Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 13 of 113
Found at i:4164567 original size:11 final size:11
Alignment explanation
Indices: 4164551--4164576 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4164541 TTATTCATGA
4164551 GAGGTGAGAAG
1 GAGGTGAGAAG
4164562 GAGGTGAGAAG
1 GAGGTGAGAAG
4164573 GAGG
1 GAGG
4164577 GACAAAGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.58, T:0.08
Consensus pattern (11 bp):
GAGGTGAGAAG
Found at i:4171426 original size:36 final size:36
Alignment explanation
Indices: 4171379--4171449 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
4171369 AGAATTAGAA
4171379 TATGGAAGTGATGGTTATATATCCCATCTATAAACT
1 TATGGAAGTGATGGTTATATATCCCATCTATAAACT
* *
4171415 TATGGAAGTGATGGTTATATGTCCTATCTATAAAC
1 TATGGAAGTGATGGTTATATATCCCATCTATAAAC
4171450 ATAAGTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (36 bp):
TATGGAAGTGATGGTTATATATCCCATCTATAAACT
Found at i:4191969 original size:20 final size:19
Alignment explanation
Indices: 4191929--4191969 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
4191919 CCGTTACATG
*
4191929 TTTTAATTTTTACTTATTT
1 TTTTAATTTTTACTTAATT
*
4191948 TTTTTATTTTTACTATAATT
1 TTTTAATTTTTACT-TAATT
4191968 TT
1 TT
4191970 ATTTGTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTAATTTTTACTTAATT
Found at i:4196896 original size:20 final size:20
Alignment explanation
Indices: 4196871--4196912 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4196861 CTCGACGCTC
4196871 TGAGGGTGGTTTCATGGTGA
1 TGAGGGTGGTTTCATGGTGA
4196891 TGAGGGTGGTTTCATGGTGA
1 TGAGGGTGGTTTCATGGTGA
4196911 TG
1 TG
4196913 GCGGCTCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.05, G:0.45, T:0.36
Consensus pattern (20 bp):
TGAGGGTGGTTTCATGGTGA
Found at i:4205520 original size:2 final size:2
Alignment explanation
Indices: 4205513--4205548 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4205503 CGTGCTGCCA
4205513 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
4205549 GAATGATGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4206366 original size:2 final size:2
Alignment explanation
Indices: 4206361--4206386 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4206351 ACACACACAC
4206361 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
4206387 GGTTTCTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4207487 original size:21 final size:21
Alignment explanation
Indices: 4207463--4207506 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
4207453 AAAGTCATCA
4207463 TTATAATAATTAATTTTATTT
1 TTATAATAATTAATTTTATTT
4207484 TTATAATAATTAATTTTATTT
1 TTATAATAATTAATTTTATTT
4207505 TT
1 TT
4207507 TTCATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATAATAATTAATTTTATTT
Found at i:4221176 original size:13 final size:13
Alignment explanation
Indices: 4221158--4221188 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4221148 ATAGAAGAAT
4221158 TAATTTGCTGAAA
1 TAATTTGCTGAAA
*
4221171 TAATTTGCTGGAA
1 TAATTTGCTGAAA
4221184 TAATT
1 TAATT
4221189 CCTTGGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (13 bp):
TAATTTGCTGAAA
Found at i:4251490 original size:6 final size:6
Alignment explanation
Indices: 4251481--4251505 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4251471 TTAAAACTCA
4251481 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
4251506 TTACTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:4252959 original size:26 final size:25
Alignment explanation
Indices: 4252929--4252986 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
4252919 AAGTTTTAAG
* *
4252929 TTTAAAAATATTCAAATTTAAAAATT
1 TTTAAAAATA-TAAAATTTAAAAACT
* *
4252955 TTTAAATATATAAAATTTGAAAACT
1 TTTAAAAATATAAAATTTAAAAACT
4252980 TTTAAAA
1 TTTAAAA
4252987 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (25 bp):
TTTAAAAATATAAAATTTAAAAACT
Found at i:4252961 original size:16 final size:16
Alignment explanation
Indices: 4252916--4253019 Score: 82
Period size: 16 Copynumber: 6.3 Consensus size: 16
4252906 TATATTTTAA
* *
4252916 AAAAAGTTTTAAGTTT
1 AAAAATTTTTAAATTT
* *
4252932 AAAAATATTCAAATTT
1 AAAAATTTTTAAATTT
*
4252948 AAAAATTTTTAAATAT
1 AAAAATTTTTAAATTT
**
4252964 ATAAAATTTGAAAACTTT
1 A-AAAATTTTTAAA-TTT
*
4252982 TAAAATTTTTAAAATTT
1 AAAAATTTTT-AAATTT
* * *
4252999 ACATATTTTGAAATTT
1 AAAAATTTTTAAATTT
4253015 AAAAA
1 AAAAA
4253020 CTTCTCAAAT
Statistics
Matches: 66, Mismatches: 19, Indels: 6
0.73 0.21 0.07
Matches are distributed among these distances:
16 35 0.53
17 26 0.39
18 5 0.08
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (16 bp):
AAAAATTTTTAAATTT
Found at i:4252986 original size:9 final size:8
Alignment explanation
Indices: 4252942--4253055 Score: 52
Period size: 8 Copynumber: 13.9 Consensus size: 8
4252932 AAAAATATTC
*
4252942 AAATTTAA
1 AAATTTTA
*
4252950 AAATTTTT
1 AAATTTTA
*
4252958 AAATATATA
1 AAAT-TTTA
*
4252967 AAATTTGA
1 AAATTTTA
4252975 AAACTTTTA
1 AAA-TTTTA
4252984 AAATTTTTA
1 AAA-TTTTA
4252993 AAA-TTTA
1 AAATTTTA
* *
4253000 CATATTTTG
1 -AAATTTTA
*
4253009 AAATTTAA
1 AAATTTTA
* *
4253017 AAACTTCTC
1 AAA-TTTTA
*
4253026 AAATTTTC
1 AAATTTTA
* *
4253034 ATATTCTA
1 AAATTTTA
*
4253042 AAA-CTTA
1 AAATTTTA
4253049 AAATTTT
1 AAATTTT
4253056 TTGTGAGATA
Statistics
Matches: 76, Mismatches: 24, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
7 9 0.12
8 38 0.50
9 29 0.38
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (8 bp):
AAATTTTA
Found at i:4252987 original size:26 final size:24
Alignment explanation
Indices: 4252933--4253018 Score: 75
Period size: 26 Copynumber: 3.5 Consensus size: 24
4252923 TTTAAGTTTA
*
4252933 AAAATATTCAAATTTAAAAATTTT
1 AAAATATTAAAATTTAAAAATTTT
* *
4252957 TAAATATATAAAATTTGAAAACTTTT
1 AAAATAT-TAAAATTT-AAAAATTTT
* * *
4252983 AAAATTTTTAAAATTTACATATTTT
1 AAAA-TATTAAAATTTAAAAATTTT
*
4253008 GAAAT-TTAAAA
1 AAAATATTAAAA
4253019 ACTTCTCAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
23 6 0.12
24 7 0.14
25 16 0.32
26 19 0.38
27 2 0.04
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.43
Consensus pattern (24 bp):
AAAATATTAAAATTTAAAAATTTT
Found at i:4254592 original size:5 final size:5
Alignment explanation
Indices: 4254578--4254644 Score: 52
Period size: 5 Copynumber: 13.8 Consensus size: 5
4254568 GAAGTGGACA
* * *
4254578 AAAAG AAAAAG AAAAAG AAAAG GAAAG -AAAG AAAAG AAAAG -TAAG AAAAT
1 AAAAG -AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
*
4254628 AAAA- AAAAT AAAA- AAAA
1 AAAAG AAAAG AAAAG AAAA
4254645 CAAACTTTTC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
4 15 0.28
5 28 0.52
6 11 0.20
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (5 bp):
AAAAG
Found at i:4254631 original size:14 final size:14
Alignment explanation
Indices: 4254579--4254644 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
4254569 AAGTGGACAA
*
4254579 AAAGAAAA-AGAA-
1 AAAGAAAAGAAAAG
*
4254591 AAAGAAAAGGAAAG
1 AAAGAAAAGAAAAG
4254605 AAAGAAAAGAAAAG
1 AAAGAAAAGAAAAG
* * *
4254619 TAAGAAAATAAAAA
1 AAAGAAAAGAAAAG
*
4254633 AAATAAAA-AAAA
1 AAAGAAAAGAAAA
4254645 CAAACTTTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
12 8 0.18
13 6 0.14
14 30 0.68
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:4258645 original size:65 final size:65
Alignment explanation
Indices: 4258475--4258675 Score: 260
Period size: 65 Copynumber: 3.1 Consensus size: 65
4258465 GGCAGGGAGT
* * * ** *
4258475 TTATCTTTCGTGTCATGACAAGCAATTACAATAAAATATTTTAATGATCTGTCTCCTCTGT-GTG
1 TTATCTCTCGTGTCATGACAAGCAATTACAATCAAATATTTTGATGATCCATCTCCTCTGTCG-A
4258539 G
65 G
* *
4258540 TTTTATCTCTTGTGTCATGACAAGCAGTTACAATCAAATATTTTGATGATCCATCTCCTCTGTCG
1 --TTATCTCTCGTGTCATGACAAGCAATTACAATCAAATATTTTGATGATCCATCTCCTCTGTCG
4258605 AG
64 AG
* * * *
4258607 TTATGTCTCGTGTCATGACAAGCAATTACAACCGAATATTTTGATGATCCATCTCCTTTGTCGAG
1 TTATCTCTCGTGTCATGACAAGCAATTACAATCAAATATTTTGATGATCCATCTCCTCTGTCGAG
4258672 TTAT
1 TTAT
4258676 ATGTTTAGTG
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
65 63 0.53
67 55 0.46
68 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (65 bp):
TTATCTCTCGTGTCATGACAAGCAATTACAATCAAATATTTTGATGATCCATCTCCTCTGTCGAG
Found at i:4271545 original size:52 final size:52
Alignment explanation
Indices: 4271425--4271580 Score: 183
Period size: 52 Copynumber: 3.0 Consensus size: 52
4271415 TATAACCATA
* * * * * *
4271425 CAAATTTACCCATTAAGAATCCCTCTCCTCTTAGAA-TCTTCTCCTGTAAGT
1 CAAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTTTCTTGCAAGT
** *
4271476 CAAACTTGTCTATTAAGAATCCCTTTCCTTTTAGAATTCTTTTCTTGCAAGT
