Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013866.1 Corchorus capsularis cultivar CVL-1 contig13887, whole genome shotgun sequence
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: 172337
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 3 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:835 original size:11 final size:11
Alignment explanation
Indices: 821--858 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
811 ATTCATAACA
821 AATTTATAATT
1 AATTTATAATT
832 AATTTATAATT
1 AATTTATAATT
843 -ATTTGATAATT
1 AATTT-ATAATT
*
854 TATTT
1 AATTT
859 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:2152 original size:136 final size:136
Alignment explanation
Indices: 1908--2157 Score: 482
Period size: 136 Copynumber: 1.8 Consensus size: 136
1898 CGGAATGTGA
* *
1908 GTTTCTTTGTAATTTGTTTGTTTATTTGGTAGGTAGGTAGTTTATTTAAGGTATATTTTCTAGTT
1 GTTTCTTTGTAATTTGTTTGTTTATTTGGTACGTAGGTAGTTTATTTAAGGTATAGTTTCTAGTT
1973 TGGGTTGAATTCTCATTTAGATGTTTGGGCATAGAGATTTATTTGAATTGTAATGAGATTTCACT
66 TGGGTTGAATTCTCATTTAGATGTTTGGGCATAGAGATTTATTTGAATTGTAATGAGATTTCACT
2038 GGGTTT
131 GGGTTT
2044 GTTTCTTTGTAATTTGTTTGTTTATTTGGTACGTAGGTAGTTTATTTAAGGTATAGTTTCTAGTT
1 GTTTCTTTGTAATTTGTTTGTTTATTTGGTACGTAGGTAGTTTATTTAAGGTATAGTTTCTAGTT
2109 TGGGTTGAATTCTCATTTAGATGTTTGGGCATAGAGATTTATTTGAATT
66 TGGGTTGAATTCTCATTTAGATGTTTGGGCATAGAGATTTATTTGAATT
2158 ATAGTTTCTA
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 112 1.00
ACGTcount: A:0.21, C:0.05, G:0.23, T:0.50
Consensus pattern (136 bp):
GTTTCTTTGTAATTTGTTTGTTTATTTGGTACGTAGGTAGTTTATTTAAGGTATAGTTTCTAGTT
TGGGTTGAATTCTCATTTAGATGTTTGGGCATAGAGATTTATTTGAATTGTAATGAGATTTCACT
GGGTTT
Found at i:2161 original size:62 final size:62
Alignment explanation
Indices: 2095--2219 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
2085 TTATTTAAGG
* *
2095 TATAGTTTCTAGTTTGGGTTGAATTCTCATTTAGATGTTTGGGCATAGAGATTTATTTGAAT
1 TATAGTTTCTAGTTTGGGTTAAATTCTCATTTAGATGTTTGGACATAGAGATTTATTTGAAT
* *
2157 TATAGTTTCTAGTTTGGTTTAAATTCTCATTTAGATTTTTGGACATAGAGATTTATTTGAAT
1 TATAGTTTCTAGTTTGGGTTAAATTCTCATTTAGATGTTTGGACATAGAGATTTATTTGAAT
2219 T
1 T
2220 GTAATGATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (62 bp):
TATAGTTTCTAGTTTGGGTTAAATTCTCATTTAGATGTTTGGACATAGAGATTTATTTGAAT
Found at i:2757 original size:45 final size:45
Alignment explanation
Indices: 2706--2795 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
2696 TAATAGAGTA
2706 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
* *
2751 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
2796 AGAAGTAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
Found at i:4900 original size:32 final size:34
Alignment explanation
Indices: 4831--4902 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
4821 TTACCTCTTG
4831 ATTACTGATTACCATTTTTACTTTTCTAAACTAA
1 ATTACTGATTACCATTTTTACTTTTCTAAACTAA
*
4865 ATTACTGATTACCCTTTTT-CTTTT-TAAACCT-A
1 ATTACTGATTACCATTTTTACTTTTCTAAA-CTAA
4897 ATTACT
1 ATTACT
4903 TAATCATCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
32 11 0.31
33 7 0.19
34 18 0.50
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.49
Consensus pattern (34 bp):
ATTACTGATTACCATTTTTACTTTTCTAAACTAA
Found at i:4965 original size:27 final size:28
Alignment explanation
Indices: 4934--4987 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
4924 GCCATTTTTA
4934 CTCTTTTCTTACTCT-TTTTACTGATTT
1 CTCTTTTCTTACTCTCTTTTACTGATTT
*
4961 CTCTTTTCTTACTCTCTTTTATTGATT
1 CTCTTTTCTTACTCTCTTTTACTGATT
4988 ACCACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (28 bp):
CTCTTTTCTTACTCTCTTTTACTGATTT
Found at i:4978 original size:13 final size:13
Alignment explanation
Indices: 4934--4980 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
4924 GCCATTTTTA
4934 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
4947 CT-TTTTACTGATTT
1 CTCTTTT-CTTA-CT
4961 CTCTTTTCTTACT
1 CTCTTTTCTTACT
4974 CTCTTTT
1 CTCTTTT
4981 ATTGATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.09, C:0.26, G:0.02, T:0.64
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:4995 original size:29 final size:28
Alignment explanation
Indices: 4936--5008 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
4926 CATTTTTACT
* *
4936 CTTTTCTTACTCT-TTTTACTGATTTCT
1 CTTTTCTTACTCTCTTTTACTGATTCCA
*
4963 CTTTTCTTACTCTCTTTTATTGATTACCA
1 CTTTTCTTACTCTCTTTTACTGATT-CCA
4992 C-TTT-TTACTCTTCTTTT
1 CTTTTCTTACTC-TCTTTT
5009 TTCTTTTACT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 19 0.47
28 19 0.47
29 2 0.05
ACGTcount: A:0.12, C:0.23, G:0.03, T:0.62
Consensus pattern (28 bp):
CTTTTCTTACTCTCTTTTACTGATTCCA
Found at i:5059 original size:26 final size:27
Alignment explanation
Indices: 5014--5068 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
5004 CTTTTTTCTT
5014 TTACTGACTACCATTTTACTCTTTGAA
1 TTACTGACTACCATTTTACTCTTTGAA
*
5041 TTACTGA-TCACC-TTTTACTTTTTGAA
1 TTACTGACT-ACCATTTTACTCTTTGAA
5067 TT
1 TT
5069 TTAATTACTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (27 bp):
TTACTGACTACCATTTTACTCTTTGAA
Found at i:5104 original size:32 final size:31
Alignment explanation
Indices: 5043--5127 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 31
5033 TCTTTGAATT
* * * *
5043 ACTGATCACCTTTTACTTTTTGAATTTTAATT
1 ACTGATCACCTCTTACTCTTTCAA-TTTAATC
5075 ACTGA-CTACCATCTTACTCTTTCAATTTAATC
1 ACTGATC-ACC-TCTTACTCTTTCAATTTAATC
*
5107 ACTGATCACCTTTTACTCTTT
1 ACTGATCACCTCTTACTCTTT
5128 AGTGATTACT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 11 0.24
32 22 0.49
33 12 0.27
ACGTcount: A:0.25, C:0.24, G:0.05, T:0.47
Consensus pattern (31 bp):
ACTGATCACCTCTTACTCTTTCAATTTAATC
Found at i:5156 original size:21 final size:22
Alignment explanation
Indices: 5117--5158 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
5107 ACTGATCACC
*
5117 TTTTACTCTTTAGTGATTACTA
1 TTTTACTCTTTACTGATTACTA
5139 TTTTACTC-TTACTGATTACT
1 TTTTACTCTTTACTGATTACT
5159 TTTAACTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.17, G:0.07, T:0.55
Consensus pattern (22 bp):
TTTTACTCTTTACTGATTACTA
Found at i:5171 original size:21 final size:21
Alignment explanation
Indices: 5130--5171 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5120 TACTCTTTAG
* *
5130 TGATTACTATTTTACTCTTAC
1 TGATTACTATTTAACTATTAC
5151 TGATTACT-TTTAACTGATTAC
1 TGATTACTATTTAACT-ATTAC
5172 CTTTTTTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (21 bp):
TGATTACTATTTAACTATTAC
Found at i:5228 original size:21 final size:20
Alignment explanation
Indices: 5177--5351 Score: 81
Period size: 20 Copynumber: 8.3 Consensus size: 20
5167 ATTACCTTTT
5177 TTTACT-TTCTACTGATTAC-C
1 TTTACTCTT-TACT-ATTACTC
* *
5197 ATTACTTTTTACTATTACTC
1 TTTACTCTTTACTATTACTC
* * *
5217 TTATACTCTTTACCATT-TTT
1 TT-TACTCTTTACTATTACTC
**
5237 TTTACTGATTACTGATTACTC
1 TTTACTCTTTACT-ATTACTC
*
5258 TTTACTCTTTACCATT-CTTC
1 TTTACTCTTTACTATTAC-TC
** *
5278 TTTACTGATTACTCTTTACTC
1 TTTACTCTTTACT-ATTACTC
5299 TTTACCATTCTTCTTTACTGATTACTC
1 TTT---A--C-TCTTTACT-ATTACTC
*
5326 TTTACTCTTTACCATT-CTTC
1 TTTACTCTTTACTATTAC-TC
5346 TTTACT
1 TTTACT
5352 GATTACTCTT
Statistics
Matches: 117, Mismatches: 23, Indels: 30
0.69 0.14 0.18
Matches are distributed among these distances:
19 15 0.13
20 43 0.37
21 39 0.33
22 2 0.02
24 2 0.02
26 1 0.01
27 15 0.13
ACGTcount: A:0.19, C:0.24, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTACTCTTTACTATTACTC
Found at i:5233 original size:34 final size:34
Alignment explanation
Indices: 5192--5375 Score: 255
Period size: 34 Copynumber: 5.2 Consensus size: 34
5182 TTTCTACTGA
5192 TTACCATTACTT-TTTACT-ATTACTCTTATACTCT
1 TTACCATT-CTTCTTTACTGATTACTCTT-TACTCT
*
5226 TTACCATTTTTTTTACTGATTACTGATTACTCTTTACTCT
1 TTACCA---TTCTT-CT--TTACTGATTACTCTTTACTCT
5266 TTACCATTCTTCTTTACTGATTACTCTTTACTCT
1 TTACCATTCTTCTTTACTGATTACTCTTTACTCT
5300 TTACCATTCTTCTTTACTGATTACTCTTTACTCT
1 TTACCATTCTTCTTTACTGATTACTCTTTACTCT
**
5334 TTACCATTCTTCTTTACTGATTACTCTTTACTGA
1 TTACCATTCTTCTTTACTGATTACTCTTTACTCT
5368 TTACCATT
1 TTACCATT
5376 TTACTTTTAA
Statistics
Matches: 138, Mismatches: 4, Indels: 16
0.87 0.03 0.10
Matches are distributed among these distances:
34 101 0.73
36 4 0.03
37 6 0.04
38 1 0.01
40 17 0.12
41 9 0.07
ACGTcount: A:0.20, C:0.24, G:0.03, T:0.53
Consensus pattern (34 bp):
TTACCATTCTTCTTTACTGATTACTCTTTACTCT
Found at i:5262 original size:7 final size:7
Alignment explanation
Indices: 5252--5365 Score: 78
Period size: 7 Copynumber: 16.7 Consensus size: 7
5242 TGATTACTGA
5252 TTACTCT
1 TTACTCT
5259 TTACTCT
1 TTACTCT
*
5266 TTAC-CA
1 TTACTCT
5272 TT-CTTCT
1 TTAC-TCT
**
5279 TTACTGA
1 TTACTCT
5286 TTACTCT
1 TTACTCT
5293 TTACTCT
1 TTACTCT
*
5300 TTAC-CA
1 TTACTCT
5306 TT-CTTCT
1 TTAC-TCT
**
5313 TTACTGA
1 TTACTCT
5320 TTACTCT
1 TTACTCT
5327 TTACTCT
1 TTACTCT
*
5334 TTAC-CA
1 TTACTCT
5340 TT-CTTCT
1 TTAC-TCT
**
5347 TTACTGA
1 TTACTCT
5354 TTACTCT
1 TTACTCT
5361 TTACT
1 TTACT
5366 GATTACCATT
Statistics
Matches: 80, Mismatches: 18, Indels: 18
0.69 0.16 0.16
Matches are distributed among these distances:
5 3 0.04
6 9 0.11
7 65 0.81
8 3 0.04
ACGTcount: A:0.18, C:0.26, G:0.03, T:0.54
Consensus pattern (7 bp):
TTACTCT
Found at i:5379 original size:22 final size:22
Alignment explanation
Indices: 5354--5920 Score: 211
Period size: 22 Copynumber: 25.4 Consensus size: 22
5344 TCTTTACTGA
5354 TTACTCTTTACTGATTACCATT
1 TTACTCTTTACTGATTACCATT
* * *
5376 TTACT-TTTAATTGGTTACCTTT
1 TTACTCTTT-ACTGATTACCATT
5398 TTACT-TTCTACTGATTACCAAAACTT
1 TTACTCTT-TACTGATTACC---A-TT
*
5424 ATTACTATTACTCTTTACTGATTACCACT
1 -TTA------CTCTTTACTGATTACCATT
* *
5453 TTGCTCTTTACTAATTACCATT
1 TTACTCTTTACTGATTACCATT
* * * *
5475 TTTCCCTTTACTGATTATCTTT
1 TTACTCTTTACTGATTACCATT
* **
5497 TTACTTTTTACTGATTAGTATT
1 TTACTCTTTACTGATTACCATT
* * *
5519 TTATTC-TTACTTATTACTATT
1 TTACTCTTTACTGATTACCATT
*
5540 TTACTTTTTACTGATTACCATT
1 TTACTCTTTACTGATTACCATT
** *
5562 TTA--CTTTA-TTTTCTTCC-TT
1 TTACTCTTTACTGAT-TACCATT
* * * *
5581 TTTCTTTCTTATTGATTACCACT
1 TTACTCT-TTACTGATTACCATT
* *
5604 TTACTTTTTACTGACTACCATT
1 TTACTCTTTACTGATTACCATT
* * **
5626 TTA-TTTTCTTCTTCTT-CC-TT
1 TTACTCTT-TACTGATTACCATT
* * *
5646 TTTCTTTCTTACTGATCACCATT
1 TTACTCT-TTACTGATTACCATT
* *
5669 TTAACTTTTTACTGACTACCATT
1 TT-ACTCTTTACTGATTACCATT
* ** *
5692 TTACTTTCTTCTTCTTCTT-CTTCCTT
1 TTAC--TCTT-TACTGATTAC--CATT
* * * *
5718 TTTCTTTCTTAGTGATCACCATT
1 TTACTCT-TTACTGATTACCATT
* * *
5741 TTACTTTTTACTTATTACTATT
1 TTACTCTTTACTGATTACCATT
* *
5763 TTACTC-TTACGGATTACTATT
1 TTACTCTTTACTGATTACCATT
* * *
5784 TTACTTTTTATTGCCGATTA-C-TA
1 TTACTCTTTA---CTGATTACCATT
5807 TTACTCTTTACTGATTA-CATT
1 TTACTCTTTACTGATTACCATT
* *
5828 TTACCCTTTACTGATTACCTTT
1 TTACTCTTTACTGATTACCATT
* *
5850 TTACTTTTTACTGTTTACCA--
1 TTACTCTTTACTGATTACCATT
* * *
5870 TTAGT-TCTTAATGATTA-C-TA
1 TTACTCT-TTACTGATTACCATT
*
5890 TTACTCTTTACTGATTACTATT
1 TTACTCTTTACTGATTACCATT
5912 TTACTCTTT
1 TTACTCTTT
5921 GAATTTAATT
Statistics
Matches: 402, Mismatches: 97, Indels: 92
0.68 0.16 0.16
Matches are distributed among these distances:
19 8 0.02
20 43 0.11
21 70 0.17
22 178 0.44
23 48 0.12
24 13 0.03
25 12 0.03
26 8 0.02
27 3 0.01
28 2 0.00
29 1 0.00
30 1 0.00
33 13 0.03
34 2 0.00
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (22 bp):
TTACTCTTTACTGATTACCATT
Found at i:5471 original size:77 final size:78
Alignment explanation
Indices: 5347--5491 Score: 188
Period size: 77 Copynumber: 1.9 Consensus size: 78
5337 CCATTCTTCT
* * ** *
5347 TTACTGATTACTCTTTACTGATTACCATTTTACTTTTAATTGGTTACC-TTTTTACTTTCTACTG
1 TTACTGATTACTCTTTACTGATTACCACTTTACTTTTAACTAATTACCATTTTTACCTT-TACTG
5411 ATTACCAAAACTTA
65 ATTACCAAAACTTA
* *
5425 TTACT-ATTACTCTTTACTGATTACCACTTTGCTCTTT-ACTAATTACCATTTTTCCCTTTACTG
1 TTACTGATTACTCTTTACTGATTACCACTTTACT-TTTAACTAATTACCATTTTTACCTTTACTG
5488 ATTA
65 ATTA
5492 TCTTTTTACT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
77 42 0.72
78 16 0.28
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.49
Consensus pattern (78 bp):
TTACTGATTACTCTTTACTGATTACCACTTTACTTTTAACTAATTACCATTTTTACCTTTACTGA
TTACCAAAACTTA
Found at i:5563 original size:43 final size:43
Alignment explanation
Indices: 5438--5919 Score: 188
