Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 171 of 204
Found at i:51171936 original size:23 final size:25
Alignment explanation
Indices: 51171888--51171935 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
51171878 AGTTGTAAAG
51171888 AGAAAATTATCTAAAGAGATTATTTT
1 AGAAAATTATCT-AAGAGATTATTTT
51171914 AGAAAATT-TCT-AGAGA-TATTTT
1 AGAAAATTATCTAAGAGATTATTTT
51171936 TCTTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
25 3 0.14
26 8 0.36
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (25 bp):
AGAAAATTATCTAAGAGATTATTTT
Found at i:51173571 original size:40 final size:40
Alignment explanation
Indices: 51173527--51173635 Score: 209
Period size: 40 Copynumber: 2.7 Consensus size: 40
51173517 CATCAATATT
*
51173527 AAACATTTATACATTATATCATGATATTAATGAACCTATG
1 AAACATTTATACATTATATCATGACATTAATGAACCTATG
51173567 AAACATTTATACATTATATCATGACATTAATGAACCTATG
1 AAACATTTATACATTATATCATGACATTAATGAACCTATG
51173607 AAACATTTATACATTATATCATGACATTA
1 AAACATTTATACATTATATCATGACATTA
51173636 TATCATGACA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (40 bp):
AAACATTTATACATTATATCATGACATTAATGAACCTATG
Found at i:51173635 original size:13 final size:13
Alignment explanation
Indices: 51173617--51173648 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
51173607 AAACATTTAT
51173617 ACATTATATCATG
1 ACATTATATCATG
51173630 ACATTATATCATG
1 ACATTATATCATG
51173643 ACATTA
1 ACATTA
51173649 AATAACCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.38
Consensus pattern (13 bp):
ACATTATATCATG
Found at i:51179319 original size:5 final size:5
Alignment explanation
Indices: 51179309--51179361 Score: 54
Period size: 5 Copynumber: 10.0 Consensus size: 5
51179299 GTCTACCTGC
*
51179309 AAAAT AAAAT AAAAT AGAAAG AAGAA- AAAAT AAAAAT AAAAAT AAAAT
1 AAAAT AAAAT AAAAT A-AAAT AA-AAT AAAAT -AAAAT -AAAAT AAAAT
51179357 AAAAT
1 AAAAT
51179362 GTGTAATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
4 2 0.05
5 24 0.56
6 17 0.40
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:51179351 original size:12 final size:11
Alignment explanation
Indices: 51179309--51179360 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
51179299 GTCTACCTGC
51179309 AAAAT-AAAAT
1 AAAATAAAAAT
* *
51179319 AAAATAGAAAG
1 AAAATAAAAAT
*
51179330 AAGA-AAAAAT
1 AAAATAAAAAT
51179340 AAAAATAAAAAT
1 -AAAATAAAAAT
51179352 AAAATAAAA
1 AAAATAAAA
51179361 TGTGTAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
10 9 0.27
11 18 0.55
12 6 0.18
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:51184239 original size:15 final size:15
Alignment explanation
Indices: 51184219--51184249 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
51184209 CATTGGGATG
51184219 CAATCAATTTATTGT
1 CAATCAATTTATTGT
51184234 CAATCAATTTATTGT
1 CAATCAATTTATTGT
51184249 C
1 C
51184250 TTTTATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.45
Consensus pattern (15 bp):
CAATCAATTTATTGT
Found at i:51189562 original size:61 final size:61
Alignment explanation
Indices: 51189467--51189587 Score: 172
Period size: 61 Copynumber: 2.0 Consensus size: 61
51189457 TTTGGGAAGT
* * * *
51189467 GAAACTAATTGACATACCAACTATCGTTTTGTTTCATTG-TTGGAGGAATTAAGTTAAAAGG
1 GAAACTAATTGACACACCAACTAACGTTTTGTTTCACTGTTTGG-GGAATTAAATTAAAAGG
**
51189528 GAAACTAATTGACACACCAGGTAACGTTTTGTTTCACTGTTTGGGGAATTAAATTAAAAG
1 GAAACTAATTGACACACCAACTAACGTTTTGTTTCACTGTTTGGGGAATTAAATTAAAAG
51189588 AGCAACTTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 49 0.92
62 4 0.08
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (61 bp):
GAAACTAATTGACACACCAACTAACGTTTTGTTTCACTGTTTGGGGAATTAAATTAAAAGG
Found at i:51190622 original size:2 final size:2
Alignment explanation
Indices: 51190617--51190665 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
51190607 TATCCCCCTC
51190617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51190659 TA TA TA T
1 TA TA TA T
51190666 TAAGGGTGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51193812 original size:37 final size:37
Alignment explanation
Indices: 51193722--51193798 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
51193712 TGTAGTGGAT
* *
51193722 ACAAGCTTGAAAATTAAGTCGAATAAAATTAAGTCAA
1 ACAAGCTTGGAAATTAAGTCGAATAAAAATAAGTCAA
51193759 ACAAGCTTGGAAATTAAGTCGAATAAAAATAAGTCAA
1 ACAAGCTTGGAAATTAAGTCGAATAAAAATAAGTCAA
51193796 ACA
1 ACA
51193799 TTTGCTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (37 bp):
ACAAGCTTGGAAATTAAGTCGAATAAAAATAAGTCAA
Found at i:51196584 original size:31 final size:31
Alignment explanation
Indices: 51196543--51196617 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
51196533 CACCGTAAAA
* * *
51196543 ATTTGAAGCAAATAACCCATTTCGGTATTTC
1 ATTTGTAGCAAACAACCCATTTCGGTAATTC
* *
51196574 TTTTGTAGCAAACGACCCATTTCGGTAATTC
1 ATTTGTAGCAAACAACCCATTTCGGTAATTC
*
51196605 ATTTGTACCAAAC
1 ATTTGTAGCAAAC
51196618 GTACCATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (31 bp):
ATTTGTAGCAAACAACCCATTTCGGTAATTC
Found at i:51196618 original size:31 final size:32
Alignment explanation
Indices: 51196557--51196626 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
51196547 GAAGCAAATA
* * *
51196557 ACCCATTTCGGTATTTCTTTTGTAGCAAACG-
1 ACCCATTTCGGTAATTCATTTGTACCAAACGT
51196588 ACCCATTTCGGTAATTCATTTGTACCAAACGT
1 ACCCATTTCGGTAATTCATTTGTACCAAACGT
51196620 A-CCATTT
1 ACCCATTT
51196627 TGATAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (32 bp):
ACCCATTTCGGTAATTCATTTGTACCAAACGT
Found at i:51203656 original size:18 final size:18
Alignment explanation
Indices: 51203633--51203669 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
51203623 CTAAAGCTTT
51203633 ATTTTAATATTTA-TATAC
1 ATTTTAAT-TTTATTATAC
51203651 ATTTTAATTTTATTATAC
1 ATTTTAATTTTATTATAC
51203669 A
1 A
51203670 CACTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAATTTTATTATAC
Found at i:51205606 original size:32 final size:31
Alignment explanation
Indices: 51205552--51205612 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 31
51205542 ATTTTTTGAC
51205552 ATAATTTGATCTTTATACTTTTATAATGTCA
1 ATAATTTGATCTTTATACTTTTATAATGTCA
51205583 ATAATTTGATCTTTATACTTTTTATAATGT
1 ATAATTTGATCTTTATAC-TTTTATAATGT
51205613 TATTAGTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 18 0.62
32 11 0.38
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.54
Consensus pattern (31 bp):
ATAATTTGATCTTTATACTTTTATAATGTCA
Found at i:51215842 original size:76 final size:78
Alignment explanation
Indices: 51215673--51215849 Score: 211
Period size: 76 Copynumber: 2.3 Consensus size: 78
51215663 AATAAGAATA
*
51215673 AAATAAAGGAAAATGCAAAAAAAAGAAGAAGAGAGAGTAGGAAATAAAATGAAGGAAGAAATTGC
1 AAAT-AAGGAAAATGCAAAAAAAAGAAGAAGAGAGAG-AGGAAATAAAATAAAGGAAGAAATTGC
*
51215738 TAAGTATAGGAAATG
64 AAAGTATAGGAAATG
*
51215753 AAATAAGGAAAATGCAAAAAAAA-AA-AA-AGAGA-AGGAAATAAAATAAAGGAA-AAATTTCAA
1 AAATAAGGAAAATGCAAAAAAAAGAAGAAGAGAGAGAGGAAATAAAATAAAGGAAGAAATTGC--
51215813 AAAAGTATAGGAAATG
64 -AAAGTATAGGAAATG
* * * *
51215829 GAATAGGGGAAATGTAAAAAA
1 AAATAAGGAAAATGCAAAAAA
51215850 TGGAGATGTA
Statistics
Matches: 87, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
73 6 0.07
74 18 0.21
76 36 0.41
77 2 0.02
78 2 0.02
79 19 0.22
80 4 0.05
ACGTcount: A:0.62, C:0.02, G:0.22, T:0.14
Consensus pattern (78 bp):
AAATAAGGAAAATGCAAAAAAAAGAAGAAGAGAGAGAGGAAATAAAATAAAGGAAGAAATTGCAA
AGTATAGGAAATG
Found at i:51217925 original size:16 final size:16
Alignment explanation
Indices: 51217904--51217937 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
51217894 AAAGTCTAAA
* *
51217904 TTTGATTTATCAATAT
1 TTTGATATAACAATAT
51217920 TTTGATATAACAATAT
1 TTTGATATAACAATAT
51217936 TT
1 TT
51217938 AAAATTAAAA
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:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (16 bp):
TTTGATATAACAATAT
Found at i:51219726 original size:21 final size:21
Alignment explanation
Indices: 51219700--51219759 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
51219690 TATATTTTTT
*
51219700 AAAATTTATAAAATTTATAAA
1 AAAATTTAAAAAATTTATAAA
*
51219721 AAAATTCTAAAAAATATAT-AA
1 AAAATT-TAAAAAATTTATAAA
51219742 AAAA-TTAAAAAATTTATA
1 AAAATTTAAAAAATTTATA
51219760 GATCAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 11 0.32
20 1 0.03
21 12 0.35
22 10 0.29
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATTTAAAAAATTTATAAA
Found at i:51223423 original size:30 final size:30
Alignment explanation
Indices: 51223382--51223447 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
51223372 TTTGTATGAG
* *
51223382 ATTTTGTTAGGAATCTTAGGAAAAGAACTT
1 ATTTTGCTAGGAATCCTAGGAAAAGAACTT
51223412 ATTTTGCTAGGAATCCTAGGAAAAGAACTT
1 ATTTTGCTAGGAATCCTAGGAAAAGAACTT
*
51223442 ACTTTG
1 ATTTTG
51223448 AGACCTATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (30 bp):
ATTTTGCTAGGAATCCTAGGAAAAGAACTT
Found at i:51225460 original size:41 final size:41
Alignment explanation
Indices: 51225347--51225463 Score: 134
Period size: 41 Copynumber: 3.0 Consensus size: 41
51225337 CCTGATCGGA
* *
51225347 TAATTCGAAGTAATAAATTGACACCCAGTGTCTCATCG-GC
1 TAATTCGAAGTAGTAAATTGACACCCAGTGTCTCATCGAAC
** ** *
51225387 TAAACCG-A--AGTAAATTGACACCCAGTACCTCATCGAAT
1 TAATTCGAAGTAGTAAATTGACACCCAGTGTCTCATCGAAC
*
51225425 TAATTCGAAGTAGTAAATTGACACTCAGTGTCTCATCGA
1 TAATTCGAAGTAGTAAATTGACACCCAGTGTCTCATCGA
51225464 CTCGAAGTCG
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
37 24 0.39
38 5 0.08
39 2 0.03
40 5 0.08
41 25 0.41
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (41 bp):
TAATTCGAAGTAGTAAATTGACACCCAGTGTCTCATCGAAC
Found at i:51227126 original size:2 final size:2
Alignment explanation
Indices: 51227114--51227157 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
51227104 NNNNNNNNNN
51227114 TA TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51227157 T
1 T
51227158 CAATTCAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51227571 original size:18 final size:19
