Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_pilon, whole genome shotgun sequence
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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 43
Found at i:3301420 original size:13 final size:12
Alignment explanation
Indices: 3301402--3301447 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
3301392 GGGTAAAATA
3301402 AAAGAAAAAGAGC
1 AAAGAAAAAGA-C
3301415 AAAG-AAAA-AC
1 AAAGAAAAAGAC
3301425 AAAGGAAAAAGCAC
1 AAA-GAAAAAG-AC
3301439 AAAGAAAAA
1 AAAGAAAAA
3301448 ATAGGATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 4 0.14
11 2 0.07
12 8 0.28
13 10 0.34
14 5 0.17
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAGAC
Found at i:3301464 original size:25 final size:24
Alignment explanation
Indices: 3301396--3301447 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3301386 AGGCGAGGGT
* *
3301396 AAAATAAAAGAAAAAG-AGCAAAGA
1 AAAACAAAGGAAAAAGCA-CAAAGA
3301420 AAAACAAAGGAAAAAGCACAAAGA
1 AAAACAAAGGAAAAAGCACAAAGA
3301444 AAAA
1 AAAA
3301448 ATAGGATAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.75, C:0.08, G:0.15, T:0.02
Consensus pattern (24 bp):
AAAACAAAGGAAAAAGCACAAAGA
Found at i:3303626 original size:42 final size:41
Alignment explanation
Indices: 3303580--3303687 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 41
3303570 AAGGAGTTCT
*
3303580 TGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
1 TGATGA-TAAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCA
* * * *
3303622 TGATGCATAAATCCTTCGGGTCATCTGTAAGGCTTTCGATCA
1 TGATG-ATAAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCA
* * *
3303664 AGATGATAAGTCCTTTGGACCATC
1 TGATGATAAGTCCTTCGGGCCATC
3303688 CATAAGACCT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 15 0.27
42 39 0.71
43 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (41 bp):
TGATGATAAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCA
Found at i:3304449 original size:36 final size:38
Alignment explanation
Indices: 3304402--3304511 Score: 152
Period size: 36 Copynumber: 2.8 Consensus size: 38
3304392 CACCCAACAA
*
3304402 TTCAAACATGTTGAAAAAAGCAAGAAAAAA-ACA-CAT
1 TTCAAACATGTTGAAAAAAGCAAGAAAAAATACATAAT
3304438 TTCAAACATGTTGAAAAAAGCAAGAAGAAAAAATACATAAT
1 TTCAAACATGTTGAAAAAAGC---AAGAAAAAATACATAAT
3304479 TTCAAACATGTTGAAAAAAAAGCAAGAAAAAAT
1 TTCAAACATGTTG--AAAAAAGCAAGAAAAAAT
3304512 GTACAAGCCG
Statistics
Matches: 66, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
36 21 0.32
39 9 0.14
40 13 0.20
41 15 0.23
43 8 0.12
ACGTcount: A:0.59, C:0.11, G:0.12, T:0.18
Consensus pattern (38 bp):
TTCAAACATGTTGAAAAAAGCAAGAAAAAATACATAAT
Found at i:3306379 original size:77 final size:78
Alignment explanation
Indices: 3306246--3306405 Score: 304
Period size: 77 Copynumber: 2.1 Consensus size: 78
3306236 TTCAAAATGA
3306246 TTTTCAAAGAGAAAACCCTGAGTCTGTATCGATCATTCCCTGCCTGGGAGAAAAAAGGTATCGAC
1 TTTTCAAAGAGAAAACCCTGAGTCTGTATCGAT-ATTCCCTGCCTGGGAGAAAAAAGGTATCGAC
3306311 AGCTTCCACCAATT
65 AGCTTCCACCAATT
3306325 TTTTCAAAGAGAAAACCCTGAGTCTGTATCGAT-TTCCCTGCCTGGGAGAAAAAAGGTATCGACA
1 TTTTCAAAGAGAAAACCCTGAGTCTGTATCGATATTCCCTGCCTGGGAGAAAAAAGGTATCGACA
3306389 GCTTCCACCAATT
66 GCTTCCACCAATT
3306402 TTTT
1 TTTT
3306406 ATTACCAATT
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
77 48 0.59
79 33 0.41
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (78 bp):
TTTTCAAAGAGAAAACCCTGAGTCTGTATCGATATTCCCTGCCTGGGAGAAAAAAGGTATCGACA
GCTTCCACCAATT
Found at i:3306745 original size:160 final size:160
Alignment explanation
Indices: 3306481--3306801 Score: 642
Period size: 160 Copynumber: 2.0 Consensus size: 160
3306471 ATATATTGTA
3306481 TTATTTAAATGTTTTGTATTATATATAGATAGAGGTGGCAAACGGGTTTTCGGATCAGGTTTGGT
1 TTATTTAAATGTTTTGTATTATATATAGATAGAGGTGGCAAACGGGTTTTCGGATCAGGTTTGGT
3306546 TTAGTTCATTTCAGTTTAGAGTTAATTCGAGTCATGTTTGGGTTGGGTTAGGTCATTTTGGGTTT
66 TTAGTTCATTTCAGTTTAGAGTTAATTCGAGTCATGTTTGGGTTGGGTTAGGTCATTTTGGGTTT
3306611 CAATTTTATTCAAGTCTATAGTAAGTAGGG
131 CAATTTTATTCAAGTCTATAGTAAGTAGGG
3306641 TTATTTAAATGTTTTGTATTATATATAGATAGAGGTGGCAAACGGGTTTTCGGATCAGGTTTGGT
1 TTATTTAAATGTTTTGTATTATATATAGATAGAGGTGGCAAACGGGTTTTCGGATCAGGTTTGGT
3306706 TTAGTTCATTTCAGTTTAGAGTTAATTCGAGTCATGTTTGGGTTGGGTTAGGTCATTTTGGGTTT
66 TTAGTTCATTTCAGTTTAGAGTTAATTCGAGTCATGTTTGGGTTGGGTTAGGTCATTTTGGGTTT
3306771 CAATTTTATTCAAGTCTATAGTAAGTAGGG
131 CAATTTTATTCAAGTCTATAGTAAGTAGGG
3306801 T
1 T
3306802 CAGGTTCGGG
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 161 1.00
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.43
Consensus pattern (160 bp):
TTATTTAAATGTTTTGTATTATATATAGATAGAGGTGGCAAACGGGTTTTCGGATCAGGTTTGGT
TTAGTTCATTTCAGTTTAGAGTTAATTCGAGTCATGTTTGGGTTGGGTTAGGTCATTTTGGGTTT
CAATTTTATTCAAGTCTATAGTAAGTAGGG
Found at i:3307508 original size:29 final size:29
Alignment explanation
Indices: 3307422--3307513 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
3307412 CATATCTTGG
* * *
3307422 GGATGAAAATGAAATGTTTAAAAGTTTGA
1 GGATTAAATTGAAATGTTTAAAAGTTTAA
* * * **
3307451 GGACTAATTTAGAATAATGGTT-GTAGTTTAA
1 GGATTAAATT-G-A-AATGTTTAAAAGTTTAA
3307482 GGATTAAATTGAAATGTTTAAAAGTTTAA
1 GGATTAAATTGAAATGTTTAAAAGTTTAA
3307511 GGA
1 GGA
3307514 CTAATTTAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
28 6 0.13
29 17 0.37
30 2 0.04
31 15 0.33
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.23, T:0.35
Consensus pattern (29 bp):
GGATTAAATTGAAATGTTTAAAAGTTTAA
Found at i:3307525 original size:29 final size:29
Alignment explanation
Indices: 3307433--3307526 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
3307423 GATGAAAATG
*
3307433 AAATGTTTAAAAGTTTGAGGACTAATTTAGA
1 AAATGTTTAAAAGTTTAAGGACTAATTT--A
* ** * * *
3307464 ATAATGGTT-GTAGTTTAAGGATTAAATTG
1 A-AATGTTTAAAAGTTTAAGGACTAATTTA
3307493 AAATGTTTAAAAGTTTAAGGACTAATTTA
1 AAATGTTTAAAAGTTTAAGGACTAATTTA
3307522 AAATG
1 AAATG
3307527 AGGGCCATAG
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
28 6 0.12
29 21 0.44
31 15 0.31
32 6 0.12
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.37
Consensus pattern (29 bp):
AAATGTTTAAAAGTTTAAGGACTAATTTA
Found at i:3307737 original size:16 final size:16
Alignment explanation
Indices: 3307702--3307751 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
3307692 ATAAATTAAA
* *
3307702 TTCAAGTTACTTTCGA
1 TTCAAGTTACTTTTGG
*
3307718 TTCAAGTTATTTTTGG
1 TTCAAGTTACTTTTGG
*
3307734 TTC-AGTTGCTTTTGG
1 TTCAAGTTACTTTTGG
3307749 TTC
1 TTC
3307752 GGTTTTGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (16 bp):
TTCAAGTTACTTTTGG
Found at i:3309392 original size:20 final size:20
Alignment explanation
Indices: 3309367--3309477 Score: 66
Period size: 20 Copynumber: 6.0 Consensus size: 20
3309357 AAAATGCTAA
3309367 AGTGTA-CCGATACACCCTG
1 AGTGTATCCGATACACCCTG
*
3309386 CAGTGTATTC-ATACA--CTG
1 -AGTGTATCCGATACACCCTG
* *
3309404 -GTGTA-CTGATACACCATG
1 AGTGTATCCGATACACCCTG
3309422 TAGTGTATCC-ATACA--CTG
1 -AGTGTATCCGATACACCCTG
* *
3309440 -GTGTA-CCGATACACTCTAC
1 AGTGTATCCGATACACCCT-G
3309459 AGTGTATCCG-TACACCCTG
1 AGTGTATCCGATACACCCTG
3309478 GCTGCAACGG
Statistics
Matches: 69, Mismatches: 9, Indels: 27
0.66 0.09 0.26
Matches are distributed among these distances:
15 2 0.03
16 20 0.29
18 9 0.13
20 33 0.48
21 5 0.07
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (20 bp):
AGTGTATCCGATACACCCTG
Found at i:3309415 original size:36 final size:36
Alignment explanation
Indices: 3309368--3309473 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 36
3309358 AAATGCTAAA
*
3309368 GTGTACCGATACACCCTGCAGTGTATTCATACACTG
1 GTGTACCGATACACCCTGCAGTGTATCCATACACTG
* * *
3309404 GTGTACTGATACACCATGTAGTGTATCCATACACTG
1 GTGTACCGATACACCCTGCAGTGTATCCATACACTG
* * *
3309440 GTGTACCGATACACTCTACAGTGTATCCGTACAC
1 GTGTACCGATACACCCTGCAGTGTATCCATACAC
3309474 CCTGGCTGCA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (36 bp):
GTGTACCGATACACCCTGCAGTGTATCCATACACTG
Found at i:3310939 original size:33 final size:34
Alignment explanation
Indices: 3310894--3310967 Score: 141
Period size: 33 Copynumber: 2.2 Consensus size: 34
3310884 CACTTTAAAG
3310894 TCAAATCTATCACATAGATTTGGTTTATAAGATC
1 TCAAATCTATCACATAGATTTGGTTTATAAGATC
3310928 TCAAAT-TATCACATAGATTTGGTTTATAAGATC
1 TCAAATCTATCACATAGATTTGGTTTATAAGATC
3310961 TCAAATC
1 TCAAATC
3310968 ACTAATTAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 33 0.85
34 6 0.15
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (34 bp):
TCAAATCTATCACATAGATTTGGTTTATAAGATC
Found at i:3319146 original size:315 final size:319
Alignment explanation
Indices: 3318712--3319344 Score: 1120
Period size: 320 Copynumber: 2.0 Consensus size: 319
3318702 TATTATTTAC
3318712 TTGTCATGTCAGTGCTAACGTGTAATTTTGTAGTACATTTCCAACACCCATCATCTGCATCCAAA
1 TTGTCATGTCAGTGCTAACGTGTAATTTTGTAGTACATTTCCAACACCCATCATCTGCATCCAAA
*
3318777 ACTGTAATTCAACCCACCCCCACCCGCTTGATCTTTGACCCAAATTCGTCCCACCATCAATTGA-
66 ACTGTAATTCAACCCACCCCCACCCACTTGATCTTTGACCCAAATTCGTCCCACCATCAATTGAG
3318841 GATGAGGCATGTGGGTCGAGTTATAAATGGG-TTCTATTACTTGAAAATCAAAATTGAAAATACA
131 GATGAGGCATGTGGGTCGAGTTATAAATGGGTTTCTATTACTTGAAAATCAAAATTGAAAATACA
* *
3318905 TGTAACATCTTACT-AAAA-A-TAAATATTT-ATACATCATCAA-CTACTATTAAAGTTTTAAAT
196 TGTAACATCTTACTAAAAATATTAAATATTTAATACAT--TAAATCAACTATTAAAGTTTTAAAT
*
3318965 TTCCAATACTCTAACATATATCAGAATTACGTAAACGAAGTTCTCACTTCCCAATAGTAAT
259 TTCCAATACTCTAACATATAACAGAATTACGTAAACGAAGTTCTCACTTCCCAATAGTAAT
3319026 TTGTCATGTCAGTGCTAACGTGTAATTTTGTAGTATACATTTCCAACACCCATCATCTGCATCCA
1 TTGTCATGTCAGTGCTAACGTGTAATTTTGTAG--TACATTTCCAACACCCATCATCTGCATCCA
*
3319091 AAACTGTAATTC-ACCCACCGCCACCCACTTGATCTTTGACCCAAATTCGTCCCACCATCAATTG
64 AAACTGTAATTCAACCCACCCCCACCCACTTGATCTTTGACCCAAATTCGTCCCACCATCAATTG
*
3319155 AGGATGAGGCATGTGGGTCGAGTTATAAATGGGTTTCTATTACTTGAAAATCAAAATTGACAATA
129 AGGATGAGGCATGTGGGTCGAGTTATAAATGGGTTTCTATTACTTGAAAATCAAAATTGAAAATA
3319220 CATGTAACATCTTACTAAAAATATTAAATATTTAATACATTAAATCAACTATTAAAGTTTTAAAT
194 CATGTAACATCTTACTAAAAATATTAAATATTTAATACATTAAATCAACTATTAAAGTTTTAAAT
3319285 TTCCAATACTCTAACATATAACAGAATTACGTAAACGAAGTTCTCACTTCCCAATAGTAA
259 TTCCAATACTCTAACATATAACAGAATTACGTAAACGAAGTTCTCACTTCCCAATAGTAA
3319345 ATAAAAGCCT
Statistics
Matches: 304, Mismatches: 6, Indels: 12
0.94 0.02 0.04
Matches are distributed among these distances:
314 33 0.11
315 51 0.17
316 73 0.24
317 46 0.15
318 4 0.01
319 4 0.01
320 87 0.29
321 6 0.02
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (319 bp):
TTGTCATGTCAGTGCTAACGTGTAATTTTGTAGTACATTTCCAACACCCATCATCTGCATCCAAA
ACTGTAATTCAACCCACCCCCACCCACTTGATCTTTGACCCAAATTCGTCCCACCATCAATTGAG
GATGAGGCATGTGGGTCGAGTTATAAATGGGTTTCTATTACTTGAAAATCAAAATTGAAAATACA
TGTAACATCTTACTAAAAATATTAAATATTTAATACATTAAATCAACTATTAAAGTTTTAAATTT
CCAATACTCTAACATATAACAGAATTACGTAAACGAAGTTCTCACTTCCCAATAGTAAT
Found at i:3324640 original size:15 final size:15
Alignment explanation
Indices: 3324607--3324642 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3324597 AATATGGAAG
*
3324607 AAGAAAGGAAATGAT
1 AAGAAAGGAAATGAC
*
3324622 AAGAAAGGAAATGGC
1 AAGAAAGGAAATGAC
3324637 AAGAAA
1 AAGAAA
3324643 TGATATAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.28, T:0.08
Consensus pattern (15 bp):
AAGAAAGGAAATGAC
Found at i:3324852 original size:13 final size:13
Alignment explanation
