Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 141 of 173
Found at i:42796001 original size:24 final size:24
Alignment explanation
Indices: 42795973--42796020 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
42795963 AAACTTTACA
42795973 TCCGCTTCCACGTTCATCCACATC
1 TCCGCTTCCACGTTCATCCACATC
42795997 TCCGCTTCCACGTTCATCCACATC
1 TCCGCTTCCACGTTCATCCACATC
42796021 ATTCTTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.46, G:0.08, T:0.29
Consensus pattern (24 bp):
TCCGCTTCCACGTTCATCCACATC
Found at i:42802286 original size:5 final size:5
Alignment explanation
Indices: 42802276--42802301 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42802266 TTTTCTTTGA
42802276 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
42802302 AAGAGATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:42802978 original size:28 final size:29
Alignment explanation
Indices: 42802926--42802990 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
42802916 CGTTTGGTTT
*
42802926 ATTTT-TTTTTTTTAAAATTCATTTTCA-
1 ATTTTATTTTATTTAAAATTCATTTTCAC
* *
42802953 ATTTTATTTTATTTATAAATT-TTTTTGAC
1 ATTTTATTTTATTTA-AAATTCATTTTCAC
42802982 ATTTTATTT
1 ATTTTATTT
42802991 AAATAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 5 0.16
28 13 0.41
29 14 0.44
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68
Consensus pattern (29 bp):
ATTTTATTTTATTTAAAATTCATTTTCAC
Found at i:42824323 original size:42 final size:42
Alignment explanation
Indices: 42824272--42824371 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
42824262 GCTCTCGGTA
*
42824272 TCGCACACTTAGTGCCCGTTATACAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTATACAACATCATCATTTTAATT
* *
42824314 TCGCACACTTAGTGCCCATTATCCAACATCATTATTTTAATT
1 TCGCACACTTAGTGCCCATTATACAACATCATCATTTTAATT
42824356 TCGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
42824372 GTTCATATAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.35
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATACAACATCATCATTTTAATT
Found at i:42825275 original size:16 final size:17
Alignment explanation
Indices: 42825242--42825275 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42825232 TATAAAGTTA
*
42825242 ATATTTACCTTATTACT
1 ATATTAACCTTATTACT
42825259 ATATTAACCTT-TTACT
1 ATATTAACCTTATTACT
42825275 A
1 A
42825276 ATAATTTTGT
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:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTAACCTTATTACT
Found at i:42830255 original size:42 final size:42
Alignment explanation
Indices: 42830187--42830337 Score: 162
Period size: 42 Copynumber: 3.6 Consensus size: 42
42830177 AGGCTGCACA
* * * *
42830187 GAAGCACATAAGTGC-CAAACAAAAACCCATAAGGGTTGAA-T
1 GAAGCTCATAAGAGCTC-AACAGAAACCCATAAGGGTTAAACT
* *
42830228 GGAAGCTCATAAGAGCTTAACAGAAACCCATAAGAGTTAAACT
1 -GAAGCTCATAAGAGCTCAACAGAAACCCATAAGGGTTAAACT
* * * *
42830271 GAAGCTCAAAAAAGCTGAACGGAAACCCATAAGGGTTAAACT
1 GAAGCTCATAAGAGCTCAACAGAAACCCATAAGGGTTAAACT
* *
42830313 GAAGCTCATGAGAGCTCAACGGAAA
1 GAAGCTCATAAGAGCTCAACAGAAA
42830338 GTAAACTCGA
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
42 91 0.99
43 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.15
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTCAACAGAAACCCATAAGGGTTAAACT
Found at i:42830259 original size:21 final size:21
Alignment explanation
Indices: 42830235--42830303 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
42830225 AATGGAAGCT
42830235 CATAAGAGCTTAACAGAAACC
1 CATAAGAGCTTAACAGAAACC
* * *
42830256 CATAAGAG-TTAAACTGAAGCT
1 CATAAGAGCTT-AACAGAAACC
* * * *
42830277 CAAAAAAGCTGAACGGAAACC
1 CATAAGAGCTTAACAGAAACC
42830298 CATAAG
1 CATAAG
42830304 GGTTAAACTG
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
20 2 0.06
21 32 0.91
22 1 0.03
ACGTcount: A:0.48, C:0.20, G:0.17, T:0.14
Consensus pattern (21 bp):
CATAAGAGCTTAACAGAAACC
Found at i:42845808 original size:7 final size:7
Alignment explanation
Indices: 42845798--42845833 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
42845788 AAAGTAAATA
42845798 ATATGTG
1 ATATGTG
42845805 ATATGTG
1 ATATGTG
42845812 ATATGTG
1 ATATGTG
42845819 ATATGTG
1 ATATGTG
42845826 ATATGTG
1 ATATGTG
42845833 A
1 A
42845834 GCATGTGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.42
Consensus pattern (7 bp):
ATATGTG
Found at i:42846656 original size:20 final size:20
Alignment explanation
Indices: 42846633--42846671 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42846623 AATTAAATCA
42846633 GTTTTCTATAAATTCAATTC
1 GTTTTCTATAAATTCAATTC
*
42846653 GTTTTCTGTAAATTCAATT
1 GTTTTCTATAAATTCAATT
42846672 GATCGGACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (20 bp):
GTTTTCTATAAATTCAATTC
Found at i:42848542 original size:104 final size:103
Alignment explanation
Indices: 42848404--42848613 Score: 384
Period size: 104 Copynumber: 2.0 Consensus size: 103
42848394 AGGAAAAATT
42848404 AAAAATTACCTGGTGCCACCACATCTAGAGTATGGACCAGGAAAAAAGAATTTTACTCATTCTGG
1 AAAAATTACCTGGTGCCACCACATCTAGAGTATGGACCAGGAAAAAAGAATTTTACTCATTCTGG
*
42848469 TGACTCCACATTGAAGTGGCAGGACCGAAAAATTTAAAA
66 TGACTCCACATTGAAGTGGCAGGAACGAAAAA-TTAAAA
*
42848508 AAAAATTACCTGGTGCCACCACATCTGGAGTATGGACCAGGAAAAAAGAATTTTACTCATTCTGG
1 AAAAATTACCTGGTGCCACCACATCTAGAGTATGGACCAGGAAAAAAGAATTTTACTCATTCTGG
*
42848573 TGACTCCACATTGAAGTGGCGGGAACGAAAAATTAAAA
66 TGACTCCACATTGAAGTGGCAGGAACGAAAAATTAAAA
42848611 AAA
1 AAA
42848614 CTATTGGTGT
Statistics
Matches: 103, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
103 9 0.09
104 94 0.91
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (103 bp):
AAAAATTACCTGGTGCCACCACATCTAGAGTATGGACCAGGAAAAAAGAATTTTACTCATTCTGG
TGACTCCACATTGAAGTGGCAGGAACGAAAAATTAAAA
Found at i:42848573 original size:52 final size:51
Alignment explanation
Indices: 42848357--42848583 Score: 141
Period size: 52 Copynumber: 4.5 Consensus size: 51
42848347 TATATAAACA
* * * **
42848357 TACTGATTTTGGTGCCACCACATCTGGAGTATGGACTAGGAAAAATTAAAAAT
1 TACTCATTCTGGTGCCACCACATCTGGAGTATGGACCAGGAAAAA--AAATTT
*
42848410 TA--C---CTGGTGCCACCACATCTAGAGTATGGACCAGGAAAAAAGAATTT
1 TACTCATTCTGGTGCCACCACATCTGGAGTATGGACCAGGAAAAAA-AATTT
* * * **
42848457 TACTCATTCTGGTGACTCCACAT-TGAAG--TGG--CAGGACCGAAAAATTT
1 TACTCATTCTGGTGCCACCACATCTGGAGTATGGACCAGGA-AAAAAAATTT
* ***
42848504 AAAAAAAAATTACCTGGTGCCACCACATCTGGAGTATGGACCAGGAAAAAAGAATTT
1 ---TACTCATT--CTGGTGCCACCACATCTGGAGTATGGACCAGGAAAAAA-AATTT
* *
42848561 TACTCATTCTGGTGACTCCACAT
1 TACTCATTCTGGTGCCACCACAT
42848584 TGAAGTGGCG
Statistics
Matches: 129, Mismatches: 27, Indels: 37
0.67 0.14 0.19
Matches are distributed among these distances:
46 1 0.01
47 15 0.12
48 37 0.29
49 4 0.03
50 4 0.03
51 3 0.02
52 39 0.30
53 6 0.05
54 4 0.03
55 3 0.02
56 3 0.02
57 10 0.08
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (51 bp):
TACTCATTCTGGTGCCACCACATCTGGAGTATGGACCAGGAAAAAAAATTT
Found at i:42850362 original size:97 final size:98
Alignment explanation
Indices: 42850057--42850373 Score: 260
Period size: 97 Copynumber: 3.2 Consensus size: 98
42850047 AGCGACACCT
* * ***
42850057 AAAAATTAAAAAAAAATTTACCTGGTGCCACCACATCTGGAGTATGAACCAGGAAAAAAGAATTT
1 AAAAATTAAAAAAAAA--TA-CTGGTGCCACCACATCTGGAGTAAGGACCAGG--AAAATTTTTT
* * * * * *
42850122 TACTGATTCTGGTGTCTCCACATTGAAGTGGCGGGACGG
61 TATTCATTTTGGTGACTCCATA-TGAAGTGGCGGGACCG
* * * * ** * *
42850161 AAAAATT-AAAAAAAATATTGGTGCCGCCATATTTGGACAAAGGACCAGGGAAATTTTATTTTTT
1 AAAAATTAAAAAAAAATACTGGTGCCACCACATCTGGAGTAAGGACCA-GGAAAATTT-TTTTAT
* *** * * * *
42850225 TACTGTTTTGGTGACTTTGTGTGAAGTGGCAGCACTG
64 T-C-ATTTTGGTGACTCCATATGAAGTGGCGGGACCG
* * *
42850262 AAAAATTAAAAAAAAATACTAGTGTCACCACATCTGGAGTAGGGACCA-GAAAATTTTTTTATTC
1 AAAAATTAAAAAAAAATACTGGTGCCACCACATCTGGAGTAAGGACCAGGAAAATTTTTTTATTC
42850326 ATTTTGGTGACTCCATATGAAGTGGCGGGACCG
66 ATTTTGGTGACTCCATATGAAGTGGCGGGACCG
42850359 AAAAATTAAAAAAAA
1 AAAAATTAAAAAAAA
42850374 CTTATTAGTG
Statistics
Matches: 163, Mismatches: 45, Indels: 17
0.72 0.20 0.08
Matches are distributed among these distances:
97 40 0.25
98 1 0.01
99 9 0.06
100 34 0.21
101 24 0.15
102 40 0.25
103 8 0.05
104 7 0.04
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (98 bp):
AAAAATTAAAAAAAAATACTGGTGCCACCACATCTGGAGTAAGGACCAGGAAAATTTTTTTATTC
ATTTTGGTGACTCCATATGAAGTGGCGGGACCG
Found at i:42852418 original size:96 final size:97
Alignment explanation
Indices: 42852318--42852500 Score: 239
Period size: 96 Copynumber: 1.9 Consensus size: 97
42852308 AGGTTTAGGG
*
42852318 TTACTTGAGTAATTTAATTA-AAAGTTATTTA-AAAA-TCAAATAAGGGTTTAGAGTTAAGGGTT
1 TTACTTGAGTAAATTAATTATAAA-TT-TTTATAAAATTCAAATAAGGG-TTAGAGTTAAGGGTT
42852380 TTTAAGGAAAAA-TCAAATAAATTAGGGTGCAAGA
63 TTTAAGGAAAAACTCAAATAAATTAGGGTGCAAGA
** * * * *
42852414 TTACTTGAGTAAATTAATTATAAATTTTTATAAAATTTGATTAAGGGTTAGTGTTTAGTGTTTTT
1 TTACTTGAGTAAATTAATTATAAATTTTTATAAAATTCAAATAAGGGTTAGAGTTAAGGGTTTTT
*
