Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 364 of 378
Found at i:109165543 original size:83 final size:84
Alignment explanation
Indices: 109165388--109165549 Score: 184
Period size: 83 Copynumber: 1.9 Consensus size: 84
109165378 TTATATATTC
* * * ** * *
109165388 TATTTTTTTTCCTTTTCTATATTTGATTTTCTATTTCTCATAAAGTATTAAATTCCCTTTTAAAT
1 TATTTTTTTTCATTTTCCATATTTGATTCTCTATTTCTCATAAAACATTAAATTCCATTTCAAAT
* *
109165453 GTTTATTTT-CATATCGAT
66 ATCTATTTTACATATCGAT
* * * *
109165471 TATTTTTTTT-ATTTTCCCATATTTGATTCTCTATTTTTCATAAAACATTCAATTCTATTTCATA
1 TATTTTTTTTCATTTT-CCATATTTGATTCTCTATTTCTCATAAAACATTAAATTCCATTTCAAA
109165535 TATCTATTTTACATA
65 TATCTATTTTACATA
109165550 ACTGTTATTC
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
82 4 0.06
83 56 0.88
84 4 0.06
ACGTcount: A:0.26, C:0.14, G:0.03, T:0.57
Consensus pattern (84 bp):
TATTTTTTTTCATTTTCCATATTTGATTCTCTATTTCTCATAAAACATTAAATTCCATTTCAAAT
ATCTATTTTACATATCGAT
Found at i:109165621 original size:19 final size:19
Alignment explanation
Indices: 109165599--109165665 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
109165589 CTCTCTCTCG
109165599 TCTCTATCTTTCTCTCATA
1 TCTCTATCTTTCTCTCATA
109165618 TCTCT-T-TTTCTCTCAT-
1 TCTCTATCTTTCTCTCATA
* * *
109165634 CCTTATATTTTTCTCTCATA
1 TC-TCTATCTTTCTCTCATA
* *
109165654 TTTCTTTCTTTC
1 TCTCTATCTTTC
109165666 GTACTCTTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
16 1 0.03
17 12 0.32
18 2 0.05
19 22 0.59
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (19 bp):
TCTCTATCTTTCTCTCATA
Found at i:109165822 original size:29 final size:30
Alignment explanation
Indices: 109165789--109165859 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
109165779 GCTTCCTTTT
109165789 TTTTTTCAATTTTATTTTCTATTTCAACT-A
1 TTTTTTCAATTTT-TTTTCTATTTCAACTAA
* * * * *
109165819 TTTTCTCAGTTTTTTTTTTGTTTCACCTAA
1 TTTTTTCAATTTTTTTTCTATTTCAACTAA
109165849 TTTTTTCAATT
1 TTTTTTCAATT
109165860 CCCATCAGTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.18, C:0.14, G:0.03, T:0.65
Consensus pattern (30 bp):
TTTTTTCAATTTTTTTTCTATTTCAACTAA
Found at i:109167172 original size:45 final size:46
Alignment explanation
Indices: 109167108--109167199 Score: 109
Period size: 45 Copynumber: 2.0 Consensus size: 46
109167098 ATAAATTTCA
* * *
109167108 TTTCTATATATTTTAAAATAAGAATTGTTTATTTAAAT-TTTATATAT
1 TTTCTATATATATTAAAATAAGAATTATTCA-TTAAATATTTA-ATAT
*
109167155 TTTCTAT-TATATT-AAATAATAATTATTCATTAAATATTTAATAT
1 TTTCTATATATATTAAAATAAGAATTATTCATTAAATATTTAATAT
109167199 T
1 T
109167200 AATATATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
44 11 0.28
45 17 0.43
46 5 0.12
47 7 0.17
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.54
Consensus pattern (46 bp):
TTTCTATATATATTAAAATAAGAATTATTCATTAAATATTTAATAT
Found at i:109174242 original size:25 final size:26
Alignment explanation
Indices: 109174201--109174307 Score: 175
Period size: 25 Copynumber: 4.2 Consensus size: 26
109174191 TGATACAAAT
109174201 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
109174227 TGATAAT-GGTTAGGTAAAT-TTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
109174251 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
109174277 TGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
109174302 TGATAA
1 TGATAA
109174308 GAATTCATGT
Statistics
Matches: 78, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
24 12 0.15
25 48 0.62
26 18 0.23
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:109176319 original size:136 final size:137
Alignment explanation
Indices: 109176074--109176359 Score: 538
Period size: 136 Copynumber: 2.1 Consensus size: 137
109176064 GAGTAGTCTC
109176074 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
109176139 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
109176204 ACTGTTA
131 ACTGTTA
*
109176211 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
109176275 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
109176340 ACTGTTA
131 ACTGTTA
**
109176347 CCTGAATGGGCTT
1 CCCAAATGGGCTT
109176360 AGGCCCAATA
Statistics
Matches: 146, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
136 126 0.86
137 20 0.14
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:109180150 original size:27 final size:27
Alignment explanation
Indices: 109180065--109180176 Score: 174
Period size: 26 Copynumber: 4.2 Consensus size: 27
109180055 TGATACAAAT
109180065 TGATAATGGGTTAGGTAAATG-TTCCA
1 TGATAATGGGTTAGGTAAATGTTTCCA
* *
109180091 TGATAATGGATTAGGTAAAT-ATTCCA
1 TGATAATGGGTTAGGTAAATGTTTCCA
109180117 TGATAATGGGTTAGGTAAATGTTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCCA
* *
109180144 TGATAATGGTTTAGGTAAATGTTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCCA
109180171 TGATAA
1 TGATAA
109180177 GAATTCATGT
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
26 43 0.54
27 36 0.46
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (27 bp):
TGATAATGGGTTAGGTAAATGTTTCCA
Found at i:109185784 original size:15 final size:14
Alignment explanation
Indices: 109185742--109185791 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
109185732 ATAACTTTGA
*
109185742 ATGCAAATGATGTG
1 ATGCAAATGATGAG
109185756 ATG-AAATGTTATGAG
1 ATGCAAATG--ATGAG
109185771 ATGCAAATGCATGA-
1 ATGCAAATG-ATGAG
109185785 ATGCAAA
1 ATGCAAA
109185792 AGAATATCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 11 0.35
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (14 bp):
ATGCAAATGATGAG
Found at i:109189630 original size:21 final size:21
Alignment explanation
Indices: 109189606--109189670 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
109189596 AAAAATAAAG
109189606 GAAAATATAATAACAATAATA
1 GAAAATATAATAACAATAATA
* * *
109189627 GAAAATACAACAATAATAATA
1 GAAAATATAATAACAATAATA
109189648 GTAAAAGATATAATAAC-ATAATA
1 G--AAA-ATATAATAACAATAATA
109189671 ATATAATAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 19 0.54
23 9 0.26
24 7 0.20
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (21 bp):
GAAAATATAATAACAATAATA
Found at i:109189751 original size:3 final size:3
Alignment explanation
Indices: 109189745--109189865 Score: 70
Period size: 3 Copynumber: 39.7 Consensus size: 3
109189735 AAAGTAGTGC
* * *
109189745 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-C TAT TAA GTTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
* * * * *
109189790 TGAA -AA TAA TGA TAA TGA TGA T-A TAT TAGA TAA TAA TAGT TAA -AA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA
* *
109189835 TAA TAA GTAA CAA TAA TAAA TTA TAA TAA TA
1 TAA TAA -TAA TAA TAA T-AA TAA TAA TAA TA
109189866 GTGATGAGAA
Statistics
Matches: 92, Mismatches: 16, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
2 7 0.08
3 71 0.77
4 14 0.15
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:109189884 original size:16 final size:16
Alignment explanation
Indices: 109189865--109189896 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
109189855 TTATAATAAT
109189865 AGTGATGAGAATAACA
1 AGTGATGAGAATAACA
*
109189881 AGTGATGATAATAACA
1 AGTGATGAGAATAACA
109189897 GTAACAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (16 bp):
AGTGATGAGAATAACA
Found at i:109190029 original size:16 final size:15
Alignment explanation
Indices: 109190000--109190042 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
109189990 TATACGTATG
*
109190000 AAAAATAATGATAGT
1 AAAAATAATAATAGT
109190015 AAAATATAATAATAGT
1 AAAA-ATAATAATAGT
*
109190031 AATAATAATAAT
1 AAAAATAATAAT
109190043 GGAATGAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
AAAAATAATAATAGT
Found at i:109190148 original size:3 final size:3
Alignment explanation
Indices: 109190140--109190178 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
109190130 CTACCATATT
109190140 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
109190179 TAGAAATACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:109190286 original size:3 final size:3
Alignment explanation
Indices: 109190272--109190307 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
109190262 AAATATACAC
109190272 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
109190308 TATTAAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:109190732 original size:30 final size:28
Alignment explanation
Indices: 109190696--109190766 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
109190686 TTTTGTTCTC
109190696 GAATCTCAAAAAAAAGAAAAATCTCCTCTT
1 GAATCTC-AAAAAAA-AAAAATCTCCTCTT
*
109190726 GAATCTC-AAAAAAAAAAATCTCTTCTT
1 GAATCTCAAAAAAAAAAAATCTCCTCTT
*
109190753 GAATCTCCAAAAAA
1 GAATCTCAAAAAAA
109190767 TCTCTTCTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 20 0.51
28 12 0.31
30 7 0.18
ACGTcount: A:0.51, C:0.20, G:0.06, T:0.24
Consensus pattern (28 bp):
GAATCTCAAAAAAAAAAAATCTCCTCTT
Found at i:109190989 original size:11 final size:11
Alignment explanation
Indices: 109190973--109191000 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
109190963 GGTTTTTTTC
109190973 TTTTTTGATTT
1 TTTTTTGATTT
109190984 TTTTTTGATTT
1 TTTTTTGATTT
109190995 TTTTTT
1 TTTTTT
109191001 TTGGGTTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (11 bp):
TTTTTTGATTT
Found at i:109190989 original size:13 final size:13
Alignment explanation
Indices: 109190967--109191003 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
109190957 AGATTAGGTT
109190967 TTTTTCTTTTTTGA
1 TTTTT-TTTTTTGA
109190981 --TTTTTTTTTGA
1 TTTTTTTTTTTGA
109190992 TTTTTTTTTTTG
