664 TGTCATTATC
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 86 1.00
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:20625220 original size:43 final size:42
Alignment explanation
Indices: 20625139--20625235 Score: 104
Period size: 43 Copynumber: 2.3 Consensus size: 42
20625129 GTCGTCAGAA
* * * *
20625139 CCAAGTCAGAAACAAAGATCAAATTATGGGAGAGGCTGTAGC
1 CCAAGTTAGAAACAAAGATCAAACTATGAGAGAAGCTGTAGC
* * * *
20625181 TCCAAGTTAGAAACAGATATCACACTATGAGAGAAGCTGTGGC
1 -CCAAGTTAGAAACAAAGATCAAACTATGAGAGAAGCTGTAGC
*
20625224 CCAAGTTCGAAA
1 CCAAGTTAGAAA
20625236 GGTAGCTGAT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 11 0.24
43 34 0.76
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (42 bp):
CCAAGTTAGAAACAAAGATCAAACTATGAGAGAAGCTGTAGC
Found at i:20627612 original size:13 final size:13
Alignment explanation
Indices: 20627594--20627620 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20627584 GATCAACATT
20627594 AAATAAATTCATA
1 AAATAAATTCATA
20627607 AAATAAATTCATA
1 AAATAAATTCATA
20627620 A
1 A
20627621 TTGCTGGAAA
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:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAATTCATA
Found at i:20632035 original size:50 final size:50
Alignment explanation
Indices: 20631921--20632059 Score: 161
Period size: 50 Copynumber: 2.8 Consensus size: 50
20631911 TAATAACATT
* * ** *
20631921 CCAAAGCCATGTCCCAGATATGGTCTTACATGGGATGTTCTCATATCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCAGTG
* * ** *
20631972 CCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGTG
* *
20632022 TCAACGCCATGTCCCAGACATGATCTTACATGGGACCT
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCT
20632060 ATTTACCCAA
Statistics
Matches: 73, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
50 43 0.59
51 30 0.41
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGTG
Found at i:20637598 original size:55 final size:55
Alignment explanation
Indices: 20637509--20637614 Score: 158
Period size: 55 Copynumber: 1.9 Consensus size: 55
20637499 GACTGGCACA
* * * *
20637509 AGAAGTTACCATTCGCTTTCCTTTCCTATCGAACATCTATCAGGACTTCTATAGG
1 AGAAATTACCATTCGCTCTCCTTGCATATCGAACATCTATCAGGACTTCTATAGG
* *
20637564 AGAAATTACCTTTCGCTCTCCTTGCATATCGAACATCTATTAGGACTTCTA
1 AGAAATTACCATTCGCTCTCCTTGCATATCGAACATCTATCAGGACTTCTA
20637615 CTGGGGCAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.35
Consensus pattern (55 bp):
AGAAATTACCATTCGCTCTCCTTGCATATCGAACATCTATCAGGACTTCTATAGG
Found at i:20639283 original size:102 final size:102
Alignment explanation
Indices: 20639148--20639490 Score: 677
Period size: 102 Copynumber: 3.4 Consensus size: 102
20639138 AGCAGACTGA
*
20639148 AGATAACAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAAATTGAAGCTAAAGATCACAAATCTT
1 AGATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAAATTGAAGCTAAAGATCACAAATCTT
20639213 ATCTTTCTGAAGTTGCAGTAGAGCAGATTGAAGCTAT
66 ATCTTTCTGAAGTTGCAGTAGAGCAGATTGAAGCTAT
20639250 AGATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAAATTGAAGCTAAAGATCACAAATCTT
1 AGATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAAATTGAAGCTAAAGATCACAAATCTT
20639315 ATCTTTCTGAAGTTGCAGTAGAGCAGATTGAAGCTAT
66 ATCTTTCTGAAGTTGCAGTAGAGCAGATTGAAGCTAT
20639352 AGATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAAATTGAAGCTAAAGATCACAAATCTT
1 AGATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAAATTGAAGCTAAAGATCACAAATCTT
20639417 ATCTTTCTGAAGTTGCAGTAGAGCAGATTGAAGCTAT
66 ATCTTTCTGAAGTTGCAGTAGAGCAGATTGAAGCTAT
20639454 AGATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAG
1 AGATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAG
20639491 CAGATCATAT
Statistics
Matches: 240, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 240 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (102 bp):
AGATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAAATTGAAGCTAAAGATCACAAATCTT
ATCTTTCTGAAGTTGCAGTAGAGCAGATTGAAGCTAT
Found at i:20639493 original size:51 final size:51
Alignment explanation
Indices: 20639147--20639495 Score: 554
Period size: 51 Copynumber: 6.8 Consensus size: 51
20639137 GAGCAGACTG
* * *
20639147 AAGATAACAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAAATTGAAGCTA
1 AAGATCACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTA
*
20639198 AAGATCACAAATCTTATCTTTCTGAAGTTGCAGTAGAGCAGATTGAAGCTA
1 AAGATCACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTA
* * * *
20639249 TAGATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAAATTGAAGCTA
1 AAGATCACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTA
*
20639300 AAGATCACAAATCTTATCTTTCTGAAGTTGCAGTAGAGCAGATTGAAGCTA
1 AAGATCACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTA
* * * *
20639351 TAGATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAAATTGAAGCTA
1 AAGATCACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTA
*
20639402 AAGATCACAAATCTTATCTTTCTGAAGTTGCAGTAGAGCAGATTGAAGCTA
1 AAGATCACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTA
* *
20639453 TAGATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 AAGATCACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
20639496 CATATCAAAT
Statistics
Matches: 271, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 271 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (51 bp):
AAGATCACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTA
Found at i:20639522 original size:41 final size:41
Alignment explanation
Indices: 20639460--20639545 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
20639450 CTATAGATTA
* * *
20639460 CAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAT
1 CAAATATTATCTCTCTAAAGTTACAGTAGAGCAGATCATAT
* *
20639501 CAAATATTTTCTCTCTAAAGTTACAGTAGAGCAGATTATAT
1 CAAATATTATCTCTCTAAAGTTACAGTAGAGCAGATCATAT
20639542 CAAA
1 CAAA
20639546 CCTTATCTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (41 bp):
CAAATATTATCTCTCTAAAGTTACAGTAGAGCAGATCATAT
Found at i:20639701 original size:44 final size:44
Alignment explanation
Indices: 20639595--20639747 Score: 144
Period size: 44 Copynumber: 3.4 Consensus size: 44
20639585 AAATCAAATA
* *
20639595 TTATCTCTCTGAAGTTATAGTGGAGCAGATTAAAGACGAGTTACAAATC
1 TTATCTCTCTGAAGTTATAGTGGAGTAGATTAAAG-C-A---ACAAACC
* * *
20639644 TTATCTCCCTGAAGTTGTAGTGGAGTAGATTAAAGCCACAAACC
1 TTATCTCTCTGAAGTTATAGTGGAGTAGATTAAAGCAACAAACC
* * * * * *
20639688 TTATCTCTTTGAAGTTACAGTAGAGTAGGTTGAAGTAACAAACC
1 TTATCTCTCTGAAGTTATAGTGGAGTAGATTAAAGCAACAAACC
* *
20639732 TTATCCCCCTGAAGTT
1 TTATCTCTCTGAAGTT
20639748 GCAATAGGTC
Statistics
Matches: 87, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
44 54 0.62
48 1 0.01
49 32 0.37
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (44 bp):
TTATCTCTCTGAAGTTATAGTGGAGTAGATTAAAGCAACAAACC
Found at i:20641364 original size:3 final size:3
Alignment explanation
Indices: 20641358--20641536 Score: 358
Period size: 3 Copynumber: 59.7 Consensus size: 3
20641348 ATTATTATTA
20641358 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
20641406 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
20641454 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
20641502 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
20641537 ATAATAATTA
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 176 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:20641694 original size:25 final size:25
Alignment explanation
Indices: 20641644--20641695 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
20641634 ATATATCTAC
* *
20641644 ATACATTTATATATTTTTCTTATAT
1 ATACATATATATATTTTTATTATAT
*
20641669 ATACATATATAT-TTTTATATTTTAT
1 ATACATATATATATTTT-TATTATAT
20641694 AT
1 AT
20641696 TTTATAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (25 bp):
ATACATATATATATTTTTATTATAT
Found at i:20641868 original size:42 final size:42
Alignment explanation
Indices: 20641777--20641868 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 42
20641767 ATGTCCATTA
* * * * *
20641777 TTATTATTATTTAAATGTTTTAGTTTTTATTTGTTTATTTAC
1 TTATTATTATTTAAATGATTGAGTTTTTATATATATATTTAC
* * *
20641819 TTGTTATTATTTACATGATTGA-TTTTTATATATATATTTCTC
1 TTATTATTATTTAAATGATTGAGTTTTTATATATATATTT-AC
20641861 TTATTATT
1 TTATTATT
20641869 TATTCATCTT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
41 14 0.35
42 26 0.65
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64
Consensus pattern (42 bp):
TTATTATTATTTAAATGATTGAGTTTTTATATATATATTTAC