Indices: 3324834--3324891 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
3324824 TAGGCATGCA
3324834 ATGGTGATGGAAG
1 ATGGTGATGGAAG
*
3324847 ATGGTGAT-G-AT
1 ATGGTGATGGAAG
* *
3324858 ATAGGCG-T-GAAA
1 AT-GGTGATGGAAG
3324870 ATGGTGATGGAAG
1 ATGGTGATGGAAG
3324883 ATGGTGATG
1 ATGGTGATG
3324892 AACAAACAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
11 8 0.22
12 8 0.22
13 20 0.56
ACGTcount: A:0.31, C:0.02, G:0.41, T:0.26
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:3324880 original size:36 final size:35
Alignment explanation
Indices: 3324777--3324892 Score: 178
Period size: 35 Copynumber: 3.3 Consensus size: 35
3324767 TGGTAAGGGA
* * *
3324777 ATGGTGATGATATAAGCGTGAAATGGAGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
* *
3324812 ATGGTGATGATATAGGCATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
3324847 ATGGTGATGATATAGGCGTGAAAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATGGAAG
3324883 ATGGTGATGA
1 ATGGTGATGA
3324893 ACAAACAGTA
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 49 0.67
36 24 0.33
ACGTcount: A:0.34, C:0.03, G:0.37, T:0.25
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
Found at i:3325406 original size:20 final size:22
Alignment explanation
Indices: 3325367--3325413 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3325357 TGCTTGAATG
3325367 ATGCACATGGCAGCCTTCTTG-A
1 ATGCACATGG-AGCCTTCTTGCA
*
3325389 ATGCACATGG-GTCTTCTTGCA
1 ATGCACATGGAGCCTTCTTGCA
3325410 ATGC
1 ATGC
3325414 TTTGGTGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 5 0.22
22 10 0.43
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (22 bp):
ATGCACATGGAGCCTTCTTGCA
Found at i:3328144 original size:16 final size:17
Alignment explanation
Indices: 3328123--3328154 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3328113 TTGACTTAAA
3328123 AGAAATGGTTA-GGTAT
1 AGAAATGGTTATGGTAT
3328139 AGAAATGGTTATGGTA
1 AGAAATGGTTATGGTA
3328155 GAGGTATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (17 bp):
AGAAATGGTTATGGTAT
Found at i:3328905 original size:35 final size:35
Alignment explanation
Indices: 3328859--3328974 Score: 187
Period size: 35 Copynumber: 3.3 Consensus size: 35
3328849 TGGTAAGGGA
*
3328859 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
* *
3328894 ATGGTGATGATATAGGCATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
*
3328929 ATGGTGATGTTATAGGCGTGAAAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATGGAAG
3328965 ATGGTGATGA
1 ATGGTGATGA
3328975 ACAGATAGAA
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 50 0.68
36 23 0.32
ACGTcount: A:0.32, C:0.03, G:0.38, T:0.27
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
Found at i:3328934 original size:13 final size:13
Alignment explanation
Indices: 3328916--3328973 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
3328906 TAGGCATGCA
3328916 ATGGTGATGGAAG
1 ATGGTGATGGAAG
** *
3328929 ATGGTGATGTTAT
1 ATGGTGATGGAAG
* *
3328942 A-GGCG-T-GAAA
1 ATGGTGATGGAAG
3328952 ATGGTGATGGAAG
1 ATGGTGATGGAAG
3328965 ATGGTGATG
1 ATGGTGATG
3328974 AACAGATAGA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 4 0.12
13 23 0.70
ACGTcount: A:0.29, C:0.02, G:0.41, T:0.28
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:3329571 original size:20 final size:22
Alignment explanation
Indices: 3329532--3329578 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3329522 TGCTTGAATG
3329532 ATGCACATGGCAGCCTTCTTG-A
1 ATGCACATGG-AGCCTTCTTGCA
*
3329554 ATGCACATGG-GTCTTCTTGCA
1 ATGCACATGGAGCCTTCTTGCA
3329575 ATGC
1 ATGC
3329579 TTTAGTGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 5 0.22
22 10 0.43
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (22 bp):
ATGCACATGGAGCCTTCTTGCA
Found at i:3333563 original size:16 final size:17
Alignment explanation
Indices: 3333537--3333569 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3333527 TTTATTTTTA
3333537 TAAATGTATAGTAATGG
1 TAAATGTATAGTAATGG
3333554 TAAA-GTATAGTAATGG
1 TAAATGTATAGTAATGG
3333570 CAATTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.33
Consensus pattern (17 bp):
TAAATGTATAGTAATGG
Found at i:3335761 original size:34 final size:35
Alignment explanation
Indices: 3335689--3335762 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
3335679 TTCATGTTCA
3335689 AAATTCCAAAACACTTCAATTACATTCTAAACCCT
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCT
* * * **
3335724 AAATTCTAAAATACTTTAATTGTATTCT-AACCCT
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCT
3335758 AAATT
1 AAATT
3335763 AAAGTATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 11 0.32
35 23 0.68
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCCT
Found at i:3336398 original size:43 final size:42
Alignment explanation
Indices: 3336342--3336439 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 42
3336332 AAGCTTTACA
* * * * **
3336342 CTTATCAACCAACACTGCCATTCATCTCATTTTCATTATTGG
1 CTTAGCAACCAACACTACCAGTAATCTCATTTTCACCATTGG
3336384 CTTAGCAAGCCAACACTACCAGTAATCTCATTTTCACCATTGG
1 CTTAGCAA-CCAACACTACCAGTAATCTCATTTTCACCATTGG
3336427 CTTAGCAAACCAA
1 CTTAGC-AACCAA
3336440 ACCGACAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 7 0.15
43 39 0.81
44 2 0.04
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.31
Consensus pattern (42 bp):
CTTAGCAACCAACACTACCAGTAATCTCATTTTCACCATTGG
Found at i:3337141 original size:15 final size:15
Alignment explanation
Indices: 3337117--3337163 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
3337107 CGGCCCGCAT
*
3337117 CCGCCTCGCATCCGC
1 CCGCCCCGCATCCGC
3337132 CCGCCCCGCATCCGC
1 CCGCCCCGCATCCGC
* *
3337147 TCGCCCCACATCCGC
1 CCGCCCCGCATCCGC
3337162 CC
1 CC
3337164 ACCTAGCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.09, C:0.64, G:0.17, T:0.11
Consensus pattern (15 bp):
CCGCCCCGCATCCGC
Found at i:3339903 original size:16 final size:17
Alignment explanation
Indices: 3339866--3339904 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3339856 CAACTTTAAA
* *
3339866 TTTATTATATTTGAAGT
1 TTTATTATATGTGAACT
3339883 TTTATTATATGTG-ACT
1 TTTATTATATGTGAACT
3339899 TTTATT
1 TTTATT
3339905 TAAAGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.26, C:0.03, G:0.10, T:0.62
Consensus pattern (17 bp):
TTTATTATATGTGAACT
Found at i:3343246 original size:23 final size:24
Alignment explanation
Indices: 3343195--3343239 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
3343185 ACTTAGTGAG
* *
3343195 ACATAATCAATAATTCAAAATAAA
1 ACATAATCAATAATACAAAACAAA
3343219 ACATAAT-AATAATACAAAACA
1 ACATAATCAATAATACAAAACA
3343240 TATCATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.64, C:0.13, G:0.00, T:0.22
Consensus pattern (24 bp):
ACATAATCAATAATACAAAACAAA
Found at i:3344629 original size:21 final size:21
Alignment explanation
Indices: 3344603--3344661 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
3344593 GTTGGGAGCG
3344603 TAGGTGCATCGGTACACCCTA
1 TAGGTGCATCGGTACACCCTA
3344624 TAGGTGCATCGGTACACCCTA
1 TAGGTGCATCGGTACACCCTA
3344645 TAGGTGCATCGGTACAC
1 TAGGTGCATCGGTACAC
3344662 TATGTGTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (21 bp):
TAGGTGCATCGGTACACCCTA
Found at i:3344791 original size:64 final size:65
Alignment explanation
Indices: 3344722--3344875 Score: 194
Period size: 64 Copynumber: 2.4 Consensus size: 65
3344712 ACACTTGGTA
* * *
3344722 TGCATCGGTACACT-AATTACATTCGA-GTTTCAA-AAGAGA-CAGGAGTGCATCGATGCATGGT
1 TGCATCGGTACACTAAAATACATTCGATGTATCAATAA-A-ATCAGGAGTGCATCAATGCATGG-
3344783 CTG
63 CTG
*
3344786 TGCATCGGTACA-TAAAATGCATTCGATGTATCAATAAAATCAGGAGTGCATCAATGCATGGCTG
1 TGCATCGGTACACTAAAATACATTCGATGTATCAATAAAATCAGGAGTGCATCAATGCATGGCTG
*
3344850 TGCATCGGTACAC-AAAATGCATTCGA
1 TGCATCGGTACACTAAAATACATTCGA
3344876 ATTAGGGTGT
Statistics
Matches: 81, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
63 1 0.01
64 51 0.63
65 27 0.33
66 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (65 bp):
TGCATCGGTACACTAAAATACATTCGATGTATCAATAAAATCAGGAGTGCATCAATGCATGGCTG
Found at i:3345032 original size:18 final size:18
Alignment explanation
Indices: 3345006--3345041 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3344996 AAAACACAAT
*
3345006 TTTATACTTTAGTAAGGA
1 TTTACACTTTAGTAAGGA
3345024 TTTACACTTTAGTAAGGA
1 TTTACACTTTAGTAAGGA
3345042 CTGAAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (18 bp):
TTTACACTTTAGTAAGGA
Found at i:3345249 original size:13 final size:13
Alignment explanation
Indices: 3345231--3345264 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
3345221 AAGATTTTTC
3345231 TTTGAAAATCAAT
1 TTTGAAAATCAAT
3345244 TTTG-AAATCAAT
1 TTTGAAAATCAAT
3345256 TTTGAAAAT
1 TTTGAAAAT
3345265 TACCCCCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:3345604 original size:30 final size:29
Alignment explanation
Indices: 3345559--3345626 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
3345549 CGTCCAAAAT
* *
3345559 ATATTC-AAAATCAAACAATCCAAA-CTAA
1 ATATTCAAAAATCAAACAA-ACAAAGCCAA
3345587 ATATTCAAAAATCCAAACAAACAAAGCCAA
1 ATATTCAAAAAT-CAAACAAACAAAGCCAA
3345617 ATATTCAAAA
1 ATATTCAAAA
3345627 TGTTTAAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 6 0.17
29 9 0.26
30 20 0.57
ACGTcount: A:0.59, C:0.21, G:0.01, T:0.19
Consensus pattern (29 bp):
ATATTCAAAAATCAAACAAACAAAGCCAA
Found at i:3347103 original size:14 final size:13
Alignment explanation
Indices: 3347059--3347103 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
3347049 TCCTAATGGG
3347059 CAAT-TTTGAAAA
1 CAATATTTGAAAA
* *
3347071 CTATGTTTGAAAA
1 CAATATTTGAAAA
3347084 CAATATTTGAAAA
1 CAATATTTGAAAA
3347097 TCAATAT
1 -CAATAT
3347104 GGAGTTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 3 0.11
13 19 0.68
14 6 0.21
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (13 bp):
CAATATTTGAAAA
Found at i:3347612 original size:23 final size:23
Alignment explanation
Indices: 3347585--3347655 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
3347575 TGAATAGTGT
3347585 ATCGATGCACATTCAATGAATGC
1 ATCGATGCACATTCAATGAATGC
* * *
3347608 ATCGATACATC-TTC-AT-AGTGT
1 ATCGATGCA-CATTCAATGAATGC
* * *
3347629 ATCAATGCATATTCAAGGAATGC
1 ATCGATGCACATTCAATGAATGC
3347652 ATCG
1 ATCG
3347656 GAACACTTTC
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
21 13 0.38
22 3 0.09
23 17 0.50
24 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (23 bp):
ATCGATGCACATTCAATGAATGC
Found at i:3347643 original size:21 final size:21
Alignment explanation
Indices: 3347578--3347643 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
3347568 GGTACACTGA
*
3347578 ATAGTGTATCGATGCACATTC
1 ATAGTGTATCGATGCATATTC
* * * *
3347599 AATGAATGCATCGATACATCTTC
1 -AT-AGTGTATCGATGCATATTC
*
3347622 ATAGTGTATCAATGCATATTC
1 ATAGTGTATCGATGCATATTC
3347643 A
1 A
3347644 AGGAATGCAT
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
21 15 0.45
22 4 0.12
23 14 0.42
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (21 bp):
ATAGTGTATCGATGCATATTC
Found at i:3347643 original size:44 final size:44
Alignment explanation
Indices: 3347578--3347683 Score: 153
Period size: 44 Copynumber: 2.4 Consensus size: 44
3347568 GGTACACTGA
*
3347578 ATAGTGTATCGATGCACATTCAATGAATGCATC-GATACA-TCTTC
1 ATAGTGTATCGATGCACATTCAAGGAATGCATCGGA-ACACT-TTC
* *
3347622 ATAGTGTATCAATGCATATTCAAGGAATGCATCGGAACACTTTC
