Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 141 of 325
Found at i:44261788 original size:144 final size:143
Alignment explanation
Indices: 44261528--44261851 Score: 425
Period size: 144 Copynumber: 2.2 Consensus size: 143
44261518 ACCGTACTAA
* * *
44261528 ATGTGCCTATGTAAGACAATGTCTAGGACATGGCATCGGCGATGATATATGTGCCAATGTAAGAC
1 ATGTGCC-ATGTAAGACCATGTCTGGGACATGGCATCGGCAATGATATATGTGCCAATGTAAGAC
* * * * *
44261593 TATGTCTAGGACATGTCATCAACGATGATATATTTGCTAATGTAAGACCATGTCTGGGACATGGC
65 TATGTCTAGGACATGGCATCAACGATGATATATGTGCCAATGTAAGACCATGTCCGGGACATGAC
*
44261658 ATCGGTAATGATAT
130 ATCGGTAATGAGAT
* *
44261672 ATGTGCCAGTGTAAGACCATGTCTGGGATATGGCATCGGCAATGATATATGTGCCAGTGTAAGAC
1 ATGTGCCA-TGTAAGACCATGTCTGGGACATGGCATCGGCAATGATATATGTGCCAATGTAAGAC
* * * * *
44261737 TATGTCTGGGACATGGCATCGACGATGGTATGTGTGCCAGTGTAAGACCATGTCCGGGACATGAC
65 TATGTCTAGGACATGGCATCAACGATGATATATGTGCCAATGTAAGACCATGTCCGGGACATGAC
*
44261802 ATCGGTGATGAGAT
130 ATCGGTAATGAGAT
* * *
44261816 GTG-GATTCATGTAAGACCATGTCGGGGACATGGCAT
1 ATGTG--CCATGTAAGACCATGTCTGGGACATGGCAT
44261852 TAGTACTTAT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
143 2 0.01
144 152 0.97
145 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (143 bp):
ATGTGCCATGTAAGACCATGTCTGGGACATGGCATCGGCAATGATATATGTGCCAATGTAAGACT
ATGTCTAGGACATGGCATCAACGATGATATATGTGCCAATGTAAGACCATGTCCGGGACATGACA
TCGGTAATGAGAT
Found at i:44262742 original size:14 final size:15
Alignment explanation
Indices: 44262709--44262744 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
44262699 AAACTAAGGT
44262709 TTTTTAAAACATCTA
1 TTTTTAAAACATCTA
* *
44262724 TTTTTAAAATATTTA
1 TTTTTAAAACATCTA
44262739 TTTTTA
1 TTTTTA
44262745 TTTAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTTAAAACATCTA
Found at i:44266827 original size:29 final size:29
Alignment explanation
Indices: 44266795--44266852 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
44266785 TTATCTGGGT
44266795 TATAACAAGACAAATCATATTATTTTAAG
1 TATAACAAGACAAATCATATTATTTTAAG
44266824 TATAACAAGACAAATCATATTATTTTAAG
1 TATAACAAGACAAATCATATTATTTTAAG
44266853 GGTGTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (29 bp):
TATAACAAGACAAATCATATTATTTTAAG
Found at i:44268620 original size:45 final size:45
Alignment explanation
Indices: 44268556--44268666 Score: 186
Period size: 45 Copynumber: 2.5 Consensus size: 45
44268546 TCTATTTTTT
*
44268556 TATTTTAAGAATTTTTTACACACTAGATATTTTTGGGAAATTACA
1 TATTTTAAGAATTTTTTACACACTAGATATTTTTAGGAAATTACA
* *
44268601 TATTTTAAGAATTTTTTACACACTAGATTTTTTTAGGAAATTACC
1 TATTTTAAGAATTTTTTACACACTAGATATTTTTAGGAAATTACA
*
44268646 TGTTTTAAGAATTTTTTACAC
1 TATTTTAAGAATTTTTTACAC
44268667 TATTATTTGT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (45 bp):
TATTTTAAGAATTTTTTACACACTAGATATTTTTAGGAAATTACA
Found at i:44269118 original size:32 final size:32
Alignment explanation
Indices: 44269082--44269148 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
44269072 GGTTGGGGTG
**
44269082 AATGGAATAGGGCTGTAAT-AGAATAGAGATGT
1 AATGGAATAGAACTGTAATGA-AATAGAGATGT
* *
44269114 AATGGAATATAACTGTAATGAAATAGAGTTGT
1 AATGGAATAGAACTGTAATGAAATAGAGATGT
44269146 AAT
1 AAT
44269149 CAGTAATTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.25, T:0.28
Consensus pattern (32 bp):
AATGGAATAGAACTGTAATGAAATAGAGATGT
Found at i:44269455 original size:58 final size:59
Alignment explanation
Indices: 44269327--44269455 Score: 190
Period size: 58 Copynumber: 2.2 Consensus size: 59
44269317 TTTTAATAAG
* * *
44269327 ATTATTACTAAATATAATTTAATAAAAATAATGATATAATTTAATAATATTTTAACATA
1 ATTATTATTAAATACAATTTAATAAAAATAATGATATAATTTAATAACATTTTAACATA
*
44269386 ATTATTATTAAATACAATTTAAT-AAAATAAT-ATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATACAATTTAATAAAAATAATGATATAATTTAATAACATT-TTAACATA
*
44269444 ATTATTTTTAAA
1 ATTATTATTAAA
44269456 ATATGAATTA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
57 17 0.27
58 26 0.41
59 21 0.33
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (59 bp):
ATTATTATTAAATACAATTTAATAAAAATAATGATATAATTTAATAACATTTTAACATA
Found at i:44269467 original size:59 final size:58
Alignment explanation
Indices: 44269327--44269469 Score: 191
Period size: 59 Copynumber: 2.4 Consensus size: 58
44269317 TTTTAATAAG
* *
44269327 ATTATTACTAAATATAATTTAATAAAAATAATGATATAATTTAATAATATTTTAACATA
1 ATTATTATTAAATATAATTTAAT-AAAATAATGATATAATTTAATAACATTTTAACATA
* *
44269386 ATTATTATTAAATACAATTTAATAAAATAAT-ATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATATAATTTAATAAAATAATGATATAATTTAATAACATT-TTAACATA
*
44269444 ATTATTTTTAAAATATGAA-TTAATAA
1 ATTATTATT-AAATAT-AATTTAATAA
44269470 GAATCATAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
57 17 0.23
58 23 0.31
59 33 0.44
60 2 0.03
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAATAATGATATAATTTAATAACATTTTAACATA
Found at i:44278052 original size:34 final size:34
Alignment explanation
Indices: 44277973--44278039 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
44277963 ATGAGTTAGC
*
44277973 ATTCAATTCCTCATTAAAAGCAATGTCTCTAACA
1 ATTCAATTCCTTATTAAAAGCAATGTCTCTAACA
44278007 ATTCAATTCCTTATTAAAAGCAATGTCTCTAAC
1 ATTCAATTCCTTATTAAAAGCAATGTCTCTAAC
44278040 CTTATTTCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (34 bp):
ATTCAATTCCTTATTAAAAGCAATGTCTCTAACA
Found at i:44283822 original size:40 final size:40
Alignment explanation
Indices: 44283760--44283840 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
44283750 GGAATTATGA
*
44283760 GGCACTGTATGTGCAAGCTCTTCAACCGAGCACTATGTGT
1 GGCACTATATGTGCAAGCTCTTCAACCGAGCACTATGTGT
* * * *
44283800 GGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGT
1 GGCACTATATGTGCAAGCTCTTCAACCGAGCACTATGTGT
44283840 G
1 G
44283841 CGAGATTGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (40 bp):
GGCACTATATGTGCAAGCTCTTCAACCGAGCACTATGTGT
Found at i:44283871 original size:29 final size:27
Alignment explanation
Indices: 44283801--44283900 Score: 137
Period size: 28 Copynumber: 3.6 Consensus size: 27
44283791 ACTATGTGTG
44283801 GCACTATGTGTGCGAGTTCTTCAATCGA
1 GCACTATGTGTGCGAGTTCTT-AATCGA
** *
44283829 GCACTATGTGTGCGAGATTGGTAATTGA
1 GCACTATGTGTGCGAG-TTCTTAATCGA
44283857 GGCACTATGTGTGCGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTC-TTAATCGA
44283886 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
44283901 AATCAGTCAG
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
28 38 0.60
29 25 0.40
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (27 bp):
GCACTATGTGTGCGAGTTCTTAATCGA
Found at i:44289302 original size:19 final size:19
Alignment explanation
Indices: 44289265--44289303 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
44289255 AAAGCTGAAT
**
44289265 TCTTTCTTCTTCTTTTCTC
1 TCTTTCTTCTTCTCATCTC
*
44289284 TCTTTCTTTTTCTCATCTC
1 TCTTTCTTCTTCTCATCTC
44289303 T
1 T
44289304 TCCTTCCTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (19 bp):
TCTTTCTTCTTCTCATCTC
Found at i:44290765 original size:60 final size:62
Alignment explanation
Indices: 44290662--44290812 Score: 170
Period size: 60 Copynumber: 2.5 Consensus size: 62
44290652 CTAACTGTGT
* * * *
44290662 TGATATGGGCAAGGCCCAATATA-TCTCA-ACTTGTAATAGGGCTACGGCCAAGATTGATAC
1 TGATATGGGCTAGGCCCAGTATACTCTGATACTTGTAATAGGGCTACGGCCAAGATTAATAC
* * *
44290722 TGATATGGGCTAGGCCCAGTATACTCTGATAC-TGT-A-AGCGGCTATGGCCCAGATTAATAT
1 TGATATGGGCTAGGCCCAGTATACTCTGATACTTGTAATAG-GGCTACGGCCAAGATTAATAC
44290782 TGATATGGGCTAAGGCCCAGT-TAACTCTGAT
1 TGATATGGGCT-AGGCCCAGTAT-ACTCTGAT
44290813 TTCTGAATAG
Statistics
Matches: 79, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
59 2 0.03
60 51 0.65
61 24 0.30
62 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (62 bp):
TGATATGGGCTAGGCCCAGTATACTCTGATACTTGTAATAGGGCTACGGCCAAGATTAATAC
Found at i:44293417 original size:22 final size:22
Alignment explanation
Indices: 44293392--44293433 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
44293382 CATAAAATTT
44293392 AAAAAGAA-AAATGAATCAATCC
1 AAAAAGAATAAA-GAATCAATCC
*
44293414 AAAAATAATAAAGAATCAAT
1 AAAAAGAATAAAGAATCAAT
44293434 TCATTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (22 bp):
AAAAAGAATAAAGAATCAATCC
Found at i:44294143 original size:21 final size:21
Alignment explanation
Indices: 44294104--44294143 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44294094 CATTTAGGCA
* *
44294104 CAATTTGCTTTGCTGGTTTTG
1 CAATTTGCTTTACTAGTTTTG
44294125 CAATTTGCTTTACTAGTTT
1 CAATTTGCTTTACTAGTTT
44294144 ATATCCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.53
Consensus pattern (21 bp):
CAATTTGCTTTACTAGTTTTG
Found at i:44297834 original size:20 final size:20
Alignment explanation
Indices: 44297809--44297848 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
44297799 AAAGAATGGT
44297809 TAAAGTAATGGTTTTTCGAA
1 TAAAGTAATGGTTTTTCGAA
44297829 TAAAGTAATGGTTTTTCGAA
1 TAAAGTAATGGTTTTTCGAA
44297849 GAGGCAATAT
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:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (20 bp):
TAAAGTAATGGTTTTTCGAA
Found at i:44298101 original size:21 final size:21
Alignment explanation
Indices: 44298077--44298165 Score: 72
Period size: 21 Copynumber: 4.2 Consensus size: 21
44298067 TTCACTTTTG
* *
44298077 TTTTGCTATTATTTGTTACTA
1 TTTTGCTATTATTTGCTACCA
* * *
44298098 TTTTGTTGTTGTTTGCTACCA