1 TTTTTTTTTTTG
109191004 GGTTGGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 8 0.38
12 3 0.14
13 10 0.48
ACGTcount: A:0.05, C:0.03, G:0.08, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTTTGA
Found at i:109190996 original size:12 final size:12
Alignment explanation
Indices: 109190968--109191001 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
109190958 GATTAGGTTT
109190968 TTTTCTTTTTTGA
1 TTTT-TTTTTTGA
109190981 -TTTTTTTTTGA
1 TTTTTTTTTTGA
109190992 TTTTTTTTTT
1 TTTTTTTTTT
109191002 TGGGTTGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTTGA
Found at i:109195991 original size:3 final size:3
Alignment explanation
Indices: 109195985--109196014 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
109195975 ATAAGAGTAT
109195985 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
109196015 TCTACAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:109196127 original size:37 final size:37
Alignment explanation
Indices: 109196056--109196127 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
109196046 CAAAAAATAT
* *
109196056 ATATAAAATATTTACAATAATGATGTAAATAAACAAC
1 ATATAAAATATTTACAATAATCATATAAATAAACAAC
109196093 ATATAAAATATTTGA-AATAA-CATATAAATGAAACA
1 ATATAAAATATTT-ACAATAATCATATAAAT-AAACA
109196128 TAAAAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.74
38 1 0.03
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29
Consensus pattern (37 bp):
ATATAAAATATTTACAATAATCATATAAATAAACAAC
Found at i:109196692 original size:20 final size:22
Alignment explanation
Indices: 109196666--109196730 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
109196656 TATGTATATA
109196666 GAAAGAAGAAGAAAAAAAA-AC
1 GAAAGAAGAAGAAAAAAAATAC
* *
109196687 -AAAGAAAAAAAGAAAAAAAATTC
1 GAAAG--AAGAAGAAAAAAAATAC
*
109196710 GAAAAAAGAGAGAAAAAAAAT
1 GAAAGAAGA-AGAAAAAAAAT
109196731 GCAAACCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 4 0.11
22 16 0.46
23 12 0.34
24 3 0.09
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (22 bp):
GAAAGAAGAAGAAAAAAAATAC
Found at i:109196716 original size:22 final size:24
Alignment explanation
Indices: 109196674--109196735 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
109196664 TAGAAAGAAG
109196674 AAGAAAAAAAA-ACAAAGAAAA-A
1 AAGAAAAAAAATACAAAGAAAAGA
* *
109196696 AAGAAAAAAAATTCGAA-AAAAGA
1 AAGAAAAAAAATACAAAGAAAAGA
* *
109196719 GAGAAAAAAAATGCAAA
1 AAGAAAAAAAATACAAA
109196736 CCTTTTTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.77, C:0.05, G:0.13, T:0.05
Consensus pattern (24 bp):
AAGAAAAAAAATACAAAGAAAAGA
Found at i:109199298 original size:31 final size:27
Alignment explanation
Indices: 109199234--109199299 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 27
109199224 TATTTTTCTC
109199234 AATTTTTAAAGTTAGGACTAAATTGAT
1 AATTTTTAAAGTTAGGACTAAATTGAT
*
109199261 AGATTTTGTAAATGTTGAGGACTAAATTTATT
1 A-ATTTT-TAAA-GTT-AGGACTAAATTGA-T
109199293 AATTTTT
1 AATTTTT
109199300 TTTAGAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 1 0.03
28 5 0.15
29 4 0.12
30 4 0.12
31 17 0.52
32 2 0.06
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.45
Consensus pattern (27 bp):
AATTTTTAAAGTTAGGACTAAATTGAT
Found at i:109199329 original size:62 final size:62
Alignment explanation
Indices: 109199236--109199356 Score: 147
Period size: 62 Copynumber: 2.0 Consensus size: 62
109199226 TTTTTCTCAA
* * * * * **
109199236 TTTTTAAAGTTAGGACTAAATTGATAGATTTTGTAAATGTTGAG-GACTAAATTTATTAATTT
1 TTTTTAAAGTTAGAACTAAAATAATAAATTTTATAAACATTGAGCG-CTAAATTTATTAATTT
109199298 TTTTTAGAA-TTAGAACTAAAATAATAAATTTTATAAACATTGAGCGCTAAATTTATTAA
1 TTTTTA-AAGTTAGAACTAAAATAATAAATTTTATAAACATTGAGCGCTAAATTTATTAA
109199357 ACATTTTATA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 47 0.94
63 3 0.06
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.42
Consensus pattern (62 bp):
TTTTTAAAGTTAGAACTAAAATAATAAATTTTATAAACATTGAGCGCTAAATTTATTAATTT
Found at i:109204661 original size:11 final size:10
Alignment explanation
Indices: 109204643--109204677 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
109204633 GAAGGGAAGG
109204643 AAAGAAAGAA
1 AAAGAAAGAA
109204653 AAGAGAAAGAA
1 AA-AGAAAGAA
109204664 AAAGAAAGGAA
1 AAAGAAA-GAA
109204675 AAA
1 AAA
109204678 TAGGGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.30
11 16 0.70
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:109204863 original size:22 final size:22
Alignment explanation
Indices: 109204838--109204882 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
109204828 CAAATGGAAG
*
109204838 AATTAAGAGTTA-AAGTGATAGA
1 AATTAA-AGTTAGAAGTGAGAGA
*
109204860 AATTCAAGTTAGAAGTGAGAGA
1 AATTAAAGTTAGAAGTGAGAGA
109204882 A
1 A
109204883 GGATTGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.49, C:0.02, G:0.24, T:0.24
Consensus pattern (22 bp):
AATTAAAGTTAGAAGTGAGAGA
Found at i:109205359 original size:17 final size:16
Alignment explanation
Indices: 109205328--109205371 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
109205318 TTAAAAATGT
109205328 ATTG-AATTGATATTG
1 ATTGAAATTGATATTG
109205343 ATTGAAATTGTATATTG
1 ATTGAAATTG-ATATTG
109205360 ATTGGAAATTGA
1 ATT-GAAATTGA
109205372 ATTATGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 10 0.38
18 7 0.27
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.43
Consensus pattern (16 bp):
ATTGAAATTGATATTG
Found at i:109205385 original size:18 final size:17
Alignment explanation
Indices: 109205328--109205386 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
109205318 TTAAAAATGT
109205328 ATTG-AATTG-ATATTG
1 ATTGAAATTGAATATTG
*
109205343 ATTGAAATTGTATATTG
1 ATTGAAATTGAATATTG
109205360 ATTGGAAATTGAAT-TATG
1 ATT-GAAATTGAATAT-TG
109205378 AATTGAAAT
1 -ATTGAAAT
109205387 ACCCTATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
15 4 0.11
16 5 0.13
17 10 0.26
18 16 0.42
19 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (17 bp):
ATTGAAATTGAATATTG
Found at i:109207603 original size:16 final size:16
Alignment explanation
Indices: 109207562--109207608 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
109207552 GGATCTAAGT
109207562 TTTCTTGTTTATTTCAG
1 TTTCTT-TTTATTTCAG
109207579 TTT-TGTTTTATTTCA-
1 TTTCT-TTTTATTTCAG
109207594 TCTTCTTTTTATTTC
1 T-TTCTTTTTATTTC
109207609 TATTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 21 0.78
17 5 0.19
ACGTcount: A:0.11, C:0.13, G:0.06, T:0.70
Consensus pattern (16 bp):
TTTCTTTTTATTTCAG
Found at i:109207618 original size:16 final size:15
Alignment explanation
Indices: 109207569--109207618 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
109207559 AGTTTTCTTG
*
109207569 TTTATTTCAGTTTTGT
1 TTTATTTCA-TTTTTT
*
109207585 TTTATTTCATCTTCTT
1 TTTATTTCAT-TTTTT
109207601 TTTATTTCTATTTTTT
1 TTTATTTC-ATTTTTT
109207617 TT
1 TT
109207619 CTTACTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 26 0.90
17 2 0.07
ACGTcount: A:0.12, C:0.10, G:0.04, T:0.74
Consensus pattern (15 bp):
TTTATTTCATTTTTT
Found at i:109208493 original size:26 final size:26
Alignment explanation
Indices: 109208464--109208742 Score: 100
Period size: 26 Copynumber: 10.8 Consensus size: 26
109208454 TTAGATACCT
109208464 TTTATTTTAAACTATTTTATATATTA
1 TTTATTTTAAACTATTTTATATATTA
* *
109208490 TTTA-TTTAAA-AATTTTATATGTTA
1 TTTATTTTAAACTATTTTATATATTA
** * * * *
109208514 TTTA-GATATATTATTCTATATGTTAA
1 TTTATTTTAAACTATTTTATATATT-A
* * *
109208540 TCT-CTTTAAGTTCCT-TTTTAT-TATT-
1 TTTATTTTAA---ACTATTTTATATATTA
* **
109208565 TTTATTTTGAACT-TTCCATATATTA
1 TTTATTTTAAACTATTTTATATATTA
* *
109208590 TTTATTTTTAAA-TATTTGTATATACTC
1 TTTA-TTTTAAACTATTT-TATATATTA
* *
109208617 TTTATTTTAAACTACTTTATGTATTA
1 TTTATTTTAAACTATTTTATATATTA
*
109208643 TTATCTATTTAAA--ATTTTCATATATAGTA
1 TT-TAT-TTTAAACTATTTT-ATATAT--TA
* * * * *
109208672 TTTAGTTTAAATTGTTTTATATGTTC
1 TTTATTTTAAACTATTTTATATATTA
* * *
109208698 CTCATTTTAAA--ACTTT-TATATTA
1 TTTATTTTAAACTATTTTATATATTA
* *
109208721 TTTATTTTAAGCTCTTTTATAT
1 TTTATTTTAAACTATTTTATAT
109208743 GTTTTCAAAA
Statistics
Matches: 180, Mismatches: 50, Indels: 46
0.65 0.18 0.17
Matches are distributed among these distances:
23 19 0.11
24 26 0.14
25 27 0.15
26 52 0.29
27 30 0.17
28 17 0.09
29 9 0.05
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (26 bp):
TTTATTTTAAACTATTTTATATATTA
Found at i:109208950 original size:23 final size:24
Alignment explanation
Indices: 109208877--109209016 Score: 86
Period size: 26 Copynumber: 5.6 Consensus size: 24
109208867 ATCTTTTTGC
* *
109208877 ATATTGTTTATTCTAAATCATTTCAT
1 ATATTATTTATTTTAAATC-TTT-AT
*
109208903 ATATTATTTATTTTAAATTTTTTTAT
1 ATATTATTTATTTTAAA--TCTTTAT
*
109208929 ATATTATTTTTTTTAAA-CTTTAT
1 ATATTATTTATTTTAAATCTTTAT
* * * * *
109208952 ATATCTTTTTACTTTAATTGGTTTCAC
1 ATAT-TATTTATTTTAAAT-CTTT-AT
* * *
109208979 CTATTAGTTATTTTAAACCTTGT-T
1 ATATTATTTATTTTAAATCTT-TAT
109209003 ATATTATTTATTTT
1 ATATTATTTATTTT
109209017 TATATTATTT
Statistics
Matches: 86, Mismatches: 21, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
23 9 0.10
24 21 0.24
25 2 0.02
26 46 0.53
27 7 0.08
28 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.61
Consensus pattern (24 bp):
ATATTATTTATTTTAAATCTTTAT
Found at i:109209120 original size:13 final size:13
Alignment explanation
Indices: 109209102--109209126 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109209092 TTGTTTTCAT
109209102 ATTATTTCATATA
1 ATTATTTCATATA
109209115 ATTATTTCATAT
1 ATTATTTCATAT
109209127 TGTCCATTAG
