Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 17 of 240
Found at i:6355650 original size:18 final size:19
Alignment explanation
Indices: 6355564--6355645 Score: 96
Period size: 18 Copynumber: 4.4 Consensus size: 19
6355554 ACTCTATTTT
* *
6355564 AGTTATTAAATGAGAATAG
1 AGTTATTAAATTAAAATAG
*
6355583 -TTTATTAAATTAAAATAG
1 AGTTATTAAATTAAAATAG
* *
6355601 AGTTATTAAATGAGAATAG
1 AGTTATTAAATTAAAATAG
*
6355620 -TTTATTAAATTAAAATAG
1 AGTTATTAAATTAAAATAG
6355638 AGTTATTA
1 AGTTATTA
6355646 CTTAATTAGA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
18 30 0.59
19 21 0.41
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (19 bp):
AGTTATTAAATTAAAATAG
Found at i:6355882 original size:37 final size:37
Alignment explanation
Indices: 6355840--6355910 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
6355830 AGTATTACTT
6355840 AATAGTTTATTAAATTAAAATAGACTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGACTTATTAAATGAG
*
6355877 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGACTTATTAAAT
6355911 AAAAAAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGACTTATTAAATGAG
Found at i:6355888 original size:18 final size:19
Alignment explanation
Indices: 6355840--6355914 Score: 93
Period size: 18 Copynumber: 4.1 Consensus size: 19
6355830 AGTATTACTT
6355840 AATAG-TTTATTAAATTAA
1 AATAGATTTATTAAATTAA
* * *
6355858 AATAGACTTATTAAATGAG
1 AATAGATTTATTAAATTAA
6355877 AATAG-TTTATTAAATTAA
1 AATAGATTTATTAAATTAA
*
6355895 AATAGAGTTATTAAA-TAA
1 AATAGATTTATTAAATTAA
6355913 AA
1 AA
6355915 AAATGAGTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 25 0.52
19 23 0.48
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.37
Consensus pattern (19 bp):
AATAGATTTATTAAATTAA
Found at i:6355915 original size:19 final size:19
Alignment explanation
Indices: 6355846--6355914 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
6355836 ACTTAATAGT
6355846 TTATTAAATTAAAATAGAC
1 TTATTAAATTAAAATAGAC
* * *
6355865 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAC
*
6355883 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAC
6355902 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
6355915 AAATGAGTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAC
Found at i:6355922 original size:20 final size:19
Alignment explanation
Indices: 6355846--6355924 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 19
6355836 ACTTAATAGT
* * *
6355846 TTATTAAATTAAAATAGAC
1 TTATTAAATAAAAAAAGAG
* * * *
6355865 TTATTAAATGAGAATAG-T
1 TTATTAAATAAAAAAAGAG
* *
6355883 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
6355902 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
6355922 TTA
1 TTA
6355925 AAGGAGAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
18 15 0.30
19 29 0.58
20 6 0.12
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:6356145 original size:29 final size:26
Alignment explanation
Indices: 6356112--6356176 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 26
6356102 TTTTTTGTGT
6356112 ATATTTTTGTAAATAATCAAAAAATAATA
1 ATATTTTTGTAAATAA--AAAAAAT-ATA
*
6356141 ATATTTTGGTAAATAAAAAAAATATA
1 ATATTTTTGTAAATAAAAAAAATATA
6356167 ATATTTTTGT
1 ATATTTTTGT
6356177 TAATTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 12 0.35
27 7 0.21
29 15 0.44
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.42
Consensus pattern (26 bp):
ATATTTTTGTAAATAAAAAAAATATA
Found at i:6366437 original size:16 final size:16
Alignment explanation
Indices: 6366416--6366459 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
6366406 TGTCAAGTTG
6366416 TTTCAAGTTTAAATCT-
1 TTTCAAGTTTAAAT-TA
*
6366432 TTTCAAGTTTGAATTA
1 TTTCAAGTTTAAATTA
*
6366448 TTTTAAGTTTAA
1 TTTCAAGTTTAA
6366460 TCTCCGAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (16 bp):
TTTCAAGTTTAAATTA
Found at i:6367880 original size:13 final size:12
Alignment explanation
Indices: 6367862--6367905 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
6367852 GATTTAAGAA
6367862 ATAAATATAATAT
1 ATAAATATAA-AT
6367875 ATAAATATAAAT
1 ATAAATATAAAT
6367887 ATTAAA-ATAAAT
1 A-TAAATATAAAT
*
6367899 TTAAATA
1 ATAAATA
6367906 AATTAACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 4 0.14
12 10 0.36
13 14 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATAAATATAAAT
Found at i:6367882 original size:6 final size:6
Alignment explanation
Indices: 6367862--6367905 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
6367852 GATTTAAGAA
*
6367862 ATAAAT ATAATAT ATAAAT ATAAAT ATTAAA- ATAAAT TTAAAT A
1 ATAAAT ATAA-AT ATAAAT ATAAAT A-TAAAT ATAAAT ATAAAT A
6367906 AATTAACAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.12
6 19 0.58
7 10 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATAAAT
Found at i:6368193 original size:19 final size:21
Alignment explanation
Indices: 6368170--6368212 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
6368160 TTATATATGC
6368170 ATATATAAAAA-ATAGTAGATT
1 ATATA-AAAAATATAGTAGATT
6368191 ATATAAAAAATATAGTAGATT
1 ATATAAAAAATATAGTAGATT
6368212 A
1 A
6368213 ATATTAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (21 bp):
ATATAAAAAATATAGTAGATT
Found at i:6369769 original size:50 final size:50
Alignment explanation
Indices: 6369713--6369991 Score: 256
Period size: 50 Copynumber: 5.6 Consensus size: 50
6369703 TCGGGGAAAC
* * *
6369713 AAGATTCGCTGTCATAGCTTCAATCTATTCCACTGCACCGCCAGGGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCAACGCCAGGGAAGT
* ** * * **
6369763 AAGATTCGCCGTTGT-GACTTCAATCTATTTAACTGCAATGTCAGGGAAAC
1 AAGATTCGCCGTCGTAG-CTTCAATCTATTCCACTGCAACGCCAGGGAAGT
* * * * * *
6369813 AAGATTCGTCGTCGTAGCTTTAATCTGTTCCACTACACCGCCAAGGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCAACGCCAGGGAAGT
* ** * *** *
6369863 AAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTTGGGGGAA-C
1 AAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCAACG-CCAGGGAAGT
* * * * *
6369913 AAGATTCGCCGTCGTAGCCTCAATCTGTTCCACTACATCGCCAGAGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCAACGCCAGGGAAGT
*
6369963 AAGATTCGCCGTTGTAGCTTCAATCTATT
1 AAGATTCGCCGTCGTAGCTTCAATCTATT
6369992 TAACTGTAAT
Statistics
Matches: 172, Mismatches: 53, Indels: 8
0.74 0.23 0.03
Matches are distributed among these distances:
49 5 0.03
50 162 0.94
51 5 0.03
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (50 bp):
AAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCAACGCCAGGGAAGT
Found at i:6369863 original size:100 final size:99
Alignment explanation
Indices: 6369680--6370002 Score: 470
Period size: 100 Copynumber: 3.2 Consensus size: 99
6369670 GGATTGGTTT
* * * *
6369680 CTTCCATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCTGTCATAGCTTCAATCTATTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGC-GTCGTAGCTTCAATCTGTTCCA
* *
6369745 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGT-G
65 CTACACCGCCAAGGAAGTAAGATTCGCCGTTGTAG
* *
6369779 ACTTCAATCTATTTAACTGCAATGTCAGGGAAACAAGATTCGTCGTCGTAGCTTTAATCTGTTCC
1 -CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCG-CGTCGTAGCTTCAATCTGTTCC
6369844 ACTACACCGCCAAGGAAGTAAGATTCGCCGTTGTAG
64 ACTACACCGCCAAGGAAGTAAGATTCGCCGTTGTAG
* * *
6369880 CTTCAATCTATTTAACTGCAATGTTGGGGGAACAAGATTCGCCGTCGTAGCCTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCG-CGTCGTAGCTTCAATCTGTTCCA
*
6369945 CTACATCGCC-AGAGAAGTAAGATTCGCCGTTGTAG
65 CTACACCGCCAAG-GAAGTAAGATTCGCCGTTGTAG
*
6369980 CTTCAATCTATTTAACTGTAATG
1 CTTCAATCTATTTAACTGCAATG
6370003 CCAAAGAGAT
Statistics
Matches: 204, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
99 2 0.01
100 200 0.98
101 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (99 bp):
CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCGTCGTAGCTTCAATCTGTTCCAC
TACACCGCCAAGGAAGTAAGATTCGCCGTTGTAG
Found at i:6372150 original size:21 final size:22
Alignment explanation
Indices: 6372114--6372162 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
6372104 CCTTAGCCTC
*
6372114 TTCATTTTTACTTTTTCCA-TTT
1 TTCATTATTACTTTTT-CATTTT
6372136 TTCATTATT-CTTTTTCATTTT
1 TTCATTATTACTTTTTCATTTT
6372157 TTCATT
1 TTCATT
6372163 TCATTCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 15 0.60
22 8 0.32
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.69
Consensus pattern (22 bp):
TTCATTATTACTTTTTCATTTT
Found at i:6372156 original size:7 final size:7
Alignment explanation
Indices: 6372114--6372174 Score: 54
Period size: 7 Copynumber: 8.3 Consensus size: 7
6372104 CCTTAGCCTC
6372114 TTCATTT
1 TTCATTT
6372121 TT-ACTTT
1 TTCA-TTT
6372128 TTCCATTT
1 TT-CATTT
*
6372136 TTCATTA
1 TTCATTT
6372143 TTC-TTT
1 TTCATTT
6372149 TTCATTTT
1 TTCA-TTT
6372157 TTCATTT
1 TTCATTT
6372164 CATTCATTT
1 --TTCATTT
6372173 TT
1 TT
6372175 TTACGATTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
6 6 0.13
7 19 0.42
8 12 0.27
9 8 0.18
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (7 bp):
TTCATTT
Found at i:6372671 original size:18 final size:17
Alignment explanation
Indices: 6372648--6372699 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 17
6372638 CCTAGTAGAG
6372648 GTTTTTGTTTCTTTTTTT
1 GTTTTT-TTTCTTTTTTT
*
6372666 GTTTTTTGTTCTTCTTTT
1 GTTTTTT-TTCTTTTTTT
6372684 GTTCTTTTTTTCTTTT
1 G-T-TTTTTTTCTTTT
6372700 GGATTGAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 1 0.03
18 16 0.55
19 7 0.24
20 5 0.17
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (17 bp):
GTTTTTTTTCTTTTTTT
Found at i:6372682 original size:21 final size:19
Alignment explanation
Indices: 6372649--6372693 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
6372639 CTAGTAGAGG
* *
6372649 TTTTTGTTTCTTTTTTTGT
1 TTTTTGTTTCTTTTGTTCT
6372668 TTTTTGTTCTTCTTTTGTTCT
