Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 110 of 325
Found at i:34994641 original size:112 final size:112
Alignment explanation
Indices: 34994525--34994781 Score: 343
Period size: 112 Copynumber: 2.3 Consensus size: 112
34994515 CTGAATGGGC
* * * * * *
34994525 TCAAACGAGCAATGTCTAATGATTATACTGAATGTACTCAAACGAGCAATATCTACTAAATCTAC
1 TCAAACGAGCAATATCCACTGATTATACCGAATGGACTCAAACGAGCAATATCTACTAAATATAC
* * * *
34994590 TGAACGTGCTCGAAAGAGCAATGTCTATTGATTATACTGAAAATTAA
66 TAAACGTGCTCAAAAAAGCAATGTCTACTGATTATACTGAAAATTAA
** * *
34994637 TCAAACGAGCAATATCCACCAATTATACCGAATGGACTCAAACGAGCAATATCTACTGAATATAG
1 TCAAACGAGCAATATCCACTGATTATACCGAATGGACTCAAACGAGCAATATCTACTAAATATAC
* **
34994702 TAAACGTGCTCAAAAAAGCAATGTCTACTGATTATACTGAAATTTGC
66 TAAACGTGCTCAAAAAAGCAATGTCTACTGATTATACTGAAAATTAA
* *
34994749 TCAAACGAGCGATATCCACTGATTATACGGAAT
1 TCAAACGAGCAATATCCACTGATTATACCGAAT
34994782 TCATGCTCAA
Statistics
Matches: 124, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
112 124 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.26
Consensus pattern (112 bp):
TCAAACGAGCAATATCCACTGATTATACCGAATGGACTCAAACGAGCAATATCTACTAAATATAC
TAAACGTGCTCAAAAAAGCAATGTCTACTGATTATACTGAAAATTAA
Found at i:34994714 original size:149 final size:149
Alignment explanation
Indices: 34994429--34994776 Score: 410
Period size: 149 Copynumber: 2.3 Consensus size: 149
34994419 AAAAATGGAA
* * *
34994429 TACTGAATATACTGAACGTGCTCAAAAGAGTAATGTCTACTGATTATACTAAAAGTTACTCAAAC
1 TACTAAATATACTGAACGTGCTCAAAAGAGCAATGTCTACTGATTATACTAAAAGTTAATCAAAC
* ** * * * * * *
34994494 GAGCAATATCCTCTGATTATACTGAATGGGCTCAAACGAGCAATGTCTAATGATTATACTGAATG
66 GAGCAATATCCACCAATTATACCGAATGGACTCAAACGAGCAATATCTAATGAATATACTAAACG
**
34994559 TACTCAAACGAGCAATATC
131 TACTCAAAAAAGCAATATC
* * *
34994578 TACTAAATCTACTGAACGTGCTCGAAAGAGCAATGTCTATTGATTATACTGAAAA-TTAATCAAA
1 TACTAAATATACTGAACGTGCTCAAAAGAGCAATGTCTACTGATTATACT-AAAAGTTAATCAAA
* *
34994642 CGAGCAATATCCACCAATTATACCGAATGGACTCAAACGAGCAATATCTACTGAATATAGTAAAC
65 CGAGCAATATCCACCAATTATACCGAATGGACTCAAACGAGCAATATCTAATGAATATACTAAAC
* *
34994707 GTGCTCAAAAAAGCAATGTC
130 GTACTCAAAAAAGCAATATC
* * ** * * * *
34994727 TACTGATTATACTGAAATTTGCTCAAACGAGCGATATCCACTGATTATAC
1 TACTAAATATACTG-AACGTGCTCAAAAGAGCAATGTCTACTGATTATAC
34994777 GGAATTCATG
Statistics
Matches: 165, Mismatches: 32, Indels: 3
0.82 0.16 0.01
Matches are distributed among these distances:
149 134 0.81
150 31 0.19
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (149 bp):
TACTAAATATACTGAACGTGCTCAAAAGAGCAATGTCTACTGATTATACTAAAAGTTAATCAAAC
GAGCAATATCCACCAATTATACCGAATGGACTCAAACGAGCAATATCTAATGAATATACTAAACG
TACTCAAAAAAGCAATATC
Found at i:34994804 original size:39 final size:37
Alignment explanation
Indices: 34994467--34994820 Score: 123
Period size: 37 Copynumber: 9.5 Consensus size: 37
34994457 AGTAATGTCT
* * * *
34994467 ACTGATTATACTAAAAGTTACTCAAACGAGCAATATCC
1 ACTGATTATACTGAAATTTGCTCAAACAAGC-ATATCC
* ** * * *
34994505 TCTGATTATACTG-AATGGGCTCAAACGAGCAATGTCT
1 ACTGATTATACTGAAATTTGCTCAAACAAGC-ATATCC
* * * * *
34994542 AATGATTATACTG-AATGTACTCAAACGAGCAATATCT
1 ACTGATTATACTGAAATTTGCTCAAACAAGC-ATATCC
* * * ** * * *
34994579 ACTAAATCTACTG-AACGTGCTCGAAA-GAGCAATGTCT
1 ACTGATTATACTGAAATTTGCTC-AAACAAGC-ATATCC
* * ** *
34994616 ATTGATTATACTGAAAATTAATCAAACGAGCAATATCC
1 ACTGATTATACTGAAATTTGCTCAAACAAGC-ATATCC
** * * * *
34994654 ACCAATTATACCG-AA-TGGACTCAAACGAGCAATATCT
1 ACTGATTATACTGAAATTTG-CTCAAACAAGC-ATATCC
* * ** * * *
34994691 ACTGAATATAGT-AAACGTGCTCAAAAAAGCAATGTCT
1 ACTGATTATACTGAAATTTGCTCAAACAAGC-ATATCC
*
34994728 ACTGATTATACTGAAATTTGCTCAAACGAGCGATATCC
1 ACTGATTATACTGAAATTTGCTCAAACAAGC-ATATCC
*
34994766 ACTGATTATAC-GGAATTCATGCTCAAACAAGCATTATCC
1 ACTGATTATACTGAAATT--TGCTCAAACAAGCA-TATCC
* *
34994805 ATTGATTACAC-GAAAT
1 ACTGATTATACTGAAAT
34994821 GAGGTCTCAC
Statistics
Matches: 244, Mismatches: 62, Indels: 19
0.75 0.19 0.06
Matches are distributed among these distances:
36 1 0.00
37 145 0.59
38 68 0.28
39 30 0.12
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (37 bp):
ACTGATTATACTGAAATTTGCTCAAACAAGCATATCC
Found at i:35002753 original size:39 final size:38
Alignment explanation
Indices: 35002695--35002774 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 38
35002685 GTGATGTATT
* *
35002695 CGGACTTAGGGTCGCAGGCTATGTGCTAGAATTATATC
1 CGGACTTAAGGTCGCAGGCTATGTGCTAGAAATATATC
* *
35002733 CGGACTTAAGGTCCGCAGGCTATGTGCTGGAAATATGTC
1 CGGACTTAAGGT-CGCAGGCTATGTGCTAGAAATATATC
35002772 CGG
1 CGG
35002775 GCTAAAGTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 11 0.30
39 26 0.70
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (38 bp):
CGGACTTAAGGTCGCAGGCTATGTGCTAGAAATATATC
Found at i:35002792 original size:39 final size:39
Alignment explanation
Indices: 35002707--35002784 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
35002697 GACTTAGGGT
* *
35002707 CGCAGGCTATGTGCTAGAATTATATCCGGACTTAAGGTC
1 CGCAGGCTATGTGCTAGAAATATATCCGGACTTAAAGTC
* * *
35002746 CGCAGGCTATGTGCTGGAAATATGTCCGGGC-TAAAGTC
1 CGCAGGCTATGTGCTAGAAATATATCCGGACTTAAAGTC
35002784 C
1 C
35002785 CGTAGGCTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
38 7 0.21
39 27 0.79
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CGCAGGCTATGTGCTAGAAATATATCCGGACTTAAAGTC
Found at i:35002839 original size:38 final size:38
Alignment explanation
Indices: 35002745--35002839 Score: 93
Period size: 39 Copynumber: 2.4 Consensus size: 38
35002735 GACTTAAGGT
*
35002745 CCGCAGGCTATGTGCTGGAAATATGTCCGGGCTAAAGTC
1 CCGCAGGCT-TGTGCTGGAAATATGACCGGGCTAAAGTC
* * * * * *
35002784 CCGTAGGCTTCGAGCTGGTATTAT-ACCGGGTTTAAATTC
1 CCGCAGGCTT-GTGCTGGAAATATGACCGGG-CTAAAGTC
35002823 CCGCAGGCTTGTGCTGG
1 CCGCAGGCTTGTGCTGG
35002840 CAATTGGTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
38 12 0.27
39 33 0.73
ACGTcount: A:0.19, C:0.23, G:0.31, T:0.27
Consensus pattern (38 bp):
CCGCAGGCTTGTGCTGGAAATATGACCGGGCTAAAGTC
Found at i:35010439 original size:12 final size:12
Alignment explanation
Indices: 35010424--35010448 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35010414 TTTTTCTTTA
35010424 TTCTTTTATTAT
1 TTCTTTTATTAT
35010436 TTCTTTTATTAT
1 TTCTTTTATTAT
35010448 T
1 T
35010449 ATAACATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCTTTTATTAT
Found at i:35010704 original size:19 final size:20
Alignment explanation
Indices: 35010670--35010707 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
35010660 AATCCTTACA
35010670 CTAAATTAACCTTAATTAAG
1 CTAAATTAACCTTAATTAAG
*
35010690 CTAAATTTA-CTTAATTAA
1 CTAAATTAACCTTAATTAA
35010708 AATCTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
CTAAATTAACCTTAATTAAG
Found at i:35017609 original size:11 final size:11
Alignment explanation
Indices: 35017593--35017632 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
35017583 TAAAACCTTA
35017593 TTTTTCTTTTC
1 TTTTTCTTTTC
35017604 TTTTTC-TTTC
1 TTTTTCTTTTC
35017614 TTTTT-TTCTT-
1 TTTTTCTT-TTC
35017624 TTTTTCTTT
1 TTTTTCTTT
35017633 CCCTGTTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:35017619 original size:12 final size:11
Alignment explanation
Indices: 35017593--35017633 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
35017583 TAAAACCTTA
*
35017593 TTTTTCTTTTC
1 TTTTTCTTTTT
35017604 TTTTTCTTTCTT
1 TTTTTCTTT-TT
35017616 TTTTTCTTTTT
1 TTTTTCTTTTT
35017627 TTCTTTC
1 TT-TTTC
35017634 CCTGTTCTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 13 0.48
12 14 0.52
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:35017623 original size:8 final size:8
Alignment explanation
Indices: 35017593--35017632 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
35017583 TAAAACCTTA
35017593 TTTTTCTT
1 TTTTTCTT
*
35017601 TTCTT-TT
1 TTTTTCTT
*
35017608 TCTTTCTT
1 TTTTTCTT
35017616 TTTTTCTT
1 TTTTTCTT
35017624 TTTTTCTT
1 TTTTTCTT
35017632 T
1 T
35017633 CCCTGTTCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 5 0.19
8 22 0.81
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTCTT
Found at i:35017688 original size:12 final size:12
Alignment explanation
Indices: 35017673--35017697 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35017663 TTTTTCTTTA
35017673 TTCTTTTATTAT
1 TTCTTTTATTAT
35017685 TTCTTTTATTAT
1 TTCTTTTATTAT
35017697 T
1 T
35017698 ATAACATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCTTTTATTAT
Found at i:35017950 original size:19 final size:19
Alignment explanation
Indices: 35017914--35017955 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
35017904 AATTTAATCC
35017914 TTAACTAAATTAACCTTAA
1 TTAACTAAATTAACCTTAA
*
35017933 TTAAGCTAAATTTA-CTTAA
1 TTAA-CTAAATTAACCTTAA
35017952 TTAA
1 TTAA
35017956 AATCTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (19 bp):
TTAACTAAATTAACCTTAA
Found at i:35021295 original size:14 final size:14
Alignment explanation
Indices: 35021276--35021303 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35021266 TCCTCGAACG
35021276 TCAGATCCGGTCTA
1 TCAGATCCGGTCTA
35021290 TCAGATCCGGTCTA
1 TCAGATCCGGTCTA
35021304 ATCTTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (14 bp):
TCAGATCCGGTCTA
Found at i:35030508 original size:41 final size:41
Alignment explanation
Indices: 35030223--35030492 Score: 379
Period size: 41 Copynumber: 6.6 Consensus size: 41
35030213 TTAAACAGAT
** * * *
35030223 TCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTG-ATTCAGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAAT--GTA
* *
35030265 -CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCA-TTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
* *
35030305 TCACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
35030346 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
35030387 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
35030428 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTG-AAT-TA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
35030467 CTTCACCGGCATTAAGCCTGCTAGAC
1 --TCACCGGCATTAAGCCTGCTAGAC
35030493 GTAACGTCCG
Statistics
Matches: 214, Mismatches: 8, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
39 2 0.01
40 8 0.04
41 200 0.93
42 4 0.02
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
Found at i:35032036 original size:13 final size:13
Alignment explanation
Indices: 35032018--35032042 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35032008 CAATCAAATG
35032018 CACACAAAATAAA
1 CACACAAAATAAA
35032031 CACACAAAATAA
1 CACACAAAATAA
35032043 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:35038180 original size:41 final size:41
Alignment explanation
Indices: 35037895--35038164 Score: 379
Period size: 41 Copynumber: 6.6 Consensus size: 41
35037885 TTAAACAGAT
** * * *
35037895 TCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTG-ATTCAGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAAT--GTA
* *
35037937 -CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCA-TTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
* *
35037977 TCACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
35038018 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
35038059 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
35038100 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTG-AAT-TA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
35038139 CTTCACCGGCATTAAGCCTGCTAGAC
1 --TCACCGGCATTAAGCCTGCTAGAC
35038165 GTAACGTCCG
Statistics
Matches: 214, Mismatches: 8, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
39 2 0.01
40 8 0.04
41 200 0.93
42 4 0.02
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
Found at i:35039706 original size:13 final size:13
Alignment explanation
Indices: 35039688--35039712 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35039678 CAATCAAATG
35039688 CACACAAAATAAA
1 CACACAAAATAAA
35039701 CACACAAAATAA
1 CACACAAAATAA
35039713 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:35047611 original size:22 final size:23
Alignment explanation
