Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 131 of 204
Found at i:40392801 original size:17 final size:18
Alignment explanation
Indices: 40392763--40392802 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
40392753 TTTTAAATTT
*
40392763 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
40392781 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
40392797 TATTAA
1 TATTAA
40392803 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:40392916 original size:15 final size:15
Alignment explanation
Indices: 40392881--40392932 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40392871 TTAAGAATTT
*
40392881 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40392895 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40392909 TATTTAATAATAAT-
1 TATTTAATTATAATA
40392923 TATGTTAATT
1 TAT-TTAATT
40392933 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40392923 original size:119 final size:118
Alignment explanation
Indices: 40392749--40393046 Score: 455
Period size: 118 Copynumber: 2.5 Consensus size: 118
40392739 ATTAGTTATA
* *
40392749 ATAATTTT-A-AATTTTATTAAATCATATA-TTTAATTA-AATCATATTTAATATTAATTAT-TT
1 ATAATTTTAAGAATTTTATTAAATTATATATTTTAATTATAAT-ATATTTAATAATAATTATGTT
* *
40392809 GAAATTT-TCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAAT
65 --AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAAT
* *
40392864 TTATTTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 ATAATT-TTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
*
40392929 AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAAT
65 AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAAT
40392983 ATAATTTTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 ATAATTTTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
40393047 TAAATATGAT
Statistics
Matches: 167, Mismatches: 9, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
115 4 0.02
116 2 0.01
117 1 0.01
118 81 0.49
119 74 0.44
120 5 0.03
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (118 bp):
ATAATTTTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTA
ATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAAT
Found at i:40392953 original size:59 final size:56
Alignment explanation
Indices: 40392871--40393046 Score: 149
Period size: 59 Copynumber: 3.0 Consensus size: 56
40392861 AATTTATTTA
* *
40392871 TTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG
1 TTAAGAATTTTATCAAATCATATATTTTAATTATAATATATTTAATAATAATTATG
* * * * * * * * *
40392927 TTAATTTATATTTTA-CAGTATCATATATTATGATT-TGAGTAAATTCATATAAGAATATAATT
1 TTAA--GA-ATTTTATCA-AATCATATATTTTAATTAT-AATATATTTA-ATAATAAT-T-ATG
* *
40392989 TTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG
1 TTAAGAATTTTATCAAATCATATATTTTAATTATAATATATTTAATAATAATTATG
40393045 TT
1 TT
40393047 TAAATATGAT
Statistics
Matches: 88, Mismatches: 22, Indels: 20
0.68 0.17 0.15
Matches are distributed among these distances:
56 8 0.09
57 1 0.01
58 10 0.11
59 52 0.59
60 10 0.11
61 1 0.01
62 6 0.07
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (56 bp):
TTAAGAATTTTATCAAATCATATATTTTAATTATAATATATTTAATAATAATTATG
Found at i:40393029 original size:16 final size:16
Alignment explanation
Indices: 40393008--40393049 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40392998 TTATTAAATT
*
40393008 ATATATTTTAATTATA
1 ATATATTTTAATAATA
40393024 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
40393039 AT-TATGTTTAA
1 ATATAT-TTTAA
40393050 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:40393034 original size:15 final size:15
Alignment explanation
Indices: 40392999--40393040 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40392989 TTAAGAATTT
*
40392999 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40393013 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40393027 TATTTAATAATAAT
1 TATTTAATTATAAT
40393041 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40393171 original size:154 final size:155
Alignment explanation
Indices: 40392984--40393296 Score: 567
Period size: 154 Copynumber: 2.0 Consensus size: 155
40392974 TATAAGAATA
*
40392984 TAATTTTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTA
1 TAATTTTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
40393049 AATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAACAATAACAATA
66 AATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATA
40393112 ATAATTTACCAAAACAAATTTATGC
131 ATAATTTACCAAAACAAATTTATGC
40393137 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATT-TTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
40393202 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
65 AAATATGATTAAATTATTTATTATTGATAAT-ATAATCTTATTAAAATTTAAATAACAATAACAA
* *
40393267 TAATCATTTACCAAAACAAATTTCTGC
129 TAATAATTTACCAAAACAAATTTATGC
40393294 TAA
1 TAA
40393297 GGGTATTCTA
Statistics
Matches: 153, Mismatches: 3, Indels: 4
0.96 0.02 0.03
Matches are distributed among these distances:
153 5 0.03
154 86 0.56
155 2 0.01
157 60 0.39
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (155 bp):
TAATTTTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATA
ATAATTTACCAAAACAAATTTATGC
Found at i:40393177 original size:18 final size:17
Alignment explanation
Indices: 40393149--40393183 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40393139 ATTATTAAGA
*
40393149 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40393166 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40393184 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40393437 original size:16 final size:16
Alignment explanation
Indices: 40393416--40393454 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40393406 TTGATTTGCT
*
40393416 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
40393432 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
40393448 ATTACAC
1 ATTACAC
40393455 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:40393455 original size:16 final size:16
Alignment explanation
Indices: 40393429--40393485 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
40393419 ACACAGCTTT
* *
40393429 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
40393445 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
40393461 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
40393477 TCCAATACA
1 TCCAATACA
40393486 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:40395032 original size:16 final size:17
Alignment explanation
Indices: 40394999--40395036 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
40394989 AGTCTGTAAG
40394999 GTAAGGGAAAAAACAAT
1 GTAAGGGAAAAAACAAT
*
40395016 GTAAGGGAAAATA-AAT
1 GTAAGGGAAAAAACAAT
40395032 GTAAG
1 GTAAG
40395037 CAATGAATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.55, C:0.03, G:0.26, T:0.16
Consensus pattern (17 bp):
GTAAGGGAAAAAACAAT
Found at i:40396939 original size:6 final size:6
Alignment explanation
Indices: 40396928--40396954 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40396918 GAATTTAGCC
40396928 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
40396955 AATTAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:40408109 original size:13 final size:13
Alignment explanation
Indices: 40408075--40408120 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
40408065 AAGATGAAAG
40408075 CTTGATG-AAAAA
1 CTTGATGAAAAAA
40408087 CTTGATGAAAAACA
1 CTTGATGAAAAA-A
*
40408101 CTTGA-GAAAAGA
1 CTTGATGAAAAAA
40408113 CTTGATGA
1 CTTGATGA
40408121 TTAAATGAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 13 0.43
13 11 0.37
14 6 0.20
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.24
Consensus pattern (13 bp):
CTTGATGAAAAAA
Found at i:40423715 original size:20 final size:20
Alignment explanation
Indices: 40423690--40423810 Score: 143
Period size: 20 Copynumber: 6.0 Consensus size: 20
40423680 TTGTACAGGA
*
40423690 TTGCACTTTGGTGCCTCTGT
1 TTGCACTTCGGTGCCTCTGT
* *
40423710 TTGCACTTTGGTGCCTCTGA
1 TTGCACTTCGGTGCCTCTGT
*
40423730 TTGCACTTCAGTGCCTCTGT
1 TTGCACTTCGGTGCCTCTGT
* * *
40423750 GTGTACTTTGGTGCCTCTGT
1 TTGCACTTCGGTGCCTCTGT
* * *
40423770 TTGTACTTCGGTGGCTCAGT
1 TTGCACTTCGGTGCCTCTGT
*
40423790 TTGCACTACGGTGCCTCTGT
1 TTGCACTTCGGTGCCTCTGT
40423810 T
1 T
40423811 ACGCATTTTT
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.08, C:0.25, G:0.26, T:0.41
Consensus pattern (20 bp):
TTGCACTTCGGTGCCTCTGT
Found at i:40423794 original size:60 final size:60
Alignment explanation
Indices: 40423694--40423809 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 60
40423684 ACAGGATTGC
* * *
40423694 ACTTTGGTGCCTCTGTTTGCACTTTGGTGCCTCTGATTGCACTTCAGTGCCTCTGTGTGT
1 ACTTTGGTGCCTCTGTTTGCACTTCGGTGCCTCAGATTGCACTACAGTGCCTCTGTGTGT
* * * *
40423754 ACTTTGGTGCCTCTGTTTGTACTTCGGTGGCTCAGTTTGCACTACGGTGCCTCTGT
1 ACTTTGGTGCCTCTGTTTGCACTTCGGTGCCTCAGATTGCACTACAGTGCCTCTGT
40423810 TACGCATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.09, C:0.25, G:0.26, T:0.41
