Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 17 of 198
Found at i:5159156 original size:22 final size:22
Alignment explanation
Indices: 5159092--5159166 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
5159082 GGGGTCAAAA
*
5159092 GCCCGTGTAAAGAGGGGCACAC
1 GCCCGTGTGAAGAGGGGCACAC
* * *
5159114 GACCGTGTGGAA-A-AGGTACAC
1 GCCCGTGT-GAAGAGGGGCACAC
*
5159135 GCCCCTGTGAAGAGGGGCACAC
1 GCCCGTGTGAAGAGGGGCACAC
5159157 AG-CCGTGTGA
1 -GCCCGTGTGA
5159167 CTGAGGCATA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
20 3 0.08
21 13 0.32
22 21 0.52
23 3 0.08
ACGTcount: A:0.27, C:0.25, G:0.36, T:0.12
Consensus pattern (22 bp):
GCCCGTGTGAAGAGGGGCACAC
Found at i:5159945 original size:5 final size:5
Alignment explanation
Indices: 5159937--5159965 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5159927 AAGAAAAGAA
5159937 AAATC AAATC AAATC AAATC AAATC AAAT
1 AAATC AAATC AAATC AAATC AAATC AAAT
5159966 TAAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATC
Found at i:5159975 original size:15 final size:15
Alignment explanation
Indices: 5159936--5159975 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
5159926 AAAGAAAAGA
5159936 AAAATCAAATCAAAT
1 AAAATCAAATCAAAT
*
5159951 CAAATCAAATCAAATT
1 AAAATCAAATCAAA-T
5159967 AAAAT-AAAT
1 AAAATCAAAT
5159976 AATAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATCAAATCAAAT
Found at i:5160367 original size:14 final size:14
Alignment explanation
Indices: 5160350--5160395 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
5160340 TAAAAAAATG
5160350 TTATTAAATTATTA
1 TTATTAAATTATTA
*
5160364 TTATTAAATTAGTA
1 TTATTAAATTATTA
5160378 TTATTAAATTATTA
1 TTATTAAATTATTA
5160392 TTAT
1 TTAT
5160396 ATTTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTATTAAATTATTA
Found at i:5160528 original size:3 final size:3
Alignment explanation
Indices: 5160522--5160556 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5160512 TATTAAAATA
5160522 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5160557 ACTAATGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5161494 original size:24 final size:27
Alignment explanation
Indices: 5161467--5161535 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 27
5161457 GTGAATTTGT
*
5161467 GAAATAATTATTG-ATTGAAAG-GTG-
1 GAAATAATGATTGAATTGAAAGTGTGA
5161491 GAAA-AATGATTGAATTGAAAGTGTGA
1 GAAATAATGATTGAATTGAAAGTGTGA
**
5161517 GAAATTGTGATTGAATTGA
1 GAAATAATGATTGAATTGA
5161536 GAATATATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 7 0.18
24 12 0.32
25 3 0.08
26 4 0.11
27 12 0.32
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (27 bp):
GAAATAATGATTGAATTGAAAGTGTGA
Found at i:5161738 original size:37 final size:39
Alignment explanation
Indices: 5161679--5161774 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
5161669 CGGATAGATT
* * * *
5161679 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTGT-C
* *
5161716 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTGTC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTGTC
5161755 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
5161775 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTGTC
Found at i:5165476 original size:17 final size:17
Alignment explanation
Indices: 5165462--5165495 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5165452 TAAGTATTTC
5165462 ATTTAGTATTTTATTTAA
1 ATTTA-TATTTTATTTAA
5165480 ATTTATATTTT-TTTAA
1 ATTTATATTTTATTTAA
5165496 TTTCATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATTTATATTTTATTTAA
Found at i:5167586 original size:17 final size:17
Alignment explanation
Indices: 5167566--5167599 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5167556 TATAATTAAG
5167566 TATATGTTGTAATATAT
1 TATATGTTGTAATATAT
5167583 TATATGTTGTAATATAT
1 TATATGTTGTAATATAT
5167600 GTTGTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (17 bp):
TATATGTTGTAATATAT
Found at i:5167598 original size:12 final size:12
Alignment explanation
Indices: 5167583--5167608 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5167573 TGTAATATAT
5167583 TATATGTTGTAA
1 TATATGTTGTAA
5167595 TATATGTTGTAA
1 TATATGTTGTAA
5167607 TA
1 TA
5167609 ATATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
TATATGTTGTAA
Found at i:5167680 original size:24 final size:27
Alignment explanation
Indices: 5167624--5167680 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 27
5167614 AAAAAATAAC
*
5167624 ATATAAAACAGTTTTAAAAATATATAT
1 ATATAAAACAGTTTGAAAAATATATAT
* *
5167651 AAATAAAA-A-TTTGAAAGATA-ATAT
1 ATATAAAACAGTTTGAAAAATATATAT
5167675 ATATAA
1 ATATAA
5167681 TGGTTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 9 0.35
25 9 0.35
26 1 0.04
27 7 0.27
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (27 bp):
ATATAAAACAGTTTGAAAAATATATAT
Found at i:5167700 original size:24 final size:25
Alignment explanation
Indices: 5167668--5167774 Score: 99
Period size: 24 Copynumber: 4.2 Consensus size: 25
5167658 AATTTGAAAG
*
5167668 ATAATATATATAATGGTTTAAAATAA
1 ATAATATATA-AATAGTTTAAAATAA
* ***
5167694 ATAATATATAAAAAACATAAAATAA
1 ATAATATATAAATAGTTTAAAATAA
5167719 ATAATA-ATAAATAGTTTAAAATAA
1 ATAATATATAAATAGTTTAAAATAA
* * **
5167743 ATAATCTATGAAAAAAACTTAAAATAA
1 ATAATATAT--AAATAGTTTAAAATAA
5167770 ATAAT
1 ATAAT
5167775 GATAAATGAG
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
24 19 0.29
25 18 0.28
26 10 0.15
27 18 0.28
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.31
Consensus pattern (25 bp):
ATAATATATAAATAGTTTAAAATAA
Found at i:5167740 original size:49 final size:50
Alignment explanation
Indices: 5167668--5167781 Score: 158
Period size: 51 Copynumber: 2.2 Consensus size: 50
5167658 AATTTGAAAG
*
5167668 ATAATATATATAATGGTTTAAAATAAATAATATAT-AAAAAACATAAAATAA
1 ATAATA-ATA-AATAGTTTAAAATAAATAATATATAAAAAAACATAAAATAA
* *
5167719 ATAATAATAAATAGTTTAAAATAAATAATCTATGAAAAAAACTTAAAATAA
1 ATAATAATAAATAGTTTAAAATAAATAATATAT-AAAAAAACATAAAATAA
*
5167770 ATAATGATAAAT
1 ATAATAATAAAT
5167782 GAGCTTTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
49 22 0.39
50 3 0.05
51 32 0.56
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (50 bp):
ATAATAATAAATAGTTTAAAATAAATAATATATAAAAAAACATAAAATAA
Found at i:5169273 original size:44 final size:43
Alignment explanation
Indices: 5169229--5169500 Score: 176
Period size: 44 Copynumber: 6.1 Consensus size: 43
5169219 GATATGAGAC
*
5169229 TTGTGGTTTTAGTCTGCTCCACTGCAACTTCAAGGAGATAAGA
1 TTGTGGTTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGA
* * * * * *
5169272 CTTGCTATAGTAGATTTAATTTGAC-CTACTACAACCTCAGAGG-TATAAGA
1 -TTG---T-G--GTTTTAATCTG-CTCCACTGCAACTTCA-AGGAGATAAGA
* * * *
5169322 TTCATTGTTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGA
1 TT-GTGGTTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGA
* * * *
5169366 TTAGTAGTTTCAATCTGCTCCACTGCAAATTCAGGGAGATAAGA
1 TT-GTGGTTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGA
* *
5169410 -T-TGGTATCTTCAACCTGCTCCACTGCAACTTC-AGAGAGATAAGGT
1 TTGTGGT-T-TT-AATCTGCTCCACTGCAACTTCAAG-GAGATAA-GA
** * *
5169455 TTGTGCCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGA
1 TTGTGGTTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGA
5169498 TTG
1 TTG
5169501 GTTTATTTTT
Statistics
Matches: 172, Mismatches: 37, Indels: 39
0.69 0.15 0.16
Matches are distributed among these distances:
41 3 0.02
42 1 0.01
43 11 0.06
44 115 0.67
45 4 0.02
46 2 0.01
47 4 0.02
48 1 0.01
49 2 0.01
50 25 0.15
51 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (43 bp):
TTGTGGTTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGA
Found at i:5169710 original size:44 final size:44
Alignment explanation
Indices: 5169603--5170055 Score: 222
Period size: 45 Copynumber: 10.0 Consensus size: 44
5169593 TTATAGCTTT
* * * * *
5169603 AATCTGTTCCACTGTAACTTCAGGGAAATAAGATTCACTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTC-GTAACTTC
* * *
5169648 AGTCTGCTCTACTACAACTTCAGGGAGATAAGACTT-GTAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGTAACTTC
* * * *
5169692 AATCTGCTCCACTGCAACTTTAAGGAGATAAGGTT--T-GCTAT-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTAACT-TC
* * * * **
5169733 GATCTACTCTACTACAACTTCAGATAGATAAGATTCGCAATTTATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCG-----TA-A-CTTC
* * * *
5169784 AATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCG-TAACTTC
* ** * *
5169829 AGTCTGCTCCACTGCAACTTCAATGAGATAAGACTAGTAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTAACTTC
* * *
5169873 AACCTGCTCCACTGCAACTTCAGGGAGATAA-AGTTTGTTA--T-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGTAACTTC
* * * * * * *
5169914 GATTTGCTCTACTGTAACTTCAGAGAGATAAGATCCGTAATTTATAGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCG-----TA-A-CTTC
* * * * * * *
5169965 AATCAGTTCCACTGTAACTTTAGGAAAATAAGATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCG-TAACTTC
* * * * *
5170010 AGTCTGCTCCACTACAACTTTAGGGAGATAAGACTAGTAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTAACTTC
5170054 AA
1 AA
5170056 AGAGATAAGG
Statistics
Matches: 300, Mismatches: 83, Indels: 51
0.69 0.19 0.12
Matches are distributed among these distances:
41 55 0.18
42 4 0.01
43 3 0.01
44 77 0.26
45 91 0.30
46 3 0.01
47 5 0.02
48 1 0.00
50 2 0.01
51 59 0.20
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTAACTTC
Found at i:5169725 original size:181 final size:181
Alignment explanation
Indices: 5169467--5170055 Score: 793
Period size: 181 Copynumber: 3.2 Consensus size: 181
5169457 GTGCCTTTAA
** * * ** * * *
5169467 TCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGTTTATTTTTAACCTGTTCCACTGTAACTTT
1 TCTGCTCCACTACAACTTCAGGGAGATAAGACTAG--TAACTTCAACCTGCTCCACTGCAACTTT
* * * *
5169532 AGGGAGATAAGGTTTGATATGATCTACTTTACTGCAAATTTAGAGAGATAAAATCTGTAATTTAT
64 AGGGAGATAAGGTTTGATATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTAT
*
5169597 AGCTTTAATCTGTTCCACTGTAACTTCAGGGAAATAAGATTCACTATCTTCAG
129 AGCTTTAATCTGTTCCACTGTAACTTCAGGGAAATAAGATTCGCTATCTTCAG
* * * *
5169650 TCTGCTCTACTACAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTTAA
1 TCTGCTCCACTACAACTTCAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTTAG
* * * *
5169715 GGAGATAAGGTTTGCTATGATCTACTCTACTACAACTTCAGATAGATAAGAT-TCGCAATTTATA
66 GGAGATAAGGTTTGATATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCT-GTAATTTATA
* **
5169779 GCTTCAATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAG
130 GCTTTAATCTGTTCCACTGTAACTTCAGGGAAATAAGATTCGCTATCTTCAG
* ** *
5169831 TCTGCTCCACTGCAACTTCAATGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTCAG
1 TCTGCTCCACTACAACTTCAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTTAG
* * * * * *
5169896 GGAGATAAAGTTTGTTATGATTTGCTCTACTGTAACTTCAGAGAGATAAGATCCGTAATTTATAG
66 GGAGATAAGGTTTGATATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAG
* * *
5169961 CTTTAATCAGTTCCACTGTAACTTTAGGAAAATAAGATTCGCTATCTTCAG
131 CTTTAATCTGTTCCACTGTAACTTCAGGGAAATAAGATTCGCTATCTTCAG
*
5170012 TCTGCTCCACTACAACTTTAGGGAGATAAGACTAGTAACTTCAA
1 TCTGCTCCACTACAACTTCAGGGAGATAAGACTAGTAACTTCAA
5170056 AGAGATAAGG
Statistics
Matches: 353, Mismatches: 51, Indels: 6
0.86 0.12 0.01
Matches are distributed among these distances:
180 1 0.00
181 322 0.91
183 30 0.08
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (181 bp):
TCTGCTCCACTACAACTTCAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTTTAG
GGAGATAAGGTTTGATATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAG
CTTTAATCTGTTCCACTGTAACTTCAGGGAAATAAGATTCGCTATCTTCAG
Found at i:5169763 original size:85 final size:85
Alignment explanation
Indices: 5169378--5169946 Score: 327
Period size: 89 Copynumber: 6.4 Consensus size: 85
5169368 AGTAGTTTCA
* * * * * *
5169378 ATCTGCTCCACTGCAAATTCAGGGAGATAAGA-TTGGTATCTTCAACCTGCTCCACTGCAACTTC
1 ATCTGCTCTACTACAACTTCAGAGAGATAAGACTT-GTAACTTCAATCTGCTCCACTGCAACTTC
* * *
5169442 AGAGAGATAAGGTTTGTGCCTTTA
65 AGGGAGATAAGG-TT-TG-CTATG
* ** * ** * * * *
5169466 ATCTGCTCCACTGTAACTTCAGGGAGATAAGA-TTGGTTTATTTTTAACCTGTTCCACTGTAACT
1 ATCTGCTCTACTACAACTTCAGAGAGATAAGACTT-G--TAACTTCAATCTGCTCCACTGCAACT
* *
5169530 TTAGGGAGATAAGGTTTGATATG
63 TCAGGGAGATAAGGTTTGCTATG
* * * * * * * * * *
5169553 ATCTACTTTACTGCAAATTTAGAGAGATAAAATCTGTAATTTATAGCTTTAATCTGTTCCACTGT
1 ATCTGCTCTACTACAACTTCAGAGAGATAAGA-C--T--TGTA-A-CTTCAATCTGCTCCACTGC
* * ** *
5169618 AACTTCAGGGAAATAAGATTCACTATCTTC
59 AACTTCAGGGAGATAAGGTTTGCTA---TG
* *
5169648 AGTCTGCTCTACTACAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTT
1 A-TCTGCTCTACTACAACTTCAGAGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTC
*
5169713 AAGGAGATAAGGTTTGCTATG
65 AGGGAGATAAGGTTTGCTATG
* * * *
5169734 ATCTACTCTACTACAACTTCAGATAGATAAGA-TTCGCAATTTATAGCTTCAATCTGTTCCACTA
1 ATCTGCTCTACTACAACTTCAGAGAGATAAGACTT-G-----TA-A-CTTCAATCTGCTCCACTG
* * * *
5169798 CAACTTCAGGGAAATAAGATTCGCTATCTTC
58 CAACTTCAGGGAGATAAGGTTTGCTA---TG
* * * *
5169829 AGTCTGCTCCACTGCAACTTCA-ATGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAACTT
1 A-TCTGCTCTACTACAACTTCAGA-GAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTT
* *
5169893 CAGGGAGATAAAGTTTGTTATG
64 CAGGGAGATAAGGTTTGCTATG
* **
5169915 ATTTGCTCTACTGTAACTTCAGAGAGATAAGA
1 ATCTGCTCTACTACAACTTCAGAGAGATAAGA
5169947 TCCGTAATTT
Statistics
Matches: 376, Mismatches: 76, Indels: 61
0.73 0.15 0.12
Matches are distributed among these distances:
84 2 0.01
85 55 0.15
86 5 0.01
87 26 0.07
88 36 0.10
89 73 0.19
90 40 0.11
91 7 0.02
92 73 0.19
93 2 0.01
95 6 0.02
96 50 0.13
97 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (85 bp):
ATCTGCTCTACTACAACTTCAGAGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCA
GGGAGATAAGGTTTGCTATG
Found at i:5169847 original size:45 final size:45
Alignment explanation
Indices: 5169333--5170042 Score: 328
Period size: 44 Copynumber: 15.7 Consensus size: 45
5169323 TCATTGTTTT
* * * *
5169333 AATCCGCTCCACTGCAACTTCAAGGAGATAGGATTAG-TAGT-TTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTA-TCTTC
* *
5169377 AATCTGCTCCACTGCAAATTCAGGGAGATAAGATT-GGTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * * * ** *
5169421 AACCTGCTCCACTGCAACTTCAGAGAGATAAGGTTTG-TGCCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * * * *
5169465 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGTTTATTTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCG-CTATCTTC
* * * * * * *
5169511 AACCTGTTCCACTGTAACTTTAGGGAGATAAGGTTTG--AT-AT-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * ** * * * * * *
5169552 GATCTACTTTACTGCAAATTTAGAGAGATAA-AATCTGTAATTTATAGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTC-G----CTAT--CTTC
* * * *
5169603 AATCTGTTCCACTGTAACTTCAGGGAAATAAGATTCACTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * * *
5169648 AGTCTGCTCTACTACAACTTCAGGGAGATAAGACTT-G-TAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCTATCTTC
* * * *
5169692 AATCTGCTCCACTGCAACTTTAAGGAGATAAGGTTTGCTA---T-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * * * **
5169733 GATCTACTCTACTACAACTTCAGATAGATAAGATTCGCAATTTATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGC----TAT--CTTC
* * *
5169784 AATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* ** * * *
5169829 AGTCTGCTCCACTGCAACTTCAATGAGATAAGACTAG-TAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * *
5169873 AACCTGCTCCACTGCAACTTCAGGGAGATAA-AGTTTG-T-T-AT-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCTATCTTC
* * * * * * * *
5169914 GATTTGCTCTACTGTAACTTCAGAGAGATAAGATCCGTAATTTATAGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCG----CTAT--CTTC
* * * * * *
5169965 AATCAGTTCCACTGTAACTTTAGGAAAATAAGATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * *
5170010 AGTCTGCTCCACTACAACTTTAGGGAGATAAGA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA
5170043 CTAGTAACTT
Statistics
Matches: 496, Mismatches: 128, Indels: 83
0.70 0.18 0.12
Matches are distributed among these distances:
40 1 0.00
41 78 0.16
42 4 0.01
43 7 0.01
44 173 0.35
45 97 0.20
46 39 0.08
47 12 0.02
50 3 0.01
51 79 0.16
52 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
Found at i:5176182 original size:25 final size:23
Alignment explanation
Indices: 5176153--5176235 Score: 85
Period size: 25 Copynumber: 3.4 Consensus size: 23
5176143 CAAAATATAT
* *
5176153 AATAAAAAGTTTCAAATAAATAAA
1 AATAAAAAATTTAAAATAAAT-AA
* *
5176177 ATATAAAAAACTAAAAATAAATAA
1 A-ATAAAAAATTTAAAATAAATAA
5176201 CAATAAAACAATTTAAAATAAATAA
1 -AATAAAA-AATTTAAAATAAATAA
*
5176226 TATAAAAAAT
1 AATAAAAAAT
5176236 AACATATAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.06
24 15 0.31
25 31 0.63
ACGTcount: A:0.70, C:0.05, G:0.01, T:0.24
Consensus pattern (23 bp):
AATAAAAAATTTAAAATAAATAA
Found at i:5176305 original size:26 final size:26
Alignment explanation
Indices: 5176276--5176384 Score: 105
Period size: 26 Copynumber: 4.2 Consensus size: 26
5176266 TATTTGAAAG
*
5176276 ATAATATATATAATGGTTTAAAATAA
1 ATAATATATATAATAGTTTAAAATAA
* **
5176302 ATAATATATA-AAAAACTTAAAATAA
1 ATAATATATATAATAGTTTAAAATAA
*
5176327 ATAATA-AAATAAATAGTTTAAAATAA
1 ATAATATATAT-AATAGTTTAAAATAA
* * **
5176353 ATAATATATGAAAAAAACTTAAAATAA
1 ATAATATAT-ATAATAGTTTAAAATAA
5176380 ATAAT
1 ATAAT
5176385 GATAAAAGAG
Statistics
Matches: 66, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
24 2 0.03
25 17 0.26
26 28 0.42
27 18 0.27
28 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (26 bp):
ATAATATATATAATAGTTTAAAATAA
Found at i:5176390 original size:51 final size:50
Alignment explanation
Indices: 5176276--5176384 Score: 164
Period size: 51 Copynumber: 2.1 Consensus size: 50
5176266 TATTTGAAAG
* *
5176276 ATAATATATATAATGGTTTAAAATAAATAATATATAAAAAACTTAAAATAA
1 ATAATAAATA-AATAGTTTAAAATAAATAATATATAAAAAACTTAAAATAA
5176327 ATAATAAAATAAATAGTTTAAAATAAATAATATATGAAAAAAACTTAAAATAA
1 ATAAT-AAATAAATAGTTTAAAATAAATAATATAT--AAAAAACTTAAAATAA
5176380 ATAAT
1 ATAAT
5176385 GATAAAAGAG
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
51 28 0.53
52 4 0.08
53 21 0.40
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (50 bp):
ATAATAAATAAATAGTTTAAAATAAATAATATATAAAAAACTTAAAATAA
Found at i:5179317 original size:9 final size:9
Alignment explanation
Indices: 5179300--5179336 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5179290 TGAGTTTTCG
5179300 AATTCGAAT
1 AATTCGAAT
*
5179309 AACTCGAAT
1 AATTCGAAT
5179318 AATTCGAAT
1 AATTCGAAT
5179327 AATTCGAAT
1 AATTCGAAT
5179336 A
1 A
5179337 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5179434 original size:20 final size:19
Alignment explanation
Indices: 5179395--5179434 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5179385 ATTTTTCTCT
*
5179395 CAAAACTTTTACTTCCTCC
1 CAAAACTTTTACTCCCTCC
5179414 CAAAACTTTTACTCCCCTCC
1 CAAAACTTTTACT-CCCTCC
5179434 C
1 C
5179435 CTCCCCTCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.25, C:0.42, G:0.00, T:0.33
Consensus pattern (19 bp):
CAAAACTTTTACTCCCTCC
Found at i:5187578 original size:11 final size:11
Alignment explanation
Indices: 5187562--5187604 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 11
5187552 TATATATCAC
5187562 ATTAATAATTA
1 ATTAATAATTA
5187573 ATTAATATATATCA
1 ATTAATA-AT-T-A
5187587 CATTAATAATTA
1 -ATTAATAATTA
5187599 ATTAAT
1 ATTAAT
5187605 TTTTTAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 13 0.46
12 3 0.11
13 2 0.07
14 3 0.11
15 7 0.25
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTAATAATTA
Found at i:5187580 original size:26 final size:26
Alignment explanation
Indices: 5187551--5187604 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
5187541 CTGCAATATT
5187551 ATATATATCACATTAATAATTAATTA
1 ATATATATCACATTAATAATTAATTA
