Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 45 of 438
Found at i:11291468 original size:41 final size:40
Alignment explanation
Indices: 11291401--11291481 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 40
11291391 CCATACTATT
11291401 AACTTAATATATATACTATACCATTGAATCGGCCTAAACCATA
1 AACTTAATATATATACTATACCATTGAA-C--CCTAAACCATA
* *
11291444 AACTTAA-A-ATATATTCTACCATTGAACCCTAAACCATA
1 AACTTAATATATATACTATACCATTGAACCCTAAACCATA
11291482 GGCTTTAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
38 11 0.31
40 1 0.03
41 16 0.44
42 1 0.03
43 7 0.19
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (40 bp):
AACTTAATATATATACTATACCATTGAACCCTAAACCATA
Found at i:11291688 original size:28 final size:28
Alignment explanation
Indices: 11291652--11291710 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
11291642 AGTTTATGTA
* *
11291652 TTAGTGTTTATGGTTT-ATGTTTTAAAAT
1 TTAGGGTTTAAGGTTTAATG-TTTAAAAT
*
11291680 TTAGGGTTTAAGGTTTAATGTTTAAGAT
1 TTAGGGTTTAAGGTTTAATGTTTAAAAT
11291708 TTA
1 TTA
11291711 AAGGTTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (28 bp):
TTAGGGTTTAAGGTTTAATGTTTAAAAT
Found at i:11291703 original size:21 final size:21
Alignment explanation
Indices: 11291656--11291718 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
11291646 TATGTATTAG
* * *
11291656 TGTTTATGGTTTATGTTTTAA
1 TGTTTAAGGTTTAAGGTTTAA
** *
11291677 AATTTAGGGTTTAAGGTTTAA
1 TGTTTAAGGTTTAAGGTTTAA
*
11291698 TGTTTAAGATTTAAAGGTTTA
1 TGTTTAAGGTTT-AAGGTTTA
11291719 CAGAAAGCCA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
21 24 0.75
22 8 0.25
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.51
Consensus pattern (21 bp):
TGTTTAAGGTTTAAGGTTTAA
Found at i:11292053 original size:41 final size:40
Alignment explanation
Indices: 11292008--11292479 Score: 459
Period size: 41 Copynumber: 11.6 Consensus size: 40
11291998 AACTTTTTGC
* *
11292008 GGCGTTTGGACAAAAAACGCCGCTATTAATCAGTTTTTAGT
1 GGCGTTTGGA-TAAAAACGCCGCTATTGATCAGTTTTTAGT
* *
11292049 GGCGTTTTGGATAAAAACGCCACAATTGATCAGATTTTT-GT
1 GGCG-TTTGGATAAAAACGCCGCTATTGATCAG-TTTTTAGT
** * * *
11292090 GGCGTTTTTATCCAAAACGCCACAATTGATCAGTTTTTAGT
1 GGCGTTTGGAT-AAAAACGCCGCTATTGATCAGTTTTTAGT
*
11292131 GGCGTTTGGGATAAAAACGCCGCAATTGATCAGTTTTTAGT
1 GGCGTTT-GGATAAAAACGCCGCTATTGATCAGTTTTTAGT
* * *
11292172 GGCGTTTGGGATTAAAACGCCACTATTGATCAGCTTTTAGT
1 GGCGTTT-GGATAAAAACGCCGCTATTGATCAGTTTTTAGT
* *
11292213 GGCGTTTAG-TGAAAAACGCCGCAATTGATCAGTTTTTAGT
1 GGCGTTTGGAT-AAAAACGCCGCTATTGATCAGTTTTTAGT
*
11292253 GGCGTTTGGGATAAAAACGCCGCAATTGATCAGTTTTTAGT
1 GGCGTTT-GGATAAAAACGCCGCTATTGATCAGTTTTTAGT
* * * *
11292294 GGCATTTGGGATTAAAACGCCACTATTGATCAGCTTTTAGT
1 GGCGTTT-GGATAAAAACGCCGCTATTGATCAGTTTTTAGT
* * * *
11292335 GGCATTTAG-TGAAAAACGCCGCTATTTACCAGTTTTTAGT
1 GGCGTTTGGAT-AAAAACGCCGCTATTGATCAGTTTTTAGT
** * * * *
11292375 GGCGTTTTGGCCAAAAATGTCGCTATTGACCAATTTTTAGT
1 GGCG-TTTGGATAAAAACGCCGCTATTGATCAGTTTTTAGT
* ** * * *
11292416 GGCGTTTTTGCCAAAAACGCCGCTATAGTTTAGTTTTTAGT
1 GGCG-TTTGGATAAAAACGCCGCTATTGATCAGTTTTTAGT
*
11292457 GGCGTTTTGG--ACAAACGCCGCTA
1 GGCG-TTTGGATAAAAACGCCGCTA
11292480 ATGTTTATTA
Statistics
Matches: 371, Mismatches: 49, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
39 14 0.04
40 71 0.19
41 272 0.73
42 14 0.04
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (40 bp):
GGCGTTTGGATAAAAACGCCGCTATTGATCAGTTTTTAGT
Found at i:11292271 original size:122 final size:122
Alignment explanation
Indices: 11292020--11292422 Score: 574
Period size: 122 Copynumber: 3.3 Consensus size: 122
11292010 CGTTTGGACA
* * * * * *
11292020 AAAAACGCCGCTATTAATCAGTTTTTAGTGGCGTTTTGGATAAAAACGCCACAATTGATCAGATT
1 AAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGATTAAAACGCCACTATTGATCAGCTT
* ** *
11292085 TTTGTGGCGTTTTTA-TCCAAAACGCCACAATTGATCAGTTTTTAGTGGCGTTTGGGAT
66 TTAGTGGCG--TTTAGTGAAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGAT
11292143 AAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGATTAAAACGCCACTATTGATCAGCTT
1 AAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGATTAAAACGCCACTATTGATCAGCTT
11292208 TTAGTGGCGTTTAGTGAAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGAT
66 TTAGTGGCGTTTAGTGAAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGAT
*
11292265 AAAAACGCCGCAATTGATCAGTTTTTAGTGGCATTTGGGATTAAAACGCCACTATTGATCAGCTT
1 AAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGATTAAAACGCCACTATTGATCAGCTT
* * * * * **
11292330 TTAGTGGCATTTAGTGAAAAACGCCGCTATTTACCAGTTTTTAGTGGCGTTTTGGCC
66 TTAGTGGCGTTTAGTGAAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGAT
* * * * *
11292387 AAAAATGTCGCTATTGACCAATTTTTAGTGGCGTTT
1 AAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTT
11292423 TTGCCAAAAA
Statistics
Matches: 255, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
121 4 0.02
122 184 0.72
123 67 0.26
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (122 bp):
AAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGATTAAAACGCCACTATTGATCAGCTT
TTAGTGGCGTTTAGTGAAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGAT
Found at i:11292433 original size:122 final size:122
Alignment explanation
Indices: 11292020--11292477 Score: 569
Period size: 122 Copynumber: 3.8 Consensus size: 122
11292010 CGTTTGGACA
* * * * *
11292020 AAAAACGCCGCTATTAATCAGTTTTTAGTGGCGTTTTGGATAAAAACGCCACAATTGATCAGATT
1 AAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGATAAAAACGCCACTATTGATCAGCTT
* ** *
11292085 TTTGTGGCGTTTTTA-TCCAAAACGCCACAATTGATCAGTTTTTAGTGGCGTTTGGGAT
66 TTAGTGGCG--TTTAGTGAAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGAT
*
11292143 AAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGATTAAAACGCCACTATTGATCAGCTT
1 AAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGATAAAAACGCCACTATTGATCAGCTT
11292208 TTAGTGGCGTTTAGTGAAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGAT
66 TTAGTGGCGTTTAGTGAAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGAT
* *
11292265 AAAAACGCCGCAATTGATCAGTTTTTAGTGGCATTTGGGATTAAAACGCCACTATTGATCAGCTT
1 AAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGATAAAAACGCCACTATTGATCAGCTT
* * * * * **
11292330 TTAGTGGCATTTAGTGAAAAACGCCGCTATTTACCAGTTTTTAGTGGCGTTTTGGCC
66 TTAGTGGCGTTTAGTGAAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGAT
* * * * * ** ** * * * * *
11292387 AAAAATGTCGCTATTGACCAATTTTTAGTGGCGTTTTTGCCAAAAACGCCGCTATAGTTTAGTTT
1 AAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGATAAAAACGCCACTATTGATCAGCTT
* *
11292452 TTAGTGGCGTTTTG-GACAAACGCCGC
66 TTAGTGGCGTTTAGTGAAAAACGCCGC
11292478 TAATGTTTAT
Statistics
Matches: 297, Mismatches: 37, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
121 15 0.05
122 215 0.72
123 67 0.23
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (122 bp):
AAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGATAAAAACGCCACTATTGATCAGCTT
TTAGTGGCGTTTAGTGAAAAACGCCGCAATTGATCAGTTTTTAGTGGCGTTTGGGAT
Found at i:11293822 original size:8 final size:8
Alignment explanation
Indices: 11293780--11293804 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11293770 ATATAGACTA
11293780 AATAAAAT
1 AATAAAAT
11293788 AATAAAAT
1 AATAAAAT
11293796 AATAAAAT
1 AATAAAAT
11293804 A
1 A
11293805 TCTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:11293828 original size:29 final size:31
Alignment explanation
Indices: 11293777--11293845 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
11293767 TATATATAGA
*
11293777 CTAAATAAAATAATAAAATAATAA-AA-TAT
1 CTAATTAAAATAATAAAATAATAATAATTAT
* *
11293806 CTTATTAAAAT-ATTAAATAAATAATAATTAT
1 CTAATTAAAATAATAAAAT-AATAATAATTAT
11293837 CTAATTAAA
1 CTAATTAAA
11293846 TAACTATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.18
29 14 0.42
30 2 0.06
31 11 0.33
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (31 bp):
CTAATTAAAATAATAAAATAATAATAATTAT
Found at i:11294125 original size:30 final size:30
Alignment explanation
Indices: 11294057--11294125 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
11294047 CCACCCTTAA
* * *
11294057 AATATTTGCACTATTAGTCCTTCAACTTTT
1 AATATTTACACTATTAATCCTTCAAATTTT
*
11294087 TATATTTACACT-TTAATCCTTCAAATTTT
1 AATATTTACACTATTAATCCTTCAAATTTT
11294116 AAGTATTTAC
1 AA-TATTTAC
11294126 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.48
Consensus pattern (30 bp):
AATATTTACACTATTAATCCTTCAAATTTT
Found at i:11296276 original size:18 final size:18
Alignment explanation
Indices: 11296253--11296288 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11296243 AATTTTTAAT
*
11296253 TTTAATTTGATAAAATTA
1 TTTAATTTGAAAAAATTA
*
11296271 TTTAATTTTAAAAAATTA
1 TTTAATTTGAAAAAATTA
11296289 AAATACAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTAATTTGAAAAAATTA
Found at i:11297363 original size:14 final size:14
Alignment explanation
Indices: 11297319--11297367 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
11297309 TTATAAAAGT
*
11297319 TTAATTTTTAA-AA
1 TTAATTTTTAACTA
11297332 TT-ATTTTTAATTCTA
1 TTAATTTTTAA--CTA
11297347 TTAATTTTTAACTA
1 TTAATTTTTAACTA
11297361 TTAATTT
1 TTAATTT
11297368 AATTATTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 8 0.26
13 2 0.06
14 10 0.32
15 3 0.10
16 8 0.26
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (14 bp):
TTAATTTTTAACTA
Found at i:11302964 original size:2 final size:2
Alignment explanation
Indices: 11302953--11302993 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
11302943 AGTTTGGGAT
