Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 14 of 182
Found at i:5617281 original size:47 final size:47
Alignment explanation
Indices: 5617212--5617305 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
5617202 TTGGTGCTTC
5617212 TATTATGCTAACAGTATTTGAACTGATGAAGAGTCTACGAGGGTGTG
1 TATTATGCTAACAGTATTTGAACTGATGAAGAGTCTACGAGGGTGTG
5617259 TATTATGCTAACAGTATTTGAACTGATGAAGAGTCTACGAGGGTGTG
1 TATTATGCTAACAGTATTTGAACTGATGAAGAGTCTACGAGGGTGTG
5617306 ATTCGAAAGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.32
Consensus pattern (47 bp):
TATTATGCTAACAGTATTTGAACTGATGAAGAGTCTACGAGGGTGTG
Found at i:5624696 original size:26 final size:26
Alignment explanation
Indices: 5624666--5624716 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
5624656 TTTTTATAAT
5624666 TTTTTAAAAAAATATAAAATTTTAAC
1 TTTTTAAAAAAATATAAAATTTTAAC
* * * *
5624692 TTTTTATAAATATTTTAAATTTTAA
1 TTTTTAAAAAAATATAAAATTTTAA
5624717 AATTATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTTTAAAAAAATATAAAATTTTAAC
Found at i:5624699 original size:18 final size:19
Alignment explanation
Indices: 5624678--5624745 Score: 70
Period size: 18 Copynumber: 3.6 Consensus size: 19
5624668 TTTAAAAAAA
*
5624678 TATAAA-ATTTTAACTTTT
1 TATAAATATTTTAAATTTT
5624696 TATAAATATTTTAAA-TTT
1 TATAAATATTTTAAATTTT
5624714 TA-AAATTATTTTAAAATTTT
1 TATAAA-TATTTT-AAATTTT
* *
5624734 AAAAAATATTTT
1 TATAAATATTTT
5624746 GATTCTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.07
18 17 0.40
19 10 0.23
20 10 0.23
21 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:5624874 original size:23 final size:22
Alignment explanation
Indices: 5624844--5624899 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
5624834 TCAATCATTC
5624844 GAATTATTTAAATCTTAAAA-TT
1 GAATTATTTAAA-CTTAAAACTT
* *
5624866 TAACTTATTCAAACTTAAAACTT
1 GAA-TTATTTAAACTTAAAACTT
5624889 GAATTATTTAA
1 GAATTATTTAA
5624900 TCAAGTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (22 bp):
GAATTATTTAAACTTAAAACTT
Found at i:5632543 original size:5 final size:5
Alignment explanation
Indices: 5632501--5632542 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
5632491 ACAAATGGCT
*
5632501 GATGA GATGA GATGA GATGA GATGA GATGA GATGA GACGA GA
1 GATGA GATGA GATGA GATGA GATGA GATGA GATGA GATGA GA
5632543 CTTCAAAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.40, C:0.02, G:0.40, T:0.17
Consensus pattern (5 bp):
GATGA
Found at i:5643241 original size:13 final size:14
Alignment explanation
Indices: 5643213--5643246 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5643203 AAAATCCTAG
5643213 TTTTCCCTCTCTTT
1 TTTTCCCTCTCTTT
*
5643227 TTTTCCTTCTCTTT
1 TTTTCCCTCTCTTT
5643241 TCTTTC
1 T-TTTC
5643247 TCCCCTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTCCCTCTCTTT
Found at i:5651113 original size:56 final size:54
Alignment explanation
Indices: 5651023--5651186 Score: 141
Period size: 55 Copynumber: 3.0 Consensus size: 54
5651013 AATTTAATTT
* * ** * *
5651023 TTTTTAAATTTTGGAAATATGATGTAGGTCATTGGATGGTAAACAACTAAAAAATA
1 TTTTTAAA-TTTGGAAAAATGATGTAGCTCATTGGATGACAAAC-ACCAAAAAAAA
*
5651079 TTTTTAAATTTGGAAAAAGTGATGTAAGCT-ATTGGGTGACAAACACCAAAAAAAA
1 TTTTTAAATTTGGAAAAA-TGATGT-AGCTCATTGGATGACAAACACCAAAAAAAA
* ** * * * * *
5651134 TTATTAAATTTGAGAAAGGTGGTGTAGATTATGGGATGACAAACACCCAAAAA
1 TTTTTAAATTTG-GAAAAATGATGTAGCTCATTGGATGACAAACACCAAAAAA
5651187 GTATTTTTTA
Statistics
Matches: 89, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
54 3 0.03
55 54 0.61
56 29 0.33
57 3 0.03
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.30
Consensus pattern (54 bp):
TTTTTAAATTTGGAAAAATGATGTAGCTCATTGGATGACAAACACCAAAAAAAA
Found at i:5655035 original size:57 final size:58
Alignment explanation
Indices: 5654933--5655165 Score: 269
Period size: 59 Copynumber: 4.0 Consensus size: 58
5654923 AAATTTTGGG
*
5654933 TCCTTTTTGTCAGATAAAAAATTCGAATTTTTTTGTGTTGGCCATGTC-ATGGCCGACAC
1 TCCTTTTTGTCAGATAAAAAATTC-AATTTTTTTGTGTTGGCCATG-CAATGGTCGACAC
* * *
5654992 TCCTTTTTTTCTGGTAAAAAA-TCAATTTTTTTGTGTTGGCCATGCAATGGTCGACAC
1 TCCTTTTTGTCAGATAAAAAATTCAATTTTTTTGTGTTGGCCATGCAATGGTCGACAC
* * * * *
5655049 CCCTTTTTGTCAGATAAAAAATTTGAA-TTTTTGGTGTTGGCCATTGC-ATGATCGATACC
1 TCCTTTTTGTCAGATAAAAAA-TTCAATTTTTTTGTGTTGGCCA-TGCAATGGTCGACA-C
* * *
5655108 TCCTTTTTTATCTGGTAAAAAATT-AATTTTTTTGTGTTGGCCATGCAATGGTCGACAC
1 TCC-TTTTTGTCAGATAAAAAATTCAATTTTTTTGTGTTGGCCATGCAATGGTCGACAC
5655166 CAACTTTCTC
Statistics
Matches: 147, Mismatches: 19, Indels: 17
0.80 0.10 0.09
Matches are distributed among these distances:
56 1 0.01
57 48 0.33
58 31 0.21
59 52 0.35
60 15 0.10
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (58 bp):
TCCTTTTTGTCAGATAAAAAATTCAATTTTTTTGTGTTGGCCATGCAATGGTCGACAC
Found at i:5655155 original size:117 final size:116
Alignment explanation
Indices: 5654934--5655166 Score: 371
Period size: 117 Copynumber: 2.0 Consensus size: 116
5654924 AATTTTGGGT
* *
5654934 CCTTTTTGTCAGATAAAAAATTCGAATTTTTTTGTGTTGGCCATGTCATGGCCGACACTCCTTTT
1 CCTTTTTGTCAGATAAAAAATTCGAATTTTTTGGTGTTGGCCATGTCATGACCGACACTCCTTTT
5654999 TTTCTGGTAAAAAATCAATTTTTTTGTGTTGGCCATGCAATGGTCGACACC
66 TTTCTGGTAAAAAATCAATTTTTTTGTGTTGGCCATGCAATGGTCGACACC
* * *
5655050 CCTTTTTGTCAGATAAAAAATTTGAA-TTTTTGGTGTTGGCCAT-TGCATGATCGATACCTCCTT
1 CCTTTTTGTCAGATAAAAAATTCGAATTTTTTGGTGTTGGCCATGT-CATGACCGACA-CTCCTT
*
5655113 TTTTATCTGGTAAAAAATTAATTTTTTTGTGTTGGCCATGCAATGGTCGACACC
64 TTTT-TCTGGTAAAAAATCAATTTTTTTGTGTTGGCCATGCAATGGTCGACACC
5655167 AACTTTCTCT
Statistics
Matches: 108, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
114 1 0.01
115 24 0.22
116 35 0.32
117 48 0.44
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (116 bp):
CCTTTTTGTCAGATAAAAAATTCGAATTTTTTGGTGTTGGCCATGTCATGACCGACACTCCTTTT
TTTCTGGTAAAAAATCAATTTTTTTGTGTTGGCCATGCAATGGTCGACACC
Found at i:5655925 original size:13 final size:13
Alignment explanation
Indices: 5655895--5655931 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5655885 ATTATCGACA
5655895 AATTAAAAAT-AT
1 AATTAAAAATAAT
5655907 -ATTAAAAATAAT
1 AATTAAAAATAAT
*
5655919 AATTAAAATTAAT
1 AATTAAAAATAAT
5655932 TTTAAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 9 0.41
12 2 0.09
13 11 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTAAAAATAAT
Found at i:5659662 original size:51 final size:51
Alignment explanation
Indices: 5659600--5659787 Score: 198
Period size: 51 Copynumber: 3.6 Consensus size: 51
5659590 GCTATAAACG
* * *
5659600 AAAGGATCCGATGACTAAGTCTCATTGTGAGTAAATGAATCCTTTACGGATT
1 AAAGG-TCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTCACGGATT
* * * * *
5659652 AAAGGTCCGATGACTAGGTGTCATCGTGAGTAAATGAATCCATGATGGGTT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTCACGGATT
* * * * * **
5659703 AAAGGTTCGATGACTCAGTGTTATCGTGAGTATATGAATTCCTACACGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTCACGGATT
5659755 AAGAGGTCCGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
5659788 TTAAATGAAA
Statistics
Matches: 111, Mismatches: 22, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 72 0.65
52 13 0.12
53 25 0.23
54 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTCACGGATT
Found at i:5661567 original size:84 final size:84
Alignment explanation
Indices: 5661440--5662156 Score: 1159
Period size: 84 Copynumber: 8.5 Consensus size: 84
5661430 AATTTAACAT
* * * * * *
5661440 TATTTAAATAAAAAAGATTATTATTATATTTCAATTTATATCAAATAATGTGTTAATTTGATAAT
1 TATTTAAAT-TAAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTGACAAT
*
5661505 ATATTATTTATCAAATTTTAA
64 ACATTATTTATCAAATTTTAA
*
5661526 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTAACAATAC
1 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTGACAATAC
5661591 ATTATTTATCAAATTTTAA
66 ATTATTTATCAAATTTTAA
* *
5661610 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATATATTGATTTGATAATAC
1 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTGACAATAC
5661675 ATTATTTATCAAATTTTAA
66 ATTATTTATCAAATTTTAA
5661694 TATTTAAATTAAAAATTATTATTATATTAC-ATTTTTATCAAATAATGTATTGATTTGACAATAC
1 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTGACAATAC
*
5661758 ATTATTTATCAAATTTGAA
66 ATTATTTATCAAATTTTAA
* *
5661777 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATTTGTTGATTTGACAATAC
1 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTGACAATAC
5661842 ATTATTTATCAAATTTTAA
66 ATTATTTATCAAATTTTAA
** *
5661861 TATTTAAA-TAAAAAAAATTATTATATTACATTTTTTATCAAATAATGTATTGATTTGACAATAC
1 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTGACAATAC
*
5661925 ATTATTTATCAAATTTGAA
66 ATTATTTATCAAATTTTAA
* * *
5661944 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATTTGTTGATTTGGCAATAC
1 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTGACAATAC
5662009 ATTATTTATCAAATTTTAA
66 ATTATTTATCAAATTTTAA
* * * *
5662028 TATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATTTGTTGATTTGATAATA
1 TATTTAAAT-TAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTGACAATA
* *
5662093 CATTATTTACCAAATTTGAA
65 CATTATTTATCAAATTTTAA
5662113 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAAT
1 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAAT
5662157 TTTAAATTTA
Statistics
Matches: 592, Mismatches: 36, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
83 157 0.27
84 343 0.58
85 83 0.14
86 9 0.02
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (84 bp):
TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTTGACAATAC
ATTATTTATCAAATTTTAA
Found at i:5661765 original size:251 final size:252
Alignment explanation
Indices: 5661440--5662156 Score: 1186
Period size: 251 Copynumber: 2.8 Consensus size: 252
5661430 AATTTAACAT
* * * * *
5661440 TATTTAAATAAAAAAGATTATTATTATATTTCAATTTATATCAAATAATGTGTTAATTTGATAAT