Period size: 43 Copynumber: 11.0 Consensus size: 43
5428 CTATTACTCT
* * * * * *
5438 TTACTGATTACCACTTTGCTCTTTACTAATTACCATTTT-TCCC
1 TTACTGATTACTATTTTACTTTTTACTGATTACCATTTTAT-TC
**
5481 TTTACTGATTATCT-TTTTACTTTTTACTGATTAGTATTTTATTC
1 -TTACTGATTA-CTATTTTACTTTTTACTGATTACCATTTTATTC
* *
5525 TTACTTATTACTATTTTACTTTTTACTGATTACCATTTTACT-
1 TTACTGATTACTATTTTACTTTTTACTGATTACCATTTTATTC
* ** * * * *
5567 TTATTTTCTTCCT-TTTT-CTTTCTTATTGATTACCACTTTACTTT
1 TTA-CTGATTACTATTTTACTTT-TTACTGATTACCATTTTA-TTC
* * * ** * *
5611 TTACTGACTACCATTTTA-TTTTCTTCTTCTT-CCTTTTTCTTTC
1 TTACTGATTACTATTTTACTTTT-TACTGATTACCATTTT-ATTC
* * *
5654 TTACTGATCACCATTTTAACTTTTTACTGACTACCATTTTACTTTC
1 TTACTGATTACTATTTT-ACTTTTTACTGATTACCATTTTA--TTC
** * * * * * *
5700 TT-CTTCTTCTTCTTCCTTTTTCTTTCTTAGTGATCACCATTTTACTTT
1 TTAC-TGAT-TAC-T-ATTTTACTTT-TTACTGATTACCATTTTA-TTC
* * * * *
5748 TTACTTATTACTATTTTAC-TCTTACGGATTACTATTTTACTTT
1 TTACTGATTACTATTTTACTTTTTACTGATTACCATTTTA-TTC
* * **
5791 TTATTGCCGATTACTA--TTACTCTTTACTGATTA-CATTTTACCC
1 TTA---CTGATTACTATTTTACTTTTTACTGATTACCATTTTATTC
*
5834 TTTACTGATTACCT-TTTTACTTTTTACTGTTTACCA--TTAGTTC
1 -TTACTGATTA-CTATTTTACTTTTTACTGATTACCATTTTA-TTC
* * * *
5877 TTAATGATTACTA--TTACTCTTTACTGATTACTATTTTACTC
1 TTACTGATTACTATTTTACTTTTTACTGATTACCATTTTATTC
5918 TT
1 TT
5920 TGAATTTAAT
Statistics
Matches: 322, Mismatches: 81, Indels: 73
0.68 0.17 0.15
Matches are distributed among these distances:
40 17 0.05
41 16 0.05
42 42 0.13
43 105 0.33
44 66 0.20
45 27 0.08
46 16 0.05
47 3 0.01
48 10 0.03
49 20 0.06
ACGTcount: A:0.20, C:0.21, G:0.05, T:0.55
Consensus pattern (43 bp):
TTACTGATTACTATTTTACTTTTTACTGATTACCATTTTATTC
Found at i:5739 original size:72 final size:67
Alignment explanation
Indices: 5522--5767 Score: 304
Period size: 64 Copynumber: 3.7 Consensus size: 67
5512 TAGTATTTTA
* * * * *
5522 TTCTTACTTATTACTATTTTACTTTTTACTGATTACCATTTTAC--TTTATT-TTCTTCCTTTTT
1 TTCTTACTGATCACCATTTTACTTTTTACTGACTACCATTTTACTTTTTCTTCTTCTTCCTTTTT
5584 CT
66 CT
* * *
5586 TTCTTATTGATTACCACTTTACTTTTTACTGACTACCATTTTA--TTTTCTTCTTCTTCCTTTTT
1 TTCTTACTGATCACCATTTTACTTTTTACTGACTACCATTTTACTTTTTCTTCTTCTTCCTTTTT
5649 CT
66 CT
5651 TTCTTACTGATCACCATTTTAACTTTTTACTGACTACCATTTTACTTTCTTCTTCTTCTTCTTCC
1 TTCTTACTGATCACCATTTT-ACTTTTTACTGACTACCATTTTAC--T-TT-TTCTTCTTCTTCC
5716 TTTTTCT
61 TTTTTCT
* * * *
5723 TTCTTAGTGATCACCATTTTACTTTTTACTTATTACTATTTTACT
1 TTCTTACTGATCACCATTTTACTTTTTACTGACTACCATTTTACT
5768 CTTACGGATT
Statistics
Matches: 160, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
64 43 0.27
65 31 0.19
66 23 0.14
69 1 0.01
71 23 0.14
72 39 0.24
ACGTcount: A:0.17, C:0.22, G:0.03, T:0.58
Consensus pattern (67 bp):
TTCTTACTGATCACCATTTTACTTTTTACTGACTACCATTTTACTTTTTCTTCTTCTTCCTTTTT
CT
Found at i:5791 original size:72 final size:71
Alignment explanation
Indices: 5522--5792 Score: 239
Period size: 72 Copynumber: 4.0 Consensus size: 71
5512 TAGTATTTTA
* * * * *
5522 TTCTTACTTATTACTATTTT-ACTTTTTACTGATTACCATTTTAC-T-TT---ATT-TTCTTCCT
1 TTCTTACTGATCACCATTTTAACTTTTTACTGACTACCATTTTACTTCTTCGGATTCTTCTTACT
5580 TTTTCT
66 TTTTCT
* * * *
5586 TTCTTATTGATTACCACTTT-ACTTTTTACTGACTACCATTTTA-TT-TTC---TTCTTCTTCCT
1 TTCTTACTGATCACCATTTTAACTTTTTACTGACTACCATTTTACTTCTTCGGATTCTTCTTACT
5645 TTTTCT
66 TTTTCT
*** *
5651 TTCTTACTGATCACCATTTTAACTTTTTACTGACTACCATTTTACTTTCTTCTTCTTCTTCTTCC
1 TTCTTACTGATCACCATTTTAACTTTTTACTGACTACCATTTTAC-TTCTTCGGATTCTTCTTAC
5716 TTTTTCT
65 TTTTTCT
* * * * *
5723 TTCTTAGTGATCACCATTTT-ACTTTTTACTTATTACTATTTTAC-TCTTACGGATTACTATTTT
1 TTCTTACTGATCACCATTTTAACTTTTTACTGACTACCATTTTACTTCTT-CGGATT-CT-TCTT
5786 ACTTTTT
63 ACTTTTT
5793 ATTGCCGATT
Statistics
Matches: 177, Mismatches: 17, Indels: 18
0.83 0.08 0.08
Matches are distributed among these distances:
64 43 0.24
65 31 0.18
66 23 0.13
68 2 0.01
69 7 0.04
70 3 0.02
71 23 0.13
72 45 0.25
ACGTcount: A:0.17, C:0.21, G:0.03, T:0.58
Consensus pattern (71 bp):
TTCTTACTGATCACCATTTTAACTTTTTACTGACTACCATTTTACTTCTTCGGATTCTTCTTACT
TTTTCT
Found at i:6045 original size:34 final size:35
Alignment explanation
Indices: 6003--6070 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
5993 TTTTTCTTAA
*
6003 GAACTTAATTA-ATGATTGCCCCTTTTACTTTTTG
1 GAACTTAATTACATGATTACCCCTTTTACTTTTTG
* *
6037 GAACTTAATTACTCTGATTACCCTTTTTACTTTT
1 GAACTTAATTAC-ATGATTACCCCTTTTACTTTT
6071 CTGACTGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 11 0.38
36 18 0.62
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.49
Consensus pattern (35 bp):
GAACTTAATTACATGATTACCCCTTTTACTTTTTG
Found at i:10072 original size:44 final size:44
Alignment explanation
Indices: 10003--10104 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
9993 AAGAGACTAG
* * *
10003 TCTGTGGTCGACTTTATAACCGCTG-AAACTGAAAAAAGACCTGT
1 TCTGAGGTCAACTTGATAACCGCTGAAAACTG-AAAAAGACCTGT
* * ***
10047 TCTGAGGTTAACTTGATAACTGCTGAAAACTGAGGGAGACCTGT
1 TCTGAGGTCAACTTGATAACCGCTGAAAACTGAAAAAGACCTGT
10091 TCTGAGGTCAACTT
1 TCTGAGGTCAACTT
10105 TGCTAACGGC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
44 42 0.88
45 6 0.12
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
TCTGAGGTCAACTTGATAACCGCTGAAAACTGAAAAAGACCTGT
Found at i:10160 original size:43 final size:43
Alignment explanation
Indices: 10101--10211 Score: 143
Period size: 43 Copynumber: 2.6 Consensus size: 43
10091 TCTGAGGTCA
* * *
10101 ACTTTGCTAACGGCTAAAAATTGAGAGACCTATTCTGAAGTTG
1 ACTTTGATAACAGCTAAAAATTGAGAGACCTATTCTAAAGTTG
* *
10144 A-TTTCGATAACTGCTAAAAATTGAGAGACCTGTTCTAAAGTTG
1 ACTTT-GATAACAGCTAAAAATTGAGAGACCTATTCTAAAGTTG
*
10187 ACTTTGATAACAGCTGAAAAGTTGA
1 ACTTTGATAACAGCT-AAAAATTGA
10212 TGATTTGAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 3 0.05
43 45 0.76
44 11 0.19
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (43 bp):
ACTTTGATAACAGCTAAAAATTGAGAGACCTATTCTAAAGTTG
Found at i:10191 original size:86 final size:87
Alignment explanation
Indices: 10039--10211 Score: 197
Period size: 86 Copynumber: 2.0 Consensus size: 87
10029 AACTGAAAAA
* * * * *
10039 AGACCTGTTCTGAGGTTAACTTGATAACTGCTGAAAACTGAGGGAGACCTGTTCTGAGGTCAACT
1 AGACCTATTCTGAAGTTAACTTGATAACTGCTAAAAACTGA-GGAGACCTGTTCTAAAGTCAACT
* *
10104 TTGCTAACGGCT-AAAAATTGAG
65 TTGATAACAGCTGAAAAATTGAG
* * * **
10126 AGACCTATTCTGAAGTTGATTTCGATAACTGCTAAAAATTGA-GAGACCTGTTCTAAAGTTGACT
1 AGACCTATTCTGAAGTTAACTT-GATAACTGCTAAAAACTGAGGAGACCTGTTCTAAAGTCAACT
*
10190 TTGATAACAGCTGAAAAGTTGA
65 TTGATAACAGCTGAAAAATTGA
10212 TGATTTGAAG
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
86 28 0.39
87 26 0.37
88 17 0.24
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (87 bp):
AGACCTATTCTGAAGTTAACTTGATAACTGCTAAAAACTGAGGAGACCTGTTCTAAAGTCAACTT
TGATAACAGCTGAAAAATTGAG
Found at i:12185 original size:12 final size:12
Alignment explanation
Indices: 12168--12201 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12158 CTTATTGGAT
12168 TGTGTCTGCTGC
1 TGTGTCTGCTGC
*
12180 TGTGTCTGCTGT
1 TGTGTCTGCTGC
*
12192 TTTGTCTGCT
1 TGTGTCTGCT
12202 ACTGAGTTTG
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:0.00, C:0.21, G:0.29, T:0.50
Consensus pattern (12 bp):
TGTGTCTGCTGC
Found at i:20276 original size:2 final size:2
Alignment explanation
Indices: 20269--20293 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20259 AATCAGTTTA
20269 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20294 AGTAAGTTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28548 original size:43 final size:43
Alignment explanation
Indices: 28449--28536 Score: 124
Period size: 43 Copynumber: 2.1 Consensus size: 43
28439 ACCAACAATT
* * *
28449 AATATTAACTTTATTTTGATGAATTATCGAGATGAAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCGAGATGAAGGAGAAG
* *
28492 AATATTAGCTTTATTTTGATGAATTACCTAGA-GATGGAGAAG
1 AATATTAGCTTTATTTTGATGAATTACCGAGATGAAGGAGAAG
28534 AAT
1 AAT
28537 TATTTGTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 11 0.28
43 29 0.73
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (43 bp):
AATATTAGCTTTATTTTGATGAATTACCGAGATGAAGGAGAAG
Found at i:31155 original size:37 final size:37
Alignment explanation
Indices: 31114--31188 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
31104 ATTTACCTTA
*
31114 TATTTTCATTTATTTTACCTTATGCTCTTCTTTGTTG
1 TATTTTCATTTATTTCACCTTATGCTCTTCTTTGTTG
*
31151 TATTTTCATTTATTTCACCTTGTGCTCTTCTTTGTTG
1 TATTTTCATTTATTTCACCTTATGCTCTTCTTTGTTG
31188 T
1 T
31189 TATATTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.12, C:0.17, G:0.09, T:0.61
Consensus pattern (37 bp):
TATTTTCATTTATTTCACCTTATGCTCTTCTTTGTTG
Found at i:35055 original size:51 final size:50
Alignment explanation
Indices: 35000--35336 Score: 319
Period size: 51 Copynumber: 7.1 Consensus size: 50
34990 TCACAAGCAT
35000 AGTTAAACCTTAATTCAGTGTAATTAAGAGGTAATTAAGAAAGTCAAGTAC
1 AGTTAAACCTTAATTCA-TGTAATTAAGAGGTAATTAAGAAAGTCAAGTAC
* * *
35051 AGTTAAA----AGA--C-T-TAATTCAG-GGTAATTAAGAAAGTCAAGCAT
1 AGTTAAACCTTA-ATTCATGTAATTAAGAGGTAATTAAGAAAGTCAAGTAC
*
35093 AGTTAAACCTTAATTCAGTGTAATTAAGAAGTAATTAAGAAAGTCAAGTAC
1 AGTTAAACCTTAATTCA-TGTAATTAAGAGGTAATTAAGAAAGTCAAGTAC
* ** * * *
35144 AGTT-AA----AAGTC-T-TAATCCA-AGGTAATTAAGGAAGTCAAGCAT
1 AGTTAAACCTTAATTCATGTAATTAAGAGGTAATTAAGAAAGTCAAGTAC
35186 AGTTAAACCTTAATTCAGTGTAATTAAGAGGTAATTAAGAAAGTCAAGTAC
1 AGTTAAACCTTAATTCA-TGTAATTAAGAGGTAATTAAGAAAGTCAAGTAC
* ** * *
35237 AGTT-AA----AAGTC-T-TAATCCA-AGGTAATTAAGAAAGTCAAGCAT
1 AGTTAAACCTTAATTCATGTAATTAAGAGGTAATTAAGAAAGTCAAGTAC
35279 AGTTAAACCTTAATTCAATGTAATTAAGAGGTAATTAAGAAAGTCAAGTAC
1 AGTTAAACCTTAATTC-ATGTAATTAAGAGGTAATTAAGAAAGTCAAGTAC
35330 AGTTAAA
1 AGTTAAA
35337 AGTCTTAATC
Statistics
Matches: 227, Mismatches: 30, Indels: 58
0.72 0.10 0.18
Matches are distributed among these distances:
42 75 0.33
43 21 0.09
44 3 0.01
45 1 0.00
46 10 0.04
47 10 0.04
48 1 0.00
49 3 0.01
50 21 0.09
51 82 0.36
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (50 bp):
AGTTAAACCTTAATTCATGTAATTAAGAGGTAATTAAGAAAGTCAAGTAC
Found at i:35080 original size:42 final size:43
Alignment explanation
Indices: 35020--35391 Score: 247
Period size: 42 Copynumber: 8.2 Consensus size: 43
35010 TAATTCAGTG
*
35020 TAATTAAGAGGTAATTAAGAAAGTCAAGTACAGTTAAAAGACT
1 TAATTAAGAGGTAATTAAGAAAGTCAAGCACAGTTAAAAGACT
* *
35063 TAATTCAG-GGTAATTAAGAAAGTCAAGCATAGTTAAACCTTA-ATTCAGT
1 TAATTAAGAGGTAATTAAGAAAGTCAAGCACAGTTAAA----AGA--C--T
* * *
35112 GTAATTAAGAAGTAATTAAGAAAGTCAAGTACAGTTAAAAGTCT
1 -TAATTAAGAGGTAATTAAGAAAGTCAAGCACAGTTAAAAGACT
** * *
35156 TAATCCA-AGGTAATTAAGGAAGTCAAGCATAGTTAAACCTTA-ATTCAGT
1 TAATTAAGAGGTAATTAAGAAAGTCAAGCACAGTTAAA----AGA--C--T
* *
35205 GTAATTAAGAGGTAATTAAGAAAGTCAAGTACAGTTAAAAGTCT
1 -TAATTAAGAGGTAATTAAGAAAGTCAAGCACAGTTAAAAGACT
** *
35249 TAATCCA-AGGTAATTAAGAAAGTCAAGCATAGTTAAACCTTA-ATTCAAT
1 TAATTAAGAGGTAATTAAGAAAGTCAAGCACAGTTAAA----AGA--C--T
* *
35298 GTAATTAAGAGGTAATTAAGAAAGTCAAGTACAGTTAAAAGTCT
1 -TAATTAAGAGGTAATTAAGAAAGTCAAGCACAGTTAAAAGACT
** * * *
35342 TAATCCA-AGGTAATTAAGAAAGTCAAACACAGTT-AAAGTCC
1 TAATTAAGAGGTAATTAAGAAAGTCAAGCACAGTTAAAAGACT
35383 TAATTAAGA
1 TAATTAAGA
35392 AAAGCAAAGT
Statistics
Matches: 257, Mismatches: 38, Indels: 69
0.71 0.10 0.19
Matches are distributed among these distances:
41 11 0.04
42 107 0.42
43 22 0.09
44 3 0.01
45 1 0.00
46 6 0.02
47 6 0.02
49 3 0.01
50 17 0.07
51 81 0.32
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.27
Consensus pattern (43 bp):
TAATTAAGAGGTAATTAAGAAAGTCAAGCACAGTTAAAAGACT
Found at i:35120 original size:93 final size:93
Alignment explanation
Indices: 34993--35378 Score: 700
Period size: 93 Copynumber: 4.2 Consensus size: 93
34983 ACATGCATCA
34993 CAAGCATAGTTAAACCTTAATTCAGTGTAATTAAGAGGTAATTAAGAAAGTCAAGTACAGTTAAA
1 CAAGCATAGTTAAACCTTAATTCAGTGTAATTAAGAGGTAATTAAGAAAGTCAAGTACAGTTAAA
* * *
35058 AGACTTAATTCAGGGTAATTAAGAAAGT
66 AGTCTTAATCCAAGGTAATTAAGAAAGT
*
35086 CAAGCATAGTTAAACCTTAATTCAGTGTAATTAAGAAGTAATTAAGAAAGTCAAGTACAGTTAAA
1 CAAGCATAGTTAAACCTTAATTCAGTGTAATTAAGAGGTAATTAAGAAAGTCAAGTACAGTTAAA
*
35151 AGTCTTAATCCAAGGTAATTAAGGAAGT
66 AGTCTTAATCCAAGGTAATTAAGAAAGT
35179 CAAGCATAGTTAAACCTTAATTCAGTGTAATTAAGAGGTAATTAAGAAAGTCAAGTACAGTTAAA
1 CAAGCATAGTTAAACCTTAATTCAGTGTAATTAAGAGGTAATTAAGAAAGTCAAGTACAGTTAAA