1 TTTTGCTATTATTTGCTACCA
* *
44298119 TTTTGATGTTATTTTGCTACCA
1 TTTTGCTATTA-TTTGCTACCA
* *
44298141 TTCTGCTATTATATTACTA-CA
1 TTTTGCTATTAT-TTGCTACCA
44298162 TTTT
1 TTTT
44298166 ATTGTTGTTG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
21 31 0.57
22 23 0.43
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.57
Consensus pattern (21 bp):
TTTTGCTATTATTTGCTACCA
Found at i:44298152 original size:22 final size:22
Alignment explanation
Indices: 44298109--44298152 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
44298099 TTTGTTGTTG
* *
44298109 TTTGCTACCATTTTGATGTTAT
1 TTTGCTACCATTCTGATATTAT
*
44298131 TTTGCTACCATTCTGCTATTAT
1 TTTGCTACCATTCTGATATTAT
44298153 ATTACTACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.52
Consensus pattern (22 bp):
TTTGCTACCATTCTGATATTAT
Found at i:44298382 original size:18 final size:17
Alignment explanation
Indices: 44298352--44298385 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
44298342 TGATGTATTA
*
44298352 TATTTTTTTTAAAAATT
1 TATTTTTTATAAAAATT
44298369 TATTTTTATATAAAAAT
1 TATTTTT-TATAAAAAT
44298386 AATATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTTTTATAAAAATT
Found at i:44301950 original size:13 final size:13
Alignment explanation
Indices: 44301932--44301966 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
44301922 TAAGTTATTA
44301932 TATATTAATATAT
1 TATATTAATATAT
* *
44301945 TATATTCATATTT
1 TATATTAATATAT
44301958 TATATTAAT
1 TATATTAAT
44301967 CTGTGTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
TATATTAATATAT
Found at i:44304247 original size:42 final size:43
Alignment explanation
Indices: 44304189--44304278 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 43
44304179 TTTATCTGAA
* *
44304189 TTTTTGTAAATATTTTGTAGTGTTAATTATAAGTTTTAT-ATT
1 TTTTTGTAAATATTTTGTAGTATTAATTATAAGTCTTATAATT
* * * *
44304231 TTTTTGTGAATCTTTTGTATTATTAATTATAGGTCTTATAATT
1 TTTTTGTAAATATTTTGTAGTATTAATTATAAGTCTTATAATT
44304274 TTTTT
1 TTTTT
44304279 TTCCATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 33 0.80
43 8 0.20
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (43 bp):
TTTTTGTAAATATTTTGTAGTATTAATTATAAGTCTTATAATT
Found at i:44304341 original size:18 final size:19
Alignment explanation
Indices: 44304289--44304342 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
44304279 TTCCATTTTT
44304289 TAGTTTTAAGTCTTATTAG
1 TAGTTTTAAGTCTTATTAG
**
44304308 TAGTGTTTCTG-C-TATTAG
1 TAGT-TTTAAGTCTTATTAG
44304326 -AGTTTTAAGTCTTATTA
1 TAGTTTTAAGTCTTATTA
44304343 TTTTTGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
16 4 0.14
17 4 0.14
18 11 0.39
19 5 0.18
20 4 0.14
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (19 bp):
TAGTTTTAAGTCTTATTAG
Found at i:44304380 original size:34 final size:33
Alignment explanation
Indices: 44304326--44304391 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
44304316 CTGCTATTAG
* *
44304326 AGTTTTAAGTCTTATTATTTTTGTTTCAATTTTT
1 AGTTTTAAGCCTTATCATTTTTGTTTC-ATTTTT
*
44304360 AGTTTTAAGCCTTGTCATTTTTGTTTCATTTT
1 AGTTTTAAGCCTTATCATTTTTGTTTCATTTT
44304392 GGTGAATACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 5 0.17
34 24 0.83
ACGTcount: A:0.18, C:0.09, G:0.11, T:0.62
Consensus pattern (33 bp):
AGTTTTAAGCCTTATCATTTTTGTTTCATTTTT
Found at i:44309636 original size:10 final size:10
Alignment explanation
Indices: 44309621--44309655 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
44309611 AAAACTCTAT
44309621 TTTTTCTTTC
1 TTTTTCTTTC
44309631 TTTTTCTTTCCC
1 TTTTTCTTT--C
44309643 TTTTTCTTTC
1 TTTTTCTTTC
44309653 TTT
1 TTT
44309656 CTTTCCCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:44309649 original size:22 final size:20
Alignment explanation
Indices: 44309621--44309663 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 20
44309611 AAAACTCTAT
44309621 TTTTTCTTTCTTTTTCTTTCCC
1 TTTTTCTTTC--TTTCTTTCCC
44309643 TTTTTCTTTCTTTCTTTCCC
1 TTTTTCTTTCTTTCTTTCCC
44309663 T
1 T
44309664 GTTCTGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.52
22 10 0.48
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTCTTTCTTTCTTTCCC
Found at i:44309708 original size:24 final size:23
Alignment explanation
Indices: 44309681--44309730 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
44309671 TTCATCCTCC
44309681 TTTCTTTCCT-TTTTCTTTATTTTA
1 TTTCTTT-CTATTTTCTTTA-TTTA
*
44309705 TTTCTTTTTATTTTCTTTATTTA
1 TTTCTTTCTATTTTCTTTATTTA
44309728 TTT
1 TTT
44309731 TAACTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTCTTTCTATTTTCTTTATTTA
Found at i:44309771 original size:23 final size:23
Alignment explanation
Indices: 44309745--44309788 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
44309735 TATTATATTA
44309745 TATTATTATTAAATTTTAATAAT
1 TATTATTATTAAATTTTAATAAT
* *
44309768 TATTATTATTTACTTTTAATA
1 TATTATTATTAAATTTTAATA
44309789 TAAGTAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTATTATTAAATTTTAATAAT
Found at i:44313501 original size:25 final size:25
Alignment explanation
Indices: 44313473--44313538 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
44313463 TGGAGCCATG
*
44313473 TAACGAGAAGCTCATGTAAGCTGTA
1 TAACGAGAAGCTCATCTAAGCTGTA
* * *
44313498 TAACGAGGTAGCTCAACTGAGCTGTA
1 TAACGA-GAAGCTCATCTAAGCTGTA
* *
44313524 TATCAAGAAGCTCAT
1 TAACGAGAAGCTCAT
44313539 ACGAGTCATA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 13 0.41
26 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (25 bp):
TAACGAGAAGCTCATCTAAGCTGTA
Found at i:44320348 original size:24 final size:24
Alignment explanation
Indices: 44320302--44320357 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
44320292 GGCATTTTGC
* *
44320302 TGGCTTTTATGGCGTACTTTGATT
1 TGGCCTTTATGGCGTACTTTGATA
*
44320326 TGGCCTTTATGGTGTA-TTCTGATA
1 TGGCCTTTATGGCGTACTT-TGATA
44320350 TGGCCTTT
1 TGGCCTTT
44320358 GTGAAATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.12, C:0.14, G:0.25, T:0.48
Consensus pattern (24 bp):
TGGCCTTTATGGCGTACTTTGATA
Found at i:44320912 original size:28 final size:28
Alignment explanation
Indices: 44320880--44320941 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
44320870 TTATCAAGAT
*
44320880 CAGTAAGGGTATT-TGCCAAAAGCATGAC
1 CAGTAAGGGT-TTCCGCCAAAAGCATGAC
* *
44320908 CAGTAAGGGTTTCCGCCAAAAGTATGAT
1 CAGTAAGGGTTTCCGCCAAAAGCATGAC
44320936 CAGTAA
1 CAGTAA
44320942 ATGATATCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 28 0.93
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (28 bp):
CAGTAAGGGTTTCCGCCAAAAGCATGAC
Found at i:44328921 original size:70 final size:71
Alignment explanation
Indices: 44328807--44328943 Score: 231
Period size: 70 Copynumber: 1.9 Consensus size: 71
44328797 ATTCCTGAAC
* * *
44328807 ATTGTAATATTATATAAAGTGAAATTTTTATAAGAAATTTTTATTATTTTCATTATTATTTATAT
1 ATTGTAATACTAGATAAAGTGAAATTTTTATAAGAAATTATTATTATTTTCATTATTATTTATAT
44328872 GAAAAT
66 GAAAAT
*
44328878 ATTGTAATACTAGATAAAGTG-AATTTTTATATGAAATTATTATTATTTTCATTATTATTTATAT
1 ATTGTAATACTAGATAAAGTGAAATTTTTATAAGAAATTATTATTATTTTCATTATTATTTATAT
44328942 GA
66 GA
44328944 TTTTTTTATT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 43 0.69
71 19 0.31
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.50
Consensus pattern (71 bp):
ATTGTAATACTAGATAAAGTGAAATTTTTATAAGAAATTATTATTATTTTCATTATTATTTATAT
GAAAAT
Found at i:44328961 original size:87 final size:89
Alignment explanation
Indices: 44328862--44329026 Score: 237
Period size: 89 Copynumber: 1.9 Consensus size: 89
44328852 ATTTTCATTA
* * *
44328862 TTATTTATATGAAAATATTGTAATACTAGATAAAG-T-GAATTTTTATATGAAATTATTAT-TAT
1 TTATTTATATGAAAATAATGTAAAACTAGATAAAGTTAAAATTTTTATATGAAATTATTATGT-T
44328924 TTTCATTATTATTTATATGATTTTT
65 TTTCATTATTATTTATATGATTTTT
* * * *
44328949 TTATTTTTATGAAAATAATGTAAAATTTGATAAAGTTAAAATTTTTATATGAAATTTTTATGTTT
1 TTATTTATATGAAAATAATGTAAAACTAGATAAAGTTAAAATTTTTATATGAAATTATTATGTTT
44329014 TTCATTATTATTT
66 TTCATTATTATTT
44329027 TTTATATAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
87 30 0.44
88 1 0.01
89 36 0.53
90 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (89 bp):
TTATTTATATGAAAATAATGTAAAACTAGATAAAGTTAAAATTTTTATATGAAATTATTATGTTT
TTCATTATTATTTATATGATTTTT
Found at i:44333021 original size:13 final size:13
Alignment explanation
Indices: 44333003--44333044 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
44332993 ATTTTTTTCT
44333003 AATTTTAAATTTA
1 AATTTTAAATTTA
44333016 AATTTTAAATTT-
1 AATTTTAAATTTA
* *
44333028 AATGTTAAATTAA
1 AATTTTAAATTTA
44333041 AATT
1 AATT
44333045 AAATGAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
AATTTTAAATTTA
Found at i:44333049 original size:18 final size:19
Alignment explanation
Indices: 44333007--44333049 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
44332997 TTTTCTAATT
*
44333007 TTAAAT-TTAAATTTTAAA
1 TTAAATGTTAAATTTAAAA
*
44333025 TTTAATGTTAAA-TTAAAA
1 TTAAATGTTAAATTTAAAA
44333043 TTAAATG
1 TTAAATG
44333050 AAATAAAGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
TTAAATGTTAAATTTAAAA
Found at i:44333154 original size:40 final size:40
Alignment explanation
Indices: 44333110--44333189 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
44333100 TAAAGGAGAA
44333110 AGAGAAAATAATTAGACATTTCGATTTATAGTGGTCCGAT
1 AGAGAAAATAATTAGACATTTCGATTTATAGTGGTCCGAT
*
44333150 AGAGAAAATAATTGGACATTTCGATTTATAGTGGTCCGAT
