Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 15 of 199
Found at i:4694526 original size:72 final size:72
Alignment explanation
Indices: 4694409--4694609 Score: 222
Period size: 72 Copynumber: 2.8 Consensus size: 72
4694399 AGCTTTATTC
* * *
4694409 GATGCTGCTCACACAAGCTTCAAAGAATCCACAACACGTGTTGGATCTTAAGCCATCGATAAAGG
1 GATGCTACTCACACAAGCTTCAAAGAATCCACAACACATGTTGGATCTCAAGCCATCGATAAAGG
4694474 ATAATTT
66 ATAATTT
* * * * * **
4694481 GATGCTACTCACACAAGTTTTAGAGAATCCATAACACATGTTGGATCTCAAGCTATCGATAAAAA
1 GATGCTACTCACACAAGCTTCAAAGAATCCACAACACATGTTGGATCTCAAGCCATCGATAAAGG
* **
4694546 ATGATCC
66 ATAATTT
* * * * * * *
4694553 AATGCTGCTCATACAAGCTTCAGAGAATCGACAACACATGCTGGAACTCAAGCCATC
1 GATGCTACTCACACAAGCTTCAAAGAATCCACAACACATGTTGGATCTCAAGCCATC
4694610 AATCATTAAA
Statistics
Matches: 106, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
72 106 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (72 bp):
GATGCTACTCACACAAGCTTCAAAGAATCCACAACACATGTTGGATCTCAAGCCATCGATAAAGG
ATAATTT
Found at i:4695668 original size:15 final size:15
Alignment explanation
Indices: 4695648--4695681 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4695638 TAATAACTAG
* *
4695648 TTAATTATAATTTAT
1 TTAATTAAAATTTAA
4695663 TTAATTAAAATTTAA
1 TTAATTAAAATTTAA
4695678 TTAA
1 TTAA
4695682 CATACTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATTAAAATTTAA
Found at i:4707483 original size:17 final size:17
Alignment explanation
Indices: 4707461--4707524 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
4707451 AATCTTAGAG
4707461 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
4707478 TTCTAATTATGTCTTAGAG-
1 TTCTAA-T-TGT-ATACAGC
4707497 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
4707514 TTTTAATTGTA
1 TTCTAATTGTA
4707525 GCCTTTGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 4 0.11
17 19 0.50
18 2 0.05
19 9 0.24
20 4 0.11
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:4707494 original size:36 final size:36
Alignment explanation
Indices: 4707453--4707521 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
4707443 GATTATTTAA
4707453 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
*
4707489 TCTTAGAGTTCTAATTGTATACAGCTTTTAATT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATT
4707522 GTAGCCTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
Found at i:4707502 original size:19 final size:18
Alignment explanation
Indices: 4707453--4707504 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
4707443 GATTATTTAA
4707453 TCTTAGAGTTCTAA-TTG
1 TCTTAGAGTTCTAATTTG
* *
4707470 T-ATACAGCTTCTAATTATG
1 TCTTAGAG-TTCTAATT-TG
4707489 TCTTAGAGTTCTAATT
1 TCTTAGAGTTCTAATT
4707505 GTATACAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 1 0.04
19 11 0.41
20 4 0.15
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (18 bp):
TCTTAGAGTTCTAATTTG
Found at i:4712665 original size:17 final size:17
Alignment explanation
Indices: 4712643--4712703 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
4712633 AATCTTAGAG
4712643 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
4712660 TTCTAATTATGTCTTAGAG-
1 TTCTAA-T-TGT-ATACAGC
4712679 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
4712696 TTTTAATT
1 TTCTAATT
4712704 ATAGCCTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 4 0.11
17 16 0.46
18 2 0.06
19 9 0.26
20 4 0.11
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:4712682 original size:36 final size:36
Alignment explanation
Indices: 4712635--4712705 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
4712625 GCTTATTTAA
4712635 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
*
4712671 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTAT
4712706 AGCCTTTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
Found at i:4712684 original size:19 final size:18
Alignment explanation
Indices: 4712635--4712686 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
4712625 GCTTATTTAA
4712635 TCTTAGAGTTCTAA-TTG
1 TCTTAGAGTTCTAATTTG
* *
4712652 T-ATACAGCTTCTAATTATG
1 TCTTAGAG-TTCTAATT-TG
4712671 TCTTAGAGTTCTAATT
1 TCTTAGAGTTCTAATT
4712687 GTATACAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 1 0.04
19 11 0.41
20 4 0.15
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (18 bp):
TCTTAGAGTTCTAATTTG
Found at i:4717487 original size:15 final size:17
Alignment explanation
Indices: 4717467--4717498 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
4717457 TAAATTACAT
4717467 TTTGAA-ATAT-TTTTA
1 TTTGAACATATATTTTA
4717482 TTTGAACATATATTTTA
1 TTTGAACATATATTTTA
4717499 AAAATATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTGAACATATATTTTA
Found at i:4723398 original size:18 final size:18
Alignment explanation
Indices: 4723350--4723398 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
4723340 TAAACGAGAG
4723350 AAAGAAATAAAAAAATTAT
1 AAAGAAATAAAAAAA-TAT
*
4723369 AAAAAAAGTAAAAAAA-AT
1 AAAGAAA-TAAAAAAATAT
4723387 AAAGAATATAAA
1 AAAGAA-ATAAA
4723399 GTGTGTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 11 0.42
19 7 0.27
20 8 0.31
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (18 bp):
AAAGAAATAAAAAAATAT
Found at i:4723731 original size:23 final size:20
Alignment explanation
Indices: 4723683--4723724 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
4723673 TACAGATTTT
*
4723683 TTAAAAAATAATTACATATA
1 TTAAAAAACAATTACATATA
4723703 -TAAAAAACAATTACAT-TA
1 TTAAAAAACAATTACATATA
4723721 TTAA
1 TTAA
4723725 TTAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAAAAACAATTACATATA
Found at i:4725258 original size:44 final size:43
Alignment explanation
Indices: 4725210--4725368 Score: 115
Period size: 44 Copynumber: 3.6 Consensus size: 43
4725200 CTAATCCACT
* * * *
4725210 CCACTACAACTTTAGGGAGATATGATTTGTTCATTCAGTCTGCC
1 CCACTGCAACTTTAGGGAGATAAGATTTCTT-ACTCAGTCTGCC
* *
4725254 CCACTGCAATTTTAGGG-GTATAAGACTTTCTTACTCAGTCTGCT
1 CCACTGCAACTTTAGGGAG-ATAAGA-TTTCTTACTCAGTCTGCC
* * * ** * * *
4725298 CCACTGTAACTTCAGGGAGATAGGATTAT-TGGCTTTAATCTGCT
1 CCACTGCAACTTTAGGGAGATAAGATT-TCTTAC-TCAGTCTGCC
* *
4725342 TCACTGCAACTTCAGGGAGATAAGATT
1 CCACTGCAACTTTAGGGAGATAAGATT
4725369 CGCCATCTTC
Statistics
Matches: 93, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
43 5 0.05
44 82 0.88
45 6 0.06
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (43 bp):
CCACTGCAACTTTAGGGAGATAAGATTTCTTACTCAGTCTGCC
Found at i:4725462 original size:50 final size:50
Alignment explanation
Indices: 4725402--4725662 Score: 200
Period size: 50 Copynumber: 5.2 Consensus size: 50
4725392 GCAATGTTGG
* *
4725402 GGGAA-CAAGATTCGCCGTCGTAGCTTCAATATGTTCCACTACACCGCCA
1 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCA
* ** * ** * * ** ***
4725451 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTTT
1 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCA
* * *
4725501 GGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCA
1 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCA
* * * ** * ** * ** ***
4725551 GGAAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTACAATGTTG
1 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCA
* *
4725601 GGGAAACAAGATTCGCCGTTGTAGCTTCAATATGTTCCACTACACCGCCA
1 GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCA
*
4725651 GGGGAGCAAGAT
1 GGGAAGCAAGAT
4725663 CCACCGTCAT
Statistics
Matches: 145, Mismatches: 66, Indels: 1
0.68 0.31 0.00
Matches are distributed among these distances:
49 5 0.03
50 140 0.97
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28
Consensus pattern (50 bp):
GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCA
Found at i:4725683 original size:100 final size:100
Alignment explanation
Indices: 4725382--4725669 Score: 468
Period size: 100 Copynumber: 2.9 Consensus size: 100
4725372 CATCTTCAGC
* *
4725382 CTTTTAAATTGCAATGTTGGGGGAACAAGATTCGCCGTCGTAGCTTCAATATGTTCCACTACACC
1 CTTTTTAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATATGTTCCACTACACC
*
4725447 GCCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAAT
66 GCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAAT
* * *
4725482 CTTTTTAATTGCAATGTTTGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACC
1 CTTTTTAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATATGTTCCACTACACC
*
4725547 GCCAGGAAAGTAAGATTCACCGTTGCGGCTTCAAT
66 GCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAAT
* *
4725582 CTTTTTAATTACAATGTTGGGGAAACAAGATTCGCCGTTGTAGCTTCAATATGTTCCACTACACC
1 CTTTTTAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATATGTTCCACTACACC
* * *
4725647 GCCAGGGGAGCAAGATCCACCGT
66 GCCAGGGAAGTAAGATTCACCGT
4725670 CATGGTTTCA
Statistics
Matches: 172, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 172 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (100 bp):
CTTTTTAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATATGTTCCACTACACC
GCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAAT
Found at i:4725822 original size:51 final size:51
Alignment explanation
Indices: 4725761--4725890 Score: 134
Period size: 51 Copynumber: 2.5 Consensus size: 51
4725751 TTCAAGTCTT
* *
4725761 AATGCCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGC
1 AATGCCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCACTAC
* * * * * * * * *
4725812 AATGCTAGGGAAACAAGGTTCGCTACCTTTAGCTTTAATCTGTTCCACTAT
1 AATGCCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCACTAC
** *
4725863 AATGCCAAAGAGATAGGATTCGCTGCCC
1 AATGCCAGGGAGATAAGATTCGCTGCCC
4725891 ATAGCTTGAA
Statistics
Matches: 59, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (51 bp):
AATGCCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCACTAC
Found at i:4725982 original size:169 final size:169
Alignment explanation
Indices: 4725686--4726290 Score: 895
Period size: 169 Copynumber: 3.6 Consensus size: 169
4725676 TTCAATCTGC
* * * * * * * *