Found at i:20647314 original size:7 final size:7
Alignment explanation
Indices: 20647304--20647352 Score: 59
Period size: 7 Copynumber: 7.1 Consensus size: 7
20647294 TAAAACTAAA
20647304 AAAAAGG
1 AAAAAGG
20647311 AAAAAGG
1 AAAAAGG
20647318 AAAAA--
1 AAAAAGG
20647323 AAAAA-G
1 AAAAAGG
20647329 AGAAAAGG
1 A-AAAAGG
20647337 AAAAAGAG
1 AAAAAG-G
20647345 AAAAAGG
1 AAAAAGG
20647352 A
1 A
20647353 GAGGCCAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.13
6 1 0.03
7 23 0.61
8 9 0.24
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:20647325 original size:19 final size:19
Alignment explanation
Indices: 20647301--20647341 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
20647291 CAATAAAACT
20647301 AAAAAAAAG-GAAAAAGGAA
1 AAAAAAAAGAG-AAAAGGAA
20647320 AAAAAAAAGAGAAAAGGAA
1 AAAAAAAAGAGAAAAGGAA
20647339 AAA
1 AAA
20647342 GAGAAAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGAGAAAAGGAA
Found at i:20647340 original size:14 final size:14
Alignment explanation
Indices: 20647305--20647348 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
20647295 AAAACTAAAA
20647305 AAAAGGAAAAAG-G
1 AAAAGGAAAAAGAG
*
20647318 AAAA-AAAAAAGAG
1 AAAAGGAAAAAGAG
20647331 AAAAGGAAAAAGAG
1 AAAAGGAAAAAGAG
20647345 AAAA
1 AAAA
20647349 AGGAGAGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 6 0.22
13 9 0.33
14 12 0.44
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAAGGAAAAAGAG
Found at i:20652034 original size:30 final size:29
Alignment explanation
Indices: 20652000--20652064 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
20651990 TAATCCACCA
20652000 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
20652030 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
20652060 CCCAA
1 CCCAA
20652065 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:20652038 original size:31 final size:30
Alignment explanation
Indices: 20652007--20652064 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
20651997 CCACCCAACT
20652007 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
20652037 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
20652065 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:20654012 original size:24 final size:25
Alignment explanation
Indices: 20653968--20654015 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
20653958 AAACAACTCT
*
20653968 AAAAGAAACTTAAAAGTAATTCTTG
1 AAAAGAAACTCAAAAGTAATTCTTG
20653993 AAAA-AAACTCAAAGAG-AATTCTT
1 AAAAGAAACTCAAA-AGTAATTCTT
20654016 ATCAACTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.25
Consensus pattern (25 bp):
AAAAGAAACTCAAAAGTAATTCTTG
Found at i:20656508 original size:103 final size:104
Alignment explanation
Indices: 20656329--20656593 Score: 417
Period size: 103 Copynumber: 2.6 Consensus size: 104
20656319 AACCGTTATT
* * * *
20656329 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
20656394 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
20656432 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
20656496 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
20656536 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
20656594 TTATGTACAA
Statistics
Matches: 149, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
102 1 0.01
103 82 0.55
104 65 0.44
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:20656955 original size:30 final size:29
Alignment explanation
Indices: 20656921--20656985 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
20656911 TAATCCACCA
20656921 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
20656951 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
20656981 CCCAA
1 CCCAA
20656986 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:20656959 original size:31 final size:30
Alignment explanation
Indices: 20656928--20656985 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
20656918 CCACCCAACT
20656928 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
20656958 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
20656986 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:20664303 original size:16 final size:16
Alignment explanation
Indices: 20664271--20664308 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20664261 TTTAGTTCTG
* *
20664271 TTCTTTTTTTTCTTTC
1 TTCTTTTTTTGCATTC
20664287 TTCTTTTTTTGCATTC
1 TTCTTTTTTTGCATTC
20664303 TT-TTTT
1 TTCTTTT
20664309 GTTCTGTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.79
Consensus pattern (16 bp):
TTCTTTTTTTGCATTC
Found at i:20670051 original size:125 final size:125
Alignment explanation
Indices: 20669848--20670199 Score: 501
Period size: 125 Copynumber: 2.8 Consensus size: 125
20669838 TAATTTCGAG
** * *
20669848 TTGACATTTCTGATAAAATAATATAAAATCGCTTCTAGTAGGATGGTATTTGAGAAGAATTTGTG
1 TTGACATTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
*
20669913 AAATTACGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACAG-AAGAAAAAAAAAATTT
66 AAATTGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCA-AGTAAGAAAAAAAAAATTT
* * *
20669973 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCGGGATGCTATTTGAGAAGAATTTGTG
1 TTGACATTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * * * ****
20670038 AAATTGCGGCCTCGT-CAGCGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTT
66 AAATTGCGCCCTCGTGGA-CGCGCTTTTGCTACAGTAGGTCAAGTAAGAAAAAAAAAATTT
20670098 TTGACATTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACATTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * *
20670163 AAATCGCGCCCTTGTGGACGCGCTTTTACTACAGTAG
66 AAATTGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
20670200 CATGTTTGGG
Statistics
Matches: 200, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
124 2 0.01
125 197 0.99
126 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (125 bp):
TTGACATTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATTGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCAAGTAAGAAAAAAAAAATTT
Found at i:20672957 original size:116 final size:116
Alignment explanation
Indices: 20672753--20672979 Score: 382
Period size: 116 Copynumber: 2.0 Consensus size: 116
20672743 TGATAAATTG
* * *
20672753 TATTAAGTCAAAAAATTGTCTTAATGGTTAGTAAAATTATCAAATTATATACAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATAATATAAAATTATTAATTGT
* *
20672818 TAGTACCAGTCAAAATATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
* *
20672869 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATAATGTAAAATTATTATTTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATAATATAAAATTATTAATTGT
*
20672934 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTTAATGT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGT
20672980 TACGGTTTTT
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 103 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (116 bp):
TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATAATATAAAATTATTAATTGT
TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
Found at i:20673004 original size:23 final size:23
Alignment explanation
Indices: 20672978--20673553 Score: 343
Period size: 23 Copynumber: 23.6 Consensus size: 23
20672968 TTACGTTAAT
*
20672978 GTTACGGTTTTTAATTAAATTAG
1 GTTAGGGTTTTTAATTAAATTAG
* *
20673001 GTTAGGGTTTTTTATTGAATTAGGCTAGG
1 GTTAGGGTTTTTAATT-AA--A--TTA-G
20673030 GTTAGGGTTTTTAATTAAATTAG
1 GTTAGGGTTTTTAATTAAATTAG
20673053 GTTAGGGTTTTTAATTAAATTAG
1 GTTAGGGTTTTTAATTAAATTAG
*
20673076 GTTAGGCTAGGGTTTTTAATCAAATTAG
1 G-T----TAGGGTTTTTAATTAAATTAG
*
20673104 GTTAGGGTTTTTAAGTT-AA-GAG
1 GTTAGGGTTTTTAA-TTAAATTAG
* * *
20673126 TTTAGAGTTTTTAATTGAATTAG
1 GTTAGGGTTTTTAATTAAATTAG
* **
20673149 GTTAGAGTTAGGGTTT--TTAGGTTAGG
1 GTTAGGGTT----TTTAATTAAATTA-G
*
20673175 GTTTAGGATTTTTAATTAAATTAG
1 G-TTAGGGTTTTTAATTAAATTAG
*
20673199 GTTAGAGTTTTTAATTAAATTAG
1 GTTAGGGTTTTTAATTAAATTAG
* * **
20673222 GTTATGGTTAGGGTT--TTAGGGTTTAGG
1 GTTAGGGTT---TTTAATTA--AATTA-G
20673249 GTTTAGGGTTTTTAATTAAATTAG
1 G-TTAGGGTTTTTAATTAAATTAG
*
20673273 GCTAGGGTTTTTAATTAAATTAG
1 GTTAGGGTTTTTAATTAAATTAG
* **
20673296 GTTAGGGTTAGGGTT--TTAGGGTTTAAG
1 GTTAGGGTT---TTTAATTA--AATT-AG
*
20673323 GTTTAGGATTTTTAATTAAATTAG
1 G-TTAGGGTTTTTAATTAAATTAG
*
20673347 GTTAGGGTTTTTAAGTT-AA--GG
1 GTTAGGGTTTTTAA-TTAAATTAG
20673368 GTTTAGGGTTTTTAATTGAATTAGGTTAGG
1 G-TTAGGGTTTTTAATT-AA--A--TTA-G
*
20673398 GTTAGGGTTTTTAATT-AA--GG
1 GTTAGGGTTTTTAATTAAATTAG