1 AGAGAAAATAATTAGACATTTCGATTTATAGTGGTCCGAT
44333190 CCTAATTGCC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (40 bp):
AGAGAAAATAATTAGACATTTCGATTTATAGTGGTCCGAT
Found at i:44333773 original size:22 final size:22
Alignment explanation
Indices: 44333725--44333783 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
44333715 AGACTTGGCA
* *
44333725 AATGTCTCGTGACATACAGACT
1 AATGTCTCGAGACATACAGACC
* * *
44333747 TATGTCTCGAGACATATAGGCC
1 AATGTCTCGAGACATACAGACC
*
44333769 AATGTCTCTAGACAT
1 AATGTCTCGAGACAT
44333784 GCAACTCTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (22 bp):
AATGTCTCGAGACATACAGACC
Found at i:44334468 original size:22 final size:20
Alignment explanation
Indices: 44334443--44334514 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
44334433 TTTATAATTT
44334443 TTTTAAAATATAAATTTTGAAA
1 TTTTAAAATAT--ATTTTGAAA
* * *
44334465 TTTTTACATATATTTTGAAT
1 TTTTAAAATATATTTTGAAA
*
44334485 TTTTGAAAAT-TATTTTGATTA
1 TTTT-AAAATATATTTTGA-AA
44334506 TTTTAAAAT
1 TTTTAAAAT
44334515 TTTTGTTGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 25 0.61
21 7 0.17
22 9 0.22
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (20 bp):
TTTTAAAATATATTTTGAAA
Found at i:44346683 original size:21 final size:20
Alignment explanation
Indices: 44346650--44346688 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
44346640 AGTAATTTAA
*
44346650 TTTTTCTTCTTTTATATTAT
1 TTTTTCTTATTTTATATTAT
*
44346670 TTTTTCTTTATTTTTTATT
1 TTTTTC-TTATTTTATATT
44346689 CACTTCTACT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTCTTATTTTATATTAT
Found at i:44357419 original size:43 final size:43
Alignment explanation
Indices: 44357363--44357473 Score: 143
Period size: 43 Copynumber: 2.6 Consensus size: 43
44357353 CATACATGTT
* * *
44357363 ATCACATATCGATGCCACTGTCCTAGACAGGGTCTTACACGAA
1 ATCAAATAACGATGCCAATGTCCTAGACAGGGTCTTACACGAA
* * *
44357406 ATCAAATAACGATGCCAATGTCCCAGACATGGTCTTACACGTA
1 ATCAAATAACGATGCCAATGTCCTAGACAGGGTCTTACACGAA
*
44357449 ATCACAAT-ACAATGCCAATGTCCTA
1 ATCA-AATAACGATGCCAATGTCCTA
44357474 TAGATGCTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
43 56 0.95
44 3 0.05
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.23
Consensus pattern (43 bp):
ATCAAATAACGATGCCAATGTCCTAGACAGGGTCTTACACGAA
Found at i:44357485 original size:43 final size:44
Alignment explanation
Indices: 44357374--44357497 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 44
44357364 TCACATATCG
* * * * * *
44357374 ATGCCACTGTCCTAGACAGGGTCTTACACGAAATCA-AATAACG
1 ATGCCAATGTCCCAGACATGCTCTTACACGTAATCACAATAACA
*
44357417 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAAT-ACA
1 ATGCCAATGTCCCAGACATGCTCTTACACGTAATCACAATAACA
* * * *
44357460 ATGCCAATGTCCTATAGATGCTCTTACATGTAATCACA
1 ATGCCAATGTCCCAGACATGCTCTTACACGTAATCACA
44357498 TCTCAATAAC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
43 67 0.96
44 3 0.04
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACATGCTCTTACACGTAATCACAATAACA
Found at i:44363476 original size:13 final size:13
Alignment explanation
Indices: 44363458--44363482 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44363448 GGGCGTGTGG
44363458 GTCCACATGGGTA
1 GTCCACATGGGTA
44363471 GTCCACATGGGT
1 GTCCACATGGGT
44363483 GTGTGGGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (13 bp):
GTCCACATGGGTA
Found at i:44365101 original size:9 final size:9
Alignment explanation
Indices: 44365087--44365112 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
44365077 TTAAAACCAT
44365087 CTAAAATCC
1 CTAAAATCC
44365096 CTAAAATCC
1 CTAAAATCC
44365105 CTAAAATC
1 CTAAAATC
44365113 TGGAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (9 bp):
CTAAAATCC
Found at i:44365955 original size:13 final size:13
Alignment explanation
Indices: 44365932--44366011 Score: 50
Period size: 12 Copynumber: 6.7 Consensus size: 13
44365922 TTTATACTTA
44365932 ATAAT-TAATAAT
1 ATAATATAATAAT
44365944 ATAATATAATAAT
1 ATAATATAATAAT
* *
44365957 TTAATA-ATTTAAT
1 ATAATATA-ATAAT
*
44365970 A-AA-ATAATAAA
1 ATAATATAATAAT
44365981 ATAA-ATAA-AAT
1 ATAATATAATAAT
*
44365992 A-AATAAAATAA-
1 ATAATATAATAAT
*
44366003 ATAAAATAA
1 ATAATATAA
44366012 AGAAACAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
10 2 0.04
11 12 0.23
12 22 0.42
13 16 0.31
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:44365975 original size:5 final size:5
Alignment explanation
Indices: 44365967--44366012 Score: 57
Period size: 5 Copynumber: 10.2 Consensus size: 5
44365957 TTAATAATTT
44365967 AATAA AAT-- AATAA AAT-A AATAA AAT-A AATAA AAT-A AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
44366012 A
1 A
44366013 GAAACAATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
3 3 0.08
4 12 0.33
5 21 0.58
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AATAA
Found at i:44365989 original size:9 final size:9
Alignment explanation
Indices: 44365967--44366012 Score: 85
Period size: 9 Copynumber: 5.2 Consensus size: 9
44365957 TTAATAATTT
44365967 AATAAAAT-
1 AATAAAATA
44365975 AATAAAATA
1 AATAAAATA
44365984 AATAAAATA
1 AATAAAATA
44365993 AATAAAATA
1 AATAAAATA
44366002 AATAAAATA
1 AATAAAATA
44366011 AA
1 AA
44366013 GAAACAATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 8 0.22
9 29 0.78
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AATAAAATA
Found at i:44373365 original size:140 final size:139
Alignment explanation
Indices: 44373113--44373366 Score: 343
Period size: 140 Copynumber: 1.8 Consensus size: 139
44373103 TGAGCTAGTG
* * *
44373113 TAAGACATGTTTGGGACATGCATCGGCTGCATTATGAGAGCCAGTGTAAGACCATGTCTGGGACA
1 TAAGACATGTCTGGGACATGCATCGGCTACATGAT-AGAGCCAGTGTAAGACCATGTCTGGGACA
* * *
44373178 TGGCATCGGCATTGAGATGAGTGCTAGTGTAAGACATGTCTAGGACATGCATTAGCCTCGGGACG
65 TGGCATCGGCATTAAGATGAATGCCAGTGTAAGACATGTCTAGGACATGCATTAGCCTCGGGACG
44373243 TAAGCCAGTA
130 TAAGCCAGTA
* * *
44373253 TAAGACATGTCTGGGACATGCATCGGCTACGA-GAT-GTGTCAGTGTAAGACCATGTTTGGGACA
1 TAAGACATGTCTGGGACATGCATCGGCTAC-ATGATAGAGCCAGTGTAAGACCATGTCTGGGACA
* *
44373316 TGGCATCGGCCTCTAAGAT-AATAGCCAGTGTAAGACCATGTCTGGGACATG
65 TGGCATCGGCAT-TAAGATGAAT-GCCAGTGTAAGA-CATGTCTAGGACATG
44373367 ACATCAGTAT
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
138 38 0.38
139 16 0.16
140 44 0.44
141 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (139 bp):
TAAGACATGTCTGGGACATGCATCGGCTACATGATAGAGCCAGTGTAAGACCATGTCTGGGACAT
GGCATCGGCATTAAGATGAATGCCAGTGTAAGACATGTCTAGGACATGCATTAGCCTCGGGACGT
AAGCCAGTA
Found at i:44376073 original size:8 final size:8
Alignment explanation
Indices: 44376060--44376101 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
44376050 ATTAAGCATG
44376060 TAATATAA
1 TAATATAA
*
44376068 TAATATAT
1 TAATATAA
44376076 TAATATAA
1 TAATATAA
*
44376084 TAATTTAA
1 TAATATAA
*
44376092 TAATAGAA
1 TAATATAA
44376100 TA
1 TA
44376102 GAAGAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (8 bp):
TAATATAA
Found at i:44376138 original size:22 final size:23
Alignment explanation
Indices: 44376093--44376139 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
44376083 ATAATTTAAT
* *
44376093 AATAGAATAGAAGAAATAAAAGA
1 AATAAAATAGAAGAAACAAAAGA
*
44376116 AATAAAATA-AAGAAACAATAGA
1 AATAAAATAGAAGAAACAAAAGA
44376138 AA
1 AA
44376140 AAGAGAACAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.72, C:0.02, G:0.13, T:0.13
Consensus pattern (23 bp):
AATAAAATAGAAGAAACAAAAGA
Found at i:44393551 original size:41 final size:43
Alignment explanation
Indices: 44393451--44393555 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
44393441 TGTGTTCTCA
* * * * *
44393451 TGTAAGACCATATCTAGGACGTTGGCATCGATATGTGATTACG
1 TGTAAGACCATATCTGGGACATCGACATCGATATGTCATTACG
* *
44393494 TGTAAGACCATGTCTGGGACATCGACATCG-TATTTCATT-CG
1 TGTAAGACCATATCTGGGACATCGACATCGATATGTCATTACG
*
44393535 TGTAAGACCCTATCTGGGACA
1 TGTAAGACCATATCTGGGACA
44393556 GTGGCATCGA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 21 0.40
42 7 0.13
43 25 0.47
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (43 bp):
TGTAAGACCATATCTGGGACATCGACATCGATATGTCATTACG
Found at i:44393564 original size:41 final size:42
Alignment explanation
Indices: 44393451--44393568 Score: 127
Period size: 41 Copynumber: 2.8 Consensus size: 42
44393441 TGTGTTCTCA
* * *
44393451 TGTAAGACCATATCTAGGAC-GTTGGCATCGATATGTGATTACG
1 TGTAAGACCATATCTGGGACAG-TGGCATCG-TATTTCATTACG
* *
44393494 TGTAAGACCATGTCTGGGACA-TCGACATCGTATTTCATT-CG
1 TGTAAGACCATATCTGGGACAGT-GGCATCGTATTTCATTACG
*
44393535 TGTAAGACCCTATCTGGGACAGTGGCATCG-ATTT
1 TGTAAGACCATATCTGGGACAGTGGCATCGTATTT
44393569 ATTGATATGT
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
40 4 0.06
41 27 0.42
42 9 0.14
43 24 0.38
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGACAGTGGCATCGTATTTCATTACG
Found at i:44400851 original size:13 final size:13
Alignment explanation
Indices: 44400835--44400863 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
44400825 CAAGTCACAC
44400835 GCCCATGTGTGAG
1 GCCCATGTGTGAG
44400848 GCCCATGTGTGAG
1 GCCCATGTGTGAG
44400861 GCC
1 GCC
44400864 GTGTGGTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.28, G:0.38, T:0.21
Consensus pattern (13 bp):
GCCCATGTGTGAG
Found at i:44405366 original size:21 final size:20
Alignment explanation
Indices: 44405337--44405375 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