1 ATAGTGTATCGATGCACATTCAAGGAATGCATCGGAACACTTTC
3347666 ATAGTGTATCGATGCACA
1 ATAGTGTATCGATGCACA
3347684 ATGTACAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
44 52 0.95
45 3 0.05
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (44 bp):
ATAGTGTATCGATGCACATTCAAGGAATGCATCGGAACACTTTC
Found at i:3351379 original size:20 final size:21
Alignment explanation
Indices: 3351340--3351379 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3351330 AACACTTTAA
* *
3351340 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
3351361 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
3351380 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:3353539 original size:65 final size:64
Alignment explanation
Indices: 3353429--3353581 Score: 220
Period size: 65 Copynumber: 2.4 Consensus size: 64
3353419 ATAAGACCTA
* *
3353429 GTGCATCGGTACACT-AATTACATTCGATGTTTCAAAAGAGCCAGGAGTGCATCGATGCATGGTC
1 GTGCATCGGTACA-TAAAATACATTCGATGTTTCAAAAGAACCAGGAGTGCATCGATGCATGG-C
3353493 T
64 T
*
3353494 GTGCATCGGTACATAAAATACATTCGATGTTTCAATAA-AATCAGGAGTGCATCGATGCATGGCT
1 GTGCATCGGTACATAAAATACATTCGATGTTTCAA-AAGAACCAGGAGTGCATCGATGCATGGCT
* *
3353558 GTGCATCGGTACACAAAATGCATT
1 GTGCATCGGTACATAAAATACATT
3353582 TGAAATAGGG
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
64 25 0.31
65 54 0.67
66 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATACATTCGATGTTTCAAAAGAACCAGGAGTGCATCGATGCATGGCT
Found at i:3357563 original size:6 final size:6
Alignment explanation
Indices: 3357455--3357564 Score: 61
Period size: 6 Copynumber: 18.2 Consensus size: 6
3357445 GATTTCAATT
*
3357455 TTATT- TTATTA TTTATT- TTAGTTA CTT-TTA TTTATTTA TTTTTA TT-TTA
1 TTATTA TTATTA -TTATTA TTA-TTA -TTATTA -TTA-TTA TTATTA TTATTA
* * * * *
3357504 TTATAA TTACTA TTATTG TTATTA TTGTTA TTA-TA TTTTTA TTAGTT-
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTA-TTA
3357551 TTAATTA TTATTA T
1 TT-ATTA TTATTA T
3357565 AGGTAAACAT
Statistics
Matches: 81, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
5 17 0.21
6 47 0.58
7 12 0.15
8 5 0.06
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (6 bp):
TTATTA
Found at i:3361102 original size:27 final size:27
Alignment explanation
Indices: 3361045--3361104 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
3361035 AAACTTTTCC
*
3361045 AAATTTATTCTTTGGTCACCAAACATT
1 AAATTTATTCTTTGGTCACCAAACATA
*
3361072 AAATTTATTCATTTTGGTCA-CTAACA-A
1 AAATTTATTC--TTTGGTCACCAAACATA
3361099 AAATTT
1 AAATTT
3361105 TAGGGTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 16 0.55
28 5 0.17
29 8 0.28
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (27 bp):
AAATTTATTCTTTGGTCACCAAACATA
Found at i:3361941 original size:22 final size:22
Alignment explanation
Indices: 3361916--3361970 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
3361906 ATGAACTACA
*
3361916 TTAGCATTGATAATAAAGTTCC
1 TTAGCATTGATAATAAAGTGCC
* * *
3361938 TTAGCAATAATATTAAAGTGCC
1 TTAGCATTGATAATAAAGTGCC
*
3361960 TTAGAATTGAT
1 TTAGCATTGAT
3361971 TGAAGTATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
TTAGCATTGATAATAAAGTGCC
Found at i:3368337 original size:23 final size:23
Alignment explanation
Indices: 3368293--3368341 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3368283 ATAAAGAACC
*
3368293 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
3368316 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
3368339 AAA
1 AAA
3368342 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:3371689 original size:21 final size:20
Alignment explanation
Indices: 3371640--3371696 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
3371630 TGAATGAAGG
* * *
3371640 AAAAAGAAAAAGTAAAAGTT
1 AAAAAGAAAGAGAAAAAATT
*
3371660 AAAATGAAAGAGAAAAAATT
1 AAAAAGAAAGAGAAAAAATT
3371680 AATAAAGAAAGAGAAAA
1 AA-AAAGAAAGAGAAAA
3371697 GAAAAAGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAAAGAAAGAGAAAAAATT
Found at i:3371717 original size:26 final size:25
Alignment explanation
Indices: 3371641--3371718 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 25
3371631 GAATGAAGGA
* *
3371641 AAAAGAAAAAG-TAAAAGTTAAAATG
1 AAAAGAAAAAGTTAAAAATTAAGA-G
* **
3371666 AAAGAGAAAAAATTAATAAAGAAAGAG
1 AAA-AGAAAAAGTTAA-AAATTAAGAG
3371693 AAAAGAAAAAGTTAAAAATTTAAGAG
1 AAAAGAAAAAGTTAAAAA-TTAAGAG
3371719 GGAAAATGTG
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
25 6 0.15
26 23 0.56
27 7 0.17
28 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (25 bp):
AAAAGAAAAAGTTAAAAATTAAGAG
Found at i:3378566 original size:23 final size:23
Alignment explanation
Indices: 3378522--3378570 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3378512 ATAAAGAACC
*
3378522 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
3378545 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
3378568 AAA
1 AAA
3378571 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:3378887 original size:12 final size:12
Alignment explanation
Indices: 3378870--3378899 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3378860 ACCGTATGTG
3378870 TCCTCCTTTTTT
1 TCCTCCTTTTTT
3378882 TCCTCCTTTTTT
1 TCCTCCTTTTTT
*
3378894 TTCTCC
1 TCCTCC
3378900 CCCATGAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (12 bp):
TCCTCCTTTTTT
Found at i:3382438 original size:20 final size:19
Alignment explanation
Indices: 3382413--3382453 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
3382403 TTACTTCTCT
3382413 AAAAACAAAAAGAGAAAACC
1 AAAAACAAAAAGA-AAAACC
3382433 AAAAACAAAAAGAAAAACC
1 AAAAACAAAAAGAAAAACC
3382452 AA
1 AA
3382454 GCATGTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAAGAAAAACC
Found at i:3384071 original size:26 final size:26
Alignment explanation
Indices: 3384038--3384105 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
3384028 AATATTATGA
3384038 AATATATTATTATCTGATTTATT-AAT
1 AATATATTATTAT-TGATTTATTAAAT
3384064 AATATATTA-TATATGCA-TTATTAAAT
1 AATATATTATTAT-TG-ATTTATTAAAT
*
3384090 AAAAT-TTATTATTGAT
1 AATATATTATTATTGAT
3384106 AAAAATATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
24 1 0.03
25 15 0.42
26 20 0.56
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (26 bp):
AATATATTATTATTGATTTATTAAAT
Found at i:3384090 original size:23 final size:23
Alignment explanation
Indices: 3384031--3384090 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
3384021 TTTATAAAAT
* *
3384031 ATTATGAAATATATTATTATCTG
1 ATTATTAAATATATTATTATATG
3384054 ATTTATTAATAATATATTA-TATATG
1 A-TTATT-A-AATATATTATTATATG
3384079 CATTATTAAATA
1 -ATTATTAAATA
3384091 AAATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
23 5 0.16
24 5 0.16
25 11 0.35
26 10 0.32
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (23 bp):
ATTATTAAATATATTATTATATG
Found at i:3386453 original size:14 final size:14
Alignment explanation
Indices: 3386434--3386461 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3386424 GTGGTCAGTT
3386434 AAGGGTCAACGGTC
1 AAGGGTCAACGGTC
3386448 AAGGGTCAACGGTC
1 AAGGGTCAACGGTC
3386462 GGTTAACGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.36, T:0.14
Consensus pattern (14 bp):
AAGGGTCAACGGTC
Found at i:3386467 original size:32 final size:32
Alignment explanation
Indices: 3386405--3386467 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
3386395 AATCAATGTC
**
3386405 GGTCAACGATCAACGGTCAGTGGTCAGTTAAG
1 GGTCAACGATCAACGGTCAACGGTCAGTTAAG
* * *
3386437 GGTCAACGGTCAAGGGTCAACGGTCGGTTAA
1 GGTCAACGATCAACGGTCAACGGTCAGTTAA
3386468 CGATCAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.21
Consensus pattern (32 bp):
GGTCAACGATCAACGGTCAACGGTCAGTTAAG
Found at i:3389193 original size:20 final size:20
Alignment explanation
Indices: 3389168--3389218 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
3389158 ATTCAATTAA
3389168 TATCGATACCAT-G-AAGGCAG
1 TATCGATACCATGGTAAGG--G
3389188 TATCGATACCATGGTAAGGG
1 TATCGATACCATGGTAAGGG
3389208 TATCGATACCA
1 TATCGATACCA
3389219 AGCAAACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 24 0.83
21 1 0.03
22 4 0.14
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (20 bp):
TATCGATACCATGGTAAGGG
Found at i:3389961 original size:45 final size:46
Alignment explanation
Indices: 3389846--3390152 Score: 405
Period size: 45 Copynumber: 6.8 Consensus size: 46
3389836 AGGATGCCAT
**
3389846 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAAAACTACTATG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTA-TACTATG
* *
3389893 -GTTGAAATGTATATGGGTACATTATCAACAGAAAATTATGCTA-G
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* *
3389937 AGTTGAAATGCATATGGGTGCATTATCAACAG-AAAGTATACTATG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* * * *
3389982 -GTTGAAATGCATATGGTTGCATTATCAACAGCAAAGTATACTAT-
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
3390026 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* *
3390072 -GTTGAAATATATATGGGTACATTATCAACAAAAAAGTATA-T-TG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* * *
3390115 TAATTGAAATGCATATGGGTGCATTATCAACAGAAAAG
1 -AGTTGAAATGTATATGGGTACATTATCAACAGAAAAG
3390153 AGGTTATAAT
Statistics
Matches: 234, Mismatches: 19, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
43 2 0.01
44 41 0.18
45 155 0.66
46 36 0.15
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (46 bp):
AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
Found at i:3397068 original size:63 final size:63
Alignment explanation
Indices: 3396997--3397123 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
3396987 CAAAAGTAGA
3396997 TAGTTCCTTTACCACACATATCAACATAAAGAACAAGTAAGCTCAAAGGAGGCAGGCTAAGTT
1 TAGTTCCTTTACCACACATATCAACATAAAGAACAAGTAAGCTCAAAGGAGGCAGGCTAAGTT
3397060 TAGTTCCTTTACCACACATATCAACATAAAGAACAAGTAAGCTCAAAGGAGGCAGGCTAAGTT
1 TAGTTCCTTTACCACACATATCAACATAAAGAACAAGTAAGCTCAAAGGAGGCAGGCTAAGTT
3397123 T
1 T
3397124 CAGGCGATCG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.23
Consensus pattern (63 bp):
TAGTTCCTTTACCACACATATCAACATAAAGAACAAGTAAGCTCAAAGGAGGCAGGCTAAGTT
Found at i:3400428 original size:26 final size:26
Alignment explanation
Indices: 3400367--3400438 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
3400357 ATTTATAAAA
*
3400367 TATTATAAAATATATTATTATCTGATT
1 TATTATATAATATATTATTATC-GATT
3400394 TATTA-ATAATATATTATATATAC-A-T
1 TATTATATAATATATTAT-TAT-CGATT
*
3400419 TATTATATAAAAT-TTATTAT
1 TATTATATAATATATTATTAT
3400439 TGATAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
24 3 0.08
25 10 0.25
26 18 0.45
27 8 0.20
28 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (26 bp):
TATTATATAATATATTATTATCGATT
Found at i:3400554 original size:3 final size:3
Alignment explanation
Indices: 3400546--3400571 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3400536 TCCATTTTAT
3400546 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3400572 TTGAACTTAA
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:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3401189 original size:15 final size:15
Alignment explanation
Indices: 3401169--3401197 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3401159 TCTGGGTTGT
3401169 TATTATTATTAATAC
1 TATTATTATTAATAC
3401184 TATTATTATTAATA
1 TATTATTATTAATA
3401198 ATTATTTCTT