35244 AGTCTTAATCCAAGGTAATTAAGAAAGT
66 AGTCTTAATCCAAGGTAATTAAGAAAGT
*
35272 CAAGCATAGTTAAACCTTAATTCAATGTAATTAAGAGGTAATTAAGAAAGTCAAGTACAGTTAAA
1 CAAGCATAGTTAAACCTTAATTCAGTGTAATTAAGAGGTAATTAAGAAAGTCAAGTACAGTTAAA
35337 AGTCTTAATCCAAGGTAATTAAGAAAGT
66 AGTCTTAATCCAAGGTAATTAAGAAAGT
* *
35365 CAAACACAGTTAAA
1 CAAGCATAGTTAAA
35379 GTCCTAATTA
Statistics
Matches: 283, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 283 1.00
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (93 bp):
CAAGCATAGTTAAACCTTAATTCAGTGTAATTAAGAGGTAATTAAGAAAGTCAAGTACAGTTAAA
AGTCTTAATCCAAGGTAATTAAGAAAGT
Found at i:35457 original size:39 final size:39
Alignment explanation
Indices: 35412--35527 Score: 117
Period size: 39 Copynumber: 3.2 Consensus size: 39
35402 CTTAATTCGG
*
35412 GGTAATTAAGAAAAGTAAGCATAGTCAAGGACTTAATTT
1 GGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTT
*
35451 GGTAATTAAG-AAA--AA-C--A---AA-GTCTTAATTCAG
1 GGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATT--T
*
35482 GGTAATTAAGAAAAGTAAGCATAGTCGAGGTCTTAATTT
1 GGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTT
35521 GGTAATT
1 GGTAATT
35528 GTCGCAACGT
Statistics
Matches: 61, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
29 8 0.13
30 2 0.03
31 10 0.16
32 3 0.05
33 1 0.02
34 2 0.03
35 2 0.03
36 2 0.03
37 1 0.02
38 3 0.05
39 17 0.28
40 1 0.02
41 9 0.15
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (39 bp):
GGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTT
Found at i:35463 original size:70 final size:70
Alignment explanation
Indices: 35383--35527 Score: 254
Period size: 70 Copynumber: 2.1 Consensus size: 70
35373 GTTAAAGTCC
* *
35383 TAATTAAGAAAAGCAAAGTCTTAATTCGGGGTAATTAAGAAAAGTAAGCATAGTCAAGGACTTAA
1 TAATTAAGAAAAACAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGACTTAA
35448 TTTGG
66 TTTGG
* *
35453 TAATTAAGAAAAACAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCGAGGTCTTAA
1 TAATTAAGAAAAACAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGACTTAA
35518 TTTGG
66 TTTGG
35523 TAATT
1 TAATT
35528 GTCGCAACGT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (70 bp):
TAATTAAGAAAAACAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGACTTAA
TTTGG
Found at i:40051 original size:22 final size:22
Alignment explanation
Indices: 40023--40079 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
40013 AAATTGGGGA
40023 ATTGAAGAATTGAAAGT-AAAGC
1 ATTGAAGAATTGAAAGTGAAA-C
*
40045 ATTGAAGAATTGAAATTGAAAC
1 ATTGAAGAATTGAAAGTGAAAC
40067 ATTGAA-AA-TGAAA
1 ATTGAAGAATTGAAA
40080 TTGGAATTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 5 0.15
21 2 0.06
22 23 0.70
23 3 0.09
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.25
Consensus pattern (22 bp):
ATTGAAGAATTGAAAGTGAAAC
Found at i:40062 original size:14 final size:14
Alignment explanation
Indices: 40045--40148 Score: 57
Period size: 14 Copynumber: 6.6 Consensus size: 14
40035 AAAGTAAAGC
40045 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
40059 ATTGAA-ACATTGAA
1 ATTGAAGA-ATTGAA
*
40073 AATGAAATTGGAATTGAA
1 ATTG-AA---GAATTGAA
*
40091 GCATTGGAGAATTGAA
1 --ATTGAAGAATTGAA
*
40107 ATTGAAGCATTTGAAGAAA
1 ATTGAAG-AATT---G-AA
40126 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
40140 ATTGTAGAA
1 ATTGAAGAA
40149 GGACCACCCC
Statistics
Matches: 70, Mismatches: 7, Indels: 26
0.68 0.07 0.25
Matches are distributed among these distances:
13 1 0.01
14 31 0.44
15 6 0.09
16 8 0.11
18 10 0.14
19 11 0.16
20 3 0.04
ACGTcount: A:0.47, C:0.03, G:0.22, T:0.28
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:40063 original size:6 final size:6
Alignment explanation
Indices: 40052--40112 Score: 50
Period size: 6 Copynumber: 9.2 Consensus size: 6
40042 AGCATTGAAG
* *
40052 AATTGA AATTGAA ACATTGA AAATGA AATTGG AATTGA AGCATTGGA GAATTGA
1 AATTGA AATTG-A A-ATTGA AATTGA AATTGA AATTGA A--ATT-GA -AATTGA
40106 AATTGA A
1 AATTGA A
40113 GCATTTGAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
6 26 0.58
7 6 0.13
8 10 0.22
9 2 0.04
10 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.21, T:0.28
Consensus pattern (6 bp):
AATTGA
Found at i:40088 original size:26 final size:28
Alignment explanation
Indices: 40052--40112 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
40042 AGCATTGAAG
40052 AATTGAAATTGAAACATT-GA-AAATGA
1 AATTGAAATTGAAACATTGGAGAAATGA
* * *
40078 AATTGGAATTGAAGCATTGGAGAATTGA
1 AATTGAAATTGAAACATTGGAGAAATGA
40106 AATTGAA
1 AATTGAA
40113 GCATTTGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 16 0.55
27 2 0.07
28 11 0.38
ACGTcount: A:0.48, C:0.03, G:0.21, T:0.28
Consensus pattern (28 bp):
AATTGAAATTGAAACATTGGAGAAATGA
Found at i:40248 original size:22 final size:23
Alignment explanation
Indices: 40206--40258 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
40196 TTTGAAGAGT
*
40206 TGAACTTGAAGCATTGAAAT-AC
1 TGAAATTGAAGCATTGAAATAAC
*
40228 TGAAATTGAAGCATTTG-AATAAT
1 TGAAATTGAAGCA-TTGAAATAAC
40251 TGAAATTG
1 TGAAATTG
40259 GAACATCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.32
Consensus pattern (23 bp):
TGAAATTGAAGCATTGAAATAAC
Found at i:40360 original size:14 final size:13
Alignment explanation
Indices: 40331--40451 Score: 50
Period size: 14 Copynumber: 8.7 Consensus size: 13
40321 TTTGAAGTAC
*
40331 TGAATTTGAAGAAT
1 TGAAATTGAAG-AT
40345 TGAAATTGAAGCAT
1 TGAAATTGAAG-AT
40359 TGGAAA-TGAA-AT
1 T-GAAATTGAAGAT
* * *
40371 TGGAACTGAAACAT
1 TGAAATTG-AAGAT
*
40385 TGAAGAATTGCA-AT
1 TG-A-AATTGAAGAT
*
40399 TGAAACATCGAAGGAT
1 TG-AA-ATTGAA-GAT
*
40415 TGAATTTGAAGAAT
1 TGAAATTGAAG-AT
*
40429 TGAAATTGAAATAT
1 TGAAATTG-AAGAT
40443 TGAAATTGA
1 TGAAATTGA
40452 GACCCTGAAG
Statistics
Matches: 84, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
11 3 0.04
12 5 0.06
13 5 0.06
14 54 0.64
15 9 0.11
16 8 0.10
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (13 bp):
TGAAATTGAAGAT
Found at i:40393 original size:22 final size:22
Alignment explanation
Indices: 40336--40440 Score: 81
Period size: 22 Copynumber: 4.7 Consensus size: 22
40326 AGTACTGAAT
*
40336 TTGAAGAATTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAACA
* *
40358 TTGGAAATGAAATTGGAACTGAAACA
1 TT-G-AA-G-AATTGAAATTGAAACA
*
40384 TTGAAGAATTGCAATTGAAACA
1 TTGAAGAATTGAAATTGAAACA
* * *
40406 TCGAAGGATTGAATTTGAAGA-A
1 TTGAAGAATTGAAATTGAA-ACA
40428 TTG-A-AATTGAAAT
1 TTGAAGAATTGAAAT
40441 ATTGAAATTG
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
20 7 0.11
21 1 0.02
22 34 0.52
23 3 0.05
24 4 0.06
25 2 0.03
26 15 0.23
ACGTcount: A:0.45, C:0.06, G:0.22, T:0.28
Consensus pattern (22 bp):
TTGAAGAATTGAAATTGAAACA
Found at i:40481 original size:8 final size:8
Alignment explanation
Indices: 40470--40819 Score: 75
Period size: 8 Copynumber: 45.8 Consensus size: 8
40460 AGGATTGAAT
40470 TTGAAGAA
1 TTGAAGAA
40478 TTGAAGAA
1 TTGAAGAA
*
40486 TTGGA-AA
1 TTGAAGAA
40493 TTG-A-AA
1 TTGAAGAA
**
40499 TTGAAGCG
1 TTGAAGAA
** *
40507 TCAAAGAT
1 TTGAAGAA
40515 TTG-A-AA
1 TTGAAGAA
40521 TTGAA-ATA
1 TTGAAGA-A
40529 TTGAA-ACA
1 TTGAAGA-A
* *
40537 TTAAATAA
1 TTGAAGAA
40545 TTG--GAA
1 TTGAAGAA
*
40551 TTGAAGCA
1 TTGAAGAA
*
40559 TTGAAGGA
1 TTGAAGAA
*
40567 TTG-A-AT
1 TTGAAGAA
*
40573 TTGGAGAA
1 TTGAAGAA
*
40581 TCG-A-AA
1 TTGAAGAA
40587 TTGAAGAA
1 TTGAAGAA
*
40595 TCGAA-ACA
1 TTGAAGA-A
40603 TTGAAGAA
1 TTGAAGAA
40611 TTG-A-AA
1 TTGAAGAA
40617 TTGAAGAA
1 TTGAAGAA
40625 TTGAA-ACA
1 TTGAAGA-A
*
40633 TTGAAGTA
1 TTGAAGAA
*
40641 CTG-A-AA
1 TTGAAGAA
**
40647 TTGAATCA
1 TTGAAGAA
40655 TTGAAGAA
1 TTGAAGAA
*
40663 TTG--CAA
1 TTGAAGAA
40669 TTGAA-ACA
1 TTGAAGA-A
40677 TTGAA-ACA
1 TTGAAGA-A
40685 TTG-A-AA
1 TTGAAGAA
* *
40691 TTGAGGCA
1 TTGAAGAA
40699 TTGAA-ATA
1 TTGAAGA-A
40707 TTG-A-AA
1 TTGAAGAA
* *
40713 CTGAAGCA
1 TTGAAGAA
*
40721 TTAAAGAA
1 TTGAAGAA
40729 TTGAAAGAAACA
1 TTG-AAG--A-A
40741 TTGAAGAA
1 TTGAAGAA
40749 TTGAAGAA
1 TTGAAGAA
40757 TTGAA-ATA
1 TTGAAGA-A
40765 TTG-A-AA
1 TTGAAGAA
40771 TTGAA-ACA
1 TTGAAGA-A
40779 TT-AAGGAA
1 TTGAA-GAA
40787 TTGAAAGAAACA
1 TTG-AAG--A-A
40799 TTGAAGAA
1 TTGAAGAA
*
40807 TT-AAAAA
1 TTGAAGAA
40814 TTGAAG
1 TTGAAG
40820 CATTAAAGAT
Statistics
Matches: 257, Mismatches: 43, Indels: 84
0.67 0.11 0.22
Matches are distributed among these distances:
6 46 0.18
7 38 0.15
8 146 0.57
9 9 0.04
10 2 0.01
11 8 0.03
12 8 0.03
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.27
Consensus pattern (8 bp):
TTGAAGAA
Found at i:40596 original size:14 final size:14
Alignment explanation
Indices: 40548--40651 Score: 91
Period size: 14 Copynumber: 7.0 Consensus size: 14
40538 TAAATAATTG
40548 GAATTGAAGCATTGAA
1 GAATTGAA--ATTGAA
* * *
40564 GGATTGAATTTGGA
1 GAATTGAAATTGAA
*
40578 GAATCGAAATTGAA
1 GAATTGAAATTGAA
*
40592 GAATCGAAACATTGAA
1 GAATTG-AA-ATTGAA
40608 GAATTGAAATTGAA
1 GAATTGAAATTGAA
40622 GAATTGAAACATTGAA
1 GAATTG-AA-ATTGAA
* *
40638 GTACTGAAATTGAA
1 GAATTGAAATTGAA
40652 TCATTGAAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
14 38 0.51
15 8 0.11
16 28 0.38
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (14 bp):
GAATTGAAATTGAA
Found at i:40617 original size:30 final size:30
Alignment explanation
Indices: 40577--40651 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
40567 TTGAATTTGG
*
40577 AGAATCGAAATTGAAGAATCGAAACATTGA
1 AGAATTGAAATTGAAGAATCGAAACATTGA
*
40607 AGAATTGAAATTGAAGAATTGAAACATTGA
1 AGAATTGAAATTGAAGAATCGAAACATTGA
* *
40637 AGTACTGAAATTGAA
1 AGAATTGAAATTGAA
40652 TCATTGAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (30 bp):
AGAATTGAAATTGAAGAATCGAAACATTGA
Found at i:40648 original size:22 final size:22
Alignment explanation
Indices: 40623--40776 Score: 140
Period size: 22 Copynumber: 7.1 Consensus size: 22
40613 GAAATTGAAG
* *
40623 AATTGAAACATTGAAGTACTGA
1 AATTGAAACATTGAAGAATTGA
* *
40645 AATTGAATCATTGAAGAATTGC
1 AATTGAAACATTGAAGAATTGA
40667 AATTGAAACATTGAA-ACATTGA
1 AATTGAAACATTGAAGA-ATTGA
**
40689 AATTGAGGCATTGAA-ATATTGA
1 AATTGAAACATTGAAGA-ATTGA
* * *
40711 AACTGAAGCATTAAAGAATTGA
1 AATTGAAACATTGAAGAATTGA
40733 AA--GAAACATTGAAGAATTGAA
1 AATTGAAACATTGAAGAATTG-A
*
40754 GAATTGAAATATTG-A-AATTGA
1 -AATTGAAACATTGAAGAATTGA
40775 AA
1 AA
40777 CATTAAGGAA
Statistics
Matches: 111, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
20 17 0.15
21 3 0.03
22 81 0.73
23 2 0.02
24 8 0.07
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27
Consensus pattern (22 bp):
AATTGAAACATTGAAGAATTGA
Found at i:40671 original size:58 final size:58
Alignment explanation
Indices: 40616--40808 Score: 212
Period size: 58 Copynumber: 3.2 Consensus size: 58
40606 AAGAATTGAA
* * * *
40616 ATTGAAGAATTGAA-ACATTGAAGTACTGAAATTGAATCATTGAAGAATTGCAATTGAAAC
1 ATTGAAGAATTGAAGACATTGAAATATTGAAATTGAAACATT-AAGAATTG-AA-AGAAAC
* *
40676 ATTGAA-ACATTGAAATTGAGGCATTGAAATATTGAAACTGAAGCATTAAAGAATTGAAAGAAAC
1 ATTGAAGA-ATTG-AA--GA--CATTGAAATATTGAAATTGAAACATT-AAGAATTGAAAGAAAC
40740 ATTGAAGAATTGAAGA-ATTGAAATATTGAAATTGAAACATTAAGGAATTGAAAGAAAC
1 ATTGAAGAATTGAAGACATTGAAATATTGAAATTGAAACATTAA-GAATTGAAAGAAAC
40798 ATTGAAGAATT
1 ATTGAAGAATT
40809 AAAAATTGAA
Statistics
Matches: 116, Mismatches: 8, Indels: 20
0.81 0.06 0.14
Matches are distributed among these distances:
57 2 0.02
58 48 0.41
59 1 0.01
60 10 0.09
61 4 0.03
63 2 0.02
64 16 0.14
65 3 0.03
66 30 0.26
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (58 bp):
ATTGAAGAATTGAAGACATTGAAATATTGAAATTGAAACATTAAGAATTGAAAGAAAC
Found at i:40968 original size:8 final size:8
Alignment explanation
Indices: 40940--41137 Score: 62
Period size: 8 Copynumber: 25.4 Consensus size: 8
40930 GTGAATGGAC
40940 GAATTGAA
1 GAATTGAA
40948 -AGATTG-A
1 GA-ATTGAA
40955 GTAATTGAA
1 G-AATTGAA
40964 GAATTGAA
1 GAATTGAA
*
40972 GCAA-TAAA
1 G-AATTGAA
*
40980 TAATTGAA
1 GAATTGAA
40988 GAATTTGAA
1 GAA-TTGAA
40997 GAA---ACA
1 GAATTGA-A
*
41003 -AATTGAT
1 GAATTGAA
*
41010 GTATTGAA
1 GAATTGAA
41018 GAATTGAA
1 GAATTGAA
*
41026 TAATTGAA
1 GAATTGAA
* *
41034 TAATTAAA
1 GAATTGAA
*
41042 GAGTTGAA
1 GAATTGAA
41050 G-A--GATA
1 GAATTGA-A
41056 -AATTGAA
1 GAATTGAA
**
41063 GTGTTGAA
1 GAATTGAA
*
41071 TG-GTT-AA
1 -GAATTGAA
*
41078 AATATTGAA
1 GA-ATTGAA
*
41087 GTATTGAA
1 GAATTGAA
41095 GAATTGAA