42852479 AAGTAAAAACTCAAATAAATTA
66 AAGGAAAAACTCAAATAAATTA
42852501 AGGTTTGGGA
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
95 4 0.05
96 48 0.64
97 23 0.31
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (97 bp):
TTACTTGAGTAAATTAATTATAAATTTTTATAAAATTCAAATAAGGGTTAGAGTTAAGGGTTTTT
AAGGAAAAACTCAAATAAATTAGGGTGCAAGA
Found at i:42852770 original size:126 final size:126
Alignment explanation
Indices: 42852545--42853087 Score: 843
Period size: 126 Copynumber: 4.3 Consensus size: 126
42852535 TTTTTAATTT
* * * **
42852545 AAAGAAGCTTCCACGTGGACGCGCTTTTGTTGCAGTAACTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
* *
42852610 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAGAAGTAATG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
*
42852671 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTAGAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
* *
42852736 GTTTCTGAGCAAATAGTGTCAAAAACGTTTTAAGCAGGATACTTTGTCAGCAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
* * *
42852797 AAAGAAGCTCCCATGTGGACGCGCTTTTGCTACAGTAGCTCCTCAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
* * **
42852862 GTTTCTGAGCAAATAGTGTCAAAAAAGCTTTAAGCAGGATGTTTTGTCAATAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
** * * *
42852923 AAAGAAGCTCTTACGTAGACGCGCTTTTGCTATAGTGGCTCCTGAAAAAATAATTTCTAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
* ** *
42852988 ATTTCTGAGCAAATAGTGTCAAAAATACTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
*
42853049 AAAGAAACTCCCACGTGGACGCGCTTTTGCTACAGTGGC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGC
42853088 GCATGTTTGG
Statistics
Matches: 377, Mismatches: 40, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 377 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
Found at i:42858554 original size:12 final size:12
Alignment explanation
Indices: 42858537--42858567 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
42858527 AGAGGAATTT
42858537 GAGAGAATACTA
1 GAGAGAATACTA
42858549 GAGAGAATACTA
1 GAGAGAATACTA
42858561 GAGAGAA
1 GAGAGAA
42858568 ATTGAGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.06, G:0.29, T:0.13
Consensus pattern (12 bp):
GAGAGAATACTA
Found at i:42858579 original size:10 final size:11
Alignment explanation
Indices: 42858518--42858578 Score: 52
Period size: 12 Copynumber: 5.5 Consensus size: 11
42858508 TCTTTTAAAT
*
42858518 AGAAATTTGAG
1 AGAAACTTGAG
* *
42858529 AGGAATTTGAG
1 AGAAACTTGAG
*
42858540 AGAATACTAGAG
1 AGAA-ACTTGAG
*
42858552 AGAATACTAGAG
1 AGAA-ACTTGAG
42858564 AGAAA-TTGAG
1 AGAAACTTGAG
42858574 AGAAA
1 AGAAA
42858579 TGATTTAGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
10 9 0.20
11 14 0.32
12 21 0.48
ACGTcount: A:0.49, C:0.03, G:0.28, T:0.20
Consensus pattern (11 bp):
AGAAACTTGAG
Found at i:42860569 original size:18 final size:18
Alignment explanation
Indices: 42860531--42860566 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42860521 TTATTATTTT
*
42860531 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
42860549 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
42860567 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:42866941 original size:6 final size:6
Alignment explanation
Indices: 42866930--42866954 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42866920 TTACAATAAT
42866930 TAATTA TAATTA TAATTA TAATTA T
1 TAATTA TAATTA TAATTA TAATTA T
42866955 TGAGATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:42884833 original size:14 final size:14
Alignment explanation
Indices: 42884814--42884850 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
42884804 TTAGCAATGC
42884814 TAAAGAAAGAAATA
1 TAAAGAAAGAAATA
42884828 TAAAGAATA-AAATA
1 TAAAGAA-AGAAATA
42884842 -AAAGAAAGA
1 TAAAGAAAGA
42884851 GATGCTCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.05
13 7 0.33
14 12 0.57
15 1 0.05
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
TAAAGAAAGAAATA
Found at i:42885675 original size:16 final size:15
Alignment explanation
Indices: 42885656--42885707 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 15
42885646 AAAATTAGCT
42885656 AAAAATAAAAATGAAA
1 AAAAATAAAAAT-AAA
42885672 AAAAATAAAAATAAACA
1 AAAAATAAAAAT-AA-A
*
42885689 AAAAAGGAAAAATAAA
1 AAAAA-TAAAAATAAA
42885705 AAA
1 AAA
42885708 TTTGACTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 18 0.56
17 8 0.25
18 6 0.19
ACGTcount: A:0.83, C:0.02, G:0.06, T:0.10
Consensus pattern (15 bp):
AAAAATAAAAATAAA
Found at i:42885691 original size:26 final size:25
Alignment explanation
Indices: 42885619--42885706 Score: 63
Period size: 26 Copynumber: 3.4 Consensus size: 25
42885609 AAAAAAATAG
*
42885619 AAAAATAAACATGAAGACAAAAAGAAA
1 AAAAATAAAAAT-AA-ACAAAAAGAAA
* ** *
42885646 AAAATTAGCTAA-AAATAAAAATGAAA
1 AAAAATA-AAAATAAACAAAAA-GAAA
**
42885672 AAAAATAAAAATAAACAAAAA-AGG
1 AAAAATAAAAATAAACAAAAAGAAA
42885696 AAAAATAAAAA
1 AAAAATAAAAA
42885707 ATTTGACTTG
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
24 12 0.26
25 8 0.17
26 20 0.43
27 6 0.13
28 1 0.02
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (25 bp):
AAAAATAAAAATAAACAAAAAGAAA
Found at i:42887596 original size:13 final size:14
Alignment explanation
Indices: 42887571--42887603 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
42887561 TGCTTTGGAA
42887571 AAATAACTAAACTC
1 AAATAACTAAACTC
42887585 AAATAA-TAAACTC
1 AAATAACTAAACTC
42887598 AAATAA
1 AAATAA
42887604 AATTCATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAACTAAACTC
Found at i:42891485 original size:24 final size:23
Alignment explanation
Indices: 42891458--42891510 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
42891448 TGCACATTAT
* * *
42891458 ATATATCCTAATTAAATTTATTTA
1 ATATATACTAAATAAATTTA-TCA
*
42891482 ATATATATTAAATAAATTTATCA
1 ATATATACTAAATAAATTTATCA
42891505 ATATAT
1 ATATAT
42891511 GTATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATATACTAAATAAATTTATCA
Found at i:42893331 original size:19 final size:21
Alignment explanation
Indices: 42893298--42893341 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
42893288 ATTGTCGCCA
42893298 TTCTCATTTTCCTCT-A-TTC
1 TTCTCATTTTCCTCTCATTTC
42893317 TTCTCCATTTT-CTCTCATTTC
1 TTCT-CATTTTCCTCTCATTTC
42893338 TTCT
1 TTCT
42893342 TCTCCATGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.36
20 7 0.32
21 7 0.32
ACGTcount: A:0.09, C:0.32, G:0.00, T:0.59
Consensus pattern (21 bp):
TTCTCATTTTCCTCTCATTTC
Found at i:42894692 original size:22 final size:22
Alignment explanation
Indices: 42894602--42894695 Score: 75
Period size: 22 Copynumber: 4.3 Consensus size: 22
42894592 TGACTTATCC
* *
42894602 CAACTTATTGGTAGCTTGTCTG
1 CAACTTACTGGCAGCTTGTCTG
* * * *
42894624 CAATTTGCTAGCAGCTTGTCTA
1 CAACTTACTGGCAGCTTGTCTG
* * *
42894646 CAACTAACTGG-TGACTTAT-TG
1 CAACTTACTGGCAG-CTTGTCTG
*
42894667 CAACTTACTGGCATCTTGTCTG
1 CAACTTACTGGCAGCTTGTCTG
42894689 CAACTTA
1 CAACTTA
42894696 TTGGTAATTC
Statistics
Matches: 52, Mismatches: 17, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
21 16 0.31
22 36 0.69
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.36
Consensus pattern (22 bp):
CAACTTACTGGCAGCTTGTCTG
Found at i:42901283 original size:36 final size:36
Alignment explanation
Indices: 42901212--42901329 Score: 141
Period size: 36 Copynumber: 3.3 Consensus size: 36
42901202 TATCTACCGT
* * *
42901212 ATATAAGGGTTCGCTTACGCATA-AGA-GTTCGCATAC
1 ATATAAGGGTTCGC--ATGCATATAAAGGTTCACATAC
*
42901248 ATATAAGGGTTTGCATGCATATAAAGGTTCACATAC
1 ATATAAGGGTTCGCATGCATATAAAGGTTCACATAC
* * *
42901284 ATATAAAGGTTCGCATGCATATAAGGGTCCACATAC
1 ATATAAGGGTTCGCATGCATATAAAGGTTCACATAC
42901320 ATATAAGGGT
1 ATATAAGGGT
42901330 ACACATACCA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
34 6 0.08
35 2 0.03
36 63 0.89
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (36 bp):
ATATAAGGGTTCGCATGCATATAAAGGTTCACATAC
Found at i:42901327 original size:18 final size:18
Alignment explanation
Indices: 42901212--42901337 Score: 117
Period size: 18 Copynumber: 7.0 Consensus size: 18
42901202 TATCTACCGT
* *
42901212 ATATAAGGGTTCGCTTAC
1 ATATAAGGGTTCACATAC
** * *
42901230 GCATAAGAGTTCGCATAC
1 ATATAAGGGTTCACATAC
** *
42901248 ATATAAGGGTTTGCATGC
1 ATATAAGGGTTCACATAC
*
42901266 ATATAAAGGTTCACATAC
1 ATATAAGGGTTCACATAC
* * *
42901284 ATATAAAGGTTCGCATGC
1 ATATAAGGGTTCACATAC
*
42901302 ATATAAGGGTCCACATAC
1 ATATAAGGGTTCACATAC
*
42901320 ATATAAGGGTACACATAC
1 ATATAAGGGTTCACATAC
42901338 CAACAATTTG
Statistics
Matches: 88, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 88 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (18 bp):
ATATAAGGGTTCACATAC
Found at i:42903544 original size:286 final size:286
Alignment explanation
Indices: 42903032--42903603 Score: 1108
Period size: 286 Copynumber: 2.0 Consensus size: 286
42903022 GTGACATAGA
* *