1 CAAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTTTCTTGCAAGT
*
4271528 CAAACTTACCTATTAAGAATCCCCTTT-CTCTTAAAATTCTTCTT-TTGCAAGT
1 CAAACTTACCTATTAAGAAT-CCCTTTCCTCTTAGAATTCTT-TTCTTGCAAGT
4271580 C
1 C
4271581 TTCTTGTCCA
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
51 30 0.34
52 51 0.57
53 8 0.09
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.40
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTTTCTTGCAAGT
Found at i:4271951 original size:25 final size:25
Alignment explanation
Indices: 4271887--4271989 Score: 109
Period size: 25 Copynumber: 4.2 Consensus size: 25
4271877 TTAAATTTTT
** *
4271887 AGCTCTTCCCACATCTCGAACTTTC
1 AGCTCTTTTCACATCTCGAACCTTC
4271912 AGCTC-TTTCACATCTCGAACCTTC
1 AGCTCTTTTCACATCTCGAACCTTC
* * *
4271936 AGCTCTTTTCATATCTTGAATCTTC
1 AGCTCTTTTCACATCTCGAACCTTC
** * *
4271961 AATTCTTCTCACATTTCGAACCTTC
1 AGCTCTTTTCACATCTCGAACCTTC
4271986 AGCT
1 AGCT
4271990 TTGATACCAT
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
24 21 0.34
25 41 0.66
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.38
Consensus pattern (25 bp):
AGCTCTTTTCACATCTCGAACCTTC
Found at i:4272023 original size:31 final size:31
Alignment explanation
Indices: 4271985--4272069 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
4271975 TTCGAACCTT
4271985 CAGCTTTGATACCATTTGTTGGGGAACACCA
1 CAGCTTTGATACCATTTGTTGGGGAACACCA
*
4272016 CAGCTTTGATACCATTTGTTGGGGATCACCA
1 CAGCTTTGATACCATTTGTTGGGGAACACCA
* *
4272047 CAGCTCTGATATCATTTGTTGGG
1 CAGCTTTGATACCATTTGTTGGG
4272070 CTAAAAGCCT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (31 bp):
CAGCTTTGATACCATTTGTTGGGGAACACCA
Found at i:4272711 original size:52 final size:51
Alignment explanation
Indices: 4272555--4272711 Score: 163
Period size: 52 Copynumber: 3.0 Consensus size: 51
4272545 TATAACCATA
* * * * **
4272555 CAAACTTGCATATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAAT-CCTTTTCTCTTAGAATTCTTTTTTTGTAAGT
* * * * *
4272607 CAAACTTGTCTATTAAAAATCCCTTTCTTTTTAGAATT-TTTTTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCTTTTC-TCTTAGAATTCTTTTT-TTGTAAGT
*
4272659 CAAACTTACCTATTAAGAATCTCTTTTCTCTTAGAATTCTTTTTTTGTAAGT
1 CAAACTTGCCTATTAAGAATC-CTTTTCTCTTAGAATTCTTTTTTTGTAAGT
4272711 C
1 C
4272712 TTCTTGTCCA
Statistics
Matches: 84, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
51 7 0.08
52 67 0.80
53 10 0.12
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCTTTTCTCTTAGAATTCTTTTTTTGTAAGT
Found at i:4274759 original size:27 final size:27
Alignment explanation
Indices: 4274729--4274782 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
4274719 TTAGAATATA
4274729 TTTAAAATATTAAT-ATAAA-ATTAATTT
1 TTTAAAAT-TTAATCATAAATA-TAATTT
*
4274756 TTTAATATTTAATCATAAATATAATTT
1 TTTAAAATTTAATCATAAATATAATTT
4274783 AATATTACAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.21
27 18 0.75
28 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TTTAAAATTTAATCATAAATATAATTT
Found at i:4276731 original size:62 final size:62
Alignment explanation
Indices: 4276634--4276761 Score: 193
Period size: 62 Copynumber: 2.1 Consensus size: 62
4276624 CTAAGAATGA
4276634 AAAGCAAGTTAAACAGCTATATTGCTCTCACATGCCACCCTAATTTGTCTGTCCACATAACG
1 AAAGCAAGTTAAACAGCTATATTGCTCTCACATGCCACCCTAATTTGTCTGTCCACATAACG
* * * * * * *
4276696 AAAGCAAGTTTAACAGCTTTATTGCTCTTATATGCCACCCTAATTTGTCTGTTCACTTAATG
1 AAAGCAAGTTAAACAGCTATATTGCTCTCACATGCCACCCTAATTTGTCTGTCCACATAACG
4276758 AAAG
1 AAAG
4276762 TAACGAGTGT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.32
Consensus pattern (62 bp):
AAAGCAAGTTAAACAGCTATATTGCTCTCACATGCCACCCTAATTTGTCTGTCCACATAACG
Found at i:4277925 original size:19 final size:19
Alignment explanation
Indices: 4277901--4277937 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
4277891 CAACCAAGAT
4277901 AAAAGAAAA-ATAGAAATGG
1 AAAAGAAAATATA-AAATGG
4277920 AAAAGAAAATATAAAATG
1 AAAAGAAAATATAAAATG
4277938 AATACGGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (19 bp):
AAAAGAAAATATAAAATGG
Found at i:4280403 original size:18 final size:18
Alignment explanation
Indices: 4280369--4280407 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4280359 AGCAATAAAC
*
4280369 AAAAAAAAAAGATATAGA
1 AAAAAAAAAAGAGATAGA
4280387 AAAATAAAAAAG-GATAGA
1 AAAA-AAAAAAGAGATAGA
4280405 AAA
1 AAA
4280408 GGCAACCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (18 bp):
AAAAAAAAAAGAGATAGA
Found at i:4281346 original size:14 final size:13
Alignment explanation
Indices: 4281297--4281347 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
4281287 TTTATCTTTT
4281297 TTAATA-TTAAAA
1 TTAATATTTAAAA
* *
4281309 TTAATATATACAA
1 TTAATATTTAAAA
*
4281322 TT-ATTTTTAAAA
1 TTAATATTTAAAA
4281334 TATAATATTTAAAA
1 T-TAATATTTAAAA
4281348 AATTTAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
12 14 0.47
13 7 0.23
14 9 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAATATTTAAAA
Found at i:4282317 original size:21 final size:21
Alignment explanation
Indices: 4282292--4282341 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
4282282 TTAAGTTTAA
*
4282292 ATTTAATTGTGTGTAAAATTG
1 ATTTAATTGTATGTAAAATTG
** *
4282313 ATTTAATTGTATGTTGAATTT
1 ATTTAATTGTATGTAAAATTG
4282334 ATTTAATT
1 ATTTAATT
4282342 ATGATATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (21 bp):
ATTTAATTGTATGTAAAATTG
Found at i:4283154 original size:3 final size:3
Alignment explanation
Indices: 4283146--4283173 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4283136 TAAATACAAG
4283146 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4283174 GGCTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4305227 original size:15 final size:17
Alignment explanation
Indices: 4305209--4305241 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
4305199 TTTAGAATAA
4305209 ATTTTTTA-TTA-AATT
1 ATTTTTTAGTTATAATT
4305224 ATTTTTTAGTTATAATT
1 ATTTTTTAGTTATAATT
4305241 A
1 A
4305242 CAATAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTTTTTAGTTATAATT
Found at i:4320974 original size:23 final size:21
Alignment explanation
Indices: 4320931--4320977 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
4320921 GAATTAAAAT
*
4320931 TTTAAAAAAATCATAAATATA
1 TTTAAAAAAATCAAAAATATA
*
4320952 TTTAATAAAATCAAAAAATTATA
1 TTTAAAAAAATC-AAAAA-TATA
4320975 TTT
1 TTT
4320978 TATATTTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 4 0.18
23 7 0.32
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAAAAAAATCAAAAATATA
Found at i:4324404 original size:98 final size:98
Alignment explanation
Indices: 4324235--4324429 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
4324225 ATGATGGAAC
*
4324235 TGATGCATAGGAAATATGAAAGATGATCTTTGGAAGCGTTGAAGAAAAAGATGTAGATTCTTGCT
1 TGATGCATAGGAAATATGAAAGATGATCTTTGGAAGCGTTAAAGAAAAAGATGTAGATTCTTGCT
*
4324300 ATTATAGAATTTTTTACGTCACTAGAATAGAAA
66 ATTATAGAATTTTTTACGCCACTAGAATAGAAA
4324333 TGATGCATAGGAAATATGAAAGATGATCTTTGGAAGCGTTAAAGAAAAAGATGTAGATTCTTGCT
1 TGATGCATAGGAAATATGAAAGATGATCTTTGGAAGCGTTAAAGAAAAAGATGTAGATTCTTGCT
* *
4324398 ATTATAGAATTTTTTATGCCACTAGGATAGAA
66 ATTATAGAATTTTTTACGCCACTAGAATAGAA
4324430 TTTTGGTAGT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (98 bp):
TGATGCATAGGAAATATGAAAGATGATCTTTGGAAGCGTTAAAGAAAAAGATGTAGATTCTTGCT
ATTATAGAATTTTTTACGCCACTAGAATAGAAA
Found at i:4329577 original size:30 final size:30
Alignment explanation
Indices: 4329532--4329588 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
4329522 GAGATTTCAC
* *
4329532 ATCCTGAAACGGGAAACATAATTGATATAA
1 ATCCTCAAACAGGAAACATAATTGATATAA
4329562 ATCCTCAAACAGGAAACATAATTGATA
1 ATCCTCAAACAGGAAACATAATTGATA
4329589 CAACGATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.23
Consensus pattern (30 bp):
ATCCTCAAACAGGAAACATAATTGATATAA
Found at i:4337760 original size:20 final size:20
Alignment explanation
Indices: 4337725--4337765 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4337715 CGCCTTTGCG
*
4337725 TAGCCATCATGCCACTACCT
1 TAGCCATCATACCACTACCT
* *
4337745 TAGCCATCATATCACTCCCT
1 TAGCCATCATACCACTACCT
4337765 T
1 T
4337766 GTCCAGTTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.07, T:0.29
Consensus pattern (20 bp):
TAGCCATCATACCACTACCT
Found at i:4338677 original size:18 final size:18
Alignment explanation
Indices: 4338624--4338677 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
4338614 AATTTTTGAA
4338624 TTTTTTATATATTAT-TAT
1 TTTTTTATAT-TTATGTAT
4338642 TTTTGTTAT-TTTGA-GTAT
1 TTTT-TTATATTT-ATGTAT
4338660 TTTTTTATATTTATGTAT
1 TTTTTTATATTTATGTAT
4338678 GATAATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
17 7 0.23