*
11302953 TA TA -A TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11302994 GTTTAGATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:11304037 original size:29 final size:27
Alignment explanation
Indices: 11303998--11304100 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 27
11303988 TTCTTTACAG
11303998 TTTTCATAATTTTCTTATGACTTTATAAAA
1 TTTT-ATAATTTT-TTATGA-TTTATAAAA
* *
11304028 TTTTATAATTTTTCTAT-ATTTCTATATA
1 TTTTATAATTTTT-TATGATTTATA-AAA
11304056 TTTTATATATTTTTTATGATTTTTATAAAA
1 TTTTATA-ATTTTTTATGA--TTTATAAAA
*
11304086 TTTTACAACTTTTTT
1 TTTTATAA-TTTTTT
11304101 TTATAATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
27 5 0.08
28 14 0.23
29 19 0.31
30 18 0.30
31 5 0.08
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTATAATTTTTTATGATTTATAAAA
Found at i:11304064 original size:9 final size:9
Alignment explanation
Indices: 11304027--11304082 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
11304017 ACTTTATAAA
11304027 ATTTTATA-
1 ATTTTATAT
*
11304035 ATTTTTCTAT
1 A-TTTTATAT
11304045 ATTTCTATAT
1 ATTT-TATAT
11304055 ATTTTATAT
1 ATTTTATAT
*
11304064 ATTTTTTAT
1 ATTTTATAT
11304073 GATTTT-TAT
1 -ATTTTATAT
11304082 A
1 A
11304083 AAATTTTACA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
8 2 0.05
9 25 0.61
10 14 0.34
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (9 bp):
ATTTTATAT
Found at i:11304089 original size:19 final size:18
Alignment explanation
Indices: 11304019--11304090 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 18
11304009 TTCTTATGAC
11304019 TTTATAAAATTTTATAATT
1 TTTATAAAATTTTAT-ATT
* *
11304038 TTTCT-ATATTTCTATATAT
1 TTTATAAAATTT-TATAT-T
**
11304057 TTTATATATTTTTTATGATT
1 TTTATA-AAATTTTAT-ATT
11304077 TTTATAAAATTTTA
1 TTTATAAAATTTTA
11304091 CAACTTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
18 7 0.17
19 18 0.43
20 10 0.24
21 7 0.17
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (18 bp):
TTTATAAAATTTTATATT
Found at i:11304105 original size:23 final size:22
Alignment explanation
Indices: 11304075--11304122 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
11304065 TTTTTTATGA
11304075 TTTTTATAAAATTTTACAACTTT
1 TTTTTATAAAATTTTACAA-TTT
**
11304098 TTTTTATAATTTTTTACAATTT
1 TTTTTATAAAATTTTACAATTT
11304120 TTT
1 TTT
11304123 AAATTCTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTTATAAAATTTTACAATTT
Found at i:11304110 original size:10 final size:10
Alignment explanation
Indices: 11304097--11304188 Score: 86
Period size: 10 Copynumber: 9.7 Consensus size: 10
11304087 TTTACAACTT
11304097 TTTTTTATAA
1 TTTTTTATAA
*
11304107 TTTTTTACAA
1 TTTTTTATAA
11304117 TTTTTTA-AA
1 TTTTTTATAA
* *
11304126 TTCTTTCTAA
1 TTTTTTATAA
*
11304136 TTTTTAATAA
1 TTTTTTATAA
11304146 -TTTTTATAA
1 TTTTTTATAA
* *
11304155 ATTTTAATAA
1 TTTTTTATAA
11304165 -TTTTT-T-A
1 TTTTTTATAA
*
11304172 TTTTTTATAT
1 TTTTTTATAA
11304182 TTTTTTA
1 TTTTTTA
11304189 CCACATGACA
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
7 1 0.01
8 6 0.09
9 20 0.30
10 40 0.60
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:11304127 original size:19 final size:20
Alignment explanation
Indices: 11304056--11304189 Score: 86
Period size: 19 Copynumber: 6.8 Consensus size: 20
11304046 TTTCTATATA
**
11304056 TTTTATATATTTTTTATGA-T
1 TTTTATA-ATTTTTTACAATT
**
11304076 TTTTATAAAATTTTACAACTTTT
1 TTTTATAATTTTTTACAA---TT
11304099 TTTTATAATTTTTTACAATT
1 TTTTATAATTTTTTACAATT
*
11304119 TTTTA-AATTCTTT-CTAATT
1 TTTTATAATTTTTTAC-AATT
*
11304138 TTTAATAATTTTTATA-AA-T
1 TTTTATAATTTTT-TACAATT
*
11304157 TTTAATAATTTTTT---ATT
1 TTTTATAATTTTTTACAATT
*
11304174 TTTTATATTTTTTTAC
1 TTTTATAATTTTTTAC
11304190 CACATGACAT
Statistics
Matches: 92, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
16 1 0.01
17 13 0.14
18 2 0.02
19 36 0.39
20 22 0.24
21 1 0.01
23 17 0.18
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (20 bp):
TTTTATAATTTTTTACAATT
Found at i:11304138 original size:29 final size:29
Alignment explanation
Indices: 11304098--11304171 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
11304088 TTACAACTTT
*
11304098 TTTTTATAATTTTTTACAATTTTT-TAAA
1 TTTTAATAATTTTTTACAATTTTTATAAA
** * *
11304126 TTCTTTCTAATTTTTAATAATTTTTATAAA
1 TT-TTAATAATTTTTTACAATTTTTATAAA
11304156 TTTTAATAATTTTTTA
1 TTTTAATAATTTTTTA
11304172 TTTTTTATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.05
29 30 0.79
30 6 0.16
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTTAATAATTTTTTACAATTTTTATAAA
Found at i:11304186 original size:9 final size:9
Alignment explanation
Indices: 11304028--11304186 Score: 70
Period size: 10 Copynumber: 16.4 Consensus size: 9
11304018 CTTTATAAAA
11304028 TTTTATAATT
1 TTTTAT-ATT
11304038 TTTCTATATT
1 TTT-TATATT
*
11304048 TCTATATATT
1 T-TTTATATT
*
11304058 TTATATATT
1 TTTTATATT
11304067 TTTTATGATT
1 TTTTAT-ATT
*
11304077 TTTATAAAATT
1 TTT-T-ATATT
** *
11304088 TTACAACTTTT
1 TT-TTA-TATT
11304099 TTTTATAATT
1 TTTTAT-ATT
*
11304109 TTTTACAATT
1 TTTTA-TATT
*
11304119 TTTTAAATT
1 TTTTATATT
11304128 CTTTCTA-ATT
1 -TTT-TATATT
* *
11304138 TTTAATAAT
1 TTTTATATT
*
11304147 TTTTATAAAT
1 TTTTAT-ATT
* *
11304157 TTTAATAAT
1 TTTTATATT
11304166 TTTT-TATT
1 TTTTATATT
11304174 TTTTATATT
1 TTTTATATT
11304183 TTTT
1 TTTT
11304187 TACCACATGA
Statistics
Matches: 118, Mismatches: 17, Indels: 29
0.72 0.10 0.18
Matches are distributed among these distances:
8 8 0.07
9 42 0.36
10 51 0.43
11 16 0.14
12 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (9 bp):
TTTTATATT
Found at i:11304455 original size:87 final size:87
Alignment explanation
Indices: 11304287--11304543 Score: 229
Period size: 87 Copynumber: 2.9 Consensus size: 87
11304277 AACATTAAAT
* * * * *
11304287 AGTCTTTTTTGATGCATTTTGACAA-TTTAAGTACCCGATTAAGT-AAAAAAAAAGTAAGAGATT
1 AGTC-TTTTTGATGCATTTTGA-AAGTTTAAGTACACAATTGAGTGAAAAAAAAA-CAAGAGCTT
* * *
11304350 AATTGTATTTTTTGAAAAAGTTTGA-A
63 AATTG-CTTTTTTAAAAAAATTT-ATA
* *
11304376 AGTCTTTTT-ATGCATTTTGAAAGTTTAAGTACACAATTGAGTGCAAAAAAAA-AAGGGCTTAAT
1 AGTCTTTTTGATGCATTTTGAAAGTTTAAGTACACAATTGAGTGAAAAAAAAACAAGAGCTTAAT
*
11304439 TGCTTTTTTAAAAAAAATTTATG
66 TGCTTTTTT-AAAAAAATTTATA
* * * * * *
11304462 GGCCTTTTTGATCCATTTTAAAAGTTTAAGTATCA-AATTGAATGAAAAAGAAAACAATAGCTTA
1 AGTCTTTTTGATGCATTTTGAAAGTTTAAGTA-CACAATTGAGTGAAAAA-AAAACAAGAGCTTA
*
11304526 ATTGCTTCTTTTGAAAAA
64 ATTGCTT-TTTTAAAAAA
11304544 GTTCGAGGAC
Statistics
Matches: 140, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
85 7 0.05
86 28 0.20
87 59 0.42
88 19 0.14
89 23 0.16
90 4 0.03
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (87 bp):
AGTCTTTTTGATGCATTTTGAAAGTTTAAGTACACAATTGAGTGAAAAAAAAACAAGAGCTTAAT
TGCTTTTTTAAAAAAATTTATA
Found at i:11306319 original size:48 final size:48
Alignment explanation
Indices: 11306231--11306339 Score: 184
Period size: 48 Copynumber: 2.2 Consensus size: 48
11306221 TTCTTTCATC
11306231 TTTTCTATTGTAACACTGTTCATTACGATAACAACCTTAAATCCAATGAA
1 TTTT-TATT-TAACACTGTTCATTACGATAACAACCTTAAATCCAATGAA
11306281 TTTTTATTTAACACTGTTCATTACGATAAC-ACCTTTAAATCCAATGAA
1 TTTTTATTTAACACTGTTCATTACGATAACAACC-TTAAATCCAATGAA
11306329 TTTTTATTTAA
1 TTTTTATTTAA
11306340 GTTATAACTG
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
47 3 0.05
48 47 0.81
49 4 0.07
50 4 0.07
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.41
Consensus pattern (48 bp):
TTTTTATTTAACACTGTTCATTACGATAACAACCTTAAATCCAATGAA
Found at i:11307203 original size:18 final size:17
Alignment explanation
Indices: 11307180--11307214 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11307170 TTGCCGGTAG
11307180 ATACATGCATATGGATGC
1 ATACATGCATA-GGATGC
*
11307198 ATACATGCTTAGGATGC
1 ATACATGCATAGGATGC
11307215 CATTTCCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (17 bp):
ATACATGCATAGGATGC
Found at i:11312982 original size:30 final size:29
Alignment explanation
Indices: 11312926--11312982 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
11312916 ATATAATAAC
*
11312926 TCTTAATGTTTAACATTCTATCAATTTTA
1 TCTTAATGTTTAACATTCAATCAATTTTA
*
11312955 TCTTAAT-TTTGACACATTCAATTAATTT
1 TCTTAATGTTT-A-ACATTCAATCAATTT
11312983 GGTCTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 8 0.33
30 13 0.54
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.51
Consensus pattern (29 bp):
TCTTAATGTTTAACATTCAATCAATTTTA
Found at i:11318924 original size:24 final size:25
Alignment explanation
Indices: 11318897--11318953 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
11318887 GAAGAGCTAT
11318897 TAACGGGAAG-TCGCA-AGAACCATA
1 TAACGGGAAGCTCG-AGAGAACCATA
* *
11318921 TAACAGGAAGCTCGAGAGGACCATA
1 TAACGGGAAGCTCGAGAGAACCATA
*
11318946 TATCGGGA
1 TAACGGGA
11318954 TTCTCATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (25 bp):
TAACGGGAAGCTCGAGAGAACCATA
Found at i:11324710 original size:25 final size:24
Alignment explanation
Indices: 11324651--11324748 Score: 79
Period size: 25 Copynumber: 4.0 Consensus size: 24
11324641 GTACATGTAT
* *
11324651 GCTCATACGAGCTGTAAATGGTAA
1 GCTCATACGAGCTGAAAACGGTAA
* * *
11324675 GCACCTTCGAGCTGAATAACGGTAA
1 GCTCATACGAGCTGAA-AACGGTAA
* * *
11324700 GCTCATACGAGCTGAGTATCGATAA
1 GCTCATACGAGCTGA-AAACGGTAA
* * *
11324725 GCTCATAAGAGTTGAAATCGGTAA
1 GCTCATACGAGCTGAAAACGGTAA
11324749 CCCTAATGAC
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
24 19 0.33
25 38 0.67
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (24 bp):
GCTCATACGAGCTGAAAACGGTAA