5187577 ATATATATCACATTAATAATTAATTA
1 ATATATATCACATTAATAATTAATTA
5187603 AT
1 AT
5187605 TTTTTAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATATATCACATTAATAATTAATTA
Found at i:5191811 original size:54 final size:54
Alignment explanation
Indices: 5191709--5191816 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
5191699 CATGCAAAAG
* * * * **
5191709 ATGTAATCAAACAATATTAAATTTAAGACATTAAAGCTCGAGTTTAACTAGAAA
1 ATGTAATCAAACAAAATTAAATGTAAGAAATTAAAACTCGAGCATAACTAGAAA
* * *
5191763 ATGTAATCAAGCAAAATTAAATGTAAGAAATTAAAACTTGAGCATAACTTGAAA
1 ATGTAATCAAACAAAATTAAATGTAAGAAATTAAAACTCGAGCATAACTAGAAA
5191817 GAAAATTTGG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (54 bp):
ATGTAATCAAACAAAATTAAATGTAAGAAATTAAAACTCGAGCATAACTAGAAA
Found at i:5192800 original size:31 final size:31
Alignment explanation
Indices: 5192748--5192824 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
5192738 CCCAAAGAGA
* **
5192748 TTAAGTACCAACTTAATAAAAAGTATAAAGT
1 TTAAGTACCAAATTAGGAAAAAGTATAAAGT
* *
5192779 TTAAGTACCAAATTAGGAAAAAGTGTCAAGT
1 TTAAGTACCAAATTAGGAAAAAGTATAAAGT
**
5192810 TTGGGTACC-AATTAG
1 TTAAGTACCAAATTAG
5192825 AACCCAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 6 0.15
31 33 0.85
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (31 bp):
TTAAGTACCAAATTAGGAAAAAGTATAAAGT
Found at i:5194312 original size:19 final size:18
Alignment explanation
Indices: 5194272--5194323 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
5194262 AAATAGTGAC
5194272 AAAATTAACAATAAAACA
1 AAAATTAACAATAAAACA
*
5194290 AAAATTATACAATAACAATA
1 AAAATTA-ACAATAA-AACA
*
5194310 AAATAGTAACAATA
1 AAA-ATTAACAATA
5194324 TAATACTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 7 0.24
19 7 0.24
20 12 0.41
21 3 0.10
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAATTAACAATAAAACA
Found at i:5194957 original size:49 final size:46
Alignment explanation
Indices: 5194894--5194999 Score: 140
Period size: 49 Copynumber: 2.2 Consensus size: 46
5194884 TCTGAATAAG
*
5194894 AAAAGGCAAAACTACATCGTTTTGATAAACATTTACATTTTCTGAAGTT
1 AAAAGGCAAAACTACATCGTTTTGATAAACATTTAC-TTGTC--AAGTT
* * *
5194943 AAAAGGTAAAACTACGTCGTTTTGATAAATATTTACTTGTCAAGTT
1 AAAAGGCAAAACTACATCGTTTTGATAAACATTTACTTGTCAAGTT
*
5194989 AAAAGACAAAA
1 AAAAGGCAAAA
5195000 TCATTATATT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
46 14 0.27
48 4 0.08
49 33 0.65
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.32
Consensus pattern (46 bp):
AAAAGGCAAAACTACATCGTTTTGATAAACATTTACTTGTCAAGTT
Found at i:5198783 original size:23 final size:22
Alignment explanation
Indices: 5198756--5198811 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
5198746 TGTTATTAAA
5198756 TTTTAATAAAATA-TTTAGTATAT
1 TTTTAATAAAATATTTTA-TAT-T
*
5198779 TTTTAAT-TAATATTTTATATT
1 TTTTAATAAAATATTTTATATT
5198800 TTTTAAATAAAA
1 TTTT-AATAAAA
5198812 ATAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 5 0.18
22 10 0.36
23 13 0.46
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTTAATAAAATATTTTATATT
Found at i:5198790 original size:22 final size:21
Alignment explanation
Indices: 5198756--5198811 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
5198746 TGTTATTAAA
5198756 TTTTAATAAAATATTTAGTATAT
1 TTTTAATAAAATATTT--TATAT
*
5198779 TTTTAAT-TAATATTTTATATT
1 TTTTAATAAAATATTTTATA-T
5198800 TTTTAAATAAAA
1 TTTT-AATAAAA
5198812 ATAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 4 0.14
21 5 0.18
22 10 0.36
23 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTTAATAAAATATTTTATAT
Found at i:5199066 original size:17 final size:17
Alignment explanation
Indices: 5199044--5199076 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5199034 AATTGATGTG
5199044 TTTTTT-TTATATTTATA
1 TTTTTTATTAT-TTTATA
5199061 TTTTTTATTATTTTAT
1 TTTTTTATTATTTTAT
5199077 TATGCTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTATTATTTTATA
Found at i:5201396 original size:14 final size:14
Alignment explanation
Indices: 5201373--5201406 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5201363 TGGTATGAGT
5201373 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
5201386 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
5201400 TTATAGG
1 TTATAGG
5201407 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:5201779 original size:31 final size:29
Alignment explanation
Indices: 5201718--5201781 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
5201708 ATAATGTAAA
* *
5201718 TGACTAAAACGTAACATTTCAAACATAAG
1 TGACTAAAACGTAACAGTTCAAACAAAAG
5201747 TGACTAAAACGTAACCTAAGTT-AAACAAAAG
1 TGACTAAAACGTAA-C--AGTTCAAACAAAAG
5201778 TGAC
1 TGAC
5201782 AATGGGTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 14 0.47
30 1 0.03
31 12 0.40
32 3 0.10
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.22
Consensus pattern (29 bp):
TGACTAAAACGTAACAGTTCAAACAAAAG
Found at i:5201843 original size:21 final size:21
Alignment explanation
Indices: 5201819--5201861 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
5201809 TTTTAGAAAA
5201819 ATATGATTTT-TAATTA-TTTTT
1 ATAT-ATTTTCTAA-TAGTTTTT
5201840 ATATATTTTCTAATAGTTTTT
1 ATATATTTTCTAATAGTTTTT
5201861 A
1 A
5201862 GTCTAAGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (21 bp):
ATATATTTTCTAATAGTTTTT
Found at i:5203138 original size:18 final size:18
Alignment explanation
Indices: 5203115--5203150 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5203105 TTCTTTTTTT
5203115 CTTTTCTATTTTTATGAA
1 CTTTTCTATTTTTATGAA
*
5203133 CTTTTCTATTTTTTTGAA
1 CTTTTCTATTTTTATGAA
5203151 ATTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.06, T:0.64
Consensus pattern (18 bp):
CTTTTCTATTTTTATGAA
Found at i:5212713 original size:18 final size:18
Alignment explanation
Indices: 5212663--5212713 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
5212653 TAAATATTTC
* *
5212663 TAAAAA-AATATTTTACA
1 TAAAAATAAAATTTTAAA
5212680 TAAAAATTAAAA-TTTAAA
1 TAAAAA-TAAAATTTTAAA
5212698 TAAAAATAAAATTTTA
1 TAAAAATAAAATTTTA
5212714 TTCAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 11 0.38
18 15 0.52
19 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAAATAAAATTTTAAA
Found at i:5213055 original size:16 final size:16
Alignment explanation
Indices: 5213026--5213069 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
5213016 CCTAAAATGG
5213026 TAAATTTT-TAATTTA
1 TAAATTTTATAATTTA
*
5213041 TATATTTTATAATTTA
1 TAAATTTTATAATTTA
5213057 TAAATTTTA-AATT
1 TAAATTTTATAATT
5213070 AGTAATGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAAATTTTATAATTTA
Found at i:5228871 original size:13 final size:12
Alignment explanation
Indices: 5228851--5228876 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5228841 CCCCAAGTTC
5228851 TTAAAAAAAATT
1 TTAAAAAAAATT
5228863 TTAAAAAAAATT
1 TTAAAAAAAATT
5228875 TT
1 TT
5228877 GATTTTCTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAAAAAAAATT
Found at i:5236414 original size:45 final size:46
Alignment explanation
Indices: 5236365--5236462 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
5236355 AGATAGAAAC
*
5236365 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
5236410 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
5236456 GAAAATA
1 CAAAATA
5236463 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:5241027 original size:45 final size:46
Alignment explanation
Indices: 5240978--5241075 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
5240968 AGATAGAAAC
*
5240978 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
5241023 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
5241069 GAAAATA
1 CAAAATA
5241076 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:5242567 original size:2 final size:2
Alignment explanation
Indices: 5242560--5242591 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5242550 ACATGGCTAC
*
5242560 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5242592 TTTATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5244418 original size:9 final size:9
Alignment explanation
Indices: 5244397--5244435 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
5244387 GTTAGTTTTG
5244397 AAAATTACAA
1 AAAATTAC-A
5244407 AAAATTACA
1 AAAATTACA
*
5244416 AAAATTATA
1 AAAATTACA
5244425 AAAATTA-A
1 AAAATTACA
5244433 AAA
1 AAA
5244436 GCTAAAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 4 0.14
9 16 0.57
10 8 0.29
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAATTACA
Found at i:5245892 original size:39 final size:39
Alignment explanation
Indices: 5245840--5245916 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
5245830 TAAACTTTTC
*
5245840 GCGGCGCAAAAAAACAAATGCCGCAATAGACCTGCATTA
1 GCGGCGCAAAAAAACAAACGCCGCAATAGACCTGCATTA
**
5245879 GCGGCGCCCAAAAACAAACGCCGCAATAGACCTGCATT
1 GCGGCGCAAAAAAACAAACGCCGCAATAGACCTGCATT
5245917 CGCAGCGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.38, C:0.30, G:0.21, T:0.12
Consensus pattern (39 bp):
GCGGCGCAAAAAAACAAACGCCGCAATAGACCTGCATTA
Found at i:5248187 original size:15 final size:16
Alignment explanation
Indices: 5248157--5248191 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5248147 ATTTATCAAT
*
5248157 TTTAATATTGATAGTA
1 TTTAATATTGAGAGTA
5248173 TTTAA-ATTGAGAGTA
1 TTTAATATTGAGAGTA
5248188 TTTA
1 TTTA
5248192 TAAATTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (16 bp):
TTTAATATTGAGAGTA
Found at i:5248876 original size:23 final size:21
Alignment explanation
Indices: 5248825--5248878 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 21
5248815 TTCGAATGTC
5248825 TGATTTTGCGTATTTATACAT
1 TGATTTTGCGTATTTATACAT
* *
5248846 TGAGTTTTGTCGTATTTTTTACTT
1 TGA-TTTTG-CGTA-TTTATACAT
5248870 TGATTTTGC
1 TGATTTTGC
5248879 TTTTTTATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 3 0.11
22 6 0.21
23 9 0.32
24 10 0.36