44405327 CAAAACTTGT
44405337 ATAATTATCATCAAACATTC
1 ATAATTATCATCAAACATTC
*
44405357 ATAATCTATCATTAAACAT
1 ATAAT-TATCATCAAACAT
44405376 CAAAATACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAATTATCATCAAACATTC
Found at i:44406397 original size:68 final size:68
Alignment explanation
Indices: 44406300--44406483 Score: 260
Period size: 68 Copynumber: 2.7 Consensus size: 68
44406290 CATAATTGAG
* * * *
44406300 CTATGGTTTTACATAATGTAACCCAATGTTTATTGTCCTAGCGGACTCCATATGTTGCCATAGCC
1 CTATGGTTTTACACAATGTAACCCCATGTTTATTGTCCTAGCGGACTCCATATGTTACCATAGCA
44406365 GAC
66 GAC
* * * * *
44406368 CTATGGTCTTATACAATGTAACCCCATGTTTATTGTCTTGGCAGACTCCATATGTTACCATAGCA
1 CTATGGTTTTACACAATGTAACCCCATGTTTATTGTCCTAGCGGACTCCATATGTTACCATAGCA
*
44406433 GAG
66 GAC
* *
44406436 CTATGGTTTTACACAATGTAACCCCATGTTTATTTTCCTAGCGAACTC
1 CTATGGTTTTACACAATGTAACCCCATGTTTATTGTCCTAGCGGACTC
44406484 TCGATTCGGA
Statistics
Matches: 99, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 99 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (68 bp):
CTATGGTTTTACACAATGTAACCCCATGTTTATTGTCCTAGCGGACTCCATATGTTACCATAGCA
GAC
Found at i:44410784 original size:31 final size:31
Alignment explanation
Indices: 44410726--44410786 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
44410716 TCAAAATTGA
* * * *
44410726 AAGTCGAATCTAATCGAGTGAAATGAAATTC
1 AAGTCGAATCGAATCAAATCAAATGAAATTC
*
44410757 AAGTCGAATCGAATCAAATCAAGTGAAATT
1 AAGTCGAATCGAATCAAATCAAATGAAATT
44410787 GTTCTAGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (31 bp):
AAGTCGAATCGAATCAAATCAAATGAAATTC
Found at i:44411029 original size:19 final size:19
Alignment explanation
Indices: 44411007--44411094 Score: 60
Period size: 19 Copynumber: 4.8 Consensus size: 19
44410997 TTTTTTAGAT
44411007 TTTTTTGAAATTTTTATAA
1 TTTTTTGAAATTTTTATAA
***
44411026 TTTTTT-AAA-AAATATAA
1 TTTTTTGAAATTTTTATAA
*
44411043 -ATTTTGAAATTTTTATAAA
1 TTTTTTGAAATTTTTAT-AA
* * *
44411062 TATTTT-AAATTTTAAAAA
1 TTTTTTGAAATTTTTATAA
44411080 TTATTTTG-AATTTTT
1 TT-TTTTGAAATTTTT
44411095 GTTCAGAGAA
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
16 4 0.08
17 8 0.15
18 9 0.17
19 26 0.50
20 5 0.10
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTTTTGAAATTTTTATAA
Found at i:44414839 original size:351 final size:351
Alignment explanation
Indices: 44414186--44414901 Score: 1180
Period size: 351 Copynumber: 2.0 Consensus size: 351
44414176 CGCGGACAGA
* * ** *
44414186 CACACGAGCGTGTGTCTAGACCGTGTGTGACACACAGCCAAGTACATAGGCGTGTAGTTAGGCTG
1 CACACGGGCATGTGTCTAGACCGTGTGTGACACACAGCCAAGTACATAGAAGTGTAGTTAGGCCG
*
44414251 TGCGTCCCCTGCACCCTAAATTTTGAGAAACAGAATGCTCAGAATTGAGCATACGGGCAGAGACA
66 TGCGTCCCCTACACCCTAAATTTTGAGAAACAGAATGCTCAGAATTGAGCATACGGGCAGAGACA
*
44414316 CAAGCGTGTGTCTCAGCCATATGTCCTACACGGCCTAGAACAAAGGCGTGTGTCTTAGCCGTGTG
131 CAAGCGTGTGTCTCAGCCATATATCCTACACGGCCTAGAACAAAGGCGTGTGTCTTAGCCGTGTG
* * *
44414381 AAACCTGCACCTAATTTCGAATTGAATTGATTAACCACATGGCCTAGCACACGGGCGTGTGGCAT
196 AAACCTACACCTAATTTCGAATTGAATTGATTAACCACACGGCCTAACACACGGGCGTGTGGCAT
* * *
44414446 GGCTGTGTGCACAAGTCAGAGAGTTACATGGGGTCGAACACGGCCTCTAACACGGGCTTGTCCCA
261 GGCCGTGTGCACAAGTCAGAGAGTTACACGGGGTCGAACACGGCCTCTAACACGGGCTTCTCCCA
*
44414511 AGGTCACATGAGCGTGTCCCTTGGAC
326 AGGTCACACGAGCGTGTCCCTTGGAC
** *
44414537 CACACGGGCATGTGTCTAGATTGTGTGTGACACACTGCCAAGTACATAGAAGTGTAGTTAGGCCG
1 CACACGGGCATGTGTCTAGACCGTGTGTGACACACAGCCAAGTACATAGAAGTGTAGTTAGGCCG
* * *
44414602 TGTGTCCCTTACACCCTAAATTTTGAGAAACAGAATGCTCAGAATTGAGCATACGTGCAGAGACA
66 TGCGTCCCCTACACCCTAAATTTTGAGAAACAGAATGCTCAGAATTGAGCATACGGGCAGAGACA
* * * **
44414667 CAAGTGTGTGTCTCAGCCATGTATGCTACACGGCCTAGAACACGGGCGTGTGTCTTAGCCGTGTG
131 CAAGCGTGTGTCTCAGCCATATATCCTACACGGCCTAGAACAAAGGCGTGTGTCTTAGCCGTGTG
*
44414732 AAACCTATACCTAATTTCGAATTGAATTGATTAACCACACGGCCTAACACACGGGCGTGTGGCAT
196 AAACCTACACCTAATTTCGAATTGAATTGATTAACCACACGGCCTAACACACGGGCGTGTGGCAT
*
44414797 GGCCGTGTGCACAAGTCAGAGAGTTACACGGGGTCGAACACGGCCTCTAACACGGGCTTCTCCTA
261 GGCCGTGTGCACAAGTCAGAGAGTTACACGGGGTCGAACACGGCCTCTAACACGGGCTTCTCCCA
*
44414862 GGGTCACACGAGCGTGTCCCTTGGAC
326 AGGTCACACGAGCGTGTCCCTTGGAC
44414888 CACACGGGCATGTG
1 CACACGGGCATGTG
44414902 AGCCCTGCAC
Statistics
Matches: 337, Mismatches: 28, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
351 337 1.00
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.23
Consensus pattern (351 bp):
CACACGGGCATGTGTCTAGACCGTGTGTGACACACAGCCAAGTACATAGAAGTGTAGTTAGGCCG
TGCGTCCCCTACACCCTAAATTTTGAGAAACAGAATGCTCAGAATTGAGCATACGGGCAGAGACA
CAAGCGTGTGTCTCAGCCATATATCCTACACGGCCTAGAACAAAGGCGTGTGTCTTAGCCGTGTG
AAACCTACACCTAATTTCGAATTGAATTGATTAACCACACGGCCTAACACACGGGCGTGTGGCAT
GGCCGTGTGCACAAGTCAGAGAGTTACACGGGGTCGAACACGGCCTCTAACACGGGCTTCTCCCA
AGGTCACACGAGCGTGTCCCTTGGAC
Found at i:44419930 original size:18 final size:19
Alignment explanation
Indices: 44419898--44419934 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
44419888 TATATTTTAT
44419898 AATTTTTTTCATAGTTTTTG
1 AATTTTTTT-ATAGTTTTTG
44419918 AATTTTTTT-TAGTTTTT
1 AATTTTTTTATAGTTTTT
44419935 CACTCATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.70
Consensus pattern (19 bp):
AATTTTTTTATAGTTTTTG
Found at i:44420270 original size:29 final size:29
Alignment explanation
Indices: 44420202--44420294 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 29
44420192 GGCCAATTGA
44420202 TTTTTTTTTTATCAGTGAA-AGCTTAATTGGG
1 TTTTTTTTTT-TCA-T-AAGAGCTTAATTGGG
****
44420233 TGCGCTTTTTTCATAAGAGCTTAATTGGG
1 TTTTTTTTTTTCATAAGAGCTTAATTGGG
*
44420262 --TTTTTTTTTCATAATG-GCTCAATT-GG
1 TTTTTTTTTTTCATAA-GAGCTTAATTGGG
44420288 TTTTTTT
1 TTTTTTT
44420295 AATTAAGGGT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
26 2 0.04
27 18 0.36
28 8 0.16
29 13 0.26
30 3 0.06
31 6 0.12
ACGTcount: A:0.19, C:0.10, G:0.18, T:0.53
Consensus pattern (29 bp):
TTTTTTTTTTTCATAAGAGCTTAATTGGG
Found at i:44420289 original size:26 final size:27
Alignment explanation
Indices: 44420238--44420294 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
44420228 TTGGGTGCGC
*
44420238 TTTTTTCATAAGAGCTTAATTGGGTTT
1 TTTTTTCATAAGAGCTCAATTGGGTTT
44420265 TTTTTTCATAATG-GCTCAATT-GGTTT
1 TTTTTTCATAA-GAGCTCAATTGGGTTT
44420291 TTTT
1 TTTT
44420295 AATTAAGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 9 0.32
27 18 0.64
28 1 0.04
ACGTcount: A:0.19, C:0.09, G:0.16, T:0.56
Consensus pattern (27 bp):
TTTTTTCATAAGAGCTCAATTGGGTTT
Found at i:44422803 original size:20 final size:21
Alignment explanation
Indices: 44422769--44422822 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
44422759 TGATGATATT
*
44422769 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
44422790 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
44422810 TTTTATTATTTTA
1 TTATATTATTTTA
44422823 TTATTATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:44422826 original size:3 final size:3
Alignment explanation
Indices: 44422808--44422856 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
44422798 TTTAATGAGA
*
44422808 TAT T-T TAT TAT T-T TAT TAT TAT T-T CAT TAT TAT T-T TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
44422853 TAT T
1 TAT T
44422857 TAGTATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:44422828 original size:11 final size:11
Alignment explanation
Indices: 44422812--44422850 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
44422802 ATGAGATATT
44422812 TTATTATTTTA
1 TTATTATTTTA
*
44422823 TTATTATTTCA
1 TTATTATTTTA
44422834 TTATTATTTTA
1 TTATTATTTTA
44422845 TTATTA
1 TTATTA
44422851 ATTATTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:44422836 original size:19 final size:19
Alignment explanation
Indices: 44422808--44422849 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
44422798 TTTAATGAGA
*
44422808 TATTTTATTATT-TTATTAT
1 TATTTCATTATTATT-TTAT
44422827 TATTTCATTATTATTTTAT
1 TATTTCATTATTATTTTAT
44422846 TATT
1 TATT
44422850 AATTATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTCATTATTATTTTAT
Found at i:44425097 original size:23 final size:23
Alignment explanation
Indices: 44424988--44425104 Score: 103
Period size: 23 Copynumber: 5.0 Consensus size: 23
44424978 CCCGATATAT
44424988 GGCTCTTCGTGAGCTTCCCGATA
1 GGCTCTTCGTGAGCTTCCCGATA
* *
44425011 GGCTTTTTGTGAGCTTCCCGATA
1 GGCTCTTCGTGAGCTTCCCGATA
* * *
44425034 GTGCTC-GCTTGAACTTCCCGATATA
1 G-GCTCTTCGTGAGCTTCCCG--ATA
* * *
44425059 TGGCTATCCG-GAGCTTTCCGATA
1 -GGCTCTTCGTGAGCTTCCCGATA
*
44425082 GGCTCTTCGTGAGCTTTCCGATA
1 GGCTCTTCGTGAGCTTCCCGATA
44425105 TGGTTCTTTG
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
22 7 0.09
23 48 0.65
24 3 0.04
25 14 0.19
26 2 0.03
ACGTcount: A:0.15, C:0.26, G:0.25, T:0.33
Consensus pattern (23 bp):
GGCTCTTCGTGAGCTTCCCGATA
Found at i:44427755 original size:50 final size:53
Alignment explanation
Indices: 44427663--44427778 Score: 166
Period size: 50 Copynumber: 2.2 Consensus size: 53
44427653 CACTTACATG
* * *
44427663 ATATGGTCTTCTTCCCATATGATTCCATAACCCACTAGTTATGGTCTTACACA
1 ATATGGTCTTCTTCCCATATGATGCCATAACCCACCAATTATGGTCTTACACA
* *
44427716 ATATGGTCTTCTT-CC-TAT-ATGCTATAACCCACCAATTATGGTCTTACACG
1 ATATGGTCTTCTTCCCATATGATGCCATAACCCACCAATTATGGTCTTACACA
44427766 ATATGGTCTTCTT
1 ATATGGTCTTCTT
44427779 TCAGTGCCAT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
50 40 0.69
51 3 0.05
52 2 0.03
53 13 0.22