4725686 TCCACTGTAATGCCAAAGAGATAGGATTTGCTGCCCACAACATTAATCCGCTTCGCTTTAGCTAC
1 TCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCCGCTCCACTTCAGCTAT
**
4725751 TTCAAGTCTTAATGCCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAATG
66 TTCAAGTCTTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAATG
* *
4725816 CTAGGGAAACAAGGTTCGCTACCTTTAGCTTTAATCTGT
131 CTAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTAT
* * *
4725855 TCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCATAGCTTGAACCCGCTCCACTTCAGCTAT
1 TCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCCGCTCCACTTCAGCTAT
* * * * *
4725920 TTCGAGTCTTAACACCAGGGAGATAAGATTCGCTGCCCTCAACTTTAATATACTCTGCTGCAATG
66 TTCAAGTCTTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAATG
4725985 CTAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTAT
131 CTAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTAT
* *
4726024 TCCACTATAATGCCAAAGAGATAGGATTCACTGCCCACAGCTTTAATCCGCTCCACTTCAGCTAA
1 TCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCCGCTCCACTTCAGCTAT
* * * * *
4726089 TCCAAGTCTTAACGCCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCACTACAAGG
66 TTCAAGTCTTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAATG
* * *
4726154 CTAGGGAAACAAGATTCACTACATTTAACTTTAATCTAT
131 CTAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTAT
* * *
4726193 TCCACTATAATGCCAACGAGATAGGATTTGCTGCCCACAGCTTTAATCCGCTCCATTTCAGCTAT
1 TCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCCGCTCCACTTCAGCTAT
* *
4726258 TTCAAGTATTAATACCAGGGAGATAAGATTCGC
66 TTCAAGTCTTAACACCAGGGAGATAAGATTCGC
4726291 CATATTCAGT
Statistics
Matches: 389, Mismatches: 47, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
169 389 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (169 bp):
TCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCCGCTCCACTTCAGCTAT
TTCAAGTCTTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAATG
CTAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTAT
Found at i:4726734 original size:87 final size:87
Alignment explanation
Indices: 4726387--4727159 Score: 856
Period size: 87 Copynumber: 8.9 Consensus size: 87
4726377 ACTGGCCTCA
* * ***
4726387 ATCTGCTCCACTACTGGTTAGGGAGATAAGATCTGTAGTTCTTCGGTCTACTCCACTGCTGCTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA-ATCTTCAACCTACTCCACTGCTGCTCA
* * * *
4726452 GGGAGATAAGACT--TG-ATGCG
65 GGGAGATAAGGCTGGGGTCTTCG
* * * ** * * * *
4726472 ATCTACTCTACTGCAACTTTAGAGAGATAAGATCTTTTATTTTCAACCTACTCCACTGCTGCTCA
1 ATCTGCTCCACTACTGC-TTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCA
* *
4726537 GGGAGACAAGGCTGGGGTCTTTG
65 GGGAGATAAGGCTGGGGTCTTCG
** * * * ** ** * * * * ** *
4726560 ATCTGCTTTACTGTCAG-TACAGAAAGGCAAGATCTGTTATCTTTAACCTGCTCCGCTGCCACTG
1 ATCTGCTCCACT-ACTGCT-TAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTC
** * *
4726624 AGGGAGGCAAGGCTAGTGTCTTCG
64 AGGGAGATAAGGCTGGGGTCTTCG
**
4726648 ATCTATTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAG
* * *
4726713 AGAGATAAGGATGGGGACTTCG
66 GGAGATAAGGCTGGGGTCTTCG
* *
4726735 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCATTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAG
*
4726800 GGAGAT-AGGCTGGGGTTTTCG
66 GGAGATAAGGCTGGGGTCTTCG
* *
4726821 ATCTGCTCTACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCACTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAG
*
4726886 GGAGACAAGGCTGGGGTCTTCG
66 GGAGATAAGGCTGGGGTCTTCG
* *
4726908 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTCCTCAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAG
*
4726973 GGAGACAAGGCTGGGGTCTTCG
66 GGAGATAAGGCTGGGGTCTTCG
* * * * * *
4726995 ATCTGCTCCGCTACTGTTTAGGGAGATAATATCTGTAATCTTCAACCTACACTACTACTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAG
* *
4727060 GGAGATAAGGCTAGGGACTTCG
66 GGAGATAAGGCTGGGGTCTTCG
* * * * *
4727082 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAACCTACTCCACTACTACTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAG
*
4727147 TGAGAT-AGGCTGG
66 GGAGATAAGGCTGG
4727160 AGTTTCATCG
Statistics
Matches: 575, Mismatches: 105, Indels: 15
0.83 0.15 0.02
Matches are distributed among these distances:
85 44 0.08
86 101 0.18
87 354 0.62
88 74 0.13
89 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAG
GGAGATAAGGCTGGGGTCTTCG
Found at i:4726907 original size:260 final size:260
Alignment explanation
Indices: 4726387--4727159 Score: 869
Period size: 260 Copynumber: 3.0 Consensus size: 260
4726377 ACTGGCCTCA
* * * ***
4726387 ATCTGCTCCACTACTGGTTAGGGAGATAAGATCTGTAGTTCTTCGGTCTACTCCACTGCTGCTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTA-ATCTTCAACCTACTCCACTGCTGCTCA
* * * * * * ** * * *
4726452 GGGAGATAA-GACT--TGA-TGCGATCTACTCTACTGCAACTTTAGAGAGATAAGATCTTTTATT
65 GAGAGATAAGGA-TGGGGACTTCGATCTGCTCCACTACTGC-TTAGGGAGATAAGATCTGTAATT
* * * *
4726513 TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTT-GATCTGCTTTACTGTCAG
128 TTCAACCTACTCCACTGCTGCTCAGGGAGA-TAGGCTGGGGT-TTTCGATCTGCTCTACT-ACTG
* ** ** * * * * * * * *
4726577 -TACAGAAAGGCAAGATCTGTTATCTTTAACCTGCTCCGCTGCCACTGAGGGAGGCAAGGCTAGT
190 CT-TAGGGAGATAAGATCTGTAATCTTTAACCTACTCCACTGCTACTCAGGGAGACAAGGCTGGG
4726641 GTCTTCG
254 GTCTTCG
*
4726648 ATCTATTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAG
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAG
4726713 AGAGATAAGGATGGGGACTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTC
66 AGAGATAAGGATGGGGACTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTC
*
4726778 AACCTACTCCATTGCTGCTCAGGGAGATAGGCTGGGGTTTTCGATCTGCTCTACTACTGCTTAGG
131 AACCTACTCCACTGCTGCTCAGGGAGATAGGCTGGGGTTTTCGATCTGCTCTACTACTGCTTAGG
* * *
4726843 GAGATAAGATCTATAATCTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCG
196 GAGATAAGATCTGTAATCTTTAACCTACTCCACTGCTACTCAGGGAGACAAGGCTGGGGTCTTCG
* *
4726908 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTCCTCA-
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAG
* * * * * * *
4726972 AGGAGACAAGGCTGGGGTCTTCGATCTGCTCCGCTACTGTTTAGGGAGATAATATCTGTAATCTT
66 A-GAGATAAGGATGGGGACTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
* * * * ** * *
4727037 CAACCTACACTACTACTGCTCAGGGAGATAAGGCTAGGGACTTCGATCTACTCCACTACTGCTTA
130 CAACCTACTCCACTGCTGCTCAGGGAGAT-AGGCTGGGGTTTTCGATCTGCTCTACTACTGCTTA
* * * *
4727102 GGGAGATAAGATCTGTAATTTTTAACCTACTCCACTACTACTCAGTGAGA-TAGGCTGG
194 GGGAGATAAGATCTGTAATCTTTAACCTACTCCACTGCTACTCAGGGAGACAAGGCTGG
4727160 AGTTTCATCG
Statistics
Matches: 439, Mismatches: 65, Indels: 17
0.84 0.12 0.03
Matches are distributed among these distances:
259 1 0.00
260 239 0.54
261 133 0.30
262 51 0.12
263 15 0.03
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (260 bp):
ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGCTCAG
AGAGATAAGGATGGGGACTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTC
AACCTACTCCACTGCTGCTCAGGGAGATAGGCTGGGGTTTTCGATCTGCTCTACTACTGCTTAGG
GAGATAAGATCTGTAATCTTTAACCTACTCCACTGCTACTCAGGGAGACAAGGCTGGGGTCTTCG
Found at i:4727069 original size:347 final size:349
Alignment explanation
Indices: 4726387--4727164 Score: 994
Period size: 347 Copynumber: 2.2 Consensus size: 349
4726377 ACTGGCCTCA
* * ***
4726387 ATCTGCTCCACTACTGGTTAGGGAGATAAGATCTGTAGTTCTTCGGTCTACTCCACTGCTGCTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATT-TTCAACCTACTCCACTGCTGCTCA
* * * * * *
4726452 GGGAGATAAGACTTGA---TGCGATCTACTCTACTGCAACTTTAGAGAGATAAGATCTTTTATTT
65 GGGAGAT-AGGCTGGAGTTTGCGATCTACTCTACTACAACTTTAGAGAGATAAGATCTATAATCT
* ** *
4726514 TCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTTGATCTGCTTTACTGTCAGTA
129 TCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTGACAGTA
* * * * * * * * *
4726579 CAGAAAGGCAAGATCTGTTATCTTTAACCTGCTCCGCTGCCACTGAGGGAGGCAAGGCTAGTGTC
194 CAGAAAGACAAGATCTGTAATCTTCAACCTACTCCACTGCCACTCAAGGAGACAAGGCTAGGGTC
* * *
4726644 TTCGATCTATTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTGC
259 TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACACCACTACTGC
*
4726709 TCAGAGAGATAAGGATGGGGACTTCG
324 TCAGAGAGATAAGGATAGGGACTTCG
*
4726735 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCATTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAG
* * * ** *
4726800 GGAGATAGGCTGGGGTTTTCGATCTGCTCTACTACTGC-TTAGGGAGATAAGATCTATAATCTTC
66 GGAGATAGGCTGGAGTTTGCGATCTACTCTACTACAACTTTAGAGAGATAAGATCTATAATCTTC
* *
4726864 AACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACT-ACTGCT-T
131 AACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTGACAG-TAC
** * *
4726927 AGGGAGATAAGATCTGTAATCTTCAACCTACTCCACTGCTC-CTCAAGGAGACAAGGCTGGGGTC
195 AGAAAGACAAGATCTGTAATCTTCAACCTACTCCACTGC-CACTCAAGGAGACAAGGCTAGGGTC
* * * * *
4726991 TTCGATCTGCTCCGCTACTGTTTAGGGAGATAATATCTGTAATCTTCAACCTACACTACTACTGC
259 TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACACCACTACTGC
* *
4727056 TCAGGGAGATAAGGCTAGGGACTTCG
324 TCAGAGAGATAAGGATAGGGACTTCG
* * * *
4727082 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAACCTACTCCACTACTACTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAG
*
4727147 TGAGATAGGCTGGAGTTT
66 GGAGATAGGCTGGAGTTT
4727165 CATCGGTTTG
Statistics
Matches: 370, Mismatches: 55, Indels: 11
0.85 0.13 0.03
Matches are distributed among these distances:
346 5 0.01
347 234 0.63
348 115 0.31
349 16 0.04
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (349 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAG
GGAGATAGGCTGGAGTTTGCGATCTACTCTACTACAACTTTAGAGAGATAAGATCTATAATCTTC
AACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTGACAGTACA
GAAAGACAAGATCTGTAATCTTCAACCTACTCCACTGCCACTCAAGGAGACAAGGCTAGGGTCTT
CGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTACACCACTACTGCTC
AGAGAGATAAGGATAGGGACTTCG
Found at i:4738263 original size:2 final size:2
Alignment explanation
Indices: 4738256--4738290 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4738246 NNNNNNCTAC
4738256 TA TA TA TA TA 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 TA TA TA TA TA T