Found at i:11326024 original size:51 final size:51
Alignment explanation
Indices: 11325951--11326064 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
11325941 CTGATCACAT
*
11325951 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGACCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
11326002 TTATCACTTGTCACTGACCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGACCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* *
11326053 TTGTCGCTTGTC
1 TTATCACTTGTC
11326065 GCTTGTCACT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
TTATCACTTGTCACTGACCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:11333839 original size:51 final size:51
Alignment explanation
Indices: 11333768--11333881 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
11333758 CTGATCACAT
11333768 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
11333819 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* *
11333870 TTGTCGCTTGTC
1 TTATCACTTGTC
11333882 GCTTGTCACT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:11344316 original size:27 final size:26
Alignment explanation
Indices: 11344268--11344399 Score: 149
Period size: 27 Copynumber: 4.9 Consensus size: 26
11344258 GTGAGGCTGC
* *
11344268 CAGATATTGTGAC-GAAGTCACCAGAT
1 CAGATATTGTGGCAG-AGCCACCAGAT
11344294 ACAGATATTGTGGCAGAGCCACCAGAT
1 -CAGATATTGTGGCAGAGCCACCAGAT
* * *
11344321 CAGATAATCGTGGCATAGCCACCAGAA
1 CAGAT-ATTGTGGCAGAGCCACCAGAT
*
11344348 CAGATATATGTGGCAGAGCCACTAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
*
11344375 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
11344400 GACGTTCCTC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.08
27 80 0.89
28 3 0.03
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAT
Found at i:11344362 original size:54 final size:54
Alignment explanation
Indices: 11344286--11344399 Score: 194
Period size: 54 Copynumber: 2.1 Consensus size: 54
11344276 GTGACGAAGT
11344286 CACCAGATACAGATATTGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGC
1 CACCAGATACAGATATTGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGC
* *
11344340 CACCAGA-ACAGATATATGTGGCAGAGCCACTAGATCAGATAATTGTGGCATAGC
1 CACCAGATACAGATAT-TGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGC
11344394 CACCAG
1 CACCAG
11344400 GACGTTCCTC
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
53 8 0.14
54 49 0.86
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATACAGATATTGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGC
Found at i:11346050 original size:26 final size:26
Alignment explanation
Indices: 11346019--11346126 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
11346009 TGAAATGCCC
*
11346019 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
11346045 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
11346071 ATTATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
11346097 ATCATGGAACATTTACATAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
11346123 ATCA
1 ATCA
11346127 ATTTGTACCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:11362474 original size:28 final size:29
Alignment explanation
Indices: 11362438--11362494 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
11362428 CAAATGACTA
11362438 TTTTCGTAATTAATCTA-T-TTTTTATATT
1 TTTTCGTAATTAAT-TATTATTTTTATATT
*
11362466 TTTTTGTAATTAATTATTATTTTTATATT
1 TTTTCGTAATTAATTATTATTTTTATATT
11362495 ATTTGGATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 2 0.08
28 14 0.54
29 10 0.38
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (29 bp):
TTTTCGTAATTAATTATTATTTTTATATT
Found at i:11363275 original size:2 final size:2
Alignment explanation
Indices: 11363264--11363296 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
11363254 ATTCAACAAT
11363264 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11363297 ACTATGACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:11366146 original size:26 final size:26
Alignment explanation
Indices: 11366117--11366172 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
11366107 AAAATGACTT
**
11366117 CCAAAACAATGCTTATTCCTTAGGTG
1 CCAAAACAATGCCCATTCCTTAGGTG
* * *
11366143 CCAAAATAATGCCCATTCTTTAGGTT
1 CCAAAACAATGCCCATTCCTTAGGTG
11366169 CCAA
1 CCAA
11366173 GCCAAACCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.30
Consensus pattern (26 bp):
CCAAAACAATGCCCATTCCTTAGGTG
Found at i:11367130 original size:45 final size:45
Alignment explanation
Indices: 11367058--11367183 Score: 171
Period size: 45 Copynumber: 2.8 Consensus size: 45
11367048 TTTTCCATGT
* * * * * *
11367058 TGCCAAAGTATCTTTCAACCATAGTCTTACACATTTGAATCGTGA
1 TGCCATAGCATCTTTCAGCTATGGTCTTACTCATTTGAATCGTGA
* * *
11367103 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTTGTATCGTGA
1 TGCCATAGCATCTTTCAGCTATGGTCTTACTCATTTGAATCGTGA
11367148 TGCCATAGCATCTTTCAGCTATGGTCTTACTCATTT
1 TGCCATAGCATCTTTCAGCTATGGTCTTACTCATTT
11367184 TTCAACCAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (45 bp):
TGCCATAGCATCTTTCAGCTATGGTCTTACTCATTTGAATCGTGA
Found at i:11372189 original size:47 final size:47
Alignment explanation
Indices: 11372075--11372340 Score: 242
Period size: 47 Copynumber: 5.7 Consensus size: 47
11372065 GATTCGTGCA
* **
11372075 CCAGTGTAAGACATGTCTGGGACATGCTTCGGCTACA-TTATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCTACAGAGATGAGAG
** *
11372121 CCAGTGTAAGACCATACCTGGGACATGGCATCGGC-ACAGAGATGAGTG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACAGAGATGAGAG
* *
11372169 CTAGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGAT---AG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGG-CT--ACAGAGATGAGAG
* ** * *
11372216 CCAGTGTAAGACGTGTCTGGGACACACATCGGCTA-AGAG-T-TGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCTACAGAGATGAGAG
* * * * *
11372260 CAAGTGTAAGACATGTCTGGGACATGCATCAGCATGCATATATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGC-TACAGAGATGAGAG
11372308 CCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCG
11372341 ATAATTTATC
Statistics
Matches: 176, Mismatches: 29, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
42 1 0.01
43 4 0.02
44 30 0.17
45 1 0.01
46 22 0.12
47 57 0.32
48 34 0.19
49 14 0.08
50 13 0.07
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (47 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGGCTACAGAGATGAGAG
Found at i:11372280 original size:44 final size:46
Alignment explanation
Indices: 11372174--11372283 Score: 127
Period size: 44 Copynumber: 2.4 Consensus size: 46
11372164 GAGTGCTAGA
** *
11372174 GTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGATAGCCAGT
1 GTAAGACATGTCTGGGACACACATCGGCCTC-ACAGAGATAGCAAGT
* * *
11372221 GTAAGACGTGTCTGGGACACACATCGG-CT-A-AGAGTTGTGCAAGT
1 GTAAGACATGTCTGGGACACACATCGGCCTCACAGAGAT-AGCAAGT
11372265 GTAAGACATGTCTGGGACA
1 GTAAGACATGTCTGGGACA
11372284 TGCATCAGCA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
43 5 0.09
44 24 0.44
46 2 0.04
47 24 0.44
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.21
Consensus pattern (46 bp):
GTAAGACATGTCTGGGACACACATCGGCCTCACAGAGATAGCAAGT
Found at i:11372289 original size:91 final size:94
Alignment explanation
Indices: 11372077--11372333 Score: 267
Period size: 94 Copynumber: 2.7 Consensus size: 94
11372067 TTCGTGCACC
* *
11372077 AGTGTAAGACATGTCTGGGACATGCTTCGGCTACATTATGAGAGCCAGTGTAAGACCATACCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACATGATGAGAGCCAGTGTAAGACCATACCTGG
** *
11372142 GACATGGCATCGGCACAGAGATGAGTGCT
66 GACATCACATCGGCACAGAGATGAGTGCA
* * * **
11372171 AGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACA-GA-GATAGCCAGTGTAAGA-CGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CT--ACATGATGAGAGCCAGTGTAAGACCATACC
*
11372233 TGGGACA-CACATCGGCTA-AGAG-T-TGTGCA
63 TGGGACATCACATCGGC-ACAGAGATGAGTGCA
* * * **
11372262 AGTGTAAGACATGTCTGGGACATGCATCAGCATGCATATATGAGAGCCAGTGTAAGACCATGTCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGC-TACAT-GATGAGAGCCAGTGTAAGACCATACCT
11372327 GGGACAT
64 GGGACAT
11372334 GGCATCGATA
Statistics
Matches: 136, Mismatches: 17, Indels: 20
0.79 0.10 0.12
Matches are distributed among these distances:
89 2 0.01
90 1 0.01
91 34 0.25
92 16 0.12
93 23 0.17
94 39 0.29
95 17 0.12
96 1 0.01
97 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.22
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACATGATGAGAGCCAGTGTAAGACCATACCTGG
GACATCACATCGGCACAGAGATGAGTGCA
Found at i:11377991 original size:26 final size:26
Alignment explanation
Indices: 11377956--11378117 Score: 254
Period size: 26 Copynumber: 6.2 Consensus size: 26
11377946 TGATACAAAT
*
11377956 TGATAATAGGTTAGGTAAATGTTCCT
1 TGATAATAGGTTAGGTAAATGTTCCA
11377982 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
11378008 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
11378034 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
11378060 TGATAAT-GCGTTAGGTAAATGTTTCA
1 TGATAATAG-GTTAGGTAAATGTTCCA
* *
11378086 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
11378112 TGATAA
1 TGATAA
11378118 GAATTTCATG
Statistics
Matches: 128, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
25 1 0.01
26 126 0.98
27 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:11378046 original size:78 final size:78
Alignment explanation
Indices: 11377956--11378117 Score: 290
Period size: 78 Copynumber: 2.1 Consensus size: 78
11377946 TGATACAAAT
*
11377956 TGATAATAGGTTAGGTAAATGTTCCTTGATAATAG-GTTAGGTAAATGTTCCATGATAATGGGTT