1 TATTTAAAT-TAAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
*
5661505 ATATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAAT
64 ACATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAAT
* * *
5661570 AATGTATTGATTTAACAATACATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTAT
129 AATTTGTTGATTTGACAATACATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTAT
* *
5661635 ATTACAATTTTTATCAAATAATATATTGATTTGATAATACATTATTTATCAAATTTTAA
194 ATTACAATTTTTATCAAATAATATATTGATTTGACAATACATTATTTATCAAATTTGAA
*
5661694 TATTTAAATTAAAAATTATTATTATATTAC-ATTTTTATCAAATAATGTATTGATTTGACAATAC
1 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
5661758 ATTATTTATCAAATTTGAATATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAA
66 ATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAA
**
5661823 TTTGTTGATTTGACAATACATTATTTATCAAATTTTAATATTTAAA-TAAAAAAAATTATTATAT
131 TTTGTTGATTTGACAATACATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTATAT
* *
5661887 TACATTTTTTATCAAATAATGTATTGATTTGACAATACATTATTTATCAAATTTGAA
196 TACAATTTTTATCAAATAATATATTGATTTGACAATACATTATTTATCAAATTTGAA
* *
5661944 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATTTGTTGATTTGGCAATAC
1 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
*
5662009 ATTATTTATCAAATTTTAATATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATA
66 ATTATTTATCAAATTTTAATATTTAAAT-TAAAAATTATTATTATATTACAATTTTTATCAAATA
* * *
5662074 ATTTGTTGATTTGATAATACATTATTTACCAAATTTGAATATTTAAATTAAAAATTATTATTATA
130 ATTTGTTGATTTGACAATACATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTATA
5662139 TTACAATTTTTATCAAAT
195 TTACAATTTTTATCAAAT
5662157 TTTAAATTTA
Statistics
Matches: 432, Mismatches: 28, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
250 99 0.23
251 194 0.45
252 94 0.22
253 36 0.08
254 9 0.02
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (252 bp):
TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
ATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAA
TTTGTTGATTTGACAATACATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTATAT
TACAATTTTTATCAAATAATATATTGATTTGACAATACATTATTTATCAAATTTGAA
Found at i:5661805 original size:167 final size:168
Alignment explanation
Indices: 5661440--5662156 Score: 1204
Period size: 167 Copynumber: 4.3 Consensus size: 168
5661430 AATTTAACAT
* * * * * *
5661440 TATTTAAATAAAAAAGATTATTATTATATTTCAATTTATATCAAATAATGTGTTAATTTGATAAT
1 TATTTAAAT-TAAAA-ATTATTATTATATTACAATTTTTATCAAATAATTTGTTGATTTGACAAT
*
5661505 ATATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAAT
64 ACATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAAT
* *
5661570 AATGTATTGATTTAACAATACATTATTTATCAAATTTTAA
129 AATGTATTGATTTGACAATACATTATTTATCAAATTTGAA
* * *
5661610 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATATATTGATTTGATAATAC
1 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATTTGTTGATTTGACAATAC
5661675 ATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTATATTAC-ATTTTTATCAAATAA
66 ATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAA
5661739 TGTATTGATTTGACAATACATTATTTATCAAATTTGAA
131 TGTATTGATTTGACAATACATTATTTATCAAATTTGAA
5661777 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATTTGTTGATTTGACAATAC
1 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATTTGTTGATTTGACAATAC
** *
5661842 ATTATTTATCAAATTTTAATATTTAAA-TAAAAAAAATTATTATATTACATTTTTTATCAAATAA
66 ATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAA
5661906 TGTATTGATTTGACAATACATTATTTATCAAATTTGAA
131 TGTATTGATTTGACAATACATTATTTATCAAATTTGAA
*
5661944 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATTTGTTGATTTGGCAATAC
1 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATTTGTTGATTTGACAATAC
*
5662009 ATTATTTATCAAATTTTAATATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATA
66 ATTATTTATCAAATTTTAATATTTAAAT-TAAAAATTATTATTATATTACAATTTTTATCAAATA
* * * *
5662074 ATTTGTTGATTTGATAATACATTATTTACCAAATTTGAA
130 ATGTATTGATTTGACAATACATTATTTATCAAATTTGAA
5662113 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAAT
1 TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAAT
5662157 TTTAAATTTA
Statistics
Matches: 520, Mismatches: 24, Indels: 7
0.94 0.04 0.01
Matches are distributed among these distances:
166 19 0.04
167 283 0.54
168 94 0.18
169 115 0.22
170 9 0.02
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (168 bp):
TATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAATTTGTTGATTTGACAATAC
ATTATTTATCAAATTTTAATATTTAAATTAAAAATTATTATTATATTACAATTTTTATCAAATAA
TGTATTGATTTGACAATACATTATTTATCAAATTTGAA
Found at i:5662280 original size:22 final size:22
Alignment explanation
Indices: 5662249--5662309 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
5662239 TGGACCACCC
* * *
5662249 AAATTTCAGCTCACCTAAACTG
1 AAATTCCAGCTCACCAAAACCG
*
5662271 AAATTCCAGCTCATCAAAACCG
1 AAATTCCAGCTCACCAAAACCG
*
5662293 AAATTCCAACTCACCAA
1 AAATTCCAGCTCACCAA
5662310 TACCCTAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.41, C:0.31, G:0.07, T:0.21
Consensus pattern (22 bp):
AAATTCCAGCTCACCAAAACCG
Found at i:5664582 original size:30 final size:30
Alignment explanation
Indices: 5664548--5664633 Score: 127
Period size: 30 Copynumber: 2.9 Consensus size: 30
5664538 CCCGTTTACT
* * * *
5664548 TTTTAAATTTAATTTGTAATTTCGTTTTTA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
5664578 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
*
5664608 TTTTAATTTTAATTTCTAATTTCCTG
1 TTTTAAATTTAATTTCTAATTTCCTG
5664634 AATAATCTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.27, C:0.08, G:0.05, T:0.60
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCCTGTATA
Found at i:5664645 original size:30 final size:30
Alignment explanation
Indices: 5664585--5664645 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
5664575 TTATTTTAAA
* * *
5664585 TTTAATTTCTAATTTCCTGTATATTTTAAT
1 TTTAATTTCTAATTTCCTGAATAATCTAAT
5664615 TTTAATTTCTAATTTCCTGAATAATCTAAT
1 TTTAATTTCTAATTTCCTGAATAATCTAAT
5664645 T
1 T
5664646 ATTATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.56
Consensus pattern (30 bp):
TTTAATTTCTAATTTCCTGAATAATCTAAT
Found at i:5665553 original size:59 final size:59
Alignment explanation
Indices: 5665450--5665565 Score: 144
Period size: 59 Copynumber: 2.0 Consensus size: 59
5665440 AAGGAAAGTT
* * * * ** *
5665450 GGTGTCTGCCATTGCATGGCCAACATCAAAAATTTGATTTTTTTTATCCGATAAATAGG
1 GGTGTCGGCCATGGCATGGCCAACATAAAAAAATTGATACTTTTTATCCGACAAATAGG
*
5665509 GGTGTCGGCCATGGCATGGCCAACATGAAAAAAATTGA-ACTTTTTATCTGACAAATA
1 GGTGTCGGCCATGGCATGGCCAACAT-AAAAAAATTGATACTTTTTATCCGACAAATA
5665566 TTTGATTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 39 0.81
60 9 0.19
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (59 bp):
GGTGTCGGCCATGGCATGGCCAACATAAAAAAATTGATACTTTTTATCCGACAAATAGG
Found at i:5665623 original size:83 final size:83
Alignment explanation
Indices: 5665476--5665628 Score: 218
Period size: 83 Copynumber: 1.8 Consensus size: 83
5665466 TGGCCAACAT
* * * * *
5665476 CAAAAATTTGATTTTTTTTATCCGATAAATAGGGGTGTCGGCCATGGCATGGCCAACATGAAAAA
1 CAAAAATTTGATTTTTTATATCAGATAAAAAGGGGTGTCGGCCATGGCATGACCAACA-CAAAAA
5665541 AATTGAACTTTTTATCTGA
65 AATTGAACTTTTTATCTGA
* * *
5665560 CAAATATTTGATTTTTTAT-TCAGATAAAAAGGGGTGTCGGTCATTGCATGACCAACACAAAAAA
1 CAAAAATTTGATTTTTTATATCAGATAAAAAGGGGTGTCGGCCATGGCATGACCAACACAAAAAA
5665624 ATTGA
66 ATTGA
5665629 TTTTTTACCA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
82 11 0.18
83 33 0.54
84 17 0.28
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (83 bp):
CAAAAATTTGATTTTTTATATCAGATAAAAAGGGGTGTCGGCCATGGCATGACCAACACAAAAAA
ATTGAACTTTTTATCTGA
Found at i:5665651 original size:58 final size:58
Alignment explanation
Indices: 5665567--5666149 Score: 381
Period size: 58 Copynumber: 9.9 Consensus size: 58
5665557 TGACAAATAT
* *
5665567 TTGATTTTTTATTCAGAT-AAAAAGGGGTGTCGGTCATTGCATGACCAACACAAAAAAA
1 TTGATTTTTTA-TCAGATAAAAAAGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAA
* * * *
5665625 TTGATTTTTTACCAGATAAAAAAGGGGAT-TCGACCA-TGCAATGGCCAATAC-CAAAAA
1 TTGATTTTTTATCAGATAAAAAAGGGG-TGTCGGCCATTGC-ATGGCCAACACAAAAAAA
* * *
5665682 TTCGAGTTTTTTATCTGA-CAAAAAGGAGTTGTCGGCCATTGCATGGCCAACACAAAAAAA
1 TT-GA-TTTTTTATCAGATAAAAAAGG-GGTGTCGGCCATTGCATGGCCAACACAAAAAAA
* * * * *
5665742 TTAATGTTTTT-CCAGA-AAAAAATGGGGCGTTGACCA-TGACATGGCCAACACAAAAAAAAA
1 TTGAT-TTTTTATCAGATAAAAAA-GGGGTGTCGGCCATTG-CATGGCCAACAC--AAAAAAA
* * * * * * * *
5665802 TTCGAAGTTTTTATCTGACAAAAAGGGGGTGTCGACCATAGCATGGCCAACACCCAAAAAT
1 TT-G-ATTTTTTATCAGATAAAAAAGGGGTGTCGGCCATTGCATGGCCAACA-CAAAAAAA
* * * *
5665863 TTGAATTTTTATTTAGAT-AAAAAGGGGTGTCGGCCA-TGCAATAGCCAACAGAAAAAAAA
1 TTGATTTTTTA-TCAGATAAAAAAGGGGTGTCGGCCATTGC-ATGGCCAACA-CAAAAAAA
* * **
5665922 TTTGAAATTTTTTATC---TGAAAAAGGAGTGTCGGCCATTGCATGATCAACACAAAAAAA
1 -TTG--ATTTTTTATCAGATAAAAAAGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAA
* * * * *
5665980 TTAATTTTTTTATCAG-T-AAATAGAGGTGTCGGCCATGGCATGGCTAACACCAAAAAAA
1 TTGA-TTTTTTATCAGATAAAAAAGGGGTGTCGGCCATTGCATGGCCAACA-CAAAAAAA
* ** * * * * *
5666038 TTGAATTTTTTATCTGATAAAAAAGGAATGTCGACCA-TGCAATAGCCAATACCCAAAAAT
1 TTG-ATTTTTTATCAGATAAAAAAGGGGTGTCGGCCATTGC-ATGGCCAACA-CAAAAAAA
* * **
5666098 TTAATTTTTTTATCAGATTAAAAAGGGGTGTCGATCA-TGCAATGGCCAACAC
1 TTGA-TTTTTTATCAGATAAAAAAGGGGTGTCGGCCATTGC-ATGGCCAACAC
5666150 CAAATTTTTT
Statistics
Matches: 410, Mismatches: 79, Indels: 71
0.73 0.14 0.13
Matches are distributed among these distances:
55 1 0.00
56 9 0.02
57 44 0.11
58 103 0.25
59 103 0.25
60 97 0.24
61 13 0.03
62 33 0.08
63 7 0.02
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (58 bp):
TTGATTTTTTATCAGATAAAAAAGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAA
Found at i:5665853 original size:120 final size:115
Alignment explanation
Indices: 5665585--5665989 Score: 417
Period size: 117 Copynumber: 3.4 Consensus size: 115
5665575 TTATTCAGAT
* *
5665585 AAAAAGGGGTGTCGGTCATTGCATGACCAACACAAAAAAATTGATTTTTTACCAGATAAAAAAGG
1 AAAAAGGGGTGTCGGCCATTGCATGACCAACACAAAAAAATTAATTTTTT-CCAGA-AAAAAAGG
* * *
5665650 GGATTCGACCATGCAATGGCCAATAC--CAAAAATTCG-AGTTTTTTATCTGAC
64 GGGTT-GACCATGCAATGGCCAACACAAAAAAAATTCGAAG-TTTTTATCTGAC
* *
5665701 AAAAAGGAGTTGTCGGCCATTGCATGGCCAACACAAAAAAATTAATGTTTTTCCAGAAAAAAATG
1 AAAAAGG-GGTGTCGGCCATTGCATGACCAACACAAAAAAATTAAT-TTTTTCCAGAAAAAAA-G
5665766 GGGCGTTGACCATG-ACATGGCCAACACAAAAAAAAATTCGAAGTTTTTATCTGAC
63 GGG-GTTGACCATGCA-ATGGCCAACAC-AAAAAAAATTCGAAGTTTTTATCTGAC
* * * * * ** *
5665821 AAAAAGGGGGTGTCGACCATAGCATGGCCAACACCCAAAAATTTGAATTTTTATTTAGATAAAAA
1 AAAAA-GGGGTGTCGGCCATTGCATGACCAACA-CAAAAAAATT-AATTTTT-TCCAGAAAAAAA
* * * * * *
5665886 GGGGTGTCGGCCATGCAATAGCCAACAGAAAAAAAATTTGAAATTTTTTATCTG--
62 GGGG-GTTGACCATGCAATGGCCAACACAAAAAAAATTCG-AAGTTTTTATCTGAC
* *
5665940 AAAAAGGAGTGTCGGCCATTGCATGATCAACACAAAAAAATTAATTTTTT
1 AAAAAGGGGTGTCGGCCATTGCATGACCAACACAAAAAAATTAATTTTTT
5665990 TATCAGTAAA
Statistics
Matches: 245, Mismatches: 29, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
115 1 0.00
116 21 0.09
117 68 0.28
118 29 0.12
119 5 0.02
120 59 0.24
121 49 0.20
122 13 0.05
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (115 bp):
AAAAAGGGGTGTCGGCCATTGCATGACCAACACAAAAAAATTAATTTTTTCCAGAAAAAAAGGGG
GTTGACCATGCAATGGCCAACACAAAAAAAATTCGAAGTTTTTATCTGAC
Found at i:5665921 original size:60 final size:58
Alignment explanation
Indices: 5665565--5666149 Score: 375
Period size: 60 Copynumber: 9.9 Consensus size: 58
5665555 TCTGACAAAT
* ** *
5665565 ATTTGATTTTTTAT-TCAGATAAAAAGGGGTGTCGGTCATTGCATGACCAACACAAAAAA
1 ATTTGAATTTTTATCT-AGATAAAAAGGGGTGTCGACCA-TGCATGGCCAACACAAAAAA
* * * *
5665624 A-TTGATTTTTTA-CCAGATAAAAAAGGGGAT-TCGACCATGCAATGGCCAATAC-CAAAA
1 ATTTGAATTTTTATCTAGAT-AAAAAGGGG-TGTCGACCATGC-ATGGCCAACACAAAAAA
* * * * *
5665681 ATTCGAGTTTTTTATCT-GACAAAAAGGAGTTGTCGGCCATTGCATGGCCAACACAAAAAA
1 ATTTGA-ATTTTTATCTAGATAAAAAGG-GGTGTCGACCA-TGCATGGCCAACACAAAAAA
* * * *
5665741 A-TT-AATGTTTT-TCCAGAAAAAAATGGGGCGTTGACCATGACATGGCCAACACAAAAAAAA
1 ATTTGAAT-TTTTATCTAGATAAAAA-GGGGTGTCGACCATG-CATGGCCAACAC--AAAAAA
* * **
5665801 ATTCGAAGTTTTTATCT-GACAAAAAGGGGGTGTCGACCATAGCATGGCCAACACCCAAAA
1 ATTTGAA-TTTTTATCTAGATAAAAA-GGGGTGTCGACCAT-GCATGGCCAACACAAAAAA
* * * *
5665861 ATTTGAATTTTTATTTAGATAAAAAGGGGTGTCGGCCATGCAATAGCCAACAGAAAAAAA
1 ATTTGAATTTTTATCTAGATAAAAAGGGGTGTCGACCATGC-ATGGCCAACA-CAAAAAA
* * **
5665921 ATTTGAAATTTTTTATCT-G--AAAAAGGAGTGTCGGCCATTGCATGATCAACACAAAAAA
1 ATTTG-AA-TTTTTATCTAGATAAAAAGGGGTGTCGACCA-TGCATGGCCAACACAAAAAA
* * * *
5665979 A-TT-AATTTTTTTATC-AG-TAAATAGAGGTGTCGGCCATGGCATGGCTAACACCAAAAAA
1 ATTTGAA--TTTTTATCTAGATAAAAAGGGGTGTCGACCAT-GCATGGCCAACA-CAAAAAA
** * * **
5666037 A-TTGAATTTTTTATCT-GATAAAAAAGGAATGTCGACCATGCAATAGCCAATACCCAAAA
1 ATTTGAA-TTTTTATCTAGAT-AAAAAGGGGTGTCGACCATGC-ATGGCCAACACAAAAAA
*
5666096 ATTT-AATTTTTTTATC-AGATTAAAAAGGGGTGTCGATCATGCAATGGCCAACAC
1 ATTTGAA--TTTTTATCTAGA-TAAAAAGGGGTGTCGACCATGC-ATGGCCAACAC
5666150 CAAATTTTTT
Statistics
Matches: 420, Mismatches: 64, Indels: 83
0.74 0.11 0.15
Matches are distributed among these distances:
55 2 0.00
56 11 0.03
57 43 0.10
58 105 0.25
59 98 0.23
60 107 0.25
61 5 0.01
62 45 0.11
63 4 0.01
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (58 bp):
ATTTGAATTTTTATCTAGATAAAAAGGGGTGTCGACCATGCATGGCCAACACAAAAAA
Found at i:5666153 original size:59 final size:57
Alignment explanation
Indices: 5665571--5666149 Score: 377
Period size: 59 Copynumber: 9.8 Consensus size: 57
5665561 AAATATTTGA
** * * *
5665571 TTTTTTATTCAGATAAAAAGGGGTGTCGGTCATTGCATGACCAACACAAAAAAATTGA-
1 TTTTTTA-TCAGATAAAAAGGGGTGTCGACCA-TGCATGGCCAACACAAAAAATTTAAT
* * * ** *
5665629 TTTTTTACCAGATAAAAAAGGGGAT-TCGACCATGCAATGGCCAATACCAAAAATTCGAG
1 TTTTTTATCAGAT-AAAAAGGGG-TGTCGACCATGC-ATGGCCAACACAAAAAATTTAAT
* * * * *
5665688 TTTTTTATCTGACAAAAAGGAGTTGTCGGCCATTGCATGGCCAACACAAAAAAATTAAT
1 TTTTTTATCAGATAAAAAGG-GGTGTCGACCA-TGCATGGCCAACACAAAAAATTTAAT
* * * * * *
5665747 GTTTTT-CCAGAAAAAAATGGGGCGTTGACCATGACATGGCCAACACAAAAAAAAATTCGAA-
1 TTTTTTATCAGATAAAAA-GGGGTGTCGACCATG-CATGGCCAACAC---AAAAAATT-TAAT
* * * *
5665808 GTTTTTATCTGACAAAAAGGGGGTGTCGACCATAGCATGGCCAACACCCAAAAATTTGAAT
1 TTTTTTATCAGATAAAAA-GGGGTGTCGACCAT-GCATGGCCAACA-CAAAAAATTT-AAT
* * * *
5665869 TTTTATT-T-AGATAAAAAGGGGTGTCGGCCATGCAATAGCCAACAGAAAAAAAATTTGAAA
1 TTTT-TTATCAGATAAAAAGGGGTGTCGACCATGC-ATGGCCAAC--ACAAAAAATTT-AAT
* * * ** *
5665929 TTTTTTATCTG--AAAAAGGAGTGTCGGCCATTGCATGATCAACACAAAAAAATTAAT
1 TTTTTTATCAGATAAAAAGGGGTGTCGACCA-TGCATGGCCAACACAAAAAATTTAAT
* * * * *
5665985 TTTTTTATCAG-TAAATAGAGGTGTCGGCCATGGCATGGCTAACACCAAAAAAATTGAA-
1 TTTTTTATCAGATAAAAAGGGGTGTCGACCAT-GCATGGCCAACA-C-AAAAAATTTAAT
* ** * * *
5666043 TTTTTTATCTGATAAAAAAGGAATGTCGACCATGCAATAGCCAATACCCAAAAATTTAAT
1 TTTTTTATCAGAT-AAAAAGGGGTGTCGACCATGC-ATGGCCAACA-CAAAAAATTTAAT
*
5666103 TTTTTTATCAGATTAAAAAGGGGTGTCGATCATGCAATGGCCAACAC
1 TTTTTTATCAGA-TAAAAAGGGGTGTCGACCATGC-ATGGCCAACAC
5666150 CAAATTTTTT
Statistics
Matches: 408, Mismatches: 79, Indels: 67
0.74 0.14 0.12
Matches are distributed among these distances:
56 13 0.03
57 43 0.11
58 86 0.21
59 110 0.27
60 99 0.24
61 20 0.05
62 35 0.09
63 2 0.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (57 bp):
TTTTTTATCAGATAAAAAGGGGTGTCGACCATGCATGGCCAACACAAAAAATTTAAT
Found at i:5667188 original size:13 final size:13
Alignment explanation
Indices: 5667170--5667211 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
5667160 TTGTTTGTTT
*
5667170 ATTATTCATTAAC
1 ATTATTCATGAAC
5667183 ATTATTCATGAAC
1 ATTATTCATGAAC
*
5667196 A-TATTCGTGAAC
1 ATTATTCATGAAC
5667208 ATTA
1 ATTA
5667212 AACAAACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (13 bp):
ATTATTCATGAAC
Found at i:5692881 original size:23 final size:23
Alignment explanation
Indices: 5692855--5692901 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
5692845 TTGTCAAAAC
5692855 ACTTTAAAATAGATGAAAAATTT
1 ACTTTAAAATAGATGAAAAATTT
* *
5692878 ACTTTAGAATGGATGAAAAATTT
1 ACTTTAAAATAGATGAAAAATTT
5692901 A
1 A
5692902 AGGGAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (23 bp):
ACTTTAAAATAGATGAAAAATTT
Found at i:5697476 original size:6 final size:6
Alignment explanation
Indices: 5697465--5697489 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5697455 ATATCGTACG
5697465 TGTATA TGTATA TGTATA TGTATA T
1 TGTATA TGTATA TGTATA TGTATA T
5697490 ATATGTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TGTATA
Found at i:5698296 original size:6 final size:6
Alignment explanation
Indices: 5698285--5698326 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
5698275 TGGCCCCAGC
*
5698285 GATGGG GATGGG GATGGG GATGGG GATGGG GATGGG CATGGG
1 GATGGG GATGGG GATGGG GATGGG GATGGG GATGGG GATGGG
5698327 TGTCATGGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.02, G:0.64, T:0.17
Consensus pattern (6 bp):
GATGGG
Found at i:5701750 original size:26 final size:25
Alignment explanation
Indices: 5701721--5701781 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 25
5701711 ATTTTGTGTT
*
5701721 AATTAAAATTTCATATAATAAACTAA
1 AATTAAAATTTAATATAATAAA-TAA
* * * * *
5701747 AATTGATATATAATATTATAAATTA
1 AATTAAAATTTAATATAATAAATAA
5701772 AATTAAAATT
1 AATTAAAATT
5701782 CACAAGTAGA
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (25 bp):
AATTAAAATTTAATATAATAAATAA
Found at i:5702870 original size:23 final size:25
Alignment explanation
Indices: 5702834--5702880 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
5702824 TTAATTTAAT
*
5702834 AAATTTGAACTTTTTA-TATAAAAC
1 AAATTTGAACTTTTGATTATAAAAC
5702858 AAATTTGAA-TTTTGATTATAAAA
1 AAATTTGAACTTTTGATTATAAAA
5702881 ACTTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (25 bp):
AAATTTGAACTTTTGATTATAAAAC
Found at i:5709195 original size:24 final size:24
Alignment explanation
Indices: 5709164--5709265 Score: 74
Period size: 24 Copynumber: 4.5 Consensus size: 24
5709154 TAAAAATAAT
5709164 TATATTAAAAATATTATTAAATTA
1 TATATTAAAAATATTATTAAATTA
* *
5709188 TATATT-AACAT-TT-TT-ATTTA
1 TATATTAAAAATATTATTAAATTA
*
5709208 T-TATT-AAAATATGATTAAATTA
1 TATATTAAAAATATTATTAAATTA
* ** * *
5709230 TTTATTATCATTTTTATTAAATTA
1 TATATTAAAAATATTATTAAATTA
*
5709254 TAT-TTAATAATA
1 TATATTAAAAATA
5709266 ATCCTATTAT
Statistics
Matches: 58, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
19 8 0.14
20 6 0.10
21 4 0.07
22 7 0.12
23 13 0.22
24 20 0.34
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (24 bp):
TATATTAAAAATATTATTAAATTA
Found at i:5709211 original size:31 final size:30
Alignment explanation
Indices: 5709175--5709235 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
5709165 ATATTAAAAA
5709175 TATTATTAAATTATAT-ATTAACATT-TTTATT
1 TATTATTAAA--ATATGATTAA-ATTATTTATT
5709206 TATTATTAAAATATGATTAAATTATTTATT
1 TATTATTAAAATATGATTAAATTATTTATT
5709236 ATCATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
29 7 0.25
30 11 0.39
31 10 0.36
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (30 bp):
TATTATTAAAATATGATTAAATTATTTATT
Found at i:5709225 original size:42 final size:43
Alignment explanation
Indices: 5709166--5709247 Score: 130
Period size: 42 Copynumber: 1.9 Consensus size: 43
5709156 AAAATAATTA
*
5709166 TATTAAAAATATTATTAAATTATATATTAACATTTTTATTTAT
1 TATTAAAAATATGATTAAATTATATATTAACATTTTTATTTAT
* *
5709209 TATT-AAAATATGATTAAATTATTTATTATCATTTTTATT
1 TATTAAAAATATGATTAAATTATATATTAACATTTTTATT
