Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 166 of 216
Found at i:52371911 original size:16 final size:15
Alignment explanation
Indices: 52371871--52371924 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
52371861 TCGTTATGTT
52371871 TGTTCGCCATTTGGATG
1 TGTTCGCCATTT--ATG
*
52371888 -GTTTGCCATTTATG
1 TGTTCGCCATTTATG
52371902 TTGTTCGCCA--TATG
1 -TGTTCGCCATTTATG
52371916 TGTTCGCCA
1 TGTTCGCCA
52371925 ATGCATGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 9 0.27
14 7 0.21
16 17 0.52
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (15 bp):
TGTTCGCCATTTATG
Found at i:52372579 original size:18 final size:19
Alignment explanation
Indices: 52372558--52372600 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
52372548 TAAAATTTGA
*
52372558 AATTTTATAAA-TATTTTC
1 AATTTTAGAAATTATTTTC
*
52372576 AATTTTAGAAATTATTTTG
1 AATTTTAGAAATTATTTTC
52372595 AATTTT
1 AATTTT
52372601 TTGTTGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (19 bp):
AATTTTAGAAATTATTTTC
Found at i:52377417 original size:9 final size:9
Alignment explanation
Indices: 52377403--52377427 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52377393 AAAGACTATC
52377403 CATTTAGCA
1 CATTTAGCA
52377412 CATTTAGCA
1 CATTTAGCA
52377421 CATTTAG
1 CATTTAG
52377428 TCATATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (9 bp):
CATTTAGCA
Found at i:52392956 original size:31 final size:31
Alignment explanation
Indices: 52392892--52392959 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
52392882 AAAGAAGAAG
* * *
52392892 AAAAA-AGCTTGTTTAACAAAACGAGATAGA
1 AAAAAGAGCTTGTTTAACAAAACGAAAAAAA
*
52392922 AAAAAGAGTTTGTTTAACAAAACGAAAAAAA
1 AAAAAGAGCTTGTTTAACAAAACGAAAAAAA
52392953 AAAAAGA
1 AAAAAGA
52392960 AGAGCTGCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.60, C:0.07, G:0.15, T:0.18
Consensus pattern (31 bp):
AAAAAGAGCTTGTTTAACAAAACGAAAAAAA
Found at i:52399268 original size:50 final size:50
Alignment explanation
Indices: 52399193--52399485 Score: 433
Period size: 50 Copynumber: 5.8 Consensus size: 50
52399183 ATTTGGGTAA
52399193 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
52399243 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
52399293 ATAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
52399343 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
52399393 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
52399443 AGAACATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
52399486 TTTTATGGTC
Statistics
Matches: 215, Mismatches: 27, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
50 182 0.85
51 33 0.15
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:52403387 original size:16 final size:16
Alignment explanation
Indices: 52403368--52403398 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52403358 TGGTAATTAG
*
52403368 TAAATAAAGTAAAAAT
1 TAAATAAAATAAAAAT
52403384 TAAATAAAATAAAAA
1 TAAATAAAATAAAAA
52403399 GCAAAGTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
TAAATAAAATAAAAAT
Found at i:52409497 original size:6 final size:6
Alignment explanation
Indices: 52409488--52409521 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
52409478 GCAAGTTCAA
52409488 GCTCAG GCTCAG GCTCAG GCTCAG GCTCAG GCTC
1 GCTCAG GCTCAG GCTCAG GCTCAG GCTCAG GCTC
52409522 GGGAGAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.15, C:0.35, G:0.32, T:0.18
Consensus pattern (6 bp):
GCTCAG
Found at i:52411547 original size:43 final size:43
Alignment explanation
Indices: 52411486--52411595 Score: 143
Period size: 42 Copynumber: 2.6 Consensus size: 43
52411476 CAATACCATC
* * *
52411486 GTCCCAAACATGGTCTTACATGTAA-TCAAATATCGATGCCACT
1 GTCCCAGACATGGTCTTACACGTAAGTCAAATA-CGATGCCAAT
*
52411529 GTCCCAGACAGGGTCTTACACG-AAGTCAAATACGATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAAGTCAAATACGATGCCAAT
* *
52411571 GTTCCAGAAATGGTCTTACACGTAA
1 GTCCCAGACATGGTCTTACACGTAA
52411596 ATCTCAAATC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 30 0.52
43 28 0.48
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGTAAGTCAAATACGATGCCAAT
Found at i:52413840 original size:28 final size:28
Alignment explanation
Indices: 52413808--52413868 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
52413798 GATGCACTTT
52413808 ACTTGAACCCGTGACCACAACATCGTCA
1 ACTTGAACCCGTGACCACAACATCGTCA
* * * *
52413836 ACTTGGAGCCGTGATCGCAACATCGTCA
1 ACTTGAACCCGTGACCACAACATCGTCA
52413864 ACTTG
1 ACTTG
52413869 GAGCCCAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (28 bp):
ACTTGAACCCGTGACCACAACATCGTCA
Found at i:52413869 original size:28 final size:28
Alignment explanation
Indices: 52413816--52413873 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
52413806 TTACTTGAAC
52413816 CCGTGACCACAACATCGTCAACTTGGAG
1 CCGTGACCACAACATCGTCAACTTGGAG
* *
52413844 CCGTGATCGCAACATCGTCAACTTGGAG
1 CCGTGACCACAACATCGTCAACTTGGAG
52413872 CC
1 CC
52413874 CAAGTTGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.33, G:0.22, T:0.19
Consensus pattern (28 bp):
CCGTGACCACAACATCGTCAACTTGGAG
Found at i:52414635 original size:13 final size:14
Alignment explanation
Indices: 52414606--52414652 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
52414596 CAAACTAAAA
*
52414606 TATAATCTTAAACAT
1 TATAATC-TAAATAT
52414621 TA-AATCTAAATAT
1 TATAATCTAAATAT
*
52414634 TATAA-ATAAATAT
1 TATAATCTAAATAT
52414647 TATAAT
1 TATAAT
52414653 ATACAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 20 0.71
14 6 0.21
15 2 0.07
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (14 bp):
TATAATCTAAATAT
Found at i:52414782 original size:19 final size:19
Alignment explanation
Indices: 52414758--52414802 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
52414748 ACTATAATCT
52414758 TAAACATTAAATCTAAAA-A
1 TAAACATTAAAT-TAAAATA
*
52414777 TAAACAATAAATTAAAATA
1 TAAACATTAAATTAAAATA
52414796 TAAACAT
1 TAAACAT
52414803 ACATATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAACATTAAATTAAAATA
Found at i:52429966 original size:16 final size:17
Alignment explanation
Indices: 52429945--52429977 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52429935 GCTTAAGTCA
*
52429945 TGTGTT-AAAGGACTTG
1 TGTGTTGAAAGAACTTG
52429961 TGTGTTGAAAGAACTTG
1 TGTGTTGAAAGAACTTG
52429978 ATAAGTGCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.06, G:0.30, T:0.36
Consensus pattern (17 bp):
TGTGTTGAAAGAACTTG
Found at i:52434690 original size:19 final size:19
Alignment explanation
Indices: 52434666--52434705 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
52434656 ATATCTGAAT
52434666 TGTGGAAGCATTCAAACTG
1 TGTGGAAGCATTCAAACTG
52434685 TGTGGAAGCATTCAAACTG
1 TGTGGAAGCATTCAAACTG
52434704 TG
1 TG
52434706 GATTTGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (19 bp):
TGTGGAAGCATTCAAACTG
Found at i:52435598 original size:27 final size:27
Alignment explanation
Indices: 52435568--52435637 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
52435558 TTTGCATTTA
* *
52435568 AGGGTTCGCACAAGTAGGCTCGCACCT
1 AGGGTTCACACAAGTAGGCTCACACCT
52435595 AGGGTTCACACAAGTAGGCTCACACCT
1 AGGGTTCACACAAGTAGGCTCACACCT
52435622 AGGGTTCACACAAGTA
1 AGGGTTCACACAAGTA
52435638 AGGGTTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.19
Consensus pattern (27 bp):
AGGGTTCACACAAGTAGGCTCACACCT
Found at i:52435798 original size:35 final size:34
Alignment explanation
Indices: 52435757--52435849 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 34
52435747 GTTGATTCGA
**
52435757 ATAATTTGACTCGCATGTAGTATTAAAAGGCTGGC
1 ATAATTTGACTCGCATGTA-TATTAAAAGGCTCAC
* *
52435792 ATAATTTGACTCGCATATTATATTAAGAGGCTCAC
1 ATAATTTGACTCGCAT-GTATATTAAAAGGCTCAC
* *
52435827 ATAATTTGGCCCGCATGTCATAT
1 ATAATTTGACTCGCATGT-ATAT
52435850 CCTAGGGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
34 1 0.02
35 46 0.94
36 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (34 bp):
ATAATTTGACTCGCATGTATATTAAAAGGCTCAC
Found at i:52441837 original size:16 final size:16
Alignment explanation
Indices: 52441816--52441883 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
52441806 TAAATTATTG
52441816 ATTACATCTCTATTCC
1 ATTACATCTCTATTCC
*
52441832 ATTACAGT-TCTATTCT
1 ATTACA-TCTCTATTCC
* * *
52441848 ATTACAGCTCTTTTCA
1 ATTACATCTCTATTCC
* *
52441864 ATTACAACCCTATTCC
1 ATTACATCTCTATTCC
52441880 ATTA
1 ATTA
52441884 TAGTGAACCA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
16 41 0.98
17 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.03, T:0.43
Consensus pattern (16 bp):
ATTACATCTCTATTCC
Found at i:52444920 original size:5 final size:5
Alignment explanation
Indices: 52444910--52444942 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
52444900 AAGAGAGGAT
*
52444910 AAGGG AAGGG AAAGG AAGGG AAGGG AAGGG AAG
1 AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AAG
52444943 AGGGACGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (5 bp):
AAGGG
Found at i:52456583 original size:16 final size:18
Alignment explanation
Indices: 52456552--52456585 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
52456542 CCAATCAATA
52456552 CCACAACCCATTCATCAC
1 CCACAACCCATTCATCAC
52456570 CCAC-ACCC-TTCATCAC
1 CCACAACCCATTCATCAC
52456586 TACCATCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.18
Consensus pattern (18 bp):
CCACAACCCATTCATCAC
Found at i:52458412 original size:111 final size:111
Alignment explanation
Indices: 52458291--52458512 Score: 342
Period size: 111 Copynumber: 2.0 Consensus size: 111
52458281 TGGTAAATTT
*
52458291 GTTTTTAAATAATTGCT-CCCCTTAATGAAAA-TCATTTTGAATTTAAGGCCAAAATAAAAAG-A
1 GTTTTCAAATAATTGCTCCCCCTTAAT-AAAAGTCATTTTGAATTTAAGGCCAAAA-AAAAAGTA
* *
52458353 TTGACATACAATTAACGTTCATTTTTACTTTAAGAAAAATGGTCACATA
64 -TGACATACAATTAACATTCATTTTAACTTTAAGAAAAATGGTCACATA
*
52458402 GTTTTCAAATAATTGCTCCCCCTTAATAAAAGTTATTTTGAATTTAAGGCCAAAAAAAAAGTATG
1 GTTTTCAAATAATTGCTCCCCCTTAATAAAAGTCATTTTGAATTTAAGGCCAAAAAAAAAGTATG
* *
52458467 ACATACAATTGACATTCATTTTAACTTTAAGGAAAATGGTCACATA
66 ACATACAATTAACATTCATTTTAACTTTAAGAAAAATGGTCACATA
52458513 ATTTGCATAA
Statistics
Matches: 102, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
111 70 0.69
112 32 0.31
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (111 bp):
GTTTTCAAATAATTGCTCCCCCTTAATAAAAGTCATTTTGAATTTAAGGCCAAAAAAAAAGTATG
ACATACAATTAACATTCATTTTAACTTTAAGAAAAATGGTCACATA
Found at i:52461467 original size:13 final size:13
Alignment explanation