18 20 0.65
19 4 0.13
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTTTTATATTTATGTAT
Found at i:4338786 original size:3 final size:3
Alignment explanation
Indices: 4338778--4338817 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
4338768 AAAAATGCTA
*
4338778 AAT AAT AAT AAT AAT AAT AAT -AT AAA AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4338818 AAATTAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4338807 original size:17 final size:17
Alignment explanation
Indices: 4338782--4338820 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
4338772 ATGCTAAATA
*
4338782 ATAATAATAATAATAAT
1 ATAAAAATAATAATAAT
4338799 ATAAAAATAATAATAAT
1 ATAAAAATAATAATAAT
4338816 A-AAAA
1 ATAAAA
4338821 TTAAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAATAATAATAAT
Found at i:4338807 original size:20 final size:20
Alignment explanation
Indices: 4338779--4338817 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4338769 AAAATGCTAA
*
4338779 ATAATAATAATAATAATAAT
1 ATAAAAATAATAATAATAAT
4338799 ATAAAAATAATAATAATAA
1 ATAAAAATAATAATAATAA
4338818 AAATTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAAAAATAATAATAATAAT
Found at i:4339152 original size:21 final size:22
Alignment explanation
Indices: 4339128--4339168 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4339118 CTAAACCTTT
*
4339128 CAAACCTTAAAAT-AAATCCCC
1 CAAACCCTAAAATCAAATCCCC
4339149 CAAACCCTAAAATCAAATCC
1 CAAACCCTAAAATCAAATCC
4339169 TTAAAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (22 bp):
CAAACCCTAAAATCAAATCCCC
Found at i:4339825 original size:92 final size:92
Alignment explanation
Indices: 4339668--4339852 Score: 343
Period size: 92 Copynumber: 2.0 Consensus size: 92
4339658 GGGGAGTCAA
4339668 GGTGATCTTATTATATTTAAGAATCAAATTTTAAATTTGCACTTCATTATCATACACAACATTTA
1 GGTGATCTTATTATATTTAAGAATCAAATTTTAAATTTGCACTTCATTATCATACACAACATTTA
*
4339733 TTGGCTTACATACATTTATTCGTTACT
66 TTAGCTTACATACATTTATTCGTTACT
* *
4339760 GGTGATCTTATTATATTTAAGAATCTAATTTTAAATTTGCACTTCATTATCATACATAACATTTA
1 GGTGATCTTATTATATTTAAGAATCAAATTTTAAATTTGCACTTCATTATCATACACAACATTTA
4339825 TTAGCTTACATACATTTATTCGTTACT
66 TTAGCTTACATACATTTATTCGTTACT
4339852 G
1 G
4339853 TTTGCACTTG
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (92 bp):
GGTGATCTTATTATATTTAAGAATCAAATTTTAAATTTGCACTTCATTATCATACACAACATTTA
TTAGCTTACATACATTTATTCGTTACT
Found at i:4344218 original size:26 final size:27
Alignment explanation
Indices: 4344189--4344241 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
4344179 AAAACCTCAG
4344189 ATTTTAA-AAATACGATAAAACAAAGT
1 ATTTTAAGAAATACGATAAAACAAAGT
* *
4344215 ATTTTAAGAAATATGATGAAACAAAGT
1 ATTTTAAGAAATACGATAAAACAAAGT
4344242 GTATTTCTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (27 bp):
ATTTTAAGAAATACGATAAAACAAAGT
Found at i:4352048 original size:110 final size:109
Alignment explanation
Indices: 4351771--4352556 Score: 754
Period size: 110 Copynumber: 7.2 Consensus size: 109
4351761 CTTATAGGTT
* * * * *
4351771 AGTCTTATTTA-TTTTCTTGACTTGCGGTTCAGTCCCAGTCATCATTAATATTTTACTCGTGGTT
1 AGTCTTTTTTATTTTTC-TAACTTGCGGTTCAGTCCCAGTCATCGTTAATCTTTGACTCGTGGTT
** * **
4351835 TAATCCTTATCATTTTTATAGTTT-TTGACTTATGGTTTAATTTC
65 TAATCCCAATCATTTTTATAGTTTCTTGACTTATGATTTAATCCC
* * * * *
4351879 AGTCTCTTTTATATTTT-TAACTTGCGGTTCAGTCTCAATCATCATTAATATTT-AGCTCGTGGT
1 AGTCTTTTTTAT-TTTTCTAACTTGCGGTTCAGTCCCAGTCATCGTTAATCTTTGA-CTCGTGGT
* *
4351942 TTAATCCCAATCATTTCTATAGTTTCTCTGACTTATGGTTTAATCCC
64 TTAATCCCAATCATTTTTATAGTTTCT-TGACTTATGATTTAATCCC
* *
4351989 AGTCTTTTTTATTTTTCTAACTTACGGTTCAGCCCCAGTCATCGTTAATCTTTGACTCGTGGTTT
1 AGTCTTTTTTATTTTTCTAACTTGCGGTTCAGTCCCAGTCATCGTTAATCTTTGACTCGTGGTTT
* * *
4352054 AATCCTAATCATTTTTATAGTTTTCCTGACTTATGATTTAATCCT
66 AATCCCAATCATTTTTATAG-TTTCTTGACTTATGATTTAATCCC
** * *
4352099 AGTCGCTTTTATTATTT-TGACTTGCGGTTTAGTCCCAG---TCGTTAATCTTTGACTCGTGGTT
1 AGTCTTTTTTATT-TTTCTAACTTGCGGTTCAGTCCCAGTCATCGTTAATCTTTGACTCGTGGTT
* * * *
4352160 CAA-CCTCGATCACTTTTATAGTTT-TTGACTTACGATTTAATCCC
65 TAATCC-CAATCATTTTTATAGTTTCTTGACTTATGATTTAATCCC
* * * * * *
4352204 AGTCTCTTTTATCTTTCTAACTTGCGGTTCAATCTCAGTCATCGTTAATATTTGGCTCGTGGTTT
1 AGTCTTTTTTATTTTTCTAACTTGCGGTTCAGTCCCAGTCATCGTTAATCTTTGACTCGTGGTTT
** * * * * *
4352269 AATCTTAGTTATTTCTATAGTTTCCCTGACTTACGATTTAATCCC
66 AATCCCAATCATTTTTATAGTTT-CTTGACTTATGATTTAATCCC
* * * *
4352314 AGT-TTCTTTTATTGTTCTAACTTACGG-TCAGTCCCAATCATCGTTAATCTTTGACTCGTGATT
1 AGTCTT-TTTTATTTTTCTAACTTGCGGTTCAGTCCCAGTCATCGTTAATCTTTGACTCGTGGTT
* * * *
4352377 TAACCCCGATCATTTTTATAGTTTCTTGACTT-TCGGTTTCATCCC
65 TAATCCCAATCATTTTTATAGTTTCTTGACTTAT-GATTTAATCCC
* * * * * * * * * * *
4352422 AGTCGTTTTTATTTTTTTGATTTACGATTTAATCCCAGTCGTCGTTAATCTTTGACTCGTGATTC
1 AGTCTTTTTTATTTTTCTAACTTGCGGTTCAGTCCCAGTCATCGTTAATCTTTGACTCGTGGTTT
* * **
4352487 AATCCCGATCATTTGTATAGTTTCTTGACTTACAATTTAATCCC
66 AATCCCAATCATTTTTATAGTTTCTTGACTTATGATTTAATCCC
* * *
4352531 GGATCGTTTTTATTTTT-TGACTTGCG
1 AG-TCTTTTTTATTTTTCTAACTTGCG
4352557 ATTTAGTCAC
Statistics
Matches: 562, Mismatches: 93, Indels: 45
0.80 0.13 0.06
Matches are distributed among these distances:
104 3 0.01
105 45 0.08
106 5 0.01
107 38 0.07
108 142 0.25
109 132 0.23
110 189 0.34
111 8 0.01
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.46
Consensus pattern (109 bp):
AGTCTTTTTTATTTTTCTAACTTGCGGTTCAGTCCCAGTCATCGTTAATCTTTGACTCGTGGTTT
AATCCCAATCATTTTTATAGTTTCTTGACTTATGATTTAATCCC
Found at i:4352561 original size:36 final size:36
Alignment explanation
Indices: 4352363--4352561 Score: 118
Period size: 36 Copynumber: 5.4 Consensus size: 36
4352353 ATCGTTAATC
* * * *
4352363 TTTGACTCGTGATTTAA-CCCCGATCATTTTTATAGTT
1 TTTGACTTGCGATTTAATCCCAGATCGTTTTTAT--TT
* * *
4352400 TCTTGACTTTCGGTTTCATCCCAG-TCGTTTTTATTTT
1 T-TTGACTTGCGATTTAATCCCAGATCGTTTTTA-TTT
* * ** * *
4352437 TTTGATTTACGATTTAATCCCAG-TCGTCGTTAATC
1 TTTGACTTGCGATTTAATCCCAGATCGTTTTTATTT
* * * *
4352472 TTTGACTCGTGATTCAATCCC-GATCATTTGTATAGTTT
1 TTTGACTTGCGATTTAATCCCAGATCGTTT-T-TA-TTT
* * * *
4352510 CTTGACTTACAATTTAATCCCGGATCGTTTTTATTT
1 TTTGACTTGCGATTTAATCCCAGATCGTTTTTATTT
4352546 TTTGACTTGCGATTTA
1 TTTGACTTGCGATTTA
4352562 GTCACTATTG
Statistics
Matches: 119, Mismatches: 35, Indels: 17
0.70 0.20 0.10
Matches are distributed among these distances:
34 1 0.01
35 20 0.17
36 42 0.35
37 8 0.07
38 36 0.30
39 12 0.10
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (36 bp):
TTTGACTTGCGATTTAATCCCAGATCGTTTTTATTT
Found at i:4352605 original size:109 final size:107
Alignment explanation
Indices: 4351778--4352658 Score: 644
Period size: 109 Copynumber: 8.1 Consensus size: 107
4351768 GTTAGTCTTA
* * * * * *
4351778 TTTATTTTCTTGACTTGCGGTTCAGTCCCAGTCATCATTAATATTTTACTCGTGGTTTAATC-CT
1 TTTATTTT-TTGACTTGCGATTTAGTCCCA-TCGTCGTTAATCTTTGACTCGTGGTTTAATCTC-
* * * **
4351842 TATCATTTTTATAGTTT-TTGACTTATGGTTTAATTTCAGTC-TCT
63 GATCATTTTTATAGTTTCTTGACTTACGATTTAATCCCAGTCGT-T
* * * * * * * *
4351886 TTTATATTTTTAACTTGCGGTTCAGTCTCAATCATCATTAATATTT-AGCTCGTGGTTTAATCCC
1 TTTAT-TTTTTGACTTGCGATTTAGTC-CCATCGTCGTTAATCTTTGA-CTCGTGGTTTAATCTC
* * * * *
4351950 AATCATTTCTATAGTTTCTCTGACTTATGGTTTAATCCCAGTCTTT
63 GATCATTTTTATAGTTTCT-TGACTTACGATTTAATCCCAGTCGTT
* * * * * *
4351996 TTTATTTTTCTAACTTACGGTTCAGCCCCAGTCATCGTTAATCTTTGACTCGTGGTTTAATC-CT
1 TTTATTTTT-TGACTTGCGATTTAGTCCCA-TCGTCGTTAATCTTTGACTCGTGGTTTAATCTC-
* * * * *
4352060 AATCATTTTTATAGTTTTCCTGACTTATGATTTAATCCTAGTCGCT
63 GATCATTTTTATAG-TTTCTTGACTTACGATTTAATCCCAGTCGTT
* * *
4352106 TTTATTATTTTGACTTGCGGTTTAGTCCCA--GTCGTTAATCTTTGACTCGTGGTTCAACCTCGA
1 TTTATT-TTTTGACTTGCGATTTAGTCCCATCGTCGTTAATCTTTGACTCGTGGTTTAATCTCGA
*
4352169 TCACTTTTATAGTTT-TTGACTTACGATTTAATCCCAGTC-TCT
65 TCATTTTTATAGTTTCTTGACTTACGATTTAATCCCAGTCGT-T
* * * * * * * * * *
4352211 TTTATCTTTCTAACTTGCGGTTCAATCTCAGTCATCGTTAATATTTGGCTCGTGGTTTAATCT-T
1 TTTAT-TTTTTGACTTGCGATTTAGTCCCA-TCGTCGTTAATCTTTGACTCGTGGTTTAATCTCG
* * * *
4352275 AGTTATTTCTATAGTTTCCCTGACTTACGATTTAATCCCAGT-TTCT
64 A-TCATTTTTATAGTTT-CTTGACTTACGATTTAATCCCAGTCGT-T
* * * * * * * * *
4352321 TTTATTGTTCTAACTTACG-GTCAGTCCCAATCATCGTTAATCTTTGACTCGTGATTTAACCCCG
1 TTTATT-TTTTGACTTGCGATTTAGTCCC-ATCGTCGTTAATCTTTGACTCGTGGTTTAATCTCG
* * *
4352385 ATCATTTTTATAGTTTCTTGACTTTCGGTTTCATCCCAGTCGTT
64 ATCATTTTTATAGTTTCTTGACTTACGATTTAATCCCAGTCGTT
* * * * * *
4352429 TTTATTTTTTTGATTTACGATTTAATCCCAGTCGTCGTTAATCTTTGACTCGTGATTCAATCCCG
1 TTTA-TTTTTTGACTTGCGATTTAGTCCCA-TCGTCGTTAATCTTTGACTCGTGGTTTAATCTCG
* * *
4352494 ATCATTTGTATAGTTTCTTGACTTACAATTTAATCCCGGATCGTT
64 ATCATTTTTATAGTTTCTTGACTTACGATTTAATCCCAG-TCGTT
* * * **