5709248 AAATTATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 32 0.89
43 4 0.11
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (43 bp):
TATTAAAAATATGATTAAATTATATATTAACATTTTTATTTAT
Found at i:5713828 original size:13 final size:13
Alignment explanation
Indices: 5713810--5713843 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
5713800 TTTTTTTATC
*
5713810 TATTCTTAAATTG
1 TATTCTAAAATTG
5713823 TATTCTAAAATTG
1 TATTCTAAAATTG
5713836 TATTCTAA
1 TATTCTAA
5713844 TCAATCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (13 bp):
TATTCTAAAATTG
Found at i:5716248 original size:17 final size:17
Alignment explanation
Indices: 5716226--5716261 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5716216 AAGGACCTGC
5716226 ACTTTCAAAAATAGTTT
1 ACTTTCAAAAATAGTTT
5716243 ACTTTCAAAAATAGTTT
1 ACTTTCAAAAATAGTTT
5716260 AC
1 AC
5716262 CCACTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.39
Consensus pattern (17 bp):
ACTTTCAAAAATAGTTT
Found at i:5741293 original size:2 final size:2
Alignment explanation
Indices: 5741286--5741310 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5741276 TCACTTAGGA
5741286 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
5741311 TTTGCAGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:5747084 original size:17 final size:17
Alignment explanation
Indices: 5747064--5747101 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5747054 ATTTTTATTT
*
5747064 ATTAA-AAATTGATTTAA
1 ATTAATAAATT-AGTTAA
5747081 ATTAATAAATTAGTTAA
1 ATTAATAAATTAGTTAA
5747098 ATTA
1 ATTA
5747102 TTTAGAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
ATTAATAAATTAGTTAA
Found at i:5753482 original size:20 final size:19
Alignment explanation
Indices: 5753440--5753490 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
5753430 AAAATCAAAA
*
5753440 GTATCGATATCCTTATCATG
1 GTATCGATA-CCTTATCAAG
*
5753460 GTATCGATACCTTCATTAAG
1 GTATCGATACCTT-ATCAAG
*
5753480 GTATCAATACC
1 GTATCGATACC
5753491 ATTTTATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (19 bp):
GTATCGATACCTTATCAAG
Found at i:5756963 original size:28 final size:28
Alignment explanation
Indices: 5756914--5756978 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
5756904 AAAAATAATT
*
5756914 TTTTTAAAGATTAAAGTTAAA-TTATAA
1 TTTTTAAAAATTAAAGTTAAATTTATAA
*
5756941 TTTTTAAATAATTAAA-TTAAAATTTTATCA
1 TTTTTAAA-AATTAAAGTT-AAA-TTTATAA
5756971 TTTTTAAA
1 TTTTTAAA
5756979 GGGTTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 10 0.31
28 9 0.28
30 13 0.41
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (28 bp):
TTTTTAAAAATTAAAGTTAAATTTATAA
Found at i:5757298 original size:28 final size:28
Alignment explanation
Indices: 5757254--5757315 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
5757244 AGTTTTAGGA
*
5757254 ATTAAATACAGGAAAAAGACATTAATAC
1 ATTAAATACAGGAAAAAGACATTAAAAC
* *
5757282 ATTAAATTCAAGG-AAAAGGCATTAAAAC
1 ATTAAATAC-AGGAAAAAGACATTAAAAC
5757310 ATTAAA
1 ATTAAA
5757316 GGCAAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 27 0.90
29 3 0.10
ACGTcount: A:0.56, C:0.10, G:0.11, T:0.23
Consensus pattern (28 bp):
ATTAAATACAGGAAAAAGACATTAAAAC
Found at i:5757325 original size:28 final size:28
Alignment explanation
Indices: 5757267--5757328 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
5757257 AAATACAGGA
* * ** *
5757267 AAAAGACATTAATACATTAAATTCAAGG
1 AAAAGGCATTAAAACATTAAAGGCAAAG
5757295 AAAAGGCATTAAAACATTAAAGGCAAAG
1 AAAAGGCATTAAAACATTAAAGGCAAAG
5757323 AAAAGG
1 AAAAGG
5757329 TTATTGTCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.56, C:0.10, G:0.16, T:0.18
Consensus pattern (28 bp):
AAAAGGCATTAAAACATTAAAGGCAAAG
Found at i:5758430 original size:58 final size:57
Alignment explanation
Indices: 5758341--5758454 Score: 133
Period size: 58 Copynumber: 2.0 Consensus size: 57
5758331 TTGGTCATGC
* *
5758341 AATGGCCGACACCCCTTTTTTGTCAGAAAAAAA-TACAATTTTTTGGTGTTGCCCATCA
1 AATGGCCGACACCCCTTTTTTG-CAAAAAAAAATTAC-ATTTTTGGGTGTTGCCCATCA
* * *
5758399 AATGGCTGACACCCCATTTTTTAG-AAAAAAAAATTGCATTTTTGGGTGTTGGCCAT
1 AATGGCCGACACCCC-TTTTTT-GCAAAAAAAAATTACATTTTTGGGTGTTGCCCAT
5758455 ATACTGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
58 39 0.81
59 8 0.17
60 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (57 bp):
AATGGCCGACACCCCTTTTTTGCAAAAAAAAATTACATTTTTGGGTGTTGCCCATCA
Found at i:5758561 original size:42 final size:42
Alignment explanation
Indices: 5758501--5758582 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
5758491 TTGGTCATCG
5758501 AATGGCCGACACCCCCTTTTCTCGAAAAAAAATGCATTTTCA
1 AATGGCCGACACCCCCTTTTCTCGAAAAAAAATGCATTTTCA
*
5758543 AATGGCCGACACCTCCTTTTCTCGAAAAAAAATGCATTTT
1 AATGGCCGACACCCCCTTTTCTCGAAAAAAAATGCATTTT
5758583 TTGGTGTTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (42 bp):
AATGGCCGACACCCCCTTTTCTCGAAAAAAAATGCATTTTCA
Found at i:5758570 original size:144 final size:144
Alignment explanation
Indices: 5758396--5758670 Score: 378
Period size: 144 Copynumber: 1.9 Consensus size: 144
5758386 GTGTTGCCCA
* *
5758396 TCAAATGGCTGACACCCCATTTTTTAGAAAAAAAAATTGCATTTTTGGGTGTTGGCCATATACTG
1 TCAAATGGCCGACACCCCATTTTCTAG-AAAAAAAA-TGCATTTTTGGGTGTTGGCCAT-TACTG
* * *
5758461 TT-T-GAGAAAAAAA-TTCAAAATTTTTTGGTGTTGGTCATCGAATGGCCGACACCCCCTTTTCT
63 TTCTCAAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCT
5758523 CGAAAAAAAATGCATTT
128 CGAAAAAAAATGCATTT
* * * *
5758540 TCAAATGGCCGACACCTCC-TTTTCTCGAAAAAAAATGCATTTTTTGGTGTTGGCCATTCCTTTT
1 TCAAATGGCCGACACC-CCATTTTCTAGAAAAAAAATGCATTTTTGGGTGTTGGCCATTACTGTT
* * *
5758604 CTCAAGAAAAAAATTTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTTTCG
65 CTCAAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCG
5758669 AA
130 AA
5758671 TTTTTTTTTT
Statistics
Matches: 115, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
141 5 0.04
142 22 0.19
143 17 0.15
144 69 0.60
145 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (144 bp):
TCAAATGGCCGACACCCCATTTTCTAGAAAAAAAATGCATTTTTGGGTGTTGGCCATTACTGTTC
TCAAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCGA
AAAAAAATGCATTT
Found at i:5758784 original size:60 final size:59
Alignment explanation
Indices: 5758598--5758942 Score: 302
Period size: 60 Copynumber: 5.7 Consensus size: 59
5758588 GTTGGCCATT
* *
5758598 CCTTTTCTCAAGAAAAAAATTTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCC
1 CCTTTTCTCGAGAAAAAAA-TTTAAA-TTTTTTGGTGTTGGCCATCAAATGGCTGACACCC
* ****** ** * *
5758659 CCTTTTTTCGA-ATTTTTTTTTTTGCATTTTTGGGTGTTGGCCATCAAATGGCTGACACAC
1 CCTTTTCTCGAGA--AAAAAATTTAAATTTTTTGGTGTTGGCCATCAAATGGCTGACACCC
* * *
5758719 CCTTTTTTCGAGAAAAAAATTTCAAACTTTTTTAGTGTTGGCAATCAAATGG-TCGACACCC
1 CCTTTTCTCGAGAAAAAAATTT-AAA-TTTTTTGGTGTTGGCCATCAAATGGCT-GACACCC
* * * * ***
5758780 CTTTTTCTCGA-AAAAAAAATTATA-TTTTTGGTGTTGACCATTTGATGGCTGACACCC
1 CCTTTTCTCGAGAAAAAAATTTAAATTTTTTGGTGTTGGCCATCAAATGGCTGACACCC
* * * * *
5758837 CCTATTCTCGAGAAAAAAATTTAAATATTTTTTGTATTGGCCATCAAATGGCCGACATCC
1 CCTTTTCTCGAGAAAAAAATTTAAAT-TTTTTGGTGTTGGCCATCAAATGGCTGACACCC
*
5758897 CCTTTTCTCGGATAAAAAAATTGTAAATTTTTTTGGTGTTGGCCAT
1 CCTTTTCTC-GAGAAAAAAATT-TAAA-TTTTTTGGTGTTGGCCAT
5758943 GTAATGCCGA
Statistics
Matches: 220, Mismatches: 51, Indels: 25
0.74 0.17 0.08
Matches are distributed among these distances:
57 34 0.15
58 12 0.05
59 5 0.02
60 87 0.40
61 62 0.28
62 19 0.09
63 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (59 bp):
CCTTTTCTCGAGAAAAAAATTTAAATTTTTTGGTGTTGGCCATCAAATGGCTGACACCC
Found at i:5759151 original size:31 final size:31
Alignment explanation
Indices: 5759116--5759175 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5759106 TACAATCGAA
* * *
5759116 TTTCGGGGTTGAGTTATATATTGTCATGTAT
1 TTTCGGAGTTGAATTATATACTGTCATGTAT
5759147 TTTCGGAGTTGAATTATATACTGTCATGT
1 TTTCGGAGTTGAATTATATACTGTCATGT
5759176 GAAGCGGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.47
Consensus pattern (31 bp):
TTTCGGAGTTGAATTATATACTGTCATGTAT
Found at i:5759694 original size:19 final size:20
Alignment explanation
Indices: 5759657--5759696 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5759647 GTTAAGAAAT
5759657 AAATATTATCTACAAATTAA
1 AAATATTATCTACAAATTAA
5759677 AAATATTAAT-TA-AAATTAA
1 AAATATT-ATCTACAAATTAA
5759696 A
1 A
5759697 TTTATGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 9 0.47
21 2 0.11
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATTATCTACAAATTAA
Found at i:5762704 original size:12 final size:12
Alignment explanation
Indices: 5762662--5762709 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
5762652 ATTTGTGTAA
*
5762662 AAATTAATTTGA
1 AAATTAATTTGG
5762674 AAATTAATTTAAGTTG
1 AAATTAATTT--G--G
5762690 AAATTAATTTGG
1 AAATTAATTTGG
5762702 AAATTAAT
1 AAATTAAT
5762710 GAACATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (12 bp):
AAATTAATTTGG
Found at i:5762987 original size:45 final size:46
Alignment explanation
Indices: 5762927--5763084 Score: 130
Period size: 45 Copynumber: 3.5 Consensus size: 46
5762917 AAAAATTATT
5762927 ATTATATTA-TAATTTT-TATCATATAATGTGTTGATTTGATAATAC
1 ATTAT-TTATTAATTTTATATCATATAATGTGTTGATTTGATAATAC
* * * **** * * *
5762972 ATTACTTATTAATTTTATATC-TTTAA-ATAAAAATTATTATTAT-T
1 ATTATTTATTAATTTTATATCATATAATGTGTTGATT-TGATAATAC
*
5763016 ATTATTATATTACAATTTT-TATCATATAATGTGTTGATTTGACAATAC
1 ATTATT-TATT--AATTTTATATCATATAATGTGTTGATTTGATAATAC
5763064 ATTATTTATTAATTTTATATC
1 ATTATTTATTAATTTTATATC
5763085 TTTAAATAAA
Statistics
Matches: 82, Mismatches: 21, Indels: 19
0.67 0.17 0.16
Matches are distributed among these distances:
44 12 0.15
45 30 0.37
46 12 0.15
47 18 0.22
48 10 0.12
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.53
Consensus pattern (46 bp):
ATTATTTATTAATTTTATATCATATAATGTGTTGATTTGATAATAC