1 GAATTGAA
* *
41103 TAATGGAA
1 GAATTGAA
*
41111 GATTTGAA
1 GAATTGAA
*
41119 GCATTGAA
1 GAATTGAA
* *
41127 TAGTTGAA
1 GAATTGAA
41135 GAA
1 GAA
41138 AGAGATTATT
Statistics
Matches: 136, Mismatches: 33, Indels: 42
0.64 0.16 0.20
Matches are distributed among these distances:
5 5 0.04
6 3 0.02
7 7 0.05
8 105 0.77
9 16 0.12
ACGTcount: A:0.46, C:0.02, G:0.22, T:0.30
Consensus pattern (8 bp):
GAATTGAA
Found at i:40983 original size:24 final size:23
Alignment explanation
Indices: 40956--41043 Score: 81
Period size: 24 Copynumber: 3.8 Consensus size: 23
40946 AAAGATTGAG
40956 TAATTGAAGAATTGAAGCAATAAA
1 TAATTGAAGAATTGAAG-AATAAA
*
40980 TAATTGAAGAATTTGAAGAA-ACA
1 TAATTGAAGAA-TTGAAGAATAAA
* * *
41003 -AATTGATGTATTGAAGAATTGAA
1 TAATTGAAGAATTGAAGAA-TAAA
* *
41026 TAATTGAATAATTAAAGA
1 TAATTGAAGAATTGAAGA
41044 GTTGAAGAGA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
21 8 0.16
22 8 0.16
23 3 0.06
24 26 0.51
25 6 0.12
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.30
Consensus pattern (23 bp):
TAATTGAAGAATTGAAGAATAAA
Found at i:41005 original size:25 final size:24
Alignment explanation
Indices: 40956--41005 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
40946 AAAGATTGAG
* *
40956 TAATTGAAGAATTGAAGCAATAAA
1 TAATTGAAGAATTGAAGAAACAAA
40980 TAATTGAAGAATTTGAAGAAACAAA
1 TAATTGAAGAA-TTGAAGAAACAAA
41005 T
1 T
41006 TGATGTATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.54, C:0.04, G:0.16, T:0.26
Consensus pattern (24 bp):
TAATTGAAGAATTGAAGAAACAAA
Found at i:42489 original size:6 final size:6
Alignment explanation
Indices: 42480--42512 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
42470 CACTTTCATT
*
42480 TTTTGA TTTTGA TCTTGA TTTTGA -TTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
42513 TTTTTTGCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.15, C:0.03, G:0.15, T:0.67
Consensus pattern (6 bp):
TTTTGA
Found at i:42990 original size:11 final size:12
Alignment explanation
Indices: 42971--42995 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42961 CATCATTTCA
42971 TTCATTTTTTTT
1 TTCATTTTTTTT
42983 TTCATTTTTTTT
1 TTCATTTTTTTT
42995 T
1 T
42996 GGCGTGGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TTCATTTTTTTT
Found at i:51019 original size:70 final size:70
Alignment explanation
Indices: 50930--51346 Score: 654
Period size: 70 Copynumber: 6.0 Consensus size: 70
50920 GGTGTCTATA
* * *
50930 GTAATTAAGAAAAGGAAAGTCTTAATTCAGGGTAACTAAGAAAAGTAAGCAAAGTCAAGGTCTTA
1 GTAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTA
50995 ATTTG
66 ATTTG
* *
51000 GTAATTAAGAAAAGTAAAGTATTAATTCAGGGTAATTAATAAAAGTAAGCATAGTCAAGGTCTTA
1 GTAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTA
51065 ATTTG
66 ATTTG
* * * *
51070 GTAATTAAGAGAAGCAAAGTCTTAATTCAGGGTATTTAAGAAAAGTAAACATAGTCAAGGTCTTA
1 GTAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTA
51135 ATTTG
66 ATTTG
*
51140 GTAATTAAGAAAAATAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTA
1 GTAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTA
51205 ATTTG
66 ATTTG
* * * * *
51210 GTAATTAAGAAAACTAAAGTCTTAATTTAGGGTAATTAAGAAATGTAAGCAAAATCAAGGTCTTA
1 GTAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTA
51275 ATTTG
66 ATTTG
** * * *
51280 GTAATTAAGAAAAACAAAGTCTTAATTCAAGGTAATTAAGAAAAGTAAACACAGTCAAGGTCTTA
1 GTAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTA
51345 AT
66 AT
51347 AATTCAGGGT
Statistics
Matches: 318, Mismatches: 29, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 318 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (70 bp):
GTAATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTA
ATTTG
Found at i:51301 original size:29 final size:30
Alignment explanation
Indices: 51242--51323 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
51232 TAATTTAGGG
* * *
51242 TAATTAA-GAAATGTAAGCAAAATCAAGGTCT
1 TAATTAAGGTAAT-TAAG-AAAAACAAAGTCT
*
51273 TAATT-TGGTAATTAAGAAAAACAAAGTCT
1 TAATTAAGGTAATTAAGAAAAACAAAGTCT
51302 TAATTCAAGGTAATTAAGAAAA
1 TAATT-AAGGTAATTAAGAAAA
51324 GTAAACACAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 16 0.37
30 4 0.09
31 23 0.53
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (30 bp):
TAATTAAGGTAATTAAGAAAAACAAAGTCT
Found at i:51345 original size:41 final size:41
Alignment explanation
Indices: 51298--51410 Score: 120
Period size: 44 Copynumber: 2.7 Consensus size: 41
51288 GAAAAACAAA
51298 GTCTTAATTCAAGGTAATTAAGAAAAGTAAACACAGTCAAG
1 GTCTTAATTCAAGGTAATTAAGAAAAGTAAACACAGTCAAG
* * * *
51339 GTCTTAATAATTCAGGGTAATTATGAAGAGTAAACACAGTCAGG
1 GTC-T--TAATTCAAGGTAATTAAGAAAAGTAAACACAGTCAAG
* *
51383 GGCTTAATTCATA-GAAATTAAGTAAAAG
1 GTCTTAATTCA-AGGTAATTAAG-AAAAG
51411 CAGCAGTTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
41 17 0.29
42 5 0.09
43 1 0.02
44 35 0.60
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (41 bp):
GTCTTAATTCAAGGTAATTAAGAAAAGTAAACACAGTCAAG
Found at i:51358 original size:44 final size:44
Alignment explanation
Indices: 51302--51390 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
51292 AACAAAGTCT
*
51302 TAATTCAAGGTAATTAAGAAAAGTAAACACAGTCAAGGTCTTAA
1 TAATTCAAGGTAATTAAGAAAAGTAAACACAGTCAAGGGCTTAA
* * * *
51346 TAATTCAGGGTAATTATGAAGAGTAAACACAGTCAGGGGCTTAA
1 TAATTCAAGGTAATTAAGAAAAGTAAACACAGTCAAGGGCTTAA
51390 T
1 T
51391 TCATAGAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (44 bp):
TAATTCAAGGTAATTAAGAAAAGTAAACACAGTCAAGGGCTTAA
Found at i:51434 original size:40 final size:39
Alignment explanation
Indices: 51385--51529 Score: 209
Period size: 40 Copynumber: 3.6 Consensus size: 39
51375 CAGTCAGGGG
*
51385 CTTAATTCATAGAAATTAAGTAAAAGCAGCAGTTAAAGGA
1 CTTAATTCATGGAAATTAAGTAAAA-CAGCAGTTAAAGGA
*
51425 GTTAATTCATGGAAATTAAGTAAGAACAGCAGTTAAAGGA
1 CTTAATTCATGGAAATTAAGTAA-AACAGCAGTTAAAGGA
* * *
51465 CTTAATTCATGGAAATTAACTGAAAACAACAGTTAAAAGA
1 CTTAATTCATGGAAATTAAGT-AAAACAGCAGTTAAAGGA
*
51505 CTTAATTCATGAAAATTAAGTAAAA
1 CTTAATTCATGGAAATTAAGTAAAA
51530 ACAGACAAGC
Statistics
Matches: 95, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.04
40 87 0.92
41 4 0.04
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (39 bp):
CTTAATTCATGGAAATTAAGTAAAACAGCAGTTAAAGGA
Found at i:51635 original size:41 final size:41
Alignment explanation
Indices: 51536--52667 Score: 1656
Period size: 41 Copynumber: 27.8 Consensus size: 41
51526 AAAAACAGAC
*
51536 AAGCACAGACTTAATTTCAGGGAAGGAAATTAGGTAAAGTAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGT-A
*
51578 AAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTAAAG-A
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
51618 TAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
* *
51660 AATCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
51701 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-A
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
*
51741 CAAGCACAGACTTAATTTCAATGAAGGAAATTAGGTAAAGTA
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
*
51783 AAGCACAGACTTAATTTCAATGAAGGAAATTAGGTAAAGTAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGT-A
*
51825 AAGCACGGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
*
51866 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA-AA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
51906 TAAGCACATG-CTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
1 -AAGCACA-GACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
*
51948 AAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAG-A
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
*
51988 TAAGCACAGACTTAATTTGAAGGAAGGAAATTAGGTAAAGTA
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
* *
52030 ACGCACATACTTAATTTC----AAGG--A--A-GTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
52062 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-A
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
* * * *
52102 CAAACACATACTTAATTTCAATGAAGGATATTAGGTAAAGTA
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
***** *
52144 AAGCACAGACTTAATTTC-ATCCTTGAAATTAAGTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
52184 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-A
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
*
52224 CAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
*
52266 AAGCACAGAATTAATTTCAAGGAAGGAAATTAGGTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
*
52307 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
*
52348 AAACACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
* *
52389 AAGCACAGGCTTAATTTCAATGAAGGAAATTAGGTAAAGTAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGT-A
*
52431 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA-AA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
* *
52471 CAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTGAAGTA
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
* *
52513 AAGCACAGACTTAAATTCAAGGAAGGAAATTAGGTGAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
* *
52554 AAGCACAAAGTTAATTTCAAGGAAGGAAATTAGGTAAAG-A
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
52594 TAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-A
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
* * * *
52635 CAGGCACATACTTAATTTCAGGGAAGGTAATTA
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTA
52668 AGTAGAGTCA
Statistics
Matches: 993, Mismatches: 68, Indels: 59
0.89 0.06 0.05
Matches are distributed among these distances:
32 24 0.02
33 1 0.00
35 1 0.00
36 4 0.00
37 4 0.00
38 1 0.00
40 43 0.04
41 794 0.80
42 121 0.12
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (41 bp):
AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA
Found at i:52068 original size:32 final size:32
Alignment explanation
Indices: 52022--52086 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
52012 AGGAAATTAG
* *
52022 GTAAAGTAACGCACATACTTAATTTCAAGGAA
1 GTAAAGTAAAGCACAGACTTAATTTCAAGGAA
52054 GTAAAGTAAAGCACAGACTTAATTTCAAGGAA
1 GTAAAGTAAAGCACAGACTTAATTTCAAGGAA
52086 G
1 G
52087 GAAATTAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (32 bp):
GTAAAGTAAAGCACAGACTTAATTTCAAGGAA
Found at i:52619 original size:606 final size:607
Alignment explanation
Indices: 51561--52660 Score: 1906
Period size: 606 Copynumber: 1.8 Consensus size: 607
51551 TTCAGGGAAG
* *
51561 GAAATTAGGTAAAGTAAAAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTAAAGATAAGCACA
1 GAAATTAAGTAAAGTAAAAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTAAAGACAAGCACA
* * * *
51626 GACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAATCATAGACTTAATTTCAAGGAAGGAAATT
66 AACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGAATTAATTTCAAGGAAGGAAATT
* *
51691 AGGTAAAGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAA
131 AGGTAAAGTAAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAACACAGACTTAA
*
51756 TTTCAATGAAGGAAATTAGGTAAAGTAAAGCACAGACTTAATTTCAATGAAGGAAATTAGGTAAA
196 TTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGACTTAATTTCAATGAAGGAAATTAGGTAAA
* *
51821 GTAAAAGCACGGACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGACTTAATTTCAA
261 GTAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAA
*
51886 GGAAGGAAATTAGGTAAAAATAAGCACATGCTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAG
326 GGAAGGAAATTAGGTAAAAATAAGCACATGCTTAAATTCAAGGAAGGAAATTAGGTAAAGTAAAG
* *
51951 CACATACTTAATTTCAAGGAAGGAAATTAGGTAAAGATAAGCACAGACTTAATTTGAAGGAAGGA
391 CACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGATAAGCACAGACTTAATTTCAAGGAAGGA
52016 AATTAGGTAAAGTA-ACGCACATACTTAATTTCAAGGAAGTAAAGTAAAGCACAGACTTAATTTC
456 AATTAGGTAAAG-ACACGCACATACTTAATTTCAAGGAAGTAAAGTAAAGCACAGACTTAATTTC
52080 AAGGAAGGAAATTAGGTAAAGACAAACACATACTTAATTTCAATGAAGGATATTAGGTAAAGTAA
520 AAGGAAGGAAATTAGGTAAAGACAAACACATACTTAATTTCAATGAAGGATATTAGGTAAAGTAA
52145 AGCACAGACTTAATTTCATCCTT
585 AGCACAGACTTAATTTCATCCTT
*
52168 GAAATTAAGTAAAGT-AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACA
1 GAAATTAAGTAAAGTAAAAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTAAAGACAAGCACA
52232 AACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGAATTAATTTCAAGGAAGGAAATT