Indices: 35047559--35047612 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
35047549 TTTTTAAAAT
35047559 TTTGGGCTTTAGGGTTTAGGTAA
1 TTTGGGCTTTAGGGTTTAGGTAA
* * *
35047582 TTTAGGCTTTAGGGTTT-TGTTA
1 TTTGGGCTTTAGGGTTTAGGTAA
35047604 TTTGGGCTT
1 TTTGGGCTT
35047613 GTTTTGGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.13, C:0.06, G:0.31, T:0.50
Consensus pattern (23 bp):
TTTGGGCTTTAGGGTTTAGGTAA
Found at i:35047961 original size:44 final size:42
Alignment explanation
Indices: 35047895--35048027 Score: 113
Period size: 44 Copynumber: 3.0 Consensus size: 42
35047885 ATAAGATTTG
* **
35047895 TTGTAGTTTCAATCCATTCCACTGCAACTTCAGGTATATAAGAT
1 TTGTAGCTTC-ATCCAGCCCACTGCAACTTCAGG-ATATAAGAT
* * * *
35047939 TTGTAGCTTCATTCCAGCCCACTGTAACTTTATGGGTATAGGAT
1 TTGTAGCTTCA-TCCAGCCCACTGCAACTTCA-GGATATAAGAT
* ** *
35047983 TTGTAGCTTTATCTTGCTCCACTGCAACTTCAGGGAGATAAGAT
1 TTGTAGCTTCATCCAGC-CCACTGCAACTTCA-GGATATAAGAT
35048027 T
1 T
35048028 CGCTATGATA
Statistics
Matches: 70, Mismatches: 16, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
43 5 0.07
44 63 0.90
45 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (42 bp):
TTGTAGCTTCATCCAGCCCACTGCAACTTCAGGATATAAGAT
Found at i:35048091 original size:94 final size:92
Alignment explanation
Indices: 35047975--35048353 Score: 352
Period size: 94 Copynumber: 4.0 Consensus size: 92
35047965 ACTTTATGGG
* * * * *
35047975 TATAGGATTTGTAGCTTTATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGATAGC
1 TATAGGATTTGTAGCTTCATCTTGCTCCACTACAACTTCAGGGAGATAAGATTTGATAT-ATAAC
* *
35048040 TTCTATCCAATCCACTTTATCTTCAACGA
65 TT-TATCTAATCCACTTCATCTTCAACGA
* * *
35048069 TATAGGATTTGTAGCTTCATCTTGCTCCACTGA-AACTTTAGGGAAATAATATTTGATATTATAA
1 TATAGGATTTGTAGCTTCATCTTGCTCCACT-ACAACTTCAGGGAGATAAGATTTGATA-TATAA
* *
35048133 CTTTGATCTAATCCA-TTGCATCTTTAAGGA
64 CTTT-ATCTAATCCACTT-CATCTTCAACGA
* * * * *
35048163 TATAGGATTTGTAGTTTCATCTTGCTCCACTACAACTTTAGGGAGTTAAGGTTTGTTATAGTAAC
1 TATAGGATTTGTAGCTTCATCTTGCTCCACTACAACTTCAGGGAGATAAGATTTGATATA-TAAC
* * * * ** *
35048228 TTTATTCTGACCCACTACAACTTCAGTGG
65 TTTA-TCTAATCCACTTCATCTTCAACGA
* * *
35048257 TATAGAATTTGTAGCTTTATCTTGCTCCACTACAACTTCAAGGAGATAAGATTTG-TCAT-TGCA
1 TATAGGATTTGTAGCTTCATCTTGCTCCACTACAACTTCAGGGAGATAAGATTTGAT-ATAT--A
* * *
35048320 ACTTTGATCCAATCCACTGCATCTTCAAGGA
63 ACTTT-ATCTAATCCACTTCATCTTCAACGA
35048351 TAT
1 TAT
35048354 GGGAGTCACT
Statistics
Matches: 232, Mismatches: 41, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
92 1 0.00
93 8 0.03
94 220 0.95
95 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (92 bp):
TATAGGATTTGTAGCTTCATCTTGCTCCACTACAACTTCAGGGAGATAAGATTTGATATATAACT
TTATCTAATCCACTTCATCTTCAACGA
Found at i:35048311 original size:44 final size:44
Alignment explanation
Indices: 35048158--35048312 Score: 106
Period size: 44 Copynumber: 3.4 Consensus size: 44
35048148 TTGCATCTTT
* * *
35048158 AAGGATATAGGATTTGTAG-TTTCATCTTGCTCCACTACAACTTT
1 AAGGAGATAAGATTTGTAGCTTT-ATCTTGCTCCACTACAACTTC
* * *
35048202 AGGGAGTTAAGGTTTGTTATAGTAACTTTAT-TCTGAC-CCACTACAACTTC
1 AAGGAGATAAGATTTG---TAG---CTTTATCT-TG-CTCCACTACAACTTC
35048252 -AGTG-G-TATAGAATTTGTAGCTTTATCTTGCTCCACTACAACTTC
1 AAG-GAGATA-AG-ATTTGTAGCTTTATCTTGCTCCACTACAACTTC
35048296 AAGGAGATAAGATTTGT
1 AAGGAGATAAGATTTGT
35048313 CATTGCAACT
Statistics
Matches: 86, Mismatches: 8, Indels: 34
0.67 0.06 0.27
Matches are distributed among these distances:
43 1 0.01
44 39 0.45
45 6 0.07
46 2 0.02
47 6 0.07
48 2 0.02
49 5 0.06
50 21 0.24
51 4 0.05
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (44 bp):
AAGGAGATAAGATTTGTAGCTTTATCTTGCTCCACTACAACTTC
Found at i:35057909 original size:17 final size:17
Alignment explanation
Indices: 35057887--35057924 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
35057877 CAGTCGGAAT
35057887 ATCCCTGAACACTTCCA
1 ATCCCTGAACACTTCCA
35057904 ATCCCTGAACACTTCCA
1 ATCCCTGAACACTTCCA
35057921 ATCC
1 ATCC
35057925 TATGGCATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.42, G:0.05, T:0.24
Consensus pattern (17 bp):
ATCCCTGAACACTTCCA
Found at i:35058736 original size:18 final size:18
Alignment explanation
Indices: 35058710--35058748 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
35058700 TCTGTTTCGT
35058710 TTTCATTCTTTCT-TTTTA
1 TTTCATTCTTT-TATTTTA
*
35058728 TTTCTTTCTTTTATTTTA
1 TTTCATTCTTTTATTTTA
35058746 TTT
1 TTT
35058749 AATTACTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTCATTCTTTTATTTTA
Found at i:35058740 original size:13 final size:14
Alignment explanation
Indices: 35058715--35058743 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
35058705 TTCGTTTTCA
35058715 TTCTTTCTTTTTAT
1 TTCTTTCTTTTTAT
35058729 TTCTTTC-TTTTAT
1 TTCTTTCTTTTTAT
35058742 TT
1 TT
35058744 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (14 bp):
TTCTTTCTTTTTAT
Found at i:35062848 original size:19 final size:19
Alignment explanation
Indices: 35062826--35062862 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
35062816 AACCAAACTA
35062826 GCAAGAGCTATGCAAAACC
1 GCAAGAGCTATGCAAAACC
35062845 GCAAGAGCTATGCAAAAC
1 GCAAGAGCTATGCAAAAC
35062863 TAATTAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.11
Consensus pattern (19 bp):
GCAAGAGCTATGCAAAACC
Found at i:35076656 original size:65 final size:65
Alignment explanation
Indices: 35076570--35076707 Score: 240
Period size: 65 Copynumber: 2.1 Consensus size: 65
35076560 GAGCACTACC
* *
35076570 GCAGCTCTTTGTGAGCGTCCTGACATATAATCGGTTGTGATCCTGAATATAGTGCAGACACAAAA
1 GCAGCTCTTTATAAGCGTCCTGACATATAATCGGTTGTGATCCTGAATATAGTGCAGACACAAAA
*
35076635 GCAGCTCTTTATAAGCTTCCTGACATATAATCGGTTGTGATCCTGAATATAGTGCAGACACAAAA
1 GCAGCTCTTTATAAGCGTCCTGACATATAATCGGTTGTGATCCTGAATATAGTGCAGACACAAAA
*
35076700 GCAACTCT
1 GCAGCTCT
35076708 CTGTTACCTT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Consensus pattern (65 bp):
GCAGCTCTTTATAAGCGTCCTGACATATAATCGGTTGTGATCCTGAATATAGTGCAGACACAAAA
Found at i:35082147 original size:10 final size:10
Alignment explanation
Indices: 35082120--35082179 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
35082110 TTAAATTCTA
35082120 AAAGATAAAT
1 AAAGATAAAT
35082130 ACAA-ATAAAT
1 A-AAGATAAAT
*
35082140 AAAGATAATT
1 AAAGATAAAT
*
35082150 AAGGATAAAT
1 AAAGATAAAT
35082160 AAAGATAAAT
1 AAAGATAAAT
35082170 GAAA-ATAAAT
1 -AAAGATAAAT
35082180 CCTAAGATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
9 2 0.05
10 36 0.84
11 5 0.12
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:35084169 original size:12 final size:11
Alignment explanation
Indices: 35084161--35084202 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 11
35084151 AAAATAATGT
35084161 AATAAATAATAA
1 AATAAATAAT-A
35084173 AATAAAGTAATA
1 AATAAA-TAATA
35084185 AATAAATAATAA
1 AATAAATAAT-A
35084197 AATAAA
1 AATAAA
35084203 AATTGGGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.14
12 20 0.71
13 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (11 bp):
AATAAATAATA
Found at i:35084174 original size:20 final size:20
Alignment explanation
Indices: 35084151--35084189 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
35084141 CCACCCAAAC
*
35084151 AAAATAATGTAATAAATAAT
1 AAAATAAAGTAATAAATAAT
35084171 AAAATAAAGTAATAAATAA
1 AAAATAAAGTAATAAATAA
35084190 ATAATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAATAAAGTAATAAATAAT
Found at i:35089336 original size:20 final size:20
Alignment explanation
Indices: 35089311--35089349 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
35089301 TACGAGTATG
35089311 TTTAAATGTTTTATATGATA
1 TTTAAATGTTTTATATGATA
35089331 TTTAAATGTTTTATATGAT
1 TTTAAATGTTTTATATGAT
35089350 GTCATAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (20 bp):
TTTAAATGTTTTATATGATA
Found at i:35089909 original size:21 final size:20
Alignment explanation
Indices: 35089878--35089917 Score: 55
Period size: 19 Copynumber: 1.9 Consensus size: 20
35089868 AGTCGAGGAC
35089878 TAAAGTGGAAACAAATTAAAAT
1 TAAAGTGG-AA-AAATTAAAAT
35089900 TAAA-TGGAAAAATTAAAA
1 TAAAGTGGAAAAATTAAAA
35089918 AGAAAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 3 0.17
22 4 0.22
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.23
Consensus pattern (20 bp):
TAAAGTGGAAAAATTAAAAT
Found at i:35091073 original size:23 final size:23
Alignment explanation
Indices: 35091045--35091096 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
35091035 TTAGGTTTTA
*
35091045 GGCTTGACGGCTTAGGTAATTTG
1 GGCTTGACGGCTTAAGTAATTTG
**
35091068 GGCTTGGGGGCTTAAGTAATTTG
1 GGCTTGACGGCTTAAGTAATTTG
35091091 GGCTTG
1 GGCTTG
35091097 TATTGGACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.15, C:0.12, G:0.38, T:0.35
Consensus pattern (23 bp):
GGCTTGACGGCTTAAGTAATTTG
Found at i:35103904 original size:174 final size:174
Alignment explanation
Indices: 35103584--35103909 Score: 368
Period size: 174 Copynumber: 1.9 Consensus size: 174
35103574 AATCCTAATA
* * * * *
35103584 TCTAAACCAACTCAGAGAATATCAAACTAAACAGGTGTACTACTAGCAAGTTAAATTTCACCTTT
1 TCTAAACCAACTCAAAGAATATCAAACTAAACAGCTGCACTAATAGCAAATTAAATTTCACCTTT
* * * * *
35103649 CCAGCATTTCTCAAACATCTAAATAAACTAATTAAGATATTCAAATCTCACAACCAATTTTCCTA
66 CCAGCATTTCTCAAACAGCCAAATAAACTAATTAAGAGATCCAAATCTCACAACCAATTTT-CAA
* * *
35103714 GACCTAATGCTAAAATGAAATTCACAGAAAACAAAATTCTTAACC
130 AACCGAAAGCTAAAATGAAATTCACAGAAAACAAAATTCTTAACC
* * * * ** *
35103759 TCTAAACCAACTCAAAGAA-ATCAAAGTTAACAGCTGCATTAATAGTAAATTGCATTTCACTTTT
1 TCTAAACCAACTCAAAGAATATCAAACTAAACAGCTGCACTAATAGCAAATTAAATTTCACCTTT
* * * * *
35103823 CCATCATTTCTCAAGCAGCCAAATAAACTGATTAAAGAGATCCTAATCTCACTACCAATTTAT-A
66 CCAGCATTTCTCAAACAGCCAAATAAACTAATT-AAGAGATCCAAATCTCACAACCAATTT-TCA
* *
35103887 AAACCGAAAGGTAAAATGTAATT
129 AAACCGAAAGCTAAAATGAAATT
35103910 TTATTTTTAA
Statistics
Matches: 122, Mismatches: 27, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
174 80 0.66
175 41 0.34
176 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (174 bp):
TCTAAACCAACTCAAAGAATATCAAACTAAACAGCTGCACTAATAGCAAATTAAATTTCACCTTT
CCAGCATTTCTCAAACAGCCAAATAAACTAATTAAGAGATCCAAATCTCACAACCAATTTTCAAA
ACCGAAAGCTAAAATGAAATTCACAGAAAACAAAATTCTTAACC
Found at i:35106604 original size:22 final size:21
Alignment explanation
Indices: 35106566--35106618 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
35106556 TGAAATTGAT
*
35106566 AATATATAA-AAAAAATTTAA
1 AATAAATAATAAAAAATTTAA
*
35106586 AGTAAATAATAAAACAATTTAA
1 AATAAATAATAAAA-AATTTAA
*
35106608 AATGAATAATA
1 AATAAATAATA
35106619 CATGAAGCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 7 0.26
21 4 0.15
22 16 0.59
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (21 bp):
AATAAATAATAAAAAATTTAA
Found at i:35107105 original size:22 final size:22
Alignment explanation
Indices: 35107080--35107121 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
35107070 CTCAATGTAT
35107080 ATAAAAAAACAATTTAAAATGG
1 ATAAAAAAACAATTTAAAATGG
* * *
35107102 ATAATAATACAATTTTAAAT
1 ATAAAAAAACAATTTAAAAT
35107122 AATCAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (22 bp):
ATAAAAAAACAATTTAAAATGG
Found at i:35111035 original size:3 final size:3
Alignment explanation
Indices: 35111027--35111060 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
35111017 ATGACAACAC
* *
35111027 ATA ATA ATA ATA ATA ATA ATG ATG ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
35111061 AATTAAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:35111662 original size:13 final size:13
Alignment explanation
Indices: 35111620--35111668 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 13
35111610 ATGGTAAACT
35111620 TTATATTTTT-T-
1 TTATATTTTTGTA
* *
35111631 TTATTTTTTTG-C
1 TTATATTTTTGTA
35111643 TTA-ATTTTTGTA
1 TTATATTTTTGTA
35111655 TTATATTTTTGTA
1 TTATATTTTTGTA
35111668 T
1 T
35111669 ATTTGGTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 15 0.48
12 6 0.19
13 10 0.32
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.73
Consensus pattern (13 bp):
TTATATTTTTGTA
Found at i:35117599 original size:22 final size:22