4738291 TGTTATGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4738784 original size:43 final size:42
Alignment explanation
Indices: 4738722--4738939 Score: 240
Period size: 43 Copynumber: 5.1 Consensus size: 42
4738712 GCGTCGCTAA
*
4738722 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCAA-AC
4738765 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCAA-AC
* * *
4738808 CTTTAGCGGCGCTTCTTCCAAAAACGCCGCTAAAGACTCTAAC
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGAC-CAAAC
* * * ** **
4738851 CTTTAACGGCACTTTTATCACAAACGCCGCTAAAGAATAAAC
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCAAAC
* * * * * *
4738893 TTTTACCGGTGCTTCTCGCAAAAACGCCGCTAAA-AACATAAC
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCA-AAC
4738935 CTTTA
1 CTTTA
4738940 AAAAATATAT
Statistics
Matches: 150, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
41 3 0.02
42 36 0.24
43 109 0.73
44 2 0.01
ACGTcount: A:0.31, C:0.32, G:0.16, T:0.22
Consensus pattern (42 bp):
CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCAAAC
Found at i:4740345 original size:15 final size:15
Alignment explanation
Indices: 4740315--4740356 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
4740305 CTCTCTTCAT
*
4740315 CATAATCGCT-AATC
1 CATAATCCCTAAATC
4740329 CATAATCCCTAAATC
1 CATAATCCCTAAATC
*
4740344 CATACTCCCTAAA
1 CATAATCCCTAAA
4740357 CCTTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.38, C:0.33, G:0.02, T:0.26
Consensus pattern (15 bp):
CATAATCCCTAAATC
Found at i:4740569 original size:8 final size:7
Alignment explanation
Indices: 4740529--4740587 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
4740519 ACCTCTGAAT
4740529 CCCTAAC
1 CCCTAAC
* *
4740536 TCTTAAC
1 CCCTAAC
4740543 CCCTAAC
1 CCCTAAC
*
4740550 ACATCTAAC
1 -C-CCTAAC
4740559 CCCTAAAC
1 CCCT-AAC
4740567 CCCTAAC
1 CCCTAAC
4740574 CCTCTAAC
1 CC-CTAAC
4740582 CCCTAA
1 CCCTAA
4740588 ACATTAAATC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
7 21 0.50
8 16 0.38
9 5 0.12
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.20
Consensus pattern (7 bp):
CCCTAAC
Found at i:4740574 original size:15 final size:15
Alignment explanation
Indices: 4740539--4740587 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
4740529 CCCTAACTCT
**
4740539 TAACCCCTAACACATC
1 TAACCCCTAA-ACCCC
4740555 TAACCCCTAAACCCC
1 TAACCCCTAAACCCC
4740570 TAACCCTCT-AACCCC
1 TAACCC-CTAAACCCC
4740585 TAA
1 TAA
4740588 ACATTAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.35, C:0.47, G:0.00, T:0.18
Consensus pattern (15 bp):
TAACCCCTAAACCCC
Found at i:4740579 original size:23 final size:24
Alignment explanation
Indices: 4740540--4740589 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
4740530 CCTAACTCTT
4740540 AACCCCTAACACATCTAACCCCTA
1 AACCCCTAACACATCTAACCCCTA
*
4740564 AACCCCTAAC-CCTCTAACCCCTA
1 AACCCCTAACACATCTAACCCCTA
4740587 AAC
1 AAC
4740590 ATTAAATCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (24 bp):
AACCCCTAACACATCTAACCCCTA
Found at i:4740617 original size:14 final size:14
Alignment explanation
Indices: 4740600--4740653 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
4740590 ATTAAATCCC
*
4740600 AATCCTTAAACCAT
1 AATCCCTAAACCAT
4740614 AATCCCTAAACCCAT
1 AATCCCTAAA-CCAT
* * *
4740629 ACTCCCTAAACTAA
1 AATCCCTAAACCAT
*
4740643 AAACCCTAAAC
1 AATCCCTAAAC
4740654 TATAGTGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 20 0.61
15 13 0.39
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.20
Consensus pattern (14 bp):
AATCCCTAAACCAT
Found at i:4740634 original size:15 final size:15
Alignment explanation
Indices: 4740600--4740639 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4740590 ATTAAATCCC
*
4740600 AATCCTTAAA-CCAT
1 AATCCCTAAACCCAT
4740614 AATCCCTAAACCCAT
1 AATCCCTAAACCCAT
*
4740629 ACTCCCTAAAC
1 AATCCCTAAAC
4740640 TAAAAACCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.23
Consensus pattern (15 bp):
AATCCCTAAACCCAT
Found at i:4741037 original size:41 final size:41
Alignment explanation
Indices: 4740925--4741037 Score: 181
Period size: 41 Copynumber: 2.8 Consensus size: 41
4740915 TAAAATGTTT
* * * *
4740925 TTAGCGGCGCTTCTTAAAAAACGCCGCGAAAGTCCTGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCA
*
4740966 TTAGCGGCGCTTCTTCAAAAACGCCACTAAAGACCAGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCA
4741007 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAA
4741038 TCCCTAAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.19
Consensus pattern (41 bp):
TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCA
Found at i:4743444 original size:90 final size:90
Alignment explanation
Indices: 4743310--4743505 Score: 252
Period size: 90 Copynumber: 2.2 Consensus size: 90
4743300 AGTCCATATC
* * * * * *
4743310 TTTTTCACTCAATTGGATACTTGAACTTTCACAATATAT-CAAAAAGA-CCCTCAAAATTTTTCA
1 TTTTTCACTCAATTGGATACTTAAACTATCAAAATACATAAAAAAAAAGCCCTCAAAATTTTTC-
*
4743373 AAAAAAAGCAATTAAGCCCCTGCTTTT
65 -AAAAAAGCAATGAAGCCCCTGCTTTT
* *
4743400 TTTTTCACTCAATTGGATACTTAAACTATCAAAATGCATAAAAAAAAAGCCCTCAAACTTTTTCA
1 TTTTTCACTCAATTGGATACTTAAACTATCAAAATACATAAAAAAAAAGCCCTCAAAATTTTTCA
* *
4743465 AAAAAGCAATGAAGGCCCTGTTTTT
66 AAAAAGCAATGAAGCCCCTGCTTTT
4743490 TTTTTGCACTCAATTG
1 TTTTT-CACTCAATTG
4743506 TCAAAATATA
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
90 62 0.67
91 16 0.17
92 14 0.15
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (90 bp):
TTTTTCACTCAATTGGATACTTAAACTATCAAAATACATAAAAAAAAAGCCCTCAAAATTTTTCA
AAAAAGCAATGAAGCCCCTGCTTTT
Found at i:4743776 original size:19 final size:19
Alignment explanation
Indices: 4743748--4743831 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 19
4743738 TTATTTTTTT
4743748 ATTA-AAAAATAGAAAAAG
1 ATTATAAAAATAGAAAAAG
* * *
4743766 ATTACAAAAATTGTAAAAG
1 ATTATAAAAATAGAAAAAG
* * ** *
4743785 TTTATAAAATTCTAAAAAA
1 ATTATAAAAATAGAAAAAG
*
4743804 ATTATAAAATATAGAAAAAT
1 ATTATAAAA-ATAGAAAAAG
4743824 A-TATAAAA
1 ATTATAAAA
4743832 TTTTATAAAG
Statistics
Matches: 50, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
18 4 0.08
19 39 0.78
20 7 0.14
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.27
Consensus pattern (19 bp):
ATTATAAAAATAGAAAAAG
Found at i:4743831 original size:29 final size:29
Alignment explanation
Indices: 4743750--4743840 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 29
4743740 ATTTTTTTAT
* * *
4743750 TAAAAAATAGAAAAAGAT-TACAAAAATTG
1 TAAAATATAGAAAAATATATA-AAAAATTA
* * * *
4743779 TAAAAGTTTATAAAATTCTA-AAAAAATTA
1 TAAAA-TATAGAAAAATATATAAAAAATTA
**
4743808 TAAAATATAGAAAAATATATAAAATTTTA
1 TAAAATATAGAAAAATATATAAAAAATTA
4743837 TAAA
1 TAAA
4743841 GTCGTAAGAA
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
28 10 0.22
29 28 0.61
30 8 0.17
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (29 bp):
TAAAATATAGAAAAATATATAAAAAATTA
Found at i:4744062 original size:10 final size:10
Alignment explanation
Indices: 4744047--4744125 Score: 51
Period size: 9 Copynumber: 8.3 Consensus size: 10
4744037 TTCTGATGCA
4744047 TTTTATAATT
1 TTTTATAATT
**
4744057 TTTTATAAGA
1 TTTTATAATT
4744067 TTTTAT-ATT
1 TTTTATAATT
*
4744076 TTTTATGA-T
1 TTTTATAATT
*
4744085 TTATAT-A-T
1 TTTTATAATT
* *
4744093 ATTTCTAATT
1 TTTTATAATT
*
4744103 TTTAATAAATT
1 TTTTAT-AATT
4744114 TTTTAT-ATT
1 TTTTATAATT
4744123 TTT
1 TTT
4744126 ATTAAAGTTT
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
8 5 0.09
9 20 0.38
10 19 0.36
11 9 0.17
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (10 bp):
TTTTATAATT
Found at i:4744433 original size:86 final size:87
Alignment explanation
Indices: 4744343--4744502 Score: 227
Period size: 86 Copynumber: 1.8 Consensus size: 87
4744333 TTTTGAGGGT
* * *
4744343 CTTTTTAATGTATTTCGACAGT-TCAAGTA-CTCAATTGAGTGTAAAAAAAAAA-AGCTTAATTG
1 CTTTTTAATGCATTTCGA-AATATCAAGTACCT-AATTGAGTGCAAAAAAAAAAGAGCTTAATTG
4744405 TTTTTTTTTTTTAAGTTTGAGTTC
64 TTTTTTTTTTTTAAGTTTGAGTTC
* *
4744429 CTTTTTAATGCATTTTGAAATATCAAGTACCTAATTGAGTGCAAAAAAAAAAGGAGTTTAATTGT
1 CTTTTTAATGCATTTCGAAATATCAAGTACCTAATTGAGTGCAAAAAAAAAA-GAGCTTAATTGT
4744494 TTTTTTTTT
65 TTTTTTTTT
4744503 AGGGATTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
85 2 0.03
86 42 0.65
87 2 0.03
88 19 0.29
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (87 bp):
CTTTTTAATGCATTTCGAAATATCAAGTACCTAATTGAGTGCAAAAAAAAAAGAGCTTAATTGTT
TTTTTTTTTTAAGTTTGAGTTC
Found at i:4744618 original size:16 final size:15
Alignment explanation
Indices: 4744588--4744616 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4744578 TTGTGTGTTT
4744588 TTTTTTTAATATTTA
1 TTTTTTTAATATTTA
4744603 TTTTTTTAATATTT
1 TTTTTTTAATATTT
4744617 TACTATTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTTAATATTTA
Found at i:4747735 original size:13 final size:13
Alignment explanation
Indices: 4747717--4747743 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4747707 TTTCTTTTTC
4747717 TTTCGTGTACGCA
1 TTTCGTGTACGCA
4747730 TTTCGTGTACGCA
1 TTTCGTGTACGCA
4747743 T
1 T
4747744 CTAAGGCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (13 bp):
TTTCGTGTACGCA
Found at i:4749640 original size:22 final size:22
Alignment explanation
Indices: 4749608--4749649 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4749598 AACCAAATAG
* * *
4749608 AATGCTGATTGTACGGCCACAT
1 AATGCTAATTGCACCGCCACAT
4749630 AATGCTAATTGCACCGCCAC
1 AATGCTAATTGCACCGCCAC
4749650 GTGTGTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (22 bp):
AATGCTAATTGCACCGCCACAT
Found at i:4750210 original size:18 final size:18
Alignment explanation
Indices: 4750165--4750211 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
4750155 TCACATCAAC
* * *
4750165 AATTATTTAATTTTTTAA
1 AATTATTAAAATTTTAAA
*
4750183 AATTA-AAAAATTTTAAA
1 AATTATTAAAATTTTAAA
4750200 AATTATTAAAAT
1 AATTATTAAAAT
4750212 AATTAAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTATTAAAATTTTAAA
Found at i:4750220 original size:20 final size:20
Alignment explanation
Indices: 4750184--4750222 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4750174 ATTTTTTAAA
*
4750184 ATTAAAAAATTTTAAAAATT
1 ATTAAAAAATTTAAAAAATT
4750204 ATTAAAATAA-TTAAAAAAT
1 ATTAAAA-AATTTAAAAAAT
4750223 GTAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTAAAAAATTTAAAAAATT
Found at i:4750252 original size:25 final size:26
Alignment explanation
Indices: 4750184--4750267 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 26
4750174 ATTTTTTAAA
* * *
4750184 ATTAAAAAATTTTAAAAATTATTAAAATA
1 ATTAAAAAA-TATAAAAA-TA-TAAATTT
* *
4750213 ATTAAAAAATGTAAAATTAT-AATTT
1 ATTAAAAAATATAAAAATATAAATTT
*
4750238 ATTAAAAAGTATAAAAATATAAATTT
1 ATTAAAAAATATAAAAATATAAATTT
4750264 -TTAA
1 ATTAA
4750268 TTTTTAATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
25 24 0.51
26 6 0.13
27 2 0.04
28 6 0.13
29 9 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
ATTAAAAAATATAAAAATATAAATTT
Found at i:4752775 original size:24 final size:24
Alignment explanation
Indices: 4752736--4752881 Score: 89
Period size: 24 Copynumber: 5.8 Consensus size: 24
4752726 AGCTCATGCG
*
4752736 AGCCATGTAACGGGAAGCTCCA-CAA
1 AGCCAT-TAACGGGAAGCT-CATAAA
4752761 AGCCATTAACGGGAAGCTCATAAA
1 AGCCATTAACGGGAAGCTCATAAA
* * *
4752785 AGCCAATAACGGGAAGGTTCA-AGCA
1 AGCCATTAACGGGAA-GCTCATA-AA
* * **
4752810 AGCCAATATCGGGAAGCTCCGAAA
1 AGCCATTAACGGGAAGCTCATAAA
* **
4752834 AGCAAATTAATTAGGAAGCTCATGAAA
1 AGC-CATTAA-CGGGAAGCTCAT-AAA
*
4752861 GAGCCTTTAATCGGGAAGCTC
1 -AGCCATTAA-CGGGAAGCTC
4752882 CGGAGATCCA
Statistics
Matches: 94, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
23 2 0.02
24 36 0.38
25 29 0.31
26 8 0.09
27 16 0.17
28 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.16
Consensus pattern (24 bp):
AGCCATTAACGGGAAGCTCATAAA
Found at i:4753578 original size:18 final size:19
Alignment explanation
Indices: 4753547--4753588 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
4753537 AGCCCATGTA
4753547 TTTCACAAAATTTA-ATTT
1 TTTCACAAAATTTACATTT
* *
4753565 TTTCATAAAGTTTACATTT
1 TTTCACAAAATTTACATTT
4753584 TTTCA
1 TTTCA
4753589 ATTTAGTCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTCACAAAATTTACATTT
Found at i:4755197 original size:28 final size:27
Alignment explanation
Indices: 4755122--4755197 Score: 64
Period size: 30 Copynumber: 2.7 Consensus size: 27
4755112 TTTGTTACCA
* *
4755122 TTTTATT-ATTATGTTGCTATAATTTTG
1 TTTTATTGTTTATATTG-TATAATTTTG
*
4755149 TTGTTATTGTTAGGATATTGTATAACTTTTG
1 TT-TTATTGTT--TATATTGTATAA-TTTTG
*
4755180 TTTTATTGTTTATTTTGT
1 TTTTATTGTTTATATTGT
4755198 TACTATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.05
28 11 0.28
29 1 0.03
30 13 0.33
31 12 0.31
ACGTcount: A:0.20, C:0.03, G:0.14, T:0.63
Consensus pattern (27 bp):
TTTTATTGTTTATATTGTATAATTTTG
Found at i:4758772 original size:77 final size:73
Alignment explanation
Indices: 4758698--4758841 Score: 166
Period size: 73 Copynumber: 1.9 Consensus size: 73
4758688 TTATTTAAAT
*
4758698 TTTAAATATATTTGTCTTATTATA-TATTATTATTATATAATTATTTATATA-TATATATATATC
1 TTTAAAT-TATTTG--TTATTATACTATTAATATTA-AT-ATTA-TTATATACT-TATATATATC
4758761 TTTTCTTTTTAAAAC
59 TTTTCTTTTTAAAAC
* * * *
4758776 TTTAGATTATTTGTTATTCTACTATTAATATTAATATTATTATTTACTTATTTATATCTTTTCTT
1 TTTAAATTATTTGTTATTATACTATTAATATTAATATTATTATATACTTATATATATCTTTTCTT
4758841 T
66 T
4758842 CATTTTAAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
73 23 0.39
74 5 0.08
75 9 0.15
76 10 0.17
77 6 0.10
78 6 0.10
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (73 bp):
TTTAAATTATTTGTTATTATACTATTAATATTAATATTATTATATACTTATATATATCTTTTCTT
TTTAAAAC
Found at i:4768293 original size:2 final size:2
Alignment explanation
Indices: 4768286--4768315 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4768276 TCCTCTGAAC
4768286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4768316 CAATCTACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4768705 original size:46 final size:46
Alignment explanation
Indices: 4768628--4768812 Score: 273
Period size: 46 Copynumber: 4.0 Consensus size: 46
4768618 ACAAGGCTAT
4768628 AACTCAGTATGGTTTTCTTCA-CGAAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCG-AAATACCATACCTACTTTTCAC
* *
4768674 AACTCAGTATGGTTTTCTTTACCGAATTACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* ** *
4768720 AACTCAGTATGCTTTTCTTCATTGAAATACCATACCTACTTTTCAG
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* * *
4768766 AACTCAGTATGGTTTTCTTCACTGGAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
4768812 A
1 A
4768813 CTTTTCCTTG
Statistics
Matches: 125, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
46 123 0.98
47 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
Found at i:4770047 original size:17 final size:17
Alignment explanation
Indices: 4770025--4770073 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
4770015 TAAATTCTTT
4770025 TTAAATCACAAAATTCA
1 TTAAATCACAAAATTCA
4770042 TTAAATCACAAAATTCA
1 TTAAATCACAAAATTCA
* *
4770059 CTAATTCA-AAAATTC
1 TTAAATCACAAAATTC
4770074 TTCTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.23
17 23 0.77
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAATCACAAAATTCA
Found at i:4773928 original size:51 final size:51
Alignment explanation
Indices: 4773823--4773955 Score: 149
Period size: 51 Copynumber: 2.6 Consensus size: 51
4773813 AAGTAGAGCG
* ** * * *
4773823 GATTAAAGCTAAAGGTAGCGAATCCTATCTCTTTGGTGTCGTAGTGGAACA
1 GATTAAAGCTAAAGGTAGCGAATCTTATCTCCCTGGTATCGCAGCGGAACA
* * * **
4773874 GATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGTATTGCAGCGGAGTA
1 GATTAAAGCTAAAGGTAGCGAATCTTATCTCCCTGGTATCGCAGCGGAACA
* *
4773925 GATTAAAGCTGAAGGCAGCGAATCTTATCTC
1 GATTAAAGCTAAAGGTAGCGAATCTTATCTC
4773956 TCTAGCGTTA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (51 bp):
GATTAAAGCTAAAGGTAGCGAATCTTATCTCCCTGGTATCGCAGCGGAACA
Found at i:4774080 original size:21 final size:21
Alignment explanation
Indices: 4774054--4774097 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4774044 CTGGTGTTGC
*
4774054 AGTGGAATAGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
* *
4774075 AGTGGAGCGGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
4774096 AG
1 AG
4774098 GCAACAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.34, T:0.20
Consensus pattern (21 bp):
AGTGGAACAGATTAAAGCTGA
Found at i:4774188 original size:51 final size:51
Alignment explanation
Indices: 4774129--4774246 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 51
4774119 GTGTTACAGT
* *
4774129 GGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCTCTGGCGTTGCAAC
1 GGAACAGATTAAAGCTAAAAGCAGCGAATCTTGTTTCTCTAGCGTTGCAAC
* * * * **
4774180 GGAGCAGATTAAAGTTAAAGGCAGCGAATCTTGTTTCTTTAGCGTTGCAGT
1 GGAACAGATTAAAGCTAAAAGCAGCGAATCTTGTTTCTCTAGCGTTGCAAC
*
4774231 GGAATAGATTAAAGCT
1 GGAACAGATTAAAGCT
4774247 GAAGTGGAGC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (51 bp):
GGAACAGATTAAAGCTAAAAGCAGCGAATCTTGTTTCTCTAGCGTTGCAAC
Found at i:4774203 original size:261 final size:261
Alignment explanation
Indices: 4773738--4774225 Score: 751
Period size: 261 Copynumber: 1.9 Consensus size: 261
4773728 ACCACCGAAG
*
4773738 TTGCAGCGAAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGTGGAATAG
1 TTGCAGCGAAACAGATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTGGCGTTGCAGTGGAATAG
* * * * **
4773803 ATTAAAGCTGAAGTAGAGCGGATTAAAGCTAAAGGTAGCGAATCCTATCTCTTTGGTGTCGTAGT
66 ATTAAAGCTGAAGTAGAGCGGATTAAAGCTAAAGGCAACAAATCCTATCTCCTTGGTGTCACAGT
* * * *
4773868 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGTATTGCAGCGGAGTAGATTAAAG
131 GGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCCTGGCATTGCAACGGAGCAGATTAAAG
*
4773933 CTGAAGGCAGCGAATCTTATCTCTCTAGCGTTAAGTCTGAGAACAGCAAATCTTATTTCCCTTAC
196 CTAAAGGCAGCGAATCTTATCTCTCTAGCGTTAAGTCTGAGAACAGCAAATCTTATTTCCCTTAC
4773998 A
261 A
* * * *
4773999 TTGCAGCGGAATAGATTAAAGCTAAAGGTAGCAAATCTTGTTTTCCTGGTGTTGCAGTGGAATAG
1 TTGCAGCGAAACAGATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTGGCGTTGCAGTGGAATAG
* * *
4774064 ATTAAAGCTGAAGTGGAGCGGATTAAAGCTGAAGGCAACAAATCCTATCTCCTTGGTGTTACAGT
66 ATTAAAGCTGAAGTAGAGCGGATTAAAGCTAAAGGCAACAAATCCTATCTCCTTGGTGTCACAGT
* *
4774129 GGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCTCTGGCGTTGCAACGGAGCAGATTAAAG
131 GGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCCTGGCATTGCAACGGAGCAGATTAAAG
* * * *
4774194 TTAAAGGCAGCGAATCTTGTTTCTTTAGCGTT
196 CTAAAGGCAGCGAATCTTATCTCTCTAGCGTT
4774226 GCAGTGGAAT
Statistics
Matches: 202, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
261 202 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (261 bp):
TTGCAGCGAAACAGATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTGGCGTTGCAGTGGAATAG
ATTAAAGCTGAAGTAGAGCGGATTAAAGCTAAAGGCAACAAATCCTATCTCCTTGGTGTCACAGT
GGAACAGATTAAAGCTAAAAGTAGCGAATCTTGTTTCCCTGGCATTGCAACGGAGCAGATTAAAG
CTAAAGGCAGCGAATCTTATCTCTCTAGCGTTAAGTCTGAGAACAGCAAATCTTATTTCCCTTAC
A
Found at i:4774273 original size:72 final size:72
Alignment explanation
Indices: 4774187--4774322 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 72
4774177 AACGGAGCAG
* * ** *
4774187 ATTAAAGTTAAAGGCAGCGAATCTTGTTTCTTTAGCGTTGCAGTGGAATAGATTAAAGCTGAAGT
1 ATTAAAGCTAAAGGCAGCGAATCTTGTTTCTCTAGCGTTGCAGCAGAACAGATTAAAGCTGAAGT
4774252 GGAGCGA
66 GGAGCGA
* * *
4774259 ATTAAAGCTGAAGGCAGCGAATCTTGTTTCTCTGGCGTTGCAGCAGAGCAGATTAAAGCTGAAG
1 ATTAAAGCTAAAGGCAGCGAATCTTGTTTCTCTAGCGTTGCAGCAGAACAGATTAAAGCTGAAG
4774323 GCTGCGAATC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (72 bp):
ATTAAAGCTAAAGGCAGCGAATCTTGTTTCTCTAGCGTTGCAGCAGAACAGATTAAAGCTGAAGT
GGAGCGA
Found at i:4774279 original size:20 final size:21
Alignment explanation
Indices: 4774238--4774280 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
4774228 AGTGGAATAG
*
4774238 ATTAAAGCTGAAGTGGAGCGA
1 ATTAAAGCTGAAGTGCAGCGA