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATTTCATATA
Found at i:109214346 original size:17 final size:17
Alignment explanation
Indices: 109214314--109214351 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
109214304 TTTATAACTT
109214314 TATTTATTTAATTTTAA
1 TATTTATTTAATTTTAA
*
109214331 GTATTT-TTTTATTTTAA
1 -TATTTATTTAATTTTAA
109214348 TATT
1 TATT
109214352 AATACTTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 10 0.53
18 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TATTTATTTAATTTTAA
Found at i:109221244 original size:24 final size:25
Alignment explanation
Indices: 109221217--109221264 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
109221207 AAATATTATA
* *
109221217 TAAAAAAGTAAAA-AAAATTAAAAT
1 TAAAAAACTAAAATAAAATAAAAAT
*
109221241 TAAAAATCTAAAATAAAATAAAAA
1 TAAAAAACTAAAATAAAATAAAAA
109221265 AAGCACTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (25 bp):
TAAAAAACTAAAATAAAATAAAAAT
Found at i:109236430 original size:17 final size:17
Alignment explanation
Indices: 109236408--109236444 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
109236398 ATTGAGGAAA
109236408 ATGGATTATATGAAACC
1 ATGGATTATATGAAACC
109236425 ATGGATTATATGAAACC
1 ATGGATTATATGAAACC
109236442 ATG
1 ATG
109236445 ATTCCATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (17 bp):
ATGGATTATATGAAACC
Found at i:109240497 original size:210 final size:210
Alignment explanation
Indices: 109240113--109240497 Score: 472
Period size: 211 Copynumber: 1.8 Consensus size: 210
109240103 CTTTAATTAA
* * ** *
109240113 TTTCCCGATTGTTTCACCTATGACACACAACAAGCTTTTCTTGTATGTAAAATCTGACAAACTCA
1 TTTCCCGATTGTTTCACCTATGACACACAACAAGCTTCTCTAGTAAATAAAATCTGACAAAATCA
* * *
109240178 ATAATCATATCCAAACAACTACCTTCAAAAGATACGATTTCGTAATAGAAAAACTTAGGAACCAT
66 ATAATCATATCCAAACAAATACCTTCAAAAGATAAGATTTCGTAATAAAAAAACTTAGGAACCAT
* * *
109240243 GGTTCAGCCATCAGATACTGATCAAACACAACCCATGGACCCTTAGTGAATACCGTTGTTTACTA
131 GGTTCAACCATCAGATACTGATCAAACACAACCCAAGCACCCTTAGTGAATACCGTTGTTTACTA
109240308 GTCAACTCTAATTGC
196 GTCAACTCTAATTGC
* ** * *
109240323 TTTCGCGATTGTTTCATTTATGACACACAATTAAGCTTCTCTAGTAAATAAAA-CTTGATAAAAT
1 TTTCCCGATTGTTTCACCTATGACACACAA-CAAGCTTCTCTAGTAAATAAAATC-TGACAAAAT
* * ** * *
109240387 CAATAATCATATCCAAGCAAATATCTTCAAGTGATAAGATTTCGTAGTAAAAAAAC-TCGGAACC
64 CAATAATCATATCCAAACAAATACCTTCAAAAGATAAGATTTCGTAATAAAAAAACTTAGGAACC
* * * *
109240451 ATGGTTCAAACC-TCAGATATTGGCTC-AACTCAATCCAAGCACCCTTA
129 ATGGTTC-AACCATCAGATACT-GATCAAACACAACCCAAGCACCCTTA
109240498 ACAAATACCC
Statistics
Matches: 145, Mismatches: 26, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
210 67 0.46
211 78 0.54
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.29
Consensus pattern (210 bp):
TTTCCCGATTGTTTCACCTATGACACACAACAAGCTTCTCTAGTAAATAAAATCTGACAAAATCA
ATAATCATATCCAAACAAATACCTTCAAAAGATAAGATTTCGTAATAAAAAAACTTAGGAACCAT
GGTTCAACCATCAGATACTGATCAAACACAACCCAAGCACCCTTAGTGAATACCGTTGTTTACTA
GTCAACTCTAATTGC
Found at i:109240713 original size:28 final size:27
Alignment explanation
Indices: 109240681--109240762 Score: 73
Period size: 28 Copynumber: 3.1 Consensus size: 27
109240671 AAATGTCTTT
109240681 TTAATTCATTTATTTATAATGCTAAATC
1 TTAATTCATTTATTTATAAT-CTAAATC
* * *
109240709 TTAATTTTATTT-TTTAT-A--TACATA
1 TTAA-TTCATTTATTTATAATCTAAATC
*
109240733 ATAATTCATTTATTTATAATCTTAAATC
1 TTAATTCATTTATTTATAATC-TAAATC
109240761 TT
1 TT
109240763 GATTTTAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
23 6 0.15
24 12 0.30
25 1 0.03
27 1 0.03
28 14 0.35
29 6 0.15
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.55
Consensus pattern (27 bp):
TTAATTCATTTATTTATAATCTAAATC
Found at i:109240904 original size:33 final size:33
Alignment explanation
Indices: 109240862--109240929 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
109240852 CTAATAAGAA
109240862 TCATTATATGCATTCCAATTGCCAGCACTTCCT
1 TCATTATATGCATTCCAATTGCCAGCACTTCCT
*
109240895 TCATTATATGCATTCCAATTGCTAGCACTTCCT
1 TCATTATATGCATTCCAATTGCCAGCACTTCCT
109240928 TC
1 TC
109240930 TCTACGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.38
Consensus pattern (33 bp):
TCATTATATGCATTCCAATTGCCAGCACTTCCT
Found at i:109246255 original size:19 final size:18
Alignment explanation
Indices: 109246231--109246278 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
109246221 ATTTTTATAT
109246231 ATTTTAATACTACGTACA
1 ATTTTAATACTACGTACA
* * *
109246249 CATTTTATTATTACGTATA
1 -ATTTTAATACTACGTACA
109246268 AGTTTTAATAC
1 A-TTTTAATAC
109246279 ATACATTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.46
Consensus pattern (18 bp):
ATTTTAATACTACGTACA
Found at i:109251671 original size:21 final size:21
Alignment explanation
Indices: 109251646--109251699 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
109251636 TGCAAGGCAT
109251646 ACACGCCCGTGTGGCCAAGGG
1 ACACGCCCGTGTGGCCAAGGG
* * *
109251667 ACACGCCCGTGAGGTCATGGG
1 ACACGCCCGTGTGGCCAAGGG
*
109251688 ACACACCCGTGT
1 ACACGCCCGTGT
109251700 CTCAGGCCGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.13
Consensus pattern (21 bp):
ACACGCCCGTGTGGCCAAGGG
Found at i:109252981 original size:41 final size:38
Alignment explanation
Indices: 109252849--109252982 Score: 110
Period size: 40 Copynumber: 3.4 Consensus size: 38
109252839 ACCAGTTTGG
* *
109252849 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAAGTTGA
1 CACCCAGTGCCTCATC-GATTATCCGAAGTAAT-AGTTGA
* * * * *
109252889 CACCCAATGTCTCATCGGCTTAACCGAAGTAA-A-TTGG
1 CACCCAGTGCCTCATC-GATTATCCGAAGTAATAGTTGA
* *
109252926 TACCCAGTACCTCATCGAATTTATCCGAAGTAATAGTTTGA
1 CACCCAGTGCCTCATCG-A-TTATCCGAAGTAATAG-TTGA
*
109252967 CACCCAGTGTCTCATC
1 CACCCAGTGCCTCATC
109252983 AACTCGAAGT
Statistics
Matches: 72, Mismatches: 17, Indels: 9
0.73 0.17 0.09
Matches are distributed among these distances:
36 1 0.01
37 15 0.21
38 13 0.18
39 1 0.01
40 26 0.36
41 16 0.22
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGATTATCCGAAGTAATAGTTGA
Found at i:109253789 original size:12 final size:12
Alignment explanation
Indices: 109253772--109253799 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
109253762 ATAAAATTTA
109253772 ATAATATAATAT
1 ATAATATAATAT
109253784 ATAATATAATAT
1 ATAATATAATAT
109253796 ATAA
1 ATAA
109253800 AACATAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATATAATAT
Found at i:109256095 original size:33 final size:32
Alignment explanation
Indices: 109256053--109256126 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
109256043 AAATAAGTAC
*
109256053 ATTTGTATTATTTATGCA-TAATTATTGAAAAGAT
1 ATTT-TATTATTTAT-CATTAATTAGT-AAAAGAT
*
109256087 ATTTTATTATTTATTATTAATTAGTAAAAGAT
1 ATTTTATTATTTATCATTAATTAGTAAAAGAT
109256119 A-TTTATTA
1 ATTTTATTA
109256127 GATGTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
31 7 0.19
32 9 0.24
33 17 0.46
34 4 0.11
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.51
Consensus pattern (32 bp):
ATTTTATTATTTATCATTAATTAGTAAAAGAT
Found at i:109256146 original size:31 final size:32
Alignment explanation
Indices: 109256071--109256146 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
109256061 TATTTATGCA
*
109256071 TAATTATTGAAAAGATATTTTATTATTTATTAT
1 TAATTATT-AAAAGATATTTTATTATGTATTAT
*
109256104 TAATTAGTAAAAGATA-TTTATTAGATGT-TTAT
1 TAATTATTAAAAGATATTTTATT--ATGTATTAT
109256136 T-ATTATTAAAA
1 TAATTATTAAAA
109256147 TTATTAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
31 15 0.39
32 13 0.34
33 10 0.26
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (32 bp):
TAATTATTAAAAGATATTTTATTATGTATTAT
Found at i:109257267 original size:18 final size:18
Alignment explanation
Indices: 109257244--109257280 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
109257234 ATGGACTAGG
109257244 TAGTATTTAATACTAAGA
1 TAGTATTTAATACTAAGA
109257262 TAGTATTTAATACTAAGA
1 TAGTATTTAATACTAAGA
109257280 T
1 T
109257281 TCTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (18 bp):
TAGTATTTAATACTAAGA
Found at i:109264258 original size:3 final size:3
Alignment explanation
Indices: 109264244--109264297 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
109264234 GACAATAAAG
*
109264244 AAT AAT AGT AAT AAT AAT AAT -AT AGAT AAT AAT -AT ATAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT
109264288 AAT AAT AAT A
1 AAT AAT AAT A
109264298 GTTAGAGATA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 6 0.14
3 32 0.73
4 6 0.14
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:109264466 original size:28 final size:28
Alignment explanation
Indices: 109264413--109264466 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
109264403 TATTTAAAAT
* *
109264413 ATATGTATATAAAAATAGTAGTAAAAGG
1 ATATGTATATAAAAATAATAGAAAAAGG
*
109264441 ATATGTATATATATAATAATA-AAAAA
1 ATATGTATATA-AAAATAATAGAAAAA
109264467 TGACATTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 15 0.68
29 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (28 bp):
ATATGTATATAAAAATAATAGAAAAAGG
Found at i:109264511 original size:3 final size:3
Alignment explanation
Indices: 109264503--109264614 Score: 63
Period size: 3 Copynumber: 37.3 Consensus size: 3
109264493 TATAAATATG
* * * *
109264503 ATA ATA ATA ATA ATG ATA ATG ATA ATA ATA ATA AT- ATA GTA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
109264550 ATA A-A AGTA A-A ATTA ATA GTA A-A TTG ATA ATA ATA AT- GTA CATTA
1 ATA ATA A-TA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA -A-TA
*
109264595 ATA ACA ATA ATA ATA TATA A