42903032 AGTTAATATACTCTTCTTGAGATGTCTTCAAGGGTATGTTGCTACACCCTTAGGCTGCATCACGA
1 AGTTAATATACTCTTCTTGAGATGTCTTCAAGGGTATGTTGCGACACACTTAGGCTGCATCACGA
42903097 CATCGAAGGCAGTCTTGTGATTTCTCTATTCTGTTCCCTATGTTGCAACATTGATCATTCTGTGT
66 CATCGAAGGCAGTCTTGTGATTTCTCTATTCTGTTCCCTATGTTGCAACATTGATCATTCTGTGT
42903162 TGCGATATAGTGACTAGAATCGGTTTAGTACGCCTTCTAATGGTCTCCTAAACACTTACAAAGTT
131 TGCGATATAGTGACTAGAATCGGTTTAGTACGCCTTCTAATGGTCTCCTAAACACTTACAAAGTT
42903227 CAATTTGAACACTTTCAAACTCCTAAAGTGCGAAAATTAGTTTAATCTATTTCACCGAATTATAG
196 CAATTTGAACACTTTCAAACTCCTAAAGTGCGAAAATTAGTTTAATCTATTTCACCGAATTATAG
*
42903292 TAGATCAAGTAATTCTTCTACAAATT
261 CAGATCAAGTAATTCTTCTACAAATT
42903318 AGTTAATATACTCTTCTTGAGATGTCTTCAAGGGTATGTTGCGACACACTTAGGCTGCATCACGA
1 AGTTAATATACTCTTCTTGAGATGTCTTCAAGGGTATGTTGCGACACACTTAGGCTGCATCACGA
42903383 CATCGAAGGCAGTCTTGTGATTTCTCTATTCTGTTCCCTATGTTGCAACATTGATCATTCTGTGT
66 CATCGAAGGCAGTCTTGTGATTTCTCTATTCTGTTCCCTATGTTGCAACATTGATCATTCTGTGT
42903448 TGCGATATAGTGACTAGAATCGGTTTAGTACGCCTTCTAATGGTCTCCTAAACACTTACAAAGTT
131 TGCGATATAGTGACTAGAATCGGTTTAGTACGCCTTCTAATGGTCTCCTAAACACTTACAAAGTT
*
42903513 CAATTTGAACACTTTCAAGCTCCTAAAGTGCGAAAATTAGTTTAATCTATTTCACCGAATTATAG
196 CAATTTGAACACTTTCAAACTCCTAAAGTGCGAAAATTAGTTTAATCTATTTCACCGAATTATAG
42903578 CAGATCAAGTAATTCTTCTACAAATT
261 CAGATCAAGTAATTCTTCTACAAATT
42903604 TGATGTTGAA
Statistics
Matches: 282, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
286 282 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (286 bp):
AGTTAATATACTCTTCTTGAGATGTCTTCAAGGGTATGTTGCGACACACTTAGGCTGCATCACGA
CATCGAAGGCAGTCTTGTGATTTCTCTATTCTGTTCCCTATGTTGCAACATTGATCATTCTGTGT
TGCGATATAGTGACTAGAATCGGTTTAGTACGCCTTCTAATGGTCTCCTAAACACTTACAAAGTT
CAATTTGAACACTTTCAAACTCCTAAAGTGCGAAAATTAGTTTAATCTATTTCACCGAATTATAG
CAGATCAAGTAATTCTTCTACAAATT
Found at i:42904345 original size:21 final size:22
Alignment explanation
Indices: 42904321--42904364 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
42904311 TAATTTTAGG
42904321 TTTAGTTTTCTCTA-AGTTTTC
1 TTTAGTTTTCTCTACAGTTTTC
*
42904342 TTTAGTTTTCTCTACATTTTTC
1 TTTAGTTTTCTCTACAGTTTTC
42904364 T
1 T
42904365 AGGGTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.14, C:0.16, G:0.07, T:0.64
Consensus pattern (22 bp):
TTTAGTTTTCTCTACAGTTTTC
Found at i:42910822 original size:16 final size:18
Alignment explanation
Indices: 42910801--42910834 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
42910791 TTCTATAAAG
42910801 ATTTTATT-TT-TATTTT
1 ATTTTATTATTATATTTT
42910817 ATTTTATTATTATATTTT
1 ATTTTATTATTATATTTT
42910835 TTAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTTATTATTATATTTT
Found at i:42911872 original size:24 final size:23
Alignment explanation
Indices: 42911845--42911898 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
42911835 TGCGCATTAT
* *
42911845 ATATATGCTAATTAAATTTATTTA
1 ATATATGCTAAATAAATTTA-TCA
**
42911869 ATATATATTAAATAAATTTATCA
1 ATATATGCTAAATAAATTTATCA
42911892 ATATATG
1 ATATATG
42911899 TATATATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (23 bp):
ATATATGCTAAATAAATTTATCA
Found at i:42912158 original size:21 final size:21
Alignment explanation
Indices: 42912128--42912167 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42912118 AATAAATACC
*
42912128 AAAAATTTATTTTAAAAATTA
1 AAAAAATTATTTTAAAAATTA
42912149 AAAAAATTATTTTAAAAAT
1 AAAAAATTATTTTAAAAAT
42912168 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAAATTATTTTAAAAATTA
Found at i:42912170 original size:11 final size:12
Alignment explanation
Indices: 42912128--42912176 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
42912118 AATAAATACC
42912128 AAAAATTTATTTT
1 AAAAA-TTATTTT
*
42912141 AAAAATTA---A
1 AAAAATTATTTT
42912150 AAAAATTATTTT
1 AAAAATTATTTT
42912162 AAAAA-TATTTT
1 AAAAATTATTTT
42912173 AAAA
1 AAAA
42912177 TTAAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
9 8 0.26
11 10 0.32
12 8 0.26
13 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAAATTATTTT
Found at i:42912239 original size:41 final size:40
Alignment explanation
Indices: 42912141--42912272 Score: 214
Period size: 39 Copynumber: 3.3 Consensus size: 40
42912131 AATTTATTTT
* *
42912141 AAAAATTAAAAAAATTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAAAAAGTATTTTAAAAGTATTTTAAAATTAA
*
42912181 AAAAA-TAAAAAATGTATTTTAAAAGTATTTTAAAATTAA
1 AAAAATTAAAAAAAGTATTTTAAAAGTATTTTAAAATTAA
42912220 AAAAATTTAAAAAAAGTATTTTAAAAGTATTTTAAAATTAA
1 AAAAA-TTAAAAAAAGTATTTTAAAAGTATTTTAAAATTAA
42912261 AAAAA-TAAAAAA
1 AAAAATTAAAAAA
42912273 TATATTTATT
Statistics
Matches: 86, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
39 43 0.50
40 5 0.06
41 38 0.44
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (40 bp):
AAAAATTAAAAAAAGTATTTTAAAAGTATTTTAAAATTAA
Found at i:42916394 original size:30 final size:30
Alignment explanation
Indices: 42916358--42916416 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
42916348 GTACATCATT
42916358 ATAACACTAAAGTCCATTTAAATAAGTTCC
1 ATAACACTAAAGTCCATTTAAATAAGTTCC
42916388 ATAACACTAAAGTCCATTTAAATAAGTTC
1 ATAACACTAAAGTCCATTTAAATAAGTTC
42916417 AATAGTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.31
Consensus pattern (30 bp):
ATAACACTAAAGTCCATTTAAATAAGTTCC
Found at i:42924858 original size:62 final size:62
Alignment explanation
Indices: 42924792--42924909 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 62
42924782 CATCAGCGTG
*
42924792 TCTCTAGGCCGTGTGAGTCACACGGTATTTCGAATGGCC-ACACGACCTAAGACACGACCATT
1 TCTCTAGGCCGTCTGAGTCACACGGTATTTCG-ATGGCCTACACGACCTAAGACACGACCATT
* * * *
42924854 TCTCTTGGCCGTCTGAGTCACACGGTATTTCGATTGCCTACACGGCCTAAGGCACG
1 TCTCTAGGCCGTCTGAGTCACACGGTATTTCGATGGCCTACACGACCTAAGACACG
42924910 GGCGTGTCTC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
61 5 0.10
62 45 0.90
ACGTcount: A:0.22, C:0.30, G:0.24, T:0.25
Consensus pattern (62 bp):
TCTCTAGGCCGTCTGAGTCACACGGTATTTCGATGGCCTACACGACCTAAGACACGACCATT
Found at i:42930332 original size:22 final size:21
Alignment explanation
Indices: 42930288--42930332 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42930278 CTGCCTTTGG
* *
42930288 TGTCGCGACACAGCCTGAGGA
1 TGTCGCGACACACCCTGAAGA
*
42930309 TGTCGTGACACACCCCTGAAGA
1 TGTCGCGACACA-CCCTGAAGA
42930331 TG
1 TG
42930333 AGTATAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (21 bp):
TGTCGCGACACACCCTGAAGA
Found at i:42941603 original size:30 final size:31
Alignment explanation
Indices: 42941537--42941609 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
42941527 ATGTTAATGG
* *
42941537 GTGACTGATTTGTCACTTTTCGATAACGTTA
1 GTGACTGTTTTGTAACTTTTCGATAACGTTA
*
42941568 GTGACTGTTTTGTAATTTTTCGA-AA-GTTGA
1 GTGACTGTTTTGTAACTTTTCGATAACGTT-A
42941598 GTGACTGTTTTG
1 GTGACTGTTTTG
42941610 CCAACTGCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.08
30 15 0.39
31 20 0.53
ACGTcount: A:0.21, C:0.11, G:0.23, T:0.45
Consensus pattern (31 bp):
GTGACTGTTTTGTAACTTTTCGATAACGTTA
Found at i:42944428 original size:17 final size:17
Alignment explanation
Indices: 42944406--42944440 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
42944396 TAATACAATG
42944406 ATCTTTATGTTTCCATT
1 ATCTTTATGTTTCCATT
42944423 ATCTTTATGTTTCCATT
1 ATCTTTATGTTTCCATT
42944440 A
1 A
42944441 CAGGAGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.57
Consensus pattern (17 bp):
ATCTTTATGTTTCCATT
Found at i:42946710 original size:16 final size:18
Alignment explanation
Indices: 42946669--42946702 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42946659 CAAAATTAGA
42946669 GTTTCTCTCATTCTTTTC
1 GTTTCTCTCATTCTTTTC
*
42946687 GATTCTCTCA-TCTTTT
1 GTTTCTCTCATTCTTTT
42946703 TTTTCTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.26, G:0.06, T:0.59
Consensus pattern (18 bp):
GTTTCTCTCATTCTTTTC
Found at i:42948146 original size:13 final size:14
Alignment explanation
Indices: 42948130--42948167 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
42948120 GAGAATTTGA
42948130 TTAAAAAATTT-TC
1 TTAAAAAATTTATC
*
42948143 TTAAAAAATTTATT
1 TTAAAAAATTTATC
42948157 TTGAAAAAATT
1 TT-AAAAAATT
42948168 CAATGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (14 bp):
TTAAAAAATTTATC
Found at i:42948716 original size:37 final size:37
Alignment explanation
Indices: 42948652--42948728 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
42948642 ATTCCAAAAA
*
42948652 TAATACTATTTTAATTATTATAATATTAAATTTAAT-T
1 TAATACTATTTTAATTAGTATAATATT-AATTTAATAT
**
42948689 TAATACTTATTTTAATT-GTATTTTATTAATTTAATAT
1 TAATAC-TATTTTAATTAGTATAATATTAATTTAATAT
42948726 TAA
1 TAA
42948729 AGTGATTATC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 8 0.23
37 17 0.49
38 10 0.29
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (37 bp):
TAATACTATTTTAATTAGTATAATATTAATTTAATAT
Found at i:42948910 original size:11 final size:9
Alignment explanation
Indices: 42948882--42948907 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