Alignment explanation
Indices: 35117555--35117600 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
35117545 CAATACTAAC
*
35117555 AATAAAATAATAACAACATAAT
1 AATAAAATAATAACAACACAAT
*
35117577 AATAAAATGATAACGAA-ACAAT
1 AATAAAATAATAAC-AACACAAT
35117599 AA
1 AA
35117601 GGAATCAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.20
Consensus pattern (22 bp):
AATAAAATAATAACAACACAAT
Found at i:35131846 original size:18 final size:18
Alignment explanation
Indices: 35131825--35131859 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35131815 AAGAAACGAT
*
35131825 AAATATGTATATATATAA
1 AAATATGTACATATATAA
35131843 AAATATGTACATATATA
1 AAATATGTACATATATA
35131860 TGGGTGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (18 bp):
AAATATGTACATATATAA
Found at i:35132436 original size:3 final size:3
Alignment explanation
Indices: 35132387--35132418 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
35132377 AACATAAACA
35132387 AAT AAGT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT A
35132419 GAATAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:35133591 original size:27 final size:27
Alignment explanation
Indices: 35133551--35133619 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
35133541 TTTTTTTGTT
*
35133551 TTGGGTT-TTGGGCTGAGGGTAGGCTA
1 TTGGGTTATTGGGCTAAGGGTAGGCTA
35133577 TTGGGTTATTGGGCTAAGGGTAGGCTA
1 TTGGGTTATTGGGCTAAGGGTAGGCTA
35133604 TTGGGTTATTGGGCTA
1 TTGGGTTATTGGGCTA
35133620 GTGGTTCTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 7 0.17
27 34 0.83
ACGTcount: A:0.14, C:0.07, G:0.42, T:0.36
Consensus pattern (27 bp):
TTGGGTTATTGGGCTAAGGGTAGGCTA
Found at i:35135539 original size:23 final size:23
Alignment explanation
Indices: 35135497--35135540 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
35135487 AATTTAATCT
*
35135497 TTTCTTTTCTCCATTTATTAAGG
1 TTTCTTTTCTCCATTAATTAAGG
**
35135520 TTTCTTTTCTTTATTAATTAA
1 TTTCTTTTCTCCATTAATTAA
35135541 AGTAAAATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.14, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTCTTTTCTCCATTAATTAAGG
Found at i:35140432 original size:14 final size:14
Alignment explanation
Indices: 35140393--35140432 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
35140383 ATTTTCTTTA
35140393 ATTATTTTCA-AAT
1 ATTATTTTCATAAT
*
35140406 ATTATTTTTATAAT
1 ATTATTTTCATAAT
*
35140420 ATTATTATCATAA
1 ATTATTTTCATAA
35140433 ATTGTATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTATTTTCATAAT
Found at i:35142169 original size:13 final size:13
Alignment explanation
Indices: 35142153--35142179 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35142143 ACTCCCAAAT
35142153 ATAATATTAAAAA
1 ATAATATTAAAAA
35142166 ATAATATTAAAAA
1 ATAATATTAAAAA
35142179 A
1 A
35142180 ATTATTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATATTAAAAA
Found at i:35142777 original size:17 final size:19
Alignment explanation
Indices: 35142747--35142789 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
35142737 TGTAATCATC
35142747 ATAATT-TTTATTAAAT-T
1 ATAATTATTTATTAAATAT
*
35142764 GTAATTATTT-TTAAATAT
1 ATAATTATTTATTAAATAT
35142782 ATAATTAT
1 ATAATTAT
35142790 CACACCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATAATTATTTATTAAATAT
Found at i:35146046 original size:16 final size:16
Alignment explanation
Indices: 35146025--35146063 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
35146015 GATCAGTGGA
35146025 TTGAATTA-TTTAGATT
1 TTGAATTATTTTAGA-T
35146041 TTGAATTATTTTAGAT
1 TTGAATTATTTTAGAT
35146057 TTGAATT
1 TTGAATT
35146064 GAAAGGTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (16 bp):
TTGAATTATTTTAGAT
Found at i:35146297 original size:14 final size:15
Alignment explanation
Indices: 35146278--35146310 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
35146268 CTTTACTTAA
*
35146278 TTTTTATATATA-AT
1 TTTTTATAAATATAT
35146292 TTTTTATAAATATAT
1 TTTTTATAAATATAT
35146307 TTTT
1 TTTT
35146311 ATGAAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTATAAATATAT
Found at i:35154461 original size:21 final size:21
Alignment explanation
Indices: 35154427--35154467 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35154417 GCATGAATAA
*
35154427 AATAGTATACAAATGAGTGAC
1 AATAGTATACAAATAAGTGAC
35154448 AATAGTATGA-AAATAAGTGA
1 AATAGTAT-ACAAATAAGTGA
35154468 ACGGATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (21 bp):
AATAGTATACAAATAAGTGAC
Found at i:35155720 original size:17 final size:18
Alignment explanation
Indices: 35155698--35155737 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
35155688 AAAAACGAAA
35155698 TAAAAAAAAAACTAGTTG
1 TAAAAAAAAAACTAGTTG
35155716 TAAAAAAAAAACTAGTTG
1 TAAAAAAAAAACTAGTTG
35155734 TAAA
1 TAAA
35155738 TAAATATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (18 bp):
TAAAAAAAAAACTAGTTG
Found at i:35155906 original size:17 final size:17
Alignment explanation
Indices: 35155851--35155895 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
35155841 GTAATACCTA
35155851 AAATAT-AA-AAATAAAG
1 AAATATAAATAAAT-AAG
35155867 AAAGTATAAATAAATAAG
1 AAA-TATAAATAAATAAG
35155885 AAATATAAATA
1 AAATATAAATA
35155896 GATGAGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.12
17 11 0.42
18 8 0.31
19 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (17 bp):
AAATATAAATAAATAAG
Found at i:35156523 original size:44 final size:44
Alignment explanation
Indices: 35156418--35156539 Score: 126
Period size: 44 Copynumber: 2.8 Consensus size: 44
35156408 TAAAAAGATT
* *
35156418 AATAATAATAATAATAATAATAA-TAAT-GATAATAGTAATAGAA
1 AATAAAAATAATAATAATAATAAGTAATAG-TAATAGCAATAGAA
* *
35156461 AATAAAAA-GATAATAATAATATAGTAATAGTAATAGCCATA-AA
1 AATAAAAATAATAATAATAATA-AGTAATAGTAATAGCAATAGAA
* * *
35156504 AATAAAAATAATAGTAATAATACGGTAATAATAATA
1 AATAAAAATAATAATAATAATA-AGTAATAGTAATA
35156540 AATAGTAATA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
42 12 0.18
43 18 0.27
44 35 0.53
45 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.28
Consensus pattern (44 bp):
AATAAAAATAATAATAATAATAAGTAATAGTAATAGCAATAGAA
Found at i:35156622 original size:3 final size:3
Alignment explanation
Indices: 35155974--35156603 Score: 190
Period size: 3 Copynumber: 208.0 Consensus size: 3
35155964 TACAAAAATG
** * *
35155974 ATA ATA ATA ATA A-A ATA AGTTA ATA ATA ATA ATA ATA ACC GTA GTA
1 ATA ATA ATA ATA ATA ATA A--TA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
35156020 GTA ATA ATA AAA AT- ATA ATA GTA AAA ATA ATA CTA A-A TATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
* * * ** * *
35156064 ATA GTA ATA TTA ATA ATA AAA ATA ATA GCA ATA AAA ATA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
35156112 ACA ATG ACA ATAA AGA ATA ATA GTA ATA ATG ATA ATA ATA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
35156158 ATA ATA ATA ATA ATA ATA ATG ATG ATG ATG ATGA A-A AT- ATGA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA AT-A ATA
** * * * * * *
35156203 ACC ATA ATC ACA ACTA TATT ATAA ATA ATAA ATA ATA ATA ATG ATA GTC
1 ATA ATA ATA ATA A-TA -ATA AT-A ATA AT-A ATA ATA ATA ATA ATA ATA
* * ** * * * ** * * *
35156252 TTA ATA ATG ATA ACG ACA ATA A-A AAA AT- GTA GGA ATG ATA ATG CTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
35156298 ATA TATA A-A ATA ATA ATA ATT GTA A-A A-A GATA ATA AGA ATA GTA
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
** ** * ** * *
35156342 GCA ATA ATA AGG GTA ATA ACG ATA ATAA ATA ATA ATA CTAA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA AT-A ATA ATA
* * * *
35156389 AAA ATA ATA ATA GA-A ATA ATA AAA AGA TTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
35156434 ATA ATA ATA ATG ATA ATA GTA ATA GAAA ATA A-A A-A GATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA ATA ATA
* * *** * * *
35156479 AT- ATA GTA ATA GTA ATA GCC ATA AAA ATA AAA ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * * *
35156526 CGGTA ATA ATA ATAA ATA GTA ATA ATA ACA ACA ACA ACA ACA ACA ACA
1 --ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
35156574 ACA ACA ACA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35156604 GCAATAATTT
Statistics
Matches: 456, Mismatches: 139, Indels: 64
0.69 0.21 0.10
Matches are distributed among these distances:
2 23 0.05
3 399 0.88
4 28 0.06
5 6 0.01
ACGTcount: A:0.60, C:0.05, G:0.08, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:35157708 original size:16 final size:16
Alignment explanation
Indices: 35157676--35157732 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
35157666 TGGGCTGTTA
*
35157676 ATTTTTGGGCTTGGGGT
1 ATTTTTGGG-TTTGGGT
35157693 ATTTTTGGGTTTGGGT
1 ATTTTTGGGTTTGGGT
* * *
35157709 A-GTTGGGGTTTAGGT
1 ATTTTTGGGTTTGGGT
35157724 -TTTTTGGGT
1 ATTTTTGGGT
35157733 CTTTTAGTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 17 0.52
16 7 0.21
17 9 0.27
ACGTcount: A:0.07, C:0.02, G:0.40, T:0.51
Consensus pattern (16 bp):
ATTTTTGGGTTTGGGT
Found at i:35158116 original size:27 final size:26
Alignment explanation
Indices: 35158086--35158137 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
35158076 ACAAGGATGT
*
35158086 GTATAAGAATTTCAAAATAAATAATAC
1 GTATAAGAATTT-AAAAGAAATAATAC
* *
35158113 GTATAATAGTTTAAAAGAAATAATA
1 GTATAAGAATTTAAAAGAAATAATA
35158138 TATGTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.56, C:0.04, G:0.10, T:0.31
Consensus pattern (26 bp):
GTATAAGAATTTAAAAGAAATAATAC
Found at i:35161981 original size:3 final size:3
Alignment explanation
Indices: 35161973--35162003 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
35161963 TATATCACTC
35161973 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
35162004 GCAACAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:35162502 original size:31 final size:32
Alignment explanation
Indices: 35162442--35162511 Score: 81
Period size: 34 Copynumber: 2.2 Consensus size: 32
35162432 CGATATGTTC
*
35162442 TTTTAATAAATAAAAAAATTAAACTAATATATAA
1 TTTTAATAAAT-AAAAAATTAAACAAATAT-TAA
* *
35162476 TTTTAATAAAT-AAAATTTAAA-AAATATTTA
1 TTTTAATAAATAAAAAATTAAACAAATATTAA
35162506 TTTTAA
1 TTTTAA
35162512 AGATTCGCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 8 0.24
31 5 0.15
32 9 0.27
34 11 0.33
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (32 bp):
TTTTAATAAATAAAAAATTAAACAAATATTAA
Found at i:35164090 original size:30 final size:30
Alignment explanation
Indices: 35164039--35164105 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
35164029 TTGATATGTT
*
35164039 TATATATTTTTAACATGTTATAAATTATAA
1 TATATATTTTTAACATCTTATAAATTATAA
* * *
35164069 TATATA-TTTTAAGTATCTTATAATTTATCA
1 TATATATTTTTAA-CATCTTATAAATTATAA
35164099 TCATATA
1 T-ATATA
35164106 AAATTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 6 0.19
30 20 0.65
31 5 0.16
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (30 bp):
TATATATTTTTAACATCTTATAAATTATAA
Found at i:35168710 original size:44 final size:44
Alignment explanation
Indices: 35168577--35169383 Score: 348
Period size: 44 Copynumber: 18.0 Consensus size: 44
35168567 CAAGATTGGT
* ** * *
35168577 GACTTGTATCTTTAATCTATTCCACTGCAACTTCAAGGAAATAA
1 GACTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
35168621 GATCCGATGT--CTTCAGTCTGCTCCATTGCATCTTCAGGGAGATAA
1 GA--C-TTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * *
35168666 GACTTGTAACTTTAACCTGCTCCACTGTAACTTCGGGGAAATAA
1 GACTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
35168710 G-GTTAGTGACTTTGATCTACTCCATTGCAACTTCAGGGAGATAA
1 GACTT-GTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * * * **
35168754 GATTTGCTATCTTCAGTCTGCTCTACTGTAACTTCATAGAGATAA
1 GACTTG-TAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
** * *
35168799 GA-TCTGTAA-TTTATAGCTCCAACCTATTCCACTGTAACTTCAGGGAAATAA
1 GACT-TGTAACTTTA-A--T-----CTGCTCCACTGCAACTTCAGGGAGATAA
* * * * * *
35168850 GATTTGCTATCTTCAGTCTGCTGCACTGCAACTTCAGAGAGATAA
1 GACTTG-TAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * *
35168895 GACTTGTAACTTTAACCTGCTCTACCGTAACTTCAGGGAGATAA