66 AACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGAATTAATTTCAAGGAAGGAAATT
52297 AGGTAAAGTAAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGTA-AAACACAGACTTA
131 AGGTAAAGTAAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAG-ACAAACACAGACTTA
*
52361 ATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGGCTTAATTTCAATGAAGGAAATTAGGTAA
195 ATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGACTTAATTTCAATGAAGGAAATTAGGTAA
*
52426 AGTAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA-AACAAGCACATACTTAATTTC
260 AGTAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA-AAGCACAGACTTAATTTC
* * *
52490 AAGGAAGGAAATTAGGT-GAAGTAAAGCACA-GACTTAAATTCAAGGAAGGAAATTAGGTGAAGT
324 AAGGAAGGAAATTAGGTAAAAAT-AAGCACATG-CTTAAATTCAAGGAAGGAAATTAGGTAAAGT
*
52553 AAAGCACAAAGTTAATTTCAAGGAAGGAAATTAGGTAAAGATAAGCACAGACTTAATTTCAAGGA
387 AAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGATAAGCACAGACTTAATTTCAAGGA
* *
52618 AGGAAATTAGGTAAAGACAGGCACATACTTAATTTCAGGGAAG
452 AGGAAATTAGGTAAAGACACGCACATACTTAATTTCAAGGAAG
52661 GTAATTAAGT
Statistics
Matches: 465, Mismatches: 23, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
605 6 0.01
606 444 0.95
607 15 0.03
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (607 bp):
GAAATTAAGTAAAGTAAAAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTAAAGACAAGCACA
AACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGAATTAATTTCAAGGAAGGAAATT
AGGTAAAGTAAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAACACAGACTTAA
TTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGACTTAATTTCAATGAAGGAAATTAGGTAAA
GTAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAA
GGAAGGAAATTAGGTAAAAATAAGCACATGCTTAAATTCAAGGAAGGAAATTAGGTAAAGTAAAG
CACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGATAAGCACAGACTTAATTTCAAGGAAGGA
AATTAGGTAAAGACACGCACATACTTAATTTCAAGGAAGTAAAGTAAAGCACAGACTTAATTTCA
AGGAAGGAAATTAGGTAAAGACAAACACATACTTAATTTCAATGAAGGATATTAGGTAAAGTAAA
GCACAGACTTAATTTCATCCTT
Found at i:52722 original size:32 final size:32
Alignment explanation
Indices: 52677--52859 Score: 206
Period size: 32 Copynumber: 5.5 Consensus size: 32
52667 AAGTAGAGTC
**
52677 AATAAAGGGCTTAATTCAGGGTAATTAAGTAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGTAG
*
52709 AATAAAGAACTTAATTCATGGTAATTAAGTAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGTAG
*
52741 AATAAAGAACTTAATTTAGGGTAATTAAGTGGAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGT--AG
*
52775 TCAATAAA-AGGCTTAATTCAGGGTAATTAAGTAG
1 --AATAAAGA-ACTTAATTCAGGGTAATTAAGTAG
* * *
52809 AATAAATAACTTATTTCTGGGTAATTAAGTGGAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGT--AG
52843 TCAATAAAGAACTTAAT
1 --AATAAAGAACTTAAT
52860 CAAAAAAAGA
Statistics
Matches: 129, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
32 82 0.64
33 1 0.01
34 6 0.05
35 1 0.01
36 39 0.30
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.31
Consensus pattern (32 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTAG
Found at i:52737 original size:68 final size:67
Alignment explanation
Indices: 52660--52859 Score: 198
Period size: 68 Copynumber: 2.9 Consensus size: 67
52650 TTTCAGGGAA
52660 GGTAATTAAGTAGAGTCAATAAAGGGCTTAATTCAGGGTAATTAAGT-AG-AATAAAGAACTTAA
1 GGTAATTAAGTAGAGT-AATAAA--GCTTAATTCAGGGTAATTAAGTGAGCAATAAAGAACTTAA
*
52723 TTCAT
63 TTCAG
* * *
52728 GGTAATTAAGTAGAATAA-AGAA-CTTAATTTAGGGTAATTAAGTGGAGTCAATAAA-AGGCTTA
1 GGTAATTAAGTAGAGTAATA-AAGCTTAATTCAGGGTAATTAAGT-GAG-CAATAAAGA-ACTTA
52790 ATTCAG
62 ATTCAG
* * *
52796 GGTAATTAAGTAGAATAA-ATAA-CTTATTTCTGGGTAATTAAGTGGAGTCAATAAAGAACTTAA
1 GGTAATTAAGTAGAGTAATA-AAGCTTAATTCAGGGTAATTAAGT-GAG-CAATAAAGAACTTAA
52859 T
63 T
52860 CAAAAAAAGA
Statistics
Matches: 116, Mismatches: 9, Indels: 14
0.83 0.06 0.10
Matches are distributed among these distances:
64 20 0.17
66 3 0.03
67 5 0.04
68 87 0.75
69 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.30
Consensus pattern (67 bp):
GGTAATTAAGTAGAGTAATAAAGCTTAATTCAGGGTAATTAAGTGAGCAATAAAGAACTTAATTC
AG
Found at i:52833 original size:100 final size:102
Alignment explanation
Indices: 52660--52859 Score: 316
Period size: 100 Copynumber: 2.0 Consensus size: 102
52650 TTTCAGGGAA
*
52660 GGTAATTAAGTAGAGTCAATAAAGGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATT
1 GGTAATTAAGTAGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATT
52725 CATGGTAATTAAGT-AG-AATAAAGAACTTAATTTAG
66 CATGGTAATTAAGTGAGCAATAAAGAACTTAATTTAG
* * *
52760 GGTAATTAAGTGGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAATAACTTATTT
1 GGTAATTAAGTAGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATT
52825 C-TGGGTAATTAAGTGGAGTCAATAAAGAACTTAAT
66 CAT-GGTAATTAAGT-GAG-CAATAAAGAACTTAAT
52860 CAAAAAAAGA
Statistics
Matches: 91, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
99 1 0.01
100 73 0.80
102 2 0.02
104 15 0.16
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.30
Consensus pattern (102 bp):
GGTAATTAAGTAGAGTCAATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATT
CATGGTAATTAAGTGAGCAATAAAGAACTTAATTTAG
Found at i:56678 original size:33 final size:33
Alignment explanation
Indices: 56609--56682 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
56599 AAAACAAATA
* **
56609 TGTTTTGGTTGATCATAGCATTGCAAATAATTC
1 TGTTTTGGTTGATCATAGCATTGAAAATAAGAC
*
56642 TGTTTTGGTTGATCATAGCATTGAAAATAGGAC
1 TGTTTTGGTTGATCATAGCATTGAAAATAAGAC
56675 TGTTTTGG
1 TGTTTTGG
56683 GTGAAAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (33 bp):
TGTTTTGGTTGATCATAGCATTGAAAATAAGAC
Found at i:57097 original size:30 final size:30
Alignment explanation
Indices: 57061--57119 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
57051 CAAGGGGGAG
57061 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
*
57091 GGAATGATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
57120 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:58712 original size:77 final size:77
Alignment explanation
Indices: 58606--58782 Score: 291
Period size: 77 Copynumber: 2.3 Consensus size: 77
58596 ACATGGTGGT
* ** **
58606 GGAGAACTTTGTAGCCATGTGATGTTTTGGTTGTTGTGATACGGCATATGAAGATCCTTATGCCA
1 GGAGACCTTTGTAGCCATGTGATACTTTGGTTGCCGTGATACGGCATATGAAGATCCTTATGCCA
58671 TTACGTGGCGGG
66 TTACGTGGCGGG
*
58683 GGAGACCTTTGTAGCTATGTGATACTTTGGTTGCCGTGATACGGCATATGAAGATCCTTATGCCA
1 GGAGACCTTTGTAGCCATGTGATACTTTGGTTGCCGTGATACGGCATATGAAGATCCTTATGCCA
*
58748 TTACGTGGCGGT
66 TTACGTGGCGGG
58760 GGAGACCTTTGTAGCCATGTGAT
1 GGAGACCTTTGTAGCCATGTGAT
58783 CATACCAAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 92 1.00
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (77 bp):
GGAGACCTTTGTAGCCATGTGATACTTTGGTTGCCGTGATACGGCATATGAAGATCCTTATGCCA
TTACGTGGCGGG
Found at i:64133 original size:3 final size:3
Alignment explanation
Indices: 64127--64158 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
64117 TTTTTTAGTT
64127 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
64159 GTATATGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:64524 original size:2 final size:2
Alignment explanation
Indices: 64512--64545 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
64502 TTACATTTTG
64512 TA TA T- TA TA 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 TA TA TA TA TA T
64546 TGTGTGTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:71716 original size:20 final size:20
Alignment explanation
Indices: 71676--71717 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
71666 TCTTACAAGA
* *
71676 TTCTAGCCGTTGGAGCTCTT
1 TTCTAGCCGTTAGAGCACTT
*
71696 TTCTAGCCGTTATAGCACTT
1 TTCTAGCCGTTAGAGCACTT
71716 TT
1 TT
71718 TCAACAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
TTCTAGCCGTTAGAGCACTT
Found at i:77891 original size:42 final size:43
Alignment explanation
Indices: 77844--77926 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
77834 CGTGTTTGGC
*
77844 TTATCGTATCT-CGTGTC-TGAATCGTGTC-GGACACGATTAAGA
1 TTATCGTAT-TACGTGTCGT-AATCGTGTCAAGACACGATTAAGA
*
77886 TTATCGTGTTACGTGTCGTAATCGTGTCAAGACACGATTAA
1 TTATCGTATTACGTGTCGTAATCGTGTCAAGACACGATTAA
77927 CACGTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
41 1 0.03
42 23 0.64
43 12 0.33
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (43 bp):
TTATCGTATTACGTGTCGTAATCGTGTCAAGACACGATTAAGA
Found at i:81669 original size:12 final size:12
Alignment explanation
Indices: 81652--81676 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
81642 AATACATATT
81652 AATATTTAATCA
1 AATATTTAATCA
81664 AATATTTAATCA
1 AATATTTAATCA
81676 A
1 A
81677 TGTTTTCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AATATTTAATCA
Found at i:85137 original size:19 final size:19
Alignment explanation
Indices: 85096--85139 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
85086 TTATCCCTCT
*
85096 TCTCTCTCCCCCCACTAAG
1 TCTCTCTCCCCCCACTAAC
* *
85115 TCTCTCTCCTCCCACTTAC
1 TCTCTCTCCCCCCACTAAC
85134 TCTCTC
1 TCTCTC
85140 ATAGTCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.11, C:0.52, G:0.02, T:0.34
Consensus pattern (19 bp):
TCTCTCTCCCCCCACTAAC
Found at i:90244 original size:31 final size:31
Alignment explanation
Indices: 90208--90273 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 31
90198 AACTTTATAT
90208 TTTCCAATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
90239 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTGTACCCTTTTCTTTAAAACATA
90270 TTTC
1 TTTC
90274 TAAATTGCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCTTTAAAACATA
Found at i:90511 original size:26 final size:27
Alignment explanation
Indices: 90463--90513 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
90453 CTTAAATTTC
* *
90463 CATTATTAAAATTTAGTATAATTTTAT
1 CATTATTAAAATTAAGTAAAATTTTAT
*
90490 CATT-TTAAAATTAATTAAAATTTT
1 CATTATTAAAATTAAGTAAAATTTT
90514 CAATTTAGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (27 bp):
CATTATTAAAATTAAGTAAAATTTTAT
Found at i:90860 original size:22 final size:22
Alignment explanation
Indices: 90835--90897 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
90825 TTCATGAGGA
* *
90835 GGTTATCAAAATTCCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
90857 GGTTACCAAAATTTCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
90879 GGTTACCAAAATTTCATAG
1 GGTTACCAAAATTTCATAG
90898 GATCAGGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGTGT
Found at i:90949 original size:22 final size:22
Alignment explanation
Indices: 90791--90951 Score: 99
Period size: 22 Copynumber: 7.2 Consensus size: 22
90781 GTGTCTATGA
* * *
90791 GGTTAACAAAATTTCATAAGAT
1 GGTTATCAAAATTTCATAGGGT
* * * *
90813 GGTTATTATAACTTCAT-GAGGA
1 GGTTATCAAAATTTCATAG-GGT
* *
90835 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAGGGT
* *
90857 GGTTACCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGGGT
* *
90879 GGTTACCAAAATTTCATAGGAT
1 GGTTATCAAAATTTCATAGGGT
* * * * * *
90901 CAGGTTTTTAAAATCTCTTAAGTT
1 --GGTTATCAAAATTTCATAGGGT
**
90925 GGTTATTGAAATTTCATAGGGT
1 GGTTATCAAAATTTCATAGGGT
90947 GGTTA
1 GGTTA
90952 ATTATCACAA
Statistics
Matches: 105, Mismatches: 30, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
22 89 0.85
23 1 0.01
24 15 0.14
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGGGT
Found at i:91012 original size:22 final size:22
Alignment explanation
Indices: 90987--91045 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
90977 ATCAAAGAGA
*
90987 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
91009 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
*
91031 TTAACAAAATTTCAT
1 TTATCAAAATTTCAT
91046 TAAATATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:91110 original size:22 final size:22
Alignment explanation
Indices: 91051--91347 Score: 113
Period size: 22 Copynumber: 13.3 Consensus size: 22
91041 TTCATTAAAT
* *
91051 ATTTCATGGGGAGGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
* *
91073 ATTTTATAGTGTGGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
* *
91095 CTTTCATA-TGAAGGTTATAAAAGTCTCA
1 ATTTCATAGTG-AGGTTAT-CAA-----A
* * **
91123 ATTTCATA-AGAAG-TGCCAAA
1 ATTTCATAGTGAGGTTATCAAA
* * *
91143 ATTTGATAG-AAGGTCATC-AA
1 ATTTCATAGTGAGGTTATCAAA
*
91163 ATTTCATAAAGTGA--TTATCGAA