42948872 ATTATAGTTG
42948882 AACTCTCTA
1 AACTCTCTA
42948891 AACTCTCTA
1 AACTCTCTA
42948900 AACTCTCT
1 AACTCTCT
42948908 CTATATAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (9 bp):
AACTCTCTA
Found at i:42951855 original size:28 final size:28
Alignment explanation
Indices: 42951815--42951899 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 28
42951805 AAAAAATTTG
*
42951815 ACCATTACAATATGGTTGTTGGAATCTA
1 ACCATTACAATATGGCTGTTGGAATCTA
** ** * *
42951843 ATTATTACAATATGGCCATTGGAATTTG
1 ACCATTACAATATGGCTGTTGGAATCTA
42951871 ACCATTACAA-ATGGCTGTTGGAATCTA
1 ACCATTACAATATGGCTGTTGGAATCTA
42951898 AC
1 AC
42951900 TGTTGCAATA
Statistics
Matches: 44, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
27 15 0.34
28 29 0.66
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (28 bp):
ACCATTACAATATGGCTGTTGGAATCTA
Found at i:42954467 original size:31 final size:31
Alignment explanation
Indices: 42954432--42954490 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
42954422 ATGTGTATAG
42954432 TTGAATCACAATAAAAATTTCATATATACAT
1 TTGAATCACAATAAAAATTTCATATATACAT
* * *
42954463 TTGAATTACAATCAAAGTTTCATATATA
1 TTGAATCACAATAAAAATTTCATATATA
42954491 TTGTTAGAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (31 bp):
TTGAATCACAATAAAAATTTCATATATACAT
Found at i:42959945 original size:21 final size:21
Alignment explanation
Indices: 42959915--42959955 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42959905 TCTGTTGCCC
42959915 TTTCTTTCTTTTTT-CTTTTA
1 TTTCTTTCTTTTTTCCTTTTA
42959935 TTTCTATTCTTTTTTCCTTTT
1 TTTCT-TTCTTTTTTCCTTTT
42959956 TTAATCTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTCTTTCTTTTTTCCTTTTA
Found at i:42968763 original size:19 final size:20
Alignment explanation
Indices: 42968722--42968763 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
42968712 TTAAAAATAA
**
42968722 TTTAATTCAATTCACTTGGT
1 TTTAATTCAATTCACTTAAT
*
42968742 TTTAATTC-ATTCATTTAAT
1 TTTAATTCAATTCACTTAAT
42968761 TTT
1 TTT
42968764 CAGTTTTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTAATTCAATTCACTTAAT
Found at i:42975834 original size:20 final size:20
Alignment explanation
Indices: 42975778--42975834 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
42975768 GATGCAAAAT
* *
42975778 AAGGGCACCAAAGTGTAATC
1 AAGGGCACCAGAGTGCAATC
**
42975798 -AGGAGCACCAGTCTGCAATC
1 AAGG-GCACCAGAGTGCAATC
42975818 AAGGGCACCAGAGTGCA
1 AAGGGCACCAGAGTGCA
42975835 TTTAGGGGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 3 0.10
20 23 0.79
21 3 0.10
ACGTcount: A:0.35, C:0.25, G:0.28, T:0.12
Consensus pattern (20 bp):
AAGGGCACCAGAGTGCAATC
Found at i:42975843 original size:20 final size:20
Alignment explanation
Indices: 42975820--42975885 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
42975810 CTGCAATCAA
42975820 GGGCACCAGAGTGCATTTAG
1 GGGCACCAGAGTGCATTTAG
* *
42975840 GGGCACGA-ATGTGC-TGCTAG
1 GGGCACCAGA-GTGCAT-TTAG
* *
42975860 GGGCACCGGAGTGCATTCAG
1 GGGCACCAGAGTGCATTTAG
42975880 GGGCAC
1 GGGCAC
42975886 GTATGTGCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.21, C:0.23, G:0.39, T:0.17
Consensus pattern (20 bp):
GGGCACCAGAGTGCATTTAG
Found at i:42975893 original size:20 final size:20
Alignment explanation
Indices: 42975830--42975894 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
42975820 GGGCACCAGA
*
42975830 GTGCATTTAGGGGCACGAAT
1 GTGCATTCAGGGGCACGAAT
* *
42975850 GTGC-TGCTAGGGGCACCGGA-
1 GTGCATTC-AGGGGCA-CGAAT
*
42975870 GTGCATTCAGGGGCACGTAT
1 GTGCATTCAGGGGCACGAAT
42975890 GTGCA
1 GTGCA
42975895 AACATGGACA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 4 0.11
20 27 0.75
21 5 0.14
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.22
Consensus pattern (20 bp):
GTGCATTCAGGGGCACGAAT
Found at i:42975907 original size:40 final size:40
Alignment explanation
Indices: 42975819--42975938 Score: 104
Period size: 40 Copynumber: 3.0 Consensus size: 40
42975809 TCTGCAATCA
* * * **
42975819 AGGG-CACCAGAGTGCATTTAGGGGCACGAATGTGC-TGC
1 AGGGACACCGGAGTGCATTCAGGGGCACGTATGTGCAAAC
*
42975857 TAGGGGCACCGGAGTGCATTCAGGGGCACGTATGTGCAAAC
1 -AGGGACACCGGAGTGCATTCAGGGGCACGTATGTGCAAAC
* * *
42975898 ATGGACACCGAAGTG-TTTACAGGGGCACAGT-TGTGCAAAC
1 AGGGACACCGGAGTGCATT-CAGGGGCAC-GTATGTGCAAAC
42975938 A
1 A
42975939 AGAACATCGA
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
39 6 0.09
40 59 0.87
41 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.34, T:0.18
Consensus pattern (40 bp):
AGGGACACCGGAGTGCATTCAGGGGCACGTATGTGCAAAC
Found at i:42975950 original size:40 final size:40
Alignment explanation
Indices: 42975877--42975954 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
42975867 GGAGTGCATT
* *
42975877 CAGGGGCACGTATGTGCAAACATGGACACCGAAGTGTTTA
1 CAGGGGCACGTATGTGCAAACAAGAACACCGAAGTGTTTA
*
42975917 CAGGGGCACAGT-TGTGCAAACAAGAACATCGAAGTGTT
1 CAGGGGCAC-GTATGTGCAAACAAGAACACCGAAGTGTT
42975955 ATGAAGGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.19
Consensus pattern (40 bp):
CAGGGGCACGTATGTGCAAACAAGAACACCGAAGTGTTTA
Found at i:42990220 original size:59 final size:62
Alignment explanation
Indices: 42990122--42990248 Score: 163
Period size: 59 Copynumber: 2.1 Consensus size: 62
42990112 ATACACCAAT
* * * *
42990122 AGTCACTCAACTTTGATTAAAACAACAAAATAGTCACTAAAC-TT-T-GAAAAGTTACAACTC
1 AGTCACTCAACTTTGATGAAAACAACAAAATAATCACT-AACGTTATCGAAAAGTGACAAATC
* *
42990182 AGTCGCTCAACTTT-ATGAAAATAACAAAATAATCACTAACGTTATCGAAAAGTGACAAATC
1 AGTCACTCAACTTTGATGAAAACAACAAAATAATCACTAACGTTATCGAAAAGTGACAAATC
42990243 AGTCAC
1 AGTCAC
42990249 CCACTAACAT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
58 3 0.05
59 22 0.39
60 14 0.25
61 18 0.32
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (62 bp):
AGTCACTCAACTTTGATGAAAACAACAAAATAATCACTAACGTTATCGAAAAGTGACAAATC
Found at i:42993243 original size:20 final size:20
Alignment explanation
Indices: 42993193--42993244 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
42993183 TAAAATAATA
*
42993193 TTATATT-AATTATATATGT
1 TTATATTAAATTATATATAT
*
42993212 TTA-ATAATAATTATATATAT
1 TTATATTA-AATTATATATAT
42993232 TTATATTAAATTA
1 TTATATTAAATTA
42993245 CTAATCCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.07
19 3 0.11
20 19 0.70
21 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTATATTAAATTATATATAT
Found at i:42996003 original size:39 final size:39
Alignment explanation
Indices: 42995907--42996005 Score: 128
Period size: 39 Copynumber: 2.5 Consensus size: 39
42995897 ATATTCACTT
* * * *
42995907 AAGCATATATCACATTACACATATAATTAGATAATGTTC
1 AAGCATATATCGCAATACTCATATAATTAGATAACGTTC
* *
42995946 AAGCACATATCGCAATACTCATATAA-TCGCATAACGTTC
1 AAGCATATATCGCAATACTCATATAATTAG-ATAACGTTC
42995985 AAGCATATATCGCAATACTCA
1 AAGCATATATCGCAATACTCA
42996006 AAAACATGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
38 2 0.04
39 50 0.96
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.28
Consensus pattern (39 bp):
AAGCATATATCGCAATACTCATATAATTAGATAACGTTC
Found at i:43004117 original size:12 final size:12
Alignment explanation
Indices: 43004079--43004130 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
43004069 GAAATATATA
*
43004079 AATAATATCAAT
1 AATAATATTAAT
*
43004091 AATAATAGTAAT
1 AATAATATTAAT
*
43004103 AATAATATTATT
1 AATAATATTAAT
* *
43004115 AATTA-ATTAAA
1 AATAATATTAAT
43004126 AATAA
1 AATAA
43004131 ATAGCAAGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
11 8 0.25
12 24 0.75
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:43010245 original size:21 final size:21
Alignment explanation
Indices: 43010213--43010253 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
43010203 GAACATTTGG
43010213 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
43010234 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
43010254 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:43013221 original size:27 final size:27
Alignment explanation
Indices: 43013176--43013241 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
43013166 TTGATTTTCG
* *
43013176 TATTTCATAATTTAATTATA-AATTATT
1 TATTT-ATATTTTAATTATATAAATATT
*
43013203 CTATTTATATTTTATTTATATAAATATT
1 -TATTTATATTTTAATTATATAAATATT
43013231 TATTTATATTT
1 TATTTATATTT
43013242 ATCTATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 23 0.68
28 11 0.32
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (27 bp):
TATTTATATTTTAATTATATAAATATT
Found at i:43014699 original size:19 final size:19
Alignment explanation
Indices: 43014677--43014714 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
43014667 GGAAATCTGC
43014677 CAAACAGCC-GAAAATATTT
1 CAAACA-CCAGAAAATATTT
43014696 CAAACACCAGAAAATATTT
1 CAAACACCAGAAAATATTT
43014715 TCCAGTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.50, C:0.21, G:0.08, T:0.21
Consensus pattern (19 bp):
CAAACACCAGAAAATATTT
