Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 176 of 211
Found at i:54606419 original size:13 final size:14
Alignment explanation
Indices: 54606384--54606427 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
54606374 CCTTCTTTTT
54606384 CTTTCTTTCCTCTC
1 CTTTCTTTCCTCTC
*
54606398 C-TTCCTTCCT-TC
1 CTTTCTTTCCTCTC
54606410 CTTTCTTTCCCTCTC
1 CTTTCTTT-CCTCTC
54606425 CTT
1 CTT
54606428 CTCCCCCCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 13 0.52
14 4 0.16
15 5 0.20
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (14 bp):
CTTTCTTTCCTCTC
Found at i:54606513 original size:27 final size:27
Alignment explanation
Indices: 54606461--54606514 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
54606451 CCCCTATTAT
* **
54606461 ACCATTGGTGCCGCCAATGGTTTTGGC
1 ACCATTGGTGCCACCAATGGCATTGGC
54606488 ACCATTGGTGCCACCAATGGCATTGGC
1 ACCATTGGTGCCACCAATGGCATTGGC
54606515 CTGACTAGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.26
Consensus pattern (27 bp):
ACCATTGGTGCCACCAATGGCATTGGC
Found at i:54606593 original size:19 final size:19
Alignment explanation
Indices: 54606556--54606594 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
54606546 CTTTTTACAA
* *
54606556 GTTTTTTTTTCTGTTTTTT
1 GTTTTTTTTTCTATATTTT
*
54606575 GTTTTTTTTTGTATATTTT
1 GTTTTTTTTTCTATATTTT
54606594 G
1 G
54606595 GTAAATAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.03, G:0.13, T:0.79
Consensus pattern (19 bp):
GTTTTTTTTTCTATATTTT
Found at i:54606641 original size:26 final size:24
Alignment explanation
Indices: 54606586--54606644 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 24
54606576 TTTTTTTTTG
*
54606586 TATATTTTGGTAAATAAAAAAATA
1 TATATTTTAGTAAATAAAAAAATA
54606610 T-T-TTTTAGTAAATAAAAAAATTA
1 TATATTTTAGTAAATAAAAAAA-TA
54606633 TAATATTTTAGT
1 T-ATATTTTAGT
54606645 TATTTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 17 0.57
23 4 0.13
24 1 0.03
25 1 0.03
26 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (24 bp):
TATATTTTAGTAAATAAAAAAATA
Found at i:54611068 original size:42 final size:42
Alignment explanation
Indices: 54610973--54611069 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
54610963 GTTATCACAT
*
54610973 GGTTTAAGACATGGTCGTGTGTATCAAGTCAGAGAGTTACAC
1 GGTTTAAGACACGGTCGTGTGTATCAAGTCAGAGAGTTACAC
* *
54611015 GAG-TTATGACACGGTCGTGTG-ATCTAAGTCAGTGAGTTACAC
1 G-GTTTAAGACACGGTCGTGTGTATC-AAGTCAGAGAGTTACAC
54611057 GGTTTAAGACACG
1 GGTTTAAGACACG
54611070 AGCTGGGACA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
41 4 0.08
42 43 0.90
43 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (42 bp):
GGTTTAAGACACGGTCGTGTGTATCAAGTCAGAGAGTTACAC
Found at i:54625621 original size:78 final size:78
Alignment explanation
Indices: 54625493--54625650 Score: 273
Period size: 78 Copynumber: 2.0 Consensus size: 78
54625483 TAGGACATTC
*
54625493 AATATGTAACTTTTTAAAGATTTCAATCTGTAATTTTAAATAACAATCTTAAGGATGTCAAGGCT
1 AATATGTAACTTTTTAAAGATTTCAATCTATAATTTTAAATAACAATCTTAAGGATGTCAAGGCT
54625558 CGAGCTCAAC-AA
66 CGAGCTCAACTAA
*
54625570 AATATGTAACTTCTTTAAAGATTTCAATCTATAATTTTAGATAACAATCTTAAGGATGTCAAGGC
1 AATATGTAACTT-TTTAAAGATTTCAATCTATAATTTTAAATAACAATCTTAAGGATGTCAAGGC
*
54625635 TCGAGCTTAACTAA
65 TCGAGCTCAACTAA
54625649 AA
1 AA
54625651 GTGCAAGCAG
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
77 12 0.16
78 60 0.79
79 4 0.05
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (78 bp):
AATATGTAACTTTTTAAAGATTTCAATCTATAATTTTAAATAACAATCTTAAGGATGTCAAGGCT
CGAGCTCAACTAA
Found at i:54630594 original size:46 final size:46
Alignment explanation
Indices: 54630544--54630682 Score: 269
Period size: 46 Copynumber: 3.0 Consensus size: 46
54630534 AGACAAACTT
*
54630544 TAACTCAAGTAGGCTATGAATAAATGGAAATTTGAATCCAACACAA
1 TAACTCAAGTAGGCTATGAGTAAATGGAAATTTGAATCCAACACAA
54630590 TAACTCAAGTAGGCTATGAGTAAATGGAAATTTGAATCCAACACAA
1 TAACTCAAGTAGGCTATGAGTAAATGGAAATTTGAATCCAACACAA
54630636 TAACTCAAGTAGGCTATGAGTAAATGGAAATTTGAATCCAACACAA
1 TAACTCAAGTAGGCTATGAGTAAATGGAAATTTGAATCCAACACAA
54630682 T
1 T
54630683 TTGACATTAG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 92 1.00
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (46 bp):
TAACTCAAGTAGGCTATGAGTAAATGGAAATTTGAATCCAACACAA
Found at i:54638315 original size:52 final size:52
Alignment explanation
Indices: 54638237--54638346 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 52
54638227 GTTAAGTAAT
54638237 TTTGTTGACAGAATTCTCAGTCTCTTTCTCTCTAATTCTCTCCATCTCTCTC
1 TTTGTTGACAGAATTCTCAGTCTCTTTCTCTCTAATTCTCTCCATCTCTCTC
*
54638289 TTTGTTGACAGAATTCTCAGTCTCTTTCTCTCTAATTCTCTCTATCTCTCTC
1 TTTGTTGACAGAATTCTCAGTCTCTTTCTCTCTAATTCTCTCCATCTCTCTC
54638341 TTTGTT
1 TTTGTT
54638347 TCTTCTACAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.15, C:0.28, G:0.08, T:0.49
Consensus pattern (52 bp):
TTTGTTGACAGAATTCTCAGTCTCTTTCTCTCTAATTCTCTCCATCTCTCTC
Found at i:54647908 original size:34 final size:35
Alignment explanation
Indices: 54647870--54647936 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
54647860 CAGTAAAATA
*
54647870 TTTTCCGTAAAATGATTT-CAGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACAGGAAAATATTTTAC
* *
54647904 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACAGGAAAATATTTT
54647937 CTGATTTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACAGGAAAATATTTTAC
Found at i:54666529 original size:17 final size:17
Alignment explanation
Indices: 54666507--54666540 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54666497 AGCAATTAAA
54666507 AAATTAGAAATTAAATT
1 AAATTAGAAATTAAATT
*
54666524 AAATTATAAATTAAATT
1 AAATTAGAAATTAAATT
54666541 CGAATTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTAGAAATTAAATT
Found at i:54672007 original size:29 final size:29
Alignment explanation
Indices: 54671936--54672009 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
54671926 TTGACACGAT
* * *
54671936 TCTCAATGAACAAATTCTTCATCGCGAAC
1 TCTCAACGAACAAGTTCTTCATCGCAAAC
54671965 TCTCAACGAACAAGTTCTTCATCGCAAAC
1 TCTCAACGAACAAGTTCTTCATCGCAAAC
54671994 TCTCAACGAACAAGTT
1 TCTCAACGAACAAGTT
54672010 TTCCACCTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.26
Consensus pattern (29 bp):
TCTCAACGAACAAGTTCTTCATCGCAAAC
Found at i:54678775 original size:41 final size:41
Alignment explanation
Indices: 54678718--54678949 Score: 358
Period size: 41 Copynumber: 5.7 Consensus size: 41
54678708 GACCTTTCGG
* *
54678718 GGCTTTAGCGGCGTTTTTGAGATAGCGCCGCTAATGCTCCT
1 GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAT
*
54678759 GGCTTTAGTGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAT
1 GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAT
* *
54678800 GGCTTTAGCGGCGTTTTTGAGAAAGCGACGCTAATACTCAT
1 GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAT
* *
54678841 GGCTTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTCAG
1 GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAT
*
54678882 GGCTTTAGCGGCGTTTTTG-GAAAAGCGCCGCTAATGCTCAG
1 GGCTTTAGCGGCGTTTTTGAG-AAAGCGCCGCTAATGCTCAT
* *
54678923 GGATTTAGCGGCGTTTTTGAAAAAGCG
1 GGCTTTAGCGGCGTTTTTGAGAAAGCG
54678950 ACGCAAAAAC
Statistics
Matches: 176, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
41 176 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (41 bp):
GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAT
Found at i:54679260 original size:14 final size:14
Alignment explanation
Indices: 54679241--54679269 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54679231 ATATATATTG
54679241 TTAGGGTATATGGT
1 TTAGGGTATATGGT
54679255 TTAGGGTATATGGT
1 TTAGGGTATATGGT
54679269 T
1 T
54679270 AATTTAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (14 bp):
TTAGGGTATATGGT
Found at i:54679429 original size:28 final size:31
Alignment explanation
Indices: 54679378--54679457 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 31
54679368 TGATTTAGGG
* *
54679378 GTTAGGGGTTAGGAGGTTAAAGATT-AA-G-A
1 GTTAGGGTTTAGG-GTTTAAAGATTCAATGCA
*
54679407 GTTAGGGTTTAGGGTTTATAGATTCAATGTCA
1 GTTAGGGTTTAGGGTTTAAAGATTCAATG-CA
*
54679439 GTTAGAGGTTTAGCGTTTA
1 GTTAG-GGTTTAGGGTTTA
54679458 GATTAATTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
28 9 0.21
29 14 0.33
30 1 0.02
32 6 0.14
33 12 0.29
ACGTcount: A:0.28, C:0.04, G:0.33, T:0.36
Consensus pattern (31 bp):
GTTAGGGTTTAGGGTTTAAAGATTCAATGCA
Found at i:54680427 original size:23 final size:21
Alignment explanation
Indices: 54680385--54680427 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
54680375 CCCTTCCCTC
*
54680385 CAAAACCCAAATTCCTTCAAG
1 CAAAACCCAAACTCCTTCAAG
54680406 CAAAACCCAAACCCTCCTTCAA
1 CAAAACCCAAA--CTCCTTCAA
54680428 ATTATCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.42, C:0.40, G:0.02, T:0.16
Consensus pattern (21 bp):
CAAAACCCAAACTCCTTCAAG
Found at i:54681362 original size:46 final size:46
Alignment explanation
Indices: 54681311--54681401 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
54681301 TTCATATTTT
54681311 CTTTATTTATTTTGTTTTCTCATTTATATCAGTAGCTTAGTAAATA
1 CTTTATTTATTTTGTTTTCTCATTTATATCAGTAGCTTAGTAAATA
54681357 CTTTATTTATTTTGTTTTCTCATTTATATCAGTAGCTTAGTAAAT
1 CTTTATTTATTTTGTTTTCTCATTTATATCAGTAGCTTAGTAAAT
54681402 TAGCGAGTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (46 bp):
CTTTATTTATTTTGTTTTCTCATTTATATCAGTAGCTTAGTAAATA
Found at i:54684647 original size:24 final size:23
Alignment explanation
Indices: 54684619--54684666 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
54684609 AATTTAAAAA
54684619 ATAAAACATAATATAATATTT-ATT
1 ATAAAA-ATAA-ATAATATTTGATT
*
54684643 ATAAAAATAAATATTATTTGATT
1 ATAAAAATAAATAATATTTGATT
54684666 A
1 A
54684667 AATTAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAAAATAAATAATATTTGATT
Found at i:54684792 original size:43 final size:42
Alignment explanation