1 ATA ATA ATA ATA ATA -ATA A
109264615 AGGATAGGAA
Statistics
Matches: 83, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
2 8 0.10
3 65 0.78
4 8 0.10
5 2 0.02
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:109264926 original size:35 final size:32
Alignment explanation
Indices: 109264884--109264977 Score: 100
Period size: 37 Copynumber: 2.8 Consensus size: 32
109264874 TATGCATAAC
109264884 AATAAAAATACAATATTAAAATATATATACGAGT
1 AATAAAAATACAATATTAAAATATATATAC-A-T
**
109264918 AATAAAAAATGTATCCGTATTAAAA-ATATATACAT
1 AAT-AAAAA--TA-CAATATTAAAATATATATACAT
109264953 AATAAAAATACAATATTTAAAATAT
1 AATAAAAATACAATA-TTAAAATAT
109264978 TTACGCAGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
31 3 0.06
32 8 0.16
33 2 0.04
34 8 0.16
35 9 0.18
36 1 0.02
37 10 0.20
38 9 0.18
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (32 bp):
AATAAAAATACAATATTAAAATATATATACAT
Found at i:109264958 original size:17 final size:17
Alignment explanation
Indices: 109264900--109264962 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
109264890 AATACAATAT
109264900 TAAAATATATATACGAGTAA
1 TAAAA-ATATATAC-A-TAA
* * * *
109264920 TAAAAAATGTATCCGTAT
1 T-AAAAATATATACATAA
109264938 TAAAAATATATACATAA
1 TAAAAATATATACATAA
109264955 TAAAAATA
1 TAAAAATA
109264963 CAATATTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 20 0.59
18 3 0.09
20 7 0.21
21 4 0.12
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (17 bp):
TAAAAATATATACATAA
Found at i:109265125 original size:23 final size:23
Alignment explanation
Indices: 109265089--109265133 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
109265079 GTACATAACA
109265089 TAAATATCATACATATA-ATATC
1 TAAATATCATACATATATATATC
109265111 TAAATATACATACATATATATAT
1 TAAATAT-CATACATATATATAT
109265134 ATAGTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.33
23 10 0.48
24 4 0.19
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAATATCATACATATATATATC
Found at i:109265885 original size:21 final size:21
Alignment explanation
Indices: 109265855--109265898 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
109265845 TTCGAAAATA
109265855 AAATAAAAAGGAAAA-AATAAT
1 AAATAAAAA-GAAAATAATAAT
*
109265876 AAATAGAAAGAAAATAATAAT
1 AAATAAAAAGAAAATAATAAT
109265897 AA
1 AA
109265899 TGTAATATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (21 bp):
AAATAAAAAGAAAATAATAAT
Found at i:109266246 original size:6 final size:6
Alignment explanation
Indices: 109266235--109266260 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
109266225 TGATTTAAGG
109266235 TTTCTT TTTCTT TTTCTT TTTCTT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TT
109266261 GTTTTGGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:109268894 original size:32 final size:32
Alignment explanation
Indices: 109268846--109268936 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 32
109268836 ATATTCAAGT
* * *
109268846 AATATTACTTG-A-AGTTATATTTATTTATGA
1 AATATTAATTGAATAGTTATATCTATTTAGGA
* *
109268876 AATGTTATTTGAATAGTTATATCTATTTAGGA
1 AATATTAATTGAATAGTTATATCTATTTAGGA
* *
109268908 TATATTAATTGAATAATTATATCTATTTA
1 AATATTAATTGAATAGTTATATCTATTTA
109268937 AAAGGTATGA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 9 0.18
31 1 0.02
32 41 0.80
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.49
Consensus pattern (32 bp):
AATATTAATTGAATAGTTATATCTATTTAGGA
Found at i:109278362 original size:14 final size:14
Alignment explanation
Indices: 109278338--109278371 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
109278328 TAGATTGGGT
109278338 TTCTT-TTGTATTC
1 TTCTTGTTGTATTC
*
109278351 TTTTTGTTGTATTC
1 TTCTTGTTGTATTC
109278365 TTCTTGT
1 TTCTTGT
109278372 AGTGTATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.06, C:0.12, G:0.12, T:0.71
Consensus pattern (14 bp):
TTCTTGTTGTATTC
Found at i:109290836 original size:2 final size:2
Alignment explanation
Indices: 109290829--109290859 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
109290819 CCCGTGAACC
109290829 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
109290860 AACAGCATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:109292858 original size:24 final size:24
Alignment explanation
Indices: 109292793--109292867 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 24
109292783 TATACATTAT
109292793 ATCAATAAATAAATTAATTTTTTTA
1 ATCAA-AAATAAATTAATTTTTTTA
* *
109292818 GTTCAAAAATTAA-TAATTTTTTTA
1 -ATCAAAAATAAATTAATTTTTTTA
* *
109292842 AT-AATGAATAAATTAATCATTTTTA
1 ATCAA-AAATAAATTAAT-TTTTTTA
109292867 A
1 A
109292868 AAAAATGATT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
22 2 0.05
23 6 0.15
24 15 0.38
25 13 0.32
26 4 0.10
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (24 bp):
ATCAAAAATAAATTAATTTTTTTA
Found at i:109292874 original size:27 final size:27
Alignment explanation
Indices: 109292824--109292875 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
109292814 TTTAGTTCAA
** *
109292824 AAATTAATAATTTTTTTAATAATGAAT
1 AAATTAATAATTTTTAAAAAAATGAAT
*
109292851 AAATTAATCATTTTTAAAAAAATGA
1 AAATTAATAATTTTTAAAAAAATGA
109292876 TTATTAATGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (27 bp):
AAATTAATAATTTTTAAAAAAATGAAT
Found at i:109295967 original size:35 final size:35
Alignment explanation
Indices: 109295921--109295993 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
109295911 GCTACAGTAT
109295921 TTTATTAATAAAAAATAGCATCGCTTTATTTGTCC
1 TTTATTAATAAAAAATAGCATCGCTTTATTTGTCC
109295956 TTTATTAATAAAAAATAGCATCGCTTTATTTGTCC
1 TTTATTAATAAAAAATAGCATCGCTTTATTTGTCC
109295991 TTT
1 TTT
109295994 TTTACTCAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (35 bp):
TTTATTAATAAAAAATAGCATCGCTTTATTTGTCC
Found at i:109296713 original size:2 final size:2
Alignment explanation
Indices: 109296706--109296751 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
109296696 TCATTTAATT
* * *
109296706 TA TA TA TA TA TA TA TA TA TA TA TT TA -A TA AA TA TA TG TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
109296746 TA TA TA
1 TA TA TA
109296752 AATTTTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:109296752 original size:17 final size:17
Alignment explanation
Indices: 109296706--109296754 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
109296696 TCATTTAATT
*
109296706 TATATATA-TATATATA
1 TATATATATTATATAAA
109296722 TATATAT-TTA-ATAAA
1 TATATATATTATATAAA
*
109296737 TATATGTATTATATAAA
1 TATATATATTATATAAA
109296754 T
1 T
109296755 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 10 0.36
16 12 0.43
17 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TATATATATTATATAAA
Found at i:109298770 original size:31 final size:32
Alignment explanation
Indices: 109298735--109298803 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
109298725 TTATAAAATG
109298735 GTCACTA-AACTATTC-AAATGTTTTCATTCAA
1 GTCACTATAACTATTCGAAA-GTTTTCATTCAA
** *
109298766 GTCAC-ATAACTATTCGAAAGTTTTTGTTTAA
1 GTCACTATAACTATTCGAAAGTTTTCATTCAA
109298797 GTCACTA
1 GTCACTA
109298804 GACAATGAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 1 0.03
31 27 0.84
32 4 0.12
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.39
Consensus pattern (32 bp):
GTCACTATAACTATTCGAAAGTTTTCATTCAA
Found at i:109301101 original size:33 final size:33
Alignment explanation
Indices: 109301064--109301130 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
109301054 TTTTTGTTTA
** *
109301064 TCTAAAGTAACCCTAATGATTTTGTATGACTTT
1 TCTAAAGTAACCAAAATGACTTTGTATGACTTT
109301097 TCTAAAGTAACCAAAATGACTTTGTATGACTTT
1 TCTAAAGTAACCAAAATGACTTTGTATGACTTT
109301130 T
1 T
109301131 TATGGAGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (33 bp):
TCTAAAGTAACCAAAATGACTTTGTATGACTTT
Found at i:109307603 original size:2 final size:2
Alignment explanation
Indices: 109307596--109307620 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
109307586 AATCAATGCT
109307596 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
109307621 TCTTTGAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:109310078 original size:30 final size:30
Alignment explanation
Indices: 109310043--109310099 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
109310033 CGTAATGAAA
109310043 AAAAGGATATTCATATATGATAGTACGTAG
1 AAAAGGATATTCATATATGATAGTACGTAG
109310073 AAAAGGATATTCATATATGATAGTACG
1 AAAAGGATATTCATATATGATAGTACG
109310100 CATACGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (30 bp):
AAAAGGATATTCATATATGATAGTACGTAG
Found at i:109314279 original size:57 final size:55
Alignment explanation
Indices: 109314150--109314345 Score: 169
Period size: 55 Copynumber: 3.5 Consensus size: 55
109314140 TTTTCAATCG
* ** * * * * * * * *
109314150 ATTGTTTTTTATGTTTAAATAAATTGTCATGTTGAAATGTTGTTTCTTTTAAATAT
1 ATTG-TTTATATGTTTAAATCGATTGTTATGATGGAATATTGCTTATTTTGAATAA
* * * **
109314206 ATTATTTATATGTTTAAATCGATTGTTATGATGGAATACTACTTCTT-TTTTTAATTG
1 ATTGTTTATATGTTTAAATCGATTGTTATGATGGAATA-T--TGCTTATTTTGAATAA
* * *
109314263 ATTGTTTATATATTTAAATGGATTGTTATGTTGGAATATTGCTTATTTTGAATAA
1 ATTGTTTATATGTTTAAATCGATTGTTATGATGGAATATTGCTTATTTTGAATAA
*
109314318 ATTGTTTATATGTTCAAATCGATTGTTA
1 ATTGTTTATATGTTTAAATCGATTGTTA
109314346 CATAACAAGT
Statistics
Matches: 112, Mismatches: 24, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
54 4 0.04
55 59 0.53
56 5 0.04
57 41 0.37
58 3 0.03
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (55 bp):
ATTGTTTATATGTTTAAATCGATTGTTATGATGGAATATTGCTTATTTTGAATAA