Found at i:43014724 original size:14 final size:15
Alignment explanation
Indices: 43014702--43014778 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
43014692 ATTTCAAACA
43014702 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
43014716 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
43014731 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
43014751 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
43014765 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
43014779 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:43014743 original size:20 final size:20
Alignment explanation
Indices: 43014718--43014757 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43014708 AATATTTTCC
*
43014718 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
43014738 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
43014758 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:43014763 original size:34 final size:35
Alignment explanation
Indices: 43014706--43014772 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
43014696 CAAACACCAG
*
43014706 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
43014741 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
43014773 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:43025022 original size:21 final size:21
Alignment explanation
Indices: 43024983--43025022 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
43024973 ACACACAAAC
*
43024983 ATTTATAAAAGTCTTTATACA
1 ATTTATAAAAGTCTCTATACA
43025004 ATTTATAAAAAGTC-CTATA
1 ATTTAT-AAAAGTCTCTATA
43025023 ACAACACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (21 bp):
ATTTATAAAAGTCTCTATACA
Found at i:43025026 original size:22 final size:21
Alignment explanation
Indices: 43024983--43025026 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
43024973 ACACACAAAC
*
43024983 ATTTATAAAAGTCTTTATACA
1 ATTTATAAAAGTCTATATACA
43025004 ATTTATAAAAAGTCCTATA-ACA
1 ATTTAT-AAAAGT-CTATATACA
43025026 A
1 A
43025027 CACAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (21 bp):
ATTTATAAAAGTCTATATACA
Found at i:43028125 original size:17 final size:16
Alignment explanation
Indices: 43028105--43028158 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
43028095 AGTTAAATTT
43028105 TTTTGTTTCTTGTTTAG
1 TTTTGTTTCTT-TTTAG
*
43028122 TTTTATTTCTATTTGTAG
1 TTTTGTTTCT-TTT-TAG
*
43028140 TTTAGGTTTCTTTTTAG
1 TTT-TGTTTCTTTTTAG
43028157 TT
1 TT
43028159 GTAATCATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 16 0.52
18 10 0.32
19 5 0.16
ACGTcount: A:0.11, C:0.06, G:0.15, T:0.69
Consensus pattern (16 bp):
TTTTGTTTCTTTTTAG
Found at i:43028160 original size:23 final size:23
Alignment explanation
Indices: 43028116--43028161 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
43028106 TTTGTTTCTT
* *
43028116 GTTTAGTTTTATTTCTATTTGTA
1 GTTTAGGTTTATTTCTAGTTGTA
* *
43028139 GTTTAGGTTTCTTTTTAGTTGTA
1 GTTTAGGTTTATTTCTAGTTGTA
43028162 ATCATAGTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.15, C:0.04, G:0.17, T:0.63
Consensus pattern (23 bp):
GTTTAGGTTTATTTCTAGTTGTA
Found at i:43038735 original size:33 final size:33
Alignment explanation
Indices: 43038698--43038767 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
43038688 CTGACCTCTC
*
43038698 TTCACTAAAAATGAATTATCTCGTTGTACAGAA
1 TTCACTAAAAATGAATTATCTCGTTGTACAAAA
*
43038731 TTCACTAAAAATGAATTATCTTGTTGTACAAAA
1 TTCACTAAAAATGAATTATCTCGTTGTACAAAA
43038764 TTCA
1 TTCA
43038768 GATGATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (33 bp):
TTCACTAAAAATGAATTATCTCGTTGTACAAAA
Found at i:43039386 original size:51 final size:51
Alignment explanation
Indices: 43039321--43039511 Score: 210
Period size: 51 Copynumber: 3.8 Consensus size: 51
43039311 TCAGTTCACA
* * * *
43039321 TAGTAGCCTGCACATAGTACTAGACATGTGACCATCACTATCAGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTACACG
* * * * * *
43039372 TAGTAGCCTGCACATAGTACTACGCACGTTATCGA--AGCTATTTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCTGGTACACG
* * *
43039423 TAGTAGGCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCTGGTACACG
43039473 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
43039512 TTCACTTTCA
Statistics
Matches: 112, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
49 4 0.04
50 41 0.37
51 64 0.57
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTACACG
Found at i:43039485 original size:101 final size:102
Alignment explanation
Indices: 43039319--43039501 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 102
43039309 TATCAGTTCA
* *
43039319 CATAGTAGCCTGCACATAGTACTAGACATGTGACCATCACTATCAGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCAGATACACGTAGTAGCCTGCA
*
43039384 CATAGTACTACGCACGTTATCGAAGCTATTTGGTACG
66 CATAGTACTACACACGTTATCGAAGCTATTTGGTACG
* * *
43039421 CATAGTAGGCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCAGATACACGTAGTAGCCTGC
43039484 ACATAGTACTACACACGT
65 ACATAGTACTACACACGT
43039502 GACCATCACT
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 37 0.50
102 33 0.45
103 4 0.05
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCAGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTTATCGAAGCTATTTGGTACG
Found at i:43040961 original size:122 final size:122
Alignment explanation
Indices: 43040761--43041002 Score: 335
Period size: 122 Copynumber: 2.0 Consensus size: 122
43040751 ACTCTAATGG
* * * *
43040761 TTTCATTTGGTATTGGTAGAACCCATCAAAATATCGATAGAAATGTAGGGGAGGCTAAACTTTGA
1 TTTCAATTGGTATTGGTAGAACCCAACAAAACATCGATAGAAATGCAGGGGAGGCTAAACTTTGA
* * * *
43040826 CTACTAATTTGACTTGTTTCAGTAAAATTCCTCAATGTAGCGGTAGAACTCTGGTGC
66 CTACTAATTTGACTTGTTTCACTAAAAGTCCTCAAGGTAGCAGTAGAACTCTGGTGC
43040883 TTTCAATTGGTATTGGTAGAACCCAACAAAACATCGATAGAAATGCAGGAGG-GGCTGAAA-TTT
1 TTTCAATTGGTATTGGTAGAACCCAACAAAACATCGATAGAAATGCAGG-GGAGGCT-AAACTTT
* * * * *
43040946 GGCTACTATTTTGACTTGTTTCACTAGAAGTCCTCAAGGTATCAGTATAACTCTGGT
64 GACTACTAATTTGACTTGTTTCACTAAAAGTCCTCAAGGTAGCAGTAGAACTCTGGT
43041003 TGGATCGATA
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
122 100 0.95
123 5 0.05
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (122 bp):
TTTCAATTGGTATTGGTAGAACCCAACAAAACATCGATAGAAATGCAGGGGAGGCTAAACTTTGA
CTACTAATTTGACTTGTTTCACTAAAAGTCCTCAAGGTAGCAGTAGAACTCTGGTGC
Found at i:43042314 original size:52 final size:51
Alignment explanation
Indices: 43042232--43042360 Score: 163
Period size: 52 Copynumber: 2.5 Consensus size: 51
43042222 ACTAGTGACT
* *
43042232 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGTTTTGG-TCA
1 CAAGTGGGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGCTTTGGCT-A
* *
43042284 CAAGTGGGGTACTATGTGAAGGCCAGTTTGTGAAGAAGGTAGCTTTGGCTA
1 CAAGTGGGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGCTA
* *
43042335 CAAG-GGTGGTATTATGTGCAGGCCAC
1 CAAGTGG-GGTACTATGTGAAGGCCAC
43042361 CGGGTATCCG
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
50 2 0.03
51 32 0.47
52 34 0.50
ACGTcount: A:0.26, C:0.13, G:0.33, T:0.28
Consensus pattern (51 bp):
CAAGTGGGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGCTA
Found at i:43042352 original size:51 final size:52
Alignment explanation
Indices: 43042232--43042360 Score: 165
Period size: 51 Copynumber: 2.5 Consensus size: 52
43042222 ACTAGTGACT
* *
43042232 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGTTTTGGTCA
1 CAAGGGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
* *
43042284 CAAGTGG-GGTACTATGTGAAGGCCAGTTTGTGAAG-AAGGTAGCTTTGG-CTA
1 CAAG-GGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTC-A
* *
43042335 CAAGGGTGGTATTATGTGCAGGCCAC
1 CAAGGGTGGTACTATGTGAAGGCCAC
43042361 CGGGTATCCG
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
50 3 0.04
51 32 0.48
52 31 0.46
53 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.33, T:0.28
Consensus pattern (52 bp):
CAAGGGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
Found at i:43044308 original size:22 final size:22
Alignment explanation
Indices: 43044273--43044328 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
43044263 TGATATAATC
*
43044273 CAACCAAAAAGTATATAAAAAG
1 CAACCAAGAAGTATATAAAAAG
*
43044295 CAATCAAGAAGTATATAAAAAG
1 CAACCAAGAAGTATATAAAAAG
43044317 CAACCAAGAAGT
1 CAACCAAGAAGT
43044329 GAGGTCATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.14
Consensus pattern (22 bp):
CAACCAAGAAGTATATAAAAAG
Found at i:43054310 original size:26 final size:26
Alignment explanation
Indices: 43054280--43054329 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
43054270 CCACTTAATC
*
43054280 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACATAGCAACCCCTT
43054306 GGGGAATCAGCACATAGCAACCCC
1 GGGGAATCAGCACATAGCAACCCC
43054330 CTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.32, G:0.24, T:0.14
Consensus pattern (26 bp):
GGGGAATCAGCACATAGCAACCCCTT
Found at i:43054412 original size:26 final size:26
