Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 53 of 316
Found at i:15439741 original size:12 final size:12
Alignment explanation
Indices: 15439724--15439754 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
15439714 AAGATATGAT
15439724 ATGGTGGTGGCG
1 ATGGTGGTGGCG
15439736 ATGGTGGTGGCG
1 ATGGTGGTGGCG
15439748 ATGGTGG
1 ATGGTGG
15439755 ATAGGGTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.06, G:0.58, T:0.26
Consensus pattern (12 bp):
ATGGTGGTGGCG
Found at i:15441733 original size:20 final size:22
Alignment explanation
Indices: 15441693--15441734 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
15441683 ATTATTCATA
*
15441693 TAATAAATATAATTTATTATTT
1 TAATAAATATAATTTAATATTT
15441715 TAATAAAT-T-ATTTAATATTT
1 TAATAAATATAATTTAATATTT
15441735 CAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAAATATAATTTAATATTT
Found at i:15442472 original size:3 final size:3
Alignment explanation
Indices: 15442464--15442499 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
15442454 AAACTCTGAT
15442464 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
15442500 GGTCTTCCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:15443694 original size:21 final size:21
Alignment explanation
Indices: 15443648--15443699 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
15443638 TTAATTATCA
* *
15443648 TTATAGTTTAGGGTTTATAGT
1 TTATGGTTAAGGGTTTATAGT
*
15443669 ATATGGTTAAGGGTTTA-ATGT
1 TTATGGTTAAGGGTTTATA-GT
15443690 TTATGAGTTA
1 TTATG-GTTA
15443700 CTATTGTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 20 0.80
22 4 0.16
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (21 bp):
TTATGGTTAAGGGTTTATAGT
Found at i:15443751 original size:14 final size:14
Alignment explanation
Indices: 15443712--15443753 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
15443702 ATTGTAAGGC
15443712 TTATGGATTATGAGT
1 TTATGGATTATG-GT
*
15443727 TTAGGGATTATGGT
1 TTATGGATTATGGT
*
15443741 TTATGGTTTATGG
1 TTATGGATTATGG
15443754 GTTAAAGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (14 bp):
TTATGGATTATGGT
Found at i:15443756 original size:15 final size:15
Alignment explanation
Indices: 15443712--15443756 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
15443702 ATTGTAAGGC
*
15443712 TTATGGATTATGAGT
1 TTATGGATTATGGGT
*
15443727 TTAGGGATTAT-GGT
1 TTATGGATTATGGGT
*
15443741 TTATGGTTTATGGGT
1 TTATGGATTATGGGT
15443756 T
1 T
15443757 AAAGGTTAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (15 bp):
TTATGGATTATGGGT
Found at i:15443790 original size:22 final size:22
Alignment explanation
Indices: 15443760--15443803 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
15443750 ATGGGTTAAA
*
15443760 GGTTAGGGTTTAAGTTTTAGGG
1 GGTTAGGGTTTAAGGTTTAGGG
*
15443782 GGTTGGGGTTTAAGGTTTAGGG
1 GGTTAGGGTTTAAGGTTTAGGG
15443804 TTAAGGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (22 bp):
GGTTAGGGTTTAAGGTTTAGGG
Found at i:15443858 original size:7 final size:7
Alignment explanation
Indices: 15443725--15443858 Score: 72
Period size: 7 Copynumber: 18.9 Consensus size: 7
15443715 TGGATTATGA
15443725 GTTTAGG
1 GTTTAGG
* *
15443732 GATTATG
1 GTTTAGG
*
15443739 GTTTATG
1 GTTTAGG
15443746 GTTTATGG
1 GTTTA-GG
* *
15443754 GTTAAAG
1 GTTTAGG
15443761 G-TTAGG
1 GTTTAGG
*
15443767 GTTTAAG
1 GTTTAGG
*
15443774 TTTTAGGG
1 GTTTA-GG
* *
15443782 GGTTGGG
1 GTTTAGG
*
15443789 GTTTAAG
1 GTTTAGG
15443796 GTTTAGG
1 GTTTAGG
*
15443803 GTTAAGG
1 GTTTAGG
**
15443810 GTTTATA
1 GTTTAGG
* *
15443817 TTTTATG
1 GTTTAGG
*
15443824 GTTTAAG
1 GTTTAGG
15443831 GTTTAGG
1 GTTTAGG
*
15443838 GGTTAGG
1 GTTTAGG
*
15443845 GAATTAGG
1 G-TTTAGG
15443853 GTTTAG
1 GTTTAG
15443859 ATTAATTAGT
Statistics
Matches: 93, Mismatches: 30, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
6 4 0.04
7 75 0.81
8 14 0.15
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:15452606 original size:21 final size:21
Alignment explanation
Indices: 15452562--15452606 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
15452552 AAAATTGCTG
* * *
15452562 TTTTTATTGTTTTCTTGTTGT
1 TTTTTACTGTTTTCTTGCTAT
*
15452583 TTTTTACTGTTTTGTTGCTAT
1 TTTTTACTGTTTTCTTGCTAT
15452604 TTT
1 TTT
15452607 CTTCACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.07, G:0.13, T:0.73
Consensus pattern (21 bp):
TTTTTACTGTTTTCTTGCTAT
Found at i:15453196 original size:15 final size:16
Alignment explanation
Indices: 15453169--15453200 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
15453159 TATATTAATT
15453169 TTTAAATAAATATAAA
1 TTTAAATAAATATAAA
15453185 TTTAAA-AAATATAAA
1 TTTAAATAAATATAAA
15453200 T
1 T
15453201 GATCAAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTTAAATAAATATAAA
Found at i:15458026 original size:10 final size:10
Alignment explanation
Indices: 15458011--15458050 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
15458001 AAAATCTTAG
15458011 ATTAAAAAAT
1 ATTAAAAAAT
15458021 ATTAAAAAAT
1 ATTAAAAAAT
*
15458031 CTGTAAAAAAT
1 AT-TAAAAAAT
15458042 -TTAAAAAAT
1 ATTAAAAAAT
15458051 CATATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 8 0.29
10 12 0.43
11 8 0.29
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (10 bp):
ATTAAAAAAT
Found at i:15458045 original size:20 final size:21
Alignment explanation
Indices: 15458013--15458051 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
15458003 AATCTTAGAT
15458013 TAAAAAATATTAAAAAATCTG
1 TAAAAAATATTAAAAAATCTG
15458034 TAAAAAAT-TTAAAAAATC
1 TAAAAAATATTAAAAAATC
15458052 ATATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (21 bp):
TAAAAAATATTAAAAAATCTG
Found at i:15460111 original size:20 final size:19
Alignment explanation
Indices: 15460061--15460111 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 19
15460051 AATAGTTCTG
15460061 TCTCTTGATGAACAATTGTA
1 TCTCTTG-TGAACAATTGTA
15460081 TCT-TT-TGAACAATTGTA
1 TCTCTTGTGAACAATTGTA
15460098 TCTCTTGGTGAACA
1 TCTCTT-GTGAACA
15460112 TATTCATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 15 0.54
18 2 0.07
19 2 0.07
20 9 0.32
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (19 bp):
TCTCTTGTGAACAATTGTA
Found at i:15468498 original size:22 final size:22
Alignment explanation
Indices: 15468473--15468516 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
15468463 AGTGCTAAGT
**
15468473 AGAGAGCATTAAAGTGCTGAAC
1 AGAGAGCAACAAAGTGCTGAAC
*
15468495 AGAGAGCAACGAAGTGCTGAAC
1 AGAGAGCAACAAAGTGCTGAAC
15468517 CCATACAAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.30, T:0.14
Consensus pattern (22 bp):
AGAGAGCAACAAAGTGCTGAAC
Found at i:15473745 original size:12 final size:12
Alignment explanation
Indices: 15473728--15473760 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
15473718 CTACTCGCCC
15473728 ATATTATTTTTT
1 ATATTATTTTTT
15473740 ATATTA-TTTTT
1 ATATTATTTTTT
*
15473751 ATATAATTTT
1 ATATTATTTT
15473761 AAAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:15473919 original size:30 final size:30
Alignment explanation
Indices: 15473883--15473945 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
15473873 ACTTAACAAG
15473883 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
15473913 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
15473943 CAA
1 CAA
15473946 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:15474434 original size:96 final size:96
Alignment explanation
Indices: 15474320--15474610 Score: 555
Period size: 96 Copynumber: 3.0 Consensus size: 96
15474310 GCAGTACTAT
15474320 CATATATGCTTAGTCTTATATATACACCCACGCATACACCGATCCGTTTCCATTCCAGCATAAGT
1 CATATATGCTTAGTCTTATATATACACCCACGCATACACCGATCCGTTTCCATTCCAGCATAAGT
15474385 GTGTACGTAGGAGTGGGTGAGCCTATCATTC
66 GTGTACGTAGGAGTGGGTGAGCCTATCATTC
*
15474416 CATATATGCTTAGTCTTATATATACACCCACGCATACACCGATCCGTTTCCATTCCAGCATGAGT
1 CATATATGCTTAGTCTTATATATACACCCACGCATACACCGATCCGTTTCCATTCCAGCATAAGT
*
15474481 GTGTACGTAGGAGTGCGTGAGCCTATCATTC
66 GTGTACGTAGGAGTGGGTGAGCCTATCATTC
*
15474512 CATGTATGCTTAGTCTTATATATACACCCACGCATACACCGATCCGTTTCCATTCCAGCATAAGT
1 CATATATGCTTAGTCTTATATATACACCCACGCATACACCGATCCGTTTCCATTCCAGCATAAGT
15474577 GTGTACGTAGGAGTGGGTGAGCCTATCATTC
66 GTGTACGTAGGAGTGGGTGAGCCTATCATTC
15474608 CAT
1 CAT
15474611 GCACATGGCA
Statistics
Matches: 190, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 190 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (96 bp):
CATATATGCTTAGTCTTATATATACACCCACGCATACACCGATCCGTTTCCATTCCAGCATAAGT
GTGTACGTAGGAGTGGGTGAGCCTATCATTC
Found at i:15475160 original size:31 final size:31
Alignment explanation
Indices: 15475124--15475183 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
15475114 TTAATTTTAC
* * *
15475124 CAATTTTAGTCTTTTTATTTTTCGAATTGAT
1 CAATTTTAGTCTCTATACTTTTCGAATTGAT
15475155 CAATTTTAGTCTCTATACTTTTCGAATTG
1 CAATTTTAGTCTCTATACTTTTCGAATTG
15475184 GGAACCCATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.53
Consensus pattern (31 bp):
CAATTTTAGTCTCTATACTTTTCGAATTGAT
Found at i:15479401 original size:27 final size:26
Alignment explanation
Indices: 15479371--15479512 Score: 151