Indices: 54684730--54684978 Score: 252
Period size: 43 Copynumber: 5.9 Consensus size: 42
54684720 AAGGTTTGTT
* *
54684730 CTATAGCGGCGTTTATGGGAAAAGTGCCGCTAAAGATATCGAG
1 CTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAG-TCTCGAG
* * * * *
54684773 CTATAGCGGCGCTTGTGGGAAAAGCGCCACCAAAGCTCTTGAG
1 CTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAG-TCTCGAG
* * *
54684816 CTATAGCGGCGTTTCTGGGAAAAGTGCCGCTAAATGTCTTGAT
1 CTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAA-GTCTCGAG
*
54684859 CTATAGCGGCGTTTGTGGAAAAAGTGCCGCTAAAGGTCTCGAG
1 CTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAA-GTCTCGAG
* * * *
54684902 CTATAGCGGCGTTT-TGGG-AAAGCGCCACTAAAG-GTCAATG
1 CTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGTCTCGA-G
* ** *
54684942 TCTTTAGCGGCGTTTGTTAGAAAAGCGCCGCTAAAGT
1 -CTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGT
54684979 TAGCGACGCT
Statistics
Matches: 172, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.02
40 2 0.01
41 25 0.15
42 5 0.03
43 136 0.79
44 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (42 bp):
CTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGTCTCGAG
Found at i:54689000 original size:35 final size:35
Alignment explanation
Indices: 54688954--54689024 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
54688944 AAAAATATAT
* *
54688954 ATTTTGGTTAACTTGATTTGCAAGTAATCTCTTAG
1 ATTTTGGTTAACTTGACTTGCAAGTAATATCTTAG
*
54688989 ATTTTGTTTAACTTGACTTGCAAGTAATATCTTAG
1 ATTTTGGTTAACTTGACTTGCAAGTAATATCTTAG
54689024 A
1 A
54689025 ATTTAGGTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (35 bp):
ATTTTGGTTAACTTGACTTGCAAGTAATATCTTAG
Found at i:54689073 original size:13 final size:14
Alignment explanation
Indices: 54689057--54689085 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54689047 AGTTTAGTTT
54689057 AATTTT-TAATTTA
1 AATTTTGTAATTTA
54689070 AATTTTGTAATTTA
1 AATTTTGTAATTTA
54689084 AA
1 AA
54689086 AAAAAGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
AATTTTGTAATTTA
Found at i:54693122 original size:15 final size:16
Alignment explanation
Indices: 54693095--54693127 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
54693085 CCACTTTGTA
54693095 TTGTTTGCCATTAATG
1 TTGTTTGCCATTAATG
54693111 TTGTTT-CCATTAATG
1 TTGTTTGCCATTAATG
54693126 TT
1 TT
54693128 AACAATCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.18, C:0.12, G:0.15, T:0.55
Consensus pattern (16 bp):
TTGTTTGCCATTAATG
Found at i:54695059 original size:21 final size:21
Alignment explanation
Indices: 54695033--54695073 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54695023 ATCTGCTCAA
* *
54695033 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
54695054 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
54695074 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:54698548 original size:39 final size:41
Alignment explanation
Indices: 54698464--54698555 Score: 125
Period size: 39 Copynumber: 2.3 Consensus size: 41
54698454 TAAAAAGTAT
* * * *
54698464 TTATATTAAAAAACACTACCATAAATATAATAAATGTTTTG
1 TTATATTAAACAACACTACAATAAATATAATAAATATTTTA
*
54698505 TTATATTAAACAACAC-A-AATAAATGTAATAAATATTTTA
1 TTATATTAAACAACACTACAATAAATATAATAAATATTTTA
54698544 TTATATTAAACA
1 TTATATTAAACA
54698556 TAATTTTTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 30 0.65
40 1 0.02
41 15 0.33
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (41 bp):
TTATATTAAACAACACTACAATAAATATAATAAATATTTTA
Found at i:54699201 original size:12 final size:11
Alignment explanation
Indices: 54699184--54699216 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
54699174 TCTTTCATAC
54699184 TTTTTTTATAA
1 TTTTTTTATAA
*
54699195 TTTTTTTATGA
1 TTTTTTTATAA
54699206 TTTTTTT-TAA
1 TTTTTTTATAA
54699216 T
1 T
54699217 ATATGTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 3 0.15
11 17 0.85
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTTTTTATAA
Found at i:54707493 original size:34 final size:34
Alignment explanation
Indices: 54707449--54707513 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
54707439 TCTTGTAAAA
* *
54707449 TACTCGTTCTCGCATGCTTCCACTAATTAATCAT
1 TACTCATTCTCGCACGCTTCCACTAATTAATCAT
54707483 TACTCATTCTCGCACGCTTCCACTAATTAAT
1 TACTCATTCTCGCACGCTTCCACTAATTAAT
54707514 ATGAACATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.25, C:0.31, G:0.08, T:0.37
Consensus pattern (34 bp):
TACTCATTCTCGCACGCTTCCACTAATTAATCAT
Found at i:54710217 original size:10 final size:10
Alignment explanation
Indices: 54710185--54710219 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
54710175 GAATATATTA
54710185 TATATTAAAT
1 TATATTAAAT
*
54710195 TAAATTAAAT
1 TATATTAAAT
*
54710205 TATATTATAT
1 TATATTAAAT
54710215 TATAT
1 TATAT
54710220 AATTTCAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TATATTAAAT
Found at i:54714573 original size:5 final size:5
Alignment explanation
Indices: 54714554--54714597 Score: 65
Period size: 5 Copynumber: 9.0 Consensus size: 5
54714544 TCATCTTCTC
54714554 TATCA TCAT-A TATCA TATCA TATCA TATCA TATCA TA-CA TATCA
1 TATCA T-ATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
54714598 AAAGTATATG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.17
5 28 0.78
6 2 0.06
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (5 bp):
TATCA
Found at i:54720329 original size:30 final size:30
Alignment explanation
Indices: 54720293--54720511 Score: 258
Period size: 30 Copynumber: 7.2 Consensus size: 30
54720283 GTATATGTTT
*
54720293 TATATATTGCTGAATTGATTTGTATATGGATA
1 TATATATTGCCGAATTGATTTGTATATGG--A
* * * *
54720325 TATATATTACCGAATTAATTTATATATAGA
1 TATATATTGCCGAATTGATTTGTATATGGA
*
54720355 TATATATAGCCGAATTGATTTGTATATGGA
1 TATATATTGCCGAATTGATTTGTATATGGA
*
54720385 TATACATTGCCGAATTGATTTGTATATGGA
1 TATATATTGCCGAATTGATTTGTATATGGA
* * **
54720415 TCTACATTGCTAAATTGATTTGTATATGGA
1 TATATATTGCCGAATTGATTTGTATATGGA
* *
54720445 TATACATTGCCGAATTGATTTGTATATGTA
1 TATATATTGCCGAATTGATTTGTATATGGA
** * *
54720475 TATATATTATCGAAATGATTTGTATATGTA
1 TATATATTGCCGAATTGATTTGTATATGGA
*
54720505 TACATAT
1 TATATAT
54720512 ATATTACCAA
Statistics
Matches: 163, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
30 139 0.85
32 24 0.15
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (30 bp):
TATATATTGCCGAATTGATTTGTATATGGA
Found at i:54727911 original size:20 final size:20
Alignment explanation
Indices: 54727874--54727912 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54727864 TAAAGATTTG
***
54727874 ATTAAATTAATTTCTTTAAC
1 ATTAAATTAATCAATTTAAC
54727894 ATTAAATTAATCAATTTAA
1 ATTAAATTAATCAATTTAA
54727913 TTTCAATACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTAAATTAATCAATTTAAC
Found at i:54728451 original size:13 final size:14
Alignment explanation
Indices: 54728420--54728457 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
54728410 GAAATTTTTA
54728420 ACTTTTCAAAAGTG
1 ACTTTTCAAAAGTG
54728434 A-TTTTCAAAAGT-
1 ACTTTTCAAAAGTG
*
54728446 ACTTTTAAAAAG
1 ACTTTTCAAAAG
54728458 AATAAGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 1 0.05
13 20 0.91
14 1 0.05
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (14 bp):
ACTTTTCAAAAGTG
Found at i:54728938 original size:13 final size:13
Alignment explanation
Indices: 54728922--54728986 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
54728912 TTTAAACTAA
54728922 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
54728935 ACTTCTCAAAAGT
1 ACTTTTCAAAAGC
* *
54728948 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
* * *
54728961 AC-TTTCCACACC
1 ACTTTTCAAAAGC
54728973 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
54728986 A
1 A
54728987 ATAAAGAACT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
12 11 0.27
13 30 0.73
ACGTcount: A:0.34, C:0.31, G:0.06, T:0.29
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:54732210 original size:49 final size:49
Alignment explanation
Indices: 54732157--54732256 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
54732147 TTCTCTTTTT
54732157 TTTCTAGAACAATCAGCAATAATTCAGCAAATCAAACAAAAGAGCATAG
1 TTTCTAGAACAATCAGCAATAATTCAGCAAATCAAACAAAAGAGCATAG
54732206 TTTCTAGAACAATCAGCAATAATTCAGCAAATCAAACAAAAGAGCATAG
1 TTTCTAGAACAATCAGCAATAATTCAGCAAATCAAACAAAAGAGCATAG
54732255 TT
1 TT
54732257 AGACAACTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (49 bp):
TTTCTAGAACAATCAGCAATAATTCAGCAAATCAAACAAAAGAGCATAG
Found at i:54742191 original size:21 final size:21
Alignment explanation
Indices: 54742165--54742205 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54742155 ATCTGCTCAA
* *
54742165 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
54742186 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
54742206 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:54748419 original size:19 final size:19
Alignment explanation
Indices: 54748381--54748429 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
54748371 TATGGTTTAG
54748381 AAAATTT-TAAAAATATAT
1 AAAATTTCTAAAAATATAT
54748399 AAAATTTCTAATAAA-ATAT
1 AAAATTTCTAA-AAATATAT
54748418 AAAATTTC-AAAA
1 AAAATTTCTAAAA
54748430 GAAAATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.07
18 9 0.31
19 15 0.52
20 3 0.10
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTTCTAAAAATATAT
Found at i:54748436 original size:20 final size:20
Alignment explanation
Indices: 54748395--54748457 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 20
54748385 TTTTAAAAAT
* *
54748395 ATATAAAATTTC-TAATAAA
1 ATATAAAATTTCAAAAGAAA
54748414 ATATAAAATTTCAAAAGAAA
1 ATATAAAATTTCAAAAGAAA
* *
54748434 ATATATAACGTCTCAAAAGAAA
1 ATATA-AA-ATTTCAAAAGAAA
54748456 AT
1 AT
54748458 CAACCTCAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 12 0.32
20 10 0.27
21 2 0.05
22 13 0.35
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.29