ACGTcount: A:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (21 bp):
TGATTTTGCGTATTTATACAT
Found at i:5249542 original size:12 final size:12
Alignment explanation
Indices: 5249525--5249552 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5249515 TTTACCTTCT
5249525 TATACATATATA
1 TATACATATATA
5249537 TATACATATATA
1 TATACATATATA
5249549 TATA
1 TATA
5249553 AGTGACGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (12 bp):
TATACATATATA
Found at i:5250901 original size:8 final size:7
Alignment explanation
Indices: 5250888--5250933 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
5250878 TAACTTATAT
5250888 ATAATAAC
1 ATAAT-AC
5250896 ATAATA-
1 ATAATAC
*
5250902 A-ATTAC
1 ATAATAC
5250908 ATAATAC
1 ATAATAC
5250915 ATAATAAC
1 ATAAT-AC
5250923 ATAATAC
1 ATAATAC
5250930 ATAA
1 ATAA
5250934 CTTATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 16 0.48
8 12 0.36
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAC
Found at i:5250926 original size:15 final size:15
Alignment explanation
Indices: 5250888--5250933 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
5250878 TAACTTATAT
5250888 ATAATAACATAAT--
1 ATAATAACATAATAC
*
5250901 A-AATTACATAATAC
1 ATAATAACATAATAC
5250915 ATAATAACATAATAC
1 ATAATAACATAATAC
5250930 ATAA
1 ATAA
5250934 CTTATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
14 1 0.04
15 16 0.57
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAACATAATAC
Found at i:5250955 original size:21 final size:20
Alignment explanation
Indices: 5250929--5250986 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
5250919 TAACATAATA
*
5250929 CATAACTTATATATAAGCTTG
1 CATAACTTATATATAA-CTTC
*
5250950 CATAACTTACATAATAACTTC
1 CATAACTTATAT-ATAACTTC
5250971 CATAACTTATATATAA
1 CATAACTTATATATAA
5250987 TAACTTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 4 0.12
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (20 bp):
CATAACTTATATATAACTTC
Found at i:5250991 original size:14 final size:14
Alignment explanation
Indices: 5250972--5250999 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5250962 AATAACTTCC
5250972 ATAACTTATATATA
1 ATAACTTATATATA
5250986 ATAACTTATATATA
1 ATAACTTATATATA
5251000 TAAGCTTGCA
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAACTTATATATA
Found at i:5251012 original size:10 final size:9
Alignment explanation
Indices: 5251008--5251425 Score: 502
Period size: 9 Copynumber: 46.7 Consensus size: 9
5250998 TATAAGCTTG
5251008 CATAACTTA
1 CATAACTTA
*
5251017 CATAAATTA
1 CATAACTTA
*
5251026 AATAACTTA
1 CATAACTTA
*
5251035 CATAAATTA
1 CATAACTTA
*
5251044 AATAACTTA
1 CATAACTTA
5251053 CATAACTTA
1 CATAACTTA
5251062 CATAACTTA
1 CATAACTTA
*
5251071 CATAAATTA
1 CATAACTTA
*
5251080 AATAACTTA
1 CATAACTTA
5251089 CATAACTTA
1 CATAACTTA
5251098 CATAACTTA
1 CATAACTTA
*
5251107 CATAAATTA
1 CATAACTTA
*
5251116 AATAACTTA
1 CATAACTTA
5251125 CATAACTTA
1 CATAACTTA
*
5251134 CATAAATTA
1 CATAACTTA
5251143 -ATAAACTTA
1 CAT-AACTTA
5251152 CATAACTTA
1 CATAACTTA
*
5251161 CATAAATTA
1 CATAACTTA
*
5251170 AATAACTTA
1 CATAACTTA
*
5251179 CATAACGTA
1 CATAACTTA
*
5251188 CATAAATTA
1 CATAACTTA
*
5251197 AATAACTTA
1 CATAACTTA
5251206 CATAACTTA
1 CATAACTTA
*
5251215 CATAAATTA
1 CATAACTTA
*
5251224 AATAACTTA
1 CATAACTTA
5251233 CATAACTTA
1 CATAACTTA
*
5251242 CATAAATTA
1 CATAACTTA
*
5251251 AATAACTTA
1 CATAACTTA
5251260 CATAACTTA
1 CATAACTTA
*
5251269 CATAAATTA
1 CATAACTTA
*
5251278 AATAACTTA
1 CATAACTTA
*
5251287 CATAAATTA
1 CATAACTTA
*
5251296 AATAACTTA
1 CATAACTTA
5251305 CATAACTTA
1 CATAACTTA
*
5251314 CATAAATTA
1 CATAACTTA
*
5251323 CATAAATTA
1 CATAACTTA
*
5251332 AATAACTTA
1 CATAACTTA
5251341 CATAACTTA
1 CATAACTTA
*
5251350 CATAAATTA
1 CATAACTTA
5251359 -ATAAACTTA
1 CAT-AACTTA
5251368 CATAACTTA
1 CATAACTTA
* *
5251377 GATTA--TA
1 CATAACTTA
*
5251384 CACAACTTA
1 CATAACTTA
*
5251393 CATAAATTA
1 CATAACTTA
*
5251402 AATAACTTA
1 CATAACTTA
*
5251411 CATAGCTTA
1 CATAACTTA
5251420 CATAAC
1 CATAAC
5251426 GGGCAAAACA
Statistics
Matches: 341, Mismatches: 62, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
7 4 0.01
8 4 0.01
9 329 0.96
10 4 0.01
ACGTcount: A:0.51, C:0.15, G:0.01, T:0.33
Consensus pattern (9 bp):
CATAACTTA
Found at i:5251684 original size:21 final size:22
Alignment explanation
Indices: 5251645--5251695 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
5251635 TTCTCTTAAA
5251645 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
5251667 CTCTCAATTTCCTTCAAAAAAT-
1 CTCTCAAATTCCTTC-CAAAATC
5251689 CTCTCAA
1 CTCTCAA
5251696 CTCCATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:5251911 original size:14 final size:15
Alignment explanation
Indices: 5251882--5251915 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5251872 AAATTTTAAA
5251882 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
5251897 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
5251911 TTTTA
1 TTTTA
5251916 GATAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:5254095 original size:30 final size:30
Alignment explanation
Indices: 5254059--5254219 Score: 202
Period size: 30 Copynumber: 5.2 Consensus size: 30
5254049 ATATTATTTG
5254059 ATTTAATTAAAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAAACCCTAACCTA
*
5254089 ATTTAATTTAAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAAACCCTAACCTA
5254119 ATTTAATTTAATTAAAACCCCTAAACCCTAACCTA
1 ATTTAA-TT-A--AAAA-CCCTAAACCCTAACCTA
**
5254154 ATTTAATTAAAAACCCTAAACATTAACCTA
1 ATTTAATTAAAAACCCTAAACCCTAACCTA
5254184 ATTTAATTAACTAAA-CCT-AA-CCTAACCTA
1 ATTTAATTAA--AAACCCTAAACCCTAACCTA
*
5254213 ACTTAAT
1 ATTTAAT
5254220 AAACCTAACN
Statistics
Matches: 117, Mismatches: 7, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
29 13 0.11
30 62 0.53
31 9 0.08
32 3 0.03
33 1 0.01
34 6 0.05
35 23 0.20
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (30 bp):
ATTTAATTAAAAACCCTAAACCCTAACCTA
Found at i:5254119 original size:35 final size:35
Alignment explanation
Indices: 5254069--5254154 Score: 120
Period size: 35 Copynumber: 2.4 Consensus size: 35
5254059 ATTTAATTAA
5254069 AAACCCTAAACCCTAACCTAATTTAATTTAAAA-CCCT
1 AAACCCT-AA-CCTAACCTAATTTAA-TTAAAACCCCT
**
5254106 AAACCCTAACCTAATTTAATTTAATTAAAACCCCT
1 AAACCCTAACCTAACCTAATTTAATTAAAACCCCT
5254141 AAACCCTAACCTAA
1 AAACCCTAACCTAA
5254155 TTTAATTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 6 0.13
35 31 0.67
36 2 0.04
37 7 0.15
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (35 bp):
AAACCCTAACCTAACCTAATTTAATTAAAACCCCT
Found at i:5254132 original size:65 final size:65
Alignment explanation
Indices: 5254054--5254191 Score: 231
Period size: 65 Copynumber: 2.1 Consensus size: 65
5254044 TTTTGATATT
* * *
5254054 ATTTGATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTTAAAACCCTAAACCCTAACCTA
1 ATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACACTAACCTA
* *
5254119 ATTTAATTTAATTAAAACCCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACATTAACCTA
1 ATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACACTAACCTA
5254184 ATTTAATT
1 ATTTAATT
5254192 AACTAAACCT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.44, C:0.22, G:0.01, T:0.33
Consensus pattern (65 bp):
ATTTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACACTAACCTA
Found at i:5254222 original size:24 final size:24
Alignment explanation
Indices: 5254177--5254228 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5254167 CCCTAAACAT
**
5254177 TAACCTAATTTAATTAACTAAACC
1 TAACCTAACCTAATTAACTAAACC
5254201 TAACCTAACCTAACTTAA-TAAACC
1 TAACCTAACCTAA-TTAACTAAACC
5254225 TAAC
1 TAAC
5254229 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (24 bp):
TAACCTAACCTAATTAACTAAACC
Found at i:5254368 original size:30 final size:30
Alignment explanation
Indices: 5254333--5254502 Score: 197
Period size: 30 Copynumber: 5.6 Consensus size: 30
5254323 NNNNNNAAAC
*
5254333 CCCTAACATAATTTAATTAAAAACCCTAAA
1 CCCTAACCTAATTTAATTAAAAACCCTAAA
*
5254363 CCCTAACCTAATTTAATTTAATTAA----AAA
1 CCCTAACCTAATTTAA-TTAA-AAACCCTAAA
* *
5254391 CCCTAACCTAATTTAATTTAAAACCCTAAG
1 CCCTAACCTAATTTAATTAAAAACCCTAAA
5254421 CCCTAACCTAATTTAATTAAAAACCCT-AA
1 CCCTAACCTAATTTAATTAAAAACCCTAAA
*
5254450 CCCTATCCTAATTTAATTTAATTAAAAACCCTAAA
1 CCCTAACC-----TAATTTAATTAAAAACCCTAAA
5254485 CCCTAACCTAATTTAATT
1 CCCTAACCTAATTTAATT
5254503 TAATTAAAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 24
0.78 0.06 0.16
Matches are distributed among these distances:
26 2 0.02
27 3 0.03
28 19 0.16
29 8 0.07
30 53 0.45
31 4 0.03
32 2 0.02
34 19 0.16
35 9 0.08
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.32
Consensus pattern (30 bp):
CCCTAACCTAATTTAATTAAAAACCCTAAA
Found at i:5254380 original size:35 final size:35
Alignment explanation
Indices: 5254341--5254518 Score: 212
Period size: 35 Copynumber: 5.6 Consensus size: 35
5254331 ACCCCTAACA
5254341 TAATTTAATTAAAAACCCTAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAAACCCTAACCTAATT
5254376 TAATTTAATT---AA----AAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAAACCCTAACCTAATT
*
5254404 TAA--T--TT-AAAACCCTAAGCCCTAACC-----
1 TAATTTAATTAAAAACCCTAAACCCTAACCTAATT
*
5254429 TAATTTAATTAAAAACCCT-AACCCTATCCTAATT
1 TAATTTAATTAAAAACCCTAAACCCTAACCTAATT
5254463 TAATTTAATTAAAAACCCTAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAAACCCTAACCTAATT
5254498 TAATTTAATTAAAAACCCTAA
1 TAATTTAATTAAAAACCCTAA
5254519 CCTAATTTGA
Statistics
Matches: 122, Mismatches: 4, Indels: 34
0.76 0.03 0.21
Matches are distributed among these distances:
24 2 0.02
25 3 0.02
26 3 0.02
27 1 0.01
28 19 0.16
29 10 0.08
30 18 0.15
32 2 0.02
34 19 0.16
35 45 0.37
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.32
Consensus pattern (35 bp):
TAATTTAATTAAAAACCCTAAACCCTAACCTAATT
Found at i:5254402 original size:23 final size:23
Alignment explanation