Consensus pattern (60 bp):
ACTTTGGTGCCTCTGTTTGCACTTCGGTGCCTCAGATTGCACTACAGTGCCTCTGTGTGT
Found at i:40425820 original size:193 final size:193
Alignment explanation
Indices: 40425491--40425877 Score: 747
Period size: 193 Copynumber: 2.0 Consensus size: 193
40425481 TTAACTATAT
40425491 TCAACTCATCCCCATGATCTTCAGTTACAAGCTCTAATTGAATCTCACCATAATTCTCATCATGG
1 TCAACTCATCCCCATGATCTTCAGTTACAAGCTCTAATTGAATCTCACCATAATTCTCATCATGG
* *
40425556 TCATCAATAATACAAAGGTCTGCATGATTCGAGTTGTGAGCATCAAACATGTCCTCTTTCCTGGG
66 TCATCAATAATACAAAGGTCTGCATGATTCGAGTTGTAAGAATCAAACATGTCCTCTTTCCTGGG
40425621 AGGTAGCGCTTCAGATATTTCTTGCATCATTTTAATTATTTGCTCTGTCATATTTGACATGTG
131 AGGTAGCGCTTCAGATATTTCTTGCATCATTTTAATTATTTGCTCTGTCATATTTGACATGTG
*
40425684 TCAACTCATCCCCATGATCTTCAGTTATAAGCTCTAATTGAATCTCACCATAATTCTCATCATGG
1 TCAACTCATCCCCATGATCTTCAGTTACAAGCTCTAATTGAATCTCACCATAATTCTCATCATGG
40425749 TCATCAATAATACAAAGGTCTGCATGATTCGAGTTGTAAGAATCAAACATGTCCTCTTTCCTGGG
66 TCATCAATAATACAAAGGTCTGCATGATTCGAGTTGTAAGAATCAAACATGTCCTCTTTCCTGGG
40425814 AGGTAGCGCTTCAGATATTTCTTGCATCATTTTAATTATTTGCTCTGTCATATTTGACATGTG
131 AGGTAGCGCTTCAGATATTTCTTGCATCATTTTAATTATTTGCTCTGTCATATTTGACATGTG
40425877 T
1 T
40425878 GACAATACTT
Statistics
Matches: 191, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
193 191 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (193 bp):
TCAACTCATCCCCATGATCTTCAGTTACAAGCTCTAATTGAATCTCACCATAATTCTCATCATGG
TCATCAATAATACAAAGGTCTGCATGATTCGAGTTGTAAGAATCAAACATGTCCTCTTTCCTGGG
AGGTAGCGCTTCAGATATTTCTTGCATCATTTTAATTATTTGCTCTGTCATATTTGACATGTG
Found at i:40431264 original size:32 final size:32
Alignment explanation
Indices: 40431161--40431264 Score: 129
Period size: 32 Copynumber: 3.3 Consensus size: 32
40431151 GAATGGCTAC
* *
40431161 AAGCCATAAGT-ATAGTAATATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
40431192 AAGCCATTAGTAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * *
40431224 CAGCCATCAGTAATGGTAATATGACCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
40431256 AAGTCATCA
1 AAGCCATCA
40431265 ATAGCATCGC
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
31 10 0.16
32 52 0.84
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATCGGCACA
Found at i:40431519 original size:24 final size:24
Alignment explanation
Indices: 40431425--40431570 Score: 193
Period size: 24 Copynumber: 6.1 Consensus size: 24
40431415 CTAGTCATAC
*
40431425 AAATCACAGACAAATCAGTCATAT
1 AAATCACAGACAAATCAGTCATTT
* *
40431449 CAATTACAGACAAATCAGTCATTT
1 AAATCACAGACAAATCAGTCATTT
40431473 AAATCACAGACAAATCAGTCATTT
1 AAATCACAGACAAATCAGTCATTT
40431497 AAATCACAGACAAATCAGTCATTT
1 AAATCACAGACAAATCAGTCATTT
* * * * *
40431521 ACATCTCAAAAAAATCAATCATTT
1 AAATCACAGACAAATCAGTCATTT
* * *
40431545 ACATCACGGACAAATCAATCATTT
1 AAATCACAGACAAATCAGTCATTT
40431569 AA
1 AA
40431571 CCCCGAGGGG
Statistics
Matches: 107, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 107 1.00
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.25
Consensus pattern (24 bp):
AAATCACAGACAAATCAGTCATTT
Found at i:40433777 original size:17 final size:17
Alignment explanation
Indices: 40433755--40433787 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40433745 TGGCTCGTTT
*
40433755 ATTTAGGTTTCATAAAA
1 ATTTAGGTTACATAAAA
40433772 ATTTAGGTTACATAAA
1 ATTTAGGTTACATAAA
40433788 TTCCTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (17 bp):
ATTTAGGTTACATAAAA
Found at i:40434839 original size:17 final size:17
Alignment explanation
Indices: 40434813--40434845 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40434803 TTAAATTTAC
*
40434813 TAAATTAATTTCTCAAT
1 TAAATCAATTTCTCAAT
40434830 TAAATCAATTTCTCAA
1 TAAATCAATTTCTCAA
40434846 CCCAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATCAATTTCTCAAT
Found at i:40435863 original size:13 final size:14
Alignment explanation
Indices: 40435844--40435881 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
40435834 CAATGACATA
40435844 GAAATAATATAAAC
1 GAAATAATATAAAC
40435858 -AAATAA-ATAAAC
1 GAAATAATATAAAC
40435870 GAAATTAATATA
1 GAAA-TAATATA
40435882 CAAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:40435988 original size:16 final size:17
Alignment explanation
Indices: 40435969--40436002 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40435959 ACAAATGATG
40435969 AAAATAAAAAATA-AAA
1 AAAATAAAAAATACAAA
*
40435985 AAAATACAAAATACAAA
1 AAAATAAAAAATACAAA
40436002 A
1 A
40436003 TATATACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAATAAAAAATACAAA
Found at i:40436346 original size:30 final size:31
Alignment explanation
Indices: 40436273--40436355 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
40436263 ACATATATAA
* ** *
40436273 AAATAATAATTATCTACATATATATAGATTAT
1 AAATAATAATAAT-TACATATATATAGAAAAC
40436305 AAA-AA-AGATAATTACATATATATA-AAAAC
1 AAATAATA-ATAATTACATATATATAGAAAAC
40436334 AAATAATAATAATTACATATAT
1 AAATAATAATAATTACATATAT
40436356 TGAAATTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 5 0.11
30 29 0.66
31 7 0.16
32 3 0.07
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (31 bp):
AAATAATAATAATTACATATATATAGAAAAC
Found at i:40436514 original size:17 final size:17
Alignment explanation
Indices: 40436492--40436535 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
40436482 TAGGAAATAA
40436492 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
40436509 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
40436526 -ATATGTATAT
1 AAAATGTATAT
40436536 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:40437014 original size:22 final size:21
Alignment explanation
Indices: 40436979--40437055 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 21
40436969 AAAGGGTATC
* *
40436979 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
40437000 TACTAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
40437023 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
40437042 TGCATATCATATCT
1 TACAAATCATATCT
40437056 AAGATTGCAC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 19 0.40
21 4 0.08
22 15 0.31
23 10 0.21
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:40437022 original size:23 final size:22
Alignment explanation
Indices: 40436979--40437036 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
40436969 AAAGGGTATC
* *
40436979 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40437000 TACTAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
40437023 TGCATATCATATCT
1 TACAAATCATATCT
40437037 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40437039 original size:19 final size:19
Alignment explanation
Indices: 40437015--40437064 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
40437005 AATCATATCT
40437015 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40437034 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40437053 TCTAAGATTGCA
1 TCTAAGATTGCA
40437065 CATCCTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:40441564 original size:23 final size:23
Alignment explanation
Indices: 40441529--40441578 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
40441519 ATTATAATAA
40441529 TTTATTTATAT-AATTAATATATT
1 TTTATTTATATAAATT-ATATATT
*
40441552 TTTATTT-TAATAAATTATTTATT
1 TTTATTTAT-ATAAATTATATATT
40441575 TTTA
1 TTTA
40441579 CAATTTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 1 0.04
23 19 0.79
24 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTATTTATATAAATTATATATT
Found at i:40441574 original size:17 final size:17
Alignment explanation
Indices: 40441523--40441576 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
40441513 CAAAAAATTA
*
40441523 TAATAATTTATTTATATAAT
1 TAATAAATTATTTAT-T--T
*
40441543 TAATATATT-TTTATTT
1 TAATAAATTATTTATTT
40441559 TAATAAATTATTTATTT
1 TAATAAATTATTTATTT
40441576 T
1 T
40441577 TACAATTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 9 0.30
17 8 0.27
18 1 0.03
19 5 0.17
20 7 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATAAATTATTTATTT
Found at i:40443367 original size:29 final size:28
Alignment explanation
Indices: 40443325--40443380 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
40443315 AAACATTCAA
* *
40443325 AAATGATTATGGTTTTCTCTGAAATGGAG
1 AAATGAATATGGTTTTCTC-AAAATGGAG
*
40443354 AAATGAATGTGGTTTTCTCAAAATGGA
1 AAATGAATATGGTTTTCTCAAAATGGA
40443381 AGTAAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (28 bp):
AAATGAATATGGTTTTCTCAAAATGGAG
Found at i:40449751 original size:13 final size:13
Alignment explanation
Indices: 40449733--40449763 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
40449723 ACAAAATAAT
40449733 TAATTTTTCATCA
1 TAATTTTTCATCA
40449746 TAA-TTTTCATCA
1 TAATTTTTCATCA
40449758 TAATTT
1 TAATTT
40449764 ACCTTTGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATTTTTCATCA
Found at i:40450395 original size:8 final size:8
Alignment explanation
Indices: 40450382--40450408 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
