Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 116 of 214
Found at i:35311810 original size:19 final size:18
Alignment explanation
Indices: 35311788--35311840 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
35311778 TAAAAAATAG
35311788 TTATAAAATTATAGAAAAA
1 TTATAAAATTAT-GAAAAA
*
35311807 TTATAAAA--ATGAGAAA
1 TTATAAAATTATGAAAAA
35311823 TTATAGAAATTATGAAAA
1 TTATA-AAATTATGAAAA
35311841 TTCTACAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 10 0.34
17 5 0.17
19 14 0.48
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (18 bp):
TTATAAAATTATGAAAAA
Found at i:35316321 original size:12 final size:13
Alignment explanation
Indices: 35316304--35316332 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
35316294 GTTTTGATTC
35316304 TTTAATTCTTT-A
1 TTTAATTCTTTAA
35316316 TTTAATTCTTTAA
1 TTTAATTCTTTAA
35316329 TTTA
1 TTTA
35316333 GTGGAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTAATTCTTTAA
Found at i:35328364 original size:20 final size:22
Alignment explanation
Indices: 35328341--35328381 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35328331 AATTAAGGAA
35328341 ATATA-TCAAAAA-TTTAAAAG
1 ATATATTCAAAAATTTTAAAAG
*
35328361 ATATATTTAAAAATTTTAAAA
1 ATATATTCAAAAATTTTAAAA
35328382 AATAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
ATATATTCAAAAATTTTAAAAG
Found at i:35329060 original size:21 final size:21
Alignment explanation
Indices: 35329036--35329092 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
35329026 CTTGAATGTC
35329036 AAGTCTTGAAACTTGACCTAT
1 AAGTCTTGAAACTTGACCTAT
* *
35329057 AAGT-TTTAATACTTAACCTAT
1 AAGTCTTGAA-ACTTGACCTAT
*
35329078 AAGTCTTGAGACTTG
1 AAGTCTTGAAACTTG
35329093 GCTTGTTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 4 0.14
21 22 0.76
22 3 0.10
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (21 bp):
AAGTCTTGAAACTTGACCTAT
Found at i:35331641 original size:44 final size:44
Alignment explanation
Indices: 35331576--35331749 Score: 190
Period size: 44 Copynumber: 3.9 Consensus size: 44
35331566 TGAGTTCAGA
* *
35331576 AAATGAGAAATACCATGGTTGAAAGATA-TCATGGCATTATACCG
1 AAATGAGAAAGACCATAGTTGAAAGATACT-ATGGCATTATACCG
*
35331620 AAATGAGAAAGACCATAGTTGAAAGATACTATGGCATTAAACCG
1 AAATGAGAAAGACCATAGTTGAAAGATACTATGGCATTATACCG
* * * * * * *
35331664 AAATGGGTAAGACCTTAGTTAAAAGATACTACGACACTATACCGG
1 AAATGAGAAAGACCATAGTTGAAAGATACTATGGCATTATACC-G
*
35331709 AAAATGA-ACAAGACCATAGTTGAAAAGATACTATGACATTA
1 -AAATGAGA-AAGACCATAGTTG-AAAGATACTATGGCATTA
35331750 AATATGATTG
Statistics
Matches: 108, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
44 74 0.69
45 2 0.02
46 16 0.15
47 16 0.15
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.22
Consensus pattern (44 bp):
AAATGAGAAAGACCATAGTTGAAAGATACTATGGCATTATACCG
Found at i:35335622 original size:17 final size:17
Alignment explanation
Indices: 35335600--35335662 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
35335590 ATTTAATCAC
35335600 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
** * *
35335617 TACATAAGTCTTTGAATTAC
1 TACATAA---TTAAAAATAT
*
35335637 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
35335654 TACATAATT
1 TACATAATT
35335663 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 21 0.62
20 13 0.38
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:35335840 original size:38 final size:39
Alignment explanation
Indices: 35335796--35335873 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
35335786 ACTTAAGAGT
*
35335796 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
35335834 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
35335873 T
1 T
35335874 TGGGTTGGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 27 0.71
39 11 0.29
ACGTcount: A:0.18, C:0.03, G:0.28, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:35335872 original size:13 final size:13
Alignment explanation
Indices: 35335854--35335878 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35335844 TTTTAGTTTT
35335854 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
35335867 ATTGGGTTGGGT
1 ATTGGGTTGGGT
35335879 TGGATAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:35345396 original size:25 final size:25
Alignment explanation
Indices: 35345368--35345431 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
35345358 ATAGTGCTAA
* *
35345368 ACATAACATTCTTTAAACATAACAT
1 ACATAACATACATTAAACATAACAT
35345393 ACATAACATACATTAAACATAACAT
1 ACATAACATACATTAAACATAACAT
*
35345418 ACATAATATACATT
1 ACATAACATACATT
35345432 CATAAATAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.30
Consensus pattern (25 bp):
ACATAACATACATTAAACATAACAT
Found at i:35345398 original size:9 final size:9
Alignment explanation
Indices: 35345384--35345430 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
35345374 CATTCTTTAA
35345384 ACATAACAT
1 ACATAACAT
35345393 ACATAACAT
1 ACATAACAT
*
35345402 ACATTA-A-
1 ACATAACAT
35345409 ACATAACAT
1 ACATAACAT
*
35345418 ACATAATAT
1 ACATAACAT
35345427 ACAT
1 ACAT
35345431 TCATAAATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 26 0.79
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (9 bp):
ACATAACAT
Found at i:35345606 original size:15 final size:15
Alignment explanation
Indices: 35345586--35345692 Score: 74
Period size: 15 Copynumber: 6.8 Consensus size: 15
35345576 CATAACTATT
35345586 ACATACATAACAACA
1 ACATACATAACAACA
*
35345601 ATATACCATGTAAC-A-A
1 ACATA-CA--TAACAACA
*
35345617 ACATACATAACAATA
1 ACATACATAACAACA
*
35345632 ATATACATAACATACA
1 ACATACATAACA-ACA
*
35345648 TACATAACAATAATAACA
1 -ACAT-AC-ATAACAACA
**
35345666 ACATACATAACAGTA
1 ACATACATAACAACA
*
35345681 ATATACATAACA
1 ACATACATAACA
35345693 TACTTTGGTA
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
13 4 0.05
14 1 0.01
15 35 0.48
16 11 0.15
17 8 0.11
18 9 0.12
19 5 0.07
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.21
Consensus pattern (15 bp):
ACATACATAACAACA
Found at i:35345624 original size:31 final size:28
Alignment explanation
Indices: 35345586--35345692 Score: 111
Period size: 31 Copynumber: 4.0 Consensus size: 28
35345576 CATAACTATT
*
35345586 ACATACATAACAACAATATACCATGTAACAA
1 ACATACATAACAATAATATA-CA--TAACAA
*
35345617 ACATACATAACAATAATATACATAACAT
1 ACATACATAACAATAATATACATAACAA
35345645 ACATACATAAC----A-ATA-ATAAC-A
1 ACATACATAACAATAATATACATAACAA
*
35345666 ACATACATAACAGTAATATACATAACA
1 ACATACATAACAATAATATACATAACA
35345693 TACTTTGGTA
Statistics
Matches: 66, Mismatches: 3, Indels: 17
0.77 0.03 0.20
Matches are distributed among these distances:
21 11 0.17
22 5 0.08
23 3 0.05
24 1 0.02
25 1 0.02
26 3 0.05
27 5 0.08
28 16 0.24
30 2 0.03
31 19 0.29
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.21
Consensus pattern (28 bp):
ACATACATAACAATAATATACATAACAA
Found at i:35345626 original size:79 final size:78
Alignment explanation
Indices: 35345459--35345628 Score: 195
Period size: 79 Copynumber: 2.2 Consensus size: 78
35345449 TACGTAATAT
* * * *
35345459 ACATACATAACAGACATGTTTATAATAGTAATATACCACATAACAGTCACATACATAATAGTAAA
1 ACATACATAACAGACATATTCATAACAGTAATATACCACATAACAGTCACATACATAACAG-AAA
*
35345524 ATACTACAGAACAT
65 ATACTACAGAACAA
* *
35345538 ACA-AGCATAACAGACATATTCATAACAGTAATATACCACATAACTA-TTACATACATAACA-AC
1 ACATA-CATAACAGACATATTCATAACAGTAATATACCACATAAC-AGTCACATACATAACAGAA
35345600 AATA-TACCATGTAACAA
64 AATACTA-CA-G-AACAA
35345617 ACATACATAACA
1 ACATACATAACA
35345629 ATAATATACA
Statistics
Matches: 78, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
76 2 0.03
77 7 0.09
78 2 0.03
79 65 0.83
80 2 0.03
ACGTcount: A:0.51, C:0.20, G:0.06, T:0.24
Consensus pattern (78 bp):
ACATACATAACAGACATATTCATAACAGTAATATACCACATAACAGTCACATACATAACAGAAAA
TACTACAGAACAA
Found at i:35345671 original size:21 final size:22
Alignment explanation
Indices: 35345616--35345695 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 22
35345606 CCATGTAACA
*
35345616 AACATACATAACAATAA-TATACAT
1 AACATACAT-AC-ATAACAATA-AT
35345640 AACATACATACATAACAATAAT
1 AACATACATACATAACAATAAT
*
35345662 AACA-ACATACATAACAGTAAT
1 AACATACATACATAACAATAAT
35345683 ATACATAACATAC
1 A-ACAT-ACATAC
35345696 TTTGGTAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
21 17 0.34
22 13 0.26
23 5 0.10
24 15 0.30
ACGTcount: A:0.57, C:0.19, G:0.01, T:0.23
Consensus pattern (22 bp):
AACATACATACATAACAATAAT
Found at i:35345837 original size:31 final size:29
Alignment explanation
Indices: 35345790--35345858 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 29
35345780 ACGAATGCCA
35345790 ACAAAAAAAAAATTGAAGTAAGATATAAT
1 ACAAAAAAAAAATTGAAGTAAGATATAAT
* **
35345819 ACGAATAAAAAAATTTGAAGTCTGATATAAT
1 AC-AA-AAAAAAAATTGAAGTAAGATATAAT
35345850 ACAAAAAAA
1 ACAAAAAAA
35345859 TACAAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.20
30 4 0.11
31 24 0.69
ACGTcount: A:0.62, C:0.06, G:0.10, T:0.22
Consensus pattern (29 bp):
ACAAAAAAAAAATTGAAGTAAGATATAAT
Found at i:35345983 original size:55 final size:58
Alignment explanation
Indices: 35345884--35345992 Score: 136
Period size: 55 Copynumber: 1.9 Consensus size: 58
35345874 ATATCAAACC
* *
35345884 AGAAAAATTTGTTTTCCCAAACCCTAAACAAAAAAAACTAAATGTTCC-AAAAAGAAT
1 AGAAAAATTTGTTTTCCCAAACCATAAACAAAAAAAACCAAATGTTCCTAAAAAGAAT
* * *
35345941 AGAAAAA-TTG-TTTCCCTAAACCATATAC-CAAAAAACCGAATGTTCCTAAAAA
1 AGAAAAATTTGTTTTCCC-AAACCATAAACAAAAAAAACCAAATGTTCCTAAAAA
35345993 ATTGTCAGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
55 21 0.47
56 17 0.38
57 7 0.16
ACGTcount: A:0.50, C:0.19, G:0.07, T:0.23
Consensus pattern (58 bp):
AGAAAAATTTGTTTTCCCAAACCATAAACAAAAAAAACCAAATGTTCCTAAAAAGAAT
Found at i:35360407 original size:40 final size:40
Alignment explanation
Indices: 35360313--35360484 Score: 294
Period size: 40 Copynumber: 4.3 Consensus size: 40
35360303 GGACTAAGAT
35360313 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGT-
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
35360352 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
35360392 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
35360432 CCGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTC
35360472 CCGAAGGCATTTG
1 CCGAAGGCATTTG
35360485 AACGAGGAGC
Statistics
Matches: 128, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
39 39 0.30
40 87 0.68
41 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:35360507 original size:79 final size:79
Alignment explanation
Indices: 35360299--35360484 Score: 295
Period size: 79 Copynumber: 2.3 Consensus size: 79
35360289 AAGTGACAAT
*
35360299 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATT
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATT
*
35360363 TGTGCGAGTTACTAA
65 TGTGCGAATTACTAA
*
35360378 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGT-CCGAAGGCATT
35360443 TGTGCGAATTACTATA
65 TGTGCGAATTACTA-A
*
35360459 A-CCGGGCTATGTCCCGAAGGCATTTG
1 ATCCGGGCTAAGTCCCGAAGGCATTTG
35360485 AACGAGGAGC
Statistics
Matches: 99, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
78 1 0.01
79 49 0.49
80 47 0.47
81 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTT
GTGCGAATTACTAA
Found at i:35368448 original size:40 final size:40
Alignment explanation
Indices: 35368210--35368434 Score: 307
Period size: 40 Copynumber: 5.7 Consensus size: 40
35368200 TTGAATGCTG
* * *
35368210 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
**
35368249 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
35368289 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
35368329 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
35368369 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
35368410 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
35368435 AACGAGGAGC
Statistics
Matches: 172, Mismatches: 8, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
39 19 0.11
40 143 0.83
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:35368452 original size:120 final size:119
Alignment explanation
Indices: 35368210--35368467 Score: 294
Period size: 120 Copynumber: 2.2 Consensus size: 119
35368200 TTGAATGCTG
*
35368210 TCCGGGCTAAGTCCCGAAGGCTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATTTG
* * ** *
35368275 TGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
66 TGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAA
* * **
35368329 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGCA
* *
35368391 TTTGTGCGAATTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
62 TTTGTGCGAATTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAA
* *
35368449 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
35368468 TACGTGATTT
Statistics
Matches: 119, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
119 36 0.30
120 73 0.61
121 10 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATTTG
TGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAA
Found at i:35375554 original size:28 final size:29
Alignment explanation
Indices: 35375514--35375580 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 29
35375504 AATTTAAAAC
* * *
35375514 GAGAAAGTTGAGAGA-CTTGAGAGGGTTT
1 GAGAGAGTTGAGAGAGCTTGAGAGAGTTG
*
35375542 GAGAGAGTTGAGAGAGTTTGAGAGAGTTG
1 GAGAGAGTTGAGAGAGCTTGAGAGAGTTG
35375571 GA-AGAGTTGA
1 GAGAGAGTTGA
35375581 AAGAAGGATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 22 0.65
29 12 0.35
ACGTcount: A:0.33, C:0.01, G:0.42, T:0.24
Consensus pattern (29 bp):
GAGAGAGTTGAGAGAGCTTGAGAGAGTTG
Found at i:35375578 original size:19 final size:19
Alignment explanation
Indices: 35375521--35375570 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
35375511 AACGAGAAAG
* *
35375521 TTGAGAGACTTGAGAGGGT
1 TTGAGAGAGTTGAGAGAGT
35375540 TTGAGAGAGTTGAGAGAGT
1 TTGAGAGAGTTGAGAGAGT
35375559 TTGAGAGAGTTG
1 TTGAGAGAGTTG
35375571 GAAGAGTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.28, C:0.02, G:0.42, T:0.28
Consensus pattern (19 bp):
TTGAGAGAGTTGAGAGAGT
Found at i:35375584 original size:9 final size:9
Alignment explanation
Indices: 35375514--35375580 Score: 73
Period size: 9 Copynumber: 7.2 Consensus size: 9
35375504 AATTTAAAAC
*
35375514 GAGAAAGTT
1 GAGAGAGTT
*
35375523 GAGAGACTT
1 GAGAGAGTT
*
35375532 GAGAGGGTTT
1 GAGAGAG-TT
35375542 GAGAGAGTT
1 GAGAGAGTT
35375551 GAGAGAGTTT
1 GAGAGAG-TT
35375561 GAGAGAGTT
1 GAGAGAGTT
35375570 G-GAAGAGTT
1 GAG-AGAGTT
35375579 GA
1 GA
35375581 AAGAAGGATG
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
8 1 0.02
9 31 0.63
10 17 0.35
ACGTcount: A:0.33, C:0.01, G:0.42, T:0.24
Consensus pattern (9 bp):
GAGAGAGTT
Found at i:35381337 original size:27 final size:26
Alignment explanation
Indices: 35381306--35381516 Score: 217
Period size: 27 Copynumber: 7.9 Consensus size: 26
35381296 TCATCTTCTA
**
35381306 GGGGTATAACAGTCATTTTACCCTAT
1 GGGGTATTTCAGTCATTTTACCCTAT
* *
35381332 GAGGGTATTTCGGTCATTTTACCCCAT
1 G-GGGTATTTCAGTCATTTTACCCTAT
* *
35381359 GGGGTATTTCACTCATTCTACCCTAT
1 GGGGTATTTCAGTCATTTTACCCTAT
*
35381385 GGGGGTATTCCAGTCATTTTACCCTAT
1 -GGGGTATTTCAGTCATTTTACCCTAT
35381412 GGGGATATTTCAGTCATTTTACCCTAT
1 GGGG-TATTTCAGTCATTTTACCCTAT
* * *
35381439 AGGGGTATTTCGGTTATTTTATCCTAT
1 -GGGGTATTTCAGTCATTTTACCCTAT
* *
35381466 GGGGGTATTTC-GCTCATTTTATCTTAT
1 -GGGGTATTTCAG-TCATTTTACCCTAT
** *
35381493 GGGGGTATTTTGGTTATTTTACCC
1 -GGGGTATTTCAGTCATTTTACCC
35381517 ATTTTAGGGT
Statistics
Matches: 157, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
26 27 0.17
27 125 0.80
28 5 0.03
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (26 bp):
GGGGTATTTCAGTCATTTTACCCTAT
Found at i:35381444 original size:54 final size:53
Alignment explanation
Indices: 35381306--35381516 Score: 253
Period size: 54 Copynumber: 3.9 Consensus size: 53
35381296 TCATCTTCTA
** * *
35381306 GGGGTATAACAGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCCAT
1 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT
* * * *
35381359 GGGGTATTTCACTCATTCTACCCTATGGGGGTATTCCAGTCATTTTACCCTAT
1 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT
* * *
35381412 GGGGATATTTCAGTCATTTTACCCTATAGGGGTATTTCGGTTATTTTATCCTAT
1 GGGG-TATTTCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT
* * * *
35381466 GGGGGTATTTC-GCTCATTTTATCTTATGGGGGTATTTTGGTTATTTTACCC
1 -GGGGTATTTCAG-TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCC
35381517 ATTTTAGGGT
Statistics
Matches: 135, Mismatches: 20, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 50 0.37
54 81 0.60
55 4 0.03
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (53 bp):
GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT
Found at i:35381494 original size:81 final size:79
Alignment explanation
Indices: 35381306--35381516 Score: 244
Period size: 81 Copynumber: 2.6 Consensus size: 79
35381296 TCATCTTCTA
**
35381306 GGGGTATAACAGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCCATGGGGTATTTCAC
1 GGGGTATTCCAGTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCCATGGGGTATTTCAC
35381371 TCATTCTACCCTATG
65 TCATTCTACCCTATG
* * *
35381386 GGGGTATTCCAGTCATTTTACCCTATGGGGATATTTCAGTCATTTTACCCTATAGGGGTATTTCG
1 GGGGTATTCCAGTCATTTTACCCTATGGGG-TATTTCGGTCATTTTACCCCAT-GGGGTATTTCA
* * * *
35381451 GTTATTTTATCCTATG
64 CTCATTCTACCCTATG
* * * * *
35381467 GGGGTATTTC-GCTCATTTTATCTTATGGGGGTATTTTGGTTATTTTACCC
1 GGGGTATTCCAG-TCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCC
35381517 ATTTTAGGGT
Statistics
Matches: 112, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
79 3 0.03
80 46 0.41
81 59 0.53
82 4 0.04
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (79 bp):
GGGGTATTCCAGTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCCCATGGGGTATTTCACT
CATTCTACCCTATG
Found at i:35383901 original size:29 final size:29
Alignment explanation
Indices: 35383838--35383905 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
35383828 TAATCAACCG
*
35383838 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
35383867 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
35383896 CGCACACTTA
1 CGCACACTTA
35383906 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:35384075 original size:29 final size:29
Alignment explanation
Indices: 35384012--35384079 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
35384002 TAATCAACCA
35384012 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
35384041 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
35384070 CGCACACTTA
1 CGCACACTTA
35384080 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:35384249 original size:29 final size:29
Alignment explanation
Indices: 35384186--35384253 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
35384176 TAATCAACCG
35384186 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
35384215 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
35384244 CGCACACTTA
1 CGCACACTTA
35384254 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:35384394 original size:29 final size:30
Alignment explanation
Indices: 35384355--35384433 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
35384345 CTTAATAATC
35384355 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
35384385 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
35384414 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
35384434 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:35384427 original size:174 final size:174
Alignment explanation
Indices: 35383727--35384402 Score: 1280
Period size: 174 Copynumber: 3.9 Consensus size: 174
35383717 AACTCAAGGT
* *
35383727 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
35383792 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
35383857 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
35383901 ACTTACCTTTTCCGCTGTCCAAAATCAACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
35383966 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
35384031 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
35384075 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
35384140 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
35384205 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
35384249 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCGTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
35384314 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