1 TTTTTG-T-TTCTTTTGTTCT
6372689 TTTTT
1 TTTTT
6372694 TCTTTTGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 1 0.05
21 15 0.68
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (19 bp):
TTTTTGTTTCTTTTGTTCT
Found at i:6372789 original size:14 final size:14
Alignment explanation
Indices: 6372766--6372799 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6372756 ATCAATGTTA
* *
6372766 TTCCAGATAAAGTC
1 TTCCACATAAAATC
6372780 TTCCACATAAAATC
1 TTCCACATAAAATC
6372794 TTCCAC
1 TTCCAC
6372800 TTTCATTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (14 bp):
TTCCACATAAAATC
Found at i:6376780 original size:18 final size:19
Alignment explanation
Indices: 6376729--6376801 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 19
6376719 ACACTAACGA
*
6376729 AATATACAAATTTAAATAT
1 AATATATAAATTTAAATAT
**
6376748 AAT-T-TAAGAAATAAATAT
1 AATATATAA-ATTTAAATAT
*
6376766 AATATATAAATTAAAATATT
1 AATATATAAATTTAAATA-T
6376786 AA-A-ATAAATTTAAATA
1 AATATATAAATTTAAATA
6376802 AATTAACAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.05
18 24 0.56
19 11 0.26
20 6 0.14
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (19 bp):
AATATATAAATTTAAATAT
Found at i:6376829 original size:29 final size:28
Alignment explanation
Indices: 6376771--6376849 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 28
6376761 AATATAATAT
*
6376771 ATAAATTAAAATATTAAAATAAATTTAA
1 ATAAATTAAAATATTAAAATAAATTGAA
* * *
6376799 ATAAATTAACAATATTGAAATGAGTTGAA
1 ATAAATTAA-AATATTAAAATAAATTGAA
* *
6376828 ATAAGTTAAAGATGTTAAAATA
1 ATAAATTAAA-ATATTAAAATA
6376850 TTTGAAAGAG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 10 0.24
29 31 0.76
ACGTcount: A:0.57, C:0.01, G:0.09, T:0.33
Consensus pattern (28 bp):
ATAAATTAAAATATTAAAATAAATTGAA
Found at i:6389100 original size:24 final size:24
Alignment explanation
Indices: 6389052--6389109 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
6389042 AACTCATTTT
6389052 ATTTAAT-TTTTTTATATATTGAC
1 ATTTAATATTTTTTATATATTGAC
* *
6389075 ATCTTAATATTTTTTA-ATGTTTAC
1 AT-TTAATATTTTTTATATATTGAC
6389099 ATTATAATATT
1 ATT-TAATATT
6389110 ATATATCACC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 3 0.10
24 20 0.67
25 7 0.23
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (24 bp):
ATTTAATATTTTTTATATATTGAC
Found at i:6393762 original size:3 final size:3
Alignment explanation
Indices: 6393756--6393812 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
6393746 AAAAAAAAAA
6393756 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
6393804 AAG AAG AAG
1 AAG AAG AAG
6393813 GGGCCTACAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6409034 original size:30 final size:30
Alignment explanation
Indices: 6408998--6409060 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
6408988 ACTTATTTTA
6408998 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
6409028 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
6409058 TTG
1 TTG
6409061 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:6411243 original size:38 final size:38
Alignment explanation
Indices: 6411201--6411277 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
6411191 CCTTAATTTG
6411201 TATTATAGGCCCTCATAAAGCCCTTAATAAATCCAAAA
1 TATTATAGGCCCTCATAAAGCCCTTAATAAATCCAAAA
6411239 TATTATAGGCCCTCATAAAGCCCTTAATAAATCCAAAA
1 TATTATAGGCCCTCATAAAGCCCTTAATAAATCCAAAA
6411277 T
1 T
6411278 TCACTACCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (38 bp):
TATTATAGGCCCTCATAAAGCCCTTAATAAATCCAAAA
Found at i:6413076 original size:5 final size:6
Alignment explanation
Indices: 6413056--6413089 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
6413046 ATGAATAGAA
* *
6413056 AAAATG GAAATG AAAATA AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
6413090 CTTACAATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:6413078 original size:18 final size:18
Alignment explanation
Indices: 6413055--6413089 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6413045 AATGAATAGA
*
6413055 AAAAATGGAAATGAAAAT
1 AAAAATGAAAATGAAAAT
6413073 AAAAATGAAAATGAAAA
1 AAAAATGAAAATGAAAA
6413090 CTTACAATCC
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:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (18 bp):
AAAAATGAAAATGAAAAT
Found at i:6433969 original size:24 final size:24
Alignment explanation
Indices: 6433932--6434043 Score: 127
Period size: 24 Copynumber: 4.7 Consensus size: 24
6433922 TCGTTCTTTG
*
6433932 GTAAATGATGAATTGAC-GAATAAT
1 GTAAAGGATGAATTGACGGAA-AAT
*
6433956 GTAAAGGATAAATTGACGGAAAAT
1 GTAAAGGATGAATTGACGGAAAAT
* * *
6433980 ATAAAGGAGGAACTGACGGAAAAT
1 GTAAAGGATGAATTGACGGAAAAT
**
6434004 GTAAAGGATGAATTGATAGAAAAT
1 GTAAAGGATGAATTGACGGAAAAT
* *
6434028 GTAAATGCTGAATTGA
1 GTAAAGGATGAATTGA
6434044 TGGCAATTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
24 71 0.96
25 3 0.04
ACGTcount: A:0.47, C:0.04, G:0.25, T:0.23
Consensus pattern (24 bp):
GTAAAGGATGAATTGACGGAAAAT
Found at i:6434805 original size:9 final size:9
Alignment explanation
Indices: 6434785--6434842 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 9
6434775 TTTGGTTAAA
*
6434785 AATTAACTG
1 AATTAACCG
*
6434794 AATTACCCG
1 AATTAACCG
*
6434803 AATTAACTG
1 AATTAACCG
6434812 AATTAACCG
1 AATTAACCG
* *
6434821 AATTACCCA
1 AATTAACCG
6434830 AATTAACCG
1 AATTAACCG
6434839 AATT
1 AATT
6434843 GAATCACTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:6434808 original size:18 final size:18
Alignment explanation
Indices: 6434785--6434842 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
6434775 TTTGGTTAAA
*
6434785 AATTAACTGAATTACCCG
1 AATTAACTGAATTAACCG
6434803 AATTAACTGAATTAACCG
1 AATTAACTGAATTAACCG
* **
6434821 AATTACCCAAATTAACCG
1 AATTAACTGAATTAACCG
6434839 AATT
1 AATT
6434843 GAATCACTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (18 bp):
AATTAACTGAATTAACCG
Found at i:6434823 original size:27 final size:27
Alignment explanation
Indices: 6434785--6434842 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
6434775 TTTGGTTAAA
* * *
6434785 AATTAACTGAATTACCCGAATTAACTG
1 AATTAACCGAATTACCCAAATTAACCG
6434812 AATTAACCGAATTACCCAAATTAACCG
1 AATTAACCGAATTACCCAAATTAACCG
6434839 AATT
1 AATT
6434843 GAATCACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (27 bp):
AATTAACCGAATTACCCAAATTAACCG
Found at i:6438360 original size:22 final size:20
Alignment explanation
Indices: 6438318--6438358 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
6438308 TGTTATAACT
6438318 TTTTTTTATTTACCAATATA
1 TTTTTTTATTTACCAATATA
*
6438338 TTTTTTTATTTACCAAAATA
1 TTTTTTTATTTACCAATATA
6438358 T
1 T
6438359 ATCAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTTTATTTACCAATATA
Found at i:6438446 original size:27 final size:27
Alignment explanation
Indices: 6438416--6438486 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 27
6438406 TGGTCACGCT
* *
6438416 AATGGCATTGGCGTCACCGATGGTGCC
1 AATGCCATTGGCGGCACCGATGGTGCC
6438443 AATGCCATTGGCGGCACCGATGGTGCC
1 AATGCCATTGGCGGCACCGATGGTGCC
6438470 ATATTG--ATTGGCGGCAC
1 A-A-TGCCATTGGCGGCAC
6438487 TATTTGTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 37 0.93
28 1 0.03
29 2 0.05
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (27 bp):
AATGCCATTGGCGGCACCGATGGTGCC
Found at i:6441670 original size:21 final size:21
Alignment explanation
Indices: 6441646--6441715 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 21
6441636 CCTTCCTTCC
6441646 CTCTTCTTCTTCCTTTTTTTT
1 CTCTTCTTCTTCCTTTTTTTT
* *
6441667 CTCTTCTCCTTTCCTTTTCTTT
1 CTCTTCTTC-TTCCTTTTTTTT
*
6441689 C-CTTCTTTCTTTCTTTTTTCTT
1 CTCTTC-TTCTTCCTTTTTT-TT
6441711 CTCTT
1 CTCTT
6441716 TTCCTTTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 20 0.50
22 17 0.43
23 3 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (21 bp):
CTCTTCTTCTTCCTTTTTTTT
Found at i:6441677 original size:34 final size:34
Alignment explanation
Indices: 6441626--6441778 Score: 104
Period size: 35 Copynumber: 4.5 Consensus size: 34
6441616 AAATTACTTT
*
6441626 CTTTTTTTT-TCCT-TCCTTCCCTCTTCTTCTTC
1 CTTTTTTTTCTCTTCTCCTTCCCTCTTCTTCTTC
* *
6441658 CTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTT
1 CTTTTTTTTCTCTTCTCC-TTCC--CTC-TT-CTTCTTC
* * *
6441697 CTTTCTTTTT-TCTTCTCTTTTCCTTTTCTTCTT-
1 CTTT-TTTTTCTCTTCTCCTTCCCTCTTCTTCTTC
* *
6441730 CTTCTTTCTTTCTCTTCTCCTTTCCTTTTC-T-TTC
1 CTT-TTT-TTTCTCTTCTCCTTCCCTCTTCTTCTTC
*
6441764 CTTCTTTTTCT-TTCT
1 CTTTTTTTTCTCTTCT
6441779 TTCCTCTCCT
Statistics
Matches: 100, Mismatches: 9, Indels: 25
0.75 0.07 0.19
Matches are distributed among these distances:
31 4 0.04
32 14 0.14
33 12 0.12
34 17 0.17
35 23 0.23
36 1 0.01
37 2 0.02
38 5 0.05
39 17 0.17
40 5 0.05
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (34 bp):
CTTTTTTTTCTCTTCTCCTTCCCTCTTCTTCTTC
Found at i:6441681 original size:39 final size:36
Alignment explanation
Indices: 6441646--6441810 Score: 140
Period size: 39 Copynumber: 4.4 Consensus size: 36
6441636 CCTTCCTTCC
6441646 CTCTTCTTCTTCCTTTTTTTTCTCTTCTCCTTTCCTT
1 CTCTTCTTCTT-CTTTTTTTTCTCTTCTCCTTTCCTT
* *
6441683 TTCTTTCCTTCTTTCTTTCTTTTT-TCTTCTCTTTTCCTT
1 CTC-TT-CTTC-TTCTTT-TTTTTCTCTTCTCCTTTCCTT
* *
6441722 TTCTTCTTCTTC-TTTCTTTCTCTTCTCCTTTCCTT
1 CTCTTCTTCTTCTTTTTTTTCTCTTCTCCTTTCCTT
* * * *
6441757 TTCTT-TCCTTCTTTTTCTTTCTTTCCTCTCCTTTCTTT
1 CTCTTCTTCTTCTTTTT-TTTC--TCTTCTCCTTTCCTT
6441795 CT-TTCTTTCTTTCTTT
1 CTCTTC-TTC-TTCTTT
6441811 CCCTCTCCTT
Statistics
Matches: 106, Mismatches: 10, Indels: 21
0.77 0.07 0.15
Matches are distributed among these distances:
34 9 0.08
35 24 0.23
36 7 0.07
37 8 0.08
38 18 0.17
39 27 0.25
40 13 0.12
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (36 bp):
CTCTTCTTCTTCTTTTTTTTCTCTTCTCCTTTCCTT