40450372 GGCTCTTTAA
40450382 AAAATTTT
1 AAAATTTT
40450390 AAAATTTT
1 AAAATTTT
40450398 AAAATTTT
1 AAAATTTT
40450406 AAA
1 AAA
40450409 TTATTAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAAATTTT
Found at i:40451487 original size:20 final size:20
Alignment explanation
Indices: 40451462--40451505 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
40451452 TTATTAATTT
40451462 TTTAGATGTCAAACTGTAAC
1 TTTAGATGTCAAACTGTAAC
40451482 TTTAGATGTCAAACTGTAAC
1 TTTAGATGTCAAACTGTAAC
40451502 TTTA
1 TTTA
40451506 TCACGTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (20 bp):
TTTAGATGTCAAACTGTAAC
Found at i:40458679 original size:24 final size:24
Alignment explanation
Indices: 40458630--40458680 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
40458620 ATTTGTTATT
**
40458630 TATTAGAATAAGGTGTTTCACTCC
1 TATTAGAATAAGGTGTTTCAAGCC
*
40458654 TATTAGAATATGGT-TTTACAAGCC
1 TATTAGAATAAGGTGTTT-CAAGCC
40458678 TAT
1 TAT
40458681 AAATAGACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (24 bp):
TATTAGAATAAGGTGTTTCAAGCC
Found at i:40462426 original size:18 final size:18
Alignment explanation
Indices: 40462399--40462434 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
40462389 AAACTTATCT
*
40462399 TGATCTTGATGGACATCC
1 TGATCCTGATGGACATCC
40462417 TGATCCTGATGGACATCC
1 TGATCCTGATGGACATCC
40462435 ACTTAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (18 bp):
TGATCCTGATGGACATCC
Found at i:40469290 original size:28 final size:28
Alignment explanation
Indices: 40469217--40469291 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 28
40469207 GAAATAAATG
* * *
40469217 GTCCTTGGTAGACATGCCACATAAGGTA
1 GTCCTTGGTGGACATTCCACATAAGGAA
* * * *
40469245 GCCCTTAGTGAACATTCCACATACGGAA
1 GTCCTTGGTGGACATTCCACATAAGGAA
*
40469273 GTCCTTGGTGGACTTTCCA
1 GTCCTTGGTGGACATTCCA
40469292 TTTTTGGTAA
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (28 bp):
GTCCTTGGTGGACATTCCACATAAGGAA
Found at i:40474065 original size:66 final size:66
Alignment explanation
Indices: 40473902--40474066 Score: 206
Period size: 66 Copynumber: 2.5 Consensus size: 66
40473892 GGTTACACGG
* * * * *
40473902 CCAAGCGACACGT-CCGTGTGCTAGGCCGTATGAAAAATGATGAGCATACTGACTTGTGACATAT
1 CCAAGCCACAC-TCCCGTGTGCTAGGCCGTGTGAAAAATGATGAGCATACTAACTTGTGACACAC
**
40473966 GT
65 AA
* * * * *
40473968 CCAAGCCACACGCCCGTGTGCTAGGCTGTGTGAAAAATGGTGAGTATACTAACTTGTGTCACACA
1 CCAAGCCACACTCCCGTGTGCTAGGCCGTGTGAAAAATGATGAGCATACTAACTTGTGACACACA
40474033 A
66 A
40474034 CCAAGCCACACTCCCGTGTGCTAGGCCGTGTGA
1 CCAAGCCACACTCCCGTGTGCTAGGCCGTGTGA
40474067 GCTTACTGAC
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
66 84 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (66 bp):
CCAAGCCACACTCCCGTGTGCTAGGCCGTGTGAAAAATGATGAGCATACTAACTTGTGACACACA
A
Found at i:40476788 original size:17 final size:17
Alignment explanation
Indices: 40476766--40476836 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
40476756 ACACAACCTG
40476766 GACACACAGTCGTGTGT
1 GACACACAGTCGTGTGT
*
40476783 GACACACAG-CCTG-G-
1 GACACACAGTCGTGTGT
*
40476797 G-CACACAGTCATGTGT
1 GACACACAGTCGTGTGT
* *
40476813 GA-AAACTAGTTGTGTGT
1 GACACAC-AGTCGTGTGT
40476830 GACACAC
1 GACACAC
40476837 GGGTATGTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
13 7 0.17
14 4 0.10
15 2 0.05
16 7 0.17
17 19 0.45
18 3 0.07
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (17 bp):
GACACACAGTCGTGTGT
Found at i:40476790 original size:30 final size:30
Alignment explanation
Indices: 40476756--40476814 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
40476746 ATAGAGAGTT
*
40476756 ACACAACCTGGACACACAGTCGTGTGTGAC
1 ACACAACCTGGACACACAGTCATGTGTGAC
* *
40476786 ACACAGCCTGGGCACACAGTCATGTGTGA
1 ACACAACCTGGACACACAGTCATGTGTGA
40476815 AAACTAGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.17
Consensus pattern (30 bp):
ACACAACCTGGACACACAGTCATGTGTGAC
Found at i:40477174 original size:6 final size:5
Alignment explanation
Indices: 40477163--40477197 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
40477153 TTTAGTTTTA
40477163 TATTT TATTTT TATTT TATTT TATTT TATTT TATT
1 TATTT TA-TTT TATTT TATTT TATTT TATTT TATT
40477198 ATGCGTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:40477179 original size:11 final size:11
Alignment explanation
Indices: 40477153--40477194 Score: 59
Period size: 10 Copynumber: 3.7 Consensus size: 11
40477143 TGTGATTTCA
40477153 TTTAGTTTTATAT
1 TTTA-TTTT-TAT
40477166 TTTATTTTTAT
1 TTTATTTTTAT
40477177 TTTA-TTTTAT
1 TTTATTTTTAT
40477187 TTTATTTT
1 TTTATTTT
40477195 ATTATGCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.36
11 10 0.36
12 4 0.14
13 4 0.14
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:40478466 original size:9 final size:9
Alignment explanation
Indices: 40478452--40478478 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
40478442 ACCATAAACA
40478452 CTTTGAGTG
1 CTTTGAGTG
40478461 CTTTGAGTG
1 CTTTGAGTG
40478470 CTTTGAGTG
1 CTTTGAGTG
40478479 AATCTTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.44
Consensus pattern (9 bp):
CTTTGAGTG
Found at i:40480304 original size:16 final size:16
Alignment explanation
Indices: 40480276--40480308 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40480266 CAAATTAAAT
40480276 ATAATAAATTAATTTA
1 ATAATAAATTAATTTA
40480292 ATAATGAAA-TAATTTA
1 ATAAT-AAATTAATTTA
40480308 A
1 A
40480309 ATTTTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
ATAATAAATTAATTTA
Found at i:40481535 original size:39 final size:42
Alignment explanation
Indices: 40481462--40481539 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
40481452 TGTTTAAAAA
*
40481462 TATTAATTAAAAATAAAATAAAAAATTTAAAAACAACATGTT
1 TATTAATTAAAAATAAAATAAAAAATCTAAAAACAACATGTT
* *
40481504 TATTAATTAAAAA-GAAA-AAAAAA-CTACAAACAACAT
1 TATTAATTAAAAATAAAATAAAAAATCTAAAAACAACAT
40481540 TAGAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 11 0.33
40 6 0.18
41 3 0.09
42 13 0.39
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.26
Consensus pattern (42 bp):
TATTAATTAAAAATAAAATAAAAAATCTAAAAACAACATGTT
Found at i:40482064 original size:19 final size:19
Alignment explanation
Indices: 40482042--40482099 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
40482032 AATGCAAAAA
40482042 AAATTATTTTATGATTTTT
1 AAATTATTTTATGATTTTT
*
40482061 AAATAATTATTATGATTTTT
1 AAATTATT-TTATGATTTTT
* *
40482081 AATTTTTTTTATGATTTTT
1 AAATTATTTTATGATTTTT
40482100 CAACATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
AAATTATTTTATGATTTTT
Found at i:40482075 original size:20 final size:20
Alignment explanation
Indices: 40482050--40482112 Score: 74
Period size: 19 Copynumber: 3.1 Consensus size: 20
40482040 AAAAATTATT
40482050 TTATGATTTTTAAATAATTA
1 TTATGATTTTTAAATAATTA
** *
40482070 TTATGATTTTT-AATTTTTT
1 TTATGATTTTTAAATAATTA
40482089 TTATGATTTTTCAACATAATTA
1 TTATGATTTTT-AA-ATAATTA
40482111 TT
1 TT
40482113 TATATAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 16 0.47
20 11 0.32
21 1 0.03
22 6 0.18
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (20 bp):
TTATGATTTTTAAATAATTA
Found at i:40482322 original size:33 final size:32
Alignment explanation
Indices: 40482259--40482342 Score: 132
Period size: 33 Copynumber: 2.6 Consensus size: 32
40482249 TTGGTTCGCT
* *
40482259 GTATTAGATTAGAGGCGTATTGGATTAGAGGC
1 GTATTGGATTAGAGGTGTATTGGATTAGAGGC
*
40482291 GTATTGGATTAGAGGTGTATTGGGATTAGAGGT
1 GTATTGGATTAGAGGTGTATT-GGATTAGAGGC
40482324 GTATTGGATTAGAGGTGTA
1 GTATTGGATTAGAGGTGTA
40482343 ATAGCTAATC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 19 0.40
33 29 0.60
ACGTcount: A:0.26, C:0.02, G:0.37, T:0.35
Consensus pattern (32 bp):
GTATTGGATTAGAGGTGTATTGGATTAGAGGC
Found at i:40482339 original size:16 final size:16
Alignment explanation
Indices: 40482258--40482342 Score: 134
Period size: 16 Copynumber: 5.2 Consensus size: 16
40482248 TTTGGTTCGC
*
40482258 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
*
40482274 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
40482290 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40482306 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
40482323 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40482339 TGTA
1 TGTA
40482343 ATAGCTAATC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
16 49 0.75
17 16 0.25
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40482407 original size:44 final size:45
Alignment explanation
Indices: 40482323--40482413 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
40482313 GGATTAGAGG
* * *
40482323 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
40482368 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
40482412 TG
1 TG
40482414 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:40482599 original size:18 final size:17
Alignment explanation
Indices: 40482578--40482612 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40482568 TTATTATTAA