Consensus pattern (20 bp):
ATATAAAATTTCAAAAGAAA
Found at i:54758836 original size:25 final size:25
Alignment explanation
Indices: 54758808--54758855 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
54758798 ATTTATTTTA
**
54758808 ATATTTTTAGTATTTTTGATATATC
1 ATATTTTTAACATTTTTGATATATC
*
54758833 ATATTTTTAACATTTTTTATATA
1 ATATTTTTAACATTTTTGATATA
54758856 CAAAATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (25 bp):
ATATTTTTAACATTTTTGATATATC
Found at i:54760672 original size:91 final size:90
Alignment explanation
Indices: 54760490--54760693 Score: 216
Period size: 91 Copynumber: 2.2 Consensus size: 90
54760480 CTTTTTTTTT
* * * *
54760490 AAAA-AATTAAGCCCCTGTTTTTATTTTTTGCACTCATTTGAGTACTTGAATTTTTAAAATACAT
1 AAAACAATTAAGCCCCTCTTTTTATTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATACAT
*
54760554 CAAAAAAGCCCTTAAACCTTT-AAA
66 CAAAAAAGCCCTCAAACCTTTAAAA
* * * *
54760578 AAAACAATTAAGCCCCTACTCTTTTTTTTTTTGCACTCAATTGGGTATTTGAACTTTCAAAATGC
1 AAAACAATTAAGCCCCT-CT-TTTTATTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATAC
* * *
54760643 AT-AAAAAAGATCCTCAAACTTTTTCAAA
64 ATCAAAAAAG-CCCTCAAAC-CTTTAAAA
* *
54760671 AAAGCAATTAATCCCCTGCTTTT
1 AAAACAATTAAGCCCCT-CTTTT
54760694 ATTAAAAAAT
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
88 4 0.04
89 12 0.12
90 8 0.08
91 46 0.48
92 6 0.06
93 20 0.21
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (90 bp):
AAAACAATTAAGCCCCTCTTTTTATTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATACAT
CAAAAAAGCCCTCAAACCTTTAAAA
Found at i:54760799 original size:18 final size:18
Alignment explanation
Indices: 54760740--54760803 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
54760730 CAATAAAAGC
* *
54760740 TATAAATATATTAAAATTT
1 TATAAAAATATTAAAA-AT
* *
54760759 TTTAAAAATA--AAATAT
1 TATAAAAATATTAAAAAT
*
54760775 TAAAAAAATATTAAAAAT
1 TATAAAAATATTAAAAAT
54760793 TATAAAAATAT
1 TATAAAAATAT
54760804 ATATAATTCG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
16 9 0.26
17 3 0.09
18 15 0.43
19 8 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TATAAAAATATTAAAAAT
Found at i:54761131 original size:19 final size:19
Alignment explanation
Indices: 54761107--54761157 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
54761097 ATTTCTAATT
54761107 TTTAATATTTTTAT-TAAAA
1 TTTAATATTTTT-TCTAAAA
54761126 TTTAATATTTTTTCTAAAA
1 TTTAATATTTTTTCTAAAA
54761145 TTTAATATTTTTT
1 TTTAATATTTTTT
54761158 TATTTTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 1 0.03
19 30 0.97
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTAATATTTTTTCTAAAA
Found at i:54761296 original size:83 final size:86
Alignment explanation
Indices: 54761196--54761365 Score: 247
Period size: 85 Copynumber: 2.0 Consensus size: 86
54761186 TAATAAGAGC
* * * *
54761196 AGGGGCTTAATTGC-TTTTTT-GAAAAATTTTGAGGGTCTTTTTGATACATTTTGAAAATTCAAG
1 AGGGGCTTAATTACTTTTTTTAAAAAAAATTTGAGGGCCTTTTTGATACATTTTGAAAATTCAAG
54761259 TACCCAATTGAGTG-AAAAAA
66 TACCCAATTGAGTGTAAAAAA
* *
54761279 AGGGGCTTAATTACTTTTTTTAAAAAAAATTTGAGGGCCTTTTTGATACATTTTTAAAGTTCAAG
1 AGGGGCTTAATTACTTTTTTTAAAAAAAATTTGAGGGCCTTTTTGATACATTTTGAAAATTCAAG
* *
54761344 TGCTCAATTGAGTGTAAAAAA
66 TACCCAATTGAGTGTAAAAAA
54761365 A
1 A
54761366 AAGCGACTTA
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
83 13 0.17
84 6 0.08
85 50 0.66
86 7 0.09
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (86 bp):
AGGGGCTTAATTACTTTTTTTAAAAAAAATTTGAGGGCCTTTTTGATACATTTTGAAAATTCAAG
TACCCAATTGAGTGTAAAAAA
Found at i:54761384 original size:85 final size:82
Alignment explanation
Indices: 54761201--54761384 Score: 206
Period size: 85 Copynumber: 2.2 Consensus size: 82
54761191 AGAGCAGGGG
** * *
54761201 CTTAATTGCTTTTTTGAAAAATTTTGAGGGTCTTTTTGATACATTTTGAAAATTCAAGTACCCAA
1 CTTAATTG-TTTTTAAAAAAAATTTGAGGGCCTTTTTGATACATTTTGAAAATTCAAGTACCCAA
* *
54761266 TTGAGTGAAAAAAAGGGG
65 TTGAGTGAAAAAAAGCGA
* * * * *
54761284 CTTAATTACTTTTTTTAAAAAAAATTTGAGGGCCTTTTTGATACATTTTTAAAGTTCAAGTGCTC
1 CTTAA-T--TGTTTTTAAAAAAAATTTGAGGGCCTTTTTGATACATTTTGAAAATTCAAGTACCC
54761349 AATTGAGTGTAAAAAAAAAGCGA
63 AATTGAGTG---AAAAAAAGCGA
54761372 CTTAATTGTTTTT
1 CTTAATTGTTTTT
54761385 TTTTAATTTA
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
83 5 0.06
84 1 0.01
85 61 0.73
86 1 0.01
87 1 0.01
88 14 0.17
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (82 bp):
CTTAATTGTTTTTAAAAAAAATTTGAGGGCCTTTTTGATACATTTTGAAAATTCAAGTACCCAAT
TGAGTGAAAAAAAGCGA
Found at i:54762859 original size:21 final size:21
Alignment explanation
Indices: 54762834--54762874 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54762824 TTAATATAAC
*
54762834 AATAC-TTGATTATATTATTTT
1 AATACTTTAATTA-ATTATTTT
54762855 AATACTTTAATTAATTATTT
1 AATACTTTAATTAATTATTT
54762875 ATGACTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (21 bp):
AATACTTTAATTAATTATTTT
Found at i:54764959 original size:24 final size:25
Alignment explanation
Indices: 54764913--54764960 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
54764903 TTTGACATTC
*
54764913 TTTTCTAATGTGGTACATGTATTTT
1 TTTTCTAATGTGGTACATATATTTT
*
54764938 TTTTC-AATGTGGTACCTATATTT
1 TTTTCTAATGTGGTACATATATTT
54764961 GACAAAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (25 bp):
TTTTCTAATGTGGTACATATATTTT
Found at i:54766159 original size:18 final size:18
Alignment explanation
Indices: 54766138--54766174 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
54766128 TTAAAATACT
54766138 AACAAAATTAACAATAAA
1 AACAAAATTAACAATAAA
54766156 AACAAAATTAACAATAAA
1 AACAAAATTAACAATAAA
54766174 A
1 A
54766175 TAAGAGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.73, C:0.11, G:0.00, T:0.16
Consensus pattern (18 bp):
AACAAAATTAACAATAAA
Found at i:54766574 original size:20 final size:21
Alignment explanation
Indices: 54766540--54766579 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
54766530 TATTCCTAAT
54766540 TTAAATTTTAATGTT-TAAAA
1 TTAAATTTTAATGTTATAAAA
**
54766560 TTAAATTTTTTTGTTATAAA
1 TTAAATTTTAATGTTATAAA
54766580 TAGATCACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
TTAAATTTTAATGTTATAAAA
Found at i:54772332 original size:33 final size:32
Alignment explanation
Indices: 54772288--54772412 Score: 99
Period size: 33 Copynumber: 3.8 Consensus size: 32
54772278 TAGATACATG
*
54772288 TGTAAGACCATAGCTGGGCTATGGCATTCTGA
1 TGTAAGACCATAGCTGGGCTATGGCATACTGA
* * * **
54772320 TGATAAGACCATAACTGGGTTATGACACTACAAA
1 TG-TAAGACCATAGCTGGGCTATGGCA-TACTGA
* * * *
54772354 TGTAAGACCATGGCAGGGCCATGGCAATGCATG-
1 TGTAAGACCATAGCTGGGCTATGGC-ATAC-TGA
* *
54772387 TGTAAGACCATAGTTGGACTATGGCA
1 TGTAAGACCATAGCTGGGCTATGGCA
54772413 CAAAAAGAAT
Statistics
Matches: 69, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
32 3 0.04
33 60 0.87
34 6 0.09
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.24
Consensus pattern (32 bp):
TGTAAGACCATAGCTGGGCTATGGCATACTGA
Found at i:54772378 original size:105 final size:99
Alignment explanation
Indices: 54772185--54772412 Score: 242
Period size: 105 Copynumber: 2.2 Consensus size: 99
54772175 TGTTTAAATT
** * * * *
54772185 TAAGACCATAGTTGGGCTATGAAATTTTAATGAAAAGACCATAATTGGGTTATGGCACCTTAAAC
1 TAAGACCATAGTTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGACACCTCAAAC
**
54772250 ATAAGACCATGGTTGGACAATGGCAGTATAGATACATGTG
66 ATAAGACCATGGCAGGACAATGGCA--AT-G---CATGTG
* * *
54772290 TAAGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGACA-CTACAAA
1 TAAGACCATAGTTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGACACCT-CAAA
** * *
54772354 TGTAAGACCATGGCAGGGCCATGGCAATGCATGTG
65 CATAAGACCATGGCAGGACAATGGCAATGCATGTG
*
54772389 TAAGACCATAGTTGGACTATGGCA
1 TAAGACCATAGTTGGGCTATGGCA
54772413 CAAAAAGAAT
Statistics
Matches: 105, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
99 28 0.27
102 1 0.01
103 2 0.02
104 2 0.02
105 72 0.69
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (99 bp):
TAAGACCATAGTTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGACACCTCAAAC
ATAAGACCATGGCAGGACAATGGCAATGCATGTG
Found at i:54774317 original size:15 final size:16
Alignment explanation
Indices: 54774292--54774321 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54774282 TATTTCTCCC
54774292 TGTTTCGTTTCTATTA
1 TGTTTCGTTTCTATTA
54774308 TGTTTC-TTTCTATT
1 TGTTTCGTTTCTATT
54774322 TCTTTTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.13, G:0.10, T:0.67
Consensus pattern (16 bp):
TGTTTCGTTTCTATTA
Found at i:54775050 original size:25 final size:24
Alignment explanation
Indices: 54775012--54775114 Score: 86
Period size: 25 Copynumber: 4.2 Consensus size: 24
54775002 TATAACGAGT
54775012 AGCTCCGAAGAGCCATTAATCAGGA
1 AGCTCCGAAGAGCCA-TAATCAGGA
* * *
54775037 AGCTCCGGATAGCCATATATCGGGA
1 AGCTCCGAAGAGCCATA-ATCAGGA
* *
54775062 AG-TTC-AAGCGAGCCAT-ATCGGGA
1 AGCTCCGAA--GAGCCATAATCAGGA
*
54775085 AGCTCCGAAGAGCCATTAATCAGAA
1 AGCTCCGAAGAGCCA-TAATCAGGA
54775110 AGCTC
1 AGCTC
54775115 ACAAAAAGCT
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
23 16 0.26
24 7 0.11
25 39 0.63
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.17
Consensus pattern (24 bp):
AGCTCCGAAGAGCCATAATCAGGA
Found at i:54775467 original size:20 final size:22
Alignment explanation
Indices: 54775428--54775470 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
54775418 TTAATTTCAT
54775428 ATATATGACAATTATACAATTC
1 ATATATGACAATTATACAATTC
*
54775450 ATATAT-ACAA-TATTCAATTC
1 ATATATGACAATTATACAATTC
54775470 A
1 A
54775471 AAAATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (22 bp):
ATATATGACAATTATACAATTC
Found at i:54775636 original size:21 final size:21
Alignment explanation
Indices: 54775612--54775651 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54775602 GTAAATTTAG
*
54775612 CTCAATTTAATACAATTCATA
1 CTCAATTCAATACAATTCATA