20673418 GTTTAGGGTTTTTAATTAAATTAG
1 G-TTAGGGTTTTTAATTAAATTAG
20673442 GTTAGGGTTTTTAATTAAATTAG
1 GTTAGGGTTTTTAATTAAATTAG
*
20673465 GCTAGGGTTTTTAATTAAATTAG
1 GTTAGGGTTTTTAATTAAATTAG
**
20673488 GTTATGGTTTTGGGTTTTTAATTATTTTAG
1 GTTA-------GGGTTTTTAATTAAATTAG
****
20673518 GTTAGGGTTTAGGGTTAAATTAG
1 GTTAGGGTTTTTAATTAAATTAG
20673541 GTTAGGGTTTTTA
1 GTTAGGGTTTTTA
20673554 TTACATCAAA
Statistics
Matches: 434, Mismatches: 57, Indels: 124
0.71 0.09 0.20
Matches are distributed among these distances:
20 2 0.00
21 21 0.05
22 31 0.07
23 207 0.48
24 23 0.05
25 22 0.05
26 13 0.03
27 22 0.05
28 39 0.09
29 31 0.07
30 23 0.05
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.47
Consensus pattern (23 bp):
GTTAGGGTTTTTAATTAAATTAG
Found at i:20673037 original size:29 final size:29
Alignment explanation
Indices: 20673000--20673112 Score: 123
Period size: 28 Copynumber: 4.1 Consensus size: 29
20672990 AATTAAATTA
* *
20673000 GGTTAGGGTTTTTTATTGAATTAGGCTAG
1 GGTTAGGGTTTTTAATTAAATTAGGCTAG
20673029 GGTTAGGGTTTTTAATTAAA-T----TA-
1 GGTTAGGGTTTTTAATTAAATTAGGCTAG
*
20673052 GGTTAGGGTTTTTAATTAAATTAGGTTA-
1 GGTTAGGGTTTTTAATTAAATTAGGCTAG
* * *
20673080 GGCTAGGGTTTTTAATCAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGCTAG
20673109 GGTT
1 GGTT
20673113 TTTAAGTTAA
Statistics
Matches: 73, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
23 20 0.27
24 3 0.04
28 29 0.40
29 21 0.29
ACGTcount: A:0.26, C:0.03, G:0.27, T:0.44
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGCTAG
Found at i:20673170 original size:20 final size:21
Alignment explanation
Indices: 20673145--20673188 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20673135 TTTAATTGAA
*
20673145 TTAGGTTAGAG-TTAGGGTTT
1 TTAGGTTAGAGTTTAGGATTT
*
20673165 TTAGGTTAGGGTTTAGGATTT
1 TTAGGTTAGAGTTTAGGATTT
20673186 TTA
1 TTA
20673189 ATTAAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (21 bp):
TTAGGTTAGAGTTTAGGATTT
Found at i:20673174 original size:14 final size:15
Alignment explanation
Indices: 20673150--20673178 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20673140 TTGAATTAGG
20673150 TTAGAGTTAGGGTTT
1 TTAGAGTTAGGGTTT
20673165 TTAG-GTTAGGGTTT
1 TTAGAGTTAGGGTTT
20673179 AGGATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.48
Consensus pattern (15 bp):
TTAGAGTTAGGGTTT
Found at i:20673248 original size:7 final size:7
Alignment explanation
Indices: 20673229--20673259 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
20673219 TAGGTTATGG
20673229 TTAGGGTT
1 TTAGGG-T
20673237 TTAGGGT
1 TTAGGGT
20673244 TTAGGGT
1 TTAGGGT
20673251 TTAGGGT
1 TTAGGGT
20673258 TT
1 TT
20673260 TTAATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.74
8 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (7 bp):
TTAGGGT
Found at i:20673285 original size:74 final size:74
Alignment explanation
Indices: 20673026--20673365 Score: 428
Period size: 74 Copynumber: 4.6 Consensus size: 74
20673016 TGAATTAGGC
*
20673026 TAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGCTAGGGTT
1 TAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTT
****
20673090 TTTAATCAAAT
66 TTT-A-GGGTT
* * * *
20673101 TA-GG-TTAGGGTTTTTAAGTT-AA-GAGTTTAGAGTTTTTAATTGAATTAGGTTAGAGTTAGGG
1 TAGGGTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAG-GTTAGGG
20673162 TTTTTA-GG-T
64 TTTTTAGGGTT
* *
20673171 TAGGGTTTAGGATTTTTAATTAAATTAGGTTAGAGTTTTTAATTAAATTAGGTTATGGTTAGGG-
1 TAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTA-GGTTAGGGT
20673235 TTTTAGGGTT
65 TTTTAGGGTT
*
20673245 TAGGGTTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG-
1 TAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTA-GGTTAGGGT
20673309 TTTTAGGGTT
65 TTTTAGGGTT
* *
20673319 TAAGGTTTAGGATTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAA
1 TAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTAA
20673366 GGGTTTAGGG
Statistics
Matches: 237, Mismatches: 18, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
70 3 0.01
71 4 0.02
72 19 0.08
73 64 0.27
74 139 0.59
75 8 0.03
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (74 bp):
TAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTT
TTTAGGGTT
Found at i:20673397 original size:96 final size:94
Alignment explanation
Indices: 20673251--20673511 Score: 348
Period size: 96 Copynumber: 2.7 Consensus size: 94
20673241 GGTTTAGGGT
20673251 TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTAGG
1 TTAGGGTTTTTAATTAAA-TAGGCTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTA--
*
20673316 GTTTAA-GGTTTAGGATTTTTAATTAAATTAGG
63 -ATTAAGGGTTTAGGATTTTTAATTAAATTAGG
* * *
20673348 TTAGGGTTTTTAAGTT-AA-GGGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTA
1 TTAGGGTTTTTAA-TTAAATAGG-CTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG-TTTTA
*
20673411 ATTAAGGGTTTAGGGTTTTTAATTAAATTAGG
63 ATTAAGGGTTTAGGATTTTTAATTAAATTAGG
* *
20673443 TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGGTTATGGTTTTGGGTTTTTA
1 TTAGGGTTTTTAATTAAA-TAGGCTAGGGTTTTTAATTAAATTAGGTTA-GGGTTAGGG-TTTTA
20673508 ATTA
63 ATTA
20673512 TTTTAGGTTA
Statistics
Matches: 146, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
94 6 0.04
95 42 0.29
96 57 0.39
97 39 0.27
98 2 0.01
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.47
Consensus pattern (94 bp):
TTAGGGTTTTTAATTAAATAGGCTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTAATT
AAGGGTTTAGGATTTTTAATTAAATTAGG
Found at i:20673503 original size:53 final size:53
Alignment explanation
Indices: 20673446--20673551 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 53
20673436 AATTAGGTTA
** *
20673446 GGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGGTTATGGTTTT
1 GGGTTTTTAATTAAATTAGGCTAGGGTTTAGAATTAAATTAGGTTAGGGTTTT
** * **
20673499 GGGTTTTTAATTATTTTAGGTTAGGGTTTAGGGTTAAATTAGGTTAGGGTTTT
1 GGGTTTTTAATTAAATTAGGCTAGGGTTTAGAATTAAATTAGGTTAGGGTTTT
20673552 TATTACATCA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.24, C:0.01, G:0.26, T:0.49
Consensus pattern (53 bp):
GGGTTTTTAATTAAATTAGGCTAGGGTTTAGAATTAAATTAGGTTAGGGTTTT
Found at i:20673634 original size:44 final size:45
Alignment explanation
Indices: 20673559--20673645 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 45
20673549 TTTTATTACA
* * * *
20673559 TCAAATAAACTTCTATTTTATTTTATCAAATAATGTCAAAATAAC
1 TCAAATAAAATTCTATTTTATTTCATAAAATAATATCAAAATAAC
20673604 TCAAA-AAAATTCTATTTT-TTTGCATAAAATAATATCAAAATA
1 TCAAATAAAATTCTATTTTATTT-CATAAAATAATATCAAAATA
20673646 TTCAAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 3 0.08
44 29 0.78
45 5 0.14
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.39
Consensus pattern (45 bp):
TCAAATAAAATTCTATTTTATTTCATAAAATAATATCAAAATAAC
Found at i:20674747 original size:7 final size:7
Alignment explanation
Indices: 20674735--20674773 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
20674725 ATACGTACAT
20674735 AATACTA
1 AATACTA
20674742 AATACTA
1 AATACTA
20674749 AATACTA
1 AATACTA
20674756 AATACTA
1 AATACTA
20674763 AATACTA
1 AATACTA
20674770 AATA
1 AATA
20674774 TCAATCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:20675975 original size:51 final size:51
Alignment explanation
Indices: 20675914--20676034 Score: 199
Period size: 51 Copynumber: 2.4 Consensus size: 51
20675904 TTATTTTAAA
* * *
20675914 AAGGCAATTGAGAGGAAATTGAAATTAAATATGGATGTGAGAGAATTTTTG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATGTGAGAGAATTTTGG
*
20675965 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATGTGAGAGAATTTTGG
20676016 AAGGAAATTGAGA-GAAATT
1 AAGGAAATTGAGAGGAAATT
20676035 TGGAAGGAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 6 0.09
51 60 0.91
ACGTcount: A:0.45, C:0.01, G:0.26, T:0.28
Consensus pattern (51 bp):
AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATGTGAGAGAATTTTGG
Found at i:20676026 original size:22 final size:22
Alignment explanation
Indices: 20676001--20676056 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
20675991 AAATATAGAT
*
20676001 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAAATTTGGAAGGAAA
20676023 TTGAGAGAAATTTGGAAGGAAA
1 TTGAGAGAAATTTGGAAGGAAA
20676045 TTGAGAGGAAAT
1 TTGAGA-GAAAT
20676057 ATGAGAGAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 27 0.84
23 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (22 bp):
TTGAGAGAAATTTGGAAGGAAA
Found at i:20676061 original size:12 final size:11
Alignment explanation