Period size: 27 Copynumber: 5.2 Consensus size: 26
15479361 GTGACGAAGT
15479371 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGA-ACAGATATTGTGGCAGAGC
*
15479398 CACCAGAACAGATATATGTGGTAGAGC
1 CACCAGAACAGATAT-TGTGGCAGAGC
* *
15479425 CACC-GAATCAAATAATTGTGGCATAGC
1 CACCAGAA-CAGAT-ATTGTGGCAGAGC
*
15479452 CACCAGGACAGATATATGTGGCAGAGC
1 CACCAGAACAGATAT-TGTGGCAGAGC
** *
15479479 CACCAGATTAGATAAATTGTGGCATAGC
1 CACCAGAACAGAT--ATTGTGGCAGAGC
15479507 CACCAG
1 CACCAG
15479513 GACGCTTCCT
Statistics
Matches: 97, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
26 13 0.13
27 62 0.64
28 20 0.21
29 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
CACCAGAACAGATATTGTGGCAGAGC
Found at i:15479467 original size:54 final size:55
Alignment explanation
Indices: 15479385--15479515 Score: 194
Period size: 54 Copynumber: 2.4 Consensus size: 55
15479375 AGATACAGAT
* * *
15479385 ATTGTGGCAGAGCCACCAGAACAGATATATGTGGTAGAGCCACC-GAATCAAAT-A
1 ATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAG-ATCAAATAA
* *
15479439 ATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAGATTAGATAA
1 ATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAGATCAAATAA
15479494 ATTGTGGCATAGCCACCAGGAC
1 ATTGTGGCATAGCCACCAGGAC
15479516 GCTTCCTCCA
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
54 46 0.66
55 24 0.34
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.19
Consensus pattern (55 bp):
ATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAGATCAAATAA
Found at i:15481141 original size:26 final size:26
Alignment explanation
Indices: 15481111--15481192 Score: 164
Period size: 26 Copynumber: 3.2 Consensus size: 26
15481101 TTGAATGCCC
15481111 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
15481137 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
15481163 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
15481189 ATCA
1 ATCA
15481193 ATTTTTATCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:15484251 original size:2 final size:2
Alignment explanation
Indices: 15484239--15484272 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
15484229 CCCTTGCATT
*
15484239 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15484273 GGTTTTGATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:15484474 original size:18 final size:16
Alignment explanation
Indices: 15484451--15484485 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
15484441 AATTTAACTT
15484451 TAATTAAATTATTTAAAA
1 TAATT-AATT-TTTAAAA
15484469 TAATTAATTTTTAAAA
1 TAATTAATTTTTAAAA
15484485 T
1 T
15484486 TATAAACGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 4 0.24
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTAATTTTTAAAA
Found at i:15484563 original size:26 final size:26
Alignment explanation
Indices: 15484499--15484555 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
15484489 AAACGAACAT
15484499 ATTTTCTTCTTTTACCATTTTTAATC
1 ATTTTCTTCTTTTACCATTTTTAATC
15484525 ATTTTCTTCTTTTACCATTTTTAATC
1 ATTTTCTTCTTTTACCATTTTTAATC
15484551 ATTTT
1 ATTTT
15484556 TAATTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.19, C:0.18, G:0.00, T:0.63
Consensus pattern (26 bp):
ATTTTCTTCTTTTACCATTTTTAATC
Found at i:15491299 original size:23 final size:25
Alignment explanation
Indices: 15491262--15491313 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
15491252 TTTAGACAGT
* *
15491262 AAAAGAAGAATAGAA-AAG-GAAGA
1 AAAAGAAGAAGAGAAGAAGAAAAGA
*
15491285 AAAAGAAGAGGAGAAGAAGAAAAGA
1 AAAAGAAGAAGAGAAGAAGAAAAGA
15491310 AAAA
1 AAAA
15491314 ATGGAGATGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 13 0.54
24 3 0.12
25 8 0.33
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (25 bp):
AAAAGAAGAAGAGAAGAAGAAAAGA
Found at i:15496702 original size:21 final size:21
Alignment explanation
Indices: 15496678--15496727 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
15496668 AGCTTCCTAC
15496678 TGAGTTGGGGTAAT-CTCTTGT
1 TGAGTTGGGGT-ATCCTCTTGT
*
15496699 TGAGTTGGGGTATCCTTTTGT
1 TGAGTTGGGGTATCCTCTTGT
15496720 TGAGTTGG
1 TGAGTTGG
15496728 AGCAACCACT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.12, C:0.08, G:0.36, T:0.44
Consensus pattern (21 bp):
TGAGTTGGGGTATCCTCTTGT
Found at i:15499255 original size:186 final size:184
Alignment explanation
Indices: 15498901--15499474 Score: 779
Period size: 186 Copynumber: 3.1 Consensus size: 184
15498891 AAACCTAGGC
* * * * ** *
15498901 AATGGTAGACAATAACCAACACAAAAACAATATAACACAAAAAAATCCATTTCTGTCATGTGCAA
1 AATGGTAGACAATAACCAATACAAAAATAATTTAACAAAAAAAAATTTATTTCTGTCATGTACAA
* * *
15498966 TAATCAAACAATAATCATGCACTTTAATCCAAAATAGTATCATGAACATGGCAAACAATCACCAA
66 TAACCAAACAATAATCATGCACTTTAATCCAAAATAGTATCATGCACATGGCAGACAAT-ACCAA
* * * *
15499031 CCAATAATCCAAAATAGAAATTGATTTGTCACTTTCCTAAGGCAATTAGTATGCA
130 ACAATAATCCAAAATAGGAACTGATTTGTCTCTTTCCTAAGGCAATTAGTATGCA
* * *
15499086 AATGGTAGGCAATAGCCAATACAAAAATAATTTAACATAAAAAAATTTATTTCTGTCATGTACAA
1 AATGGTAGACAATAACCAATACAAAAATAATTTAACAAAAAAAAATTTATTTCTGTCATGTACAA
* *
15499151 TAACCAAACAATAATCATGCACTTTTTACCCAAAATAGTATCATGCACATGGCAGACAATAGCCA
66 TAACCAAACAATAATCATGCAC-TTTAATCCAAAATAGTATCATGCACATGGCAGACAATA-CCA
*
15499216 AACAATAATCCAAAATAGGGACTGATTTGTCTCTTTCCTAAGGCAATTAGTATGCA
129 AACAATAATCCAAAATAGGAACTGATTTGTCTCTTTCCTAAGGCAATTAGTATGCA
*
15499272 AATGGTAGACAATAACCAATACAAAAATAGTTTTAAACAAAAAAAAATTCTATTTCTGTCATGTA
1 AATGGTAGACAATAACCAATACAAAAATA-ATTT-AACAAAAAAAAATT-TATTTCTGTCATGTA
* * * *
15499337 AAATAACCAAACAATAATCATGCACTTTAATCCTAAATAGTATCATACAAATGGCAGACAATAAC
63 CAATAACCAAACAATAATCATGCACTTTAATCCAAAATAGTATCATGCACATGGCAGACAAT-AC
* * * * * * * * *
15499402 CAAACAGTAATCTAAATTAGGAACTAATTTATCTATTTCTTATGGCAATTATTATGCA
127 CAAACAATAATCCAAAATAGGAACTGATTTGTCTCTTTCCTAAGGCAATTAGTATGCA
15499460 AATGGTAGACAATAA
1 AATGGTAGACAATAA
15499475 GTTTACAAAA
Statistics
Matches: 344, Mismatches: 39, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
185 78 0.23
186 114 0.33
187 3 0.01
188 109 0.32
189 40 0.12
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.27
Consensus pattern (184 bp):
AATGGTAGACAATAACCAATACAAAAATAATTTAACAAAAAAAAATTTATTTCTGTCATGTACAA
TAACCAAACAATAATCATGCACTTTAATCCAAAATAGTATCATGCACATGGCAGACAATACCAAA
CAATAATCCAAAATAGGAACTGATTTGTCTCTTTCCTAAGGCAATTAGTATGCA
Found at i:15504479 original size:47 final size:45
Alignment explanation
Indices: 15504408--15504769 Score: 237
Period size: 47 Copynumber: 7.7 Consensus size: 45
15504398 TGATTTGTGC
** * * *
15504408 GCCAGTGCCAGACATGTCTAGGACATGCTTCGGCCACATTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACA-GATGAGA
** *
15504454 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATCCAGACAAGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA--CAGATGAGA
* * * * *
15504502 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACA-GATGAGA
* * * *
15504548 GCCAGTGTAAAACCATGTCTGGGACATGAAATCGGCACAGAGATGAGT
1 GCCAGTGTAAGA-CATGTCTGGGACATG-CATCGGC-CACAGATGAGA
* *
15504596 GCCAGTGTAAGATATGTCTGGGACATGCATCGGCCTCGACAGA-GATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGG-C-C-ACAGATGAGA
* * ** * *
15504643 GCCAGTGTAAGACGTGTCTGGGACACGCATCGG-CTTAGA-GTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGATG-AGA
* * * * * *
15504687 GCTAGTGTAAGACATGCCTGAGACATGCATCAGCACGCGTATATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGC-CAC--AGATGAGA
* *
15504735 GCCAGTGTAATACCATGTTTGGGACATGGCATCGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGG
15504770 TAATATATCC
Statistics
Matches: 241, Mismatches: 56, Indels: 34
0.73 0.17 0.10
Matches are distributed among these distances:
43 4 0.02
44 28 0.12
45 1 0.00
46 34 0.14
47 94 0.39
48 57 0.24
49 17 0.07
50 6 0.02
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.22
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGATGAGA
Found at i:15504582 original size:94 final size:92
Alignment explanation
Indices: 15504417--15504769 Score: 333
Period size: 94 Copynumber: 3.8 Consensus size: 92
15504407 CGCCAGTGCC
* * * * *
15504417 AGACATGTCTAGGACATGCTTCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATG
1 AGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATGTCTGGGACAT-
* *
15504482 GCATCGGCATCCAGACAAGGGCTAGTGTA
65 GCATCGGCAT-CAGAGAAGTGCTAGTGTA
* *
15504511 AGACATGTCTGGGACATGCATCAGCCATACTATGATAGCCAGTGTAAAACCATGTCTGGGACATG
1 AGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATGTCTGGGACATG
* *
15504576 AAATCGGCA-CAGAGATGAGTGCCAGTGTA
66 -CATCGGCATCAGAGA--AGTGCTAGTGTA
* * *
15504605 AGATATGTCTGGGACATGCATCGGCC-TCGAC-A-GAGATAGCCAGTGTAAGA-CGTGTCTGGGA
1 AGACATGTCTGGGACATGCATCAGCCAT--ACTATGAG--AGCCAGTGTAAGACCATGTCTGGGA
* * **
15504666 CACGCATCGGC-TTAGAGTTGTGCTAGTGTA
62 CATGCATCGGCATCAGAGAAGTGCTAGTGTA
* * * * *
15504696 AGACATGCCTGAGACATGCATCAGCACGCGTA-TATGAGAGCCAGTGTAATACCATGTTTGGGAC
1 AGACATGTCTGGGACATGCATCAG--C-CATACTATGAGAGCCAGTGTAAGACCATGTCTGGGAC
15504760 ATGGCATCGG
63 AT-GCATCGG
15504770 TAATATATCC
Statistics
Matches: 213, Mismatches: 30, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