1 TGATAATAGGTTAGGTAAATGTTCCATGATAAT-GCGTTAGGTAAATGTTCCATGATAATGGGTT
11378020 AGGTAAATGTTTCA
65 AGGTAAATGTTTCA
*
11378034 TGATAATAGGTTAGGTAAATGTTCCATGATAATGCGTTAGGTAAATGTTTCATGATAATGGGTTA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGCGTTAGGTAAATGTTCCATGATAATGGGTTA
11378099 GGTAAATGTTTCA
66 GGTAAATGTTTCA
11378112 TGATAA
1 TGATAA
11378118 GAATTTCATG
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
77 1 0.01
78 80 0.99
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (78 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATGCGTTAGGTAAATGTTCCATGATAATGGGTTA
GGTAAATGTTTCA
Found at i:11383701 original size:26 final size:25
Alignment explanation
Indices: 11383591--11383747 Score: 239
Period size: 26 Copynumber: 6.2 Consensus size: 25
11383581 TGATACAAAT
11383591 TGATAATAGGTTAGGTAAATGTT--
1 TGATAATAGGTTAGGTAAATGTTCA
11383614 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
11383640 TGATAAT-GGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
11383664 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
*
11383690 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
*
11383716 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
11383742 TGATAA
1 TGATAA
11383748 GAATTTCATG
Statistics
Matches: 127, Mismatches: 1, Indels: 9
0.93 0.01 0.07
Matches are distributed among these distances:
23 23 0.18
24 9 0.07
25 30 0.24
26 63 0.50
27 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Found at i:11383708 original size:76 final size:75
Alignment explanation
Indices: 11383591--11383747 Score: 255
Period size: 76 Copynumber: 2.1 Consensus size: 75
11383581 TGATACAAAT
11383591 TGATAATAGGTTAGGTAAATGTTTGATAATAGGTTAGGTAAATGTTCCATGATAAT-GGTTAGGT
1 TGATAATAGGTTAGGTAAATGTTTGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGT
11383655 AAATG-TTCA
66 AAATGTTTCA
* *
11383664 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCATGATAATGGGTTA
1 TGATAATAGGTTAGGTAAATGTT---TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTA
11383729 GGTAAATGTTTCA
63 GGTAAATGTTTCA
11383742 TGATAA
1 TGATAA
11383748 GAATTTCATG
Statistics
Matches: 77, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
73 23 0.30
76 31 0.40
77 13 0.17
78 10 0.13
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (75 bp):
TGATAATAGGTTAGGTAAATGTTTGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGT
AAATGTTTCA
Found at i:11385259 original size:26 final size:26
Alignment explanation
Indices: 11385230--11385282 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
11385220 TTTACAGTTT
11385230 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
11385256 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
11385282 T
1 T
11385283 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:11389976 original size:26 final size:26
Alignment explanation
Indices: 11389945--11390052 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
11389935 TGAAATTCCC
*
11389945 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
11389971 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
11389997 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
11390023 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
11390049 ATCA
1 ATCA
11390053 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:11396219 original size:2 final size:2
Alignment explanation
Indices: 11396207--11396241 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11396197 TGAGATTGAT
*
11396207 TA TA CA 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
11396242 GCATTTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11400149 original size:26 final size:26
Alignment explanation
Indices: 11400120--11400223 Score: 181
Period size: 26 Copynumber: 4.0 Consensus size: 26
11400110 ATTCCCATCT
*
11400120 TGGAACATTTACCTAAACCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
11400146 TGGAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
* *
11400172 TGGAATATTTACCTAATCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
11400198 TGGAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
11400224 ATTTGTATCA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.33
Consensus pattern (26 bp):
TGGAACATTTACCTAACCCATTATCA
Found at i:11401692 original size:47 final size:46
Alignment explanation
Indices: 11401578--11401842 Score: 191
Period size: 47 Copynumber: 5.7 Consensus size: 46
11401568 GATTTGTGCA
* * * * * *
11401578 CCAGTGTAAGACATATCTGGGACATGCTTCGGC-TACATTATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCATAGA-GATGAGTG
** *
11401624 CCAGTGTAAGACCATACCTGGGACATGGCATCAGCATAGGGATGAGTG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCATAGAGATGAGTG
* * * * *
11401672 CCAGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACA-GAGATAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCATAGAGATGAG-T-G
* * * *
11401719 CCAGTGTAAGACGTGTCTGGGACACGCATCGGC-TA-AGA-GTTGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCATAGAGATG-AGTG
* * * *
11401763 CAAGTGTAAGACATGTCTGGGACATGCATCAACAT-GCATATAAGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCATAG-AGAT--GAGTG
11401811 CCAGTGTAAGACCATGTCTGGGACATGGCATC
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATC
11401843 GACAATTTAT
Statistics
Matches: 175, Mismatches: 30, Indels: 24
0.76 0.13 0.10
Matches are distributed among these distances:
44 29 0.17
45 8 0.05
46 26 0.15
47 56 0.32
48 34 0.19
49 17 0.10
50 5 0.03
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (46 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCAGCATAGAGATGAGTG
Found at i:11401784 original size:44 final size:46
Alignment explanation
Indices: 11401677--11401843 Score: 151
Period size: 44 Copynumber: 3.6 Consensus size: 46
11401667 GAGTGCCAGA
*
11401677 GTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGATAGCCAGT
1 GTAAGACATGTCTGGGACATGCATCGGCCTC-ACAGAGATAGCAAGT
* * * *
11401724 GTAAGACGTGTCTGGGACACGCATCGG-CT-A-AGAGTTGTGCAAGT
1 GTAAGACATGTCTGGGACATGCATCGGCCTCACAGAGAT-AGCAAGT
** * * * * *
11401768 GTAAGACATGTCTGGGACATGCATCAACATGCATATAAGAGAGCCAGT
1 GTAAGACATGTCTGGGACATGCATCGGCCT-CACA-GAGATAGCAAGT
11401816 GTAAGACCATGTCTGGGACATGGCATCG
1 GTAAGA-CATGTCTGGGACAT-GCATCG
11401844 ACAATTTATC
Statistics
Matches: 96, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
43 5 0.05
44 29 0.30
45 1 0.01
46 2 0.02
47 26 0.27
48 12 0.12
49 16 0.17
50 5 0.05
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (46 bp):
GTAAGACATGTCTGGGACATGCATCGGCCTCACAGAGATAGCAAGT
Found at i:11405092 original size:12 final size:12
Alignment explanation
Indices: 11405059--11405094 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
11405049 TCTAGCCTGC
*
11405059 TATATATATATA
1 TATATATATTTA
11405071 TATATATATTTA
1 TATATATATTTA
*
11405083 TATTTATATTTA
1 TATATATATTTA
11405095 ATAATTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATATATATTTA
Found at i:11408495 original size:1 final size:1
Alignment explanation
Indices: 11408489--11408514 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
11408479 GCTAGTTCAT
11408489 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
11408515 CTCAATGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11409459 original size:21 final size:22
Alignment explanation
Indices: 11409434--11409474 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
11409424 TGTTTTTATT
11409434 TATTTAT-AATATAATCATTAA
1 TATTTATAAATATAATCATTAA
*
11409455 TATTTATAAATATGATCATT
1 TATTTATAAATATAATCATT
11409475 TATTGTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTTATAAATATAATCATTAA
Found at i:11413583 original size:18 final size:19
Alignment explanation
Indices: 11413560--11413601 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
11413550 TGTAGAAGAA
*
11413560 TGAAATT-AAGATCAATTT
1 TGAAATTGAAGATCAAATT
*
11413578 TGAAATTGAAGCTCAAATT
1 TGAAATTGAAGATCAAATT
11413597 TGAAA
1 TGAAA
11413602 GTTATGGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (19 bp):
TGAAATTGAAGATCAAATT
Found at i:11421864 original size:79 final size:78
Alignment explanation
Indices: 11421730--11421963 Score: 335
Period size: 79 Copynumber: 3.0 Consensus size: 78
11421720 CTCGAGTCAC
* * * *
11421730 ATATCATGTAACTGTAGTGAATCAGGATAACCTTTTTAGGTCAAATCCTACCCACCTTAAGTTAT
1 ATATCATGTAACTGTAGCGAATCAGGATTACCTTTTTAGGTCAAATCCTATCCACCTTAAGTTAC
11421795 CATAAGGAATCAT
66 CATAAGGAATCAT
* * * *
11421808 ATATCGTGTAACCGTAGCGAATTAGGATTACCCTTTTTAGGTCAAATCCTATCCACCTTAGGTTA
1 ATATCATGTAACTGTAGCGAATCAGGATTA-CCTTTTTAGGTCAAATCCTATCCACCTTAAGTTA
*
11421873 CCATAATGAATCAT
65 CCATAAGGAATCAT
* * *
11421887 ATATCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCTCCTTTAGTTAC
1 ATATCATGTAACTGTAGCGAATCAGGATTACCTTTTTAGGTCAAATCCTATCCACCTTAAGTTAC
11421952 CAT-AGTGAATCA
66 CATAAG-GAATCA
11421964 GGAATAAATC
Statistics
Matches: 137, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
77 1 0.01
78 65 0.47
79 71 0.52
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.33
Consensus pattern (78 bp):
ATATCATGTAACTGTAGCGAATCAGGATTACCTTTTTAGGTCAAATCCTATCCACCTTAAGTTAC
CATAAGGAATCAT
Found at i:11422060 original size:40 final size:40
Alignment explanation
Indices: 11421928--11422065 Score: 163
Period size: 40 Copynumber: 3.5 Consensus size: 40
11421918 CTTTTCAGGT
*
11421928 CAAATCCTATCCTCCTTT--AGTTACCATAGTGAATCAGGAA
1 CAAATCCTATCC-ACTTTAAAG-TACCATAGTGAATCAGGAA
* * *
11421968 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAAGTACCATAGTGAATCAGGAA
* * **
11422008 CAAATCCTATCCACTTTGAGGTATTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAAGTACCATAGTGAATCAGGAA
*
11422048 CGAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
11422066 TATTCTCGAG
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 78 0.94
41 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAAGTACCATAGTGAATCAGGAA
Found at i:11427154 original size:26 final size:24
Alignment explanation
Indices: 11427109--11427156 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
11427099 GTATCATTTT
*
11427109 TATTTGTTTTTATGTTTTTAAATA
1 TATTTGTTTTTATATTTTTAAATA
11427133 TATTTGATTTATTATATTTTTAAA
1 TATTTG-TTT-TTATATTTTTAAA
11427157 ATTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (24 bp):
TATTTGTTTTTATATTTTTAAATA
Found at i:11427341 original size:16 final size:16
Alignment explanation
Indices: 11427320--11427361 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
11427310 ATTTTATTTG
11427320 GGCCCGGCCCGAACCT
1 GGCCCGGCCCGAACCT
11427336 GGCCCGGCCCGAACCT
1 GGCCCGGCCCGAACCT
11427352 GGCCCGGCCC
1 GGCCCGGCCC
11427362 TTGATCACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.10, C:0.52, G:0.33, T:0.05
Consensus pattern (16 bp):
GGCCCGGCCCGAACCT
Found at i:11432890 original size:5 final size:5
Alignment explanation
Indices: 11432880--11432908 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
11432870 AAAACTGTAC
11432880 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
11432909 ATATTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:11434720 original size:15 final size:17
Alignment explanation
Indices: 11434702--11434742 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
11434692 TTAATTTTTA
11434702 TTTAAAAAATA-AAT-T
1 TTTAAAAAATATAATAT
11434717 TTTAAAAAATATAATAT
1 TTTAAAAAATATAATAT
*
11434734 ATTAAAAAA
1 TTTAAAAAA
11434743 ATATTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.48
16 3 0.13
17 9 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTTAAAAAATATAATAT
Found at i:11434730 original size:17 final size:18
Alignment explanation
Indices: 11434700--11434746 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 18
11434690 AATTAATTTT
*
11434700 TATTTAAAAAATA-AAT-
1 TATTAAAAAAATATAATA
*
11434716 T-TTTAAAAAATATAATA
1 TATTAAAAAAATATAATA
11434733 TATTAAAAAAATAT
1 TATTAAAAAAATAT
11434747 TAAAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 11 0.41
16 4 0.15
17 1 0.04
18 11 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TATTAAAAAAATATAATA
Found at i:11442541 original size:33 final size:34
Alignment explanation
Indices: 11442478--11442546 Score: 81
Period size: 32 Copynumber: 2.1 Consensus size: 34
11442468 AGATCCACCT
*
11442478 ACTCTAAATACATTCATTAAACTAGATACAT-CA
1 ACTCTAAATACATTCATTAAAATAGATACATGCA
*
11442511 ACTCT-AATTCATTCATTAAATATA-AGTACATGCA
1 ACTCTAAATACATTCATTAAA-ATAGA-TACATGCA
11442545 AC
1 AC
11442547 AAGTAATGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 15 0.48
33 12 0.39
34 4 0.13
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.32
Consensus pattern (34 bp):
ACTCTAAATACATTCATTAAAATAGATACATGCA
Found at i:11446900 original size:32 final size:33
Alignment explanation
Indices: 11446840--11446905 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
11446830 ATGCATGAGT
11446840 ACTAGATACATCTACTCTAAATACATTCATTAA
1 ACTAGATACATCTACTCTAAATACATTCATTAA
11446873 ACTAGATACATCTACTCT-AATACATTCATTAA
1 ACTAGATACATCTACTCTAAATACATTCATTAA
11446905 A
1 A
11446906 TATAAGTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 15 0.45
33 18 0.55
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.33
Consensus pattern (33 bp):
ACTAGATACATCTACTCTAAATACATTCATTAA
Found at i:11447473 original size:81 final size:81
Alignment explanation
Indices: 11447385--11447547 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 81
11447375 TAACAATAGC
* *
11447385 ATCCAATTCATCAAATTAATTAACAATATTCATAAATAATTCAAAATGAAGCAATACATACATTC
1 ATCCAATTCATCAAATTAATTAAAAATATTCATAAATAATTCAAAATGAAGCAAGACATACATTC
11447450 ACGGGTCTTAAATCAA
66 ACGGGTCTTAAATCAA
11447466 ATCCAATTCATCAAATTAATTAAAAATATTCATAAATAATTCAAAATGAAGCAAGACATACATTC
1 ATCCAATTCATCAAATTAATTAAAAATATTCATAAATAATTCAAAATGAAGCAAGACATACATTC
11447531 ACGGGTCTTAAATCAA
66 ACGGGTCTTAAATCAA
11447547 A
1 A
11447548 CTTACGAGAC
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.29
Consensus pattern (81 bp):
ATCCAATTCATCAAATTAATTAAAAATATTCATAAATAATTCAAAATGAAGCAAGACATACATTC
ACGGGTCTTAAATCAA
Found at i:11447511 original size:20 final size:22
Alignment explanation
Indices: 11447471--11447512 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
11447461 ATCAAATCCA
11447471 ATTCATCAAATTAATTAAAAAT
1 ATTCATCAAATTAATTAAAAAT
*
11447493 ATTCAT-AAA-TAATTCAAAAT
1 ATTCATCAAATTAATTAAAAAT
11447513 GAAGCAAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 3 0.16
22 6 0.32
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (22 bp):
ATTCATCAAATTAATTAAAAAT
Found at i:11451369 original size:61 final size:58
Alignment explanation
Indices: 11451266--11451381 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 58
11451256 ATCATTTTAA
* * *
11451266 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTTAATTTAATATTAAATC
1 TATTAAATTAATAGAATAATTATCAAGATAAATATTAAATTTAATTTAATATTAAATC
* *
11451324 TATTAAATTAATAGAATAATTATCTGCAAGATAATTATTAAATTTAATTTAATTTTAA
1 TATTAAATTAATAGAATAATTA--T-CAAGATAAATATTAAATTTAATTTAATATTAA
11451382 GATAGTTACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 20 0.40
60 1 0.02
61 29 0.58
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (58 bp):
TATTAAATTAATAGAATAATTATCAAGATAAATATTAAATTTAATTTAATATTAAATC
Found at i:11451462 original size:17 final size:17
Alignment explanation
Indices: 11451427--11451459 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11451417 TTAAGATATG
*
11451427 TATTAAATTTAATTTAA
1 TATTAAATTTAATTAAA
11451444 TATTAAATTT-ATTAAA
1 TATTAAATTTAATTAAA
11451460 ATAATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAAATTTAATTAAA
Found at i:11451465 original size:68 final size:71
Alignment explanation
Indices: 11451324--11451469 Score: 160
Period size: 68 Copynumber: 2.1 Consensus size: 71
11451314 ATATTAAATC
* * *
11451324 TATTAAATTAATAGAATAATTATCTGCAAGATAATTATTAAATTTAATTTAATTTTAAGATAGTT
1 TATTAAATTAATAAAATAACTATCT-CAAGATAATTATTAAATTTAATTTAATATTAAGATAGTT
***
11451389 ACTTTAA
65 AAAATAA
11451396 TATTAAATTAATAAAAT-ACTAT-T-AAGAT-ATGTATTAAATTTAATTTAATATTAA-ATTTA-
1 TATTAAATTAATAAAATAACTATCTCAAGATAAT-TATTAAATTTAATTTAATATTAAGA--TAG
11451455 TTAAAATAA
63 TTAAAATAA
11451464 TATTAA
1 TATTAA
11451470 TTTTAGAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
67 3 0.05
68 39 0.60
69 2 0.03
70 1 0.02
71 4 0.06
72 16 0.25
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (71 bp):
TATTAAATTAATAAAATAACTATCTCAAGATAATTATTAAATTTAATTTAATATTAAGATAGTTA
AAATAA
Found at i:11453506 original size:16 final size:17
Alignment explanation
Indices: 11453473--11453506 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11453463 TCGGGCTATA
*
11453473 ACCATGCATTTCCAAAC
1 ACCATGCATATCCAAAC
11453490 ACCATGCATAT-CAAAC
1 ACCATGCATATCCAAAC
11453506 A
1 A
11453507 TAGTATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.32, G:0.06, T:0.21
Consensus pattern (17 bp):
ACCATGCATATCCAAAC
Found at i:11454118 original size:77 final size:74
Alignment explanation
Indices: 11453966--11454109 Score: 182
Period size: 77 Copynumber: 1.9 Consensus size: 74
11453956 TTCTCTTATC
* *
11453966 AATAGAGAACGCAAATGGATAGTTAGAAAAAGGAATTATATTCTTTCCAAAAAAATATAGGATTT
1 AATAGAGAACGCAAATGAAAAGTTAGAAAAAGGAATTATATTCTTTCCAAAAAAATATA-GATTT
*
11454031 TCCCCTTTTT
65 TCACCTTTTT
* * * *
11454041 AATAGATAATGCAAATGAAAAGTTAGAAAAAAAGGAATTATATTCTTTTCAAAAGAATATTA-AT
1 AATAGAGAACGCAAATGAAAAGTTAG--AAAAAGGAATTATATTCTTTCCAAAAAAATA-TAGAT
11454105 TTTCA
63 TTTCA
11454110 TGTCTTTTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
75 22 0.37
76 6 0.10
77 29 0.49
78 2 0.03
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (74 bp):
AATAGAGAACGCAAATGAAAAGTTAGAAAAAGGAATTATATTCTTTCCAAAAAAATATAGATTTT
CACCTTTTT
Found at i:11454256 original size:112 final size:112
Alignment explanation
Indices: 11454097--11454330 Score: 342
Period size: 112 Copynumber: 2.1 Consensus size: 112
11454087 TTTCAAAAGA
* * ** * * * *
11454097 ATATTAATTTTCATGTCTTTTATATTTTGACTGAAATTAATGAATATAATTGTTTATATTAATAT
1 ATATTAATTTCCATATCTTTTATATTTTGACCAAAACTAATGAATATAACTATTTATATTAATAA
* * *
11454162 ATTCGGTAAAATATATACAATAAATATTTTGTATGAGTCTAATTCAT
66 ATTCAGTAAAATATATACAATAAATATTTTGTATGAATCAAATTCAT
* *
11454209 ATATTAATTTCCATATCTTTTATATTTTGACCAAAACTAATTAATATAACTATTTCTATTAATAA
1 ATATTAATTTCCATATCTTTTATATTTTGACCAAAACTAATGAATATAACTATTTATATTAATAA
*
11454274 ATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCAT
66 ATTCAGTAAAATATATACAATAAATATTTTGTATGAATCAAATTCAT
11454321 ATATTAATTT
1 ATATTAATTT
11454331 TTTCTATGTT
Statistics
Matches: 108, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
112 108 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (112 bp):
ATATTAATTTCCATATCTTTTATATTTTGACCAAAACTAATGAATATAACTATTTATATTAATAA
ATTCAGTAAAATATATACAATAAATATTTTGTATGAATCAAATTCAT
Found at i:11455540 original size:20 final size:19
Alignment explanation
Indices: 11455505--11455544 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
11455495 TATTAATACC
11455505 ATTATTATTAAATATTATT