Indices: 5254376--5254451 Score: 89
Period size: 23 Copynumber: 3.0 Consensus size: 23
5254366 TAACCTAATT
5254376 TAATTTAATTAAAAACCCTAACC
1 TAATTTAATTAAAAACCCTAACC
5254399 TAATTTAATTTAAAACCCTAAGCCCTAACC
1 TAATTTAA-TT-AAA----AA-CCCTAACC
5254429 TAATTTAATTAAAAACCCTAACC
1 TAATTTAATTAAAAACCCTAACC
5254452 CTATCCTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
23 16 0.35
24 4 0.09
25 3 0.07
28 3 0.07
29 4 0.09
30 16 0.35
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.30
Consensus pattern (23 bp):
TAATTTAATTAAAAACCCTAACC
Found at i:5258134 original size:124 final size:125
Alignment explanation
Indices: 5257765--5258169 Score: 633
Period size: 125 Copynumber: 3.2 Consensus size: 125
5257755 CACGAGGGCA
* *
5257765 CGATTTGACACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCG
1 CGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCG
*
5257830 AAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAA
66 AAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAG
5257890 CGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCG
1 CGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCG
*
5257955 AAATCGCGTCCACG-GGGTCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAG
66 AAATCGCGTCCACGAGGG-CACGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAG
* * *
5258015 CGATTTTATACTATTTGTTCAGAAAACGTCAAAAAA-AA-TATTTCTTACATGACCAACTAT-GC
1 CGATTTTATACTATTTGCTCAG-AAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAG-
* **
5258077 CGAAATGGCGTCCACGAGGGCACGATTTCACAATTTCTTCTC-TGATAGCATCCTGGTAGAAG
64 CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAT-ATAGCATCCTGGTATCAG
5258139 CGATTTTATACTATTTGAC-CAGAAACGTCAA
1 CGATTTTATACTATTTG-CTCAGAAACGTCAA
5258170 CTCGAAATAA
Statistics
Matches: 262, Mismatches: 12, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
123 11 0.04
124 95 0.36
125 143 0.55
126 13 0.05
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (125 bp):
CGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAG
Found at i:5258422 original size:28 final size:27
Alignment explanation
Indices: 5258363--5258421 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
5258353 GATTTTGGGG
*
5258363 AAAATGGGCCATTCCGGTAAATAATTAA
1 AAAATGGCCCATTCCGGTAAAT-ATTAA
*
5258391 AAAATCGGCCCATTTCGGTAAAT-TTAA
1 AAAAT-GGCCCATTCCGGTAAATATTAA
5258418 AAAA
1 AAAA
5258422 AGGGCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.29
28 5 0.18
29 15 0.54
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (27 bp):
AAAATGGCCCATTCCGGTAAATATTAA
Found at i:5258457 original size:9 final size:9
Alignment explanation
Indices: 5258445--5258512 Score: 70
Period size: 9 Copynumber: 7.8 Consensus size: 9
5258435 GTGTTTTGCC
5258445 CTTACATAA
1 CTTACATAA
5258454 CTTACATAA
1 CTTACATAA
* *
5258463 ATTAAATAA
1 CTTACATAA
5258472 CTTACATAA
1 CTTACATAA
*
5258481 CTTACATTA
1 CTTACATAA
5258490 --TACATAA
1 CTTACATAA
*
5258497 CCTT-CTTAA
1 -CTTACATAA
5258506 CTTACAT
1 CTTACAT
5258513 TATACACAAC
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
7 6 0.13
8 3 0.06
9 37 0.79
10 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.37
Consensus pattern (9 bp):
CTTACATAA
Found at i:5258539 original size:25 final size:25
Alignment explanation
Indices: 5258511--5258572 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
5258501 CTTAACTTAC
*
5258511 ATTATACACAACTCACATAATTAAT
1 ATTATACACAACTCACAGAATTAAT
5258536 ATTATACACAACTCACAGAATTAAT
1 ATTATACACAACTCACAGAATTAAT
*
5258561 ATTATACCCAAC
1 ATTATACACAAC
5258573 CCAATATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.29
Consensus pattern (25 bp):
ATTATACACAACTCACAGAATTAAT
Found at i:5258748 original size:21 final size:21
Alignment explanation
Indices: 5258722--5258761 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5258712 CTACAACTTA
5258722 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGGG
*
5258743 AAGCAGAGGCTGCAGCGAG
1 AAGCAGAGGCGGCAGCGAG
5258762 AATGCAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.47, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGGG
Found at i:5259311 original size:42 final size:41
Alignment explanation
Indices: 5259173--5259315 Score: 214
Period size: 41 Copynumber: 3.5 Consensus size: 41
5259163 AATCCCAAAA
* *
5259173 TTAGTGGCGTTTTTCGTTAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTT-TTTAAGCGCCGCTAAAGAACATGATCT
* *
5259215 TTGGCGGTGTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
* * *
5259256 TTAGCCGCGTTTTTTTTAAGTGCCACTAAAGAACATGATCT
1 TTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
5259297 TTAGCGGCGTTTTTTTTAA
1 TTAGCGGCGTTTTTTTTAA
5259316 AAGCGCTGCA
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 80 0.88
42 11 0.12
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
TTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
Found at i:5266963 original size:20 final size:20
Alignment explanation
Indices: 5266924--5266969 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
5266914 TTTAATAGTA
5266924 ATTTAATATTAAAATCATAT
1 ATTTAATATTAAAATCATAT
* * *
5266944 ATTTGATATTAAATTTATAT
1 ATTTAATATTAAAATCATAT
5266964 -TTTAAT
1 ATTTAAT
5266970 TGAATTATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTAATATTAAAATCATAT
Found at i:5268247 original size:26 final size:26
Alignment explanation
Indices: 5268218--5268269 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
5268208 AATAAAAGAG
*
5268218 TTCAATATCTTGAGTCTATTGACAAT
1 TTCAATATCTTGAGTCCATTGACAAT
5268244 TTCAATATCTTGAGTCCATTGACAAT
1 TTCAATATCTTGAGTCCATTGACAAT
5268270 AGGGTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (26 bp):
TTCAATATCTTGAGTCCATTGACAAT
Found at i:5268508 original size:49 final size:50
Alignment explanation
Indices: 5268407--5268510 Score: 174
Period size: 51 Copynumber: 2.1 Consensus size: 50
5268397 ATGGTATTGA
*
5268407 TTGTGGTTTAAGGTTTACTTAGAAAAGACACATGTATATTATGTAATTCGC
1 TTGTGATTTAAGGTTTACTTAGAAAAGA-ACATGTATATTATGTAATTCGC
*
5268458 TTGTGATTTAAGGTTTACTTAGAAAAG-ACATGTATATTATGTAGTTCGC
1 TTGTGATTTAAGGTTTACTTAGAAAAGAACATGTATATTATGTAATTCGC
5268507 TTGT
1 TTGT
5268511 TACGAACACA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
49 25 0.49
51 26 0.51
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (50 bp):
TTGTGATTTAAGGTTTACTTAGAAAAGAACATGTATATTATGTAATTCGC
Found at i:5280091 original size:22 final size:22
Alignment explanation
Indices: 5280061--5280103 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5280051 TAATCAGAAT
*
5280061 ATTAAAAAAAATAAAAAGATGG
1 ATTAAAAAAAAGAAAAAGATGG
* *
5280083 ATTAGAAAAAAGAAGAAGATG
1 ATTAAAAAAAAGAAAAAGATG
5280104 TTAATAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (22 bp):
ATTAAAAAAAAGAAAAAGATGG
Found at i:5284450 original size:46 final size:46
Alignment explanation
Indices: 5284383--5284537 Score: 246
Period size: 46 Copynumber: 3.5 Consensus size: 46
5284373 TGATCAGTGA
5284383 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
**
5284429 CAAGTGACAAAGTGATAAGTGGTAATTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
5284475 CAAGTGACAAAGTG-TAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
5284519 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
5284538 ATCATACTTA
Statistics
Matches: 102, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
42 5 0.05
43 11 0.11
44 19 0.19
45 9 0.09
46 58 0.57
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:5285515 original size:24 final size:24
Alignment explanation
Indices: 5285488--5285539 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5285478 GGAGACAAAA
5285488 ATGAAG-CCAAGAGTAGAGATGAAG
1 ATGAAGACCAAG-GTAGAGATGAAG
* * *
5285512 ATGATGACGACGGTAGAGATGAAG
1 ATGAAGACCAAGGTAGAGATGAAG
5285536 ATGA
1 ATGA
5285540 GTACAAGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.42, C:0.08, G:0.35, T:0.15
Consensus pattern (24 bp):
ATGAAGACCAAGGTAGAGATGAAG
Found at i:5286411 original size:18 final size:18
Alignment explanation
Indices: 5286370--5286411 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
5286360 ACATTGTAAC
*
5286370 GCGTTTCAATCTGTACAT
1 GCGTTTCAATCTGTACAG
*
5286388 GAGTTTCAATCTGTACAG
1 GCGTTTCAATCTGTACAG
5286406 GCGTTT
1 GCGTTT
5286412 ACTTAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (18 bp):
GCGTTTCAATCTGTACAG
Found at i:5291456 original size:37 final size:37
Alignment explanation
Indices: 5291387--5291542 Score: 130
Period size: 37 Copynumber: 4.3 Consensus size: 37
5291377 CGAATATAAT
* ** *
5291387 AAATATTTTTATT-ATTTTTTATTTTTTTAA-TTTTA
1 AAATACTTTTATTAATTTTTTAAATTTTAAATTTTTA
5291422 AAATACTTTTATTAAATTTTTTAAATTTTAAATTTTTTTA
1 AAATACTTTTATT-AATTTTTTAAATTTTAAA--TTTTTA
*
5291462 AAATAC-TTT-TTAATTTTTTTAATTTTAAAATATTTTTA
1 AAATACTTTTATTAATTTTTTAAATTTT--AA-ATTTTTA
* *
5291500 AAATACTTTTTTTAA--TATT-AATTTT-AATTTTTA
1 AAATACTTTTATTAATTTTTTAAATTTTAAATTTTTA
*
5291533 AAATAATTTT
1 AAATACTTTT
5291543 TTGGTATTTA
Statistics
Matches: 104, Mismatches: 7, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
33 16 0.15
34 1 0.01
35 12 0.12
37 34 0.33
38 17 0.16
39 8 0.08
40 16 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (37 bp):
AAATACTTTTATTAATTTTTTAAATTTTAAATTTTTA
Found at i:5291476 original size:21 final size:21
Alignment explanation
Indices: 5291417--5291483 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
5291407 ATTTTTTTAA
*
5291417 TTTTAAAATACTTTTATTAAATT
1 TTTTAAAATAC-TTT-TTAATTT
*
5291440 TTTT--AA-A-TTTTAAATTT
1 TTTTAAAATACTTTTTAATTT
5291457 TTTTAAAATACTTTTTAATTT
1 TTTTAAAATACTTTTTAATTT
5291478 TTTTAA
1 TTTTAA
5291484 TTTTAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
17 9 0.24
18 3 0.08
19 2 0.05
20 2 0.05
21 17 0.46
23 4 0.11
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTAAAATACTTTTTAATTT
Found at i:5291480 original size:38 final size:38
Alignment explanation