1 ATTTCAT--AGTGAGGTTATCAAA
* *
91185 ATTTCATAGAGATCGAATTATCAAA
1 ATTTCATAGTGA--G-GTTATCAAA
**
91210 ATTTCATAGTGTTGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
* *
91232 ATTTCAAAGCGAGGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
* * * * *
91254 ATTACATAATGTGGTTATTAGA
1 ATTTCATAGTGAGGTTATCAAA
* * * *
91276 ATTTCATAGAGGGGTCAACAAA
1 ATTTCATAGTGAGGTTATCAAA
* ***
91298 ATTTTATAAAAAGGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
**
91320 ATTTCATAAAGAGGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
*
91342 TTTTCA
1 ATTTCA
91348 AAATGTAATT
Statistics
Matches: 200, Mismatches: 57, Indels: 36
0.68 0.19 0.12
Matches are distributed among these distances:
20 22 0.11
21 7 0.04
22 137 0.69
23 3 0.01
25 19 0.09
26 1 0.00
27 2 0.01
28 9 0.05
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
ATTTCATAGTGAGGTTATCAAA
Found at i:91211 original size:25 final size:22
Alignment explanation
Indices: 91161--91372 Score: 99
Period size: 22 Copynumber: 9.5 Consensus size: 22
91151 GAAGGTCATC
* *
91161 AAATTTCATAAAGTGATTATCG
1 AAATTTCATAGAGTGATTATCA
91183 AAATTTCATAGAGATCGAATTATCA
1 AAATTTCATAGAG-T-G-ATTATCA
*
91208 AAATTTCATAGTGTTG-TTATCA
1 AAATTTCATAGAG-TGATTATCA
* * * *
91230 AAATTTCAAAGCGAGGTTATCA
1 AAATTTCATAGAGTGATTATCA
* * *
91252 AAATTACATA-ATGTGGTTATTA
1 AAATTTCATAGA-GTGATTATCA
* * * * *
91274 GAATTTCATAGAGGGGTCAACA
1 AAATTTCATAGAGTGATTATCA
* * ** *
91296 AAATTTTATAAAAAGGTTATCA
1 AAATTTCATAGAGTGATTATCA
* * *
91318 AAATTTCATAAAGAGGTTATCA
1 AAATTTCATAGAGTGATTATCA
* * *
91340 AATTTTCA-AAATGTAATTA-CAA
1 AAATTTCATAGA-GTGATTATC-A
91362 AAATTTCATAG
1 AAATTTCATAG
91373 TGGTATTTCT
Statistics
Matches: 148, Mismatches: 33, Indels: 17
0.75 0.17 0.09
Matches are distributed among these distances:
21 5 0.03
22 119 0.80
23 3 0.02
24 2 0.01
25 19 0.13
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (22 bp):
AAATTTCATAGAGTGATTATCA
Found at i:91271 original size:44 final size:44
Alignment explanation
Indices: 91139--91353 Score: 157
Period size: 44 Copynumber: 4.9 Consensus size: 44
91129 TAAGAAGTGC
* * * * *
91139 CAAAATTTGATAGA-AGGTCATC-AAATTTCATAAAGTGATTAT
1 CAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTGGTTAT
* * * * *
91181 CGAAATTTCATAGAGATCGAATTATCAAAATTTCATAGTGTTGTTAT
1 CAAAATTTCAAAGAGA--G-GTTATCAAAATTTCATAATGTGGTTAT
* *
91228 CAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTGGTTAT
1 CAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTGGTTAT
* * * * * * * ***
91272 TAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAAAGGTTAT
1 CAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTGGTTAT
* *
91316 CAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 CAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
91354 AATTACAAAA
Statistics
Matches: 128, Mismatches: 39, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
42 12 0.09
43 1 0.01
44 79 0.62
45 3 0.02
46 4 0.03
47 29 0.23
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (44 bp):
CAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTGGTTAT
Found at i:91478 original size:20 final size:20
Alignment explanation
Indices: 91453--91522 Score: 88
Period size: 19 Copynumber: 3.5 Consensus size: 20
91443 TTATGGAGTA
91453 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
91473 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
* *
91492 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCA-A-GGAGGAT
91514 ATCAAAATT
1 ATCAAAATT
91523 GCATAGTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.42
20 11 0.26
22 14 0.33
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:91519 original size:22 final size:22
Alignment explanation
Indices: 91491--91971 Score: 154
Period size: 22 Copynumber: 22.1 Consensus size: 22
91481 TCAGGGAGGA
91491 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
91513 TATCAAAATTGCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
91535 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
*
91557 TATCAAAATTTCATA--ATATGT
1 TATCAAAATTTCATATGA-AGGT
* * * * *
91578 AGATCAAAATTCCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
91601 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* ** * *
91623 TATGAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
91645 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * * *
91661 TATCAAGATTTTATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
91683 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
91706 TATCAAAATTTTATAGGAAGTT
1 TATCAAAATTTCATATGAAGGT
* *
91728 TATCAAAAATTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
91750 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
91772 TATCAAAATTTCAGA-GTATGAT
1 TATCAAAATTTCATATG-AAGGT
* *
91794 TA-CTAACAA-TTCATATGGAGAT
1 TATC-AA-AATTTCATATGAAGGT
* * * ** *
91816 TTTTAAATTTTCATAACATGGT
1 TATCAAAATTTCATATGAAGGT
* *
91838 TATCAATATATCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
91860 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
*
91883 TATCAAAATTTCAT-TGGAA-CT
1 TATCAAAATTTCATAT-GAAGGT
*
91904 TATCAAAATTTCATATTG-AGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
91926 CT-TCAAAATTCCTTAAGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * *
91948 TAACCAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
91970 TA
1 TA
91972 AAAAAAAAAT
Statistics
Matches: 337, Mismatches: 89, Indels: 66
0.68 0.18 0.13
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
20 4 0.01
21 28 0.08
22 243 0.72
23 48 0.14
24 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:96595 original size:1 final size:1
Alignment explanation
Indices: 96589--96617 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
96579 GATTATTCTC
96589 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
96618 CCTCTTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:100549 original size:28 final size:28
Alignment explanation
Indices: 100518--100588 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 28
100508 GCCCAAGGGT
*
100518 ATTTTGGTCATTTTTGCAC-CTAGGGGGC
1 ATTTTGGTCATTTTTGCACTC-AGGGAGC
100546 ATTTTGGTCATTTTTGCACTCAGGGAGC
1 ATTTTGGTCATTTTTGCACTCAGGGAGC
*
100574 ATTTTAGTCATTTTT
1 ATTTTGGTCATTTTT
100589 AGGTTCACCT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 39 0.98
29 1 0.03
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45
Consensus pattern (28 bp):
ATTTTGGTCATTTTTGCACTCAGGGAGC
Found at i:103416 original size:51 final size:51
Alignment explanation
Indices: 103347--103795 Score: 385
Period size: 51 Copynumber: 8.7 Consensus size: 51
103337 ATCTTTATGT
* * *
103347 TAAAAGATTGAATATTTAAGTAATTAGTAAATAAAGATGTAATCTTTATG-T
1 TAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATGTAACCTTT-TGAA
* ** *
103398 TAAAAGATTGAATTTTTAAATAATTAGTTTATAAAGATGTAACCTTTTGAC
1 TAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAA
* * * * * *
103449 TAAAAGATGGAAAAATTTTTTAGTAATTAGTAAGTAAAAATGTCA-CTTTTGAG
1 TAAAAGATTG---AATTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAA
*
103502 CAAAAGATAT-AATTTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAA
1 TAAAAGAT-TGAA-TTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAA
* * ** *
103554 TAAAAGATTGAACTTTTAAATAATTAGTTTATAAAGATGTAACCTTTTGAC
1 TAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAA
* * * * * *
103605 TAAAAGATGGAATTTTTTTTAGTAATTAGTAAGTAAAAATGTCA-CTTTTGAG
1 TAAAAGATTGAA--TTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAA
* * * *
103657 CAAAAGATAGAATTTTTTAAGTAATTAGTAAATAAGGATAT-ACCTTTTGAA
1 TAAAAGATTGAA-TTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAA
* * *
103708 TAAAAGATTGAATTTTTTTTTTAGTAATTGGTAAATAAA-ATGTCACC-TTTGAA
1 TAAAAGATTGAA----TTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAA
* * *
103761 TTAAAGTTTGAACTTTT-AG-ACCATTAGTAAATAAA
1 TAAAAGATTGAATTTTTAAGTA--ATTAGTAAATAAA
103796 TTGATTAGTT
Statistics
Matches: 325, Mismatches: 56, Indels: 36
0.78 0.13 0.09
Matches are distributed among these distances:
47 1 0.00
48 2 0.01
49 16 0.05
50 5 0.02
51 164 0.50
52 33 0.10
53 55 0.17
54 49 0.15
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (51 bp):
TAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAA
Found at i:103662 original size:103 final size:103
Alignment explanation
Indices: 103514--103795 Score: 316
Period size: 104 Copynumber: 2.7 Consensus size: 103
103504 AAAGATATAA
* * *
103514 TTTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAATAAAAGATTGAACTTTTAAATAATT
1 TTTTTTTAGTAATTAGTAAATAAAAATGTCA-CTTTTGAATAAAAGATTGAACTTTTAAATAATT
** * *
103579 AGTTTATAAAGATGTAACCTTTTGACTAAAAGATGGAA-T
65 AGTAAATAAAGATAT-ACCTTTTGAATAAAAGATGGAATT
* ** * * *
103618 TTTTTTTAGTAATTAGTAAGTAAAAATGTCACTTTTGAGCAAAAGATAGAATTTTTTAAGTAATT
1 TTTTTTTAGTAATTAGTAAATAAAAATGTCACTTTTGAATAAAAGATTGAA-CTTTTAAATAATT
* *
103683 AGTAAATAAGGATATACCTTTTGAATAAAAGATTGAATTT
65 AGTAAATAAAGATATACCTTTTGAATAAAAGATGGAA-TT
* * * * * **
103723 TTTTTTTAGTAATTGGTAAAT-AAAATGTCACCTTTGAATTAAAGTTTGAACTTTTAGACCATTA
1 TTTTTTTAGTAATTAGTAAATAAAAATGTCACTTTTGAATAAAAGATTGAACTTTTAAATAATTA
103787 GTAAATAAA
66 GTAAATAAA
103796 TTGATTAGTT
Statistics
Matches: 146, Mismatches: 29, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
103 54 0.37
104 72 0.49
105 20 0.14
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (103 bp):
TTTTTTTAGTAATTAGTAAATAAAAATGTCACTTTTGAATAAAAGATTGAACTTTTAAATAATTA
GTAAATAAAGATATACCTTTTGAATAAAAGATGGAATT
Found at i:103674 original size:156 final size:156
Alignment explanation
Indices: 103348--103724 Score: 627
Period size: 156 Copynumber: 2.4 Consensus size: 156
103338 TCTTTATGTT
* * * *
103348 AAAAGATTGAA-TATTTAAGTAATTAGTAAATAAAGATGTAATCTTTATG-TTAAAAGATTGAAT
1 AAAAGATAGAATTTTTTAAGTAATTAGTAAATAAAGATGTAACCTTT-TGAATAAAAGATTGAAT
103411 TTTTAAATAATTAGTTTATAAAGATGTAACCTTTTGACTAAAAGATGGAAAAATTTTTTAGTAAT
65 TTTTAAATAATTAGTTTATAAAGATGTAACCTTTTGACTAAAAGATGGAAAAATTTTTTAGTAAT
103476 TAGTAAGTAAAAATGTCACTTTTGAGC
130 TAGTAAGTAAAAATGTCACTTTTGAGC
* *
103503 AAAAGATATAATTTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAATAAAAGATTGAACT
1 AAAAGATAGAATTTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAATAAAAGATTGAATT
**
103568 TTTAAATAATTAGTTTATAAAGATGTAACCTTTTGACTAAAAGATGG-AATTTTTTTTAGTAATT
66 TTTAAATAATTAGTTTATAAAGATGTAACCTTTTGACTAAAAGATGGAAAAATTTTTTAGTAATT
103632 AGTAAGTAAAAATGTCACTTTTGAGC
131 AGTAAGTAAAAATGTCACTTTTGAGC
* *
103658 AAAAGATAGAATTTTTTAAGTAATTAGTAAATAAGGATAT-ACCTTTTGAATAAAAGATTGAATT
1 AAAAGATAGAATTTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAATAAAAGATTGAATT
103722 TTT
66 TTT
103725 TTTTTAGTAA
Statistics
Matches: 208, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
154 26 0.12
155 89 0.43
156 93 0.45
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (156 bp):
AAAAGATAGAATTTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAATAAAAGATTGAATT
TTTAAATAATTAGTTTATAAAGATGTAACCTTTTGACTAAAAGATGGAAAAATTTTTTAGTAATT
AGTAAGTAAAAATGTCACTTTTGAGC
Found at i:103759 original size:104 final size:102
Alignment explanation
Indices: 103348--103795 Score: 300
Period size: 105 Copynumber: 4.3 Consensus size: 102
103338 TCTTTATGTT
* * * * * *
103348 AAAAGATTGAA-TATTTAAGTAATTAGTAAATAAAGATGTAATCTTTATG-TTAAAAGATTGAA-
1 AAAAGATAGAACT-TTTAAATAATTAGTAAATAAAGATATAACCTTT-TGAATAAAAGATGGAAT
* * ** *
103410 -TTTTTAAATAATTAGTTTATAAAGATGTAACCTTTTG-AC
64 TTTTTTTAGTAATTAGTAAATAAA-ATGTCACC-TTTGAAC
* * * * * * * * ** **
103449 TAAAAGATGGAAAAATTTTTTAGTAATTAGTAAGTAAAAATGTCA-CTTTTGAGCAAAAGATATA
1 -AAAAGAT---AGAACTTTTAAATAATTAGTAAATAAAGATATAACCTTTTGAATAAAAGATGGA
* * *
103513 A-TTTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTTGAAT
62 ATTTTTTTTAGTAATTAGTAAATAAA-ATGTCACC-TTTGAAC
* ** * *
103555 AAAAGATTGAACTTTTAAATAATTAGTTTATAAAGATGTAACCTTTTGACTAAAAGATGGAATTT
1 AAAAGATAGAACTTTTAAATAATTAGTAAATAAAGATATAACCTTTTGAATAAAAGATGGAATTT
* * *
103620 TTTTTAGTAATTAGTAAGTAAAAATGTCACTTTTGAGC
66 TTTTTAGTAATTAGTAAAT-AAAATGTCACCTTTGAAC
* * * *
103658 AAAAGATAGAATTTTTTAAGTAATTAGTAAATAAGGATAT-ACCTTTTGAATAAAAGATTGAATT
1 AAAAGATAGAA-CTTTTAAATAATTAGTAAATAAAGATATAACCTTTTGAATAAAAGATGGAA--
* *
103722 TTTTTTTTAGTAATTGGTAAATAAAATGTCACCTTTGAAT