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (53 bp):
ATATGGTCTTCTTCCCATATGATGCCATAACCCACCAATTATGGTCTTACACA
Found at i:44429751 original size:9 final size:9
Alignment explanation
Indices: 44429726--44429775 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
44429716 ATAAATTCCA
44429726 AAAAATATTT
1 AAAAAT-TTT
*
44429736 TAAAATTTT
1 AAAAATTTT
44429745 AAAAATTATT
1 AAAAATT-TT
*
44429755 AAAAA-TAT
1 AAAAATTTT
44429763 AAAAATTTT
1 AAAAATTTT
44429772 AAAA
1 AAAA
44429776 TAAAAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
8 6 0.18
9 16 0.47
10 12 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AAAAATTTT
Found at i:44429756 original size:18 final size:17
Alignment explanation
Indices: 44429727--44429776 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
44429717 TAAATTCCAA
*
44429727 AAAATATTTTAAAATTTT
1 AAAA-ATTTTAAAATTAT
*
44429745 AAAAATTATTAAAAATAT
1 AAAAATT-TTAAAATTAT
44429763 AAAAATTTTAAAAT
1 AAAAATTTTAAAAT
44429777 AAAAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAAATTTTAAAATTAT
Found at i:44433949 original size:20 final size:19
Alignment explanation
Indices: 44433915--44433965 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
44433905 TTGCACTTTG
44433915 GTGCCTCTGATTGCATATTCA
1 GTGCCTCT-ATTGCA-ATTCA
*
44433936 -TGCCTCTATCTGCAGTTCA
1 GTGCCTCTAT-TGCAATTCA
44433955 GTGCCTCTATT
1 GTGCCTCTATT
44433966 ATGCATCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.16, C:0.27, G:0.18, T:0.39
Consensus pattern (19 bp):
GTGCCTCTATTGCAATTCA
Found at i:44438522 original size:26 final size:26
Alignment explanation
Indices: 44438486--44438541 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
44438476 TGAAATTCCA
44438486 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
44438512 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
44438538 ATCA
1 ATCA
44438542 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:44448414 original size:3 final size:3
Alignment explanation
Indices: 44448406--44448484 Score: 140
Period size: 3 Copynumber: 26.3 Consensus size: 3
44448396 TTCGATCTTA
* *
44448406 ATG ATG ATG ATG ATG ATG ATT ATG ATG ATG ATG ATG ATA ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
44448454 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
44448485 GGTTAGAAAG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:44449048 original size:14 final size:14
Alignment explanation
Indices: 44449029--44449058 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
44449019 TATTTTCAAG
44449029 ATAGATTAACGCAT
1 ATAGATTAACGCAT
*
44449043 ATAGATTCACGCAT
1 ATAGATTAACGCAT
44449057 AT
1 AT
44449059 TTATAAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (14 bp):
ATAGATTAACGCAT
Found at i:44452758 original size:33 final size:33
Alignment explanation
Indices: 44452716--44452783 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
44452706 CGAGTCACAC
44452716 ATACATAGTTTATCATCCACTCAAGATTAAGGT
1 ATACATAGTTTATCATCCACTCAAGATTAAGGT
** *
44452749 ATACATAGTTTATCATCCACTTGAGATTAATGT
1 ATACATAGTTTATCATCCACTCAAGATTAAGGT
44452782 AT
1 AT
44452784 GTCCCACTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (33 bp):
ATACATAGTTTATCATCCACTCAAGATTAAGGT
Found at i:44453799 original size:20 final size:20
Alignment explanation
Indices: 44453774--44453814 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
44453764 GTTTAGTGTT
44453774 AGATGAAAATGAAATCTTTA
1 AGATGAAAATGAAATCTTTA
44453794 AGATGAAAATGAAATCTTTA
1 AGATGAAAATGAAATCTTTA
44453814 A
1 A
44453815 AACTGAGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (20 bp):
AGATGAAAATGAAATCTTTA
Found at i:44454970 original size:19 final size:20
Alignment explanation
Indices: 44454940--44454985 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
44454930 CGGAAAATGA
44454940 TTTCTAGAAAATGATTTACT
1 TTTCTAGAAAATGATTTACT
44454960 TTTCT-GAAAATGATTTACT
1 TTTCTAGAAAATGATTTACT
44454979 TTTCTAG
1 TTTCTAG
44454986 TGTTTGGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (20 bp):
TTTCTAGAAAATGATTTACT
Found at i:44455826 original size:15 final size:15
Alignment explanation
Indices: 44455806--44455838 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
44455796 TTCCATCAGT
44455806 AAGTTGCCAAGCATA
1 AAGTTGCCAAGCATA
*
44455821 AAGTTGCCAGGCATA
1 AAGTTGCCAAGCATA
44455836 AAG
1 AAG
44455839 ATACAAGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (15 bp):
AAGTTGCCAAGCATA
Found at i:44456884 original size:22 final size:23
Alignment explanation
Indices: 44456858--44456903 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
44456848 CAACCAAACC
44456858 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
44456880 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
44456903 A
1 A
44456904 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:44456909 original size:23 final size:23
Alignment explanation
Indices: 44456865--44456909 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
44456855 ACCAATTCAA
*
44456865 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
44456888 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
44456910 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:44461896 original size:25 final size:25
Alignment explanation
Indices: 44461868--44461917 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
44461858 GGAAGAGAAC
44461868 ATGAAGAAC-GAAAGAAGGAAAAGGA
1 ATGAAGAACAG-AAGAAGGAAAAGGA
*
44461893 ATGAAGAACAGAAGAAGGAGAAGGA
1 ATGAAGAACAGAAGAAGGAAAAGGA
44461918 GAATGAGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.58, C:0.04, G:0.34, T:0.04
Consensus pattern (25 bp):
ATGAAGAACAGAAGAAGGAAAAGGA
Found at i:44467810 original size:24 final size:24
Alignment explanation
Indices: 44467778--44467823 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
44467768 ATTGAGTTAG
44467778 TACCGAAGAAGAAAAAAAAAAAGA
1 TACCGAAGAAGAAAAAAAAAAAGA
44467802 TACCGAAGAAGAAAAAAAAAAA
1 TACCGAAGAAGAAAAAAAAAAA
44467824 AAGATAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.72, C:0.09, G:0.15, T:0.04
Consensus pattern (24 bp):
TACCGAAGAAGAAAAAAAAAAAGA
Found at i:44492466 original size:13 final size:13
Alignment explanation
Indices: 44492448--44492473 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44492438 ACGGAGATTG
44492448 ACATGGCCGTGTA
1 ACATGGCCGTGTA
44492461 ACATGGCCGTGTA
1 ACATGGCCGTGTA
44492474 CACCAATGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (13 bp):
ACATGGCCGTGTA
Found at i:44496923 original size:42 final size:43
Alignment explanation
Indices: 44496827--44496985 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 43
44496817 AACAAGTACA
* * *
44496827 ATGCCAATGTCTCAGAC-GTGGTCTTACATGTAATTCAATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGTAAATCAATATCG
** * *
44496870 ATGCCTCTGTCCTAGATAGGGTCTTACACG-AAATCAGATAT-G
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAAATCA-ATATCG
*
44496912 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTTAA-ATCG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAAATC--AATATCG
* ** *
44496956 AAGCCTGTGTCCCAGACACGGTCTTACACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACG
44496986 ATATTTCAGA
Statistics
Matches: 94, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
42 31 0.33
43 33 0.35
44 29 0.31
45 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAAATCAATATCG
Found at i:44506240 original size:34 final size:34
Alignment explanation
Indices: 44506197--44506265 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
44506187 TGTTGAACCC
44506197 TGCACCCATAAGGAAAATACTTTAAAGCACAAAT
1 TGCACCCATAAGGAAAATACTTTAAAGCACAAAT
44506231 TGCACCCATAAGGAAAATACTTTAAAGCACAAAT
1 TGCACCCATAAGGAAAATACTTTAAAGCACAAAT
44506265 T
1 T
44506266 AAGTAAGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.22
Consensus pattern (34 bp):
TGCACCCATAAGGAAAATACTTTAAAGCACAAAT
Found at i:44510735 original size:24 final size:21
Alignment explanation
Indices: 44510696--44510745 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
44510686 GCAAAAAACT
* *
44510696 AAAAAATATATTAAATTTTAGA
1 AAAAAAAATATTAAATTGTA-A
44510718 AAAAAAAATATTAAAAATTGTAA
1 AAAAAAAATATT--AAATTGTAA
44510741 AAAAA
1 AAAAA
44510746 GGAAAGAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.46
23 6 0.25
24 7 0.29
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAAAAAATATTAAATTGTAA
Found at i:44519171 original size:18 final size:18
Alignment explanation
Indices: 44519144--44519192 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
44519134 ATTGCTTTTC
44519144 AGAAGCACTTTTGGGACA
1 AGAAGCACTTTTGGGACA
*
44519162 AGAAGTACTTTTGGGACA
1 AGAAGCACTTTTGGGACA
*
44519180 AAAAGCACTTTTG
1 AGAAGCACTTTTG
44519193 AGATAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (18 bp):
AGAAGCACTTTTGGGACA
Found at i:44521420 original size:23 final size:23
Alignment explanation
Indices: 44521378--44521422 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
44521368 TCATGACTTA
*
44521378 TAAAATTTATGATTTGAAATTTT
1 TAAAATTTATGATTTAAAATTTT
44521401 TAAAATTT-TGATTTTAAAATTT
1 TAAAATTTATGA-TTTAAAATTT
44521423 AGGATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (23 bp):
TAAAATTTATGATTTAAAATTTT
Found at i:44522495 original size:30 final size:31
Alignment explanation
Indices: 44522461--44522522 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