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:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTATTATTAATAC
Found at i:3402224 original size:2 final size:2
Alignment explanation
Indices: 3402217--3402286 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
3402207 TTTAGGTGTA
3402217 AT AT AT AT AT AT 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 AT AT AT AT AT AT
3402259 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
3402287 TGCATGATGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3403432 original size:22 final size:22
Alignment explanation
Indices: 3403405--3403446 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3403395 GTAATCCCTC
3403405 AAACTT-AAAAATAAAGTAAAAA
1 AAACTTGAAAAATAAA-TAAAAA
3403427 AAACTTGAAAAATAAATAAA
1 AAACTTGAAAAATAAATAAA
3403447 GAAGAGAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (22 bp):
AAACTTGAAAAATAAATAAAAA
Found at i:3403696 original size:26 final size:26
Alignment explanation
Indices: 3403658--3403707 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3403648 CCAGAAGGAG
3403658 CGCTGACTAGATCTTCTAGAAACTGC
1 CGCTGACTAGATCTTCTAGAAACTGC
* *
3403684 CGCTGATTGGATCTTCTAGAAACT
1 CGCTGACTAGATCTTCTAGAAACT
3403708 ACCACGTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (26 bp):
CGCTGACTAGATCTTCTAGAAACTGC
Found at i:3403991 original size:2 final size:2
Alignment explanation
Indices: 3403984--3404011 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3403974 AGGTAATTTA
3403984 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
3404012 TTCGTAATAT
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:3405999 original size:2 final size:2
Alignment explanation
Indices: 3405992--3406047 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
3405982 TTAGGTGTAA
3405992 AT AT AT AT AT AT 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 AT AT AT AT AT AT
3406034 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
3406048 GCATGATGTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3406289 original size:16 final size:17
Alignment explanation
Indices: 3406258--3406291 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3406248 TGGTAAAATA
3406258 AGATTAAATAGTAAAAAG
1 AGATTAAATAG-AAAAAG
3406276 AGATTAAATA-AAAAAG
1 AGATTAAATAGAAAAAG
3406292 GCAATTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.21
Consensus pattern (17 bp):
AGATTAAATAGAAAAAG
Found at i:3407471 original size:26 final size:26
Alignment explanation
Indices: 3407433--3407482 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3407423 CCAGAAGGAG
3407433 CGCTGACTAGATCTTCTAGAAACTGC
1 CGCTGACTAGATCTTCTAGAAACTGC
* *
3407459 CGCTGATTGGATCTTCTAGAAACT
1 CGCTGACTAGATCTTCTAGAAACT
3407483 ACCACGTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (26 bp):
CGCTGACTAGATCTTCTAGAAACTGC
Found at i:3407766 original size:2 final size:2
Alignment explanation
Indices: 3407759--3407786 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3407749 AGGTAATTTA
3407759 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
3407787 TTTCGTAATA
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:3409777 original size:2 final size:2
Alignment explanation
Indices: 3409770--3409830 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
3409760 GCGTTAGGTG
3409770 TA TA TA TA TA TA TA 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 TA TA TA TA
3409812 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
3409831 TGCTTGATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3411242 original size:26 final size:26
Alignment explanation
Indices: 3411204--3411253 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3411194 CCAGAAGGAG
3411204 CGCTGACTAGATCTTCTAGAAACTGC
1 CGCTGACTAGATCTTCTAGAAACTGC
* *
3411230 CGCTGATTGGATCTTCTAGAAACT
1 CGCTGACTAGATCTTCTAGAAACT
3411254 ACCACGTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (26 bp):
CGCTGACTAGATCTTCTAGAAACTGC
Found at i:3411533 original size:2 final size:2
Alignment explanation
Indices: 3411526--3411559 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3411516 AGGTAATTTA
3411526 AT AT 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 AT AT
3411560 TTCGTAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3416772 original size:25 final size:22
Alignment explanation
Indices: 3416714--3416757 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3416704 ATTCTACTTC
3416714 AAGATTTAACAACATATTTGAT
1 AAGATTTAACAACATATTTGAT
3416736 AAGATTTAACAACATATTTGAT
1 AAGATTTAACAACATATTTGAT
3416758 GAGGTTGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (22 bp):
AAGATTTAACAACATATTTGAT
Found at i:3420196 original size:16 final size:16
Alignment explanation
Indices: 3420164--3420197 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3420154 TAAATATAAG
*
3420164 AATTAAAACTATGAAT
1 AATTAAAACAATGAAT
*
3420180 AATTAAAACAATTAAT
1 AATTAAAACAATGAAT
3420196 AA
1 AA
3420198 CCTAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (16 bp):
AATTAAAACAATGAAT
Found at i:3420234 original size:15 final size:15
Alignment explanation
Indices: 3420208--3420263 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
3420198 CCTAATTTAA
3420208 AAAAAT-AAAATAAC
1 AAAAATAAAAATAAC
*
3420222 AATAATAAAAATAA-
1 AAAAATAAAAATAAC
* *
3420236 AAACAGTAAAAACAAC
1 AAA-AATAAAAATAAC
3420252 ATAAAATAAAAA
1 A-AAAATAAAAA
3420264 ATAAATAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
14 7 0.21
15 16 0.48
16 8 0.24
17 2 0.06
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (15 bp):
AAAAATAAAAATAAC
Found at i:3420631 original size:110 final size:110
Alignment explanation
Indices: 3420500--3420768 Score: 357
Period size: 110 Copynumber: 2.4 Consensus size: 110
3420490 AAAAAACACA
* **
3420500 AAAGTTTTGGGGACCAAGAATGATATTTTACCAAAAAATACGAAA-CATACAGTAAAAT-GGAAA
1 AAAGTTTGGGGGACCTGGAATGATATTTTACCAAAAAATAC-AAAGCATACAGTAAAATAGG-AA
* * *
3420563 AATTATGAAAACAATCTCTAAAAGTGGCTATTTTACAATAAACACAG-T
64 AATTATGAAAACAATCCCTAAAAGTGACTATTTTACAA-AAACA-AGAC
* *
3420611 AAAGTTT-GGGGATCTGGAATGATATTTTACCAAAAAATACAAAGCATATAGTAAAATAGGAAAA
1 AAAGTTTGGGGGACCTGGAATGATATTTTACCAAAAAATACAAAGCATACAGTAAAATAGGAAAA
* * *
3420675 TTATGAAAACAATCCCTAAAGGTGACTATTTTGCAAAAACATGAC
66 TTATGAAAACAATCCCTAAAAGTGACTATTTTACAAAAACAAGAC
* *
3420720 AAAGTTTGGGGGACCTTGAATGATATTTTACCAAAAAATACAATGCATA
1 AAAGTTTGGGGGACCTGGAATGATATTTTACCAAAAAATACAAAGCATA
3420769 TAAAATGGGA
Statistics
Matches: 141, Mismatches: 13, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
108 1 0.01
109 15 0.11
110 116 0.82
111 9 0.06
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (110 bp):
AAAGTTTGGGGGACCTGGAATGATATTTTACCAAAAAATACAAAGCATACAGTAAAATAGGAAAA
TTATGAAAACAATCCCTAAAAGTGACTATTTTACAAAAACAAGAC
Found at i:3420769 original size:110 final size:109
Alignment explanation
Indices: 3420493--3420798 Score: 353
Period size: 110 Copynumber: 2.8 Consensus size: 109
3420483 AAAATGCAAA
* * *
3420493 AAACACA--AAAGTTTTGGGGACCAAGAATGATATTTTACCAAAAAATACGAAACATACAGTAAA
1 AAACACAGCAAAG-TTTGGGGACCTAGAATGATATTTTACCAAAAAATAC-AAGCATATAGTAAA
* *
3420556 ATGGAAAAATTATGAAAACAATCTCTAAAAGTGGCTATTTTACAAT
64 ATGGAAAAATTATGAAAACAATCCCTAAAAGTGACTATTTTACAAT
* * *
3420602 AAACACAGTAAAGTTTGGGGATCTGGAATGATATTTTACCAAAAAATACAAAGCATATAGTAAAA
1 AAACACAGCAAAGTTTGGGGACCTAGAATGATATTTTACCAAAAAATAC-AAGCATATAGTAAAA
* *
3420667 TAGG-AAAATTATGAAAACAATCCCTAAAGGTGACTATTTTGCAA-
65 T-GGAAAAATTATGAAAACAATCCCTAAAAGTGACTATTTTACAAT
* *
3420711 AAACA-TGACAAAGTTTGGGGGACCTTGAATGATATTTTACCAAAAAATACAATGC--ATA-TAA
1 AAACACAG-CAAAGTTT-GGGGACCTAGAATGATATTTTACCAAAAAATACAA-GCATATAGTAA
3420772 AATGGGAAAAATTAT-AAAA-AATGCCCT
63 AAT-GGAAAAATTATGAAAACAAT-CCCT
3420799 TCGAGTAACC
Statistics
Matches: 174, Mismatches: 15, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
106 3 0.02
107 16 0.09
108 12 0.07
109 21 0.12
110 116 0.67
111 6 0.03
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (109 bp):
AAACACAGCAAAGTTTGGGGACCTAGAATGATATTTTACCAAAAAATACAAGCATATAGTAAAAT
GGAAAAATTATGAAAACAATCCCTAAAAGTGACTATTTTACAAT
Found at i:3422088 original size:59 final size:59
Alignment explanation
Indices: 3422006--3422149 Score: 198
Period size: 59 Copynumber: 2.4 Consensus size: 59
3421996 ATCCTCTTCT
* * * *
3422006 GGAAATGTTGGTCCCTCATGTGAGGCGTCGCTGATTCGAAGTGTTGTGAATCGAGCAAA
1 GGAAATGTTGATCCCTCAAGTGAGGCGTCACTGATTCGAAGTGTTATGAATCGAGCAAA
* * *
3422065 GGAAATGTTGATCCTTCAAGTGAGGCGTTACTGATTTGAAGTGTTATGAATCGAGCAAA
1 GGAAATGTTGATCCCTCAAGTGAGGCGTCACTGATTCGAAGTGTTATGAATCGAGCAAA
* * *
3422124 CGAAATGTTAATCCCTCGAGTGAGGC
1 GGAAATGTTGATCCCTCAAGTGAGGC
3422150 ATAGTTTTCT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 74 1.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (59 bp):
GGAAATGTTGATCCCTCAAGTGAGGCGTCACTGATTCGAAGTGTTATGAATCGAGCAAA
Found at i:3422461 original size:116 final size:116
Alignment explanation
Indices: 3422167--3422849 Score: 802
Period size: 116 Copynumber: 5.8 Consensus size: 116
3422157 TCTTTAAGGA
** * * *
3422167 AAACAATCTCAATTGAGATAAATCTTATGTTTCGAGTGAAACTAGCTCAAGCAAGATAAAATCTT
1 AAACAATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
* * * *
3422232 CTGTTTCGAGCGAAACTATCTTAAGCGAGATAAAATATTCTT-TTTCGAGCG
66 CTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT-TTGTTTCGAGTG
* * * * ** * *
3422283 AAA-ATATCTTAAGAGATATAAAAT-ATCTGTTTCGAACGAAACTATATCAAGCGATATAAAATC
1 AAACA-ATCTCAAGCGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
* *
3422346 TGT-TGTTTCGAGTGAAACTATCTCAAGCGAGATAAAAATCTTCTGTTTCAAGTG
64 T-TCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTTTGTTTCGAGTG
*
3422400 AAACAATCTCAAGCGAGATAAATCTTCTGTTTCAAGTGAAACTATCTCAAGCGAGAT-AAATCTT
1 AAACAATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
* * * **
3422464 CTGTTTCGAGTGAAAATATCTCAAGCTAAATAAAATCTTTTGTTTCGTTTG
66 CTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGTG
* * *
3422515 AAACTATCTCAAGCGAGATAAAAATCTTCTGATTCGAGTGAAACTATCTCAAGCGAGACAAAAAT
1 AAACAATCTCAAGCGAGAT--AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGA-TAAAAT
* * *
3422580 CTTATGTTTCGGGTGAAACTATCTCAAGCGAGATAAAAATCTTTTGATTCGAGTG
63 CTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTTTGTTTCGAGTG
* * *
3422635 AAACTATCTCAAGCGAGACAAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGTGAGATAAAAAT
1 AAACAATCTCAAGCGAG--ATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAAT
* * * * *
3422700 CCTCTCTTTCGAATGAAACTATCTCAAGCGAGAT-AAATCTTTTGTTTCAAATG
63 CTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGTG
* * * ***
3422753 AAACTATCTCAAGCAAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGAGAGATGATGGTCT
1 AAACAATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCT
3422818 TCTGTTTCGAGTGAAACTATCTCAAGCGAGAT
65 TCTGTTTCGAGTGAAACTATCTCAAGCGAGAT
3422850 GTTTATCCTT
Statistics
Matches: 483, Mismatches: 68, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
115 36 0.07
116 182 0.38
117 95 0.20
118 33 0.07
119 33 0.07
120 103 0.21
122 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (116 bp):
AAACAATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
CTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGTG
Found at i:3422850 original size:40 final size:39
Alignment explanation
Indices: 3422167--3422849 Score: 813
Period size: 40 Copynumber: 17.5 Consensus size: 39