4774259 ATTAAAGCTGAAG-GCAGCGA
1 ATTAAAGCTGAAGTGCAGCGA
4774279 AT
1 AT
4774281 CTTGTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.19
Consensus pattern (21 bp):
ATTAAAGCTGAAGTGCAGCGA
Found at i:4774438 original size:51 final size:51
Alignment explanation
Indices: 4774361--4774486 Score: 162
Period size: 51 Copynumber: 2.5 Consensus size: 51
4774351 GACTGAGAGC
* * * *
4774361 AGCGAATCTTATTTCCCTGACGTTGCAGCGGAGCATATTAAAGCTAAAGGT
1 AGCGAATCTTATTTCCCTGGCATTGCAACGGAGCAGATTAAAGCTAAAGGT
* * * *
4774412 AGCGAATCTTGTTTCTCTGGCATTGCAACGGATCAGATTAAAGCTGAAGGT
1 AGCGAATCTTATTTCCCTGGCATTGCAACGGAGCAGATTAAAGCTAAAGGT
* *
4774463 AGCAAATCTTATCTCCCTGGCATT
1 AGCGAATCTTATTTCCCTGGCATT
4774487 AAAATTGAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (51 bp):
AGCGAATCTTATTTCCCTGGCATTGCAACGGAGCAGATTAAAGCTAAAGGT
Found at i:4774694 original size:44 final size:44
Alignment explanation
Indices: 4774636--4775113 Score: 180
Period size: 44 Copynumber: 10.8 Consensus size: 44
4774626 AAGGTTACAG
* * * *
4774636 ATCCTGTCCCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
* * * * *
4774680 ATCTTATCTTCCTAAG--GTAGTAGGAAAGCAGATTTAAG-CCACCA
1 ATCCTATCTCCCTAAGCAGTAGT-GG--AGCAGATTGAAGACCGCGA
* * * * * **
4774724 GTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGC-A
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
* ** *
4774767 GATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACAGCGA
1 -ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
* * * * *
4774812 ATCTTATCTTCCC-AAGGTAGTAG-GGAAGC-GTATTTAA-ACCACCA
1 ATCCTATC-TCCCTAA-GCAGTAGTGG-AGCAG-ATTGAAGACCGCGA
* * * * **
4774856 GTCCTATCTCCCTGAGCAGCAGTGGAGTA-AGTTGAAGATTGC-A
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGA-TTGAAGACCGCGA
* * * *
4774899 GATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGTAGACAGCGA
1 -ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
** * * * *
4774944 ATATTATCTTTCC-AAG--GTAGTAGAGAGGCAGATTTAAG-CCACCA
1 ATCCTATC-TCCCTAAGCAGTAGT-G-GA-GCAGATTGAAGACCGCGA
* * * * **
4774988 GTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGC-A
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
* * * * *
4775031 GATCTTGTCTCCCTAAGCAGTAGTGGAGCAGA-TCAAGGACGGTGA
1 -ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATTGAA-GACCGCGA
* * *
4775076 ATCTTATCTTCCTAAGGTAGTAG-GGAAGCAGATTGAAG
1 ATCCTATCTCCCTAA-GCAGTAGTGG-AGCAGATTGAAG
4775114 CCACTAGTCT
Statistics
Matches: 308, Mismatches: 92, Indels: 67
0.66 0.20 0.14
Matches are distributed among these distances:
42 11 0.04
43 44 0.14
44 183 0.59
45 58 0.19
46 12 0.04
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (44 bp):
ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
Found at i:4775135 original size:132 final size:132
Alignment explanation
Indices: 4774538--4775128 Score: 900
Period size: 132 Copynumber: 4.5 Consensus size: 132
4774528 GGGGCAAACT
* * *
4774538 GAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGAGAAGTAGATTTAAGCCACCAGTCCTATCTC
1 GAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTC
* * * * *
4774603 CC-CAGCAGCAGTGGAGTAGGTTAAAGGTTACAGATCCTGTCCCCCTAAGCAGTAGTGGAGCAGA
66 CCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGA
4774667 TC
131 TC
* *
4774669 GAAGACGGCGAATCTTATCTTCCTAAGGTAGTAGGAAAGCAGATTTAAGCCACCAGTCCTATCTC
1 GAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTC
4774734 CCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGA
66 CCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGA
4774799 TC
131 TC
* * *
4774801 AAAGACAGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGC-GTATTTAAACCACCAGTCCTATCT
1 GAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAG-ATTTAAGCCACCAGTCCTATCT
*
4774865 CCCTGAGCAGCAGTGGAGTAAGTTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAG
65 CCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAG
4774930 ATC
130 ATC
* * * * * *
4774933 GTAGACAGCGAATATTATCTTTCCAAGGTAGTAGAGAGGCAGATTTAAGCCACCAGTCCTATCTC
1 GAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTC
* *
4774998 CCTGAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGA
66 CCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGA
4775063 TC
131 TC
* * * * *
4775065 -AAGGACGGTGAATCTTATCTTCCTAAGGTAGTAGGGAAGCAGATTGAAGCCACTAGTCTTATCT
1 GAA-GACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCT
4775129 TACTGAGGTT
Statistics
Matches: 419, Mismatches: 37, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
131 64 0.15
132 354 0.84
133 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (132 bp):
GAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTC
CCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGA
TC
Found at i:4775230 original size:45 final size:45
Alignment explanation
Indices: 4775121--4775237 Score: 137
Period size: 45 Copynumber: 2.6 Consensus size: 45
4775111 AAGCCACTAG
* * * *
4775121 TCTTATCTTACTGAGGTTGCAGTATAGAAGACTGAAGATAGCAAC
1 TCTTATCTCACTGAGGTTGCAGTAGAGAAGACTGAAAAGAGCAAC
* *
4775166 TTTTATCTCACTGAGGTTGCAGTAGAGTAGACTGAAAAGAGCAGA-
1 TCTTATCTCACTGAGGTTGCAGTAGAGAAGACTGAAAAGAGCA-AC
* * *
4775211 TCTTATTTCTCTGAAGTTGCAGTAGAG
1 TCTTATCTCACTGAGGTTGCAGTAGAG
4775238 CAGATCACGA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
45 60 0.98
46 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (45 bp):
TCTTATCTCACTGAGGTTGCAGTAGAGAAGACTGAAAAGAGCAAC
Found at i:4777319 original size:10 final size:10
Alignment explanation
Indices: 4777304--4777344 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
4777294 TATATTTGCC
4777304 TTATTATATA
1 TTATTATATA
4777314 TTATTATATAA
1 TTATTATAT-A
4777325 TTAGTTATATA
1 TTA-TTATATA
4777336 -TA-TATATA
1 TTATTATATA
4777344 T
1 T
4777345 CTTTTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
8 6 0.21
10 11 0.39
11 5 0.18
12 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
TTATTATATA
Found at i:4777499 original size:18 final size:17
Alignment explanation
Indices: 4777468--4777528 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
4777458 TAAATAGATT
*
4777468 TTTACTTTTATATTTTTA
1 TTTA-TTTTGTATTTTTA
*
4777486 TTTATTTTCGTATTGTTA
1 TTTATTTT-GTATTTTTA
*
4777504 -TTATTGTTTTATCTTTTA
1 TTTATT-TTGTAT-TTTTA
4777522 TTTATTT
1 TTTATTT
4777529 ATTTATGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 12 0.34
18 18 0.51
19 5 0.14
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (17 bp):
TTTATTTTGTATTTTTA
Found at i:4777549 original size:44 final size:42
Alignment explanation
Indices: 4777467--4777549 Score: 98
Period size: 44 Copynumber: 1.9 Consensus size: 42
4777457 ATAAATAGAT
*
4777467 TTTTACTTTTATATTTTTATTTATTTTCGTATTGTTATTATTG
1 TTTTACTTTTATATTTTTATTTATTTTCG-ATTATTATTATTG
4777510 TTTTATCTTTTAT-TTATTTATTTATGTGTTC-ATTATTATT
1 TTTTA-CTTTTATATT-TTTATTTAT-T-TTCGATTATTATT
4777550 TTTATGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
43 7 0.20
44 24 0.69
45 1 0.03
46 3 0.09
ACGTcount: A:0.19, C:0.05, G:0.06, T:0.70
Consensus pattern (42 bp):
TTTTACTTTTATATTTTTATTTATTTTCGATTATTATTATTG
Found at i:4777956 original size:73 final size:73
Alignment explanation
Indices: 4777837--4777978 Score: 232
Period size: 73 Copynumber: 1.9 Consensus size: 73
4777827 TATTTTCAGA
** * *
4777837 CAAGTTTTAAGTGATCTCGAGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATGATTCCTT
1 CAAGTTTTAAACGATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCCTT
4777902 TTTTTTCT
66 TTTTTTCT
4777910 CAAGTTTTAAACGATCTC-AGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCCT
1 CAAGTTTTAAACGATCTCGA-GAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCCT
4777974 TTTTT
65 TTTTT
4777979 AAAATCCGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 1 0.02
73 63 0.98
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (73 bp):
CAAGTTTTAAACGATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCCTT
TTTTTTCT
Found at i:4791202 original size:24 final size:24
Alignment explanation
Indices: 4791175--4791246 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
4791165 AAAGTCAAAC
*
4791175 ATATTATGCTAATAAATGCTAAAT
1 ATATTATACTAATAAATGCTAAAT
4791199 ATATTATACTAATAAATGCTAAAT
1 ATATTATACTAATAAATGCTAAAT
* *
4791223 ATATTATACTCATAAATACTAAAT
1 ATATTATACTAATAAATGCTAAAT
4791247 CTTCTAGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.38
Consensus pattern (24 bp):
ATATTATACTAATAAATGCTAAAT
Found at i:4793682 original size:3 final size:3
Alignment explanation
Indices: 4793676--4793701 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4793666 TGCTTCTGCT
4793676 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
4793702 TAAATCATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:4814419 original size:109 final size:109
Alignment explanation
Indices: 4814167--4814505 Score: 515
Period size: 109 Copynumber: 3.1 Consensus size: 109
4814157 TAGATTGAGA
* **
4814167 TTTAAGAGAATATTTGGCTATTTGGTCAAACGAG--AAATCGAAACCCAGCACATTAGGGCATAT
1 TTTAAAAGAATATTTGGCTATTTGGTCAAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
* *
4814230 TTTCT--AATTTCCAAACGCAAAAAATTGCCTTATTTTGAAATTT
66 TTTCTCGAATTTCCAAACGCAAAACATTACCTTATTTTGAAA-TT
* *
4814273 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGAATATTTGGCTATTTGGTCAAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
*
4814338 TTTCTCGAATTTCCAAATGCAAAACATTACCTTATTTTGAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTACCTTATTTTGAAATT
* * *
4814382 TTTAAAAGAATATTTGGTTATTTGGTCAAAAGAGAAAAATCGAAACCTAGCACATTAGGGCACGT
1 TTTAAAAGAATATTTGGCTATTTGGTCAAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
*
4814447 TTTCTCGAATTTCCAAACGCAAAACATTACCTTACTTTGAAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTACCTTATTTTG-AAATT
*
4814492 TTTAAAAGGATATT
1 TTTAAAAGAATATT
4814506 AATATGCGTA
Statistics
Matches: 212, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
106 31 0.15
108 32 0.15
109 99 0.47
110 50 0.24