44522451 TTTAAAGGAT
*
44522461 TAAAT-CAAAATTTTATCATTTTT-AGGGGCC
1 TAAATGCAAAATTTT-CCATTTTTGAGGGGCC
*
44522491 TAAATGGAAAATTTTCCATTTTTGAGGGGCC
1 TAAATGCAAAATTTTCCATTTTTGAGGGGCC
44522522 T
1 T
44522523 TGCTAGCCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.39
Consensus pattern (31 bp):
TAAATGCAAAATTTTCCATTTTTGAGGGGCC
Found at i:44531557 original size:55 final size:54
Alignment explanation
Indices: 44531450--44531600 Score: 178
Period size: 55 Copynumber: 2.8 Consensus size: 54
44531440 AATCGATTAG
* * * *
44531450 ACATATAAACAATCGATTCAAAATAAGTAATATTCCAACATAAAACTTTATTTGA
1 ACATATAAACAATCGATTCAAAAGAAGCAATATTCCAACA-AAAACTCTATTTAA
* * * *
44531505 ACATAAAAAAAATTGATTCAAAAGAAGCAGTATTCCAACAAGACAA-TCTATTTAA
1 ACATATAAACAATCGATTCAAAAGAAGCAATATTCCAACAA-A-AACTCTATTTAA
* *
44531560 ACATATAAACAATCGATTCAATAGAAGCAATATCCCAACAA
1 ACATATAAACAATCGATTCAAAAGAAGCAATATTCCAACAA
44531601 TTAAGAAGAA
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
54 1 0.01
55 77 0.96
56 2 0.03
ACGTcount: A:0.51, C:0.17, G:0.07, T:0.25
Consensus pattern (54 bp):
ACATATAAACAATCGATTCAAAAGAAGCAATATTCCAACAAAAACTCTATTTAA
Found at i:44540425 original size:414 final size:414
Alignment explanation
Indices: 44539646--44541315 Score: 3232
Period size: 414 Copynumber: 4.0 Consensus size: 414
44539636 CCAATGACTC
* * *
44539646 CATCTCTAGTTCTTTCAAACTGTAAGCAAACATTAGTAGTACCTCGTAAGTATATTAAAATCAAC
1 CATCTCAAATTCTTTCAAACTGTAAGCAAACATTAGTAGTACCTCGTAAGTATCTTAAAATCAAC
44539711 TAAACTACTTTCTAATATTCTTTATCGGGATTCGCCATGTATCTGCTAACTGCACTGACTGCATA
66 TAAACTACTTTCTAATATTCTTTATCGGGATTCGCCATGTATCTGCTAACTGCACTGACTGCATA
*
44539776 TTATATATCTGGACATAAACAAACCATAGCATACATGAAAGATCTCATTGCACTAGAATATGGAA
131 TTATATATCTGGACATAAACAAACCATAGCATACATGAAAGATCCCATTGCACTAGAATATGGAA
*
44539841 CATGTGACATATAATCAATCTCATCATCTGATTGTGGAGACAAAGCCGATGAAAGTCTGAAATAG
196 CATGTGACATGTAATCAATCTCATCATCTGATTGTGGAGACAAAGCCGATGAAAGTCTGAAATAG
44539906 ACTACTAAAGGAGTACTAACAGGCTTAGCACTTTGCATTTTGAACCTGCAAAGAACTTTCTCAAT
261 ACTACTAAAGGAGTACTAACAGGCTTAGCACTTTGCATTTTGAACCTGCAAAGAACTTTCTCAAT
44539971 GTACCCTTTTGAATTAGGTACAATTTACTTGTTTTTCTATTTCTGAGAATCTCCATACCAAGTAT
326 GTACCCTTTTGAATTAGGTACAATTTACTTGTTTTTCTATTTCTGAGAATCTCCATACCAAGTAT
44540036 TTTCTTTGCTGGTCCCAAATCTTT
391 TTTCTTTGCTGGTCCCAAATCTTT
44540060 CATCTCAAATTCTTTCAAACTGTAAGCAAACATTAGTAGTACCTCGTAAGTATCTTAAAATCAAC
1 CATCTCAAATTCTTTCAAACTGTAAGCAAACATTAGTAGTACCTCGTAAGTATCTTAAAATCAAC
* *
44540125 TAAACTACTTTCTAATATTCTTTATCGGGATTCGCCATGTATATGCTAACTGCACTGATTGCATA
66 TAAACTACTTTCTAATATTCTTTATCGGGATTCGCCATGTATCTGCTAACTGCACTGACTGCATA
*
44540190 TTATATATCTGGACATAAACAAACCATAACATACATGAAAGATCCCATTGCACTAGAATATGGAA
131 TTATATATCTGGACATAAACAAACCATAGCATACATGAAAGATCCCATTGCACTAGAATATGGAA
44540255 CATGTGACATGTAATCAATCTCATCATCTGATTGTGGAGACAAAGCCGATGAAAGTCTGAAATAG
196 CATGTGACATGTAATCAATCTCATCATCTGATTGTGGAGACAAAGCCGATGAAAGTCTGAAATAG
44540320 ACTACTAAAGGAGTACTAACAGGCTTAGCACTTTGCATTTTGAACCTGCAAAGAACTTTCTCAAT
261 ACTACTAAAGGAGTACTAACAGGCTTAGCACTTTGCATTTTGAACCTGCAAAGAACTTTCTCAAT
44540385 GTACCCTTTTGAATTAGGTACAATTTACTTGTTTTTCTATTTCTGAGAATCTCCATACCAAGTAT
326 GTACCCTTTTGAATTAGGTACAATTTACTTGTTTTTCTATTTCTGAGAATCTCCATACCAAGTAT
44540450 TTTCTTTGCTGGTCCCAAATCTTT
391 TTTCTTTGCTGGTCCCAAATCTTT
44540474 CATCTCAAATTCTTTCAAACTGTAAGCAAACATTAGTAGTACCTCGTAAGTATCTTAAAATCAAC
1 CATCTCAAATTCTTTCAAACTGTAAGCAAACATTAGTAGTACCTCGTAAGTATCTTAAAATCAAC
*
44540539 TAAGCTACTTTCTAATATTCTTTATCGGGATTCGCCATGTATCTGCTAACTGCACTGACTGCATA
66 TAAACTACTTTCTAATATTCTTTATCGGGATTCGCCATGTATCTGCTAACTGCACTGACTGCATA
44540604 TTATATATCTGGACATAAACAAACCATAGCATACATGAAAGATCCCATTGCACTAGAATATGGAA
131 TTATATATCTGGACATAAACAAACCATAGCATACATGAAAGATCCCATTGCACTAGAATATGGAA
44540669 CATGTGACATGTAATCAATCTCATCATCTGATTGTGGAGACAAAGCCGATGAAAGTCTGAAATAG
196 CATGTGACATGTAATCAATCTCATCATCTGATTGTGGAGACAAAGCCGATGAAAGTCTGAAATAG
*
44540734 ACTACTAAAGGAGTACTAACAGGCTTAGCACTTTGCATTTTGAACCTGCAAAGAACTTTCTTAAT
261 ACTACTAAAGGAGTACTAACAGGCTTAGCACTTTGCATTTTGAACCTGCAAAGAACTTTCTCAAT
*
44540799 GTACCCTTTTGAATTAGGTACAATTTACTTGTTTTTCTATTTCTGATAATCTCCATACCAAGTAT
326 GTACCCTTTTGAATTAGGTACAATTTACTTGTTTTTCTATTTCTGAGAATCTCCATACCAAGTAT
44540864 TTTCTTTGCTGGTCCCAAATCTTT
391 TTTCTTTGCTGGTCCCAAATCTTT
44540888 CATCTCAAATTCTTTCAAACTGTAAGCAAACATTAGTAGTACCTCGTAAGTATCTTAAAATCAAC
1 CATCTCAAATTCTTTCAAACTGTAAGCAAACATTAGTAGTACCTCGTAAGTATCTTAAAATCAAC
44540953 TAAACTACTTTCTAATATTCTTTATCGGGATTCGCCATGTATCTGCTAACTGCACTGACTGCATA
66 TAAACTACTTTCTAATATTCTTTATCGGGATTCGCCATGTATCTGCTAACTGCACTGACTGCATA
44541018 TTATATATCTGGACATAAACAAACCATAGCATACATGAAAGATCCCATTGCACTAGAATATGGAA
131 TTATATATCTGGACATAAACAAACCATAGCATACATGAAAGATCCCATTGCACTAGAATATGGAA
44541083 CATGTGACATGTAATCAATCTCATCATCTGATTGTGGAGACAAAGCCGATGAAAGTCTGAAATAG
196 CATGTGACATGTAATCAATCTCATCATCTGATTGTGGAGACAAAGCCGATGAAAGTCTGAAATAG
44541148 ACTACTAAAGGAGTACTAACAGGCTTAGCACTTTGCATTTTGAACCTGCAAAGAACTTTCTCAAT
261 ACTACTAAAGGAGTACTAACAGGCTTAGCACTTTGCATTTTGAACCTGCAAAGAACTTTCTCAAT
44541213 GTACCCTTTTGAATTAGGTACAATTTACTTGTTTTTCTATTTCTGAGAATCTCCATACCAAGTAT
326 GTACCCTTTTGAATTAGGTACAATTTACTTGTTTTTCTATTTCTGAGAATCTCCATACCAAGTAT
*
44541278 TTTCTTTGTTGGTCCCAAATCTTT
391 TTTCTTTGCTGGTCCCAAATCTTT
44541302 CATCTCAAATTCTT
1 CATCTCAAATTCTT
44541316 CACTAAGCTG
Statistics
Matches: 1238, Mismatches: 18, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
414 1238 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (414 bp):
CATCTCAAATTCTTTCAAACTGTAAGCAAACATTAGTAGTACCTCGTAAGTATCTTAAAATCAAC
TAAACTACTTTCTAATATTCTTTATCGGGATTCGCCATGTATCTGCTAACTGCACTGACTGCATA
TTATATATCTGGACATAAACAAACCATAGCATACATGAAAGATCCCATTGCACTAGAATATGGAA
CATGTGACATGTAATCAATCTCATCATCTGATTGTGGAGACAAAGCCGATGAAAGTCTGAAATAG
ACTACTAAAGGAGTACTAACAGGCTTAGCACTTTGCATTTTGAACCTGCAAAGAACTTTCTCAAT
GTACCCTTTTGAATTAGGTACAATTTACTTGTTTTTCTATTTCTGAGAATCTCCATACCAAGTAT
TTTCTTTGCTGGTCCCAAATCTTT
Found at i:44547786 original size:6 final size:6
Alignment explanation
Indices: 44547775--44547803 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
44547765 GTTAACGAAC
44547775 AAATAT AAATAT AAATAT AAATAT AAATA
1 AAATAT AAATAT AAATAT AAATAT AAATA
44547804 AATATTTATA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATAT
Found at i:44550309 original size:16 final size:17
Alignment explanation
Indices: 44550277--44550309 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44550267 ATTAAATAAA
*
44550277 ATTATTTTAATTAAAAT
1 ATTATTTCAATTAAAAT
44550294 ATTATTTCAA-TAAAAT
1 ATTATTTCAATTAAAAT
44550310 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTATTTCAATTAAAAT
Found at i:44550533 original size:32 final size:32
Alignment explanation
Indices: 44550454--44550516 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
44550444 TCATAAACTT
* * *
44550454 ATAAATTGATTACTTAAATTTAATAACTCATG
1 ATAAATTAATTAATTTAATTTAATAACTCATG
44550486 ATAAATTAATTAATTTAATTTAATAACTCAT
1 ATAAATTAATTAATTTAATTTAATAACTCAT
44550517 ACTGATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (32 bp):
ATAAATTAATTAATTTAATTTAATAACTCATG
Found at i:44550541 original size:35 final size:32
Alignment explanation
Indices: 44550454--44550542 Score: 92
Period size: 32 Copynumber: 2.7 Consensus size: 32
44550444 TCATAAACTT
* *
44550454 ATAAATTGATTACTTAAATTTAATAACTCATG
1 ATAAATTAATTATTTAAATTTAATAACTCATG
44550486 ATAAATTAATTAATTT-AATTTAATAACTCATACTG
1 ATAAATTAATT-ATTTAAATTTAATAACTC--A-TG
*
44550521 ATTAATTAAATT-TTTAAATTTA
1 ATAAATT-AATTATTTAAATTTA
44550543 TAAACTTCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
32 23 0.48
33 3 0.06
34 4 0.08
35 14 0.29
36 4 0.08
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (32 bp):
ATAAATTAATTATTTAAATTTAATAACTCATG
Found at i:44550736 original size:24 final size:24
Alignment explanation
Indices: 44550706--44550755 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
44550696 AATTTTATGA
44550706 TAGATTTACAATAATTACCCTTTT
1 TAGATTTACAATAATTACCCTTTT
*
44550730 TAGATTTACAATAATTATCCTTTT
1 TAGATTTACAATAATTACCCTTTT
44550754 TA
1 TA
44550756 TAATAGCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.48
Consensus pattern (24 bp):
TAGATTTACAATAATTACCCTTTT
Found at i:44551481 original size:71 final size:71
Alignment explanation
Indices: 44551399--44551538 Score: 271
Period size: 71 Copynumber: 2.0 Consensus size: 71
44551389 AAAAACAACT
*
44551399 TTTTTTCACTCTTTTCTTTGATTTGTAAAACCTACACCAAACTTTTCTTTAATTATATATTGCTT
1 TTTTTTCACTCTTTTCTTTGATTTGTAAAACCTAAACCAAACTTTTCTTTAATTATATATTGCTT
44551464 ATTGAC
66 ATTGAC
44551470 TTTTTTCACTCTTTTCTTTGATTTGTAAAACCTAAACCAAACTTTTCTTTAATTATATATTGCTT
1 TTTTTTCACTCTTTTCTTTGATTTGTAAAACCTAAACCAAACTTTTCTTTAATTATATATTGCTT
44551535 ATTG
66 ATTG
44551539 GATTGTCTTC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (71 bp):
TTTTTTCACTCTTTTCTTTGATTTGTAAAACCTAAACCAAACTTTTCTTTAATTATATATTGCTT
ATTGAC
Found at i:44552245 original size:17 final size:17
Alignment explanation
Indices: 44552223--44552259 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
44552213 TAAGAAAGAA
44552223 TAATTAAAAAATTTAAT
1 TAATTAAAAAATTTAAT
**
44552240 TAATTAAAATTTTTAAT
1 TAATTAAAAAATTTAAT
44552257 TAA
1 TAA
44552260 AAATCTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATTAAAAAATTTAAT
Found at i:44558418 original size:17 final size:16
Alignment explanation
Indices: 44558366--44558470 Score: 68