Alignment explanation
Indices: 43054382--43054431 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
43054372 CCAATGAACT
*
43054382 GGGGAATCAGCACTTAGCAACCCCTC
1 GGGGAATCAGCACATAGCAACCCCTC
43054408 GGGGAATCAGCACATAGCAACCCC
1 GGGGAATCAGCACATAGCAACCCC
43054432 CTTTCACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.34, G:0.24, T:0.12
Consensus pattern (26 bp):
GGGGAATCAGCACATAGCAACCCCTC
Found at i:43054423 original size:102 final size:103
Alignment explanation
Indices: 43054247--43054509 Score: 413
Period size: 102 Copynumber: 2.6 Consensus size: 103
43054237 AACCGTTATT
* * * *
43054247 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGAA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
** *
43054312 TCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
43054349 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGA
43054413 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
43054452 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
43054510 TTATGTACAA
Statistics
Matches: 148, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
101 1 0.01
102 81 0.55
103 65 0.44
104 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (103 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:43054871 original size:30 final size:30
Alignment explanation
Indices: 43054844--43054901 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
43054834 CCACCCAATT
43054844 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
43054874 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
43054902 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:43061363 original size:41 final size:41
Alignment explanation
Indices: 43061296--43061377 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
43061286 TCGCTCCAAC
* *
43061296 CTCTTTATAACCTCCCACAGACAAGTACCACAAGGCAAATG
1 CTCTTTATAACCTCCCACAAACAAGTACCACAAAGCAAATG
* * *
43061337 CTCTTTATAATCTCCCTCAAATAAGTACCACAAAGCAAATG
1 CTCTTTATAACCTCCCACAAACAAGTACCACAAAGCAAATG
43061378 GTCGAGAGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.23
Consensus pattern (41 bp):
CTCTTTATAACCTCCCACAAACAAGTACCACAAAGCAAATG
Found at i:43069753 original size:19 final size:19
Alignment explanation
Indices: 43069706--43069755 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
43069696 TAAACTATTT
* *
43069706 CAACCCAAATGAGCTAAAT
1 CAACCCAAATGAACTAAAA
*
43069725 GAAGCCCAAATGAACTAAAA
1 CAA-CCCAAATGAACTAAAA
43069745 CAACCCAAATG
1 CAACCCAAATG
43069756 GCCATATTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.50, C:0.26, G:0.12, T:0.12
Consensus pattern (19 bp):
CAACCCAAATGAACTAAAA
Found at i:43072725 original size:12 final size:12
Alignment explanation
Indices: 43072708--43072732 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43072698 GTTCAAAGTG
43072708 AAAATTAAATTA
1 AAAATTAAATTA
43072720 AAAATTAAATTA
1 AAAATTAAATTA
43072732 A
1 A
43072733 TTGGTTATCA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTAAATTA
Found at i:43078438 original size:23 final size:25
Alignment explanation
Indices: 43078394--43078443 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
43078384 AAAATAAATT
43078394 AGAAAGAAAGATACAGAAAAAATGTAA
1 AGAAAGAAAGATACAG-AAAAAT-TAA
43078421 AGAAAGAAAGA-A-AG-AAAATTAA
1 AGAAAGAAAGATACAGAAAAATTAA
43078443 A
1 A
43078444 AGATTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 4 0.17
23 5 0.22
25 2 0.09
26 1 0.04
27 11 0.48
ACGTcount: A:0.70, C:0.02, G:0.18, T:0.10
Consensus pattern (25 bp):
AGAAAGAAAGATACAGAAAAATTAA
Found at i:43078445 original size:23 final size:22
Alignment explanation
Indices: 43078384--43078469 Score: 61
Period size: 23 Copynumber: 3.6 Consensus size: 22
43078374 TAAAAATAAA
43078384 AAAATAAATTAGAAAGAAAGATACAG
1 AAAA-AAATTA-AAAGAAAGA-A-AG
43078410 -AAAAAATGT-AAAGAAAGAAAG
1 AAAAAAAT-TAAAAGAAAGAAAG
43078431 AAAGAAAATTAAAAGATTAA-AAAG
1 AAA-AAAATTAAAAGA--AAGAAAG
43078455 AAAAATAAATTAAAA
1 -AAAA-AAATTAAAA
43078470 ATAAGTAAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 17
0.75 0.00 0.25
Matches are distributed among these distances:
21 2 0.04
22 4 0.08
23 19 0.37
24 9 0.17
25 18 0.35
ACGTcount: A:0.71, C:0.01, G:0.13, T:0.15
Consensus pattern (22 bp):
AAAAAAATTAAAAGAAAGAAAG
Found at i:43078547 original size:21 final size:21
Alignment explanation
Indices: 43078508--43078547 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
43078498 TTATTAGTTT
*
43078508 TTTTAAAAATATATTTTTATA
1 TTTTAAAAATATATATTTATA
43078529 TTTT-AAAATAATATATTTA
1 TTTTAAAAAT-ATATATTTA
43078548 ATAGATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTAAAAATATATATTTATA
Found at i:43078623 original size:16 final size:16
Alignment explanation
Indices: 43078604--43078637 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43078594 GCTTTTCTAT
*
43078604 TTTTCTATTTTTACAA
1 TTTTCTATTTTTAAAA
*
43078620 TTTTTTATTTTTAAAA
1 TTTTCTATTTTTAAAA
43078636 TT
1 TT
43078638 ATTTGATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTCTATTTTTAAAA
Found at i:43084566 original size:28 final size:26
Alignment explanation
Indices: 43084531--43084582 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
43084521 TTTAAACCAA
43084531 ACTTTTCAAAAACACTTCTCTCAAAAAC
1 ACTTTTCAAAAACACTT-T-TCAAAAAC
43084559 ACTTTTCAAAAACACTTTTCAAAA
1 ACTTTTCAAAAACACTTTTCAAAA
43084583 GTATTGCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 6 0.25
27 1 0.04
28 17 0.71
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (26 bp):
ACTTTTCAAAAACACTTTTCAAAAAC
Found at i:43084569 original size:13 final size:13
Alignment explanation
Indices: 43084531--43084582 Score: 86
Period size: 13 Copynumber: 3.8 Consensus size: 13
43084521 TTTAAACCAA
43084531 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
43084544 ACTTCTCTCAAAAAC
1 ACTT-T-TCAAAAAC
43084559 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
43084572 ACTTTTCAAAA
1 ACTTTTCAAAA
43084583 GTATTGCTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
13 23 0.62
14 2 0.05
15 12 0.32
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:43090177 original size:98 final size:98
Alignment explanation
Indices: 43090008--43090208 Score: 393
Period size: 98 Copynumber: 2.1 Consensus size: 98
43089998 GTGTATTCTG
*
43090008 TTCTACTACCAAAACTCGATAGTTTAGTATTTTGGAAATAGGCCATGGATGATGATCCACTCACT
1 TTCTACTACCAAAACTCGATAGTTTAGTATTTTGGAAATAAGCCATGGATGATGATCCACTCACT
43090073 TACGAGGAGGCTATACAGGATGTTGATTCCAAT
66 TACGAGGAGGCTATACAGGATGTTGATTCCAAT
43090106 TTCTACTACCAAAACTCGATAGTTTAGTATTTTGGAAATAAGCCATGGATGATGATCCACTCACT
1 TTCTACTACCAAAACTCGATAGTTTAGTATTTTGGAAATAAGCCATGGATGATGATCCACTCACT
43090171 TACGAGGAGGCTATACAGGATGTTGATTCCAAT
66 TACGAGGAGGCTATACAGGATGTTGATTCCAAT
43090204 TTCTA
1 TTCTA
43090209 GAAACAGGCC
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 102 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (98 bp):
TTCTACTACCAAAACTCGATAGTTTAGTATTTTGGAAATAAGCCATGGATGATGATCCACTCACT
TACGAGGAGGCTATACAGGATGTTGATTCCAAT
Found at i:43090883 original size:11 final size:11
Alignment explanation
Indices: 43090867--43090905 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
43090857 TTTATAAATA
43090867 TATAAATTAAT
1 TATAAATTAAT
*
43090878 TATAAAGTATAT
1 TATAAATTA-AT
43090890 TATTAAATTAAT
1 TA-TAAATTAAT
43090902 TATA
1 TATA
43090906 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:43090903 original size:28 final size:28
Alignment explanation
Indices: 43090871--43090924 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
43090861 TAAATATATA
43090871 AATTA-ATTATAAAGTA-TATTATTAAATT
1 AATTATATTATAAA-TATTA-TATTAAATT
43090899 AATTATATTATAAATATTATATTAAA
1 AATTATATTATAAATATTATATTAAA
43090925 AAATAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
AATTATATTATAAATATTATATTAAATT
Found at i:43090917 original size:14 final size:17
Alignment explanation
Indices: 43090885--43090922 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
43090875 AATTATAAAG
43090885 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
43090902 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
43090916 TATATTA
1 TATATTA
43090923 AAAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:43091166 original size:19 final size:20
Alignment explanation
Indices: 43091131--43091169 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
43091121 ACATGTCTAA
43091131 TAATAATAAACATATGTATT
1 TAATAATAAACATATGTATT
43091151 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
43091170 GCTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:43091236 original size:10 final size:10
Alignment explanation
Indices: 43091218--43091250 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
43091208 TAATTAAAAC
43091218 AAAAT-AAAT
1 AAAATGAAAT
43091227 AAAATGAAAT
1 AAAATGAAAT
*
43091237 GAAATGAAAT
1 AAAATGAAAT
43091247 AAAA
1 AAAA