Alignment explanation
Indices: 51227542--51227577 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
51227532 TTAAACTAAA
*
51227542 TTAAACTCCCTATTTTCAC
1 TTAAACTCCCTAATTTCAC
51227561 TTAAA-TCCCTAATTTCA
1 TTAAACTCCCTAATTTCA
51227578 AATTTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAACTCCCTAATTTCAC
Found at i:51227862 original size:4 final size:4
Alignment explanation
Indices: 51227853--51227909 Score: 61
Period size: 4 Copynumber: 15.2 Consensus size: 4
51227843 AAGGCCGTGG
*
51227853 CTTT CTTT C-TT CTTT CTCTT -TTT CTTT CCTT -TTT C-TT -TTT CTTT
1 CTTT CTTT CTTT CTTT CT-TT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
51227897 CTTT CTTT CTTT C
1 CTTT CTTT CTTT C
51227910 CAATTTCGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
3 11 0.24
4 32 0.71
5 2 0.04
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:51227878 original size:6 final size:6
Alignment explanation
Indices: 51227854--51227896 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
51227844 AGGCCGTGGC
* *
51227854 TTTCTT TCTTCTT TCTCTT TTTC-T TTCCTT TTTCTT TTTCTT T
1 TTTCTT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
51227897 CTTTCTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 4 0.13
6 21 0.68
7 6 0.19
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:51227879 original size:12 final size:12
Alignment explanation
Indices: 51227856--51227906 Score: 59
Period size: 11 Copynumber: 4.1 Consensus size: 12
51227846 GCCGTGGCTT
51227856 TCTTTCTTCTTTC
1 TCTTT-TTCTTTC
51227869 TCTTTTTCTTTC
1 TCTTTTTCTTTC
*
51227881 -CTTTTTCTTTT
1 TCTTTTTCTTTC
51227892 TCTTTCTTTCTTTC
1 TC-TT-TTTCTTTC
51227906 T
1 T
51227907 TTCCAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 10 0.30
12 8 0.24
13 7 0.21
14 8 0.24
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
TCTTTTTCTTTC
Found at i:51227884 original size:17 final size:17
Alignment explanation
Indices: 51227854--51227902 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
51227844 AGGCCGTGGC
51227854 TTTCTTTCTTCTTTCTCTT
1 TTTCTTTC--CTTTCTCTT
*
51227873 TTTCTTTCCTTTTTCTT
1 TTTCTTTCCTTTCTCTT
51227890 TTTCTTT-CTTTCT
1 TTTCTTTCCTTTCT
51227903 TTCTTTCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 5 0.18
17 15 0.54
19 8 0.29
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTTTCCTTTCTCTT
Found at i:51227894 original size:29 final size:30
Alignment explanation
Indices: 51227854--51227910 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
51227844 AGGCCGTGGC
51227854 TTTCTTTCTTCTTTCTCTT-TTTCTTTCCTT
1 TTTCTTTCTTCTTTCT-TTCTTTCTTTCCTT
51227884 TTTCTTT-TTCTTTCTTTCTTTCTTTCC
1 TTTCTTTCTTCTTTCTTTCTTTCTTTCC
51227911 AATTTCGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 2 0.08
29 17 0.65
30 7 0.27
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (30 bp):
TTTCTTTCTTCTTTCTTTCTTTCTTTCCTT
Found at i:51227916 original size:29 final size:29
Alignment explanation
Indices: 51227854--51227934 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 29
51227844 AGGCCGTGGC
**
51227854 TTTCTTTCTTCTTTCTCTT-TTTCTTTCCTT
1 TTTCTTT-TTCTTTCT-TTCTTTCTTTCCAA
51227884 TTTCTTTTTCTTTCTTTCTTTCTTTCCAA
1 TTTCTTTTTCTTTCTTTCTTTCTTTCCAA
* *
51227913 TTTCGTTTTGCTTTGTTTCTTT
1 TTTC-TTTTTCTTTCTTTCTTT
51227935 TTCTTTTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 2 0.04
29 21 0.47
30 22 0.49
ACGTcount: A:0.02, C:0.22, G:0.04, T:0.72
Consensus pattern (29 bp):
TTTCTTTTTCTTTCTTTCTTTCTTTCCAA
Found at i:51228687 original size:22 final size:20
Alignment explanation
Indices: 51228660--51228701 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
51228650 CCGGCCCGAT
51228660 TTTTAATAAACACAAAAAAATA
1 TTTTAA-AAACA-AAAAAAATA
*
51228682 TTTTAAAAATAAAAAAAATA
1 TTTTAAAAACAAAAAAAATA
51228702 AAAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
TTTTAAAAACAAAAAAAATA
Found at i:51228704 original size:8 final size:9
Alignment explanation
Indices: 51228686--51228710 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
51228676 AAAATATTTT
51228686 AAAAATAAA
1 AAAAATAAA
51228695 AAAAATAAA
1 AAAAATAAA
51228704 AAAAATA
1 AAAAATA
51228711 TATTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAATAAA
Found at i:51233713 original size:41 final size:40
Alignment explanation
Indices: 51233600--51233713 Score: 101
Period size: 41 Copynumber: 2.9 Consensus size: 40
51233590 CCTGATCGGA
* * * * *
51233600 TAATTCGAAGTAATAAATTGACACACAGTCTCTCATCGGT
1 TAATCCGAAGTAGTAAATTGACACCCAGTGTCTCATCGAT
* ** *
51233640 TAAACC-AA--AGTAAATT-AGCACCCAAAGCCTCATCGAAT
1 TAATCCGAAGTAGTAAATTGA-CACCCAGTGTCTCATCG-AT
51233678 TAATCCGAAGTAGTAAATTGACACCCAGTGTCTCAT
1 TAATCCGAAGTAGTAAATTGACACCCAGTGTCTCAT
51233714 TGACTCGAAG
Statistics
Matches: 55, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
36 1 0.02
37 19 0.35
38 6 0.11
39 4 0.07
40 4 0.07
41 20 0.36
42 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (40 bp):
TAATCCGAAGTAGTAAATTGACACCCAGTGTCTCATCGAT
Found at i:51233886 original size:2 final size:2
Alignment explanation
Indices: 51233879--51233921 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
51233869 CAAATAATCA
*
51233879 AT AT AT AT -T CAT A- AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51233920 AT
1 AT
51233922 CAATTCAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 33 0.92
3 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:51234653 original size:6 final size:6
Alignment explanation
Indices: 51234615--51234702 Score: 63
Period size: 6 Copynumber: 14.3 Consensus size: 6
51234605 AGGCCGTGAC
* * * * *
51234615 TTTCTT TCTTCTT TCTCTA TTTC-T TTCCTT TTTCTT TTTC-T TTCCTG
1 TTTCTT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* *
51234662 TTTCGTT TTGCTT TGGTTCTT TTTCTT TTTCTA TTTCTT TT
1 TTTC-TT TTTCTT T--TTCTT TTTCTT TTTCTT TTTCTT TT
51234703 ATTTATTTGT
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
5 7 0.11
6 40 0.65
7 10 0.16
8 5 0.08
ACGTcount: A:0.02, C:0.20, G:0.06, T:0.72
Consensus pattern (6 bp):
TTTCTT
Found at i:51234654 original size:17 final size:17
Alignment explanation
Indices: 51234615--51234675 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
51234605 AGGCCGTGAC
51234615 TTTCTTT-CTTCTTTCTCT
1 TTTCTTTCCTT-TTTCT-T
51234633 ATTTCTTTCCTTTTTCTT
1 -TTTCTTTCCTTTTTCTT
*
51234651 TTTCTTTCCTGTTTCGTT
1 TTTCTTTCCTTTTTC-TT
*
51234669 TTGCTTT
1 TTTCTTT
51234676 GGTTCTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
17 14 0.37
18 9 0.24
19 12 0.32
20 3 0.08
ACGTcount: A:0.02, C:0.23, G:0.05, T:0.70
Consensus pattern (17 bp):
TTTCTTTCCTTTTTCTT
Found at i:51238541 original size:17 final size:17
Alignment explanation
Indices: 51238502--51238545 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
51238492 GCCGTATAAT
*
51238502 AAATATTTTT-ATTTTT
1 AAATATTTTTAATTTTA
*
51238518 TAA-ATTTTTAATTTTA
1 AAATATTTTTAATTTTA
51238534 AAATATTTTTAA
1 AAATATTTTTAA
51238546 AATACTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 6 0.26
16 9 0.39
17 8 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:51238545 original size:11 final size:11
Alignment explanation
Indices: 51238529--51238592 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
51238519 AAATTTTTAA
51238529 TTTTAAAATAT
1 TTTTAAAATAT
51238540 TTTTAAAATACT
1 TTTTAAAATA-T
*
51238552 TTTT---TTAT
1 TTTTAAAATAT
*
51238560 TTTT--TA-AT
1 TTTTAAAATAT
51238568 -TTTAAAATAT
1 TTTTAAAATAT
51238578 TTTTAAAATAT
1 TTTTAAAATAT
51238589 TTTT
1 TTTT
51238593 TTAATTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
7 3 0.07
8 7 0.16
9 3 0.07
10 2 0.05
11 24 0.55
12 5 0.11
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:51238555 original size:38 final size:37
Alignment explanation
Indices: 51238511--51238603 Score: 159
Period size: 38 Copynumber: 2.5 Consensus size: 37
51238501 TAAATATTTT
*
51238511 TATTTTTTAAATTTTTAATTTTAAAATATTTTTAAAA
1 TATTTTTTTAATTTTTAATTTTAAAATATTTTTAAAA
*
51238548 TACTTTTTTTATTTTTTAATTTTAAAATATTTTTAAAA
1 TA-TTTTTTTAATTTTTAATTTTAAAATATTTTTAAAA
51238586 TATTTTTTTAATTTTTAA
1 TATTTTTTTAATTTTTAA
51238604 AATAAATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
37 17 0.33
38 35 0.67
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (37 bp):
TATTTTTTTAATTTTTAATTTTAAAATATTTTTAAAA
Found at i:51238562 original size:20 final size:19
Alignment explanation
Indices: 51238537--51238628 Score: 71
Period size: 20 Copynumber: 4.6 Consensus size: 19
51238527 AATTTTAAAA
51238537 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATA-TTTTTT
* ***
51238557 TATTTTT-TAAT-TTTAAAA
1 TATTTTTAAAATATTT-TTT
51238575 TATTTTTAAAATATTTTTT
1 TATTTTTAAAATATTTTTT
51238594 TAATTTTTAAAATAAATTTTTT
1 T-ATTTTTAAAAT--ATTTTTT
51238616 GTATTTATTAAAA
1 -TATTT-TTAAAA
51238629 AATGGGCCGG
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.05
18 7 0.12
19 7 0.12
20 21 0.38
22 11 0.20
23 7 0.12
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (19 bp):
TATTTTTAAAATATTTTTT
Found at i:51238631 original size:21 final size:19
Alignment explanation
Indices: 51238575--51238631 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 19
51238565 AATTTTAAAA
*
51238575 TATTTTTAAAATATTTTTT
1 TATTTTTAAAAAATTTTTT
51238594 TAATTTTTAAAATAAATTTTTT
1 T-ATTTTT-AAA-AAATTTTTT
51238616 GTATTTATTAAAAAAT
1 -TATTT-TTAAAAAAT
51238632 GGGCCGGACC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 1 0.03
20 6 0.19
21 7 0.22
22 15 0.47
23 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TATTTTTAAAAAATTTTTT
Found at i:51250810 original size:61 final size:61
Alignment explanation
Indices: 51250732--51250969 Score: 449
Period size: 61 Copynumber: 3.9 Consensus size: 61
51250722 ATAAATTTAA
* *
51250732 TATTTAATTTAATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTAATGTGAGT
1 TATTAAATTTGATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTAATGTGAGT
51250793 TATTAAATTTGATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTAATGTGAGT
1 TATTAAATTTGATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTAATGTGAGT
51250854 TATTAAATTTGATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTAATGTGAGT
1 TATTAAATTTGATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTAATGTGAGT
*
51250915 TATTAAATTTGATTTAATTTTTATCTTGATAGTATTTTATTAATTTAATATTAAT
1 TATTAAATTTGATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTAAT
51250970 CTAAGTAATT
Statistics
Matches: 174, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 174 1.00
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.55
Consensus pattern (61 bp):
TATTAAATTTGATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTAATGTGAGT
Found at i:51252514 original size:17 final size:18
Alignment explanation
Indices: 51252492--51252525 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
51252482 AATCCATACA
51252492 AACTCAATCATT-TCATC
1 AACTCAATCATTATCATC
*
51252509 AACTCATTCATTATCAT
1 AACTCAATCATTATCAT
51252526 TTCTATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (18 bp):
AACTCAATCATTATCATC
Found at i:51253533 original size:2 final size:2
Alignment explanation
Indices: 51253521--51253558 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
51253511 TTCAATATCA
* *
51253521 AT AT GT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51253559 TTCATTCGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:51254247 original size:26 final size:27
Alignment explanation
Indices: 51254202--51254253 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
51254192 AAACCTCAAA
*
51254202 TTTTCTTTCTTTCCTTCCCT-TTTTCT
1 TTTTCTTTCTTTCCTCCCCTGTTTTCT
51254228 TTTTCTTTCCTTT-CTCCCCTGTTTTC
1 TTTTCTTT-CTTTCCTCCCCTGTTTTC
51254254 GTTTGCCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTCTTTCTTTCCTCCCCTGTTTTCT
Found at i:51254485 original size:14 final size:13
Alignment explanation
Indices: 51254459--51254508 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
51254449 ATTTATTTGA
51254459 AATATAATAATAT
1 AATATAATAATAT
51254472 AATATAATTAATAT
1 AATATAA-TAATAT
* *
51254486 AAT-TTACAATAT
1 AATATAATAATAT
51254498 AATA-AATAATA
1 AATATAATAATA
51254509 ATATACTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 13 0.42
13 9 0.29
14 9 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:51258245 original size:19 final size:19
Alignment explanation
Indices: 51258218--51258254 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
51258208 TTGAACTTAG
* *
51258218 TAAATCTTAATTGATTAAT
1 TAAAACTTAATTAATTAAT
51258237 TAAAACTTAATTAATTAA
1 TAAAACTTAATTAATTAA
51258255 ACATTAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (19 bp):
TAAAACTTAATTAATTAAT
Found at i:51259101 original size:36 final size:40
Alignment explanation
Indices: 51259048--51259137 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 40
51259038 TATATTTAAA
51259048 AATTTTAATTTTATT-AAAA-TAT-AAT-A-ATATTTTTT
1 AATTTTAATTTTATTAAAAACTATAAATAACATATTTTTT
51259083 AATTTTAAATTTTATTAAAAACTTATAAATAACATATTTTTT
1 AATTTT-AATTTTATTAAAAAC-TATAAATAACATATTTTTT
51259125 AATTTTAATTTTA
1 AATTTTAATTTTA
51259138 ATTTTTTTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
35 6 0.12
36 9 0.19
37 4 0.08
39 3 0.06
40 3 0.06
41 8 0.17
42 15 0.31
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (40 bp):
AATTTTAATTTTATTAAAAACTATAAATAACATATTTTTT
Found at i:51259168 original size:28 final size:26
Alignment explanation
Indices: 51259131--51259212 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 26
51259121 TTTTAATTTT
51259131 AATTTT-AATTTTTTTATTATTTTTAA
1 AATTTTAAATTTTTTTA-TATTTTTAA
51259157 AAGTTTTAAATTATTTTTACTATTTTTAA
1 AA-TTTTAAATT-TTTTTA-TATTTTTAA
*
51259186 AATTTTAAAATATTTTTATATTGTTTA
1 AATTTT-AAATTTTTTTATATT-TTTA
51259213 TAATATTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
26 2 0.04
27 8 0.16
28 18 0.37
29 21 0.43
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (26 bp):
AATTTTAAATTTTTTTATATTTTTAA
Found at i:51259174 original size:29 final size:27
Alignment explanation
Indices: 51259131--51259212 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 27
51259121 TTTTAATTTT
51259131 AATTTT-AATT-TTTTTATTATTTTTAA
1 AATTTTAAATTATTTTTA-TATTTTTAA
51259157 AAGTTTTAAATTATTTTTACTATTTTTAA
1 AA-TTTTAAATTATTTTTA-TATTTTTAA
*
51259186 AATTTTAAAATATTTTTATATTGTTTA
1 AATTTTAAATTATTTTTATATT-TTTA
51259213 TAATATTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
26 2 0.04
27 8 0.16
28 23 0.46
29 17 0.34
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (27 bp):
AATTTTAAATTATTTTTATATTTTTAA
Found at i:51259304 original size:19 final size:20
Alignment explanation
Indices: 51259280--51259324 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
51259270 ATTTTTATAA
51259280 TTTTTTAT-AA-TTTATATG
1 TTTTTTATAAATTTTATATG
*
51259298 TTGTTTTCTAAATTTTATATG
1 TT-TTTTATAAATTTTATATG
51259319 TTTTTT
1 TTTTTT
51259325 GAATTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 5 0.22
20 6 0.26
21 10 0.43
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (20 bp):
TTTTTTATAAATTTTATATG
Found at i:51259332 original size:19 final size:21
Alignment explanation
Indices: 51259290--51259336 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
51259280 TTTTTTATAA
*
51259290 TTTATATGTTGTTTTCTAAAT
1 TTTATATGTTGTTTTCGAAAT
*
51259311 TTTATATGTT-TTTT-GAATT
1 TTTATATGTTGTTTTCGAAAT
51259330 TTTATAT
1 TTTATAT
51259337 ATTTATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.42
20 4 0.17
21 10 0.42
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (21 bp):
TTTATATGTTGTTTTCGAAAT
Found at i:51259355 original size:20 final size:21
Alignment explanation
Indices: 51259313--51259360 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
51259303 TTCTAAATTT
*
51259313 TATATGTT-TTTTGAATTTTTA
1 TATAT-TTATTTTGAATTTATA
51259334 TATATTTATTTTG-ATTTATA
1 TATATTTATTTTGAATTTATA
51259354 TATATTT
1 TATATTT
51259361 TAATGTGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (21 bp):
TATATTTATTTTGAATTTATA
Found at i:51259362 original size:21 final size:22
Alignment explanation
Indices: 51259313--51259362 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
51259303 TTCTAAATTT
* *
51259313 TATATGTT-TTTTGAATTTTTA
1 TATATTTTATTTTGAATTTATA
51259334 TATA-TTTATTTTG-ATTTATA
1 TATATTTTATTTTGAATTTATA
51259354 TATATTTTA
1 TATATTTTA
51259363 ATGTGTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (22 bp):
TATATTTTATTTTGAATTTATA
Found at i:51261075 original size:15 final size:16
Alignment explanation
Indices: 51261057--51261090 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
51261047 CTAAACCCCG
51261057 AAAACCC-AAAAACAT
1 AAAACCCTAAAAACAT
*
51261072 AAAACCCTCAAAACAT
1 AAAACCCTAAAAACAT
51261088 AAA
1 AAA
51261091 CACAAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.65, C:0.26, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAACCCTAAAAACAT
Found at i:51266272 original size:20 final size:19
Alignment explanation
Indices: 51266226--51266296 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
51266216 TAGAATTTTT
*
51266226 TTTATAAAAAATAATAAAT
1 TTTATAAAAAATAATAAAA
51266245 TTTAATAAAAACATTAA-AAAA
1 TTT-ATAAAAA-A-TAATAAAA
*
51266266 TTTAT-AAAATTATATAAAA
1 TTTATAAAAAATA-ATAAAA
* *
51266285 ATCATAAAAAAT
1 TTTATAAAAAAT
51266297 TAATGACCTC
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
17 2 0.05
18 1 0.02
19 14 0.34
20 14 0.34
21 7 0.17
22 3 0.07
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
TTTATAAAAAATAATAAAA
Found at i:51266273 original size:30 final size:30
Alignment explanation
Indices: 51266229--51266300 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
51266219 AATTTTTTTT
*
51266229 ATAAAAAA-TAAT-AAATTTTAATAAAAA-C
1 ATAAAAAATTAATAAAATTAT-ATAAAAATC
*
51266257 ATTAAAAAATTTATAAAATTATATAAAAATC
1 A-TAAAAAATTAATAAAATTATATAAAAATC
51266288 ATAAAAAATTAAT
1 ATAAAAAATTAAT
51266301 GACCTCTAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 1 0.03
29 7 0.19
30 21 0.57
31 8 0.22
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (30 bp):
ATAAAAAATTAATAAAATTATATAAAAATC
Found at i:51266490 original size:20 final size:22
Alignment explanation
Indices: 51266462--51266505 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
51266452 TAAATTTATA
* *
51266462 TTTCTTTAC-ATTTTATATAAT
1 TTTCTTTACTACTTTATAAAAT
51266483 TTTC-TTACTACTTTATAAAAT
1 TTTCTTTACTACTTTATAAAAT
51266504 TT
1 TT
51266506 ATAGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTCTTTACTACTTTATAAAAT
Found at i:51266528 original size:29 final size:30
Alignment explanation
Indices: 51266496--51266573 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
51266486 CTTACTACTT
* *
51266496 TATAAAATTTATAG-TTTTTTTTA-TATTTC
1 TATAAAATTT-TAGAATTTTTTTACGATTTC
* *
51266525 TAT-ATATTTTAGAATTTTTTTACGATTTT
1 TATAAAATTTTAGAATTTTTTTACGATTTC
*
51266554 TATAAAATTTTACAATTTTT
1 TATAAAATTTTAGAATTTTT
51266574 ATATATATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 3 0.08
28 13 0.32
29 10 0.25
30 14 0.35
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (30 bp):
TATAAAATTTTAGAATTTTTTTACGATTTC
Found at i:51266564 original size:20 final size:20
Alignment explanation
Indices: 51266541--51266596 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
51266531 TTTTAGAATT
51266541 TTTTTACGATTTTTATAAAA
1 TTTTTACGATTTTTATAAAA
* *
51266561 -TTTTACAATTTTTAT-ATA
1 TTTTTACGATTTTTATAAAA
51266579 TATTTTACGATTTTTATA
1 T-TTTTACGATTTTTATA
51266597 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.07
19 14 0.47
20 14 0.47
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTTTACGATTTTTATAAAA
Found at i:51266597 original size:20 final size:20
Alignment explanation
Indices: 51266542--51266597 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
51266532 TTTAGAATTT
51266542 TTTTACGATTTTTATA-AAA
1 TTTTACGATTTTTATATAAA
* *
51266561 TTTTACAATTTTTATATATA
1 TTTTACGATTTTTATATAAA
51266581 TTTTACGATTTTTATAT
1 TTTTACGATTTTTATAT