Indices: 52461431--52461476 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
52461421 TCTACATTGC
52461431 TTTTGAAAAGTGT
1 TTTTGAAAAGTGT
* *
52461444 TGTGGAAAAGTGT
1 TTTTGAAAAGTGT
* *
52461457 TTTTGAGAAGTGC
1 TTTTGAAAAGTGT
52461470 TTTTGAA
1 TTTTGAA
52461477 GAATAAAATG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.41
Consensus pattern (13 bp):
TTTTGAAAAGTGT
Found at i:52463556 original size:14 final size:14
Alignment explanation
Indices: 52463539--52463571 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
52463529 TATTAAATTG
52463539 TAGAACTAAAATGC
1 TAGAACTAAAATGC
52463553 TAGAACTAAAATGC
1 TAGAACTAAAATGC
*
52463567 CAGAA
1 TAGAA
52463572 ATTGTTCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.18
Consensus pattern (14 bp):
TAGAACTAAAATGC
Found at i:52464686 original size:19 final size:20
Alignment explanation
Indices: 52464662--52464710 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
52464652 TTTTCTTACG
52464662 AGTATCGATATTTTATAAA-
1 AGTATCGATATTTTATAAAT
*
52464681 AGTATCGATATTTTTTAAAT
1 AGTATCGATATTTTATAAAT
*
52464701 GGTATCGATA
1 AGTATCGATA
52464711 CCAAATTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (20 bp):
AGTATCGATATTTTATAAAT
Found at i:52464945 original size:36 final size:36
Alignment explanation
Indices: 52464904--52464972 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
52464894 TAAAATTTAG
52464904 TCTATTCTAACAAGTTCAAGAGCAAAAAAAAAAAAT
1 TCTATTCTAACAAGTTCAAGAGCAAAAAAAAAAAAT
52464940 TCTATTCTAACAAGTTCAAGAGCAAAAAAAAAA
1 TCTATTCTAACAAGTTCAAGAGCAAAAAAAAAA
52464973 TTAAGTCATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.22
Consensus pattern (36 bp):
TCTATTCTAACAAGTTCAAGAGCAAAAAAAAAAAAT
Found at i:52469463 original size:8 final size:8
Alignment explanation
Indices: 52469450--52469474 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
52469440 TATACTAAAC
52469450 AATAAAAT
1 AATAAAAT
52469458 AATAAAAT
1 AATAAAAT
52469466 AATAAAAT
1 AATAAAAT
52469474 A
1 A
52469475 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:52472563 original size:21 final size:21
Alignment explanation
Indices: 52472539--52472578 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
52472529 TGAAGCAATT
* *
52472539 TTGACTTGTTTAAATGATATC
1 TTGACTTGATAAAATGATATC
52472560 TTGACTTGATAAAATGATA
1 TTGACTTGATAAAATGATA
52472579 AAAGACCTTT
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:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (21 bp):
TTGACTTGATAAAATGATATC
Found at i:52478457 original size:27 final size:28
Alignment explanation
Indices: 52478369--52478611 Score: 253
Period size: 28 Copynumber: 8.8 Consensus size: 28
52478359 AACACGTCAG
*
52478369 GAAAGAATAAGCCTTTGTGGTGAACTAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAT
* *
52478397 GAAAGAATAAGCCTTTATGGCAAACTAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAT
*
52478425 GAAAGAATAAGCCTTTG-GGAGAACTAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAT
*
52478452 GAAAGAATAAGCCTTTGTGGTGAA-TAAT
1 GAAAGAATAAGCCTTTGTGGCGAACT-AT
*
52478480 GAAAGAATAAGCCCTTGT-GCGAA-TAAT
1 GAAAGAATAAGCCTTTGTGGCGAACT-AT
* *
52478507 AAAAGAATAAGCCTTTGT-GCGAACAAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAT
* * *
52478534 GAAAGACTAAGCCCTTGCGGCGAACTAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAT
** * * *
52478562 CTAAGACTAAGCCCTTGTGGTGAACTAT
1 GAAAGAATAAGCCTTTGTGGCGAACTAT
* * * *
52478590 CAAAGACTAAGCCCTTATGGCG
1 GAAAGAATAAGCCTTTGTGGCG
52478612 GACTCCGTAT
Statistics
Matches: 187, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
27 71 0.38
28 116 0.62
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (28 bp):
GAAAGAATAAGCCTTTGTGGCGAACTAT
Found at i:52478461 original size:55 final size:56
Alignment explanation
Indices: 52478369--52478605 Score: 250
Period size: 55 Copynumber: 4.3 Consensus size: 56
52478359 AACACGTCAG
* * * * *
52478369 GAAAGAATAAGCCTTTGTGGTGAACTATGAAAGAATAAGCCTTTATGGCAAACTAT
1 GAAAGAATAAGCCCTTGCGGCGAACTATGAAAGAATAAGCCTTTGTGGCGAACTAT
* * *
52478425 GAAAGAATAAGCCTTTG-GGAGAACTATGAAAGAATAAGCCTTTGTGGTGAA-TAAT
1 GAAAGAATAAGCCCTTGCGGCGAACTATGAAAGAATAAGCCTTTGTGGCGAACT-AT
* * *
52478480 GAAAGAATAAGCCCTTG-TGCGAA-TAATAAAAGAATAAGCCTTTGT-GCGAACAAT
1 GAAAGAATAAGCCCTTGCGGCGAACT-ATGAAAGAATAAGCCTTTGTGGCGAACTAT
* ** * * *
52478534 GAAAGACTAAGCCCTTGCGGCGAACTATCTAAGACTAAGCCCTTGTGGTGAACTAT
1 GAAAGAATAAGCCCTTGCGGCGAACTATGAAAGAATAAGCCTTTGTGGCGAACTAT
* *
52478590 CAAAGACTAAGCCCTT
1 GAAAGAATAAGCCCTT
52478606 ATGGCGGACT
Statistics
Matches: 156, Mismatches: 19, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
54 24 0.15
55 92 0.59
56 40 0.26
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (56 bp):
GAAAGAATAAGCCCTTGCGGCGAACTATGAAAGAATAAGCCTTTGTGGCGAACTAT
Found at i:52478573 original size:82 final size:82
Alignment explanation
Indices: 52478369--52478580 Score: 205
Period size: 82 Copynumber: 2.6 Consensus size: 82
52478359 AACACGTCAG
* * * * * * * *
52478369 GAAAGAATAAGCCTTTGTGGTGAACT-ATGAAAGAATAAGCCTTTATGGCAAACT-ATGAAAGAA
1 GAAAGAATAAGCCCTTGCGGCGAA-TAATCAAAGAATAAGCCCTTGT-GCGAA-TAATAAAAGAA
*
52478432 TAAGCCTTTGGGAGAACTAT
63 TAAGCCTTTGGGAGAACAAT
* * * *
52478452 GAAAGAATAAGCCTTTGTGGTGAATAATGAAAGAATAAGCCCTTGTGCGAATAATAAAAGAATAA
1 GAAAGAATAAGCCCTTGCGGCGAATAATCAAAGAATAAGCCCTTGTGCGAATAATAAAAGAATAA
* *
52478517 GCCTTTGTGCGAACAAT
66 GCCTTTGGGAGAACAAT
* * *
52478534 GAAAGACTAAGCCCTTGCGGCGAACT-ATCTAAGACTAAGCCCTTGTG
1 GAAAGAATAAGCCCTTGCGGCGAA-TAATCAAAGAATAAGCCCTTGTG
52478581 GTGAACTATC
Statistics
Matches: 112, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
81 1 0.01
82 68 0.61
83 43 0.38
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (82 bp):
GAAAGAATAAGCCCTTGCGGCGAATAATCAAAGAATAAGCCCTTGTGCGAATAATAAAAGAATAA
GCCTTTGGGAGAACAAT
Found at i:52491726 original size:41 final size:41
Alignment explanation
Indices: 52491675--52491861 Score: 191
Period size: 41 Copynumber: 4.6 Consensus size: 41
52491665 TTTAAACAGA
* * ** *
52491675 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTTTAATTCCG
1 TTCACCGGCACTT-AGCCTGCTAGGCTTATAGCCTAATTCAG
* * *
52491716 TTCACCGGCACTTAGCCTGCTATGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
* * *
52491757 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
* * * *
52491798 CTCACCGGCACTTAGCCTGCT-GGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGCTAGG-CTTATAG-CCTAATTCAG
52491839 TTCACCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAG
52491862 ACGTATAGTC
Statistics
Matches: 126, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
40 3 0.02
41 120 0.95
42 3 0.02
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.29
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
Found at i:52491884 original size:41 final size:41
Alignment explanation
Indices: 52491716--52491874 Score: 214
Period size: 41 Copynumber: 3.9 Consensus size: 41
52491706 TTTAATTCCG
* *
52491716 TTCACCGGCACTTAGCCTGCTATG-CCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTA-GACGTATAGCCTGATTCAA
* * *
52491757 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
* *
52491798 CTCACCGGCACTTAGCCTGCTGGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAG-CCTGATTCAA
*
52491839 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGA
52491875 ATAATTTCAC
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 2 0.02
41 100 0.96
42 2 0.02
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
Found at i:52499629 original size:41 final size:41
Alignment explanation
Indices: 52499578--52499764 Score: 200
Period size: 41 Copynumber: 4.6 Consensus size: 41
52499568 TTTAAACAGA
* * ** *
52499578 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTTTAATTCCG
1 TTCACCGGCACTT-AGCCTGCTAGGCTTATAGCCTAATTCAG
* *
52499619 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
* * *
52499660 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
* * * *
52499701 CTCACCGGCACTTAGCCTGCT-GGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGCTAGG-CTTATAG-CCTAATTCAG
52499742 TTCACCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAG
52499765 ACGTATAGTC
Statistics
Matches: 128, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
40 3 0.02
41 122 0.95
42 3 0.02
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.29
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATTCAG
Found at i:52499787 original size:41 final size:41
Alignment explanation
Indices: 52499619--52499777 Score: 221
Period size: 41 Copynumber: 3.9 Consensus size: 41
52499609 TTTAATTCCG
* * *
52499619 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
* * *
52499660 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
* *
52499701 CTCACCGGCACTTAGCCTGCTGGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAG-CCTGATTCAA
*
52499742 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGA
52499778 ATAATTTCAC
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 1 0.01
41 102 0.97
42 2 0.02
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
Found at i:52504535 original size:6 final size:7
Alignment explanation
Indices: 52504512--52504552 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
52504502 AAAAGTGATG
52504512 TGAAAAA
1 TGAAAAA
52504519 TGAAAAGA
1 TGAAAA-A
52504527 TG-AAAA
1 TGAAAAA
52504533 TGAAAAA
1 TGAAAAA
52504540 TGAAAAA
1 TGAAAAA
*
52504547 AGAAAA
1 TGAAAA
52504553 TGGAGAGGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 3 0.10
7 25 0.81
8 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (7 bp):
TGAAAAA
Found at i:52506070 original size:133 final size:132
Alignment explanation
Indices: 52505838--52506142 Score: 522
Period size: 133 Copynumber: 2.3 Consensus size: 132
52505828 TCCCTCGGTT
52505838 GTAGTGGAGCAGATCAAAGATGGC-GAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAG
1 GTAGTGGAGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAG
* *
52505902 CCAATAATTCTACTTCCCTGGGCAGCAGCGAAATAGATTGAATATTTCAGAATCTTGTCTCCCTA
65 CCAATAATTCTACTTCCCTAGGCAGCAGCGAAATAGATTGAAGATTTCA-AATCTTGTCTCCCTA
52505967 AGCA
129 AGCA
*
52505971 GTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGC
1 GTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGC
* *
52506036 CAGTAATTCTACTTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAG
66 CAATAATTCTACTTCCCTAGGCAGCAGCGAAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAG
52506101 CA
131 CA
* *
52506103 GTAGCGGAGCAGATAAAAGATGGCAGATTTTACCTCCCTG
1 GTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTG
52506143 GGCAGCAGCG
Statistics
Matches: 164, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
132 57 0.35
133 106 0.65
134 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (132 bp):
GTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGC
CAATAATTCTACTTCCCTAGGCAGCAGCGAAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAG
CA
Found at i:52506109 original size:44 final size:44
Alignment explanation
Indices: 52506049--52506191 Score: 151
Period size: 44 Copynumber: 3.2 Consensus size: 44
52506039 TAATTCTACT
* *
52506049 TCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAAATCTTGTC
1 TCCCTAAGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTC
* ** ** ** * **
52506093 TCCCTAAGCAGTAGCGGAGCAGATAAAAGATGGCAGATTTTACC
1 TCCCTAAGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTC
** *
52506137 TCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAGATCTTGTC
1 TCCCTAAGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTC
52506181 TCCCTAAGCAG
1 TCCCTAAGCAG
52506192 TAGTGGAGCA
Statistics
Matches: 72, Mismatches: 27, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (44 bp):
TCCCTAAGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTC
Found at i:52506149 original size:88 final size:88
Alignment explanation
Indices: 52506040--52506230 Score: 285
Period size: 88 Copynumber: 2.2 Consensus size: 88
52506030 TGAAGCCAGT
* * * *
52506040 AATTCTACTTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAGCAGT
1 AATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAAATCTTGTCTCCCTAAGCAGT
52506105 AGCGGAGCAGATAAAAGATGGCAG
66 AGCGGAGCAGATAAAAGATGG-AG
*
52506129 -ATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAGATCTTGTCTCCCTAAGCAGT
1 AATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAAATCTTGTCTCCCTAAGCAGT
* * * *
52506193 AGTGGAGCAGATCAAATATGGTG
66 AGCGGAGCAGATAAAAGATGGAG
52506216 AATTTTACCTCCCTG
1 AATTTTACCTCCCTG
52506231 TGGTTACAGT
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
87 1 0.01
88 91 0.99
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (88 bp):
AATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAAATCTTGTCTCCCTAAGCAGT
AGCGGAGCAGATAAAAGATGGAG
Found at i:52506228 original size:132 final size:131
Alignment explanation
Indices: 52506137--52506779 Score: 969
Period size: 132 Copynumber: 4.9 Consensus size: 131
52506127 AGATTTTACC
*
52506137 TCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCA
1 TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCA
*
52506202 GATCAAATATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
66 GATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAG-AATTCTA
52506267 CT
130 CT
* * *
52506269 TCCTTGGGCAGTAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCA
1 TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCA
* *
52506334 GATCAAAAATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTA
66 GATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC-AGAATTCTA
52506399 CT
130 CT
* *
52506401 TCCCTGGGTAGCAGCGAAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCA
1 TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCA
*
52506466 GATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGAAGTACATTGAAGCCAGTAATTCTA
66 GATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAG-AATTCTA
52506531 CT
130 CT
* * *
52506533 TCCCTGGGCAGCAGTGGAATAGATTGAGGATTTCAGATCTTGTCTCCCCAAGCAGTAGTGGAGCA
1 TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCA
* * *
52506598 GATCAAAGATGGTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCTAGTAATTCTA
66 GATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAG-AATTCTA
52506663 -T
130 CT
* * * *
52506664 CTCCCTGGGCAGCAGTGGAATAGATTAAAGA-TT---A-C--ATATCCCTAAGCAGTAGTGGAGC
1 -TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGC
* * * *
52506722 AGATCAAGGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAG
65 AGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAG
52506780 TATCCCTATC
Statistics
Matches: 475, Mismatches: 33, Indels: 13
0.91 0.06 0.02
Matches are distributed among these distances:
125 73 0.15
127 1 0.00
128 1 0.00
131 4 0.01
132 395 0.83
133 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (131 bp):
TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCA
GATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGAATTCTAC
T
Found at i:52506299 original size:220 final size:221
Alignment explanation
Indices: 52505907--52506362 Score: 731
Period size: 220 Copynumber: 2.1 Consensus size: 221
52505897 TGAAGCCAAT
* * *
52505907 AATTCTACTTCCCTGGGCAGCAGCGAAATAGATTGAATATTTCAGAATCTTGTCTCCCTAAGCAG
1 AATTTTACCTCCCTGGGCAGCAGCGAAATAGATTGAAAATTTCAGAATCTTGTCTCCCTAAGCAG
*
52505972 TAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGCC
66 TAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
52506037 AGTAATTCTACTTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAGC
131 AGTAATTCTACTTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAGC
52506102 AGTAGCGGAGCAGAT-AAAAGATGGCAG
196 AGTAGCGGAGCAGATCAAAA-ATGG-AG
*
52506129 -ATTTTACCTCCCTGGGCAGCAGCGGAATAGATTGAAAATTTCAG-ATCTTGTCTCCCTAAGCAG
1 AATTTTACCTCCCTGGGCAGCAGCGAAATAGATTGAAAATTTCAGAATCTTGTCTCCCTAAGCAG
* *
52506192 TAGTGGAGCAGATCAAATATGG-TGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGC
66 TAGTGGAGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGC
* * * * *
52506256 CAGTAATTCTACTTCCTTGGGCAGTAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAG
130 CAGTAATTCTACTTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAG
* *
52506321 CAGTAGTGGAGCAGATCAAAAATGGTG
195 CAGTAGCGGAGCAGATCAAAAATGGAG
52506348 AATTTTACCTCCCTG
1 AATTTTACCTCCCTG
52506363 TGGTTACAGT
Statistics
Matches: 217, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
219 2 0.01
220 171 0.79
221 44 0.20
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (221 bp):
AATTTTACCTCCCTGGGCAGCAGCGAAATAGATTGAAAATTTCAGAATCTTGTCTCCCTAAGCAG
TAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
AGTAATTCTACTTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAGC
AGTAGCGGAGCAGATCAAAAATGGAG
Found at i:52507674 original size:21 final size:22
Alignment explanation
Indices: 52507639--52507679 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
52507629 GAGACTATTT
52507639 TTTTTTATTTATTTTTATTTTA
1 TTTTTTATTTATTTTTATTTTA
52507661 TTTTTTATTT-TTTTTATTT
1 TTTTTTATTTATTTTTATTT
52507680 ATAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (22 bp):
TTTTTTATTTATTTTTATTTTA
Found at i:52508399 original size:24 final size:24
Alignment explanation
Indices: 52508328--52508407 Score: 90
Period size: 26 Copynumber: 3.3 Consensus size: 24
52508318 TTTTACATAA
* * *
52508328 TATATATACATTTTTTTCATATAG
1 TATATATGCATATTTTTAATATAG
* *
52508352 TACATACGCATATTTTTTATATATAG
1 TATATATGCATA-TTTTTA-ATATAG
52508378 TATATATGCATATTTTTAATATA-
1 TATATATGCATATTTTTAATATAG
52508401 TATATAT
1 TATATAT
52508408 TTTAAGCTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
23 7 0.15
24 13 0.28
25 11 0.23
26 16 0.34
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.51
Consensus pattern (24 bp):
TATATATGCATATTTTTAATATAG
Found at i:52512086 original size:33 final size:33
Alignment explanation
Indices: 52512044--52512108 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
52512034 ACTTGAGAAG
*
52512044 ATTTGATCCAAGTTATGTAATTGGGATGCGAAT
1 ATTTGATCCAAGTTATGTAATTAGGATGCGAAT
52512077 ATTTGATCCAAGTTATGTAATTAGGATGCGAA
1 ATTTGATCCAAGTTATGTAATTAGGATGCGAA
52512109 ACAACTCTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.35
Consensus pattern (33 bp):
ATTTGATCCAAGTTATGTAATTAGGATGCGAAT
Found at i:52513591 original size:15 final size:15
Alignment explanation
Indices: 52513561--52513606 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
52513551 ATAATGTAAA
52513561 TTCAATACTTGATTTT
1 TTCAATACTT-ATTTT
*
52513577 TT-AGTACTTATTTT
1 TTCAATACTTATTTT
*
52513591 TTCAATGCTTATTTT
1 TTCAATACTTATTTT
52513606 T
1 T
52513607 CATCATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 7 0.27
15 17 0.65
16 2 0.08
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.61
Consensus pattern (15 bp):
TTCAATACTTATTTT
Found at i:52513807 original size:18 final size:18
Alignment explanation
Indices: 52513786--52513830 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
52513776 AAATTCAAAC
*
52513786 TAACAATAATCTAA-ATT
1 TAACAATAAACTAACATT
52513803 ATAACAATAAACTAACATT
1 -TAACAATAAACTAACATT
52513822 TAA-AATAAA
1 TAACAATAAA
52513831 AAATTTCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 6 0.24
18 16 0.64
19 3 0.12
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (18 bp):
TAACAATAAACTAACATT
Found at i:52514244 original size:19 final size:19
Alignment explanation
Indices: 52514220--52514260 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
52514210 GAGAAGCTGT
52514220 TGGAAGAATGAAAAGAATG
1 TGGAAGAATGAAAAGAATG
*
52514239 TGGAAGAATGGAAAGAATG
1 TGGAAGAATGAAAAGAATG
52514258 TGG
1 TGG
52514261 CTTTATATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (19 bp):
TGGAAGAATGAAAAGAATG
Found at i:52514608 original size:32 final size:29
Alignment explanation
Indices: 52514561--52514674 Score: 88
Period size: 31 Copynumber: 3.8 Consensus size: 29
52514551 TGCCAACTTC
52514561 AAAAGTTATACTTAAATTCATTAAATTATTA
1 AAAAGTTATACTTAAATT-ATTAAATT-TTA
* * *
52514592 ATAAATTTATATTTAAATTATTTAATTTTA
1 A-AAAGTTATACTTAAATTATTAAATTTTA
**
52514622 AAAAGTTATA-AAATAATTATTAAACTATTT-
1 AAAAGTTATACTTA-AATTATTAAA-T-TTTA
* *
52514652 AAAAGTTTTTATTTAAATTATTA
1 AAAAG-TTATACTTAAATTATTA
52514675 GACTACTAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
28 1 0.01
29 17 0.25
30 10 0.15
31 23 0.34
32 16 0.24
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (29 bp):
AAAAGTTATACTTAAATTATTAAATTTTA
Found at i:52518965 original size:9 final size:10
Alignment explanation
Indices: 52518949--52519022 Score: 62
Period size: 10 Copynumber: 7.1 Consensus size: 10
52518939 GCCAAGGTAA
52518949 GAAAAAAAAT
1 GAAAAAAAAT
52518959 GAAAAAAAAT
1 GAAAAAAAAT
52518969 GAAAAAAAA-
1 GAAAAAAAAT
*
52518978 -AAGGAAAAAT
1 GAA-AAAAAAT
*
52518988 GAAAAAGAAAAA
1 G-AAAA-AAAAT
*
52519000 GAAAAAGAAAAA
1 G-AAAA-AAAAT
52519012 GAAAAAAAAT
1 GAAAAAAAAT
52519022 G
1 G
52519023 TACAAAGAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
8 2 0.04
9 5 0.09
10 24 0.44
11 5 0.09
12 19 0.35
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (10 bp):