Found at i:109314326 original size:112 final size:113
Alignment explanation
Indices: 109314140--109314345 Score: 270
Period size: 112 Copynumber: 1.8 Consensus size: 113
109314130 TAGAATATTC
* * * * *
109314140 TTTTCAATCGATTGTTTTTTATGTTTAAATAAATTGTCATGTTGAAATGTTGTTTCTTTTAAATA
1 TTTTCAATCGATTGTTTTATATATTTAAATAAATTGTCATGTTGAAATATTGCTTATTTTAAATA
* *
109314205 TATTATTTATATGTTTAAATCGATTGTTATGATGGAATACTACTTCTT
66 AATTATTTATATGTTCAAATCGATTGTTATGATGGAATACTACTTCTT
* * ** * * *
109314253 TTTTTAATTGATTG-TTTATATATTTAAATGGATTGTTATGTTGGAATATTGCTTATTTTGAATA
1 TTTTCAATCGATTGTTTTATATATTTAAATAAATTGTCATGTTGAAATATTGCTTATTTTAAATA
*
109314317 AATTGTTTATATGTTCAAATCGATTGTTA
66 AATTATTTATATGTTCAAATCGATTGTTA
109314346 CATAACAAGT
Statistics
Matches: 78, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
112 66 0.85
113 12 0.15
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (113 bp):
TTTTCAATCGATTGTTTTATATATTTAAATAAATTGTCATGTTGAAATATTGCTTATTTTAAATA
AATTATTTATATGTTCAAATCGATTGTTATGATGGAATACTACTTCTT
Found at i:109314838 original size:190 final size:189
Alignment explanation
Indices: 109314515--109314895 Score: 645
Period size: 190 Copynumber: 2.0 Consensus size: 189
109314505 ATCTCACCCC
*
109314515 TTCAATATGCTTTTCCACGTCCAAGAGTCAGGTGATCATCTCTGCACGTCTAGAAATTTTTTATT
1 TTCAATATGCTTTTCCACGTCCAAGAGTCAGGTGATCATCTCTGCACATCTAGAAATTTTTTATT
* * *
109314580 AGAGCAGTATTTAGTTAAGAACGTAGCATGGGCCACAGCATGTAGCCTTGTGAGTATTCATCAGG
66 AGAGCAGTATTTAGTTAAGAACGTAGCATGAGCCACAGCATGCAACCTTGTGAGTATTCATCAGG
109314645 CTTGTTTGCAAAGAACTGCATCGTTCATTACTTCAGCTTAACGGATGTCCAATCCATCCT
131 CTTGTTTGCAAAGAACTGCATCGTTCATTA-TTCAGCTTAACGGATGTCCAATCCATCCT
* * *
109314705 TTCAATATGCTTTTCCACGTCCAAGAGTCGGGTGATCGTCTCTGTACATCTAGAAATTTTTTATT
1 TTCAATATGCTTTTCCACGTCCAAGAGTCAGGTGATCATCTCTGCACATCTAGAAATTTTTTATT
*
109314770 AGAGCAGTATTTAGTTAAGAACGTAGCATGAGCCTCAGCATGCAACCTTGTGAGTATTCATCAGG
66 AGAGCAGTATTTAGTTAAGAACGTAGCATGAGCCACAGCATGCAACCTTGTGAGTATTCATCAGG
* * * *
109314835 CTTGTTTGCAAAGAAGTGCATCGTTCATTATTCAGCTTAACGTATGTCGAATCTATCCT
131 CTTGTTTGCAAAGAACTGCATCGTTCATTATTCAGCTTAACGGATGTCCAATCCATCCT
109314894 TT
1 TT
109314896 TGTTTTCACC
Statistics
Matches: 179, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
189 28 0.16
190 151 0.84
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (189 bp):
TTCAATATGCTTTTCCACGTCCAAGAGTCAGGTGATCATCTCTGCACATCTAGAAATTTTTTATT
AGAGCAGTATTTAGTTAAGAACGTAGCATGAGCCACAGCATGCAACCTTGTGAGTATTCATCAGG
CTTGTTTGCAAAGAACTGCATCGTTCATTATTCAGCTTAACGGATGTCCAATCCATCCT
Found at i:109322704 original size:3 final size:3
Alignment explanation
Indices: 109322696--109322730 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
109322686 AATTTATACT
109322696 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
109322731 TTCTTTCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:109324094 original size:14 final size:14
Alignment explanation
Indices: 109324070--109324103 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
109324060 TCTCTACTTC
109324070 GTTTCTGTTTCTTTT
1 GTTTCTGTTTC-TTT
109324085 GTTT-TGTTTCTTT
1 GTTTCTGTTTCTTT
109324098 GTTTCT
1 GTTTCT
109324104 TTAATTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.39
14 7 0.39
15 4 0.22
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.74
Consensus pattern (14 bp):
GTTTCTGTTTCTTT
Found at i:109330045 original size:14 final size:14
Alignment explanation
Indices: 109330021--109330054 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
109330011 TCTCTACTTC
109330021 GTTTCTGTTTCTTTT
1 GTTTCTGTTTC-TTT
109330036 GTTT-TGTTTCTTT
1 GTTTCTGTTTCTTT
109330049 GTTTCT
1 GTTTCT
109330055 TTAATTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.39
14 7 0.39
15 4 0.22
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.74
Consensus pattern (14 bp):
GTTTCTGTTTCTTT
Found at i:109330104 original size:11 final size:12
Alignment explanation
Indices: 109330088--109330137 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
109330078 TTTATTAACA
109330088 TAATATA-ATAT
1 TAATATATATAT
109330099 TAATATCATATAT
1 TAATAT-ATATAT
* *
109330112 TAATATATCTTT
1 TAATATATATAT
*
109330124 TAATTTA-ATAT
1 TAATATATATAT
109330135 TAA
1 TAA
109330138 GTAAATTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
11 11 0.34
12 11 0.34
13 10 0.31
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATATATATAT
Found at i:109345140 original size:6 final size:7
Alignment explanation
Indices: 109345122--109345153 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
109345112 TAATTAATAA
109345122 ATTTTTT
1 ATTTTTT
109345129 ATTTTTT
1 ATTTTTT
109345136 ATTTTTT
1 ATTTTTT
*
109345143 ATTTTTA
1 ATTTTTT
109345150 ATTT
1 ATTT
109345154 ATCTTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (7 bp):
ATTTTTT
Found at i:109345242 original size:15 final size:15
Alignment explanation
Indices: 109345213--109345251 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
109345203 AAATATAATT
109345213 ATTTTTAGTAAATATA
1 ATTTTTA-TAAATATA
*
109345229 ATTTTTATATATATA
1 ATTTTTATAAATATA
*
109345244 ATATTTAT
1 ATTTTTAT
109345252 TTTTCAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
ATTTTTATAAATATA
Found at i:109345249 original size:17 final size:18
Alignment explanation
Indices: 109345203--109345249 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
109345193 TAATTATTGC
109345203 AAATATAATTATTTTTAGT
1 AAATATAA-TATTTTTAGT
109345222 AAATAT-A-ATTTTTA-T
1 AAATATAATATTTTTAGT
*
109345237 ATATATAATATTT
1 AAATATAATATTT
109345250 ATTTTTCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 6 0.24
16 8 0.32
17 4 0.16
18 1 0.04
19 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
AAATATAATATTTTTAGT
Found at i:109345512 original size:22 final size:22
Alignment explanation
Indices: 109345482--109345523 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
109345472 AATACTTTAT
*
109345482 TAATGATATAATTATTATTAAA
1 TAATAATATAATTATTATTAAA
**
109345504 TAATAATATTTTTATTATTA
1 TAATAATATAATTATTATTA
109345524 TGTAGGTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TAATAATATAATTATTATTAAA
Found at i:109347196 original size:23 final size:23
Alignment explanation
Indices: 109347152--109347196 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
109347142 ATTAATATTT
* *
109347152 ATATTATTAAACTATATTTAATA
1 ATATTACTAAACTATATATAATA
109347175 ATATTACT-AACTATAATATAAT
1 ATATTACTAAACTAT-ATATAAT
109347197 TGAATTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATTACTAAACTATATATAATA
Found at i:109350127 original size:32 final size:32
Alignment explanation
Indices: 109350081--109350143 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
109350071 TCAACTTTGT
*
109350081 ATACTAATTTTAATTAAATTATATAATATTTC
1 ATACCAATTTTAATTAAATTATATAATATTTC
109350113 ATACCAATTTTAATTAAATTATATAATATTT
1 ATACCAATTTTAATTAAATTATATAATATTT
109350144 ATTATTAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.49
Consensus pattern (32 bp):
ATACCAATTTTAATTAAATTATATAATATTTC
Found at i:109350480 original size:11 final size:11
Alignment explanation
Indices: 109350466--109350506 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
109350456 TGTTTTCTCC
109350466 CTATTTTGCTA
1 CTATTTTGCTA
*
109350477 CTATTTTACTA
1 CTATTTTGCTA
* *
109350488 TTATGTTGCTA
1 CTATTTTGCTA
109350499 CTATTTTG
1 CTATTTTG
109350507 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:109350746 original size:12 final size:12
Alignment explanation
Indices: 109350725--109350758 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
109350715 TATATATTTT
*
109350725 AAAATTATATAA
1 AAAATAATATAA
109350737 AAAATAATATAA
1 AAAATAATATAA
*
109350749 AAATTAATAT
1 AAAATAATAT
109350759 GGGCGGACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:109353869 original size:22 final size:22
Alignment explanation
Indices: 109353844--109353940 Score: 97
Period size: 22 Copynumber: 4.5 Consensus size: 22
109353834 AGAGCATTAT
*
109353844 AGTGCTAAACAGAGAGTACCGA
1 AGTGCTAAACAGAGAGCACCGA
* *
109353866 AGTGCCAAGCAGAGAGCACC-A
1 AGTGCTAAACAGAGAGCACCGA
* * * *
109353887 AATGCTAAGCAAACAGCACCGA
1 AGTGCTAAACAGAGAGCACCGA
* *
109353909 AGTGCTAAATAGAGAGCACCAA
1 AGTGCTAAACAGAGAGCACCGA
*
109353931 AGTGCAAAAC
1 AGTGCTAAAC
109353941 TCGTACAAGC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
21 17 0.29
22 42 0.71
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.10
Consensus pattern (22 bp):
AGTGCTAAACAGAGAGCACCGA
Found at i:109353894 original size:43 final size:44
Alignment explanation
Indices: 109353844--109353940 Score: 115
Period size: 43 Copynumber: 2.2 Consensus size: 44
109353834 AGAGCATTAT
* * * *
109353844 AGTGCTAAACAGAGAGTACCGAAGTGCCAAGCAGAGAGCACCAA
1 AGTGCTAAACAAACAGCACCGAAGTGCCAAACAGAGAGCACCAA
* * *
109353888 A-TGCTAAGCAAACAGCACCGAAGTGCTAAATAGAGAGCACCAA
1 AGTGCTAAACAAACAGCACCGAAGTGCCAAACAGAGAGCACCAA
*
109353931 AGTGCAAAAC
1 AGTGCTAAAC
109353941 TCGTACAAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
43 36 0.84
44 7 0.16
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.10
Consensus pattern (44 bp):
AGTGCTAAACAAACAGCACCGAAGTGCCAAACAGAGAGCACCAA
Found at i:109357281 original size:49 final size:49
Alignment explanation
Indices: 109357159--109357605 Score: 662
Period size: 49 Copynumber: 9.1 Consensus size: 49
109357149 GTACGTAATA
109357159 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATG----TAT
*
109357212 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