51266598 TTTTTATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTTACGATTTTTATATAAA
Found at i:51269326 original size:191 final size:191
Alignment explanation
Indices: 51268981--51269342 Score: 521
Period size: 191 Copynumber: 1.9 Consensus size: 191
51268971 AGGCAAAATC
*** * *
51268981 AAATTTTTTTTAGGGGGGATTGAAATTAAATTGTGATTTTTAAGATAGCAAAAATACAATTTCAC
1 AAATTTTTTTTAGGGGGGACCAAAATTAAATTGTAATTTTTAAGATAACAAAAATACAATTTCAC
* *
51269046 CATTTTAATAGCCTATATCTTTATAATTTTTAAAGGATTAAATCAAATTTTTATGTTTTTAGGGG
66 CATCTTAATAGCCTATATCTTTATAATTTTTAAAGGATTAAATCAAATTTTTATATTTTTAGGGG
* * * *
51269111 GCCAAAGTGTAATTTTACCTTTATTAATTTGAAATTTTAAAGGGGGCCGAGGTGAAACCAG
131 GCCAAAATATAAATTTACCTTTATTAATTTAAAATTTTAAAGGGGGCCGAGGTGAAACCAG
* * **
51269172 AAATTTTTTTTAGGGGTGG-CCAAAATTAAATTGTAATTTTTACGATAATAAAAATGTAATTTCA
1 AAATTTTTTTTAGGGG-GGACCAAAATTAAATTGTAATTTTTAAGATAACAAAAATACAATTTCA
* *
51269236 CCATCTTAATAGCTTATATCTTTATAA-TTTTAAAGTATTAAATCAAATTTTTATATTTTTAGGG
65 CCATCTTAATAGCCTATATCTTTATAATTTTTAAAGGATTAAATCAAATTTTTATATTTTTAGGG
* *
51269300 GAGTCAAAATATAAATTTATCTTTATTAATTTAAAATTTTAAA
130 G-GCCAAAATATAAATTTACCTTTATTAATTTAAAATTTTAAA
51269343 AATTTTAAAA
Statistics
Matches: 150, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
190 36 0.24
191 112 0.75
192 2 0.01
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.42
Consensus pattern (191 bp):
AAATTTTTTTTAGGGGGGACCAAAATTAAATTGTAATTTTTAAGATAACAAAAATACAATTTCAC
CATCTTAATAGCCTATATCTTTATAATTTTTAAAGGATTAAATCAAATTTTTATATTTTTAGGGG
GCCAAAATATAAATTTACCTTTATTAATTTAAAATTTTAAAGGGGGCCGAGGTGAAACCAG
Found at i:51269945 original size:3 final size:3
Alignment explanation
Indices: 51269937--51269969 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
51269927 GGGAAATTAA
51269937 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
51269970 GTGATTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:51287008 original size:232 final size:232
Alignment explanation
Indices: 51286596--51287063 Score: 713
Period size: 232 Copynumber: 2.0 Consensus size: 232
51286586 ATCGGATGAT
* * *
51286596 AGAAAAGATCATATCTGACAATGCATTCAGCCTGAACAACAACCCGATAGTAGAGGTCTGTAGTC
1 AGAAAAGATCATATCTGACAATGCATTCAACCTGAACAACAACACGATAGTAGAGGTCTATAGTC
* * * *
51286661 AGTTCAAGATCAAACATCACAACTCATTACTATATCGCCCAAAAATAAATGGTGCAATGGAGGCA
66 AGTTCAAGATCAAACATCACAACTCATCACCAGACCGCCCAAAAATAAATGGTGCAATGGAGGCA
51286726 GCCAATAAGAACATTAAGAAGATCGTGGGGAAAATGACAGAAACTTATAAAGATTGGCATAAAAA
131 GCCAATAAGAACATTAAGAAGATCGTGGGGAAAATGACAGAAACTTATAAAGATTGGCATAAAAA
* *
51286791 GTTATCATTTG-TCCTCTATGCTTATCAAACTTCTGTC
196 GTTACCATTTGCT-CTCTATGCTTATCAAACGTCTGTC
* * * * *
51286828 AGAAAGGATCATATCTGACAATGCATTGAACTTGAACAACAACACGATAGTAGAGTTCTATAGTT
1 AGAAAAGATCATATCTGACAATGCATTCAACCTGAACAACAACACGATAGTAGAGGTCTATAGTC
** *
51286893 AGTTCAAGATCAAACATCACAACTCATCACCAGACCTTCCAAAAATGAATGGTGCAATGGAGGCA
66 AGTTCAAGATCAAACATCACAACTCATCACCAGACCGCCCAAAAATAAATGGTGCAATGGAGGCA
* * * *
51286958 GCCAATAAGAACATTAAGAAGATCGTGGGGGAAATGACAGAAACTTATAAAGATTGGTATGAGAA
131 GCCAATAAGAACATTAAGAAGATCGTGGGGAAAATGACAGAAACTTATAAAGATTGGCATAAAAA
**
51287023 GTTACCATTTGCTCTCTATGCTTATTGAACGTCTGTC
196 GTTACCATTTGCTCTCTATGCTTATCAAACGTCTGTC
51287060 AGAA
1 AGAA
51287064 CCTCCATCAG
Statistics
Matches: 212, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
232 211 1.00
233 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (232 bp):
AGAAAAGATCATATCTGACAATGCATTCAACCTGAACAACAACACGATAGTAGAGGTCTATAGTC
AGTTCAAGATCAAACATCACAACTCATCACCAGACCGCCCAAAAATAAATGGTGCAATGGAGGCA
GCCAATAAGAACATTAAGAAGATCGTGGGGAAAATGACAGAAACTTATAAAGATTGGCATAAAAA
GTTACCATTTGCTCTCTATGCTTATCAAACGTCTGTC
Found at i:51289535 original size:22 final size:20
Alignment explanation
Indices: 51289510--51289561 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
51289500 CTTTTATTTA
51289510 TTATTATTGTTGTTATTCATT
1 TTATTATTGTTGTTATTC-TT
*
51289531 GTTATTACTT-ATGTTATTCTT
1 -TTATTA-TTGTTGTTATTCTT
51289552 TT-TTATTGTT
1 TTATTATTGTT
51289562 AATATTAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 2 0.08
19 4 0.15
20 2 0.08
21 2 0.08
22 14 0.54
23 2 0.08
ACGTcount: A:0.17, C:0.06, G:0.10, T:0.67
Consensus pattern (20 bp):
TTATTATTGTTGTTATTCTT
Found at i:51293128 original size:19 final size:19
Alignment explanation
Indices: 51293104--51293149 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
51293094 TAGATGTCTT
*
51293104 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
51293123 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
51293142 TATGCATT
1 TTTGCATT
51293150 GAAGTCCACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.46
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:51301824 original size:143 final size:143
Alignment explanation
Indices: 51301566--51301936 Score: 546
Period size: 143 Copynumber: 2.6 Consensus size: 143
51301556 TTGAAGTCAT
* * ** **
51301566 TTATGGCGGATCTTATCTCCCTAAAGTTGCAGT-GAAGCAGATTAAAGCCATTAATCTTATCTCC
1 TTATGGCGGATCTTATCTTCCTAAAGTTGCAGTGGAA-CAGATTGAAGCCACCAGCCTTATCTCC
* * *
51301630 CTGAAGTTGTAGCGGAGTAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAATAG
65 CTGAAGTTGCAGCGGAGTAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAATGGAACAG
51301695 ATTAAAGCTACAAA
130 ATTAAAGCTACAAA
* * *
51301709 TTATGGCGGATCTTATCTTCTTGAAGTTGCAGTGGAACATATTGAAGCCACCAGCCTTATCTCCC
1 TTATGGCGGATCTTATCTTCCTAAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTTATCTCCC
* *
51301774 TGAAGTTGCAGCGGAGTAGACTGAAGATAGCGAATCTTCTTTCCCTGGCGTTGCAATGGAACAGA
66 TGAAGTTGCAGCGGAGTAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAATGGAACAGA
*
51301839 TTAAAGCTACAAG
131 TTAAAGCTACAAA
* * *
51301852 TTATGGCAGATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCT
1 TTATGGCGGATCTTATCTTCCTAAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTTATCTCCC
* *
51301917 TGAAGTTCCAGTGGAGTAGA
66 TGAAGTTGCAGCGGAGTAGA
51301937 TCGAAGCTAC
Statistics
Matches: 204, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
143 201 0.99
144 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (143 bp):
TTATGGCGGATCTTATCTTCCTAAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTTATCTCCC
TGAAGTTGCAGCGGAGTAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAATGGAACAGA
TTAAAGCTACAAA
Found at i:51302022 original size:44 final size:44
Alignment explanation
Indices: 51301865--51302069 Score: 144
Period size: 44 Copynumber: 4.6 Consensus size: 44
51301855 TGGCAGATCT
* * * * * * *
51301865 TATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGAATGAAGCCACAATCCC
* * * * *
51301909 TATCTCCTTGAAGTTCCAGTGGAGTAG-ATCGAAGCTACAAATCTC
1 TATCTCCCTGAAGTTACAGTGGAGCAGAAT-GAAGCCAC-AATCCC
* * * * *
51301954 T-TCTCCCTAAAATTACATTAGAGCAGAATGACGCCACAATCCC
1 TATCTCCCTGAAGTTACAGTGGAGCAGAATGAAGCCACAATCCC
** *** * *
51301997 TATCTCCCTGAAGTTACAGTGGAGCAGGATAAAAATATACAAACCT
1 TATCTCCCTGAAGTTACAGTGGAGCA-GA-ATGAAGCCACAATCCC
51302043 TATCTCCCTGAAGTTACAGTGGAGCAG
1 TATCTCCCTGAAGTTACAGTGGAGCAG
51302070 GTTGAAATTA
Statistics
Matches: 122, Mismatches: 33, Indels: 11
0.73 0.20 0.07
Matches are distributed among these distances:
43 7 0.06
44 73 0.60
45 8 0.07
46 34 0.28
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (44 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGAATGAAGCCACAATCCC
Found at i:51303607 original size:22 final size:20
Alignment explanation
Indices: 51303582--51303633 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
51303572 CTTTTATTTA
51303582 TTATTATTGTTGTTATTCATT
1 TTATTATTGTTGTTATTC-TT
*
51303603 GTTATTACTT-ATGTTATTCTT
1 -TTATTA-TTGTTGTTATTCTT
51303624 TT-TTATTGTT
1 TTATTATTGTT
51303634 AATATTAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 2 0.08
19 4 0.15
20 2 0.08
21 2 0.08
22 14 0.54
23 2 0.08
ACGTcount: A:0.17, C:0.06, G:0.10, T:0.67
Consensus pattern (20 bp):
TTATTATTGTTGTTATTCTT
Found at i:51304727 original size:44 final size:44
Alignment explanation
Indices: 51304640--51305079 Score: 338
Period size: 44 Copynumber: 9.7 Consensus size: 44
51304630 AGTCACCATA
* * *
51304640 ACAAACCTTATCTCCCTGAAGTTCCCCAGTGGAGCAGATTAAAGCT
1 ACAAATCTTATCTCCCTGAAGTT--GCAGTGGAGCAGATTGAAGCT
* * *
51304686 ACAAATCTTATCTCCCT-ACAGTTGTAGTGGAGTAGATTAAAGCT
1 ACAAATCTTATCTCCCTGA-AGTTGCAGTGGAGCAGATTGAAGCT
* * *
51304730 ACAAATCTTATTTCCCAGAAGTTGCAGTGAAGCAGATTGAAGCT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
*
51304774 ACAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
* * * *
51304818 ACAAATCTTATCTTCCTGAAATTGTAGTGGAGCAGATTGAAGCG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
* * * *
51304862 ACAAATCCTATAC-CTCTGAAGTTGCAGTGG-GTCAGATTAAATCT
1 ACAAATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGCT
* * *
51304906 ACCATAGTGAGTCTTATTTCCCTAAAGTTGTAGTGGAGCAAGA-TGAAGCT
1 A-CA-A---A-TCTTATCTCCCTGAAGTTGCAGTGGAGC-AGATTGAAGCT
** * * * *
51304956 ACATCTCCTATAC-CCCTGAAGTTGCAGTGG-GTCAAAATGAATCT
1 ACAAATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGCT
* *
51305000 ACCATAGTGAATATTATCTCCCTGAAGTTGCAGTAGAGCAAGA-TGAAGCT
1 A-C--A---AATCTTATCTCCCTGAAGTTGCAGTGGAGC-AGATTGAAGCT
* * *
51305050 ACAAATCCTATAC-CCCTAAAGTTGTAGTGG
1 ACAAATCTTAT-CTCCCTGAAGTTGCAGTGG
51305080 GTCGAAATGA
Statistics
Matches: 316, Mismatches: 52, Indels: 54
0.75 0.12 0.13
Matches are distributed among these distances:
43 4 0.01
44 216 0.68
45 7 0.02
46 21 0.07
47 2 0.01
49 5 0.02
50 54 0.17
51 7 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT
Found at i:51304965 original size:94 final size:94
Alignment explanation
Indices: 51304821--51305095 Score: 342
Period size: 94 Copynumber: 2.9 Consensus size: 94
51304811 TGAAGCTACA
* *
51304821 AATCTTATCTT-CCTGAAA-TTGTAGTGGAGC-AGATTGAAGCGACAAATCCTATACCTCTGAAG
1 AATCTTAT-TTCCCT-AAAGTTGTAGTGGAGCAAGA-TGAAGCTACAAATCCTATACCCCTGAAG
* *
51304883 TTGCAGTGGGTCAGATTAAATCTACCATAGTG
63 TTGCAGTGGGTCAAAATAAATCTACCATAGTG
* **
51304915 AGTCTTATTTCCCTAAAGTTGTAGTGGAGCAAGATGAAGCTACATCTCCTATACCCCTGAAGTTG
1 AATCTTATTTCCCTAAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