GAAAAAAAAT
Found at i:52518973 original size:6 final size:6
Alignment explanation
Indices: 52518963--52519017 Score: 76
Period size: 6 Copynumber: 8.8 Consensus size: 6
52518953 AAAAATGAAA
52518963 AAAAATG AAAAA- AAAAAGG AAAAATG AAAAAG AAAAAG AAAAAG AAAAAG
1 AAAAA-G AAAAAG AAAAA-G AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG
52519013 AAAAA
1 AAAAA
52519018 AAATGTACAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
5 5 0.11
6 24 0.53
7 16 0.36
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:52518975 original size:19 final size:18
Alignment explanation
Indices: 52518949--52519017 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 18
52518939 GCCAAGGTAA
*
52518949 GAAAAAAAATGAAAAAAAAT
1 GAAAAAAAA--AAGAAAAAT
52518969 GAAAAAAAAAAGGAAAAAT
1 GAAAAAAAAAA-GAAAAAT
52518988 GAAAAAGAAAAAGAAAAA-
1 GAAAAA-AAAAAGAAAAAT
52519006 GAAAAAGAAAAA
1 GAAAAA-AAAAA
52519018 AAATGTACAA
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
18 14 0.30
19 18 0.39
20 14 0.30
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.04
Consensus pattern (18 bp):
GAAAAAAAAAAGAAAAAT
Found at i:52526781 original size:25 final size:24
Alignment explanation
Indices: 52526740--52526786 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
52526730 TTTCTTTTTA
* *
52526740 CTTTTTTTTTAGTTTAGGTTTTCT
1 CTTTTTTTTTAGGTTAGATTTTCT
52526764 CTTTTCTTTTTAGGTTAGATTTT
1 CTTTT-TTTTTAGGTTAGATTTT
52526787 AGTTTTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.11, C:0.09, G:0.13, T:0.68
Consensus pattern (24 bp):
CTTTTTTTTTAGGTTAGATTTTCT
Found at i:52532251 original size:39 final size:39
Alignment explanation
Indices: 52532181--52532289 Score: 130
Period size: 39 Copynumber: 2.8 Consensus size: 39
52532171 GGTAAGAGGA
* * *
52532181 GTACTAAAATACAACAGGGGCACGTAGGTGCG-TTCAGGG
1 GTACCAAAGTACAACAGGGGCACGTAAGTGCGATT-AGGG
*
52532220 GTACCAAAGTATAACAGGGGCACGTAAGTGCGATTAGGG
1 GTACCAAAGTACAACAGGGGCACGTAAGTGCGATTAGGG
* * * *
52532259 GTACCGAAGTACAACAAGGGCATGAAAGTGC
1 GTACCAAAGTACAACAGGGGCACGTAAGTGC
52532290 AATCATGGTA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
39 58 0.97
40 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.32, T:0.17
Consensus pattern (39 bp):
GTACCAAAGTACAACAGGGGCACGTAAGTGCGATTAGGG
Found at i:52533227 original size:16 final size:17
Alignment explanation
Indices: 52533205--52533243 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
52533195 TTGATTTTAA
52533205 ATTTTATT-TTATGTTAT
1 ATTTTATTGTTA-GTTAT
52533222 -TTTTATTGTTAGTTAT
1 ATTTTATTGTTAGTTAT
52533238 ATTTTA
1 ATTTTA
52533244 GGATTTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (17 bp):
ATTTTATTGTTAGTTAT
Found at i:52550728 original size:27 final size:28
Alignment explanation
Indices: 52550681--52550759 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
52550671 AAAAGGGTAC
*
52550681 AAAATATATACATGTACATATA-TA-AA
1 AAAATATATACATATACATATATTATAA
* *
52550707 AAAATTATATAGATATATATATATTATAA
1 AAAA-TATATACATATACATATATTATAA
* *
52550736 AAAAGATAATTACATATATATATA
1 AAAATAT-A-TACATATACATATA
52550760 AACAACTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.09
27 15 0.35
28 4 0.09
29 7 0.16
30 13 0.30
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAATATATACATATACATATATTATAA
Found at i:52550737 original size:30 final size:30
Alignment explanation
Indices: 52550701--52550759 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
52550691 CATGTACATA
* *
52550701 TATAAAAAA-ATTATATAGATATATATATAT
1 TATAAAAAAGATAAT-TACATATATATATAT
52550731 TATAAAAAAGATAATTACATATATATATA
1 TATAAAAAAGATAATTACATATATATATA
52550760 AACAACTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (30 bp):
TATAAAAAAGATAATTACATATATATATAT
Found at i:52550824 original size:24 final size:24
Alignment explanation
Indices: 52550796--52550845 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
52550786 AAAATTAATT
52550796 AATTTA-GAAAAATATATATAAAAA
1 AATTTATGAAAAATA-ATATAAAAA
* *
52550820 AATTTATGAAGAATAATATAAGAA
1 AATTTATGAAAAATAATATAAAAA
52550844 AA
1 AA
52550846 CATACGTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (24 bp):
AATTTATGAAAAATAATATAAAAA
Found at i:52551101 original size:3 final size:3
Alignment explanation
Indices: 52551093--52551184 Score: 55
Period size: 3 Copynumber: 30.0 Consensus size: 3
52551083 GTATATATAG
* * *
52551093 TAA TAA TAA TAA TGA TAA TAA TAA CAA TAA TAA TAA CTTAA TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA --TAA TAA TAA
* * * *
52551140 GAA -AA TCA -AA T-T TAA TAA AAA TAAA TAA TAAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA T-AA TAA T-AA TAA TAA
52551185 AGACTAAATC
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
2 4 0.06
3 53 0.77
4 9 0.13
5 3 0.04
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:52551171 original size:7 final size:7
Alignment explanation
Indices: 52551152--52551185 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
52551142 AAATCAAATT
52551152 TAATAAA
1 TAATAAA
52551159 -AATAAA
1 TAATAAA
52551165 TAATAAA
1 TAATAAA
52551172 TAATAAA
1 TAATAAA
52551179 TAATAAA
1 TAATAAA
52551186 GACTAAATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
TAATAAA
Found at i:52551479 original size:23 final size:24
Alignment explanation
Indices: 52551451--52551495 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
52551441 AAATTAAATC
52551451 TCTAAGATTACA-AAATCATATAT
1 TCTAAGATTACATAAATCATATAT
*
52551474 TCTAAGATTGCATAAATCATAT
1 TCTAAGATTACATAAATCATAT
52551496 CTAAGATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATAT
Found at i:52551500 original size:21 final size:21
Alignment explanation
Indices: 52551451--52551527 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 21
52551441 AAATTAAATC
52551451 TCTAAGATTACA-AAATCATATA
1 TCTAAGATTACATAAATC--ATA
*
52551473 TTCTAAGATTGCATAAATCATA
1 -TCTAAGATTACATAAATCATA
*
52551495 TCTAAGATTGCAT--ATCATA
1 TCTAAGATTACATAAATCATA
*
52551514 TATAAGATTACATA
1 TCTAAGATTACATA
52551528 TCCTTGAAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
19 17 0.35
21 13 0.27
22 3 0.06
23 11 0.22
24 5 0.10
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (21 bp):
TCTAAGATTACATAAATCATA
Found at i:52551992 original size:128 final size:128
Alignment explanation
Indices: 52551812--52552063 Score: 305
Period size: 128 Copynumber: 2.0 Consensus size: 128
52551802 AGATGAATTT
* * *
52551812 GATGCGATCTGCTCTACTGTAATTTCAGAGAGATAAGATCCATCATTCTAATCCACTCCGCTACA
1 GATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
* *
52551877 ACCTT-AGGGAGATAGGATTTGTTTA-TTTAGTCTGCTCCACTGC-AACTTCAGAGAGATAAGAC
66 A-CTTCAGGGAGATAGGA-TT-ATTACTTTAATCTGCTCCACT-CTAACTTCAGAGAGATAAGAC
52551939 TA
127 TA
* * ** * * * *
52551941 GATGCGTTCTGCTCT-CTGTAACTTCAGAGAGATAAGATCGAAGGTTTTAATCCGCTTCACTGCA
1 GATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
*
52552005 ACTTCAGGGAGATAGGATTATTAGCTTTAATCTGCTCCACTCTAACTTCAGGGAGATAA
66 ACTTCAGGGAGATAGGATTATTA-CTTTAATCTGCTCCACTCTAACTTCAGAGAGATAA
52552064 AATTTGCCAT
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
126 3 0.03
127 6 0.06
128 82 0.78
129 14 0.13
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (128 bp):
GATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
ACTTCAGGGAGATAGGATTATTACTTTAATCTGCTCCACTCTAACTTCAGAGAGATAAGACTA
Found at i:52552436 original size:44 final size:44
Alignment explanation
Indices: 52552378--52552745 Score: 367
Period size: 44 Copynumber: 8.5 Consensus size: 44
52552368 CCACCTACTG
* *
52552378 CACTGCTG-CTCAGGGAGATAGGGTTCACGATCTTCAACCTATTC
1 CACTGCTGAC-CAGGGAGATAGGATTCACAATCTTCAACCTATTC
* * *
52552422 TACTGCTGACCAGGGAGATAGGA-CCTACAATCTTCAATCTATTC
1 CACTGCTGACCAGGGAGATAGGATTC-ACAATCTTCAACCTATTC
* * * * * * *
52552466 CACTACTGCCCAGAGAGATAGAATTCTCAATTTTCAACCTATTT
1 CACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTC
* *
52552510 CACTGCAGACCAGGGAGATAGGATTCACAATCTTTAACCTATTC
1 CACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTC
* * * * *
52552554 CACTACTGTCGATGGAGATAGGATT--C--T-TT-AATCTATTC
1 CACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTC
* * * *
52552592 TACTGCTG-CCTAGGGAGATAGAATTCTCAATCTTCAACATATTC
1 CACTGCTGACC-AGGGAGATAGGATTCACAATCTTCAACCTATTC
* *
52552636 CACTGCTAACCAGGGAGATAGGATTCACAATCTTTAACCTATTC
1 CACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTC
* * * * * *
52552680 CACTGTTGTCTAGGGAGATAGGATTCACAATTTTTAACCTATTT
1 CACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTC
52552724 CACTGCTGACCAGGGAGATAGG
1 CACTGCTGACCAGGGAGATAGG
52552746 GCTGGGGTCA
Statistics
Matches: 261, Mismatches: 52, Indels: 22
0.78 0.16 0.07
Matches are distributed among these distances:
37 1 0.00
38 26 0.10
39 2 0.01
40 2 0.01
42 2 0.01
43 3 0.01
44 221 0.85
45 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
CACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTC
Found at i:52552591 original size:38 final size:38
Alignment explanation
Indices: 52552540--52552618 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
52552530 GGATTCACAA
* * *
52552540 TCTTTAACCTATTCCACTACTGTCGATGGAGATAGGAT
1 TCTTTAACCTATTCCACTACTGCCGAGGGAGATAGAAT
* * * *
52552578 TCTTTAATCTATTCTACTGCTGCCTAGGGAGATAGAAT
1 TCTTTAACCTATTCCACTACTGCCGAGGGAGATAGAAT
52552616 TCT
1 TCT
52552619 CAATCTTCAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (38 bp):
TCTTTAACCTATTCCACTACTGCCGAGGGAGATAGAAT
Found at i:52552599 original size:170 final size:170
Alignment explanation
Indices: 52552416--52552745 Score: 425
Period size: 170 Copynumber: 1.9 Consensus size: 170
52552406 GATCTTCAAC
* **
52552416 CTATTCTACTGCTGACC-AGGGAGATAGGA-CCTACAATCTTCAATC-TATTCCACTACTGCCCA
1 CTATTCTACTGCTG-CCTAGGGAGATAGAATCCT-CAATCTTCAA-CATATTCCACTACTAACCA
* *
52552478 GAGAGATAGAATTCTCAAT-TTTCAACCTATTTCACTGCAGACCAGGGAGATAGGATTCACAATC
63 GAGAGATAGAATTCACAATCTTT-AACCTATTCCACTGCAGACCAGGGAGATAGGATTCACAATC
* * *
52552542 TTTAACCTATTCCACTACTGTCGATGGAGATAGGATTCTTTAAT
127 TTTAACCTATTCCACTACTGACCAGGGAGATAGGATTCTTTAAT
* * *
52552586 CTATTCTACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCAACATATTCCACTGCTAACCAGGG
1 CTATTCTACTGCTGCCTAGGGAGATAGAATCCTCAATCTTCAACATATTCCACTACTAACCAGAG
* ** * * *
52552651 AGATAGGATTCACAATCTTTAACCTATTCCACTGTTGTCTAGGGAGATAGGATTCACAATTTTTA
66 AGATAGAATTCACAATCTTTAACCTATTCCACTGCAGACCAGGGAGATAGGATTCACAATCTTTA
* *
52552716 ACCTATTTCACTGCTGACCAGGGAGATAGG
131 ACCTATTCCACTACTGACCAGGGAGATAGG
52552746 GCTGGGGTCA
Statistics