35384379 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
35384403 TGTACAATTT
Statistics
Matches: 492, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 492 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:35392393 original size:29 final size:29
Alignment explanation
Indices: 35392330--35392397 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
35392320 TAATCAACCG
*
35392330 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
35392359 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
35392388 CGCACACTTA
1 CGCACACTTA
35392398 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:35392510 original size:174 final size:174
Alignment explanation
Indices: 35392219--35392837 Score: 1175
Period size: 174 Copynumber: 3.6 Consensus size: 174
35392209 AACTCAAGGT
* *
35392219 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
35392284 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
35392349 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
35392393 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
35392458 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
35392523 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
35392567 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
35392632 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
35392697 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
35392741 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCATTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
35392806 GAAAATATATATTGCGTTCGCACACTTAGTGC
66 GAAAATATATATTGGGTTCGCACACATAGTGC
35392838 CATGTACTTT
Statistics
Matches: 437, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 437 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:35392567 original size:29 final size:29
Alignment explanation
Indices: 35392504--35392571 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
35392494 TAATCAACCA
35392504 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
35392533 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
35392562 CGCACACTTA
1 CGCACACTTA
35392572 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:35392741 original size:29 final size:29
Alignment explanation
Indices: 35392678--35392745 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
35392668 TAATCAACCG
35392678 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
35392707 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
35392736 CGCACACTTA
1 CGCACACTTA
35392746 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:35392865 original size:29 final size:30
Alignment explanation
Indices: 35392823--35392897 Score: 111
Period size: 29 Copynumber: 2.6 Consensus size: 30
35392813 TATATTGCGT
35392823 TCGCACACTTAGTGCCATGTAC-TTTAAAC
1 TCGCACACTTAGTGCCATGTACATTTAAAC
35392852 TCGCACACTTAGTG-C-TGTACAATTTAAAC
1 TCGCACACTTAGTGCCATGTAC-ATTTAAAC
*
35392881 CCGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
35392898 ATCTCATGAC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 34 0.83
30 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (30 bp):
TCGCACACTTAGTGCCATGTACATTTAAAC
Found at i:35401055 original size:12 final size:12
Alignment explanation
Indices: 35401038--35401071 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35401028 TTAGAGCAAT
35401038 TGCAAGAACAGA
1 TGCAAGAACAGA
**
35401050 TGCAAGCCCAGA
1 TGCAAGAACAGA
35401062 TGCAAGAACA
1 TGCAAGAACA
35401072 ACTAGAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.09
Consensus pattern (12 bp):
TGCAAGAACAGA
Found at i:35403324 original size:5 final size:5
Alignment explanation
Indices: 35403311--35403352 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
35403301 AAGAATGTTC
* *
35403311 AAAAA AAAAG AAAAG AAAA- AATA- AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
35403353 AGGAGAGGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
4 6 0.18
5 27 0.82
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:35403338 original size:18 final size:17
Alignment explanation
Indices: 35403311--35403353 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 17
35403301 AAGAATGTTC
35403311 AAAAAAAAAGAAAAGAA
1 AAAAAAAAAGAAAAGAA
35403328 AAAATAAAAAGAAAAGAA
1 AAAA-AAAAAGAAAAGAA
35403346 AAGAAAAA
1 AA-AAAAA
35403354 GGAGAGGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.17
18 18 0.75
19 2 0.08
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAGAAAAGAA
Found at i:35403342 original size:23 final size:22
Alignment explanation
Indices: 35403311--35403353 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
35403301 AAGAATGTTC
35403311 AAAAAAAAAGAAAAGAAAAAAT
1 AAAAAAAAAGAAAAGAAAAAAT
35403333 AAAAAGAAAAGAAAAGAAAAA
1 AAAAA-AAAAGAAAAGAAAAA
35403354 GGAGAGGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAGAAAAGAAAAAAT
Found at i:35403819 original size:108 final size:108
Alignment explanation
Indices: 35403628--35403829 Score: 314
Period size: 108 Copynumber: 1.9 Consensus size: 108
35403618 TTCATCTTAT
* * * *
35403628 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTTTGCACTCAATAAAATTC
1 TATCTTAGCAAAATTTGCTATATTAATTAATTTATTCATTTCGAGCCTTACACTCAATAAAATTC
35403693 CATCTTATCCATTATGATAATATTTTTCATCTTATTCAGTTCG
66 CATCTTATCCATTATGATAATATTTTTCATCTTATTCAGTTCG
* **
35403736 TATCTTAGCAAAATTTGCTATATTAATTAATTTATTCATTTTGAGCCTTATTCTCAATAAAATTC
1 TATCTTAGCAAAATTTGCTATATTAATTAATTTATTCATTTCGAGCCTTACACTCAATAAAATTC
* * *
35403801 CATCTTGTCCATTTTGATAATCTTTTTCA
66 CATCTTATCCATTATGATAATATTTTTCA
35403830 AGCATATTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
108 84 1.00
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (108 bp):
TATCTTAGCAAAATTTGCTATATTAATTAATTTATTCATTTCGAGCCTTACACTCAATAAAATTC
CATCTTATCCATTATGATAATATTTTTCATCTTATTCAGTTCG
Found at i:35404342 original size:24 final size:24
Alignment explanation
Indices: 35404297--35404351 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
35404287 ATGTCCCAAA
*
35404297 ATTACAGTGGACTTAACCTTGAAG
1 ATTACAGCGGACTTAACCTTGAAG
*
35404321 ATTACAGCGGA-TTGAACTTTGAAG
1 ATTACAGCGGACTT-AACCTTGAAG
35404345 ATTACAG
1 ATTACAG
35404352 TGGGGGCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (24 bp):
ATTACAGCGGACTTAACCTTGAAG
Found at i:35405034 original size:44 final size:44
Alignment explanation
Indices: 35404985--35405284 Score: 166
Period size: 44 Copynumber: 6.8 Consensus size: 44
35404975 AAGCACCAGC
* * *
35404985 CTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTGTAGAT
1 CTTATCTCCCTGAGGAGCAGTGGAGCAGATCGAAGATTGTAGAT
* * * * * *
35405029 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAAT
1 CTTATCTCCCTGAGGAGCAGTGGAGCAGATCGAAGATTGTAGAT
* * ** *****
35405073 CTTATCTTCCC--AAGA-TAGTAGGAAGCAGATTTAAGCCACCAG-T
1 CTTATC-TCCCTGAGGAGCAGT-GG-AGCAGATCGAAGATTGTAGAT
* * * * *
35405116 CCTATCTCCCTGAGTAGCAGTGGAGTAGGTCAAAGATTGTAGAT
1 CTTATCTCCCTGAGGAGCAGTGGAGCAGATCGAAGATTGTAGAT
* * * * * *
35405160 CTTGTCTTCCTGTACTG-GCAGTGAAGCAGATCGAAAGCA--CTAG-C
1 CTTATCTCCCTG-A-GGAGCAGTGGAGCAGATCG-AAG-ATTGTAGAT
* * *
35405204 CTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTGTAGAT
1 CTTATCTCCCTGAGGAGCAGTGGAGCAGATCGAAGATTGTAGAT
* * *
35405248 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT
1 CTTATCTCCCTGAGGAGCAGTGGAGCAGATCGAAGAT
35405285 GGCGAATCTT
Statistics
Matches: 184, Mismatches: 57, Indels: 30
0.68 0.21 0.11
Matches are distributed among these distances:
41 1 0.01
42 12 0.07
43 36 0.20
44 108 0.59
45 23 0.12
46 3 0.02
47 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (44 bp):
CTTATCTCCCTGAGGAGCAGTGGAGCAGATCGAAGATTGTAGAT
Found at i:35405143 original size:219 final size:219
Alignment explanation
Indices: 35404680--35405652 Score: 1537
Period size: 219 Copynumber: 4.5 Consensus size: 219
35404670 CATCATATCA
* * *
35404680 AGTCTTATCTCCCTGAGCAGCAATGGAGTAGGTCGAAGATTGCAGATCTTGTCTTCCTGTACTGG
1 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG
* * * *
35404745 CAGTGAAGTAGATTGAAAGCACCACCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTG
66 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG
* * * *
35404810 CAG-----ATCTCCCTAAGAAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGAT
131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT
35404870 AGTAGGAAGCAGATTTAAGCCACC
196 AGTAGGAAGCAGATTTAAGCCACC
* *
35404894 AGTCCTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTATAGATCTTGTCTTCCTGTACTGG
1 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG
*
35404959 CAGTGAAGCAGATCAAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG
66 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG
*
35405024 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTCCCAAGAT
131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT
35405089 AGTAGGAAGCAGATTTAAGCCACC
196 AGTAGGAAGCAGATTTAAGCCACC
* *
35405113 AGTCCTATCTCCCTGAGTAGCAGTGGAGTAGGTCAAAGATTGTAGATCTTGTCTTCCTGTACTGG
1 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG
*
35405178 CAGTGAAGCAGATCGAAAGCACTAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG
66 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG
*
35405243 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGAT
131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT
*
35405308 AGTAGGAAGTAGATTTAAGCCACC
196 AGTAGGAAGCAGATTTAAGCCACC
* *
35405332 AGTCCTATCTCCCTGAGCAGCAGCGAAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG
1 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG
* * * *
35405397 CAGTGAAGCAGATCAAAAGCACCAGCCTTATCTCCCTGAGGAGTAGTGGGGTAGATTGAAGATTG
66 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG
* * ** *
35405462 TAGATCTTATCTCCCGAGGCAGTAGTGGAGCAGATTAAAGATGGCGAATCTTATCTTCCCAAGGT
131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT
* **
35405527 AGTAGGGAAGTAGATTTAAGCCATT
196 AGTA-GGAAGCAGATTTAAGCCACC
* * *
35405552 AG-CCTTATCTCCCTAAGCAGCAGTGGAGTAGGTCGATGATTGTAGATCTTGTCTTCCTGTATTG
1 AGTCC-TATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTG
*
35405616 GCAGTGAAGCAGATTGAAAGCACCAGCCTTATC-CCCT
65 GCAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCT
35405653 AAATTTGCAG
Statistics