Indices: 5291417--5291543 Score: 139
Period size: 38 Copynumber: 3.1 Consensus size: 38
5291407 ATTTTTTTAA
*
5291417 TTTTAAAATACTTTTATTAAATTTTTTAAATTTT-AAATTT
1 TTTTAAAATAC-TTT-TTAAATTTTTT-AATTTTAAAATAT
*
5291457 TTTTAAAATACTTTTTAATTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTAAATTTTTTAATTTTAAAATAT
5291495 TTTTAAAATACTTTTTTTAATATTAATTTTAATTTTTAAAATAAT
1 TTTTAAAATAC--TTTTTAA-ATT--TTTTAA-TTTTAAAAT-AT
5291540 TTTT
1 TTTT
5291544 TGGTATTTAT
Statistics
Matches: 76, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
37 6 0.08
38 26 0.34
39 3 0.04
40 18 0.24
41 2 0.03
43 6 0.08
44 9 0.12
45 6 0.08
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (38 bp):
TTTTAAAATACTTTTTAAATTTTTTAATTTTAAAATAT
Found at i:5293234 original size:14 final size:14
Alignment explanation
Indices: 5293204--5293237 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5293194 AAAGTAAGTC
*
5293204 ATTTTCCAAAAATT
1 ATTTTCCAAAAACT
*
5293218 ATTTTCCAAAAGCT
1 ATTTTCCAAAAACT
5293232 ATTTTC
1 ATTTTC
5293238 AGTGAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (14 bp):
ATTTTCCAAAAACT
Found at i:5301456 original size:19 final size:19
Alignment explanation
Indices: 5301432--5301470 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5301422 AATAAAAAAA
*
5301432 TATTTT-TAATAATATAATT
1 TATTTTGTAA-AAAATAATT
5301451 TATTTTGTAAAAAATAATT
1 TATTTTGTAAAAAATAATT
5301470 T
1 T
5301471 TTATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TATTTTGTAAAAAATAATT
Found at i:5307873 original size:17 final size:18
Alignment explanation
Indices: 5307853--5307886 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5307843 CGAAAATGGT
5307853 ATAAAA-TTAAAAAAAAC
1 ATAAAAGTTAAAAAAAAC
5307870 ATAAAAGTTAAAAAAAA
1 ATAAAAGTTAAAAAAAA
5307887 GTTGGGGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (18 bp):
ATAAAAGTTAAAAAAAAC
Found at i:5308004 original size:10 final size:10
Alignment explanation
Indices: 5307991--5308105 Score: 87
Period size: 10 Copynumber: 11.5 Consensus size: 10
5307981 AGAAGGAGAA
5307991 GAAAGAAAAG
1 GAAAGAAAAG
*
5308001 GAAAGGAAAG
1 GAAAGAAAAG
5308011 GAGAAG-AAAG
1 GA-AAGAAAAG
*
5308021 GAAAGGAAAG
1 GAAAGAAAAG
5308031 GAGAAG-AAA-
1 GA-AAGAAAAG
*
5308040 GAAAAAGAAAG
1 GAAAGA-AAAG
*
5308051 GAAAGGAGAA-
1 GAAA-GAAAAG
*
5308061 GAAAGGAAAG
1 GAAAGAAAAG
*
5308071 GAAAGGAGAA-
1 GAAA-GAAAAG
*
5308081 GAAAGAAAAA
1 GAAAGAAAAG
5308091 GAAAGAAAAG
1 GAAAGAAAAG
5308101 GAAAG
1 GAAAG
5308106 GAGAAGAGGG
Statistics
Matches: 85, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
8 2 0.02
9 12 0.14
10 55 0.65
11 15 0.18
12 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:5308017 original size:25 final size:25
Alignment explanation
Indices: 5307983--5308112 Score: 157
Period size: 25 Copynumber: 5.4 Consensus size: 25
5307973 GAGAAGAAAG
5307983 AAGGAGAAGAAAGAAAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAGGAAAGGA
5308008 AA-G-G-AG-AAG-AAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAGGAAAGGA
*
5308028 AAGGAGAAGAAAGAAAAAGAAAGGA
1 AAGGAGAAGAAAGAAAAGGAAAGGA
*
5308053 AAGGAGAAGAAAGGAAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAGGAAAGGA
* *
5308078 GAA-GA-AAGAAAAAGAAAGAAAAGGA
1 -AAGGAGAAGAAAGA-AAAGGAAAGGA
5308103 AAGGAGAAGA
1 AAGGAGAAGA
5308113 GGGAGGGAAG
Statistics
Matches: 90, Mismatches: 6, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
20 13 0.14
21 4 0.04
22 3 0.03
23 3 0.03
24 12 0.13
25 49 0.54
26 6 0.07
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (25 bp):
AAGGAGAAGAAAGAAAAGGAAAGGA
Found at i:5308037 original size:45 final size:45
Alignment explanation
Indices: 5307983--5308102 Score: 222
Period size: 45 Copynumber: 2.7 Consensus size: 45
5307973 GAGAAGAAAG
*
5307983 AAGGAGAAGAAAGAAAAGGAAAGGAAAGGAGAAGAAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAAGAAAGGAAAGGAGAAGAAAGGAAAGGA
5308028 AAGGAGAAGAAAGAAAAAGAAAGGAAAGGAGAAGAAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAAGAAAGGAAAGGAGAAGAAAGGAAAGGA
*
5308073 AAGGAGAAGAAAGAAAAAGAAAGAAAAGGA
1 AAGGAGAAGAAAGAAAAAGAAAGGAAAGGA
5308103 AAGGAGAAGA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 73 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (45 bp):
AAGGAGAAGAAAGAAAAAGAAAGGAAAGGAGAAGAAAGGAAAGGA
Found at i:5308112 original size:20 final size:20
Alignment explanation
Indices: 5307970--5308095 Score: 143
Period size: 20 Copynumber: 6.2 Consensus size: 20
5307960 CATTCGGCTG
5307970 AAGGAGAAGAAA-G-AAGGA
1 AAGGAGAAGAAAGGAAAGGA
5307988 GAA-GA-AAGAAAAGGAAAGGA
1 -AAGGAGAAG-AAAGGAAAGGA
5308008 AAGGAGAAGAAAGGAAAGGA
1 AAGGAGAAGAAAGGAAAGGA
5308028 AAGGAGAAGAAAGAAAAAGAAAGGA
1 AAGGAGAAGAAAG-----GAAAGGA
5308053 AAGGAGAAGAAAGGAAAGGA
1 AAGGAGAAGAAAGGAAAGGA
* *
5308073 AAGGAGAAGAAAGAAAAAGA
1 AAGGAGAAGAAAGGAAAGGA
5308093 AAG
1 AAG
5308096 AAAAGGAAAG
Statistics
Matches: 95, Mismatches: 2, Indels: 19
0.82 0.02 0.16
Matches are distributed among these distances:
17 3 0.03
18 5 0.05
19 5 0.05
20 59 0.62
21 3 0.03
25 20 0.21
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (20 bp):
AAGGAGAAGAAAGGAAAGGA
Found at i:5308246 original size:26 final size:27
Alignment explanation
Indices: 5308217--5308271 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
5308207 ATGTACATTG
*
5308217 TATATGTTTTATT-ATTTTATTTAGCA
1 TATATGTTTTATTAAATTTATTTAGCA
*
5308243 TATATTTTTTATTAAAATTTATTTAGCA
1 TATATGTTTTATT-AAATTTATTTAGCA
5308271 T
1 T
5308272 GAAAAAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.48
28 13 0.52
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (27 bp):
TATATGTTTTATTAAATTTATTTAGCA
Found at i:5308381 original size:17 final size:17
Alignment explanation
Indices: 5308359--5308393 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5308349 TTTTTTTACA
*
5308359 AAAATAACATTAAAAAT
1 AAAATAACAATAAAAAT
*
5308376 AAAATAATAATAAAAAT
1 AAAATAACAATAAAAAT
5308393 A
1 A
5308394 TGTTTAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATAACAATAAAAAT
Found at i:5308689 original size:129 final size:131
Alignment explanation
Indices: 5308534--5308799 Score: 428
Period size: 129 Copynumber: 2.0 Consensus size: 131
5308524 AAAAACACTC
*
5308534 TAAATTAATACATTTCAAACATAATGTACTAAAAGAATGTAAAATAATAAAATACGAAAATAATA
1 TAAATTAATACATTTCAAAAATAATGTACTAAAAGAATGTAAAATAATAAAATACGAAAATAATA
* * *
5308599 TA-TTTTTGAAAGTAATAAAATC-CGAAAAAAATATGAACAAATGGCCAAAATAAGAGTTTTTTA
66 TATTTTTTGAAAGTAATAAAATCTCGAAAAAAATACGAACAAAGGGCCAAAATAAGAGTCTTTTA
5308662 A
131 A
* *
5308663 TAAATTAATACATTTCAAAAATAATGTACTAAAATAATGTATAATAATAAAATACGAAAATAATA
1 TAAATTAATACATTTCAAAAATAATGTACTAAAAGAATGTAAAATAATAAAATACGAAAATAATA
* * *
5308728 TATTTTTTGAAAGTAATAAAATCTGGGAAAAAATACGAACAAAGGGCCAAAATAAGGGTCTTTTA
66 TATTTTTTGAAAGTAATAAAATCTCGAAAAAAATACGAACAAAGGGCCAAAATAAGAGTCTTTTA
*
5308793 C
131 A
5308794 TAAATT
1 TAAATT
5308800 TATTTAAAGA
Statistics
Matches: 125, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
129 64 0.51
130 20 0.16
131 41 0.33
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (131 bp):
TAAATTAATACATTTCAAAAATAATGTACTAAAAGAATGTAAAATAATAAAATACGAAAATAATA
TATTTTTTGAAAGTAATAAAATCTCGAAAAAAATACGAACAAAGGGCCAAAATAAGAGTCTTTTA
A
Found at i:5308696 original size:13 final size:13
Alignment explanation
Indices: 5308680--5308726 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
5308670 ATACATTTCA
5308680 AAAATAATGTACT
1 AAAATAATGTACT
5308693 AAAATAATGTA-T
1 AAAATAATGTACT
** *
5308705 AATAATAAAATACG
1 AA-AATAATGTACT
5308719 AAAATAAT
1 AAAATAAT
5308727 ATATTTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 3 0.11
13 23 0.82
14 2 0.07
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (13 bp):
AAAATAATGTACT
Found at i:5309180 original size:152 final size:152
Alignment explanation
Indices: 5308663--5309403 Score: 1068
Period size: 153 Copynumber: 4.9 Consensus size: 152
5308653 AGTTTTTTAA
* * *
5308663 TAAATTAATACATTTCAAAAATAATGTACTAAAATAATGTATAATAATAAAATACGAAAATAATA
1 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACAAAAATAATA
*
5308728 TA-TTTT-TTGAAAGTAATAAAA-TCTGGG-AAAAAATACGAACAAAGGGCCAAAATAAGGGTCT
66 TATTTTTATTGAAAGTAATAAAATTC-GGGAAAAAAATACGAACAAAGGGCCGAAATAA-GGT-T
* *
5308789 TTTACTAAATTTATTTAAAGAACACAG
128 TTT--TTAATTTATTTAAAAAACACAG
* * *
5308816 TAAATTAATAGATTTCAAACACAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATA
1 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACAAAAATAATA
5308881 TATTTTTATTGAAAGTAATAAAATTCGGG-AAAAAATACGAACAAAGGGCCGAAATAAGGATTTT
66 TATTTTTATTGAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGG--TTT
5308945 TTTTAATTTATTTAAAAAACACAG
129 TTTTAATTTATTTAAAAAACACAG
* * *
5308969 TAAATTAATACATTTTAAACATAACGTACTAAAATAATGTAAAATAATAAAAAACAAAAATAATA
1 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACAAAAATAATA
* * *
5309034 TATTTTTATTGAAAGTAATAAAATTTGGGAAAAAAATACGAACAAATGGTCGAAATAAGGTTTTT
66 TATTTTTATTGAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTT
5309099 TTAATTTATTTAAAAAACACAG
131 TTAATTTATTTAAAAAACACAG
* * *
5309121 TAAATTAATACATTTCAAATATAATGTACTAAAGTAATGTAAAATAATAAAATATAAAAATAATA
1 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACAAAAATAATA
* *
5309186 TATTTTTATTGAAAGTAATAAAATCCGGAAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTT
66 TATTTTTATTGAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGG-TTTT
*
5309251 TTTAATTTATTTAAAAAACACAC
130 TTTAATTTATTTAAAAAACACAG
*
5309274 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTA-AAAAATAGT
1 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA-TACAAAAATAAT
* ** * * * * *
5309338 ATA-TTTT-TTAAAAGTAAT-AAATTCCAGAAAAAAATACGAATAAATGGTCAAAATAAGGGTTT
65 ATATTTTTATTGAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTT
5309400 TTTA
130 TTTA
5309404 CTAAATTTGT
Statistics
Matches: 539, Mismatches: 41, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