4352539 TTTATTTTTTGACTTGCGATTTAGTCACTATTGTCTTTAATCTTTGACTCACGGTTTAATCTCGA
1 TTTATTTTTTGACTTGCGATTTAGTC-CCATCGTCGTTAATCTTTGACTCGTGGTTTAATCTCGA
* ** *
4352604 TC-CTCAT-TA-TTTCTCTGACTTACGATTTAATCTCAGT--TT
65 TCATTTTTATAGTTTCT-TGACTTACGATTTAATCCCAGTCGTT
4352643 CTTTATTTTCTTGACT
1 -TTTATTTT-TTGACT
4352659 CATGATTCAA
Statistics
Matches: 644, Mismatches: 94, Indels: 72
0.80 0.12 0.09
Matches are distributed among these distances:
104 2 0.00
105 53 0.08
106 16 0.02
107 60 0.09
108 141 0.22
109 183 0.28
110 180 0.28
111 9 0.01
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (107 bp):
TTTATTTTTTGACTTGCGATTTAGTCCCATCGTCGTTAATCTTTGACTCGTGGTTTAATCTCGAT
CATTTTTATAGTTTCTTGACTTACGATTTAATCCCAGTCGTT
Found at i:4352670 original size:433 final size:432
Alignment explanation
Indices: 4351778--4352658 Score: 1057
Period size: 433 Copynumber: 2.0 Consensus size: 432
4351768 GTTAGTCTTA
* *
4351778 TTTATTTTCTTGACTTGCGGTTCAGTCCCAGTCATCATTAATATTTTACTCGTGGTTTAATCCTT
1 TTTATTTTCTTGACTTGCGGTTCAATCCCAGTCATCATTAATATTTGACTCGTGGTTTAATCCTT
* * * * ** * *
4351843 ATCATTTTTATAGTTTTTGACTTATGGTTTAATTTCAGTCTCTTTTATATTTTTAACTTGCGGTT
66 ATCATTTCTATAGTTTCTGACTTACGATTTAATCCCAGTCTCTTTTATATTTCTAACTTACGGTT
* * *
4351908 CAGTCTCAATCATCATTAATATTTAGCTCGTGGTTTAATCCCAATCATTTCTATAGTTTCTCTGA
131 CAGTCCCAATCATCATTAATATTTAGCTCGTGATTTAACCCCAATCATTTCTATAGTTTCTCTGA
* * *
4351973 CTTATGGTTTAATCCCAGTCTTTTTTATTTTTCTAACTTACGGTTCAGCCCCAGTCATCGTTAAT
196 CTTATGGTTTAATCCCAGTCGTTTTTATTTTTCTAACTTACGATTCAACCCCAGTCATCGTTAAT
* * * * ** *
4352038 CTTTGACTCGTGGTTTAATCCTAATCATTTTTATAGTTTTCCTGACTTATGATTTAATCCTAGTC
261 CTTTGACTCGTGATTCAATCCCAATCATTTGTATAGTTTTCCTGACTTACAATTTAATCCCAGTC
* **
4352103 GCTTTTATTATTTTGACTTGCGGTTTAGTCCCAGTCGTTAATCTTTGACTCGTGGTTCAACCTCG
326 GCTTTTATTATTTTGACTTGCGATTTAGTCCCAGTCGTTAATCTTTGACTCACGGTTCAACCTCG
* *
4352168 ATCACTTTTATAGTTTTTGACTTACGATTTAATCCCAGTCTCT
391 ATCACTATTATA-TTTCTGACTTACGATTTAATCCCAGTCTCT
* * * *
4352211 TTTATCTTTC-TAACTTGCGGTTCAATCTCAGTCATCGTTAATATTTGGCTCGTGGTTTAAT-CT
1 TTTAT-TTTCTTGACTTGCGGTTCAATCCCAGTCATCATTAATATTTGACTCGTGGTTTAATCCT
* *
4352274 TAGTTATTTCTATAGTTTCCCTGACTTACGATTTAATCCCAGTTTCTTTTAT-TGTTCTAACTTA
65 TA-TCATTTCTATAGTTT--CTGACTTACGATTTAATCCCAGTCTCTTTTATAT-TTCTAACTTA
* * * *
4352338 CGG-TCAGTCCCAATCATCGTTAATCTTT-GACTCGTGATTTAACCCCGATCATTTTTATAGTTT
126 CGGTTCAGTCCCAATCATCATTAATATTTAG-CTCGTGATTTAACCCCAATCATTTCTATAGTTT
* * * * * * *
4352401 CT-TGACTT-TCGGTTTCATCCCAGTCGTTTTTATTTTTTTGATTTACGATTTAATCCCAGTCGT
190 CTCTGACTTAT-GGTTTAATCCCAGTCGTTTTTATTTTTCTAACTTACGATTCAACCCCAGTCAT
* *
4352464 CGTTAATCTTTGACTCGTGATTCAATCCCGATCATTTGTATAG-TTTCTTGACTTACAATTTAAT
254 CGTTAATCTTTGACTCGTGATTCAATCCCAATCATTTGTATAGTTTTCCTGACTTACAATTTAAT
* * * *
4352528 CCCGGATCGTTTTTATT-TTTTGACTTGCGATTTAGTCACTATTGTCTTTAATCTTTGACTCACG
319 CCCAG-TCGCTTTTATTATTTTGACTTGCGATTTAGTC-CCA--GTCGTTAATCTTTGACTCACG
* * * *
4352592 GTTTAATCTCGATC-CTCATTAT-TTCTCTGACTTACGATTTAATCTCAGTTTC-
380 GTTCAACCTCGATCACT-ATTATATT-TCTGACTTACGATTTAATCCCAGTCTCT
4352644 TTTATTTTCTTGACT
1 TTTATTTTCTTGACT
4352659 CATGATTCAA
Statistics
Matches: 378, Mismatches: 56, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
432 49 0.13
433 174 0.46
434 84 0.22
435 71 0.19
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (432 bp):
TTTATTTTCTTGACTTGCGGTTCAATCCCAGTCATCATTAATATTTGACTCGTGGTTTAATCCTT
ATCATTTCTATAGTTTCTGACTTACGATTTAATCCCAGTCTCTTTTATATTTCTAACTTACGGTT
CAGTCCCAATCATCATTAATATTTAGCTCGTGATTTAACCCCAATCATTTCTATAGTTTCTCTGA
CTTATGGTTTAATCCCAGTCGTTTTTATTTTTCTAACTTACGATTCAACCCCAGTCATCGTTAAT
CTTTGACTCGTGATTCAATCCCAATCATTTGTATAGTTTTCCTGACTTACAATTTAATCCCAGTC
GCTTTTATTATTTTGACTTGCGATTTAGTCCCAGTCGTTAATCTTTGACTCACGGTTCAACCTCG
ATCACTATTATATTTCTGACTTACGATTTAATCCCAGTCTCT
Found at i:4352710 original size:104 final size:105
Alignment explanation
Indices: 4352587--4352814 Score: 291
Period size: 105 Copynumber: 2.2 Consensus size: 105
4352577 AATCTTTGAC
* * * *
4352587 TCACGGTTTAAT-CTCGATCCTCATTATTTCTCTGACTTACGATTTAATCTCAGTT-TCTTTA-T
1 TCACGGTTTAATCCT-GATCCTCAGTATTTCTCTAACTTACGATTTAATCCCA-TTCTATTTATT
* * ** * *
4352649 TTTCTTGACTCATGATTCAATCCTGATCTCTTTAGTTTTAAG
64 TTTCTTGACTCACGAATCAATCCCAATCTCTTTACTTCTAAG
* *
4352691 TCACGGTTTAATCCTGATCCTCAGTCTTTCTCTAACTTGCGATTTAATCCCATTCTATTTATTTT
1 TCACGGTTTAATCCTGATCCTCAGTATTTCTCTAACTTACGATTTAATCCCATTCTATTTATTTT
*
4352756 TTTTGACTCACGAATCAATCCCAATCTCTTTACTTCTAAG
66 TCTTGACTCACGAATCAATCCCAATCTCTTTACTTCTAAG
*
4352796 TCACGGTTTAATCCCGATC
1 TCACGGTTTAATCCTGATC
4352815 GTTGTTCTTT
Statistics
Matches: 107, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
103 2 0.02
104 49 0.46
105 56 0.52
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (105 bp):
TCACGGTTTAATCCTGATCCTCAGTATTTCTCTAACTTACGATTTAATCCCATTCTATTTATTTT
TCTTGACTCACGAATCAATCCCAATCTCTTTACTTCTAAG
Found at i:4352863 original size:105 final size:103
Alignment explanation
Indices: 4352587--4352862 Score: 247
Period size: 105 Copynumber: 2.7 Consensus size: 103
4352577 AATCTTTGAC
* * * * ** * *
4352587 TCACGGTTTAATCTCGATCCTCATTATTTCTCTGACTTACGATTTAATCTCAGTT-TCTTTA-TT
1 TCACGGTTTAATCCCGA--CTCAGTCTTTCTCTAACTCGCGATTTAATCCCA-TTCTATTTATTT
* * * ** * *
4352650 TTCTTGACTCATGATTCAATCCTGATCTCTTTAGTTTTAAG
63 TTTTTGACTCACGAATCAATCCCAATCTCTTTACTTCTAAG
* *
4352691 TCACGGTTTAATCCTGATCCTCAGTCTTTCTCTAACTTGCGATTTAATCCCATTCTATTTATTTT
1 TCACGGTTTAATCCCGA--CTCAGTCTTTCTCTAACTCGCGATTTAATCCCATTCTATTTATTTT
4352756 TTTTGACTCACGAATCAATCCCAATCTCTTTACTTCTAAG
64 TTTTGACTCACGAATCAATCCCAATCTCTTTACTTCTAAG
* * * * *
4352796 TCACGGTTTAATCCCGA-TC-GT-TGTTCTTTGACTCGTGATTTAATCCCAGTCTTTTTTTATTT
1 TCACGGTTTAATCCCGACTCAGTCT-TTCTCTAACTCGCGATTTAATCCCA-T-TCTATTTATTT
4352858 TTTTT
63 TTTTT
4352863 TAACTTGTGA
Statistics
Matches: 145, Mismatches: 22, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
100 1 0.01
101 23 0.16
102 3 0.02
103 16 0.11
104 50 0.34
105 52 0.36
ACGTcount: A:0.20, C:0.22, G:0.11, T:0.47
Consensus pattern (103 bp):
TCACGGTTTAATCCCGACTCAGTCTTTCTCTAACTCGCGATTTAATCCCATTCTATTTATTTTTT
TTGACTCACGAATCAATCCCAATCTCTTTACTTCTAAG
Found at i:4354514 original size:3 final size:3
Alignment explanation
Indices: 4354508--4354550 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
4354498 AAAAATGCTA
* *
4354508 AAT AAT AAT AAT AAT AAT AAT -CT AA- AAA AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4354551 TGAATAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 3 0.09
3 32 0.91
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4354566 original size:25 final size:23
Alignment explanation
Indices: 4354508--4354558 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
4354498 AAAAATGCTA
4354508 AATAATAATAATAATAATAATCT
1 AATAATAATAATAATAATAATCT
*
4354531 AA-AAAAATAATAATAATAAT-T
1 AATAATAATAATAATAATAATCT
4354552 GAATAAT
1 -AATAAT
4354559 TAATTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.04
22 19 0.79
23 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (23 bp):
AATAATAATAATAATAATAATCT
Found at i:4354665 original size:3 final size:3
Alignment explanation
Indices: 4354657--4354687 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4354647 GGGGAATTAT
4354657 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4354688 AAAAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4355043 original size:14 final size:13
Alignment explanation
Indices: 4354995--4355045 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 13
4354985 CCTTCCAAGT
4354995 CCTAAAATTGAAA
1 CCTAAAATTGAAA
4355008 CTCTAAACATCT-AAA
1 C-CTAAA-AT-TGAAA
4355023 CCCTAAAATTGAAA
1 -CCTAAAATTGAAA
4355037 CCATAAAAT
1 CC-TAAAAT
4355046 CCAAAATGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 4 0.12
14 16 0.50
15 10 0.31
16 2 0.06
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.24
Consensus pattern (13 bp):
CCTAAAATTGAAA
Found at i:4356678 original size:25 final size:25
Alignment explanation
Indices: 4356607--4356681 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
4356597 ATTTAATAAA
* **
4356607 ATAAAATATATTTTTTATA-TTTAT
1 ATAAAATATAATTTAAATATTTTAT
* * **
4356631 ATAAATTATTATACATAAT-TTTTAT
1 ATAAAATATAATTTA-AATATTTTAT
4356656 ATAAAATATAATTTAAATATTTTAT
1 ATAAAATATAATTTAAATATTTTAT
4356681 A
1 A
4356682 CTATATAAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
24 12 0.32
25 25 0.68
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (25 bp):
ATAAAATATAATTTAAATATTTTAT
Found at i:4360788 original size:27 final size:27
Alignment explanation
Indices: 4360757--4360809 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
4360747 AGTTTTGGTA