Matches: 704, Mismatches: 48, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
214 122 0.17
219 477 0.68
220 105 0.15
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (219 bp):
AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG
CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG
TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT
AGTAGGAAGCAGATTTAAGCCACC
Found at i:35405298 original size:88 final size:88
Alignment explanation
Indices: 35405118--35405281 Score: 206
Period size: 88 Copynumber: 1.9 Consensus size: 88
35405108 CCACCAGTCC
* * * * *
35405118 TATCTCCCTGAGTAGCAGTGGAGTAGGTCAAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTG
1 TATCTCCCTGAGGAGCAGTGGAGTAGGTCAAAGATTGTAGATCTTATCTCCCTGAACTAGCAGTG
* *
35405183 AAGCAGATCGAAAGCACTAGCCT
66 AAGCAGATCGAAAGCACGAACCT
** *
35405206 TATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCT-AAGC-AGTAGT
1 TATCTCCCTGAGGAGCAGTGGAGTAGGTCAAAGATTGTAGATCTTATCTCCCTGAA-CTAGCAGT
*
35405269 GGAGCAGATCGAA
65 GAAGCAGATCGAA
35405282 GATGGCGAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
87 17 0.26
88 49 0.74
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (88 bp):
TATCTCCCTGAGGAGCAGTGGAGTAGGTCAAAGATTGTAGATCTTATCTCCCTGAACTAGCAGTG
AAGCAGATCGAAAGCACGAACCT
Found at i:35405513 original size:44 final size:43
Alignment explanation
Indices: 35405423--35405531 Score: 112
Period size: 44 Copynumber: 2.4 Consensus size: 43
35405413 AAGCACCAGC
* * * * *
35405423 CTTATCTCCCTGAGGAGTAGTGGGGTAGATTGAAGATTGTAGAT
1 CTTATCTCCC-GAGGAGTAGTGGAGCAGATTAAAGATGGGAGAT
35405467 CTTATCTCCCGAGGCAGTAGTGGAGCAGATTAAAGATGGCGA-AT
1 CTTATCTCCCGAGG-AGTAGTGGAGCAGATTAAAGATGG-GAGAT
*
35405511 CTTATCTTCCCAAGGTAGTAG
1 CTTATC-TCCCGAGG-AGTAG
35405532 GGAAGTAGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
43 4 0.07
44 38 0.69
45 13 0.24
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (43 bp):
CTTATCTCCCGAGGAGTAGTGGAGCAGATTAAAGATGGGAGAT
Found at i:35407652 original size:48 final size:52
Alignment explanation
Indices: 35407576--35407673 Score: 125
Period size: 48 Copynumber: 2.0 Consensus size: 52
35407566 ATACCCGTAG
* * *
35407576 ATATTTTTATAACTTATTTATAATATATATATATAC-CTTCTTATATATATAC
1 ATATTTTTATAACTTATTCATAATATATATAGATACAC-ACTTATATATATAC
35407628 ATATTTTT-TAA-TT-TTCATAA-ATATATAGATACACACTTATATATAT
1 ATATTTTTATAACTTATTCATAATATATATAGATACACACTTATATATAT
35407674 TCTTTAGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
48 22 0.52
49 7 0.17
50 2 0.05
51 3 0.07
52 8 0.19
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (52 bp):
ATATTTTTATAACTTATTCATAATATATATAGATACACACTTATATATATAC
Found at i:35407932 original size:18 final size:18
Alignment explanation
Indices: 35407891--35407929 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
35407881 TTATTTTATT
*
35407891 TTTATTTTTATAATTTTA
1 TTTATTTTCATAATTTTA
*
35407909 TTTATTTTCATTATTGTTA
1 TTTATTTTCATAATT-TTA
35407928 TT
1 TT
35407930 ATTGTCTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTATTTTCATAATTTTA
Found at i:35410445 original size:15 final size:16
Alignment explanation
Indices: 35410419--35410450 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
35410409 AATTTCTATA
35410419 TAATCAAGTTAAAATT
1 TAATCAAGTTAAAATT
35410435 TAATC-AGTTAAAATT
1 TAATCAAGTTAAAATT
35410450 T
1 T
35410451 GATATTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (16 bp):
TAATCAAGTTAAAATT
Found at i:35410921 original size:27 final size:27
Alignment explanation
Indices: 35410882--35410959 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 27
35410872 TCATGTTAGC
*
35410882 AATTAATTAATTTTTTAAAATT-AAAA
1 AATTAATAAATTTTTTAAAATTCAAAA
*
35410908 AATTACATAAATTTTTTAGAAATTCAAAG
1 AATTA-ATAAATTTTTTA-AAATTCAAAA
* * *
35410937 AAGTATATATATATTTTAAAATT
1 AATTA-ATAAATTTTTTAAAATT
35410960 TAAATAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
26 5 0.12
27 11 0.26
28 10 0.23
29 17 0.40
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (27 bp):
AATTAATAAATTTTTTAAAATTCAAAA
Found at i:35410978 original size:21 final size:21
Alignment explanation
Indices: 35410949--35411024 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 21
35410939 GTATATATAT
*
35410949 ATTTTAAAATTTAAATAAAAA
1 ATTTAAAAATTTAAATAAAAA
* *
35410970 ATTTCAAAATTCAGAA-AAAATA
1 ATTTAAAAATTTA-AATAAAA-A
*
35410992 ATTTAAAAGCATATAAATAAAAAA
1 ATTTAAAA--ATTTAAAT-AAAAA
*
35411016 ATATAAAAA
1 ATTTAAAAA
35411025 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
21 15 0.35
22 11 0.26
23 2 0.05
24 11 0.26
25 4 0.09
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (21 bp):
ATTTAAAAATTTAAATAAAAA
Found at i:35417338 original size:43 final size:41
Alignment explanation
Indices: 35417246--35417394 Score: 149
Period size: 43 Copynumber: 3.6 Consensus size: 41
35417236 GTTACTCTGT
* * *
35417246 GGAATCAGCACTTAACAACCACC-TTATATTC-AGTGATACGG
1 GGAATCAGCACTTAGCAACC-CCTTTACAATCAAG-GATACGG
* *
35417287 GAAATCAGCACATAGCAACCCCTTTCACAATCAAGGATACGG
1 GGAATCAGCACTTAGCAACCCCTTT-ACAATCAAGGATACGG
* ** *
35417329 TGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGG
1 -GGAATCAGCACTTAGCAACC-CCTTTACAATCAAGGATACGG
*
35417372 GGAATCAACACTTAGCAACCCCT
1 GGAATCAGCACTTAGCAACCCCT
35417395 CAAGGAATTT
Statistics
Matches: 91, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
40 2 0.02
41 22 0.24
42 30 0.33
43 32 0.35
44 5 0.05
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (41 bp):
GGAATCAGCACTTAGCAACCCCTTTACAATCAAGGATACGG
Found at i:35417386 original size:42 final size:42
Alignment explanation
Indices: 35417246--35417391 Score: 161
Period size: 42 Copynumber: 3.5 Consensus size: 42
35417236 GTTACTCTGT
* * * *
35417246 GGAATCAGCACTTAACAACCACC-TTATATTCAGTGATACGG
1 GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG
* * *
35417287 GAAATCAGCACATAGCAACC-CCTTTCACAATCAAGGATACGG
1 GGAATCAGCACTTAGCAACCACCTTT-ACAATCAATGATACGG
* * *
35417329 TGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGG
1 -GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG
*
35417372 GGAATCAACACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
35417392 CCTCAAGGAA
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
40 2 0.02
41 19 0.22
42 31 0.36
43 30 0.34
44 5 0.06
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.21
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG
Found at i:35424146 original size:30 final size:30
Alignment explanation
Indices: 35424108--35424273 Score: 117
Period size: 30 Copynumber: 5.5 Consensus size: 30
35424098 TTCAACTATC
35424108 AATTATGAAAAGGGATGGTGATGACCATCA
1 AATTATGAAAAGGGATGGTGATGACCATCA
* * * *
35424138 ACTTATGAAAAGGGATGGCT--TCGGCTAT-T
1 AATTATGAAAAGGGATGG-TGAT-GACCATCA
* * * * *
35424167 GATATCTGAAAAGGGATGGCT-TTGGCTATCA
1 AAT-TATGAAAAGGGATGG-TGATGACCATCA
*
35424198 AATTATGAAAAGGAATGGTGATGACCATCA
1 AATTATGAAAAGGGATGGTGATGACCATCA
** * *
35424228 AAAAAT-AGAAAGGAATGGTGAAGACCATCA
1 AATTATGA-AAAGGGATGGTGATGACCATCA
*
35424258 AATTATGAAAATGGAT
1 AATTATGAAAAGGGAT
35424274 AGCTTCAGCT
Statistics
Matches: 107, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
29 4 0.04
30 98 0.92
31 5 0.05
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (30 bp):
AATTATGAAAAGGGATGGTGATGACCATCA
Found at i:35424256 original size:120 final size:120
Alignment explanation
Indices: 35424116--35424333 Score: 294
Period size: 120 Copynumber: 1.8 Consensus size: 120
35424106 TCAATTATGA
* * * * * * *
35424116 AAAGGGATGGTGATGACCATCAACTTATGAAAAGGGATGGCTTCGGCTATTGATA-TCTGAAAAG
1 AAAGGAATGGTGAAGACCATCAAATTATGAAAAGGGATAGCTTCAGCTATCGA-ACTATGAAAAG
** * *
35424180 GGATGGCTTTGGCTATCAAATTATGAAAAGGAATGGTGATGACCATCAAAAAATAG
65 GGATAACTTCGGCTATCAAATTACGAAAAGGAATGGTGATGACCATCAAAAAATAG
*
35424236 AAAGGAATGGTGAAGACCATCAAATTATGAAAATGGATAGCTTCAGCTATCGAACTATGAAAAGG
1 AAAGGAATGGTGAAGACCATCAAATTATGAAAAGGGATAGCTTCAGCTATCGAACTATGAAAAGG
* *
35424301 GATAACTTCGGTTATCGAATTACGAAAAGGAAT
66 GATAACTTCGGCTATCAAATTACGAAAAGGAAT
35424334 ATGTCAACCA
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
119 1 0.01
120 82 0.99
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (120 bp):
AAAGGAATGGTGAAGACCATCAAATTATGAAAAGGGATAGCTTCAGCTATCGAACTATGAAAAGG
GATAACTTCGGCTATCAAATTACGAAAAGGAATGGTGATGACCATCAAAAAATAG
Found at i:35424297 original size:30 final size:30
Alignment explanation
Indices: 35424261--35424330 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
35424251 ACCATCAAAT
* *
35424261 TATGAAAATGGATAGCTTCAGCTATCGAAC
1 TATGAAAAGGGATAACTTCAGCTATCGAAC
* * *
35424291 TATGAAAAGGGATAACTTCGGTTATCGAAT
1 TATGAAAAGGGATAACTTCAGCTATCGAAC
*
35424321 TACGAAAAGG
1 TATGAAAAGG
35424331 AATATGTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.26
Consensus pattern (30 bp):
TATGAAAAGGGATAACTTCAGCTATCGAAC
Found at i:35424300 original size:60 final size:59
Alignment explanation
Indices: 35424083--35424303 Score: 166
Period size: 60 Copynumber: 3.7 Consensus size: 59
35424073 TCATCAACGA
* *
35424083 ATGAAAATGGATAGCTTCAACTATC-AATTATGAAAAGGGATGGTGATGACCATCAACTT
1 ATGAAAATGGATAGCTTCAGCTATCGAA-TATGAAAAGGGATGGTGATGACCATCAAATT
* * * * * * * *
35424142 ATGAAAAGGGATGGCTTCGGCTATTGATATCTGAAAAGGGATGGCT-TTGGCTATCAAATT
1 ATGAAAATGGATAGCTTCAGCTATCGA-ATATGAAAAGGGATGG-TGATGACCATCAAATT
* * * * * * *
35424202 ATGAAAA-GGA-ATG-GTGATGACCATCAAAAAAT-AGAAAGGAATGGTGAAGACCATCAAATT
1 ATGAAAATGGATA-GCTTCA-G-CTATC-GAATATGA-AAAGGGATGGTGATGACCATCAAATT
35424262 ATGAAAATGGATAGCTTCAGCTATCGAACTATGAAAAGGGAT
1 ATGAAAATGGATAGCTTCAGCTATCGAA-TATGAAAAGGGAT
35424304 AACTTCGGTT
Statistics
Matches: 118, Mismatches: 30, Indels: 27
0.67 0.17 0.15
Matches are distributed among these distances:
58 1 0.01
59 29 0.25
60 76 0.64
61 9 0.08
62 3 0.03
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (59 bp):
ATGAAAATGGATAGCTTCAGCTATCGAATATGAAAAGGGATGGTGATGACCATCAAATT
Found at i:35427011 original size:51 final size:51
Alignment explanation
Indices: 35426952--35427142 Score: 194
Period size: 51 Copynumber: 3.8 Consensus size: 51
35426942 AACTATTATC
35426952 ATTCGATACACGTAGTAGCCTTA-ACATAGTACTACACACGTGATCATTAAT
1 ATTCGATACACGTAGTAGCC-TACACATAGTACTACACACGTGATCATTAAT