1 ATTATTATTAAATATTATT
*
11455524 ATTATTATTTTAATATTATT
1 ATTATTA-TTAAATATTATT
11455544 A
1 A
11455545 GCTAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATTATTAAATATTATT
Found at i:11456219 original size:31 final size:31
Alignment explanation
Indices: 11456181--11456239 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
11456171 GATGACATAA
11456181 AATCTTTCTACGTATTTGAATTAAATGTAAT
1 AATCTTTCTACGTATTTGAATTAAATGTAAT
11456212 AATCTTTCTACGTATTTGAATTAAATGT
1 AATCTTTCTACGTATTTGAATTAAATGT
11456240 TCACTTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (31 bp):
AATCTTTCTACGTATTTGAATTAAATGTAAT
Found at i:11462044 original size:15 final size:15
Alignment explanation
Indices: 11462024--11462054 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11462014 CCTCAGAGGG
11462024 CAGTTCGGCAGCCAC
1 CAGTTCGGCAGCCAC
11462039 CAGTTCGGCAGCCAC
1 CAGTTCGGCAGCCAC
11462054 C
1 C
11462055 TAGGGTCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.42, G:0.26, T:0.13
Consensus pattern (15 bp):
CAGTTCGGCAGCCAC
Found at i:11465482 original size:20 final size:20
Alignment explanation
Indices: 11465457--11465501 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
11465447 AGGGACTAAA
*
11465457 ATGAAAAGTTGT-AAAATTT
1 ATGAAAAATTGTGAAAATTT
*
11465476 GATGAAAAATTTTGAAAATTT
1 -ATGAAAAATTGTGAAAATTT
11465497 ATGAA
1 ATGAA
11465502 TACATGTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTGTGAAAATTT
Found at i:11467561 original size:2 final size:2
Alignment explanation
Indices: 11467554--11467586 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
11467544 TCATGAATGA
*
11467554 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11467587 AAAATCACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:11472653 original size:55 final size:55
Alignment explanation
Indices: 11472528--11472640 Score: 149
Period size: 55 Copynumber: 2.1 Consensus size: 55
11472518 CGAGCCTGCC
* *
11472528 AAAACAACACAGGCGTGCGACACGCCCGTGTGGAAGAACCGTGGGTGAACCTGTT
1 AAAACAACACGGGCGTGCGACACGCCCGGGTGGAAGAACCGTGGGTGAACCTGTT
* * *
11472583 AAAACAACACGGGCGTTCGACACGCTCGGGTGGAA-CACC-TGTGGTCGAACCTGTT
1 AAAACAACACGGGCGTGCGACACGCCCGGGTGGAAGAACCGTG-GGT-GAACCTGTT
11472638 AAA
1 AAA
11472641 TTAACATGGG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
53 2 0.04
54 6 0.12
55 43 0.84
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.16
Consensus pattern (55 bp):
AAAACAACACGGGCGTGCGACACGCCCGGGTGGAAGAACCGTGGGTGAACCTGTT
Found at i:11475057 original size:25 final size:25
Alignment explanation
Indices: 11475029--11475109 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
11475019 CGACTGGCAA
11475029 ATGTGATAAATGTGAACATGCATAT
1 ATGTGATAAATGTGAACATGCATAT
* * *
11475054 ATGTGAT-AAGGCCG-A-ATGGC-CA-
1 ATGTGATAAATG-TGAACAT-GCATAT
11475076 ATGTGATAAATGTGAACATGCATAT
1 ATGTGATAAATGTGAACATGCATAT
11475101 ATGTGATAA
1 ATGTGATAA
11475110 GGCAGAATGG
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
22 8 0.19
23 9 0.21
24 9 0.21
25 17 0.40
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.28
Consensus pattern (25 bp):
ATGTGATAAATGTGAACATGCATAT
Found at i:11475097 original size:47 final size:47
Alignment explanation
Indices: 11475023--11475129 Score: 196
Period size: 47 Copynumber: 2.3 Consensus size: 47
11475013 ATTTAACGAC
* *
11475023 TGGCAAATGTGATAAATGTGAACATGCATATATGTGATAAGGCCGAA
1 TGGCCAATGTGATAAATGTGAACATGCATATATGTGATAAGGCAGAA
11475070 TGGCCAATGTGATAAATGTGAACATGCATATATGTGATAAGGCAGAA
1 TGGCCAATGTGATAAATGTGAACATGCATATATGTGATAAGGCAGAA
11475117 TGGCCAATGTGAT
1 TGGCCAATGTGAT
11475130 GAACGTGGAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.26
Consensus pattern (47 bp):
TGGCCAATGTGATAAATGTGAACATGCATATATGTGATAAGGCAGAA
Found at i:11475129 original size:22 final size:22
Alignment explanation
Indices: 11475054--11475129 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
11475044 ACATGCATAT
*
11475054 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCAGAATGGCCA
*
11475076 ATGTGATAAATGTG-A-ACAT-GCATA
1 ATGTGAT-AA-G-GCAGA-ATGGC-CA
11475100 TATGTGATAAGGCAGAATGGCCA
1 -ATGTGATAAGGCAGAATGGCCA
11475123 ATGTGAT
1 ATGTGAT
11475130 GAACGTGGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
22 15 0.36
23 10 0.24
24 9 0.21
25 8 0.19
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCAGAATGGCCA
Found at i:11475205 original size:46 final size:46
Alignment explanation
Indices: 11475146--11475236 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
11475136 GGAAGTGTAT
* * *
11475146 ATATGTGGGAAAGCCGAATGGTTAATGTGAAATGTGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGTGAAATATGTATGAGATGG
* *
11475192 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGTGAAATATGTATGAGATG
11475237 TGTATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.34, C:0.05, G:0.32, T:0.29
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGTGAAATATGTATGAGATGG
Found at i:11476771 original size:39 final size:40
Alignment explanation
Indices: 11476690--11476954 Score: 387
Period size: 40 Copynumber: 6.7 Consensus size: 40
11476680 TGTTATATTT
* *
11476690 GGGCTAAGTCCCAAAGAGCATTCGTGCTAGTGATGTATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCC
11476730 GGGCTAAGTCCCGAAGAGCATTCGTG-TAGTGATATATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCC
*
11476769 GGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATATATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCC
**
11476809 GGGCTAAGTCTTGAA-AGCATTCGTGCTAGTGATATATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCC
*
11476848 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCC
** *
11476888 GGGCTAAGTTCTGGAA-AGCATTAGTGCTAGTGATATATCC
1 GGGCTAAG-TCCCGAAGAGCATTCGTGCTAGTGATATATCC
*
11476928 GGGCTAA-ACCTCGAAG-GCATTCGTGCT
1 GGGCTAAGTCC-CGAAGAGCATTCGTGCT
11476955 GGAATCATGA
Statistics
Matches: 203, Mismatches: 17, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.00
39 87 0.43
40 110 0.54
41 5 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCC
Found at i:11476779 original size:79 final size:79
Alignment explanation
Indices: 11476690--11476954 Score: 410
Period size: 79 Copynumber: 3.4 Consensus size: 79
11476680 TGTTATATTT
* *
11476690 GGGCTAAGTCCCAAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGT
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCTCGAA-AGCATTCGT
11476755 G-TAGTGATATATCC
65 GCTAGTGATATATCC
* * *
11476769 GGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATATATCCGGGCTAAGTCTTGAAAGCATTCGTG
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCTCGAAAGCATTCGTG
11476834 CTAGTGATATATCC
66 CTAGTGATATATCC
* *
11476848 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCTGGAAAGCATTAGT
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAG-TCTCGAAAGCATTCGT
11476913 GCTAGTGATATATCC
65 GCTAGTGATATATCC
*
11476928 GGGCTAA-ACCTCGAAG-GCATTCGTGCT
1 GGGCTAAGTCC-CGAAGAGCATTCGTGCT
11476955 GGAATCATGA
Statistics
Matches: 173, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
78 10 0.06
79 122 0.71
80 41 0.24
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCTCGAAAGCATTCGTG
CTAGTGATATATCC
Found at i:11477029 original size:29 final size:28
Alignment explanation
Indices: 11476994--11477091 Score: 99
Period size: 29 Copynumber: 3.4 Consensus size: 28
11476984 CTTCAACCAA
* *
11476994 GCACTATGTGTGCCAGATCAGTAGTTGAG
1 GCACTATGTGTGCAAGATC-GTAATTGAG
* * *
11477023 GCACTATGTGTGCAAGTTCTTCAATCGA-
1 GCACTATGTGTGCAAGATCGT-AATTGAG
* *
11477051 GCACTATGTGTGCGAGATTGGTAATTGAG
1 GCACTATGTGTGCAAGA-TCGTAATTGAG
11477080 GCACTATGTGTG
1 GCACTATGTGTG
11477092 TGAGTTCTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
28 21 0.38
29 35 0.62
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (28 bp):
GCACTATGTGTGCAAGATCGTAATTGAG
Found at i:11477054 original size:57 final size:57
Alignment explanation
Indices: 11476962--11477129 Score: 228
Period size: 57 Copynumber: 2.9 Consensus size: 57
11476952 GCTGGAATCA
* * * * *
11476962 TGAGGCACTGTGTGTGCAAGTTCTTCAACCAAGCACTATGTGTGCCAGATCAGTAGT
1 TGAGGCACTATGTGTGCAAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
**
11477019 TGAGGCACTATGTGTGCAAGTTCTTCAATCGAGCACTATGTGTGCGAGATTGGTAAT
1 TGAGGCACTATGTGTGCAAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
** * * *
11477076 TGAGGCACTATGTGTGTGAGTTCTTTAATCGAGCGCTATGTGTGCGAAATCAGT
1 TGAGGCACTATGTGTGCAAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGT
11477130 CAGTGGGCAC
Statistics
Matches: 97, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 97 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (57 bp):
TGAGGCACTATGTGTGCAAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
Found at i:11477104 original size:29 final size:28
Alignment explanation
Indices: 11476966--11477122 Score: 118
Period size: 28 Copynumber: 5.5 Consensus size: 28
11476956 GAATCATGAG
* * * * *
11476966 GCACTGTGTGTGCAAGTTCTTCAACCAA
1 GCACTATGTGTGCGAGTTCTTTAATCGA
* * ** * *
11476994 GCACTATGTGTGCCAGATCAGTAGTTGA
1 GCACTATGTGTGCGAGTTCTTTAATCGA
* *
11477022 GGCACTATGTGTGCAAGTTCTTCAATCGA
1 -GCACTATGTGTGCGAGTTCTTTAATCGA
** *
11477051 GCACTATGTGTGCGAGATT-GGTAATTGA
1 GCACTATGTGTGCGAG-TTCTTTAATCGA
*
11477079 GGCACTATGTGTGTGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTCTTTAATCGA
*
11477108 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
11477123 AATCAGTCAG
Statistics
Matches: 97, Mismatches: 28, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