Indices: 20676017--20676063 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
20676007 GAATTTTGGA
20676017 AGGAAATTGAG
1 AGGAAATTGAG
20676028 A-GAAATTTG-G
1 AGGAAA-TTGAG
20676038 AAGGAAATTGAG
1 -AGGAAATTGAG
20676050 AGGAAATATGAG
1 AGGAAAT-TGAG
20676062 AG
1 AG
20676064 AGGATTTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
10 5 0.16
11 15 0.48
12 11 0.35
ACGTcount: A:0.47, C:0.00, G:0.34, T:0.19
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:20676766 original size:30 final size:29
Alignment explanation
Indices: 20676730--20676794 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
20676720 TAATTCCAGC
* *
20676730 CTTTTTACTTTACTTATATTAAAATTTAAT
1 CTTTTTACTTTAATT-TAGTAAAATTTAAT
* *
20676760 CTTTTTATTTTAATTTAGTATAATTTAAT
1 CTTTTTACTTTAATTTAGTAAAATTTAAT
*
20676789 TTTTTT
1 CTTTTT
20676795 TTCAATGTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (29 bp):
CTTTTTACTTTAATTTAGTAAAATTTAAT
Found at i:20678267 original size:16 final size:16
Alignment explanation
Indices: 20678246--20678298 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
20678236 TTGGTTGGCT
20678246 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
20678262 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
*
20678278 GTAATAGAATAGAGGC
1 GTAATGGAATAGAGGC
20678294 GTAAT
1 GTAAT
20678299 AGATAATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.40, C:0.06, G:0.32, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:20678333 original size:45 final size:44
Alignment explanation
Indices: 20678278--20678374 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
20678268 GAATAGATGC
* *
20678278 GTAATAGAATAGAGGCGTAATAGATAATCTTTTGTTTGGTTGAAT
1 GTAATAGAATAGAGGCATAAT-GATAATCTTGTGTTTGGTTGAAT
* * *
20678323 GTAATTGAATAGAGGCATAATGGTATTCTTGTGTTTGGTTGAAT
1 GTAATAGAATAGAGGCATAATGATAATCTTGTGTTTGGTTGAAT
*
20678367 GGAATAGA
1 GTAATAGA
20678375 GATGTAATAG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 26 0.58
45 19 0.42
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (44 bp):
GTAATAGAATAGAGGCATAATGATAATCTTGTGTTTGGTTGAAT
Found at i:20678512 original size:18 final size:18
Alignment explanation
Indices: 20678483--20678543 Score: 79
Period size: 18 Copynumber: 3.3 Consensus size: 18
20678473 GCTTATTAAT
20678483 ATAAATAATATATAATTTA
1 ATAAA-AATATATAATTTA
*
20678502 ATAAAAATATATAAATTA
1 ATAAAAATATATAATTTA
20678520 AT-AAAATATATGAATTTA
1 ATAAAAATATAT-AATTTA
*
20678538 CTAAAA
1 ATAAAA
20678544 TCATAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 9 0.24
18 20 0.54
19 8 0.22
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAAAAATATATAATTTA
Found at i:20680243 original size:22 final size:22
Alignment explanation
Indices: 20680218--20680261 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20680208 TAAATATGGC
20680218 AATGCAAATATTAAAATTCCAT
1 AATGCAAATATTAAAATTCCAT
*
20680240 AATGCACATATTAAAATTCCAT
1 AATGCAAATATTAAAATTCCAT
20680262 TAGGTTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.32
Consensus pattern (22 bp):
AATGCAAATATTAAAATTCCAT
Found at i:20682401 original size:14 final size:14
Alignment explanation
Indices: 20682382--20682411 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20682372 AAATTCTATA
20682382 TTTCGTGTATTAAT
1 TTTCGTGTATTAAT
20682396 TTTCGTGTATTAAT
1 TTTCGTGTATTAAT
20682410 TT
1 TT
20682412 AGTATGTGTA
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:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (14 bp):
TTTCGTGTATTAAT
Found at i:20682637 original size:90 final size:90
Alignment explanation
Indices: 20682524--20682849 Score: 465
Period size: 90 Copynumber: 3.6 Consensus size: 90
20682514 TTGTATCTGC
* *
20682524 AAATTTAATTTAGTCTGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCCA
1 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTATCCA
20682589 TCTGTTTGTAGTTTGTTGGGTGTTT
66 TCTGTTTGTAGTTTGTTGGGTGTTT
** * * * * *
20682614 AAATTTAATTTAGTATGTGTTATATATAGTTTGAATTTAAAATTTTCGTGCACTAATGTTATCCA
1 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTATCCA
* * *
20682679 TCAGTTTGTAGATTGTTGGATGTTT
66 TCTGTTTGTAGTTTGTTGGGTGTTT
*
20682704 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCATGTATTAATTTTATCCA
1 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTATCCA
*
20682769 TCTGTTTGTGGTTTGTTGGGTGTTT
66 TCTGTTTGTAGTTTGTTGGGTGTTT
* * * * * *
20682794 AAATTTAATTTAGTGCGTATTATAT-TTGTTCGAATTTTATATTTTTGTGTATTAAT
1 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAAT
20682850 ATTCTAGAAT
Statistics
Matches: 207, Mismatches: 29, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
89 25 0.12
90 182 0.88
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (90 bp):
AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTATCCA
TCTGTTTGTAGTTTGTTGGGTGTTT
Found at i:20686003 original size:25 final size:25
Alignment explanation
Indices: 20685924--20685990 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
20685914 GTAGTTTTGA
* **
20685924 AGAGCCAT-TAATCAGGAAGCTCCGG
1 AGAGCCATAT-ATCGGGAAGCTCTAG
*
20685949 ATAGCCATATATCGGGAAGCTCTAG
1 AGAGCCATATATCGGGAAGCTCTAG
20685974 AGAGCCATATATCGGGA
1 AGAGCCATATATCGGGA
20685991 CACTCATAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
25 35 0.97
26 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (25 bp):
AGAGCCATATATCGGGAAGCTCTAG
Found at i:20686091 original size:25 final size:25
Alignment explanation
Indices: 20686078--20686125 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
20686068 GGAAGTTTGC
20686078 AAGAACCATATAACGGGAAGCTCTT
1 AAGAACCATATAACGGGAAGCTCTT
*
20686103 AAGAACCATATAATGGGAAGCTC
1 AAGAACCATATAACGGGAAGCTC
20686126 GAGAGGGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (25 bp):
AAGAACCATATAACGGGAAGCTCTT
Found at i:20687207 original size:17 final size:17
Alignment explanation
Indices: 20687178--20687210 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20687168 GACTTCAAAT
20687178 TTTGAATACTATAGCTA
1 TTTGAATACTATAGCTA
20687195 TTTG-ATACTTATAGCT
1 TTTGAATAC-TATAGCT
20687211 CTAGAACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (17 bp):
TTTGAATACTATAGCTA
Found at i:20688425 original size:23 final size:22
Alignment explanation
Indices: 20688394--20688461 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
20688384 AGCCCTGTCC
*
20688394 TTTCAACTTTTTTTTTCATTTCA
1 TTTC-ACTTTTATTTTCATTTCA
* *
20688417 TTTCTACTTTCATTTCCATTTCA
1 TTTC-ACTTTTATTTTCATTTCA
20688440 TTTCA-TTTTCATTTTCATTTCA
1 TTTCACTTTT-ATTTTCATTTCA
20688462 CTTAAATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 3 0.08
22 12 0.32
23 23 0.61
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTCACTTTTATTTTCATTTCA
Found at i:20688438 original size:6 final size:5
Alignment explanation
Indices: 20688407--20688639 Score: 66
Period size: 5 Copynumber: 43.4 Consensus size: 5
20688397 CAACTTTTTT
20688407 TTTCA TTTCA TTTCTA CTTTCA TTTCCA TTTCA TTTCA TTTTCA TTTTCA
1 TTTCA TTTCA TTTC-A -TTTCA TTT-CA TTTCA TTTCA -TTTCA -TTTCA
* * * * * * *
20688457 TTTCA CTTAA ATT-A TTT-T TTTCA TTTAAA TTTAA TTT-T TTCTCA TTTCAA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTT-CA TTTCA TTTCA TT-TCA TTTC-A
* * *
20688507 TTT-T TTTCA TTTCA GTTTTTA TTTTCA TTTCAA TTTGTAA TTT-A TTTTCA
1 TTTCA TTTCA TTTCA --TTTCA -TTTCA TTTC-A -TT-TCA TTTCA -TTTCA
* * * * *
20688557 TTTAAA CTTTCA TTCCA TTTCA TAATCA --TCA TTTCA TTACAAA TTACA
1 TTT-CA -TTTCA TTTCA TTTCA T-TTCA TTTCA TTTCA TTTC--A TTTCA
*
20688605 TTTCA TTTCA TATTCA TTTAACA TTTTA TTTCA TT
1 TTTCA TTTCA T-TTCA TTT--CA TTTCA TTTCA TT
20688640 AATTTTTTTT
Statistics
Matches: 178, Mismatches: 23, Indels: 54
0.70 0.09 0.21
Matches are distributed among these distances:
3 3 0.02
4 12 0.07
5 91 0.51
6 47 0.26
7 24 0.13
8 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.01, T:0.58
Consensus pattern (5 bp):
TTTCA
Found at i:20688440 original size:11 final size:11
Alignment explanation
Indices: 20688410--20688461 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
20688400 CTTTTTTTTT
20688410 CATTTCATTTC
1 CATTTCATTTC
*
20688421 TACTTTCATTTC
1 CA-TTTCATTTC
20688433 CATTTCATTT-
1 CATTTCATTTC
*
20688443 CATTTTCATTTT
1 CA-TTTCATTTC
20688455 CATTTCA
1 CATTTCA
20688462 CTTAAATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 2 0.06
11 22 0.61
12 12 0.33
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (11 bp):
CATTTCATTTC
Found at i:20688440 original size:28 final size:28