*
40482578 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40482596 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40482613 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40482731 original size:17 final size:17
Alignment explanation
Indices: 40482698--40482731 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40482688 TTATTATTAA
* *
40482698 ATATATTTTAATTAAAT
1 ATATAATTTAATAAAAT
40482715 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40482732 TCTTAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40482773 original size:119 final size:119
Alignment explanation
Indices: 40482561--40482964 Score: 679
Period size: 119 Copynumber: 3.4 Consensus size: 119
40482551 ATCATATTTA
40482561 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
40482626 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGT-AAATATAAATT
40482681 AACATAATTATTATTAAATATATTTTAATT-AAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
40482745 TATTCTTATATTAATTTACAGAAATCATAATATATGATACTGTAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAATATAAATT
*
40482799 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* * *
40482864 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGA-AAATTT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAT-ATAAA-TT
* * *
40482919 GAA-ATAATTAATATTAAATATATTTTAATTATAATATATGATTTAA
1 -AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAA
40482965 AATAATTTAA
Statistics
Matches: 271, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
118 41 0.15
119 155 0.57
120 73 0.27
121 2 0.01
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (119 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAATATAAATT
Found at i:40483082 original size:91 final size:91
Alignment explanation
Indices: 40482987--40483194 Score: 233
Period size: 91 Copynumber: 2.3 Consensus size: 91
40482977 TAATTATAAC
* * * *
40482987 TAATAAATTATATTTTATGAATTTGTATAATCTAAAATAA-TAATTATTACATATAATTT-ATAA
1 TAATAAATTATATTATATGAATTTATACAATCTAAAATAATTAA-TATTAAATATAATTTAAT-A
* **
40483050 TTAATAT-TAAATTTCATAAAATACTTGA
64 GTAATATAT-AATTTCATAAAATACTCAA
* * *
40483078 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAATTATATTATATGAATTTATACAATCTAAAATAATTAATATTAAATATAATTTAATAGT
* *
40483143 GATATATAATTTCATAAAATTCTCAA
66 AATATATAATTTCATAAAATACTCAA
* *
40483169 TAATAAATTGTTCTTATATGAATTTA
1 TAATAAATT-ATATTATATGAATTTA
40483195 CTAAAATCAA
Statistics
Matches: 101, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
91 79 0.78
92 22 0.22
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATCTAAAATAATTAATATTAAATATAATTTAATAGT
AATATATAATTTCATAAAATACTCAA
Found at i:40489692 original size:40 final size:40
Alignment explanation
Indices: 40489633--40489864 Score: 290
Period size: 40 Copynumber: 5.8 Consensus size: 40
40489623 GAGAATTGAG
*
40489633 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
* **
40489673 AGTTATATATCCGGACTAAGTTTCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
* * *
40489713 AGTGATATATCCAGG-TTAAATCCCGAAGCGCATTCGTGCT
1 AGTGATATATCC-GGACTAAGTCCCGAAGAGCATTCGTGCT
* *
40489753 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
**
40489793 AGTGATATATCCGTG-CTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCG-GACTAAGTCCCGAAGAGCATTCGTGCT
* * *
40489833 GGTGTTATATCCGGGA-TAGGTCCCGAAGAGCA
1 AGTGATATATCC-GGACTAAGTCCCGAAGAGCA
40489865 ATCATGCTGG
Statistics
Matches: 163, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.01
40 157 0.96
41 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (40 bp):
AGTGATATATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
Found at i:40489766 original size:80 final size:79
Alignment explanation
Indices: 40489633--40489864 Score: 322
Period size: 80 Copynumber: 2.9 Consensus size: 79
40489623 GAGAATTGAG
* * *
40489633 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTTATATATCCGGACTAAGTTTCG
1 AGTGATATATCC-GGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATCCGGACTAAGTTCCG
40489698 AAGAGCATTCGTGCT
65 AAGAGCATTCGTGCT
* * *
40489713 AGTGATATATCCAGGTTAAATCCCGAAGCGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCG
1 AGTGATATATCC-GGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATCCGGACTAAGTTCCG
40489778 AAGAGCATTCGTGCT
65 AAGAGCATTCGTGCT
* * * * *
40489793 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGA-TAGGTCCC
1 AGTGATATATCCG-GCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATCC-GGACTAAGTTCC
40489857 GAAGAGCA
64 GAAGAGCA
40489865 ATCATGCTGG
Statistics
Matches: 135, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
79 1 0.01
80 131 0.97
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (79 bp):
AGTGATATATCCGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATCCGGACTAAGTTCCGA
AGAGCATTCGTGCT
Found at i:40490081 original size:25 final size:25
Alignment explanation
Indices: 40490040--40490091 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
40490030 TGTGTAATAA
40490040 TGAATGAATAAGAGCACTATGTGTG
1 TGAATGAATAAGAGCACTATGTGTG
* *
40490065 TGAATG-ATTAGAGGCACTGTGTGTG
1 TGAATGAATAAGA-GCACTATGTGTG
40490090 TG
1 TG
40490092 CGAATTCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.31
Consensus pattern (25 bp):
TGAATGAATAAGAGCACTATGTGTG
Found at i:40493818 original size:47 final size:47
Alignment explanation
Indices: 40493708--40494164 Score: 774
Period size: 47 Copynumber: 9.7 Consensus size: 47
40493698 TTAGGATTCT
* * *
40493708 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGG-CG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
*
40493754 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40493801 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40493848 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
40493895 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40493942 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40493989 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40494036 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
40494083 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
40494130 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
40494165 TCCCGAAGGG
Statistics
Matches: 392, Mismatches: 17, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
45 1 0.00
46 38 0.10
47 353 0.90
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:40494339 original size:37 final size:37
Alignment explanation
Indices: 40494283--40494361 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40494273 CCGAGCTCTA
* * *
40494283 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
40494320 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40494357 AAGAC
1 AAGAC
40494362 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40495524 original size:47 final size:47
Alignment explanation
Indices: 40495473--40495882 Score: 680
Period size: 47 Copynumber: 8.7 Consensus size: 47
40495463 TTAGGATTCT
* * *
40495473 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
*
40495520 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40495567 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
40495614 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40495661 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT-GCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40495707 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40495754 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
40495801 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
40495848 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
40495883 TCCCGAAGGG
Statistics
Matches: 345, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
46 47 0.14
47 298 0.86
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:40495746 original size:187 final size:188
Alignment explanation
Indices: 40495473--40495882 Score: 689
Period size: 187 Copynumber: 2.2 Consensus size: 188
40495463 TTAGGATTCT
* *
40495473 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATGGATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
40495537 GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
65 GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
* * *
40495602 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
130 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATAGCCA
*
40495661 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT-GCCGATGTGATGAATGTGAAAG
1 ATGTGATGGATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
40495725 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
66 TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
* * *
40495790 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
131 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATAGCCA
* *
40495848 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGGATGTGAAAGTGTATATATGTGATAAG
40495883 TCCCGAAGGG
Statistics
Matches: 208, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