Period size: 17 Copynumber: 6.2 Consensus size: 16
44558356 ACACAATTTC
*
44558366 TTTAAAA-ACGAGAAT
1 TTTAAAACACGAAAAT
*
44558381 TTTAGAAACATGAAAATT
1 TTTA-AAACACGAAAA-T
*
44558399 TTTAAAACACGACAACT
1 TTTAAAACACGA-AAAT
* *
44558416 TTTGAAGCACGAGAAATT
1 TTTAAAACACGA-AAA-T
* *
44558434 TATTCAAAACACAAAAAA
1 T-TT-AAAACACGAAAAT
*
44558452 TTTAAAACACGAACAT
1 TTTAAAACACGAAAAT
44558468 TTT
1 TTT
44558471 TTGAAACAAT
Statistics
Matches: 68, Mismatches: 15, Indels: 13
0.71 0.16 0.14
Matches are distributed among these distances:
15 4 0.06
16 16 0.24
17 27 0.40
18 10 0.15
19 5 0.07
20 6 0.09
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.28
Consensus pattern (16 bp):
TTTAAAACACGAAAAT
Found at i:44558527 original size:17 final size:17
Alignment explanation
Indices: 44558491--44558706 Score: 123
Period size: 18 Copynumber: 12.4 Consensus size: 17
44558481 TTTTATTTTT
*
44558491 ATTTTT-AAACAAGAAAA
1 ATTTTTAAAACACG-AAA
*
44558508 ATTTTTAAAACACGAGA
1 ATTTTTAAAACACGAAA
*
44558525 A-TTTTAGAGACACGAAA
1 ATTTTTA-AAACACGAAA
*
44558542 ATTCTTAAAACACGAAA
1 ATTTTTAAAACACGAAA
* *
44558559 ATTTTTGAGAACACGACA
1 ATTTTT-AAAACACGAAA
* *
44558577 ATTTTGAAATACACGAAT
1 ATTTTTAAA-ACACGAAA
* **
44558595 TTTTTTGAAAAC-CTGATTT
1 ATTTTT-AAAACAC-GA-AA
* * * *
44558614 TTTTTTGAAGCGCGAAA
1 ATTTTTAAAACACGAAA
** * * *
44558631 ATTCGTGAAACATGAGA
1 ATTTTTAAAACACGAAA
*
44558648 ATTGTTGAAAACACGAAA
1 ATT-TTTAAAACACGAAA
44558666 ATTTTTGAAAACACGAAA
1 ATTTTT-AAAACACGAAA
* *
44558684 ATTTTTGAAACATGAAA
1 ATTTTTAAAACACGAAA
44558701 ATTTTT
1 ATTTTT
44558707 TGAAAACACA
Statistics
Matches: 152, Mismatches: 36, Indels: 22
0.72 0.17 0.10
Matches are distributed among these distances:
16 5 0.03
17 65 0.43
18 71 0.47
19 11 0.07
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (17 bp):
ATTTTTAAAACACGAAA
Found at i:44558543 original size:34 final size:35
Alignment explanation
Indices: 44558505--44558705 Score: 122
Period size: 35 Copynumber: 5.7 Consensus size: 35
44558495 TTAAACAAGA
*
44558505 AAAATTTTTAAAACACGAGAATTTTAGAG-ACACG
1 AAAATTTTTAAAACACGAAAATTTTAGAGAACACG
* *
44558539 AAAATTCTTAAAACACGAAAATTTTTGAGAACACG
1 AAAATTTTTAAAACACGAAAATTTTAGAGAACACG
* * ** * *
44558574 ACAATTTTGAAATACACGAATTTTTTTGAAAAC-CTG
1 AAAATTTTTAAA-ACACGAAAATTTTAGAGAACAC-G
*** * * * * *
44558610 ATTTTTTTTTGAAGCGCGAAAATTCGT-GA-AACATG
1 A-AAATTTTTAAAACACGAAAATT-TTAGAGAACACG
* * * *
44558645 AGAATTGTTGAAAACACGAAAATTTTTGAAAACACG
1 AAAATT-TTTAAAACACGAAAATTTTAGAGAACACG
* *
44558681 AAAATTTTTGAAACATGAAAATTTT
1 AAAATTTTTAAAACACGAAAATTTT
44558706 TTGAAAACAC
Statistics
Matches: 125, Mismatches: 33, Indels: 17
0.71 0.19 0.10
Matches are distributed among these distances:
34 29 0.23
35 51 0.41
36 38 0.30
37 7 0.06
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (35 bp):
AAAATTTTTAAAACACGAAAATTTTAGAGAACACG
Found at i:44558573 original size:18 final size:18
Alignment explanation
Indices: 44558505--44558715 Score: 159
Period size: 17 Copynumber: 11.9 Consensus size: 18
44558495 TTAAACAAGA
44558505 AAAATTTTT-AAAACACG
1 AAAATTTTTGAAAACACG
* * *
44558522 AGAATTTTAG-AGACACG
1 AAAATTTTTGAAAACACG
*
44558539 AAAATTCTT-AAAACACG
1 AAAATTTTTGAAAACACG
*
44558556 AAAATTTTTGAGAACACG
1 AAAATTTTTGAAAACACG
*
44558574 ACAA-TTTTGAAATACACG
1 AAAATTTTTGAAA-ACACG
**
44558592 AATTTTTTTGAAAAC-CTG
1 AAAATTTTTGAAAACAC-G
*** * *
44558610 ATTTTTTTTTG-AAGCGCG
1 A-AAATTTTTGAAAACACG
** *
44558628 AAAATTCGTG-AAACATG
1 AAAATTTTTGAAAACACG
* *
44558645 AGAATTGTTGAAAACACG
1 AAAATTTTTGAAAACACG
44558663 AAAATTTTTGAAAACACG
1 AAAATTTTTGAAAACACG
*
44558681 AAAATTTTTG-AAACATG
1 AAAATTTTTGAAAACACG
44558698 AAAATTTTTTGAAAACAC
1 AAAA-TTTTTGAAAACAC
44558716 ATTTTTTTTT
Statistics
Matches: 151, Mismatches: 32, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
17 66 0.44
18 63 0.42
19 22 0.15
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (18 bp):
AAAATTTTTGAAAACACG
Found at i:44558692 original size:36 final size:36
Alignment explanation
Indices: 44558505--44558715 Score: 159
Period size: 36 Copynumber: 6.0 Consensus size: 36
44558495 TTAAACAAGA
* * *
44558505 AAAATTTTT-AAAACACGAGAATTTTAG-AGACACG
1 AAAATTTTTGAAAACACGAAAATTTTTGAAAACACG
* *
44558539 AAAATTCTT-AAAACACGAAAATTTTTGAGAACACG
1 AAAATTTTTGAAAACACGAAAATTTTTGAAAACACG
* **
44558574 ACAA-TTTTGAAATACACGAATTTTTTTGAAAAC-CTG
1 AAAATTTTTGAAA-ACACGAAAATTTTTGAAAACAC-G
*** * * ** *
44558610 ATTTTTTTTTG-AAGCGCGAAAATTCGTG-AAACATG
1 A-AAATTTTTGAAAACACGAAAATTTTTGAAAACACG
* *
44558645 AGAATTGTTGAAAACACGAAAATTTTTGAAAACACG
1 AAAATTTTTGAAAACACGAAAATTTTTGAAAACACG
*
44558681 AAAATTTTTG-AAACATGAAAATTTTTTGAAAACAC
1 AAAATTTTTGAAAACACGAAAA-TTTTTGAAAACAC
44558716 ATTTTTTTTT
Statistics
Matches: 135, Mismatches: 32, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
34 32 0.24
35 41 0.30
36 55 0.41
37 2 0.01
38 5 0.04
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (36 bp):
AAAATTTTTGAAAACACGAAAATTTTTGAAAACACG
Found at i:44558706 original size:89 final size:89
Alignment explanation
Indices: 44558537--44558710 Score: 208
Period size: 89 Copynumber: 2.0 Consensus size: 89
44558527 TTTAGAGACA
* * * * **
44558537 CGAAAATTCTTAAAACACGAAAATTTTTGAGAACACGACAATTTTGAAATACACGAATTTTTTTG
1 CGAAAATTCGTAAAACACGAAAATTGTTGAAAACACGAAAATTTTGAAATACACGAAAATTTTTG
* **
44558602 AAAACCTGATTTTTTTTTGAAGCG
66 AAAACATGAAATTTTTTTGAAGCG
* * *
44558626 CGAAAATTCGTGAAACATGAGAATTGTTGAAAACACGAAAATTTTTGAAA-ACACGAAAATTTTT
1 CGAAAATTCGTAAAACACGAAAATTGTTGAAAACACGAAAA-TTTTGAAATACACGAAAATTTTT
*
44558690 G-AAACATGAAAATTTTTTGAA
65 GAAAACATGAAATTTTTTTGAA
44558711 AACACATTTT
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
88 16 0.23
89 47 0.66
90 8 0.11
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (89 bp):
CGAAAATTCGTAAAACACGAAAATTGTTGAAAACACGAAAATTTTGAAATACACGAAAATTTTTG
AAAACATGAAATTTTTTTGAAGCG
Found at i:44558771 original size:17 final size:17
Alignment explanation
Indices: 44558736--44558777 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
44558726 TGATCATGGG
44558736 AATTTTTGAAAACGTGAA
1 AATTTTTGAAAACG-GAA
44558754 AATTTTTGAAACAC-GAA
1 AATTTTTGAAA-ACGGAA
*
44558771 AGTTTTT
1 AATTTTT
44558778 TTTTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 11 0.50
19 2 0.09
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (17 bp):
AATTTTTGAAAACGGAA
Found at i:44558845 original size:19 final size:19
Alignment explanation
Indices: 44558804--44558849 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
44558794 CGAAAATTTT
* *
44558804 TTTTTGAACACGAGAAAAT
1 TTTTTGAAAACGAGAAAAA
44558823 TTTTTGAAAAC-ATGAAAAA
1 TTTTTGAAAACGA-GAAAAA
44558842 -TTTTGAAA
1 TTTTTGAAA
44558850 CACCGAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.35
Consensus pattern (19 bp):
TTTTTGAAAACGAGAAAAA
Found at i:44558883 original size:18 final size:17
Alignment explanation
Indices: 44558823--44558886 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 17
44558813 ACGAGAAAAT
*
44558823 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACG-AAA
*
44558841 ATTTTG-AAACACCGAAA
1 TTTTTGAAAACA-CGAAA
*
44558858 -TCTTGAAAACACGAAGA
1 TTTTTGAAAACACGAA-A
44558875 TTTTTGAAAACA
1 TTTTTGAAAACA
44558887 ATTATTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 8 0.21
17 14 0.37
18 16 0.42
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
TTTTTGAAAACACGAAA
Found at i:44558963 original size:17 final size:17
Alignment explanation
Indices: 44558941--44559031 Score: 65
Period size: 18 Copynumber: 5.2 Consensus size: 17
44558931 TTTTAAAAAA
*
44558941 AAAACACAAAAATTTTC
1 AAAACACAAAAATTTTG
* *
44558958 AAAACACTGAAATTTTTG
1 AAAACAC-AAAAATTTTG
** ** *
44558976 AAAACATGAGGATTTTT
1 AAAACACAAAAATTTTG
*
44558993 AAAACACGCAAAATTTTG
1 AAAACAC-AAAAATTTTG
*
44559011 GAAACACAAAAATTTTTG
1 AAAACACAAAAA-TTTTG
44559029 AAA
1 AAA
44559032 TACGAAATTA
Statistics
Matches: 55, Mismatches: 16, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
17 23 0.42
18 32 0.58
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (17 bp):
AAAACACAAAAATTTTG
Found at i:44559008 original size:18 final size:17
Alignment explanation
Indices: 44558941--44559038 Score: 72
Period size: 17 Copynumber: 5.6 Consensus size: 17
44558931 TTTTAAAAAA
* *
44558941 AAAACACAAAAATTTTC
1 AAAACACGAAAATTTTT
44558958 AAAACACTG-AAATTTTT
1 AAAACAC-GAAAATTTTT
* **
44558975 GAAAACATGAGGATTTTT
1 -AAAACACGAAAATTTTT
*
44558993 AAAACACGCAAAATTTTG
1 AAAACACG-AAAATTTTT
* *
44559011 GAAACACAAAAATTTTT
1 AAAACACGAAAATTTTT
* *
44559028 GAAATACGAAA
1 AAAACACGAAA
44559039 TTATTTTTTT
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
17 39 0.62
18 24 0.38
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (17 bp):
AAAACACGAAAATTTTT
Found at i:44559026 original size:35 final size:35
Alignment explanation
Indices: 44558941--44559027 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 35
44558931 TTTTAAAAAA
* *
44558941 AAAACACAAAAATTTTCAAAACACTGAAATTTTTG
1 AAAACACAAAAATTTTTAAAACACTGAAAATTTTG
** **
44558976 AAAACATGAGGATTTTTAAAACAC-GCAAAATTTTG
1 AAAACACAAAAATTTTTAAAACACTG-AAAATTTTG
*
44559011 GAAACACAAAAATTTTT
1 AAAACACAAAAATTTTT
44559028 GAAATACGAA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
34 1 0.03
35 39 0.98
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (35 bp):