Alignment explanation
Indices: 20688407--20688460 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
20688397 CAACTTTTTT
20688407 TTTCATTTCA-TTTCTACTTTCATTTCCA
1 TTTCATTTCATTTTC-ACTTTCATTTCCA
*
20688435 TTTCATTTCATTTTCATTTTCATTTC
1 TTTCATTTCATTTTCACTTTCATTTC
20688461 ACTTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.17, C:0.22, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTCATTTCATTTTCACTTTCATTTCCA
Found at i:20688484 original size:18 final size:18
Alignment explanation
Indices: 20688457--20688513 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
20688447 TTCATTTTCA
*
20688457 TTTCACTTAAATTATTTT
1 TTTCATTTAAATTATTTT
20688475 TTTCATTTAAATTTAATTTT
1 TTTCATTTAAA-TT-ATTTT
*
20688495 TTCTCATTTCAATT-TTTT
1 TT-TCATTTAAATTATTTT
20688513 T
1 T
20688514 CATTTCAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 15 0.44
19 2 0.06
20 9 0.26
21 8 0.24
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTCATTTAAATTATTTT
Found at i:20688492 original size:23 final size:21
Alignment explanation
Indices: 20688402--20688509 Score: 74
Period size: 23 Copynumber: 4.9 Consensus size: 21
20688392 CCTTTCAACT
* *
20688402 TTTTTTTTCATTTCATTTCTAC
1 TTTTTTTTCATTTCAATT-TAA
* * *
20688424 TTTCATTTCCATTTC-ATTTCA
1 TTT-TTTTTCATTTCAATTTAA
* *
20688445 TTTTCATTTTCATTTCACTTAAA
1 TTTT--TTTTCATTTCAATTTAA
*
20688468 TTATTTTTTTCATTTAAATTTAA
1 -T-TTTTTTTCATTTCAATTTAA
*
20688491 TTTTTTCTCATTTCAATTT
1 TTTTTTTTCATTTCAATTT
20688510 TTTTCATTTC
Statistics
Matches: 65, Mismatches: 15, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
21 20 0.31
22 15 0.23
23 26 0.40
24 1 0.02
25 3 0.05
ACGTcount: A:0.21, C:0.16, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTTTTCATTTCAATTTAA
Found at i:20688660 original size:17 final size:17
Alignment explanation
Indices: 20688619--20688669 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
20688609 ATTTCATATT
*
20688619 CATTTAACATTTTATTT-
1 CATTTAA-ATTTTTTTTC
20688636 CA-TT-AATTTTTTTTC
1 CATTTAAATTTTTTTTC
20688651 CATTTAAATTTATTTTTC
1 CATTTAAATTT-TTTTTC
20688669 C
1 C
20688670 TAATATACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 8 0.28
15 3 0.10
16 4 0.14
17 7 0.24
18 7 0.24
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (17 bp):
CATTTAAATTTTTTTTC
Found at i:20688828 original size:21 final size:21
Alignment explanation
Indices: 20688786--20688828 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
20688776 TATCAGGGTC
*
20688786 ATTTAAAATTTTTCATATTTT
1 ATTTAAAATTTTTCATAATTT
*
20688807 ATTTAAATTTTTTC-TCAATTT
1 ATTTAAAATTTTTCAT-AATTT
20688828 A
1 A
20688829 AAAATAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTAAAATTTTTCATAATTT
Found at i:20689346 original size:113 final size:112
Alignment explanation
Indices: 20689171--20689733 Score: 421
Period size: 114 Copynumber: 4.9 Consensus size: 112
20689161 TTTACCACGC
* * *
20689171 AGCGCCGCAAAATATC-AAGACCAACACGCAGCGTTCTGGTCTTGATGTATATTGGC-ATTAGTG
1 AGCGCCGCAAAAGATCTTA-ACCAAAACGCAGCGTT-TGGTCTTGATGTATATT-GCAATTAGTG
*
20689234 GCGCTTATGAACAAACGCCAG-TAATGTACAGTATTAGCGGCGCTTAGCGGA
63 GCGCTTATGAA-AAACGCC-GCTAATGTATAGTATTAGCGGCGCTTAGCGGA
* * *
20689285 AGCGCCGCAAAAGATGTTAACCAAAACGCAGAGTTTAGTCTTGATGTATATTGCAATTAGTGGCG
1 AGCGCCGCAAAAGATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTGCAATTAGTGGCG
* * * * ** *
20689350 CTTATAAAGAAAACACCGCTAATGTATAGTATTAACTGCGCAGAGCGTTA
66 CTTAT-GA-AAAACGCCGCTAATGTATAGTATTAGCGGCGCTTAGCG-GA
* * * * * * **
20689400 AACGCCGCAAGATATCTTAATCAAAACGCACCGTTTTGGTCTTGATGTATACTATAATTAGTGGC
1 AGCGCCGCAAAAGATCTTAACCAAAACGCAGCG-TTTGGTCTTGATGTATATTGCAATTAGTGGC
* * * * * * * *
20689465 GTTTAAGGAAAACGCCAG-TAA-GGATAGT-TATAGCAGCGTTTTGTGGTA
65 GCTTATGAAAAACGCC-GCTAATGTATAGTAT-TAGCGGCGCTTAGCGG-A
* * * * *
20689513 AGCGCCTCCAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGA-GGATTATTAG-AATTAGTGG
1 AGCGCCGCAAAAGATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTA-TATT-GCAATTAGTGG
* * * *
20689576 CGCTTGATGAAAAACGCCGCTAAAGTATA-TCATTAGCGGCG-TTTGTGTA
64 CGCTT-ATGAAAAACGCCGCTAATGTATAGT-ATTAGCGGCGCTTAGCGGA
* * * *
20689625 ACGCGCCGC-AAAGTATCTTAACCAAAACACAGCGTTTAGTTCTTGATGTATACTGTAATTAGTG
1 A-GCGCCGCAAAAG-ATCTTAACCAAAACGCAGCGTTT-GGTCTTGATGTATATTGCAATTAGTG
** * * *
20689689 GCGCACATGGGAAAACGCCGTTGAA-GCATAGTATTAGCGGCGCTT
63 GCGCTTAT-GAAAAACGCCGCT-AATGTATAGTATTAGCGGCGCTT
20689734 TTACCGAAAC
Statistics
Matches: 356, Mismatches: 67, Indels: 51
0.75 0.14 0.11
Matches are distributed among these distances:
111 2 0.01
112 36 0.10
113 123 0.35
114 126 0.35
115 38 0.11
116 31 0.09
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (112 bp):
AGCGCCGCAAAAGATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTGCAATTAGTGGCG
CTTATGAAAAACGCCGCTAATGTATAGTATTAGCGGCGCTTAGCGGA
Found at i:20689588 original size:112 final size:112
Alignment explanation
Indices: 20689402--20689692 Score: 281
Period size: 113 Copynumber: 2.6 Consensus size: 112
20689392 GAGCGTTAAA
* * * * * *
20689402 CGCCGCAAGATATCTTAATCAAAACGCACCGTTTTGGTCTTGATGTATACTATAATTAGTGGCGT
1 CGCCCCAA-ATATCTTAACCAAAACGCAGCG-TTTGGTCTTGAGGTATACTAGAATTAGTGGCGC
*
20689467 TTAAGG-AAAACGCCAG-T-AAGGATAGTTA-TAGCAGCGTTTTGTGGTAA-G
64 TTAAGGAAAAACGCC-GCTAAAGGATA-TCATTAGCAGCG-TTTGT-GTAACG
* *
20689515 CGCCTCCAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGG-ATTATTAGAATTAGTGGCGC
1 CGCC-CCAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTA-TACTAGAATTAGTGGCGC
* * * *
20689579 TTGATGAAAAACGCCGCTAAAGTATATCATTAGCGGCGTTTGTGTAACG
64 TTAAGGAAAAACGCCGCTAAAGGATATCATTAGCAGCGTTTGTGTAACG
* * * *
20689628 CGCCGCAAAGTATCTTAACCAAAACACAGCGTTTAGTTCTTGATGTATACT-GTAATTAGTGGCG
1 CGCCCCAAA-TATCTTAACCAAAACGCAGCGTTT-GGTCTTGAGGTATACTAG-AATTAGTGGCG
20689692 C
63 C
20689693 ACATGGGAAA
Statistics
Matches: 148, Mismatches: 19, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
111 1 0.01
112 40 0.27
113 67 0.45
114 39 0.26
115 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (112 bp):
CGCCCCAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCTT
AAGGAAAAACGCCGCTAAAGGATATCATTAGCAGCGTTTGTGTAACG
Found at i:20690342 original size:81 final size:82
Alignment explanation
Indices: 20690246--20690397 Score: 184
Period size: 81 Copynumber: 1.9 Consensus size: 82
20690236 GGATTCGGTG
* * * * * *
20690246 TCAGGTTAGGTTTTA-GCATTTAGATTAATTAGTGTGTTTTAATTT-T-TATAAAATATGGTTTA
1 TCAGGTTACGATTTAGGC-TTTAGATTAATTAATATGTTTTAATTTATGTATAAAACAAGGTTT-
20690308 AGGGTTAGGGGTTAGGGAT
64 AGGGTTAGGGGTTAGGGAT
* * *
20690327 TCAGGTTACGATTTAGGCTTTTGATTAATTAATATTTTTTAATTTATGTATTAAACAAGGTTTAG
1 TCAGGTTACGATTTAGGCTTTAGATTAATTAATATGTTTTAATTTATGTATAAAACAAGGTTTAG
20690392 GGTTAG
66 GGTTAG
20690398 TACAAGTTAG
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
81 36 0.61
82 11 0.19
83 12 0.20
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.45
Consensus pattern (82 bp):
TCAGGTTACGATTTAGGCTTTAGATTAATTAATATGTTTTAATTTATGTATAAAACAAGGTTTAG
GGTTAGGGGTTAGGGAT
Found at i:20692983 original size:13 final size:12
Alignment explanation
Indices: 20692957--20693005 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
20692947 TTTTTACTAA
*
20692957 AATTAACTTGAAT
1 AATT-ACTTAAAT
20692970 ATATTACTTAAAT
1 A-ATTACTTAAAT
20692983 AATTTACTTAAAT
1 AA-TTACTTAAAT
20692996 ACATTACTTA
1 A-ATTACTTA
20693006 CTAAAATGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 1 0.03
13 27 0.84
14 4 0.12
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (12 bp):
AATTACTTAAAT
Found at i:20693274 original size:16 final size:16
Alignment explanation
Indices: 20693253--20693454 Score: 64
Period size: 16 Copynumber: 12.1 Consensus size: 16
20693243 ACACTTATAA
20693253 AACTTACATAATACAT
1 AACTTACATAATACAT
*
20693269 AACTTACAT-GT---T
1 AACTTACATAATACAT
20693281 AACTTACATAATACAT
1 AACTTACATAATACAT
* * *
20693297 GACTTATATAAAATTCTCAAAT
1 AACTTACAT--AA---T-ACAT
20693319 AAACTTACATAATACAT
1 -AACTTACATAATACAT
* *
20693336 TAGTTACATAATAACTTATAT
1 AACTTACATAAT-AC----AT
20693357 AAGCTTACATAATACA-
1 AA-CTTACATAATACAT
*
20693373 CA-TTAC-T--TACAT
1 AACTTACATAATACAT
* * *
20693385 AGCATACATAACTTACAC
1 AACTTACATAA--TACAT
*
20693403 AACTT-CAATAATACAA
1 AACTTAC-ATAATACAT
20693419 AACTTACATAACTTACAT
1 AACTTACATAA--TACAT
*
20693437 AACCTACATAATACAT
1 AACTTACATAATACAT
20693453 AA
1 AA
20693455 TAACTTACAA
Statistics
Matches: 136, Mismatches: 22, Indels: 56
0.64 0.10 0.26