* * *
35427003 ATTCGATACACGTAGTAGCCTGCACATAGTACTACACACATGATCGA--AGCT
1 ATTCGATACACGTAGTAGCCTACACATAGTACTACACACGTGATC-ATTA-AT
* * * * * * * *
35427054 A-TCTGGTACGCATAGTAGCCTACACATAGTACTACACATGCGACCTTTCAT
1 ATTC-GATACACGTAGTAGCCTACACATAGTACTACACACGTGATCATTAAT
* *
35427105 -TCCGGTACACGTAGTAGCCTACACATAGTACTACACAC
1 ATTCGATACACGTAGTAGCCTACACATAGTACTACACAC
35427143 TTGACCATCA
Statistics
Matches: 115, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
50 36 0.31
51 78 0.68
52 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (51 bp):
ATTCGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCATTAAT
Found at i:35436308 original size:43 final size:43
Alignment explanation
Indices: 35436261--35436344 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
35436251 TATGTGATTT
35436261 ATATTGAAATGGAAAAA-ATGAAAAATGAATATGAGATGAGAAA
1 ATATTGAAAT-GAAAAATATGAAAAATGAATATGAGATGAGAAA
* *
35436304 ATATTGAAATGAAAAATATGATAAATGATTATGAGATGAGA
1 ATATTGAAATGAAAAATATGAAAAATGAATATGAGATGAGA
35436345 TATGAGATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 6 0.16
43 32 0.84
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (43 bp):
ATATTGAAATGAAAAATATGAAAAATGAATATGAGATGAGAAA
Found at i:35436319 original size:15 final size:16
Alignment explanation
Indices: 35436276--35436331 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
35436266 GAAATGGAAA
35436276 AAATGAAAAATGAATATG
1 AAATGAAAAAT--ATATG
*
35436294 AGATGAGAAAATAT-TG
1 AAATGA-AAAATATATG
35436310 AAATGAAAAATATGAT-
1 AAATGAAAAATAT-ATG
35436326 AAATGA
1 AAATGA
35436332 TTATGAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 7 0.21
16 13 0.39
17 3 0.09
18 5 0.15
19 5 0.15
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23
Consensus pattern (16 bp):
AAATGAAAAATATATG
Found at i:35440404 original size:54 final size:54
Alignment explanation
Indices: 35440334--35440492 Score: 147
Period size: 54 Copynumber: 3.1 Consensus size: 54
35440324 TATTATAAAG
* *
35440334 AATTTTATGAAATCATATATTATTATTAAATTATATTTAATAATAATTATTTTA
1 AATTGTATCAAATCATATATTATTATTAAATTATATTTAATAATAATTATTTTA
* *
35440388 AATTGTA-CAAATTCATATA--A-GA--AAATT-TA-TTAGTAATAATTATTTTA
1 AATTGTATCAAA-TCATATATTATTATTAAATTATATTTAATAATAATTATTTTA
* * * * * *
35440435 AATTTTATTAAAGCATATATT-TTAATTAAAATATATTTAATAATTATTATTTCA
1 AATTGTATCAAATCATATATTATT-ATTAAATTATATTTAATAATAATTATTTTA
35440489 AATT
1 AATT
35440493 ATATTTTATA
Statistics
Matches: 83, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
47 29 0.35
48 5 0.06
49 5 0.06
50 1 0.01
51 1 0.01
52 5 0.06
53 5 0.06
54 32 0.39
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (54 bp):
AATTGTATCAAATCATATATTATTATTAAATTATATTTAATAATAATTATTTTA
Found at i:35440501 original size:59 final size:58
Alignment explanation
Indices: 35440436--35440850 Score: 212
Period size: 59 Copynumber: 6.9 Consensus size: 58
35440426 ATTATTTTAA
*
35440436 ATTTTATTAAAGCATATATTTTAATTAAAATATATTTAATAATTATTATTTCAAATTAT
1 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTATTT-AAATTAT
* * * * * * * *
35440495 ATTTTA-TAGTATCATATACTATGATTTTAGTAAAT-TCATATAAGAA-TATTGATTATTAA-GA
1 ATTTTATTA-AATCATATA-TTTTA-ATTA--AAATAT-ATTTAATAATTATT-ATT-TAAATTA
35440556 -
58 T
35440556 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTATTTCAAATTAT
1 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTATTT-AAATTAT
* * * * * * *
35440615 ATTTTA-TAGTATCATATATTATGATTTTAGTAAAT-TCATATAAGAA-TATTGATTATTAA-GA
1 ATTTTATTA-AATCATATATT-TTA-ATTA--AAATAT-ATTTAATAATTATT-ATT-TAAATTA
35440676 -
58 T
* * *
35440676 ATTTTATTAATTTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTAT
1 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTAT-TTAAATTAT
* * * * * * *
35440735 ATTTTA-TAGTATCATATATTATGATTTTAGTAAAT-TCATATAAGAA-TATTGATTATTAA-GA
1 ATTTTATTA-AATCATATATT-TTA-ATTA--AAATAT-ATTTAATAATTATT-ATT-TAAATTA
35440796 -
58 T
* * *
35440796 ATTTTATTAATTTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTAT-TTAAA
35440851 ATATGATTAA
Statistics
Matches: 263, Mismatches: 53, Indels: 82
0.66 0.13 0.21
Matches are distributed among these distances:
56 1 0.00
57 48 0.18
58 23 0.09
59 52 0.20
60 14 0.05
61 51 0.19
62 24 0.09
63 48 0.18
64 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (58 bp):
ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTATTTAAATTAT
Found at i:35440850 original size:120 final size:120
Alignment explanation
Indices: 35440435--35440844 Score: 732
Period size: 120 Copynumber: 3.4 Consensus size: 120
35440425 AATTATTTTA
* *
35440435 AATTTTATTAAAGCATATATTTTAATTAAAATATATTTAATAATTATTATTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
*
35440500 ATAGTATCATATACTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
35440555 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTATTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
35440620 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
* *
35440675 AATTTTATTAATTTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTT
35440739 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
65 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
* *
35440795 AATTTTATTAATTTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT
35440845 GTTAAAATAT
Statistics
Matches: 284, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
120 282 0.99
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:35441091 original size:16 final size:16
Alignment explanation
Indices: 35441063--35441127 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
35441053 TTGAATTGCT
35441063 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
* *
35441079 ATTGCGTCTCTATTCC
1 ATTACGCCTCTATTCC
35441095 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
35441111 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
35441127 A
1 A
35441128 ATACAGCGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.18, C:0.35, G:0.08, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:35448181 original size:18 final size:18
Alignment explanation
Indices: 35448158--35448193 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35448148 TACGGTGTGC
*
35448158 GAAACTATTTTTATGCTT
1 GAAACTATTTTGATGCTT
35448176 GAAACTATTTTGATGCTT
1 GAAACTATTTTGATGCTT
35448194 CCTATTCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (18 bp):
GAAACTATTTTGATGCTT
Found at i:35453815 original size:30 final size:30
Alignment explanation
Indices: 35453779--35453840 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
35453769 AATCCCTAAT
35453779 TCCCCAAATTCTCTCAAATCTTTCAAAACC
1 TCCCCAAATTCTCTCAAATCTTTCAAAACC
35453809 TCCCCAAATTCTCTCAAATCTTTCAAAACC
1 TCCCCAAATTCTCTCAAATCTTTCAAAACC
35453839 TC
1 TC
35453841 TTAAACCCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.37, G:0.00, T:0.31
Consensus pattern (30 bp):
TCCCCAAATTCTCTCAAATCTTTCAAAACC
Found at i:35468555 original size:15 final size:15
Alignment explanation
Indices: 35468535--35468563 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35468525 GTAATCAGAT
35468535 ATCTTTGTTCAAACC
1 ATCTTTGTTCAAACC
35468550 ATCTTTGTTCAAAC
1 ATCTTTGTTCAAAC
35468564 TGGGTACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (15 bp):
ATCTTTGTTCAAACC
Found at i:35475002 original size:39 final size:39
Alignment explanation
Indices: 35474944--35475081 Score: 224
Period size: 39 Copynumber: 3.5 Consensus size: 39
35474934 AACATGTTTT
* *
35474944 TGAGTATTGTGATAGATGCTTGAATGTTATGTGATTAAA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
35474983 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
35475022 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
35475061 T-ATGTAATGTGATATATGCTT
1 TGA-GTATTGTGATATATGCTT
35475082 AAAAGTGCAT
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
38 1 0.01
39 93 0.99
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
Found at i:35475015 original size:22 final size:22
Alignment explanation
Indices: 35474990--35475061 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
35474980 AAATGAGTAT
35474990 TGTGATATATGCTTGAATGTTA
1 TGTGATATATGCTTGAATGTTA
*
35475012 TGTGAT-TAT--ATG-A-G-TA
1 TGTGATATATGCTTGAATGTTA
*
35475028 TTGTGATATATGCTTAAATGTTA
1 -TGTGATATATGCTTGAATGTTA
35475051 TGTGATTATAT
1 TGTGA-TATAT
35475062 ATGTAATGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 15
0.68 0.05 0.26
Matches are distributed among these distances:
16 2 0.05
17 7 0.18
18 4 0.10
19 2 0.05
20 1 0.03
21 4 0.10
22 12 0.31
23 7 0.18
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (22 bp):
TGTGATATATGCTTGAATGTTA
Found at i:35475082 original size:39 final size:39
Alignment explanation
Indices: 35474944--35475098 Score: 222
Period size: 39 Copynumber: 3.9 Consensus size: 39
35474934 AACATGTTTT
* * *
35474944 TGAGTATTGTGATAGATGCTTGAATGTTATGTGATTAAA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
35474983 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
35475022 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
35475061 T-ATGTAATGTGATATATGCTTAAAAGTGCATGTGATTA
1 TGA-GTATTGTGATATATGCTTAAATGT-TATGTGATTA
35475099 CCATGTAAAT
Statistics
Matches: 108, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
38 1 0.01
39 98 0.91
40 9 0.08
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.43
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:35478006 original size:20 final size:20
Alignment explanation
Indices: 35477978--35478045 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
35477968 CTTACGTGCT
*
35477978 CCTATTTGTACTTCGATACC
1 CCTAATTGTACTTCGATACC
* *
35477998 CCTGATTGTACTTGCG-TGCC
1 CCTAATTGTACTT-CGATACC
*
35478018 CCTAATTGTACTTCAATACC
1 CCTAATTGTACTTCGATACC
*
35478038 CCTTATTG
1 CCTAATTG
35478046 CAGTTACGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.03
20 36 0.92
21 2 0.05
ACGTcount: A:0.19, C:0.29, G:0.13, T:0.38
Consensus pattern (20 bp):
CCTAATTGTACTTCGATACC
Found at i:35478016 original size:40 final size:40
Alignment explanation
Indices: 35477960--35478088 Score: 159
Period size: 40 Copynumber: 3.2 Consensus size: 40
35477950 AATTATACCT
* *
35477960 TGATTGCACTTACGTGCTCCTATTTGTACTTCGATACCCC