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (109 bp):
TTTAAAAGAATATTTGGCTATTTGGTCAAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
TTTCTCGAATTTCCAAACGCAAAACATTACCTTATTTTGAAATT
Found at i:4816782 original size:13 final size:13
Alignment explanation
Indices: 4816764--4816789 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4816754 AATTCTTTTT
4816764 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
4816777 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
4816790 GCATTCAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:4819207 original size:37 final size:37
Alignment explanation
Indices: 4819166--4819242 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
4819156 AGAACAGACG
4819166 TTTGTTTATAATTTAAAAAATTAATTATTTTAAGTAA
1 TTTGTTTATAATTTAAAAAATTAATTATTTTAAGTAA
4819203 TTTGTTTATAATTTAAAAAATTAATTATTTTAAGTAA
1 TTTGTTTATAATTTAAAAAATTAATTATTTTAAGTAA
4819240 TTT
1 TTT
4819243 TAACTAAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (37 bp):
TTTGTTTATAATTTAAAAAATTAATTATTTTAAGTAA
Found at i:4819224 original size:20 final size:20
Alignment explanation
Indices: 4819166--4819224 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
4819156 AGAACAGACG
4819166 TTTGTTTATAATTTAAAAAA
1 TTTGTTTATAATTTAAAAAA
** **
4819186 -TTAATTAT--TTTAAGTAA
1 TTTGTTTATAATTTAAAAAA
4819203 TTTGTTTATAATTTAAAAAA
1 TTTGTTTATAATTTAAAAAA
4819223 TT
1 TT
4819225 AATTATTTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 7 0.25
18 6 0.21
19 6 0.21
20 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTGTTTATAATTTAAAAAA
Found at i:4838568 original size:30 final size:27
Alignment explanation
Indices: 4838510--4838611 Score: 77
Period size: 27 Copynumber: 3.6 Consensus size: 27
4838500 AAAAGGGTAC
* * *
4838510 AAAATATATACATGTACATATATAAAA
1 AAAATATATACATATATATAGATAAAA
4838537 AAAACTATATACATATATATAGATTATAAA
1 AAAA-TATATACATATATATAGA-TA-AAA
4838567 AAAGATA-ATTACATATATAT--ATAAACA
1 AAA-ATATA-TACATATATATAGATAAA-A
4838594 AATAATA-ATTACATATAT
1 AA-AATATA-TACATATAT
4838612 TAAAATTAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
26 2 0.03
27 23 0.35
28 17 0.26
29 3 0.05
30 19 0.29
31 1 0.02
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (27 bp):
AAAATATATACATATATATAGATAAAA
Found at i:4838775 original size:17 final size:17
Alignment explanation
Indices: 4838753--4838798 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
4838743 TAGGAAATAA
4838753 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
* *
4838770 AAAATGTAAATGTATGT
1 AAAATGTATATGTATAT
*
4838787 ATATATGTATAT
1 A-AAATGTATAT
4838799 AAATGTTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:4838808 original size:23 final size:22
Alignment explanation
Indices: 4838754--4838808 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
4838744 AGGAAATAAA
*
4838754 AAATGTATATGTATATAAAATGT
1 AAATGT-TATGTATATAAAATAT
**
4838777 AAATG-TATGTATATATGTATAT
1 AAATGTTATGTATATA-AAATAT
4838799 AAATGTTATG
1 AAATGTTATG
4838809 CAAATATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 10 0.37
22 8 0.30
23 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.42
Consensus pattern (22 bp):
AAATGTTATGTATATAAAATAT
Found at i:4838913 original size:3 final size:3
Alignment explanation
Indices: 4838905--4838945 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
4838895 GTATATATAG
* * *
4838905 TAA TAA TAA TAA TAA TGA TAA TGA TAA CAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4838946 GCTTAATAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:4839307 original size:24 final size:22
Alignment explanation
Indices: 4839260--4839309 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
4839250 TACAAATTAA
4839260 ATCTTTAAGATTACAAAATCAT
1 ATCTTTAAGATTACAAAATCAT
* *
4839282 ATCTTCTAAGATTGCATATATCAT
1 ATCTT-TAAGATTACA-AAATCAT
4839306 ATCT
1 ATCT
4839310 AAGATCATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.21
23 9 0.38
24 10 0.42
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (22 bp):
ATCTTTAAGATTACAAAATCAT
Found at i:4839318 original size:12 final size:12
Alignment explanation
Indices: 4839301--4839338 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
4839291 GATTGCATAT
4839301 ATCATATCTAAG
1 ATCATATCTAAG
4839313 ATCATATCTAAG
1 ATCATATCTAAG
4839325 ATCATATCTAAG
1 ATCATATCTAAG
4839337 AT
1 AT
4839339 TGCATATCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (12 bp):
ATCATATCTAAG
Found at i:4841094 original size:14 final size:15
Alignment explanation
Indices: 4841067--4841096 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4841057 TTTTTTGTAC
4841067 AAATAAATAATAAAA
1 AAATAAATAATAAAA
4841082 AAATAAA-AATAAAA
1 AAATAAATAATAAAA
4841096 A
1 A
4841097 TTTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAATAATAAAA
Found at i:4841095 original size:49 final size:50
Alignment explanation
Indices: 4841018--4841112 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
4841008 AACAAATCCA
* * * *
4841018 AAATAAATAAT-AAAAATTTAAATTTAAAATAT-ATTTAAATTTTTTGTAC
1 AAATAAATAATAAAAAAATAAAAATAAAAATATAATTT-AATTTTTTGTAC
*
4841067 AAATAAATAATAAAAAAATAAAAATAAAAATTTAATTTAATTTTTT
1 AAATAAATAATAAAAAAATAAAAATAAAAATATAATTTAATTTTTT
4841113 AGGTACCGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
49 11 0.28
50 24 0.62
51 4 0.10
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (50 bp):
AAATAAATAATAAAAAAATAAAAATAAAAATATAATTTAATTTTTTGTAC
Found at i:4843982 original size:27 final size:27
Alignment explanation
Indices: 4843952--4844046 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 27
4843942 CTCTTTTATC
*
4843952 ATTATTTATTTTAAATTTTTTACATTT
1 ATTATTTATTTTAAATTTTTTATATTT
*
4843979 ATTATTTATTTGAAACTGTTTTTATA-TT
1 ATTATTTATTTTAAA-T-TTTTTATATTT
* *
4844007 A-AATTTA-TTTAAATTTCTTT-TATAT
1 ATTATTTATTTTAAATTT-TTTATATTT
*
4844032 ATTATTTATTGTAAA
1 ATTATTTATTTTAAA
4844047 CTTATGTATG
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
24 4 0.07
25 6 0.11
26 10 0.18
27 24 0.44
28 4 0.07
29 7 0.13
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (27 bp):
ATTATTTATTTTAAATTTTTTATATTT
Found at i:4845276 original size:12 final size:12
Alignment explanation
Indices: 4845259--4845283 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4845249 ATTTTCCAAG
4845259 AAAATGAAAATA
1 AAAATGAAAATA
4845271 AAAATGAAAATA
1 AAAATGAAAATA
4845283 A
1 A
4845284 CCTTTATTTC
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATGAAAATA
Found at i:4845736 original size:14 final size:14
Alignment explanation
Indices: 4845717--4845745 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4845707 GACCTCAGTT
4845717 TTCTAAAGTGTTGA
1 TTCTAAAGTGTTGA
4845731 TTCTAAAGTGTTGA
1 TTCTAAAGTGTTGA
4845745 T
1 T
4845746 GGAGCCACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TTCTAAAGTGTTGA
Found at i:4847745 original size:11 final size:11
Alignment explanation
Indices: 4847717--4847747 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4847707 GTTGTTACAG
*
4847717 GAAAATATGTT
1 GAAAATTTGTT
4847728 GAAAATTTGTT
1 GAAAATTTGTT
4847739 GAAAATTTG
1 GAAAATTTG
4847748 GGTTCTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (11 bp):
GAAAATTTGTT
Found at i:4848834 original size:26 final size:27
Alignment explanation
Indices: 4848805--4848860 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
4848795 AAATCACAGA
* *
4848805 CCCAAAATCT-AACCCAATTAGCCTAG
1 CCCAAAACCTAAACCCAATTAACCTAG
4848831 CCC-AAACCTAAACCCAATTAACCTAG
1 CCCAAAACCTAAACCCAATTAACCTAG
4848857 CCCA
1 CCCA
4848861 GCTAATGTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.39, C:0.39, G:0.05, T:0.16
Consensus pattern (27 bp):
CCCAAAACCTAAACCCAATTAACCTAG
Found at i:4853716 original size:19 final size:19
Alignment explanation
Indices: 4853692--4853738 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
4853682 AAAAAAATCA
* * *
4853692 AAATAATTTTTAAATTTTT
1 AAATAATTATAAAAATTTT
4853711 AAATAATTATAAAAATTTT
1 AAATAATTATAAAAATTTT
*
4853730 AATTAATTA
1 AAATAATTA
4853739 ATTTTGAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATAATTATAAAAATTTT
Found at i:4854570 original size:26 final size:26
Alignment explanation
Indices: 4854514--4854579 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 26
4854504 AAAAATCAAA
*
4854514 ATAAATTTTA-AATTTTAAAAAAATT
1 ATAAAATTTATAATTTTAAAAAAATT
** **
4854539 CCAAAATTTATAATTTTTTAAAAATT
1 ATAAAATTTATAATTTTAAAAAAATT
4854565 ATAAAAATTT-TAATT
1 AT-AAAATTTATAATT
4854580 AATTAATTTC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
25 7 0.22
26 18 0.56
27 7 0.22
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (26 bp):
ATAAAATTTATAATTTTAAAAAAATT
Found at i:4855277 original size:43 final size:43
Alignment explanation
Indices: 4855229--4855355 Score: 218
Period size: 43 Copynumber: 3.0 Consensus size: 43
4855219 TCGCTAACTT
* *
4855229 CCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGTTATAGA
1 CCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGA
4855272 CCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGA
1 CCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGA
* *
4855315 CCAAGACCTTTAGCGCCGCTTTTCCCATAAACGCCGCTAAA
1 CCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
4855356 AACTATGACA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 80 1.00
ACGTcount: A:0.27, C:0.35, G:0.17, T:0.21
Consensus pattern (43 bp):
CCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGA
Found at i:4855636 original size:19 final size:20
Alignment explanation
Indices: 4855601--4855642 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
4855591 AAGTTGTCGT
4855601 AAAAATTAAAGTAAAAA-TA
1 AAAAATTAAAGTAAAAACTA
*
4855620 AAAAATTAGAA-TCAAAACTA
1 AAAAATTA-AAGTAAAAACTA
4855640 AAA
1 AAA
4855643 TAAATAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (20 bp):
AAAAATTAAAGTAAAAACTA
Found at i:4856370 original size:53 final size:53
Alignment explanation
Indices: 4856304--4856418 Score: 212