*
54775633 CTCAATTCAATCCAATTCA
1 CTCAATTCAATACAATTCA
54775652 CATCTTAGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (21 bp):
CTCAATTCAATACAATTCATA
Found at i:54776829 original size:47 final size:47
Alignment explanation
Indices: 54776755--54776888 Score: 117
Period size: 47 Copynumber: 2.9 Consensus size: 47
54776745 TTGGCAGTTT
* * * * ** *
54776755 ATCTGTTCGACCAGTGGTTTATCCACAATGTATTTTA-TTCAGCAATC
1 ATCTGCTCAACCAATGGTTCATCCACAACATATTTTAGTTC-CCAATC
* *
54776802 ATCTGCTCAACCAATGGTTCATTCACAACATATTTTAGTTCCCAGTC
1 ATCTGCTCAACCAATGGTTCATCCACAACATATTTTAGTTCCCAATC
* * * * * *
54776849 ATCTGCTCAGCCAGTGTTTTATCCATAACGTATTTTAGTT
1 ATCTGCTCAACCAATGGTTCATCCACAACATATTTTAGTT
54776889 GGCAGTTCAT
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
47 67 0.96
48 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.38
Consensus pattern (47 bp):
ATCTGCTCAACCAATGGTTCATCCACAACATATTTTAGTTCCCAATC
Found at i:54778648 original size:34 final size:35
Alignment explanation
Indices: 54778604--54778670 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
54778594 TAGTAAAATA
*
54778604 TTTTCCGTAAAATGATTT-C-GAAAAAATATTTTAT
1 TTTTCCGTAAAATAATTTACTG-AAAAATATTTTAT
*
54778638 TTTTCTGTAAAATAATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTT
54778671 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 16 0.55
35 12 0.41
36 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGAAAAATATTTTAT
Found at i:54779060 original size:21 final size:21
Alignment explanation
Indices: 54779034--54779085 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
54779024 AAGGGTGAGA
*
54779034 CATTTTCCCTAAAATGTAACT
1 CATTTTCCCTAAAATGTAACC
54779055 CATTTTCCCTAAAATGTAACC
1 CATTTTCCCTAAAATGTAACC
54779076 CATTTTCCCT
1 CATTTTCCCT
54779086 TGTTTTGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.04, T:0.38
Consensus pattern (21 bp):
CATTTTCCCTAAAATGTAACC
Found at i:54791147 original size:18 final size:19
Alignment explanation
Indices: 54791114--54791151 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
54791104 AGACTCCAGG
*
54791114 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
54791133 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
54791151 T
1 T
54791152 GCTTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:54795891 original size:18 final size:19
Alignment explanation
Indices: 54795859--54795898 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
54795849 TTGTTGAAGA
*
54795859 GCTTGCAGCTTGTATGCAT
1 GCTTGCAGCTCGTATGCAT
*
54795878 GCTT-CAGCTCGTATGCTT
1 GCTTGCAGCTCGTATGCAT
54795896 GCT
1 GCT
54795899 GCAATAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.12, C:0.25, G:0.25, T:0.38
Consensus pattern (19 bp):
GCTTGCAGCTCGTATGCAT
Found at i:54806183 original size:12 final size:12
Alignment explanation
Indices: 54806166--54806190 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54806156 ACGTGAAAAA
54806166 ACCCCTCCAAAG
1 ACCCCTCCAAAG
54806178 ACCCCTCCAAAG
1 ACCCCTCCAAAG
54806190 A
1 A
54806191 GGATAAAAAA
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:0.36, C:0.48, G:0.08, T:0.08
Consensus pattern (12 bp):
ACCCCTCCAAAG
Found at i:54812782 original size:9 final size:9
Alignment explanation
Indices: 54812761--54812813 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
54812751 TTTACATCTT
*
54812761 TCTCTTAAC
1 TCTCTCAAC
*
54812770 TCTCTCAAT
1 TCTCTCAAC
54812779 TCTCTCAAAC
1 TCTCTC-AAC
* *
54812789 CCTCTCAAG
1 TCTCTCAAC
*
54812798 TCTCTCAAG
1 TCTCTCAAC
54812807 TCTCTCA
1 TCTCTCA
54812814 TTTTTAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
9 30 0.81
10 7 0.19
ACGTcount: A:0.23, C:0.38, G:0.04, T:0.36
Consensus pattern (9 bp):
TCTCTCAAC
Found at i:54830763 original size:21 final size:19
Alignment explanation
Indices: 54830713--54830768 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 19
54830703 AATCTTCAAG
54830713 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
54830732 GATATGCAATCTTAGATAT
1 GATATGTAATCTTAGATAT
54830751 GATATATGTAATCTTAGA
1 G--ATATGTAATCTTAGA
54830769 AGATATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.58
21 14 0.42
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (19 bp):
GATATGTAATCTTAGATAT
Found at i:54830790 original size:23 final size:24
Alignment explanation
Indices: 54830745--54830791 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
54830735 ATGCAATCTT
* *
54830745 AGATATGATATATGTAATCTTAGA
1 AGATATGATATATATAATATTAGA
*
54830769 AGATATGAT-TTTATAATATTAGA
1 AGATATGATATATATAATATTAGA
54830792 GATTTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.43, C:0.02, G:0.15, T:0.40
Consensus pattern (24 bp):
AGATATGATATATATAATATTAGA
Found at i:54836482 original size:25 final size:26
Alignment explanation
Indices: 54836433--54836499 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
54836423 ATAAAATACA
**
54836433 TCTTTGCATTCATTTTTGAGCTAA-TAT
1 TCTTT-CATTC-TTTTTGAAATAATTAT
*
54836460 TTTTTCATTCTTTTTGAAATAATTAT
1 TCTTTCATTCTTTTTGAAATAATTAT
54836486 TCTTTCATTCTTTT
1 TCTTTCATTCTTTT
54836500 GGATTTTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.29
26 21 0.60
27 4 0.11
ACGTcount: A:0.21, C:0.13, G:0.06, T:0.60
Consensus pattern (26 bp):
TCTTTCATTCTTTTTGAAATAATTAT
Found at i:54838848 original size:88 final size:88
Alignment explanation
Indices: 54838680--54838986 Score: 427
Period size: 88 Copynumber: 3.5 Consensus size: 88
54838670 ATCAGTGAAG
* * * **
54838680 ATAGCAAATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCTTTA
1 ATAGCAGATCTTGTCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTA
*
54838745 AGTTGCAGCGGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
* * * *
54838768 ATTA-CATATATTGTCTTCTTGCACCGACAGCGAAGCAGATCGAAGACACCAGCTTTGCCTCCCT
1 A-TAGCAGATCTTGTCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT
* *
54838832 GGGTTGTAGCGGAGCAGGTTAAAA
65 AGGTTGCAGCGGAGCAGGTTAAAA
** * *
54838856 ATAGCAGATCTTACCTTCCTGCACCAACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTA
1 ATAGCAGATCTTGTCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTA
* *
54838921 GGTTACAGCAGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
*
54838944 ATAGTAGATCTTGTCTTCCTGCACCGACAGCGAAGCAGATCGA
1 ATAGCAGATCTTGTCTTCCTGCACCGACAGCGAAGCAGATCGA
54838987 TGACCCCAAC
Statistics
Matches: 189, Mismatches: 28, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
87 2 0.01
88 185 0.98
89 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (88 bp):
ATAGCAGATCTTGTCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTA
GGTTGCAGCGGAGCAGGTTAAAA
Found at i:54839047 original size:44 final size:45
Alignment explanation
Indices: 54838997--54839118 Score: 137
Period size: 44 Copynumber: 2.8 Consensus size: 45
54838987 TGACCCCAAC
54838997 CCTATCTCCT-TGGACAGCAGTGGAATAGGTTGAAGATTGT-AAGT
1 CCTATCTCCTCTGGACAGCAGTGGAATAGGTTGAAGATTGTGAA-T
* * *
54839041 TCTATCT-CTCTGGTCAGTAGTGGAATAGGTTGAAGATTGTGAAT
1 CCTATCTCCTCTGGACAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
54839085 CCTATCTCC-CT-GAGCAACAATGGAGTAGGTTGAA
1 CCTATCTCCTCTGGA-CAGCAGTGGAATAGGTTGAA
54839119 AATAGCAGAT
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
43 3 0.05
44 59 0.91
45 3 0.05
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (45 bp):
CCTATCTCCTCTGGACAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:54839579 original size:44 final size:45
Alignment explanation
Indices: 54839482--54839820 Score: 138
Period size: 44 Copynumber: 7.8 Consensus size: 45
54839472 GAAGATTGAG
* * *
54839482 AATCTTATCT-CTCTGAAGTTGCAGTGGAGTAGATTAAAGCCAAT
1 AATCTTATCTCCTCTAAAGTTGCAGTGGAGCAGATTAAAACCAAT
* * *
54839526 AATCCTATCTCCT-TAAAGTTGCAGTGGAGCGGATTAAAATCACA-
1 AATCTTATCTCCTCTAAAGTTGCAGTGGAGCAGATTAAAACCA-AT
* * * * *** *
54839570 GATCTTATCT-CTCTGAAGTTACAG-AGAGCAGA-TCGCATC--T
1 AATCTTATCTCCTCTAAAGTTGCAGTGGAGCAGATTAAAACCAAT
* * * * *
54839610 AGTCTTATCTCC-CTGAAGTTCCAGTGGAGCAGACTAAGTAATC-A-
1 AATCTTATCTCCTCTAAAGTTGCAGTGGAGCAGATTAA--AACCAAT
* * * * *****
54839654 AGTCTTA--TCCTCCTAAAGTTGTAGT-GAGGCAGACTGAAGATGGCG
1 AATCTTATCTCCT-CTAAAGTTGCAGTGGA-GCAGA-TTAAAACCAAT
* * *
54839699 AATCTTATCTCC-CTGAAGTTGCAGTGGAGTAGATTAAAGCCAAT
1 AATCTTATCTCCTCTAAAGTTGCAGTGGAGCAGATTAAAACCAAT
* * * * *
54839743 AATCCTATTTCC-CTGAAGTTGCAGTGGAGCGGATTAAAA-CAACA
1 AATCTTATCTCCTCTAAAGTTGCAGTGGAGCAGATTAAAACCAA-T
* * *
54839787 AATCTTATCT-CTCTGAAGTTGCAGTAGAGTAGAT
1 AATCTTATCTCCTCTAAAGTTGCAGTGGAGCAGAT
54839821 CACATCGGGT
Statistics
Matches: 221, Mismatches: 53, Indels: 42
0.70 0.17 0.13
Matches are distributed among these distances:
40 19 0.09
41 8 0.04
42 8 0.04
43 16 0.07
44 139 0.63
45 26 0.12
46 2 0.01
47 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (45 bp):
AATCTTATCTCCTCTAAAGTTGCAGTGGAGCAGATTAAAACCAAT
Found at i:54839763 original size:89 final size:88
Alignment explanation
Indices: 54839612--54839820 Score: 192
Period size: 89 Copynumber: 2.4 Consensus size: 88
54839602 TCGCATCTAG
* * * * * *
54839612 TCTTATCTCCCTGAAGTTCCAGTGGAGCAGACTAAGTAATCAAGTCTTATCCTCCTAAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAGCAATCAAGTCCTATCCTCCTAAAGTTGCA
* *** *
54839677 GT-GAGGCAGACTGAAGATGGCGAA
66 GTGGA-GCAGA-TGAAAACAACAAA
* *
54839701 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAAT-AA-TCCTAT-TTCCCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT-AAG-CAATCAAGTCCTATCCT-CCTAAAGTT
* *
54839763 GCAGTGGAGCGGATTAAAACAACAAA
63 GCAGTGGAGCAGATGAAAACAACAAA
* *
54839789 TCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
54839821 CACATCGGGT
Statistics
Matches: 99, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
88 38 0.38
89 51 0.52
90 7 0.07
91 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAGCAATCAAGTCCTATCCTCCTAAAGTTGCA
GTGGAGCAGATGAAAACAACAAA
Found at i:54839793 original size:133 final size:129