Found at i:5763078 original size:92 final size:92
Alignment explanation
Indices: 5762921--5763201 Score: 450
Period size: 92 Copynumber: 3.1 Consensus size: 92
5762911 TAAAGTAAAA
* * *
5762921 ATTATTATTATATTATAATTTTTATCATATAATGTGTTGATTTGATAATACATTACTTATTAATT
1 ATTATTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATT
5762986 TTATATCTTTAAATAAAAATTATTATT
66 TTATATCTTTAAATAAAAATTATTATT
5763013 ATTATTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATT
1 ATTATTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATT
5763078 TTATATCTTTAAAT--AAA--A--ATT
66 TTATATCTTTAAATAAAAATTATTATT
**
5763099 ATTATTATTATATTACAATTTTTATCATATTTTGAATGTTGATTTGACAATACATTATTTATTAA
1 ATTATTATTATATTACAATTTTTATCATATAATG--TGTTGATTTGACAATACATTATTTATTAA
5763164 TTTTATATCTTTAAATAAAAATTATTATT
64 TTTTATATCTTTAAATAAAAATTATTATT
5763193 ATTA-TATTA
1 ATTATTATTA
5763202 CAATTTTTAC
Statistics
Matches: 176, Mismatches: 5, Indels: 15
0.90 0.03 0.08
Matches are distributed among these distances:
86 35 0.20
88 46 0.26
90 6 0.03
92 77 0.44
93 5 0.03
94 7 0.04
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (92 bp):
ATTATTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATT
TTATATCTTTAAATAAAAATTATTATT
Found at i:5763219 original size:88 final size:86
Alignment explanation
Indices: 5762841--5763216 Score: 519
Period size: 88 Copynumber: 4.3 Consensus size: 86
5762831 AAAAAGATAG
* * * *
5762841 TTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATTATATTACAATTTTTATCATATATTGTGTTGATTTGACAATACATTATTTAT-TAATTTT-
5762906 ATA--TTTAAAGT-AAAA--ATTA
64 ATATCTTTAAA-TAAAAATTATTA
* * * *
5762925 TTATTATATTATAATTTTTATCATATAATGTGTTGATTTGATAATACATTACTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATATTGTGTTGATTTGACAATACATTATTTATTAATTTTAT
5762990 ATCTTTAAATAAAAATTATTATTATTA
66 ATCTTTAAAT--AAA--A--ATTATTA
*
5763017 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATATTGTGTTGATTTGACAATACATTATTTATTAATTTTAT
5763082 ATCTTTAAATAAAAATTATTA
66 ATCTTTAAATAAAAATTATTA
*
5763103 TTATTATATTACAATTTTTATCATATTTTGAATGTTGATTTGACAATACATTATTTATTAATTTT
1 TTATTATATTACAATTTTTATCATATATTG--TGTTGATTTGACAATACATTATTTATTAATTTT
5763168 ATATCTTTAAATAAAAATTATTA
64 ATATCTTTAAATAAAAATTATTA
*
5763191 TTATTATATTACAATTTTTACCATAT
1 TTATTATATTACAATTTTTATCATAT
5763217 TTTAAATTTA
Statistics
Matches: 265, Mismatches: 14, Indels: 22
0.88 0.05 0.07
Matches are distributed among these distances:
82 3 0.01
83 7 0.03
84 55 0.21
86 37 0.14
88 83 0.31
90 4 0.02
92 76 0.29
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (86 bp):
TTATTATATTACAATTTTTATCATATATTGTGTTGATTTGACAATACATTATTTATTAATTTTAT
ATCTTTAAATAAAAATTATTA
Found at i:5765688 original size:30 final size:30
Alignment explanation
Indices: 5765637--5765702 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
5765627 TCCCTTTACT
* * *
5765637 TTTTAAATTTAATTTATAATTTCGTT-TTTA
1 TTTTAAATTAAATTTAGAATTTC-TTGTATA
*
5765667 TTTTAAATTAAATTTCGAATTTCTTGTATA
1 TTTTAAATTAAATTTAGAATTTCTTGTATA
5765697 TTTTAA
1 TTTTAA
5765703 TTTTTCTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (30 bp):
TTTTAAATTAAATTTAGAATTTCTTGTATA
Found at i:5767996 original size:6 final size:6
Alignment explanation
Indices: 5767985--5768041 Score: 71
Period size: 6 Copynumber: 9.5 Consensus size: 6
5767975 GGTTTATTCA
* * *
5767985 ATTTTG ATTTTG ATTTTG ATTCTG ATTTTC ATTTTCG ATTTTG A-TTGG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTT-G ATTTTG ATTTTG
5768033 ATTTTG ATT
1 ATTTTG ATT
5768042 GCTACTGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
5 4 0.09
6 34 0.79
7 5 0.12
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (6 bp):
ATTTTG
Found at i:5768012 original size:24 final size:24
Alignment explanation
Indices: 5767985--5768041 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
5767975 GGTTTATTCA
*
5767985 ATTTTGATTTT-GATTTTGATTCTG
1 ATTTTGATTTTCGATTTTGATT-GG
*
5768009 ATTTTCATTTTCGATTTTGATTGG
1 ATTTTGATTTTCGATTTTGATTGG
5768033 ATTTTGATT
1 ATTTTGATT
5768042 GCTACTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 19 0.66
25 10 0.34
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (24 bp):
ATTTTGATTTTCGATTTTGATTGG
Found at i:5771605 original size:24 final size:24
Alignment explanation
Indices: 5771568--5771614 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5771558 TTAATATGTA
*
5771568 GTGTAATATGTAAATTTTAATTTG
1 GTGTAATATGTAAACTTTAATTTG
*
5771592 GTGTACATAT-TAAACTTTGATTT
1 GTGTA-ATATGTAAACTTTAATTT
5771615 TAATATGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (24 bp):
GTGTAATATGTAAACTTTAATTTG
Found at i:5774806 original size:85 final size:85
Alignment explanation
Indices: 5774420--5775514 Score: 1710
Period size: 86 Copynumber: 12.9 Consensus size: 85
5774410 TTAAAATCTA
*
5774420 ATAAAAATTGTAATATAATAATAATCTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
1 ATAAAAATTGTATTATAATAATAAT-TTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
5774485 GTCAAATCAACACATTATTTG
65 GTCAAATCAACACATTATTTG
* * *
5774506 ATAAAAATTGTAATACAATAATAA-TTTTTTATTTAAATATTTAAATTTAGTAAGTAATGTATTG
1 ATAAAAATTGTATTATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
5774570 TCAAATCAACACATTATTTG
66 TCAAATCAACACATTATTTG
*
5774590 ATAAAAATCT-TATTATAATAAT-A-TTTTTTATTTAAATATTTAAATTTAGTAAATAATATATT
1 ATAAAAAT-TGTATTATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
5774652 GTCAAATCAACACATTATTTG
65 GTCAAATCAACACATTATTTG
*
5774673 ATAAAAATTGTATTATAATAATAA---TCTT-TTT---TATTTAAATTTAGTAAATAATGTATTG
1 ATAAAAATTGTATTATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
*
5774731 TCAAATCAATACATTATTTG
66 TCAAATCAACACATTATTTG
* * * *
5774751 ATAAAAATTGTATTATAATAATAATATTTTTATTTAAATATTTGAATTTAGTAAATAATATATTA
1 ATAAAAATTGTATTATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
*
5774816 TCAAATCAACATATTATTTG
66 TCAAATCAACACATTATTTG
* * *
5774836 ATAAAAATTGTAATATAATAATAATCTTTTTTATTTAAATATTTAAATTTCGTAAATAATGTGTT
1 ATAAAAATTGTATTATAATAATAAT-TTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
*
5774901 ATCAAATCAACACATTATTTG
65 GTCAAATCAACACATTATTTG
5774922 ATAAAAATTGTATTATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
1 ATAAAAATTGTATTATAATAATAAT-TTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
* *
5774987 ATTAAATCAACACATTATTTG
65 GTCAAATCAACACATTATTTG
* * *
5775008 ATAAAAATTGTATTATAATAATAATCATTTTTGTTTAAATATTTAAATTTAGTAAATAATATATT
1 ATAAAAATTGTATTATAATAATAAT-TTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
* *
5775073 GTTATATCAACACATTATTTG
65 GTCAAATCAACACATTATTTG
*
5775094 ATAAAAATTGTAATATAATAATAATTTTTCTTATTTAAATATTTAAATTTAGTAAATAATGTATT
1 ATAAAAATTGTATTATAATAATAATTTTT-TTATTTAAATATTTAAATTTAGTAAATAATGTATT
* *
5775159 ATCAAATCAACATATTATTTG
65 GTCAAATCAACACATTATTTG
*
5775180 ATAAAAATTGTATTATAATAATAATCTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
1 ATAAAAATTGTATTATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
* *
5775245 TTAAATCAACAAATTATTTG
66 TCAAATCAACACATTATTTG
*
5775265 AT-AAAATTATATTATAATAATAATCTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
1 ATAAAAATTGTATTATAATAATAAT-TTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
*
5775329 GTAAAATCAACACATTATTTG
65 GTCAAATCAACACATTATTTG
*
5775350 ATAAAAATTATATTATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
1 ATAAAAATTGTATTATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
* *
5775415 TTAAATCAACATATTATTTG
66 TCAAATCAACACATTATTTG
* * *
5775435 ATAAAAATTATAATATAATTATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
1 ATAAAAATTGTATTATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
5775500 TCAAATCAACACATT
66 TCAAATCAACACATT
5775515 GCATGGTCAA
Statistics
Matches: 939, Mismatches: 56, Indels: 29
0.92 0.05 0.03
Matches are distributed among these distances:
78 69 0.07
81 6 0.01
82 7 0.01
83 79 0.08
84 99 0.11
85 318 0.34
86 361 0.38
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (85 bp):
ATAAAAATTGTATTATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTG
TCAAATCAACACATTATTTG
Found at i:5777869 original size:27 final size:25
Alignment explanation
Indices: 5777809--5777871 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 25
5777799 GGGTTTCAAA
5777809 TCTATTTAAAATTAATTTTTTAAAG
1 TCTATTTAAAATTAATTTTTTAAAG
*
5777834 TTTATTTAAAATTAAATATATTTT-AAG
1 TCTATTTAAAATT-AAT-T-TTTTAAAG
5777861 TCTATTTAAAA
1 TCTATTTAAAA
5777872 ATTTTCATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 12 0.36
26 3 0.09
27 14 0.42
28 4 0.12
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (25 bp):
TCTATTTAAAATTAATTTTTTAAAG
Found at i:5778325 original size:23 final size:23
Alignment explanation
Indices: 5778295--5778339 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
5778285 CAATCATTTT
5778295 TTAAATATATATTAATTTTAAAA
1 TTAAATATATATTAATTTTAAAA
5778318 TTAAATATATATTAATTTTAAA
1 TTAAATATATATTAATTTTAAA
5778340 TAGTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAAATATATATTAATTTTAAAA
Found at i:5792043 original size:29 final size:29
Alignment explanation
Indices: 5792001--5792057 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
5791991 ATGAAAATTC
5792001 AAATGTATAGAAATCATGGGTTAATCATG
1 AAATGTATAGAAATCATGGGTTAATCATG
5792030 AAATGTATAGAAATCATGGGTTAATCAT
1 AAATGTATAGAAATCATGGGTTAATCAT
5792058 AGTCTAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (29 bp):
AAATGTATAGAAATCATGGGTTAATCATG
Found at i:5793846 original size:32 final size:33
Alignment explanation
Indices: 5793810--5793883 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
5793800 CATCTTCATA
5793810 AATG-CTTTTTGCATAA-TATCTCCCTTGAAATT
1 AATGCCTTTTTGCATAACT-TCTCCCTTGAAATT
* *
5793842 AATGCCTTTTTGCCTAACTTCTTCCTTGAAATT