Matches are distributed among these distances:
11 4 0.03
12 10 0.07
13 5 0.04
14 5 0.04
15 1 0.01
16 48 0.35
17 8 0.06
18 28 0.21
21 8 0.06
22 12 0.09
23 7 0.05
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:20693401 original size:9 final size:9
Alignment explanation
Indices: 20693346--20693583 Score: 146
Period size: 9 Copynumber: 27.4 Consensus size: 9
20693336 TAGTTACATA
*
20693346 ATAACTTAT
1 ATAACTTAC
20693355 ATAAGCTTAC
1 ATAA-CTTAC
*
20693365 ATAA-TACAC
1 ATAACT-TAC
*
20693374 ATTACTTAC
1 ATAACTTAC
* *
20693383 ATAGCATAC
1 ATAACTTAC
20693392 ATAACTTAC
1 ATAACTTAC
*
20693401 ACAACTT-C
1 ATAACTTAC
20693409 AATAA--TAC
1 -ATAACTTAC
*
20693417 AAAACTTAC
1 ATAACTTAC
20693426 ATAACTTAC
1 ATAACTTAC
*
20693435 ATAACCTAC
1 ATAACTTAC
*
20693444 ATAATACATA-
1 AT-A-ACTTAC
20693454 ATAACTTAC
1 ATAACTTAC
20693463 --AACTTAC
1 ATAACTTAC
20693470 --AACTTAC
1 ATAACTTAC
*
20693477 ATAACATAC
1 ATAACTTAC
* **
20693486 ATTACTTTG
1 ATAACTTAC
20693495 ATAACTTAC
1 ATAACTTAC
20693504 ATAACTTAC
1 ATAACTTAC
20693513 AT-AC-TAC
1 ATAACTTAC
* *
20693520 ACAACTTAA
1 ATAACTTAC
* *
20693529 ATAGCCTAC
1 ATAACTTAC
*
20693538 TTAA--TAC
1 ATAACTTAC
20693545 ATAACTTAC
1 ATAACTTAC
20693554 ATAACTT--
1 ATAACTTAC
*
20693561 ATACACGTAC
1 ATA-ACTTAC
20693571 ATAACTTAC
1 ATAACTTAC
20693580 ATAA
1 ATAA
20693584 TTGACTTAAT
Statistics
Matches: 175, Mismatches: 35, Indels: 38
0.71 0.14 0.15
Matches are distributed among these distances:
7 31 0.18
8 14 0.08
9 111 0.63
10 15 0.09
11 4 0.02
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (9 bp):
ATAACTTAC
Found at i:20693448 original size:34 final size:34
Alignment explanation
Indices: 20693389--20693527 Score: 99
Period size: 34 Copynumber: 4.1 Consensus size: 34
20693379 TTACATAGCA
* *
20693389 TACATAACTTACACAA-CTTCAATAATACAAAACT
1 TACATAACTTACATAACCTAC-ATAATACAAAACT
20693423 TACATAACTTACATAACCTACATAATACATAATAACT
1 TACATAACTTACATAACCTACATAATAC--AA-AACT
* **
20693460 TAC--AACTTAC--AACTTACATAACATACATTACT
1 TACATAACTTACATAACCTACAT-A-ATACAAAACT
** * * *
20693492 TTGATAACTTACATAACTTACATACTACACAACT
1 TACATAACTTACATAACCTACATAATACAAAACT
20693526 TA
1 TA
20693528 AATAGCCTAC
Statistics
Matches: 84, Mismatches: 11, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
32 4 0.05
33 9 0.11
34 38 0.45
35 15 0.18
36 11 0.13
37 7 0.08
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30
Consensus pattern (34 bp):
TACATAACTTACATAACCTACATAATACAAAACT
Found at i:20693501 original size:94 final size:93
Alignment explanation
Indices: 20693377--20693548 Score: 204
Period size: 94 Copynumber: 1.8 Consensus size: 93
20693367 AATACACATT
* * *
20693377 ACTTACATAGCATACATAACTTACACAACTT-CAATAA-TACAAAACTTACATAACTTACATAAC
1 ACTTACATAACATACATAACTTACACAACTTAC-ATAACTAC-AAAC-TACACAACTTAAATAAC
20693440 CTACATAATACATAATAACTTACAACTTACA
63 CTACATAATACATAATAACTTACAACTTACA
* ** * * *
20693471 ACTTACATAACATACATTACTTTGATAACTTACATAACTTACATACTACACAACTTAAATAGCCT
1 ACTTACATAACATACATAACTTACACAACTTACATAAC-TACAAACTACACAACTTAAATAACCT
*
20693536 ACTTAATACATAA
65 ACATAATACATAA
20693549 CTTACATAAC
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
94 58 0.89
95 4 0.06
96 3 0.05
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.30
Consensus pattern (93 bp):
ACTTACATAACATACATAACTTACACAACTTACATAACTACAAACTACACAACTTAAATAACCTA
CATAATACATAATAACTTACAACTTACA
Found at i:20693597 original size:51 final size:50
Alignment explanation
Indices: 20693495--20693599 Score: 131
Period size: 51 Copynumber: 2.1 Consensus size: 50
20693485 CATTACTTTG
* *
20693495 ATAACTTACATAACTTACATACTACACAACTTAAATAGCCTACTTAATAC
1 ATAACTTACATAACTTACACACTACACAACTTAAATAGACTACTTAATAC
* * * *
20693545 ATAACTTACATAACTTATACACGTACATAACTTACATA-ATTGACTTAATAC
1 ATAACTTACATAACTTACACAC-TACACAACTTAAATAGACT-ACTTAATAC
20693596 ATAA
1 ATAA
20693600 ATATATATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
50 21 0.45
51 26 0.55
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.31
Consensus pattern (50 bp):
ATAACTTACATAACTTACACACTACACAACTTAAATAGACTACTTAATAC
Found at i:20699114 original size:42 final size:42
Alignment explanation
Indices: 20699067--20699311 Score: 402
Period size: 42 Copynumber: 5.8 Consensus size: 42
20699057 TGTATAAAAA
* *
20699067 CGCCGCTAAAGAACATGATCTTTAGCGGCCTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* *
20699109 CGCCGCTAAAGAACATGTTCTTTAGCGTCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
20699151 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTT-TAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* * *
20699192 CACCGCTAAAGAACATGGTCTTTAGAGGCATTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGC-GTTTTTTTCTAAG
20699235 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
20699277 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
20699312 GTTTGTAAAC
Statistics
Matches: 190, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
41 30 0.16
42 129 0.68
43 31 0.16
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:20699383 original size:22 final size:22
Alignment explanation
Indices: 20699352--20699396 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
20699342 TTTCGTTAGT
* *
20699352 GGCCTTAAAAAGCGCCGCTAAA
1 GGCCTAAAAAAACGCCGCTAAA
20699374 GGCCTAAAAAAACGCCGCTAAA
1 GGCCTAAAAAAACGCCGCTAAA
20699396 G
1 G
20699397 ACCTGTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.27, G:0.22, T:0.11
Consensus pattern (22 bp):
GGCCTAAAAAAACGCCGCTAAA
Found at i:20699560 original size:49 final size:47
Alignment explanation
Indices: 20699463--20699652 Score: 292
Period size: 47 Copynumber: 4.0 Consensus size: 47
20699453 ATTTCCATTT
*
20699463 TCATTTCATTTAAATTATCTTTTTTT-CATTTAAATTTAACTTTTTTC
1 TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTT-ATTTTTTTC
*
20699510 TCATTTCGTTTAAATTATCTTTTTTTCCATTTAAATTTAATTTTTTTTC
1 TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTT-A-TTTTTTTC
*
20699559 TCATTTCATTTAAATTATCTTTTTTTTCATTTAAATTTATTTTTTTC
1 TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTATTTTTTTC
* *
20699606 TCATTTCATTTAAATTATCTTTCTTTCCATTTTAATTTATGTTTTTT
1 TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAT-TTTTTT
20699653 TTTCATATTA
Statistics
Matches: 133, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
47 70 0.53
48 20 0.15
49 43 0.32
ACGTcount: A:0.23, C:0.12, G:0.01, T:0.64
Consensus pattern (47 bp):
TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTATTTTTTTC
Found at i:20699603 original size:96 final size:96
Alignment explanation
Indices: 20699463--20699658 Score: 315
Period size: 96 Copynumber: 2.0 Consensus size: 96
20699453 ATTTCCATTT
*
20699463 TCATTTCATTTAAATTATCTTTTTTTCATTTAAATTTAACTTTTTTCTCATTTCGTTTAAATTAT
1 TCATTTCATTTAAATTATCTTTTTTTCATTTAAATTTAACTTTTTTCTCATTTCATTTAAATTAT
*
20699528 CTTTTTTTCCATTTAAATTTAAT-TTTTTTTC
66 CTTTCTTTCCATTTAAATTT-ATGTTTTTTTC
*
20699559 TCATTTCATTTAAATTATCTTTTTTTTCATTTAAATTT-ATTTTTTTCTCATTTCATTTAAATTA
1 TCATTTCATTTAAATTATC-TTTTTTTCATTTAAATTTAACTTTTTTCTCATTTCATTTAAATTA
* *
20699623 TCTTTCTTTCCATTTTAATTTATGTTTTTTTT
65 TCTTTCTTTCCATTTAAATTTATGTTTTTTTC
20699655 TCAT
1 TCAT
20699659 ATTAATTTTT
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
95 2 0.02
96 73 0.78
97 18 0.19
ACGTcount: A:0.23, C:0.12, G:0.01, T:0.64
Consensus pattern (96 bp):
TCATTTCATTTAAATTATCTTTTTTTCATTTAAATTTAACTTTTTTCTCATTTCATTTAAATTAT
CTTTCTTTCCATTTAAATTTATGTTTTTTTC
Found at i:20699637 original size:21 final size:21
Alignment explanation
Indices: 20699461--20699642 Score: 107
Period size: 21 Copynumber: 7.9 Consensus size: 21
20699451 TCATTTCCAT
*
20699461 TTTCATTTCATTTAAATTATC
1 TTTCTTTTCATTTAAATTATC
*
20699482 TTT-TTTTCATTTAAATTTAACTTT
1 TTTCTTTTCATTTAAA-TT-A--TC
*
20699506 TTTCTCATTTCGTTTAAATTATC
1 TTTCT--TTTCATTTAAATTATC
*
20699529 TTT-TTTTCCATTTAAATTTAATTTTT
1 TTTCTTTT-CATTTAAA-TT-A---TC
20699555 TTTCTCATTTCATTTAAATTATC
1 TTTCT--TTTCATTTAAATTATC
* *
20699578 TTTTTTTTCATTTAAATTTATTTT
1 TTTCTTTTCATTTAAA-TTA--TC
20699602 TTTCTCATTTCATTTAAATTATC
1 TTTCT--TTTCATTTAAATTATC
* *
20699625 TTTCTTTCCATTTTAATT
1 TTTCTTTTCATTTAAATT
20699643 TATGTTTTTT
Statistics
Matches: 127, Mismatches: 13, Indels: 42
0.70 0.07 0.23
Matches are distributed among these distances:
20 14 0.11
21 34 0.27
22 7 0.06
23 16 0.13
24 9 0.07
25 5 0.04
26 18 0.14
27 13 0.10
28 8 0.06
29 3 0.02
ACGTcount: A:0.24, C:0.13, G:0.01, T:0.63