*
109357261 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGGAAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
109357310 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATG--TAT
109357361 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATG--TAT
* * *
109357412 ATATATGTGTGATAAGGCCTAATGGTCGATGTGATGAATATGAAAGTGTAT
1 ATATA--TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
*
109357463 ATATATGTG---A----TAA-GGCC--TGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
109357502 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
* *
109357551 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
109357600 ATATAT
1 ATATAT
109357606 ATGTGGTAAA
Statistics
Matches: 368, Mismatches: 12, Indels: 32
0.89 0.03 0.08
Matches are distributed among these distances:
39 30 0.08
41 3 0.01
42 4 0.01
46 4 0.01
47 4 0.01
49 173 0.47
51 67 0.18
53 83 0.23
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.31
Consensus pattern (49 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTAT
Found at i:109357484 original size:39 final size:39
Alignment explanation
Indices: 109357441--109357519 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
109357431 TAATGGTCGA
109357441 TGTGATGAATATGAAAGTGTATATATATGTGATAAGGCC
1 TGTGATGAATATGAAAGTGTATATATATGTGATAAGGCC
*
109357480 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TGTGATGAATATGAAAGTGTATATATATGTGATAAGGCC
109357519 T
1 T
109357520 AATGGCCGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (39 bp):
TGTGATGAATATGAAAGTGTATATATATGTGATAAGGCC
Found at i:109357530 original size:88 final size:91
Alignment explanation
Indices: 109357388--109357568 Score: 296
Period size: 88 Copynumber: 2.0 Consensus size: 91
109357378 TAATGGCCGA
*
109357388 TGTGATGAATGTGAAAATGTATATATATATGTGTGATAAGGCCTAATGGTCGATGTGATGAATAT
1 TGTGATGAATGTGAAAATGTATATATATA-GTGTGATAAGGCCTAATGGCCGATGTGATGAATAT
*
109357453 GAAAGTGTATATATATGTGATAAGGCC
65 GAAAATGTATATATATGTGATAAGGCC
* *
109357480 TGTGATGAATGTG-AAA-GTGTATATATA-TGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
1 TGTGATGAATGTGAAAATGTATATATATAGTGTGATAAGGCCTAATGGCCGATGTGATGAATATG
109357542 AAAATGTATATATATGTGATAAGGCC
66 AAAATGTATATATATGTGATAAGGCC
109357568 T
1 T
109357569 AATGGCCGAC
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
88 59 0.69
90 10 0.12
91 3 0.04
92 13 0.15
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (91 bp):
TGTGATGAATGTGAAAATGTATATATATAGTGTGATAAGGCCTAATGGCCGATGTGATGAATATG
AAAATGTATATATATGTGATAAGGCC
Found at i:109364449 original size:17 final size:17
Alignment explanation
Indices: 109364427--109364460 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
109364417 CTTCCTTTTT
109364427 GACTCTTTAATAAACGA
1 GACTCTTTAATAAACGA
109364444 GACTCTTTAATAAACGA
1 GACTCTTTAATAAACGA
109364461 AGTTGTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (17 bp):
GACTCTTTAATAAACGA
Found at i:109364879 original size:24 final size:24
Alignment explanation
Indices: 109364851--109364897 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
109364841 ATTTTAGCCC
*
109364851 TTAACTTTTA-TATTTTTTGTTAAT
1 TTAACCTTTATTATTTTTT-TTAAT
109364875 TTAACCTTTATTATTTTTTTTAA
1 TTAACCTTTATTATTTTTTTTAA
109364898 AGTTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (24 bp):
TTAACCTTTATTATTTTTTTTAAT
Found at i:109364903 original size:25 final size:24
Alignment explanation
Indices: 109364851--109364903 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
109364841 ATTTTAGCCC
* *
109364851 TTAACTTTTATATTTTTTGTTAAT
1 TTAACCTTTATATTTTTTGTTAAG
109364875 TTAACCTTTATTATTTTTT-TTAAAG
1 TTAACCTTTA-TATTTTTTGTT-AAG
109364900 TTAA
1 TTAA
109364904 ATTTAGTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (24 bp):
TTAACCTTTATATTTTTTGTTAAG
Found at i:109368604 original size:16 final size:17
Alignment explanation
Indices: 109368579--109368612 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
109368569 TATTATTTAA
109368579 ATTTAATTTTAA-AAAT
1 ATTTAATTTTAATAAAT
*
109368595 ATTTATTTTTAATAAAT
1 ATTTAATTTTAATAAAT
109368612 A
1 A
109368613 ATAAATTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTAATTTTAATAAAT
Found at i:109370129 original size:16 final size:16
Alignment explanation
Indices: 109370108--109370142 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
109370098 TAAAGTGAAA
*
109370108 AGAAAATAGGAAGGAT
1 AGAAAATAGGAAGAAT
*
109370124 AGAAAATTGGAAGAAT
1 AGAAAATAGGAAGAAT
109370140 AGA
1 AGA
109370143 TCAATAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (16 bp):
AGAAAATAGGAAGAAT
Found at i:109373449 original size:293 final size:292
Alignment explanation
Indices: 109372920--109373462 Score: 681
Period size: 293 Copynumber: 1.9 Consensus size: 292
109372910 CTATTGTTCA
* *
109372920 TAGTTGGAGTCAGAATTGTGCTTACGGTTAGAGTTTTCATTTATTTGTTTTATTTAGATTTAATT
1 TAGTTGGAGTCAAAATAGTGCTTACGGTTAGAGTTTTCATTTATTTGTTTTATTTAGATTTAATT
* * **
109372985 TTGTTTTCTTTATTTTTATTTCATTTTTATTTAATTTCTATTATTTATTTTAGATTTAGATCCAA
66 TTGTTTTCTTTATTTTTATTTAATTTTTATTTAA-TTCTAATATAGATTTTAGATTTAGATCCAA
* * * * ** *
109373050 TATTTATTTTCTTTAATTTAGCAAATTTGTCTACTTTTGGTCATAAGAAATTGTAAAATTAATCA
130 TATTTATTCTCTTTAATTTAGAAAATTTGTCTAATCTTGGTCATAAGAAATCATAAAATTAACCA
* * ** * ** *
109373115 GTTCAATCTCAGTGGGATTGATCCTACTTGCTATTCTGTAAATTTAATTTAATTTTGATTTAGGC
195 ATTCAATCTCAGTGAGATCAACCCTACTCACTATACTGTAAATTTAATTTAATTTTGATTTAGGC
109373180 GAAGGAGAAAATTTATTGTCTGAGATCAATTTG
260 GAAGGAGAAAATTTATTGTCTGAGATCAATTTG
109373213 TAGTTGGAGTCAAAATCAG-GCTTGA-GGTTAGAGTTTTCATTTATTTGTTTTATTTAGATTTAA
1 TAGTTGGAGTCAAAAT-AGTGCTT-ACGGTTAGAGTTTTCATTTATTTGTTTTATTTAGATTTAA
*
109373276 TTTTGTTTTAC-TTATTTTTATTTAATTTTTA-TT-A-TCTAATATAGA-TTTAGATTTAGAT-T
64 TTTTGTTTT-CTTTATTTTTATTTAATTTTTATTTAATTCTAATATAGATTTTAGATTTAGATCC
*
109373335 TATATTTAATCTCTCTTTATTTATTTTCA-AAAATTTGTCTAATCTTGGTCATAAGAAATCATAA
128 AATATTT-AT-TCTCTTTA---A-TTT-AGAAAATTTGTCTAATCTTGGTCATAAGAAATCATAA
* ** *
109373399 AATTAACCAATTCAGTCTTTGTGAGATCAACCCTACTCATTATACTGTAAATTTAATTTAATTT
186 AATTAACCAATTCAATCTCAGTGAGATCAACCCTACTCACTATACTGTAAATTTAATTTAATTT
109373463 CGGTTTAAGC
Statistics
Matches: 213, Mismatches: 27, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
287 6 0.03
288 15 0.07
289 15 0.07
291 1 0.00
292 3 0.01
293 169 0.79
294 4 0.02
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.49
Consensus pattern (292 bp):
TAGTTGGAGTCAAAATAGTGCTTACGGTTAGAGTTTTCATTTATTTGTTTTATTTAGATTTAATT
TTGTTTTCTTTATTTTTATTTAATTTTTATTTAATTCTAATATAGATTTTAGATTTAGATCCAAT
ATTTATTCTCTTTAATTTAGAAAATTTGTCTAATCTTGGTCATAAGAAATCATAAAATTAACCAA
TTCAATCTCAGTGAGATCAACCCTACTCACTATACTGTAAATTTAATTTAATTTTGATTTAGGCG
AAGGAGAAAATTTATTGTCTGAGATCAATTTG
Found at i:109379827 original size:19 final size:19
Alignment explanation
Indices: 109379803--109379842 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
109379793 TGAGGCAAAT
109379803 CCTCCAGTACGTGGACAAG
1 CCTCCAGTACGTGGACAAG
109379822 CCTCCAGTACGTGGACAAG
1 CCTCCAGTACGTGGACAAG
109379841 CC
1 CC
109379843 ACTTTCAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.35, G:0.25, T:0.15
Consensus pattern (19 bp):
CCTCCAGTACGTGGACAAG
Found at i:109379968 original size:24 final size:26
Alignment explanation
Indices: 109379932--109379979 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
109379922 TCAAACATGC
109379932 ATTTAGGTCAATTTAAC-CCTAGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGT
* *
109379957 ATTTCGGT-AATTTATCTCCTAGG
1 ATTTAGGTCAATTTAACTCCTAGG
109379980 TAAAACTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACTCCTAGGGT
Found at i:109381493 original size:26 final size:26
Alignment explanation
Indices: 109381462--109381569 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
109381452 ATGAAATTCC
*
109381462 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
109381488 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
109381514 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
109381540 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
109381566 ATCA
1 ATCA
109381570 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:109386374 original size:11 final size:12
Alignment explanation
Indices: 109386356--109386385 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
109386346 AGTACTACCT
109386356 CGGCCTCGACCA
1 CGGCCTCGACCA
109386368 C-GCCTCGACCA
1 CGGCCTCGACCA
109386379 CGGCCTC
1 CGGCCTC
109386386 TTCCCCGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.13, C:0.53, G:0.23, T:0.10
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:109388012 original size:24 final size:26
Alignment explanation
Indices: 109387976--109388026 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
109387966 TCAAACATGC
109387976 ATTTAGGTCAATTTAAC-CCTAGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGT
* *
109388001 ATTTCGGT-AATTTATCTCCTAGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGT
109388026 A
1 A
109388027 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACTCCTAGGGT
Found at i:109389545 original size:26 final size:25
Alignment explanation
Indices: 109389509--109389586 Score: 111
Period size: 26 Copynumber: 3.0 Consensus size: 25
109389499 ATTCCCATCG
109389509 TGGAACATTTACCTAACCTATTATCA
1 TGGAACATTTACCTAACC-ATTATCA
*
109389535 TGGAATATTTACCTAATCCATTATCA
1 TGGAACATTTACCTAA-CCATTATCA
*
109389561 TGAAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAA-CCATTATCA
109389587 ATTTGTATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