1 AATGCCTTTTTGCATAACTTCTCCCTTGAAATT
*
5793875 AATGTCTTT
1 AATGCCTTT
5793884 ATGAATGCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 4 0.11
33 32 0.86
34 1 0.03
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.46
Consensus pattern (33 bp):
AATGCCTTTTTGCATAACTTCTCCCTTGAAATT
Found at i:5796303 original size:20 final size:20
Alignment explanation
Indices: 5796278--5796317 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5796268 TTTCGAGATA
5796278 CATATATACTATATTTACAT
1 CATATATACTATATTTACAT
5796298 CATATATACTATATTTACAT
1 CATATATACTATATTTACAT
5796318 GCACATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (20 bp):
CATATATACTATATTTACAT
Found at i:5799316 original size:2 final size:2
Alignment explanation
Indices: 5799309--5799352 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5799299 AACCCTAGCC
5799309 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5799351 CT
1 CT
5799353 TCTGTGCTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5801658 original size:21 final size:21
Alignment explanation
Indices: 5801625--5801665 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5801615 ATAACTATTT
*
5801625 TATTTAAACATAACTAAATAA
1 TATTTAAACATAAATAAATAA
**
5801646 TATTTAATTATAAATAAATA
1 TATTTAAACATAAATAAATA
5801666 CTAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
TATTTAAACATAAATAAATAA
Found at i:5807631 original size:19 final size:20
Alignment explanation
Indices: 5807589--5807634 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5807579 TATTTATTAC
5807589 AATTTATGTATTGATAAGTA
1 AATTTATGTATTGATAAGTA
*
5807609 AATTTATGATGTTGA-AA-TA
1 AATTTATG-TATTGATAAGTA
5807628 AATTTAT
1 AATTTAT
5807635 AATAATTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 9 0.38
20 10 0.42
21 5 0.21
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (20 bp):
AATTTATGTATTGATAAGTA
Found at i:5809160 original size:31 final size:31
Alignment explanation
Indices: 5809122--5809184 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
5809112 TGGGGTGATG
5809122 TGATTTTGAACCAGTAGACCTAGCTTTTAAT
1 TGATTTTGAACCAGTAGACCTAGCTTTTAAT
5809153 TGATTTTGAACCAGTAGACCTAGCTTTTAAT
1 TGATTTTGAACCAGTAGACCTAGCTTTTAAT
5809184 T
1 T
5809185 AATCTATTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (31 bp):
TGATTTTGAACCAGTAGACCTAGCTTTTAAT
Found at i:5812019 original size:20 final size:19
Alignment explanation
Indices: 5811977--5812029 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
5811967 ATTAATTGAT
* *
5811977 TATTATATATTTTTAAATT
1 TATTATATATTTTCAAATA
*
5811996 TATTATTATATTTTCGAATA
1 TATTA-TATATTTTCAAATA
*
5812016 TATTTATGTATTTT
1 TA-TTATATATTTT
5812030 ATATATTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.18
20 20 0.71
21 3 0.11
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (19 bp):
TATTATATATTTTCAAATA
Found at i:5819480 original size:15 final size:16
Alignment explanation
Indices: 5819456--5819485 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5819446 ATTTAATAAC
5819456 TTTATATAATTTTTTG
1 TTTATATAATTTTTTG
5819472 TTTAT-TAATTTTTT
1 TTTATATAATTTTTT
5819486 ATATAGTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTATATAATTTTTTG
Found at i:5833088 original size:21 final size:22
Alignment explanation
Indices: 5833050--5833096 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
5833040 ATAAAATAGA
*
5833050 AAAATGACAGCAAAACAACATC
1 AAAATGACAGCAAAACAACAAC
*
5833072 AAAATGGCAGC-AAACAACAAC
1 AAAATGACAGCAAAACAACAAC
5833093 AAAA
1 AAAA
5833097 CAACAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.62, C:0.21, G:0.11, T:0.06
Consensus pattern (22 bp):
AAAATGACAGCAAAACAACAAC
Found at i:5861126 original size:32 final size:32
Alignment explanation
Indices: 5861077--5861141 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
5861067 CTTAACCTGT
*
5861077 TGGATTTTGTTTAAATTT-AAAAATTATCAAAA
1 TGGAGTTTGTTTAAATTTGAAAAA-TATCAAAA
*
5861109 TGGAGTTTGTTTCAATTTGAAAAATATCAAAA
1 TGGAGTTTGTTTAAATTTGAAAAATATCAAAA
5861141 T
1 T
5861142 CATTTCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 25 0.83
33 5 0.17
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (32 bp):
TGGAGTTTGTTTAAATTTGAAAAATATCAAAA
Found at i:5861201 original size:21 final size:21
Alignment explanation
Indices: 5861162--5861202 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5861152 ACAAAATAAA
* *
5861162 AAATATTATTATGAGAATATG
1 AAATATTAATATGAAAATATG
*
5861183 AAATATTAATATTAAAATAT
1 AAATATTAATATGAAAATAT
5861203 ATATTCGTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
AAATATTAATATGAAAATATG
Found at i:5884450 original size:18 final size:17
Alignment explanation
Indices: 5884418--5884451 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5884408 TTTTGAATTT
*
5884418 TTAAAACATAAATATTA
1 TTAAAACAAAAATATTA
5884435 TTAAATACAAAAATATT
1 TTAAA-ACAAAAATATT
5884452 TTGAGATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAACAAAAATATTA
Found at i:5884853 original size:14 final size:14
Alignment explanation
Indices: 5884835--5884882 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
5884825 TTATAATTTG
*
5884835 AAAAATATAAAATAT
1 AAAAATA-AATATAT
* *
5884850 AAAAATTAAATTTTT
1 AAAAA-TAAATATAT
5884865 AAAAATAAATATAT
1 AAAAATAAATATAT
5884879 AAAA
1 AAAA
5884883 TTATATTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 11 0.41
15 14 0.52
16 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAATAAATATAT
Found at i:5884862 original size:29 final size:28
Alignment explanation
Indices: 5884829--5884890 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
5884819 TAAATTTTAT
5884829 AATTTGAAAAATATAAA-ATATAAAAATTA
1 AATTTGAAAAA-ATAAATATAT-AAAATTA
**
5884858 AATTTTTAAAAATAAATATATAAAATTA
1 AATTTGAAAAAATAAATATATAAAATTA
*
5884886 TATTT
1 AATTT
5884891 TAATTTTACC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (28 bp):
AATTTGAAAAAATAAATATATAAAATTA
Found at i:5885061 original size:18 final size:22
Alignment explanation
Indices: 5885038--5885083 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 22
5885028 TGCGGACTTT
5885038 CTTTTTGTT-TT-TT-TTC-TC
1 CTTTTTGTTGTTCTTCTTCTTC
5885056 CTTTTTGTTGTTCTTCTTCTTC
1 CTTTTTGTTGTTCTTCTTCTTC
5885078 CTTTTT
1 CTTTTT
5885084 TTATATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.38
19 2 0.08
20 2 0.08
21 3 0.12
22 8 0.33
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.74
Consensus pattern (22 bp):
CTTTTTGTTGTTCTTCTTCTTC
Found at i:5914531 original size:29 final size:30
Alignment explanation
Indices: 5914463--5914531 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
5914453 ATTGTATTAA
*
5914463 TAATTTATAAGAATTAGATCAAATTAAAATT
1 TAATTTAT-AGAATTACATCAAATTAAAATT
* *
5914494 TCATGTATAGAATTACA-CAAATT-AAATT
1 TAATTTATAGAATTACATCAAATTAAAATT
5914522 TAAGTTTATA
1 TAA-TTTATA
5914532 TATACAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 11 0.34
30 8 0.25
31 6 0.19
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (30 bp):
TAATTTATAGAATTACATCAAATTAAAATT
Found at i:5914561 original size:31 final size:31
Alignment explanation
Indices: 5914490--5914566 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
5914480 ATCAAATTAA
* *
5914490 AATTTCATGTATAGAATTACACAAATTAAATTT
1 AATTT-ATGTATACAATTACAC-AATTAAATAT
*
5914523 AAGTTTATATATACAATTACAC-ATTAAATCAT
1 AA-TTTATGTATACAATTACACAATTAAAT-AT
5914555 AATTTATGTATA
1 AATTTATGTATA
5914567 ATTTTGAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
31 16 0.42
32 3 0.08
33 16 0.42
34 3 0.08
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTTATGTATACAATTACACAATTAAATAT
Found at i:5915493 original size:3 final size:3
Alignment explanation
Indices: 5915485--5915509 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5915475 TATTTTTTAT
5915485 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
5915510 CTCCATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:5917510 original size:23 final size:23
Alignment explanation
Indices: 5917461--5917513 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5917451 TGATTCAAAT
* * *
5917461 AAATACTCATATTTATATTATTG
1 AAATATTCATATTTATAGTATTA
5917484 AAATATTCATATTGTATAGTA-TA
1 AAATATTCATATT-TATAGTATTA
5917507 AAATATT
1 AAATATT
5917514 TATGGCTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (23 bp):
AAATATTCATATTTATAGTATTA
Found at i:5922693 original size:23 final size:23
Alignment explanation
Indices: 5922650--5922693 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5922640 AGTTTGAAGT
*
5922650 TTGAAGAGAAGGCAAATGATGAC
1 TTGAAGAGAAGGCAAAAGATGAC
5922673 TTGAAGA-AAGGCAAAGAGATG
1 TTGAAGAGAAGGCAAA-AGATG
5922694 GGAGGTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.45, C:0.07, G:0.32, T:0.16
Consensus pattern (23 bp):
TTGAAGAGAAGGCAAAAGATGAC
Found at i:5932316 original size:18 final size:18
Alignment explanation
Indices: 5932293--5932328 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5932283 CACCAAATAG
5932293 AAGATCTAGTCTTTCTAA
1 AAGATCTAGTCTTTCTAA
5932311 AAGATCTAGTCTTTCTAA
1 AAGATCTAGTCTTTCTAA
5932329 GCTAAGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (18 bp):
AAGATCTAGTCTTTCTAA
Found at i:5937492 original size:32 final size:31
Alignment explanation
Indices: 5937454--5937517 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
5937444 ATTATGCACT
* *
5937454 TGAAACTTGAATTGTGATTCATATGTAATACA
1 TGAAACTTGAATTGTGAATCAAATGT-ATACA
* *
5937486 TGAAACTTTAATTTTGAATCAAATGTATACA
1 TGAAACTTGAATTGTGAATCAAATGTATACA
5937517 T
1 T
5937518 TTAAAGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (31 bp):
TGAAACTTGAATTGTGAATCAAATGTATACA
Found at i:5939528 original size:6 final size:6
Alignment explanation
Indices: 5939517--5939561 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