Consensus pattern (21 bp):
TTTCTTTTCATTTAAATTATC
Found at i:20699926 original size:44 final size:44
Alignment explanation
Indices: 20699689--20699928 Score: 354
Period size: 44 Copynumber: 5.5 Consensus size: 44
20699679 AATTTATTTC
* * * *
20699689 ATTTAATGTGTTTTAAGTTAAATATGTAAGTCTGTTGTATTATA
1 ATTTAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATA
*
20699733 ATTTAATGTGTTTTAAAGTAAATATGTATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATA
* *
20699777 GTTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATA
* * *
20699821 GTTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTTTA
1 ATTTAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATA
* *
20699865 ATTTAATGTGCTTTAAATTAAATATGCATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATA
* *
20699909 ATTTAACGTATTTTAAATTA
1 ATTTAATGTGTTTTAAATTA
20699929 GGAACAAGAA
Statistics
Matches: 180, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 180 1.00
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (44 bp):
ATTTAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATA
Found at i:20703374 original size:46 final size:44
Alignment explanation
Indices: 20703323--20703453 Score: 126
Period size: 45 Copynumber: 2.9 Consensus size: 44
20703313 TTTTGACATA
*
20703323 TAGTATTATTTAATATTTAAGCT-TAAC-ATTGTTTTAAATTTATCAT
1 TAGTATTATTTAATATTTAA--TAT-ACTATTATTTTAAA-TTATCAT
*
20703369 TAGTATTATTTTAATATTTAATATACTATTATTTTAAATTATTAT
1 TAGTATTA-TTTAATATTTAATATACTATTATTTTAAATTATCAT
* *
20703414 TAATATTATTTAA-ATTTATCATATA-TCAATATTTTAAATT
1 TAGTATTATTTAATATTTA--ATATACT-ATTATTTTAAATT
20703454 CATTATGTAC
Statistics
Matches: 75, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
43 5 0.07
44 6 0.08
45 33 0.44
46 19 0.25
47 12 0.16
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (44 bp):
TAGTATTATTTAATATTTAATATACTATTATTTTAAATTATCAT
Found at i:20703380 original size:23 final size:23
Alignment explanation
Indices: 20703354--20703453 Score: 95
Period size: 23 Copynumber: 4.4 Consensus size: 23
20703344 CTTAACATTG
20703354 TTTTAAATTTATCAT-TAGTATTA
1 TTTTAAATTTATCATATA-TATTA
20703377 TTTTAATATTTA--ATATACTATTA
1 TTTTAA-ATTTATCATATA-TATTA
*
20703400 TTTTAAA-TTATTAT-TAATATTA
1 TTTTAAATTTATCATAT-ATATTA
*
20703422 -TTTAAATTTATCATATATCAATA
1 TTTTAAATTTATCATATAT-ATTA
20703445 TTTTAAATT
1 TTTTAAATT
20703454 CATTATGTAC
Statistics
Matches: 65, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
21 9 0.14
22 17 0.26
23 26 0.40
24 13 0.20
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (23 bp):
TTTTAAATTTATCATATATATTA
Found at i:20703432 original size:22 final size:23
Alignment explanation
Indices: 20703345--20703459 Score: 94
Period size: 23 Copynumber: 5.0 Consensus size: 23
20703335 ATATTTAAGC
* * *
20703345 TTAACATTGTTTTAAATTTATCA
1 TTAATATTATTTTAAATTTATTA
* *
20703368 TTAGTATTATTTTAATATTTAATA
1 TTAATATTATTTTAA-ATTTATTA
*
20703392 -TACTATTATTTTAAA-TTATTA
1 TTAATATTATTTTAAATTTATTA
*
20703413 TTAATATTA-TTTAAATTTATCA
1 TTAATATTATTTTAAATTTATTA
* *
20703435 -TATATCAATATTTTAAATTCATTA
1 TTA-AT-ATTATTTTAAATTTATTA
20703459 T
1 T
20703460 GTACTATTTT
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
21 13 0.18
22 15 0.21
23 28 0.38
24 17 0.23
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (23 bp):
TTAATATTATTTTAAATTTATTA
Found at i:20703438 original size:45 final size:43
Alignment explanation
Indices: 20703354--20703473 Score: 118
Period size: 45 Copynumber: 2.7 Consensus size: 43
20703344 CTTAACATTG
* * *
20703354 TTTTAAATTTATCATTAGTATTATTTTAATATTTAATATA-CTATTA
1 TTTTAAA-TTATTATTAATATTA-TTTAA-ATTTAATATATC-AATA
20703400 TTTTAAATTATTATTAATATTATTTAAATTTATCATATATCAATA
1 TTTTAAATTATTATTAATATTATTTAAATTTA--ATATATCAATA
*
20703445 TTTTAAATTCATTATGTACTATT-TTTAAA
1 TTTTAAATT-ATTAT-TAATATTATTTAAA
20703474 AAAAAACTTA
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
43 5 0.08
44 5 0.08
45 30 0.46
46 19 0.29
47 6 0.09
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (43 bp):
TTTTAAATTATTATTAATATTATTTAAATTTAATATATCAATA
Found at i:20703473 original size:22 final size:20
Alignment explanation
Indices: 20703400--20703473 Score: 58
Period size: 24 Copynumber: 3.4 Consensus size: 20
20703390 TATACTATTA
*
20703400 TTTTAAATTATTATTAATAT
1 TTTTAAATTATTATTACTAT
* *
20703420 TATTTAAATTTATCATATATCAAT
1 T-TTTAAA-TTATTAT-TA-CTAT
20703444 ATTTTAAATTCATTATGTACTAT
1 -TTTTAAATT-ATTAT-TACTAT
20703467 TTTTAAA
1 TTTTAAA
20703474 AAAAAACTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
20 1 0.02
21 6 0.14
22 13 0.31
23 7 0.17
24 14 0.33
25 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.54
Consensus pattern (20 bp):
TTTTAAATTATTATTACTAT
Found at i:20703900 original size:14 final size:14
Alignment explanation
Indices: 20703865--20703901 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
20703855 TCGATCTTTT
20703865 TATATATA-TA-TA
1 TATATATATTAGTA
20703877 TATATATATTAGTA
1 TATATATATTAGTA
*
20703891 TATATGTATTA
1 TATATATATTA
20703902 TTACTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.36
13 2 0.09
14 12 0.55
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
TATATATATTAGTA
Found at i:20705208 original size:12 final size:12
Alignment explanation
Indices: 20705177--20705202 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20705167 TTCAACTAAT
20705177 AAAGCAAACAAA
1 AAAGCAAACAAA
20705189 AAAGCAAACAAA
1 AAAGCAAACAAA
20705201 AA
1 AA
20705203 CTCAAATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAGCAAACAAA
Found at i:20705448 original size:56 final size:56
Alignment explanation
Indices: 20705344--20705458 Score: 148
Period size: 55 Copynumber: 2.1 Consensus size: 56
20705334 TTAATGTGAT
20705344 AAAGTAGGTGTCGACCATCGATGTCCCAAAACAAAAAAACAATTTCGGGACCCGAA
1 AAAGTAGGTGTCGACCATCGATGTCCCAAAACAAAAAAACAATTTCGGGACCCGAA
**
20705400 AAAGTA-GTGTC-AGCCATC-AGTGTCCCAAAGTAAAAAAA-AATTCCTCGGGACCCGAA
1 AAAGTAGGTGTCGA-CCATCGA-TGTCCCAAAACAAAAAAACAATT--TCGGGACCCGAA
20705456 AAA
1 AAA
20705459 TGTACTTGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
54 6 0.11
55 26 0.49
56 21 0.40
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (56 bp):
AAAGTAGGTGTCGACCATCGATGTCCCAAAACAAAAAAACAATTTCGGGACCCGAA
Found at i:20712756 original size:19 final size:20
Alignment explanation
Indices: 20712711--20712763 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
20712701 CATATACGAA
*
20712711 ATATAAATTTTAATTTAAAT
1 ATATAAATTATAATTTAAAT
* *
20712731 ATATAAATTATATTTTAAGT
1 ATATAAATTATAATTTAAAT
*
20712751 AT-TAAAATATAAT
1 ATATAAATTATAAT
20712764 AATTACAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATAAATTATAATTTAAAT
Found at i:20713185 original size:31 final size:32
Alignment explanation
Indices: 20713147--20713213 Score: 102
Period size: 31 Copynumber: 2.1 Consensus size: 32
20713137 CTTTAAATCC
20713147 ATACATTTGAA-TCAAAATCAAAATTT-TATGT
1 ATACATTTGAACT-AAAATCAAAATTTATATGT
20713178 ATACATTTGAACTAAAATCAAAATTTAATATGT
1 ATACATTTGAACTAAAATCAAAATTT-ATATGT
20713211 ATA
1 ATA
20713214 ATTGCAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 24 0.73
32 1 0.03
33 8 0.24
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (32 bp):
ATACATTTGAACTAAAATCAAAATTTATATGT
Found at i:20716848 original size:15 final size:15
Alignment explanation
Indices: 20716822--20716877 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
20716812 AAGTTCAAAT
20716822 TTTTTAAA--TTTAA
1 TTTTTAAATTTTTAA
*
20716835 TTTTTATATTTTT-A
1 TTTTTAAATTTTTAA
*
20716849 TTTTTAAGAATTTTTAT
1 TTTTT-A-AATTTTTAA
20716866 TTTTTAAATTTT
1 TTTTTAAATTTT
20716878 AACAACTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
13 7 0.20
14 6 0.17
15 10 0.29
16 7 0.20
17 5 0.14
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTTTAAATTTTTAA
Found at i:20716877 original size:24 final size:24
Alignment explanation
Indices: 20716833--20716879 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
20716823 TTTTAAATTT
*
20716833 AATTTTTATATTTTTATTTTTAAG
1 AATTTTTATATTTTTAATTTTAAG
20716857 AATTTTTAT-TTTTTAAATTTTAA
1 AATTTTTATATTTTT-AATTTTAA
20716880 CAACTAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
AATTTTTATATTTTTAATTTTAAG
Found at i:20722267 original size:15 final size:15
Alignment explanation
Indices: 20722247--20722298 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
20722237 AATAATTAGT
20722247 AAAAATTATAAATTA
1 AAAAATTATAAATTA
*
20722262 AAAAATTATTAA--A