3422157 TCTTTAAGGA
* ** *
3422167 AAACAATCTCAATTGAGAT-AAATCTTATGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * *
3422205 AAACTAGCTCAAGCAAGATAAAATCTTCTGTTTCGAGCG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * * *
3422244 AAACTATCTTAAGCGAGATAAAATATTCTTTTTCGAGCG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * * * * **
3422283 AAAATATCTTAAGAGATATAAAAT-ATCTGTTTCGAACG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
3422321 AAACTATATCAAGCGATATAAAATCTGT-TGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCT-TCTGTTTCGAGTG
*
3422360 AAACTATCTCAAGCGAGATAAAAATCTTCTGTTTCAAGTG
1 AAACTATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTG
* *
3422400 AAACAATCTCAAGCGAGAT-AAATCTTCTGTTTCAAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
3422438 AAACTATCTCAAGCGAGAT-AAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * * * **
3422476 AAAATATCTCAAGCTAAATAAAATCTTTTGTTTCGTTTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
*
3422515 AAACTATCTCAAGCGAGATAAAAATCTTCTGATTCGAGTG
1 AAACTATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTG
* * *
3422555 AAACTATCTCAAGCGAGACAAAAATCTTATGTTTCGGGTG
1 AAACTATCTCAAGCGAGA-TAAAATCTTCTGTTTCGAGTG
* *
3422595 AAACTATCTCAAGCGAGATAAAAATCTTTTGATTCGAGTG
1 AAACTATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTG
*
3422635 AAACTATCTCAAGCGAGACAAAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGA-TAAAATCTTCTGTTTCGAGTG
* * * *
3422675 AAACTATCTCAAGTGAGATAAAAATCCTCTCTTTCGAATG
1 AAACTATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTG
* * *
3422715 AAACTATCTCAAGCGAGAT-AAATCTTTTGTTTCAAATG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
*
3422753 AAACTATCTCAAGCAAGAT-AAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* ***
3422791 AAACTATCTCAAGAGAGATGATGGTCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTG
3422831 AAACTATCTCAAGCGAGAT
1 AAACTATCTCAAGCGAGAT
3422850 GTTTATCCTT
Statistics
Matches: 557, Mismatches: 75, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
38 182 0.33
39 131 0.24
40 244 0.44
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
Found at i:3423166 original size:52 final size:52
Alignment explanation
Indices: 3423100--3423404 Score: 238
Period size: 52 Copynumber: 5.7 Consensus size: 52
3423090 TTTCAGTTTT
*
3423100 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTATAAAAACTCATTTAAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAACTCATTTAAAAA
* * * * *
3423152 CATCAAGAACCCCCTAAAAA-TAGGCTTAATTTCTTTTAAAAATTCATTAGTAATCAT
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTC---TAAAAACTCATT--TAA-AAA
* * ** * *
3423209 CATCAAGAAAACCCT-GAAATTCAAACTTATTTTCTAAAAACTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATT-AGGCTTAGTTTCTAAAAACTCATTTAAAAA
* * * *
3423261 TATCAAGAAACCCCTAAAAATTAGGCTTTGCTTATTTAAAAATTC-TTTGGAAATAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAG-TT-TCTAAAAACTCATTT--AAA-AA
** * * * * *
3423317 TCATCAAGGTACCCTTGAAAATCAGCCTTAGTTTCTAAAAACTCATTTACAAA
1 -CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAACTCATTTAAAAA
* * *
3423370 CATCAAGAAGCCTCTAAAAATTAGGCTTAGCTTCT
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCT
3423405 TTTAAAAGTT
Statistics
Matches: 191, Mismatches: 46, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
51 11 0.06
52 63 0.33
53 14 0.07
54 22 0.12
55 22 0.12
56 13 0.07
57 37 0.19
58 9 0.05
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (52 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAACTCATTTAAAAA
Found at i:3423247 original size:109 final size:110
Alignment explanation
Indices: 3423099--3423411 Score: 364
Period size: 109 Copynumber: 2.9 Consensus size: 110
3423089 TTTTCAGTTT
* * * * *
3423099 TCATCAAGAAACCCCTAAAAATT-AGGCTTAGTTTATAAAAACTCATTTAAAAACATCAAGAACC
1 TCATCAAGAAAACCCT-GAAATTCAGACTTAGTTTCTAAAAACTCATTTAAAAACATCAAGAAAC
** * *
3423163 CCCTAAAAA-TAGGCTTAATTTCTTTTAAAAATTCATTAGTAATCA
65 CCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTAGAAATAA
* * * *
3423208 TCATCAAGAAAACCCTGAAATTCAAACTTATTTTCTAAAAACTCATTTGAAAATATCAAGAAACC
1 TCATCAAGAAAACCCTGAAATTCAGACTTAGTTTCTAAAAACTCATTTAAAAACATCAAGAAACC
* * * *
3423273 CCTAAAAATTAGGCTTTGCTT-ATTTAAAAATTCTTTGGAAATAA
66 CCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTAGAAATAA
** * * * *
3423317 TCATCAAG-GTACCCTTGAAAATCAGCCTTAGTTTCTAAAAACTCATTTACAAACATCAAGAAGC
1 TCATCAAGAAAACCC-TGAAATTCAGACTTAGTTTCTAAAAACTCATTTAAAAACATCAAGAAAC
*
3423381 CTCTAAAAATTAGGCTTAGCTTCTTTTAAAA
65 CCCTAAAAATTAGGCTTAGCTTCTTTTAAAA
3423412 GTTTATTTGA
Statistics
Matches: 170, Mismatches: 30, Indels: 7
0.82 0.14 0.03
Matches are distributed among these distances:
108 9 0.05
109 145 0.85
110 16 0.09
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.31
Consensus pattern (110 bp):
TCATCAAGAAAACCCTGAAATTCAGACTTAGTTTCTAAAAACTCATTTAAAAACATCAAGAAACC
CCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTAGAAATAA
Found at i:3423680 original size:2 final size:2
Alignment explanation
Indices: 3423673--3423729 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
3423663 TATGAATGCA
3423673 AT AT AT AT AT AT 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 AT AT AT AT AT AT
3423715 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
3423730 ATTGTAATGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3425583 original size:42 final size:42
Alignment explanation
Indices: 3425535--3425622 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
3425525 TTTCTTTTAT
*
3425535 TTTTGTTCCTCTTTT-TCTCT-TCTTTCTTTTCTTTTCTATCTC
1 TTTTGTT-CTCTTTTCTCTCTAT-TTTCCTTTCTTTTCTATCTC
* *
3425577 TTTTGTTTTCTTTTCTCTCTATTTTCCTTTCTTTTCTCTCTC
1 TTTTGTTCTCTTTTCTCTCTATTTTCCTTTCTTTTCTATCTC
3425619 TTTT
1 TTTT
3425623 CCTTTCTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
41 6 0.15
42 34 0.83
43 1 0.02
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.70
Consensus pattern (42 bp):
TTTTGTTCTCTTTTCTCTCTATTTTCCTTTCTTTTCTATCTC
Found at i:3425643 original size:21 final size:21
Alignment explanation
Indices: 3425547--3425633 Score: 115
Period size: 21 Copynumber: 4.2 Consensus size: 21
3425537 TTGTTCCTCT
*
3425547 TTTTCTCT-TC-TTTCTTTTC
1 TTTTCTCTCTCTTTTCCTTTC
* **
3425566 TTTTCTATCTCTTTTGTTTTC
1 TTTTCTCTCTCTTTTCCTTTC
*
3425587 TTTTCTCTCTATTTTCCTTTC
1 TTTTCTCTCTCTTTTCCTTTC
3425608 TTTTCTCTCTCTTTTCCTTTC
1 TTTTCTCTCTCTTTTCCTTTC
3425629 TTTTC
1 TTTTC
3425634 GTGTGTTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 7 0.12
20 2 0.03
21 50 0.85
ACGTcount: A:0.02, C:0.26, G:0.01, T:0.70
Consensus pattern (21 bp):
TTTTCTCTCTCTTTTCCTTTC
Found at i:3429509 original size:108 final size:109
Alignment explanation
Indices: 3429247--3429564 Score: 385
Period size: 108 Copynumber: 2.9 Consensus size: 109
3429237 ACCACGGAAA
* * * *
3429247 ATTGAATCGGGGCAGAATTATTCCGCTTACTCTAAAAGGAAAATCAAATCTTGGAAAAGTGAGAC
1 ATTGAATCGGGGCAGATTTATTCCGCTTACTCTAAGA-GAATATCAAATCTTAGAAAA--GAGAC
3429312 ATGTTCCGCTTACTCTGAAGGG-AAATCAGATCTGTGGGAGTTTATCC
63 ATGTT-CGCTTACTCTGAAGGGAAAATCAGATCTGTGGGAGTTTATCC
* *
3429359 ATTGAATCGGGGAAGATTTATTCCGCTTACTCTAAAGGGAATATCAAATCTTAGAAAAGAGACAT
1 ATTGAATCGGGGCAGATTTATTCCGCTTACTCT-AAGAGAATATCAAATCTTAGAAAAGAGACAT
3429424 GTTCTGCTTACTCTGAAGGGAAAATCAGATCTG-GGGAG-TT-TCC
65 GTTC-GCTTACTCTGAAGGGAAAATCAGATCTGTGGGAGTTTATCC
* * * * *
3429467 ATTGAATCGGGCCAGATTTGTTCCGATTACTCTGAAGAGAATATCAAATCTTGAAAAAAAAGACC
1 ATTGAATCGGGGCAGATTTATTCCGCTTACTCT-AAGAGAATATCAAATCTT-AGAAAAGAGA-C
* * *
3429532 TAT-TTCACTTACTCTGAAGGGAATATCAAATCT
63 -ATGTTCGCTTACTCTGAAGGGAAAATCAGATCT
3429565 TGGAAAAGAG
Statistics
Matches: 183, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
108 49 0.27
109 35 0.19
110 34 0.19
111 14 0.08
112 49 0.27
113 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (109 bp):
ATTGAATCGGGGCAGATTTATTCCGCTTACTCTAAGAGAATATCAAATCTTAGAAAAGAGACATG
TTCGCTTACTCTGAAGGGAAAATCAGATCTGTGGGAGTTTATCC
Found at i:3429599 original size:48 final size:47
Alignment explanation
Indices: 3429493--3429612 Score: 134
Period size: 48 Copynumber: 2.5 Consensus size: 47
3429483 TTTGTTCCGA
* *
3429493 TTACTCTGAAGAGAATATCAAATCTTGAAAAAAAAGACCTATTTCAC
1 TTACTCTGAAGGGAATATCAAATCTTGAAAAAAAAGACATATTTCAC
* * * *
3429540 TTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTAT-GC
1 TTACTCTGAAGGGAATATCAAATCTT-GAAAAAAAAGACATATT-TCAC
* * *
3429588 TTACTCCGAAGGGAAAATCAGATCT
1 TTACTCTGAAGGGAATATCAAATCT
3429613 GAGGGAGTTG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
47 25 0.40
48 36 0.58
49 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (47 bp):
TTACTCTGAAGGGAATATCAAATCTTGAAAAAAAAGACATATTTCAC
Found at i:3429686 original size:157 final size:153
Alignment explanation
Indices: 3429384--3429684 Score: 415
Period size: 160 Copynumber: 1.9 Consensus size: 153
3429374 ATTTATTCCG
* *
3429384 CTTACTCTAAAGGGAATATCAAATCTTAGAAAAGAGACATGTTCTGCTTACTCTGAAGGGAAAAT
1 CTTACTCTAAAGGGAATATCAAATCTTAGAAAAGAGACATGTTATGCTTACTCCGAAGGGAAAAT
*
3429449 CAGATCTGGGGAGTTTCCATTGAATCGGGCCAGATTTGTTCCGATTACTCTGAAGAGAATATCAA
66 CAGATCTGGGGAGTTTCCATTGAATCGGGCCAGATTTGTTCCGATTACTCCGAAGAGAATATCAA
3429514 ATCTTGAAAAAAAAGACCTATTTCA
131 ATCTTG--AAAAAAGACCTATTTCA
* *
3429539 CTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTATGCTTACTCCGAAGGGAAA
1 CTTACTCTAAAGGGAATATCAAATCTTAG-AAA-AGAGACATGTTATGCTTACTCCGAAGGGAAA
** * ** *
3429604 ATCAGATCTGAGGGAGTTGATCCATTGAATCGGGGTATACTTT-TTTTGCTTACTCCGAAGAGAA
64 ATCAGATCTG-GGGAGTT--TCCATTGAATCGGGCCAGA-TTTGTTCCGATTACTCCGAAGAGAA
*
3429668 TATCAAATCTTGGAAAA
125 TATCAAATCTTGAAAAA
3429685 GAGAGACTTG
Statistics
Matches: 128, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
155 27 0.21
156 3 0.02
157 39 0.30
158 11 0.09
160 45 0.35
161 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.29
Consensus pattern (153 bp):
CTTACTCTAAAGGGAATATCAAATCTTAGAAAAGAGACATGTTATGCTTACTCCGAAGGGAAAAT
CAGATCTGGGGAGTTTCCATTGAATCGGGCCAGATTTGTTCCGATTACTCCGAAGAGAATATCAA
ATCTTGAAAAAAGACCTATTTCA
Found at i:3429816 original size:113 final size:112
Alignment explanation
Indices: 3429539--3429841 Score: 371
Period size: 113 Copynumber: 2.7 Consensus size: 112
3429529 ACCTATTTCA
**
3429539 CTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTATGCTTACTCCGAAGGGAAA
1 CTTACTCTGAA-GGAATATCAAATCTTGGAAAAGAGAGACATGTTATGCTTACTTTGAAGGGAAA
* * * * **
3429604 ATCAGATCTGAGGGAGTTGATCCATTGAATCGGGGTATACTTTTTTTG
65 ATCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCG
* * ** *
3429652 CTTACTCCGAAGAGAATATCAAATCTTGGAAAAGAGAGACTTGTTCCGCTTACTTTGAATGGAAA
1 CTTACTCTGAAG-GAATATCAAATCTTGGAAAAGAGAGACATGTTATGCTTACTTTGAAGGGAAA
3429717 ATCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCG
65 ATCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCG
* *
3429765 CTTACTCTAAAGGTAATATCAAATCTT-G-AAGGAGATGGATC-TGTTATGCTTA-TCTTGAAGG
1 CTTACTCTGAAGG-AATATCAAATCTTGGAAAAGAGA--GA-CATGTTATGCTTACT-TTGAAGG
*
3429826 GAATATCAGATCTGGG
61 GAAAATCAGATCTGGG
3429842 AGGATACGTG
Statistics
Matches: 164, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
111 6 0.04
112 4 0.02
113 153 0.93
114 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (112 bp):
CTTACTCTGAAGGAATATCAAATCTTGGAAAAGAGAGACATGTTATGCTTACTTTGAAGGGAAAA
TCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCG
Found at i:3430051 original size:136 final size:134
Alignment explanation
Indices: 3429740--3430125 Score: 376
Period size: 134 Copynumber: 2.9 Consensus size: 134
3429730 GAGTTGATCC
* * *
3429740 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTAAAGGTAATATCAAATCTT-G-AAGGAGATGG
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTAAAGG-AAAATCAAAACTTGGAAAAGAGA--G
* * * *
3429803 ATCTGTTATGCTTA-TCTTGAAGGGAATATCAGATCTGGGAGGA-TACGTGATTCATTCCTCTGT
63 ACCTGTTACGCTTACT-TTGAAGGGAATATCAGATCT-GGAGGAGT---TGATCCATTCCGCTGT
**
3429866 TCTTCAGGGAAG
123 TCCCCAGGGAAG
* ** * *
3429878 TTTGAATCAAGGTAGACTTGTTCCGCTGT-CACT-AAGGAAAATCAAAACTTGGAAAAGAGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCT-TACTCTAAAGGAAAATCAAAACTTGGAAAAGAGAGAC
* * * *
3429941 CTCTTCCCCTTACTTTGAAGGGAATATCAGATCTGGAGGAGGTTGATCCATTTCGCTG-TCACCC
65 CTGTTACGCTTACTTTGAAGGGAATATCAGATCTGGAGGA-GTTGATCCATTCCGCTGTTC-CCC
3430005 AGGGAAG
128 AGGGAAG
* *
3430012 ATTGAATCGGGGCAGACTTGTTCTGCTTACTCTGAAAGG-AAATCAAAACTTGGAAAAGTGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCT-AAAGGAAAATCAAAACTTGGAAAAGAGAGAC
* * * * *
3430076 CTGTTTCGCTTACTCTGAA-GGAAAATCAGATCTGGGGGAGTTTATCCATT
65 CTGTTACGCTTACTTTGAAGGGAATATCAGATCTGGAGGAGTTGATCCATT
3430126 GAATCAGGGT
Statistics
Matches: 206, Mismatches: 32, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
133 13 0.06
134 63 0.31
135 45 0.22
136 45 0.22
137 7 0.03
138 32 0.16
139 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (134 bp):
ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTAAAGGAAAATCAAAACTTGGAAAAGAGAGACC
TGTTACGCTTACTTTGAAGGGAATATCAGATCTGGAGGAGTTGATCCATTCCGCTGTTCCCCAGG
GAAG
Found at i:3430347 original size:111 final size:113
Alignment explanation
Indices: 3430012--3430776 Score: 957
Period size: 111 Copynumber: 6.9 Consensus size: 113
3430002 CCCAGGGAAG
* * * *
3430012 ATTGAATCGGGGCAGACTTGTTCTGCTTACTCTGAAAGGAA-ATCAAAACTTGGAAAAGTGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
* * * *
3430076 CTGTTTCGCTTACTCTGAA-GGAAAATCAGATCTGGGGGAGTTTATCC
66 ATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTAGGGGAGTTGATCC
* * * * *
3430123 ATTGAATCAGGGTAGATTTGTTCCGCTTACTCTGAAAGGAATAACAAATCTTGGAAAAGAGAGAT
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGA-
*
3430188 C-TGTTCCGCTTACTCTGAAGGGAAAATCAGATCTAGGGGAGTTAATCC
65 CATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTAGGGGAGTTGATCC
* * *
3430236 AATGAATTGGGGCAGACTTGTTCCTCTTACTCTGAAGGGAATATCAAATC-T-GAAAAGAGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
*
3430299 ATGTTCCGCTTACTCTGAAGGGAAAATC-GAATTTAGGGGAGTTGATCC
66 ATGTTCCGCTTACTCTGAAGGGAAAATCAG-ATCTAGGGGAGTTGATCC
* * * *
3430347 ATT-AATCGGGGTAGATTTATTCCGCTTACTCTAAAGGGAATATCAAATCTTGGAAAAGAGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
3430411 ATGTTCCGCTTACT-TAGAAGGGAAAATCAGATCT-GAGGGAGTTGA-CC
66 ATGTTCCGCTTACTCT-GAAGGGAAAATCAGATCTAG-GGGAGTTGATCC
*
3430458 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAGGGAATATC-AATC-TCGAAAAGAGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
* * * * *
3430521 TTGTTCTGCTTACTCTGAAGGGAAAATCAGTTATAGGGGAGTTGGTCC
66 ATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTAGGGGAGTTGATCC
* * ** *
3430569 ATTG-ATCGGGGTATA-TTGTTTTGTTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
* * * *
3430632 ATGTTCTGCTTACTCTAAAAGGAAAATCAGATAT-GGGGCAGTTGATCC
66 ATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTAGGGG-AGTTGATCC
* * * **
3430680 ATTGAATCGAGGCAGACTTGTTCCGCTTACTCTGAAAGGAATATCAAATATTCTAAAAGAGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
* ** * *
3430745 TTGTTCATCTTATTCTGAAGGGAATATCAGAT
66 ATGTTCCGCTTACTCTGAAGGGAAAATCAGAT
3430777 TTTTCAAAAA
Statistics
Matches: 569, Mismatches: 66, Indels: 36
0.85 0.10 0.05
Matches are distributed among these distances:
109 25 0.04
110 108 0.19
111 168 0.30
112 132 0.23
113 136 0.24
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (113 bp):
ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
ATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTAGGGGAGTTGATCC
Found at i:3437567 original size:15 final size:15
Alignment explanation
Indices: 3437534--3437570 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3437524 TGAGACCTTA
**
3437534 CCCGCCCCGCATCTT
1 CCCGCCCCGCATCCG
3437549 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
3437564 CCCGCCC
1 CCCGCCC
3437571 AGTTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.68, G:0.16, T:0.11
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:3437749 original size:28 final size:28
Alignment explanation
Indices: 3437709--3437774 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
3437699 TAATTTTTTT
**
3437709 TCTTTCAAACCTCTCCTTACTGTGCCGA
1 TCTTTCAAACCTCTCCTTACTGCACCGA
3437737 TCTTTCAAACCTCTCCTTACTGCACCGA
1 TCTTTCAAACCTCTCCTTACTGCACCGA
3437765 TCTTTCAAAC
1 TCTTTCAAAC
3437775 ATCTGGTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.21, C:0.36, G:0.08, T:0.35
Consensus pattern (28 bp):
TCTTTCAAACCTCTCCTTACTGCACCGA
Found at i:3441952 original size:3 final size:3
Alignment explanation
Indices: 3441939--3441977 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
3441929 CTCAACATAT
* *
3441939 TCA TAA TCA TCA TCA T-A TTA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
3441978 TATTATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:3441982 original size:3 final size:3
Alignment explanation
Indices: 3441976--3442022 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
3441966 CATCATCATC
3441976 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
3442022 A
1 A
3442023 ATTAGTATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3442183 original size:3 final size:3
Alignment explanation
Indices: 3442175--3442222 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
3442165 TTTGTGCAAC
3442175 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3442223 GTTGAAAACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3442555 original size:2 final size:2
Alignment explanation
Indices: 3442550--3442594 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3442540 TATCATAACT
3442550 TA TA TA TA TA TA TA 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 TA TA TA TA
3442592 TA T
1 TA T
3442595 TTTCTAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3445088 original size:23 final size:23
Alignment explanation
Indices: 3445062--3445111 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3445052 ATCAAGCACA
* *
3445062 ATAACATATTA-GATAGTGCTTAT
1 ATAACATAATATG-TAGCGCTTAT
*
3445085 ATAACGTAATATGTAGCGCTTAT
1 ATAACATAATATGTAGCGCTTAT
3445108 ATAA
1 ATAA
3445112 TAAAATAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (23 bp):
ATAACATAATATGTAGCGCTTAT
Found at i:3445246 original size:23 final size:23
Alignment explanation
Indices: 3445220--3445279 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
3445210 ATCAAGCACA
* *
3445220 ATAACATATTAGGTATCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
3445243 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
3445266 ATAATAAAATAGGT
1 ATAACATAATAGGT
3445280 TAATTACTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:3445405 original size:23 final size:24
Alignment explanation
Indices: 3445379--3445424 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
3445369 TCAAGCATAA
*
3445379 TAACATATTAGGTAGCGC-TTATG
1 TAACATAATAGGTAGCGCATTATG
* *
3445402 TAACGTAATAGGTTGCGCATTAT
1 TAACATAATAGGTAGCGCATTAT
3445425 TAAAGCTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (24 bp):
TAACATAATAGGTAGCGCATTATG
Found at i:3445412 original size:158 final size:158
Alignment explanation
Indices: 3444903--3445424 Score: 764
Period size: 158 Copynumber: 3.3 Consensus size: 158
3444893 TATCAAATAT
* * * * ** * **
3444903 AATAATATATTAGATAGCGTTTATATAATGTAATAAGTAATGTTTATATAATAAAATATTTTAAT
1 AATAACATATTAGATAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAAT
* *
3444968 TACTTAATTTGTTATTACAACATATTAGATAAACGCCTAAAATGTTACTAATGATAACATAACCG
66 TACTTAATTTGTTATTACAACATATTAGGTAAACTCCTAAAATGTTAC-AATGATAACATAACCG
3445033 GTTAATTACT-GGAAACATTATCAAGCAC
130 GTTAATTACTAGGAAACATTATCAAGCAC
* *
3445061 AATAACATATTAGATAGTGCTTATATAACGTAATATGTAGCGCTTATATAATAAAATAGGTTAAT
1 AATAACATATTAGATAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAAT
* *
3445126 TACTTAATTTGTTATTACAACATATTAGGTAAA-TGCCTAAAATGTTAACAAGGATAGCATAACC
66 TACTTAATTTGTTATTACAACATATTAGGTAAACT-CCTAAAATGTT-ACAATGATAACATAACC
3445190 GGTTAATTACTA-GAAACATTATCAAGCAC
129 GGTTAATTACTAGGAAACATTATCAAGCAC
* *
3445219 AATAACATATTAGGTATCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAAT
1 AATAACATATTAGATAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAAT
*
3445284 TACTTAATTTGTTATTACAACATATTAGGTAAACTCCTAAAATGTTGTCAATGATAACATAACCG
66 TACTTAATTTGTTATTACAACATATTAGGTAAACTCCTAAAATGTT-ACAATGATAACATAACCG
* *
3445349 ATTAATTA-TAGGAAACATTATCAAGCAT
130 GTTAATTACTAGGAAACATTATCAAGCAC
* * *
3445377 AATAACATATTAGGTAGCGCTTATGTAACGTAATAGGTTGCGCATTAT
1 AATAACATATTAGATAGCGCTTATATAACGTAATAGGTAGCGC-TTAT
3445425 TAAAGCTGAT
Statistics
Matches: 331, Mismatches: 27, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
157 2 0.01
158 322 0.97
159 7 0.02
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.34
Consensus pattern (158 bp):
AATAACATATTAGATAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAAT
TACTTAATTTGTTATTACAACATATTAGGTAAACTCCTAAAATGTTACAATGATAACATAACCGG
TTAATTACTAGGAAACATTATCAAGCAC
Found at i:3445652 original size:75 final size:73
Alignment explanation
Indices: 3445538--3445784 Score: 327
Period size: 75 Copynumber: 3.4 Consensus size: 73
3445528 AAAATTTAAA
* * * * * *
3445538 CTACCTATTACATTAAAATACTTACAGGTTTTTTTAAGGTTGTTAATAATGTAAACGATAAAAAA
1 CTACCTATTACATTAAAATACCTACCGATTTTTTGAAGGTTGCTAATAATGTAAACGGT--AAAA
3445603 AAAATAGGCG
64 AAAATAGGCG
*
3445613 TTACCTATTACATTAAAATACCTACCGATTTTTTGAAGGTTGCTAATAATGTAAACGGT-AAAAA
1 CTACCTATTACATTAAAATACCTACCGATTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAAAA
3445677 AATA-GCG
66 AATAGGCG
* * *
3445684 CTACATATTACATTAAAATACCTACCGATTATTTTGAAGGTTGCTAATAATATAAATGGTAAAAA
1 CTACCTATTACATTAAAATACCTACCGATT-TTTTGAAGGTTGCTAATAATGTAAACGGTAAAAA
* *
3445749 AAATTGGCA
65 AAATAGGCG
* *
3445758 CTACCTATTACATTAAACTACATACCG
1 CTACCTATTACATTAAAATACCTACCG
3445785 GATATGTAGA
Statistics
Matches: 153, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
71 31 0.20
72 36 0.24
73 8 0.05
74 26 0.17
75 52 0.34
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (73 bp):
CTACCTATTACATTAAAATACCTACCGATTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAAAA
AATAGGCG
Found at i:3446062 original size:112 final size:112
Alignment explanation
Indices: 3445865--3446217 Score: 546
Period size: 112 Copynumber: 3.2 Consensus size: 112
3445855 TAGCGCCTAT
* *
3445865 AAAGTATCGATACTTTATAAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
* *
3445930 ATCAGTTTCATTATGACAAAACTGGTAAAGAGCTACCAAATATGTTA
66 ATCAGTTTCATTATGACAAAACTGGTAAAGAGCTACCAGATATGTTG
* ** * *
3445977 AAAGTATCGATACTTTTTGTACATGTATCGATACTTTACAATATAACAGGTAAAAATATGAAAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
* *
3446042 ATCAGTTTCATTATGACAAAACCGGTAAAGAGTTACCAGATATGTTG