91 30 0.14
92 17 0.08
93 28 0.13
94 123 0.58
95 15 0.07
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (92 bp):
AGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATGTCTGGGACATG
CATCGGCATCAGAGAAGTGCTAGTGTA
Found at i:15504767 original size:141 final size:142
Alignment explanation
Indices: 15504447--15504769 Score: 340
Period size: 141 Copynumber: 2.3 Consensus size: 142
15504437 TCGGCCACAT
* *
15504447 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAGACAAGGGCTAGTGTAA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAGACAAGAGCCAGTGTAA
* * * *
15504512 GACATGTCTGGGACATGCATCAGCCATACTATGATAGCCAGTGTAAAACCATGTCTGGGACATGA
66 GACATGTCTGGGACACGCATCAGCCAGACTATGATAGCCAGTGTAAAACCATGCCTGAGACATGA
*
15504577 AATCGGCACAGA
131 AATCAGCACAGA
* * * *
15504589 GATGAGTGCCAGTGTAAGA-TATGTCTGGGACAT-GCATCGGCCT-C-GACAGAGATAGCCAGTG
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAGACA-AG--AGCCAGTG
* * * * * *
15504650 TAAGACGTGTCTGGGACACGCATCGGCTTAGAGT-TG-T-GCTAGTGTAAGA-CATGCCTGAGAC
63 TAAGACATGTCTGGGACACGCATCAGC-CAGACTATGATAGCCAGTGTAAAACCATGCCTGAGAC
* *
15504711 ATG-CATCAGCACGCGTA
127 ATGAAATCAGCAC-AG-A
* *
15504728 TATGAGAGCCAGTGTAATACCATGTTTGGGACATGGCATCGG
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG
15504770 TAATATATCC
Statistics
Matches: 149, Mismatches: 24, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
137 7 0.05
138 18 0.12
139 30 0.20
140 22 0.15
141 52 0.35
142 20 0.13
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.22
Consensus pattern (142 bp):
TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAGACAAGAGCCAGTGTAA
GACATGTCTGGGACACGCATCAGCCAGACTATGATAGCCAGTGTAAAACCATGCCTGAGACATGA
AATCAGCACAGA
Found at i:15505659 original size:11 final size:13
Alignment explanation
Indices: 15505629--15505653 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15505619 GAGACACGGC
15505629 CGTGTGTATCGGT
1 CGTGTGTATCGGT
15505642 CGTGTGTATCGG
1 CGTGTGTATCGG
15505654 CTGTGTGAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.40, T:0.36
Consensus pattern (13 bp):
CGTGTGTATCGGT
Found at i:15512397 original size:13 final size:13
Alignment explanation
Indices: 15512381--15512413 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
15512371 TTTAATTAAA
*
15512381 TTAGTTAATTAGT
1 TTAGATAATTAGT
15512394 TTAGATAATTAGT
1 TTAGATAATTAGT
15512407 TTA-ATAA
1 TTAGATAA
15512414 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:15520186 original size:7 final size:6
Alignment explanation
Indices: 15520134--15520196 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
15520124 CCTATTTGTT
* * * *
15520134 TTTTTA TTATTTA CTCTTA TTTTTA -TTTTA TTTTTA TTTTTC TTTTGA
1 TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
15520182 TTTTTA TTTTCA TTT
1 TTTTTA TTTTTA TTT
15520197 CAATTTTATT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
5 5 0.11
6 36 0.78
7 5 0.11
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:15523129 original size:13 final size:13
Alignment explanation
Indices: 15523113--15523145 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
15523103 TTTAATTAAA
*
15523113 TTAGTTAATTAGT
1 TTAGATAATTAGT
15523126 TTAGATAATTAGT
1 TTAGATAATTAGT
15523139 TTA-ATAA
1 TTAGATAA
15523146 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:15531441 original size:42 final size:42
Alignment explanation
Indices: 15531367--15531478 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 42
15531357 ATTCATATGC
* * * *
15531367 CACATGGCTTGGACACACGCCTATATCCTTGCCTGTATAGCT
1 CACATGGCCTGGGCACACGCCTATGTCCTTGCCCGTATAGCT
* * * *
15531409 CACATGGCCTGGGCACACGCCTTTGTCTTTGCCCGTGTGGCT
1 CACATGGCCTGGGCACACGCCTATGTCCTTGCCCGTATAGCT
* * *
15531451 TACACGGACTGGGCACACGCCTATGTCC
1 CACATGGCCTGGGCACACGCCTATGTCC
15531479 CTAGCCGTGT
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.17, C:0.33, G:0.24, T:0.26
Consensus pattern (42 bp):
CACATGGCCTGGGCACACGCCTATGTCCTTGCCCGTATAGCT
Found at i:15532797 original size:17 final size:18
Alignment explanation
Indices: 15532775--15532809 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
15532765 GTAAATAAAC
15532775 ATAAAAGAAT-AAAGAAA
1 ATAAAAGAATAAAAGAAA
15532792 ATAAAAGAATAAAAGAAA
1 ATAAAAGAATAAAAGAAA
15532810 GAAATGAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (18 bp):
ATAAAAGAATAAAAGAAA
Found at i:15532802 original size:8 final size:8
Alignment explanation
Indices: 15532775--15532808 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
15532765 GTAAATAAAC
15532775 ATAAAAGA
1 ATAAAAGA
*
15532783 ATAAAGAAA
1 ATAAA-AGA
15532792 ATAAAAGA
1 ATAAAAGA
15532800 ATAAAAGA
1 ATAAAAGA
15532808 A
1 A
15532809 AGAAATGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
ATAAAAGA
Found at i:15534173 original size:43 final size:43
Alignment explanation
Indices: 15534116--15534299 Score: 246
Period size: 43 Copynumber: 4.3 Consensus size: 43
15534106 GCTTTCAAGA
* * * *
15534116 AAACGCCTCTAAAGAACGTGACCTTTAGAGGCG-TGTTTTGGAC
1 AAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCT-TTCTGTAC
15534159 AAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTCTGTAC
1 AAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTCTGTAC
*
15534202 AAACGCCGCTAAAGAACTTGACCTTTAGCGGCGCTTTCTGTAC
1 AAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTCTGTAC
** * ** *
15534245 AAACG-CGCTAAAGGCCATGTTCTTTAGCGGCGCTTTCTCTAC
1 AAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTCTGTAC
15534287 AAACGCCGCTAAA
1 AAACGCCGCTAAA
15534300 AATGTATGTT
Statistics
Matches: 128, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
42 36 0.28
43 91 0.71
44 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTCTGTAC
Found at i:15534270 original size:42 final size:43
Alignment explanation
Indices: 15534079--15534299 Score: 243
Period size: 43 Copynumber: 5.1 Consensus size: 43
15534069 AAAAAACACT
* * *
15534079 GCTAAAGAACAAGACTTTTAGCGGCGCGCTTTCAAG-A-AAACGCC
1 GCTAAAGAACATGACCTTTAGC-G-GCGCTTTC-TGTACAAACGCC
* * * * *
15534123 TCTAAAGAACGTGACCTTTAGAGGCG-TGTTTTGGACAAACGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCT-TTCTGTACAAACGCC
*
15534166 GCTAAAGAACGTGACCTTTAGCGGCGCTTTCTGTACAAACGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTCTGTACAAACGCC
*
15534209 GCTAAAGAACTTGACCTTTAGCGGCGCTTTCTGTACAAACG-C
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTCTGTACAAACGCC
** ** *
15534251 GCTAAAGGCCATGTTCTTTAGCGGCGCTTTCTCTACAAACGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTCTGTACAAACGCC
15534294 GCTAAA
1 GCTAAA
15534300 AATGTATGTT
Statistics
Matches: 154, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
41 2 0.01
42 42 0.27
43 92 0.60
44 18 0.12
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.24
Consensus pattern (43 bp):
GCTAAAGAACATGACCTTTAGCGGCGCTTTCTGTACAAACGCC
Found at i:15534280 original size:85 final size:86
Alignment explanation
Indices: 15534079--15534299 Score: 250
Period size: 85 Copynumber: 2.6 Consensus size: 86
15534069 AAAAAACACT
* * * * * *
15534079 GCTAAAGAACAAGACTTTTAGCGGCGCGCTT-TCAAGAAAACGCCTCTAAAGAACGTGACCTTTA
1 GCTAAAGAACATGACCTTTAGCGGCGC-TTTCTCTA-CAAACGCCGCTAAAGAACGTGACCTTTA
*
15534143 GAGGCGTGTTTTGGACAAACGCC
64 GAGGCGTGTTCTGGACAAACGCC
* * * *
15534166 GCTAAAGAACGTGACCTTTAGCGGCGCTTTCTGTACAAACGCCGCTAAAGAACTTGACCTTTAGC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTCTCTACAAACGCCGCTAAAGAACGTGACCTTTAGA
*
15534231 GGCGCT-TTCTGTACAAACG-C
66 GGCG-TGTTCTGGACAAACGCC
** **
15534251 GCTAAAGGCCATGTTCTTTAGCGGCGCTTTCTCTACAAACGCCGCTAAA
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTCTCTACAAACGCCGCTAAA
15534300 AATGTATGTT
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
85 44 0.39
86 43 0.38
87 27 0.24
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.24
Consensus pattern (86 bp):
GCTAAAGAACATGACCTTTAGCGGCGCTTTCTCTACAAACGCCGCTAAAGAACGTGACCTTTAGA
GGCGTGTTCTGGACAAACGCC
Found at i:15534470 original size:47 final size:47
Alignment explanation
Indices: 15534393--15534533 Score: 228
Period size: 47 Copynumber: 3.0 Consensus size: 47
15534383 AATCCTTCCT
* *
15534393 GCAACATCAAATCCAACCAATGACAGCAAATCTGAATGATACTTCAA
1 GCAACATCAAATCCAACCAATAACAGCAAATCTAAATGATACTTCAA
*
15534440 GCAACATCAAATCCAACCAATAACAACAAATCTAAATGATACTTCAA
1 GCAACATCAAATCCAACCAATAACAGCAAATCTAAATGATACTTCAA
* * *
15534487 GAAACATCAAATCCAACCAATAATAGCAAATCTAAATGATACATCAA
1 GCAACATCAAATCCAACCAATAACAGCAAATCTAAATGATACTTCAA
15534534 AAATTTAATG
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 87 1.00
ACGTcount: A:0.50, C:0.24, G:0.07, T:0.19
Consensus pattern (47 bp):
GCAACATCAAATCCAACCAATAACAGCAAATCTAAATGATACTTCAA
Found at i:15549840 original size:25 final size:24
Alignment explanation
Indices: 15549794--15549842 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
15549784 ACATATATAT
*
15549794 TTAAAAATATTTTCAAAAAAAAAC
1 TTAAAAATATTTGCAAAAAAAAAC
*
15549818 TTAAAAATAATTTGGAAACAAAAAA
1 TTAAAAAT-ATTTGCAAA-AAAAAA
15549843 GGTTTTGCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 7 0.33
26 6 0.29