28 53 0.55
29 44 0.45
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (28 bp):
GCACTATGTGTGCGAGTTCTTTAATCGA
Found at i:11477859 original size:2 final size:2
Alignment explanation
Indices: 11477852--11477883 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11477842 CATGTATAAA
11477852 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
11477884 TTTCATAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11480826 original size:47 final size:47
Alignment explanation
Indices: 11480769--11481102 Score: 483
Period size: 47 Copynumber: 7.1 Consensus size: 47
11480759 GGATTTTATA
* ** * * * *
11480769 TGATGGATGTGAATGTGTATATATGAGCTAAGGCCGAATGGCAAATG
1 TGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATG
* *
11480816 TGATGAATGTGAACATGCATTTGTGTGATAAGGCCGAATGGCCAATG
1 TGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATG
* *
11480863 TGATGAATGTGAACATGTACATATGTGATAAGGCCGAATGGCCAATG
1 TGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATG
* *
11480910 TGATGAATGTGAACGTGCATATGTGTGATAAGGCCGAATGGCCAATG
1 TGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATG
* * *
11480957 TGATGAATATGAACATGCACATATGTGATATGGCCGAATGG-CAATG
1 TGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATG
*
11481003 TGATAAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATG
1 TGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATG
* *
11481050 TGATAAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAA-G
1 TGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATG
11481096 TGATGAA
1 TGATGAA
11481103 CGTGGAAGTG
Statistics
Matches: 258, Mismatches: 28, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
46 49 0.19
47 209 0.81
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
TGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATG
Found at i:11481166 original size:46 final size:46
Alignment explanation
Indices: 11481116--11481206 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
11481106 GGAAGTGTAT
** * *
11481116 ATATGTGGGAAAGCCGGATGGTTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
* * *
11481162 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATG
11481207 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.27
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
Found at i:11483859 original size:6 final size:6
Alignment explanation
Indices: 11483848--11483876 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
11483838 TTACAACTAC
11483848 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
11483877 CAGCAGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:11486261 original size:14 final size:15
Alignment explanation
Indices: 11486242--11486271 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
11486232 ATATTTAACT
11486242 TATTCTTAATT-TTG
1 TATTCTTAATTCTTG
11486256 TATTCTTAATTCTTG
1 TATTCTTAATTCTTG
11486271 T
1 T
11486272 TTTGATATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.20, C:0.10, G:0.07, T:0.63
Consensus pattern (15 bp):
TATTCTTAATTCTTG
Found at i:11487142 original size:16 final size:16
Alignment explanation
Indices: 11487121--11487154 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
11487111 AAAATGACTC
11487121 TAACCACAA-TCAAACA
1 TAACCA-AATTCAAACA
11487137 TAACCAAATTCAAACA
1 TAACCAAATTCAAACA
11487153 TA
1 TA
11487155 GAAATTAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (16 bp):
TAACCAAATTCAAACA
Found at i:11493199 original size:19 final size:20
Alignment explanation
Indices: 11493167--11493211 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
11493157 TGATTCAACG
11493167 GACA-GAAAACTCTTGACAT
1 GACATGAAAACTCTTGACAT
*
11493186 GACATGAAAA-TCTTGAGAT
1 GACATGAAAACTCTTGACAT
*
11493205 GAAATGA
1 GACATGA
11493212 TAATAACTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.22
Consensus pattern (20 bp):
GACATGAAAACTCTTGACAT
Found at i:11497521 original size:39 final size:39
Alignment explanation
Indices: 11497428--11497579 Score: 216
Period size: 39 Copynumber: 3.9 Consensus size: 39
11497418 AGTGTTACAA
* *
11497428 GGTATGGCTCGATTGAGCATACTTTCAATAGAATCCA-TAG
1 GGTATGGCTCAATTGAGCATACTTTCAGTAGAAT-CAGT-G
* *
11497468 GGTATGACTCAATTGAGCATACTTTCAGTCGAATCAGTG
1 GGTATGGCTCAATTGAGCATACTTTCAGTAGAATCAGTG
*
11497507 GGTATGGCTCAATTGAGCATACTTTCAGTAGAATTAGTG
1 GGTATGGCTCAATTGAGCATACTTTCAGTAGAATCAGTG
* *
11497546 GGTATGGCTCGATTGAGCATACTTTTAGTAGAAT
1 GGTATGGCTCAATTGAGCATACTTTCAGTAGAAT
11497580 AATATCCCAT
Statistics
Matches: 102, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
39 71 0.70
40 31 0.30
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (39 bp):
GGTATGGCTCAATTGAGCATACTTTCAGTAGAATCAGTG
Found at i:11499202 original size:24 final size:22
Alignment explanation
Indices: 11499160--11499210 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 22
11499150 AAAAACGGGC
*
11499160 TATTATAATAAATATATATCAAA
1 TATTATAATAAACATATAT-AAA
11499183 -ATTATAATATAACATAATATAAA
1 TATTATAATA-AACAT-ATATAAA
11499206 TATTA
1 TATTA
11499211 CACAGTTCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 9 0.38
23 7 0.29
24 8 0.33
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
TATTATAATAAACATATATAAA
Found at i:11516408 original size:20 final size:21
Alignment explanation
Indices: 11516364--11516420 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
11516354 GCAAACTCTT
*
11516364 GATTTCCAAAAGAAAAAAAAG
1 GATTTTCAAAAGAAAAAAAAG
*
11516385 GATTTTCAAAAGACAAAAAA-
1 GATTTTCAAAAGAAAAAAAAG
*
11516405 GATTTTCAATAGAAAA
1 GATTTTCAAAAGAAAA
11516421 CTGAGGCGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (21 bp):
GATTTTCAAAAGAAAAAAAAG
Found at i:11518005 original size:26 final size:26
Alignment explanation
Indices: 11517976--11518083 Score: 153
Period size: 26 Copynumber: 4.2 Consensus size: 26
11517966 TGGTACAAAT
11517976 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
11518002 TGATAATGGATTAGGTAAATATTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
11518028 TGATAATGGGTTAGATAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
11518054 TTATAATGGTTTAAGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
11518080 TGAT
1 TGAT
11518084 GGGCATTTCA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 70 1.00
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:11519779 original size:27 final size:27
Alignment explanation
Indices: 11519696--11519800 Score: 108
Period size: 27 Copynumber: 3.9 Consensus size: 27
11519686 AGGAAGCGTC
* * *
11519696 CTGGTGGCTATGCCACGATTATCT-AAT
1 CTGGTGGCTCTGCCAC-AATATCTGTAT
*
11519723 CTAGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
11519750 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
11519777 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
11519801 GCAGCCTCGC
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
26 10 0.15
27 57 0.85
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:11520796 original size:17 final size:16
Alignment explanation
Indices: 11520765--11520795 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
11520755 TGGGTTTACA
11520765 AAAAACAAAATTTTTC
1 AAAAACAAAATTTTTC
11520781 AAAAACAAAATTTTT
1 AAAAACAAAATTTTT
11520796 TTTTGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAACAAAATTTTTC
Found at i:11527669 original size:27 final size:26
Alignment explanation
Indices: 11527629--11527715 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 26
11527619 AGGAAGTGTC
*
11527629 CTGGTGGCTATGCCACGATTATCTAAT
1 CTGGTGGCTCTGCCAC-ATTATCTAAT
**
11527656 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTAAT
* *
11527683 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACATTATCT-AAT
11527710 CTGGTG
1 CTGGTG
11527716 ACTTCGTCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 7 0.13
27 45 0.87
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.34
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTAAT
Found at i:11527726 original size:27 final size:26
Alignment explanation
Indices: 11527655--11527733 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 26
11527645 GATTATCTAA
*
11527655 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGACTCTGCCACA-ATATCTGT
*
11527682 TCTGGTGGCTCTGCCACAATATCTGT
1 TCTGGTGACTCTGCCACAATATCTGT
*
11527708 ATCTGGTGACT-TCGTCACAATATCTG
1 -TCTGGTGACTCT-GCCACAATATCTG
11527734 GCAGCCTCGC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
26 9 0.19
27 39 0.81
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (26 bp):
TCTGGTGACTCTGCCACAATATCTGT
Found at i:11528794 original size:13 final size:13
Alignment explanation
Indices: 11528771--11528835 Score: 76
Period size: 13 Copynumber: 4.6 Consensus size: 13
11528761 GGCAACCCAA
11528771 TTTTTATTTTTATT
1 TTTTTA-TTTTATT
11528785 TTTTTATTTTATT
1 TTTTTATTTTATT
11528798 TTTTTATTTTATT
1 TTTTTATTTTATT
*
11528811 CTTTATTACTTTAATT
1 -TTT-TTA-TTTTATT
11528827 TATTTTATT
1 T-TTTTATT
11528836 ATTTATTACT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
13 20 0.43
14 11 0.24
15 7 0.15
16 8 0.17
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:11528815 original size:25 final size:26
Alignment explanation
Indices: 11528771--11528842 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 26
11528761 GGCAACCCAA
*
11528771 TTTTTATTTTTATTTTTTTATTTTA-TT
1 TTTTTA-TTTTA-TTATTTATTTTACTT
*
11528798 TTTTTATTTTATTCTTTA--TTACTT
1 TTTTTATTTTATTATTTATTTTACTT
*
11528822 TAATTTATTTTATTATTTATT
1 T-TTTTATTTTATTATTTATT