187 171 0.82
188 37 0.18
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (188 bp):
ATGTGATGGATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
CCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATAGCCA
Found at i:40496057 original size:37 final size:37
Alignment explanation
Indices: 40496001--40496079 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40495991 CCGAGCTCTA
* * *
40496001 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
40496038 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40496075 AAGAC
1 AAGAC
40496080 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40508977 original size:18 final size:17
Alignment explanation
Indices: 40508939--40508982 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
40508929 TATATTTTTA
40508939 TGAATTGTGAATTATATT
1 TGAA-TGTGAATTATATT
40508957 TGATATGTGAATTA-ATAT
1 TGA-ATGTGAATTATAT-T
40508975 TGAATGTG
1 TGAATGTG
40508983 GAAGGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 7 0.29
18 16 0.67
19 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.45
Consensus pattern (17 bp):
TGAATGTGAATTATATT
Found at i:40509236 original size:23 final size:23
Alignment explanation
Indices: 40509208--40509329 Score: 165
Period size: 23 Copynumber: 5.3 Consensus size: 23
40509198 AGTGTTATTG
40509208 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
40509231 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
40509254 ATCAATGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
40509277 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
40509300 ATCAGTGGTTGCTAT-GGCTACAT
1 ATCAGTGGTAGCT-TCGGCTACAT
40509323 ATCAGTG
1 ATCAGTG
40509330 CGGCACTTAT
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
23 85 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:40509263 original size:46 final size:46
Alignment explanation
Indices: 40509208--40509329 Score: 192
Period size: 46 Copynumber: 2.7 Consensus size: 46
40509198 AGTGTTATTG
40509208 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
* *
40509254 ATCAATGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
* *
40509300 ATCAGTGGTTGCTAT-GGCTACATATCAGTG
1 ATCAGTGGTAGCT-TCGGCTACATTTCAGTG
40509330 CGGCACTTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
46 69 0.99
47 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:40513682 original size:73 final size:73
Alignment explanation
Indices: 40513531--40513670 Score: 235
Period size: 73 Copynumber: 1.9 Consensus size: 73
40513521 TCTCGGATTT
* *
40513531 AAAAATGGATCATGCCCAGTAAGTTAGGACACGATCTTTTATTAATTCCCGAGATAGTTTAAAAC
1 AAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTATTAATTCCCGAGATAGTTTAAAAC
40513596 TTAAAAAA
66 TTAAAAAA
* * *
40513604 AAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCTCGAGATCGTTTAAAAC
1 AAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTATTAATTCCCGAGATAGTTTAAAAC
40513669 TT
66 TT
40513671 GAGTTTGAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Consensus pattern (73 bp):
AAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTATTAATTCCCGAGATAGTTTAAAAC
TTAAAAAA
Found at i:40514166 original size:23 final size:23
Alignment explanation
Indices: 40514114--40514180 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
40514104 AAATATAAGT
* * *
40514114 ATGTATATATATAAATTATAAAA
1 ATGTATGTATGTATATTATAAAA
**
40514137 AAATATGTATGTATATTATAAAA
1 ATGTATGTATGTATATTATAAAA
* *
40514160 ATGTATGCATGCATATATATA
1 ATGTATGTATGTATAT-TATA
40514181 TATATAACGA
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
23 30 0.88
24 4 0.12
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (23 bp):
ATGTATGTATGTATATTATAAAA
Found at i:40514236 original size:3 final size:3
Alignment explanation
Indices: 40514228--40514323 Score: 59
Period size: 3 Copynumber: 31.0 Consensus size: 3
40514218 GTAAAAAATT
** *
40514228 ATA ATA ATA ATA ATA AGGTA AGTA ATA ATA ATA A-A CACG ATA ATA GTA
1 ATA ATA ATA ATA ATA A--TA A-TA ATA ATA ATA ATA -ATA ATA ATA ATA
* * * * * * *
40514276 ATA GTA ACA TTA AAA ATA ATA ATA ATA ATA GTA AAA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40514324 CTATTAAAAT
Statistics
Matches: 70, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
2 1 0.01
3 62 0.89
4 4 0.06
5 3 0.04
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:40514331 original size:21 final size:21
Alignment explanation
Indices: 40514269--40514337 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
40514259 TAAACACGAT
* * *
40514269 AATAGTAATAGTAACATTAAA
1 AATAATAATAATAATATTAAA
*
40514290 AATAATAATAATAATAGTAAA
1 AATAATAATAATAATATTAAA
* *
40514311 AATAATGATAATACTATTAAA
1 AATAATAATAATAATATTAAA
*
40514332 ATTAAT
1 AATAAT
40514338 TAATTTAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (21 bp):
AATAATAATAATAATATTAAA
Found at i:40516151 original size:131 final size:132
Alignment explanation
Indices: 40515999--40516243 Score: 404
Period size: 131 Copynumber: 1.9 Consensus size: 132
40515989 GTTTAGTCAG
*
40515999 TCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCCTCAACCTACTCCACTACTGCTTAG-
1 TCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCCTCAACCTACTCCACTACTGCTTAGA
* *
40516063 GAAGATAAGGCTGGT-GCTTAAATCTGCTTCCTTGCTACCTTGAGAAGATAAGATTCGCTATCTT
66 G-AGATAAGGCTGGTGGCTTAAATCTGCTTCCATACTACCTTGAGAAGATAAGATTCGCTATCTT
40516127 CGA
130 CGA
* * *
40516130 TCTGCTCCACTACTGCTTAGGGAGACAGGATCTGCAATCTTCAACCTACTCCACTGCTGCTTAGA
1 TCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCCTCAACCTACTCCACTACTGCTTAGA
*
40516195 GAGATAAGGCTGGTGGCTTAAATCTGCTTCCATACTACCTTGGGAAGAT
66 GAGATAAGGCTGGTGGCTTAAATCTGCTTCCATACTACCTTGAGAAGAT
40516244 TCACCGTCTT
Statistics
Matches: 105, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
131 73 0.70
132 32 0.30
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (132 bp):
TCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCCTCAACCTACTCCACTACTGCTTAGA
GAGATAAGGCTGGTGGCTTAAATCTGCTTCCATACTACCTTGAGAAGATAAGATTCGCTATCTTC
GA
Found at i:40516405 original size:50 final size:51
Alignment explanation
Indices: 40516306--40516455 Score: 167
Period size: 50 Copynumber: 3.0 Consensus size: 51
40516296 CTTTAATTTT
* * * * *
40516306 AACACCAAGGAGATAAGATTCACTACCTTTAGCTTTAATCTGCTCCACTAC
1 AACACCAAAGAAACAAGATTCGCTACCTTTAGCTTTAATCTACTCCACTAC
* * *
40516357 AACGCCAGAGAAACAAGATTCGCTACCTTTA-CTTTAATCTATTCCACTAC
1 AACACCAAAGAAACAAGATTCGCTACCTTTAGCTTTAATCTACTCCACTAC
* * * * * *
40516407 GACACCAAAGAGATATGATTCGCTGCCTTTAGCTTTAATCCACTCCACT
1 AACACCAAAGAAACAAGATTCGCTACCTTTAGCTTTAATCTACTCCACT
40516456 GCAGCTTTAA
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
50 41 0.51
51 40 0.49
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (51 bp):
AACACCAAAGAAACAAGATTCGCTACCTTTAGCTTTAATCTACTCCACTAC
Found at i:40516628 original size:87 final size:87
Alignment explanation
Indices: 40516482--40516641 Score: 216
Period size: 87 Copynumber: 1.8 Consensus size: 87
40516472 CCACAATAAT
* * * *
40516482 GCCAGGGAAACAAGATTCGCTACTTTTAGCTTTAATCTGTTCCGCTGCAACATCAGGGAAATAAG
1 GCCAGGGAAACAAGATTCACTACCTTTAGCTTTAATCTGCTCCGCTGCAACATCAGGGAAACAAG
40516547 ATTCGCTACTCTCAATCTTAAC
66 ATTCGCTACTCTCAATCTTAAC
* * * *
40516569 GCCAGGGAGATAAGATTCACTACCTTTAGCTTTAATCTGCTCTGTTG-AA-ATGCCAGGGAAACA
1 GCCAGGGAAACAAGATTCACTACCTTTAGCTTTAATCTGCTCCGCTGCAACAT--CAGGGAAACA
40516632 AGATTCGCTA
64 AGATTCGCTA
40516642 ACTTTAGCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
85 2 0.03
86 2 0.03
87 59 0.94
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (87 bp):
GCCAGGGAAACAAGATTCACTACCTTTAGCTTTAATCTGCTCCGCTGCAACATCAGGGAAACAAG
ATTCGCTACTCTCAATCTTAAC
Found at i:40516706 original size:138 final size:138
Alignment explanation
Indices: 40516479--40516843 Score: 430
Period size: 138 Copynumber: 2.6 Consensus size: 138
40516469 ATTCCACAAT
* * * * * *
40516479 AATGCCAGGGAAACAAGATTCGCT-ACTTTTAGCTTTAATCTGTTCCGCTGCAACATCAGGGAAA
1 AATGCCAGGGAAACAAGATTCGCTAAC-TTTAGCTTTAATTTGTTCCACTGAAACACCAAGGAGA
* * * * *
40516543 TAAGATTCGCT-ACTCTCAATCTTAACGCCAGGGAGATAAGATTCACTACCTTTAGCTTTAATCT
65 TAAGATTCGCTGCCT-TCAGTTTTAACGACAGGGAGATAAGATTCACTACCTTCAGCTTTAATCT
*
40516607 GCTCT-GTTGA
129 GCT-TAGCTGA
* * *
40516617 AATGCCAGGGAAACAAGATTCGCTAACTTTAGCTTTAATTTGTTCTACTAAAACACCAAAGAGAT
1 AATGCCAGGGAAACAAGATTCGCTAACTTTAGCTTTAATTTGTTCCACTGAAACACCAAGGAGAT
* ** *
40516682 AAGATTCGCTGCCTTCAGTTTTAACGACATGGAGATAAGATTTGCTGCCTTCAGCTTTAATCTGC
66 AAGATTCGCTGCCTTCAGTTTTAACGACAGGGAGATAAGATTCACTACCTTCAGCTTTAATCTGC
*
40516747 TTAGCTGT
131 TTAGCTGA
* * * *
40516755 AATGCCAGGGAAACAAGATTTGCTACCTTTAGCTTTAATTTGTTCCACTGTAACGCCAAGGAGAT
1 AATGCCAGGGAAACAAGATTCGCTAACTTTAGCTTTAATTTGTTCCACTGAAACACCAAGGAGAT
* * * *
40516820 AGGATTCACTGCCTTTAGCTTTAA
66 AAGATTCGCTGCCTTCAGTTTTAA
40516844 TCCGCTCCAC
Statistics
Matches: 193, Mismatches: 31, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
137 1 0.01
138 188 0.97
139 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (138 bp):