Alignment explanation
Indices: 54839619--54839860 Score: 285
Period size: 133 Copynumber: 1.8 Consensus size: 129
54839609 TAGTCTTATC
* * * *
54839619 TCCCTGAAGTTCCAGTGGAGCAGACTAAGTAATCAAGTCTTATC-CTCCTAAAGTTGTAGT-GAG
1 TCCCTGAAGTTCCAGTGGAGCAGACTAAGAAAACAAATCTTATCTCT-CTAAAGTTGCAGTAGA-
*
54839682 GCAGACTGAAGAT-GGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAATAAT
64 GCAGA-T-AACATCGG-G--TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAATAAT
54839746 CCTATT
124 CCTATT
* * * *
54839752 TCCCTGAAGTTGCAGTGGAGCGGATTAA-AACAACAAATCTTATCTCTCTGAAGTTGCAGTAGAG
1 TCCCTGAAGTTCCAGTGGAGCAGACTAAGAA-AACAAATCTTATCTCTCTAAAGTTGCAGTAGAG
* *
54839816 TAGATCACATCGGGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGA
65 CAGATAACATCGGGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGA
54839861 CTCAAGAAAG
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
129 31 0.33
131 4 0.04
132 4 0.04
133 51 0.54
134 4 0.04
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (129 bp):
TCCCTGAAGTTCCAGTGGAGCAGACTAAGAAAACAAATCTTATCTCTCTAAAGTTGCAGTAGAGC
AGATAACATCGGGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAATAATCCTATT
Found at i:54840276 original size:21 final size:21
Alignment explanation
Indices: 54840251--54840307 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
54840241 ATCTTCAAGG
*
54840251 ATATGTAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
54840272 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
54840293 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
54840308 AGATATGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:54840329 original size:23 final size:24
Alignment explanation
Indices: 54840263--54840330 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 24
54840253 ATGTAATCTT
54840263 AGATATGATATATGCAATCTT---
1 AGATATGATATATGCAATCTTAGA
54840284 AGATATGATATATGCAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
* *
54840308 AGATATGAT-TTTGTAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
54840331 GATTTAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.50
23 12 0.29
24 9 0.21
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (24 bp):
AGATATGATATATGCAATCTTAGA
Found at i:54840558 original size:23 final size:23
Alignment explanation
Indices: 54840514--54840558 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
54840504 TTTTATTTTG
* *
54840514 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
54840537 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
54840559 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:54842451 original size:146 final size:146
Alignment explanation
Indices: 54842246--54842512 Score: 365
Period size: 146 Copynumber: 1.8 Consensus size: 146
54842236 ATTCAGGTAG
* * * *
54842246 ATTAATAATATGTATATCTATATATAGCTATGCTATTATAATGTATATTTTTACATTAATGAGAT
1 ATTAATAATATGTATATCTATATAAAACTATGATATTATAATGTATATTTTTACATTAATGAGAC
* ** * *
54842311 GTAAGCTGAAACCCTAAATTTATAACTAACTGTATGGTAGATTATAATATATACAACAAACATAT
66 GCAAAATGAAACCCTAAACTTATAACTAACTGTATAGTAGATTATAATATATACAACAAACATAT
54842376 ATAATTAAGATACATT
131 ATAATTAAGATACATT
* * *
54842392 ATTAATAATATGTA-ATCCTATATAAAATTATGATATTATAATGTATATTTTTATATTAATGATA
1 ATTAATAATATGTATAT-CTATATAAAACTATGATATTATAATGTATATTTTTACATTAATGAGA
* * * * *
54842456 CGCAAAATTAAACTCTAAACTTGTAATTAACTTTATAGTAGATTATAATATATACAA
65 CGCAAAATGAAACCCTAAACTTATAACTAACTGTATAGTAGATTATAATATATACAA
54842513 TTAGCATGGA
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
145 2 0.02
146 101 0.98
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (146 bp):
ATTAATAATATGTATATCTATATAAAACTATGATATTATAATGTATATTTTTACATTAATGAGAC
GCAAAATGAAACCCTAAACTTATAACTAACTGTATAGTAGATTATAATATATACAACAAACATAT
ATAATTAAGATACATT
Found at i:54843251 original size:66 final size:66
Alignment explanation
Indices: 54843122--54843254 Score: 169
Period size: 66 Copynumber: 2.0 Consensus size: 66
54843112 ATTCTGAAGC
* * *
54843122 TATAGCTAGAGTTAATCATATTTTCTTGTTGCCTCTGCTTCCCTCGCTGCTGCCTCTGCTTTAAG
1 TATAGCTAGAGTTAATCATATTTTCTTGTAGCCTCTGCTTCCCTCGATGCTGCCTCCGCTTTAAG
54843187 T
66 T
* * * * * *
54843188 TATAGCTGGAGTTCATCATATTTTCTT-TAAGCCTCTGCTTCTCTCGATGTTGCTTCCGTTTTAA
1 TATAGCTAGAGTTAATCATATTTTCTTGT-AGCCTCTGCTTCCCTCGATGCTGCCTCCGCTTTAA
54843252 GT
65 GT
54843254 T
1 T
54843255 GAGCAATTTG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 1 0.02
66 56 0.98
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.44
Consensus pattern (66 bp):
TATAGCTAGAGTTAATCATATTTTCTTGTAGCCTCTGCTTCCCTCGATGCTGCCTCCGCTTTAAG
T
Found at i:54844082 original size:11 final size:11
Alignment explanation
Indices: 54844066--54844110 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
54844056 TGGCTATTTA
54844066 TAATAAAATAT
1 TAATAAAATAT
54844077 TAATAAAATATCT
1 TAATAAAATA--T
*
54844090 TATTAAAATAT
1 TAATAAAATAT
*
54844101 TAATTAAATA
1 TAATAAAATA
54844111 ATATTTATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 19 0.66
13 10 0.34
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:54846725 original size:23 final size:24
Alignment explanation
Indices: 54846693--54846757 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 24
54846683 TATCAAATTT
54846693 TCATAATCAATCTCATTTTCT-CTC
1 TCAT-ATCAATCTCATTTTCTACTC
*
54846717 TCATATCAATTTCA-TTTCTACTC
1 TCATATCAATCTCATTTTCTACTC
* *
54846740 TCATTTCCATTCTCATTT
1 TCATAT-CAATCTCATTT
54846758 CCATTCTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
22 5 0.15
23 17 0.50
24 10 0.29
25 2 0.06
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (24 bp):
TCATATCAATCTCATTTTCTACTC
Found at i:54846745 original size:12 final size:12
Alignment explanation
Indices: 54846715--54846770 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
54846705 TCATTTTCTC
* *
54846715 TCTCATATCAAT
1 TCTCATTTCCAT
* *
54846727 T-TCATTTCTAC
1 TCTCATTTCCAT
54846738 TCTCATTTCCAT
1 TCTCATTTCCAT
54846750 TCTCATTTCCAT
1 TCTCATTTCCAT
54846762 TCTCATTTC
1 TCTCATTTC
54846771 AGTCTCAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
11 8 0.21
12 30 0.79
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (12 bp):
TCTCATTTCCAT
Found at i:54848852 original size:11 final size:11
Alignment explanation
Indices: 54848836--54848880 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
54848826 TAGCTATTTA
54848836 TAATAAAATAT
1 TAATAAAATAT
54848847 TAATAAAATATCT
1 TAATAAAATA--T
*
54848860 TATTAAAATAT
1 TAATAAAATAT
*
54848871 TAATTAAATA
1 TAATAAAATA
54848881 ATATTTATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 19 0.66
13 10 0.34
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:54849848 original size:43 final size:43
Alignment explanation
Indices: 54849800--54849885 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
54849790 TATGTGATTG
* *
54849800 ATATTGAAAT-GGAAATGGCGAGAAATGAAAATGAGATGAGAAA
1 ATATTGAAATAGCAAA-GACGAGAAATGAAAATGAGATGAGAAA
* **
54849843 ATATTGAAATAGCAAAGATGAGAAATGATTATGAGATGAGAAA
1 ATATTGAAATAGCAAAGACGAGAAATGAAAATGAGATGAGAAA
54849886 TGAAATATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
43 33 0.89
44 4 0.11
ACGTcount: A:0.51, C:0.02, G:0.26, T:0.21
Consensus pattern (43 bp):
ATATTGAAATAGCAAAGACGAGAAATGAAAATGAGATGAGAAA
Found at i:54855010 original size:34 final size:33
Alignment explanation
Indices: 54854927--54855011 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 33
54854917 AATACATAAA
* * *
54854927 AAGCATTATTTTTGCTACTGAGTTGATCTATCAT
1 AAGCA-TATTTTTGCTACTGAATCGAACTATCAT
* * *
54854961 AAGCATATTAATTGCTACTGAATCGAACTGTTAT
1 AAGCATATT-TTTGCTACTGAATCGAACTATCAT
54854995 AAGCATATTGTTTGCTA
1 AAGCATATT-TTTGCTA
54855012 TTGTATTATT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 4 0.10
34 38 0.90
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (33 bp):
AAGCATATTTTTGCTACTGAATCGAACTATCAT
Found at i:54861349 original size:20 final size:18
Alignment explanation
Indices: 54861296--54861353 Score: 53
Period size: 20 Copynumber: 3.0 Consensus size: 18
54861286 TATCTTTTTG
*
54861296 AATTTTTTTATTTTTATT
1 AATTTTTTTATTTTAATT
* *
54861314 TATTTTTTACAATTTTAATCT
1 AATTTTTT--TATTTTAAT-T
54861335 AATTTTTTTAGTTTTAATT
1 AATTTTTTTA-TTTTAATT
54861354 TTGTAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
18 7 0.23
19 2 0.06
20 14 0.45
21 8 0.26
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (18 bp):
AATTTTTTTATTTTAATT
Found at i:54864010 original size:40 final size:40
Alignment explanation
Indices: 54863962--54864042 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
54863952 ATTGGACTTA
54863962 TAGAAGACATAATAGTCCTAACTAGATTCATTTACTTAAT
1 TAGAAGACATAATAGTCCTAACTAGATTCATTTACTTAAT
54864002 TAGAAGACATAATAGTCCTAACTAGATTCATTTACTTAAT
1 TAGAAGACATAATAGTCCTAACTAGATTCATTTACTTAAT
54864042 T
1 T
54864043 TAACTCTACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.36
Consensus pattern (40 bp):
TAGAAGACATAATAGTCCTAACTAGATTCATTTACTTAAT
Found at i:54864837 original size:22 final size:23
Alignment explanation
Indices: 54864787--54864850 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 23
54864777 CTTTTTTATT
*
54864787 ACTTTAATATTTGAAGTTATTTC
1 ACTTTAATATTTGAAGTTTTTTC
*
54864810 ACTTTAATA-TTGAAGTTTTTTT
1 ACTTTAATATTTGAAGTTTTTTC
**
54864832 TTTTTAA-ATTTGAAGTTTT
1 ACTTTAATATTTGAAGTTTT
54864851 GCCACACAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.03
22 26 0.72
23 9 0.25
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (23 bp):
ACTTTAATATTTGAAGTTTTTTC
Found at i:54866296 original size:21 final size:22
Alignment explanation
Indices: 54866272--54866321 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
54866262 ATTTGCTTAT
54866272 TTGAATCGATTATGT-TGTTGA
1 TTGAATCGATTATGTATGTTGA
* * * *
54866293 TTGACTCGATTCTTTATGTTGT
1 TTGAATCGATTATGTATGTTGA
54866315 TTGAATC
1 TTGAATC