66 ATCAGTTTCATTATGACAAAACTGGTAAAGAGCTACCAGATATGTTG
* * *
3446089 AAAGTGTCGATACTTTATAAAAATGTATCAATACTTTACAATATAACAAGTAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
* *
3446154 A-CTAGTTTCATTATGACAAAACTAGTAAAGAGCTACCGGATATGTTG
66 ATC-AGTTTCATTATGACAAAACTGGTAAAGAGCTACCAGATATGTTG
3446201 AAAGTATCGATACTTTA
1 AAAGTATCGATACTTTA
3446218 CAATATAACA
Statistics
Matches: 216, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
111 1 0.00
112 215 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (112 bp):
AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
ATCAGTTTCATTATGACAAAACTGGTAAAGAGCTACCAGATATGTTG
Found at i:3446289 original size:90 final size:91
Alignment explanation
Indices: 3446113--3446307 Score: 311
Period size: 90 Copynumber: 2.2 Consensus size: 91
3446103 TTATAAAAAT
* * *
3446113 GTATCAATACTTTACAATATAACAAGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACTA
1 GTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCA
* *
3446178 GTAAAGAGCTACCGGATATGTTGAAA
66 GTAAAGAACTACCAGATATGTTGAAA
* *
3446204 GTATCGATACTTTACAATATAACACGTAAAAATATGAC-AAACCAGTTTCATTATGACAAAACCG
1 GTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCA
3446268 GTAAAGAACTACCAGATATGTTGAAA
66 GTAAAGAACTACCAGATATGTTGAAA
*
3446294 GTAACGATACTTTA
1 GTATCGATACTTTA
3446308 TAAAATGTAT
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 60 0.62
91 36 0.38
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (91 bp):
GTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCA
GTAAAGAACTACCAGATATGTTGAAA
Found at i:3446325 original size:110 final size:111
Alignment explanation
Indices: 3446204--3446417 Score: 331
Period size: 111 Copynumber: 1.9 Consensus size: 111
3446194 TATGTTGAAA
* *
3446204 GTATCGATACTTTACAATATAACACGTAAAAATATGAC-AAACCAGTTTCATTATGACAAAACCG
1 GTATCGATACTTTACAATATAACACGTAAAAATATGACAAAACCAATTTCATTATGACAAAAACG
* *
3446268 GTAAAGAACTACCAGATATGTTGAAAGTAACGATACTTTATAAAAT
66 ATAAAGAACTACCAGATATGTCGAAAGTAACGATACTTTATAAAAT
* * *
3446314 GTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAATCAATTTCATTTTGACAAAAACG
1 GTATCGATACTTTACAATATAACACGTAAAAATATGACAAAACCAATTTCATTATGACAAAAACG
* * *
3446379 ATAAAGAGCTACCGGATATGTCGAAAGTATCGATACTTT
66 ATAAAGAACTACCAGATATGTCGAAAGTAACGATACTTT
3446418 TTGTACATGT
Statistics
Matches: 93, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
110 37 0.40
111 56 0.60
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (111 bp):
GTATCGATACTTTACAATATAACACGTAAAAATATGACAAAACCAATTTCATTATGACAAAAACG
ATAAAGAACTACCAGATATGTCGAAAGTAACGATACTTTATAAAAT
Found at i:3446386 original size:201 final size:203
Alignment explanation
Indices: 3446001--3446417 Score: 671
Period size: 201 Copynumber: 2.1 Consensus size: 203
3445991 TTTTGTACAT
* *
3446001 GTATCGATACTTTACAATATAACAGGTAAAAATATGAAAAAATCAGTTTCATTATGACAAAACCG
1 GTATCGATACTTTACAATATAACACGTAAAAATATGAAAAAACCAGTTTCATTATGACAAAACCG
** **
3446066 GTAAAGAGTTACCAGATATGTTGAAAGTGTCGATACTTTATAAAAATGTATCAATACTTTACAAT
66 GTAAAGAACTACCAGATATGTTGAAAGTAACGATACTTTATAAAAATGTATCAATACTTTACAAT
* *
3446131 ATAACAAGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACTAGTAAAGAGCTACCGGATA
131 ATAACAAGTAAAAATATGACAAAACTAATTTCATTATGACAAAACGAGTAAAGAGCTACCGGATA
*
3446196 TGTTGAAA
196 TGTCGAAA
*
3446204 GTATCGATACTTTACAATATAACACGTAAAAATATG-ACAAACCAGTTTCATTATGACAAAACCG
1 GTATCGATACTTTACAATATAACACGTAAAAATATGAAAAAACCAGTTTCATTATGACAAAACCG
*
3446268 GTAAAGAACTACCAGATATGTTGAAAGTAACGATACTTTAT-AAAATGTATCGATACTTTACAAT
66 GTAAAGAACTACCAGATATGTTGAAAGTAACGATACTTTATAAAAATGTATCAATACTTTACAAT
* *
3446332 ATAACAGGTAAAAATATGACAAAA-TCAATTTCATTTTGACAAAAACGA-TAAAGAGCTACCGGA
131 ATAACAAGTAAAAATATGACAAAACT-AATTTCATTATGAC-AAAACGAGTAAAGAGCTACCGGA
3446395 TATGTCGAAA
194 TATGTCGAAA
3446405 GTATCGATACTTT
1 GTATCGATACTTT
3446418 TTGTACATGT
Statistics
Matches: 199, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
200 1 0.01
201 94 0.47
202 69 0.35
203 35 0.18
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (203 bp):
GTATCGATACTTTACAATATAACACGTAAAAATATGAAAAAACCAGTTTCATTATGACAAAACCG
GTAAAGAACTACCAGATATGTTGAAAGTAACGATACTTTATAAAAATGTATCAATACTTTACAAT
ATAACAAGTAAAAATATGACAAAACTAATTTCATTATGACAAAACGAGTAAAGAGCTACCGGATA
TGTCGAAA
Found at i:3447029 original size:7 final size:7
Alignment explanation
Indices: 3447013--3447042 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3447003 TTTTAAATCA
*
3447013 ATAAAAT
1 ATAAATT
3447020 ATAAATT
1 ATAAATT
3447027 ATAAATT
1 ATAAATT
3447034 ATAAATT
1 ATAAATT
3447041 AT
1 AT
3447043 TTGAGTTGAG
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAAATT
Found at i:3447249 original size:19 final size:19
Alignment explanation
Indices: 3447169--3447251 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 19
3447159 AGTTTAAAAA
3447169 TGATTGTAATATGTT-CGTT
1 TGATTGTAATATGTTAC-TT
* *
3447188 TGATATATTTATAGTGTTACTT
1 TGAT-T-GTAATA-TGTTACTT
* * **
3447210 TAATTGTAATATTTTGTTT
1 TGATTGTAATATGTTACTT
3447229 TGATTGTAATATGTTACTT
1 TGATTGTAATATGTTACTT
3447248 TGAT
1 TGAT
3447252 GTATTTGTGA
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
19 28 0.58
20 5 0.10
21 5 0.10
22 9 0.19
23 1 0.02
ACGTcount: A:0.25, C:0.04, G:0.16, T:0.55
Consensus pattern (19 bp):
TGATTGTAATATGTTACTT
Found at i:3456092 original size:2 final size:2
Alignment explanation
Indices: 3456085--3456129 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3456075 ATATTTTGAT
3456085 TA TA TA TA TA TA TA 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 TA TA TA TA
3456127 TA T
1 TA T
3456130 TATTAATAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3457731 original size:13 final size:14
Alignment explanation
Indices: 3457707--3457735 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3457697 CGTTTCTAAT
3457707 TTATTACAATTTTA
1 TTATTACAATTTTA
3457721 TTATT-CAATTTTA
1 TTATTACAATTTTA
3457734 TT
1 TT
3457736 TTATTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTACAATTTTA
Found at i:3463170 original size:38 final size:38
Alignment explanation
Indices: 3463033--3463664 Score: 527
Period size: 38 Copynumber: 15.9 Consensus size: 38
3463023 AAAAAATCGG
*
3463033 TTTTTGAAACATATATATATTATATAG-TTTTGAAAACA
1 TTTTTGAAA-ATATATATAATATATAGTTTTTGAAAACA
*
3463071 -TTTTGAAAATATATATAATATGTAGTTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
3463108 TTTTTAAAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTT-GAAAATATATATAATATATAGTTTTTGAAAACA
* * *
3463147 TTTTTGAAAATATATATATTATATAGTTTTTGGAAATA
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* * *
3463185 ATTTTGAAAACATATATATATTATATA-ATTTTGAAAACA
1 TTTTTG-AAA-ATATATATAATATATAGTTTTTGAAAACA
**
3463224 -TTTTGAAAACATATATATAATATATAGTTTTCAAAAAACA
1 TTTTTG-AAA-ATATATATAATATATAGTTTT-TGAAAACA
*
3463264 -TTTTGAAAATACATATATATATATATATTATATAGTTTTTGGAAACA
1 TTTTTG-----A-A-A-ATATATATA-A-TATATAGTTTTTGAAAACA
* * *
3463311 TTTTTAAAAACATATATATAATATACAGTTTTTAAAAAAAACA
1 TTTTT-GAAA-ATATATATAATATATAGTTTTT---GAAAACA
*
3463354 -TTTTGAAAACATATATATAATATATAGTTTTTAAAAACA
1 TTTTTG-AAA-ATATATATAATATATAGTTTTTGAAAACA
3463393 -TTTTGAAAAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTTG---AAAATATATATAATATATAGTTTTTGAAAACA
* *
3463433 TTTTTGAAAATATATATATTATATAGTTTTTGCAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* * * *
3463471 TTTTTGAAAACATATAT-ATACATA--TATT--ATACA
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
** *
3463504 GTTTTGAAAACATATATATAATATATAGGTTTTTAAAAAACA
1 -TTTTTGAAA-ATATATATAATATATA-GTTTTT-GAAAACA
*
3463546 -TTTTGAAAATATATATATAATATATAACTTTTTGAAAAAAAACA
1 TTTTTG-AAA-ATATATATAATATAT-AGTTTTTG----AAAACA
* *
3463590 -TTTTGAAAAAATATATATAATATATAGTTTTTAAAAAAA
1 TTTTTG--AAAATATATATAATATATAGTTTTTGAAAACA
* *
3463629 TGTTTTAAAAATATATATAATATATAGTTTTGGAAA
1 T-TTTTGAAAATATATATAATATATAGTTTTTGAAA
3463665 TATATTATAT
Statistics
Matches: 499, Mismatches: 53, Indels: 83
0.79 0.08 0.13
Matches are distributed among these distances:
33 4 0.01
34 7 0.01
35 10 0.02
36 21 0.04
37 24 0.05
38 109 0.22
39 98 0.20
40 69 0.14
41 37 0.07
42 44 0.09
43 12 0.02
44 28 0.06
45 5 0.01
46 10 0.02
47 6 0.01
48 15 0.03
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (38 bp):
TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:3463200 original size:40 final size:40
Alignment explanation
Indices: 3463034--3463659 Score: 525
Period size: 40 Copynumber: 15.8 Consensus size: 40
3463024 AAAAATCGGT
* *
3463034 TTTTG-AAACATATATATATTATATAG-TTTT-GAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
* *
3463071 TTTTG-AAA-ATATATATAATATGTAGTTTTT-GAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
* * *
3463108 TTTTTAAAAAATATATATAATATATAGTTTTT-GAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
* * *
3463147 TTTTTG-AAA-ATATATATATTATATAGTTTTTGGAAATA-A
1 -TTTTGAAAACATATATATAATATATAGTTTTT-AAAAAACA
* * *
3463186 TTTTGAAAACATATATATATTATATA-ATTTT-GAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
*
3463224 TTTTGAAAACATATATATAATATATAGTTTTCAAAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
**
3463264 TTTTGAAAATACATATATATATATATATTATATAGTTTTT-GGAAACA
1 TTTTG-AAA-AC----ATATATATA-A-TATATAGTTTTTAAAAAACA
* *
3463311 TTTTTAAAAACATATATATAATATACAGTTTTTAAAAAAAACA
1 -TTTTGAAAACATATATATAATATATAGTTTTT--AAAAAACA
3463354 TTTTGAAAACATATATATAATATATAGTTTTT-AAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
* *
3463393 TTTTGAAAAAAATATATATAATATATAGTTTTT-GAAAACA
1 TTTTG-AAAACATATATATAATATATAGTTTTTAAAAAACA
* **
3463433 TTTTTG-AAA-ATATATATATTATATAGTTTTT-GCAAACA
1 -TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
* * * **
3463471 TTTTTGAAAACATATATAT-ACATATA----TT-ATACAGT
1 -TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
** * *
3463506 TTTGAAAACATATATATA-ATATATA-GGTTTTTAAAAAACA
1 TTTTGAAA-ACATATATATA-ATATATAGTTTTTAAAAAACA
* *
3463546 TTTTGAAAATATATATATAATATATAACTTTTTGAAAAAAAACA
1 TTTTGAAAACATATATATAATATAT-AGTTTTT---AAAAAACA
*
3463590 TTTTGAAAAAATATATATAATATATAGTTTTTAAAAAA-A
1 TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
*
3463629 TGTTTTAAAA-ATATATATAATATATAGTTTT
1 T-TTTGAAAACATATATATAATATATAGTTTT
3463660 GGAAATATAT
Statistics
Matches: 496, Mismatches: 51, Indels: 82
0.79 0.08 0.13
Matches are distributed among these distances:
34 6 0.01
35 12 0.02
36 19 0.04
37 26 0.05
38 88 0.18
39 104 0.21
40 108 0.22
41 14 0.03
42 41 0.08
43 11 0.02
44 32 0.06
46 11 0.02
47 9 0.02
48 15 0.03
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (40 bp):
TTTTGAAAACATATATATAATATATAGTTTTTAAAAAACA
Found at i:3463608 original size:112 final size:110
Alignment explanation
Indices: 3463393--3463613 Score: 275
Period size: 112 Copynumber: 1.9 Consensus size: 110
3463383 TTTAAAAACA
*
3463393 TTTTGAAAAAAATATATATAATATATAGTTTTTGAAAACATTTTTGAAAATATATATATTATATA
1 TTTTG-AAAAAATATATATAATATATAGTTTTTAAAAACATTTTTGAAAATATATATATTATATA
* * *
3463458 GTTTTTGCAAACATTTTTGAAAACATATATATACATATATTATACAG
65 CTTTTTGAAAACATTTTTGAAAACATATATATA-ATATAATATACAG
*
3463505 TTTTGAAAACATATATATAATATATAGGTTTTTAAAAAACA-TTTTGAAAATATATATATAATAT
1 TTTTGAAAAAATATATATAATATATA-GTTTTT-AAAAACATTTTTGAAAATATATATAT--TAT
*
3463569 ATAACTTTTTGAAAAAAAACA-TTTTGAAAAAATATATATAATATA
62 AT-ACTTTTTG----AAAACATTTTTGAAAACATATATATAATATA
3463614 TAGTTTTTAA
Statistics
Matches: 95, Mismatches: 5, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