1 GACTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* ** * *
35168939 G-GTTAGTGGCTTTGATTTGCTCCACTGCAACTTCAGGGAGATAA
1 GACTT-GTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * *
35168983 GA-TT-TACTATTTTCAGTCTACTCCGCTGCAACTTCAGGGAGATAA
1 GACTTGTA--ACTTT-AATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
35169028 GACTTGTAACTTCAACCTACTCCACTGCATCTTTAGGGAGATAA
1 GACTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* ** * * * * *
35169072 G-GTTAGTGGCTTCAATCAGCTTCACTGCAACTTCAAGAAGATAA
1 GACTT-GTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * * * *
35169116 GA-TTCGCCATCTTCAGTCTGCTCCACTGTAATTTTAGGGAGATAA
1 GACTT-G-TAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * *
35169161 GACTTGTAACTTCAACCTACTCCACTGCATCTTCAGAGG-GAT-A
1 GACTTGTAACTTTAATCTGCTCCACTGCAACTTCAG-GGAGATAA
** * ** ** * * *
35169204 GGGTTAATGGCTTCGATATGCTCCACTGCAACTTTAGGGTGATAA
1 GACTT-GTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
35169249 GA-TT-CACCTTCTTCAGTCTGCCCCACTGTAACTTCAGGGAGATAA
1 GACTTGTAAC-T-TT-AATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * *
35169294 GACTTGTAACTTCAAACTACTCCACTGCATCTTCAGGGAGATAA
1 GACTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* ** ** * * *
35169338 GA-TTAATGGCTTTAATCTATTTCACTGCAACTTTAGGAAGATAA
1 GACTT-GTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
35169382 GA
1 GA
35169384 TTTGCCATAA
Statistics
Matches: 557, Mismatches: 165, Indels: 82
0.69 0.21 0.10
Matches are distributed among these distances:
42 5 0.01
43 19 0.03
44 303 0.54
45 181 0.32
46 9 0.02
47 7 0.01
50 1 0.00
51 26 0.05
52 3 0.01
53 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
GACTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
Found at i:35168998 original size:133 final size:133
Alignment explanation
Indices: 35168826--35169386 Score: 676
Period size: 133 Copynumber: 4.2 Consensus size: 133
35168816 TCCAACCTAT
* * * * *
35168826 TCCACTGTAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTGCACTGCAACTTCAGAGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTTACTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
* * * * * * * ** *
35168891 ATAAGACTTGTAACTTTAACCTGCTCTACCGTAACTTCAGGGAGATAAGGTTAGTGGCTTTGATT
66 ATAAGACTTGTAACTTCAACCTACTCCACTGCATCTTCAGGGAGATAAGGTTAATGGCTTCAATC
35168956 TGC
131 TGC
* * *
35168959 TCCACTGCAACTTCAGGGAGATAAGATTTACTATTTTCAGTCTACTCCGCTGCAACTTCAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTTACTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
* *
35169024 ATAAGACTTGTAACTTCAACCTACTCCACTGCATCTTTAGGGAGATAAGGTTAGTGGCTTCAATC
66 ATAAGACTTGTAACTTCAACCTACTCCACTGCATCTTCAGGGAGATAAGGTTAATGGCTTCAATC
*
35169089 AGC
131 TGC
* * * ** * * * *
35169092 TTCACTGCAACTTCAAGAAGATAAGATTCGCCATCTTCAGTCTGCTCCACTGTAATTTTAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTTACTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
* *
35169157 ATAAGACTTGTAACTTCAACCTACTCCACTGCATCTTCAGAGG-GATAGGGTTAATGGCTTCGAT
66 ATAAGACTTGTAACTTCAACCTACTCCACTGCATCTTCAG-GGAGATAAGGTTAATGGCTTCAAT
*
35169221 ATGC
130 CTGC
* * * * *
35169225 TCCACTGCAACTTTAGGGTGATAAGATTCACCT-TCTTCAGTCTGCCCCACTGTAACTTCAGGGA
1 TCCACTGCAACTTCAGGGAGATAAGATTTA-CTATCTTCAGTCTGCTCCACTGCAACTTCAGGGA
* * *
35169289 GATAAGACTTGTAACTTCAAACTACTCCACTGCATCTTCAGGGAGATAAGATTAATGGCTTTAAT
65 GATAAGACTTGTAACTTCAACCTACTCCACTGCATCTTCAGGGAGATAAGGTTAATGGCTTCAAT
**
35169354 CTAT
130 CTGC
* * *
35169358 TTCACTGCAACTTTAGGAAGATAAGATTT
1 TCCACTGCAACTTCAGGGAGATAAGATTT
35169387 GCCATAATTC
Statistics
Matches: 366, Mismatches: 59, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
132 2 0.01
133 361 0.99
134 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (133 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTACTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
ATAAGACTTGTAACTTCAACCTACTCCACTGCATCTTCAGGGAGATAAGGTTAATGGCTTCAATC
TGC
Found at i:35169000 original size:229 final size:229
Alignment explanation
Indices: 35168593--35169029 Score: 640
Period size: 229 Copynumber: 1.9 Consensus size: 229
35168583 TATCTTTAAT
* * *
35168593 CTATTCCACTGCAACTTCAAGGAAATAAGATCCGATGTCTTCAGTCTGCTCCATTGCATCTTCAG
1 CTATTCCACTGCAACTTCAAGGAAATAAGATCCGATATCTTCAGTCTGCTCCACTGCAACTTCAG
* * *
35168658 GGAGATAAGACTTGTAACTTTAACCTGCTCCACTGTAACTTCGGGGAAATAAGGTTAGTGACTTT
66 AGAGATAAGACTTGTAACTTTAACCTGCTCCACCGTAACTTCAGGGAAATAAGGTTAGTGACTTT
* * * * *
35168723 GATCTACTCCATTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCTACTGTAACTT
131 GATCTACTCCACTGCAACTTCAGGGAGATAAGATTTACTATCTTCAGTCTACTCCACTGCAACTT
*
35168788 CATAGAGATAAGATCTGTAATTTATAGCTCCAAC
196 CAGAGAGATAAGATCTGTAATTTATAGCTCCAAC
* * ** * *
35168822 CTATTCCACTGTAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTGCACTGCAACTTCAG
1 CTATTCCACTGCAACTTCAAGGAAATAAGATCCGATATCTTCAGTCTGCTCCACTGCAACTTCAG
* * *
35168887 AGAGATAAGACTTGTAACTTTAACCTGCTCTACCGTAACTTCAGGGAGATAAGGTTAGTGGCTTT
66 AGAGATAAGACTTGTAACTTTAACCTGCTCCACCGTAACTTCAGGGAAATAAGGTTAGTGACTTT
* * * *
35168952 GATTTGCTCCACTGCAACTTCAGGGAGATAAGATTTACTATTTTCAGTCTACTCCGCTGCAACTT
131 GATCTACTCCACTGCAACTTCAGGGAGATAAGATTTACTATCTTCAGTCTACTCCACTGCAACTT
*
35169017 CAGGGAGATAAGA
196 CAGAGAGATAAGA
35169030 CTTGTAACTT
Statistics
Matches: 182, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
229 182 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (229 bp):
CTATTCCACTGCAACTTCAAGGAAATAAGATCCGATATCTTCAGTCTGCTCCACTGCAACTTCAG
AGAGATAAGACTTGTAACTTTAACCTGCTCCACCGTAACTTCAGGGAAATAAGGTTAGTGACTTT
GATCTACTCCACTGCAACTTCAGGGAGATAAGATTTACTATCTTCAGTCTACTCCACTGCAACTT
CAGAGAGATAAGATCTGTAATTTATAGCTCCAAC
Found at i:35169160 original size:266 final size:266
Alignment explanation
Indices: 35168828--35169391 Score: 758
Period size: 266 Copynumber: 2.1 Consensus size: 266
35168818 CAACCTATTC
* * *
35168828 CACTGTAACTTCAGGGAA-ATAAGATTTGCTATCTTCAGTCTGCTGCACTGCAACTTCAGAGAGA
1 CACTGCAACTTCA-GGAAGATAAGATTTGCCATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGA
* * * * * * *
35168892 TAAGACTTGTAACTTTAACCTGCTCTACCGTAACTTCAG-GGAGATAAGGTTAGTGGCTTTGATT
65 TAAGACTTGTAACTTCAACCTACTCCACCGCAACTTCAGAGG-GATAAGGTTAATGGCTTCGATA
* * * *
35168956 TGCTCCACTGCAACTTCAGGGAGATAAGATTTA-CTATTTTCAGTCTACTCCGCTGCAACTTCAG
129 TGCTCCACTGCAACTTCAGGGAGATAAGATTCACCT-TCTTCAGTCTACCCCACTGCAACTTCAG
* * * *
35169020 GGAGATAAGACTTGTAACTTCAACCTACTCCACTGCATCTTTAGGGAGATAAGGTTAGTGGCTTC
193 GGAGATAAGACTTGTAACTTCAAACTACTCCACTGCATCTTCAGGGAGATAAGATTAATGGCTTC
35169085 AATC-AGCTT
258 AATCTA-CTT
* * * * * *
35169094 CACTGCAACTTCAAGAAGATAAGATTCGCCATCTTCAGTCTGCTCCACTGTAATTTTAGGGAGAT
1 CACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGAT
* * *
35169159 AAGACTTGTAACTTCAACCTACTCCACTGCATCTTCAGAGGGATAGGGTTAATGGCTTCGATATG
66 AAGACTTGTAACTTCAACCTACTCCACCGCAACTTCAGAGGGATAAGGTTAATGGCTTCGATATG
* * * *
35169224 CTCCACTGCAACTTTAGGGTGATAAGATTCACCTTCTTCAGTCTGCCCCACTGTAACTTCAGGGA
131 CTCCACTGCAACTTCAGGGAGATAAGATTCACCTTCTTCAGTCTACCCCACTGCAACTTCAGGGA
*
35169289 GATAAGACTTGTAACTTCAAACTACTCCACTGCATCTTCAGGGAGATAAGATTAATGGCTTTAAT
196 GATAAGACTTGTAACTTCAAACTACTCCACTGCATCTTCAGGGAGATAAGATTAATGGCTTCAAT
*
35169354 CTATTT
261 CTACTT
*
35169360 CACTGCAACTTTAGGAAGATAAGATTTGCCAT
1 CACTGCAACTTCAGGAAGATAAGATTTGCCAT
35169392 AATTCGTAGC
Statistics
Matches: 258, Mismatches: 36, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
265 3 0.01
266 250 0.97
267 5 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (266 bp):
CACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGAT
AAGACTTGTAACTTCAACCTACTCCACCGCAACTTCAGAGGGATAAGGTTAATGGCTTCGATATG
CTCCACTGCAACTTCAGGGAGATAAGATTCACCTTCTTCAGTCTACCCCACTGCAACTTCAGGGA
GATAAGACTTGTAACTTCAAACTACTCCACTGCATCTTCAGGGAGATAAGATTAATGGCTTCAAT
CTACTT
Found at i:35169187 original size:89 final size:90
Alignment explanation
Indices: 35168682--35169391 Score: 342
Period size: 89 Copynumber: 7.9 Consensus size: 90
35168672 TAACTTTAAC
* * * * * ** * *
35168682 CTGCTCCACTGTAACTTCGGGGAAATAAG-GTTAGTGACTTTGATCTACTCCATTGCAACTTCAG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTAGTAACTTCAACCTACTCCACTGCAACTTCAG
* *
35168746 GGAGATAAGATTTGCTATCTTCAGT
66 GAAGATAAGATTTGCCATCTTCAGT
* * ** * * * *
35168771 CTGCTCTACTGTAACTTCATAGAGATAAGATCTGTAATTTATAGCTCCAACCTATTCCACTGTAA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-T-A-GTA-A-CTTCAACCTACTCCACTGCAA
*
35168836 CTTCAGGGAA-ATAAGATTTGCTATCTTCAGT
60 CTTCA-GGAAGATAAGATTTGCCATCTTCAGT
* * * * * * *
35168867 CTGCTGCACTGCAACTTCAGAGAGATAAGACTT-GTAACTTTAACCTGCTCTACCGTAACTTCAG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTAGTAACTTCAACCTACTCCACTGCAACTTCAG
* * * *
35168931 GGAGATAAGGTTAGTGGC-T-TTGA-T
66 GAAGATAAGATT--TGCCATCTTCAGT
* * * ** ** *
35168955 TTGCTCCACTGCAACTTCAGGGAGATAAGATTTACTATTTTCAGTCTACTCCGCTGCAACTTCAG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTAGTAACTTCAACCTACTCCACTGCAACTTCAG
* * * * **
35169020 GGAGATAAGACTTG-TAACTTCAAC
66 GAAGATAAGATTTGCCATCTTCAGT
* * * * ** * *
35169044 CTACTCCACTGCATCTTTAGGGAGATAAG-GTTAGTGGCTTCAATC-AGCTTCACTGCAACTTCA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTAGTAACTTCAACCTA-CTCCACTGCAACTTCA
* *
35169107 AGAAGATAAGATTCGCCATCTTCAGT
65 GGAAGATAAGATTTGCCATCTTCAGT
* * * *
35169133 CTGCTCCACTGTAATTTTAGGGAGATAAGACTT-GTAACTTCAACCTACTCCACTGCATCTTCA-
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTAGTAACTTCAACCTACTCCACTGCAACTTCAG
* * * *
35169196 GAGGGATAGGGTTAATG---GCTTC-GAT
66 GA-AGATAAGATT--TGCCATCTTCAG-T
* * * * * ** * * *
35169221 ATGCTCCACTGCAACTTTAGGGTGATAAGA-TTCACCT-TCTTCAGTCTGCCCCACTGTAACTTC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTT-A-GTAACTTCAACCTACTCCACTGCAACTTC
* * * * **
35169284 AGGGAGATAAGACTTG-TAACTTCAAA
64 AGGAAGATAAGATTTGCCATCTTCAGT
* * * ** * * * * *
35169310 CTACTCCACTGCATCTTCAGGGAGATAAGA-TTAATGGCTTTAATCTATTTCACTGCAACTTTAG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTAGTAACTTCAACCTACTCCACTGCAACTTCAG
35169374 GAAGATAAGATTTGCCAT
66 GAAGATAAGATTTGCCAT
35169392 AATTCGTAGC
Statistics
Matches: 462, Mismatches: 127, Indels: 64
0.71 0.19 0.10
Matches are distributed among these distances:
87 9 0.02
88 136 0.29
89 228 0.49
90 7 0.02
91 6 0.01
92 1 0.00
93 1 0.00
94 2 0.00
95 3 0.01
96 66 0.14
97 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (90 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTAGTAACTTCAACCTACTCCACTGCAACTTCAG
GAAGATAAGATTTGCCATCTTCAGT
Found at i:35181159 original size:254 final size:253
Alignment explanation
Indices: 35180709--35181174 Score: 619
Period size: 254 Copynumber: 1.8 Consensus size: 253
35180699 GTGAATATTG
* * * *
35180709 AGATTCTCTTATTTTGAAGAAATAAAACATCACTTCCAGCACGTAGGACACAACATTCAAACCTT
1 AGATTCTCTTATTTCGAAGAAATAAAACATCACATCCAACACGTAGCACACAACATTCAAACCTT
* * * * *
35180774 TGATATCAAAATCATCTCATAATTCCCAGAATTTATGCATTCAAAAGTTAAAAAGGATATTCGGT
66 CGATACCAAAACCATCTCATAATTCCCAGAACTCATGCATTCAAAAGTTAAAAAGGATATTCGGT
* * * * * * * *
35180839 CGTTCGGTCAAACGATAAATTGAAACCCAGCACGTTGGGCATAATTTCTCTAAATTTCCGAACAC
131 CGTTCGGTCAAACGACAAATCGAAACCCAACACGTAGGGCACAATCTCTCGAAATTTCCAAACAC
*
35180904 GAAATATTGCCTTGTTTAAAAAAATCTTGAATAAAAATGTAATAGTATGAAACGATTA
196 GAAATATTACCTTGTTTAAAAAAATCTTGAATAAAAATGTAATAGTATGAAACGATTA
* * * *
35180962 AGATTCTCTTGTTTCGAAGAAATAAAATATCACATCCAACACGTAGCACACGATATTTCAAACCT
1 AGATTCTCTTATTTCGAAGAAATAAAACATCACATCCAACACGTAGCACACAACA-TTCAAACCT
* ** * ** *
35181027 TCGATACCAAAACCATCTCATAATTTCC-GAAACTCATGTTTTGAAATTTTAAAAAGGATATTTG
65 TCGATACCAAAACCATCTCATAATTCCCAG-AACTCATGCATTCAAAAGTTAAAAAGGATATTCG
* * *
35181091 GTTGTTCGGTCAAATGACAAATCGAAACCCAACACGTAGGGCACAATCTCTCGAAATTTGCAAAC
129 GTCGTTCGGTCAAACGACAAATCGAAACCCAACACGTAGGGCACAATCTCTCGAAATTTCCAAAC
35181156 ACGAAATATTACCTTGTTT
194 ACGAAATATTACCTTGTTT
35181175 TGAATAAAAC
Statistics
Matches: 179, Mismatches: 32, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
253 48 0.27
254 131 0.73
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (253 bp):
AGATTCTCTTATTTCGAAGAAATAAAACATCACATCCAACACGTAGCACACAACATTCAAACCTT