1 AAAAATTATAAATTA
*
20722275 AAAAAGTATAAATTA
1 AAAAATTATAAATTA
*
20722290 TAAAATTAT
1 AAAAATTAT
20722299 TAATACTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 11 0.37
15 19 0.63
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
AAAAATTATAAATTA
Found at i:20722284 original size:28 final size:28
Alignment explanation
Indices: 20722247--20722301 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
20722237 AATAATTAGT
*
20722247 AAAAATTATAAATTAAAAAATTATTAAA
1 AAAAAGTATAAATTAAAAAATTATTAAA
*
20722275 AAAAAGTATAAATTATAAAATTATTAA
1 AAAAAGTATAAATTAAAAAATTATTAA
20722302 TACTTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (28 bp):
AAAAAGTATAAATTAAAAAATTATTAAA
Found at i:20724546 original size:18 final size:17
Alignment explanation
Indices: 20724523--20724557 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
20724513 TGTGTGAACT
20724523 AATTAATTAATTAAATTA
1 AATTAATT-ATTAAATTA
20724541 AATTAATTATTAAATTA
1 AATTAATTATTAAATTA
20724558 GTACTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAATTATTAAATTA
Found at i:20731755 original size:95 final size:99
Alignment explanation
Indices: 20731546--20731777 Score: 339
Period size: 95 Copynumber: 2.4 Consensus size: 99
20731536 AATAAAGTAA
*
20731546 TGGCGCTATTTAGAATGACTCCACCAAATAAAATATTATTTTTTAAAAAATTTTAAATATAAAAA
1 TGGCGCCATTTAGAATGACTCCACCAAATAAAATATTATTTTTTAAAAAATTTTAAATATAAAAA
**
20731611 AATAGATTTTTTTTAAAAAGTCTTAAAATGAATTGG
66 AATAGA--TTTTAAAAAAAGTCTTAAAATGAATTGG
* *
20731647 TGACGCCATTTAGAATGGCTCCACCAAATAAAATATTA-TTTTT-AAAAATTTTAAATAT-AAAA
1 TGGCGCCATTTAGAATGACTCCACCAAATAAAATATTATTTTTTAAAAAATTTTAAATATAAAAA
20731709 AATAGA-TTTAAAAAAAGTCTTAAAATGAATTGG
66 AATAGATTTTAAAAAAAGTCTTAAAATGAATTGG
* *
20731742 TGGCGCCATTTAGAATAACTCTACCAAA-AAGAATAT
1 TGGCGCCATTTAGAATGACTCCACCAAATAA-AATAT
20731778 ACATTTAAAA
Statistics
Matches: 121, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
94 2 0.02
95 54 0.45
98 10 0.08
99 15 0.12
100 5 0.04
101 35 0.29
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (99 bp):
TGGCGCCATTTAGAATGACTCCACCAAATAAAATATTATTTTTTAAAAAATTTTAAATATAAAAA
AATAGATTTTAAAAAAAGTCTTAAAATGAATTGG
Found at i:20737009 original size:22 final size:22
Alignment explanation
Indices: 20736980--20737071 Score: 87
Period size: 22 Copynumber: 4.0 Consensus size: 22
20736970 TGCACTAATG
20736980 AACAGAGAGCACTGAAGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
* * * *
20737002 TACAGAGAGTACAGATGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
*
20737024 AACAGAGAGCACTGACGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
*
20737046 GTAATCAAAGAGCACT-AACGTGCTA
1 --AA-CAGAGAGCACTGAA-GTGCTA
20737071 A
1 A
20737072 TAATGAGAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
22 36 0.64
23 1 0.02
24 3 0.05
25 16 0.29
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (22 bp):
AACAGAGAGCACTGAAGTGCTA
Found at i:20737059 original size:25 final size:25
Alignment explanation
Indices: 20737026--20737107 Score: 119
Period size: 25 Copynumber: 3.3 Consensus size: 25
20737016 ATGTGCTAAA
* *
20737026 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACTAACGTGCTAATAAT
*
20737051 CAAAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCTAATAAT
* *
20737076 GAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCTAATAAT
20737101 CAGAGAG
1 CAGAGAG
20737108 TGCGCTAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (25 bp):
CAGAGAGCACTAACGTGCTAATAAT
Found at i:20738060 original size:5 final size:5
Alignment explanation
Indices: 20738052--20738094 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
20738042 CTTTTTCTTT
20738052 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT
20738095 TTATACTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:20746817 original size:24 final size:24
Alignment explanation
Indices: 20746790--20746841 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
20746780 TTAGTAAGTC
*
20746790 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
20746814 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
20746838 AAAT
1 AAAT
20746842 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:20757093 original size:16 final size:16
Alignment explanation
Indices: 20757068--20757101 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20757058 AACATATTAT
*
20757068 ATTATTAATTAATAAA
1 ATTATAAATTAATAAA
*
20757084 ATTATAAATTTATAAA
1 ATTATAAATTAATAAA
20757100 AT
1 AT
20757102 CATTGAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTATAAATTAATAAA
Found at i:20758641 original size:29 final size:29
Alignment explanation
Indices: 20758609--20758674 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
20758599 ACCAATAAAA
20758609 GCCGTTTTTTTCAAAATTTACCGAAATGG
1 GCCGTTTTTTTCAAAATTTACCGAAATGG
* * ** *
20758638 GCCGATTTTTTGATTATTTACCGGAATGG
1 GCCGTTTTTTTCAAAATTTACCGAAATGG
*
20758667 GCCATTTT
1 GCCGTTTT
20758675 CCGTGAAATC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.41
Consensus pattern (29 bp):
GCCGTTTTTTTCAAAATTTACCGAAATGG
Found at i:20760484 original size:54 final size:54
Alignment explanation
Indices: 20760402--20760507 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
20760392 ACCAAACCCT
* *
20760402 TATATTACTCGTTTTGGTCCATCTATTGTGTTAAATATTGAGATTTAATGGATC
1 TATATTACTCATTTTGATCCATCTATTGTGTTAAATATTGAGATTTAATGGATC
* *
20760456 TATATTACTCATTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAATGGA
1 TATATTACTCATTTTGATCCATCTATTGTGTTAAATATTGAGATTTAATGGA
20760508 GCAATTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.48
Consensus pattern (54 bp):
TATATTACTCATTTTGATCCATCTATTGTGTTAAATATTGAGATTTAATGGATC
Found at i:20760524 original size:128 final size:124
Alignment explanation
Indices: 20760298--20760578 Score: 402
Period size: 128 Copynumber: 2.2 Consensus size: 124
20760288 TTGATATATT
* *
20760298 TATTGTGTTAAATATTGAGATTTAATGGATCCATATTACTCGATTGATTTATCTATTTTGTTAAA
1 TATTGTGTTAAATATTGAGATTTAATGGATCCATATTACTCGATTGATCTATCTATTGTGTTAAA
* * **
20760363 ATTTGAGATTTAATGGAGCAATTAAATTAACCAAACCCTTATATTACTCGTTTTGGTCCATC
66 ATTTGAGATTTAATGGAGCAATTAAATCAACCAAACCC-CA-A-TACTCGTTTTCATCCATC
*
20760425 TATTGTGTTAAATATTGAGATTTAATGGATCTATATTACTC-ATTTTGATCTATCTATTGTGTTA
1 TATTGTGTTAAATATTGAGATTTAATGGATCCATATTACTCGA--TTGATCTATCTATTGTGTTA
* * *
20760489 AATTTTGAGATTTAATGGAGCAATTAAATCCACCAAACCCCAATACTCGTTTTCATCTATC
64 AAATTTGAGATTTAATGGAGCAATTAAATCAACCAAACCCCAATACTCGTTTTCATCCATC
* *
20760550 TATTGTGTTAAATTTTGAGATTTTATGGA
1 TATTGTGTTAAATATTGAGATTTAATGGA
20760579 GCGGTTAAAT
Statistics
Matches: 140, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
125 42 0.30
126 2 0.01
127 41 0.29
128 55 0.39
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (124 bp):
TATTGTGTTAAATATTGAGATTTAATGGATCCATATTACTCGATTGATCTATCTATTGTGTTAAA
ATTTGAGATTTAATGGAGCAATTAAATCAACCAAACCCCAATACTCGTTTTCATCCATC
Found at i:20760643 original size:76 final size:72
Alignment explanation
Indices: 20760458--20760651 Score: 273
Period size: 71 Copynumber: 2.7 Consensus size: 72
20760448 AATGGATCTA
* *
20760458 TATTACTCATTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAATGGAGCAATTAAATCCACC
1 TATTACTCGTTTTCATCTATCTATTGTGTTAAATTTTGAGATTTAATGGAGCAATTAAATCCACC
20760523 AAACCCC
66 AAACCCC
* * **
20760530 -AATACTCGTTTTCATCTATCTATTGTGTTAAATTTTGAGATTTTATGGAGCGGTTAAATCCACC
1 TATTACTCGTTTTCATCTATCTATTGTGTTAAATTTTGAGATTTAATGGAGCAATTAAATCCACC
20760594 AAACCCCGCC
66 AAA--CC-CC
* *
20760604 GTATTACTCGTTTTCATCTATCTAATGTGTTGAATTTTGAGATTTAAT
1 -TATTACTCGTTTTCATCTATCTATTGTGTTAAATTTTGAGATTTAAT
20760652 TTTTAAGTAT
Statistics
Matches: 107, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
71 61 0.57
73 2 0.02
74 2 0.02
76 42 0.39
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (72 bp):
TATTACTCGTTTTCATCTATCTATTGTGTTAAATTTTGAGATTTAATGGAGCAATTAAATCCACC
AAACCCC
Found at i:20763956 original size:20 final size:19
Alignment explanation
Indices: 20763924--20763995 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
20763914 TCCCTCTAAA
20763924 AAAAAGATT-AAAATAATATT
1 AAAAA-ATTCAAAATAATA-T
* **
20763944 TAAAAATTCAAAATTTTAT
1 AAAAAATTCAAAATAATAT
**
20763963 AAAAAATTCAAAATTTTAT
1 AAAAAATTCAAAATAATAT
20763982 AAAAAATTCTAAAA
1 AAAAAATTC-AAAA
20763996 ATTTATAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 31 0.67
20 15 0.33
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (19 bp):
AAAAAATTCAAAATAATAT
Done.