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (24 bp):
TTAAAAATATTTGCAAAAAAAAAC
Found at i:15551509 original size:12 final size:12
Alignment explanation
Indices: 15551492--15551516 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15551482 CATAAGGAGT
15551492 AAACAATGATGA
1 AAACAATGATGA
15551504 AAACAATGATGA
1 AAACAATGATGA
15551516 A
1 A
15551517 CTAAAAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (12 bp):
AAACAATGATGA
Found at i:15552942 original size:15 final size:15
Alignment explanation
Indices: 15552919--15552950 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
15552909 AAATAATAAT
15552919 TTATATATATTTATC
1 TTATATATATTTATC
*
15552934 TTATTTATATTTATC
1 TTATATATATTTATC
15552949 TT
1 TT
15552951 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATATATATTTATC
Found at i:15553008 original size:14 final size:14
Alignment explanation
Indices: 15552976--15553030 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
15552966 AAATTATACT
*
15552976 CTAAACTTGAAACC
1 CTAAACCTGAAACC
* *
15552990 TTAAACCTGAGACC
1 CTAAACCTGAAACC
15553004 CTAAACCCT-AAACC
1 CTAAA-CCTGAAACC
*
15553018 CTAAACCTTAAAC
1 CTAAACCTGAAAC
15553031 AACAAACACC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 3 0.09
14 28 0.82
15 3 0.09
ACGTcount: A:0.42, C:0.33, G:0.05, T:0.20
Consensus pattern (14 bp):
CTAAACCTGAAACC
Found at i:15553011 original size:7 final size:7
Alignment explanation
Indices: 15553001--15553030 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
15552991 TAAACCTGAG
15553001 ACCCTAA
1 ACCCTAA
15553008 ACCCTAA
1 ACCCTAA
15553015 ACCCTAA
1 ACCCTAA
*
15553022 ACCTTAA
1 ACCCTAA
15553029 AC
1 AC
15553031 AACAAACACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.43, C:0.40, G:0.00, T:0.17
Consensus pattern (7 bp):
ACCCTAA
Found at i:15557821 original size:25 final size:26
Alignment explanation
Indices: 15557784--15557836 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
15557774 TCAAACATGC
15557784 ATTTAGGTCAATTTAACC-CTAGGGGT
1 ATTTAGGTCAATTT-ACCACTAGGGGT
*
15557810 ATTTTGGT-AATTTACCTACTAGGGGT
1 ATTTAGGTCAATTTACC-ACTAGGGGT
15557836 A
1 A
15557837 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 3 0.12
25 5 0.21
26 16 0.67
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTACCACTAGGGGT
Found at i:15559354 original size:26 final size:26
Alignment explanation
Indices: 15559318--15559425 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
15559308 TGAAATTCCG
15559318 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
15559344 ATCATGGAACAATTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
15559370 ATCATGAAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
15559396 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
15559422 ATCA
1 ATCA
15559426 ATTTGTACCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:15566445 original size:26 final size:26
Alignment explanation
Indices: 15566409--15566516 Score: 207
Period size: 26 Copynumber: 4.2 Consensus size: 26
15566399 TGAAATTCCG
15566409 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
15566435 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
15566461 ATCATGGAACATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
15566487 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
15566513 ATCA
1 ATCA
15566517 ATTTGTACCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:15571360 original size:36 final size:35
Alignment explanation
Indices: 15571277--15571361 Score: 116
Period size: 36 Copynumber: 2.4 Consensus size: 35
15571267 TTAGTAATAT
*
15571277 TCAATTATTCAGTAGAATTAGTTATTCAGTAACAA
1 TCAATTATTCAGTAGAATCAGTTATTCAGTAACAA
* ** *
15571312 TCATTTGCTCAGTAGGAATCAGTTATTCAGTAACGA
1 TCAATTATTCAGTA-GAATCAGTTATTCAGTAACAA
15571348 TCAATTATTCAGTA
1 TCAATTATTCAGTA
15571362 ACAGTCAGTC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 11 0.27
36 30 0.73
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (35 bp):
TCAATTATTCAGTAGAATCAGTTATTCAGTAACAA
Found at i:15571362 original size:18 final size:19
Alignment explanation
Indices: 15571277--15571363 Score: 76
Period size: 18 Copynumber: 4.8 Consensus size: 19
15571267 TTAGTAATAT
15571277 TCAATTATTCAGT-A-GAA
1 TCAATTATTCAGTAACGAA
* *
15571294 TTAGTTATTCAGTAAC-AA
1 TCAATTATTCAGTAACGAA
* ** *
15571312 TCATTTGCTCAGT-AGGAA
1 TCAATTATTCAGTAACGAA
*
15571330 TCAGTTATTCAGTAACG-A
1 TCAATTATTCAGTAACGAA
15571348 TCAATTATTCAGTAAC
1 TCAATTATTCAGTAAC
15571364 AGTCAGTCAT
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
17 12 0.22
18 40 0.74
19 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (19 bp):
TCAATTATTCAGTAACGAA
Found at i:15571370 original size:36 final size:34
Alignment explanation
Indices: 15571277--15571376 Score: 101
Period size: 36 Copynumber: 2.8 Consensus size: 34
15571267 TTAGTAATAT
*
15571277 TCAATTATTCAGTAGAATTAGTTATTCAGTAACAA
1 TCAATTATTCAGTA-AATCAGTTATTCAGTAACAA
* ** *
15571312 TCATTTGCTCAGTAGGAATCAGTTATTCAGTAACGA
1 TCAATTATTCAGTA--AATCAGTTATTCAGTAACAA
*
15571348 TCAATTATTCAGTAACAGTCAGTCATTCA
1 TCAATTATTCAGTAA-A-TCAGTTATTCA
15571377 ATACTTTTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
34 1 0.02
35 12 0.23
36 40 0.75
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (34 bp):
TCAATTATTCAGTAAATCAGTTATTCAGTAACAA
Found at i:15571375 original size:18 final size:18
Alignment explanation
Indices: 15571296--15571376 Score: 67
Period size: 18 Copynumber: 4.5 Consensus size: 18
15571286 CAGTAGAATT
*
15571296 AGTTATTCAGTAACAATC
1 AGTTATTCAGTAACGATC
* ** *
15571314 ATTTGCTCAGT-AGGAATC
1 AGTTATTCAGTAACG-ATC
15571332 AGTTATTCAGTAACGATC
1 AGTTATTCAGTAACGATC
*
15571350 AATTATTCAGTAAC-AGTC
1 AGTTATTCAGTAACGA-TC
*
15571368 AGTCATTCA
1 AGTTATTCA
15571377 ATACTTTTAT
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
17 2 0.04
18 44 0.92
19 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (18 bp):
AGTTATTCAGTAACGATC
Found at i:15577078 original size:17 final size:18
Alignment explanation
Indices: 15577046--15577089 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
15577036 AATAATAAAG
*
15577046 TAAATAAACATAAAAGAA
1 TAAAGAAACATAAAAGAA
15577064 TAAAGAAAC-TAAAAGAA
1 TAAAGAAACATAAAAGAA
15577081 TAAAAGAAA
1 T-AAAGAAA
15577090 GAAATGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.14
Consensus pattern (18 bp):
TAAAGAAACATAAAAGAA
Found at i:15583885 original size:17 final size:19
Alignment explanation
Indices: 15583863--15583903 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
15583853 TATAATATAT
15583863 TATATTA-T-TATATAGAG
1 TATATTACTATATATAGAG
15583880 TATATTACTATATATAGAG
1 TATATTACTATATATAGAG
15583899 TATAT
1 TATAT
15583904 AGCATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 7 0.32
18 1 0.05
19 14 0.64
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (19 bp):
TATATTACTATATATAGAG
Found at i:15597714 original size:107 final size:107
Alignment explanation
Indices: 15597507--15597774 Score: 293
Period size: 107 Copynumber: 2.5 Consensus size: 107
15597497 CCTATCATCG
* * *
15597507 CGATGGCTGAGATCCTACATATGTTGCGGATTCTTAACAACTTGTATGAGCAGCATCGTAAACTA
1 CGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGACAACTTGTGTGAGCAGCATCGTAAACTA
* * ** * ** * * * *
15597572 TTGAATTGAATGGCTACTCTATTTTGATGACATAGACCGTTT
66 GTGAAATGAATAACTACACTATACTGACGAAATAGACCATTA
* * * *
15597614 CGATGGCTGAGATCCTGCACATGTTTCGGATTCTTGACAACTTGTGTGAGCAGCATCGTGAACTG
1 CGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGACAACTTGTGTGAGCAGCATCGTAAACTA
* * **
15597679 GTGAAATGACTAACTACACTGTACTGACGAAATAGATTATTA
66 GTGAAATGAATAACTACACTATACTGACGAAATAGACCATTA
* ** * *
15597721 CGATGGTTGAGATCCTGCATATGTTGCAAATTCTTGTCAACATGTGTGAGCAGC
1 CGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGACAACTTGTGTGAGCAGC
15597775 CTTATGAACC
Statistics
Matches: 132, Mismatches: 29, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
107 132 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (107 bp):
CGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGACAACTTGTGTGAGCAGCATCGTAAACTA
GTGAAATGAATAACTACACTATACTGACGAAATAGACCATTA
Found at i:15598762 original size:21 final size:21
Alignment explanation
Indices: 15598731--15598779 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
15598721 GCATACGGTT
15598731 GAGCC-CATGGGCT-TGTGGGA
1 GAGCCACATGGG-TGTGTGGGA
15598751 TG-GCCACATGGGTGTGTGGGA
1 -GAGCCACATGGGTGTGTGGGA
15598772 GAGCCACA
1 GAGCCACA
15598780 CGGCTGAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.18, C:0.20, G:0.43, T:0.18
Consensus pattern (21 bp):
GAGCCACATGGGTGTGTGGGA
Found at i:15601513 original size:42 final size:42
Alignment explanation
Indices: 15601464--15601606 Score: 170
Period size: 41 Copynumber: 3.5 Consensus size: 42
15601454 GTAACAGTGA
15601464 TATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTAT
1 TATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTAT
* *
15601506 GT-TATCAGGCTTATTGCCTGGCAGGCTTT-ATTCCGGTGTAT
1 -TATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTAT
* * * *