*
51304980 CAGTGGGTCAAAATGAATCTACCATAGTG
66 CAGTGGGTCAAAATAAATCTACCATAGTG
* * * * * *
51305009 AATATTATCTCCCTGAAGTTGCAGTAGAGCAAGATGAAGCTACAAATCCTATACCCCTAAAGTTG
1 AATCTTATTTCCCTAAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
* *
51305074 TAGTGGGTCGAAATGAAA-CTAC
66 CAGTGGGTCAAAAT-AAATCTAC
51305096 AACAACAAAT
Statistics
Matches: 157, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
93 5 0.03
94 147 0.94
95 5 0.03
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (94 bp):
AATCTTATTTCCCTAAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
CAGTGGGTCAAAATAAATCTACCATAGTG
Found at i:51305046 original size:50 final size:49
Alignment explanation
Indices: 51304877--51305051 Score: 130
Period size: 50 Copynumber: 3.6 Consensus size: 49
51304867 TCCTATACCT
* * * * * *
51304877 CTGAAGTTGCAGTGGGTC-AGATTAAATCTACCATAGTGAGTCTTATTTCC
1 CTGAAGTTGCAGTGAG-CAAGA-TGAAGCTACCATAGTGAATATTATCTCC
* * * **
51304927 CTAAAGTTGTAGTGGAGCAAGATGAAGCTA-CAT-CT-CCTA-TA-C-CC
1 CTGAAGTTGCAGT-GAGCAAGATGAAGCTACCATAGTGAATATTATCTCC
* * *
51304971 CTGAAGTTGCAGTGGGTCAAAATGAATCTACCATAGTGAATATTATCTCC
1 CTGAAGTTGCAGTGAG-CAAGATGAAGCTACCATAGTGAATATTATCTCC
51305021 CTGAAGTTGCAGTAGAGCAAGATGAAGCTAC
1 CTGAAGTTGCAGT-GAGCAAGATGAAGCTAC
51305052 AAATCCTATA
Statistics
Matches: 94, Mismatches: 21, Indels: 20
0.70 0.16 0.15
Matches are distributed among these distances:
43 2 0.02
44 24 0.26
45 3 0.03
46 3 0.03
47 3 0.03
48 3 0.03
49 4 0.04
50 45 0.48
51 7 0.07
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (49 bp):
CTGAAGTTGCAGTGAGCAAGATGAAGCTACCATAGTGAATATTATCTCC
Found at i:51305122 original size:94 final size:94
Alignment explanation
Indices: 51304847--51305125 Score: 247
Period size: 94 Copynumber: 3.0 Consensus size: 94
51304837 AATTGTAGTG
* * * * * *
51304847 GAGC-AGATTGAAGCGACAAATCCTATACCTCTGAAGTTGCAGTGGGTC-AGATTAAATCTACCA
1 GAGCAAGA-TGAAGCTACAAATCCTATACCCCTAAAGTTGCAGTGGGTCAAAATGAAA-CTACAA
* *** * * * * * *
51304910 TAGTGAGTCTTATTTCCCTAAAGTTGTAGTG
64 CAACAAATATTATCTCACTAAAGTTGCAGTA
** * * * *
51304941 GAGCAAGATGAAGCTACATCTCCTATACCCCTGAAGTTGCAGTGGGTCAAAATGAATCTACCATA
1 GAGCAAGATGAAGCTACAAATCCTATACCCCTAAAGTTGCAGTGGGTCAAAATGAAACTACAACA
*** * *
51305006 GTGAATATTATCTCCCTGAAGTTGCAGTA
66 ACAAATATTATCTCACTAAAGTTGCAGTA
* *
51305035 GAGCAAGATGAAGCTACAAATCCTATACCCCTAAAGTTGTAGTGGGTCGAAATGAAACTACAACA
1 GAGCAAGATGAAGCTACAAATCCTATACCCCTAAAGTTGCAGTGGGTCAAAATGAAACTACAACA
* *
51305100 ACAAATATTATCTTATTAAAGTTGCA
66 ACAAATATTATCTCACTAAAGTTGCA
51305126 ATGGAGCATG
Statistics
Matches: 155, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
94 147 0.95
95 8 0.05
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (94 bp):
GAGCAAGATGAAGCTACAAATCCTATACCCCTAAAGTTGCAGTGGGTCAAAATGAAACTACAACA
ACAAATATTATCTCACTAAAGTTGCAGTA
Found at i:51308808 original size:28 final size:30
Alignment explanation
Indices: 51308776--51308837 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
51308766 TCATGCACTG
**
51308776 AATTTAGTCC-CCTACTTTT-ATTTTTAAA
1 AATTTAGTCCTCCTACTTTTCAAATTTAAA
*
51308804 AATTTAGTCCTTCTACTTTTCAAATTTAAA
1 AATTTAGTCCTCCTACTTTTCAAATTTAAA
51308834 AATT
1 AATT
51308838 CAGGTCCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 10 0.34
29 8 0.28
30 11 0.38
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.48
Consensus pattern (30 bp):
AATTTAGTCCTCCTACTTTTCAAATTTAAA
Found at i:51309841 original size:13 final size:13
Alignment explanation
Indices: 51309817--51309853 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
51309807 GATTTAAACA
51309817 CTTTAC-AATATC
1 CTTTACAAATATC
51309829 CTTTACAAATATC
1 CTTTACAAATATC
51309842 CTTTACAAATAT
1 CTTTACAAATAT
51309854 TCACTACGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 6 0.25
13 18 0.75
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (13 bp):
CTTTACAAATATC
Found at i:51311368 original size:9 final size:9
Alignment explanation
Indices: 51311333--51311381 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
51311323 TCTGCTTATG
51311333 CTTCTTT-T
1 CTTCTTTCT
*
51311341 CTATTTTTCTT
1 CT-TCTTTC-T
51311352 CTTC-TTCT
1 CTTCTTTCT
51311360 CTTCTTTCT
1 CTTCTTTCT
51311369 CTTCTTTCT
1 CTTCTTTCT
51311378 CTTC
1 CTTC
51311382 ATCTTCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 7 0.20
9 24 0.69
10 1 0.03
11 3 0.09
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (9 bp):
CTTCTTTCT
Found at i:51311389 original size:18 final size:16
Alignment explanation
Indices: 51311348--51311388 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
51311338 TTTCTATTTT
51311348 TCTTCTTCTTCTCTTC
1 TCTTCTTCTTCTCTTC
51311364 T-TTC-TCTTCT-TTC
1 TCTTCTTCTTCTCTTC
*
51311377 TCTTCATCTTCT
1 TCTTCTTCTTCT
51311389 TTTACCATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.17
14 9 0.39
15 9 0.39
16 1 0.04
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (16 bp):
TCTTCTTCTTCTCTTC
Found at i:51318506 original size:19 final size:19
Alignment explanation
Indices: 51318482--51318519 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
51318472 ATTTTTATTG
51318482 ATACAAGTCCACTTCTATC
1 ATACAAGTCCACTTCTATC
* *
51318501 ATACAAGTTCACTTTTATC
1 ATACAAGTCCACTTCTATC
51318520 TATAAATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (19 bp):
ATACAAGTCCACTTCTATC
Found at i:51324535 original size:60 final size:60
Alignment explanation
Indices: 51324463--51324577 Score: 221
Period size: 60 Copynumber: 1.9 Consensus size: 60
51324453 TTTTTATAAA
*
51324463 TATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTGTAAT
1 TATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTGTAAT
51324523 TATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTT
1 TATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTT
51324578 AGTTTAGTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (60 bp):
TATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTGTAAT
Found at i:51334561 original size:20 final size:20
Alignment explanation
Indices: 51334536--51334576 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
51334526 GTACACAATT
51334536 TCAATGGGTTCGCCAAGATG
1 TCAATGGGTTCGCCAAGATG
51334556 TCAATGGGTTCGCCAAGATG
1 TCAATGGGTTCGCCAAGATG
51334576 T
1 T
51334577 GGATGAAGAT
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:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (20 bp):
TCAATGGGTTCGCCAAGATG
Found at i:51336802 original size:43 final size:42
Alignment explanation
Indices: 51336731--51336968 Score: 228
Period size: 42 Copynumber: 5.6 Consensus size: 42
51336721 GGCGCTTTTC
* * ** * *
51336731 AAAAACGCCGCTAAAGGACATGACCTTTAGCCAAGTTTTAGGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTT-GGG
* * *
51336774 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGTGATGTTTTTGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTTGGG
* *
51336816 AAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTT-TGGG
* * *
51336859 -AAAGCGCCGCTAAAAGTCATGTTCTTTAACGGCG-TTTGTGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTTG-GG
* * * * *
51336900 TAAAGCGCCGCTGAAGGTCATGTTCTTTAGTGGCATTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTT-TGGG
* * *
51336943 GAAAGCACCGTTAAAGGTCATGTTCT
1 AAAAGCGCCGCTAAAGGTCATGTTCT
51336969 ATAACGTCAT
Statistics
Matches: 167, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
40 2 0.01
41 4 0.02
42 98 0.59
43 61 0.37
44 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (42 bp):
AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTTGGG
Found at i:51336836 original size:42 final size:42
Alignment explanation
Indices: 51336772--51336968 Score: 241
Period size: 42 Copynumber: 4.7 Consensus size: 42
51336762 CAAGTTTTAG
* * ** *
51336772 GGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTGATGTTTTT
1 GGAAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT
51336814 GGAAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT
1 GGAAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT
* *
51336856 GGGAAAGCGCCGCTAAAAGTCATGTTCTTTAACGGCGTTTGT
1 GGAAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT
* * * * *
51336898 GGTAAAGCGCCGCTGAAGGTCATGTTCTTTAGTGGCATTTGT
1 GGAAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT
* * * *
51336940 GGGGAAAGCACCGTTAAAGGTCATGTTCT
1 -GGAAAAGCGCCGCTAAAAGTCATGTTCT
51336969 ATAACGTCAT
Statistics
Matches: 137, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 113 0.82
43 24 0.18
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (42 bp):
GGAAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT
Found at i:51336878 original size:84 final size:85
Alignment explanation
Indices: 51336775--51336984 Score: 269
Period size: 84 Copynumber: 2.5 Consensus size: 85
51336765 GTTTTAGGGA
** * *
51336775 AAAGCGCCGCTAAAGGTCATGTTCTTTAGTGATGTTTTTGGAAAAGCGCCGCTAAAAGTCATGTT
1 AAAGCGCCGCTAAAGGTCATGTTCTTTAACGACGTTTGTGGAAAAGCGCCGCTAAAAGTCATGTT
*
51336840 CTTTAGCGGCGTTTGT-GGG
66 CTTTAGCGGCATTTGTGGGG
* * * * *
51336859 AAAGCGCCGCTAAAAGTCATGTTCTTTAACGGCGTTTGTGGTAAAGCGCCGCTGAAGGTCATGTT
1 AAAGCGCCGCTAAAGGTCATGTTCTTTAACGACGTTTGTGGAAAAGCGCCGCTAAAAGTCATGTT
*
51336924 CTTTAGTGGCATTTGTGGGG
66 CTTTAGCGGCATTTGTGGGG
* * * * *
51336944 AAAGCACCGTTAAAGGTCATGTTCTATAACGTCATTTGTGG
1 AAAGCGCCGCTAAAGGTCATGTTCTTTAACGACGTTTGTGG
51336985 GGTAGTGCCG
Statistics
Matches: 108, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
84 70 0.65
85 38 0.35
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (85 bp):
AAAGCGCCGCTAAAGGTCATGTTCTTTAACGACGTTTGTGGAAAAGCGCCGCTAAAAGTCATGTT
CTTTAGCGGCATTTGTGGGG
Found at i:51336996 original size:85 final size:84
Alignment explanation
Indices: 51336817--51336985 Score: 230
Period size: 85 Copynumber: 2.0 Consensus size: 84
51336807 TGTTTTTGGA
* *
51336817 AAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAAGTCATGTT
1 AAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCATTTGTGGGAAAGCACCGCTAAAAGTCATGTT
* * *