Found at i:6441698 original size:4 final size:4
Alignment explanation
Indices: 6441682--6441811 Score: 94
Period size: 4 Copynumber: 32.0 Consensus size: 4
6441672 CTCCTTTCCT
*
6441682 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTC TTTTCC TTT- TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTT-C TTTC T-TTC
* *
6441728 -TTC -TTC TTTC TTTC TCTTC -TCC TTTCC TTTTC TTTC CTTC -TT- TTTC
1 TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC TTTC TTTC
*
6441774 TTTC TTTCC TCTCC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC
6441812 CCTCTCCTTC
Statistics
Matches: 104, Mismatches: 7, Indels: 30
0.74 0.05 0.21
Matches are distributed among these distances:
3 16 0.15
4 66 0.63
5 15 0.14
6 7 0.07
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:6441731 original size:22 final size:21
Alignment explanation
Indices: 6441650--6441734 Score: 61
Period size: 22 Copynumber: 4.0 Consensus size: 21
6441640 CCTTCCCTCT
*
6441650 TCTTCTTCCTTTTTTTTCTCTTC
1 TCTT-TTCCTTTTTTCT-TCTTC
* * *
6441673 TCCTTTCCTTTTCT-TTCCT-
1 TCTTTTCCTTTTTTCTTCTTC
*
6441692 TC-TTT-CTTTCTTTTTTCTTC
1 TCTTTTCCTTT-TTTCTTCTTC
6441712 TCTTTTCCTTTTCTTCTTCTTC
1 TCTTTTCCTTTT-TTCTTCTTC
6441734 T
1 T
6441735 TTCTTTCTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
17 4 0.08
18 5 0.10
19 6 0.12
20 5 0.10
21 5 0.10
22 22 0.44
23 3 0.06
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (21 bp):
TCTTTTCCTTTTTTCTTCTTC
Found at i:6441734 original size:40 final size:40
Alignment explanation
Indices: 6441647--6441781 Score: 152
Period size: 40 Copynumber: 3.4 Consensus size: 40
6441637 CTTCCTTCCC
* *
6441647 TCTTCTTCTTCCTTT-TTTTTCTCTTCTCCTTTCCTTTTCT
1 TCTTCTTCTTTCTTTCTTTTT-TCTTCTCTTTTCCTTTTCT
*
6441687 T-TCCTTCTTTCTTTCTTTTTTCTTCTCTTTTCCTTTTCT
1 TCTTCTTCTTTCTTTCTTTTTTCTTCTCTTTTCCTTTTCT
* * *
6441726 TCTTCTTCTTTCTTTCTCTTCTCCTT-TCCTTTT-CTTTCCT
1 TCTTCTTCTTTCTTTCT-TTTTTCTTCT-CTTTTCCTTTTCT
*
6441766 TCTTTTTCTTTCTTTC
1 TCTTCTTCTTTCTTTC
6441782 CTCTCCTTTC
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
39 30 0.36
40 42 0.51
41 11 0.13
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (40 bp):
TCTTCTTCTTTCTTTCTTTTTTCTTCTCTTTTCCTTTTCT
Found at i:6441747 original size:22 final size:22
Alignment explanation
Indices: 6441648--6441805 Score: 70
Period size: 21 Copynumber: 7.3 Consensus size: 22
6441638 TTCCTTCCCT
6441648 CTTCTTCTTCCTT-TTT-TTTCT
1 CTTCTTCTT-CTTCTTTCTTTCT
* *
6441669 CTTCTCCTT-TCCTTTTCTTTC-
1 CTTCTTCTTCTTC-TTTCTTTCT
*
6441690 CTTCTTTCTTTCTTTTTTCTTCTCT
1 CTTC-TTC-TTCTTCTTTCTT-TCT
*
6441715 TTTCCTT-TTCTTCTTCTTCTTTCT
1 CTT-CTTCTTCTTC-T-TTCTTTCT
*
6441739 -TTC-TCTTCTCCTTTCCTTT-T
1 CTTCTTCTTCTTCTTT-CTTTCT
*
6441759 CTT-TCCTTCTT-TTTCTTTCT
1 CTTCTTCTTCTTCTTTCTTTCT
* *
6441779 -TTCCTCTCCTTTCTTTCTTTCT
1 CTTCTTCTTC-TTCTTTCTTTCT
6441801 -TTCTT
1 CTTCTT
6441806 TCTTTCCCTC
Statistics
Matches: 104, Mismatches: 14, Indels: 37
0.67 0.09 0.24
Matches are distributed among these distances:
19 7 0.07
20 10 0.10
21 30 0.29
22 25 0.24
23 15 0.14
24 7 0.07
25 9 0.09
26 1 0.01
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (22 bp):
CTTCTTCTTCTTCTTTCTTTCT
Found at i:6441747 original size:74 final size:73
Alignment explanation
Indices: 6441622--6441820 Score: 231
Period size: 74 Copynumber: 2.8 Consensus size: 73
6441612 AATAAAATTA
* *
6441622 CTTTCTTT-TTTTTTCCTTC-CTTCCCTCTTCTTCTTCCTT-TTT-TTTCTCTTCTCCTTTCCTT
1 CTTTCTTTCTTTTTT-CTTCTCTTTCCTTTTCTTCTT-CTTCTTTCTTTCTCTTCTCCTTTCCTT
6441683 TTCTTTCCTT
64 TTCTTTCCTT
6441693 CTTTCTTTCTTTTTTCTTCTCTTTTCCTTTTCTTCTTCTTCTTTCTTTCTCTTCTCCTTTCCTTT
1 CTTTCTTTCTTTTTTCTTCTC-TTTCCTTTTCTTCTTCTTCTTTCTTTCTCTTCTCCTTTCCTTT
6441758 TCTTTCCTT
65 TCTTTCCTT
* *
6441767 C-TT-TTTCTTTCTTTCCTCTCCTTT-C-TTTC-T-TTCTTTCTTTCTTTC-CCTCTCCTT
1 CTTTCTTTCTTT-TTTCTTCT-CTTTCCTTTTCTTCTTC-TTCTTTCTTTCTCTTCTCCTT
6441821 CTGCCCCCCA
Statistics
Matches: 116, Mismatches: 4, Indels: 18
0.84 0.03 0.13
Matches are distributed among these distances:
69 11 0.09
70 12 0.10
71 16 0.14
72 18 0.16
73 28 0.24
74 31 0.27
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (73 bp):
CTTTCTTTCTTTTTTCTTCTCTTTCCTTTTCTTCTTCTTCTTTCTTTCTCTTCTCCTTTCCTTTT
CTTTCCTT
Found at i:6441800 original size:40 final size:42
Alignment explanation
Indices: 6441675--6441810 Score: 131
Period size: 40 Copynumber: 3.3 Consensus size: 42
6441665 TTCTCTTCTC
* **
6441675 CTTTCCTT-TTCTTTCCTTCTTTCT-TTCTTTTTTCTTCTCTTTT
1 CTTTCCTTCTT-TTTCTTTCTTTCTCTTCTCCTTTCTT-TC-TTT
* * *
6441718 CCTTTTCTTCTTCTTCTTTCTTTCTCTTCTCCTTTC-CT-TTT
1 -CTTTCCTTCTTTTTCTTTCTTTCTCTTCTCCTTTCTTTCTTT
6441759 CTTTCCTTCTTTTTCTTTCTTTC-C-TCTCCTTTCTTTCTTT
1 CTTTCCTTCTTTTTCTTTCTTTCTCTTCTCCTTTCTTTCTTT
*
6441799 CTTTCTTTCTTT
1 CTTTCCTTCTTT
6441811 CCCTCTCCTT
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
38 9 0.12
39 2 0.03
40 35 0.45
41 3 0.04
43 1 0.01
44 18 0.23
45 10 0.13
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (42 bp):
CTTTCCTTCTTTTTCTTTCTTTCTCTTCTCCTTTCTTTCTTT
Found at i:6441806 original size:30 final size:30
Alignment explanation
Indices: 6441682--6441820 Score: 119
Period size: 30 Copynumber: 4.5 Consensus size: 30
6441672 CTCCTTTCCT
6441682 TTTCTTTCCT-T-CTTTCTTTCTTT-TTTC
1 TTTCTTTCCTCTCCTTTCTTTCTTTCTTTC
* *
6441709 TTCTCTTTTCCTTTTC-TTC-TTC-TTCTTTC
1 TT-TC-TTTCCTCTCCTTTCTTTCTTTCTTTC
* *
6441738 TTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTC
1 -TT-TCTT-TCCTCTCC-TTTCTTT-CTT-TCTTTC
6441774 TTTCTTTCCTCTCCTTTCTTTCTTTCTTTC
1 TTTCTTTCCTCTCCTTTCTTTCTTTCTTTC
6441804 TTTCTTTCCCTCTCCTT
1 TTTCTTT-CCTCTCCTT
6441821 CTGCCCCCCA
Statistics
Matches: 94, Mismatches: 4, Indels: 24
0.77 0.03 0.20
Matches are distributed among these distances:
27 2 0.02
28 4 0.04
29 15 0.16
30 28 0.30
31 13 0.14
32 10 0.11
33 9 0.10
34 5 0.05
35 3 0.03
36 5 0.05
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (30 bp):
TTTCTTTCCTCTCCTTTCTTTCTTTCTTTC
Found at i:6441990 original size:28 final size:28
Alignment explanation
Indices: 6441958--6442012 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
6441948 TTTTTACAAG
6441958 TTTTTTTATATATTTTGGTAAATAAAAT
1 TTTTTTTATATATTTTGGTAAATAAAAT
6441986 TTTTTTTATATATTTTGGTAAATAAAA
1 TTTTTTTATATATTTTGGTAAATAAAA
6442013 AAAGTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (28 bp):
TTTTTTTATATATTTTGGTAAATAAAAT
Found at i:6442783 original size:14 final size:13
Alignment explanation
Indices: 6442757--6442807 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
6442747 ATTTATTTTA
6442757 AATATAATAATAT
1 AATATAATAATAT
6442770 AATATAATTAATAT
1 AATATAA-TAATAT
* *
6442784 AAT-TTACAATAT
1 AATATAATAATAT
*
6442796 AATAAAATAATA
1 AATATAATAATA
6442808 ACATACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:6445136 original size:23 final size:23
Alignment explanation
Indices: 6445081--6445130 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
6445071 ACGTTCCAAC
*
6445081 TTTTTTTTTAAAATTATATTTAA
1 TTTTTATTTAAAATTATATTTAA
*
6445104 TTTTTATTTAAAATT-T-TTTAG
1 TTTTTATTTAAAATTATATTTAA
6445125 TTTTTA
1 TTTTTA
6445131 AATTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 1 0.04
23 14 0.56
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTTTATTTAAAATTATATTTAA
Found at i:6445306 original size:16 final size:16
Alignment explanation
Indices: 6445262--6445313 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
6445252 ATCAATAAGA
6445262 AAAACATTTTTAAAATT
1 AAAA-ATTTTTAAAATT
**
6445279 AAAAATGATTAAAATT
1 AAAAATTTTTAAAATT
*
6445295 ATAAATTTTTAAAAATT
1 AAAAATTTTT-AAAATT
6445312 AA
1 AA
6445314 TTAAATATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAAATTTTTAAAATT
Found at i:6445454 original size:23 final size:21
Alignment explanation
Indices: 6445414--6445461 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
6445404 AATTTGACAA
* *
6445414 AAAAATATAAATTTAATAACT
1 AAAAATAAAAATTTAATAAAT
6445435 AAAAATAAAAATATTAAATAAAT
1 AAAAATAAAAAT-TT-AATAAAT
6445458 AAAA
1 AAAA
6445462 CTATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 2 0.09
23 10 0.43
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAATAAAAATTTAATAAAT
Found at i:6445719 original size:13 final size:13
Alignment explanation
Indices: 6445698--6445746 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
6445688 CTCCACATCT
* *
6445698 ATTTGATTAATTA
1 ATTTTATTAATTG
6445711 ATTTTATTAATTG
1 ATTTTATTAATTG
*
6445724 ATTTAATTAATTG
1 ATTTTATTAATTG
*
6445737 ATTCTATTAA
1 ATTTTATTAA
6445747 CTGTTTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (13 bp):
ATTTTATTAATTG
Found at i:6460792 original size:24 final size:24
Alignment explanation
Indices: 6460760--6460813 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
6460750 TCTTTCTAGA
6460760 ATATTTAGTATTTATTAGCATAAT
1 ATATTTAGTATTTATTAGCATAAT
6460784 ATATTTAGTATTTATTAGCATAAT
1 ATATTTAGTATTTATTAGCATAAT
*
6460808 TTATTT
1 ATATTT
6460814 GACCTACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (24 bp):
ATATTTAGTATTTATTAGCATAAT
Found at i:6462877 original size:24 final size:24
Alignment explanation
Indices: 6462850--6462896 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
6462840 GCTTATAATA
6462850 GGTAGCTCCAAAGAGCAATTAACG
1 GGTAGCTCCAAAGAGCAATTAACG
* *
6462874 GGTAGCTTCGAAGAGCAATTAAC
1 GGTAGCTCCAAAGAGCAATTAAC
6462897 AGGAAGTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (24 bp):
GGTAGCTCCAAAGAGCAATTAACG
Found at i:6462976 original size:26 final size:26
Alignment explanation
Indices: 6462941--6463006 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
6462931 AAGCGAGGAC
*
6462941 TAATGGGAAGCTCACAAAGAGCC-TT
1 TAATGGGAAGCTCACAAAGAGCCATA
*
6462966 TAATCGGGAAGCTCACGAAGAGCCATA