111 20 0.21
112 29 0.31
113 6 0.06
114 5 0.05
115 7 0.07
117 5 0.05
118 18 0.19
119 5 0.05
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (110 bp):
TTTTGAAAAAATATATATAATATATAGTTTTTAAAAACATTTTTGAAAATATATATATTATATAC
TTTTTGAAAACATTTTTGAAAACATATATATAATATAATATACAG
Found at i:3463620 original size:112 final size:110
Alignment explanation
Indices: 3463282--3463614 Score: 305
Period size: 122 Copynumber: 2.8 Consensus size: 110
3463272 ATACATATAT
* ** * * *
3463282 ATATATATATTATATAGTTTTTGGAAACATTTTTAAAAACATATATATAATATACAGTTTTTAAA
1 ATATATATAATATATAGTTTTTAAAAACATTTTTGAAAATATATATATTATATAC--TTTTT---
* *
3463347 AAAAACA-TTTTGAAAACATATATATAATATATAGTTTTTAAAAACA-TTTTGAAAAAA
61 GAAAACATTTTTGAAAACATATATAT-A-ATATA----TT--ATACAGTTTTG-AAAAA
* * *
3463404 ATATATATAATATATAGTTTTTGAAAACATTTTTGAAAATATATATATTATATAGTTTTTGCAAA
1 ATATATATAATATATAGTTTTTAAAAACATTTTTGAAAATATATATATTATATACTTTTTGAAAA
*
3463469 CATTTTTGAAAACATATATATACATATATTATACAGTTTTGAAAAC
66 CATTTTTGAAAACATATATATA-ATATATTATACAGTTTTGAAAAA
3463515 ATATATATAATATATAGGTTTTTAAAAAACA-TTTTGAAAATATATATATAATATATAACTTTTT
1 ATATATATAATATATA-GTTTTT-AAAAACATTTTTGAAAATATATATAT--TATAT-ACTTTTT
*
3463579 GAAAAAAAACA-TTTTGAAAAAATATATATAATATAT
61 G----AAAACATTTTTGAAAACATATATATAATATAT
3463615 AGTTTTTAAA
Statistics
Matches: 185, Mismatches: 15, Indels: 27
0.81 0.07 0.12
Matches are distributed among these distances:
111 24 0.13
112 29 0.16
113 8 0.04
114 5 0.03
115 7 0.04
117 17 0.09
118 36 0.19
119 5 0.03
120 5 0.03
122 49 0.26
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (110 bp):
ATATATATAATATATAGTTTTTAAAAACATTTTTGAAAATATATATATTATATACTTTTTGAAAA
CATTTTTGAAAACATATATATAATATATTATACAGTTTTGAAAAA
Found at i:3463659 original size:25 final size:22
Alignment explanation
Indices: 3463630--3463685 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 22
3463620 TTAAAAAAAT
3463630 GTTTTAAAAATATATATAATATATA
1 GTTTTAAAAATATAT-T-ATATA-A
**
3463655 GTTTTGGAAATATATTATATAA
1 GTTTTAAAAATATATTATATAA
3463677 -TTTTAAAAA
1 GTTTTAAAAA
3463686 CAATGTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 7 0.26
22 1 0.04
23 5 0.19
24 1 0.04
25 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (22 bp):
GTTTTAAAAATATATTATATAA
Found at i:3463685 original size:85 final size:88
Alignment explanation
Indices: 3463492--3463685 Score: 228
Period size: 85 Copynumber: 2.2 Consensus size: 88
3463482 ATATATATAC
*
3463492 ATATATTATACAGTTTTGAAAACATATATATAATATATAGGTTTTTAAAAAACATTTTGAAAATA
1 ATATATTATA-AATTTTGAAAA-ATATATATAATATATAGGTTTTTAAAAAACATTTTGAAAATA
*
3463557 TATATATAATATATAACTTTTTGAA
64 TATATATAATATATAACTTTTGGAA
*
3463582 A-A-A--A-AACATTTTGAAAAAATATATATAATATATA-GTTTTTAAAAAA-ATGTTTTAAAA-
1 ATATATTATAA-ATTTTG-AAAAATATATATAATATATAGGTTTTTAAAAAACAT-TTTGAAAAT
*
3463639 ATATATATAATATAT-AGTTTTGGAA
63 ATATATATAATATATAACTTTTGGAA
3463664 ATATATTATATAATTTT-AAAAA
1 ATATATTATA-AATTTTGAAAAA
3463686 CAATGTTTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 23
0.77 0.03 0.19
Matches are distributed among these distances:
82 9 0.10
83 18 0.20
84 21 0.23
85 27 0.30
86 6 0.07
87 6 0.07
88 2 0.02
89 1 0.01
90 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (88 bp):
ATATATTATAAATTTTGAAAAATATATATAATATATAGGTTTTTAAAAAACATTTTGAAAATATA
TATATAATATATAACTTTTGGAA
Found at i:3463691 original size:60 final size:60
Alignment explanation
Indices: 3463604--3463719 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
3463594 GAAAAAATAT
* *
3463604 ATATAATATATAGTTTTTAAAAAAATG-TTTTAAAAATATATATAATATATAGTTTTGGAA
1 ATATAATATATAGATTTTAAAAAAATGTTTTTAAAAA-ATATATAATATATAATTTTGGAA
* **
3463664 ATATATTATATA-ATTTTAAAAACAATGTTTTTTGAAAATATATAATATATAATTTT
1 ATATAATATATAGATTTTAAAAA-AATGTTTTTAAAAAATATATAATATATAATTTT
3463720 AAAAATGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 9 0.18
60 33 0.67
61 7 0.14
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (60 bp):
ATATAATATATAGATTTTAAAAAAATGTTTTTAAAAAATATATAATATATAATTTTGGAA
Found at i:3465104 original size:16 final size:17
Alignment explanation
Indices: 3465083--3465123 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
3465073 CTTTTTTTGT
3465083 TTTATTATTATTA-TTA
1 TTTATTATTATTATTTA
*
3465099 TTTATTTTTATTATTTA
1 TTTATTATTATTATTTA
*
3465116 TTTTTTAT
1 TTTATTAT
3465124 CCTTTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTATTATTATTTA
Found at i:3465109 original size:13 final size:13
Alignment explanation
Indices: 3465087--3465120 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3465077 TTTTGTTTTA
*
3465087 TTATTATTATTAT
1 TTATTTTTATTAT
3465100 TTATTTTTATTAT
1 TTATTTTTATTAT
3465113 TTATTTTT
1 TTATTTTT
3465121 TATCCTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTTATTAT
Found at i:3465724 original size:22 final size:21
Alignment explanation
Indices: 3465705--3465745 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3465695 CGTATTAATA
*
3465705 AAGAAAATTTCTAATTTTAAAG
1 AAGAAAA-TTCAAATTTTAAAG
*
3465727 AAGTAAATTCAAATTTTAA
1 AAGAAAATTCAAATTTTAA
3465746 GAAATTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (21 bp):
AAGAAAATTCAAATTTTAAAG
Found at i:3471017 original size:233 final size:232
Alignment explanation
Indices: 3470610--3471074 Score: 921
Period size: 233 Copynumber: 2.0 Consensus size: 232
3470600 GTAATAAAAC
3470610 CATAAATATAGGACTCAAATGGAATAACATAAACATCAGTACCCCATTTCGAACAAAAAAATAGA
1 CATAAATATAGGACTCAAATGGAATAACATAAACATCAGTACCCCATTTCGAACAAAAAAATAGA
3470675 TACAATAGAGGACTAAATTAAAATAATAAAAAACAAAGTATCCAATTCCCAAATCATGTAAAATA
66 TACAATAGAGGACTAAATTAAAATAATAAAAAACAAAGTATCCAATTCCCAAATCATGTAAAATA
3470740 AAAGAAAATGGTGACCAAATCACAAAAAACGCTAAACTTGAAGGGACCTAAGGCATGATTAACTC
131 AAAGAAAATGGTGACCAAATCACAAAAAACGCTAAACTTGAAGGGACCTAAGGCATGATTAACTC
3470805 TAAAAAAATTATTAAAACGCGAATCGCACTAAACAAAT
196 T-AAAAAATTATTAAAACGCGAATCGCACTAAACAAAT
3470843 CATAAATATAGGACTCAAATGGAATAACATAAACATCAGTACCCCATTTCGAACAAAAAAATAGA
1 CATAAATATAGGACTCAAATGGAATAACATAAACATCAGTACCCCATTTCGAACAAAAAAATAGA
3470908 TACAATAGAGGACTAAATTAAAATAATAAAAAACAAAGTATCCAATTCCCAAATCATGTAAAATA
66 TACAATAGAGGACTAAATTAAAATAATAAAAAACAAAGTATCCAATTCCCAAATCATGTAAAATA
3470973 AAAGAAAATGGTGACCAAATCACAAAAAACGCTAAACTTGAAGGGACCTAAGGCATGATTAACTC
131 AAAGAAAATGGTGACCAAATCACAAAAAACGCTAAACTTGAAGGGACCTAAGGCATGATTAACTC
3471038 TAAAAAATTATTAAAACGCGAATCGCACTAAACAAAT
196 TAAAAAATTATTAAAACGCGAATCGCACTAAACAAAT
3471075 AAGACCTACG
Statistics
Matches: 232, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
232 36 0.16
233 196 0.84
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (232 bp):
CATAAATATAGGACTCAAATGGAATAACATAAACATCAGTACCCCATTTCGAACAAAAAAATAGA
TACAATAGAGGACTAAATTAAAATAATAAAAAACAAAGTATCCAATTCCCAAATCATGTAAAATA
AAAGAAAATGGTGACCAAATCACAAAAAACGCTAAACTTGAAGGGACCTAAGGCATGATTAACTC
TAAAAAATTATTAAAACGCGAATCGCACTAAACAAAT
Found at i:3472574 original size:44 final size:43
Alignment explanation
Indices: 3472526--3472826 Score: 135
Period size: 44 Copynumber: 6.9 Consensus size: 43
3472516 GATGTCGGTA
* *
3472526 CTGATCTACCTCCTTTTGTGATAGAATTGAGCTAAAAGTTGATG
1 CTGATCTACCTCCTTCTGTGATAGAATCGAGCTAAAA-TTGATG
* * * * * * **
3472570 CTGATCAAACTCCTTCTGCGATGGATTTGAG-TGAAAATAAAAATG
1 CTGATCTACCTCCTTCTGTGATAGAATCGAGCT-AAAAT--TGATG
* * * * * * *
3472615 -TCGATCCATCTCCTTCTGTGATGGAATCGAACGAGATATTGGTG
1 CT-GATCTACCTCCTTCTGTGATAGAATCGAGCTA-AAATTGATG
* *
3472659 CTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACG
1 CTGATCTACCTCCTTCTGTGATAGAATCGAGCTAAAA-TTGATG
* * * * * * * ***
3472703 CTGATCCAACTCATTCTGCGATGGATTTGAGGC-AAAAAAAATG
1 CTGATCTACCTCCTTCTGTGATAGAATCGA-GCTAAAATTGATG
* * * * * ** *
3472746 -TCAATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTG
1 CT-GATCTACCTCCTTCTGTGATAGAATCGAGCTA-AAATTGATG
*
3472790 CTGATCTACCTCCTTCTGTGATAGATTCGAGC-AAAAT
1 CTGATCTACCTCCTTCTGTGATAGAATCGAGCTAAAAT
3472827 GTTGAACAAT
Statistics
Matches: 186, Mismatches: 58, Indels: 28
0.68 0.21 0.10
Matches are distributed among these distances:
42 4 0.02
43 30 0.16
44 118 0.63
45 31 0.17
46 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (43 bp):
CTGATCTACCTCCTTCTGTGATAGAATCGAGCTAAAATTGATG
Found at i:3472806 original size:131 final size:132
Alignment explanation
Indices: 3472180--3472831 Score: 774
Period size: 131 Copynumber: 5.0 Consensus size: 132
3472170 AATATGTTGA
* * * * *
3472180 TGATGCTGATCCAACTCCA-TATGTGATGGA--TAAGTGAAATAAAAATGTCGAT-CTCCTTCTT
1 TGATGCTGATCCAACT-CATTCTGCGATGGATTTGAGTGAAATAAAAATGTCGATCCACCTCCTT
* ** * * * **
3472241 CTGTGATGGAATCGAACAAGATGTCAGTTCTGATCTACCTCCTTCTGTGATAGATTTGAG-TGAA
65 CTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAA
3472305 AGT
130 AGT
* * * * * *
3472308 TGATGTTGATCTAACTCATTATGCGATGGATTTGAGTGAAATTAAAATGCCGATCCACCTCTTTC
1 TGATGCTGATCCAACTCATTCTGCGATGGATTTGAGTGAAATAAAAATGTCGATCCACCTCCTTC
* * *
3472373 TGTGATGGAATTGAACGAGATG-T-GT--TGATCTACCTCATTCTGTGATAAAATCGAGCAAAAA
66 TGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAA
3472434 GT
131 GT
* * * * * * * *
3472436 TGATGCTGATCCAACTCCTTCTGTGATGGATTTGAG-G-GA-ACAAATATCAATCTACCTCTTTC
1 TGATGCTGATCCAACTCATTCTGCGATGGATTTGAGTGAAATAAAAATGTCGATCCACCTCCTTC
* * * * * * *
3472498 TATGCTGGAATCGAACGAGATGTCGGTACTGATCTACCTCCTTTTGTGATAGAATTGAGCTAAAA
66 TGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAA
3472563 GT
131 GT
* * *
3472565 TGATGCTGATCAAACTCCTTCTGCGATGGATTTGAGTGAAAATAAAAATGTCGATCCATCTCCTT
1 TGATGCTGATCCAACTCATTCTGCGATGGATTTGAGTG-AAATAAAAATGTCGATCCACCTCCTT
*
3472630 CTGTGATGGAATCGAACGAGATATTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAA
65 CTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAA
3472695 AGT
130 AGT
* *
3472698 TGACGCTGATCCAACTCATTCTGCGATGGATTTGAG-GCAAA-AAAAATGTCAATCCACCTCCTT
1 TGATGCTGATCCAACTCATTCTGCGATGGATTTGAGTG-AAATAAAAATGTCGATCCACCTCCTT
*
3472761 CTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGATTCGAGCAAAA
65 CTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAA
*
3472826 TGT
130 AGT
3472829 TGA
1 TGA
3472832 ACAATCTCTT
Statistics
Matches: 446, Mismatches: 65, Indels: 23
0.84 0.12 0.04
Matches are distributed among these distances:
125 36 0.08
126 1 0.00
127 31 0.07
128 60 0.13
129 69 0.15
130 20 0.04
131 115 0.26
132 5 0.01
133 109 0.24
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (132 bp):
TGATGCTGATCCAACTCATTCTGCGATGGATTTGAGTGAAATAAAAATGTCGATCCACCTCCTTC
TGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAA
GT
Found at i:3472807 original size:87 final size:86
Alignment explanation
Indices: 3472666--3472825 Score: 194
Period size: 87 Copynumber: 1.8 Consensus size: 86
3472656 GTGCTGATCT
* * *
3472666 ACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCATTCTGCGATGGATTT
1 ACCTCCTTCTGTGATAGAATCGAACAAAAAGTTGACGCTGATCCAACTCATTCTGCGATAGATTC
3472731 GAGGCAAAAAAAATGTCAATCC
66 GA-GCAAAAAAAATGTCAATCC
* * * * ** * * * *
3472753 ACCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGATTC
1 ACCTCCTTCTGTGATAGAATCGAACAAAAAGTTGACGCTGATCCAACTCATTCTGCGATAGATTC
3472818 GAGCAAAA
66 GAGCAAAA
3472826 TGTTGAACAA
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
86 6 0.10
87 54 0.90
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (86 bp):
ACCTCCTTCTGTGATAGAATCGAACAAAAAGTTGACGCTGATCCAACTCATTCTGCGATAGATTC
GAGCAAAAAAAATGTCAATCC
Done.