54866322 AATTCTTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (22 bp):
TTGAATCGATTATGTATGTTGA
Found at i:54866318 original size:22 final size:22
Alignment explanation
Indices: 54866287--54866331 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
54866277 TCGATTATGT
* *
54866287 TGTTGATTGACTCGATTCTTTA
1 TGTTGATTGAATCAATTCTTTA
*
54866309 TGTTGTTTGAATCAATTCTTTA
1 TGTTGATTGAATCAATTCTTTA
54866331 T
1 T
54866332 TGTAAAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.11, G:0.16, T:0.53
Consensus pattern (22 bp):
TGTTGATTGAATCAATTCTTTA
Found at i:54867949 original size:18 final size:19
Alignment explanation
Indices: 54867917--54867952 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
54867907 TACAAAATAA
54867917 AAAATATATAAGTATATAT
1 AAAATATATAAGTATATAT
54867936 AAAATATA-AAGTATATA
1 AAAATATATAAGTATATA
54867953 AAAGTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (19 bp):
AAAATATATAAGTATATAT
Found at i:54870161 original size:89 final size:91
Alignment explanation
Indices: 54869994--54870168 Score: 282
Period size: 89 Copynumber: 1.9 Consensus size: 91
54869984 CCTGATGTCC
*
54869994 TTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTCTTCCTTTGATCTGCTTCGCCACC
1 TTGATCTACTTCACACCAGTACATGAAGACAAGATCT-CTACTTCCTTTGATCTGCTTCGCCACC
*
54870059 AGTATGGGAAGGCAATATCTGTTACCT
65 AGTATGGGAAGGCAAGATCTGTTACCT
** *
54870086 TTGATCTACTTCATGCCAGTACATGAAGACAAGAT-T-TACTTTCTTTGATCTGCTTCGCCACCA
1 TTGATCTACTTCACACCAGTACATGAAGACAAGATCTCTACTTCCTTTGATCTGCTTCGCCACCA
54870149 GTATGGGAAGGCAAGATCTG
66 GTATGGGAAGGCAAGATCTG
54870169 CTGCTTTTCA
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
89 44 0.56
91 1 0.01
92 33 0.42
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (91 bp):
TTGATCTACTTCACACCAGTACATGAAGACAAGATCTCTACTTCCTTTGATCTGCTTCGCCACCA
GTATGGGAAGGCAAGATCTGTTACCT
Found at i:54870164 original size:45 final size:45
Alignment explanation
Indices: 54870034--54870167 Score: 130
Period size: 45 Copynumber: 3.0 Consensus size: 45
54870024 AAGATCTGCT
*
54870034 TCTT-CCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAATATC
1 TCTTACCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATC
* * *** *** * *
54870078 TGTTACCTTTGATCTACTTC-ATGCCAGTACATGAAGACAAGATT
1 TCTTACCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATC
*
54870122 TACTT-TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATC
1 T-CTTACCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATC
54870167 T
1 T
54870168 GCTGCTTTTC
Statistics
Matches: 65, Mismatches: 22, Indels: 5
0.71 0.24 0.05
Matches are distributed among these distances:
44 32 0.49
45 33 0.51
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (45 bp):
TCTTACCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATC
Found at i:54881060 original size:18 final size:19
Alignment explanation
Indices: 54881028--54881063 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
54881018 TACAAAATAA
54881028 AAAATATATAAGTATATAT
1 AAAATATATAAGTATATAT
54881047 AAAATATA-AAGTATATA
1 AAAATATATAAGTATATA
54881064 AAAGTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (19 bp):
AAAATATATAAGTATATAT
Found at i:54885488 original size:32 final size:32
Alignment explanation
Indices: 54885447--54885511 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
54885437 GCTTAGTCAC
54885447 TAGTTTTGGCCCTTTGGAGCTATCCATCTTTG
1 TAGTTTTGGCCCTTTGGAGCTATCCATCTTTG
54885479 TAGTTTTGGCCCTTTGGAGCTATCCATCTTTG
1 TAGTTTTGGCCCTTTGGAGCTATCCATCTTTG
54885511 T
1 T
54885512 TGCAAAATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (32 bp):
TAGTTTTGGCCCTTTGGAGCTATCCATCTTTG
Found at i:54891003 original size:32 final size:30
Alignment explanation
Indices: 54890961--54891051 Score: 73
Period size: 32 Copynumber: 3.0 Consensus size: 30
54890951 ATCTTATTTA
54890961 ATTCTTTTAATAATATAAGAATTAATTAATT
1 ATTC-TTTAATAATATAAGAATTAATTAATT
* * * *
54890992 ATTTCATTTAATTTATTTAA-TATT-ATT--TG
1 A-TTC-TTTAA-TAATATAAGAATTAATTAATT
54891021 ATTCTTTCAATAATATAAGAATTAATTAATT
1 ATTCTTT-AATAATATAAGAATTAATTAATT
54891052 CATATAATAG
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
27 9 0.20
28 8 0.18
29 5 0.11
31 5 0.11
32 11 0.25
33 6 0.14
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (30 bp):
ATTCTTTAATAATATAAGAATTAATTAATT
Found at i:54891676 original size:24 final size:26
Alignment explanation
Indices: 54891618--54891677 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 26
54891608 TTAAACATAC
54891618 ATATTTAATTATTTATATTTAATAAA
1 ATATTTAATTATTTATATTTAATAAA
**
54891644 ATAAATAATTA-TTA-ATTTAATAAA
1 ATATTTAATTATTTATATTTAATAAA
*
54891668 TTATTTAATT
1 ATATTTAATT
54891678 TAATATCTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 17 0.59
25 3 0.10
26 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATATTTAATTATTTATATTTAATAAA
Found at i:54891690 original size:17 final size:17
Alignment explanation
Indices: 54891650--54891682 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54891640 TAAAATAAAT
54891650 AATTA-TTAATTTAATA
1 AATTATTTAATTTAATA
54891666 AATTATTTAATTTAATA
1 AATTATTTAATTTAATA
54891683 TCTTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTATTTAATTTAATA
Found at i:54892050 original size:14 final size:14
Alignment explanation
Indices: 54892031--54892063 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54892021 ATTTTAATTA
54892031 AAAATAACTTTT-AG
1 AAAATAA-TTTTAAG
54892045 AAAATAATTTTAAG
1 AAAATAATTTTAAG
54892059 AAAAT
1 AAAAT
54892064 TTGTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (14 bp):
AAAATAATTTTAAG
Found at i:54893040 original size:3 final size:3
Alignment explanation
Indices: 54893032--54893056 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54893022 TAATTTTTGT
54893032 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
54893057 TATTACTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:54895963 original size:16 final size:17
Alignment explanation
Indices: 54895942--54895975 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
54895932 TTCTATCATG
54895942 TAAGAATCATT-TTGAT
1 TAAGAATCATTATTGAT
54895958 TAAGAATCATTATTGAT
1 TAAGAATCATTATTGAT
54895975 T
1 T
54895976 TGTCCTGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (17 bp):
TAAGAATCATTATTGAT
Found at i:54899597 original size:21 final size:21
Alignment explanation
Indices: 54899573--54899628 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
54899563 AACAGCGGTG
* *
54899573 GCGGTAAGATTAGTTACAGTA
1 GCGGTGAGATTAGATACAGTA
*
54899594 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACAGTA
*
54899615 GTGGTGAGATTAGA
1 GCGGTGAGATTAGA
54899629 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.07, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACAGTA
Found at i:54899639 original size:21 final size:21
Alignment explanation
Indices: 54899596--54899639 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
54899586 TTACAGTAGC
* **
54899596 GGTGAGATTAGATACTGTAGT
1 GGTGAGATTAGAAACAATAGT
*
54899617 GGTGAGATTAGAAACAATGGT
1 GGTGAGATTAGAAACAATAGT
54899638 GG
1 GG
54899640 AGTTTGTGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.36, T:0.27
Consensus pattern (21 bp):
GGTGAGATTAGAAACAATAGT
Found at i:54905389 original size:12 final size:12
Alignment explanation
Indices: 54905358--54905400 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
54905348 ATGATTAAAA
* *
54905358 ACTTGATGGAAA
1 ACTTGATTGAAG
54905370 ACTTGATTGAAG
1 ACTTGATTGAAG
* *
54905382 ACTTGATTTATG
1 ACTTGATTGAAG
54905394 ACTTGAT
1 ACTTGAT
54905401 GAATAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (12 bp):
ACTTGATTGAAG
Found at i:54906786 original size:6 final size:6
Alignment explanation
Indices: 54906775--54906804 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
54906765 GAATAGAAGG
54906775 AATAAA AATAAA AATAAA AAT-AA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA AATAAA A
54906805 TGTGTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:54906792 original size:12 final size:11
Alignment explanation
Indices: 54906775--54906804 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
54906765 GAATAGAAGG
54906775 AATAAAAATAAA
1 AATAAAAAT-AA
54906787 AATAAAAATAA
1 AATAAAAATAA
54906798 AATAAAA
1 AATAAAA
54906805 TGTGTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:54919022 original size:12 final size:12
Alignment explanation
Indices: 54919005--54919029 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54918995 GGTGTGCATT
54919005 CGGTTAACCGAC
1 CGGTTAACCGAC
54919017 CGGTTAACCGAC
1 CGGTTAACCGAC
54919029 C
1 C
54919030 CGAATTAGTT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:54919191 original size:9 final size:9
Alignment explanation
Indices: 54919177--54919260 Score: 98
Period size: 9 Copynumber: 9.4 Consensus size: 9
54919167 TGGTTAAAAA
54919177 TTAACCGAT
1 TTAACCGAT
*
54919186 TTAACCTAT
1 TTAACCGAT
54919195 TTAACCGA-
1 TTAACCGAT
*
54919203 TTAACCGAC
1 TTAACCGAT
54919212 TTAACCGAT
1 TTAACCGAT
*
54919221 TTAACCGAC
1 TTAACCGAT
*
54919230 TTAACTGAT
1 TTAACCGAT
* *
54919239 TTAACCAAC
1 TTAACCGAT
*
54919248 TTAATCGAT
1 TTAACCGAT
54919257 TTAA
1 TTAA
54919261 ATCACTATAT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
8 8 0.13
9 54 0.87
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (9 bp):
TTAACCGAT
Found at i:54919200 original size:18 final size:18
Alignment explanation
Indices: 54919177--54919260 Score: 116
Period size: 18 Copynumber: 4.7 Consensus size: 18
54919167 TGGTTAAAAA
* *
54919177 TTAACCGATTTAACCTAT
1 TTAACCGATTTAACCGAC
54919195 TTAACCGA-TTAACCGAC
1 TTAACCGATTTAACCGAC
54919212 TTAACCGATTTAACCGAC
1 TTAACCGATTTAACCGAC
* *
54919230 TTAACTGATTTAACCAAC
1 TTAACCGATTTAACCGAC
*
54919248 TTAATCGATTTAA
1 TTAACCGATTTAA
54919261 ATCACTATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