Period size: 53 Copynumber: 2.2 Consensus size: 53
4856294 AGAATTAATA
*
4856304 AAACTGAAAGGAGAATGCAATAGCATGATGGCTTGACCCAAAAGTTCTGATTT
1 AAACTGAAAGGAGAATGCAATAGCATGATGACTTGACCCAAAAGTTCTGATTT
*
4856357 AAACTGAAAGGAGAATGCAATAGCATGATGACTTGACCTAAAAGTTCTGATTT
1 AAACTGAAAGGAGAATGCAATAGCATGATGACTTGACCCAAAAGTTCTGATTT
4856410 AAACTGAAA
1 AAACTGAAA
4856419 ATTATCCCTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 60 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (53 bp):
AAACTGAAAGGAGAATGCAATAGCATGATGACTTGACCCAAAAGTTCTGATTT
Found at i:4860160 original size:28 final size:29
Alignment explanation
Indices: 4860118--4860172 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
4860108 CTGAATCTCT
* * *
4860118 AAACCCTAAATCACTAA-CTCTTAACCCC
1 AAACCCCAAACCACTAACCTCTAAACCCC
4860146 AAACCCCAAACCACTAACCTCTAAACC
1 AAACCCCAAACCACTAACCTCTAAACC
4860173 ATATTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (29 bp):
AAACCCCAAACCACTAACCTCTAAACCCC
Found at i:4860328 original size:89 final size:89
Alignment explanation
Indices: 4860115--4860320 Score: 243
Period size: 89 Copynumber: 2.3 Consensus size: 89
4860105 ACCCTGAATC
* *
4860115 TCTAAACCCTAAATCACTAACTCTTAACCCCAAACCCCAAACCACTAACCTCTAAACCATATTTA
1 TCTAAACCCTAAATC-CTAAC-C-TAACCCCAAATCCCAAACCACTAACCCCTAAACCATATTTA
4860180 ATATAGAAATTAAAAAACACTAATTAA
63 ATATAGAAATTAAAAAACACTAATTAA
* * * ** * * * *
4860207 TCTAAATCATAAACCCTAACCCGACCCCAAATCCCTAACCCCTAACCCCTAAA-TATTATTTAGT
1 TCTAAACCCTAAATCCTAACCTAACCCCAAATCCCAAACCACTAACCCCTAAACCA-TATTTAAT
* * *
4860271 ATATAAATTAAAACACACTATTTAA
65 ATAGAAATTAAAAAACACTAATTAA
4860296 TCTAAACCCTAAATCCTAACCTAAC
1 TCTAAACCCTAAATCCTAACCTAAC
4860321 ACTAAATCTA
Statistics
Matches: 94, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
88 1 0.01
89 75 0.80
90 1 0.01
91 5 0.05
92 12 0.13
ACGTcount: A:0.44, C:0.30, G:0.01, T:0.25
Consensus pattern (89 bp):
TCTAAACCCTAAATCCTAACCTAACCCCAAATCCCAAACCACTAACCCCTAAACCATATTTAATA
TAGAAATTAAAAAACACTAATTAA
Found at i:4860376 original size:14 final size:14
Alignment explanation
Indices: 4860359--4860397 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4860349 CTCTTAATCT
4860359 CTAACCCTTAACCC
1 CTAACCCTTAACCC
*
4860373 CTAACCCCTAACCC
1 CTAACCCTTAACCC
* *
4860387 ATAAACCTTAA
1 CTAACCCTTAA
4860398 ATCACAACTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.44, G:0.00, T:0.21
Consensus pattern (14 bp):
CTAACCCTTAACCC
Found at i:4860434 original size:14 final size:15
Alignment explanation
Indices: 4860417--4860448 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
4860407 CTTAAATCAG
4860417 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
4860431 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
4860446 AAT
1 AAT
4860449 TTATAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:4860883 original size:41 final size:41
Alignment explanation
Indices: 4860826--4861063 Score: 379
Period size: 41 Copynumber: 5.8 Consensus size: 41
4860816 ATGTTTTTGT
* **
4860826 GGCGCTTTTTCAAAAACGCCGTTAAAGCCCTGAGCATTAGC
1 GGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGC
*
4860867 GGCGCTTTTTCAAAAACGCCACTAAAGATCTGAGCATTAGC
1 GGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGC
4860908 GGCGCTTTTTCAAAAACGCCGCTAAAGATCT-AGCATTAGC
1 GGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGC
*
4860948 GGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTAGC
1 GGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGC
* *
4860989 GGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTAGT
1 GGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGC
* *
4861030 GGCGCTTTTTTTAAAAACGCGGCTAAAGATCTGA
1 GGCGC-TTTTTCAAAAACGCCGCTAAAGATCTGA
4861064 AAGGTACAAA
Statistics
Matches: 185, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
40 39 0.21
41 121 0.65
42 25 0.14
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (41 bp):
GGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGC
Found at i:4860965 original size:81 final size:82
Alignment explanation
Indices: 4860826--4861063 Score: 379
Period size: 81 Copynumber: 2.9 Consensus size: 82
4860816 ATGTTTTTGT
* ** *
4860826 GGCGCTTTTTCAAAAACGCCGTTAAAGCCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCACTA
1 GGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTA
4860891 AAGATCTGAGCATTAGC
66 AAGATCTGAGCATTAGC
*
4860908 GGCGCTTTTTCAAAAACGCCGCTAAAGATCT-AGCATTAGCGGCGCTTTCTCAAAAACGCCGCTA
1 GGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTA
4860972 AAGATCTGAGCATTAGC
66 AAGATCTGAGCATTAGC
* * * *
4860989 GGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTAGTGGCGCTTTTTTTAAAAACGCGGCT
1 GGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGC-TTTTTCAAAAACGCCGCT
4861054 AAAGATCTGA
65 AAAGATCTGA
4861064 AAGGTACAAA
Statistics
Matches: 144, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
81 78 0.54
82 41 0.28
83 25 0.17
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (82 bp):
GGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTA
AAGATCTGAGCATTAGC
Found at i:4861251 original size:12 final size:12
Alignment explanation
Indices: 4861234--4861259 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4861224 TTTTTTGTCC
4861234 AAACGCCGCTAA
1 AAACGCCGCTAA
4861246 AAACGCCGCTAA
1 AAACGCCGCTAA
4861258 AA
1 AA
4861260 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:4861412 original size:16 final size:17
Alignment explanation
Indices: 4861391--4861431 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
4861381 TAAATATGTT
*
4861391 ATTTTTAG-GTTTTATA
1 ATTTTTAGAGTTTTAAA
4861407 ATTTTT-GAGTTTTAAA
1 ATTTTTAGAGTTTTAAA
4861423 ATTTTTAGA
1 ATTTTTAGA
4861432 TTCGGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 19 0.86
17 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (17 bp):
ATTTTTAGAGTTTTAAA
Found at i:4864088 original size:18 final size:19
Alignment explanation
Indices: 4864065--4864106 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
4864055 GAAGTTTTCT
4864065 ATTATTGTAATAT-TATTA
1 ATTATTGTAATATATATTA
* *
4864083 ATTATTTTAATATATTTTA
1 ATTATTGTAATATATATTA
4864102 ATTAT
1 ATTAT
4864107 ATATTAACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTATTGTAATATATATTA
Found at i:4864092 original size:9 final size:9
Alignment explanation
Indices: 4864065--4864106 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
4864055 GAAGTTTTCT
*
4864065 ATTATTGTA
1 ATTATTTTA
4864074 A-TATTATTA
1 ATTATT-TTA
4864083 ATTATTTTA
1 ATTATTTTA
4864092 ATATATTTTA
1 AT-TATTTTA
4864102 ATTAT
1 ATTAT
4864107 ATATTAACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
8 4 0.14
9 12 0.41
10 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (9 bp):
ATTATTTTA
Found at i:4865302 original size:21 final size:20
Alignment explanation
Indices: 4865285--4865335 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
4865275 GAGGTTCAGT
*
4865285 GTTCGGTGTTCATGGTTCGAG
1 GTTCGG-GTTCATGGTTCAAG
*
4865306 GTTTAGGGTTCATGGTTCAAG
1 G-TTCGGGTTCATGGTTCAAG
4865327 GTTCGGGTT
1 GTTCGGGTT
4865336 TGAGATTCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.27
21 15 0.58
22 4 0.15
ACGTcount: A:0.12, C:0.12, G:0.37, T:0.39
Consensus pattern (20 bp):
GTTCGGGTTCATGGTTCAAG
Found at i:4865886 original size:2 final size:2
Alignment explanation
Indices: 4865879--4865906 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4865869 ATATGTCGTA
4865879 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4865907 TTATTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4873881 original size:18 final size:18
Alignment explanation
Indices: 4873801--4873881 Score: 58
Period size: 18 Copynumber: 4.6 Consensus size: 18
4873791 ACACTGTTGG
* *
4873801 AGATGAAGATGAAGATCA
1 AGATGAAGATGGAGATGA
* * *
4873819 AGATCAAGATGGAGGTGG
1 AGATGAAGATGGAGATGA
* * *
4873837 AGGTGGAGGTGGAGAT-A
1 AGATGAAGATGGAGATGA
* *
4873854 GGAT-AAGATGGAGGTGA
1 AGATGAAGATGGAGATGA
4873871 AGATGAAGATG
1 AGATGAAGATG
4873882 AAGAGCCGGA
Statistics
Matches: 44, Mismatches: 17, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
16 8 0.18
17 6 0.14
18 30 0.68
ACGTcount: A:0.38, C:0.02, G:0.42, T:0.17
Consensus pattern (18 bp):
AGATGAAGATGGAGATGA
Found at i:4878825 original size:16 final size:17
Alignment explanation
Indices: 4878804--4878858 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 17
4878794 TCACTTAAAA
4878804 AATTTT-ATTTTTTTAT
1 AATTTTAATTTTTTTAT
*
4878820 AATTTTAATAATTTTTA-
1 AATTTTAAT-TTTTTTAT
*
4878837 GATTTTAATTTTTTT-T
1 AATTTTAATTTTTTTAT
4878853 AATTTT
1 AATTTT
4878859 CAAGTAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
16 16 0.50
17 10 0.31
18 6 0.19
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
AATTTTAATTTTTTTAT
Found at i:4878841 original size:17 final size:16
Alignment explanation
Indices: 4878814--4878858 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
4878804 AATTTTATTT
4878814 TTTTATAATTTTAATAA
1 TTTT-TAATTTTAATAA
**
4878831 TTTTTAGATTTTAATTT
1 TTTTTA-ATTTTAATAA
4878848 TTTTTAATTTT
1 TTTTTAATTTT
4878859 CAAGTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTTTAATTTTAATAA
Found at i:4884862 original size:42 final size:42
Alignment explanation
Indices: 4884803--4884884 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
4884793 GTGTATCCTG
4884803 CAATTCCATGCCAATTACATGAATGGAAGTCTTTCCTTTTGC
1 CAATTCCATGCCAATTACATGAATGGAAGTCTTTCCTTTTGC
*
4884845 CAATTCCATGCCAATTACATGAATGGAAGTCTTTTCTTTT
1 CAATTCCATGCCAATTACATGAATGGAAGTCTTTCCTTTT
4884885 ATTGGAAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (42 bp):
CAATTCCATGCCAATTACATGAATGGAAGTCTTTCCTTTTGC
Found at i:4893170 original size:20 final size:21
Alignment explanation
Indices: 4893139--4893181 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
4893129 TATAAAAAAT
*
4893139 ATAATGGTAATAATGATAGTA
1 ATAATGGTAATAATAATAGTA
4893160 ATAAT-GTAATAATAATAGTA
1 ATAATGGTAATAATAATAGTA