149 7 0.01
150 32 0.06
151 10 0.02
152 145 0.27
153 257 0.48
154 36 0.07
155 49 0.09
156 3 0.01
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (152 bp):
TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACAAAAATAATA
TATTTTTATTGAAAGTAATAAAATTCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTT
TTAATTTATTTAAAAAACACAG
Found at i:5309252 original size:305 final size:303
Alignment explanation
Indices: 5308663--5309403 Score: 1130
Period size: 305 Copynumber: 2.4 Consensus size: 303
5308653 AGTTTTTTAA
* * *
5308663 TAAATTAATACATTTCAAAAATAATGTACTAAAATAATGTATAATAATAAAATACGAAAATAATA
1 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACAAAAATAATA
* * *
5308728 TATTTTTTGAAAGTAATAAAATCTGGG-AAAAAATACGAACAAAGGGCCAAAATAAGGGTCTTTT
66 TATTTTTTGAAAGTAATAAAATTTGGGAAAAAAATACGAACAAATGGTCAAAATAA-GGT-TTTT
* * *
5308792 ACTAAATTTATTTAAAGAACACAGTAAATTAATAGATTTCAAACACAATGTACTAAAATAATGTA
129 --TTAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACACAATGTACTAAAATAATGTA
* * *
5308857 AAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGAAAAAATACGAA
192 AAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGAAAAAAATACGAA
*
5308922 CAAAGGGCCGAAATAAGGATTTTTTTTAATTTATTTAAAAAACACAG
257 CAAAGGGCCGAAATAAGGATTTTTTTTAATTTATTTAAAAAACACAC
* * *
5308969 TAAATTAATACATTTTAAACATAACGTACTAAAATAATGTAAAATAATAAAAAACAAAAATAATA
1 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACAAAAATAATA
*
5309034 TATTTTTATTGAAAGTAATAAAATTTGGGAAAAAAATACGAACAAATGGTCGAAATAAGGTTTTT
66 TA-TTTT-TTGAAAGTAATAAAATTTGGGAAAAAAATACGAACAAATGGTCAAAATAAGGTTTTT
* * *
5309099 TTAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAATATAATGTACTAAAGTAATGTAAA
129 TTAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACACAATGTACTAAAATAATGTAAA
*
5309164 ATAATAAAATATAAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGAAAAAAAATACGAAC
194 ATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATCCGG-AAAAAAATACGAAC
5309229 AAAGGGCCGAAATAAGG-TTTTTTTTAATTTATTTAAAAAACACAC
258 AAAGGGCCGAAATAAGGATTTTTTTTAATTTATTTAAAAAACACAC
*
5309274 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTA-AAAAATAGT
1 TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA-TACAAAAATAAT
* *** * *
5309338 ATATTTTTTAAAAGTAAT-AAATTCCAGAAAAAAATACGAATAAATGGTCAAAATAAGGGTTTTT
65 ATATTTTTTGAAAGTAATAAAATTTGGGAAAAAAATACGAACAAATGGTCAAAATAAGGTTTTTT
5309402 TA
130 TA
5309404 CTAAATTTGT
Statistics
Matches: 398, Mismatches: 32, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
302 42 0.11
303 10 0.03
304 4 0.01
305 194 0.49
306 92 0.23
307 8 0.02
308 23 0.06
309 25 0.06
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (303 bp):
TAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACAAAAATAATA
TATTTTTTGAAAGTAATAAAATTTGGGAAAAAAATACGAACAAATGGTCAAAATAAGGTTTTTTT
AATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACACAATGTACTAAAATAATGTAAAAT
AATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGAAAAAAATACGAACAAA
GGGCCGAAATAAGGATTTTTTTTAATTTATTTAAAAAACACAC
Found at i:5309549 original size:41 final size:40
Alignment explanation
Indices: 5309451--5309565 Score: 110
Period size: 42 Copynumber: 2.8 Consensus size: 40
5309441 TAATATAAAA
*
5309451 ACTAACAATCATACTAACTAAAATAATAATTAGGGTTTTT
1 ACTAACAATAATACTAACTAAAATAATAATTAGGGTTTTT
* *
5309491 ACTAATC-CTAATAACTAACCATAATAATAAT-ATTA-GTTTTTT
1 ACTAA-CAATAAT-ACTAA-C-TAA-AATAATAATTAGGGTTTTT
* *
5309533 ACTAACAATAATACTAAGTAACAATAATTATTA
1 ACTAACAATAATACTAACTAA-AATAATAATTA
5309566 ATAACTAAAC
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
39 9 0.15
40 12 0.19
41 12 0.19
42 16 0.26
43 7 0.11
44 6 0.10
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (40 bp):
ACTAACAATAATACTAACTAAAATAATAATTAGGGTTTTT
Found at i:5309710 original size:31 final size:29
Alignment explanation
Indices: 5309640--5309713 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
5309630 GGCTCAAATT
* *
5309640 ACATTTTAGTCACTTATGTTTGAGATGTT
1 ACATTTTAGTCACTTATGTTTCAGATGTA
* *
5309669 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-GATGTA
5309700 ACATTTTAGTCACT
1 ACATTTTAGTCACT
5309714 GAGCCATTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 19 0.50
30 2 0.05
31 17 0.45
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAGATGTA
Found at i:5310589 original size:3 final size:3
Alignment explanation
Indices: 5310583--5310616 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
5310573 CCGGCACCAC
* *
5310583 CTT CTT CTT CTT CTT CTT TTT CTT TTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
5310617 AGCTAGACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
CTT
Found at i:5311200 original size:16 final size:16
Alignment explanation
Indices: 5311179--5311211 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5311169 TTCACATTGC
5311179 AAACG-AAAGTGATAGG
1 AAACGAAAAGTGA-AGG
5311195 AAACGAAAAGTGAAGG
1 AAACGAAAAGTGAAGG
5311211 A
1 A
5311212 GAAAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.55, C:0.06, G:0.30, T:0.09
Consensus pattern (16 bp):
AAACGAAAAGTGAAGG
Found at i:5311304 original size:21 final size:20
Alignment explanation
Indices: 5311254--5311306 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
5311244 CAAATGAATA
5311254 AAAGAGAGAAAAACGAAAGAG
1 AAAGAGA-AAAAACGAAAGAG
*
5311275 ATAGCAGAAAAAACGAAAGAG
1 AAAG-AGAAAAAACGAAAGAG
5311296 AGAAGAGAAAA
1 A-AAGAGAAAA
5311307 GAGGTTGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.66, C:0.06, G:0.26, T:0.02
Consensus pattern (20 bp):
AAAGAGAAAAAACGAAAGAG
Found at i:5312901 original size:16 final size:16
Alignment explanation
Indices: 5312880--5312951 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
5312870 TTTTGTATTA
5312880 TTTTAATATTAAATAT
1 TTTTAATATTAAATAT
* *
5312896 TTTTAAAATTAAATAA
1 TTTTAATATTAAATAT
* *
5312912 CTTTAATA-TAATTGAT
1 TTTTAATATTAAAT-AT
*
5312928 TTTAAATTAGTTAAATAT
1 TTTTAA-TA-TTAAATAT
5312946 TTTTAA
1 TTTTAA
5312952 AAATATTTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
15 4 0.10
16 25 0.60
17 2 0.05
18 7 0.17
19 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (16 bp):
TTTTAATATTAAATAT
Found at i:5319739 original size:45 final size:46
Alignment explanation
Indices: 5319690--5319800 Score: 136
Period size: 45 Copynumber: 2.5 Consensus size: 46
5319680 TGCCATAGTG
*
5319690 TCTTTCAATTATGGTCTTACTTAATT-ATGTCATGATGTCAAAGCA
1 TCTTTCAACTATGGTCTTACTTAATTCATGTCATGATGTCAAAGCA
* * * * * *
5319735 TCTTTCAACTATGGTCGTA-TTTATTCTTGTTATGGTGTCATAGCA
1 TCTTTCAACTATGGTCTTACTTAATTCATGTCATGATGTCAAAGCA
*
5319780 TCTTTCAGCTATGGTCTTACT
1 TCTTTCAACTATGGTCTTACT
5319801 CATTTTAGGC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
44 5 0.09
45 49 0.89
46 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (46 bp):
TCTTTCAACTATGGTCTTACTTAATTCATGTCATGATGTCAAAGCA
Found at i:5321190 original size:13 final size:13
Alignment explanation
Indices: 5321174--5321227 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
5321164 TTTAAACCAA
*
5321174 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
*
5321187 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
5321200 ACTTTTTACATAGC
1 ACTTTTCA-AAAGC
5321214 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
5321227 A
1 A
5321228 TTGCCAAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
13 22 0.67
14 11 0.33
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:5324605 original size:29 final size:30
Alignment explanation
Indices: 5324545--5324606 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
5324535 ACGTACACAT
* *
5324545 TTGTACCAAAATCAAAGTTTATGTTTATAA
1 TTGTACCAAAATCAAAGTTAATGTTCATAA
5324575 TTGTA-CAAAATCAAAGTTAATGTATCA-AA
1 TTGTACCAAAATCAAAGTTAATGT-TCATAA
5324604 TTG
1 TTG
5324607 CACATTGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (30 bp):
TTGTACCAAAATCAAAGTTAATGTTCATAA
Found at i:5328169 original size:40 final size:40
Alignment explanation
Indices: 5328125--5328213 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 40
5328115 CGTTAACACA
5328125 TGAACTATTAATTTTTGCTA-ATCTGTTACATATAAATGGT
1 TGAACTATTAATTTTTGCTATATCT-TTACATATAAATGGT
* *
5328165 TGAAC-AGTTAATTTTTGCTATTTCTTTACATATAAATTGT
1 TGAACTA-TTAATTTTTGCTATATCTTTACATATAAATGGT
*
5328205 TGAATTATT
1 TGAACTATT
5328214 GATTAGCGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
39 1 0.02
40 38 0.88
41 4 0.09
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.48
Consensus pattern (40 bp):
TGAACTATTAATTTTTGCTATATCTTTACATATAAATGGT
Found at i:5346120 original size:109 final size:111
Alignment explanation
Indices: 5346000--5346219 Score: 309
Period size: 111 Copynumber: 2.0 Consensus size: 111
5345990 GTAAATTATT
* * * * * *
5346000 TTTTTTTGTGGTGGCTTGCCAATGACCTGCATCACCTTTTTTGTGAGAA-TTTTTTT-TACTTTT
1 TTTTTTGGTGGTGGCCTGCCAATGACCGGCACCACATTTTTTGTGAGAATTTTTTTTATACATTT
*
5346063 TTCGTGTCAAAAAAAGGTATCAGTACACGAAAAAAGTTAAAAAAAA
66 TTCGTGTCAAAAAAAGGTATCAGTACACGAAAAAAGTAAAAAAAAA
* *
5346109 TTTTTTGGTGGTGGCCTGCCAATGGCCGGCACCACATTTTTTGTGGGAATTTTTTTTATACATTT
1 TTTTTTGGTGGTGGCCTGCCAATGACCGGCACCACATTTTTTGTGAGAATTTTTTTTATACATTT
* * * *
5346174 TTCGTGTCAAAAGAAGGTATTAGTATACGGAAAAAGTAAAAAAAAA
66 TTCGTGTCAAAAAAAGGTATCAGTACACGAAAAAAGTAAAAAAAAA
5346220 AAATTGTGGT
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
109 42 0.44
110 7 0.07
111 47 0.49
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (111 bp):
TTTTTTGGTGGTGGCCTGCCAATGACCGGCACCACATTTTTTGTGAGAATTTTTTTTATACATTT
TTCGTGTCAAAAAAAGGTATCAGTACACGAAAAAAGTAAAAAAAAA
Found at i:5346240 original size:22 final size:22
Alignment explanation
Indices: 5346213--5346256 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5346203 GAAAAAGTAA
5346213 AAAAAAAAAATTGTGGTGGCCT
1 AAAAAAAAAATTGTGGTGGCCT
5346235 AAAAAAAAAATTGTGGTGGCCT
1 AAAAAAAAAATTGTGGTGGCCT