CGATACCAAAACCATCTCATAATTCCCAGAACTCATGCATTCAAAAGTTAAAAAGGATATTCGGT
CGTTCGGTCAAACGACAAATCGAAACCCAACACGTAGGGCACAATCTCTCGAAATTTCCAAACAC
GAAATATTACCTTGTTTAAAAAAATCTTGAATAAAAATGTAATAGTATGAAACGATTA
Found at i:35185767 original size:33 final size:33
Alignment explanation
Indices: 35185725--35185800 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
35185715 TGAGCGTGAA
*
35185725 AGGAAAGATTGTGAGAGAGCTCAGAGTAAGGGG
1 AGGAAAGATTGAGAGAGAGCTCAGAGTAAGGGG
*
35185758 AGGAAAGATTGAGAGAGAGCTTAGAGTAAGGGG
1 AGGAAAGATTGAGAGAGAGCTCAGAGTAAGGGG
35185791 AGGAAAGATT
1 AGGAAAGATT
35185801 CAGGTCCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.39, C:0.04, G:0.41, T:0.16
Consensus pattern (33 bp):
AGGAAAGATTGAGAGAGAGCTCAGAGTAAGGGG
Found at i:35191000 original size:34 final size:34
Alignment explanation
Indices: 35190936--35191002 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
35190926 TTTATACTAA
* *
35190936 TCAAATTTATATATTTACTGAATTATTATAAAAC
1 TCAAAGTTATATATTTAATGAATTATTATAAAAC
35190970 TCAAAGTTATATATTGTAAT-AATT-TATATAAAA
1 TCAAAGTTATATATT-TAATGAATTAT-TATAAAA
35191003 TAATAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 1 0.03
34 25 0.86
35 3 0.10
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (34 bp):
TCAAAGTTATATATTTAATGAATTATTATAAAAC
Found at i:35191006 original size:17 final size:18
Alignment explanation
Indices: 35190986--35191021 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
35190976 TTATATATTG
*
35190986 TAATAATTTA-TATAAAA
1 TAATAAATTATTATAAAA
35191003 TAATAAATTATTATAAAA
1 TAATAAATTATTATAAAA
35191021 T
1 T
35191022 TTTGTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAAATTATTATAAAA
Found at i:35191198 original size:18 final size:17
Alignment explanation
Indices: 35191157--35191203 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
35191147 TTATGTCATT
35191157 TTTATAATAA-TA-AAA
1 TTTATAATAATTATAAA
*
35191172 TTT-TCATAATTATTAAA
1 TTTATAATAATTA-TAAA
35191189 TTTATAATAATTATA
1 TTTATAATAATTATA
35191204 TAATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 5 0.19
15 5 0.19
17 8 0.31
18 8 0.31
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTATAATAATTATAAA
Found at i:35192714 original size:13 final size:13
Alignment explanation
Indices: 35192696--35192720 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35192686 GGCCTACACG
35192696 GGTGAACCACATA
1 GGTGAACCACATA
35192709 GGTGAACCACAT
1 GGTGAACCACAT
35192721 GGGCATGTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (13 bp):
GGTGAACCACATA
Found at i:35197867 original size:37 final size:37
Alignment explanation
Indices: 35197826--35197899 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
35197816 TAGAGGACAT
*
35197826 GTTGAGGGGCTGCATTATAGATTTTTGAGGTAGTTGG
1 GTTGAGGGGCTGCATTATAGATTTTTGAGGCAGTTGG
*
35197863 GTTGAGGGGTTGCATTATAGATTTTTGAGGCAGTTGG
1 GTTGAGGGGCTGCATTATAGATTTTTGAGGCAGTTGG
35197900 AAGGAGTACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.19, C:0.05, G:0.38, T:0.38
Consensus pattern (37 bp):
GTTGAGGGGCTGCATTATAGATTTTTGAGGCAGTTGG
Found at i:35210632 original size:72 final size:72
Alignment explanation
Indices: 35210515--35210658 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
35210505 AACGGAGAAG
35210515 TAAGTTTAATCTGCTCTCTCTGTATCGGTTCTGTTAAGCGGTCAAAGATAATTAAATTCTTTCTA
1 TAAGTTTAATCTGCTCTCTCTGTATCGGTTCTGTTAAGCGGTCAAAGATAATTAAATTCTTTCTA
35210580 AATAACC
66 AATAACC
35210587 TAAGTTTAATCTGCTCTCTCTGTATCGGTTCTGTTAAGCGGTCAAAGATAATTAAATTCTTTCTA
1 TAAGTTTAATCTGCTCTCTCTGTATCGGTTCTGTTAAGCGGTCAAAGATAATTAAATTCTTTCTA
35210652 AATAACC
66 AATAACC
35210659 ATGGCTGACC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (72 bp):
TAAGTTTAATCTGCTCTCTCTGTATCGGTTCTGTTAAGCGGTCAAAGATAATTAAATTCTTTCTA
AATAACC
Found at i:35217503 original size:213 final size:214
Alignment explanation
Indices: 35217131--35217560 Score: 691
Period size: 213 Copynumber: 2.0 Consensus size: 214
35217121 TCGGGGTGAA
* *
35217131 GGGGTATTGTTAGTCCAGAGGTGTTGAGCCAAAAATATCCTCAATATTAGGTGTAGGTGCTTACT
1 GGGGTATTGTTAGTCCAGAGGTGCTGAGCCAAAAATATCCTCAATATTAGGTGTAGGTGCTTACC
*
35217196 GATGGAGCTCTGGGTGGTATGAGAACGATCCAGAGTATGCTGAGTGTTGAGGCTCAAGGTCGTTG
66 GATGGAGCTCTGGGTGGTATGAGAACGATCCAGAGTATGCTGAGTATTGAGGCTCAAGGTCGTTG
* *
35217261 CCAAATATGTCCTCGAACGAAGGAGGATTCGGAT-GGGGGTTTGTGAGGCTTCTTCAGATGATTC
131 CCAAATATGTCCTCGAACGAAGAAGGATTCGGATGGGGGGTTTGTGAGGCTTCCTCAGATGATTC
*
35217325 ATATTCATGCTCGGGATCG
196 ATATTCATGCTCAGGATCG
* *
35217344 GGGGTATTGTTAGTCCAGAGGTGCTGAGCCAAAAATATCCTTAATATTAGGTGTAGGTGCTTGCC
1 GGGGTATTGTTAGTCCAGAGGTGCTGAGCCAAAAATATCCTCAATATTAGGTGTAGGTGCTTACC
* * * * * * *
35217409 GATGGGGCTTTGGGTGGTATGATAATGATCCCGAGTTTGTTGAGTATTGAGGCTCAAGGTCGTTG
66 GATGGAGCTCTGGGTGGTATGAGAACGATCCAGAGTATGCTGAGTATTGAGGCTCAAGGTCGTTG
* * *
35217474 CCAAATATGTCCTCGAATGAAGAAGGATTCGGATGGGGGGTTTGTGAGGTTTCCTCGGATGATTC
131 CCAAATATGTCCTCGAACGAAGAAGGATTCGGATGGGGGGTTTGTGAGGCTTCCTCAGATGATTC
35217539 ATATTCATGCTCAGGATCG
196 ATATTCATGCTCAGGATCG
35217558 GGG
1 GGG
35217561 TTTGAGACAG
Statistics
Matches: 198, Mismatches: 18, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
213 150 0.76
214 48 0.24
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (214 bp):
GGGGTATTGTTAGTCCAGAGGTGCTGAGCCAAAAATATCCTCAATATTAGGTGTAGGTGCTTACC
GATGGAGCTCTGGGTGGTATGAGAACGATCCAGAGTATGCTGAGTATTGAGGCTCAAGGTCGTTG
CCAAATATGTCCTCGAACGAAGAAGGATTCGGATGGGGGGTTTGTGAGGCTTCCTCAGATGATTC
ATATTCATGCTCAGGATCG
Found at i:35218823 original size:140 final size:140
Alignment explanation
Indices: 35218670--35218921 Score: 459
Period size: 140 Copynumber: 1.8 Consensus size: 140
35218660 TTTAATTAGT
* *
35218670 TATAATCTATTCAATTGAAATGTATTAAATTATTTTTTATTTAATCTTTAAATTAATTTTTTCAA
1 TATAATCTATTCAATTGAAATGGATTAAATTATTTTTTATTTAATCTTTAAATTAATTTTTTAAA
*
35218735 TTAAAATTAAGAAATTCAATTAATTTTTAATTTAAACTTTAAGTATTTAATTTTTATTTTTTAAT
66 TAAAAATTAAGAAATTCAATTAATTTTTAATTTAAACTTTAAGTATTTAATTTTTATTTTTTAAT
35218800 TGAAGTTATC
131 TGAAGTTATC
*
35218810 TATAATCTATTCAATTGAAATGGATTAAATTATTTTTTATTTAATCTTTAAATTGATTTTTTAAA
1 TATAATCTATTCAATTGAAATGGATTAAATTATTTTTTATTTAATCTTTAAATTAATTTTTTAAA
*
35218875 TAAAAATTAAGAAATTCAATTAATTTTTAATTTAAACTTTAATTATT
66 TAAAAATTAAGAAATTCAATTAATTTTTAATTTAAACTTTAAGTATT
35218922 AAGTTAAACT
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 107 1.00
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (140 bp):
TATAATCTATTCAATTGAAATGGATTAAATTATTTTTTATTTAATCTTTAAATTAATTTTTTAAA
TAAAAATTAAGAAATTCAATTAATTTTTAATTTAAACTTTAAGTATTTAATTTTTATTTTTTAAT
TGAAGTTATC
Found at i:35218940 original size:19 final size:19
Alignment explanation
Indices: 35218894--35218934 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
35218884 AGAAATTCAA
* *
35218894 TTAATTTTTAATTTAAACT
1 TTAATTATTAAGTTAAACT
35218913 TTAATTATTAAGTTAAACT
1 TTAATTATTAAGTTAAACT
35218932 TTA
1 TTA
35218935 TGTATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (19 bp):
TTAATTATTAAGTTAAACT
Found at i:35219077 original size:170 final size:175
Alignment explanation
Indices: 35218810--35219246 Score: 598
Period size: 170 Copynumber: 2.4 Consensus size: 175
35218800 TGAAGTTATC
* *
35218810 TATAATCTATTCAATTGAAATGGATTAAATTATTTTTTATTTAATCTTTAAATTGATTTTTTAAA
1 TATAATATATTCAATTGAAATGTATTAAATTA-TTTTTATTTAATCTTTAAATTGA-TTTTT-AA
* * * *
35218875 TAAAAATTAAGAAATTCAATTAATTTTTAATTTAAACTTTAATTATTAAGTTAAACTTTATGTAT
63 TTAAAATTAAGAAATCCAATTAATTTTTAATTTAAACTTTAATTATCAAGTTAAACTTAATGTAT
35218940 TTAA-TTTTTA-TTTTTAATTGAAATTATCTATACTTTAATTGGT-TA
128 TTAATTTTTTATTTTTTAATTGAAATTATCTATACTTTAATTGGTATA
* *
35218985 -A-AATATATTCAATTGAAATGTATTAAAATATTTTTATTTAATCTTTAAATTGAGTTTTAATTA
1 TATAATATATTCAATTGAAATGTATTAAATTATTTTTATTTAATCTTTAAATTGATTTTTAATTA
35219048 AAATTAAGAAATCCAATTAATTTTTAATTTAAACTTTAATTATCAAGTTAAACTTAATGTATTTA
66 AAATTAAGAAATCCAATTAATTTTTAATTTAAACTTTAATTATCAAGTTAAACTTAATGTATTTA
35219113 ATTTTTTTATTTTTTAATTGAAATTATCTATACTTTAATTGGTATA
131 A-TTTTTTATTTTTTAATTGAAATTATCTATACTTTAATTGGTATA
* *
35219159 TTAGTTGGTTTTAATCT-TTCAATTGAAATGTTTTAAATTATTATTTATTTAATCTTTAAATTGA
1 -TA--------TAATATATTCAATTGAAATGTATTAAATTATT-TTTATTTAATCTTTAAATTGA
*
35219223 TTTTATAATTAAAATTAAAAAATC
56 TTTT-TAATTAAAATTAAGAAATC
35219247 ATGGGAAATC
Statistics
Matches: 232, Mismatches: 13, Indels: 23
0.87 0.05 0.09
Matches are distributed among these distances:
170 67 0.29
171 4 0.02
172 29 0.12
173 59 0.25
174 3 0.01
176 1 0.00
184 23 0.10
185 28 0.12
186 18 0.08
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.51
Consensus pattern (175 bp):
TATAATATATTCAATTGAAATGTATTAAATTATTTTTATTTAATCTTTAAATTGATTTTTAATTA
AAATTAAGAAATCCAATTAATTTTTAATTTAAACTTTAATTATCAAGTTAAACTTAATGTATTTA
ATTTTTTATTTTTTAATTGAAATTATCTATACTTTAATTGGTATA
Found at i:35219086 original size:19 final size:18
Alignment explanation
Indices: 35219064--35219116 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
35219054 AGAAATCCAA
35219064 TTAATTTTTAATTTAAAC
1 TTAATTTTTAATTTAAAC
* * *
35219082 TTTAATTATCAAGTTAAAC
1 -TTAATTTTTAATTTAAAC
35219101 TTAATGTATTTAATTT
1 TTAAT-T-TTTAATTT
35219117 TTTTATTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 5 0.19
19 16 0.62
20 5 0.19
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.53
Consensus pattern (18 bp):
TTAATTTTTAATTTAAAC
Found at i:35221635 original size:3 final size:3
Alignment explanation
Indices: 35221584--35221677 Score: 52
Period size: 3 Copynumber: 32.7 Consensus size: 3
35221574 GCTGATAATG
* * * * * * *
35221584 TAA TAG TAA TGA TAA TAG TAA TAA TAG TAA AAA TAA AAA TAA -CA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
35221631 TAA TAA -AA AAA TAA -GA TAA TAA TAA TAG CAA TAA -AA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35221676 TA
1 TA
35221678 GTGATATTAG
Statistics
Matches: 65, Mismatches: 22, Indels: 8
0.68 0.23 0.08
Matches are distributed among these distances:
2 6 0.09
3 59 0.91
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:35221642 original size:19 final size:19
Alignment explanation
Indices: 35221618--35221655 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
35221608 TAGTAAAAAT
35221618 AAAAATAACATAATAATAA
1 AAAAATAACATAATAATAA
*
35221637 AAAAATAAGATAATAATAA
1 AAAAATAACATAATAATAA
35221656 TAGCAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (19 bp):
AAAAATAACATAATAATAA
Found at i:35224470 original size:15 final size:15
Alignment explanation
Indices: 35224452--35224502 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
35224442 TCACTCAAAT
*
35224452 CTTCACTATCGAACC
1 CTTCATTATCGAACC
*
35224467 CTTCTTTATCAGAA-C
1 CTTCATTATC-GAACC
35224482 CTTCATTATC-AGACC
1 CTTCATTATCGA-ACC
35224497 CTTCAT
1 CTTCAT
35224503 CACCATCTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 1 0.03
15 25 0.83
16 3 0.10
ACGTcount: A:0.25, C:0.33, G:0.06, T:0.35
Consensus pattern (15 bp):
CTTCATTATCGAACC
Found at i:35225364 original size:107 final size:108
Alignment explanation
Indices: 35225236--35225431 Score: 290
Period size: 107 Copynumber: 1.8 Consensus size: 108
35225226 TGATGTCGGT
* * * *
35225236 CATCTAGTTCCCCAAATCCAAATTTTTTTTATCTGATAAAGT-AGGTGCCGACCATTACTGTGCC
1 CATCTAGTTCCCCAAACCCAAATTTTATTTATCTGATAAAGTGA-GTGCCGACCATCAATGTGCC
*
35225300 AACA-CAAAAAAATTATTTTTTAATCCGAAAAGCTGATGATGAC
65 AACACCAAAAAAAATATTTTTTAATCCGAAAAGCTGATGATGAC
*
35225343 CATCTAGTATTCCC-AACCCAAATTTTATTTATCTGATAAAGTGAGTGCCGACCATCAATGTGCC
1 CATCTAGT-TCCCCAAACCCAAATTTTATTTATCTGATAAAGTGAGTGCCGACCATCAATGTGCC
35225407 AACACCCAAAAAAAATATTTTTTAA
65 AACA-CCAAAAAAAATATTTTTTAA
35225432 AAATTATAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
107 56 0.71
108 5 0.06
109 18 0.23
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (108 bp):
CATCTAGTTCCCCAAACCCAAATTTTATTTATCTGATAAAGTGAGTGCCGACCATCAATGTGCCA
ACACCAAAAAAAATATTTTTTAATCCGAAAAGCTGATGATGAC
Found at i:35225414 original size:52 final size:52
Alignment explanation
Indices: 35225253--35225416 Score: 129
Period size: 52 Copynumber: 3.1 Consensus size: 52
35225243 TTCCCCAAAT
* *
35225253 CCAAATTTTTTTTATCTGATAAAGT-AGGTGCCGACCATTACTGTGCCAACAC