4360757 TGTACAATAGAATCTTAAACGTTTTTG
1 TGTACAATAGAATCTTAAACGTTTTTG
4360784 TGTACAATAGAATCTTAAACGTTTTT
1 TGTACAATAGAATCTTAAACGTTTTT
4360810 ATTTGCTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (27 bp):
TGTACAATAGAATCTTAAACGTTTTTG
Found at i:4361216 original size:27 final size:27
Alignment explanation
Indices: 4361183--4361235 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
4361173 CAATAATATT
4361183 TTCAACATCATCATTATTGGAAAATAC
1 TTCAACATCATCATTATTGGAAAATAC
*
4361210 TTCAACATCGTCATTATTGGAAAATA
1 TTCAACATCATCATTATTGGAAAATA
4361236 GTTAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (27 bp):
TTCAACATCATCATTATTGGAAAATAC
Found at i:4364218 original size:2 final size:2
Alignment explanation
Indices: 4364211--4364251 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4364201 CTGTTTTTGT
4364211 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4364252 TCATTCAGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4364772 original size:24 final size:24
Alignment explanation
Indices: 4364741--4364878 Score: 177
Period size: 24 Copynumber: 5.8 Consensus size: 24
4364731 CCCCTATTAC
* *
4364741 TGCACCTGAGCCTTCCGGTCCTTT
1 TGCACCTGAGCCTTCCAGTCCTCT
*
4364765 TACACCTGAGCCTTCCAGTCCTCT
1 TGCACCTGAGCCTTCCAGTCCTCT
* * **
4364789 TGCACCCGAGCCTTCAAGTTGTCT
1 TGCACCTGAGCCTTCCAGTCCTCT
4364813 TGCACCTGAGCCTTCCAGTCCTCT
1 TGCACCTGAGCCTTCCAGTCCTCT
* * *
4364837 TGCACCTGAGCCTTCAAGTTCACT
1 TGCACCTGAGCCTTCCAGTCCTCT
*
4364861 TGCATCTGAGCCTTCCAG
1 TGCACCTGAGCCTTCCAG
4364879 GTCCCCTAGT
Statistics
Matches: 97, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 97 1.00
ACGTcount: A:0.15, C:0.37, G:0.18, T:0.30
Consensus pattern (24 bp):
TGCACCTGAGCCTTCCAGTCCTCT
Found at i:4364863 original size:72 final size:72
Alignment explanation
Indices: 4364741--4364875 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 72
4364731 CCCCTATTAC
* * * *
4364741 TGCACCTGAGCCTTCCGGTCCTTTTACACCTGAGCCTTCCAGTCCTCTTGCACCCGAGCCTTCAA
1 TGCACCTGAGCCTTCCAGTCCTCTTACACCTGAGCCTTCAAGTCCACTTGCACCCGAGCCTTCAA
4364806 GTTGTCT
66 GTTGTCT
* * * *
4364813 TGCACCTGAGCCTTCCAGTCCTCTTGCACCTGAGCCTTCAAGTTCACTTGCATCTGAGCCTTC
1 TGCACCTGAGCCTTCCAGTCCTCTTACACCTGAGCCTTCAAGTCCACTTGCACCCGAGCCTTC
4364876 CAGGTCCCCT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 55 1.00
ACGTcount: A:0.15, C:0.37, G:0.18, T:0.30
Consensus pattern (72 bp):
TGCACCTGAGCCTTCCAGTCCTCTTACACCTGAGCCTTCAAGTCCACTTGCACCCGAGCCTTCAA
GTTGTCT
Found at i:4368935 original size:24 final size:24
Alignment explanation
Indices: 4368882--4368935 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
4368872 CTGGTACCGT
*
4368882 AATATTCGATTTAAATAAAATTTT
1 AATATTCGATTTAAATAAAATTTA
** * *
4368906 TTTATTCGATTTGAATTAAATTTA
1 AATATTCGATTTAAATAAAATTTA
4368930 AATATT
1 AATATT
4368936 AAATATTACT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (24 bp):
AATATTCGATTTAAATAAAATTTA
Found at i:4371784 original size:29 final size:28
Alignment explanation
Indices: 4371751--4371828 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 28
4371741 AAAAGATTTA
4371751 AATATTTTAAAGATTTAATTAGAT-AAAAT
1 AATATTTTAAA-ATTTAATTA-ATAAAAAT
* *
4371780 AATATTTCAAAAACTTAATTTAATAAAAAT
1 AATATTT-TAAAATTTAA-TTAATAAAAAT
* *
4371810 ATTACTTTAAAATTTAATT
1 AATATTTTAAAATTTAATT
4371829 TAAATACGAC
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
28 2 0.05
29 22 0.55
30 16 0.40
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (28 bp):
AATATTTTAAAATTTAATTAATAAAAAT
Found at i:4375403 original size:2 final size:2
Alignment explanation
Indices: 4375390--4375429 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
4375380 AGGCCTGGCA
* *
4375390 AT AT AC AT AT AT AT AT AT AT AT AT AT AC 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
4375430 CATCATCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4377132 original size:12 final size:12
Alignment explanation
Indices: 4377115--4377147 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4377105 AAAAGTCAAT
4377115 AGTAAAAAAAAA
1 AGTAAAAAAAAA
*
4377127 AGTAAAAGAAAA
1 AGTAAAAAAAAA
4377139 A-TAAAAAAA
1 AGTAAAAAAA
4377148 TGAGGGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (12 bp):
AGTAAAAAAAAA
Found at i:4377144 original size:19 final size:19
Alignment explanation
Indices: 4377099--4377146 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
4377089 ACTTGTTTTG
* *
4377099 AAAAAAAAAAGTCAATAGT
1 AAAAAAAAAAGTCAAAAGA
4377118 AAAAAAAAAAGT-AAAAGA
1 AAAAAAAAAAGTCAAAAGA
4377136 AAAATAAAAAA
1 AAAA-AAAAAA
4377147 ATGAGGGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.10
Consensus pattern (19 bp):
AAAAAAAAAAGTCAAAAGA
Found at i:4377503 original size:45 final size:45
Alignment explanation
Indices: 4377417--4377503 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
4377407 TTTTATTTTG
* * * * *
4377417 TTCTGAGTTTGATTTGATTTACTTTTGGGTTTCCTGAATTTTAAT
1 TTCTAAGTTTGATTTCATTTACTGTTGAGTTTCCAGAATTTTAAT
*
4377462 TTCTAAGTTTGATTTCATTTTCTGTTGAGTTT-CAGAGATTTT
1 TTCTAAGTTTGATTTCATTTACTGTTGAGTTTCCAGA-ATTTT
4377504 TACTGGAGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.18, C:0.09, G:0.17, T:0.55
Consensus pattern (45 bp):
TTCTAAGTTTGATTTCATTTACTGTTGAGTTTCCAGAATTTTAAT
Found at i:4377690 original size:11 final size:11
Alignment explanation
Indices: 4377674--4377705 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
4377664 TTACATGTTT
4377674 TTTTTATTTTC
1 TTTTTATTTTC
4377685 TTTTTATTTTC
1 TTTTTATTTTC
4377696 TTTTTATTTT
1 TTTTTATTTT
4377706 TTGATTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTATTTTC
Found at i:4377707 original size:19 final size:19
Alignment explanation
Indices: 4377680--4377732 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
4377670 GTTTTTTTTA
* *
4377680 TTTTCTTTTTATTTT-CTT
1 TTTTTTTTTTATTTTGATT
*
4377698 TTTATTTTTTGATTTTGATT
1 TTT-TTTTTTTATTTTGATT
*
4377718 TTTTTTCTTTATTTT
1 TTTTTTTTTTATTTT
4377733 TTTACTTCGT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (19 bp):
TTTTTTTTTTATTTTGATT
Found at i:4377745 original size:26 final size:27
Alignment explanation
Indices: 4377698--4377762 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
4377688 TTATTTTCTT
* * *
4377698 TTTATTTTTTGATTTTGATTTTTTTTC
1 TTTATTTTTTGACTTCGATTTTTATTC
*
4377725 TTTATTTTTTTACTTCG-TTTTTATTC
1 TTTATTTTTTGACTTCGATTTTTATTC
4377751 TCTTATTTTTTG
1 T-TTATTTTTTG
4377763 TATTTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 9 0.28
27 23 0.72
ACGTcount: A:0.11, C:0.08, G:0.06, T:0.75
Consensus pattern (27 bp):
TTTATTTTTTGACTTCGATTTTTATTC
Found at i:4377905 original size:21 final size:20
Alignment explanation
Indices: 4377879--4377935 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
4377869 AATTAATTTT
*
4377879 CATGATATTTCATCTTAATTA
1 CATGATATTT-ATATTAATTA
*
4377900 CATGATAGTTTATATTAATTG
1 CATGATA-TTTATATTAATTA
4377921 CATGATA-TTATATTA
1 CATGATATTTATATTA
4377936 TTATTTGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.24
21 22 0.67
22 3 0.09
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (20 bp):
CATGATATTTATATTAATTA
Found at i:4377943 original size:22 final size:21
Alignment explanation
Indices: 4377855--4377953 Score: 62
Period size: 21 Copynumber: 4.7 Consensus size: 21
4377845 GTGATTCATT
*
4377855 TTTGCATGATTATTA-AT-TAA
1 TTTGCATGA-TATTATATATTA
* *
4377875 TTTTCATGATATT-TCATCTTA
1 TTTGCATGATATTAT-ATATTA
* *
4377896 ATTACATGATAGTT-TATATTA
1 TTTGCATGATA-TTATATATTA
*
4377917 ATTGCATGATATTATATTATTA
1 TTTGCATGATATTATA-TATTA
**
4377939 TTTGCAAAATATTAT
1 TTTGCATGATATTAT
4377954 TTTGTACGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
19 4 0.06
20 12 0.19
21 28 0.44
22 20 0.31
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (21 bp):
TTTGCATGATATTATATATTA
Found at i:4382605 original size:22 final size:22
Alignment explanation
Indices: 4382580--4382626 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4382570 TTTCGAATGA
* * *
4382580 GAATTTTTAAAATTTTGGATGT
1 GAATCTTTAAAATTTTAGATAT
4382602 GAATCTTTAAAATTTTAGATAT
1 GAATCTTTAAAATTTTAGATAT
4382624 GAA
1 GAA
4382627 ACCCTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.45
Consensus pattern (22 bp):
GAATCTTTAAAATTTTAGATAT
Found at i:4382877 original size:15 final size:15
Alignment explanation
Indices: 4382838--4382881 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
4382828 TTATATATGA
4382838 AATTTTAAATCATTTG
1 AATTTTAAATC-TTTG
**
4382854 AA-TGCAAATCTTTG
1 AATTTTAAATCTTTG
4382868 AATTTTAAATCTTT
1 AATTTTAAATCTTT
4382882 ACAAATTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 6 0.26