63 TTTTTTTTAGTAATTAGTAAATAAAATGTCACCTTTGAAC
* * * * **
103762 TAAAGTTTGAACTTTTAGACCATTAGTAAATAAA
1 AAAAGATAGAACTTTTAAATAATTAGTAAATAAA
103796 TTGATTAGTT
Statistics
Matches: 276, Mismatches: 57, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
102 31 0.11
103 70 0.25
104 83 0.30
105 90 0.33
106 2 0.01
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (102 bp):
AAAAGATAGAACTTTTAAATAATTAGTAAATAAAGATATAACCTTTTGAATAAAAGATGGAATTT
TTTTTAGTAATTAGTAAATAAAATGTCACCTTTGAAC
Found at i:104533 original size:47 final size:47
Alignment explanation
Indices: 104475--104789 Score: 407
Period size: 47 Copynumber: 6.4 Consensus size: 47
104465 AAAAAGGGGC
*
104475 AATCAGT-AATCAGTAAAAAGAGATTAATCAGAGTCAAGTTGATGGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGT
*
104521 AATCAGTAAATCAGTAAATCAGTAGAAAGAGATTAATCAAAGTCAAGGTGATGGT
1 AATCAGTAAATCAG----T-A--A-AAAGAGATTAATCAGAGTCAAGGTGATGGT
*
104576 AATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAGGTGATGGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGT
*
104623 AATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAGGTGATGGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGT
*
104670 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTAATGGTAATCAGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGG---T-G--AT-GGT
* *
104724 CAATCAGTAAATCAGTAAAAAGAGATTAATCAAGAGTCAAGGTAATAGT
1 -AATCAGTAAATCAGTAAAAAGAGATTAATC-AGAGTCAAGGTGATGGT
104773 AATCAGTAAATCAGTAA
1 AATCAGTAAATCAGTAA
104790 TCAAGTAAAA
Statistics
Matches: 244, Mismatches: 7, Indels: 34
0.86 0.02 0.12
Matches are distributed among these distances:
46 7 0.03
47 120 0.49
48 18 0.07
49 3 0.01
50 4 0.02
51 3 0.01
52 1 0.00
53 3 0.01
54 3 0.01
55 72 0.30
56 10 0.04
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.24
Consensus pattern (47 bp):
AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGT
Found at i:104644 original size:94 final size:99
Alignment explanation
Indices: 104475--104789 Score: 453
Period size: 94 Copynumber: 3.2 Consensus size: 99
104465 AAAAAGGGGC
*
104475 AATCAGT-AATCAGTAAAAAGAGATTAATCAGAGTCAAGTTGATGGTAATCAGTAAATCAGTAAA
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAG--GATGG-AATCAGTCAATCAGTAAA
*
104539 TCAGTAGAAAGAGATTAATCAAAGTCAAGGTGATGGT
63 TCAGTAAAAAGAGATTAATCAAAGTCAAGGTGATGGT
* *
104576 AATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAGG-T-G-AT-GGT-AATCAGTAAATCA
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGATGGAATCAGTCAATCAGTAAATCA
**
104636 GTAAAAAGAGATTAATCGGAGTCAAGGTGATGGT
66 GTAAAAAGAGATTAATCAAAGTCAAGGTGATGGT
104670 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTAATGGTAATCAGTCAATCAGTAAA
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGG--ATGG-AATCAGTCAATCAGTAAA
* *
104735 TCAGTAAAAAGAGATTAATCAAGAGTCAAGGTAATAGT
63 TCAGTAAAAAGAGATTAATCAA-AGTCAAGGTGATGGT
104773 AATCAGTAAATCAGTAA
1 AATCAGTAAATCAGTAA
104790 TCAAGTAAAA
Statistics
Matches: 193, Mismatches: 11, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
94 83 0.43
95 2 0.01
96 2 0.01
97 1 0.01
98 2 0.01
99 1 0.01
100 3 0.02
101 9 0.05
102 60 0.31
103 30 0.16
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.24
Consensus pattern (99 bp):
AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGATGGAATCAGTCAATCAGTAAATCA
GTAAAAAGAGATTAATCAAAGTCAAGGTGATGGT
Found at i:104786 original size:56 final size:56
Alignment explanation
Indices: 104670--104811 Score: 225
Period size: 56 Copynumber: 2.6 Consensus size: 56
104660 AGGTGATGGT
* *
104670 AATCAGTAAATCAGTAAAAAGAGATTAATC-AGAGTCAAGGTAATGGTAATCAGTC
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAAGAGTCAAGGTAATAGTAATCAGTA
104725 AATCAGTAAATCAGTAAAAAGAGATTAATCAAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAAGAGTCAAGGTAATAGTAATCAGTA
* *
104781 AATCAGT-AATCAAGTAAAAAGATAGTAATCA
1 AATCAGTAAATC-AGTAAAAAGAGATTAATCA
104812 GTAAATTGAT
Statistics
Matches: 81, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
55 34 0.42
56 47 0.58
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (56 bp):
AATCAGTAAATCAGTAAAAAGAGATTAATCAAGAGTCAAGGTAATAGTAATCAGTA
Found at i:104830 original size:71 final size:70
Alignment explanation
Indices: 104750--104905 Score: 183
Period size: 71 Copynumber: 2.2 Consensus size: 70
104740 AAAAAGAGAT
* * *
104750 TAATCAAGAGTCAAGGTAATAG-TAATCAGTAAATCAGTAATCAA-GTAAAAAGATAGTAATCAG
1 TAATTAAGAGTCAAGGTAAGAGATAATCAGTAAATAAG-AATCAAGGT-AAAA-ATAGTAATCAG
*
104813 TAAAT-TG
63 TAAATCAG
* *
104820 ATAATTAAGAGTCAAGGTAAGAGATTAATCAGTAATTAAGAGTCAAGGTAAAAATAGTAATCAGT
1 -TAATTAAGAGTCAAGGTAAGAGA-TAATCAGTAAATAAGAATCAAGGTAAAAATAGTAATCAGT
104885 AAATCAG
64 AAATCAG
*
104892 TAATTAAAAGTCAA
1 TAATTAAGAGTCAA
104906 TGGATTGATC
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
71 49 0.66
72 10 0.14
73 15 0.20
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (70 bp):
TAATTAAGAGTCAAGGTAAGAGATAATCAGTAAATAAGAATCAAGGTAAAAATAGTAATCAGTAA
ATCAG
Found at i:104886 original size:32 final size:31
Alignment explanation
Indices: 104821--104886 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
104811 AGTAAATTGA
*
104821 TAATTAAGAGTCAAGGTAAGAGATTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
104852 TAATTAAGAGTCAAGGTAA-AAATAGTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAAT--TAATCAG
104884 TAA
1 TAA
104887 ATCAGTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 3 0.09
31 19 0.59
32 10 0.31
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAGAAATTAATCAG
Found at i:105042 original size:14 final size:14
Alignment explanation
Indices: 105025--105060 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
105015 AATGGTAAAG
105025 AGTAAAGAATAATC
1 AGTAAAGAATAATC
* *
105039 AGTAAGGAATAATT
1 AGTAAAGAATAATC
105053 AGTAAAGA
1 AGTAAAGA
105061 GTAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (14 bp):
AGTAAAGAATAATC
Found at i:105042 original size:35 final size:35
Alignment explanation
Indices: 104999--105065 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
104989 TTCAAGAGAG
*
104999 TAATCAGTAAAGGAA-AAATGGTAAAGAGTAAAGAA
1 TAATCAGT-AAGGAATAAATAGTAAAGAGTAAAGAA
*
105034 TAATCAGTAAGGAATAATTAGTAAAGAGTAAA
1 TAATCAGTAAGGAATAAATAGTAAAGAGTAAA
105066 ATGATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 6 0.21
35 23 0.79
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (35 bp):
TAATCAGTAAGGAATAAATAGTAAAGAGTAAAGAA
Found at i:105089 original size:51 final size:49
Alignment explanation
Indices: 104999--105094 Score: 129
Period size: 51 Copynumber: 1.9 Consensus size: 49
104989 TTCAAGAGAG
* *
104999 TAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGGAA
1 TAATCAGTAAAGGAAAAATGATAAAAAGTAAAGAATAATCAGTAAGGAA
* * *
105048 TAATTAGTAAAGAGTAAAATGATAAAAAAGTAAAGAGTAATCAGTAA
1 TAATCAGTAAAG-GAAAAATGAT-AAAAAGTAAAGAATAATCAGTAA
105095 AAGAAGAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 11 0.28
50 8 0.20
51 21 0.52
ACGTcount: A:0.56, C:0.03, G:0.20, T:0.21
Consensus pattern (49 bp):
TAATCAGTAAAGGAAAAATGATAAAAAGTAAAGAATAATCAGTAAGGAA
Found at i:105090 original size:86 final size:85
Alignment explanation
Indices: 104995--105151 Score: 235
Period size: 86 Copynumber: 1.8 Consensus size: 85
104985 TAAATTCAAG
* * *
104995 AGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGT-AAGGAATAATTAGTAAA
1 AGAGTAATCAGTAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAAGGAAGAA-TAGTAAA
105059 GAGTAAAATGATAAAAAAGTAA
65 GAG-AAAATGATAAAAAAGTAA
* * *
105081 AGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTAAAGAGTAATCAGTAAAGGAAGAATGGTAAAG
1 AGAGTAATCAGTAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAAGGAAGAATAGTAAAG
105146 AGAAAA
66 AGAAAA
105152 GGGTAATCAG
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
85 4 0.06
86 52 0.81
87 8 0.12
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.18
Consensus pattern (85 bp):
AGAGTAATCAGTAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAAGGAAGAATAGTAAAG
AGAAAATGATAAAAAAGTAA
Found at i:105117 original size:35 final size:35
Alignment explanation
Indices: 105072--105166 Score: 154
Period size: 35 Copynumber: 2.7 Consensus size: 35
105062 TAAAATGATA
105072 AAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGGT
1 AAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGGT
*
105107 AAAAAGTAAAGAGTAATCAGTAAAGGAAGAATGGT
1 AAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGGT
* * *
105142 AAAGAGAAAAGGGTAATCAGTAAAA
1 AAAAAGTAAAGAGTAATCAGTAAAA
105167 AGTAAAAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.57, C:0.03, G:0.24, T:0.16
Consensus pattern (35 bp):
AAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGGT
Found at i:105180 original size:22 final size:22
Alignment explanation
Indices: 105140--105372 Score: 104
Period size: 22 Copynumber: 10.3 Consensus size: 22
105130 AGGAAGAATG
* *
105140 GTAAAGAG-AAAAGGGTAATCA
1 GTAAAAAGTAAAAAGGTAATCA
*
105161 GTAAAAAGTAAAAAGATAATCA
1 GTAAAAAGTAAAAAGGTAATCA
105183 GTAAAGAATGAAATAGTAAAAGGTAATCCA
1 GTAAA-AA-G---TA--AAAAGGTAAT-CA
* *
105213 -TAAAAA-AAAAGTAATGATAATCA
1 GTAAAAAGTAAA--AA-GGTAATCA
105236 GTAAAAAGGTAAAATA-GTAATCA
1 GTAAAAA-GTAAAA-AGGTAATCA
* * *
105259 GT-AAGAGCAAAATGGTAATCA
1 GTAAAAAGTAAAAAGGTAATCA
* * * * *
105280 AT-GAGAGCAAAATGGTAATCA
1 GTAAAAAGTAAAAAGGTAATCA
*
105301 GTAAAGAGTAAAATA-GTAATCA
1 GTAAAAAGTAAAA-AGGTAATCA
* *
105323 TTAAAAAGTAAGAAGGTAATCA
1 GTAAAAAGTAAAAAGGTAATCA
**
105345 GTAAAGCGTAAAATA-GTAATCA
1 GTAAAAAGTAAAA-AGGTAATCA
*
105367 GCAAAA
1 GTAAAA
105373 GGCAATCAGT
Statistics
Matches: 165, Mismatches: 26, Indels: 41
0.71 0.11 0.18
Matches are distributed among these distances:
21 42 0.25
22 71 0.43
23 16 0.10
24 13 0.08
25 1 0.01
26 3 0.02
27 2 0.01
28 2 0.01
29 13 0.08
30 2 0.01
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.20
Consensus pattern (22 bp):
GTAAAAAGTAAAAAGGTAATCA
Found at i:105204 original size:29 final size:25
Alignment explanation
Indices: 105163--105242 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 25
105153 GGTAATCAGT
105163 AAAAAGTAAAAAGATAATCAGTAAAGA
1 AAAAAGT-AAAAGATAATCAGTAAA-A
*
105190 ATGAAATAGTAAAAGGTAATCCA-TAAAA
1 A--AAA-AGTAAAAGATAAT-CAGTAAAA
*
105218 AAAAAGT-AATGATAATCAGTAAAA
1 AAAAAGTAAAAGATAATCAGTAAAA
105242 A
1 A
105243 GGTAAAATAG
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
23 2 0.04
24 13 0.29
25 3 0.07
26 3 0.07
27 1 0.02
28 2 0.04
29 16 0.36
30 5 0.11
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.19
Consensus pattern (25 bp):
AAAAAGTAAAAGATAATCAGTAAAA
Found at i:105276 original size:21 final size:21
Alignment explanation
Indices: 105246--105633 Score: 110
Period size: 21 Copynumber: 18.8 Consensus size: 21
105236 GTAAAAAGGT
105246 AAAATAGTAATCAGTAAGAGC
1 AAAATAGTAATCAGTAAGAGC
* * *
105267 AAAATGGTAATCAATGAGAGC
1 AAAATAGTAATCAGTAAGAGC
* *
105288 AAAATGGTAATCAGTAAAGAGT
1 AAAATAGTAATCAGT-AAGAGC
* * *
105310 AAAATAGTAATCATTAAAAAGT
1 AAAATAGTAATCAGT-AAGAGC
*
105332 AAGAA-GGTAATCAGTAA-AGC
1 AA-AATAGTAATCAGTAAGAGC
* *
105352 GTAAAATAGTAATCAGCAAAAGGC
1 --AAAATAGTAATCAGTAAGA-GC
*
105376 --AATCAGT-A--AG----AGT
1 AAAAT-AGTAATCAGTAAGAGC
105389 AAAATAGTAATCAGT---AG-
1 AAAATAGTAATCAGTAAGAGC
* *
105406 --AA-GGTAATCAGTAAAGAGT
1 AAAATAGTAATCAGT-AAGAGC
105425 AAAATAGTAATCAGT------
1 AAAATAGTAATCAGTAAGAGC
* *
105440 AAAAGA-TAATCAGTAAGAGT
1 AAAATAGTAATCAGTAAGAGC
* * *
105460 AAAACAGTAACCAGTGAGAGC
1 AAAATAGTAATCAGTAAGAGC
* * *
105481 AAAGTGGTAATTAGTAAGAGTC
1 AAAATAGTAATCAGTAAGAG-C
*
105503 -AAATAGTAATCAGTAAGAAGT
1 AAAATAGTAATCAGTAAG-AGC
*
105524 AAAAGAGTAATCAGTAAAAAAGGAGC
1 AAAATAGTAATCAGT----AA-GAGC
*
105550 AGAAAATAGTAATCAGTAAAAGAGT
1 --AAAATAGTAATCAGT--AAGAGC
* * *
105575 AAAATGGTAATCAGTAAAAAGT
1 AAAATAGTAATCAGT-AAGAGC
* ** *
105597 AAGAA-GGTAATCAACAAGAGT
1 AA-AATAGTAATCAGTAAGAGC
105618 AAAATAGTAATCAGTA
1 AAAATAGTAATCAGTA
105634 CAAAGTAAAG
Statistics
Matches: 282, Mismatches: 44, Indels: 82
0.69 0.11 0.20
Matches are distributed among these distances:
13 1 0.00
14 21 0.07
15 11 0.04
17 2 0.01
18 6 0.02
20 13 0.05
21 95 0.34
22 86 0.30
23 19 0.07
24 2 0.01
25 3 0.01
26 8 0.03
27 1 0.00
28 14 0.05