1 TGATTGCACTTACGTGCCCCTATTTGTACTTCAATACCCC
* * *
35478000 TGATTGTACTTGCGTGCCCCTAATTGTACTTCAATACCCC
1 TGATTGCACTTACGTGCCCCTATTTGTACTTCAATACCCC
* * * * *
35478040 TTATTGCAGTTACGTGCCCCTGTTTGTACTTCAGTACCCT
1 TGATTGCACTTACGTGCCCCTATTTGTACTTCAATACCCC
*
35478080 TGAATGCAC
1 TGATTGCAC
35478089 ATCGGTGCCC
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.36
Consensus pattern (40 bp):
TGATTGCACTTACGTGCCCCTATTTGTACTTCAATACCCC
Found at i:35478116 original size:20 final size:20
Alignment explanation
Indices: 35478053--35478118 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
35478043 TTGCAGTTAC
* *
35478053 GTGCCCCTGTTTGTACTTCA
1 GTGCCCATGTTTGCACTTCA
* * ** * *
35478073 GTACCCTTGAATGCACATCG
1 GTGCCCATGTTTGCACTTCA
35478093 GTGCCCATGTTTGCACTTCA
1 GTGCCCATGTTTGCACTTCA
35478113 GTGCCC
1 GTGCCC
35478119 CTAGTTGCAC
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.32, G:0.21, T:0.32
Consensus pattern (20 bp):
GTGCCCATGTTTGCACTTCA
Found at i:35478120 original size:80 final size:81
Alignment explanation
Indices: 35477957--35478112 Score: 174
Period size: 80 Copynumber: 1.9 Consensus size: 81
35477947 GTAAATTATA
* * * * *
35477957 CCTTGATTGCACTTACGTGCTCCTATTTGTACTTCGATACCCCTGATTGTACTTGCGTGCCCCTA
1 CCTTGATTGCACTTACGTGCCCCTATTTGTACTTCGATACCCCTGAATGCACTCGCGTGCCCATA
*
35478022 ATTGTACTTCAATACC
66 ATTGCACTTCAATACC
* * *
35478038 CCTT-ATTGCAGTTACGTGCCCCTGTTTGTACTTC-AGTACCCTTGAATGCACATCG-GTGCCCA
1 CCTTGATTGCACTTACGTGCCCCTATTTGTACTTCGA-TACCCCTGAATGCAC-TCGCGTGCCCA
**
35478100 TGTTTGCACTTCA
64 TAATTGCACTTCA
35478113 GTGCCCCTAG
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
79 1 0.02
80 55 0.89
81 6 0.10
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (81 bp):
CCTTGATTGCACTTACGTGCCCCTATTTGTACTTCGATACCCCTGAATGCACTCGCGTGCCCATA
ATTGCACTTCAATACC
Found at i:35490673 original size:18 final size:18
Alignment explanation
Indices: 35490650--35490687 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
35490640 AATTTGAAAT
35490650 AAAACAAAAAATTTTGGA
1 AAAACAAAAAATTTTGGA
**
35490668 AAAACATGAAATTTTGGA
1 AAAACAAAAAATTTTGGA
35490686 AA
1 AA
35490688 CAGAGGTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.05, G:0.13, T:0.24
Consensus pattern (18 bp):
AAAACAAAAAATTTTGGA
Found at i:35493327 original size:41 final size:41
Alignment explanation
Indices: 35493267--35493344 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
35493257 CTCACTTATC
35493267 GAAATCATGGTCCCAAAACCATTATTTCTGACACCACCAAA
1 GAAATCATGGTCCCAAAACCATTATTTCTGACACCACCAAA
* *
35493308 GAAATCATGGTCCCGAAACCATTATTTCTGGCACCAC
1 GAAATCATGGTCCCAAAACCATTATTTCTGACACCAC
35493345 TGAAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (41 bp):
GAAATCATGGTCCCAAAACCATTATTTCTGACACCACCAAA
Found at i:35493993 original size:2 final size:2
Alignment explanation
Indices: 35493986--35494015 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
35493976 CTACTCGTAA
*
35493986 CT CT CT CT CT CT GT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
35494016 TACTAATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:35498214 original size:20 final size:19
Alignment explanation
Indices: 35498190--35498237 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
35498180 TTTTTAACCC
* *
35498190 AAATTAATTATTTTCTCTA
1 AAATTAATTAATTACTCTA
* *
35498209 ATAATTATTTAATTACTTTA
1 A-AATTAATTAATTACTCTA
35498229 AAATTAATT
1 AAATTAATT
35498238 TTCCCAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATTAATTAATTACTCTA
Found at i:35499063 original size:37 final size:37
Alignment explanation
Indices: 35499013--35499087 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
35499003 AGAGTATGAG
* *
35499013 TACAGTGGACGACATCCCTTAGTATTCCTGCTAGGGT
1 TACAGTGGACGACACCCCTTAGTATTCCTCCTAGGGT
35499050 TACAGTGGACGACACCCCTTAGTATTCCTCCTAGGGT
1 TACAGTGGACGACACCCCTTAGTATTCCTCCTAGGGT
35499087 T
1 T
35499088 GTTGCCCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (37 bp):
TACAGTGGACGACACCCCTTAGTATTCCTCCTAGGGT
Found at i:35499478 original size:6 final size:6
Alignment explanation
Indices: 35499456--35499497 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
35499446 GCAAATATAT
*
35499456 CATTTC TCATTTC CATTTT CATTTC CATTTC CATTTC CATTT
1 CATTTC -CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
35499498 TGAGAAACCT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.55
Consensus pattern (6 bp):
CATTTC
Found at i:35507383 original size:7 final size:6
Alignment explanation
Indices: 35507371--35507429 Score: 64
Period size: 6 Copynumber: 9.7 Consensus size: 6
35507361 TAAATGTATC
* * * *
35507371 ATTTCT AATTTCT ATTTCT ATTTCT ATTTCC ATTTCC ATTTCC ATTTCC
1 ATTTCT -ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT ATTTCT
*
35507420 ATTTCC ATTT
1 ATTTCT ATTT
35507430 TAAGAAACCT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
6 45 0.88
7 6 0.12
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.58
Consensus pattern (6 bp):
ATTTCT
Found at i:35507387 original size:6 final size:6
Alignment explanation
Indices: 35507378--35507429 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
35507368 ATCATTTCTA
* * *
35507378 ATTTCT ATTTCT ATTTCT ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC
35507426 ATTT
1 ATTT
35507430 TAAGAAACCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (6 bp):
ATTTCC
Found at i:35507405 original size:18 final size:18
Alignment explanation
Indices: 35507370--35507429 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
35507360 GTAAATGTAT
*
35507370 CATTTCTAATTTCTATTTC
1 CATTTCT-ATTTCCATTTC
*
35507389 TATTTCTATTTCCATTTC
1 CATTTCTATTTCCATTTC
*
35507407 CATTTCCATTTCCATTTC
1 CATTTCTATTTCCATTTC
35507425 CATTT
1 CATTT
35507430 TAAGAAACCT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
18 31 0.84
19 6 0.16
ACGTcount: A:0.18, C:0.25, G:0.00, T:0.57
Consensus pattern (18 bp):
CATTTCTATTTCCATTTC
Found at i:35519847 original size:40 final size:40
Alignment explanation
Indices: 35519803--35519974 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
35519793 GGACTAAGAT
*
35519803 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
*
35519843 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * *
35519883 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
35519923 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
35519962 CCGAAGGCATTTG
1 CCGAAGGCATTTG
35519975 AACGAGGAGC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 34 0.29
40 81 0.69
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:35519888 original size:80 final size:79
Alignment explanation
Indices: 35519803--35519974 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
35519793 GGACTAAGAT
*
35519803 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
35519867 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
35519883 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
35519948 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
35519962 CCGAAGGCATTTG
1 CCGAAGGCATTTG
35519975 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:35519992 original size:79 final size:80
Alignment explanation
Indices: 35519830--35520007 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
35519820 AGATACAAAT
* * * *
35519830 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
35519895 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
35519910 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
35519974 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
35519989 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
35520008 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:35527786 original size:40 final size:40
Alignment explanation
Indices: 35527742--35527913 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
35527732 GGACTAAGAT
*
35527742 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
*
35527782 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * *
35527822 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
35527862 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
35527901 CCGAAGGCATTTG
1 CCGAAGGCATTTG
35527914 AACGAGGAGC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 34 0.29
40 81 0.69
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:35527827 original size:80 final size:79
Alignment explanation
Indices: 35527742--35527913 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
35527732 GGACTAAGAT
*
35527742 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
35527806 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
35527822 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
35527887 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
35527901 CCGAAGGCATTTG
1 CCGAAGGCATTTG
35527914 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:35527931 original size:79 final size:80
Alignment explanation
Indices: 35527769--35527946 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
35527759 AGATACAAAT
* * * *
35527769 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
35527834 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
35527849 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
35527913 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
35527928 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
35527947 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:35531251 original size:19 final size:19
Alignment explanation
Indices: 35531215--35531253 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
35531205 GATGGCAAAA
*
35531215 TTACTATTTTGTCTATTTT
1 TTACTATTTTGTCAATTTT
35531234 TTACT-TTTTGTACAATTTT
1 TTACTATTTTGT-CAATTTT
35531253 T
1 T
35531254 CACAGTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.18, C:0.10, G:0.05, T:0.67
Consensus pattern (19 bp):
TTACTATTTTGTCAATTTT
Found at i:35546946 original size:40 final size:40
Alignment explanation
Indices: 35546902--35547073 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
35546892 GGACTAAGAT
*
35546902 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
*
35546942 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * *
35546982 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
35547022 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
35547061 CCGAAGGCATTTG
1 CCGAAGGCATTTG
35547074 AACGAGGAGC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 34 0.29
40 81 0.69
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:35546987 original size:80 final size:79
Alignment explanation
Indices: 35546902--35547073 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
35546892 GGACTAAGAT
*
35546902 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
35546966 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
35546982 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
35547047 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
35547061 CCGAAGGCATTTG
1 CCGAAGGCATTTG
35547074 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:35547091 original size:79 final size:80
Alignment explanation
Indices: 35546929--35547106 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
35546919 AGATACAAAT
* * * *
35546929 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
35546994 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
35547009 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
35547073 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
35547088 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
35547107 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:35550414 original size:18 final size:20
Alignment explanation
Indices: 35550385--35550424 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
35550375 GATGGCAAAA
*
35550385 TTACTATTTTGT-CTATTTT
1 TTACTATTTTGTACAATTTT
35550404 TTACT-TTTTGTACAATTTT
1 TTACTATTTTGTACAATTTT
35550423 TT
1 TT
35550425 CACAGTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.68
Consensus pattern (20 bp):
TTACTATTTTGTACAATTTT
Found at i:35558044 original size:5 final size:5
Alignment explanation
Indices: 35558025--35558061 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
35558015 TTGAAAAGCA
*
35558025 ATAAA ATAAT AATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT A
35558062 AAGAAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:35558348 original size:24 final size:25
Alignment explanation
Indices: 35558314--35558360 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
35558304 AACAGTAGAA
35558314 GAAGAGAAGAAGAAGAA-GAATAAG
1 GAAGAGAAGAAGAAGAAGGAATAAG
* *
35558338 GAAGAGGAGAAGGAGAAGGAATA
1 GAAGAGAAGAAGAAGAAGGAATA
35558361 GGAGAAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.38, T:0.04
Consensus pattern (25 bp):
GAAGAGAAGAAGAAGAAGGAATAAG
Found at i:35558397 original size:20 final size:20
Alignment explanation
Indices: 35558317--35558398 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 20
35558307 AGTAGAAGAA
*
35558317 GAGAAGAAGAAGAAGAATAAG
1 GAGAAGAAGAAAAAGAAT-AG
* *
35558338 GAAGAGGAGAAGGAGAAGGAATAG
1 G-AGA--AGAA-GAAAAAGAATAG
**
35558362 GAGAAGAAGACTAAGAATAG
1 GAGAAGAAGAAAAAGAATAG
*
35558382 GCGAAGAAGAAAAAGAA
1 GAGAAGAAGAAAAAGAA
35558399 GAGAAGAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
20 23 0.48
21 5 0.10
22 3 0.06
23 3 0.06
24 7 0.15
25 7 0.15
ACGTcount: A:0.57, C:0.02, G:0.35, T:0.05
Consensus pattern (20 bp):
GAGAAGAAGAAAAAGAATAG
Found at i:35559316 original size:20 final size:20
Alignment explanation
Indices: 35559291--35559340 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
35559281 TATCGATCCA
*
35559291 GTATCGATACT-TTTCTTAAG
1 GTATCGATA-TATTTCCTAAG
35559311 GTATCGATATATTTCCTAAG
1 GTATCGATATATTTCCTAAG
35559331 GTATCGATAT
1 GTATCGATAT
35559341 TCCTGCTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (20 bp):
GTATCGATATATTTCCTAAG
Found at i:35560117 original size:19 final size:19
Alignment explanation
Indices: 35560093--35560130 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
35560083 AATAGAATGG
35560093 CCTTTCATATCAGGAAATT
1 CCTTTCATATCAGGAAATT
35560112 CCTTTCATATCAGGAAATT
1 CCTTTCATATCAGGAAATT
35560131 GGCTTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (19 bp):
CCTTTCATATCAGGAAATT
Found at i:35560146 original size:3 final size:3
Alignment explanation
Indices: 35560133--35560258 Score: 195
Period size: 3 Copynumber: 43.0 Consensus size: 3
35560123 AGGAAATTGG
35560133 CTT CTT C-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* *
35560180 CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT CTT CTT C-T CTT TTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* *
35560227 CTT CTT TTT CTT C-T CTT TTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
35560259 ATCCTCACTA
Statistics
Matches: 112, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
2 6 0.05
3 106 0.95
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:35560464 original size:43 final size:43
Alignment explanation
Indices: 35560413--35560555 Score: 216
Period size: 43 Copynumber: 3.3 Consensus size: 43
35560403 TTATTTCTAA
* *
35560413 AAACGCCGCTAAAGGTCATGGTCTTTAGCGGTGCTTACCACAC
1 AAACGCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAAC
* *
35560456 AAACGCCGCTAAAGGTTATGGTCTTTAGCAGCGCTT-CCAAAAC
1 AAACGCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACC-AAAC
**
35560499 AAACGCCGCTGGAGGTCATGGTCTTTAGCGGCGCTTACCAAAC
1 AAACGCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAAC
35560542 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
35560556 ACAACGACCT
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
42 2 0.02
43 84 0.95
44 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAAC
Found at i:35560591 original size:86 final size:86
Alignment explanation
Indices: 35560413--35560579 Score: 226
Period size: 86 Copynumber: 1.9 Consensus size: 86
35560403 TTATTTCTAA
* * *** * **
35560413 AAACGCCGCTAAAGGTCATGGTCTTTAGCGGTGCTTACCACACAAACGCCGCTAAAGGTTATGGT
1 AAACGCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAACGCCGCTAAAGACAACGAC
35560478 CTTTAGCAGCGCTTCCAAAAC
66 CTTTAGCAGCGCTTCCAAAAC
**
35560499 AAACGCCGCTGGAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAACGCCGCTAAAGACAACGAC
1 AAACGCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAACGCCGCTAAAGACAACGAC
**
35560564 CTTTAGTGGCGCTTCC
66 CTTTAGCAGCGCTTCC
35560580 CTTACAAACG
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
86 69 1.00
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (86 bp):
AAACGCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAACGCCGCTAAAGACAACGAC
CTTTAGCAGCGCTTCCAAAAC
Found at i:35560646 original size:43 final size:43
Alignment explanation
Indices: 35560520--35560746 Score: 162
Period size: 43 Copynumber: 5.3 Consensus size: 43
35560510 GAGGTCATGG
* * *
35560520 TCTTTAGCGGCGCTT-ACCAAACAAACGCCGCTAAAGACAAC-GA
1 TCTTTAGCGGCGCTTCTCCATA-AAACGCCGCTAAAGAC-CCTGA
* * * **
35560563 CCTTTAGTGGCGCTTC-CCTTACAAACGCC-CTTAATTACCCTGA
1 TCTTTAGCGGCGCTTCTCCATA-AAACGCCGC-TAAAGACCCTGA
* * * *
35560606 TCTTTAGTGGCACTTCTGCATAAAACGCCGCTAAAGACCCTAA
1 TCTTTAGCGGCGCTTCTCCATAAAACGCCGCTAAAGACCCTGA
* * *
35560649 TCTTTAGCGGCGTTTTTCTCC--AAAATGCCGCTGAAGACCCTGA
1 TCTTTAGCGGCG--CTTCTCCATAAAACGCCGCTAAAGACCCTGA
* * * *
35560692 TCTTTAGCGGCGCTTTTACCA-CAAACGCCGCTAAAGACCATTA
1 TCTTTAGCGGCGCTTCT-CCATAAAACGCCGCTAAAGACCCTGA
*
35560735 CCTTTAGCGGCG
1 TCTTTAGCGGCG
35560747 TTTTTTTAAA
Statistics
Matches: 146, Mismatches: 29, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
41 3 0.02
42 4 0.03
43 130 0.89
44 4 0.03
45 5 0.03
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (43 bp):
TCTTTAGCGGCGCTTCTCCATAAAACGCCGCTAAAGACCCTGA
Found at i:35560891 original size:10 final size:10
Alignment explanation
Indices: 35560872--35560903 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
35560862 AATCTGTAAT
35560872 ATAT-AATAA
1 ATATCAATAA
35560881 ATATCAATAA
1 ATATCAATAA
35560891 ATATCAATAA
1 ATATCAATAA
35560901 ATA
1 ATA
35560904 AAATAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (10 bp):
ATATCAATAA
Found at i:35560912 original size:20 final size:19
Alignment explanation
Indices: 35560872--35560910 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
35560862 AATCTGTAAT
*
35560872 ATATAATAAATATCAATAA
1 ATATAATAAATATAAATAA
35560891 ATATCAATAAATA-AAATAA
1 ATAT-AATAAATATAAATAA
35560910 A
1 A
35560911 ATTCGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
ATATAATAAATATAAATAA
Found at i:35561172 original size:66 final size:66
Alignment explanation
Indices: 35561100--35561240 Score: 196
Period size: 66 Copynumber: 2.1 Consensus size: 66
35561090 GCAGCTTCTG
*
35561100 CTTCTCTCGCTGCCGTATCTGCTTTAAGCTACT-GCTGGAGTTCTTCATA-CTTTCGTTGAACCT
1 CTTCTCTCGCTGCCGCATCTGCTTTAAG-TACTAGCTGGAGTTCTTCATATCTTT-GTTGAACCT
35561163 CAA
64 CAA
* ** *
35561166 CTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACCTCA
1 CTTCTCTCGCTGCCGCATCTGCTTTAAGTACTAGCTGGAGTTCTTCATATCTTTGTTGAACCTCA
*
35561231 G
66 A
35561232 CTTCTCTCG
1 CTTCTCTCG
35561241 ATGTTGCCTC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 2 0.03
66 61 0.91
67 4 0.06
ACGTcount: A:0.15, C:0.28, G:0.17, T:0.40
Consensus pattern (66 bp):
CTTCTCTCGCTGCCGCATCTGCTTTAAGTACTAGCTGGAGTTCTTCATATCTTTGTTGAACCTCA
A
Found at i:35561256 original size:66 final size:66
Alignment explanation
Indices: 35561133--35561261 Score: 188
Period size: 66 Copynumber: 2.0 Consensus size: 66
35561123 TTAAGCTACT
* *
35561133 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAACTTCTCTCGCTGCTGCATCTGCTTTAAGTTGT
1 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAACTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
35561198 A
66 A
* * * *
35561199 GCTGGAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTT
1 GCTGGAGTTCTTCATA-CTTTCGTTGAACCTCAACTTCTCTCGATGCTGCATCCGCTTTAAGTT
35561262 TTGTAATTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 52 0.93
67 4 0.07
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.41
Consensus pattern (66 bp):
GCTGGAGTTCTTCATACTTTCGTTGAACCTCAACTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
A
Found at i:35567306 original size:27 final size:27
Alignment explanation
Indices: 35567276--35567506 Score: 264