5939507 ACAATTCATA
* *
5939517 TCACTT TCACTT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
5939562 ATTTTGACCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:5942890 original size:21 final size:21
Alignment explanation
Indices: 5942842--5942892 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5942832 TTTTCCATTT
*
5942842 ATCTTCTTTTGGATTCCAAGA
1 ATCTTCTTTTGGATTCCAAAA
* * **
5942863 ATGTTCTTTTGGCTTTTAAAA
1 ATCTTCTTTTGGATTCCAAAA
5942884 ATCTTCTTT
1 ATCTTCTTT
5942893 CAACATCTTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.51
Consensus pattern (21 bp):
ATCTTCTTTTGGATTCCAAAA
Found at i:5947872 original size:19 final size:21
Alignment explanation
Indices: 5947840--5947878 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
5947830 AAAATTCGAA
5947840 TTTTATTTTCTATTTCTTAAC
1 TTTTATTTTCTATTTCTTAAC
*
5947861 TTTT-TTTT-TATTTTTTAA
1 TTTTATTTTCTATTTCTTAA
5947879 ATTTCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTATTTTCTATTTCTTAAC
Found at i:5961799 original size:18 final size:18
Alignment explanation
Indices: 5961778--5961820 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5961768 TTTTCAGTTG
5961778 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
5961796 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
5961814 TAATTAA
1 TAATTAA
5961821 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:5961968 original size:15 final size:15
Alignment explanation
Indices: 5961948--5961998 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
5961938 ACAAAATGAG
*
5961948 AATATAAATGACTAA
1 AATATAAATGATTAA
*
5961963 AATATAAA--ATTTTA
1 AATATAAATGA-TTAA
5961977 AATATAAATGATTAA
1 AATATAAATGATTAA
5961992 AATATAA
1 AATATAA
5961999 CTTGAACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 10 0.33
15 18 0.60
16 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (15 bp):
AATATAAATGATTAA
Found at i:5966282 original size:14 final size:14
Alignment explanation
Indices: 5966265--5966294 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5966255 AATATTTAAT
5966265 AATATTTAAAACAA
1 AATATTTAAAACAA
5966279 AATATTTAAAACAA
1 AATATTTAAAACAA
5966293 AA
1 AA
5966295 GTATAAGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (14 bp):
AATATTTAAAACAA
Found at i:5971617 original size:38 final size:38
Alignment explanation
Indices: 5971566--5971642 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
5971556 TCATAAGTAT
5971566 GCATAAGACAGAGTGAAGTAACAATATATTTTTATACG
1 GCATAAGACAGAGTGAAGTAACAATATATTTTTATACG
* *
5971604 GCATAAGACAGAGTGACGTAACGATATATTTTTATACG
1 GCATAAGACAGAGTGAAGTAACAATATATTTTTATACG
5971642 G
1 G
5971643 AAACACATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.29
Consensus pattern (38 bp):
GCATAAGACAGAGTGAAGTAACAATATATTTTTATACG
Found at i:5980792 original size:41 final size:38
Alignment explanation
Indices: 5980692--5980795 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
5980682 TTCGAAGCAA
* *
5980692 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
5980729 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
5980767 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
5980796 CTCAAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:5980929 original size:6 final size:6
Alignment explanation
Indices: 5980920--5980948 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5980910 CCAATTCCAA
5980920 TTTCAC TTTCAC TTTCAC TTTCAC TTTCA
1 TTTCAC TTTCAC TTTCAC TTTCAC TTTCA
5980949 ATTTTGATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTCAC
Found at i:5982273 original size:10 final size:11
Alignment explanation
Indices: 5982248--5982274 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5982238 GATTTTTGTT
5982248 TTTTTCCTGTA
1 TTTTTCCTGTA
5982259 TTTTTCCTGTA
1 TTTTTCCTGTA
5982270 TTTTT
1 TTTTT
5982275 TATGATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.15, G:0.07, T:0.70
Consensus pattern (11 bp):
TTTTTCCTGTA
Found at i:6002696 original size:20 final size:20
Alignment explanation
Indices: 6002663--6002700 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6002653 ACTAGTTATA
6002663 AGTAAAAATATAATAAAAGT
1 AGTAAAAATATAATAAAAGT
6002683 AGTAGAAAAT-TAATAAAA
1 AGTA-AAAATATAATAAAA
6002701 TCACAGACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (20 bp):
AGTAAAAATATAATAAAAGT
Found at i:6009651 original size:6 final size:7
Alignment explanation
Indices: 6009605--6009632 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
6009595 ATTTTGATCC
6009605 TAAATTT
1 TAAATTT
6009612 TAAATTT
1 TAAATTT
6009619 TAAATTT
1 TAAATTT
6009626 TAAATTT
1 TAAATTT
6009633 AATCATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TAAATTT
Found at i:6013895 original size:15 final size:15
Alignment explanation
Indices: 6013874--6013918 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
6013864 TATCTATAAA
6013874 ATATTTTTCATCTTTT
1 ATATTTTT-ATCTTTT
6013890 -TATTTTTATCTTTT
1 ATATTTTTATCTTTT
*
6013904 ACATTTTTATCTTTT
1 ATATTTTTATCTTTT
6013919 CAATTATCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 7 0.26
15 20 0.74
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (15 bp):
ATATTTTTATCTTTT
Found at i:6014326 original size:15 final size:15
Alignment explanation
Indices: 6014306--6014351 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
6014296 GAATAATTAT
6014306 ATATTAAAAATAATA
1 ATATTAAAAATAATA
6014321 ATATTAAAAA-AATA
1 ATATTAAAAATAATA
6014335 CATATTAAAAATAATA
1 -ATATTAAAAATAATA
6014351 A
1 A
6014352 ACCCATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.14
15 21 0.72
16 4 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
ATATTAAAAATAATA
Found at i:6019867 original size:33 final size:33
Alignment explanation
Indices: 6019830--6019902 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
6019820 TACCGGTATC
*
6019830 GGTGCTGGAGTT-GGACTTGT-GGGAAGTGGCGTT
1 GGTGCTGGAGTTGGGA-TTGTCGGG-AGTGGCCTT
6019863 GGTGCTGGAGTTGGGATTGTCGGGAGTGGCCTT
1 GGTGCTGGAGTTGGGATTGTCGGGAGTGGCCTT
*
6019896 GGAGCTG
1 GGTGCTG
6019903 TTGGCAGTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.11, C:0.11, G:0.49, T:0.29
Consensus pattern (33 bp):
GGTGCTGGAGTTGGGATTGTCGGGAGTGGCCTT
Found at i:6021682 original size:5 final size:5
Alignment explanation
Indices: 6021672--6021701 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
6021662 TTAGCAGCGG
6021672 AGCAC AGCAC AGCAC AGCAC AGCAC AGCAC
1 AGCAC AGCAC AGCAC AGCAC AGCAC AGCAC
6021702 TGCGCCCAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (5 bp):
AGCAC
Found at i:6030808 original size:2 final size:2
Alignment explanation
Indices: 6030801--6030852 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
6030791 TTAGGTAATA
6030801 AT AT AT AT AT 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 AT AT AT AT AT
6030843 AT AT AT AT AT
1 AT AT AT AT AT
6030853 GCTTCTTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6034070 original size:22 final size:22
Alignment explanation
Indices: 6034042--6034087 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
6034032 ATTGCAATTG
6034042 AAGCTTAGACTGTTTATGGTTA
1 AAGCTTAGACTGTTTATGGTTA
6034064 AAGCTTAGACTGTTTATGGTTA
1 AAGCTTAGACTGTTTATGGTTA
6034086 AA
1 AA
6034088 CTTTACAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (22 bp):
AAGCTTAGACTGTTTATGGTTA
Found at i:6035829 original size:21 final size:21
Alignment explanation
Indices: 6035803--6035845 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
6035793 AACAAGCTAA
* *
6035803 CAAATCTCCTTAGGACTTAGT
1 CAAATCTCCCTAGGACTCAGT
6035824 CAAATCTCCCTAGGACTCAGT
1 CAAATCTCCCTAGGACTCAGT
6035845 C
1 C
6035846 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (21 bp):
CAAATCTCCCTAGGACTCAGT
Found at i:6053155 original size:30 final size:30
Alignment explanation
Indices: 6053120--6053176 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
6053110 GACTTTCGAC
*
6053120 CGAATTAGATCGATTAATTGATCAATTAAT
1 CGAATTAAATCGATTAATTGATCAATTAAT
* * *
6053150 CGAATTAAATCGTTTGATTGATTAATT
1 CGAATTAAATCGATTAATTGATCAATT
6053177 CGGTTTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (30 bp):
CGAATTAAATCGATTAATTGATCAATTAAT
Found at i:6055918 original size:60 final size:59
Alignment explanation
Indices: 6055794--6055926 Score: 176
Period size: 60 Copynumber: 2.2 Consensus size: 59
6055784 AAATTTGATA
* * * * ** *
6055794 TTTTTCCTAATTTAGTACTTAAATTTTTTTTGACCTAATTTGGTACTTGAACTTAACAC
1 TTTTTCCTAATTTGGTACTTAAATTTCTTTGGACCTAATCTAATACCTGAACTTAACAC
* *
6055853 TTTTTCCTAATTTGGTACTTAAACTTTCTTTGGACCTAATCTAATACCTGAACTTGACAT
1 TTTTTCCTAATTTGGTACTTAAA-TTTCTTTGGACCTAATCTAATACCTGAACTTAACAC
6055913 TTTTTCCTAATTTG
1 TTTTTCCTAATTTG
6055927 ACACCTAAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
59 22 0.34
60 42 0.66
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (59 bp):
TTTTTCCTAATTTGGTACTTAAATTTCTTTGGACCTAATCTAATACCTGAACTTAACAC
Found at i:6069147 original size:25 final size:25
Alignment explanation
Indices: 6069113--6069169 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
6069103 AAAAGCGTAC
6069113 AAATTGTACAATCCTATCACCAAGA
1 AAATTGTACAATCCTATCACCAAGA
6069138 AAATTGTACAATCCTATCACCAAGA
1 AAATTGTACAATCCTATCACCAAGA
6069163 AAATTGT
1 AAATTGT
6069170 CATTAGTCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (25 bp):
AAATTGTACAATCCTATCACCAAGA
Found at i:6071406 original size:20 final size:21
Alignment explanation
Indices: 6071368--6071421 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
6071358 ACTCATAACC
* * *
6071368 TTAAACTTTAAACCTTAAACT
1 TTAAACCTCAAACCCTAAACT
6071389 TTAAACC-CAAACCCTAAACT
1 TTAAACCTCAAACCCTAAACT
6071409 TTAAACCTCAAAC
1 TTAAACCTCAAAC