51336882 CTTTAACGGCGTTTGTGGT
66 CTATAACGGCATTTGTGGG
* * * * *
51336901 AAAGCGCCGCTGAAGGTCATGTTCTTTAGTGGCATTTGTGGGGAAAGCACCGTTAAAGGTCATGT
1 AAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCATTTGT-GGGAAAGCACCGCTAAAAGTCATGT
*
51336966 TCTATAACGTCATTTGTGGG
65 TCTATAACGGCATTTGTGGG
51336986 GTAGTGCCGC
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
84 35 0.48
85 38 0.52
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (84 bp):
AAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCATTTGTGGGAAAGCACCGCTAAAAGTCATGTT
CTATAACGGCATTTGTGGG
Found at i:51339244 original size:21 final size:21
Alignment explanation
Indices: 51339194--51339245 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
51339184 CAATTCTGAA
*
51339194 AATTTTAAAATATCTTAAAAT
1 AATTTTAAAATAACTTAAAAT
* * *
51339215 AAATATAAAATAAGTTAAAAT
1 AATTTTAAAATAACTTAAAAT
*
51339236 ATTTTTAAAA
1 AATTTTAAAA
51339246 ATAATTTGAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
AATTTTAAAATAACTTAAAAT
Found at i:51339564 original size:10 final size:11
Alignment explanation
Indices: 51339537--51339575 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
51339527 TAAGGTCAAC
*
51339537 ATATTTTAAAA
1 ATATATTAAAA
51339548 ATATATTAAAA
1 ATATATTAAAA
51339559 AT-TATTAAAA
1 ATATATTAAAA
51339569 ATATATT
1 ATATATT
51339576 GAAGGTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATATATTAAAA
Found at i:51342475 original size:18 final size:18
Alignment explanation
Indices: 51342452--51342486 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
51342442 ACACGGGCGT
*
51342452 GTGGCTTGGCCTTGTGGC
1 GTGGCTTGGCCGTGTGGC
51342470 GTGGCTTGGCCGTGTGG
1 GTGGCTTGGCCGTGTGG
51342487 TACAAGTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.49, T:0.31
Consensus pattern (18 bp):
GTGGCTTGGCCGTGTGGC
Found at i:51343904 original size:21 final size:21
Alignment explanation
Indices: 51343865--51343906 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
51343855 TTTGCCTAAG
* *
51343865 ATATGAATTGGATTGAATTGA
1 ATATGAATTAGATTAAATTGA
*
51343886 ATATGAATTATATTAAATTGA
1 ATATGAATTAGATTAAATTGA
51343907 GTTAAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (21 bp):
ATATGAATTAGATTAAATTGA
Found at i:51344398 original size:26 final size:26
Alignment explanation
Indices: 51344369--51344426 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
51344359 CTCGATGTAT
51344369 GGCT-TTTCGTGAGCTTCCTGATTAAA
1 GGCTCTTT-GTGAGCTTCCTGATTAAA
* *
51344395 GGCTCTTTGTGAGCTTCTTGATTAAT
1 GGCTCTTTGTGAGCTTCCTGATTAAA
51344421 GGCTCT
1 GGCTCT
51344427 CCAGAGCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 26 0.90
27 3 0.10
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (26 bp):
GGCTCTTTGTGAGCTTCCTGATTAAA
Found at i:51346275 original size:13 final size:13
Alignment explanation
Indices: 51346254--51346284 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
51346244 AAAATACATA
*
51346254 TAAATGAAAAAGT
1 TAAAAGAAAAAGT
51346267 TAAAAGAAAAAGT
1 TAAAAGAAAAAGT
51346280 TAAAA
1 TAAAA
51346285 TTTTAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (13 bp):
TAAAAGAAAAAGT
Found at i:51355270 original size:14 final size:12
Alignment explanation
Indices: 51355243--51355277 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 12
51355233 TAATTTAAAC
51355243 AAATAAAAACAA
1 AAATAAAAACAA
51355255 AAATAAATAGACAA
1 AAATAAA-A-ACAA
51355269 AAATAAAAA
1 AAATAAAAA
51355278 AATAACAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.38
13 2 0.10
14 11 0.52
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (12 bp):
AAATAAAAACAA
Found at i:51361258 original size:3 final size:3
Alignment explanation
Indices: 51361250--51361280 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
51361240 CAAAACTTGC
51361250 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
51361281 GTCATCACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:51362301 original size:15 final size:15
Alignment explanation
Indices: 51362281--51362311 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
51362271 ATTAAAACGC
51362281 ATTATCTTTTTATTT
1 ATTATCTTTTTATTT
51362296 ATTATCTTTTTATTT
1 ATTATCTTTTTATTT
51362311 A
1 A
51362312 AAAATTAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTATCTTTTTATTT
Found at i:51364420 original size:21 final size:22
Alignment explanation
Indices: 51364394--51364439 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
51364384 TTGTATTCAC
*
51364394 AAAAAATAATATTATTTATATTTA
1 AAAAAAT-A-ATTATATATATTTA
51364418 AAAAAATAAATTATATATATTT
1 AAAAAAT-AATTATATATATTT
51364440 TACTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAAAATAATTATATATATTTA
Found at i:51364430 original size:23 final size:25
Alignment explanation
Indices: 51364377--51364439 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
51364367 TCTTAAATTT
* *
51364377 ATATTATTTGTATTCACAAAAAATA
1 ATATTATTTATATTTACAAAAAATA
51364402 ATATTATTTATATTTA-AAAAAATA
1 ATATTATTTATATTTACAAAAAATA
*
51364426 A-ATTATATATATTT
1 ATATTATTTATATTT
51364440 TACTTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 12 0.34
24 9 0.26
25 14 0.40
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (25 bp):
ATATTATTTATATTTACAAAAAATA
Found at i:51367141 original size:28 final size:27
Alignment explanation
Indices: 51367101--51367158 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
51367091 TTCAATTTAT
* *
51367101 TGTCATTTCAAATAAAAATAAAAATTGA
1 TGTCAATTAAAATAAAAAT-AAAATTGA
* * *
51367129 TGTCAATTAAAATTAAGATAAATTTGA
1 TGTCAATTAAAATAAAAATAAAATTGA
51367156 TGT
1 TGT
51367159 ATTTTAGGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.36
Consensus pattern (27 bp):
TGTCAATTAAAATAAAAATAAAATTGA
Found at i:51368248 original size:3 final size:3
Alignment explanation
Indices: 51368240--51368274 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
51368230 TTTTATTGAG
51368240 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
51368275 TGTCTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:51378752 original size:66 final size:66
Alignment explanation
Indices: 51378646--51378771 Score: 234
Period size: 66 Copynumber: 1.9 Consensus size: 66
51378636 CATTTCAGAG
*
51378646 AGCACACTCCCGCAAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
1 AGCACACTCCCGCAAACCTCATCCTTACAGCGGGATTACCAGTACAGGCTAAATCCCCTGCAAGA
51378711 T
66 T
*
51378712 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTACAGGCTAAATCCCCTG
1 AGCACACTCCCGCAAACCTCATCCTTACAGCGGGATTACCAGTACAGGCTAAATCCCCTG
51378772 TAATATAAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.28, C:0.37, G:0.17, T:0.18
Consensus pattern (66 bp):
AGCACACTCCCGCAAACCTCATCCTTACAGCGGGATTACCAGTACAGGCTAAATCCCCTGCAAGA
T
Found at i:51381420 original size:30 final size:30
Alignment explanation
Indices: 51381348--51381421 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
51381338 CTTGGGCTGT
*
51381348 CACATGCTCGTGTGACACACATGACCTAGCTA
1 CACA-GCT-GTGTGACACACACGACCTAGCTA
* * *
51381380 TACGGTTGTGTGACACACACGACCTAGCTA
1 CACAGCTGTGTGACACACACGACCTAGCTA
51381410 CACAGCTGTGTG
1 CACAGCTGTGTG
51381422 TCACTTGTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 31 0.89
31 2 0.06
32 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (30 bp):
CACAGCTGTGTGACACACACGACCTAGCTA
Found at i:51388196 original size:2 final size:2
Alignment explanation
Indices: 51388189--51388221 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
51388179 AATGGTAGAG
51388189 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51388222 GTAGATGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51389244 original size:15 final size:15
Alignment explanation
Indices: 51389224--51389253 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
51389214 AGCTTACATC
51389224 ATGATTTTAAAATAT
1 ATGATTTTAAAATAT
*
51389239 ATGATTTTTAAATAT
1 ATGATTTTAAAATAT
51389254 TAATAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
ATGATTTTAAAATAT
Found at i:51391755 original size:105 final size:105
Alignment explanation
Indices: 51391630--51391829 Score: 285
Period size: 105 Copynumber: 1.9 Consensus size: 105
51391620 AAAGTACATC
* ** *
51391630 TTATTTATATTTTTATTAAGTAGCAAATGTACATACTGGACGTGTTTTTATGTA-CAAAGGAATT
1 TTATTTATATTTTTATTAAGTAACAAACATACATACTGGACGCGTTTTTATGTACCAAA-GAATT
** *
51391694 TGATTGGAAAGTGCTCTTCCTCGTGGTAGCAGTACTATTGG
65 TGATCAGAAAGAGCTCTTCCTCGTGGTAGCAGTACTATTGG
* *
51391735 TTATTTATATTTTTATTAAGTAACAAACATACGTAGTGGACGCGTTTTTATGTACCAAAGAATTT
1 TTATTTATATTTTTATTAAGTAACAAACATACATACTGGACGCGTTTTTATGTACCAAAGAATTT
* *
51391800 GATCAGAAAGAGCTCTTTCTTGTGGTAGCA
66 GATCAGAAAGAGCTCTTCCTCGTGGTAGCA
51391830 ATTTTGAAGG
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
105 79 0.95
106 4 0.05
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (105 bp):
TTATTTATATTTTTATTAAGTAACAAACATACATACTGGACGCGTTTTTATGTACCAAAGAATTT
GATCAGAAAGAGCTCTTCCTCGTGGTAGCAGTACTATTGG
Found at i:51401704 original size:2 final size:2
Alignment explanation
Indices: 51401649--51401688 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
51401639 CTTTAATTGC
* *
51401649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51401689 GTGTGTATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:51403978 original size:2 final size:2
Alignment explanation
Indices: 51403971--51404002 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
51403961 GTTTAAAGTA
51403971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51404003 GAGAAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51404256 original size:6 final size:6
Alignment explanation
Indices: 51404245--51404285 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
51404235 ACAGTATAAT
51404245 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
51404286 TAATTAGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:51410229 original size:123 final size:124
Alignment explanation
Indices: 51409974--51410276 Score: 378
Period size: 123 Copynumber: 2.4 Consensus size: 124