Matches: 137, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
169 3 0.02
170 129 0.94
171 5 0.04
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (170 bp):
CTATTCTACTGCTGCCTAGGGAGATAGAATCCTCAATCTTCAACATATTCCACTACTAACCAGAG
AGATAGAATTCACAATCTTTAACCTATTCCACTGCAGACCAGGGAGATAGGATTCACAATCTTTA
ACCTATTCCACTACTGACCAGGGAGATAGGATTCTTTAAT
Found at i:52552648 original size:126 final size:126
Alignment explanation
Indices: 52552388--52552705 Score: 404
Period size: 126 Copynumber: 2.5 Consensus size: 126
52552378 CACTGCTGCT
* * * * *
52552388 CAGGGAGATAGGGTTCACGATCTTCAACCTATTCTACTGCTGACCAGGGAGATAGGACCTACAAT
1 CAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAGGGAGATAGGA--T----T
* * *
52552453 CTTCAATCTATTCCACTACTGCCCAGAGAGATAGAATTCTCAATTTTCAACCTATTTCACTGCAG
60 CTTCAATCTATTCCACTACTGCCCAGAGAGATAGAATTCTCAATCTTCAACATATTCCACTGCAG
52552518 AC
125 AC
* * * *
52552520 CAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGTCGATGGAGATAGGATTCTTTAA
1 CAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAGGGAGATAGGATTCTTCAA
* * * *
52552585 TCTATTCTACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCAACATATTCCACTGCTA-AC
66 TCTATTCCACTACTGCCCAGAGAGATAGAATTCTCAATCTTCAACATATTCCACTGC-AGAC
* *
52552646 CAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGTTGTCTAGGGAGATAGGATTC
1 CAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAGGGAGATAGGATTC
52552706 ACAATTTTTA
Statistics
Matches: 165, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
126 114 0.69
127 1 0.01
130 1 0.01
132 49 0.30
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (126 bp):
CAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAGGGAGATAGGATTCTTCAA
TCTATTCCACTACTGCCCAGAGAGATAGAATTCTCAATCTTCAACATATTCCACTGCAGAC
Found at i:52552802 original size:88 final size:88
Alignment explanation
Indices: 52552745--52553067 Score: 538
Period size: 88 Copynumber: 3.7 Consensus size: 88
52552735 AGGGAGATAG
* * * *
52552745 GGCTGGGGTCATCAATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
52552810 TCCGTTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCTAGGGAGGCAA
* * *
52552833 GGCTGGTGTCTTCGATTTGATTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
52552898 TCCGCTGCAACCTAGGGAGGCAA
66 TCCGCTGCAACCTAGGGAGGCAA
* * *
52552921 GGCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
52552986 TCCGCTGCAACCTAGGGAGGCAA
66 TCCGCTGCAACCTAGGGAGGCAA
52553009 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
52553068 CTGATCTGCT
Statistics
Matches: 217, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 217 1.00
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.28
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTGCAACCTAGGGAGGCAA
Found at i:52552833 original size:44 final size:44
Alignment explanation
Indices: 52552783--52553009 Score: 143
Period size: 44 Copynumber: 5.2 Consensus size: 44
52552773 CGGTGTAGGA
*
52552783 AGGCAAGATCTGCTATTTTTAACCTGCTCCGTTGCAACCCAGGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGG
* * * * ** ** * * **** *
52552827 AGGCAAG-GCTGGTGTCTTCGATTTGATTCGCTGTCGGTGCAGGA
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACCCAGGG
* *
52552871 AGGCAAGATCTACTATTTTTAACCTGCTCCGCTGCAACCTAGGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGG
* * * ** * * * * ** *
52552915 AGGCAAG-GCTGGTATCTTCGATCTGCTTCACTGTCGATGCAGGA
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACCCAGGG
*
52552959 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCTAGGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGG
52553003 AGGCAAG
1 AGGCAAG
52553010 GCTGGTGTCT
Statistics
Matches: 119, Mismatches: 60, Indels: 8
0.64 0.32 0.04
Matches are distributed among these distances:
43 32 0.27
44 54 0.45
45 33 0.28
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (44 bp):
AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGG
Found at i:52553035 original size:43 final size:43
Alignment explanation
Indices: 52552894--52553035 Score: 133
Period size: 43 Copynumber: 3.3 Consensus size: 43
52552884 TATTTTTAAC
52552894 CTGCTCCGCTGCAACCTAGGGAGGCAAGGCTGGTATCTTCGAT
1 CTGCTCCGCTGCAACCTAGGGAGGCAAGGCTGGTATCTTCGAT
* * ** * * * * ** *
52552937 CTGCTTCACTGTCGATGC-AGGAAGGCAAGATCTGCTATTTTTAAC
1 CTGCTCCGCTG-C-AACCTAGGGAGGCAAG-GCTGGTATCTTCGAT
*
52552982 CTGCTCCGCTGCAACCTAGGGAGGCAAGGCTGGTGTCTTCGAT
1 CTGCTCCGCTGCAACCTAGGGAGGCAAGGCTGGTATCTTCGAT
*
52553025 CTGCTTCGCTG
1 CTGCTCCGCTG
52553036 TCGGTGCAGG
Statistics
Matches: 71, Mismatches: 24, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
43 29 0.41
44 22 0.31
45 20 0.28
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (43 bp):
CTGCTCCGCTGCAACCTAGGGAGGCAAGGCTGGTATCTTCGAT
Found at i:52553051 original size:44 final size:44
Alignment explanation
Indices: 52552822--52553053 Score: 139
Period size: 44 Copynumber: 5.3 Consensus size: 44
52552812 CGTTGCAACC
* * * * *
52552822 CAGGGAGGCAAGGCTGGTGTCTTCGATTTGATTCGCTGTCGGTG
1 CAGGAAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATG
* ** * ** * * **
52552866 CAGGAAGGCAAGATCTACTATTTTTAACCTGCTCCGCTG-C-AAC
1 CAGGAAGGCAAG-GCTGGTATCTTCGATCTGCTTCGCTGTCGATG
* *
52552909 CTAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCACTGTCGATG
1 C-AGGAAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATG
* * * ** * * **
52552954 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-C-AAC
1 CAGGAAGGCAAG-GCTGGTATCTTCGATCTGCTTCGCTGTCGATG
* * *
52552997 CTAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 C-AGGAAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATG
52553042 CAGGAAGGCAAG
1 CAGGAAGGCAAG
52553054 ATCTGCTATT
Statistics
Matches: 129, Mismatches: 51, Indels: 16
0.66 0.26 0.08
Matches are distributed among these distances:
43 38 0.29
44 55 0.43
45 36 0.28
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.26
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGATG
Found at i:52559275 original size:22 final size:21
Alignment explanation
Indices: 52559241--52559285 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
52559231 AATGGAATAA
*
52559241 AAATAATATAAACAAATAAAT
1 AAATAATAAAAACAAATAAAT
*
52559262 AAATAAATAAAAACAAATCAAT
1 AAAT-AATAAAAACAAATAAAT
52559284 AA
1 AA
52559286 CATGCAAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (21 bp):
AAATAATAAAAACAAATAAAT
Found at i:52559647 original size:17 final size:17
Alignment explanation
Indices: 52559625--52559668 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
52559615 TAGGAAATAA
52559625 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
52559642 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
52559659 -ATATGTATAT
1 AAAATGTATAT
52559669 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:52559799 original size:3 final size:3
Alignment explanation
Indices: 52559791--52559832 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
52559781 GTATATATAG
* *
52559791 TAA TAA TAA TAA TAA TAA TAA TGA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52559833 CTTAATAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:52560197 original size:21 final size:21
Alignment explanation
Indices: 52560148--52560245 Score: 121
Period size: 21 Copynumber: 4.7 Consensus size: 21
52560138 AAATTAAATC
*
52560148 TCTAAGATTACA-AAATCATATA
1 TCTAAGATTGCATAAATC--ATA
52560170 TTCTAAGATTGCATAAATCATA
1 -TCTAAGATTGCATAAATCATA
*
52560192 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATAAATCATA
52560213 TCTAAGATTGCAT--ATCATA
1 TCTAAGATTGCATAAATCATA
*
52560232 TCTAAGATTACATA
1 TCTAAGATTGCATA
52560246 TCCTTGAAGA
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
19 18 0.26
21 33 0.47
22 3 0.04
23 11 0.16
24 5 0.07
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (21 bp):
TCTAAGATTGCATAAATCATA
Found at i:52566399 original size:28 final size:27
Alignment explanation
Indices: 52566366--52566542 Score: 198
Period size: 26 Copynumber: 6.6 Consensus size: 27
52566356 ATTAAATTTC
52566366 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
52566393 TGCCACTAAGTGTGCGAAATGAATATG-
1 AG-CACTAAGTGTGCGATTTGACTATGT
* *
52566420 ATGCACTAAGTGTGCGA-TTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
52566447 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
52566475 AGCACTAAGTGTGCGATTTGA-TACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
52566501 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
52566528 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52566543 GACTCAATTC
Statistics
Matches: 127, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
26 45 0.35
27 37 0.29
28 45 0.35
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:52566486 original size:54 final size:54
Alignment explanation
Indices: 52566366--52566542 Score: 207
Period size: 54 Copynumber: 3.3 Consensus size: 54
52566356 ATTAAATTTC
* **
52566366 AGCACTAAGTGTGCGATTTGACTATGTTGCCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATG-TGGCACTAAGTGTGCGAGTTGAATATGT
* * *
52566420 ATGCACTAAGTGTGCGA-TTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGT
1 A-GCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAG-TTGAATATGT
* * * *
52566475 AGCACTAAGTGTGCGATTTGA-TACGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGT
*
52566528 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52566543 GACTCAATTC
Statistics
Matches: 106, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
53 37 0.35
54 49 0.46
55 20 0.19
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGT
Found at i:52566533 original size:81 final size:81
Alignment explanation
Indices: 52566365--52566542 Score: 218
Period size: 81 Copynumber: 2.2 Consensus size: 81
52566355 GATTAAATTT
* *
52566365 CAGCACTAAGTGTGCGATTTGACTATGTTGCCACTAAGTGTGCGAAATGAATATGATGCACTAAG
1 CAGCACTAAGTGTGCGATTTGACTATGTAGCCACTAAGTGTGCGAAATGAATACGATGCACTAAG
*
52566430 TGTGCGATTGACCATG
66 TGTGCGATTGACCATA
* **
52566446 CGGCACTAAGTGTGCGAGTTTGACTATGTAG-CACTAAGTGTGCGATTTG-ATACG-TAGCACTA
1 CAGCACTAAGTGTGCGA-TTTGACTATGTAGCCACTAAGTGTGCGAAATGAATACGAT-GCACTA
**
52566508 AGTGTGCGAGTTGATTATA
64 AGTGTGCGA-TTGACCATA
* *
52566527 TAGCACTGAGTGTGCG
1 CAGCACTAAGTGTGCG
52566543 GACTCAATTC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
79 1 0.01
80 19 0.23
81 51 0.61
82 12 0.14
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
CAGCACTAAGTGTGCGATTTGACTATGTAGCCACTAAGTGTGCGAAATGAATACGATGCACTAAG
TGTGCGATTGACCATA
Found at i:52568329 original size:40 final size:40