6071422 TCAAACCTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (21 bp):
TTAAACCTCAAACCCTAAACT
Found at i:6071414 original size:14 final size:14
Alignment explanation
Indices: 6071364--6071395 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
6071354 CCAAACTCAT
6071364 AACCTTAAACTTTA
1 AACCTTAAACTTTA
6071378 AACCTTAAACTTTA
1 AACCTTAAACTTTA
6071392 AACC
1 AACC
6071396 CAAACCCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (14 bp):
AACCTTAAACTTTA
Found at i:6071421 original size:27 final size:27
Alignment explanation
Indices: 6071376--6071428 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
6071366 CCTTAAACTT
* *
6071376 TAAACCTTAAACTTTAAACCCAAACCC
1 TAAACCTTAAACCTCAAACCCAAACCC
* *
6071403 TAAACTTTAAACCTCAAACTCAAACC
1 TAAACCTTAAACCTCAAACCCAAACC
6071429 TTGAACCTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (27 bp):
TAAACCTTAAACCTCAAACCCAAACCC
Found at i:6071427 original size:20 final size:20
Alignment explanation
Indices: 6071355--6071437 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 20
6071345 ACTCAAGCCC
*
6071355 CAAACTCATAACCTTAAACTT
1 CAAACTCA-AACCTTAAACCT
* * *
6071376 TAAACCTTAAACTTTAAACC-
1 CAAA-CTCAAACCTTAAACCT
* *
6071396 CAAACCCTAAACTTTAAACCT
1 CAAACTC-AAACCTTAAACCT
*
6071417 CAAACTCAAACCTTGAACCT
1 CAAACTCAAACCTTAAACCT
6071437 C
1 C
6071438 GTCAATGTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.02
20 27 0.55
21 18 0.37
22 3 0.06
ACGTcount: A:0.42, C:0.31, G:0.01, T:0.25
Consensus pattern (20 bp):
CAAACTCAAACCTTAAACCT
Found at i:6079822 original size:20 final size:20
Alignment explanation
Indices: 6079785--6079822 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6079775 ATTAAAAATG
*
6079785 GAAAATGAATAAACAATATA
1 GAAAATGAATAAAAAATATA
6079805 GAAAAT-AATAAATAAATA
1 GAAAATGAATAAA-AAATA
6079823 ATAACAATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (20 bp):
GAAAATGAATAAAAAATATA
Found at i:6080621 original size:30 final size:30
Alignment explanation
Indices: 6080556--6080621 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
6080546 CAACTTAACA
* * *
6080556 AACAAATGCCTCTAAAATAGTAACAAAATT
1 AACAATTGCCTATAAAATAATAACAAAATT
6080586 AACAATTGCCTATAAAATAATAACAAAATT
1 AACAATTGCCTATAAAATAATAACAAAATT
6080616 AACAAT
1 AACAAT
6080622 AAAATAAGTT
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:0.56, C:0.15, G:0.05, T:0.24
Consensus pattern (30 bp):
AACAATTGCCTATAAAATAATAACAAAATT
Found at i:6096669 original size:10 final size:11
Alignment explanation
Indices: 6096641--6096687 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 11
6096631 TGCAACCCGT
6096641 TCTATATCTATA
1 TCTATA-CTATA
6096653 TCTATACTATA
1 TCTATACTATA
6096664 -CTATACTATAAA
1 TCTATACTAT--A
*
6096676 TCTATAATATA
1 TCTATACTATA
6096687 T
1 T
6096688 ATTTGTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 9 0.29
11 7 0.23
12 7 0.23
13 8 0.26
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (11 bp):
TCTATACTATA
Found at i:6103526 original size:19 final size:21
Alignment explanation
Indices: 6103497--6103535 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
6103487 TATTATATGT
6103497 TATTCTTAAATATA-AATTTA
1 TATTCTTAAATATATAATTTA
6103517 TATT-TTAAATATATAATTT
1 TATTCTTAAATATATAATTT
6103536 TCATACATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTCTTAAATATATAATTTA
Found at i:6104151 original size:3 final size:3
Alignment explanation
Indices: 6104145--6104178 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
6104135 AGAATCATCA
6104145 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
6104179 TTTTTCCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:6110040 original size:25 final size:26
Alignment explanation
Indices: 6110007--6110075 Score: 104
Period size: 25 Copynumber: 2.7 Consensus size: 26
6109997 GTGAAAAATT
* *
6110007 AAATAAAATAAATTTTTTGTTAT-AA
1 AAATTAAATAAAATTTTTGTTATAAA
6110032 AAATTAAATAAAATTTTTGTTATAAA
1 AAATTAAATAAAATTTTTGTTATAAA
6110058 AAATTAATATAAAATTTT
1 AAATTAA-ATAAAATTTT
6110076 AAATATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 21 0.52
26 9 0.22
27 10 0.25
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (26 bp):
AAATTAAATAAAATTTTTGTTATAAA
Found at i:6111313 original size:21 final size:20
Alignment explanation
Indices: 6111287--6111356 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 20
6111277 ACAGTAAGCA
6111287 CACACAGTGCAATCCAGTAGG
1 CACACAGTGCAAT-CAGTAGG
6111308 CACACACAGTGCAATCAGTAGCG
1 --CACACAGTGCAATCAGTAG-G
* *
6111331 CACATAGCGCAAATCAGTAGG
1 CACACAGTGC-AATCAGTAGG
6111352 CACAC
1 CACAC
6111357 GAAGTGCGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 13 0.31
22 15 0.36
23 14 0.33
ACGTcount: A:0.36, C:0.30, G:0.21, T:0.13
Consensus pattern (20 bp):
CACACAGTGCAATCAGTAGG
Found at i:6111378 original size:44 final size:44
Alignment explanation
Indices: 6111274--6111379 Score: 110
Period size: 44 Copynumber: 2.4 Consensus size: 44
6111264 AAGTGCTGGG
* *
6111274 GAAACAGTAAGCACACACAGTGCAATCCAGTAGGCACACACAGTGC
1 GAAACAGTAAG--CACATAGCGCAATCCAGTAGGCACACACAGTGC
* *
6111320 -AATCAGTAGCGCACATAGCGCAAAT-CAGTAGGCACACGA-AGTGC
1 GAAACAGTA-AGCACATAGCGC-AATCCAGTAGGCACAC-ACAGTGC
6111364 GAAACAGTAAGCACAT
1 GAAACAGTAAGCACAT
6111380 GAAGTGCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
44 31 0.62
45 18 0.36
46 1 0.02
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.12
Consensus pattern (44 bp):
GAAACAGTAAGCACATAGCGCAATCCAGTAGGCACACACAGTGC
Found at i:6111383 original size:23 final size:23
Alignment explanation
Indices: 6111250--6111398 Score: 98
Period size: 23 Copynumber: 6.4 Consensus size: 23
6111240 CGAAGTACTT
6111250 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACGAAGTGC----GA
6111276 AACAGTAAGCACAC-ACAGTGC-A
1 AACAGTAAGCACACGA-AGTGCGA
* *
6111298 ATCCAGTAGGCACAC-ACAGTGC-A
1 A-ACAGTAAGCACACGA-AGTGCGA
* * *
6111321 ATCAGT-AGCGCAC-ATAGCGC-A
1 AACAGTAAGCACACGA-AGTGCGA
*
6111342 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACACGAAGTGCGA
*
6111366 AACAGTAAGCACATGAAGTGCGA
1 AACAGTAAGCACACGAAGTGCGA
6111389 AACAGTAAGC
1 AACAGTAAGC
6111399 GCGTTAGCGT
Statistics
Matches: 104, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
21 12 0.12
22 10 0.10
23 58 0.56
24 4 0.04
26 15 0.14
27 5 0.05
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACGAAGTGCGA
Found at i:6117484 original size:23 final size:24
Alignment explanation
Indices: 6117458--6117506 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
6117448 CTATCACAAC
6117458 AAAAC-AGAAGCAA-TATTTGAGAG
1 AAAACAAGAA-CAAGTATTTGAGAG
*
6117481 AAAACAAGAACAAGTTTTTGAGAG
1 AAAACAAGAACAAGTATTTGAGAG
6117505 AA
1 AA
6117507 CAAAAGTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.53, C:0.08, G:0.20, T:0.18
Consensus pattern (24 bp):
AAAACAAGAACAAGTATTTGAGAG
Found at i:6118359 original size:35 final size:32
Alignment explanation
Indices: 6118320--6118394 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 32
6118310 TTGAAGTAAA
6118320 TTTTTTTTAAAAGATTAAAAAATAACAATTTAACT
1 TTTTTTTTAAAAGATT-AAAAATAA-AATTTAA-T
* * *
6118355 TTTTTTTAAAAAGATTTAAAATCAAATTTAAT
1 TTTTTTTTAAAAGATTAAAAATAAAATTTAAT
6118387 TTTTTTTT
1 TTTTTTTT
6118395 GTGAATATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 8 0.22
33 7 0.19
34 6 0.17
35 15 0.42
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.51
Consensus pattern (32 bp):
TTTTTTTTAAAAGATTAAAAATAAAATTTAAT
Found at i:6118383 original size:33 final size:34
Alignment explanation
Indices: 6118320--6118394 Score: 100
Period size: 33 Copynumber: 2.2 Consensus size: 34
6118310 TTGAAGTAAA
6118320 TTTTTTTTAAAAGATTAAAAAATAACAATTTAAC
1 TTTTTTTTAAAAGATTAAAAAATAACAATTTAAC
* * *
6118354 TTTTTTTTAAAAAGATT-TAAAATCA-AATTTAAT
1 TTTTTTTT-AAAAGATTAAAAAATAACAATTTAAC
6118387 TTTTTTTT
1 TTTTTTTT
6118395 GTGAATATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 15 0.41
34 14 0.38
35 8 0.22
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.51
Consensus pattern (34 bp):
TTTTTTTTAAAAGATTAAAAAATAACAATTTAAC
Found at i:6120030 original size:42 final size:42
Alignment explanation
Indices: 6119971--6120055 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
6119961 AAGTAACCCG
** * * *
6119971 CAATCATCCTCCACTTATCAGCAGCCTGCAGAATATCCTCCT
1 CAATCATCCTCCACTTATCAAAAACCTGCACAATATACTCCT
*
6120013 CAATCATCCTCCTCTTATCAAAAACCTGCACAATATACTCCT
1 CAATCATCCTCCACTTATCAAAAACCTGCACAATATACTCCT
6120055 C
1 C
6120056 CTGAAAGTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.29, C:0.38, G:0.06, T:0.27
Consensus pattern (42 bp):
CAATCATCCTCCACTTATCAAAAACCTGCACAATATACTCCT
Found at i:6120292 original size:126 final size:126
Alignment explanation
Indices: 6120061--6120318 Score: 437
Period size: 126 Copynumber: 2.0 Consensus size: 126
6120051 TCCTCCTGAA
* * * *
6120061 AGTAATTCTGAGCTCCTCTCCACACACATTAGCTTCTCTGGTCATAACCGGCAAGACAGTACAAG
1 AGTAATTCCGAGCCCCTCTCCACACACATTAGCTTCTCTGGTCATAACAGGCAAGACAATACAAG
* *
6120126 TTCCTTAGCAGCAAATACGGGAAGTGCCTCACCTCTTTACCCGCCTTTGGATTATCAGTTG
66 TTCCTTAGCAGCAAATACGGGAAGTGCCTCACCTCTTTACCCGCCTTTGGATCATCAATTG
6120187 AGTAATTCCGAGCCCCTCTCCACACACATTAGCTTCTCTGGTCATAACAGGCAAGACAATACAAG
1 AGTAATTCCGAGCCCCTCTCCACACACATTAGCTTCTCTGGTCATAACAGGCAAGACAATACAAG
*
6120252 TTCCTTAGCAGCAAATACGGGAAGTGCCTCACCTGC-TTACCCGCTTTTGGATCATCAATTG
66 TTCCTTAGCAGCAAATACGGGAAGTGCCTCACCT-CTTTACCCGCCTTTGGATCATCAATTG
6120313 AGTAAT
1 AGTAAT
6120319 ATGCATTTGT
Statistics
Matches: 124, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
126 123 0.99
127 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (126 bp):
AGTAATTCCGAGCCCCTCTCCACACACATTAGCTTCTCTGGTCATAACAGGCAAGACAATACAAG
TTCCTTAGCAGCAAATACGGGAAGTGCCTCACCTCTTTACCCGCCTTTGGATCATCAATTG
Done.