51409964 AAACGACGCC
* * * * *
51409974 GTTTCACTACAGG-AAGTAAGTTTTTTTAGTAGCGTTTTGATTGAAAATGCCGCAAAGGTGATAC
1 GTTTCACTACAGGAAATTAA--ATTTTTAGTGGCGTTTTGACTGAAAACGCCGCAAAGGTGATAC
* * * * * * *
51410038 ATTAGTGGCGTTTTTTATAAACGCTGCAAAATTGCAATACCAATTCGAGTTAAACGTCGTT
64 ATTAGTGGCGATTTTCATAAACGCCGCAAAATTACAATACAAATTCGACTTAAACGGCGTT
* * *
51410099 GTTTCACTACA-GAACATTAAATTTTTAGTGGCATTTTGACTGAAAACGCTGCAAAGGTTATACA
1 GTTTCACTACAGGAA-ATTAAATTTTTAGTGGCGTTTTGACTGAAAACGCCGCAAAGGTGATACA
*
51410163 TTAGTGGC-ATTTTCATAAACGCCGCAAAATTACAATACAAATTTGACTTAAACGGCGTT
65 TTAGTGGCGATTTTCATAAACGCCGCAAAATTACAATACAAATTCGACTTAAACGGCGTT
* ** *
51410222 GTTTCACTACAGGGAATTAAGGTTTTAGTGGCGTTTTGACCGAAAACGCCGCAAA
1 GTTTCACTACAGGAAATTAAATTTTTAGTGGCGTTTTGACTGAAAACGCCGCAAA
51410277 ATTACAATAC
Statistics
Matches: 153, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
123 89 0.58
124 48 0.31
125 12 0.08
126 4 0.03
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (124 bp):
GTTTCACTACAGGAAATTAAATTTTTAGTGGCGTTTTGACTGAAAACGCCGCAAAGGTGATACAT
TAGTGGCGATTTTCATAAACGCCGCAAAATTACAATACAAATTCGACTTAAACGGCGTT
Found at i:51410392 original size:84 final size:84
Alignment explanation
Indices: 51410163--51410427 Score: 399
Period size: 84 Copynumber: 3.1 Consensus size: 84
51410153 AGGTTATACA
* * *
51410163 TTAGTGGCA-TTTTCATAAACGCCGCAAAATTACAATACAAATTTGACTTAAACGGCGTTGTTTC
1 TTAGTGGCATTTTTCATAAACGCCGCAAAATTACAATACCAATTTGACTTAAACGGTGTCGTTTC
* *
51410227 ACTACAGGGAATTAAGGTT
66 ACTATAGGGAATTAAGTTT
* *
51410246 TTAGTGGCGTTTTGACCGA-AAACGCCGCAAAATTACAATACCAATTTGACTTAAACGGTGTCGT
1 TTAGTGGCATTTT--TC-ATAAACGCCGCAAAATTACAATACCAATTTGACTTAAACGGTGTCGT
51410310 TTCACTATAGGGAATTAAGTTT
63 TTCACTATAGGGAATTAAGTTT
* *
51410332 TTAGTGGCATTTTTCATAAACGCCGCAAAATTGCAATACCAATTTGACTTAAACGTTGTCGTTTC
1 TTAGTGGCATTTTTCATAAACGCCGCAAAATTACAATACCAATTTGACTTAAACGGTGTCGTTTC
*
51410397 ACTATAAGGAATTAAGTTT
66 ACTATAGGGAATTAAGTTT
51410416 TTAGTGGCATTT
1 TTAGTGGCATTT
51410428 GGCTTGAAAA
Statistics
Matches: 165, Mismatches: 12, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
83 9 0.05
84 80 0.48
86 75 0.45
87 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (84 bp):
TTAGTGGCATTTTTCATAAACGCCGCAAAATTACAATACCAATTTGACTTAAACGGTGTCGTTTC
ACTATAGGGAATTAAGTTT
Found at i:51412742 original size:43 final size:44
Alignment explanation
Indices: 51412636--51412887 Score: 234
Period size: 43 Copynumber: 5.9 Consensus size: 44
51412626 ATGTTTTTGG
* * *
51412636 GAAAAGCGCTGCTAAAGGTCATGTTTTTTAGCGGCGTTTG-TGT
1 GAAAAGCGCTGCTAAAGGTCATGTTCTTTAGTGGCATTTGTTGT
*** *
51412679 G-AAAGCGCCATTAAATGTCATGTTCTTTAGTGGCATTTGTTG-
1 GAAAAGCGCTGCTAAAGGTCATGTTCTTTAGTGGCATTTGTTGT
* * * *
51412721 GAAAAGCGTTGCTAAAGGTCATGTTCTTTAGCGGCGTATGTTG-
1 GAAAAGCGCTGCTAAAGGTCATGTTCTTTAGTGGCATTTGTTGT
* * * *
51412764 GAAGAGTGCTGCAAAAGGTCATGTTCTTTAGCT-ACATTTG-TGT
1 GAAAAGCGCTGCTAAAGGTCATGTTCTTTAG-TGGCATTTGTTGT
* * * * *
51412807 TAAAAGCGCCGCTAAAGGTCATGTTCTATAGTGGCGTTT-TCGT
1 GAAAAGCGCTGCTAAAGGTCATGTTCTTTAGTGGCATTTGTTGT
*
51412850 GAGAAA-CGCTGCTAAAGGTCATG-TCTATAGTGGCATTT
1 GA-AAAGCGCTGCTAAAGGTCATGTTCTTTAGTGGCATTT
51412888 TTCACATAAA
Statistics
Matches: 167, Mismatches: 35, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
42 49 0.29
43 115 0.69
44 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (44 bp):
GAAAAGCGCTGCTAAAGGTCATGTTCTTTAGTGGCATTTGTTGT
Found at i:51414682 original size:25 final size:27
Alignment explanation
Indices: 51414646--51414709 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 27
51414636 TAATTTATAC
*
51414646 AATA-AAACATTTATTATT-AAATA-T
1 AATATAAATATTTATTATTAAAATATT
* *
51414670 GATATATATATTTATTATTAAAATATT
1 AATATAAATATTTATTATTAAAATATT
51414697 AATATAAATATTT
1 AATATAAATATTT
51414710 CCAATAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 3 0.09
25 12 0.38
26 5 0.16
27 12 0.38
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
AATATAAATATTTATTATTAAAATATT
Found at i:51421568 original size:15 final size:16
Alignment explanation
Indices: 51421543--51421575 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
51421533 TATCCCTTTC
*
51421543 TTTATATTTTATTATA
1 TTTATATTTTATGATA
51421559 TTTA-ATTTTATGATA
1 TTTATATTTTATGATA
51421574 TT
1 TT
51421576 ATTTTGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTATATTTTATGATA
Found at i:51422264 original size:20 final size:20
Alignment explanation
Indices: 51422241--51422280 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
51422231 CCCTAGCCCT
51422241 GCCACCGCCACGGTCACGTC
1 GCCACCGCCACGGTCACGTC
*
51422261 GCCACCGCCATGGTCACGTC
1 GCCACCGCCACGGTCACGTC
51422281 ACCGCCTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.47, G:0.25, T:0.12
Consensus pattern (20 bp):
GCCACCGCCACGGTCACGTC
Found at i:51422285 original size:17 final size:18
Alignment explanation
Indices: 51422242--51422286 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
51422232 CCTAGCCCTG
51422242 CCACCGCCACGGTCACGT
1 CCACCGCCACGGTCACGT
*
51422260 CGCCACCGCCATGGTCACGT
1 --CCACCGCCACGGTCACGT
51422280 -CACCGCC
1 CCACCGCC
51422287 TACCCACTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 7 0.29
20 17 0.71
ACGTcount: A:0.16, C:0.51, G:0.22, T:0.11
Consensus pattern (18 bp):
CCACCGCCACGGTCACGT
Found at i:51423228 original size:594 final size:583
Alignment explanation
Indices: 51422280--51423781 Score: 2376
Period size: 594 Copynumber: 2.5 Consensus size: 583
51422270 ATGGTCACGT
*
51422280 CACCGCCTACCCACTTGCACCGCCACTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
1 CACCGCCTACCCACTTGCACCGCCAGTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
*
51422345 GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTCTTTTTTTTCGGTAACAT
66 GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTCTTTTTTTTTGGTAACAT
*
51422410 TTTCACAGAAATAAAAGCAAAAAAACAAAGGTGATTTCTTTTTTTTTTTTCATTTTCGCATCTCT
131 TTTCACAGAAATAAAAGCAAAAAAACAAAGATGATTTC-TTTTTTTTTTTCATTTTCGCATCTCT
* * *
51422475 GCTCTTTTCATACCTGTTCATTTTATTTTTATACATATATACATATATTTTTTTAAAAAGAGTTT
195 GCTCTTTTCATACCTGTTCATTTTATTTTTATACGTATATACATATATATTTTAAAAAAGAGTTT
*
51422540 ATATTCGCGCAAAATACAAAAAGTAAAATTTTTACCTTTTTTTAAATTTTTCGACCACCGCGTAA
260 ATATTCGCGCAAAATACAAAAAGTAAATTTTTTACCTTTTTTTAAATTTTTCGACCACCGCGTAA
*
51422605 TATTCTCGTTACCCGACAACGAGCAAAGAGGGGCAGCTGTACAAGCCCAATTTTAGCCCAGGCTT
325 TATTCTCGTTACCCGACAACGAACAAAGAGGGGCAGCTGTACAAGCCCAATTTTAGCCCAGGCTT
51422670 AAGACCCAATTAAACCCCAAACCCAAACCACCTAAACCCAAAACCCAAATACAACCCAACAAAAT
390 AAGACCCAATT-------------AAACC-CC-AAACCCAAAACCCAAATACAACCCAACAAAAT
*
51422735 TAAACCCAATACCCAAACCCAACAACCCCAATACCCCAGGCCCAAAATAACCCTAGCCCAAAAAC
440 TAAACCCAATACCCAAACCCAACAAACCCAATACCCCAGGCCCAAAATAACCCTAGCCCAAAAAC
*
51422800 AAATCAG-AAAAAAAAATAATTTTTTCAAGCCCTAGGTGC-G-G-C-CTTCTGACCAGCAGGCGC
505 AAATCAGAAAAAAAAAACAATTTTTTCAAGCCCTAGGTGCGGTGCCGCTTCTGACCAGCAGGCGC
51422860 CGCCCTAGCCCTGC
570 CGCCCTAGCCCTGC
51422874 CACCGCCTACCCACTTGCACCGCCAGTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
1 CACCGCCTACCCACTTGCACCGCCAGTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
*
51422939 GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTCTTTTTTTTTGGTAATAT
66 GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTCTTTTTTTTTGGTAACAT
*
51423004 TTTCACAGAAATAAAAGCAAAAAAACAAAGATGATTTC-TTTTTTTTTTCATTTTCGCATCTCTA
131 TTTCACAGAAATAAAAGCAAAAAAACAAAGATGATTTCTTTTTTTTTTTCATTTTCGCATCTCTG
51423068 CTCTTTTCATACCTGTTCATTTTATTTTTATACGTATATACATATATATTTTAAAAAAGAGTTTA
196 CTCTTTTCATACCTGTTCATTTTATTTTTATACGTATATACATATATATTTTAAAAAAGAGTTTA
*
51423133 TATTCGTGCAAAATACAAAAAAGTAAATTTTTTTACCTTTTTTTAAA-TTTTCTGACCACCGCGT
261 TATTCGCGCAAAATAC-AAAAAGTAAA-TTTTTTACCTTTTTTTAAATTTTTC-GACCACCGCGT
51423197 AATATTCTCGTTACCCGACAACGAACAAAGAGGGGCAGCTGTACAAGCCCAATTTTAGCCCAGGC
323 AATATTCTCGTTACCCGACAACGAACAAAGAGGGGCAGCTGTACAAGCCCAATTTTAGCCCAGGC
* *
51423262 TTAAGACTCAATTAAACCCCAAACCCAAAACCCAAATACAACTCAACAAAATTAAACCCAATACC
388 TTAAGACCCAATTAAACCCCAAACCCAAAACCCAAATACAACCCAACAAAATTAAACCCAATACC
* *
51423327 CAAACCCAGCAAACCCAATACCCCAGGCCCAAAATAACCCTAGCCCAGAAACAAATCAGAAAAAA
453 CAAACCCAACAAACCCAATACCCCAGGCCCAAAATAACCCTAGCCCAAAAACAAATCAG---AAA
51423392 AAAAAAACAATTTTTTCAAGCCCTAGGTGCGGTGCACCTAGGGTCTTCTGACCAGCAGGCGCCGC
515 AAAAAAACAATTTTTTCAAGCCCTAGGTGCGGTG--CC----G-CTTCTGACCAGCAGGCGCCGC
*
51423457 CCTAGCCTTGC
573 CCTAGCCCTGC
* * *
51423468 CATCGTCTACTCACTTGCACCGCCAGTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
1 CACCGCCTACCCACTTGCACCGCCAGTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
51423533 GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTCTTTTTTTTTTTGGTAAC
66 GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTC--TTTTTTTTTGGTAAC
* * * *
51423598 ATTTTCACAGAAATAAAAGCAAAAAATCAAAGCTGA---CGTTTTTTTTATCATTTTCGCATCTC
129 ATTTTCACAGAAATAAAAGCAAAAAAACAAAGATGATTTCTTTTTTTTTTTCATTTTCGCATCTC
*
51423660 TGCTCTTTTCATACCTGTTCATTTTATTTTTATACGTATATGCATATATATTTTTAAAAAAAGAG
194 TGCTCTTTTCATACCTGTTCATTTTATTTTTATACGTATATACATATATA-TTTT-AAAAAAGAG
* *
51423725 TTTTTATTCGCGCAAAATACAAAAAGTAAAATTTTTTACCCTTTTTTAAATTTTTCG
257 TTTATATTCGCGCAAAATACAAAAAGT-AAATTTTTTACCTTTTTTTAAATTTTTCG
51423782 CGATGGCCGG
Statistics
Matches: 853, Mismatches: 30, Indels: 49
0.92 0.03 0.05
Matches are distributed among these distances:
579 100 0.12
580 2 0.00
581 5 0.01
583 31 0.04
584 1 0.00
585 1 0.00
588 1 0.00
592 102 0.12
593 16 0.02
594 481 0.56
595 30 0.04
596 83 0.10
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (583 bp):
CACCGCCTACCCACTTGCACCGCCAGTCACCTGCAAAGAAGAAAGCAAACAAGACAACAGAAGCA
GTAGCAATCGGCTATAAAAGCCGAAGAAAATGTAATTTTTGGGGGTTCTTTTTTTTTGGTAACAT
TTTCACAGAAATAAAAGCAAAAAAACAAAGATGATTTCTTTTTTTTTTTCATTTTCGCATCTCTG
CTCTTTTCATACCTGTTCATTTTATTTTTATACGTATATACATATATATTTTAAAAAAGAGTTTA
TATTCGCGCAAAATACAAAAAGTAAATTTTTTACCTTTTTTTAAATTTTTCGACCACCGCGTAAT
ATTCTCGTTACCCGACAACGAACAAAGAGGGGCAGCTGTACAAGCCCAATTTTAGCCCAGGCTTA
AGACCCAATTAAACCCCAAACCCAAAACCCAAATACAACCCAACAAAATTAAACCCAATACCCAA