4893180 AT
1 AT
4893182 GGAAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (21 bp):
ATAATGGTAATAATAATAGTA
Found at i:4893212 original size:26 final size:26
Alignment explanation
Indices: 4893183--4893232 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
4893173 AATAGTAATG
4893183 GAAATAATAAAAAAACAA-AATAAAAA
1 GAAATAATAAAAAAA-AACAATAAAAA
**
4893209 GAAATTGTAAAAAAAAACAATAAA
1 GAAATAATAAAAAAAAACAATAAA
4893233 TGTAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (26 bp):
GAAATAATAAAAAAAAACAATAAAAA
Found at i:4895281 original size:23 final size:22
Alignment explanation
Indices: 4895250--4895296 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
4895240 TTTAATATAG
4895250 ATATTCTATTATTATATTACAA
1 ATATTCTATTATTATATTACAA
*
4895272 ATATGTCTATTATTATTTTACAA
1 ATAT-TCTATTATTATATTACAA
4895295 AT
1 AT
4895297 TATAAAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATTCTATTATTATATTACAA
Found at i:4900020 original size:20 final size:19
Alignment explanation
Indices: 4899977--4900021 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
4899967 CCCATTTATT
*
4899977 TATTTTTTTCTTTTTCAAC
1 TATTTTTTTCATTTTCAAC
* *
4899996 GATTTCTTTTCATTTTCACC
1 TATTT-TTTTCATTTTCAAC
4900016 TATTTT
1 TATTTT
4900022 GTTTTTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.16, C:0.18, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTTTTTTCATTTTCAAC
Found at i:4906866 original size:27 final size:27
Alignment explanation
Indices: 4906833--4906888 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
4906823 TTAGTCTCTC
* *
4906833 TCAAAAAAATTAAAATAAATTTTAAAAT
1 TCAAAATAATTAAAA-AAATTTCAAAAT
* *
4906861 TCAAAATATTTATAAAAATTTCAAAAT
1 TCAAAATAATTAAAAAAATTTCAAAAT
4906888 T
1 T
4906889 TATATTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (27 bp):
TCAAAATAATTAAAAAAATTTCAAAAT
Found at i:4906876 original size:18 final size:19
Alignment explanation
Indices: 4906837--4906901 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
4906827 TCTCTCTCAA
4906837 AAAAATT-AAAATAAATTTT
1 AAAAATTCAAAAT-AATTTT
4906856 -AAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
4906874 AAAAATTTCAAAATTTATATTTT
1 AAAAA-TTCAAAA--TA-ATTTT
4906897 AAAAA
1 AAAAA
4906902 AGATAATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
17 4 0.11
18 7 0.18
19 9 0.24
20 7 0.18
22 1 0.03
23 6 0.16
24 4 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:4914635 original size:26 final size:27
Alignment explanation
Indices: 4914564--4914640 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 27
4914554 AAATATTAAT
4914564 AAAATATTATAAAGAAATTAGAAATGATAGA
1 AAAATA-TAT-AA-AAATTA-AAATGATAGA
*
4914595 AAATTATATCAAAAATTAAAATGATA-A
1 AAAATATAT-AAAAATTAAAATGATAGA
4914622 AAGAATATATAAAAATTAA
1 AA-AATATATAAAAATTAA
4914641 TAAAAAAAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.29
28 14 0.33
29 6 0.14
30 5 0.12
31 5 0.12
ACGTcount: A:0.64, C:0.01, G:0.08, T:0.27
Consensus pattern (27 bp):
AAAATATATAAAAATTAAAATGATAGA
Found at i:4914961 original size:30 final size:32
Alignment explanation
Indices: 4914901--4914963 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
4914891 AAAAATTACT
*
4914901 AAAATATTATAAATTTTTAGAAAATTATAAAA
1 AAAATATTATAAATTATTAGAAAATTATAAAA
**
4914933 AAAATA-TATAAATTATTA-AATGTTATAAAA
1 AAAATATTATAAATTATTAGAAAATTATAAAA
4914963 A
1 A
4914964 CTTAAAGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 11 0.39
31 11 0.39
32 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (32 bp):
AAAATATTATAAATTATTAGAAAATTATAAAA
Found at i:4915209 original size:34 final size:34
Alignment explanation
Indices: 4915154--4915218 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
4915144 TTTACAAATT
4915154 ATTTTTAATAAAATAAATA-TTTTATTATTTTCCA
1 ATTTTTAATAAAATAAATATTTTTATT-TTTTCCA
**
4915188 ATTTTT-ATATAAATATTTATTTTTATTTTTT
1 ATTTTTAATA-AAATAAATATTTTTATTTTTT
4915219 AAAATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 3 0.11
34 17 0.63
35 7 0.26
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (34 bp):
ATTTTTAATAAAATAAATATTTTTATTTTTTCCA
Found at i:4916505 original size:22 final size:22
Alignment explanation
Indices: 4916426--4916497 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
4916416 TTGGATCAAA
* **
4916426 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
4916448 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
4916470 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
4916492 CATGAG
1 CATGAG
4916498 GGTTTAGTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:4917016 original size:9 final size:9
Alignment explanation
Indices: 4917002--4917031 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
4916992 TTAATAATTT
4917002 AAAATTTTA
1 AAAATTTTA
4917011 AAAATTTTA
1 AAAATTTTA
4917020 AAAATTTTA
1 AAAATTTTA
4917029 AAA
1 AAA
4917032 GACCAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAAATTTTA
Found at i:4917419 original size:17 final size:19
Alignment explanation
Indices: 4917399--4917441 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
4917389 CATTAAAAAA
4917399 ATAAACATA-TACT-AAAT
1 ATAAACATACTACTCAAAT
*
4917416 ATAAA-ATACTACTCTAAT
1 ATAAACATACTACTCAAAT
4917434 ATAAACAT
1 ATAAACAT
4917442 TAAATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 9 0.41
18 8 0.36
19 2 0.09
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAAACATACTACTCAAAT
Found at i:4918913 original size:29 final size:29
Alignment explanation
Indices: 4918871--4918927 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
4918861 ATAAAAAAAG
*
4918871 GTTGAAACTAATACATTCTTGGCAAATTA
1 GTTGAAACTAATACATTCTTGACAAATTA
*
4918900 GTTGAAATTAATACATTCTTGACAAATT
1 GTTGAAACTAATACATTCTTGACAAATT
4918928 TAACTTCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (29 bp):
GTTGAAACTAATACATTCTTGACAAATTA
Found at i:4924220 original size:27 final size:25
Alignment explanation
Indices: 4924181--4924245 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
4924171 ACTAGAGCAC
4924181 ATAATCGGGAAGCCCTCTCTTAAGCCAA
1 ATAA-CGGGAAGCCCT-TC-TAAGCCAA
* * *
4924209 ATAACGGGAAGCTCTTCTGAGCCAT
1 ATAACGGGAAGCCCTTCTAAGCCAA
*
4924234 ATAACGAGAAGC
1 ATAACGGGAAGC
4924246 TTATCCAGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 17 0.52
26 2 0.06
27 10 0.30
28 4 0.12
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.20
Consensus pattern (25 bp):
ATAACGGGAAGCCCTTCTAAGCCAA
Found at i:4924379 original size:25 final size:25
Alignment explanation
Indices: 4924324--4924403 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
4924314 ATAGCTCCGA
* *
4924324 AGAGCCATATATCGGGACGCTCTAG
1 AGAGCCATATATCGGGAAGCTCAAG
* *
4924349 ATAGCCATATATCGGGAAGTTCAAG
1 AGAGCCATATATCGGGAAGCTCAAG
* *
4924374 CGAGCC--ATATCGGGAAGCTCACAA
1 AGAGCCATATATCGGGAAGCTCA-AG
4924398 AGAGCC
1 AGAGCC
4924404 TTTAATCAAG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 14 0.31
24 6 0.13
25 25 0.56
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (25 bp):
AGAGCCATATATCGGGAAGCTCAAG
Found at i:4928001 original size:30 final size:30
Alignment explanation
Indices: 4927967--4928035 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
4927957 TTTCTTTTGT
* *
4927967 TTTGTTGTTGT-TATTGTTTGTGTTTTGCAA
1 TTTGTTGTTGTGT-GTGTTGGTGTTTTGCAA
* * *
4927997 TTTGTTTTTGTGTGTGTTGGTGTTTTGTAT
1 TTTGTTGTTGTGTGTGTTGGTGTTTTGCAA
4928027 TTTGTTGTT
1 TTTGTTGTT
4928036 TGTTTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.06, C:0.01, G:0.26, T:0.67
Consensus pattern (30 bp):
TTTGTTGTTGTGTGTGTTGGTGTTTTGCAA
Found at i:4930159 original size:66 final size:66
Alignment explanation
Indices: 4930038--4930179 Score: 167
Period size: 66 Copynumber: 2.2 Consensus size: 66
4930028 TGTTTAGTAA
* * * * * * * * *
4930038 CTTGAGAAGACTCGATATCTCGTTTAGGATCTTGGGATTGAGAAGGCTTGTTATCTTGTTCAAGA
1 CTTGGGAAGACTCGATATCGCGTTCAAGAGCTTGGGATTGAGAAGACCTGATATCTCGTTCAAGA
4930103 G
66 G
* * *
4930104 TTTGGGAAGACTCGATATCGCGTTCAAGAGCTTGGGATTGAGAATACCTGATATCTCGTTCAGGA
1 CTTGGGAAGACTCGATATCGCGTTCAAGAGCTTGGGATTGAGAAGACCTGATATCTCGTTCAAGA
4930169 G
66 G
*
4930170 CTTGGCAAGA
1 CTTGGGAAGA
4930180 TCTGGTATTT
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.31
Consensus pattern (66 bp):
CTTGGGAAGACTCGATATCGCGTTCAAGAGCTTGGGATTGAGAAGACCTGATATCTCGTTCAAGA
G
Found at i:4930164 original size:36 final size:35
Alignment explanation
Indices: 4930051--4930174 Score: 96
Period size: 36 Copynumber: 3.6 Consensus size: 35
4930041 GAGAAGACTC
* * * * *
4930051 GATATCTCGTTTAGGATCTTGGGATTGAGAAGGCTT
1 GATATCTCGTTCAAGAGCTTGGGATTGAGAA-TCCT
* * * *
4930087 GTTATCTTGTTCAAGAGTTTGGGA---AGACT-C-
1 GATATCTCGTTCAAGAGCTTGGGATTGAGAATCCT
*
4930117 GATATCGCGTTCAAGAGCTTGGGATTGAGAATACCT
1 GATATCTCGTTCAAGAGCTTGGGATTGAGAAT-CCT
*
4930153 GATATCTCGTTCAGGAGCTTGG
1 GATATCTCGTTCAAGAGCTTGG
4930175 CAAGATCTGG
Statistics
Matches: 66, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
30 20 0.30
33 7 0.11
35 1 0.02
36 38 0.58
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (35 bp):
GATATCTCGTTCAAGAGCTTGGGATTGAGAATCCT
Found at i:4938823 original size:27 final size:23
Alignment explanation
Indices: 4938774--4938819 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
4938764 GATAGCCTGA
4938774 AAACCCACACATTTGACTCTGTT
1 AAACCCACACATTTGACTCTGTT
4938797 AAACCCACACATTTGACTCTGTT
1 AAACCCACACATTTGACTCTGTT
4938820 TGTTCTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.30
Consensus pattern (23 bp):
AAACCCACACATTTGACTCTGTT
Found at i:4940354 original size:15 final size:17
Alignment explanation
Indices: 4940323--4940356 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
4940313 ATACAGGATG
4940323 TTTAAATATATTTATTA
1 TTTAAATATATTTATTA
4940340 TTTAAA-ATA-TTATTA
1 TTTAAATATATTTATTA
4940355 TT
1 TT
4940357 AAAGAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 3 0.18
17 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAAATATATTTATTA
Done.