11528843 ACTTTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 3 0.08
24 3 0.08
25 21 0.55
26 5 0.13
27 6 0.16
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTATTTTATTATTTATTTTACTT
Found at i:11528816 original size:33 final size:33
Alignment explanation
Indices: 11528772--11528852 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
11528762 GCAACCCAAT
* *
11528772 TTTTATT-TTTATTTTTTTATTTTATTTTTTTA
1 TTTTATTCTTTATTTTTTTAATTTATTTTATTA
**
11528804 TTTTATTCTTTATTACTTTAATTTATTTTATTA
1 TTTTATTCTTTATTTTTTTAATTTATTTTATTA
11528837 -TTTATTACTTTATTTT
1 TTTTATT-CTTTATTTT
11528853 GTTTGGATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
32 13 0.32
33 28 0.68
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.77
Consensus pattern (33 bp):
TTTTATTCTTTATTTTTTTAATTTATTTTATTA
Found at i:11528843 original size:25 final size:25
Alignment explanation
Indices: 11528800--11528848 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
11528790 ATTTTATTTT
*
11528800 TTTATTTTATTCTTTATTACTTTAA
1 TTTATTTTATTATTTATTACTTTAA
11528825 TTTATTTTATTATTTATTACTTTA
1 TTTATTTTATTATTTATTACTTTA
11528849 TTTTGTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTATTTTATTATTTATTACTTTAA
Found at i:11528848 original size:8 final size:8
Alignment explanation
Indices: 11528805--11528850 Score: 51
Period size: 7 Copynumber: 5.8 Consensus size: 8
11528795 ATTTTTTTAT
11528805 TTTATT-C
1 TTTATTAC
11528812 TTTATTAC
1 TTTATTAC
*
11528820 TTTAATTTAT
1 TTT-A-TTAC
11528830 TTTATTA-
1 TTTATTAC
11528837 TTTATTAC
1 TTTATTAC
11528845 TTTATT
1 TTTATT
11528851 TTGTTTGGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
7 13 0.38
8 13 0.38
9 2 0.06
10 6 0.18
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTATTAC
Found at i:11528863 original size:25 final size:25
Alignment explanation
Indices: 11528800--11528857 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
11528790 ATTTTATTTT
* *
11528800 TTTATTTTATTCTTTATTACTTTAA
1 TTTATTTGATTATTTATTACTTTAA
* *
11528825 TTTATTTTATTATTTATTACTTTAT
1 TTTATTTGATTATTTATTACTTTAA
*
11528850 TTTGTTTG
1 TTTATTTG
11528858 GATATTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (25 bp):
TTTATTTGATTATTTATTACTTTAA
Found at i:11543403 original size:20 final size:20
Alignment explanation
Indices: 11543378--11543421 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
11543368 CGTGGGGCAC
11543378 GCCCGTGTACCCTAATTTTA
1 GCCCGTGTACCCTAATTTTA
* *
11543398 GCCCGTGTGCCCTAATTTTG
1 GCCCGTGTACCCTAATTTTA
11543418 GCCC
1 GCCC
11543422 ATGTGTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.34, G:0.20, T:0.32
Consensus pattern (20 bp):
GCCCGTGTACCCTAATTTTA
Found at i:11543426 original size:20 final size:20
Alignment explanation
Indices: 11543387--11543426 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11543377 CGCCCGTGTA
*
11543387 CCCTAATTTTAGCCCGTGTG
1 CCCTAATTTTAGCCCATGTG
*
11543407 CCCTAATTTTGGCCCATGTG
1 CCCTAATTTTAGCCCATGTG
11543427 TATCGTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.30, G:0.20, T:0.35
Consensus pattern (20 bp):
CCCTAATTTTAGCCCATGTG
Found at i:11557317 original size:46 final size:46
Alignment explanation
Indices: 11557249--11557340 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
11557239 ACATATTTAC
11557249 CTATTGAAGTTTCATTACTACTTCAATCGATATACTACTATAGAGG
1 CTATTGAAGTTTCATTACTACTTCAATCGATATACTACTATAGAGG
* *
11557295 CTATTGAAGTTTCATTATTACTTCAATCGATATGCTACTATAGAGG
1 CTATTGAAGTTTCATTACTACTTCAATCGATATACTACTATAGAGG
11557341 TTATCAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (46 bp):
CTATTGAAGTTTCATTACTACTTCAATCGATATACTACTATAGAGG
Found at i:11562290 original size:38 final size:38
Alignment explanation
Indices: 11562248--11562336 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 38
11562238 CTCCATTCAC
* *
11562248 CCCTACACACCACG-TGAGGATAATATCAACCCA-CCTAG
1 CCCTACACACCAAGATGAGGATAA-ATCAACCCATCC-AA
*
11562286 CCCTACACACCAAGTATGGGGATAAATCAACCCATCCAA
1 CCCTACACACCAAG-ATGAGGATAAATCAACCCATCCAA
*
11562325 CCATACACACCA
1 CCCTACACACCA
11562337 TAAGGTACCG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
38 13 0.30
39 21 0.48
40 10 0.23
ACGTcount: A:0.37, C:0.37, G:0.11, T:0.15
Consensus pattern (38 bp):
CCCTACACACCAAGATGAGGATAAATCAACCCATCCAA
Found at i:11562715 original size:18 final size:18
Alignment explanation
Indices: 11562692--11562731 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
11562682 CATATGGCCT
11562692 GCCCGTGTGAGCCCACAC-
1 GCCCGTGTG-GCCCACACA
*
11562710 GCCCGTGTGGCTCACACA
1 GCCCGTGTGGCCCACACA
11562728 GCCC
1 GCCC
11562732 AAATTGGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.15, C:0.45, G:0.28, T:0.12
Consensus pattern (18 bp):
GCCCGTGTGGCCCACACA
Found at i:11580016 original size:36 final size:36
Alignment explanation
Indices: 11579976--11580048 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
11579966 TCACTTTACC
11579976 TATGGTTCAGTTGACCTCTCAAATCGATGTTGAAAA
1 TATGGTTCAGTTGACCTCTCAAATCGATGTTGAAAA
11580012 TATGGTTCAGTTGACCTCTCAAATCGATGTTGAAAA
1 TATGGTTCAGTTGACCTCTCAAATCGATGTTGAAAA
11580048 T
1 T
11580049 CATCAATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (36 bp):
TATGGTTCAGTTGACCTCTCAAATCGATGTTGAAAA
Found at i:11581094 original size:4 final size:4
Alignment explanation
Indices: 11581087--11581113 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
11581077 AATAATAAAT
11581087 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
11581114 ATTCCTGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:11588605 original size:13 final size:14
Alignment explanation
Indices: 11588575--11588612 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
11588565 TTTACAAAAA
11588575 AATATTTTTTATAAT
1 AATATTTTTTAT-AT
11588590 AATATTTTTTAT-T
1 AATATTTTTTATAT
11588603 AATATTTTTT
1 AATATTTTTT
11588613 TCTAACTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.48
15 12 0.52
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
AATATTTTTTATAT
Found at i:11590536 original size:17 final size:17
Alignment explanation
Indices: 11590501--11590533 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11590491 GTACTTTTTT
*
11590501 TAAATTATTTTTTATAA
1 TAAATTATTTTTTAAAA
11590518 TAAATT-TTTTTTAAAA
1 TAAATTATTTTTTAAAA
11590534 ATATCTCGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TAAATTATTTTTTAAAA
Found at i:11596746 original size:66 final size:66
Alignment explanation
Indices: 11596640--11596768 Score: 258
Period size: 66 Copynumber: 2.0 Consensus size: 66
11596630 TAGTATATAT
11596640 TAATTTTTGTTAAGCTTAATATAAAAATGGGATGAGTTGAGAAGCTGATTTAAAGTTAATGTCTA
1 TAATTTTTGTTAAGCTTAATATAAAAATGGGATGAGTTGAGAAGCTGATTTAAAGTTAATGTCTA
11596705 C
66 C
11596706 TAATTTTTGTTAAGCTTAATATAAAAATGGGATGAGTTGAGAAGCTGATTTAAAGTTAATGTC
1 TAATTTTTGTTAAGCTTAATATAAAAATGGGATGAGTTGAGAAGCTGATTTAAAGTTAATGTC
11596769 ATCCCATACT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.38
Consensus pattern (66 bp):
TAATTTTTGTTAAGCTTAATATAAAAATGGGATGAGTTGAGAAGCTGATTTAAAGTTAATGTCTA
C
Found at i:11601283 original size:2 final size:2
Alignment explanation
Indices: 11601276--11601309 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
11601266 TTTTCTACCA
11601276 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
11601310 TCACATATTT
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:11601571 original size:27 final size:25
Alignment explanation
Indices: 11601542--11601655 Score: 88
Period size: 27 Copynumber: 4.2 Consensus size: 25
11601532 ATTGAATTAA
11601542 ATATTAATTTATATTATAAATTAAAT
1 ATATTAATTTA-ATTATAAATTAAAT
* *
11601568 AATATTAA-ATAATTAAAAATTTATAAT
1 -ATATTAATTTAATTATAAA-TTA-AAT
*
11601595 ATAATTATATATTAATTTTGAAA-TAAAT
1 AT-ATTA-AT-TTAATTAT-AAATTAAAT
*
11601623 ATATTAATTTATTTATTAAATATAAAT
1 ATATTAATTTAATTA-TAAAT-TAAAT
11601650 ATATTA
1 ATATTA
11601656 GCATTAATAA
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
25 15 0.21
26 10 0.14
27 29 0.41
28 6 0.09
29 2 0.03
30 5 0.07
31 3 0.04
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (25 bp):
ATATTAATTTAATTATAAATTAAAT
Found at i:11601579 original size:19 final size:18
Alignment explanation
Indices: 11601547--11601601 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 18
11601537 ATTAAATATT
11601547 AATTTATATTATAAATTAAA
1 AATTTATA--ATAAATTAAA
11601567 TAATATTA-AAT-AATTAAA
1 -AAT-TTATAATAAATTAAA
11601585 AATTTATAATATAATTA
1 AATTTATAATA-AATTA
11601602 TATATTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.10
17 6 0.20
18 7 0.23
19 7 0.23
21 4 0.13
22 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTATAATAAATTAAA
Found at i:11601700 original size:21 final size:21
Alignment explanation
Indices: 11601671--11601719 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
11601661 AATAAAAATA
*
11601671 AATAGATTAAATGTTGTTAAT
1 AATAAATTAAATGTTGTTAAT
* * **
11601692 AATAAATTAACTTTTGTTGTT
1 AATAAATTAAATGTTGTTAAT
11601713 AATAAAT
1 AATAAAT
11601720 ATAATTTGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (21 bp):
AATAAATTAAATGTTGTTAAT
Found at i:11603293 original size:29 final size:30
Alignment explanation
Indices: 11603246--11603313 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
11603236 TGGCCCAAGA
* *
11603246 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
11603276 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
11603306 GAAAATAT
1 GTAAATAT
11603314 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Done.