1 TAAT-GGGAAGCTCACAAAGAGCCATA
*
6462993 TAATGGGATGCTCA
1 TAATGGGAAGCTCA
6463007 TAAGAGTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.11
26 27 0.75
27 5 0.14
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (26 bp):
TAATGGGAAGCTCACAAAGAGCCATA
Found at i:6464297 original size:21 final size:21
Alignment explanation
Indices: 6464231--6464297 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
6464221 ATACACCAAT
* *
6464231 AGAAGCTCGTAAGAGCTAAAC
1 AGAAGCTCATAAGAGCTGAAC
* * * * *
6464252 AAAAACTCATAAGAGTTGTAT
1 AGAAGCTCATAAGAGCTGAAC
6464273 AGAAGCTCATAAGAGCTGAAC
1 AGAAGCTCATAAGAGCTGAAC
6464294 AGAA
1 AGAA
6464298 AGTAAAACAC
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTGAAC
Found at i:6466211 original size:27 final size:26
Alignment explanation
Indices: 6466164--6466216 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
6466154 TTTTAAAAAA
* ** *
6466164 TAAATTTTAAAATTTTTTTAATTGTT
1 TAAATTTTAAAAATTAATTAAATGTT
6466190 TAAATTTTTAAAAATTAATTAAATGTT
1 TAAA-TTTTAAAAATTAATTAAATGTT
6466217 GATGTGTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (26 bp):
TAAATTTTAAAAATTAATTAAATGTT
Found at i:6469450 original size:529 final size:529
Alignment explanation
Indices: 6468452--6469504 Score: 2081
Period size: 529 Copynumber: 2.0 Consensus size: 529
6468442 TTTATATAAT
*
6468452 TAAATTACTTAAAGTTCATTTCCCTTTTTTTGATCCAAACTTTTCTTTTGTACAAAATTACTCTC
1 TAAATTACTCAAAGTTCATTTCCCTTTTTTTGATCCAAACTTTTCTTTTGTACAAAATTACTCTC
6468517 TTTCTTAACTTTTTATATTATATATATATGTTTTATAAGATTAGCTTTAGCTCTCAGTTTTCACT
66 TTTCTTAACTTTTTATATTATATATATATGTTTTATAAGATTAGCTTTAGCTCTCAGTTTTCACT
6468582 TTCACATTGAGTTATTTGAGCATTTTTCATTTTTCTTTCTAATGTGGGACAGATTTCATTTTTTT
131 TTCACATTGAGTTATTTGAGCATTTTTCATTTTTCTTTCTAATGTGGGACAGATTTCATTTTTTT
6468647 AAAAAGAAAAAAATATATTGTTTTTGTTGCCTCAATCCTCTTTATTTGTCTCTTTAACCTCATTG
196 AAAAAGAAAAAAATATATTGTTTTTGTTGCCTCAATCCTCTTTATTTGTCTCTTTAACCTCATTG
6468712 GATATGGAGTCTATATTGTCTTTTCTTTTCAGTTTTTCCATTTTAGATTTATAGTTAAACTTCAA
261 GATATGGAGTCTATATTGTCTTTTCTTTTCAGTTTTTCCATTTTAGATTTATAGTTAAACTTCAA
6468777 AGTAGTTCTGCTTCAAGTTAAAACAGTGGGGTTTTTTACATTGATCATCTTAAGTTTTCAGAAAA
326 AGTAGTTCTGCTTCAAGTTAAAACAGTGGGGTTTTTTACATTGATCATCTTAAGTTTTCAGAAAA
6468842 TATTTTTCCTGTTGATTTTGGATTTTTTAAGGTTATTTTTGTTTTTCCTTCCTCAAATGCTTTTT
391 TATTTTTCCTGTTGATTTTGGATTTTTTAAGGTTATTTTTGTTTTTCCTTCCTCAAATGCTTTTT
6468907 TTTTTCTGATTTAATGAATATGGCAGGATTAAGCTCTAGAAATCCATGATTAACTGAGGACTTTA
456 TTTTTCTGATTTAATGAATATGGCAGGATTAAGCTCTAGAAATCCATGATTAACTGAGGACTTTA
6468972 TATTTTTTA
521 TATTTTTTA
6468981 TAAATTACTCAAAGTTCATTTCCCTTTTTTTGATCCAAACTTTTCTTTTGTACAAAATTACTCTC
1 TAAATTACTCAAAGTTCATTTCCCTTTTTTTGATCCAAACTTTTCTTTTGTACAAAATTACTCTC
6469046 TTTCTTAACTTTTTATATTATATATATATGTTTTATAAGATTAGCTTTAGCTCTCAGTTTTCACT
66 TTTCTTAACTTTTTATATTATATATATATGTTTTATAAGATTAGCTTTAGCTCTCAGTTTTCACT
6469111 TTCACATTGAGTTATTTGAGCATTTTTCATTTTTCTTTCTAATGTGGGACAGATTTCATTTTTTT
131 TTCACATTGAGTTATTTGAGCATTTTTCATTTTTCTTTCTAATGTGGGACAGATTTCATTTTTTT
6469176 AAAAAGAAAAAAAATATATTGTTTTTGTTGCCTCAATCCTCTTTATTTGTCTCTTTAACCTCATT
196 AAAAAG-AAAAAAATATATTGTTTTTGTTGCCTCAATCCTCTTTATTTGTCTCTTTAACCTCATT
6469241 GGATATGGAGTCTATATTGTCTTTTCTTTTCAGTTTTTCCATTTTAGATTTATAGTTAAACTTCA
260 GGATATGGAGTCTATATTGTCTTTTCTTTTCAGTTTTTCCATTTTAGATTTATAGTTAAACTTCA
6469306 AAGTAGTTCTGCTTCAAGTTAAAACAGTGGGGTTTTTTACATTGATCATCTTAAGTTTTCAGAAA
325 AAGTAGTTCTGCTTCAAGTTAAAACAGTGGGGTTTTTTACATTGATCATCTTAAGTTTTCAGAAA
6469371 ATATTTTTCCTGTTGATTTTGGATTTTTTAAGGTTATTTTTGTTTTTCCTTCCTCAAATGC-TTT
390 ATATTTTTCCTGTTGATTTTGGATTTTTTAAGGTTATTTTTGTTTTTCCTTCCTCAAATGCTTTT
6469435 TTTTTTCTGATTTAATGAATATGGCAGGATTAAGCTCTAGAAATCCATGATTAACTGAGGACTTT
455 TTTTTTCTGATTTAATGAATATGGCAGGATTAAGCTCTAGAAATCCATGATTAACTGAGGACTTT
6469500 ATATT
520 ATATT
6469505 GGGTCCTCAG
Statistics
Matches: 522, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
529 273 0.52
530 249 0.48
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (529 bp):
TAAATTACTCAAAGTTCATTTCCCTTTTTTTGATCCAAACTTTTCTTTTGTACAAAATTACTCTC
TTTCTTAACTTTTTATATTATATATATATGTTTTATAAGATTAGCTTTAGCTCTCAGTTTTCACT
TTCACATTGAGTTATTTGAGCATTTTTCATTTTTCTTTCTAATGTGGGACAGATTTCATTTTTTT
AAAAAGAAAAAAATATATTGTTTTTGTTGCCTCAATCCTCTTTATTTGTCTCTTTAACCTCATTG
GATATGGAGTCTATATTGTCTTTTCTTTTCAGTTTTTCCATTTTAGATTTATAGTTAAACTTCAA
AGTAGTTCTGCTTCAAGTTAAAACAGTGGGGTTTTTTACATTGATCATCTTAAGTTTTCAGAAAA
TATTTTTCCTGTTGATTTTGGATTTTTTAAGGTTATTTTTGTTTTTCCTTCCTCAAATGCTTTTT
TTTTTCTGATTTAATGAATATGGCAGGATTAAGCTCTAGAAATCCATGATTAACTGAGGACTTTA
TATTTTTTA
Found at i:6476482 original size:22 final size:21
Alignment explanation
Indices: 6476431--6476483 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
6476421 TTTGCTTGTT
* * *
6476431 TTACTGTTTTTTATTGTTTTG
1 TTACTATTTTTTATTATATTG
6476452 TTA-TCATTTTATTATTATATTG
1 TTACT-ATTTT-TTATTATATTG
6476474 TTACTATTTT
1 TTACTATTTT
6476484 GTTGTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 7 0.27
22 17 0.65
23 1 0.04
ACGTcount: A:0.19, C:0.06, G:0.08, T:0.68
Consensus pattern (21 bp):
TTACTATTTTTTATTATATTG
Found at i:6477530 original size:18 final size:17
Alignment explanation
Indices: 6477513--6477580 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 17
6477503 TAATAATATA
6477513 TTAAAATTTAATTTTA-
1 TTAAAATTTAATTTTAT
* *
6477529 TAAATTAATTTAA-TGTAT
1 TTAA--AATTTAATTTTAT
*
6477547 TTAAAATTTTTAAGTTTAT
1 TTAAAA--TTTAATTTTAT
*
6477566 TTAAAATTAAATTTT
1 TTAAAATTTAATTTT
6477581 TAAATACTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
16 5 0.12
17 10 0.25
18 15 0.38
19 10 0.25
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTAAAATTTAATTTTAT
Found at i:6477765 original size:13 final size:12
Alignment explanation
Indices: 6477723--6477764 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
6477713 ATTGTGCATG
6477723 TTAATTTTAAAT
1 TTAATTTTAAAT
*
6477735 TAAATTTTAAAT
1 TTAATTTTAAAT
6477747 TTAATATTTAAAT
1 TTAAT-TTTAAAT
6477760 TTAAT
1 TTAAT
6477765 AATAACGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAATTTTAAAT
Found at i:6488841 original size:21 final size:21
Alignment explanation
Indices: 6488808--6488849 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6488798 TCATAAATTT
* * *
6488808 TTTTACATCATATAATTAAAA
1 TTTTAAATAATATAATAAAAA
6488829 TTTTAAATAATATAATAAAAA
1 TTTTAAATAATATAATAAAAA
6488850 AAATTAAATT
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:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTTAAATAATATAATAAAAA
Found at i:6517635 original size:25 final size:26
Alignment explanation
Indices: 6517607--6517664 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 26
6517597 CATCAAAATC
6517607 TATTTTCTTTA-GAAATATAA-ATTAA
1 TATTTTCTTTATGAAA-ATAATATTAA
*
6517632 TATTTTTTTTATGAAAATAATTATTAA
1 TATTTTCTTTATGAAAATAA-TATTAA
6517659 TATTTT
1 TATTTT
6517665 TAAGAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 14 0.48
26 4 0.14
27 11 0.38
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (26 bp):
TATTTTCTTTATGAAAATAATATTAA
Found at i:6517649 original size:27 final size:25
Alignment explanation
Indices: 6517607--6517665 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
6517597 CATCAAAATC
*
6517607 TATTTTCTTTAGAAAT-ATAAATTAA
1 TATTTTTTTTAGAAATAAT-AATTAA
*
6517632 TATTTTTTTTATGAAAATAATTATTAA
1 TATTTTTTTTA-G-AAATAATAATTAA
6517659 TATTTTT
1 TATTTTT
6517666 AAGAAAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 10 0.34
26 1 0.03
27 16 0.55
28 2 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (25 bp):
TATTTTTTTTAGAAATAATAATTAA
Found at i:6518536 original size:30 final size:30
Alignment explanation
Indices: 6518502--6518564 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
6518492 GCGGAAAATA
* *
6518502 GCCCATTCCGGTAAATAATT-AAAAAAACCG
1 GCCCATTCCGATAAAT-ATTGAAAAAAAACG
* *
6518532 GCCCATTTCGATAAATTTTGAAAAAAAACG
1 GCCCATTCCGATAAATATTGAAAAAAAACG
6518562 GCC
1 GCC
6518565 TTTTTTGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (30 bp):
GCCCATTCCGATAAATATTGAAAAAAAACG
Found at i:6532252 original size:27 final size:27
Alignment explanation
Indices: 6532195--6532253 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
6532185 TCGAAAAATT
** *
6532195 TATTGTAATTTATATTTTTAAGTTAAT
1 TATTGTAATTTATATTAATAAGTTAAA
*
6532222 TATTGTAATTTATGTTAAATAAG-TAAA
1 TATTGTAATTTATATT-AATAAGTTAAA
6532249 TATTG
1 TATTG
6532254 ATTTTGAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (27 bp):
TATTGTAATTTATATTAATAAGTTAAA
Found at i:6532632 original size:44 final size:43
Alignment explanation
Indices: 6532432--6532800 Score: 161
Period size: 44 Copynumber: 8.4 Consensus size: 43
6532422 GATTCGCCAC
* * * * * *
6532432 CGTAACCTCAGGGAGGTAAAATTTGCCATCTTCGATCTGCTCCA
1 CGTAACCT-AGGGAGATAAGATCTGACATCTTCAATCTACTCCA
* * * * *
6532476 C-TACCGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTTCA
1 CGTAAC-C-TAGGGAGATAAGATCTGACATCTTCAATCTACTCCA
* * *
6532520 CTGCCAA-CTAGGGGGAT-AGAAT-T-AC-TGGCTTCAATGTACTCCA
1 C-G-TAACCTAGGGAGATAAG-ATCTGACAT--CTTCAATCTACTCCA
* * * * *
6532563 CTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCA
1 C-GTAACCT-AGGGAGATAAGATCTGACATCTTCAATCTACTCCA
* *
6532608 C-TAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCA
1 CGTAA--CCTAGGGAGATAAGATCTGACATCTTCAATCTACTCCA
** *
6532652 CTGTCAACC-AGGGAGAT-AGAAT-T-ACGGCTTCAATGTACTCCA
1 C-GT-AACCTAGGGAGATAAG-ATCTGACATCTTCAATCTACTCCA
* * * * * *
6532694 CTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCA
1 C-GTAACC-TAGGGAGATAAGATCTGACATCTTCAATCTACTCCA
* *
6532739 C-TAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCA
1 CGTAA--CCTAGGGAGATAAGATCTGACATCTTCAATCTACTCCA
*
6532783 CTGCCAACC-AGGGAGATA
1 C-G-TAACCTAGGGAGATA
6532801 GAATTACGGC