Alignment explanation
Indices: 52568274--52568504 Score: 315
Period size: 40 Copynumber: 5.8 Consensus size: 40
52568264 ATTTGAATGA
*
52568274 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
*
52568314 GATCCGGGCTAAG-TCCGAAGGCATTTGTGCTAGTGATTT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
*
52568353 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
* *
52568393 GATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTT
* * * *
52568434 -ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTT
* * *
52568474 G-CCCGGGTTAAGACCCGAAGGCAATTGTGCT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCT
52568505 TGTGGTAATA
Statistics
Matches: 176, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
39 38 0.22
40 133 0.76
41 5 0.03
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (40 bp):
GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
Found at i:52568516 original size:80 final size:80
Alignment explanation
Indices: 52568275--52568532 Score: 310
Period size: 80 Copynumber: 3.2 Consensus size: 80
52568265 TTTGAATGAG
*
52568275 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAG-TCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGACCCGAAGGCATT
* *
52568339 TGTGCTAGTGAT-TT
66 TGTGCTAGTGGTAAT
52568353 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGACCCGAAGGCAT
1 -ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGACCCGAAGGCAT
* *
52568418 TTGTGCGAGTTG-ATAT
65 TTGTGCTAGTGGTA-AT
* * * * * * * *
52568434 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATG-CCCGGGTTAAGACCCGAAGGCAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTTGATCCGGGCTAAGACCCGAAGGCAT
*
52568498 TTGTGCTTGTGGTAAT
65 TTGTGCTAGTGGTAAT
* *
52568514 ATCC-GGCTAAATTCCGAAG
1 ATCCGGGCTAAGTCCCGAAG
52568533 AAACTTGGGT
Statistics
Matches: 155, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
79 64 0.41
80 84 0.54
81 7 0.05
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGACCCGAAGGCATT
TGTGCTAGTGGTAAT
Found at i:52576701 original size:26 final size:26
Alignment explanation
Indices: 52576671--52576723 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
52576661 TGATTTGATC
52576671 CGGGCTAAGTCCCGAAGGCATTTGTG
1 CGGGCTAAGTCCCGAAGGCATTTGTG
52576697 CGGGCTAAGTCCCGAAGGCATTTGTG
1 CGGGCTAAGTCCCGAAGGCATTTGTG
52576723 C
1 C
52576724 TAGTGATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.25, G:0.34, T:0.23
Consensus pattern (26 bp):
CGGGCTAAGTCCCGAAGGCATTTGTG
Found at i:52576707 original size:66 final size:66
Alignment explanation
Indices: 52576631--52576763 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
52576621 GAATGAGATC
52576631 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGTCCCGAAGGCATTTGT
52576696 G
66 G
52576697 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGTCCCGAAGGCATTTGT
52576762 G
66 G
52576763 C
1 C
52576764 TAGTGATTTG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.20, C:0.22, G:0.32, T:0.27
Consensus pattern (66 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGTCCCGAAGGCATTTGT
G
Found at i:52576744 original size:40 final size:41
Alignment explanation
Indices: 52576697--52576884 Score: 249
Period size: 40 Copynumber: 4.7 Consensus size: 41
52576687 GGCATTTGTG
* *
52576697 CGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTTGATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGATATGATC
* *
52576737 CGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTTGATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGATATGATC
*
52576777 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT-ATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGATATGATC
* * * *
52576817 CGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATG-CC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGATATGATC
* *
52576857 CGGGTTAAGACCCGAAGGCAATTGTGCT
1 CGGGCTAAGACCCGAAGGCATTTGTGCT
52576885 TGTGGTAATA
Statistics
Matches: 136, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
40 131 0.96
41 5 0.04
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.26
Consensus pattern (41 bp):
CGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGATATGATC
Found at i:52582714 original size:18 final size:18
Alignment explanation
Indices: 52582691--52582726 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52582681 ATTTATTTAC
52582691 TATTAACATAAATATTAA
1 TATTAACATAAATATTAA
* *
52582709 TATTAATATAAATTTTAA
1 TATTAACATAAATATTAA
52582727 ATTTATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTAACATAAATATTAA
Found at i:52582739 original size:21 final size:20
Alignment explanation
Indices: 52582709--52582747 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52582699 TAAATATTAA
52582709 TATTAATATAAATTTTAAATT
1 TATTAATAT-AATTTTAAATT
* *
52582730 TATTATTATATTTTTAAA
1 TATTAATATAATTTTAAA
52582748 ATATTTATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTAATATAATTTTAAATT
Found at i:52589686 original size:33 final size:33
Alignment explanation
Indices: 52589649--52589932 Score: 165
Period size: 33 Copynumber: 7.8 Consensus size: 33
52589639 TCCCCCAAGA
52589649 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
52589682 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTAAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T----GGT
*
52589724 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * * * *
52589757 GGCTGCTAAATGCTGATTTCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGA-TTCCCCG-A--TT-CAT-T---GGT
* *
52589799 GGTTGCTAAGTGCTGATTCCCCTAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
52589832 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
*
52589874 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
52589907 GGTTGCTAAGTGTTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
52589933 AACGGATAAC
Statistics
Matches: 193, Mismatches: 28, Indels: 59
0.69 0.10 0.21
Matches are distributed among these distances:
32 2 0.01
33 74 0.38
34 15 0.08
35 3 0.02
36 4 0.02
37 10 0.05
38 9 0.05
39 4 0.02
40 3 0.02
41 11 0.06
42 56 0.29
43 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:52589772 original size:75 final size:75
Alignment explanation
Indices: 52589649--52589930 Score: 465
Period size: 75 Copynumber: 3.8 Consensus size: 75
52589639 TCCCCCAAGA
*
52589649 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAA
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAA
*
52589714 ATGTAAAAGG
66 ATGTGAAAGG
* * *
52589724 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGCTGCTAAATGCTGATTTCACCGTATCTTAA
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAA
*
52589789 ATGTGAAGGG
66 ATGTGAAAGG
* * *
52589799 GGTTGCTAAGTGCTGATTCCCCTAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTTAA
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAA
52589864 ATGTGAAAGG
66 ATGTGAAAGG
* *
52589874 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGTTGAATCCACCG
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
52589931 ATAACGGATA
Statistics
Matches: 189, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 189 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.32
Consensus pattern (75 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAA
ATGTGAAAGG
Found at i:52597229 original size:33 final size:33
Alignment explanation
Indices: 52597192--52597319 Score: 148
Period size: 33 Copynumber: 3.6 Consensus size: 33
52597182 TCTCCCAAGG
52597192 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
52597225 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
*
52597267 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
52597300 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
52597320 ACCGTATCTT
Statistics
Matches: 81, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
33 41 0.51
34 3 0.04
35 1 0.01
36 2 0.02
37 4 0.05
38 3 0.04
39 2 0.02
40 1 0.01
41 3 0.04
42 21 0.26
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:52597284 original size:42 final size:42
Alignment explanation
Indices: 52597225--52597403 Score: 250
Period size: 42 Copynumber: 4.5 Consensus size: 42
52597215 ATTCATTGGT
52597225 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
* *
52597267 GGTTGCTAAGTGCTGATTCC-CCG-A-C-T-CAT-TG---GT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
*
52597300 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
*
52597342 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
*
52597384 GGTTGCTAAGTGTTGATTCC
1 GGTTGCTAAGTGCTGATTCC
52597404 CCGACTCATT
Statistics
Matches: 120, Mismatches: 8, Indels: 18
0.82 0.05 0.12
Matches are distributed among these distances:
33 21 0.17
34 3 0.03
35 1 0.01
36 3 0.03
37 3 0.03
38 3 0.03
39 3 0.03
40 1 0.01
41 3 0.03
42 79 0.66
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
Found at i:52597311 original size:75 final size:75
Alignment explanation
Indices: 52597188--52597358 Score: 324
Period size: 75 Copynumber: 2.3 Consensus size: 75
52597178 TGATTCTCCC
*
52597188 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
52597253 TTAAATGTGA
66 TTAAATGTGA
52597263 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
52597328 TTAAATGTGA
66 TTAAATGTGA
*
52597338 AGGGGGTTGCTAAGTGCTGAT
1 AAGGGGTTGCTAAGTGCTGAT
52597359 CCCACCGTAT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 94 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:52597431 original size:117 final size:117
Alignment explanation
Indices: 52597225--52597440 Score: 396
Period size: 117 Copynumber: 1.8 Consensus size: 117
52597215 ATTCATTGGT
*
52597225 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCG
1 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCG
* *
52597290 ACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
66 ACTCATTGGTGGGTGCTAAGTGCTGAATCCACCGTATCTTAAATGTGAAGGG
*
52597342 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCCG
1 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCG
52597407 ACTCATTGGTGGGTGCTAAGTGCTGAATCCACCG
66 ACTCATTGGTGGGTGCTAAGTGCTGAATCCACCG
52597441 ATAACGGATA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
117 95 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (117 bp):
GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCG
ACTCATTGGTGGGTGCTAAGTGCTGAATCCACCGTATCTTAAATGTGAAGGG
Found at i:52604199 original size:37 final size:37
Alignment explanation
Indices: 52604157--52604228 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