AATGCCAGGGAAACAAGATTCGCTAACTTTAGCTTTAATTTGTTCCACTGAAACACCAAGGAGAT
AAGATTCGCTGCCTTCAGTTTTAACGACAGGGAGATAAGATTCACTACCTTCAGCTTTAATCTGC
TTAGCTGA
Found at i:40516806 original size:51 final size:51
Alignment explanation
Indices: 40516718--40517004 Score: 227
Period size: 51 Copynumber: 5.5 Consensus size: 51
40516708 ACATGGAGAT
* *
40516718 AAGATTTGCTGCCTTCAGCTTTAATCTGCTT--AGCTGTAATGCCAGGGAAAC
1 AAGATTCGCTGCCTTTAGCTTTAATCTG-TTCCA-CTGTAATGCCAGGGAAAC
* * * * * * *
40516769 AAGATTTGCTACCTTTAGCTTTAATTTGTTCCACTGTAACGCCAAGGAGAT
1 AAGATTCGCTGCCTTTAGCTTTAATCTGTTCCACTGTAATGCCAGGGAAAC
* * * * * * * *
40516820 AGGATTCACTGCCTTTAGCTTTAATCCGCTCCACTTCAGCTTTAACGACAGGGAGAT
1 AAGATTCGCTGCCTTTAGCTTTAATCTGTTCCAC-T--G---TAATGCCAGGGAAAC
* * **
40516877 AAGATTCGCTGCCTTTAGCTTTAATCTGCTCCATTGTAATGATAGGGAAAC
1 AAGATTCGCTGCCTTTAGCTTTAATCTGTTCCACTGTAATGCCAGGGAAAC
* * ** * *
40516928 AAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGAT
1 AAGATTCGCTGCCTTTAGCTTTAATCTGTTCCACTGTAATGCCAGGGAAAC
* *
40516979 AAGATTCGCTGTCTTCAGCTTTAATC
1 AAGATTCGCTGCCTTTAGCTTTAATC
40517005 CGCTCCATTT
Statistics
Matches: 191, Mismatches: 37, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
50 2 0.01
51 141 0.74
52 2 0.01
54 2 0.01
56 1 0.01
57 43 0.23
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (51 bp):
AAGATTCGCTGCCTTTAGCTTTAATCTGTTCCACTGTAATGCCAGGGAAAC
Found at i:40516985 original size:159 final size:159
Alignment explanation
Indices: 40516694--40517023 Score: 482
Period size: 159 Copynumber: 2.1 Consensus size: 159
40516684 GATTCGCTGC
* * * *
40516694 CTTCAGTTTTAACGACATGGAGATAAGATTTGCTGCCTTCAGCTTTAATCTGCTTAGCTGTAATG
1 CTTCAGCTTTAACGACAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCAGCTGTAATG
* * * * * *
40516759 CCAGGGAAACAAGATTTGCTACCTTTAGCTTTAATTTGTTCCACTGTAACGCCAAGGAGATAGGA
66 ACAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAACGCCAAAGAGATAAGA
*
40516824 TTCACTGCCTTTAGCTTTAATCCGCTCCA
131 TTCACTGCCTTCAGCTTTAATCCGCTCCA
* *
40516853 CTTCAGCTTTAACGACAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCA-TTGTAAT
1 CTTCAGCTTTAACGACAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCT-CAGCTGTAAT
* *
40516917 GATAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAAG
65 GACAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAACGCCAAAGAGATAAG
* *
40516982 ATTCGCTGTCTTCAGCTTTAATCCGCTCCA
130 ATTCACTGCCTTCAGCTTTAATCCGCTCCA
*
40517012 TTTCAGCTTTAA
1 CTTCAGCTTTAA
40517024 TCTATTCCAC
Statistics
Matches: 152, Mismatches: 18, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
159 151 0.99
160 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (159 bp):
CTTCAGCTTTAACGACAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCAGCTGTAATG
ACAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAACGCCAAAGAGATAAGA
TTCACTGCCTTCAGCTTTAATCCGCTCCA
Found at i:40518490 original size:6 final size:6
Alignment explanation
Indices: 40518479--40518541 Score: 60
Period size: 6 Copynumber: 10.7 Consensus size: 6
40518469 TCTCCTCTTT
* * *
40518479 TTTTTC TTTTTC TTTTTC -TTTTC TTCTTC TTCTT- TATTTC TTTCTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT-TTC
40518526 TTTTTC TCTTTT- TTTT
1 TTTTTC T-TTTTC TTTT
40518542 AAATATTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
5 11 0.22
6 28 0.57
7 10 0.20
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:40523165 original size:73 final size:73
Alignment explanation
Indices: 40523013--40523156 Score: 243
Period size: 73 Copynumber: 2.0 Consensus size: 73
40523003 TCTCGGATTT
* * ** *
40523013 AAAAAATGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTTTCGAGATTGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATGCTCGAGATCGTTTAAAA
40523078 CTTGAGAA
66 CTTGAGAA
40523086 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATGCTCGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATGCTCGAGATCGTTTAAAA
40523151 CTTGAG
66 CTTGAG
40523157 TTGGAAAAGA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (73 bp):
AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATGCTCGAGATCGTTTAAAA
CTTGAGAA
Found at i:40523767 original size:18 final size:18
Alignment explanation
Indices: 40523746--40523792 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
40523736 ACGATAATTC
* *
40523746 TAATAGTAACATTAAAAA
1 TAATAATAACAGTAAAAA
*
40523764 TAATAATAATAGTAAAAA
1 TAATAATAACAGTAAAAA
*
40523782 TAATGATAACA
1 TAATAATAACA
40523793 CTATTAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (18 bp):
TAATAATAACAGTAAAAA
Found at i:40525555 original size:16 final size:17
Alignment explanation
Indices: 40525525--40525559 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40525515 AAATGGGTAA
*
40525525 TATGTATTTTAAATAAT
1 TATGTATGTTAAATAAT
40525542 TATGTATGTT-AATAAT
1 TATGTATGTTAAATAAT
40525558 TA
1 TA
40525560 CAGATTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (17 bp):
TATGTATGTTAAATAAT
Found at i:40534102 original size:10 final size:10
Alignment explanation
Indices: 40534083--40534112 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
40534073 ATCTACTCTT
*
40534083 GAAAAGAAAA
1 GAAAAAAAAA
40534093 GAAAAAAAAA
1 GAAAAAAAAA
40534103 GAAAAAAAAA
1 GAAAAAAAAA
40534113 AGAGAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:40534104 original size:15 final size:14
Alignment explanation
Indices: 40534084--40534113 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
40534074 TCTACTCTTG
40534084 AAAAGAAAAGAAAAA
1 AAAAGAAAA-AAAAA
40534099 AAAAGAAAAAAAAA
1 AAAAGAAAAAAAAA
40534113 A
1 A
40534114 GAGAAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAA
Found at i:40552414 original size:18 final size:18
Alignment explanation
Indices: 40552393--40552429 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40552383 ACTCATTCCA
* *
40552393 CATCACTTATAATCATTT
1 CATCACTTACAACCATTT
40552411 CATCACTTACAACCATTT
1 CATCACTTACAACCATTT
40552429 C
1 C
40552430 GAAACATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.00, T:0.38
Consensus pattern (18 bp):
CATCACTTACAACCATTT
Found at i:40554198 original size:3 final size:3
Alignment explanation
Indices: 40554190--40554233 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
40554180 ACCTACTTCT
40554190 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40554234 CTCTTTTATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40555767 original size:16 final size:16
Alignment explanation
Indices: 40555738--40555770 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40555728 CCAAACCATA
40555738 TGAAAAATTCCAAATT
1 TGAAAAATTCCAAATT
40555754 TGAAAGAATT-CAAATT
1 TGAAA-AATTCCAAATT
40555770 T
1 T
40555771 AGTATCAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.33
Consensus pattern (16 bp):
TGAAAAATTCCAAATT
Found at i:40567006 original size:171 final size:171
Alignment explanation
Indices: 40566721--40567065 Score: 672
Period size: 171 Copynumber: 2.0 Consensus size: 171
40566711 CACCACGATC
40566721 TTTAATCTTTTAATTAAGTTGGCTTTTAACTTCTTACTTATAGAGAATAAATTCTCTTCGAATTA
1 TTTAATCTTTTAATTAAGTTGGCTTTTAACTTCTTACTTATAGAGAATAAATTCTCTTCGAATTA
*
40566786 GCTCGTAGCAATGAAGGTAATAAACATTTTTATTCCTTCCTTTAATTTAAACAAGTTTTACGAGC
66 GCTCGTAGCAATGAAGGTAATAAACATTTTTATTCCTTCCTCTAATTTAAACAAGTTTTACGAGC
40566851 ATTGCTATGCATTAGATCAAGTGGTTTTTGACCTTTGTTAA
131 ATTGCTATGCATTAGATCAAGTGGTTTTTGACCTTTGTTAA
*
40566892 TTTAATCTTTTAATTAAGTTGGTTTTTAACTTCTTACTTATAGAGAATAAATTCTCTTCGAATTA
1 TTTAATCTTTTAATTAAGTTGGCTTTTAACTTCTTACTTATAGAGAATAAATTCTCTTCGAATTA
40566957 GCTCGTAGCAATGAAGGTAATAAACATTTTTATTCCTTCCTCTAATTTAAACAAGTTTTACGAGC
66 GCTCGTAGCAATGAAGGTAATAAACATTTTTATTCCTTCCTCTAATTTAAACAAGTTTTACGAGC
40567022 ATTGCTATGCATTAGATCAAGTGGTTTTTGACCTTTGTTAA
131 ATTGCTATGCATTAGATCAAGTGGTTTTTGACCTTTGTTAA
40567063 TTT
1 TTT
40567066 TGCCTCAAAA
Statistics
Matches: 172, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 172 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (171 bp):
TTTAATCTTTTAATTAAGTTGGCTTTTAACTTCTTACTTATAGAGAATAAATTCTCTTCGAATTA
GCTCGTAGCAATGAAGGTAATAAACATTTTTATTCCTTCCTCTAATTTAAACAAGTTTTACGAGC
ATTGCTATGCATTAGATCAAGTGGTTTTTGACCTTTGTTAA
Found at i:40568887 original size:86 final size:87
Alignment explanation
Indices: 40568769--40569020 Score: 246
Period size: 86 Copynumber: 2.9 Consensus size: 87
40568759 TCTTTGTTTG
* * * * *
40568769 GAAACAAAA-CAATAT-TGAATAAATCTTGTTAAATGGCAGGAATAAATCCCGAAACAGATTTTA
1 GAAACAAAATCAAAATAAGAATAAAACTTATTAAACGGCAGGAATAAATCCCGAAACAGATTTTA
*
40568832 TTTA-ATTTAATTTCTCATTTTTA
66 TTTACATTTAATTTC-C-TATTTA
* * * * * *
40568855 GCAACAAAATC-AAATCA-AATAAAACTTATTAAACGGAAGGAATCAATCCCAAAACGGATTTTA
1 GAAACAAAATCAAAATAAGAATAAAACTTATTAAACGGCAGGAATAAATCCCGAAACAGATTTTA
* *
40568918 TTTACCTTTAATTTCCTATTTG
66 TTTACATTTAATTTCCTATTTA
* * * *
40568940 GAAATAAAATCAAAATAATGGAATAAAA-TCAGTTGAACGGCGGGAATAAATCCCGAAACAGATT
1 GAAACAAAATCAAAATAA--GAATAAAACTTA-TTAAACGGCAGGAATAAATCCCGAAACAGATT
*