Statistics
Matches: 239, Mismatches: 56, Indels: 60
0.67 0.16 0.17
Matches are distributed among these distances:
41 5 0.02
42 21 0.09
43 41 0.17
44 124 0.52
45 40 0.17
46 2 0.01
47 6 0.03
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (43 bp):
CGTAACCTAGGGAGATAAGATCTGACATCTTCAATCTACTCCA
Found at i:6532670 original size:132 final size:131
Alignment explanation
Indices: 6532428--6532832 Score: 693
Period size: 131 Copynumber: 3.1 Consensus size: 131
6532418 ATTGGATTCG
* * ** * *
6532428 CCACCGTAACCTCAGGGAGGTAAAATTTGCCATCTTCGATCTGCTCCACTACCGCTTAAGGAGAT
1 CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
* * *
6532493 AAGATCTGAAATCTTCAATCTATTTCACTGCCAACTAGGGGGATAGAATTACTGGCTTCAATGTA
66 AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTAC-GGCTTCAATGTA
6532558 CT
130 CT
6532560 CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
1 CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
*
6532625 AAGATCTGAAATCTTCAATCTATTCCACTGTCAACCAGGGAGATAGAATTACGGCTTCAATGTAC
66 AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTCAATGTAC
6532690 T
131 T
*
6532691 CCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
1 CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
*
6532756 AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTCAATATAC
66 AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTCAATGTAC
6532821 T
131 T
6532822 CCACTGTAACC
1 CCACTGTAACC
6532833 ACAGTCCACT
Statistics
Matches: 260, Mismatches: 13, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
131 153 0.59
132 107 0.41
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (131 bp):
CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTCAATGTAC
T
Found at i:6532696 original size:42 final size:43
Alignment explanation
Indices: 6532487--6532833 Score: 162
Period size: 44 Copynumber: 8.0 Consensus size: 43
6532477 TACCGCTTAA
* * * * * *
6532487 GGAGATA-AGATCTGAAATCTTCAATCTATTTCACTGCCAACTAG
1 GGAGATAGA-ATCTGACAGCTTCAATCTACTCCACTG-TAACCAG
* * *
6532531 GGGGATAGAAT-T-ACTGGCTTCAATGTACTCCACTGTAACCTCAG
1 GGAGATAGAATCTGAC-AGCTTCAATCTACTCCACTGTAA-C-CAG
* * * * * *
6532575 GGAGGTAAAATCTGCCATCTTCGATCTGCTCCAC--TAATGCCTAG
1 GGAGATAGAATCTGACAGCTTCAATCTACTCCACTGTAA--CC-AG
* * *
6532619 GGAGATA-AGATCTGAAATCTTCAATCTATTCCACTGTCAACCAG
1 GGAGATAGA-ATCTGACAGCTTCAATCTACTCCACTGT-AACCAG
* *
6532663 GGAGATAGAAT-T-ACGGCTTCAATGTACTCCACTGTAACCACAG
1 GGAGATAGAATCTGACAGCTTCAATCTACTCCACTGTAA-C-CAG
* * * * * *
6532706 GGAGGTAAAATCTGCCATCTTCGATCTGCTCCAC--TAATGCCTAG
1 GGAGATAGAATCTGACAGCTTCAATCTACTCCACTGTAA--CC-AG
* * * *
6532750 GGAGATA-AGATCTGAAATCTTCAATCTATTCCACTGCCAACCAG
1 GGAGATAGA-ATCTGACAGCTTCAATCTACTCCACTG-TAACCAG
* *
6532794 GGAGATAGAAT-T-ACGGCTTCAATATACTCCACTGTAACCA
1 GGAGATAGAATCTGACAGCTTCAATCTACTCCACTGTAACCA
6532834 CAGTCCACTA
Statistics
Matches: 227, Mismatches: 52, Indels: 51
0.69 0.16 0.15
Matches are distributed among these distances:
41 7 0.03
42 39 0.17
43 41 0.18
44 99 0.44
45 35 0.15
46 2 0.01
47 4 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (43 bp):
GGAGATAGAATCTGACAGCTTCAATCTACTCCACTGTAACCAG
Found at i:6532900 original size:44 final size:44
Alignment explanation
Indices: 6532847--6533140 Score: 169
Period size: 44 Copynumber: 6.7 Consensus size: 44
6532837 TCCACTAATG
*
6532847 CCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
1 CCTAGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTG-CAA
*** * *
6532892 CC-AGGGAGAT-AGAAT-T-ACGGCTTCAATGTACTCCACTGTAA
1 CCTAGGGAGATAAG-ATCTGAAATCTTCAATCTACTCCACTGCAA
* * ** * *
6532933 CC-ACGGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT--AA
1 CCTA--GGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCAA
*
6532976 TGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
1 --CCTAGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTG-CAA
*** * *
6533023 CCTA-GGAGAT-AGAAT-T-ACGGCTTCAATGTACTCCACTGTAA
1 CCTAGGGAGATAAG-ATCTGAAATCTTCAATCTACTCCACTGCAA
* * * ** * * **
6533064 CCACAGGGAGGTAAAATCTGTCATCTTCGATCTACTCCACTACTG
1 CC-TAGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCAA
* *
6533109 CTTAGGGAAATAAGATCTGAAATCTTCAATCT
1 CCTAGGGAGATAAGATCTGAAATCTTCAATCT
6533141 TTTAAATTGC
Statistics
Matches: 184, Mismatches: 47, Indels: 37
0.69 0.18 0.14
Matches are distributed among these distances:
41 9 0.05
42 35 0.19
43 23 0.12
44 74 0.40
45 40 0.22
46 1 0.01
47 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (44 bp):
CCTAGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCAA
Found at i:6532911 original size:102 final size:102
Alignment explanation
Indices: 6532735--6532936 Score: 395
Period size: 102 Copynumber: 2.0 Consensus size: 102
6532725 TTCGATCTGC
6532735 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
1 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
6532800 AGAATTACGGCTTCAATATACTCCACTGTAACCACAG
66 AGAATTACGGCTTCAATATACTCCACTGTAACCACAG
6532837 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
1 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
*
6532902 AGAATTACGGCTTCAATGTACTCCACTGTAACCAC
66 AGAATTACGGCTTCAATATACTCCACTGTAACCAC
6532937 GGGGAGGTAA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.25
Consensus pattern (102 bp):
TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
AGAATTACGGCTTCAATATACTCCACTGTAACCACAG
Found at i:6533011 original size:233 final size:233
Alignment explanation
Indices: 6532604--6533069 Score: 889
Period size: 233 Copynumber: 2.0 Consensus size: 233
6532594 TTCGATCTGC
*
6532604 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTCAACCAGGGAGAT
1 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
6532669 AGAATTACGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTG
66 AGAATTACGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTG
6532734 CTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACC-AGGGAG
131 CTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCTA-GGAG
6532798 ATAGAATTACGGCTTCAATATACTCCACTGTAACCACAG
195 ATAGAATTACGGCTTCAATATACTCCACTGTAACCACAG
6532837 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
1 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
*
6532902 AGAATTACGGCTTCAATGTACTCCACTGTAACCACGGGGAGGTAAAATCTGCCATCTTCGATCTG
66 AGAATTACGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTG
6532967 CTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCTAGGAGA
131 CTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCTAGGAGA
*
6533032 TAGAATTACGGCTTCAATGTACTCCACTGTAACCACAG
196 TAGAATTACGGCTTCAATATACTCCACTGTAACCACAG
6533070 GGAGGTAAAA
Statistics
Matches: 229, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
233 228 1.00
234 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (233 bp):
TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
AGAATTACGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTG
CTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCTAGGAGA
TAGAATTACGGCTTCAATATACTCCACTGTAACCACAG
Found at i:6533073 original size:131 final size:131
Alignment explanation
Indices: 6532837--6533140 Score: 538
Period size: 131 Copynumber: 2.3 Consensus size: 131
6532827 GTAACCACAG
6532837 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
1 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
* *
6532902 AGAATTACGGCTTCAATGTACTCCACTGTAACCACGGGGAGGTAAAATCTGCCATCTTCGATCTG
66 AGAATTACGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTA
6532967 C
131 C
6532968 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCTA-GGAGA
1 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACC-AGGGAGA
*
6533032 TAGAATTACGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGTCATCTTCGATCT
65 TAGAATTACGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCT
6533097 AC
130 AC
* * *
6533099 TCCACTACTGCTTAGGGAAATAAGATCTGAAATCTTCAATCT
1 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCT
6533141 TTTAAATTGC
Statistics
Matches: 166, Mismatches: 6, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
131 165 0.99
132 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (131 bp):
TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
AGAATTACGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTA
C
Found at i:6534616 original size:23 final size:24
Alignment explanation
Indices: 6534590--6534637 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
6534580 CCTTAGCCTC
6534590 TCCATTTTTACTTTTTC-CATTTT
1 TCCATTTTTACTTTTTCACATTTT
*
6534613 TCCATTTTTATTTTTTCACATTTT
1 TCCATTTTTACTTTTTCACATTTT
6534637 T
1 T
6534638 TTTTGCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.67
Consensus pattern (24 bp):
TCCATTTTTACTTTTTCACATTTT
Found at i:6534628 original size:16 final size:15
Alignment explanation
Indices: 6534609--6534641 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
6534599 ACTTTTTCCA
6534609 TTTTTC-CATTTTTAT
1 TTTTTCACATTTTT-T
6534624 TTTTTCACATTTTTT
1 TTTTTCACATTTTTT
6534639 TTT
1 TTT
6534642 GCAACTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTCACATTTTTT
Found at i:6535120 original size:1 final size:1
Alignment explanation
Indices: 6535114--6535229 Score: 88
Period size: 1 Copynumber: 116.0 Consensus size: 1
6535104 CCGGTAGAGG
* * * * * * * * * * *
6535114 TTTTTTTGTTTCTTTTTATTTTTTGTTTTTTGTTCTCTTTTTTTCTTTTTTTCTCTTTTTTTATT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
6535179 TTTTTGTTTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6535230 AACTGAATCT
Statistics
Matches: 83, Mismatches: 32, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 83 1.00
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.86
Consensus pattern (1 bp):
T
Found at i:6535137 original size:18 final size:18