AAAACACAAAAATTTTTAAAACACTGAAAATTTTG
Found at i:44559675 original size:8 final size:8
Alignment explanation
Indices: 44559651--44559731 Score: 87
Period size: 8 Copynumber: 10.2 Consensus size: 8
44559641 ATTGAACCCC
44559651 CTTTTTCTT
1 CTTTTT-TT
*
44559660 CCTTTTTT
1 CTTTTTTT
44559668 CTTTTTTT
1 CTTTTTTT
44559676 C-TTTTTT
1 CTTTTTTT
44559683 CTTTTTTT
1 CTTTTTTT
44559691 C-TTTTTT
1 CTTTTTTT
*
44559698 CCTTTTTT
1 CTTTTTTT
44559706 CTTCTTTTT
1 CTT-TTTTT
**
44559715 CTTCCTTT
1 CTTTTTTT
44559723 -TTTTTTT
1 CTTTTTTT
44559730 CT
1 CT
44559732 GCTGGGCTGC
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
7 19 0.31
8 29 0.48
9 13 0.21
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
CTTTTTTT
Found at i:44559681 original size:15 final size:15
Alignment explanation
Indices: 44559651--44559731 Score: 92
Period size: 15 Copynumber: 5.1 Consensus size: 15
44559641 ATTGAACCCC
44559651 CTTTTTCTTCCTTTTTT
1 CTTTTT-TT-CTTTTTT
44559668 CTTTTTTTCTTTTTT
1 CTTTTTTTCTTTTTT
44559683 CTTTTTTTCTTTTTT
1 CTTTTTTTCTTTTTT
*
44559698 CCTTTTTTCTTCTTTTT
1 CTTTTTTTC-T-TTTTT
*
44559715 CTTCCTTTT-TTTTTT
1 CTT-TTTTTCTTTTTT
44559730 CT
1 CT
44559732 GCTGGGCTGC
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
15 37 0.64
16 4 0.07
17 13 0.22
18 4 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
CTTTTTTTCTTTTTT
Found at i:44559692 original size:23 final size:23
Alignment explanation
Indices: 44559653--44559731 Score: 97
Period size: 23 Copynumber: 3.3 Consensus size: 23
44559643 TGAACCCCCT
*
44559653 TTTTCTTCCTTTTTTCTTTTTTTC
1 TTTT-TTCTTTTTTTCTTTTTTTC
*
44559677 TTTTTTCTTTTTTTCTTTTTTCC
1 TTTTTTCTTTTTTTCTTTTTTTC
*
44559700 TTTTTTCTTCTTTTTCTTCCTTTT-
1 TTTTTTCTT-TTTTTCTT-TTTTTC
44559724 TTTTTTCT
1 TTTTTTCT
44559732 GCTGGGCTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
23 26 0.53
24 20 0.41
25 3 0.06
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTTCTTTTTTTCTTTTTTTC
Found at i:44560017 original size:3 final size:3
Alignment explanation
Indices: 44560011--44560066 Score: 67
Period size: 3 Copynumber: 17.0 Consensus size: 3
44560001 TTTCTTTTTT
44560011 TTC TTC TTTC TTC TTC TCTC TTTC TTTC TTC TTC TTC TTTC TTC TTC
1 TTC TTC -TTC TTC TTC T-TC -TTC -TTC TTC TTC TTC -TTC TTC TTC
44560058 TTC TTC TTC
1 TTC TTC TTC
44560067 AAAACCGAGC
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
3 34 0.69
4 14 0.29
5 1 0.02
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:44560026 original size:10 final size:10
Alignment explanation
Indices: 44560002--44560066 Score: 73
Period size: 10 Copynumber: 6.6 Consensus size: 10
44559992 TAAATTTTTT
*
44560002 TTCTT-TTTT
1 TTCTTCTTTC
44560011 TTCTTCTTTC
1 TTCTTCTTTC
*
44560021 TTCTTCTCTC
1 TTCTTCTTTC
44560031 TTTCTT-TCTTC
1 -TTCTTCT-TTC
44560042 TTCTTCTTTC
1 TTCTTCTTTC
44560052 TTCTTC-TTC
1 TTCTTCTTTC
44560061 TTCTTC
1 TTCTTC
44560067 AAAACCGAGC
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
9 14 0.29
10 27 0.55
11 8 0.16
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (10 bp):
TTCTTCTTTC
Found at i:44560027 original size:13 final size:13
Alignment explanation
Indices: 44560002--44560066 Score: 73
Period size: 13 Copynumber: 5.0 Consensus size: 13
44559992 TAAATTTTTT
*
44560002 TTCTT-TTTTTTC
1 TTCTTCTTTCTTC
44560014 TTCTT-TCTTCTTC
1 TTCTTCT-TTCTTC
44560027 TCTCTTTCTTTCTTC
1 T-TC-TTCTTTCTTC
44560042 TTCTTCTTTCTTC
1 TTCTTCTTTCTTC
44560055 TTCTTC-TTCTTC
1 TTCTTCTTTCTTC
44560067 AAAACCGAGC
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
12 12 0.25
13 22 0.46
14 4 0.08
15 9 0.19
16 1 0.02
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TTCTTCTTTCTTC
Found at i:44560463 original size:29 final size:29
Alignment explanation
Indices: 44560430--44560546 Score: 103
Period size: 30 Copynumber: 3.9 Consensus size: 29
44560420 TGTAATTTTT
*
44560430 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* *
44560459 TGAAAGTTTAGGGGTCT-AAATGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
44560489 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
44560518 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
44560547 TTATTTTTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
29 14 0.19
30 58 0.78
31 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:44560482 original size:30 final size:30
Alignment explanation
Indices: 44560445--44560546 Score: 143
Period size: 30 Copynumber: 3.4 Consensus size: 30
44560435 ATTTAGGATT
*
44560445 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
44560475 TAAATGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
44560505 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
44560535 AAAATGCAATTT
1 AAAATGAAATTT
44560547 TTATTTTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
29 2 0.03
30 62 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:44560525 original size:60 final size:59
Alignment explanation
Indices: 44560411--44560546 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 59
44560401 CAAAACTTCT
* ** * *
44560411 GGGG-CTAAATGTAATTTTTAGAAAATTTAGGATTAAAATGAAATTTAATGAAAGTTTA
1 GGGGTCTAAATGAAATTTAAAGAAAATTTAGGATCAAAATGAAATTTAAGGAAAGTTTA
* *
44560469 GGGGTCTAAATGAAATTTAAAGAAAGTTTAAGGGTCAAAATGAAATTT-AGGAAAAGTTTA
1 GGGGTCTAAATGAAATTTAAAGAAAATTT-AGGATCAAAATGAAATTTAAGG-AAAGTTTA
* *
44560529 GGGGTCAAAATGCAATTT
1 GGGGTCTAAATGAAATTT
44560547 TTATTTTTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 4 0.06
59 22 0.33
60 40 0.61
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.32
Consensus pattern (59 bp):
GGGGTCTAAATGAAATTTAAAGAAAATTTAGGATCAAAATGAAATTTAAGGAAAGTTTA
Found at i:44560994 original size:54 final size:55
Alignment explanation
Indices: 44560817--44561034 Score: 324
Period size: 54 Copynumber: 4.1 Consensus size: 55
44560807 CACGTGAGCC
* * *
44560817 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTG-AA
*
44560872 AAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAATAGAAATTGAA
*
44560923 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
44560977 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
44561032 AAG
1 AAG
44561035 TAGAAATTGA
Statistics
Matches: 149, Mismatches: 7, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
50 14 0.09
51 33 0.22
52 1 0.01
54 53 0.36
55 36 0.24
56 6 0.04
57 6 0.04
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
Found at i:44561032 original size:14 final size:14
Alignment explanation
Indices: 44561013--44561047 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
44561003 GAGTTGATTT
44561013 TTGAAAAATAGAAA
1 TTGAAAAATAGAAA
*
44561027 TTGAAAAGTAGAAA
1 TTGAAAAATAGAAA
44561041 TTGAAAA
1 TTGAAAA
44561048 TACCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:44561142 original size:15 final size:15
Alignment explanation
Indices: 44561122--44561150 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
44561112 TTTTGGAAAC
44561122 ACAGAAATTAAAAAA
1 ACAGAAATTAAAAAA
44561137 ACAGAAATTAAAAA
1 ACAGAAATTAAAAA
44561151 CAGAATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (15 bp):
ACAGAAATTAAAAAA
Found at i:44561151 original size:13 final size:14
Alignment explanation
Indices: 44561122--44561155 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
44561112 TTTTGGAAAC
44561122 ACAGAAATTAAAAAA
1 ACAGAAATT-AAAAA
44561137 ACAGAAATT-AAAA
1 ACAGAAATTAAAAA
44561150 ACAGAA
1 ACAGAA
44561156 TTTGAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
15 9 0.47
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.12
Consensus pattern (14 bp):
ACAGAAATTAAAAA
Found at i:44561693 original size:193 final size:192
Alignment explanation
Indices: 44561358--44562162 Score: 1490
Period size: 193 Copynumber: 4.2 Consensus size: 192
44561348 CATGTGAGCC
* * *
44561358 GAGGCTCCACTCATCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
44561423 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
*
44561488 AACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAAAAATTTAAAAATACCTCAACGTGTCTT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTTTT-AAAATTTAAAAATACCTCAACGTGTCTT
44561552 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
44561617 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
**
44561682 ACTCGTTTCTCGCAATATGAGTTGATTTTTTTTTAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAATTTAAAAATACCTCAACGTGTCTT
44561744 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
44561809 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTG-CCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
44561873 ACTCACTTCTCGCAATATGAGTTGA--TTTTTTTAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAATTTAAAAATACCTCAACGTGTCTT
44561933 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
44561998 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
*
44562063 ACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTT-TAAAATTTAAAAATACCTCAACGTGTCTT
*
44562126 GAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
44562163 CCTTGGAAAG
Statistics
Matches: 599, Mismatches: 8, Indels: 9
0.97 0.01 0.01
Matches are distributed among these distances:
189 153 0.26
190 36 0.06
191 34 0.06
192 152 0.25
193 194 0.32
194 30 0.05
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (192 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAATTTAAAAATACCTCAACGTGTCTT
Done.