Period size: 27 Copynumber: 8.5 Consensus size: 27
35567266 AAATTGTACA
35567276 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTT
** * *
35567303 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGATTTGACTATGTT
35567330 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTT
** * *
35567357 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGATTTGACTATGTT
* * **
35567384 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTT
*
35567411 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTT
* * *
35567439 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGATTTGACTATGTT
* * * *
35567466 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGACTATGTT
*
35567493 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
35567507 GACTCAATAT
Statistics
Matches: 176, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
27 153 0.87
28 23 0.13
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTT
Found at i:35567336 original size:54 final size:55
Alignment explanation
Indices: 35567275--35567506 Score: 301
Period size: 54 Copynumber: 4.3 Consensus size: 55
35567265 TAAATTGTAC
35567275 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
35567330 -GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
* * ** ** *
35567384 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGA-AATGAATATGAT
* * * ** *
35567438 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
*
35567492 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35567507 GACTCAATAT
Statistics
Matches: 158, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
54 115 0.73
55 43 0.27
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
Found at i:35575459 original size:27 final size:27
Alignment explanation
Indices: 35575429--35575659 Score: 255
Period size: 27 Copynumber: 8.5 Consensus size: 27
35575419 AAATTGTACA
35575429 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTT
** * *
35575456 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGATTTGACTATGTT
35575483 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTT
* ** * *
35575510 GCACTAAGTGTACGAAATGAATATGAT
1 GCACTAAGTGTGCGATTTGACTATGTT
* * **
35575537 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTT
*
35575564 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTT
* * *
35575592 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGATTTGACTATGTT
* * * *
35575619 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGACTATGTT
*
35575646 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
35575660 GACTCAATAT
Statistics
Matches: 174, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
27 151 0.87
28 23 0.13
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTT
Found at i:35575489 original size:54 final size:55
Alignment explanation
Indices: 35575428--35575659 Score: 292
Period size: 54 Copynumber: 4.3 Consensus size: 55
35575418 TAAATTGTAC
35575428 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
*
35575483 -GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTACGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
* * ** ** *
35575537 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGA-AATGAATATGAT
* * * ** *
35575591 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
*
35575645 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35575660 GACTCAATAT
Statistics
Matches: 156, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
54 113 0.72
55 43 0.28
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
Found at i:35578289 original size:15 final size:16
Alignment explanation
Indices: 35578246--35578295 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
35578236 TTATTATGTC
*
35578246 GTATTATGTAAGTTAT
1 GTATTATATAAGTTAT
*
35578262 ATATTATATAAGTTAT
1 GTATTATATAAGTTAT
35578278 GTATTA-ATAAGTTAT
1 GTATTATATAAGTTAT
35578293 GTA
1 GTA
35578296 AGTTATGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
15 12 0.39
16 19 0.61
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (16 bp):
GTATTATATAAGTTAT
Found at i:35578302 original size:9 final size:9
Alignment explanation
Indices: 35578249--35578304 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
35578239 TTATGTCGTA
35578249 TTATGTAAG
1 TTATGTAAG
*
35578258 TTATAT-A-
1 TTATGTAAG
*
35578265 TTATATAAG
1 TTATGTAAG
35578274 TTATGT-A-
1 TTATGTAAG
*
35578281 TTA-ATAAG
1 TTATGTAAG
35578289 TTATGTAAG
1 TTATGTAAG
35578298 TTATGTA
1 TTATGTA
35578305 TCATTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 1 0.03
7 10 0.26
8 6 0.16
9 21 0.55
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:35578978 original size:15 final size:15
Alignment explanation
Indices: 35578950--35578985 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
35578940 TTAATAAAAG
*
35578950 GAAAA-AGTAGAAAT
1 GAAAACAGTACAAAT
35578964 GAAAACAGTACAAAT
1 GAAAACAGTACAAAT
35578979 GAAAACA
1 GAAAACA
35578986 AATTGGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (15 bp):
GAAAACAGTACAAAT
Found at i:35583490 original size:41 final size:41
Alignment explanation
Indices: 35583445--35583722 Score: 242
Period size: 41 Copynumber: 6.8 Consensus size: 41
35583435 GCTCAAGTAT
*
35583445 TTAGCGGCGCTTTTTAAGAAACGCCGTTAAAGACCGGAGCA
1 TTAGCGGCGCTTTTTAAGAAACGCCGCTAAAGACCGGAGCA
* * * * *
35583486 TTAGCAGCGCTTTCTGAGAAACGCTGCTAAAGACCGTAGCA
1 TTAGCGGCGCTTTTTAAGAAACGCCGCTAAAGACCGGAGCA
* * * **
35583527 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGAACTAAGCA
1 TTAGCGGCGCTTTTTAAGAAACGCCGCTAAAGACCGGAGCA
* * * *
35583568 TTAGCGGCGCCTCTTACA-AAGCGCCGCTAAAGACCTGAGCA
1 TTAGCGGCGCTTTTTA-AGAAACGCCGCTAAAGACCGGAGCA
* * * **
35583609 TTAGCGGCGCATCTT-AGAAAACGCCACTAAAGACCTCAGCA
1 TTAGCGGCGCTTTTTAAG-AAACGCCGCTAAAGACCGGAGCA
* * * * *
35583650 CTAGCGGTGATTATTCAA-AAACGCCGCTAAAGACAGGAGCA
1 TTAGCGGCGCTT-TTTAAGAAACGCCGCTAAAGACCGGAGCA
*
35583691 TTAGCGGCG-TGTTTTGAA-AAGCGCCGCTAAAG
1 TTAGCGGCGCT-TTTT-AAGAAACGCCGCTAAAG
35583723 GCCCAAAAAA
Statistics
Matches: 192, Mismatches: 38, Indels: 14
0.79 0.16 0.06
Matches are distributed among these distances:
39 1 0.01
40 3 0.02
41 185 0.96
42 2 0.01
43 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTAAGAAACGCCGCTAAAGACCGGAGCA
Found at i:35583597 original size:82 final size:81
Alignment explanation
Indices: 35583445--35583722 Score: 272
Period size: 82 Copynumber: 3.4 Consensus size: 81
35583435 GCTCAAGTAT
* * ** * * *
35583445 TTAGCGGCGCTTTTTAAGAAACGCCGTTAAAGACCGGAGCATTAGCAGCGCTTTCTGAGAAACGC
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGC-TTCTTACAAACGC
*
35583510 TGCTAAAGACCGTAGCA
65 CGCTAAAGACCGTAGCA
* * *
35583527 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGAACTAAGCATTAGCGGCGCCTCTTACAAAGCGC
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGCTTCTTACAAA-CGC
35583592 CGCTAAAGACC-TGAGCA
65 CGCTAAAGACCGT-AGCA
* * * * * * * * * *
35583609 TTAGCGGCGCATCTTAGAAAACGCCACTAAAGACCTCAGCACTAGCGGTGATTATTCAAAAACGC
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGCTTCTT-ACAAACGC
* *
35583674 CGCTAAAGACAGGAGCA
65 CGCTAAAGACCGTAGCA
* *
35583691 TTAGCGGCG-TGTTTTGAAAAGCGCCGCTAAAG
1 TTAGCGGCGCT-TTTTAAAAAACGCCGCTAAAG
35583723 GCCCAAAAAA
Statistics
Matches: 159, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
81 8 0.05
82 147 0.92
83 4 0.03
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (81 bp):
TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGCTTCTTACAAACGCC
GCTAAAGACCGTAGCA
Found at i:35583599 original size:123 final size:122
Alignment explanation
Indices: 35583466--35583722 Score: 290
Period size: 123 Copynumber: 2.1 Consensus size: 122
35583456 TTTTAAGAAA
* * ** *
35583466 CGCCGTTAAAGACCGGAGCATTAGCAGCGCTTTCTGAG-AAACGCTGCTAAAGACCGT-AGCATT
1 CGCCGCTAAAGACCGGAGCATTAGCAGCGC-ATCTGAGAAAACGCCACTAAAGACC-TCAGCACT
*
35583529 AGCGGCGCTT-TGTAAAAAACGCCGCTAAAGAACTA-AGCATTAGCGGCGCCTCTT-ACAAAG
64 AGCGGCGATTAT-TAAAAAACGCCGCTAAAG-AC-AGAGCATTAGCGGCGCCTCTTGA-AAAG
* * *
35583589 CGCCGCTAAAGACCTGAGCATTAGCGGCGCATCTTAGAAAACGCCACTAAAGACCTCAGCACTAG
1 CGCCGCTAAAGACCGGAGCATTAGCAGCGCATCTGAGAAAACGCCACTAAAGACCTCAGCACTAG
* * ** *
35583654 CGGTGATTATTCAAAAACGCCGCTAAAGACAGGAGCATTAGCGGCGTGTTTTGAAAAG
66 CGGCGATTATTAAAAAACGCCGCTAAAGACA-GAGCATTAGCGGCGCCTCTTGAAAAG
35583712 CGCCGCTAAAG
1 CGCCGCTAAAG
35583723 GCCCAAAAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
121 1 0.01
122 8 0.07
123 103 0.90
124 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (122 bp):
CGCCGCTAAAGACCGGAGCATTAGCAGCGCATCTGAGAAAACGCCACTAAAGACCTCAGCACTAG
CGGCGATTATTAAAAAACGCCGCTAAAGACAGAGCATTAGCGGCGCCTCTTGAAAAG
Found at i:35583799 original size:39 final size:38
Alignment explanation
Indices: 35583754--35583910 Score: 138
Period size: 41 Copynumber: 3.9 Consensus size: 38
35583744 CGTTCGGCTT
35583754 TCGTTTTTTGCGGCGCTTATTTGTAAA-CGCCGCTAATGC
1 TCGTTTTTTGCGGCG-TT-TTTGTAAAGCGCCGCTAATGC
* * ***
35583793 TTGTTTTTAGCGGCGTTTTACAAATAGCGCCGCTAATGC
1 TCGTTTTTTGCGGCGTTTTTGTAA-AGCGCCGCTAATGC
* *
35583832 TCGTATCTTTGGCGGCGTTTTGCGTAAAGCGCCGCTAATGC
1 TCGT-T-TTTTGCGGCGTTTT-TGTAAAGCGCCGCTAATGC
*
35583873 TCGATTTTTTGTGGCGTTTTTTGTCCAAA-CGCCGCTAA
1 TCG-TTTTTTGCGGCG-TTTTTGT--AAAGCGCCGCTAA
35583911 AAACGCCGCT
Statistics
Matches: 96, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
37 4 0.04
38 3 0.03
39 28 0.29
40 11 0.11
41 44 0.46
42 6 0.06
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (38 bp):
TCGTTTTTTGCGGCGTTTTTGTAAAGCGCCGCTAATGC
Found at i:35583914 original size:12 final size:12
Alignment explanation
Indices: 35583899--35583924 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35583889 TTTTTTGTCC
35583899 AAACGCCGCTAA
1 AAACGCCGCTAA
35583911 AAACGCCGCTAA
1 AAACGCCGCTAA
35583923 AA
1 AA
35583925 CCCTATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:35583952 original size:3 final size:3
Alignment explanation
Indices: 35583944--35584008 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
35583934 GGTGTAGTGC
35583944 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
35583992 CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CT
35584009 ACTACTACTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Done.