Alignment explanation
Indices: 6535114--6535228 Score: 110
Period size: 18 Copynumber: 6.4 Consensus size: 18
6535104 CCGGTAGAGG
*
6535114 TTTTTTTGTTTCTTTTT-
1 TTTTTTTGTTTTTTTTTC
*
6535131 ATTTTTTGTTTTTTGTTCTC
1 TTTTTTTGTTTTTT-TT-TC
* *
6535151 TTTTTTTCTTTTTTTCTC
1 TTTTTTTGTTTTTTTTTC
*
6535169 TTTTTTTATTTTTTTGTT-
1 TTTTTTTGTTTTTTT-TTC
* *
6535187 TTTTTTT-TGTTTTTTTG
1 TTTTTTTGTTTTTTTTTC
*
6535204 TTTTTTTGTTTTTTTTTG
1 TTTTTTTGTTTTTTTTTC
6535222 TTTTTTT
1 TTTTTTT
6535229 TAACTGAATC
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
16 2 0.02
17 25 0.30
18 41 0.49
19 3 0.04
20 12 0.14
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.86
Consensus pattern (18 bp):
TTTTTTTGTTTTTTTTTC
Found at i:6535228 original size:45 final size:45
Alignment explanation
Indices: 6535113--6535228 Score: 144
Period size: 45 Copynumber: 2.6 Consensus size: 45
6535103 CCCGGTAGAG
* *
6535113 GTTTTTTTGTTTCTTTTTATTTTTTGTTTTTTGTTCTCTTTTTTT
1 GTTTTTTTGTTTTTTTTTTTTTTTTGTTTTTTGTTCTCTTTTTTT
* * * * *
6535158 CTTTTTTTCTCTTTTTTTATTTTTTTGTTTTTT-TTTTGTTTTTTT
1 GTTTTTTTGT-TTTTTTTTTTTTTTTGTTTTTTGTTCTCTTTTTTT
6535203 GTTTTTTTGTTTTTTTTTGTTTTTTT
1 GTTTTTTTGTTTTTTTTT-TTTTTTT
6535229 TAACTGAATC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 7 0.12
45 33 0.56
46 19 0.32
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (45 bp):
GTTTTTTTGTTTTTTTTTTTTTTTTGTTTTTTGTTCTCTTTTTTT
Found at i:6539439 original size:3 final size:3
Alignment explanation
Indices: 6539431--6539489 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
6539421 ACATACATGC
* *
6539431 AAT AAT AAT -AT AGT AAT AATT AAA AAT AAAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT -AAT AAT AAT AAT AAT AAT
* *
6539476 CAT AAT AAA AAT AA
1 AAT AAT AAT AAT AA
6539490 ACTAAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
2 3 0.07
3 35 0.80
4 6 0.14
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:6539466 original size:17 final size:17
Alignment explanation
Indices: 6539444--6539483 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
6539434 AATAATATAG
6539444 TAATAATTAAAAATAA-A
1 TAATAA-TAAAAATAACA
*
6539461 TAATAATAATAATAACA
1 TAATAATAAAAATAACA
6539478 TAATAA
1 TAATAA
6539484 AAATAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TAATAATAAAAATAACA
Found at i:6539481 original size:31 final size:27
Alignment explanation
Indices: 6539431--6539490 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 27
6539421 ACATACATGC
*
6539431 AATAATAATATAGTAATAATTAAAAATA
1 AATAATAATATAATAATAA-TAAAAATA
6539459 AATAATAATAATAATAACATAATAAAAATA
1 AATAATAAT-ATAAT-A-ATAATAAAAATA
6539489 AA
1 AA
6539491 CTAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 9 0.32
29 4 0.14
30 11 0.39
31 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (27 bp):
AATAATAATATAATAATAATAAAAATA
Found at i:6539488 original size:17 final size:16
Alignment explanation
Indices: 6539455--6539489 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
6539445 AATAATTAAA
*
6539455 AATAAATAATAATAAT
1 AATAAATAATAAAAAT
6539471 AATAACATAATAAAAAT
1 AATAA-ATAATAAAAAT
6539488 AA
1 AA
6539490 ACTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAATAATAAAAAT
Found at i:6543124 original size:20 final size:20
Alignment explanation
Indices: 6543099--6543141 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
6543089 GTTACCCTCC
6543099 AAAAAACACTTAAAACGTGA
1 AAAAAACACTTAAAACGTGA
6543119 AAAAAACACTTAAAACGTGA
1 AAAAAACACTTAAAACGTGA
6543139 AAA
1 AAA
6543142 CATTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.63, C:0.14, G:0.09, T:0.14
Consensus pattern (20 bp):
AAAAAACACTTAAAACGTGA
Found at i:6544901 original size:27 final size:27
Alignment explanation
Indices: 6544856--6544909 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
6544846 AACTTTAATT
*
6544856 GTGCCAATAAAAATGGCACCATTGGTG
1 GTGCCAATAAAAATAGCACCATTGGTG
* *
6544883 GTGCCAATGAGAATAGCACCATTGGTG
1 GTGCCAATAAAAATAGCACCATTGGTG
6544910 TCGCCATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (27 bp):
GTGCCAATAAAAATAGCACCATTGGTG
Found at i:6561594 original size:19 final size:20
Alignment explanation
Indices: 6561564--6561604 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
6561554 AAATTTTGAG
*
6561564 AAATTATTATTTATTTTTTA
1 AAATTATTATTTATCTTTTA
6561584 AAATT-TTATTTATCTTTTA
1 AAATTATTATTTATCTTTTA
6561603 AA
1 AA
6561605 GAAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTATTATTTATCTTTTA
Found at i:6566690 original size:3 final size:3
Alignment explanation
Indices: 6566682--6566729 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
6566672 AACTAGCCCT
6566682 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6566730 GATATAAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6566881 original size:41 final size:42
Alignment explanation
Indices: 6566831--6566911 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
6566821 CTATTTTCTG
*
6566831 GACTAATATAA-AAACATAGTGAAACATCACATCTAATTTAT
1 GACTAATATAACAAACATAATGAAACATCACATCTAATTTAT
* * *
6566872 GACTCATATAACAAACATAATGAAACATCACTTTTAATTT
1 GACTAATATAACAAACATAATGAAACATCACATCTAATTT
6566912 GGCAAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 10 0.29
42 25 0.71
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (42 bp):
GACTAATATAACAAACATAATGAAACATCACATCTAATTTAT
Found at i:6568753 original size:37 final size:37
Alignment explanation
Indices: 6568688--6568796 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
6568678 TACATATGAT
* *
6568688 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
6568723 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
6568760 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
6568797 AAAAGCTATC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 10 0.14
36 3 0.04
37 56 0.81
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:6568813 original size:46 final size:46
Alignment explanation
Indices: 6568760--6569011 Score: 292
Period size: 52 Copynumber: 5.3 Consensus size: 46
6568750 TAAGTGTAGC
* **
6568760 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCAAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
6568806 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
6568852 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAACCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
6568904 CACTTATCACTTTCCACTTGTCACTTGATTAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
6568956 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAA--TAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
6569000 CACTTGTCACTT
1 CACTTATCACTT
6569012 GATCAGAAGT
Statistics
Matches: 186, Mismatches: 13, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
44 14 0.08
46 80 0.43
49 1 0.01
50 1 0.01
51 3 0.02
52 87 0.47
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:6568971 original size:98 final size:94
Alignment explanation
Indices: 6568760--6569011 Score: 296
Period size: 98 Copynumber: 2.6 Consensus size: 94
6568750 TAAGTGTAGC
* ** *
6568760 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCAAAAGCTATCACTTATCAC--TTTGTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTTGTCA
6568823 CTTGATCAGATAAGTATAGCCGAAGCTAT
66 CTTGATCAGATAAGTATAGCCGAAGCTAT
*
6568852 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAACCGAAGCTATCACTTATCACTTT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
* * *
6568917 CCACTTGTCACTTGATTAGATAAGTGTAGCTGAAGCTAT
60 ----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
6568956 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAA--TATCACTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTT
6569012 GATCAGAAGT
Statistics
Matches: 137, Mismatches: 11, Indels: 20
0.82 0.07 0.12
Matches are distributed among these distances:
92 10 0.07
95 1 0.01
96 14 0.10
98 69 0.50
100 1 0.01
101 1 0.01
104 41 0.30
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (94 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTTGTCA
CTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:6569010 original size:44 final size:44
Alignment explanation
Indices: 6568908--6569011 Score: 131
Period size: 46 Copynumber: 2.3 Consensus size: 44
6568898 AGCTATCACT
* * *
6568908 TATCACTTTCCAC-TTGTCACTTGATTAGATAAGTGTAGCTGAAGC
1 TATCACTTT-CACTTTGTCACTTGATCAGATAAGTATAGCCGAA-C
6568953 TATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAA-
1 TATCACTT-TCACTTTGTCACTTGATCAGATAAGTATAGCCGAAC
6568997 TATCACTTGTCACTT
1 TATCACTT-TCACTT
6569012 GATCAGAAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
44 14 0.26
45 11 0.21
46 28 0.53
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (44 bp):
TATCACTTTCACTTTGTCACTTGATCAGATAAGTATAGCCGAAC
Found at i:6570284 original size:45 final size:45
Alignment explanation
Indices: 6570235--6570453 Score: 330
Period size: 45 Copynumber: 4.9 Consensus size: 45
6570225 TCGGCCATGG
* * * *
6570235 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
6570280 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
6570325 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
6570370 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
* * * **
6570415 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
6570454 TCCACCTCTT
Statistics
Matches: 162, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 162 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
Found at i:6570588 original size:16 final size:16
Alignment explanation
Indices: 6570567--6570598 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6570557 CATTCTGCAT
6570567 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
6570583 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