17 15 0.25
18 44 0.75
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (18 bp):
TTAACCGATTTAACCGAC
Found at i:54919205 original size:26 final size:26
Alignment explanation
Indices: 54919176--54919244 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
54919166 TTGGTTAAAA
*
54919176 ATTAACCGATTTAACCTATTTAACCG
1 ATTAACCGATTTAACCGATTTAACCG
*
54919202 ATTAACCGACTTAACCGATTTAACCG
1 ATTAACCGATTTAACCGATTTAACCG
*
54919228 ACTTAACTGATTTAACC
1 A-TTAACCGATTTAACC
54919245 AACTTAATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
26 25 0.66
27 13 0.34
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.32
Consensus pattern (26 bp):
ATTAACCGATTTAACCGATTTAACCG
Found at i:54919383 original size:37 final size:37
Alignment explanation
Indices: 54919260--54919369 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 37
54919250 AATCGATTTA
*
54919260 AATCACTATATAATTTAAAAA-ATTACATAAGTCTTTG
1 AATCACTAAATAA-TTAAAAACATTACATAAGTCTTTG
* * * *
54919297 AATCACTACATAACTAAAAACATTACATAAATTTTTG
1 AATCACTAAATAATTAAAAACATTACATAAGTCTTTG
54919334 AATCACTAAATAATTAAAAACATTACATAAGTCTTT
1 AATCACTAAATAATTAAAAACATTACATAAGTCTTT
54919370 AACACATAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 6 0.09
37 58 0.91
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.35
Consensus pattern (37 bp):
AATCACTAAATAATTAAAAACATTACATAAGTCTTTG
Found at i:54919598 original size:7 final size:7
Alignment explanation
Indices: 54919586--54919651 Score: 87
Period size: 7 Copynumber: 9.3 Consensus size: 7
54919576 GTACAGAAGA
54919586 AAACATG
1 AAACATG
54919593 AAACATG
1 AAACATG
* **
54919600 CAGTATG
1 AAACATG
54919607 AAACATG
1 AAACATG
*
54919614 AAATCGTG
1 AAA-CATG
54919622 AAACATG
1 AAACATG
54919629 AAACATG
1 AAACATG
54919636 AAACATG
1 AAACATG
54919643 AAACATG
1 AAACATG
54919650 AA
1 AA
54919652 TTGTTCTTGG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
7 44 0.88
8 6 0.12
ACGTcount: A:0.53, C:0.14, G:0.17, T:0.17
Consensus pattern (7 bp):
AAACATG
Found at i:54919672 original size:13 final size:13
Alignment explanation
Indices: 54919654--54919680 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54919644 AACATGAATT
54919654 GTTCTTGGGCTTA
1 GTTCTTGGGCTTA
54919667 GTTCTTGGGCTTA
1 GTTCTTGGGCTTA
54919680 G
1 G
54919681 AGCCTGGAGG
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:0.07, C:0.15, G:0.33, T:0.44
Consensus pattern (13 bp):
GTTCTTGGGCTTA
Found at i:54919904 original size:18 final size:19
Alignment explanation
Indices: 54919869--54919920 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
54919859 AACCGACCGA
**
54919869 TTAACCGAATTCGGTCGG-
1 TTAACCGAATTTTGTCGGT
*
54919887 TTAACCGAATTTTTTCGGTT
1 TTAACCGAATTTTGTCGG-T
54919907 TTAACCGAATTTTG
1 TTAACCGAATTTTG
54919921 CACACTCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 15 0.54
20 13 0.46
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (19 bp):
TTAACCGAATTTTGTCGGT
Found at i:54923622 original size:62 final size:62
Alignment explanation
Indices: 54923522--54923697 Score: 272
Period size: 62 Copynumber: 2.9 Consensus size: 62
54923512 CTCTTTTTTG
*
54923522 CATTCATGCATCAACATTACATTGCA-TGC----AATAAATTTCCTAAAATCCAAAAATACA
1 CATTCATGCATCAACATTACATTTCATTGCATATAATAAATTTCCTAAAATCCAAAAATACA
* *
54923579 CATTCATGCATCAACATTACATTTCATTGCATATAATAAATTTCCTAAAATTCAAAAATACG
1 CATTCATGCATCAACATTACATTTCATTGCATATAATAAATTTCCTAAAATCCAAAAATACA
**
54923641 CATTCATGCATCAACATTACATTTCATTTTATATAATAAATTTCCTAAAATCCAAAA
1 CATTCATGCATCAACATTACATTTCATTGCATATAATAAATTTCCTAAAATCCAAAA
54923698 GTACGTCGAG
Statistics
Matches: 108, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
57 25 0.23
58 3 0.03
62 80 0.74
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (62 bp):
CATTCATGCATCAACATTACATTTCATTGCATATAATAAATTTCCTAAAATCCAAAAATACA
Found at i:54925010 original size:24 final size:23
Alignment explanation
Indices: 54924983--54925056 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
54924973 AGTAGAGGCA
54924983 AAAAAAAAGAGCAAAAATAAAAAG
1 AAAAAAAA-AGCAAAAATAAAAAG
54925007 -AAAAAAAA-CTAGAAAATAAAAAG
1 AAAAAAAAAGC-A-AAAATAAAAAG
* *
54925030 CAAAAAAAAACCAAAAA-GAAAAG
1 -AAAAAAAAAGCAAAAATAAAAAG
54925053 AAAA
1 AAAA
54925057 GACCTCTACT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
21 1 0.02
22 6 0.14
23 23 0.52
24 4 0.09
25 9 0.20
26 1 0.02
ACGTcount: A:0.80, C:0.07, G:0.09, T:0.04
Consensus pattern (23 bp):
AAAAAAAAAGCAAAAATAAAAAG
Found at i:54925056 original size:11 final size:10
Alignment explanation
Indices: 54924996--54925056 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 10
54924986 AAAAAGAGCA
54924996 AAAATAAAAAG
1 AAAA-AAAAAG
54925007 AAAAAAAACTAG
1 AAAAAAAA--AG
54925019 AAAATAAAAAG
1 AAAA-AAAAAG
*
54925030 CAAAAAAAAACC
1 -AAAAAAAAA-G
54925042 AAAAAGAAAAG
1 AAAAA-AAAAG
54925053 AAAA
1 AAAA
54925057 GACCTCTACT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
10 4 0.10
11 20 0.48
12 14 0.33
13 4 0.10
ACGTcount: A:0.80, C:0.07, G:0.08, T:0.05
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:54926596 original size:44 final size:44
Alignment explanation
Indices: 54926533--54926985 Score: 274
Period size: 44 Copynumber: 10.3 Consensus size: 44
54926523 GAAGTCATAA
* * * * *
54926533 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCA
1 AAGATAGCAGATCCTGTCTTCATATATTGGAGTGAAGTAGATCG
* * * * * *
54926577 AAAATAGTAGGTCCTGTCTTCCTATACTGGTAG-GAAGTGGATCG
1 AAGATAGCAGATCCTGTCTTCATATATTGG-AGTGAAGTAGATCG
* * * * *
54926621 AAGAT-GCAGATCTTGTCTTTC-CATACTGGTAGCGAAGTAGATCA
1 AAGATAGCAGATCCTGTC-TTCATATATTGG-AGTGAAGTAGATCG
* * * * * *
54926665 AAGAAAGAAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCG
1 AAGATAGCAGATCCTGTCTTCATATATTGGAGTGAAGTAGATCG
* * * * * * *
54926709 AAGATGGCTGGTCCTGTCTTCTTATATTGATAG-GAAGTGGATCC
1 AAGATAGCAGATCCTGTCTTCATATATTG-GAGTGAAGTAGATCG
* *
54926753 AAGAT-GCAGATCTTGTCTTCATGTATT-GACGTGAAGTAGATCG
1 AAGATAGCAGATCCTGTCTTCATATATTGGA-GTGAAGTAGATCG
* * * * * *
54926796 AAGATAACAGGTCCTGTCTCCCTATATTGGTAG-GGAGTGGATCG
1 AAGATAGCAGATCCTGTCTTCATATATTGG-AGTGAAGTAGATCG
* * * * * * *
54926840 AAGAAAGCAAAACTTGTCTTCTTGTATTGGCGTGAAGTAGATCG
1 AAGATAGCAGATCCTGTCTTCATATATTGGAGTGAAGTAGATCG
* * *
54926884 AAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTAGATTG
1 AAGATAGCAGATCCTGTCTTCATATATTGG-AGTGAAGTAGATCG
* * * * * * *
54926928 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCG
1 AAGATAGCAGATCCTGTCTTCATATA-TTGG-AGTGAAGTAGATCG
*
54926974 AAGATGGCAGAT
1 AAGATAGCAGAT
54926986 TTTACCTCCC
Statistics
Matches: 308, Mismatches: 86, Indels: 28
0.73 0.20 0.07
Matches are distributed among these distances:
41 1 0.00
42 1 0.00
43 51 0.17
44 208 0.68
45 26 0.08
46 21 0.07
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (44 bp):
AAGATAGCAGATCCTGTCTTCATATATTGGAGTGAAGTAGATCG
Found at i:54926694 original size:132 final size:132
Alignment explanation
Indices: 54926532--54926771 Score: 383
Period size: 132 Copynumber: 1.8 Consensus size: 132
54926522 TGAAGTCATA
* *
54926532 AAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAAATAG-TAGGTCCTGTCT
1 AAAGAAAGAAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAAAATAGCT-GGTCCTGTCT
* *
54926596 TCCTATACTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTTCCATACTGGTAGCGAAGTAG
65 TCCTATACTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTTCCATACTGGTAGCGAAGTAG
54926661 ATC
130 ATC
* * *
54926664 AAAGAAAGAAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGATGGCTGGTCCTGTCTT
1 AAAGAAAGAAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAAAATAGCTGGTCCTGTCTT
* *
54926729 CTTATATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTT
66 CCTATACTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTT
54926772 CATGTATTGA
Statistics
Matches: 98, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
132 97 0.99
133 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (132 bp):
AAAGAAAGAAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAAAATAGCTGGTCCTGTCTT
CCTATACTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTTCCATACTGGTAGCGAAGTAGA
TC
Found at i:54926702 original size:88 final size:88
Alignment explanation
Indices: 54926610--54926983 Score: 396
Period size: 88 Copynumber: 4.2 Consensus size: 88
54926600 ATACTGGTAG
* * * *
54926610 GAAGTGGATCGAAGAT-GCAGATCTTGTCTTTCC-ATACTGGTAGCGAAGTAGATCAAAGAAAGA
1 GAAGTAGATCGAAGATAGCAGGTCCTGTC-TTCCTATATTGGTAG-GAAGTAGATCAAAGAAAGA
*
54926673 AGATCTTATCTTCATGTATTGGCGT
64 AGATCTTGTCTTCATGTATTGGCGT
* * * * * * * *
54926698 GAAGTAGATCGAAGATGGCTGGTCCTGTCTTCTTATATTGATAGGAAGTGGATCCAAG-ATGCAG
1 GAAGTAGATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTAGATCAAAGAAAGAAG
*
54926762 ATCTTGTCTTCATGTATTGACGT
66 ATCTTGTCTTCATGTATTGGCGT
* * * * *
54926785 GAAGTAGATCGAAGATAACAGGTCCTGTCTCCCTATATTGGTAGGGAGTGGATCGAAGAAAGCAA
1 GAAGTAGATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTAGATCAAAGAAAG-AA
* *
54926850 -AACTTGTCTTCTTGTATTGGCGT
65 GATCTTGTCTTCATGTATTGGCGT
** ** *
54926873 GAAGTAGATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTAGATTGAAGATTGCAG
1 GAAGTAGATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTAGATCAAAGAAAGAAG
* * *
54926938 ATCTTGCCTTCCTGTATTTGGCAGC
66 ATCTTGTCTTCATGTA-TTGGC-GT
* *
54926963 GAAGCAGATCGAAGATGGCAG
1 GAAGTAGATCGAAGATAGCAG
54926984 ATTTTACCTC
Statistics
Matches: 239, Mismatches: 40, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
87 76 0.32
88 120 0.50
89 23 0.10
90 20 0.08
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (88 bp):
GAAGTAGATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTAGATCAAAGAAAGAAG
ATCTTGTCTTCATGTATTGGCGT
Found at i:54927089 original size:134 final size:134
Alignment explanation
Indices: 54926916--54927296 Score: 618