43091251 AAAAGGGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 5 0.24
10 16 0.76
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (10 bp):
AAAATGAAAT
Found at i:43091308 original size:6 final size:6
Alignment explanation
Indices: 43091297--43091327 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
43091287 CAGGGAAAGG
43091297 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
43091328 TTAAAGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:43091717 original size:17 final size:18
Alignment explanation
Indices: 43091695--43091728 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
43091685 TAAATGAGTT
43091695 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
43091712 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
43091729 AATAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:43092049 original size:18 final size:18
Alignment explanation
Indices: 43092026--43092063 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
43092016 GTATATTGAT
43092026 TTGAAT-GTGAAATTGAAA
1 TTGAATAGTGAAATT-AAA
*
43092044 TTGAATAGTGATATTAAA
1 TTGAATAGTGAAATTAAA
43092062 TT
1 TT
43092064 TGGTATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (18 bp):
TTGAATAGTGAAATTAAA
Found at i:43092170 original size:23 final size:23
Alignment explanation
Indices: 43092140--43092202 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
43092130 TTTTTCGATT
43092140 AGGCACTTTATGTGTCGTATTTC
1 AGGCACTTTATGTGTCGTATTTC
**
43092163 AGGCACTTCGTGTGTCG--TTTC
1 AGGCACTTTATGTGTCGTATTTC
*
43092184 AGGCAC-TTATGTGTGGTAT
1 AGGCACTTTATGTGTCGTAT
43092203 ACTGATCAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
20 7 0.21
21 10 0.30
22 1 0.03
23 15 0.45
ACGTcount: A:0.16, C:0.17, G:0.27, T:0.40
Consensus pattern (23 bp):
AGGCACTTTATGTGTCGTATTTC
Found at i:43096993 original size:15 final size:15
Alignment explanation
Indices: 43096953--43096993 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
43096943 TTAATTTCAC
43096953 ATTTTACTA-TTATGT
1 ATTTTA-TATTTATGT
43096968 ATTTTATATTTATGT
1 ATTTTATATTTATGT
*
43096983 CTTTTATATTT
1 ATTTTATATTT
43096994 TGCATGCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 22 0.92
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (15 bp):
ATTTTATATTTATGT
Found at i:43098683 original size:31 final size:29
Alignment explanation
Indices: 43098648--43098706 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
43098638 AGTTGTATTT
*
43098648 TATTAATTTAATATTAAAGTGATTATCTTAA
1 TATTAAATTAA-ATTAAA-TGATTATCTTAA
* *
43098679 TATTAAATTAAATTTAATGTTTATCTTA
1 TATTAAATTAAATTAAATGATTATCTTA
43098707 TAGATAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.40
30 5 0.20
31 10 0.40
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (29 bp):
TATTAAATTAAATTAAATGATTATCTTAA
Found at i:43099830 original size:29 final size:29
Alignment explanation
Indices: 43099798--43099868 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
43099788 AATCTCGAGA
*
43099798 TATTTTTTCAGGA-TCCATCT-AGTCAAAAT
1 TATTTTTTCAGAACT-CATCTCA-TCAAAAT
*
43099827 TATTTTTTTAGAACTCATCTCATCAAAAT
1 TATTTTTTCAGAACTCATCTCATCAAAAT
*
43099856 TATTTTTTTAGAA
1 TATTTTTTCAGAA
43099869 TCCCTAAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 36 0.95
30 2 0.05
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (29 bp):
TATTTTTTCAGAACTCATCTCATCAAAAT
Found at i:43099916 original size:14 final size:14
Alignment explanation
Indices: 43099899--43099926 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43099889 ATTTATGAAC
43099899 AATAAAACCCTAAA
1 AATAAAACCCTAAA
43099913 AATAAAACCCTAAA
1 AATAAAACCCTAAA
43099927 CCCTAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.14
Consensus pattern (14 bp):
AATAAAACCCTAAA
Found at i:43100072 original size:22 final size:22
Alignment explanation
Indices: 43100032--43100094 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
43100022 AACTTAAATA
*
43100032 AAACACAAAAACCCTAATTTAAT
1 AAACACCAAAA-CCTAATTTAAT
*
43100055 TAACACCAAAACCTAATTTAAT
1 AAACACCAAAACCTAATTTAAT
*
43100077 AAAC-CCTAAACCCTAATT
1 AAACACC-AAAACCTAATT
43100095 AAACAATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.06
22 24 0.69
23 9 0.26
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (22 bp):
AAACACCAAAACCTAATTTAAT
Found at i:43100096 original size:21 final size:22
Alignment explanation
Indices: 43100040--43100094 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
43100030 TAAAACACAA
*
43100040 AAACCCTAATTTAATTAACACC
1 AAACCCTAATTTAATAAACACC
*
43100062 AAAACCTAATTTAATAAAC-CC
1 AAACCCTAATTTAATAAACACC
43100083 TAAACCCTAATT
1 -AAACCCTAATT
43100095 AAACAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (22 bp):
AAACCCTAATTTAATAAACACC
Found at i:43106346 original size:3 final size:3
Alignment explanation
Indices: 43106340--43106385 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
43106330 ATAAATTACG
* * * *
43106340 TTA TTA TTA TTA GTA TTA TTA TTA ATA TTA TTG TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43106386 ATTTTCATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:43106575 original size:28 final size:28
Alignment explanation
Indices: 43106544--43106605 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
43106534 ATATACTTAT
*
43106544 ATATTTTTATAT-TTTATAACTTATATAC
1 ATATTTTTATATCTATATAAC-TATATAC
* * *
43106572 ATATCTATATATCTATATATCTATATAC
1 ATATTTTTATATCTATATAACTATATAC
43106600 AT-TTTT
1 ATATTTT
43106606 AAATTTTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
27 2 0.07
28 19 0.70
29 6 0.22
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (28 bp):
ATATTTTTATATCTATATAACTATATAC
Found at i:43106585 original size:8 final size:8
Alignment explanation
Indices: 43106572--43106598 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
43106562 ACTTATATAC
43106572 ATATCTAT
1 ATATCTAT
43106580 ATATCTAT
1 ATATCTAT
43106588 ATATCTAT
1 ATATCTAT
43106596 ATA
1 ATA
43106599 CATTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (8 bp):
ATATCTAT
Found at i:43106622 original size:52 final size:51
Alignment explanation
Indices: 43106463--43106622 Score: 129
Period size: 50 Copynumber: 3.2 Consensus size: 51
43106453 AATTTTGTTA
* * * * *
43106463 TATGTATATACATAC-ATACATTTATATATATATGTACATATTTT-AATTTT
1 TATGAATATACATACTATATATCTATATATCTATATACAT-TTTTAAATTTT
* * * *
43106513 TATAAATATACATA-TGTATA-C-ATATA-CT-TATATATTTTTATATTTT
1 TATGAATATACATACTATATATCTATATATCTATATACATTTTTAAATTTT
*
43106559 ATAACT-TATATACATATCTATATATCTATATATCTATATACATTTTTAAATTTT
1 -T-A-TGAATATACATA-CTATATATCTATATATCTATATACATTTTTAAATTTT
43106613 TATGAATATA
1 TATGAATATA
43106623 TAAATACATG
Statistics
Matches: 84, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
45 4 0.05
46 10 0.12
47 2 0.02
48 15 0.18
49 1 0.01
50 20 0.24
51 2 0.02
52 11 0.13
53 3 0.04
54 16 0.19
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (51 bp):
TATGAATATACATACTATATATCTATATATCTATATACATTTTTAAATTTT
Found at i:43106623 original size:54 final size:52
Alignment explanation
Indices: 43106467--43106629 Score: 146
Period size: 54 Copynumber: 3.2 Consensus size: 52
43106457 TTGTTATATG
* * * *
43106467 TATATACATAC-ATACATTTATATATATATGTACATATTTT-AATTTTTATAA
1 TATATACATACTATATATCTATATATCTATATACAT-TTTTAAATTTTTATAA
* * *
43106518 -ATATACATA-TGTATA-C-ATATA-CT-TATATATTTTTATA-TTTTATAA
1 TATATACATACTATATATCTATATATCTATATACATTTTTAAATTTTTATAA
43106563 CTTATATACATATCTATATATCTATATATCTATATACATTTTTAAATTTTTATGAA
1 --TATATACATA-CTATATATCTATATATCTATATACATTTTTAAATTTTTAT-AA
*
43106619 TATATAAATAC
1 TATATACATAC
43106630 ATGCTTATAT
Statistics
Matches: 88, Mismatches: 11, Indels: 24
0.72 0.09 0.20
Matches are distributed among these distances:
45 12 0.14
46 6 0.07
47 1 0.01
48 14 0.16
50 17 0.19
51 1 0.01
52 5 0.06
53 3 0.03
54 21 0.24
55 6 0.07
56 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (52 bp):
TATATACATACTATATATCTATATATCTATATACATTTTTAAATTTTTATAA
Found at i:43110011 original size:60 final size:60
Alignment explanation
Indices: 43109854--43110021 Score: 176
Period size: 60 Copynumber: 2.8 Consensus size: 60
43109844 TATATTTTTT
* *
43109854 ATTTTTAGAGTTAGGACTAAATTGATAGATTTTTGTAAATATTGAAGGCTAAATTTATTGA
1 ATTTTTAGAATTAGGACTAAATTGATAGA-ATTTGTAAATATTGAAGGCTAAATTTATTGA
* * ** * * * *
43109915 ATTTTTAGAATTAGAACCAAAACGACA-AATTTTGTAAACATTGAAGGTTAAATTTGTTGA
1 ATTTTTAGAATTAGGACTAAATTGATAGAA-TTTGTAAATATTGAAGGCTAAATTTATTGA
* * * * *
43109975 ATTTTTATATTTAGGATTAAATTGATAGAATGTGTAAATATTAAAGG
1 ATTTTTAGAATTAGGACTAAATTGATAGAATTTGTAAATATTGAAGG
43110022 GATAATTTTA
Statistics
Matches: 84, Mismatches: 21, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
60 61 0.73
61 23 0.27
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.40
Consensus pattern (60 bp):
ATTTTTAGAATTAGGACTAAATTGATAGAATTTGTAAATATTGAAGGCTAAATTTATTGA
Found at i:43110963 original size:125 final size:123