26 45 0.96
27 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.35
Consensus pattern (25 bp):
TGGAACATTTACCTAACCATTATCA
Found at i:109414656 original size:33 final size:33
Alignment explanation
Indices: 109414593--109414659 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
109414583 CCTAACCCCC
109414593 CCCCAAAAAAAAGAAGAAAAAAGAAAAACCTAA
1 CCCCAAAAAAAAGAAGAAAAAAGAAAAACCTAA
*
109414626 CCCCAAAAAAAAGAAGAAAACAGAAAAACCTAA
1 CCCCAAAAAAAAGAAGAAAAAAGAAAAACCTAA
109414659 C
1 C
109414660 AAAAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.67, C:0.21, G:0.09, T:0.03
Consensus pattern (33 bp):
CCCCAAAAAAAAGAAGAAAAAAGAAAAACCTAA
Found at i:109414663 original size:30 final size:31
Alignment explanation
Indices: 109414595--109414668 Score: 112
Period size: 33 Copynumber: 2.3 Consensus size: 31
109414585 TAACCCCCCC
109414595 CCAAAAAAAAGAAGAAAAAAGAAAAACCTAA
1 CCAAAAAAAAGAAGAAAAAAGAAAAACCTAA
*
109414626 CCCCAAAAAAAAGAAGAAAACAGAAAAACCTAA
1 --CCAAAAAAAAGAAGAAAAAAGAAAAACCTAA
*
109414659 CAAAAAAAAA
1 CCAAAAAAAA
109414669 ACTAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 9 0.23
33 30 0.77
ACGTcount: A:0.73, C:0.16, G:0.08, T:0.03
Consensus pattern (31 bp):
CCAAAAAAAAGAAGAAAAAAGAAAAACCTAA
Found at i:109415864 original size:23 final size:21
Alignment explanation
Indices: 109415838--109415879 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
109415828 TATTTCTATT
*
109415838 TTATTTTTATTTGTCAATATTAA
1 TTATTATTA-TTGT-AATATTAA
109415861 TTATTATTATTGTAATATT
1 TTATTATTATTGTAATATT
109415880 TTGATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 4 0.22
23 8 0.44
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (21 bp):
TTATTATTATTGTAATATTAA
Found at i:109415892 original size:16 final size:15
Alignment explanation
Indices: 109415868--109415902 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
109415858 TAATTATTAT
109415868 TATTGTAATATTTTGA
1 TATTGTAATATTTT-A
*
109415884 TATTTTAATATTTTA
1 TATTGTAATATTTTA
109415899 TATT
1 TATT
109415903 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (15 bp):
TATTGTAATATTTTA
Found at i:109419750 original size:17 final size:16
Alignment explanation
Indices: 109419725--109419782 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
109419715 CGACAGTCAT
*
109419725 AAAAGAAAAGAAAAACA
1 AAAAAAAAAGAAAAA-A
109419742 AAAAAAAAAG-AAAAA
1 AAAAAAAAAGAAAAAA
* *
109419757 GAAAAAAAGGACAAAAA
1 AAAAAAAAAGA-AAAAA
109419774 AAAAAAAAA
1 AAAAAAAAA
109419783 ATCAAATGCC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 9 0.26
16 4 0.12
17 21 0.62
ACGTcount: A:0.86, C:0.03, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAA
Found at i:109419770 original size:28 final size:27
Alignment explanation
Indices: 109419725--109419783 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 27
109419715 CGACAGTCAT
109419725 AAAAGAAAAGAAAAACAAAAAAAAAAGA
1 AAAAGAAAAGAAAAACAAAAAAAAAA-A
*
109419753 AAAAGAAAA-AAAGGACAAAAAAAAAAA
1 AAAAGAAAAGAAA-AACAAAAAAAAAAA
109419780 AAAA
1 AAAA
109419784 TCAAATGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.86, C:0.03, G:0.10, T:0.00
Consensus pattern (27 bp):
AAAAGAAAAGAAAAACAAAAAAAAAAA
Found at i:109422269 original size:76 final size:74
Alignment explanation
Indices: 109422128--109422828 Score: 516
Period size: 72 Copynumber: 9.4 Consensus size: 74
109422118 TTTTCAAAAA
*
109422128 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
109422193 TCTGTTGTC
66 TCTGTTGTC
* * *
109422202 AAAAAAATCAACTCGTATTGCGAGCGGCGAGTTGAGCCTCAGGTCACACG-TCGAGGTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG--ACACGCT-GAGGTAATTTCA
* *
109422266 ATTTCCGTTTTTC
63 ATTTCTG-TTGTC
*** * * *
109422279 AATTTTTGTTTTTCAAAAA--AA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
1 AA------------AAAAATCAACTC-A-T-ATTGCGAGAG--GCGAGTTGAGCCTCAGGACACG
*
109422341 CTGAGGTAATTTCAATTTCTGTTTTC
49 CTGAGGTAATTTCAATTTCTGTTGTC
* *** * * *
109422367 --AAAAATGAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
* *
109422430 TTTGTCTTTC
66 TCTGT-TGTC
* * * * *
109422440 -AAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
*
109422504 TTTG-TGT-
66 TCTGTTGTC
*** ** * * *
109422511 TTTAATTTCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
*
109422576 TCTGTTTTC
66 TCTGTTGTC
*** * * * *
109422585 --AAAAATCAACTCATATTGCGAGAAATGAGTTGAGTCTCAAGACATGCTGAGGTATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
* *
109422648 TTTGTCTTTC
66 TCTGT-TGTC
*** * * *
109422658 -AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
*
109422722 TTTG-TGT-
66 TCTGTTGTC
*** ** * * *
109422729 TTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGATGAGGTAATTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
109422794 TCTGTTTGTC
66 TCTG-TTGTC
*
109422804 --AAGAATCAACTCATATTGCGAGAGG
1 AAAAAAATCAACTCATATTGCGAGAGG
109422829 TGGGTTGAAC
Statistics
Matches: 511, Mismatches: 80, Indels: 73
0.77 0.12 0.11
Matches are distributed among these distances:
72 213 0.42
73 31 0.06
74 174 0.34
75 2 0.00
76 25 0.05
77 8 0.02
86 2 0.00
87 2 0.00
88 6 0.01
89 32 0.06
90 1 0.00
91 15 0.03
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (74 bp):
AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
TCTGTTGTC
Found at i:109422279 original size:14 final size:14
Alignment explanation
Indices: 109422260--109422294 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
109422250 CGTCGAGGTA
109422260 TTTTCAATTTCCGT
1 TTTTCAATTTCCGT
**
109422274 TTTTCAATTTTTGT
1 TTTTCAATTTCCGT
109422288 TTTTCAA
1 TTTTCAA
109422295 AAAAATCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.14, G:0.06, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTCCGT
Found at i:109422396 original size:72 final size:73
Alignment explanation
Indices: 109422274--109422836 Score: 704
Period size: 72 Copynumber: 7.7 Consensus size: 73
109422264 CAATTTCCGT
*
109422274 TTTTCAATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
1 TTTTCAATTTTTGTCTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
109422339 CGCTGAGGTA
64 CGCTGAGGTA
* * * ** ** *
109422349 ATTTCAATTTCTGT-TTTCAAAAATGAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATG
1 TTTTCAATTTTTGTCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
109422413 CTGAGGTA
66 CTGAGGTA
* *
109422421 TTTTCAATTTTTGTCTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCAC
1 TTTTCAATTTTTGTCTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
109422486 GCTGAGGTA
65 GCTGAGGTA
* * ** *
109422495 TTTTCAATTTTTGTGTTT-TAATTTCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACG
1 TTTTCAATTTTTGTCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
109422559 CTGAGGTA
66 CTGAGGTA
* * ** * ** *
109422567 ATTTCAATTTCTGT-TTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGTCTCAAGACATG
1 TTTTCAATTTTTGTCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
109422631 CTGAGGTA
66 CTGAGGTA
** *
109422639 TTTTCAATTTTTGTCTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCAC
1 TTTTCAATTTTTGTCTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
109422704 GCTGAGGTA
65 GCTGAGGTA
* * ** * *
109422713 TTTTCAATTTTTGTGTTT-TAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATG
1 TTTTCAATTTTTGTCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
*
109422777 ATGAGGTA
66 CTGAGGTA
* * * *
109422785 ATTTCAATTTCTGT-TTGTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGA
1 TTTTCAATTTTTGTCTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
109422837 ACCTTTTAAT
Statistics
Matches: 420, Mismatches: 61, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
71 5 0.01
72 234 0.56
73 36 0.09
74 133 0.32
75 12 0.03
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (73 bp):
TTTTCAATTTTTGTCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
CTGAGGTA
Found at i:109422542 original size:146 final size:144
Alignment explanation
Indices: 109422274--109422826 Score: 714
Period size: 146 Copynumber: 3.8 Consensus size: 144
109422264 CAATTTCCGT
*
109422274 TTTTCAATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
1 TTTTCAATTTTTG-TTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
*
109422339 CGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATGAACTCATATTGCGAGAAATGAGTTGAGCCT
63 CGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
** *
109422404 CAAGACATGCTGAGGTA
128 CGGGACACGCTGAGGTA
* * *
109422421 TTTTCAATTTTTGTCTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCAC
1 TTTTCAATTTTTGT-TTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* * * ** * **
109422486 GCTGAGGTATTTTCAATTTTTGTGTTT-TAATTTCAACTCATATTGTGAGAGGTGAGTTGAGCCT
64 GCTGAGGTAATTTCAATTTCTGT-TTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
109422550 CGGGACACGCTGAGGTA
128 CGGGACACGCTGAGGTA
* * ** * * *
109422567 ATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGTCTCAAGACATGC
1 TTTTCAATTTTTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
* *
109422632 TGAGGTATTTTCAATTTTTGTCTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
66 TGAGGTAATTTCAATTTCTGT-TTTC-AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
*
109422697 GGGGCACGCTGAGGTA
129 GGGACACGCTGAGGTA
* ** *
109422713 TTTTCAATTTTTGTGTTT-TAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATG
1 TTTTCAATTTTTGT-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
* *
109422777 ATGAGGTAATTTCAATTTCTGTTTGTCAAGAATCAACTCATATTGCGAGA