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.20
Consensus pattern (21 bp):
AAAATAGTAATCAGTAAGAGC
Found at i:105279 original size:44 final size:43
Alignment explanation
Indices: 105230--105591 Score: 181
Period size: 35 Copynumber: 8.7 Consensus size: 43
105220 AAAGTAATGA
* *
105230 TAATCAGTAAAAAGGTAAAATAGTAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAAAA-GTAAAATGGTAATCAGTAAGAGCAAAATAG
* * * * *
105274 TAATCAAT-GAGAGCAAAATGGTAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAAAGTAAAATGGTAATCAGT-AAGAGCAAAATAG
*
105317 TAATCATTAAAAAGTAAGAA-GGTAATCAGTAA-AGCGTAAAATAG
1 TAATCAGTAAAAAGTAA-AATGGTAATCAGTAAGAGC--AAAATAG
* * *
105361 TAATC-------AGCAAAA-GGCAATCAGTAAGAGTAAAATAG
1 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATAG
*
105396 TAATCAGT----AG---AA-GGTAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAAAGTAAAATGGTAATCAGT-AAGAGCAAAATAG
* *
105432 TAATCAGT-AAAAG----A---TAATCAGTAAGAGTAAAACAG
1 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATAG
* * * * * *
105467 TAACCAGT-GAGAGCAAAGTGGTAATTAGTAAGAGTC-AAATAG
1 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAG-CAAAATAG
*
105509 TAATCAGTAAGAAGTAAAA-GAGTAATCAGTAAAAAAGGAGCAGAAAATAG
1 TAATCAGTAAAAAGTAAAATG-GTAATCAGT----AA-GAGC--AAAATAG
105559 TAATCAGTAAAAGAGTAAAATGGTAATCAGTAA
1 TAATCAGTAAAA-AGTAAAATGGTAATCAGTAA
105592 AAAGTAAGAA
Statistics
Matches: 253, Mismatches: 32, Indels: 63
0.73 0.09 0.18
Matches are distributed among these distances:
35 45 0.18
36 42 0.17
37 6 0.02
38 3 0.01
39 2 0.01
42 42 0.17
43 35 0.14
44 34 0.13
45 2 0.01
47 5 0.02
48 3 0.01
50 17 0.07
51 16 0.06
52 1 0.00
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.20
Consensus pattern (43 bp):
TAATCAGTAAAAAGTAAAATGGTAATCAGTAAGAGCAAAATAG
Found at i:105381 original size:36 final size:35
Alignment explanation
Indices: 105329--105598 Score: 213
Period size: 36 Copynumber: 7.3 Consensus size: 35
105319 ATCATTAAAA
*
105329 AGTAAGAAGGTAATCAGTAAAGCGTAAAATAGTAATC
1 AGTAA-AAGGTAATCAGT-AAGAGTAAAATAGTAATC
* *
105366 AGCAAAAGGCAATCAGTAAGAGTAAAATAGTAATC
1 AGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATC
*
105401 AGTAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
1 AGTAAAAGGTAATCAGT-AAGAGTAAAATAGTAATC
* * *
105437 AGTAAAAGATAATCAGTAAGAGTAAAACAGTAACC
1 AGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATC
* *
105472 AGTGAGAGCAAAGTGGTAATTAGTAAGAGTCAAATAGTAATC
1 AGT---A--AAA--GGTAATCAGTAAGAGTAAAATAGTAATC
** * * * *
105514 AGTAAGAA-GTAAAAGAGTAATCAGTAAAAAAG-GAGC
1 AGTAA-AAGGT-AATCAGTAA-GAGTAAAATAGTAATC
* *
105550 AG-AAAATAGTAATCAGTAAAAGAGTAAAATGGTAATC
1 AGTAAAA-GGTAATCAGT--AAGAGTAAAATAGTAATC
*
105587 AGTAAAAAGTAA
1 AGTAAAAGGTAA
105599 GAAGGTAATC
Statistics
Matches: 187, Mismatches: 29, Indels: 34
0.75 0.12 0.14
Matches are distributed among these distances:
34 2 0.01
35 59 0.32
36 65 0.35
37 24 0.13
38 7 0.04
39 1 0.01
40 3 0.02
42 26 0.14
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.20
Consensus pattern (35 bp):
AGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATC
Found at i:105411 original size:71 final size:71
Alignment explanation
Indices: 105333--105474 Score: 230
Period size: 71 Copynumber: 2.0 Consensus size: 71
105323 TTAAAAAGTA
* * *
105333 AGAAGGTAATCAGTAAAGCGTAAAATAGTAATCAGCAAAAGGCAATCAGTAAGAGTAAAATAGTA
1 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGACAATCAGTAAGAGTAAAACAGTA
*
105398 ATCAGT
66 ACCAGT
* *
105404 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGATAATCAGTAAGAGTAAAACAGTA
1 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGACAATCAGTAAGAGTAAAACAGTA
105469 ACCAGT
66 ACCAGT
105475 GAGAGCAAAG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.20
Consensus pattern (71 bp):
AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGACAATCAGTAAGAGTAAAACAGTA
ACCAGT
Found at i:105426 original size:14 final size:15
Alignment explanation
Indices: 105394--105426 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
105384 AGAGTAAAAT
105394 AGTAATCAGTAGAAG
1 AGTAATCAGTAGAAG
105409 -GTAATCAGTA-AAG
1 AGTAATCAGTAGAAG
105422 AGTAA
1 AGTAA
105427 AATAGTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.48, C:0.06, G:0.24, T:0.21
Consensus pattern (15 bp):
AGTAATCAGTAGAAG
Found at i:105451 original size:14 final size:15
Alignment explanation
Indices: 105422--105455 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
105412 ATCAGTAAAG
*
105422 AGTAAAATAGTAATC
1 AGTAAAAGAGTAATC
105437 AGTAAAAGA-TAATC
1 AGTAAAAGAGTAATC
105451 AGTAA
1 AGTAA
105456 GAGTAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:105539 original size:15 final size:15
Alignment explanation
Indices: 105521--105576 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
105511 ATCAGTAAGA
105521 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
105536 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
105550 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
105564 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
105577 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:105649 original size:21 final size:22
Alignment explanation
Indices: 105557--105675 Score: 83
Period size: 21 Copynumber: 5.5 Consensus size: 22
105547 AGCAGAAAAT
*
105557 AGTAATCAGTAAAAGAGTAAA-A
1 AGTAATCAGTACAA-AGTAAAGA
* *
105579 TGGTAATCAGTAAAAAGT-AAGA
1 -AGTAATCAGTACAAAGTAAAGA
105601 AGGTAATCA--ACAAGAGTAAA-A
1 A-GTAATCAGTACAA-AGTAAAGA
105622 TAGTAATCAGTACAAAGTAAAGA
1 -AGTAATCAGTACAAAGTAAAGA
*
105645 A-TAATCAGTA-AAA-TAATGA
1 AGTAATCAGTACAAAGTAAAGA
*
105664 TGGTAATCAGTA
1 -AGTAATCAGTA
105676 ATTCAGTAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
19 5 0.06
20 6 0.07
21 31 0.38
22 21 0.26
23 18 0.22
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (22 bp):
AGTAATCAGTACAAAGTAAAGA
Found at i:110806 original size:8 final size:8
Alignment explanation
Indices: 110793--110818 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
110783 TTTGCTCTGC
110793 CTCTGCCT
1 CTCTGCCT
110801 CTCTGCCT
1 CTCTGCCT
110809 CTCTGCCT
1 CTCTGCCT
110817 CT
1 CT
110819 GCTCTACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.50, G:0.12, T:0.38
Consensus pattern (8 bp):
CTCTGCCT
Found at i:112608 original size:2 final size:2
Alignment explanation
Indices: 112601--112634 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
112591 ATAATTGCTA
*
112601 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112635 GTAGTAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116694 original size:2 final size:2
Alignment explanation
Indices: 116687--116720 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
116677 CTTGATAATA
116687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
116721 GGCNTAAAAN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:117445 original size:33 final size:33
Alignment explanation
Indices: 117403--117468 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
117393 TGGTGTATTG
117403 TATAATTTGCCTATATTATATAACTGAATCAAA
1 TATAATTTGCCTATATTATATAACTGAATCAAA
117436 TATAATTTGCCTATATTATATAACTGAATCAAA
1 TATAATTTGCCTATATTATATAACTGAATCAAA
117469 CGTGATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (33 bp):
TATAATTTGCCTATATTATATAACTGAATCAAA
Found at i:124175 original size:2 final size:2
Alignment explanation
Indices: 124160--124199 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
124150 TATTCAAATA
*
124160 AT AT AT GT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
124200 GGGGCTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:124462 original size:8 final size:8
Alignment explanation
Indices: 124439--124473 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
124429 AAAATAACAG
124439 AAATTATAA
1 AAATTA-AA
*
124448 GAATTAAA
1 AAATTAAA
124456 AAATTAAA
1 AAATTAAA
124464 AAATTAAA
1 AAATTAAA
124472 AA
1 AA
124474 GTAAAAGGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 19 0.79
9 5 0.21
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (8 bp):
AAATTAAA
Found at i:125071 original size:13 final size:13
Alignment explanation
Indices: 125053--125077 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
125043 AGATTTAGCC
125053 ATGTTAATATTGA
1 ATGTTAATATTGA
125066 ATGTTAATATTG
1 ATGTTAATATTG
125078 TTTGCTTGGC
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:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
ATGTTAATATTGA
Found at i:125909 original size:30 final size:30
Alignment explanation
Indices: 125871--125977 Score: 160
Period size: 30 Copynumber: 3.6 Consensus size: 30
125861 ATGAAGTAGT
*
125871 AGTGGAAGACAACAATGGAAACCAGCAGCA
1 AGTGGAAGATAACAATGGAAACCAGCAGCA
* * *
125901 AATGGAAGATAACAATGGAAACGAGCAACA
1 AGTGGAAGATAACAATGGAAACCAGCAGCA
**
125931 AGTGGAAGATAACAATGGGGACCAGCAGCA
1 AGTGGAAGATAACAATGGAAACCAGCAGCA
125961 AGTGGAAGATAACAATG
1 AGTGGAAGATAACAATG
125978 TTGGAGAGGG
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.47, C:0.15, G:0.28, T:0.10
Consensus pattern (30 bp):
AGTGGAAGATAACAATGGAAACCAGCAGCA
Found at i:125919 original size:13 final size:13
Alignment explanation
Indices: 125901--125948 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
125891 ACCAGCAGCA
125901 AATGGAAGATAAC
1 AATGGAAGATAAC
*
125914 AATGGAAACGAGCAAC
1 AATGG-AA-GA-TAAC
125930 AAGTGGAAGATAAC
1 AA-TGGAAGATAAC
125944 AATGG
1 AATGG
125949 GGACCAGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 8 0.28
14 7 0.24
15 4 0.14
16 7 0.24
17 3 0.10
ACGTcount: A:0.50, C:0.10, G:0.27, T:0.12
Consensus pattern (13 bp):
AATGGAAGATAAC
Found at i:126252 original size:15 final size:15
Alignment explanation
Indices: 126232--126273 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
126222 TGGGGTTGGG
126232 CCATCTACTGCAGGT
1 CCATCTACTGCAGGT
126247 CCATCTACTGCAGGT
1 CCATCTACTGCAGGT
* *
126262 CCTTCTAATGCA
1 CCATCTACTGCA
126274 TCTCAGCCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.21, C:0.33, G:0.17, T:0.29
Consensus pattern (15 bp):
CCATCTACTGCAGGT
Found at i:127309 original size:23 final size:24
Alignment explanation
Indices: 127279--127341 Score: 101
Period size: 24 Copynumber: 2.6 Consensus size: 24
127269 AACACAAGGT
127279 ACTTTCTGTTTTTTATAAATG-TA
1 ACTTTCTGTTTTTTATAAATGCTA
127302 ACTTTCTGTTTTTTTATAAATGTCTA
1 ACTTTCTG-TTTTTTATAAATG-CTA
127328 ACTTTCTGTTTTTT
1 ACTTTCTGTTTTTT
127342 TAAGGCTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
23 8 0.22
24 13 0.35
25 6 0.16
26 10 0.27
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.60
Consensus pattern (24 bp):
ACTTTCTGTTTTTTATAAATGCTA
Found at i:127319 original size:24 final size:25
Alignment explanation
Indices: 127279--127343 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 25
127269 AACACAAGGT
127279 ACTTTCTG-TTTTTTATAAATG-TA
1 ACTTTCTGTTTTTTTATAAATGCTA
127302 ACTTTCTGTTTTTTTATAAATGTCTA
1 ACTTTCTGTTTTTTTATAAATG-CTA
127328 ACTTTCTGTTTTTTTA
1 ACTTTCTGTTTTTTTA
127344 AGGCTCTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
23 8 0.21
24 13 0.33
26 18 0.46
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.60
Consensus pattern (25 bp):
ACTTTCTGTTTTTTTATAAATGCTA
Found at i:127339 original size:25 final size:25
Alignment explanation
Indices: 127279--127366 Score: 103
Period size: 25 Copynumber: 3.6 Consensus size: 25
127269 AACACAAGGT
127279 ACTTTCTGTTTTTTATAAATG--TA
1 ACTTTCTGTTTTTTATAAATGTCTA
127302 ACTTTCTGTTTTTTTATAAATGTCTA
1 ACTTTCTG-TTTTTTATAAATGTCTA
*
127328 ACTTTCTGTTTTTT-T-AAGGCTCTTA
1 ACTTTCTGTTTTTTATAAATG-TC-TA
*
127353 ACTTACTGTTTTTT
1 ACTTTCTGTTTTTT
127367 GGTAAAATGG
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
23 11 0.19
24 16 0.28
25 21 0.36
26 10 0.17
ACGTcount: A:0.20, C:0.12, G:0.09, T:0.58
Consensus pattern (25 bp):
ACTTTCTGTTTTTTATAAATGTCTA
Found at i:128529 original size:15 final size:14
Alignment explanation
Indices: 128505--128537 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
128495 AAGTACAAGA
128505 AACACCCACTGCCC
1 AACACCCACTGCCC
128519 AACACCCCACTGCCC
1 AACA-CCCACTGCCC
128534 AACA
1 AACA
128538 ATCATCAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.33, C:0.55, G:0.06, T:0.06
Consensus pattern (14 bp):
AACACCCACTGCCC
Done.