52604147 CAAAACATGC
* *
52604157 CAAACTCTCATTAGA-GCTAATCCAACCGGTAACACAA
1 CAAACTCTCATGAGAGGC-AATCCAACCGATAACACAA
52604194 CAAACTCTCATGAGAGGCAATCCAACCGATAACAC
1 CAAACTCTCATGAGAGGCAATCCAACCGATAACAC
52604229 GCCTCAACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 30 0.94
38 2 0.06
ACGTcount: A:0.40, C:0.31, G:0.12, T:0.17
Consensus pattern (37 bp):
CAAACTCTCATGAGAGGCAATCCAACCGATAACACAA
Found at i:52612192 original size:22 final size:25
Alignment explanation
Indices: 52612167--52612214 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 25
52612157 ATGTACATTG
52612167 TTTATTTCAAAT-CT-ATT-TCCAA
1 TTTATTTCAAATACTAATTATCCAA
52612189 TTTATTTCAAATACTAATTATCCAA
1 TTTATTTCAAATACTAATTATCCAA
52612214 T
1 T
52612215 GTTCTATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 12 0.52
23 2 0.09
24 3 0.13
25 6 0.26
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTATTTCAAATACTAATTATCCAA
Found at i:52613624 original size:17 final size:17
Alignment explanation
Indices: 52613602--52613634 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
52613592 TAGAATTGGG
52613602 TTGAGAAAATTATTTAA
1 TTGAGAAAATTATTTAA
*
52613619 TTGAGAAATTTATTTA
1 TTGAGAAAATTATTTA
52613635 TTTATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (17 bp):
TTGAGAAAATTATTTAA
Found at i:52614022 original size:19 final size:22
Alignment explanation
Indices: 52613984--52614032 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
52613974 AAATAGTGAG
*
52613984 AATT-TATTTTCTAAGTAT-A-
1 AATTCTATTTTCTAAGAATAAC
52614003 AATTCTATTTTCTAA-AATAAC
1 AATTCTATTTTCTAAGAATAAC
52614024 AATTCTATT
1 AATTCTATT
52614033 GGTTTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 6 0.23
20 11 0.42
21 9 0.35
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (22 bp):
AATTCTATTTTCTAAGAATAAC
Found at i:52642448 original size:99 final size:99
Alignment explanation
Indices: 52642277--52642751 Score: 737
Period size: 98 Copynumber: 4.9 Consensus size: 99
52642267 AAAACATGCG
* * * * * **
52642277 AGGTATGAAAGTGTTAACATATCATGTTGCGTATTTGATATTCTGTATGATTAATAAAGTGACCG
1 AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTCG
** *
52642342 CACTTATTATGTTGAAAATGAATGGGAATGAATC
66 CACTTATTATGTTGAAAATGAATGAAAATTAATC
52642376 AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTCG
1 AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTCG
52642441 CACTTATTATGTTGAAAATGAATGAAAATTAATC
66 CACTTATTATGTTGAAAATGAATGAAAATTAATC
52642475 AGGTATGAAAATGTTAAT-TATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTCG
1 AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTCG
52642539 CACTTATTATGTTGAAAATGAATGAAAATTAATC
66 CACTTATTATGTTGAAAATGAATGAAAATTAATC
* * *
52642573 AGGTATGAAAATGTTAAT-TATCATGTTGCATACTTGATATTCTATATGATTAATAAAGTGTTTG
1 AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTCG
** *
52642637 CACTTATTATGTTGAAAATGAATGGGAATAAATC
66 CACTTATTATGTTGAAAATGAATGAAAATTAATC
* *
52642671 AGGTATGAAAGTGTTAATATATCATGTTGCATACTTGATATACTGTATG-TTGATAAAGTGTTCG
1 AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTCG
*
52642735 --CTCATTATG-TGAAAATG
66 CACTTATTATGTTGAAAATG
52642752 TTTTTGGTTT
Statistics
Matches: 353, Mismatches: 22, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
95 8 0.02
96 8 0.02
98 202 0.57
99 135 0.38
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (99 bp):
AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTCG
CACTTATTATGTTGAAAATGAATGAAAATTAATC
Found at i:52642502 original size:48 final size:48
Alignment explanation
Indices: 52642444--52642600 Score: 119
Period size: 48 Copynumber: 3.2 Consensus size: 48
52642434 GTGTTCGCAC
*
52642444 TTATTATGTTGAAAATGAATGAAAATTAATCAGGTATGAAAATGTTAA
1 TTATCATGTTGAAAATGAATGAAAATTAATCAGGTATGAAAATGTTAA
* * * * * * *
52642492 TTATCATGTTG--CAT-ACTTG-ATATT-CTGTATG-ATTGATAAAGTGTTCGCAC
1 TTATCATGTTGAAAATGA-ATGAAAATTAAT-CAGGTA-TGA-AAA-TGTT---AA
*
52642542 TTATTATGTTGAAAATGAATGAAAATTAATCAGGTATGAAAATGTTAA
1 TTATCATGTTGAAAATGAATGAAAATTAATCAGGTATGAAAATGTTAA
52642590 TTATCATGTTG
1 TTATCATGTTG
52642601 CATACTTGAT
Statistics
Matches: 78, Mismatches: 17, Indels: 28
0.63 0.14 0.23
Matches are distributed among these distances:
44 2 0.03
45 10 0.13
46 7 0.09
47 4 0.05
48 21 0.27
50 11 0.14
51 4 0.05
52 7 0.09
53 10 0.13
54 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (48 bp):
TTATCATGTTGAAAATGAATGAAAATTAATCAGGTATGAAAATGTTAA
Found at i:52646862 original size:81 final size:82
Alignment explanation
Indices: 52646727--52646884 Score: 255
Period size: 81 Copynumber: 1.9 Consensus size: 82
52646717 TAGTATTACC
* * * * *
52646727 TTAACATTTTATGGTGATTCATAGATGTTTTGAGATTTTTGTTTTTCATCCAAGATTAAAAGAAC
1 TTAACATTTTATAGTGATTCAAAGATGTTTTAAGATTTTCGTTTTTCATCCAAGATTAAAACAAC
52646792 CAATAAA-AAAATTATG
66 CAATAAAGAAAATTATG
*
52646808 TTAACATTTTATAGTGATTCAAAGATGTTTTAAGATTTTCGTTTTTCATCCAAGATTAACACAAC
1 TTAACATTTTATAGTGATTCAAAGATGTTTTAAGATTTTCGTTTTTCATCCAAGATTAAAACAAC
52646873 CAATAAAGAAAA
66 CAATAAAGAAAA
52646885 ATAAAATGGT
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 66 0.94
82 4 0.06
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (82 bp):
TTAACATTTTATAGTGATTCAAAGATGTTTTAAGATTTTCGTTTTTCATCCAAGATTAAAACAAC
CAATAAAGAAAATTATG
Found at i:52650886 original size:5 final size:5
Alignment explanation
Indices: 52650873--52650904 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
52650863 AGGAATTGGG
*
52650873 GCCAG GCCAT GCCAT GCCAT GCCAT GCCAT GC
1 GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT GC
52650905 AATCGACTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.41, G:0.25, T:0.16
Consensus pattern (5 bp):
GCCAT
Found at i:52654028 original size:42 final size:42
Alignment explanation
Indices: 52653971--52654119 Score: 147
Period size: 42 Copynumber: 3.5 Consensus size: 42
52653961 CTAAAGGCTA
* * * ** * *
52653971 AACAGAAACACATAAGTGCTAAACAGAAACCCGTGAGGGTTG
1 AACAGAAGCTCATAAGAGCTAAATGGAAACCCATAAGGGTTG
* * *
52654013 AATAGAAGCTCATAAGAGCTGAATGGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAATGGAAACCCATAAGGGTTG
*
52654055 AACAGAAGCTCA-ACAGAGCTAAATGGAAACCCATTAGGGTTG
1 AACAGAAGCTCATA-AGAGCTAAATGGAAACCCATAAGGGTTG
* * * *
52654097 AACGGAAACTCATATGAGTTAAA
1 AACAGAAGCTCATAAGAGCTAAA
52654120 CAGAAGCTCG
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
41 1 0.01
42 85 0.98
43 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAATGGAAACCCATAAGGGTTG
Found at i:52654391 original size:42 final size:42
Alignment explanation
Indices: 52654345--52654457 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
52654335 GTGCTAAACA
* * * *
52654345 GAAACCCGTGAGGGTTGAATAGAAGCTCATA-AGAGCTGAATG
1 GAAACCCATAAGGGTTGAACAGAAGCTCA-ACAGAGCTAAATG
*
52654387 GAAACCCATAAGGGTTAAACAGAAGCTCAACAGAGCTAAATG
1 GAAACCCATAAGGGTTGAACAGAAGCTCAACAGAGCTAAATG
* * *
52654429 GAAACCCATTAGGGTTGAACGGAAACTCA
1 GAAACCCATAAGGGTTGAACAGAAGCTCA
52654458 TATGAGTTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 1 0.02
42 60 0.98
ACGTcount: A:0.40, C:0.18, G:0.26, T:0.17
Consensus pattern (42 bp):
GAAACCCATAAGGGTTGAACAGAAGCTCAACAGAGCTAAATG
Found at i:52654471 original size:349 final size:349
Alignment explanation
Indices: 52653832--52654532 Score: 1384
Period size: 349 Copynumber: 2.0 Consensus size: 349
52653822 TAAATTGATG
52653832 AGTACACTTCTTTCAAATCAATATCAATAATAAACAATAAATATTTCAATTTCACTCACATAATT
1 AGTACACTTCTTTCAAATCAATATCAATAATAAACAATAAATATTTCAATTTCACTCACATAATT
*
52653897 CATTTACCAAATCTTACCGAATTGGAGAAAGGCTTACGGATATGAGTACATCATTTTCAGAAGCC
66 CATTTACCAAATCTTACCGAATTGGAGAAAGGCTTACGGATATGAGTACATCATTTTCAAAAGCC
52653962 TAAAGGCTAAACAGAAACACATAAGTGCTAAACAGAAACCCGTGAGGGTTGAATAGAAGCTCATA
131 TAAAGGCTAAACAGAAACACATAAGTGCTAAACAGAAACCCGTGAGGGTTGAATAGAAGCTCATA
52654027 AGAGCTGAATGGAAACCCATAAGGGTTAAACAGAAGCTCAACAGAGCTAAATGGAAACCCATTAG
196 AGAGCTGAATGGAAACCCATAAGGGTTAAACAGAAGCTCAACAGAGCTAAATGGAAACCCATTAG
52654092 GGTTGAACGGAAACTCATATGAGTTAAACAGAAGCTCGAGAGAACTAAACAAAAAGTAAATAGAA
261 GGTTGAACGGAAACTCATATGAGTTAAACAGAAGCTCGAGAGAACTAAACAAAAAGTAAATAGAA
52654157 AGTACGCAACAAATGCTAAACCTC
326 AGTACGCAACAAATGCTAAACCTC
52654181 AGTACACTTCTTTCAAATCAATATCAATAATAAACAATAAATATTTCAATTTCACTCACATAATT
1 AGTACACTTCTTTCAAATCAATATCAATAATAAACAATAAATATTTCAATTTCACTCACATAATT
*
52654246 CATTTACCAAATCTTACCGAATTGGAGAAAGGCTTACGGATATGAGTACATCGTTTTCAAAAGCC
66 CATTTACCAAATCTTACCGAATTGGAGAAAGGCTTACGGATATGAGTACATCATTTTCAAAAGCC
52654311 TAAAGGCTAAACAGAAACACATAAGTGCTAAACAGAAACCCGTGAGGGTTGAATAGAAGCTCATA
131 TAAAGGCTAAACAGAAACACATAAGTGCTAAACAGAAACCCGTGAGGGTTGAATAGAAGCTCATA
52654376 AGAGCTGAATGGAAACCCATAAGGGTTAAACAGAAGCTCAACAGAGCTAAATGGAAACCCATTAG
196 AGAGCTGAATGGAAACCCATAAGGGTTAAACAGAAGCTCAACAGAGCTAAATGGAAACCCATTAG
52654441 GGTTGAACGGAAACTCATATGAGTTAAACAGAAGCTCGAGAGAACTAAACAAAAAGTAAATAGAA
261 GGTTGAACGGAAACTCATATGAGTTAAACAGAAGCTCGAGAGAACTAAACAAAAAGTAAATAGAA
52654506 AGTACGCAACAAATGCTAAACCTC
326 AGTACGCAACAAATGCTAAACCTC
52654530 AGT
1 AGT
52654533 TTACTTGGGT
Statistics
Matches: 350, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
349 350 1.00
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (349 bp):
AGTACACTTCTTTCAAATCAATATCAATAATAAACAATAAATATTTCAATTTCACTCACATAATT
CATTTACCAAATCTTACCGAATTGGAGAAAGGCTTACGGATATGAGTACATCATTTTCAAAAGCC
TAAAGGCTAAACAGAAACACATAAGTGCTAAACAGAAACCCGTGAGGGTTGAATAGAAGCTCATA
AGAGCTGAATGGAAACCCATAAGGGTTAAACAGAAGCTCAACAGAGCTAAATGGAAACCCATTAG
GGTTGAACGGAAACTCATATGAGTTAAACAGAAGCTCGAGAGAACTAAACAAAAAGTAAATAGAA
AGTACGCAACAAATGCTAAACCTC
Found at i:52657584 original size:54 final size:54
Alignment explanation
Indices: 52657502--52657604 Score: 179
Period size: 54 Copynumber: 1.9 Consensus size: 54
52657492 AAATTATGAG
52657502 TAAGTTTTTATTTTGGTCACTCAATTAAAAAATTTACAATTTGACCACTGAAGA
1 TAAGTTTTTATTTTGGTCACTCAATTAAAAAATTTACAATTTGACCACTGAAGA
* * *
52657556 TAAGTTTTTGTTTTGGTCACTCAATTAAAAAATTTATAATTTGATCACT
1 TAAGTTTTTATTTTGGTCACTCAATTAAAAAATTTACAATTTGACCACT
52657605 AAATTATTCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (54 bp):
TAAGTTTTTATTTTGGTCACTCAATTAAAAAATTTACAATTTGACCACTGAAGA
Found at i:52666346 original size:24 final size:23
Alignment explanation
Indices: 52666319--52666369 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
52666309 ATCTATATAT
52666319 TTTTAATAAATTT-ATAAATTTTTA
1 TTTT-ATAAATTTAATAAA-TTTTA
**
52666343 TTTTATATTTTTAATAAATTTTA
1 TTTTATAAATTTAATAAATTTTA
52666366 TTTT
1 TTTT
52666370 TTATTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTATAAATTTAATAAATTTTA
Found at i:52666351 original size:32 final size:30
Alignment explanation
Indices: 52666314--52666379 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 30
52666304 TATGTATCTA
52666314 TATATTTTTAATAAATTTATAAATTTTTATTT
1 TATATTTTTAATAAATTT-T-AATTTTTATTT
*
52666346 TATATTTTTAATAAATTTTATTTTTTATTT
1 TATATTTTTAATAAATTTTAATTTTTATTT
52666376 TATA
1 TATA
52666380 ACTTATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 14 0.42
31 1 0.03
32 18 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (30 bp):
TATATTTTTAATAAATTTTAATTTTTATTT
Found at i:52666364 original size:23 final size:24
Alignment explanation
Indices: 52666332--52666376 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
52666322 TAATAAATTT
52666332 ATAAATTTTTATTTTATATTTTTA
1 ATAAATTTTTATTTTATATTTTTA
*
52666356 ATAAA-TTTTATTTTTTATTTT
1 ATAAATTTTTATTTTATATTTT
52666377 ATAACTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
ATAAATTTTTATTTTATATTTTTA
Found at i:52666388 original size:21 final size:23
Alignment explanation
Indices: 52666332--52666391 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
52666322 TAATAAATTT
* *
52666332 ATAAATTTTTATTTTATATTTTTA
1 ATAAA-TTATATTTTTTATTTTTA
*
52666356 ATAAATTTTATTTTTTA-TTTT-
1 ATAAATTATATTTTTTATTTTTA
*
52666377 ATAACTTATATTTTT
1 ATAAATTATATTTTT
52666392 CATAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.39
22 4 0.12
23 11 0.33
24 5 0.15
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
ATAAATTATATTTTTTATTTTTA
Found at i:52666462 original size:26 final size:26
Alignment explanation
Indices: 52666382--52666469 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
52666372 ATTTTATAAC
52666382 TTATATTTTTCATAATATTT-TATGCTTT
1 TTATATTTTT-ATAA-ATTTATATG-TTT
* * *
52666410 TTAT-TTATTT-TTAATTGTATGTATTT
1 TTATATT-TTTATAAATT-TATATGTTT
*
52666436 TTATATTTTTATAAATTTATTTGTTT
1 TTATATTTTTATAAATTTATATGTTT
52666462 TTATATTT
1 TTATATTT
52666470 AATATGTTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
25 3 0.06
26 28 0.57
27 11 0.22
28 7 0.14
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (26 bp):
TTATATTTTTATAAATTTATATGTTT
Found at i:52666682 original size:17 final size:18
Alignment explanation
Indices: 52666662--52666696 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
52666652 ACATGATATT
52666662 ATATAAAA-AATAAAAAC
1 ATATAAAATAATAAAAAC
52666679 ATATAAAATTAATAAAAA
1 ATATAAAA-TAATAAAAA
52666697 TGCGTTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
ATATAAAATAATAAAAAC
Found at i:52670943 original size:23 final size:23
Alignment explanation
Indices: 52670911--52670954 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
52670901 TAATTATCAT
*
52670911 TAAAATAATAAAGTAAA-TAAACA
1 TAAAAGAATAAAG-AAACTAAACA
52670934 TAAAAGAATAAAGAAACTAAA
1 TAAAAGAATAAAGAAACTAAA
52670955 AGAGAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.18
Consensus pattern (23 bp):
TAAAAGAATAAAGAAACTAAACA
Found at i:52670956 original size:17 final size:19
Alignment explanation
Indices: 52670924--52670966 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
52670914 AATAATAAAG
*
52670924 TAAATAAACATAAAAGA-A
1 TAAAGAAACATAAAAGAGA
52670942 TAAAGAAAC-TAAAAGAGA
1 TAAAGAAACATAAAAGAGA
52670960 -AAAGAAA
1 TAAAGAAA
52670967 ACAAATAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.72, C:0.05, G:0.12, T:0.12
Consensus pattern (19 bp):
TAAAGAAACATAAAAGAGA
Found at i:52674795 original size:39 final size:39
Alignment explanation
Indices: 52674747--52674857 Score: 141
Period size: 39 Copynumber: 3.1 Consensus size: 39
52674737 TTAAAAATTT
52674747 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
52674786 TTAAAAAATTAAAAAAAGTATTTT--AAA-A--TT-AAA
1 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
* *
52674819 --AAAAAATT-AAAAAAGTATGTAAAAAATATTTTAAAA
1 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
52674855 TTA
1 TTA
52674858 TGTAAAAAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 17
0.77 0.02 0.21
Matches are distributed among these distances:
30 11 0.18
31 8 0.13
32 3 0.05
33 4 0.06
34 2 0.03
35 2 0.03
36 4 0.06
37 3 0.05
38 1 0.02
39 24 0.39
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (39 bp):
TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:52674867 original size:22 final size:22
Alignment explanation
Indices: 52674797--52674877 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
52674787 TAAAAAATTA
52674797 AAAAAAGTATTTTAAAATTA---
1 AAAAAA-TATTTTAAAATTATGT
* ** *
52674817 AAAAAAAATTAAAAAAGTATGT
1 AAAAAATATTTTAAAATTATGT
52674839 AAAAAATATTTTAAAATTATGT
1 AAAAAATATTTTAAAATTATGT
52674861 AAAAAATATTTTAAAAT
1 AAAAAATATTTTAAAAT
52674878 AAAAAATAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.18
20 6 0.12
22 35 0.70
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (22 bp):
AAAAAATATTTTAAAATTATGT
Found at i:52674875 original size:12 final size:11
Alignment explanation
Indices: 52674814--52674876 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
52674804 TATTTTAAAA
* *
52674814 TTAAAAAAAAA
1 TTAAAAAATAT
52674825 TTAAAAAAGTAT
1 TTAAAAAA-TAT
*
52674837 GTAAAAAATAT
1 TTAAAAAATAT
* *
52674848 TTTAAAATTAT
1 TTAAAAAATAT
*
52674859 GTAAAAAATATT
1 TTAAAAAATA-T
52674871 TTAAAA
1 TTAAAA
52674877 TAAAAAATAA
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
11 26 0.65
12 14 0.35
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (11 bp):
TTAAAAAATAT
Found at i:52674876 original size:11 final size:11
Alignment explanation
Indices: 52674733--52674785 Score: 65
Period size: 10 Copynumber: 4.9 Consensus size: 11
52674723 AGCCCATTTT
52674733 TATTTTAAAAA
1 TATTTTAAAAA
52674744 T-TTTTAAAAA
1 TATTTTAAAAA
**
52674754 -ATTAAAAAAA
1 TATTTTAAAAA
52674764 GTATTTTAAAAA
1 -TATTTTAAAAA
52674776 TATTTTAAAA
1 TATTTTAAAA
52674786 TTAAAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 16 0.46
11 11 0.31
12 8 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:52674890 original size:21 final size:22
Alignment explanation
Indices: 52674795--52674895 Score: 77
Period size: 22 Copynumber: 4.7 Consensus size: 22
52674785 ATTAAAAAAT
*
52674795 TAAAAAAAGTATTTTAAAA-T-
1 TAAAAAAAATATTTTAAAATTA
** *
52674815 TAAAAAAAA-ATTAAAAAAGTA
1 TAAAAAAAATATTTTAAAATTA
**
52674836 TGTAAAAAATATTTTAAAATTA
1 TAAAAAAAATATTTTAAAATTA
**
52674858 TGTAAAAAATATTTTAAAA-TA
1 TAAAAAAAATATTTTAAAATTA
52674879 -AAAAATAAATATATTTA
1 TAAAAA-AAATAT-TTTA
52674896 TTATATATGG
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
19 7 0.11
20 12 0.18
21 15 0.23
22 32 0.48
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (22 bp):
TAAAAAAAATATTTTAAAATTA
Found at i:52676411 original size:16 final size:16
Alignment explanation
Indices: 52676389--52676457 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
52676379 TTTGGTTCGC
52676389 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
52676405 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
52676421 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
52676438 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
52676454 TGTA
1 TGTA
52676458 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:52676435 original size:33 final size:32
Alignment explanation
Indices: 52676389--52676457 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
52676379 TTTGGTTCGC
52676389 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
52676421 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
52676454 TGTA
1 TGTA
52676458 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:52676522 original size:44 final size:45
Alignment explanation
Indices: 52676438--52676528 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
52676428 GGATTAGAGG
* * *
52676438 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
52676483 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
52676527 TG
1 TG
52676529 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:52676714 original size:18 final size:17
Alignment explanation
Indices: 52676693--52676727 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52676683 TTATTATTAA
*
52676693 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
52676711 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
52676728 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:52679891 original size:33 final size:33
Alignment explanation
Indices: 52679842--52679950 Score: 127
Period size: 33 Copynumber: 3.3 Consensus size: 33
52679832 ATTATAAAGC
52679842 ATGTATAA-TGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
52679874 ATGTATAATTGACCTAAAATTACTTGTTGGTTT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
52679907 AATGT-T-ATTGTCCCTAAAA-AACATTGTTGGTGT
1 -ATGTATAATTG-ACCTAAAATTA-ATTGTTGGTGT
52679940 ATGTATAATTG
1 ATGTATAATTG
52679951 TTGGTTTAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
32 17 0.26
33 40 0.62
34 8 0.12
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.42
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTGT
Found at i:52679957 original size:51 final size:50
Alignment explanation
Indices: 52679897--52679999 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 50
52679887 CTAAAATTAC
52679897 TTGTTGGTTTAATGTTATTGT-CCCTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATT-TACCCTAAAAAACATTGTTGGTGTATG-ATAA
52679948 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGATAA
52679998 TT
1 TT
52680000 TTTACGTATA
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
50 7 0.14
51 44 0.86
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (50 bp):
TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGATAA
Found at i:52680173 original size:86 final size:86
Alignment explanation
Indices: 52680066--52680246 Score: 355
Period size: 86 Copynumber: 2.1 Consensus size: 86
52680056 TTCTCTCCAC
52680066 ATAA-AATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
1 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
52680130 TTAATATTAAAGATAAAAATT
66 TTAATATTAAAGATAAAAATT
52680151 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
1 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
52680216 TTAATATTAAAGATAAAAATT
66 TTAATATTAAAGATAAAAATT
52680237 ATAATAATTA
1 ATAATAATTA
52680247 CAATTATATT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 4 0.04
86 91 0.96
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (86 bp):
ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
TTAATATTAAAGATAAAAATT
Done.