15601547 TAAATCAGGTTTATTACCTAGCAGGCTCTG-TGCCGGTGTAT
1 TATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTAT
*
15601588 TAT-TTAGGCTT-TATGCCTA
1 TATATCAGGCTTAT-TGCCTA
15601607 ACAAATTTTA
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
39 1 0.01
40 12 0.14
41 45 0.53
42 26 0.31
43 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (42 bp):
TATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTAT
Found at i:15602273 original size:39 final size:37
Alignment explanation
Indices: 15602173--15602265 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
15602163 ATGGCATGTA
* *
15602173 TATTTTGTCCGATCTTGGATATGTATAGGCTAATATG
1 TATTATGTCTGATCTTGGATATGTATAGGCTAATATG
*
15602210 TATTTTGTCTGATCTTGGATATGTATAGGCTAACTTATG
1 TATTATGTCTGATCTTGGATATGTATAGGCTAA--TATG
* *
15602249 T-TTATGTTTGATTTTGG
1 TATTATGTCTGATCTTGG
15602266 GTTATGTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
37 32 0.64
38 13 0.26
39 5 0.10
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.48
Consensus pattern (37 bp):
TATTATGTCTGATCTTGGATATGTATAGGCTAATATG
Found at i:15609541 original size:27 final size:27
Alignment explanation
Indices: 15609493--15609651 Score: 166
Period size: 27 Copynumber: 5.9 Consensus size: 27
15609483 ACGAGGCTGC
* *
15609493 CAGATATTGT-GAAGAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
**
15609520 CAGATATTGTCACAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
15609546 CAGATATATGTGGCAGAGCCACTAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
15609573 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
15609600 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
15609627 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
15609652 GACGCTTCCT
Statistics
Matches: 112, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
26 10 0.09
27 96 0.86
28 6 0.05
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:15609601 original size:54 final size:54
Alignment explanation
Indices: 15609535--15609651 Score: 216
Period size: 54 Copynumber: 2.2 Consensus size: 54
15609525 ATTGTCACAG
*
15609535 AGCCACCAGAACAGATATATGTGGCAGAGCCACTAGATCAGATAATCGTGGCAT
1 AGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAT
*
15609589 AGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCAT
1 AGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAT
15609643 AGCCACCAG
1 AGCCACCAG
15609652 GACGCTTCCT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (54 bp):
AGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAT
Found at i:15611306 original size:26 final size:26
Alignment explanation
Indices: 15611271--15611378 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
15611261 TGAAATGCCC
* *
15611271 ATCATTGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
15611297 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* **
15611323 ATCATGGAATATTTACCTAATTCATT
1 ATCATGGAACATTTACCTAACCCATT
15611349 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
15611375 ATCA
1 ATCA
15611379 ATTTGTACCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:15616440 original size:19 final size:19
Alignment explanation
Indices: 15616412--15616449 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
15616402 GTCTCATTTT
*
15616412 TATTTGTTTTTTGTTTTAA
1 TATTTGTTTTATGTTTTAA
*
15616431 TATTTTTTTTATGTTTTAA
1 TATTTGTTTTATGTTTTAA
15616450 ATGTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (19 bp):
TATTTGTTTTATGTTTTAA
Found at i:15616458 original size:18 final size:19
Alignment explanation
Indices: 15616418--15616460 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
15616408 TTTTTATTTG
* * *
15616418 TTTTTTGTTTTAATATTTT
1 TTTTATGTTTTAATATGTA
15616437 TTTTATGTTTTAA-ATGTA
1 TTTTATGTTTTAATATGTA
15616455 TTTTAT
1 TTTTAT
15616461 TTATTATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (19 bp):
TTTTATGTTTTAATATGTA
Found at i:15616467 original size:25 final size:24
Alignment explanation
Indices: 15616439--15616487 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
15616429 AATATTTTTT
*
15616439 TTATGTTTTAAATGTATTTTATTTA
1 TTATATTTTAAA-GTATTTTATTTA
*
15616464 TTATATTTTAAAGTTTTTTATTTA
1 TTATATTTTAAAGTATTTTATTTA
15616488 ATTAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (24 bp):
TTATATTTTAAAGTATTTTATTTA
Found at i:15619039 original size:26 final size:26
Alignment explanation
Indices: 15618999--15619096 Score: 151
Period size: 26 Copynumber: 3.8 Consensus size: 26
15618989 TGCTATTGGG
*
15618999 TTAGGTAAATGTTCCATGATAATAGA
1 TTAGGTAAATGTTCCATGATAATGGA
* *
15619025 TTAGGTAAATATTCCATGATAATGGG
1 TTAGGTAAATGTTCCATGATAATGGA
*
15619051 TTAGGTAAATGTTCCATGATAATGGT
1 TTAGGTAAATGTTCCATGATAATGGA
*
15619077 TTAGTTAAATGTTCCATGAT
1 TTAGGTAAATGTTCCATGAT
15619097 GGGCATTTCA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 66 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (26 bp):
TTAGGTAAATGTTCCATGATAATGGA
Found at i:15619057 original size:52 final size:52
Alignment explanation
Indices: 15618995--15619096 Score: 168
Period size: 52 Copynumber: 2.0 Consensus size: 52
15618985 AAATTGCTAT
15618995 TGGGTTAGGTAAATGTTCCATGATAATAGATTAGGTAAATATTCCATGATAA
1 TGGGTTAGGTAAATGTTCCATGATAATAGATTAGGTAAATATTCCATGATAA
* * * *
15619047 TGGGTTAGGTAAATGTTCCATGATAATGGTTTAGTTAAATGTTCCATGAT
1 TGGGTTAGGTAAATGTTCCATGATAATAGATTAGGTAAATATTCCATGAT
15619097 GGGCATTTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (52 bp):
TGGGTTAGGTAAATGTTCCATGATAATAGATTAGGTAAATATTCCATGATAA
Found at i:15627206 original size:26 final size:26
Alignment explanation
Indices: 15627177--15627284 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
15627167 TGGTACAAAT
15627177 TGATAAT-GAGTTAGGTAAATGTTCCA
1 TGATAATGGA-TTAGGTAAATGTTCCA
*
15627203 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
15627229 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
15627255 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
15627281 TGAT
1 TGAT
15627285 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
26 75 0.97
27 2 0.03
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:15629854 original size:19 final size:19
Alignment explanation
Indices: 15629808--15629855 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
15629798 GTATATATTT
15629808 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
15629826 TAAATCTTATTT-GGTTAGA
1 TAAATTTTATTTAGG-TAGA
*
15629845 TAAGTTTTATT
1 TAAATTTTATT
15629856 CATATTCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:15629917 original size:43 final size:43
Alignment explanation
Indices: 15629869--15629961 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
15629859 ATTCTAGAAA
15629869 TATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
1 TATTTTCT-TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
* *
15629912 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
15629955 TATTTTC
1 TATTTTC
15629962 CCAATTAGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (43 bp):
TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
Found at i:15633668 original size:19 final size:19
Alignment explanation
Indices: 15633622--15633669 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
15633612 GTATATATTT
15633622 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
15633640 TAAATCTTATTT-GGATAGA
1 TAAATTTTATTTAGG-TAGA
*
15633659 TAAGTTTTATT
1 TAAATTTTATT
15633670 CATATTCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:15633731 original size:43 final size:43
Alignment explanation
Indices: 15633683--15633775 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
15633673 ATTCTAGAAA
15633683 TATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
1 TATTTTCT-TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
* *
15633726 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
15633769 TATTTTC
1 TATTTTC
15633776 CCAATTAGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (43 bp):
TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
Found at i:15634606 original size:7 final size:7
Alignment explanation
Indices: 15634594--15634634 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
15634584 CTTGTGAAAA
15634594 ATAATAT
1 ATAATAT
*
15634601 ATAATAA
1 ATAATAT
15634608 ATAATA-
1 ATAATAT
*
15634614 AT-ATAA
1 ATAATAT
15634620 ATAATAT
1 ATAATAT
15634627 ATAATAT
1 ATAATAT
15634634 A
1 A
15634635 AAAATAAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 3 0.10
6 4 0.13
7 23 0.77
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:15634609 original size:14 final size:14
Alignment explanation
Indices: 15634549--15634632 Score: 70
Period size: 14 Copynumber: 6.0 Consensus size: 14
15634539 CTTTAATGAT
15634549 AATAATATATAGATA
1 AATAATATATA-ATA
*
15634564 AA-AATGTATAATGA
1 AATAATATATAAT-A
*
15634578 TAATAACT-TGTGAA-A
1 -AATAA-TATAT-AATA
15634593 AATAATATATAATA
1 AATAATATATAATA
15634607 AATAATA-AT-ATA
1 AATAATATATAATA
15634619 AATAATATATAATA
1 AATAATATATAATA
15634633 TAAAAATAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 19
0.72 0.04 0.24