40569004 TTATTTACTTTTAATTT
63 TTATTTACATTTAATTT
40569021 TGAAAACAAA
Statistics
Matches: 134, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
85 13 0.10
86 60 0.45
87 10 0.07
88 2 0.01
89 49 0.37
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (87 bp):
GAAACAAAATCAAAATAAGAATAAAACTTATTAAACGGCAGGAATAAATCCCGAAACAGATTTTA
TTTACATTTAATTTCCTATTTA
Found at i:40572618 original size:22 final size:23
Alignment explanation
Indices: 40572591--40572670 Score: 85
Period size: 22 Copynumber: 3.5 Consensus size: 23
40572581 AACTAATGAA
40572591 CAGAGAGCACTAAAGTGCTATA-
1 CAGAGAGCACTAAAGTGCTATAT
*
40572613 CAGAGAGCAC-AGATGTGCTA-AT
1 CAGAGAGCACTA-AAGTGCTATAT
* *
40572635 CAGAGAGCACTAACGTACTAATAAT
1 CAGAGAGCACTAAAGTGCT-AT-AT
40572660 CAGAGAGCACT
1 CAGAGAGCACT
40572671 GATGTCCTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
21 2 0.04
22 32 0.65
23 2 0.04
25 13 0.27
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (23 bp):
CAGAGAGCACTAAAGTGCTATAT
Found at i:40572665 original size:25 final size:25
Alignment explanation
Indices: 40572631--40572691 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
40572621 ACAGATGTGC
40572631 TAATCAGAGAGCACTAACGTACTAA
1 TAATCAGAGAGCACTAACGTACTAA
* * *
40572656 TAATCAGAGAGCACTGATGTCCTAA
1 TAATCAGAGAGCACTAACGTACTAA
*
40572681 TAAGCAGAGAG
1 TAATCAGAGAG
40572692 TGCGCTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (25 bp):
TAATCAGAGAGCACTAACGTACTAA
Found at i:40572667 original size:47 final size:44
Alignment explanation
Indices: 40572591--40572681 Score: 119
Period size: 47 Copynumber: 2.0 Consensus size: 44
40572581 AACTAATGAA
* *
40572591 CAGAGAGCACTAAAGTGCTATACAGAGAGCACAGATGTGCTAAT
1 CAGAGAGCACTAAAGTACTATACAGAGAGCACAGATGTCCTAAT
* *
40572635 CAGAGAGCACTAACGTACTAATAATCAGAGAGCACTGATGTCCTAAT
1 CAGAGAGCACTAAAGTACT-AT-A-CAGAGAGCACAGATGTCCTAAT
40572682 AAGCAGAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 17 0.43
45 2 0.05
46 1 0.03
47 20 0.50
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (44 bp):
CAGAGAGCACTAAAGTACTATACAGAGAGCACAGATGTCCTAAT
Found at i:40577653 original size:16 final size:17
Alignment explanation
Indices: 40577622--40577656 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40577612 TTGTGTTTTG
40577622 TGCAAAAAGGACTAAAA
1 TGCAAAAAGGACTAAAA
*
40577639 TGCAAAAAGTA-TAAAA
1 TGCAAAAAGGACTAAAA
40577655 TG
1 TG
40577657 TCAGGGGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (17 bp):
TGCAAAAAGGACTAAAA
Found at i:40578036 original size:17 final size:18
Alignment explanation
Indices: 40578016--40578049 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40578006 AATTTAGTTA
40578016 AAGTATAAACA-GTATAT
1 AAGTATAAACATGTATAT
*
40578033 AAGTATATACATGTATA
1 AAGTATAAACATGTATA
40578050 AATTATTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (18 bp):
AAGTATAAACATGTATAT
Found at i:40578757 original size:41 final size:41
Alignment explanation
Indices: 40578700--40578857 Score: 167
Period size: 41 Copynumber: 3.9 Consensus size: 41
40578690 AATAAGATGG
* *
40578700 TTCAGACTTTACGTCTAGGAGGCTTGATGCCGATGAAATGT
1 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGATGAAATGT
* * **
40578741 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGATGAAATGT
*
40578782 TTCAGACTTTATGTTTAGCAGGCTTTG-TGCC-AGTGAAATGT
1 TTCAGACTTTATGTCTAGCAGGC-TTGATGCCGA-TGAAATGT
* * * * * *
40578823 ATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGATG
1 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGATG
40578858 TTTTATACAA
Statistics
Matches: 95, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
40 2 0.02
41 89 0.94
42 4 0.04
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (41 bp):
TTCAGACTTTATGTCTAGCAGGCTTGATGCCGATGAAATGT
Found at i:40578841 original size:82 final size:82
Alignment explanation
Indices: 40578700--40578854 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 82
40578690 AATAAGATGG
* * *
40578700 TTCAGACTTTACGTCTAGGAGGCTTGATGCCGATGAAATGTTTCAGACTTTATGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGATGAAATGTATCAGACTTTATGCCTAGCAGGCT
40578765 TGATGCCGGTGAATTAC
66 TGATGCCGGTGAATTAC
* * * * *
40578782 TTCAGACTTTATGTTTAGCAGGCTTTG-TGCC-AGTGAAATGTATCGGGCTTTGTGCCTAGCAGG
1 TTCAGACTTTACGTCTAGCAGGC-TTGATGCCGA-TGAAATGTATCAGACTTTATGCCTAGCAGG
*
40578845 CTTTATGCCG
64 CTTGATGCCG
40578855 ATGTTTTATA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 1 0.02
82 58 0.94
83 3 0.05
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (82 bp):
TTCAGACTTTACGTCTAGCAGGCTTGATGCCGATGAAATGTATCAGACTTTATGCCTAGCAGGCT
TGATGCCGGTGAATTAC
Found at i:40580408 original size:16 final size:17
Alignment explanation
Indices: 40580387--40580424 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
40580377 TTCTATAGGG
*
40580387 ATTTTACT-TTTATTTT
1 ATTTTACTATGTATTTT
40580403 ATTTTACTACTGTATTTT
1 ATTTTACTA-TGTATTTT
40580421 ATTT
1 ATTT
40580425 AAATAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTACTATGTATTTT
Found at i:40582781 original size:20 final size:19
Alignment explanation
Indices: 40582750--40582798 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
40582740 TAAATAAATC
40582750 ATAAAAATATTACAAA-TTT
1 ATAAAAATATTA-AAATTTT
40582769 ATAAAAGATATTAAAATTTT
1 ATAAAA-ATATTAAAATTTT
40582789 ATAAAAATAT
1 ATAAAAATAT
40582799 ATTAAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAAAAATATTAAAATTTT
Found at i:40583414 original size:40 final size:38
Alignment explanation
Indices: 40583365--40583457 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 38
40583355 CATATTTATA
* *
40583365 ATTTATTAAATTTTTATAAGCTTATATAAAAAATTTAAAT
1 ATTTTTTAAATTTTTATAA-ATT-TATAAAAAATTTAAAT
* *
40583405 ATTTTTTAAATTTTTATAAATTTATATAAAATTTTAAT
1 ATTTTTTAAATTTTTATAAATTTATAAAAAATTTAAAT
40583443 ATTTTGTTAATATTT
1 ATTTT-TTAA-ATTT
40583458 CACGTGTCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
38 19 0.40
39 6 0.13
40 22 0.47
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (38 bp):
ATTTTTTAAATTTTTATAAATTTATAAAAAATTTAAAT
Found at i:40596735 original size:51 final size:51
Alignment explanation
Indices: 40596680--40596791 Score: 152
Period size: 51 Copynumber: 2.2 Consensus size: 51
40596670 TACTCTTAGA
* * * * * * *
40596680 CAAAGTCCGAATGTCCAGGTGGCTTGTGATCAAGGTGTCTCGACTTCTAGT
1 CAAAGTCAGAACGTACAAGTGGCTTGTAATCAAGGTGTCTCAACTGCTAGT
*
40596731 CAAAGTCAGAACGTACAATTGGCTTGTAATCAAGGTGTCTCAACTGCTAGT
1 CAAAGTCAGAACGTACAAGTGGCTTGTAATCAAGGTGTCTCAACTGCTAGT
40596782 CAAAGTCAGA
1 CAAAGTCAGA
40596792 CAGTACAGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (51 bp):
CAAAGTCAGAACGTACAAGTGGCTTGTAATCAAGGTGTCTCAACTGCTAGT
Found at i:40601297 original size:18 final size:19
Alignment explanation
Indices: 40601276--40601317 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
40601266 ACCATTATTA
*
40601276 TTATTATCATTA-TTGCTT
1 TTATTATCATTATTTGCCT
* *
40601294 TTATTTTTATTATTTGCCT
1 TTATTATCATTATTTGCCT
40601313 TTATT
1 TTATT
40601318 GTTTACTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.67
Consensus pattern (19 bp):
TTATTATCATTATTTGCCT
Found at i:40601315 original size:19 final size:19
Alignment explanation
Indices: 40601284--40601322 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40601274 TATTATTATC
*
40601284 ATTATTGCTTTTATT-TTT
1 ATTATTGCCTTTATTGTTT
40601302 ATTATTTGCCTTTATTGTTT
1 ATTA-TTGCCTTTATTGTTT
40601322 A
1 A
40601323 CTCATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.67
Consensus pattern (19 bp):
ATTATTGCCTTTATTGTTT
Found at i:40601658 original size:26 final size:24
Alignment explanation
Indices: 40601627--40601690 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 24
40601617 AAATATATAA
*
40601627 ATATATACTTTATATCTTATTTA-TTT
1 ATATATACTTTATA-C--ATATACTTT
*
40601653 ATATATCCTTGTATACATATACTTT
1 ATATATACTT-TATACATATACTTT
40601678 -TATATACTTTATA
1 ATATATACTTTATA
40601691 ATGCATACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 4 0.12
24 12 0.36
25 3 0.09
26 10 0.30
27 4 0.12
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.55
Consensus pattern (24 bp):
ATATATACTTTATACATATACTTT
Found at i:40611659 original size:10 final size:10
Alignment explanation
Indices: 40611641--40611670 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
40611631 TGGCATATCA
*
40611641 TATTGTCCCC
1 TATTCTCCCC
40611651 TATTCTCCCC
1 TATTCTCCCC
40611661 TATTCTCCCC
1 TATTCTCCCC
40611671 ATTGGTAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.47, G:0.03, T:0.40
Consensus pattern (10 bp):
TATTCTCCCC
Found at i:40621420 original size:21 final size:21
Alignment explanation
Indices: 40621396--40621455 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
40621386 TTTAAATTAA
40621396 TATTAATTTTAAATATATTT-T
1 TATTAATTTTAAATA-ATTTCT
*
40621417 TATTAATTTTTAATAATTTCT
1 TATTAATTTTAAATAATTTCT
40621438 TA-TAATTCTT-AATAATTT
1 TATTAATT-TTAAATAATTT
40621456 ATAAATAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTAATTTTAAATAATTTCT
Found at i:40621427 original size:10 final size:10
Alignment explanation
Indices: 40621399--40621469 Score: 63
Period size: 10 Copynumber: 6.8 Consensus size: 10
40621389 AAATTAATAT
*
40621399 TAATTTTAAA
1 TAATTTTTAA
*
40621409 TATATTTTTAT
1 TA-ATTTTTAA
40621420 TAATTTTTAA
1 TAATTTTTAA
40621430 TAATTTCTT-A
1 TAATTT-TTAA
*
40621440 TAATTCTTAA
1 TAATTTTTAA
*
40621450 TAATTTATAAA
1 TAATTT-TTAA
40621461 TAAATTTTT
1 T-AATTTTT
40621470 GTATTTTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
9 2 0.04
10 27 0.55
11 15 0.31
12 5 0.10
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:40621443 original size:20 final size:20
Alignment explanation
Indices: 40621396--40621455 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
40621386 TTTAAATTAA
*
40621396 TATTAATTTTAAATATATTTT
1 TATTAATTTTTAATA-ATTTT
40621417 TATTAATTTTTAATAATTTCT
1 TATTAATTTTTAATAATTT-T
*
40621438 TA-TAATTCTTAATAATTT
1 TATTAATTTTTAATAATTT
40621456 ATAAATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTAATTTTTAATAATTTT
Found at i:40623149 original size:12 final size:13
Alignment explanation
Indices: 40623119--40623149 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40623109 AGAATTTTGC
40623119 TTTCTTCTCCCTA
1 TTTCTTCTCCCTA
40623132 TTTCTTCTCCCT-
1 TTTCTTCTCCCTA
40623144 TTTCTT
1 TTTCTT
40623150 TTCCATCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTCTTCTCCCTA
Found at i:40625451 original size:35 final size:34
Alignment explanation
Indices: 40625339--40625496 Score: 147
Period size: 34 Copynumber: 4.6 Consensus size: 34
40625329 ATTTACTGCT
* * * *
40625339 GTATTGATCTATTATAAGGATATTAATTGCTACG
1 GTATTGATCTGTTATAAGCATATTAATTACTACC
* * * * * *
40625373 GTGTTTATTTGTTATAATCACATTAATTGCGT-CC
1 GTATTGATCTGTTATAAGCATATTAATTAC-TACC
* *
40625407 GTATTGATCTGTTATAAGCATTTTGAATTACTATC
1 GTATTGATCTGTTATAAGCATATT-AATTACTACC
* * **
40625442 GTATCGATCTGTTATATGCATATTAATTGGTACC
1 GTATTGATCTGTTATAAGCATATTAATTACTACC
40625476 GTATTGATCTGTTATAAGCAT
1 GTATTGATCTGTTATAAGCAT
40625497 GTCAAATTGC
Statistics
Matches: 97, Mismatches: 24, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
34 69 0.71
35 28 0.29
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (34 bp):
GTATTGATCTGTTATAAGCATATTAATTACTACC
Found at i:40634510 original size:22 final size:22
Alignment explanation
Indices: 40634482--40634527 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
40634472 ATAAGTCATT
40634482 TTGCCTTCTTATTATTTTTTCC
1 TTGCCTTCTTATTATTTTTTCC
40634504 TTGCCTTCTTATTATTTTTTCC
1 TTGCCTTCTTATTATTTTTTCC
40634526 TT
1 TT
40634528 TGTCCTCCTC
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:0.09, C:0.22, G:0.04, T:0.65
Consensus pattern (22 bp):
TTGCCTTCTTATTATTTTTTCC
Found at i:40650738 original size:19 final size:19
Alignment explanation
Indices: 40650714--40650786 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 19
40650704 ACCTAATTAC
40650714 CCAACCCAATTACCATTTA
1 CCAACCCAATTACCATTTA
* * *
40650733 CCAACCCAATAAACTAAAGTCTA
1 CCAACCCAAT-TAC--CA-TTTA
40650756 CCCAAACCCAATTACCATTTA
1 -CC-AACCCAATTACCATTTA
40650777 CCAACCCAAT
1 CCAACCCAAT
40650787 AAAACAAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 18 0.43
20 4 0.10
21 3 0.07
22 2 0.05
23 3 0.07
24 4 0.10
25 8 0.19
ACGTcount: A:0.41, C:0.37, G:0.01, T:0.21
Consensus pattern (19 bp):
CCAACCCAATTACCATTTA
Found at i:40651333 original size:8 final size:8
Alignment explanation
Indices: 40651322--40651362 Score: 73
Period size: 8 Copynumber: 5.0 Consensus size: 8
40651312 TATTTGCTGG
40651322 GGTTAATC
1 GGTTAATC
40651330 GGTTAATC
1 GGTTAATC
40651338 GGTTAAATC
1 GGTT-AATC
40651347 GGTTAATC
1 GGTTAATC
40651355 GGTTAATC
1 GGTTAATC
40651363 TTTAACCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 24 0.75
9 8 0.25
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (8 bp):
GGTTAATC
Found at i:40651348 original size:17 final size:17
Alignment explanation
Indices: 40651322--40651360 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
40651312 TATTTGCTGG
40651322 GGTT-AATCGGTTAATC
1 GGTTAAATCGGTTAATC
40651338 GGTTAAATCGGTTAATC
1 GGTTAAATCGGTTAATC
40651355 GGTTAA
1 GGTTAA
40651361 TCTTTAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (17 bp):
GGTTAAATCGGTTAATC
Found at i:40652404 original size:115 final size:114
Alignment explanation
Indices: 40652184--40652411 Score: 266
Period size: 115 Copynumber: 2.0 Consensus size: 114
40652174 GTTTTGAACT
* *
40652184 ACTCATAACCCCTTCTAACCTATAAATAGGAGGATAATACGTTTCAGCGTACTCAAACCTACTTC
1 ACTCATAACCCCTTCCAACCTATAAATAGGAGGATAATACGCTTCAGCGTACTCAAACCTACTTC
* * * *
40652249 CTCTTGTATTGACAACAATATCAGTCCCAATTGAGATAAAATTCAATCA
66 CTCCTGCATTGACAACAATATCAGTACCAATTGAGATAAAACTCAATCA
* * * *
40652298 ACTCATAAACCTCTTCCAACCTATAAATAGTAGGATAATGCGCTTCAGC-TCACTCAAA-ATCAC
1 ACTCAT-AACCCCTTCCAACCTATAAATAGGAGGATAATACGCTTCAGCGT-ACTCAAACCT-AC
* * *
40652361 TTCCTCCTGCATTGAGAGCAATGTCCA-TACCAATTGA-ATTAAAACTCAATC
63 TTCCTCCTGCATTGACAACAATAT-CAGTACCAATTGAGA-TAAAACTCAATC
40652412 GACTATTGTT
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
114 9 0.09
115 85 0.89
116 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.28
Consensus pattern (114 bp):
ACTCATAACCCCTTCCAACCTATAAATAGGAGGATAATACGCTTCAGCGTACTCAAACCTACTTC
CTCCTGCATTGACAACAATATCAGTACCAATTGAGATAAAACTCAATCA
Found at i:40652517 original size:9 final size:9
Alignment explanation
Indices: 40652503--40652533 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40652493 GTTAAACGAA
40652503 TCGAGTTAT
1 TCGAGTTAT
*
40652512 TCGAGTTAA
1 TCGAGTTAT
40652521 TCGAGTTAT
1 TCGAGTTAT
40652530 TCGA
1 TCGA
40652534 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:40652616 original size:9 final size:9
Alignment explanation
Indices: 40652587--40652623 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
40652577 TGAGTTTTCG
40652587 AATTCGAAT
1 AATTCGAAT
*
40652596 AACTCGAAT
1 AATTCGAAT
40652605 AATTCGAAT
1 AATTCGAAT
*
40652614 AATTTGAAT
1 AATTCGAAT
40652623 A
1 A
40652624 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:40652841 original size:30 final size:30
Alignment explanation
Indices: 40652807--40652864 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40652797 AAACCTTTTA
* *
40652807 TTTTCCCCCAAAATTTTTACTCCCTTCCAC
1 TTTTCACCCAAAACTTTTACTCCCTTCCAC
* *
40652837 TTTTCACCTAAAACTTTTATTCCCTTCC
1 TTTTCACCCAAAACTTTTACTCCCTTCC
40652865 CATCTCACCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.43
Consensus pattern (30 bp):
TTTTCACCCAAAACTTTTACTCCCTTCCAC
Found at i:40653636 original size:5 final size:5
Alignment explanation
Indices: 40653626--40653662 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
40653616 AAATTTTTTT
40653626 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG AT
40653663 CGAACGCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:40655951 original size:2 final size:2
Alignment explanation
Indices: 40655944--40655979 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40655934 TGCTCAAGTT
40655944 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40655980 ACACATATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:40659525 original size:9 final size:9
Alignment explanation
Indices: 40659511--40659537 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
40659501 GAGTTTTCGC
40659511 ATTCGAATA
1 ATTCGAATA
40659520 ATTCGAATA
1 ATTCGAATA
40659529 ATTCGAATA
1 ATTCGAATA
40659538 TCAAACCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (9 bp):
ATTCGAATA
Found at i:40660435 original size:5 final size:5
Alignment explanation
Indices: 40660425--40660450 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40660415 GAACAAATAT
40660425 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
40660451 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:40665899 original size:8 final size:8
Alignment explanation
Indices: 40665886--40665916 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
40665876 GAACGGTAAA
40665886 AAAAAAAC
1 AAAAAAAC
40665894 AAAAAAA-
1 AAAAAAAC
40665901 AAAAAAAC
1 AAAAAAAC
40665909 AAAAAAAC
1 AAAAAAAC
40665917 CTCTACCGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:40665901 original size:15 final size:15
Alignment explanation
Indices: 40665883--40665915 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
40665873 AATGAACGGT
40665883 AAAAAAAAAACAAAA
1 AAAAAAAAAACAAAA
40665898 AAAAAAAAAACAAAA
1 AAAAAAAAAACAAAA
40665913 AAA
1 AAA
40665916 CCTCTACCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAACAAAA
Found at i:40666374 original size:23 final size:23
Alignment explanation
Indices: 40666348--40666399 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
40666338 TACTTCACTT
*
40666348 GAAAAAAAAATGAA-AAGAAAAAA
1 GAAAAAAAAA-GAAGAACAAAAAA
*
40666371 GAAAAGAAAAGAAGAACAAAAAA
1 GAAAAAAAAAGAAGAACAAAAAA
40666394 GAAAAA
1 GAAAAA
40666400 GGAGAGGCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (23 bp):
GAAAAAAAAAGAAGAACAAAAAA
Done.