Period size: 134 Copynumber: 2.8 Consensus size: 134
54926906 TATATTGGTA
*
54926916 GGAAGTAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGG
1 GGAA-TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGAGAAGCAGATCGAAGATGG
54926981 CAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCCGTATTTG
65 CAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCCGTATTTG
54927046 GCAGT
130 GCAGT
* * * *
54927051 GGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGTAAAGAAGCAGATTGATGATGGC
1 GGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGAGAAGCAGATCGAAGATGGC
* *
54927116 AGATTTTACCTCTCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGG
66 AGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCCGTATTTGG
54927181 CAGT
131 CAGT
* * *
54927185 GGAATAGATTGAAGATTACAGATCTTGCCTTCCTGTATTTGGCAGAGAAGCAGATCGAATATGAC
1 GGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGAGAAGCAGATCGAAGATGGC
* * *
54927250 GGATTTTACCTCCCTGAGATTACAGTGGAGTACATTGAAGCCAATAA
66 AGATTTTACCTCCCT--GACTACAGTGGAGTACATTGAAGCCGATAA
54927297 TCTTACTTTC
Statistics
Matches: 226, Mismatches: 18, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
134 194 0.86
135 4 0.02
136 28 0.12
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (134 bp):
GGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGAGAAGCAGATCGAAGATGGC
AGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCCGTATTTGG
CAGT
Found at i:54927319 original size:134 final size:131
Alignment explanation
Indices: 54926916--54927343 Score: 540
Period size: 134 Copynumber: 3.2 Consensus size: 131
54926906 TATATTGGTA
* * *
54926916 GGAAGTAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGG
1 GGAA-TAGATTGAAGATTACAGATCTTGCCTTCCTGTATTTGGCAGAGAAGCAGATCGAATATGG
* *
54926981 CAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCCGTATTTG
65 CAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT-TTCCTGTA--TG
54927046 GCAGT
127 GCAGT
* * * *
54927051 GGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGTAAAGAAGCAGATTG-ATGATGG
1 GGAATAGATTGAAGATTACAGATCTTGCCTTCCTGTATTTGGCAGAGAAGCAGATCGAAT-ATGG
* *
54927115 CAGATTTTACCTCTCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTG
65 CAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT-TTCCTGTA--TG
54927180 GCAGT
127 GCAGT
*
54927185 GGAATAGATTGAAGATTACAGATCTTGCCTTCCTGTATTTGGCAGAGAAGCAGATCGAATATGAC
1 GGAATAGATTGAAGATTACAGATCTTGCCTTCCTGTATTTGGCAGAGAAGCAGATCGAATATGGC
* * * *
54927250 GGATTTTACCTCCCTGAGATTACAGTGGAGTACATTGAAGCCAATAA-TCTTACTTTCCTGGGA-
66 AGATTTTACCTCCCT--GACTACAGTGGAGTACATTGAAGCCGATAACTC-TA-TTTCCT-GTAT
**
54927313 AACAGT
126 GGCAGT
*
54927319 GGAATAGATCGAAGATTACAG-TCTT
1 GGAATAGATTGAAGATTACAGATCTT
54927344 ATCTCCCTAA
Statistics
Matches: 265, Mismatches: 21, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
133 5 0.02
134 215 0.81
135 8 0.03
136 34 0.13
137 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (131 bp):
GGAATAGATTGAAGATTACAGATCTTGCCTTCCTGTATTTGGCAGAGAAGCAGATCGAATATGGC
AGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATTTCCTGTATGGCAG
T
Found at i:54927436 original size:82 final size:82
Alignment explanation
Indices: 54927336--54927835 Score: 768
Period size: 82 Copynumber: 6.1 Consensus size: 82
54927326 ATCGAAGATT
*
54927336 ACAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCCAGTCTTATCTCCCTAAGCAGTA
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
*
54927400 GTGGAGCAGACAAAACC
66 GCGGAGCAGACAAAACC
* * * *
54927417 ATAGATCTTATCTCTCTAAGCAGTAGTGGAGTAGATCGCATTAAGTCTTATCTCCCTAAGCAGTA
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
*
54927482 GCGGAGCGGACAAAACC
66 GCGGAGCAGACAAAACC
* *
54927499 ACAGATCTTATCTCCCTAAGTAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
*
54927564 GTGGAGCAGACAAAACC
66 GCGGAGCAGACAAAACC
* *
54927581 ACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAACAGTA
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
* *
54927646 GCGGAGCGGACGAAACC
66 GCGGAGCAGACAAAACC
54927663 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
*
54927728 GCGGAGCAGACGAAACC
66 GCGGAGCAGACAAAACC
* * * * **
54927745 ACAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCACATCCAGTCTTATCTCCCTAAATAGTA
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
* *
54927810 GTGGAGCAGACTAAAAAC
66 GCGGAGCAGAC-AAAACC
*
54927828 ACAAATCT
1 ACAGATCT
54927836 CATCCCCATG
Statistics
Matches: 384, Mismatches: 33, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
81 3 0.01
82 370 0.96
83 11 0.03
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (82 bp):
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTA
GCGGAGCAGACAAAACC
Found at i:54929229 original size:20 final size:21
Alignment explanation
Indices: 54929182--54929229 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
54929172 CCCTTATTTG
*
54929182 TTATT-TTAGTTATTTTATCA
1 TTATTATTAGTTATTTAATCA
*
54929202 TTA-AATTAGTTATTTAAT-A
1 TTATTATTAGTTATTTAATCA
54929221 TTATTATTA
1 TTATTATTA
54929230 CTATTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (21 bp):
TTATTATTAGTTATTTAATCA
Found at i:54934079 original size:108 final size:108
Alignment explanation
Indices: 54933895--54934184 Score: 503
Period size: 108 Copynumber: 2.7 Consensus size: 108
54933885 ATATTTGGCA
* * * * * * *
54933895 ATTTGGTTAAACGAG-AAATCGAAACCTAGCACCTTAGGGCACG-TTCCTCAAATTTCCAAACGC
1 ATTTGGTTAAACGAGAAAAACGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAATGC
54933958 AAAACATTGCCTCATTGTAAAATTTTTAAAAGGATATTAAGCC
66 AAAACATTGCCTCATTGTAAAATTTTTAAAAGGATATTAAGCC
54934001 ATTTGGTTAAACGAGAAAAACGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAATGC
1 ATTTGGTTAAACGAGAAAAACGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAATGC
54934066 AAAACATTGCCTCATTGTAAAATTTTTAAAAGGATATTAAGCC
66 AAAACATTGCCTCATTGTAAAATTTTTAAAAGGATATTAAGCC
54934109 ATTTGGTTAAACGAGAAAAACGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAATGC
1 ATTTGGTTAAACGAGAAAAACGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAATGC
54934174 AAAACATTGCC
66 AAAACATTGCC
54934185 CTTTTTGAAA
Statistics
Matches: 175, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
106 15 0.09
107 24 0.14
108 136 0.78
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (108 bp):
ATTTGGTTAAACGAGAAAAACGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAATGC
AAAACATTGCCTCATTGTAAAATTTTTAAAAGGATATTAAGCC
Found at i:54934673 original size:27 final size:28
Alignment explanation
Indices: 54934642--54934696 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
54934632 TAAGGAAAAT
* *
54934642 ATATATAG-ATCT-AAATGTATATATAA
1 ATATATAGAATATAAAATATATATATAA
54934668 AT-TATAGAATATAAAATATATATATAA
1 ATATATAGAATATAAAATATATATATAA
54934695 AT
1 AT
54934697 GGGTACATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 5 0.20
27 15 0.60
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (28 bp):
ATATATAGAATATAAAATATATATATAA
Found at i:54936608 original size:49 final size:49
Alignment explanation
Indices: 54936555--54936903 Score: 349
Period size: 49 Copynumber: 7.1 Consensus size: 49
54936545 TTATGGCCTA
* *** * * * *
54936555 AATCTTTTAATTGCAATGTCGGGGAAGCGTGATTCGCCGATGTAGCCTC
1 AATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
** * * *
54936604 AATCTGTTCCATTGCATTGCCTGGGAAGTAAGATCCGCTGTTGTAGCTTC
1 AATCT-TTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
*
54936654 AATCTTTTAATTGTAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
1 AATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
* *
54936703 AATCTTTTGATTGCAATGTCAGGGAAGTAAGATCCTCTGTTGTAGCTTC
1 AATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
* *
54936752 AATCTTTTAATTGCAATATCATGGAAGTAAGATCCGCTGTTGTAGCTTC
1 AATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
** * * *** * ** * * *
54936801 AATCTGTTCCACTGCAAAG-CCTCGAAATAAGATTTGCCGTTGTGGCCTC
1 AATCT-TTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
* * ** *
54936850 AATCTTTTGATTGCAATGTCAGGGAAGTGAGATTTGCCGTTGTAGCTTC
1 AATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
54936899 AATCT
1 AATCT
54936904 GTTCCGCTGC
Statistics
Matches: 248, Mismatches: 49, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
48 9 0.04
49 194 0.78
50 45 0.18
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (49 bp):
AATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
Found at i:54936756 original size:98 final size:98
Alignment explanation
Indices: 54936555--54936908 Score: 388
Period size: 98 Copynumber: 3.6 Consensus size: 98
54936545 TTATGGCCTA
* *** * * *
54936555 AATCTTTTAATTGCAATGTCGGGGAAGCGTGATTCGCCGATGTAGCCTCAATCTGTTCCATTGCA
1 AATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTGTTCCATTGCA
* * *
54936620 TTGCCTGGGAAGTAAGATCCGCTGTTGTAGCTTC
66 ATG-CAGGGAAGTAAGATCCTCTGTTGTAGCTTC
* * **
54936654 AATCTTTTAATTGTAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT-TTTGATTGCA
1 AATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTGTTCCATTGCA
54936718 ATGTCAGGGAAGTAAGATCCTCTGTTGTAGCTTC
66 ATG-CAGGGAAGTAAGATCCTCTGTTGTAGCTTC
* * * *
54936752 AATCTTTTAATTGCAATATCATGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCA
1 AATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTGTTCCATTGCA
* *** * * * * *
54936817 AAGCCTCGAAATAAGAT-TTGCCGTTGTGGCCTC
66 ATGCAGGGAAGTAAGATCCT-CTGTTGTAGCTTC
* * **
54936850 AATCTTTTGATTGCAATGTCAGGGAAGTGAGATTTGCCGTTGTAGCTTCAATCTGTTCC
1 AATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTGTTCC
54936909 GCTGCACCGC
Statistics
Matches: 216, Mismatches: 37, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
97 1 0.00
98 161 0.75
99 54 0.25
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (98 bp):
AATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCCGTTGTAGCTTCAATCTGTTCCATTGCA
ATGCAGGGAAGTAAGATCCTCTGTTGTAGCTTC
Done.