15 15 0.65
16 2 0.09
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (15 bp):
AATTTTAAATCTTTG
Found at i:4383270 original size:64 final size:64
Alignment explanation
Indices: 4383199--4383322 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 64
4383189 GAAATTCAAA
* * * * *
4383199 TATTTGATTTCTTTTGAACTTGAAATTTTTGCAAATATGAGTTCTTACAAATATGAAATTTGAG
1 TATTTGATTTCTTGTGAACCTAAAATTCTTGCAAATATAAGTTCTTACAAATATGAAATTTGAG
* * * *
4383263 TATTTGATTTCTTGTGATCCTAAAATTCTTGCGAATCTAAGTTCTTACAAATTTGAAATT
1 TATTTGATTTCTTGTGAACCTAAAATTCTTGCAAATATAAGTTCTTACAAATATGAAATT
4383323 CAAAATTTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (64 bp):
TATTTGATTTCTTGTGAACCTAAAATTCTTGCAAATATAAGTTCTTACAAATATGAAATTTGAG
Found at i:4384746 original size:19 final size:20
Alignment explanation
Indices: 4384710--4384751 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
4384700 TGATCACAGG
* *
4384710 TTTTCTTATTTTC-TTTTTA
1 TTTTCTAATTTTCATTTTGA
*
4384729 TTTTCTAATTTTGATTTTGA
1 TTTTCTAATTTTCATTTTGA
4384749 TTT
1 TTT
4384752 GATTTGATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTCTAATTTTCATTTTGA
Found at i:4384839 original size:28 final size:28
Alignment explanation
Indices: 4384808--4384869 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
4384798 ATATTTTTCG
4384808 TATTTAATTT-TTGCATGATATGATT-ATA
1 TATTTAATTTATTGCATGAT-T-ATTGATA
*
4384836 TATTTTATTTAATTGCATGATTATTGATA
1 TATTTAATTT-ATTGCATGATTATTGATA
4384865 TATTT
1 TATTT
4384870 GTTAACATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 12 0.40
29 9 0.30
30 9 0.30
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (28 bp):
TATTTAATTTATTGCATGATTATTGATA
Found at i:4384950 original size:21 final size:21
Alignment explanation
Indices: 4384915--4384973 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
4384905 ATGATTATTA
*
4384915 ATTAATTTGCATGATATTTTAT
1 ATTAA-TTACATGATATTTTAT
* *
4384937 CTTAATTACATGATAGTTTAT
1 ATTAATTACATGATATTTTAT
*
4384958 ATTAATTGCATGATAT
1 ATTAATTACATGATAT
4384974 CATATTGTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (21 bp):
ATTAATTACATGATATTTTAT
Found at i:4384986 original size:21 final size:21
Alignment explanation
Indices: 4384957--4385016 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
4384947 TGATAGTTTA
4384957 TATTAATTGCATGATATCATAT
1 TATT-ATTGCATGATATCATAT
* *
4384979 TGTTATTGCATGATATTATAT
1 TATTATTGCATGATATCATAT
*
4385000 TATTATTTGCATAATAT
1 TATTA-TTGCATGATAT
4385017 TATTTTGCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 20 0.61
22 13 0.39
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (21 bp):
TATTATTGCATGATATCATAT
Found at i:4385004 original size:43 final size:43
Alignment explanation
Indices: 4384909--4385016 Score: 105
Period size: 42 Copynumber: 2.5 Consensus size: 43
4384899 TTTTGCATGA
**
4384909 TTATTAATTAATTTGCATGATATTTTATCTTAATTACATGATAGT
1 TTATT-ATTAA-TTGCATGATATCATATCTTAATTACATGATAGT
* *
4384954 TTA-TATTAATTGCATGATATCATAT-TGTTATTGCATGATA-T
1 TTATTATTAATTGCATGATATCATATCT-TAATTACATGATAGT
* *
4384995 TATATTATTATTTGCATAATAT
1 T-TATTATTAATTGCATGATAT
4385017 TATTTTGCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
41 3 0.06
42 27 0.50
43 20 0.37
44 1 0.02
45 3 0.06
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.51
Consensus pattern (43 bp):
TTATTATTAATTGCATGATATCATATCTTAATTACATGATAGT
Found at i:4385047 original size:19 final size:18
Alignment explanation
Indices: 4384997--4385048 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
4384987 CATGATATTA
4384997 TATTATTATTTGCATAATAT
1 TATT-TTATTTG-ATAATAT
** *
4385017 TATTTTGCTTGATAATTTT
1 TATTTTATTTGATAA-TAT
4385036 TATTTTATTTGAT
1 TATTTTATTTGAT
4385049 TTTTTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.62
Consensus pattern (18 bp):
TATTTTATTTGATAATAT
Found at i:4385201 original size:104 final size:103
Alignment explanation
Indices: 4385097--4385428 Score: 313
Period size: 104 Copynumber: 3.2 Consensus size: 103
4385087 ATTTACAATC
4385097 TTACCAAACTATTGGAGTACATAATAAATTTTTTAAATAAAATAAAATAATAAATATTTTTAATT
1 TTACCAAACTATTGGAGTACATAATAAATTTTTTAAATAAAATAAAATAATAAATATTTTTAATT
*
4385162 CTATTAAACTATTAGAGAATCAAAATTTTGAATTAAATC
66 CTATTAAACTATT-GAGAATCAAAATTTTGAATTAAATA
* ** * * * *
4385201 TTAGCAAACTATTGGAAG-ATTTAATATATTTTCTCAAAGTAAAAT---TTTATAAATGATTTTT
1 TTACCAAACTATTGG-AGTACATAATAAATTTT-TTAAA-TAAAATAAAATAATAAAT-ATTTTT
* * * * *
4385262 AAATAAAATCTCATCAAACTATT--GAA--AGATTTGTATCAAAGTAAAATA
62 -AAT----TCT-ATTAAACTATTGAGAATCAAAATT-T-T-GAA-TTAAATA
* *
4385310 TTACCAAACTATTGGAGTACATAATGAATTTTTTAAATAAAATAAAATAATATAT-TTTTTAATT
1 TTACCAAACTATTGGAGTACATAATAAATTTTTTAAATAAAATAAAATAATAAATATTTTTAATT
4385374 CTATTAAACTATTGGAGAATCAAAATTTTGAATTAAATA
66 CTATTAAACTATT-GAGAATCAAAATTTTGAATTAAATA
*
4385413 TTAGCAAACTATTGGA
1 TTACCAAACTATTGGA
4385429 AGATTTAATA
Statistics
Matches: 177, Mismatches: 28, Indels: 47
0.70 0.11 0.19
Matches are distributed among these distances:
102 10 0.06
103 31 0.18
104 33 0.19
105 17 0.10
106 8 0.05
107 17 0.10
108 13 0.07
109 32 0.18
110 16 0.09
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (103 bp):
TTACCAAACTATTGGAGTACATAATAAATTTTTTAAATAAAATAAAATAATAAATATTTTTAATT
CTATTAAACTATTGAGAATCAAAATTTTGAATTAAATA
Found at i:4385444 original size:103 final size:104
Alignment explanation
Indices: 4385101--4385457 Score: 324
Period size: 103 Copynumber: 3.4 Consensus size: 104
4385091 ACAATCTTAC
* *
4385101 CAAACTATTGGAGTACATAATAAATTTT-TTAAA-TAAAATAAAATAATAAATATTTTTAATTCT
1 CAAACTATTGGAGTACATAATATATTTTCTTAAAGTAAAATAAAATAATATAT-TTTTTAATTCT
*
4385164 ATTAAACTATTAGAGAATCAAAATTTTGAATTAAATCTTAG
65 ATTAAACTATT-GAGAATCAAAATTTTGAATTAAATATTAG
** * ***
4385205 CAAACTATTGGAAG-ATTTAATATATTTTCTCAAAGTAAAATTTTATAA-ATGATTTTTAAATAA
1 CAAACTATTGG-AGTACATAATATATTTTCTTAAAGTAAAATAAAATAATAT-ATTTTT---T-A
* * * * * * *
4385268 AATCTCATCAAACTATT--GAA--AGATTTGTATCAAAGTAAAATATTAC
60 ATTCT-ATTAAACTATTGAGAATCAAAATT-T-T-GAA-TTAAATATTAG
4385314 CAAACTATTGGAGTACATAATGA-ATTTT-TTAAA-TAAAATAAAATAATATATTTTTTAATTCT
1 CAAACTATTGGAGTACATAAT-ATATTTTCTTAAAGTAAAATAAAATAATATATTTTTTAATTCT
4385376 ATTAAACTATTGGAGAATCAAAATTTTGAATTAAATATTAG
65 ATTAAACTATT-GAGAATCAAAATTTTGAATTAAATATTAG
**
4385417 CAAACTATTGGAAG-ATTTAATATATTTTCTTAAAGTAAAAT
1 CAAACTATTGG-AGTACATAATATATTTTCTTAAAGTAAAAT
4385458 TTTATAAATA
Statistics
Matches: 197, Mismatches: 31, Indels: 49
0.71 0.11 0.18
Matches are distributed among these distances:
102 11 0.06
103 35 0.18
104 32 0.16
105 25 0.13
106 14 0.07
107 24 0.12
108 11 0.06
109 34 0.17
110 11 0.06
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (104 bp):
CAAACTATTGGAGTACATAATATATTTTCTTAAAGTAAAATAAAATAATATATTTTTTAATTCTA
TTAAACTATTGAGAATCAAAATTTTGAATTAAATATTAG
Found at i:4385465 original size:212 final size:213
Alignment explanation
Indices: 4385097--4385534 Score: 779
Period size: 212 Copynumber: 2.1 Consensus size: 213
4385087 ATTTACAATC
4385097 TTACCAAACTATTGGAGTACATAATAAATTTTTTAAATAAAATAAAATAATAAATATTTTTAATT
1 TTACCAAACTATTGGAGTACATAATAAATTTTTTAAATAAAATAAAATAATAAATATTTTTAATT
*
4385162 CTATTAAACTATTAGAGAATCAAAATTTTGAATTAAATCTTAGCAAACTATTGGAAGATTTAATA
66 CTATTAAACTATTAGAGAATCAAAATTTTGAATTAAATATTAGCAAACTATTGGAAGATTTAATA
*
4385227 TATTTTCTCAAAGTAAAATTTTATAAATGATTTTTAAATAAAATCTCATCAAACTATTGAAAGAT
131 TATTTTCTCAAAGTAAAATTTTATAAATAATTTTTAAATAAAATCTCATCAAACTATTGAAAGAT
4385292 TTGTATCAAAGTAAAATA
196 TTGTATCAAAGTAAAATA
* *
4385310 TTACCAAACTATTGGAGTACATAATGAATTTTTTAAATAAAATAAAATAATATAT-TTTTTAATT
1 TTACCAAACTATTGGAGTACATAATAAATTTTTTAAATAAAATAAAATAATAAATATTTTTAATT
*
4385374 CTATTAAACTATTGGAGAATCAAAATTTTGAATTAAATATTAGCAAACTATTGGAAGATTTAATA
66 CTATTAAACTATTAGAGAATCAAAATTTTGAATTAAATATTAGCAAACTATTGGAAGATTTAATA
* * *
4385439 TATTTTCTTAAAGTAAAATTTTATAAATAATTTTTAAATAAAATCTTATCAAACTATTGAGAGAT
131 TATTTTCTCAAAGTAAAATTTTATAAATAATTTTTAAATAAAATCTCATCAAACTATTGAAAGAT
*
4385504 TTGTATCAAAGTAAAATC
196 TTGTATCAAAGTAAAATA
*
4385522 TTACCAAATTATT
1 TTACCAAACTATT
4385535 AAAAGATTTT
Statistics
Matches: 215, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
212 162 0.75
213 53 0.25
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (213 bp):
TTACCAAACTATTGGAGTACATAATAAATTTTTTAAATAAAATAAAATAATAAATATTTTTAATT
CTATTAAACTATTAGAGAATCAAAATTTTGAATTAAATATTAGCAAACTATTGGAAGATTTAATA
TATTTTCTCAAAGTAAAATTTTATAAATAATTTTTAAATAAAATCTCATCAAACTATTGAAAGAT
TTGTATCAAAGTAAAATA
Found at i:4385543 original size:109 final size:109
Alignment explanation
Indices: 4385196--4385543 Score: 333
Period size: 109 Copynumber: 3.2 Consensus size: 109