6570599 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:6572383 original size:19 final size:20
Alignment explanation
Indices: 6572349--6572395 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
6572339 ACTCTTAAAA
*
6572349 TTTTAGAAATTATTATTTATT
1 TTTTA-AAATTATTATTTATC
*
6572370 TTTTAAAATT-TTATTTCTC
1 TTTTAAAATTATTATTTATC
6572389 TTTTAAA
1 TTTTAAA
6572396 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.58
20 5 0.21
21 5 0.21
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTAAAATTATTATTTATC
Found at i:6578198 original size:3 final size:3
Alignment explanation
Indices: 6578190--6578237 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
6578180 AACTAGCCCT
6578190 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6578237 T
1 T
6578238 ATAAATTAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6578378 original size:41 final size:42
Alignment explanation
Indices: 6578333--6578414 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
6578323 CCTATTTTCT
* *
6578333 TGACTAATATAA-AAACATAGTGAAAGATCACATCTAATTTA
1 TGACTAATATAACAAACATAATGAAACATCACATCTAATTTA
*
6578374 TGACTCATATAACAAACATAATGAAACATCACATCTAATTT
1 TGACTAATATAACAAACATAATGAAACATCACATCTAATTT
6578415 GGCAAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 11 0.30
42 26 0.70
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (42 bp):
TGACTAATATAACAAACATAATGAAACATCACATCTAATTTA
Found at i:6579641 original size:19 final size:20
Alignment explanation
Indices: 6579611--6579651 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
6579601 AAATTTTGAG
*
6579611 AAATTATTATTTATTTTTTA
1 AAATTATTATTTATCTTTTA
*
6579631 AAATT-TTATTTCTCTTTTA
1 AAATTATTATTTATCTTTTA
6579650 AA
1 AA
6579652 GTAAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTATTATTTATCTTTTA
Found at i:6580147 original size:16 final size:16
Alignment explanation
Indices: 6580126--6580157 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6580116 TCTCCTCTTC
6580126 TTTTTTTGTTGCCCTT
1 TTTTTTTGTTGCCCTT
6580142 TTTTTTTGTTGCCCTT
1 TTTTTTTGTTGCCCTT
6580158 CCACCTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.12, T:0.69
Consensus pattern (16 bp):
TTTTTTTGTTGCCCTT
Found at i:6582711 original size:82 final size:82
Alignment explanation
Indices: 6582624--6582787 Score: 276
Period size: 82 Copynumber: 2.0 Consensus size: 82
6582614 TTAGTACATA
*
6582624 AAACACATTAAATTATAAATAATGCTTAAAAATGTCACTTGACTTTAAATA-TGTTTTTTCCAAG
1 AAACACATTAAATTATAAATAATGCTTAAAAATGTCACTTGACTTTAAA-ACTGTTTTTTCCAAA
6582688 GATTCAAAAGCATTTTCT
65 GATTCAAAAGCATTTTCT
* * *
6582706 AAACACATTAAATTATAAATAATGGTTAAAAATGTGACTTGACTTTAAAACTGTTTTTTTCAAAG
1 AAACACATTAAATTATAAATAATGCTTAAAAATGTCACTTGACTTTAAAACTGTTTTTTCCAAAG
6582771 ATTCAAAAGCATTTTCT
66 ATTCAAAAGCATTTTCT
6582788 TACTTCTGAA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
81 1 0.01
82 76 0.99
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (82 bp):
AAACACATTAAATTATAAATAATGCTTAAAAATGTCACTTGACTTTAAAACTGTTTTTTCCAAAG
ATTCAAAAGCATTTTCT
Found at i:6586739 original size:18 final size:18
Alignment explanation
Indices: 6586716--6586836 Score: 110
Period size: 18 Copynumber: 6.7 Consensus size: 18
6586706 AAAACAAAAA
6586716 TTTTGAAACACGAGAATT
1 TTTTGAAACACGAGAATT
*
6586734 TTTTGAAAACACGA-AAAT
1 TTTTG-AAACACGAGAATT
* *
6586752 TTTTGAAACAAGAAAATT
1 TTTTGAAACACGAGAATT
6586770 TTTTGAAA-AC-ATGAATTTT
1 TTTTGAAACACGA-GAA--TT
*
6586789 TTTTAAAACAC-A-AAGTT
1 TTTTGAAACACGAGAA-TT
6586806 TTTT-AAACACGAGAATT
1 TTTTGAAACACGAGAATT
6586823 TTTTGAAAACACGA
1 TTTTG-AAACACGA
6586837 AAACACGAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
16 7 0.08
17 23 0.27
18 28 0.33
19 25 0.29
20 3 0.03
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.35
Consensus pattern (18 bp):
TTTTGAAACACGAGAATT
Found at i:6586857 original size:43 final size:41
Alignment explanation
Indices: 6586793--6586920 Score: 122
Period size: 43 Copynumber: 3.1 Consensus size: 41
6586783 AATTTTTTTT
*
6586793 AAAACAC-AAAGTTTTTTAAACACGAGAATTTTTTGAAAACAC
1 AAAACACGAAAG-TTTTGAAACACG-GAATTTTTTGAAAACAC
*
6586835 GAAAACACGAAAGTTTTGAAACAC-GAA-TTTTT-AAAA-AA
1 -AAAACACGAAAGTTTTGAAACACGGAATTTTTTGAAAACAC
* * *
6586873 AAAACAAGAAAATTTTGAAAGACGGGAATTTTTTTTGAAAACAC
1 AAAACACGAAAGTTTTGAAACAC-GGAA--TTTTTTGAAAACAC
6586917 AAAA
1 AAAA
6586921 TTTTTTTAGC
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
37 20 0.28
38 1 0.01
39 7 0.10
40 5 0.07
41 3 0.04
42 5 0.07
43 21 0.30
44 9 0.13
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (41 bp):
AAAACACGAAAGTTTTGAAACACGGAATTTTTTGAAAACAC
Found at i:6586924 original size:18 final size:18
Alignment explanation
Indices: 6586903--6586993 Score: 64
Period size: 18 Copynumber: 5.1 Consensus size: 18
6586893 GACGGGAATT
6586903 TTTTTTGAAAACACAAAA
1 TTTTTTGAAAACACAAAA
* *
6586921 TTTTTT--TAGCACAAAA
1 TTTTTTGAAAACACAAAA
* *
6586937 -ATTTTG-AAACACTAGAA
1 TTTTTTGAAAACAC-AAAA
*
6586954 TTTTTCTGAAAACACTAAA
1 TTTTT-TGAAAACACAAAA
* *
6586973 TTTTTTTAAAATACGAAAA
1 TTTTTTGAAAACAC-AAAA
6586992 TT
1 TT
6586994 GTGATAAATT
Statistics
Matches: 55, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
15 4 0.07
16 12 0.22
17 3 0.05
18 16 0.29
19 14 0.25
20 6 0.11
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (18 bp):
TTTTTTGAAAACACAAAA
Found at i:6586980 original size:52 final size:53
Alignment explanation
Indices: 6586881--6586980 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 53
6586871 AAAAAACAAG
* * *
6586881 AAAATTTTGAAAGACGGGAATTTTTTTTGAAAACACAAAATTTTTTTAGCACA
1 AAAATTTTGAAACACGAGAATTTTTTCTGAAAACACAAAATTTTTTTAGCACA
* *
6586934 AAAATTTTGAAACACTAGAA-TTTTTCTGAAAACACTAAATTTTTTTA
1 AAAATTTTGAAACACGAGAATTTTTTCTGAAAACACAAAATTTTTTTA
6586981 AAATACGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 25 0.60
53 17 0.40
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (53 bp):
AAAATTTTGAAACACGAGAATTTTTTCTGAAAACACAAAATTTTTTTAGCACA
Found at i:6587978 original size:23 final size:24
Alignment explanation
Indices: 6587952--6588007 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
6587942 TTCTTTTTCC
6587952 TTTTGGTTGCTG-TTTTTTTTCTT
1 TTTTGGTTGCTGTTTTTTTTTCTT
**
6587975 TTTTACTTGCTGTTTTTTTTTCTT
1 TTTTGGTTGCTGTTTTTTTTTCTT
6587999 TTTTGGTTG
1 TTTTGGTTG
6588008 TTGCCTTGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.02, C:0.09, G:0.16, T:0.73
Consensus pattern (24 bp):
TTTTGGTTGCTGTTTTTTTTTCTT
Found at i:6588274 original size:23 final size:23
Alignment explanation
Indices: 6588226--6588276 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
6588216 GTGAGGGCCC
* **
6588226 TTTTGCTGCTGTTTTCTTGGTGT
1 TTTTGCTGCTATTTTCTTCATGT
*
6588249 TTTTGCTGCTATTTTCTTTCATTT
1 TTTTGCTGCTATTTTC-TTCATGT
6588273 TTTT
1 TTTT
6588277 TTTGCTTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.04, C:0.14, G:0.16, T:0.67
Consensus pattern (23 bp):
TTTTGCTGCTATTTTCTTCATGT
Found at i:6588799 original size:23 final size:24
Alignment explanation
Indices: 6588767--6588811 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
6588757 TTAATTAAAC
*
6588767 TTTATAAATAATTAATATTTATTG
1 TTTATAAATAATTAAAATTTATTG
*
6588791 TTTA-AAATATTTAAAATTTAT
1 TTTATAAATAATTAAAATTTAT
6588812 ATTGCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTATAAATAATTAAAATTTATTG
Found at i:6589859 original size:31 final size:31
Alignment explanation
Indices: 6589822--6589881 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
6589812 TGGGTTGTCT
6589822 TTTAGTTTTAGTTTTATTGGATTGGGTAAAC
1 TTTAGTTTTAGTTTTATTGGATTGGGTAAAC
*
6589853 TTTAGTTTTAGTTTTATTGGGTTGGGTAA
1 TTTAGTTTTAGTTTTATTGGATTGGGTAA
6589882 TTGAGTTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.02, G:0.25, T:0.53
Consensus pattern (31 bp):
TTTAGTTTTAGTTTTATTGGATTGGGTAAAC
Found at i:6595549 original size:21 final size:21
Alignment explanation
Indices: 6595509--6595566 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
6595499 TTCCAAAAGG
*
6595509 CAAAACGGTAGAAATGTAGGGA
1 CAAAACGGTA-AAATATAGGGA
*
6595531 CAAAACGGTAAAATATAGGGG
1 CAAAACGGTAAAATATAGGGA
*
6595552 CAAAAAGGATAAAAT
1 CAAAACGG-TAAAAT
6595567 TCTATAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.52, C:0.09, G:0.26, T:0.14
Consensus pattern (21 bp):
CAAAACGGTAAAATATAGGGA
Found at i:6599912 original size:33 final size:33
Alignment explanation
Indices: 6599865--6599928 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
6599855 GGGAGGAGGC
6599865 GGTGGAGGCAGCATGGTTTTTGAAGGCGGAGCT
1 GGTGGAGGCAGCATGGTTTTTGAAGGCGGAGCT
* * * *
6599898 GGTGGAGTCTGCATGGTTTTTGGAGGTGGAG
1 GGTGGAGGCAGCATGGTTTTTGAAGGCGGAG
6599929 GCGGCAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.16, C:0.09, G:0.47, T:0.28
Consensus pattern (33 bp):
GGTGGAGGCAGCATGGTTTTTGAAGGCGGAGCT
Found at i:6627291 original size:14 final size:14
Alignment explanation
Indices: 6627272--6627310 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
6627262 ATTATGTGTT
6627272 TTATTTAATTTTAA
1 TTATTTAATTTTAA
**
6627286 TTATTTGTTTTTAA
1 TTATTTAATTTTAA
*
6627300 TTTTTTAATTT
1 TTATTTAATTT
6627311 ACAATAAGTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TTATTTAATTTTAA
Found at i:6629227 original size:224 final size:222
Alignment explanation
Indices: 6628827--6629274 Score: 806
Period size: 224 Copynumber: 2.0 Consensus size: 222
6628817 AAAATGTTAC
* * * *
6628827 AACATGATAACATAAGTGATTTAAACGTAGCATTTCAAATATAAGTGACTAAAATATAACCTGAG
1 AACATGATAACATAAGAGACTAAAACGTAACATTTCAAATATAAGTGACTAAAATATAACCTGAG
6628892 GCAAACAAAAGTGATTATTTAGTAGTTTACCCTTTTTTTGAATTATATAATATTAATAACTATTT
66 GCAAACAAAAGTGATTATTTAGTAGTTTACCCTTTTTTTGAATTATATAATATTAATAACTATTT
* *