5346257 GCCAATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (22 bp):
AAAAAAAAAATTGTGGTGGCCT
Found at i:5346340 original size:129 final size:129
Alignment explanation
Indices: 5346116--5346362 Score: 433
Period size: 129 Copynumber: 1.9 Consensus size: 129
5346106 AAATTTTTTG
5346116 GTGGTGGCCTGCCAATGGCCGGCACCACATTTTTTGTGGGAATTTTTTTTATACATTTTTCGTGT
1 GTGGTGGCCTGCCAATGGCCGGCACCACATTTTTTGT-GGAATTTTTTTTATACATTTTTCGTGT
*
5346181 CAAAAGAAGGTATTAGTATACGGAAAAAGTAAAAAAAAAAAATTGTGGTGGCCTAAAAAAAAAAT
65 CAAAAGAAGGTATTAGTATACGAAAAAAGT-AAAAAAAAAAATTGTGGTGGCCTAAAAAAAAAAT
5346246 T
129 T
* *
5346247 GTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGT-GAATTTTTTTTTTACATTTTTCGTGTC
1 GTGGTGGCCTGCCAATGGCCGGCACCACATTTTTTGTGGAATTTTTTTTATACATTTTTCGTGTC
*
5346311 AAAAGAAGGTATTAGTATACGAAAAAAGTAAAAAAAAAATTTGTGGTGGCCT
66 AAAAGAAGGTATTAGTATACGAAAAAAGTAAAAAAAAAAATTGTGGTGGCCT
5346363 GCCAATGGTC
Statistics
Matches: 112, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
128 22 0.20
129 54 0.48
131 36 0.32
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.32
Consensus pattern (129 bp):
GTGGTGGCCTGCCAATGGCCGGCACCACATTTTTTGTGGAATTTTTTTTATACATTTTTCGTGTC
AAAAGAAGGTATTAGTATACGAAAAAAGTAAAAAAAAAAATTGTGGTGGCCTAAAAAAAAAATT
Found at i:5346493 original size:106 final size:105
Alignment explanation
Indices: 5346234--5346482 Score: 392
Period size: 106 Copynumber: 2.4 Consensus size: 105
5346224 TGTGGTGGCC
*
5346234 TAAAAAAAAAATTGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTGAATTTTTTTTTTAC
1 TAAAAAAAAAATTGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTGAATATTTTTTTTAC
* *
5346299 ATTTTTCGTGTCAAAAGAAGGTATTAGTATACGAAAAAAG
66 ATTTTTCGTGTCAAAAGAAGGTATCAGTATACAAAAAAAG
*
5346339 TAAAAAAAAAATTTGTGGTGGCCTGCCAATGGTCGGCACCACCTTTTTTGTGGAA-ATTTTTTTT
1 TAAAAAAAAAA-TTGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGT-GAATATTTTTTTT
* * *
5346403 ACTTTTTTCGTGTCAATAGCAGGTATCAGTATACAAAAAAAG
64 ACATTTTTCGTGTCAAAAGAAGGTATCAGTATACAAAAAAAG
* *
5346445 TAAAAAAAAAATTGTGGTGGCTTGGCAATGGCCGGCAC
1 TAAAAAAAAAATTGTGGTGGCCTGCCAATGGCCGGCAC
5346483 AAATTTTTTT
Statistics
Matches: 132, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
105 35 0.27
106 94 0.71
107 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (105 bp):
TAAAAAAAAAATTGTGGTGGCCTGCCAATGGCCGGCACCACCTTTTTTGTGAATATTTTTTTTAC
ATTTTTCGTGTCAAAAGAAGGTATCAGTATACAAAAAAAG
Found at i:5357850 original size:26 final size:26
Alignment explanation
Indices: 5357812--5357901 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
5357802 TGCTCTGGTA
5357812 AAAAAACAT-AGGTACTTAATTGGGAC
1 AAAAAAC-TCAGGTACTTAATTGGGAC
** *
5357838 AAAAAACTCAGGTACCGAATT-GAAC
1 AAAAAACTCAGGTACTTAATTGGGAC
*
5357863 ATTAAAGCCAAATTCAGGTACTTAATTGGGAC
1 ---AAA---AAACTCAGGTACTTAATTGGGAC
5357895 AAAAAAC
1 AAAAAAC
5357902 AACTCAAGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
25 4 0.08
26 20 0.42
28 3 0.06
29 3 0.06
31 15 0.31
32 3 0.06
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.21
Consensus pattern (26 bp):
AAAAAACTCAGGTACTTAATTGGGAC
Found at i:5360208 original size:33 final size:33
Alignment explanation
Indices: 5360166--5360232 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
5360156 AAAAGAGAAA
5360166 CAAAATCACAAAAAAATTTCCTACAATAGGGTG
1 CAAAATCACAAAAAAATTTCCTACAATAGGGTG
5360199 CAAAATCACAAAAAAATTTCCTACAATAGGGTG
1 CAAAATCACAAAAAAATTTCCTACAATAGGGTG
5360232 C
1 C
5360233 CAACTCCTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (33 bp):
CAAAATCACAAAAAAATTTCCTACAATAGGGTG
Found at i:5368240 original size:18 final size:19
Alignment explanation
Indices: 5368200--5368244 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
5368190 AAAATCATAA
* *
5368200 AAATATTTAAAATTTTAAC
1 AAATTTTTAAAATGTTAAC
*
5368219 AAATTTTTAAAA-GTTAAT
1 AAATTTTTAAAATGTTAAC
5368237 AAATTTTT
1 AAATTTTT
5368245 TAGAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
AAATTTTTAAAATGTTAAC
Found at i:5369505 original size:41 final size:41
Alignment explanation
Indices: 5369448--5369528 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
5369438 GTTAACTTCT
5369448 GTTATAGTGCCTGCCTTTCTCTATCCATTTATGTTTTTGAA
1 GTTATAGTGCCTGCCTTTCTCTATCCATTTATGTTTTTGAA
5369489 GTTATAGTGCCTGCCTTTCTCTATCCATTTATGTTTTTGA
1 GTTATAGTGCCTGCCTTTCTCTATCCATTTATGTTTTTGA
5369529 TAAAATAATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.16, C:0.20, G:0.15, T:0.49
Consensus pattern (41 bp):
GTTATAGTGCCTGCCTTTCTCTATCCATTTATGTTTTTGAA
Found at i:5374478 original size:13 final size:15
Alignment explanation
Indices: 5374449--5374480 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
5374439 TTGGCTTCCA
5374449 TTCTTTTATTGTTTT
1 TTCTTTTATTGTTTT
5374464 TTCTTTT-TT-TTTT
1 TTCTTTTATTGTTTT
5374477 TTCT
1 TTCT
5374481 GGACAACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 2 0.12
15 7 0.41
ACGTcount: A:0.03, C:0.09, G:0.03, T:0.84
Consensus pattern (15 bp):
TTCTTTTATTGTTTT
Found at i:5385067 original size:2 final size:2
Alignment explanation
Indices: 5385060--5385100 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
5385050 ATACTGAAGA
*
5385060 AC AC AC AC AC AC AC AC AA AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5385101 TGTATATGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5390402 original size:20 final size:20
Alignment explanation
Indices: 5390377--5390420 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5390367 AAGTACAAAT
*
5390377 TATATACATATAGACATACA
1 TATATACATATACACATACA
* *
5390397 TATATATATATACATATACA
1 TATATACATATACACATACA
5390417 TATA
1 TATA
5390421 GGCCTTATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (20 bp):
TATATACATATACACATACA
Found at i:5390405 original size:18 final size:18
Alignment explanation
Indices: 5390378--5390412 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5390368 AGTACAAATT
5390378 ATATACATATAGACATAC
1 ATATACATATAGACATAC
* *
5390396 ATATATATATATACATA
1 ATATACATATAGACATA
5390413 TACATATAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.34
Consensus pattern (18 bp):
ATATACATATAGACATAC
Found at i:5393669 original size:21 final size:21
Alignment explanation
Indices: 5393644--5393684 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
5393634 CAATATCAAG
5393644 GGCGACATAATGATCAAACTC
1 GGCGACATAATGATCAAACTC
5393665 GGCGACATAATGATCAAACT
1 GGCGACATAATGATCAAACT
5393685 GCTGAGAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (21 bp):
GGCGACATAATGATCAAACTC
Found at i:5407268 original size:9 final size:9
Alignment explanation
Indices: 5407256--5407291 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
5407246 GCCCATATTA
5407256 AATATATAT
1 AATATATAT
5407265 AATATATAT
1 AATATATAT
5407274 AATATATA-
1 AATATATAT
*
5407282 AAAATATAT
1 AATATATAT
5407291 A
1 A
5407292 TTTGATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
AATATATAT
Found at i:5408656 original size:76 final size:76
Alignment explanation
Indices: 5408530--5408678 Score: 280
Period size: 76 Copynumber: 2.0 Consensus size: 76
5408520 TTTATCACAT
* *
5408530 ATTACTTAATAAATACAGTCAATTTATTATCTATTATATTTAATCATTATCAAGCCTTATTCTTC
1 ATTACTTAATAAATACAATCAATTCATTATCTATTATATTTAATCATTATCAAGCCTTATTCTTC
5408595 ACTTATTCTTC
66 ACTTATTCTTC
5408606 ATTACTTAATAAATACAATCAATTCATTATCTATTATATTTAATCATTATCAAGCCTTATTCTTC
1 ATTACTTAATAAATACAATCAATTCATTATCTATTATATTTAATCATTATCAAGCCTTATTCTTC
5408671 ACTTATTC
66 ACTTATTC
5408679 AACATATAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.46
Consensus pattern (76 bp):
ATTACTTAATAAATACAATCAATTCATTATCTATTATATTTAATCATTATCAAGCCTTATTCTTC
ACTTATTCTTC
Found at i:5408715 original size:18 final size:18
Alignment explanation
Indices: 5408694--5408742 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
5408684 ATAAATTTGT
5408694 AATTAAATATCATATTAA-
1 AATTAAAT-TCATATTAAC
* *
5408712 AATTATATTCATTTTAAC
1 AATTAAATTCATATTAAC
*
5408730 AATTAACTTCATA
1 AATTAAATTCATA
5408743 ATCAAAACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTAAATTCATATTAAC
Found at i:5413628 original size:15 final size:15
Alignment explanation
Indices: 5413603--5413637 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5413593 AACTCTATTT
*
5413603 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
5413617 TAATTAATATTAAGA
1 TAATTAATATTAAGA
5413632 TAATTA
1 TAATTA
5413638 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:5414265 original size:28 final size:28
Alignment explanation
Indices: 5414225--5414282 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
5414215 TTGGCTAGAG
5414225 TCAGGTTCCACTAAATCGTAAGTCTAAA
1 TCAGGTTCCACTAAATCGTAAGTCTAAA
*
5414253 TCAGGTTCCACTAAATCGTATGTCTAAA
1 TCAGGTTCCACTAAATCGTAAGTCTAAA
5414281 TC
1 TC
5414283 CTTGGAGCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (28 bp):
TCAGGTTCCACTAAATCGTAAGTCTAAA
Found at i:5419476 original size:50 final size:50
Alignment explanation
Indices: 5419284--5419475 Score: 267
Period size: 50 Copynumber: 3.8 Consensus size: 50
5419274 TTTCCTGTAC
* * * * ** *
5419284 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * **
5419334 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
5419384 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
5419434 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5419476 TTACCCAAAT
Statistics
Matches: 126, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 126 1.00
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:5422266 original size:21 final size:22
Alignment explanation
Indices: 5422237--5422277 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5422227 ACAGCAAGCA
*
5422237 ATTTTTTTTCCTTCT-TTTTCG
1 ATTTATTTTCCTTCTCTTTTCG
*
5422258 ATTTATTTTCTTTCTCTTTT
1 ATTTATTTTCCTTCTCTTTT
5422278 TCGGCCTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.73
Consensus pattern (22 bp):
ATTTATTTTCCTTCTCTTTTCG
Done.