4385186 ATTTTGAATT
* * * *
4385196 AAATCTTAGCAAACTATTGGAAGATTTAATATATTTTCTCAAAGTAAAATTTTATAAATGATTTT
1 AAATATTACCAAACTATTGGAAGATTTAATATATTTTCTTAAAGTAAAATTTTATAAATAATTTT
* *
4385261 TAAATAAAATCTCATCAAACTATTGAAAGATTTGTATCAAAGTA
66 TAAATAAAATCTTATCAAACTATTGAGAGATTTGTATCAAAGTA
** ***
4385305 AAATATTACCAAACTATTGG-AGTACATAATGA-ATTTT-TTAAA-TAAAATAAAAT-AATATAT
1 AAATATTACCAAACTATTGGAAG-ATTTAAT-ATATTTTCTTAAAGTAAAATTTTATAAATA-AT
* * *** * ** *
4385365 TTTT---T-AATTC-TATTAAACTATTG-GAGAATCAAAATTTTGAA-TT
63 TTTTAAATAAAATCTTATCAAACTATTGAGAG-AT--TTGTATCAAAGTA
*
4385408 AAATATTAGCAAACTATTGGAAGATTTAATATATTTTCTTAAAGTAAAATTTTATAAATAATTTT
1 AAATATTACCAAACTATTGGAAGATTTAATATATTTTCTTAAAGTAAAATTTTATAAATAATTTT
4385473 TAAATAAAATCTTATCAAACTATTGAGAGATTTGTATCAAAGTA
66 TAAATAAAATCTTATCAAACTATTGAGAGATTTGTATCAAAGTA
* * **
4385517 AAATCTTACCAAATTATTAAAAGATTT
1 AAATATTACCAAACTATTGGAAGATTT
4385544 TGTTGATTAT
Statistics
Matches: 181, Mismatches: 40, Indels: 36
0.70 0.16 0.14
Matches are distributed among these distances:
101 2 0.01
102 14 0.08
103 34 0.19
104 12 0.07
105 14 0.08
106 7 0.04
107 14 0.08
108 11 0.06
109 55 0.30
110 15 0.08
111 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (109 bp):
AAATATTACCAAACTATTGGAAGATTTAATATATTTTCTTAAAGTAAAATTTTATAAATAATTTT
TAAATAAAATCTTATCAAACTATTGAGAGATTTGTATCAAAGTA
Found at i:4389053 original size:21 final size:23
Alignment explanation
Indices: 4389028--4389069 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4389018 AAACATGAAA
4389028 ATAAT-ATGATTTA-AAATTTTT
1 ATAATAATGATTTATAAATTTTT
*
4389049 ATAATAATTATTTATAAATTT
1 ATAATAATGATTTATAAATTT
4389070 AATAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATAATAATGATTTATAAATTTTT
Found at i:4389074 original size:22 final size:21
Alignment explanation
Indices: 4389027--4389074 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
4389017 AAAACATGAA
4389027 AATAATATGATTTAAAATTTT
1 AATAATATGATTTAAAATTTT
* *
4389048 TATAATAATTATTTATAAA-TTT
1 AATAAT-ATGATTTA-AAATTTT
4389070 AATAA
1 AATAA
4389075 AATAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 5 0.23
22 14 0.64
23 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AATAATATGATTTAAAATTTT
Found at i:4389078 original size:24 final size:24
Alignment explanation
Indices: 4389025--4389079 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
4389015 AAAAAACATG
*
4389025 AAAATAATATGATTTAAAATTTTT
1 AAAATAATATGATTTAAAATTTAT
*
4389049 ATAATAAT-T-ATTTATAAATTTAAT
1 AAAATAATATGATTTA-AAATTT-AT
4389073 AAAATAA
1 AAAATAA
4389080 AAAATTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 5 0.19
23 7 0.27
24 14 0.54
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
AAAATAATATGATTTAAAATTTAT
Found at i:4389168 original size:32 final size:33
Alignment explanation
Indices: 4389125--4389188 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
4389115 TTTATATAAA
* * *
4389125 ATATTATATAAATAAATTAA-TATTAATATTTT
1 ATATTACATAAATAAATAAATTATTAAGATTTT
*
4389157 ATATTACATAAATATATAAATTATTAAGATTT
1 ATATTACATAAATAAATAAATTATTAAGATTT
4389189 CAAAAGGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (33 bp):
ATATTACATAAATAAATAAATTATTAAGATTTT
Found at i:4390692 original size:13 final size:13
Alignment explanation
Indices: 4390676--4390701 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4390666 AGAAGGAACC
4390676 AAAAGGAAAAGGA
1 AAAAGGAAAAGGA
4390689 AAAAGGAAAAGGA
1 AAAAGGAAAAGGA
4390702 GGAAGACAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAAAGGAAAAGGA
Found at i:4391472 original size:2 final size:2
Alignment explanation
Indices: 4391465--4391494 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4391455 ATCCCTCGAG
4391465 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
4391495 TACATAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4400077 original size:2 final size:2
Alignment explanation
Indices: 4400070--4400104 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4400060 GGAACACCCA
4400070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4400105 TAATACTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4411738 original size:71 final size:70
Alignment explanation
Indices: 4411622--4411768 Score: 233
Period size: 71 Copynumber: 2.1 Consensus size: 70
4411612 GTAGGCATTT
* * *
4411622 TACTTTATAAGAAGAATTTGCTTTGTGTTGCTGTCTCTTCTGTAGATAGTCCTAATATTTTGTTA
1 TACTTTATAAGAAGAATTGGCTTTGTGTTGCTGCCTCTTCTGTAGATAGTCCTAACATTTTGTTA
4411687 CAATTG
66 CAA-TG
* *
4411693 TACTTTATAATAAGAATTGGCTTTGTGTTGCTGCCTCTTTTGTAGATAGTCCTAACATTTTGTTA
1 TACTTTATAAGAAGAATTGGCTTTGTGTTGCTGCCTCTTCTGTAGATAGTCCTAACATTTTGTTA
4411758 CAATG
66 CAATG
4411763 TA-TTTA
1 TACTTTA
4411769 GTCAATTTTG
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 4 0.06
70 4 0.06
71 63 0.89
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.46
Consensus pattern (70 bp):
TACTTTATAAGAAGAATTGGCTTTGTGTTGCTGCCTCTTCTGTAGATAGTCCTAACATTTTGTTA
CAATG
Found at i:4421023 original size:16 final size:16
Alignment explanation
Indices: 4420987--4421017 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4420977 TTTCATCACA
4420987 TTTATATTATTAATTC
1 TTTATATTATTAATTC
*
4421003 TTTATATTCTTAATT
1 TTTATATTATTAATT
4421018 ACTTATGTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATATTATTAATTC
Found at i:4438015 original size:2 final size:2
Alignment explanation
Indices: 4438008--4438036 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4437998 AAATCAATTG
4438008 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4438037 GTCTTCCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4439999 original size:21 final size:22
Alignment explanation
Indices: 4439942--4440009 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 22
4439932 AAAAAATATA
* *
4439942 AATATAATATAAATATAAATTTT
1 AATAAAATA-AAAAATAAATTTT
* *
4439965 AA-AAAATTATAAATAAA-TTT
1 AATAAAATAAAAAATAAATTTT
4439985 AATAAAATAAAAAATATATATTTT
1 AATAAAATAAAAAATA-A-ATTTT
4440009 A
1 A
4440010 TATTTTCGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
20 5 0.14
21 18 0.51
22 5 0.14
23 3 0.09
24 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAAAATAAAAAATAAATTTT
Found at i:4454043 original size:25 final size:25
Alignment explanation
Indices: 4454015--4454069 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
4454005 ATATTAAGTG
4454015 TATATATTCATGAATATATAAA-AAA
1 TATATATTCATGAATA-ATAAATAAA
* *
4454040 TATATGTTTATGAATAATAAATAAA
1 TATATATTCATGAATAATAAATAAA
4454065 T-TATA
1 TATATA
4454070 ATTAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (25 bp):
TATATATTCATGAATAATAAATAAA
Found at i:4454070 original size:14 final size:14
Alignment explanation
Indices: 4454053--4454094 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
4454043 ATGTTTATGA
4454053 ATAATAAATAAATT
1 ATAATAAATAAATT
4454067 ATAATTAAATAAATT
1 ATAA-TAAATAAATT
4454082 -TAAATAAATAAAT
1 AT-AATAAATAAAT
4454095 CTTAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAATAAATAAATT
Found at i:4454075 original size:11 final size:11
Alignment explanation
Indices: 4454056--4454157 Score: 51
Period size: 11 Copynumber: 9.8 Consensus size: 11
4454046 TTTATGAATA
4454056 ATAAATAAATT
1 ATAAATAAATT
*
4454067 ATAATTAAA-T
1 ATAAATAAATT
* *
4454077 A-AATTTAA--
1 ATAAATAAATT
4454085 ATAAATAAATCT
1 ATAAATAAAT-T
4454097 -TAAATAAA-T
1 ATAAATAAATT
4454106 ATAAATAAATT
1 ATAAATAAATT
* **
4454117 -CAAACGAA-T
1 ATAAATAAATT
4454126 ATAAATAAATT
1 ATAAATAAATT
*
4454137 TTAAAATAAGATT
1 AT-AAATAA-ATT
4454150 A-AAATAAA
1 ATAAATAAA
4454158 AAATATAATT
Statistics
Matches: 69, Mismatches: 12, Indels: 21
0.68 0.12 0.21
Matches are distributed among these distances:
8 1 0.01
9 13 0.19
10 21 0.30
11 25 0.36
12 6 0.09
13 3 0.04
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (11 bp):
ATAAATAAATT
Found at i:4454085 original size:25 final size:25
Alignment explanation
Indices: 4454056--4454121 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
4454046 TTTATGAATA
4454056 ATAAATAAATTATAA-TTAAATAAAT
1 ATAAATAAATTA-AACTTAAATAAAT
*
4454081 TTAAATAAA-TAAATCTTAAATAAAT
1 ATAAATAAATTAAA-CTTAAATAAAT
4454106 ATAAATAAATTCAAAC
1 ATAAATAAATT-AAAC
4454122 GAATATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
23 2 0.06
24 2 0.06
25 26 0.74
26 2 0.06
27 3 0.09
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (25 bp):
ATAAATAAATTAAACTTAAATAAAT
Found at i:4454099 original size:15 final size:14
Alignment explanation
Indices: 4454055--4454106 Score: 77
Period size: 15 Copynumber: 3.6 Consensus size: 14
4454045 GTTTATGAAT