Matches are distributed among these distances:
12 10 0.18
13 9 0.16
14 26 0.46
15 5 0.09
16 4 0.07
17 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (14 bp):
AATAATATATAATA
Found at i:15634689 original size:18 final size:19
Alignment explanation
Indices: 15634649--15634699 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
15634639 TAAGGTTAAA
*
15634649 GATAAAACAAAT-TACAAT
1 GATAAAAAAAATATACAAT
*
15634667 TATAAAAAAAATATAC-AT
1 GATAAAAAAAATATACAAT
* *
15634685 GATAATAAATATATA
1 GATAAAAAAAATATA
15634700 TATATATAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (19 bp):
GATAAAAAAAATATACAAT
Found at i:15639602 original size:27 final size:27
Alignment explanation
Indices: 15639562--15639623 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
15639552 AGATTCCAAT
*
15639562 CAAACACACCAGAACAAAGAATCCTCC
1 CAAACACACAAGAACAAAGAATCCTCC
* * *
15639589 CAAACACACAAGAATAAATAATCCTTC
1 CAAACACACAAGAACAAAGAATCCTCC
15639616 CAAACACA
1 CAAACACA
15639624 ACAGAAAGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.52, C:0.32, G:0.05, T:0.11
Consensus pattern (27 bp):
CAAACACACAAGAACAAAGAATCCTCC
Found at i:15640813 original size:18 final size:18
Alignment explanation
Indices: 15640770--15640816 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
15640760 CTTGTCCTGA
* *
15640770 TTTAATTTAATTTATTTG
1 TTTAATATAATTTATATG
*
15640788 TTTTATATAATTTAATAT-
1 TTTAATATAATTT-ATATG
15640806 TTTAATATAAT
1 TTTAATATAAT
15640817 AAAAATCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTAATATAATTTATATG
Found at i:15642425 original size:40 final size:40
Alignment explanation
Indices: 15642370--15642448 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
15642360 GTACGGTACC
*
15642370 ACTTGGTGTGTAGGGTTGGATGGGTTGATTCTATCCCCAT
1 ACTTGGTGTGTAGGGTTGGATGGGTCGATTCTATCCCCAT
* *
15642410 ACTTGGTGTGTAGGGTTGGGTGGGTCGATTTTATCCCCA
1 ACTTGGTGTGTAGGGTTGGATGGGTCGATTCTATCCCCA
15642449 AATGGTGTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.14, C:0.15, G:0.34, T:0.37
Consensus pattern (40 bp):
ACTTGGTGTGTAGGGTTGGATGGGTCGATTCTATCCCCAT
Found at i:15642465 original size:38 final size:40
Alignment explanation
Indices: 15642373--15642467 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 40
15642363 CGGTACCACT
* *
15642373 TGGTGTGTAGGGTTGGATGGGTTGATTCTATCCCCATACT
1 TGGTGTGTAGGGTTGGATGGGTCGATTCTATCCCCATACA
* *
15642413 TGGTGTGTAGGGTTGGGTGGGTCGATTTTATCCCCA-A-A
1 TGGTGTGTAGGGTTGGATGGGTCGATTCTATCCCCATACA
15642451 TGGTGTGTTA-GGTTGGA
1 TGGTGTG-TAGGGTTGGA
15642468 CGGAGTTGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 13 0.27
39 3 0.06
40 33 0.67
ACGTcount: A:0.15, C:0.12, G:0.37, T:0.37
Consensus pattern (40 bp):
TGGTGTGTAGGGTTGGATGGGTCGATTCTATCCCCATACA
Found at i:15644120 original size:23 final size:23
Alignment explanation
Indices: 15644092--15644203 Score: 93
Period size: 23 Copynumber: 4.8 Consensus size: 23
15644082 AACTATATTA
15644092 GGAAGCTCACAAAGAGCCTATCG
1 GGAAGCTCACAAAGAGCCTATCG
* *** *
15644115 AGAAGCTC-TGGATAGCCATATATCG
1 GGAAGCTCACAAAGAGCC---TATCG
* **
15644140 GGAAGTTCA-AGCGAGCACTATCG
1 GGAAGCTCACAAAGAGC-CTATCG
15644163 GGAAGCTCACAAAGAGCCTATCG
1 GGAAGCTCACAAAGAGCCTATCG
*
15644186 GGAAGCTCACGAAGAGCC
1 GGAAGCTCACAAAGAGCC
15644204 ATATATCGGG
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
22 5 0.07
23 43 0.62
24 5 0.07
25 15 0.22
26 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.28, T:0.15
Consensus pattern (23 bp):
GGAAGCTCACAAAGAGCCTATCG
Found at i:15644132 original size:71 final size:71
Alignment explanation
Indices: 15644057--15644193 Score: 152
Period size: 71 Copynumber: 1.9 Consensus size: 71
15644047 AGCTCAATAG
* * *
15644057 AGCCA-AAATTAGGTAGTTCATAAAGAACTA-TATTAGGAAGCTCACAAAGAGCCTATCGAGAAG
1 AGCCATAAATCAGGAAGTTCA-AAAGAAC-ACTATCAGGAAGCTCACAAAGAGCCTATCGAGAAG
15644120 CTCTGGAT
64 CTCTGGAT
* * ** * * *
15644128 AGCCATATATCGGGAAGTTCAAGCGAGCACTATCGGGAAGCTCACAAAGAGCCTATCGGGAAGCT
1 AGCCATAAATCAGGAAGTTCAAAAGAACACTATCAGGAAGCTCACAAAGAGCCTATCGAGAAGCT
15644193 C
66 C
15644194 ACGAAGAGCC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
70 1 0.02
71 42 0.78
72 11 0.20
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (71 bp):
AGCCATAAATCAGGAAGTTCAAAAGAACACTATCAGGAAGCTCACAAAGAGCCTATCGAGAAGCT
CTGGAT
Found at i:15646389 original size:18 final size:20
Alignment explanation
Indices: 15646362--15646410 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
15646352 TAATTAATAA
* *
15646362 TAAAATAATAAAATATCTCAT
1 TAAAATAAT-ATATATCTAAT
15646383 TAAAATAATATATATCTAAT
1 TAAAATAATATATATCTAAT
15646403 T-AAATAAT
1 TAAAATAAT
15646411 CATAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 7 0.27
20 10 0.38
21 9 0.35
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAATAATATATATCTAAT
Found at i:15646399 original size:20 final size:21
Alignment explanation
Indices: 15646362--15646421 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
15646352 TAATTAATAA
*
15646362 TAAAATAATAAAATATCTCAT
1 TAAAATAATAAAATATCTAAT
*
15646383 TAAAATAAT-ATATATCTAAT
1 TAAAATAATAAAATATCTAAT
*
15646403 TAAATAATCATAAAATATC
1 T-AA-AATAATAAAATATC
15646422 ATCAACATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.31
21 11 0.34
22 5 0.16
23 6 0.19
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATAATAAAATATCTAAT
Found at i:15654465 original size:40 final size:40
Alignment explanation
Indices: 15654404--15654479 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
15654394 ACTTGATATC
* * *
15654404 TCGCACACTAAGTGCCGTATATAGTCGAAGCTATCTCAAA
1 TCGCACACTAAGTGCCATATATAGCCAAAGCTATCTCAAA
* *
15654444 TCGCACACTAAGTTCTATATATAGCCAAAGCTATCT
1 TCGCACACTAAGTGCCATATATAGCCAAAGCTATCT
15654480 TGATCTCACA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATATATAGCCAAAGCTATCTCAAA
Found at i:15661780 original size:41 final size:40
Alignment explanation
Indices: 15661727--15661873 Score: 204
Period size: 41 Copynumber: 3.6 Consensus size: 40
15661717 CTTTCTCAAA
*
15661727 TCGCACACTAAGTGCCATATATAGCCGAAGTTATCTCGACC
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCGA-C
* *
15661768 TCGCACACTAAGTGCCATATATAGTCGAAGCTATCTTGATC
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCGA-C
* * * *
15661809 TCGCACACTAAATGACATATATAGCCGAAGCTATGTCGAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCGAC
*
15661849 TCGCACACTAAGTGCCACATATAGC
1 TCGCACACTAAGTGCCATATATAGC
15661874 TGATTTGTCG
Statistics
Matches: 93, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 22 0.24
41 71 0.76
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCGAC
Found at i:15668344 original size:27 final size:26
Alignment explanation
Indices: 15668307--15668421 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
15668297 AGCATGGCTG
* *
15668307 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
15668333 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
15668361 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
15668388 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
15668415 CCAGAAC
1 CCAGAAC
15668422 GCTTGCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:15668366 original size:54 final size:54
Alignment explanation
Indices: 15668307--15668421 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
15668297 AGCATGGCTG
*
15668307 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
15668361 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
15668415 CCAGAAC
1 CCAGAAC
15668422 GCTTGCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:15670079 original size:26 final size:26
Alignment explanation
Indices: 15670038--15670145 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
15670028 ACATGAAATC
*
15670038 TATCAT-GAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCTAT
* *
15670063 TATCATGAAACATTTACCTAACCGAT
1 TATCATGGAACATTTACCTAACCTAT
15670089 TATCATGGAACATTTACCTAACCTAT
1 TATCATGGAACATTTACCTAACCTAT
*
15670115 TATCATGGAACATATACCTAACCTAT
1 TATCATGGAACATTTACCTAACCTAT
15670141 TATCA
1 TATCA
15670146 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 6 0.08
26 71 0.92
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
TATCATGGAACATTTACCTAACCTAT
Found at i:15676402 original size:27 final size:26
Alignment explanation
Indices: 15676365--15676479 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
15676355 AGCATGGCTG
* *
15676365 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
15676391 CCAGATACAGATAATCATGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
15676419 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
15676446 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
15676473 CCAGAAC
1 CCAGAAC
15676480 GCTTCCTCCA
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
26 5 0.06
27 57 0.73
28 16 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:15676429 original size:54 final size:54
Alignment explanation
Indices: 15676365--15676479 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
15676355 AGCATGGCTG
*