1 CCAAATTTTTTTTATCTGATAAAGTGA-GTGCCGACCATCAATGTGCCAACAC
** * ** * * * *
35225305 AAAAAAATTATTTTTTAATCCGA-AAAGCTGA-TGATGACCATCTAGTATTCCCA-AC
1 --CCAAATT-TTTTTT-ATCTGATAAAG-TGAGTGCCGACCATC-AATGTGCCAACAC
*
35225360 CCAAATTTTATTTATCTGATAAAGTGAGTGCCGACCATCAATGTGCCAACAC
1 CCAAATTTTTTTTATCTGATAAAGTGAGTGCCGACCATCAATGTGCCAACAC
35225412 CCAAA
1 CCAAA
35225417 AAAAATATTT
Statistics
Matches: 82, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
51 14 0.17
52 25 0.30
53 5 0.06
54 5 0.06
55 20 0.24
56 12 0.15
57 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (52 bp):
CCAAATTTTTTTTATCTGATAAAGTGAGTGCCGACCATCAATGTGCCAACAC
Found at i:35235901 original size:13 final size:13
Alignment explanation
Indices: 35235868--35235910 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
35235858 TTTTAAATTA
*
35235868 TTTTGGTTTTA-T
1 TTTTTGTTTTATT
*
35235880 TTTAT-TTTTATT
1 TTTTTGTTTTATT
35235892 TTTTTGTTTTATT
1 TTTTTGTTTTATT
35235905 TTTTTG
1 TTTTTG
35235911 GTTGTGGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 5 0.19
12 8 0.31
13 13 0.50
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.81
Consensus pattern (13 bp):
TTTTTGTTTTATT
Found at i:35236341 original size:176 final size:174
Alignment explanation
Indices: 35236057--35236969 Score: 814
Period size: 176 Copynumber: 5.2 Consensus size: 174
35236047 AGACTGGCTT
** * *
35236057 AAATCTGCTCCATTGCCTG-TACATGGAGATAAGATTTGCCCTCTTCGA--T-CTACTGCAACGT
1 AAATCTGCTCCATTGCC-GATACATGGAGATAAGATTCACCATCTTCGATCTACTACTGCAACTT
* * * *
35236118 CAGGGAAATAAGATCTTCAATCTTCAGTCTGCTCCCTTGA-TACCTCAGGAAGATAAGACTTATT
65 CAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTT-ACTACCTCAGAAAGATAAGACTCATT
** *
35236182 CTTCAATTTGTTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGTA
129 CTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGTA
* *
35236228 AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATTTTTGATCTACTCCACTGCAACT
1 AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTACT--ACTGCAACT
* *
35236293 TCATGGAGATAAGATCTTCAATCTTCAGTCTGCTTTCTTACTACCTCAGAAAGATAAGACTCATT
64 TCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTACTACCTCAGAAAGATAAGACTCATT
* * * * *
35236358 CTTCAACTTGCTCTCTTGCTACCTCAAAGAGGTGAGGCGGGTGGTA
129 CTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGTA
* * * * *
35236404 AAATCTGCTTCATTGTCGATACATGGAGATAAAATTCACCATATTCGATGC-ACTCCTTTGCAAC
1 AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGAT-CTACTAC--TGCAAC
* * * *
35236468 TTCAGGGAGATAAGATCTTTAATCTTCAGTCTTCTTTCC-TGCTACCTGAGAAAGATAAGACTCA
63 TTCAGGGAGATAAGATCTTCAATCTTCAGTCTGC-TTCCTTACTACCTCAGAAAGATAAGACTCA
* * * * * *
35236532 TTCTTTAACCTGCTCTTTTGCTACCTCAGAGAGATAAGGCTTGCGACTT
127 TTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTG-GTA
* * * *
35236581 CAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCCTCCG-TC-AGCT-CTGCTACT
1 AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCAT-CTTCGATCTA-CTACTGCAACT
* * * * * * *
35236643 GCTCAGGGAGATAAAATCTTCAATCTTTAGTCTACTTCCTTGCTACATCAGGACGATAAGACT-A
64 --TCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTACTACCTCAGAAAGATAAGACTCA
* * * *
35236707 TTATCTTCAACCTACTCTCTTGTTACCTTAGAGAGATAAGG-TCAGTGGCTA
127 -T-TCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT-GGTGG-TA
* * * * * * *
35236758 AAATCCGCT-CATTGCCAATACATGGAGATAAGATTTACCATCTTCGATCT-GTTCCGCTACTGC
1 AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTACTACTGCAACT--
* * *** * * * * * *
35236821 TTAGGAAGATAAGATCTGGGATTTTCATTCTGC-TCCACTGCAATCTCAGAAAGATAAGACTTCA
64 TCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCC-TTACTACCTCAGAAAGATAAGAC-TCA
* * * * * *
35236885 ATCTTCAACATCCTCTCTTACTACCTCAGAGAGATAAGGTTTGG-GGCTT
127 TTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGG-CTGGTGG-TA
* * *
35236934 AAATCTACTCTATTGCCGATACATGGTGATAAGATT
1 AAATCTGCTCCATTGCCGATACATGGAGATAAGATT
35236970 TGCCTCCTCC
Statistics
Matches: 609, Mismatches: 103, Indels: 54
0.80 0.13 0.07
Matches are distributed among these distances:
170 1 0.00
171 41 0.07
173 1 0.00
174 9 0.01
175 14 0.02
176 425 0.70
177 113 0.19
178 5 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (174 bp):
AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTACTACTGCAACTTC
AGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTACTACCTCAGAAAGATAAGACTCATTCT
TCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGTA
Found at i:35236833 original size:352 final size:346
Alignment explanation
Indices: 35236051--35236984 Score: 880
Period size: 353 Copynumber: 2.7 Consensus size: 346
35236041 GAGATAAGAC
* ** * * * * *
35236051 TGGCTTAAATCTGCTCCATTGCCTGTACATGGAGATAAGATTTGCCCTCTTCGATCTACTGCAAC
1 TGGCTAAAATCTGCT-CATTGCCAATACATGGAGATAAGATTTACCATCTTCGATCTTCCGCTAC
* * * *
35236116 G-TCAGGGAA-ATAAGATCTTCAATCTTCAGTCTGCTCCCTTGATACCTCAGGAAGATAAGACTT
65 GCTTA-GGAAGATAAGATCTTCAATCTTCAGTCTGCTCCC-TGCTACCTCAGAAAGATAAGACTC
** * * * * *
35236179 ATTCTTCAATTTGTTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGTAAAATCTGCTCCATTGC
128 ATTCTTCAACATGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGCGCTTAAATCTGCTCCATTGC
* * ** * *
35236244 CGATACATGGAGATAAGATTCACCAT-TTTTGATCTACTCCACTGCAACTTCATGGAGATAAGAT
193 CGATACATGGAGATAAGATTCGCCATCCTCCGATCTACT-C-CTGCAACTTCAGGGAGATAAAAT
* * * * *
35236308 CTTCAATCTTCAGTCTGCTTTCTTACTACCTCAGAAAGATAAGACTCATTCTTCAACTTGCTCTC
256 CTTCAATCTTCAGTCTACTTCCTTACTACATCAGAAAGATAAGACTCATTCTTCAACCTACTCTC
* * *
35236373 TTGCTACCTCAAAGAGGTGAGGCGGG
321 TTGCTACCTCAAAGAGATAAGGCGAG
* * * * * * **
35236399 TGG-TAAAATCTGCTTCATTGTCGATACATGGAGATAAAATTCACCATATTCGATGCACTCCTTT
1 TGGCTAAAATCTGC-TCATTGCCAATACATGGAGATAAGATTTACCATCTTCGAT-C-TTCCGCT
* * * * * * *
35236463 GCAACTTCAGGGAGATAAGATCTTTAATCTTCAGTCTTCTTTCCTGCTACCTGAGAAAGATAAGA
63 AC-GCTT-AGGAAGATAAGATCTTCAATCTTCAGTCTGC-TCCCTGCTACCTCAGAAAGATAAGA
* * * *
35236528 CTCATTCTTTAACCTGCTCTTTTGCTACCTCAGAGAGATAAGGCTTGCGACTTCAATCTGCTCCA
125 CTCATTCTTCAACATGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGCG-CTTAAATCTGCTCCA
*
35236593 TTGCCGATACATGGAGATAAGATTCGCCATCCTCCG-TC-AGCT-CTGCTACTGCTCAGGGAGAT
189 TTGCCGATACATGGAGATAAGATTCGCCATCCTCCGATCTA-CTCCTGCAACT--TCAGGGAGAT
* * * *
35236655 AAAATCTTCAATCTTTAGTCTACTTCCTTGCTACATCAGGACGATAAGACT-ATTATCTTCAACC
251 AAAATCTTCAATCTTCAGTCTACTTCCTTACTACATCAGAAAGATAAGACTCA-T-TCTTCAACC
* * *
35236719 TACTCTCTTGTTACCTTAGAGAGATAAGGTC-AG
314 TACTCTCTTGCTACCTCAAAGAGATAAGG-CGAG
*
35236752 TGGCTAAAATCCGCTCATTGCCAATACATGGAGATAAGATTTACCATCTTCGATCTGTTCCGCTA
1 TGGCTAAAATCTGCTCATTGCCAATACATGGAGATAAGATTTACCATCTTCGATC--TTCCGCTA
*** * * * *
35236817 CTGCTTAGGAAGATAAGATCTGGGATTTTCATTCTGCTCCACTGCAATCTCAGAAAGATAAGACT
64 C-GCTTAGGAAGATAAGATCTTCAATCTTCAGTCTGCTCC-CTGCTACCTCAGAAAGATAAGAC-
* * * * * * *
35236882 TCAATCTTCAACATCCTCTCTTACTACCTCAGAGAGATAAGGTTTGGGGCTTAAATCTACTCTAT
126 TCATTCTTCAACATGCTCTCTTGCTACCTCAGAGAGATAAGGCTT-GCGCTTAAATCTGCTCCAT
* * *
35236947 TGCCGATACATGGTGATAAGATTTGCC-TCCTCCAATCT
190 TGCCGATACATGGAGATAAGATTCGCCATCCTCCGATCT
35236985 TCAATCTTCA
Statistics
Matches: 467, Mismatches: 96, Indels: 40
0.77 0.16 0.07
Matches are distributed among these distances:
347 40 0.09
348 5 0.01
349 2 0.00
350 7 0.01
351 7 0.01
352 188 0.40
353 204 0.44
354 14 0.03
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (346 bp):
TGGCTAAAATCTGCTCATTGCCAATACATGGAGATAAGATTTACCATCTTCGATCTTCCGCTACG
CTTAGGAAGATAAGATCTTCAATCTTCAGTCTGCTCCCTGCTACCTCAGAAAGATAAGACTCATT
CTTCAACATGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGCGCTTAAATCTGCTCCATTGCCGA
TACATGGAGATAAGATTCGCCATCCTCCGATCTACTCCTGCAACTTCAGGGAGATAAAATCTTCA
ATCTTCAGTCTACTTCCTTACTACATCAGAAAGATAAGACTCATTCTTCAACCTACTCTCTTGCT
ACCTCAAAGAGATAAGGCGAG
Found at i:35237283 original size:133 final size:133
Alignment explanation
Indices: 35237084--35237334 Score: 389
Period size: 133 Copynumber: 1.9 Consensus size: 133
35237074 GTGGCTAAAA
* *
35237084 TCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCATCAATCTGCCCCACTACTGCCTAG
1 TCTGATCCATTGCCGATACATGGAGATAAGATTCACCATCATCAATCTGCCCCACTACTGCCTAG
*
35237149 GGAGATAAGATCTACAAAT-TTCAGTCTGCTTCCTTGCTACCTCAGAAAGATAAGACTACTATTG
66 GGAGATAAGATCTAC-AATCTTCAGTCTGCTTCCTTGCTACCACAGAAAGATAAGACTACTATTG
35237213 CCAG
130 CCAG
* * * *
35237217 TCTGATCCATTGCCGATACATGGAGATAAGATTCACTAT-ATTCGATCTGCTCCACTACTGCTTA
1 TCTGATCCATTGCCGATACATGGAGATAAGATTCACCATCA-TCAATCTGCCCCACTACTGCCTA
* *
35237281 GGGAGGTAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCACAGAAAGATAA
65 GGGAGATAAGATCTACAATCTTCAGTCTGCTTCCTTGCTACCACAGAAAGATAA
35237335 TACTCAACTT
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
132 4 0.04
133 103 0.96
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (133 bp):
TCTGATCCATTGCCGATACATGGAGATAAGATTCACCATCATCAATCTGCCCCACTACTGCCTAG
GGAGATAAGATCTACAATCTTCAGTCTGCTTCCTTGCTACCACAGAAAGATAAGACTACTATTGC
CAG
Found at i:35237699 original size:64 final size:64
Alignment explanation
Indices: 35237575--35237729 Score: 186
Period size: 64 Copynumber: 2.4 Consensus size: 64
35237565 TGATAAAAAA
* * * * * *
35237575 GAATCAAATGCTCCTAACTAAATGAGATATGAGTGATGTTAAATAATTAGGACACTATAATTGAA
1 GAATCAAATGCTCCTAACTAGATG-TA-ATG-CTTATGTCAAATAATTAGGACACTATAA-TCAA
35237640 A-T
62 ACT
* **
35237642 GAATCAAATGCTCTTAACTAGATGTAATGCTTATGTCAAATAATTAGGATGCTATAATCAAACT
1 GAATCAAATGCTCCTAACTAGATGTAATGCTTATGTCAAATAATTAGGACACTATAATCAAACT
35237706 GAATCAAATGCTCCTAACTAGATG
1 GAATCAAATGCTCCTAACTAGATG
35237730 CGTGATTTAT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 4 0.05
64 47 0.61
65 3 0.04
66 1 0.01
67 22 0.29
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (64 bp):
GAATCAAATGCTCCTAACTAGATGTAATGCTTATGTCAAATAATTAGGACACTATAATCAAACT
Found at i:35238768 original size:18 final size:17
Alignment explanation
Indices: 35238722--35238776 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 17
35238712 TCTCTTTTTC
35238722 TTTCTTTTTTTTTTAATT
1 TTTC-TTTTTTTTTAATT
35238740 TTT-TGATTTTTTTTAATT
1 TTTCT--TTTTTTTTAATT
35238758 TTTCTTCTTTTTTT-ATT
1 TTTCTT-TTTTTTTAATT
35238775 TT
1 TT
35238777 GATTTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.03
17 6 0.18
18 25 0.76
19 1 0.03
ACGTcount: A:0.11, C:0.05, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTCTTTTTTTTTAATT
Found at i:35239365 original size:28 final size:27
Alignment explanation
Indices: 35239326--35239388 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 27
35239316 TCACTATGAC
35239326 CTTTGTTTTATTGTTTG-CTTTTCCTTTT
1 CTTT-TTTTATT-TTTGACTTTTCCTTTT
**
35239354 CTTTTTTCTATTTTTGTACTTTTGTTTTT
1 CTTTTTT-TATTTTTG-ACTTTTCCTTTT
35239383 CTTTTT
1 CTTTTT
35239389 GGATGCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 7 0.23
28 8 0.27
29 15 0.50
ACGTcount: A:0.05, C:0.13, G:0.08, T:0.75
Consensus pattern (27 bp):
CTTTTTTTATTTTTGACTTTTCCTTTT
Found at i:35245675 original size:12 final size:12
Alignment explanation
Indices: 35245643--35245682 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
35245633 TTTTAAATTA
*
35245643 TTTTGGTTTTAT
1 TTTTTGTTTTAT
*
35245655 TTTAT-TTTTAT
1 TTTTTGTTTTAT
35245666 TTTTTGTTTTAT
1 TTTTTGTTTTAT
35245678 TTTTT
1 TTTTT
35245683 TGGTTGTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.82
Consensus pattern (12 bp):
TTTTTGTTTTAT
Found at i:35245681 original size:11 final size:11
Alignment explanation
Indices: 35245640--35245681 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
35245630 GACTTTTAAA
*
35245640 TTATTTTGGTT
1 TTATTTTTGTT
35245651 TTATTTTAT-TT
1 TTATTTT-TGTT
35245662 TTATTTTTTGTT
1 TTA-TTTTTGTT
35245674 TTATTTTT
1 TTATTTTT
35245682 TTGGTTGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.81
Consensus pattern (11 bp):
TTATTTTTGTT
Found at i:35246115 original size:176 final size:175
Alignment explanation
Indices: 35245816--35246745 Score: 853
Period size: 176 Copynumber: 5.3 Consensus size: 175
35245806 TTTTTTTGGG
* * * ** * *
35245816 GAGATAAGACTGG-CTTAAATCTGCTCCATTGCATG-TACATGGAGATAAGATTTGCCCTCTTCG