65 CTGAGGTAATTTCAATTTCTGTTT-TCAAAAATCAACTCATATTGCGAGA
109422827 GGTGGGTTGA
Statistics
Matches: 355, Mismatches: 45, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
144 63 0.18
145 28 0.08
146 241 0.68
147 23 0.06
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (144 bp):
TTTTCAATTTTTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGG
GACACGCTGAGGTA
Found at i:109422690 original size:218 final size:218
Alignment explanation
Indices: 109422300--109422826 Score: 955
Period size: 218 Copynumber: 2.4 Consensus size: 218
109422290 TTCAAAAAAA
109422300 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTT
*
109422365 TCAAAAATGAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATT
66 TCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATT
* **
109422430 TTTGTCTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTA
131 TTTGTCTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCTGAGGTA
109422495 TTTTCAATTTTTGTGTTTTAATT
196 TTTTCAATTTTTGTGTTTTAATT
*
109422518 TCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTT
*
109422583 TCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGTCTCAAGACATGCTGAGGTATTTTCAATT
66 TCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATT
109422648 TTTGTCTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCTGAGGTA
131 TTTGTCTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCTGAGGTA
109422713 TTTTCAATTTTTGTGTTTTAATT
196 TTTTCAATTTTTGTGTTTTAATT
* * *
109422736 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGATGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTT
*
109422801 GTCAAGAATCAACTCATATTGCGAGA
66 -TCAAAAATCAACTCATATTGCGAGA
109422827 GGTGGGTTGA
Statistics
Matches: 297, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
218 273 0.92
219 24 0.08
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (218 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTT
TCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATT
TTTGTCTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCTGAGGTA
TTTTCAATTTTTGTGTTTTAATT
Found at i:109423020 original size:116 final size:117
Alignment explanation
Indices: 109422812--109423031 Score: 327
Period size: 116 Copynumber: 1.9 Consensus size: 117
109422802 TCAAGAATCA
* *
109422812 ACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTGAACATTTTAATTTCTACTTTTTCAAAATCAACTCATATTGC
* *
109422877 GAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTTTAAATTG
66 GAGAAGTGAGTCGAGCCTCAGGGCACGCTGAGGTATTTTTAGTTTTAAATTG
* **
109422929 ACTCATATTGCGAGAGGTGAGTT-AAGCATTTTTATTT-TTGTTTTTCAAAATCAACTCATATTG
1 ACTCATATTGCGAGAGGTGAGTTGAA-CATTTTAATTTCTACTTTTTCAAAATCAACTCATATTG
* * *
109422992 CTAGAGGTGAGTCGAGCCTCAGGTCACGCTGAGGTATTTT
65 CGAGAAGTGAGTCGAGCCTCAGGGCACGCTGAGGTATTTT
109423032 CAATTTTTGT
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
116 61 0.66
117 31 0.34
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (117 bp):
ACTCATATTGCGAGAGGTGAGTTGAACATTTTAATTTCTACTTTTTCAAAATCAACTCATATTGC
GAGAAGTGAGTCGAGCCTCAGGGCACGCTGAGGTATTTTTAGTTTTAAATTG
Found at i:109423202 original size:87 final size:86
Alignment explanation
Indices: 109423051--109423462 Score: 355
Period size: 87 Copynumber: 4.8 Consensus size: 86
109423041 TGTTTTAATT
* * **
109423051 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGAGTTACATA-TCGAGGTATTTTCAAAATCTG
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTG-GTCACACACT-GAGGTATTTTCAATTTCTG
109423115 TTTTTCAAGTTAAGTTTCAAAAA
64 TTTTTCAAGTTAAGTTTCAAAAA
* * *
109423138 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTTCAATTTCTGT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG-TCACACACTGAGGTATTTTCAATTTCTGT
* * * *
109423203 TTTT-AATGTCT-ATTTTTAGAGAG
65 TTTTCAA-GT-TAAGTTTCA-AAAA
* * ** * *
109423226 TCAATTAATATTGCGA-AAATGAGTTGA-ACTTCAGATCACACACTGAGGTA--TT---TTT-T-
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTT--GGTCACACACTGAGGTATTTTCAATTTCTG
* *
109423282 TTTTTCAATTTATATTTTTCAAAAA
64 TTTTTCAAGTTA-A-GTTTCAAAAA
* * *
109423307 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGAGTCACATATTGAGGTATTTTCAAAATT-TG
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTG-GTCACACACTGAGGTATTTTC-AATTTCTG
*
109423371 CTTTTCAAGTTAAGTTTCAAAAA
64 TTTTTCAAGTTAAGTTTCAAAAA
* * * * * *
109423394 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTAACGCGCTGAGCTATTTTCAATGTCTAT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG-TCACACACTGAGGTATTTTCAATTTCTGT
109423459 TTTT
65 TTTT
109423463 AGAGAGTCAA
Statistics
Matches: 256, Mismatches: 46, Indels: 46
0.74 0.13 0.13
Matches are distributed among these distances:
79 1 0.00
80 6 0.02
81 21 0.08
82 30 0.12
83 3 0.01
84 2 0.01
85 2 0.01
86 10 0.04
87 148 0.58
88 23 0.09
89 10 0.04
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (86 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGTCACACACTGAGGTATTTTCAATTTCTGTT
TTTCAAGTTAAGTTTCAAAAA
Found at i:109424204 original size:33 final size:32
Alignment explanation
Indices: 109424167--109424239 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 32
109424157 TAACCCCCCC
109424167 AAAAAAAAAGAAGAAAAAAGAAAAACCTAACCA
1 AAAAAAAAAGAAGAAAAAAGAAAAACCTAA-CA
*
109424200 AAAAAAAAAGAAGAAAACAGAAAAACCTAACA
1 AAAAAAAAAGAAGAAAAAAGAAAAACCTAACA
109424232 AAAAAAAA
1 AAAAAAAA
109424240 CTAAAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 10 0.26
33 29 0.74
ACGTcount: A:0.78, C:0.11, G:0.08, T:0.03
Consensus pattern (32 bp):
AAAAAAAAAGAAGAAAAAAGAAAAACCTAACA
Found at i:109424234 original size:18 final size:17
Alignment explanation
Indices: 109424181--109424239 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 17
109424171 AAAAAGAAGA
109424181 AAAAAGAAAAACCTAACC
1 AAAAAGAAAAACCTAA-C
* *
109424199 AAAAA-AAAAA--GAAG
1 AAAAAGAAAAACCTAAC
109424213 AAAACAGAAAAACCTAAC
1 AAAA-AGAAAAACCTAAC
109424231 AAAAA-AAAA
1 AAAAAGAAAA
109424240 CTAAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 4 0.12
15 3 0.09
16 9 0.27
17 6 0.18
18 11 0.33
ACGTcount: A:0.76, C:0.14, G:0.07, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAACCTAAC
Found at i:109424250 original size:33 final size:32
Alignment explanation
Indices: 109424165--109424250 Score: 104
Period size: 32 Copynumber: 2.6 Consensus size: 32
109424155 CCTAACCCCC
*
109424165 CCAAAAAAAAAGAAGAAAAA-AGAAAAACCTAA
1 CCAAAAAAAAA-AAAAAAAACAGAAAAACCTAA
*
109424197 CCAAAAAAAAAAGAAGAAAACAGAAAAACCTAA
1 CCAAAAAAAAAA-AAAAAAACAGAAAAACCTAA
109424230 -CAAAAAAAAACTAAAAAAAAC
1 CCAAAAAAAAA--AAAAAAAAC
109424251 CTAGCCACCT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
31 1 0.02
32 26 0.55
33 19 0.40
34 1 0.02
ACGTcount: A:0.76, C:0.14, G:0.07, T:0.03
Consensus pattern (32 bp):
CCAAAAAAAAAAAAAAAAACAGAAAAACCTAA
Found at i:109425274 original size:18 final size:20
Alignment explanation
Indices: 109425253--109425290 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
109425243 ACCTTTTTGT
109425253 GTATA-TAA-TATTATTTTC
1 GTATATTAATTATTATTTTC
109425271 GTATATTTAATTATTATTTT
1 GTATA-TTAATTATTATTTT
109425291 AAAAAAGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (20 bp):
GTATATTAATTATTATTTTC
Found at i:109425457 original size:16 final size:15
Alignment explanation
Indices: 109425433--109425467 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
109425423 TAATTATTAT
109425433 TATTGTAATATTTTGA
1 TATTGTAATATTTT-A
*
109425449 TATTTTAATATTTTA
1 TATTGTAATATTTTA
109425464 TATT
1 TATT
109425468 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (15 bp):
TATTGTAATATTTTA
Found at i:109427492 original size:25 final size:27
Alignment explanation
Indices: 109427444--109427495 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
109427434 TAAATAAAAA
* *
109427444 ATTTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAAACATAATAAATCAAATAT
109427471 ATTTAAAAAACATAA-AAA-CAAATAT
1 ATTTAAAAAACATAATAAATCAAATAT
109427496 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 3 0.13
27 13 0.57
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (27 bp):
ATTTAAAAAACATAATAAATCAAATAT
Found at i:109427507 original size:22 final size:22
Alignment explanation
Indices: 109427473--109427524 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
109427463 TCAAATATAT
109427473 TTAAAA-AACATAAAAACAAATA
1 TTAAAACAACATAAAAA-AAATA
*
109427495 TTAAAACAA-ATAAAAATAATA
1 TTAAAACAACATAAAAAAAATA
*
109427516 CTAAAACAA
1 TTAAAACAA
109427525 TTTTTAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
22 13 0.48
23 2 0.07
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (22 bp):
TTAAAACAACATAAAAAAAATA
Found at i:109427509 original size:21 final size:20
Alignment explanation
Indices: 109427477--109427524 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
109427467 ATATATTTAA
* *
109427477 AAAACATAAAAACA-AATATT
1 AAAACA-AAAAAAATAATACT
109427497 AAAACAAATAAAAATAATACT
1 AAAACAAA-AAAAATAATACT
109427518 AAAACAA
1 AAAACAA
109427525 TTTTTAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 10 0.42
21 12 0.50
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAACAAAAAAAATAATACT
Found at i:109430586 original size:21 final size:20
Alignment explanation
Indices: 109430562--109430601 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
109430552 TAGTTGTTAG
*
109430562 GAAGCTAAGTTTCAAGACTTA
1 GAAGCTAAGTCTCAA-ACTTA
109430583 GAAGCTAAGTCTCAAACTT
1 GAAGCTAAGTCTCAAACTT
109430602 GGAGGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (20 bp):
GAAGCTAAGTCTCAAACTTA
Done.