ACCCAACAAACCCAATACCCCAGGCCCAAAATAACCCTAGCCCAAAAACAAATCAGAAAAAAAAA
ACAATTTTTTCAAGCCCTAGGTGCGGTGCCGCTTCTGACCAGCAGGCGCCGCCCTAGCCCTGC
Found at i:51424342 original size:3 final size:3
Alignment explanation
Indices: 51424334--51424401 Score: 91
Period size: 3 Copynumber: 22.7 Consensus size: 3
51424324 TTATTTTAAC
* * *
51424334 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT GTT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
51424382 ATT ATT GTT ATT ATA ATT AT
1 ATT ATT ATT ATT ATT ATT AT
51424402 ATTTCCATTT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:51425072 original size:43 final size:42
Alignment explanation
Indices: 51425024--51425160 Score: 118
Period size: 43 Copynumber: 3.2 Consensus size: 42
51425014 GTTTTTCTCT
* *
51425024 CAAACGCCGTACTAGGCCCTGATCTATAGCTGCGCTTCGACCA
1 CAAACGCCGAAATA-GCCCTGATCTATAGCTGCGCTTCGACCA
* * * * *
51425067 CAAACGCCACGAAATA-ACCTAATCTTTAG-TGGCGCTTTC-CCCT
1 CAAACG-C-CGAAATAGCCCTGATCTATAGCT-GCGC-TTCGACCA
* *
51425110 CAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTCGACCA
1 CAAACGCCGAAATAG-CCCTGATCTATAGCTGCGCTTCGACCA
51425153 CAAACGCC
1 CAAACGCC
51425161 ACTAAAGAAC
Statistics
Matches: 72, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
41 6 0.08
42 5 0.07
43 52 0.72
44 4 0.06
45 5 0.07
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.20
Consensus pattern (42 bp):
CAAACGCCGAAATAGCCCTGATCTATAGCTGCGCTTCGACCA
Found at i:51425148 original size:86 final size:86
Alignment explanation
Indices: 51425003--51425229 Score: 312
Period size: 86 Copynumber: 2.6 Consensus size: 86
51424993 AAGATCAGGG
* * * * * * *
51425003 TCTTTAGCGGCGTTTTTCTCTCAAACGCCGTACTAGGCCCTGATCTATAGCTGCGCTTCGACCAC
1 TCTTTAGCGGCGCTTTCCCCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTCGACCAC
*
51425068 AAACGCCACGAAATAACCTAA
66 AAACGCCACGAAAGAACCTAA
*
51425089 TCTTTAGTGGCGCTTTCCCCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTCGACCAC
1 TCTTTAGCGGCGCTTTCCCCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTCGACCAC
*
51425154 AAACGCCACTAAAGAACCTAA
66 AAACGCCACGAAAGAACCTAA
* * * *
51425175 TCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAA-AGACCATGATCTTTAGTGGCG
1 TCTTTAGCGGCGCTTTCCCCTCAAACGCCGC-AATAGACCCTGATCTATAGCGGCG
51425230 TTTTTTTTAA
Statistics
Matches: 125, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 123 0.98
87 2 0.02
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.24
Consensus pattern (86 bp):
TCTTTAGCGGCGCTTTCCCCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTCGACCAC
AAACGCCACGAAAGAACCTAA
Found at i:51425183 original size:43 final size:43
Alignment explanation
Indices: 51425045--51425229 Score: 171
Period size: 43 Copynumber: 4.3 Consensus size: 43
51425035 CTAGGCCCTG
* * * *
51425045 ATCTATAGCTGCGC-TTCGACCACAAACGCCACGAAATAACCTA
1 ATCTTTAGCGGCGCTTTC-ACCACAAACGCCACTAAAGAACCTA
* * * * * *
51425088 ATCTTTAGTGGCGCTTTCCCCTCAAACGCCGC-AATAGACCCTG
1 ATCTTTAGCGGCGCTTTCACCACAAACGCCACTAA-AGAACCTA
*
51425131 ATCTATAGCGGCGC-TTCGACCACAAACGCCACTAAAGAACCTA
1 ATCTTTAGCGGCGCTTTC-ACCACAAACGCCACTAAAGAACCTA
* * *
51425174 ATCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAG-ACCATG
1 ATCTTTAGCGGCGCTTTCACCACAAACGCCACTAAAGAACC-TA
*
51425217 ATCTTTAGTGGCG
1 ATCTTTAGCGGCG
51425230 TTTTTTTTAA
Statistics
Matches: 115, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
42 8 0.07
43 99 0.86
44 8 0.07
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (43 bp):
ATCTTTAGCGGCGCTTTCACCACAAACGCCACTAAAGAACCTA
Found at i:51425582 original size:21 final size:21
Alignment explanation
Indices: 51425556--51425668 Score: 118
Period size: 21 Copynumber: 5.4 Consensus size: 21
51425546 TTTGACGCTG
*
51425556 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCTCTCGCTGCAGC
* **
51425577 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCTCTCGCTGCAGC
51425598 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCTCTCGCTGCAGC
* * * * *
51425619 TTGTACTTCTCTCGTTGCCGC
1 CTCTGCTTCTCTCGCTGCAGC
* *
51425640 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCTCTCGCTGCAGC
*
51425661 ATCTGCTT
1 CTCTGCTT
51425669 TAAACTGCTG
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.04, C:0.41, G:0.18, T:0.37
Consensus pattern (21 bp):
CTCTGCTTCTCTCGCTGCAGC
Found at i:51425723 original size:66 final size:66
Alignment explanation
Indices: 51425639--51425785 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 66
51425629 CTCGTTGCCG
* *
51425639 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAACTGCT-GTTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAACTG-TAGTTGGAGTTCTTCATATCTTT-GTT
51425702 GAA
64 GAA
* * ** *
51425705 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGTTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAACTGTAGTTGGAGTTCTTCATATCTTTGTTGA
51425770 A
66 A
*
51425771 CCTCAACTTCTCTCG
1 CCTCAGCTTCTCTCG
51425786 ATGTTGCCTC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
65 1 0.01
66 66 0.93
67 4 0.06
ACGTcount: A:0.14, C:0.28, G:0.17, T:0.41
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAACTGTAGTTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:51425801 original size:66 final size:66
Alignment explanation
Indices: 51425678--51425808 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
51425668 TTAAACTGCT
* * * *
51425678 GTTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGT
1 GTTGGAGTTCTTCATACTTTCGTTGAACCTCAACTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
51425743 A
66 A
* * *
51425744 GTTGGAGTTCTTCATATCTTT-TTTGAACCTCAACTTCTCTCGATGTTGCCTCCGCTTTAAGTTG
1 GTTGGAGTTCTTCATA-CTTTCGTTGAACCTCAACTTCTCTCGATGCTGCATCCGCTTTAAGTTG
51425808 T
65 T
51425809 GTAATTTGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 53 0.93
67 4 0.07
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.43
Consensus pattern (66 bp):
GTTGGAGTTCTTCATACTTTCGTTGAACCTCAACTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
A
Found at i:51427189 original size:115 final size:114
Alignment explanation
Indices: 51426987--51427567 Score: 921
Period size: 114 Copynumber: 5.1 Consensus size: 114
51426977 CATGTATCAT
*
51426987 GCTAATACTCATATTATTAGCGGCGCTATTCAAAAAACGCCACTAATGTCACCGAAGTGTCTCCA
1 GCTAATACTCATATTATTAGCGGCGCTATTCGAAAAACGCCACTAATGTCACCGAAGTGTCTCCA
*
51427052 AACGACGTCGTCTGGGTTTTAGTTTTTGCGGCGTTTTTATACAAAACGCC
66 AACGACGTCGTCTGGGTTTTAGTTTTTGCGGCATTTTTATA-AAAACGCC
* *
51427102 GCTAATACTCATATTATTAGCGGCGCTACTCGGAAAACGCCACTAATGTCACCGAAGTGTCTCCA
1 GCTAATACTCATATTATTAGCGGCGCTATTCGAAAAACGCCACTAATGTCACCGAAGTGTCTCCA
* * * * * *
51427167 AATGAAGTCGTTTGGGTTTTAGTTTTTCCGGCATTTTTGTAGAAACGCC
66 AACGACGTCGTCTGGGTTTTAGTTTTTGCGGCATTTTTATAAAAACGCC
* *
51427216 GCTAATACTCATATTATTAGCGGCGCTATTAGAAAAACGCCACTAAAGTCACCGAAGTGTCTCCA
1 GCTAATACTCATATTATTAGCGGCGCTATTCGAAAAACGCCACTAATGTCACCGAAGTGTCTCCA
* * *
51427281 AACGACGTCGTTTGGGGTTTAGTTTTTGTGGCATTTTTATAAAAACGCC
66 AACGACGTCGTCTGGGTTTTAGTTTTTGCGGCATTTTTATAAAAACGCC
* * *
51427330 ACTAATACTCATATTATTAGCGGCACTATTCAAAAAACGCCACTAATGTCACCGAAGTGTCTCCA
1 GCTAATACTCATATTATTAGCGGCGCTATTCGAAAAACGCCACTAATGTCACCGAAGTGTCTCCA
* *
51427395 AACGACGTCGTCTGGGTTTTAGTTTTTGCGGCATTTTTACAGAAACGCC
66 AACGACGTCGTCTGGGTTTTAGTTTTTGCGGCATTTTTATAAAAACGCC
*
51427444 GCTAATACTCATATTATTAGCGGCGCTATTCGAAAAACGCCACTAATGTCACCGAAGTTTCTCCA
1 GCTAATACTCATATTATTAGCGGCGCTATTCGAAAAACGCCACTAATGTCACCGAAGTGTCTCCA
* * * *
51427509 AATGACGTCATCTGGG-TTTAGTTTTTGCGGCGTTTTTATAGAAACGCC
66 AACGACGTCGTCTGGGTTTTAGTTTTTGCGGCATTTTTATAAAAACGCC
51427557 GCTAATACTCA
1 GCTAATACTCA
51427568 ATCGGTTGCA
Statistics
Matches: 427, Mismatches: 39, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
113 41 0.10
114 289 0.68
115 97 0.23
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (114 bp):
GCTAATACTCATATTATTAGCGGCGCTATTCGAAAAACGCCACTAATGTCACCGAAGTGTCTCCA
AACGACGTCGTCTGGGTTTTAGTTTTTGCGGCATTTTTATAAAAACGCC
Found at i:51428287 original size:35 final size:34
Alignment explanation
Indices: 51428225--51428324 Score: 127
Period size: 35 Copynumber: 3.0 Consensus size: 34
51428215 ACCAAAAATT
51428225 TATTTTAAAAA--TTAAAA-T-AAAATTAAAAAG
1 TATTTTAAAAATTTTAAAATTAAAAATTAAAAAG
51428255 TATTTTAAAATATTTTAAAATTAAAAATTAAAAAG
1 TATTTTAAAA-ATTTTAAAATTAAAAATTAAAAAG
* *
51428290 TATTTTAAAAATTTCAAAAATTTTAAAATTAAAAA
1 TATTTTAAAAATTT-TAAAA-TTAAAAATTAAAAA
51428325 ATTAAAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
30 10 0.16
31 1 0.02
33 6 0.10
34 5 0.08
35 26 0.43
36 13 0.21
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (34 bp):
TATTTTAAAAATTTTAAAATTAAAAATTAAAAAG
Found at i:51428308 original size:9 final size:9
Alignment explanation
Indices: 51428256--51428317 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
51428246 ATTAAAAAGT
51428256 ATTTTAAAA
1 ATTTTAAAA
51428265 TATTTT-AAA
1 -ATTTTAAAA
51428274 A--TTAAAA
1 ATTTTAAAA
*
51428281 A-TTAAAAA
1 ATTTTAAAA
51428289 GTATTTTAAAA
1 --ATTTTAAAA
*
51428300 ATTTCAAAA
1 ATTTTAAAA
51428309 ATTTTAAAA
1 ATTTTAAAA
51428318 TTAAAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
6 2 0.05
7 4 0.09
8 6 0.14
9 19 0.44
10 6 0.14
11 6 0.14
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:51428352 original size:43 final size:41
Alignment explanation
Indices: 51428259--51428377 Score: 120
Period size: 43 Copynumber: 2.9 Consensus size: 41
51428249 AAAAAGTATT
*
51428259 TTAAAATATTTTAAAATTAAAAATTAAAAAGTATTTTAAAAAT
1 TTAAAA-ATTTTAAAATTAAAAATTAAAAAGTATTTT-AAAAG
51428302 TTCAAAAATTTTAAAATTAAAAAATTAAAAAAAGTATTTT-AAAG
1 TT-AAAAATTTTAAAATT-AAAAATT--AAAAAGTATTTTAAAAG
* * *
51428346 TTAAAAA--TAAAAAATAAAAAATAAAAA-TATTT
1 TTAAAAATTTTAAAATTAAAAATTAAAAAGTATTT
51428378 ATTATTCGGG
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
37 5 0.07
38 5 0.07
40 6 0.09
41 6 0.09
43 18 0.26
44 16 0.24
46 12 0.18
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (41 bp):
TTAAAAATTTTAAAATTAAAAATTAAAAAGTATTTTAAAAG
Done.