15676365 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCATGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCATGGCAGAGCCA
* * ** *
15676419 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCATGGCAGAGCCA
15676473 CCAGAAC
1 CCAGAAC
15676480 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCATGGCAGAGCCA
Found at i:15678114 original size:26 final size:26
Alignment explanation
Indices: 15678078--15678186 Score: 157
Period size: 26 Copynumber: 4.2 Consensus size: 26
15678068 CATGAAATTC
15678078 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
15678104 TTATCATGAAACA-TTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
15678129 TTATCATGGAATATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* * *
15678155 TTATCATGGAACATATACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
15678181 TTATCA
1 TTATCA
15678187 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 23 0.30
26 54 0.70
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:15678158 original size:51 final size:52
Alignment explanation
Indices: 15678078--15678186 Score: 166
Period size: 51 Copynumber: 2.1 Consensus size: 52
15678068 CATGAAATTC
15678078 TTATCATGAAACATTTACCTAACCCATTATCATGAAACAT-TACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATATACCTAACCCA
* * * * *
15678129 TTATCATGGAATATTTACCTAACCTATTATCATGGAACATATACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATATACCTAACCCA
15678181 TTATCA
1 TTATCA
15678187 ATTTGTATCA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
51 36 0.69
52 16 0.31
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.33
Consensus pattern (52 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGAAACATATACCTAACCCA
Found at i:15687132 original size:26 final size:26
Alignment explanation
Indices: 15687086--15687138 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
15687076 TCAAACATGC
*
15687086 ATTTAGGTCAATTTAACCCTATGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* *
15687112 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAAC-CCTAGGGGT
15687138 A
1 A
15687139 AAAGTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:15688655 original size:26 final size:26
Alignment explanation
Indices: 15688624--15688731 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
15688614 TGAAATGCCC
*
15688624 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
15688650 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
15688676 ATCATGGAATATTTACCCAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
15688702 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
15688728 ATCA
1 ATCA
15688732 ATTTGTATCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:15689805 original size:47 final size:47
Alignment explanation
Indices: 15689735--15689863 Score: 186
Period size: 47 Copynumber: 2.7 Consensus size: 47
15689725 CACAATTGAT
*
15689735 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTTATCCCA
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCA
* * * * *
15689782 GAGTACCTATACAATGGCCCATAGCCAAATCAAGGTAGCTCCTCTCA
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCA
* *
15689829 AAATACCTATACCATGGCCCGTAGCCAAATCAAGG
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGG
15689864 CATTATTCAC
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.20
Consensus pattern (47 bp):
AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCA
Found at i:15695136 original size:17 final size:17
Alignment explanation
Indices: 15695095--15695160 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 17
15695085 CTTCGCAACT
***
15695095 TTGATGAGCTCACAGCC
1 TTGATGAGCTCACAAAA
*
15695112 TTGGTGAGCTCACAAAA
1 TTGATGAGCTCACAAAA
** * *
15695129 TTGATGAGCTCGTACAT
1 TTGATGAGCTCACAAAA
15695146 TTGATGAGCTCACAA
1 TTGATGAGCTCACAA
15695161 TCTTAGTGAG
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (17 bp):
TTGATGAGCTCACAAAA
Found at i:15695217 original size:35 final size:35
Alignment explanation
Indices: 15695129--15695233 Score: 101
Period size: 34 Copynumber: 3.1 Consensus size: 35
15695119 GCTCACAAAA
* * *
15695129 TTGATGAGCTCGTACATTT-GATGAGCTCACAATCT
1 TTGATGAGCTCGTACCTTTGGGTAAGCTCAC-ATCT
* *
15695164 TAG-TGAGCTC-TCAACTTTGGGTAAGCTCACATCT
1 TTGATGAGCTCGT-ACCTTTGGGTAAGCTCACATCT
* *
15695198 TTGATGAGCTCGTACCTTTGGG-AAGTTCGCATCT
1 TTGATGAGCTCGTACCTTTGGGTAAGCTCACATCT
15695232 TT
1 TT
15695234 ACGACTTGTG
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
33 1 0.02
34 29 0.51
35 26 0.46
36 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (35 bp):
TTGATGAGCTCGTACCTTTGGGTAAGCTCACATCT
Found at i:15698631 original size:26 final size:26
Alignment explanation
Indices: 15698602--15698705 Score: 181
Period size: 26 Copynumber: 4.0 Consensus size: 26
15698592 ATTCCCATCT
*
15698602 TGGAACATTTACCTAAACCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
15698628 TGGAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
* *
15698654 TGGAATATTTACCTAATCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
15698680 TGGAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
15698706 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.33
Consensus pattern (26 bp):
TGGAACATTTACCTAACCCATTATCA
Found at i:15699344 original size:18 final size:18
Alignment explanation
Indices: 15699316--15699362 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
15699306 AATTTAAAAC
15699316 TTTTAATAAATAAATTTAA
1 TTTTAA-AAATAAATTTAA
**
15699335 TTTTAAAAATATTTTTAA
1 TTTTAAAAATAAATTTAA
*
15699353 TATTAAAAAT
1 TTTTAAAAAT
15699363 TTATAAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTAAAAATAAATTTAA
Found at i:15699756 original size:15 final size:14
Alignment explanation
Indices: 15699734--15699765 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
15699724 TGGATGAAAT
15699734 TTTAATTTTTATAA
1 TTTAATTTTTATAA
15699748 TTTATATTTTTATAA
1 TTTA-ATTTTTATAA
15699763 TTT
1 TTT
15699766 GTAAAGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTAATTTTTATAA
Found at i:15702926 original size:2 final size:2
Alignment explanation
Indices: 15702919--15702943 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15702909 TAACGTTATT
15702919 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15702944 TTGTAATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15703863 original size:24 final size:23
Alignment explanation
Indices: 15703803--15703863 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
15703793 TTATATATTC
* *
15703803 AAATTAAATTTTACAAATAATTT
1 AAATTAAATTTTAAAAATAATTA
* *
15703826 ATATTAATTATTTAAAAATAATTA
1 AAATTAAAT-TTTAAAAATAATTA
15703850 AAATTTAAATTTTA
1 AAA-TTAAATTTTA
15703864 TATATCATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 7 0.23
24 18 0.60
25 5 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATTAAATTTTAAAAATAATTA
Found at i:15706843 original size:26 final size:26
Alignment explanation
Indices: 15706814--15706866 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
15706804 TTTACAGTTT
15706814 TACCCCTAGGAGATAAATT-ACTGAAA
1 TACCCCTAGG-GATAAATTGACTGAAA
* *
15706840 TACCCCTAGGGTTAAATTGACTTAAA
1 TACCCCTAGGGATAAATTGACTGAAA
15706866 T
1 T
15706867 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACTGAAA
Found at i:15712357 original size:26 final size:26
Alignment explanation
Indices: 15712328--15712431 Score: 172
Period size: 26 Copynumber: 4.0 Consensus size: 26
15712318 TGGTACAAAT
15712328 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
15712354 TGATAGTGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
15712380 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
15712406 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
15712432 AGATGGGAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 71 1.00
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:15718277 original size:40 final size:40
Alignment explanation
Indices: 15718214--15718316 Score: 134
Period size: 40 Copynumber: 2.6 Consensus size: 40
15718204 GTTGAATAGT
* *
15718214 TATCAAAACTATTGAATCATATGAGCTTATGAGCCATACC
1 TATCAAAACTATTGAATCATATGAGCCTAAGAGCCATACC
* **
15718254 TATCGAAACTATTGAATTGTATGAGCCTAAGAGCCATACC
1 TATCAAAACTATTGAATCATATGAGCCTAAGAGCCATACC
* * *
15718294 TATCAAAACCACTAAATCATATG
1 TATCAAAACTATTGAATCATATG
15718317 CGCTTTCGAG
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (40 bp):
TATCAAAACTATTGAATCATATGAGCCTAAGAGCCATACC
Found at i:15719224 original size:15 final size:15
Alignment explanation
Indices: 15719204--15719234 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15719194 GTGACCCTTG
15719204 ACTTCAAAATTTTTA
1 ACTTCAAAATTTTTA
15719219 ACTTCAAAATTTTTA
1 ACTTCAAAATTTTTA
15719234 A
1 A
15719235 TTTCTCTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (15 bp):
ACTTCAAAATTTTTA
Found at i:15732637 original size:2 final size:2
Alignment explanation
Indices: 15732630--15732704 Score: 60
Period size: 2 Copynumber: 37.5 Consensus size: 2
15732620 AATCACCTCA
* * * * * *
15732630 AT AT AT AT AT AT GT GT GT AT AT AT AT AT GT AT AT AT AT AC AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