6628957 ACGGGAAATAACAAATTAAGTTTAAAAAAATGTATAAATCGACCTTAAAGATAATATTGGAAGCT
131 ACGGAAAATAACAAATTAAGTTAAAAAAAATGTATAAATCGACCTTAAAGATAATATTGGAAGCT
*
6629022 AAATTCCTAACGACTACTAGGGCCCTA
196 AAATTCCTAACGACTACTAGGGCCATA
6629049 AACATGATAACATAAGAGACTAAAACGTAACATTTCAAATATAAGTGACTAAAATATAACCTGAG
1 AACATGATAACATAAGAGACTAAAACGTAACATTTCAAATATAAGTGACTAAAATATAACCTGAG
*
6629114 GCAAACAAAAGTGATTATTTTAGTAGTTTATCCTTTTTTTTGAATTATATAATATTAATAACTAT
66 GCAAACAAAAGTGATTA-TTTAGTAGTTTA-CCCTTTTTTTGAATTATATAATATTAATAACTAT
6629179 TTACGGAAAATAACAAATTAAGTTAAAAAAAATGTATAAATCGACCTTAAAGATAATATTGGAAG
129 TTACGGAAAATAACAAATTAAGTTAAAAAAAATGTATAAATCGACCTTAAAGATAATATTGGAAG
6629244 CTAAATTCCTAACGACTACTAGGGCCATA
194 CTAAATTCCTAACGACTACTAGGGCCATA
6629273 AA
1 AA
6629275 TTGACGGTGC
Statistics
Matches: 216, Mismatches: 8, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
222 78 0.36
223 12 0.06
224 126 0.58
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (222 bp):
AACATGATAACATAAGAGACTAAAACGTAACATTTCAAATATAAGTGACTAAAATATAACCTGAG
GCAAACAAAAGTGATTATTTAGTAGTTTACCCTTTTTTTGAATTATATAATATTAATAACTATTT
ACGGAAAATAACAAATTAAGTTAAAAAAAATGTATAAATCGACCTTAAAGATAATATTGGAAGCT
AAATTCCTAACGACTACTAGGGCCATA
Found at i:6640232 original size:18 final size:18
Alignment explanation
Indices: 6640209--6640299 Score: 146
Period size: 18 Copynumber: 5.1 Consensus size: 18
6640199 CAATCCCAAC
*
6640209 TACTGTATACGTGAACAG
1 TACTGTATACGTGAATAG
6640227 TACTGTATACGTGAATAG
1 TACTGTATACGTGAATAG
*
6640245 TACCGTATACGTGAATAG
1 TACTGTATACGTGAATAG
6640263 TACTGTATACGTGAATAG
1 TACTGTATACGTGAATAG
* *
6640281 TGCCGTATACGTGAATAG
1 TACTGTATACGTGAATAG
6640299 T
1 T
6640300 TCCGTAAACG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (18 bp):
TACTGTATACGTGAATAG
Found at i:6642731 original size:14 final size:15
Alignment explanation
Indices: 6642708--6642737 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6642698 TAAATTTAAT
6642708 TAAATCAATTAAAAA
1 TAAATCAATTAAAAA
6642723 TAAAT-AATTAAAAA
1 TAAATCAATTAAAAA
6642737 T
1 T
6642738 TTGAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATCAATTAAAAA
Found at i:6645174 original size:5 final size:5
Alignment explanation
Indices: 6645145--6645228 Score: 90
Period size: 5 Copynumber: 17.4 Consensus size: 5
6645135 TCAGTTTATT
6645145 TAATA T-ATAA TAATA T-ATAA TAATA TAATA TAATA TAAT- TAATA TAATA
1 TAATA TAAT-A TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA
*
6645194 TAATA TAATA T-ATAA TAAAA TAATA T-AT- TAATA TA
1 TAATA TAATA TAAT-A TAATA TAATA TAATA TAATA TA
6645229 TTTAAAACAT
Statistics
Matches: 68, Mismatches: 2, Indels: 18
0.77 0.02 0.20
Matches are distributed among these distances:
3 1 0.01
4 14 0.21
5 48 0.71
6 5 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:6645190 original size:29 final size:28
Alignment explanation
Indices: 6645149--6645228 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 28
6645139 TTTATTTAAT
6645149 ATATAATAATAT-ATAATAATATAATATA
1 ATATAATAATATAAT-ATAATATAATATA
6645177 ATATAATTAATATAATATAATATAATATATA
1 ATATAA-TAATATAATATAATAT-A-ATATA
*
6645208 ATAAAATAATAT-AT-TAATATA
1 ATATAATAATATAATATAATATA
6645229 TTTAAAACAT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
27 1 0.02
28 12 0.26
29 15 0.32
30 9 0.19
31 10 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
ATATAATAATATAATATAATATAATATA
Found at i:6650077 original size:18 final size:18
Alignment explanation
Indices: 6650050--6650098 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
6650040 TAAAAAATTC
6650050 AAATATTAAAATTAG-AAA
1 AAATA-TAAAATTAGTAAA
* *
6650068 AAATTATAAAAATCGTAAA
1 AAA-TATAAAATTAGTAAA
6650087 AAATATAAAATT
1 AAATATAAAATT
6650099 TTATAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (18 bp):
AAATATAAAATTAGTAAA
Found at i:6650078 original size:9 final size:9
Alignment explanation
Indices: 6650066--6650162 Score: 70
Period size: 10 Copynumber: 10.4 Consensus size: 9
6650056 TAAAATTAGA
6650066 AAAAATTAT
1 AAAAATTAT
**
6650075 AAAAATCGT
1 AAAAATTAT
*
6650084 AAAAAATAT
1 AAAAATTAT
*
6650093 AAAATTTTAT
1 AAAA-ATTAT
*
6650103 AAAATTTTAT
1 AAAA-ATTAT
*
6650113 AAAAATCAT
1 AAAAATTAT
6650122 AAAAATATAT
1 AAAAAT-TAT
*
6650132 AGAAATATAT
1 AAAAAT-TAT
*
6650142 AGAAA-TAT
1 AAAAATTAT
*
6650150 GAAAATTAT
1 AAAAATTAT
6650159 AAAA
1 AAAA
6650163 TTTTATAAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
8 6 0.08
9 32 0.45
10 33 0.46
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:6650078 original size:71 final size:72
Alignment explanation
Indices: 6649981--6650117 Score: 167
Period size: 72 Copynumber: 1.9 Consensus size: 72
6649971 CTCCTACTTT
*
6649981 TATTAAAAATTAGAAAAAAAACT-AAAATC-AATAAAACTAT-AAATATTATTAAATTTTAATAA
1 TATTAAAAATTAGAAAAAAAACTAAAAATCGAA-AAAA-TATAAAATATTATAAAATTTT-ATAA
6650043 AAAATTCAAA
63 AAAATTCAAA
* *
6650053 TATT-AAAATTAGAAAAAATTA-TAAAAATCGTAAAAAATATAAAATTTTATAAAATTTTATAAA
1 TATTAAAAATTAGAAAAAA-AACTAAAAATCG-AAAAAATATAAAATATTATAAAATTTTATAAA
6650116 AA
64 AA
6650118 TCATAAAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
71 15 0.26
72 21 0.37
73 19 0.33
74 2 0.04
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (72 bp):
TATTAAAAATTAGAAAAAAAACTAAAAATCGAAAAAATATAAAATATTATAAAATTTTATAAAAA
ATTCAAA
Found at i:6650115 original size:29 final size:27
Alignment explanation
Indices: 6650085--6650171 Score: 88
Period size: 29 Copynumber: 3.1 Consensus size: 27
6650075 AAAAATCGTA
6650085 AAAAATATAAAATTTTATAAAATTTTAT
1 AAAAATATAAAA-TTTATAAAATTTTAT
* *
6650113 AAAAATCATAAAAATATATAGAAA-TATAT
1 AAAAAT-AT-AAAATTTATA-AAATTTTAT
*
6650142 AGAAATATGAAAA-TTATAAAATTTTAT
1 AAAAATAT-AAAATTTATAAAATTTTAT
6650169 AAA
1 AAA
6650172 TTCGTAAGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
26 3 0.06
27 10 0.21
28 12 0.25
29 16 0.33
30 7 0.15
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (27 bp):
AAAAATATAAAATTTATAAAATTTTAT
Found at i:6650219 original size:57 final size:55
Alignment explanation
Indices: 6650066--6650209 Score: 159
Period size: 57 Copynumber: 2.5 Consensus size: 55
6650056 TAAAATTAGA
6650066 AAAAATTATAAAAATCGTAAA-AAATATAAAATTTTATAAAATTTTATAAAAATCAT
1 AAAAATTATAAAAAT-GTAAAGAAATATAAAA-TTTATAAAATTTTATAAAAATCAT
* * * * *
6650122 AAAAATATATAGAAATATATAGAAATATGAAAA-TTATAAAATTTTAT-AAATTCGT
1 AAAAAT-TATAAAAATGTAAAGAAATAT-AAAATTTATAAAATTTTATAAAAATCAT
6650177 AAGAAAATTATACAAAATGTAAAGAAATATAAA
1 -A-AAAATTATA-AAAATGTAAAGAAATATAAA
6650210 TTTCGTAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
55 6 0.08
56 31 0.42
57 33 0.45
58 4 0.05
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (55 bp):
AAAAATTATAAAAATGTAAAGAAATATAAAATTTATAAAATTTTATAAAAATCAT
Found at i:6650462 original size:19 final size:20
Alignment explanation
Indices: 6650431--6650483 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
6650421 AAAAATCTAC
* *
6650431 TTTTTAAT-GAATTTAA-AT
1 TTTTTAATAAAATTTAATAA
6650449 TTTTTAATAAAATTTAATAA
1 TTTTTAATAAAATTTAATAA
*
6650469 TTTTT-CTAAAATTTA
1 TTTTTAATAAAATTTA
6650484 TTTTTTTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.27
19 16 0.53
20 6 0.20
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTTTAATAAAATTTAATAA
Found at i:6650669 original size:88 final size:86
Alignment explanation
Indices: 6650510--6650683 Score: 235
Period size: 88 Copynumber: 2.0 Consensus size: 86
6650500 TAATAAGAGC
* * *
6650510 AGGGGCTTAATTGCTTTTTTGAAAATTTTTGAGGGTCTTTTTGATACATTTTGAAAGTTCAAGTA
1 AGGGGCTTAATTGCTTTTTTGAAAATGTTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAG-A
* *
6650575 TCCAATTGAGTGAGAAAAAAAGT
65 TCCAATTAAGTG-CAAAAAAAGT
*
6650598 AGGGGCTTAATTGCTTTTTTGAAGAA-GTTTGAGGGCCTTTTTGATGCATTTTAAAAGTTCAA-A
1 AGGGGCTTAATTGCTTTTTTGAA-AATGTTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAGA
6650661 TGCTCAATTAAGTGCAAAAAAAG
65 T-C-CAATTAAGTGCAAAAAAAG
6650684 GGCTTAATTG
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
86 2 0.03
87 9 0.12
88 64 0.83
89 2 0.03
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (86 bp):
AGGGGCTTAATTGCTTTTTTGAAAATGTTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAGAT
CCAATTAAGTGCAAAAAAAGT
Found at i:6651467 original size:14 final size:15
Alignment explanation
Indices: 6651444--6651473 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6651434 TAAATTTAAT
6651444 TAAATCAATTAAAAA
1 TAAATCAATTAAAAA
6651459 TAAAT-AATTAAAAA
1 TAAATCAATTAAAAA
6651473 T
1 T
6651474 TTGAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATCAATTAAAAA
Found at i:6652021 original size:17 final size:17
Alignment explanation
Indices: 6652002--6652073 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 17
6651992 TATATTTATT
*
6652002 TTTTTAAAT-TTTTTAA
1 TTTTAAAATATTTTTAA
6652018 TTTTAAAATATTTTTAAAA
1 TTTTAAAATATTTTT--AA
** *
6652037 TACTTTTTATTATTTTTAAA
1 T--TTTAAAATATTTTT-AA
6652057 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
6652074 AATACTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
16 8 0.18
17 7 0.16
18 11 0.25
19 3 0.07
20 4 0.09
21 11 0.25
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:6652032 original size:11 final size:11
Alignment explanation
Indices: 6652018--6652098 Score: 79
Period size: 11 Copynumber: 7.9 Consensus size: 11
6652008 AATTTTTTAA
6652018 TTTTAAAATAT
1 TTTTAAAATAT
6652029 TTTTAAAATACT
1 TTTTAAAATA-T
*
6652041 TTTT--ATTAT
1 TTTTAAAATAT
6652050 TTTT--AA-A-
1 TTTTAAAATAT
6652057 TTTTAAAATAT
1 TTTTAAAATAT
6652068 TTTTAAAATACT
1 TTTTAAAATA-T
6652080 TTTT-AAA-AT
1 TTTTAAAATAT
6652089 TTTTAAAATA
1 TTTTAAAATA
6652099 AATTTTTAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
7 4 0.07
8 1 0.02
9 13 0.22
10 8 0.13
11 24 0.40
12 10 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Done.