Alignment explanation
Indices: 43110720--43111143 Score: 546
Period size: 125 Copynumber: 3.4 Consensus size: 123
43110710 ACGTGAACGC
* * * * * *
43110720 GAAGAATTTGTGAAATCGCGCCCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACACGCTTTTGCTACAGTAGGTCCT-GAAAAAATAA
* * *
43110785 TTTTGAATTAACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACTAGGATGCTTTATGA
65 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAC-AGGATGCTTTATGA
* * * *
43110845 GAAGAATTTGTTAAATCGTGCCCACGTGGACACGCTTTTCCTACAGTAGGTCCTGAAAAAATTAT
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACACGCTTTTGCTACAGTAGGTCCTGAAAAAATAAT
* * *
43110910 TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACACTT-TAAGCAGAATGCTATT-TGA
66 TTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTCT-A-CAGGATGCT-TTATGA
* * * * * * *
43110970 GAAGAATTTCTGAAATCGTGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCTTGAAAGAACTAA
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACACGCTTTTGCTACAGTAGGTCCTGAAA-AAATAA
43111035 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
65 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTA-CAGGATGCTTTATGA
*
43111095 GAAGAATTTGTGAAATCGCGCTCACGTGGACACGCTTTTGCTACAGTAG
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACACGCTTTTGCTACAGTAG
43111144 CATGTTTGGG
Statistics
Matches: 257, Mismatches: 35, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
124 39 0.15
125 179 0.70
126 39 0.15
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (123 bp):
GAAGAATTTGTGAAATCGCGCCCACGTGGACACGCTTTTGCTACAGTAGGTCCTGAAAAAATAAT
TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACAGGATGCTTTATGA
Found at i:43112213 original size:9 final size:9
Alignment explanation
Indices: 43112195--43112226 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
43112185 ATTCTCAAAT
43112195 AATA-TCAA
1 AATATTCAA
43112203 AATATTCAA
1 AATATTCAA
43112212 AATATTCAA
1 AATATTCAA
43112221 AATATT
1 AATATT
43112227 TGTACAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (9 bp):
AATATTCAA
Found at i:43112331 original size:70 final size:69
Alignment explanation
Indices: 43112250--43112379 Score: 224
Period size: 70 Copynumber: 1.9 Consensus size: 69
43112240 TAAGCTCATG
* *
43112250 TTATTACATCAAATAATATCAAAATAAATCAAAAAAATTTCTATTTTATTACATCAAATAAACTT
1 TTATTACATCAAATAATATCAAAATAAATCAAAAAAA-TTCTATTTAATTACATAAAATAAACTT
43112315 ATATT
65 ATATT
*
43112320 TTATTACATCAAATAATATCAAAATAACTCAAAAAAATTCTATTTAATTACATAAAATAA
1 TTATTACATCAAATAATATCAAAATAAATCAAAAAAATTCTATTTAATTACATAAAATAA
43112380 TATCAAAATA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
69 21 0.37
70 36 0.63
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (69 bp):
TTATTACATCAAATAATATCAAAATAAATCAAAAAAATTCTATTTAATTACATAAAATAAACTTA
TATT
Found at i:43112333 original size:25 final size:25
Alignment explanation
Indices: 43112277--43112335 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
43112267 ATCAAAATAA
* * *
43112277 ATCAAAAAAATTTCTATTTTATTAC
1 ATCAAATAAACTTATATTTTATTAC
43112302 ATCAAATAAACTTATATTTTATTAC
1 ATCAAATAAACTTATATTTTATTAC
43112327 ATCAAATAA
1 ATCAAATAA
43112336 TATCAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (25 bp):
ATCAAATAAACTTATATTTTATTAC
Found at i:43114146 original size:11 final size:12
Alignment explanation
Indices: 43114132--43114174 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
43114122 TTAAATATGG
43114132 ATTTGAGA-GAA
1 ATTTGAGAGGAA
43114143 ATTTTGA-AGGAA
1 A-TTTGAGAGGAA
43114155 A-TTGAGAGGAA
1 ATTTGAGAGGAA
43114166 ATTTGAGAG
1 ATTTGAGAG
43114175 AGGATTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.14
11 8 0.29
12 16 0.57
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:43116389 original size:55 final size:55
Alignment explanation
Indices: 43116323--43116516 Score: 361
Period size: 55 Copynumber: 3.5 Consensus size: 55
43116313 AAAAATAGAG
43116323 TGTTTATACGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCGAT
1 TGTTTATACGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCGAT
*
43116378 TGTTTATACGTTTAAATCGATTATTATGTTGGAATATAGCTTCTTTTGAATCGAT
1 TGTTTATACGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCGAT
*
43116433 TGTTTATATGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCGAT
1 TGTTTATACGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCGAT
*
43116488 TGTTTATACGTTTAAATCGATTGTTATGT
1 TGTTTATACGTTTAAATCGATTATTATGT
43116517 AGCACATATA
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 134 1.00
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.49
Consensus pattern (55 bp):
TGTTTATACGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCGAT
Found at i:43116640 original size:13 final size:13
Alignment explanation
Indices: 43116618--43116650 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
43116608 AGATATAACT
*
43116618 ATAAATCTCGAAA
1 ATAAACCTCGAAA
43116631 ATAAACCTCGAAA
1 ATAAACCTCGAAA
43116644 ATAAACC
1 ATAAACC
43116651 GTAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.18
Consensus pattern (13 bp):
ATAAACCTCGAAA
Found at i:43116667 original size:8 final size:8
Alignment explanation
Indices: 43116654--43116682 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
43116644 ATAAACCGTA
43116654 AAAAATAT
1 AAAAATAT
43116662 AAAAATAT
1 AAAAATAT
43116670 AAAAATAT
1 AAAAATAT
43116678 AAAAA
1 AAAAA
43116683 GAAAACATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAT
Found at i:43117398 original size:8 final size:9
Alignment explanation
Indices: 43117310--43117438 Score: 73
Period size: 10 Copynumber: 13.4 Consensus size: 9
43117300 ACATGTGACA
43117310 AAAAATTAT
1 AAAAATTAT
43117319 AAAAA--AT
1 AAAAATTAT
*
43117326 AAAAATCAAT
1 AAAAAT-TAT
*
43117336 AAAAGTTAT
1 AAAAATTAT
43117345 AAAAATTATT
1 AAAAATTA-T
**
43117355 AAATTTTAAT
1 AAAAATT-AT
43117365 AAAAATATAATT
1 AAAAAT-T-A-T
* * *
43117377 TAAAATGAA
1 AAAAATTAT
43117386 AAAAATTAT
1 AAAAATTAT
43117395 AAAAATTAT
1 AAAAATTAT
*
43117404 AAAAAATTGT
1 -AAAAATTAT
*
43117414 AAAATTTTAT
1 AAAA-ATTAT
43117424 AAAAAATTTAT
1 -AAAAA-TTAT
43117435 AAAA
1 AAAA
43117439 TGCATCAAAA
Statistics
Matches: 92, Mismatches: 17, Indels: 21
0.71 0.13 0.16
Matches are distributed among these distances:
7 7 0.08
9 33 0.36
10 34 0.37
11 12 0.13
12 6 0.07
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:43117409 original size:19 final size:19
Alignment explanation
Indices: 43117309--43117438 Score: 81
Period size: 19 Copynumber: 6.7 Consensus size: 19
43117299 AACATGTGAC
43117309 AAAAAATTATAAAAA--AT
1 AAAAAATTATAAAAATTAT
* *
43117326 -AAAAATCAATAAAAGTTAT
1 AAAAAAT-TATAAAAATTAT
**
43117345 -AAAAATTATTAAATTTTAAT
1 AAAAAATTA-TAAAAATT-AT
* * *
43117365 AAAAATATAATTTAAAATGA-
1 AAAAA-ATTA-TAAAAATTAT
43117385 AAAAAATTATAAAAATTAT
1 AAAAAATTATAAAAATTAT
* *
43117404 AAAAAATTGTAAAATTTTAT
1 AAAAAATTATAAAA-ATTAT
43117424 AAAAAATTTATAAAA
1 AAAAAA-TTATAAAA
43117439 TGCATCAAAA
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
16 6 0.07
17 6 0.07
18 8 0.09
19 30 0.34
20 17 0.20
21 12 0.14
22 8 0.09
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAAATTATAAAAATTAT
Found at i:43117623 original size:10 final size:9
Alignment explanation
Indices: 43117608--43117786 Score: 72
Period size: 9 Copynumber: 18.4 Consensus size: 9
43117598 TTTTGGTACG
43117608 ATAATTCTTT
1 ATAATT-TTT
43117618 ATAATTTTT
1 ATAATTTTT
* *
43117627 TTACGAATTTT
1 ATA--ATTTTT
*
43117638 ATATTTCTTT
1 ATAATT-TTT
*
43117648 ATATTTTTT
1 ATAATTTTT
*
43117657 ATAATTTTC
1 ATAATTTTT
*
43117666 ATACGA-CTTT
1 ATA--ATTTTT
43117676 ATAATATTTT
1 ATAAT-TTTT
43117686 ATAATTTTT
1 ATAATTTTT
* *
43117695 CCCTATATTTCT
1 --ATA-ATTTTT
* *
43117707 ACATTTTTTT
1 ATA-ATTTTT
*
43117717 ATATTTTTT
1 ATAATTTTT
*
43117726 ATGATTTTT
1 ATAATTTTT
*
43117735 ATAAAATTTTA
1 AT--AATTTTT
**
43117746 ATTTTTTTT
1 ATAATTTTT
43117755 ATAATTTCTT
1 ATAATTT-TT
**
43117765 ACGATTTTT
1 ATAATTTTT
43117774 ATAATTTTT
1 ATAATTTTT
43117783 ATAA
1 ATAA
43117787 CTTTAATTTA
Statistics
Matches: 126, Mismatches: 30, Indels: 27
0.69 0.16 0.15
Matches are distributed among these distances:
8 1 0.01
9 60 0.48
10 43 0.34
11 17 0.13
12 5 0.04
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:43117693 original size:39 final size:38
Alignment explanation
Indices: 43117608--43117694 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 38
43117598 TTTTGGTACG
* **
43117608 ATAATTCTTTATAATTTTTTTACGAATTTTATATTTCT
1 ATAATTTTTTATAATTTTCATACGAATTTTATATTTCT
* *
43117646 TTATATTTTTTATAATTTTCATACGACTTTATAATATTT-T
1 ATA-ATTTTTTATAATTTTCATACGAATTT-T-ATATTTCT
43117686 ATAATTTTT
1 ATAATTTTT
43117695 CCCTATATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
38 2 0.05
39 28 0.70
40 4 0.10
41 6 0.15
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (38 bp):
ATAATTTTTTATAATTTTCATACGAATTTTATATTTCT
Done.