15732672 AT AT AC AT AT AT AT AT AC AC AC AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15732705 CATACTTTGA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.41
Consensus pattern (2 bp):
AT
Found at i:15732675 original size:20 final size:20
Alignment explanation
Indices: 15732652--15732709 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
15732642 GTGTGTATAT
*
15732652 ATATATGTATATATATACAC
1 ATATATATATATATATACAC
*
15732672 ATATACATATATATATACAC
1 ATATATATATATATATACAC
* *
15732692 ACATATATATATACATAC
1 ATATATATATATATATAC
15732710 TTTGAAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (20 bp):
ATATATATATATATATACAC
Found at i:15732703 original size:22 final size:22
Alignment explanation
Indices: 15732650--15732704 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
15732640 ATGTGTGTAT
* *
15732650 ATATATATGTATATATATACAC
1 ATATATATATATATATACACAC
*
15732672 ATATACATATATATATACACAC
1 ATATATATATATATATACACAC
15732694 ATATATATATA
1 ATATATATATA
15732705 CATACTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (22 bp):
ATATATATATATATATACACAC
Found at i:15735124 original size:14 final size:15
Alignment explanation
Indices: 15735107--15735135 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
15735097 TCACAAAAAT
15735107 TTCACACAT-ATAAA
1 TTCACACATAATAAA
15735121 TTCACACATAATAAA
1 TTCACACATAATAAA
15735136 CACAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:15751773 original size:42 final size:42
Alignment explanation
Indices: 15751723--15751848 Score: 114
Period size: 43 Copynumber: 3.0 Consensus size: 42
15751713 AATGCCTTCA
*
15751723 TCCCAGACAGGGTCTTACACGAAATCAGATACGATGTCAATG
1 TCCCAGACACGGTCTTACACGAAATCAGATACGATGTCAATG
* * *** *
15751765 TCCCAGACATGGTCTTATACGTAAATCTCA-AT-CGAACCCTATG
1 TCCCAGACACGGTCTTACACG-AAA--TCAGATACGATGTCAATG
*
15751808 TCCCAGACACGGTCTTACACGATATCTCAGATA-GATGTCAA
1 TCCCAGACACGGTCTTACACGA-A-ATCAGATACGATGTCAA
15751849 CCTTCCTTTA
Statistics
Matches: 64, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
42 23 0.36
43 36 0.56
44 2 0.03
45 3 0.05
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (42 bp):
TCCCAGACACGGTCTTACACGAAATCAGATACGATGTCAATG
Found at i:15759809 original size:41 final size:41
Alignment explanation
Indices: 15759758--15759947 Score: 290
Period size: 41 Copynumber: 4.6 Consensus size: 41
15759748 AACTGTACAA
* *
15759758 TAGCGACGCTTTTAGAAAAATGCCGCTATAGGCCGAGGTTT
1 TAGCGGCGCTTTTGGAAAAATGCCGCTATAGGCCGAGGTTT
* *
15759799 TAGCGGCGCTTTTGGAAAAACGCTGCTATAGGCCGAGGTTT
1 TAGCGGCGCTTTTGGAAAAATGCCGCTATAGGCCGAGGTTT
* * *
15759840 TAGCGGCGCTTATGGAAAAATGCCGTTATAGGCCGATGTTT
1 TAGCGGCGCTTTTGGAAAAATGCCGCTATAGGCCGAGGTTT
*
15759881 TAGCGGCGCTTTTGGAAAAATGCCGCTATAGGCCGATGTTT
1 TAGCGGCGCTTTTGGAAAAATGCCGCTATAGGCCGAGGTTT
* *
15759922 TAGCGGCGCTTATGGAAAAACGCCGC
1 TAGCGGCGCTTTTGGAAAAATGCCGC
15759948 AAAAAAGTAA
Statistics
Matches: 136, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 136 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.26
Consensus pattern (41 bp):
TAGCGGCGCTTTTGGAAAAATGCCGCTATAGGCCGAGGTTT
Found at i:15760281 original size:18 final size:18
Alignment explanation
Indices: 15760254--15760302 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
15760244 TTGTCCCTTG
15760254 TTAT-ATATATATTAA-A
1 TTATAATATATATTAAGA
*
15760270 CTTCTAATATATATTAAGA
1 -TTATAATATATATTAAGA
15760289 TTATAATATATATT
1 TTATAATATATATT
15760303 TAGGGTGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.11
18 24 0.86
19 1 0.04
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (18 bp):
TTATAATATATATTAAGA
Found at i:15760742 original size:15 final size:15
Alignment explanation
Indices: 15760722--15760753 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
15760712 TTTAATGTAG
*
15760722 AAGATAAATGTATAT
1 AAGATAAATATATAT
15760737 AAGATAAATATATAT
1 AAGATAAATATATAT
15760752 AA
1 AA
15760754 ATCATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (15 bp):
AAGATAAATATATAT
Found at i:15760792 original size:24 final size:24
Alignment explanation
Indices: 15760725--15760792 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
15760715 AATGTAGAAG
* * *
15760725 ATAAATGTATATAAGATAAATATAT
1 ATAAATATATATATGA-AAAAATAT
* *
15760750 ATAAATCAT-TATTTTAAAAAATAT
1 ATAAAT-ATATATATGAAAAAATAT
15760774 ATAAATATATATATGAAAA
1 ATAAATATATATATGAAAA
15760793 GTGGTTTAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
23 2 0.06
24 21 0.62
25 10 0.29
26 1 0.03
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (24 bp):
ATAAATATATATATGAAAAAATAT
Found at i:15765618 original size:24 final size:24
Alignment explanation
Indices: 15765591--15765658 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
15765581 ATTATTATTG
*
15765591 AAATATTCTTGTCCGTTTTATCAC
1 AAATATTATTGTCCGTTTTATCAC
* *
15765615 AAATATTATTCTCCATTTTATCAC
1 AAATATTATTGTCCGTTTTATCAC
*
15765639 AAATATTATCGTCCGTTTTA
1 AAATATTATTGTCCGTTTTA
15765659 CCATTTAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (24 bp):
AAATATTATTGTCCGTTTTATCAC
Found at i:15765879 original size:15 final size:15
Alignment explanation
Indices: 15765835--15765890 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
15765825 AACGACATGT
15765835 ATATTATTTAATTAAA
1 ATATTATTTAATT-AA
15765851 ATAATT-TTT-A-TAA
1 AT-ATTATTTAATTAA
15765864 ATATTATTTAATTAA
1 ATATTATTTAATTAA
15765879 ATATTATTTAAT
1 ATATTATTTAAT
15765891 CCCGCTACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.08
13 7 0.19
14 2 0.06
15 16 0.44
16 5 0.14
17 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:15766007 original size:9 final size:9
Alignment explanation
Indices: 15766005--15766220 Score: 141
Period size: 9 Copynumber: 23.4 Consensus size: 9
15765995 CATAATTTAC
15766005 ATAACTTAT
1 ATAACTTAT
*
15766014 ATAACATAT
1 ATAACTTAT
*
15766023 ATAACTTAC
1 ATAACTTAT
15766032 ATAACTTAT
1 ATAACTTAT
* *
15766041 ATAACATAC
1 ATAACTTAT
15766050 ATAACTTAT
1 ATAACTTAT
15766059 ATAACTTAT
1 ATAACTTAT
*
15766068 ATAACTTAG
1 ATAACTTAT
*
15766077 ATAA-ATAT
1 ATAACTTAT
15766085 ATAACTTAT
1 ATAACTTAT
*
15766094 ATAACTTAC
1 ATAACTTAT
15766103 ATAATACTTAAAT
1 AT-A-ACTT--AT
**
15766116 ATATTTTATAT
1 ATA-ACT-TAT
* *
15766127 CATAATTTAC
1 -ATAACTTAT
*
15766137 ATAACTTAC
1 ATAACTTAT
15766146 ATAACTTAT
1 ATAACTTAT
*
15766155 ATAACTTAG
1 ATAACTTAT
*
15766164 ATAA-ATAT
1 ATAACTTAT
* *
15766172 ATAATTTAC
1 ATAACTTAT
*
15766181 ATAA-ATAT
1 ATAACTTAT
* *
15766189 ATATCATAT
1 ATAACTTAT
* *
15766198 CATAAATTAC
1 -ATAACTTAT
*
15766208 ATAACTTAC
1 ATAACTTAT
15766217 ATAA
1 ATAA
15766221 TACTTAAATA
Statistics
Matches: 164, Mismatches: 33, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
8 17 0.10
9 121 0.74
10 8 0.05
11 8 0.05
12 6 0.04
13 4 0.02
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (9 bp):
ATAACTTAT
Found at i:15766017 original size:18 final size:18
Alignment explanation
Indices: 15765995--15766220 Score: 170
Period size: 18 Copynumber: 12.3 Consensus size: 18
15765985 TATTTGATAT
* *
15765995 CATAATTTACATAACTTA
1 CATAACTTATATAACTTA
* *
15766013 TATAACATATATAACTTA
1 CATAACTTATATAACTTA
*
15766031 CATAACTTATATAACATA
1 CATAACTTATATAACTTA
15766049 CATAACTTATATAACTTA
1 CATAACTTATATAACTTA
* * *
15766067 TATAACTTAGATAA-ATA
1 CATAACTTATATAACTTA
*
15766084 TATAACTTATATAACTTA
1 CATAACTTATATAACTTA
**
15766102 CATAATACTTAAATATATTTTATA
1 CAT-A-ACTT--ATATA-ACT-TA
* *
15766126 TCATAATTTACATAACTTA
1 -CATAACTTATATAACTTA
15766145 CATAACTTATATAACTTA
1 CATAACTTATATAACTTA
* * *
15766163 GATAA-ATATATAATTTA
1 CATAACTTATATAACTTA
* * *
15766180 CATAA-ATATATATCATA
1 CATAACTTATATAACTTA
* *
15766197 TCATAAATTACATAACTTA
1 -CATAACTTATATAACTTA
15766216 CATAA
1 CATAA
15766221 TACTTAAATA
Statistics
Matches: 165, Mismatches: 33, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
17 38 0.23
18 92 0.56
19 11 0.07
20 5 0.03
21 4 0.02
22 5 0.03
23 4 0.02
24 3 0.02
25 3 0.02
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (18 bp):
CATAACTTATATAACTTA
Found at i:15766212 original size:114 final size:114
Alignment explanation
Indices: 15766023--15766244 Score: 304
Period size: 114 Copynumber: 1.9 Consensus size: 114
15766013 TATAACATAT
* * *
15766023 ATAACTTACATAACTTATATAACATACATAACTTATATAACTTATATAACTTAGATAAATATATA
1 ATAACTTACATAACTTATATAACATACATAACATATATAACTTACATAAATTAGATAAATATATA
* * * *
15766088 ACTTATATAACTTACATAATACTTAAATATATTTTATATCATAATTTAC
66 AATTACATAACTTACATAATACTTAAATATATATCATATCATAATTTAC
* * * * *
15766137 ATAACTTACATAACTTATATAACTTAGATAA-ATATATAATTTACATAAA-TATATATCATATCA
1 ATAACTTACATAACTTATATAACATACATAACATATATAACTTACATAAATTAGATA-AATAT-A
15766200 TAAATTACATAACTTACATAATACTTAAATATATATCATATCATA
64 TAAATTACATAACTTACATAATACTTAAATATATATCATATCATA
15766245 CATAACTAGT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
112 5 0.05
113 18 0.19
114 71 0.76
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (114 bp):
ATAACTTACATAACTTATATAACATACATAACATATATAACTTACATAAATTAGATAAATATATA
AATTACATAACTTACATAATACTTAAATATATATCATATCATAATTTAC
Done.