1 GAGATAAGGCTGGTGTTAAATCTGCTCCATTGC-CGATACATGGAGATAAGATTCACCATTTTCG
* * * * * *
35245879 ATCTACT--GC-A-A-CGTCAGGGAAATAAGATCTTCAATCTTCAGTCTGCTCCCTTGTTACCTC
65 ATCTGCTCCGCTACAGCTTCAAGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTC
* * *
35245939 AGGAAGATAAGACTTATTCTTCAATTTATTCTCTTGCTACCTCAGA
130 AGGAAGATAAGACTCATTCTTCAACTTACTCTCTTGCTACCTCAGA
* **
35245985 GAGATAAGGCTGGTGATAAAGTCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATTTTTT
1 GAGATAAGGCTGGTGTTAAA-TCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATTTTCG
* * * *
35246050 ATCTGCTCCACTGCAGCTTCAAGGAGATAAGATCTTCAATCTTCAGTCTGCTTTCTTACTACCTC
65 ATCTGCTCCGCTACAGCTTCAAGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTC
* * *
35246115 AGAAAGATAAGACTCATTCTTCAACTTGCTCTCTTGCTACCTCAAA
130 AGGAAGATAAGACTCATTCTTCAACTTACTCTCTTGCTACCTCAGA
* * * * * * *
35246161 GAGGTGAGGCGGGTGGTAAAATCTTCTCCATTGCCGATACATGGAGATAAAATTCACCATATTCG
1 GAGATAAGGCTGGT-GTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATTTTCG
* * * * * * *
35246226 ATCCGCTCCTCTGCAAG-TGCAGGGAGATAAGATCTTTAATCTTCAGTCTGCTTTCTTGCTACCT
65 ATCTGCTCCGCTAC-AGCTTCAAGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCT
* * * * *
35246290 CAGAAAGATAAGACTCATTCTTTAACTTTCTCTATTGCTACCCCAGA
129 CAGGAAGATAAGACTCATTCTTCAACTTACTCTCTTGCTACCTCAGA
* * * * ** *
35246337 GAGATAAGGCTTGGGGCTTCAATCTGCTCCATTGTCGATACATGGAGATAAGATTCGCCATCCTG
1 GAGATAAGGC-TGGTG-TTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATTTTC
* * * * *
35246402 GATCTGCTCCGCTACTGC-TGAAGGAGATAAGATCTTTAATCTTTAGTCTACTTCCTTGCTACCT
64 GATCTGCTCCGCTACAGCTTCAAGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCT
* * * *
35246466 CAGGAAGATAAGACT-ATTATCTTCAACCTACTCTCTTGTTACTTCAAA
129 CAGGAAGATAAGACTCA-T-TCTTCAACTTACTCTCTTGCTACCTCAGA
* * *
35246514 GAGATAAGGTCAGTGG-CTAAAATCTGCTCCATTGCCAATACATGGAGATAAGATTCACCATTTT
1 GAGATAAGG-C--TGGTGTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATTTT
* * * * * * * * * * *
35246578 CAATCTGTTCTGCTACTGCTT-AGGGAGATAATATCTGT-GATTTTCAGTCTGC-TCCACTACAA
63 CGATCTGCTCCGCTACAGCTTCAAGGAGATAAGATCT-TCAATCTTCAGTCTGCTTCC-TTGCTA
* * * * * *
35246640 CCTTAAGAAGATAAGACATCAATCTTCAACATGCTCTCTTACTACCTCAGA
126 CCTCAGGAAGATAAGAC-TCATTCTTCAACTTACTCTCTTGCTACCTCAGA
* * * *
35246691 AAGATAAGGTTTGGGGCTTAAATCTACTCCATTGCCGATACATGGAGATAAGATT
1 GAGATAAGG-CTGGTG-TTAAATCTGCTCCATTGCCGATACATGGAGATAAGATT
35246746 TGCCTCTTCC
Statistics
Matches: 621, Mismatches: 116, Indels: 40
0.80 0.15 0.05
Matches are distributed among these distances:
169 12 0.02
170 5 0.01
171 41 0.07
173 1 0.00
175 5 0.01
176 297 0.48
177 252 0.41
178 4 0.01
179 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (175 bp):
GAGATAAGGCTGGTGTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATTTTCGA
TCTGCTCCGCTACAGCTTCAAGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCA
GGAAGATAAGACTCATTCTTCAACTTACTCTCTTGCTACCTCAGA
Found at i:35247059 original size:133 final size:133
Alignment explanation
Indices: 35246858--35247114 Score: 381
Period size: 133 Copynumber: 1.9 Consensus size: 133
35246848 CAGTGGCTAA
* *
35246858 AATCTGCTCCATTACCGATACATGGAGATAAGATTCACCGTCATCAATCTGCCCCACTACTGCCT
1 AATCTACTCCATTACCGATACATGGAGATAAGATTCACCATCATCAATCTGCCCCACTACTGCCT
* *
35246923 AGGGAGATAAGATCTACAAAT-TCCAGTCTGCTTTCTTGCTACCTCAGGAAGATAAGACTACAAT
66 AGGGAGATAAGATCTAC-AATCTCCAGTCTGCTTCCTTCCTACCTCAGGAAGATAAGACTACAAT
35246987 CGCC
130 CGCC
* * * * * *
35246991 AATCTACTCCATTATCGATACATGGAGATAAGATTCACTATCTTCGATCTGCTCCACTACTGCTT
1 AATCTACTCCATTACCGATACATGGAGATAAGATTCACCATCATCAATCTGCCCCACTACTGCCT
* * *
35247056 AGGGAGGTAAGATCTTCAATCTTCAGTCTGCTTCCTTCCTACCTCAGGAAGATAAGACT
66 AGGGAGATAAGATCTACAATCTCCAGTCTGCTTCCTTCCTACCTCAGGAAGATAAGACT
35247115 CAACTTTTAA
Statistics
Matches: 110, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
132 3 0.03
133 107 0.97
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (133 bp):
AATCTACTCCATTACCGATACATGGAGATAAGATTCACCATCATCAATCTGCCCCACTACTGCCT
AGGGAGATAAGATCTACAATCTCCAGTCTGCTTCCTTCCTACCTCAGGAAGATAAGACTACAATC
GCC
Found at i:35247482 original size:64 final size:67
Alignment explanation
Indices: 35247347--35247505 Score: 200
Period size: 64 Copynumber: 2.4 Consensus size: 67
35247337 GCCATGATAA
* * * *
35247347 AAAAT-AATCAAATGCTCTTAACTAAATGATATATGAGTGATGTCAAATAATTAGGACGCTATGA
1 AAAATGAATCAAATGCTCTTAACTAGATGATATATGACTGATGTCAAATAATTAGGACACTATAA
35247411 TC
66 TC
* * * * *
35247413 GAAATGAATCAAATGCTCTTAACTAGA-GGTA-ATG-CTTATGTCAAATAATTAGGATACTTTAA
1 AAAATGAATCAAATGCTCTTAACTAGATGATATATGACTGATGTCAAATAATTAGGACACTATAA
35247475 TC
66 TC
*
35247477 AAAATGAATCAAATGCTCCTAACTAGATG
1 AAAATGAATCAAATGCTCTTAACTAGATG
35247506 CGAGATTTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
64 49 0.61
65 4 0.05
66 7 0.09
67 20 0.25
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (67 bp):
AAAATGAATCAAATGCTCTTAACTAGATGATATATGACTGATGTCAAATAATTAGGACACTATAA
TC
Found at i:35248556 original size:17 final size:18
Alignment explanation
Indices: 35248494--35248556 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 18
35248484 CTTTTCTTTC
*
35248494 TTTTTTTTTAAATTTTTTGA
1 TTTTTTTTTTAA--TTTTGA
**
35248514 TTTTCTTTTTTAATTTTTC
1 TTTT-TTTTTTAATTTTGA
*
35248533 TTCTTTTTTT-ATTTTGA
1 TTTTTTTTTTAATTTTGA
35248550 TTTTTTT
1 TTTTTTT
35248557 ATTTTAATCT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
17 11 0.31
18 6 0.17
19 7 0.20
20 4 0.11
21 7 0.20
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTTAATTTTGA
Found at i:35248581 original size:36 final size:36
Alignment explanation
Indices: 35248508--35248583 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
35248498 TTTTTAAATT
* *
35248508 TTTTGATTTTCTTTTTTAATTTTTCTTCTTTTTTTA
1 TTTTGATTTTCTTTTTTAATTCTTCTTCTTTTCTTA
*
35248544 TTTTGATTTTTTTATTTTAATCTCTT-TT-TTTTCTTA
1 TTTTGATTTTCTT-TTTTAAT-TCTTCTTCTTTTCTTA
35248580 TTTT
1 TTTT
35248584 TTAAGGTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 23 0.66
37 9 0.26
38 3 0.09
ACGTcount: A:0.12, C:0.08, G:0.03, T:0.78
Consensus pattern (36 bp):
TTTTGATTTTCTTTTTTAATTCTTCTTCTTTTCTTA
Found at i:35249142 original size:28 final size:28
Alignment explanation
Indices: 35249106--35249168 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
35249096 TCACTATGAC
*
35249106 CTTTGTTCTATTGTTTG-CTTTTCCTTTT
1 CTTTTTTCTATT-TTTGACTTTTCCTTTT
**
35249134 CTTTTTTCTATTTTTGTACTTTTGTTTTT
1 CTTTTTTCTATTTTTG-ACTTTTCCTTTT
35249163 CTTTTT
1 CTTTTT
35249169 GGATGCCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 4 0.13
28 11 0.37
29 15 0.50
ACGTcount: A:0.05, C:0.14, G:0.08, T:0.73
Consensus pattern (28 bp):
CTTTTTTCTATTTTTGACTTTTCCTTTT
Found at i:35258040 original size:13 final size:13
Alignment explanation
Indices: 35258016--35258059 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
35258006 TTCCTGTAAA
*
35258016 CATTTCACATAAC
1 CATTTCATATAAC
**
35258029 CATTTTGTATAAC
1 CATTTCATATAAC
*
35258042 CAATTCATATAAC
1 CATTTCATATAAC
35258055 CATTT
1 CATTT
35258060 GTCATCTGGT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (13 bp):
CATTTCATATAAC
Found at i:35258204 original size:46 final size:46
Alignment explanation
Indices: 35258142--35258277 Score: 175
Period size: 46 Copynumber: 3.0 Consensus size: 46
35258132 TTATATTTGA
* * * *** *
35258142 CATGATGCCATAGTATCTTTCAACTATGGTCTTACTTGTTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTAC-ACATTTCATAT
*
35258188 CATGTTGCCATGGTATCTTTCAGCCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
35258234 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
35258278 TTCAGAGAGC
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 4 0.05
46 75 0.95
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:35258701 original size:23 final size:23
Alignment explanation
Indices: 35258669--35258784 Score: 92
Period size: 23 Copynumber: 5.0 Consensus size: 23
35258659 CAAAGAATCA
*
35258669 TATCGTGAAGCTCACGAAGAGCC
1 TATCGGGAAGCTCACGAAGAGCC
* *
35258692 TATCGGGAAGCTC-CGGATAGCC
1 TATCGGGAAGCTCACGAAGAGCC
* * * *
35258714 ATATATCGAGAAGTTCAAG-CGAGCAC
1 ---TATCGGGAAGCTCACGAAGAGC-C
* * *
35258740 TATAGGGAGGCTCACAAAGAGCC
1 TATCGGGAAGCTCACGAAGAGCC
35258763 TATCGGGAAGCTCACGAAGAGC
1 TATCGGGAAGCTCACGAAGAGC
35258785 TGTATTTTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
22 7 0.10
23 42 0.61
24 4 0.06
25 14 0.20
26 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.16
Consensus pattern (23 bp):
TATCGGGAAGCTCACGAAGAGCC
Found at i:35262875 original size:61 final size:62
Alignment explanation
Indices: 35262737--35262887 Score: 152
Period size: 60 Copynumber: 2.5 Consensus size: 62
35262727 CCAACTGTGT
* * *
35262737 TAATATGGGC-AAGGCCCAATATA-TCTCGA-CTTGTAATAGGGCTACGGCCCAAATTGATAC
1 TAATATGGGCTAAGGCCCAGTATACTCT-GATATTGTAATAGGGCTACGGCCCAAATTAATAC
* * * * * *
35262797 TAATATAGGCT-CGGCCCAGTATACTCTGATATTGTAA-GGGGCTATGGCCCAGATTAATAT
1 TAATATGGGCTAAGGCCCAGTATACTCTGATATTGTAATAGGGCTACGGCCCAAATTAATAC
*
35262857 TGATATGGGCTAAGGCCCAGT-TAACTCTGAT
1 TAATATGGGCTAAGGCCCAGTAT-ACTCTGAT
35262888 TTCTGAATAG
Statistics
Matches: 74, Mismatches: 12, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
60 49 0.66
61 25 0.34
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (62 bp):
TAATATGGGCTAAGGCCCAGTATACTCTGATATTGTAATAGGGCTACGGCCCAAATTAATAC
Found at i:35263995 original size:29 final size:27
Alignment explanation
Indices: 35263920--35263995 Score: 64
Period size: 29 Copynumber: 2.7 Consensus size: 27
35263910 TATCATATAA
*
35263920 ATATCTTATAATATAATTATAATAAATT
1 ATATTTTATAATA-AATTATAATAAATT
* **
35263948 A-ATTTAATATCATTTATTACTAATAAATAT
1 ATATTT--TATAATAAATTA-TAATAAAT-T
35263978 ATATTTTATAATAAATTA
1 ATATTTTATAATAAATTA
35263996 GATTTTTACT
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
27 3 0.08
28 5 0.14
29 22 0.61
30 2 0.06
31 4 0.11
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
ATATTTTATAATAAATTATAATAAATT
Found at i:35264000 original size:17 final size:18
Alignment explanation
Indices: 35263968--35264001 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35263958 CATTTATTAC
*
35263968 TAATAAATATATATTTTA
1 TAATAAATATAGATTTTA
35263986 TAATAAAT-TAGATTTT
1 TAATAAATATAGATTTT
35264002 TACTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATAAATATAGATTTTA
Found at i:35264172 original size:23 final size:19
Alignment explanation
Indices: 35264127--35264174 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 19
35264117 AATTATCCTT
*
35264127 AATTAAACTAAATTCACTT
1 AATTAAACTAAATTCACTC
35264146 AATTAAACTATAATTAACCACTC
1 AATTAAACTA-AATT---CACTC
35264169 AATTAA
1 AATTAA
35264175 CTTTTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.42
20 4 0.17
23 10 0.42
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTAAACTAAATTCACTC
Found at i:35267223 original size:50 final size:50
Alignment explanation
Indices: 35267147--35267260 Score: 185
Period size: 51 Copynumber: 2.3 Consensus size: 50
35267137 CTCAAAATAT
* * *
35267147 AAAAATAA-GTAAATAAGAATTAAAAAATGAATGTGAAATGGATCTTTGAA
1 AAAAATAATGAAAACAAGAATTAAAAAATAAATGTGAAATGGATCTTT-AA
35267197 AAAAATAATGAAAACAAGAATTAAAAAATAAATGTGAAATGGATCTTTAA
1 AAAAATAATGAAAACAAGAATTAAAAAATAAATGTGAAATGGATCTTTAA
35267247 AAAAATAATGAAAA
1 AAAAATAATGAAAA
35267261 AAACTCAATT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 24 0.40
51 36 0.60
ACGTcount: A:0.61, C:0.03, G:0.13, T:0.24
Consensus pattern (50 bp):
AAAAATAATGAAAACAAGAATTAAAAAATAAATGTGAAATGGATCTTTAA
Found at i:35267246 original size:26 final size:26
Alignment explanation
Indices: 35267166--35267250 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
35267156 TAAATAAGAA
*
35267166 TTAAAAAATGAATGTGAAATGGATCT
1 TTAAAAAATAAATGTGAAATGGATCT
* ** *
35267192 TTGAAAAAA-ATAATG-AAAACAAGA--A
1 TT-AAAAAATA-AATGTGAAA-TGGATCT
35267217 TTAAAAAATAAATGTGAAATGGATCT
1 TTAAAAAATAAATGTGAAATGGATCT
35267243 TTAAAAAA
1 TTAAAAAA
35267251 ATAATGAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 14
0.65 0.14 0.21
Matches are distributed among these distances:
24 12 0.28
25 6 0.14
26 13 0.30
27 12 0.28
ACGTcount: A:0.56, C:0.04, G:0.14, T:0.26
Consensus pattern (26 bp):
TTAAAAAATAAATGTGAAATGGATCT
Found at i:35267256 original size:26 final size:27
Alignment explanation
Indices: 35267168--35267254 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
35267158 AATAAGAATT
*
35267168 AAAAAATGAATGTGAAATGGATCTTTGA
1 AAAAAATAAATGTGAAATGGATCTTT-A
* ** *
35267196 AAAAAAT-AATG-AAAACAAGA--ATT-
1 AAAAAATAAATGTGAAA-TGGATCTTTA
35267219 AAAAAATAAATGTGAAATGGATCTTTA
1 AAAAAATAAATGTGAAATGGATCTTTA
35267246 AAAAAATAA
1 AAAAAATAA
35267255 TGAAAAAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 13
0.68 0.12 0.20
Matches are distributed among these distances:
23 7 0.16
24 6 0.13
25 5 0.11
26 5 0.11
27 15 0.33
28 7 0.16
ACGTcount: A:0.59, C:0.03, G:0.14, T:0.24
Consensus pattern (27 bp):
AAAAAATAAATGTGAAATGGATCTTTA
Found at i:35267275 original size:50 final size:50
Alignment explanation
Indices: 35267147--35267278 Score: 153
Period size: 51 Copynumber: 2.6 Consensus size: 50
35267137 CTCAAAATAT
* * * *
35267147 AAAAATAA-GTAAATAAGAATTAAAAAATGAATGTGAAATGGATCTTTGAA
1 AAAAATAATGAAAAAAACAATT-AAAAATAAATGTGAAATGGATCTTTGAA
* *
35267197 AAAAATAATGAAAACAAGAATTAAAAAATAAATGTGAAATGGATCTTT-AA
1 AAAAATAATGAAAAAAACAATT-AAAAATAAATGTGAAATGGATCTTTGAA
35267247 AAAAATAATGAAAAAAACTCAATT-AAAATAAA
1 AAAAATAATGAAAAAAA--CAATTAAAAATAAA
35267279 ACTAAAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
50 34 0.46
51 36 0.49
52 4 0.05
ACGTcount: A:0.61, C:0.04, G:0.11, T:0.23
Consensus pattern (50 bp):
AAAAATAATGAAAAAAACAATTAAAAATAAATGTGAAATGGATCTTTGAA
Found at i:35267287 original size:50 final size:50
Alignment explanation
Indices: 35267182--35267287 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
35267172 AATGAATGTG
* * ** *
35267182 AAATGGATCTTTGAAAAAAATAATGAAAACAAGAATTAAAAAATAAATGTG
1 AAATGGATCTTTGAAAAAAATAATGAAAAAAACAATT-AAAAATAAAACTA
35267233 AAATGGATCTTT-AAAAAAATAATGAAAAAAACTCAATT-AAAATAAAACTA
1 AAATGGATCTTTGAAAAAAATAATGAAAAAAA--CAATTAAAAATAAAACTA
35267283 AAATG
1 AAATG
35267288 AAAGGGATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
50 32 0.67
51 12 0.25
52 4 0.08
ACGTcount: A:0.60, C:0.06, G:0.10, T:0.24
Consensus pattern (50 bp):
AAATGGATCTTTGAAAAAAATAATGAAAAAAACAATTAAAAATAAAACTA
Found at i:35268422 original size:17 final size:17
Alignment explanation
Indices: 35268400--35268445 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
35268390 TTGGACTTTA
35268400 ATTTTGGTTTTTTTATT
1 ATTTTGGTTTTTTTATT
* *
35268417 ATTTTGATTTATTTTGTT
1 ATTTTGGTTT-TTTTATT
35268435 -TTTTGGTTTTT
1 ATTTTGGTTTTT
35268446 GTATAAGCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 17 0.68
18 6 0.24
ACGTcount: A:0.11, C:0.00, G:0.13, T:0.76
Consensus pattern (17 bp):
ATTTTGGTTTTTTTATT
Found at i:35285579 original size:25 final size:25
Alignment explanation
Indices: 35285545--35285600 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
35285535 GTTTTAGTTG
35285545 TTGGGCCATTTGGGCCTTGTATTTT
1 TTGGGCCATTTGGGCCTTGTATTTT
*
35285570 TTGGGCCATTTGGGCTTTGTATTTT
1 TTGGGCCATTTGGGCCTTGTATTTT
35285595 TTGGGC
1 TTGGGC
35285601 TGGGTTTTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.07, C:0.14, G:0.30, T:0.48
Consensus pattern (25 bp):
TTGGGCCATTTGGGCCTTGTATTTT
Found at i:35286121 original size:44 final size:44
Alignment explanation
Indices: 35286062--35286266 Score: 108
Period size: 44 Copynumber: 4.4 Consensus size: 44
35286052 TGCTCTGCTA
* * *
35286062 CAACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTG
1 CAACTTCAGGAAGATAAGGCTGGTAGCTTCAATCTACTCCACTG
* * * *
35286106 CAACTTCAGGAAGATAAAAGTCACCATAATTTGTAGCTTTAATCTATTCCACTG
1 CAACTTCAGGAAGAT--AAG---GC-----TGGTAGCTTCAATCTACTCCACTG
* ** * * * * *
35286160 CAACGTCAAGGAA-ATAAGATTCGCTATCTTCAGTCTGCTCCGCTG
1 CAACTTC-AGGAAGATAAGGCT-GGTAGCTTCAATCTACTCCACTG
* * *
35286205 CAAATTCTAGG-AGATAAGGCTGGTGGCTTCAATCTGCTCCACTG
1 CAACTTC-AGGAAGATAAGGCTGGTAGCTTCAATCTACTCCACTG
*
35286249 CAACTTTAGGAAGATAAG
1 CAACTTCAGGAAGATAAG
35286267 ATCCGCCATA
Statistics
Matches: 117, Mismatches: 30, Indels: 28
0.67 0.17 0.16
Matches are distributed among these distances:
43 3 0.03
44 45 0.38
45 29 0.25
46 3 0.03
49 1 0.01
52 3 0.03
54 28 0.24
55 5 0.04
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (44 bp):
CAACTTCAGGAAGATAAGGCTGGTAGCTTCAATCTACTCCACTG
Found at i:35286276 original size:143 final size:143
Alignment explanation
Indices: 35286026--35286704 Score: 943
Period size: 143 Copynumber: 4.7 Consensus size: 143
35286016 GGAACTTTAG
* * * *
35286026 GGAAATAAGATTCACTATCTTCAGTCTGCTCTGCTACAACTT-TAGGGAGATAAGGCTGGTGGCT
1 GGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCTA-GGAGATAAGGCTGGTGGCT
* * * *
35286090 TCAATCTACTCCACTGCAACTTCAGGAAGATAAAAGT-CACCATAATTTGTAGCTTTAATCTATT
65 TCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA-TCCGCCATAATTTGTAACTTTAATCTATT
35286154 CCACTGCAACGTCAA
129 CCACTGCAACGTCAA
* *
35286169 GGAAATAAGATTCGCTATCTTCAGTCTGCTCCGCTGCAAATTCTAGGAGATAAGGCTGGTGGCTT
1 GGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCTAGGAGATAAGGCTGGTGGCTT
*
35286234 CAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCGCCATAATTTGTAACTTTAATCTATTCC
66 CAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAACTTTAATCTATTCC
* * *
35286299 ACTGCAACATTAG
131 ACTGCAACGTCAA
* * * * * *
35286312 GGAAATAAGATTCACTGTCTTTAGTCTGCTCCACTACAACTTCAAGGAGATAAGGGTGGTGGCTT
1 GGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCTAGGAGATAAGGCTGGTGGCTT
* * * *
35286377 CAATCTGTTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTACCTTTAATATGTTCC
66 CAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAACTTTAATCTATTCC
* *
35286442 ACTACAATGTCAA
131 ACTGCAACGTCAA
* * * * *
35286455 GGAAATAAAATTCGCTGTCTTCAGTTTGCTCTGTTGCAACTT-TAGGCAGATAAGGCGGGTGGCT
1 GGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCTAGG-AGATAAGGCTGGTGGCT
* *
35286519 TCAATCTGCTCTACTGCAACTTCAGGAAGATAAGATCTGCCATAATTTGTAACTTTAATCTATTC
65 TCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAACTTTAATCTATTC
*
35286584 CACTGCAACGTTAA
130 CACTGCAACGTCAA
* * *
35286598 GGAAATGAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAAGTTC-AGGGAGATAAGGTTGGTGGCT
1 GGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCTA-GGAGATAAGGCTGGTGGCT
* *
35286662 TCAATCTGCTCCACTGCAACTTCAGGAATATAAGATCTGCCAT
65 TCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCAT
35286705 CTTTGATCTA
Statistics
Matches: 471, Mismatches: 60, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
142 4 0.01
143 463 0.98
144 4 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (143 bp):
GGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCTAGGAGATAAGGCTGGTGGCTT
CAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAACTTTAATCTATTCC
ACTGCAACGTCAA
Found at i:35286748 original size:20 final size:20
Alignment explanation
Indices: 35286723--35286771 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
35286713 TACTCCATTG
35286723 CAACTTCAAGGAGATATCTA
1 CAACTTCAAGGAGATATCTA
35286743 CAACTTCAAGGAGATATCTA
1 CAACTTCAAGGAGATATCTA
35286763 CAACTTCAA
1 CAACTTCAA
35286772 TTTGTTCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.24
Consensus pattern (20 bp):
CAACTTCAAGGAGATATCTA
Found at i:35287047 original size:30 final size:30
Alignment explanation
Indices: 35287011--35287072 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
35287001 ATCATTGCTC
35287011 ATTGTTCATCAAGATTCTATCATTGACACA
1 ATTGTTCATCAAGATTCTATCATTGACACA
35287041 ATTGTTCATCAAGATTCTATCATTGACACA
1 ATTGTTCATCAAGATTCTATCATTGACACA
35287071 AT
1 AT
35287073 ATCTTATCTT
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:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (30 bp):
ATTGTTCATCAAGATTCTATCATTGACACA
Found at i:35287396 original size:65 final size:65
Alignment explanation
Indices: 35287321--35287444 Score: 194
Period size: 65 Copynumber: 1.9 Consensus size: 65
35287311 AATGATGGAC
* * * *
35287321 AAGAAAGAAATTGATTGAGAGCATAGCTCGAGACGAATAAGTTAATCAAATATGGCAAATAAAAT
1 AAGAAAGAAATTGATTGAGAGCATAGCTCGAAACGAATAAATTAATCAAAGATAGCAAATAAAAT
* *
35287386 AAGAAAGAAATTGATTGAGAGTATAGCTCGAAATGAATAAATTAATCAAAGATAGCAAA
1 AAGAAAGAAATTGATTGAGAGCATAGCTCGAAACGAATAAATTAATCAAAGATAGCAAA
35287445 CTTTGCTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.22
Consensus pattern (65 bp):
AAGAAAGAAATTGATTGAGAGCATAGCTCGAAACGAATAAATTAATCAAAGATAGCAAATAAAAT
Found at i:35287913 original size:12 final size:12
Alignment explanation
Indices: 35287896--35288003 Score: 68
Period size: 11 Copynumber: 9.3 Consensus size: 12
35287886 TGTTTCTCCT
35287896 TTTTCTCTTTTC
1 TTTTCTCTTTTC
35287908 TTTTCT-TTTCTC
1 TTTTCTCTTT-TC
* *
35287920 TTTTGT-TTTTA
1 TTTTCTCTTTTC
*
35287931 TTTTTTGCTTTTTC
1 TTTTCT-C-TTTTC
35287945 TTTTC-CTTTT-
1 TTTTCTCTTTTC
* * *
35287955 ATTTCTTTTTTA
1 TTTTCTCTTTTC
*
35287967 TTTTCT-TTTTG
1 TTTTCTCTTTTC
35287978 TTTT-TCTTTTC
1 TTTTCTCTTTTC
*
35287989 TTTTTTCTTTT-
1 TTTTCTCTTTTC
35288000 TTTT
1 TTTT
35288004 TATTTTTTTA
Statistics
Matches: 78, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
10 5 0.06
11 37 0.47
12 28 0.36
14 8 0.10
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.81
Consensus pattern (12 bp):
TTTTCTCTTTTC
Found at i:35287942 original size:7 final size:6
Alignment explanation
Indices: 35287894--35288018 Score: 73
Period size: 6 Copynumber: 20.0 Consensus size: 6
35287884 TTTGTTTCTC
35287894 CTTTTT CTCTTTT C-TTTT CTTTTCT CTTTTGT -TTTTAT -TTTTT GCTTTTT
1 CTTTTT CT-TTTT CTTTTT CTTTT-T CTTTT-T CTTTT-T CTTTTT -CTTTTT
* *
35287944 CTTTTCCT TTTATTT CTTTTT -TATTTT CTTTTT GTTTTT C-TTTT CTTTTTT
1 CTTTT--T CTT-TTT CTTTTT CT-TTTT CTTTTT CTTTTT CTTTTT C-TTTTT
* *
35287995 CTTTTT -TTTTAT TTTTTT ATTTTT
1 CTTTTT CTTTT-T CTTTTT CTTTTT
35288019 TTAAGGTGAA
Statistics
Matches: 98, Mismatches: 7, Indels: 28
0.74 0.05 0.21
Matches are distributed among these distances:
5 16 0.16
6 47 0.48
7 30 0.31
8 3 0.03
9 2 0.02
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:35287976 original size:1 final size:1
Alignment explanation
Indices: 35287960--35288020 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
35287950 CTTTTATTTC
* * * * * * * *
35287960 TTTTTTATTTTCTTTTTGTTTTTCTTTTCTTTTTTCTTTTTTTTTATTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
35288021 AAGGTGAAAT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.05, C:0.07, G:0.02, T:0.87
Consensus pattern (1 bp):
T
Found at i:35287976 original size:47 final size:46
Alignment explanation
Indices: 35287909--35288017 Score: 112
Period size: 47 Copynumber: 2.3 Consensus size: 46
35287899 TCTCTTTTCT
* * * *
35287909 TTTCTTTTCTCTTTTGTTTTTATTTTTTGCTTTT-TCTTTTCCTTTTA
1 TTTCTTTTTTATTTTCTTTTT-GTTTTT-CTTTTCTCTTTTCCTTTTA
* * *
35287956 TTTCTTTTTTATTTTCTTTTTGTTTTTCTTTTCTTTTTTCTTTTTT
1 TTTCTTTTTTATTTTCTTTTTGTTTTTCTTTTCTCTTTTCCTTTTA
*
35288002 TTTATTTTTTTATTTT
1 TTT-CTTTTTTATTTT
35288018 TTTAAGGTGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
45 5 0.10
46 18 0.35
47 29 0.56
ACGTcount: A:0.05, C:0.11, G:0.03, T:0.82
Consensus pattern (46 bp):
TTTCTTTTTTATTTTCTTTTTGTTTTTCTTTTCTCTTTTCCTTTTA
Found at i:35287999 original size:17 final size:17
Alignment explanation
Indices: 35287894--35288011 Score: 85
Period size: 17 Copynumber: 6.4 Consensus size: 17
35287884 TTTGTTTCTC
35287894 CTTTTTCTCTTTTCTTTT
1 CTTTTT-TCTTTTCTTTT
* *
35287912 CTTTTCTCTTTTGTTTTT
1 CTTTTTTCTTTT-CTTTT
*
35287930 ATTTTTTGCTTTTTCTTTT
1 CTTTTTT-C-TTTTCTTTT
*
35287949 CCTTTTATTTCTTTTTTATTTT
1 -C-TTT-TTTC--TTTTCTTTT
35287971 CTTTTTGT-TTTTCTTTT
1 CTTTTT-TCTTTTCTTTT
*
35287988 CTTTTTTCTTTTTTTTT
1 CTTTTTTCTTTTCTTTT
*
35288005 ATTTTTT
1 CTTTTTT
35288012 TATTTTTTTA
Statistics
Matches: 81, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.01
17 34 0.42
18 14 0.17
19 7 0.09
20 8 0.10
21 5 0.06
22 12 0.15
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.81
Consensus pattern (17 bp):
CTTTTTTCTTTTCTTTT
Done.