4454055 AATAAATAAATTATA
1 AATAAATAAATT-TA
*
4454070 ATTAAATAAATTTA
1 AATAAATAAATTTA
4454084 AATAAATAAATCTTA
1 AATAAATAAAT-TTA
4454099 AATAAATA
1 AATAAATA
4454107 TAAATAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.35
15 22 0.65
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
AATAAATAAATTTA
Found at i:4454100 original size:21 final size:21
Alignment explanation
Indices: 4454085--4454141 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
4454075 ATAAATTTAA
4454085 ATAAATAAATCTTAAATAAAT
1 ATAAATAAATCTTAAATAAAT
* **
4454106 ATAAATAAAT-TCAAACGAAT
1 ATAAATAAATCTTAAATAAAT
*
4454126 ATAAATAAATTTTAAA
1 ATAAATAAATCTTAAA
4454142 ATAAGATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAAATAAATCTTAAATAAAT
Found at i:4454198 original size:11 final size:11
Alignment explanation
Indices: 4454182--4454222 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
4454172 TAATATTATT
*
4454182 ATAAATAAATA
1 ATAAATGAATA
4454193 ATAAATGAATA
1 ATAAATGAATA
*
4454204 ATAAGTGAATA
1 ATAAATGAATA
4454215 ATAAATGA
1 ATAAATGA
4454223 TAAACAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (11 bp):
ATAAATGAATA
Found at i:4459266 original size:23 final size:21
Alignment explanation
Indices: 4459239--4459286 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
4459229 TCTGATTCGA
*
4459239 TTTAAAATTAATAAAGTATTATT
1 TTTAAAA-T-ATAAAATATTATT
4459262 TTT-AAATATAAAATATTATT
1 TTTAAAATATAAAATATTATT
4459282 TTTAA
1 TTTAA
4459287 TGTAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 15 0.65
21 2 0.09
22 3 0.13
23 3 0.13
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTAAAATATAAAATATTATT
Found at i:4459292 original size:19 final size:20
Alignment explanation
Indices: 4459249--4459286 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4459239 TTTAAAATTA
*
4459249 ATAAAGTATTATTTTTAAAT
1 ATAAAATATTATTTTTAAAT
4459269 ATAAAATATTATTTTTAA
1 ATAAAATATTATTTTTAA
4459287 TGTAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATAAAATATTATTTTTAAAT
Found at i:4463371 original size:20 final size:20
Alignment explanation
Indices: 4463338--4463376 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4463328 ATATTTTTTG
*
4463338 TTAATAAATATATATTAATT
1 TTAATAAATATATAATAATT
* *
4463358 TTAATTAATCTATAATAAT
1 TTAATAAATATATAATAAT
4463377 AATTTATATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAATAAATATATAATAATT
Found at i:4465896 original size:21 final size:21
Alignment explanation
Indices: 4465870--4465909 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
4465860 AGCTAGGGGT
4465870 CTTACAAGGTCAAGAAAAGGC
1 CTTACAAGGTCAAGAAAAGGC
4465891 CTTACAAGGTCAAGAAAAG
1 CTTACAAGGTCAAGAAAAG
4465910 AATATGGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (21 bp):
CTTACAAGGTCAAGAAAAGGC
Found at i:4476369 original size:19 final size:19
Alignment explanation
Indices: 4476321--4476372 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
4476311 AAAAAAATCA
4476321 TAGAT-ATTTTGTACATTTTT
1 TAGATAATTTT-TA-ATTTTT
* *
4476341 AAG-TAGTTTTTAATTTTT
1 TAGATAATTTTTAATTTTT
4476359 TAGATAATTTTTAA
1 TAGATAATTTTTAA
4476373 AAGCTACATA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 8 0.31
19 12 0.46
20 6 0.23
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (19 bp):
TAGATAATTTTTAATTTTT
Found at i:4487999 original size:24 final size:24
Alignment explanation
Indices: 4487954--4487999 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
4487944 TATTATTCTT
*
4487954 TTATTATTATAATTAGTTTATAAG
1 TTATTATTATAATTAGTATATAAG
*
4487978 TTATGTATTA-AATTTGTATATA
1 TTAT-TATTATAATTAGTATATA
4488000 TTGTCATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (24 bp):
TTATTATTATAATTAGTATATAAG
Found at i:4491514 original size:46 final size:46
Alignment explanation
Indices: 4491447--4491672 Score: 172
Period size: 46 Copynumber: 5.0 Consensus size: 46
4491437 GGTTTTACAT
* * * *
4491447 CTCAAATATTCTCATTTGAAAATGTCTTAAAGGTTCTCATTT-AAGA
1 CTCAAAGATTCTCATTTGAAAACGTCGTAAAGATTCTCATTTGAA-A
*
4491493 CTCAAAGATGCTCATTTGAAAACGTCGTAAAGATTCTCATTTGAAA
1 CTCAAAGATTCTCATTTGAAAACGTCGTAAAGATTCTCATTTGAAA
* *
4491539 CTCAAAGATTCTCATTTG-AAAC-TC--AAAGATTTTCATTTAAAAATA
1 CTCAAAGATTCTCATTTGAAAACGTCGTAAAGATTCTCATTT--GAA-A
* *
4491584 TCTTAAAGATTCTTATTT-AAAAC-TC--AAAGATTCTCATTTGAAAATA
1 -CTCAAAGATTCTCATTTGAAAACGTCGTAAAGATTCTCATTTG--AA-A
* * *
4491630 TCTTAAAGATTTTCATTT-AAGAC-T--TAAAGATTCTCATTTGAAA
1 -CTCAAAGATTCTCATTTGAAAACGTCGTAAAGATTCTCATTTGAAA
4491673 ATGTCTTAAA
Statistics
Matches: 156, Mismatches: 15, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
42 13 0.08
43 1 0.01
44 6 0.04
45 5 0.03
46 129 0.83
47 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (46 bp):
CTCAAAGATTCTCATTTGAAAACGTCGTAAAGATTCTCATTTGAAA
Found at i:4491566 original size:67 final size:67
Alignment explanation
Indices: 4491475--4491719 Score: 214
Period size: 67 Copynumber: 3.6 Consensus size: 67
4491465 AAAATGTCTT
* * * *
4491475 AAAGGTTCTCATTT-AAGACTCAAAGATGCTCATTTGAAAACGTCGTAAAGATTCTCATTTGAAA
1 AAAGATTCTCATTTGAA-ACTCAAAGATGCTCATTTAAAAACATCGTAAAGATTCTCATTTAAAA
4491539 CTC
65 CTC
** * * *
4491542 AAAGATTCTCATTTGAAACTCAAAGATTTTCATTTAAAAATATCTTAAAGATTCTTATTTAAAAC
1 AAAGATTCTCATTTGAAACTCAAAGATGCTCATTTAAAAACATCGTAAAGATTCTCATTTAAAAC
4491607 TC
66 TC
* ** *
4491609 AAAGATTCTCATTTGAAAATATCTTAAAGATTTTCATTT-AAGAC-T--TAAAGATTCTCATTTG
1 AAAGATTCTCATTTG--AA-A-CTCAAAGATGCTCATTTAAAAACATCGTAAAGATTCTCATTT-
*
4491670 AAAATGTCTT
61 AAAA---CTC
* *
4491680 AAAGATTTTCATTT-AAGACTCAAAGATTCTCATTTAAAAA
1 AAAGATTCTCATTTGAA-ACTCAAAGATGCTCATTTAAAAA
4491720 TTTAAGACTT
Statistics
Matches: 149, Mismatches: 19, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
67 99 0.66
68 12 0.08
69 3 0.02
70 4 0.03
71 31 0.21
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (67 bp):
AAAGATTCTCATTTGAAACTCAAAGATGCTCATTTAAAAACATCGTAAAGATTCTCATTTAAAAC
TC
Found at i:4491646 original size:113 final size:115
Alignment explanation
Indices: 4491445--4491718 Score: 328
Period size: 113 Copynumber: 2.4 Consensus size: 115
4491435 GAGGTTTTAC
* * * * * *
4491445 ATCTCAAATATTCTCATTTGAAAATGTCTTAAAGGTTCTCATTTAAGACTCAAAGATGCTCATTT
1 ATCTCAAAGATTTTCATTTAAAAATATCTTAAAGATTCTCATTTAAAACTCAAAGATGCTCATTT
*
4491510 GAAAACGTCGTAAAGATTCTCATTTGAA-ACTCAAAGATTCTCATTTG-AA
66 GAAAACATCGTAAAGATTCTCATTT-AAGACTCAAAGATTCTCATTTGAAA
* *
4491559 A-CTCAAAGATTTTCATTTAAAAATATCTTAAAGATTCTTATTTAAAACTCAAAGATTCTCATTT
1 ATCTCAAAGATTTTCATTTAAAAATATCTTAAAGATTCTCATTTAAAACTCAAAGATGCTCATTT
* * * *
4491623 GAAAATATCTTAAAGATTTTCATTTAAGACTTAAAGATTCTCATTTGAAA
66 GAAAACATCGTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAA
* * *
4491673 ATGTCTTAAAGATTTTCATTT---AAGA-CTCAAAGATTCTCATTTAAAA
1 A--TCTCAAAGATTTTCATTTAAAAATATCTTAAAGATTCTCATTTAAAA
4491719 ATTTAAGACT
Statistics
Matches: 138, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
112 2 0.01
113 113 0.82
114 7 0.05
117 16 0.12
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (115 bp):
ATCTCAAAGATTTTCATTTAAAAATATCTTAAAGATTCTCATTTAAAACTCAAAGATGCTCATTT
GAAAACATCGTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAA
Found at i:4491673 original size:46 final size:46
Alignment explanation
Indices: 4491521--4491720 Score: 268
Period size: 46 Copynumber: 4.4 Consensus size: 46
4491511 AAAACGTCGT
* *
4491521 AAAGATTCTCATTTG--AA-A-CTCAAAGATTCTCATTTGAA-ACTC
1 AAAGATTCTCATTTGAAAATATCTTAAAGATTTTCATTT-AAGACTC
* * *
4491563 AAAGATTTTCATTTAAAAATATCTTAAAGATTCTT-ATTTAAAACTC
1 AAAGATTCTCATTTGAAAATATCTTAAAGATT-TTCATTTAAGACTC
*
4491609 AAAGATTCTCATTTGAAAATATCTTAAAGATTTTCATTTAAGACTT
1 AAAGATTCTCATTTGAAAATATCTTAAAGATTTTCATTTAAGACTC
*
4491655 AAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTTAAGACTC
1 AAAGATTCTCATTTGAAAATATCTTAAAGATTTTCATTTAAGACTC
*
4491701 AAAGATTCTCATTTAAAAAT
1 AAAGATTCTCATTTGAAAAT
4491721 TTAAGACTTC
Statistics
Matches: 140, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
42 13 0.09
44 2 0.01
45 5 0.04
46 119 0.85
47 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.39
Consensus pattern (46 bp):
AAAGATTCTCATTTGAAAATATCTTAAAGATTTTCATTTAAGACTC
Found at i:4491726 original size:21 final size:21
Alignment explanation
Indices: 4491454--4491718 Score: 206
Period size: 21 Copynumber: 11.7 Consensus size: 21
4491444 CATCTCAAAT
4491454 ATTCTCATTTGAAAATGTCTTAAAG
1 ATTCTCATTT-AAAA---CTTAAAG
* * *
4491479 GTTCTCATTTAAGACTCAAAG
1 ATTCTCATTTAAAACTTAAAG
*
4491500 ATGCTCATTTGAAAACGTCGTAAAG
1 ATTCTCATTT-AAAAC-T--TAAAG
* *
4491525 ATTCTCATTTGAAACTCAAAG
1 ATTCTCATTTAAAACTTAAAG
* *
4491546 ATTCTCATTTGAAACTCAAAG
1 ATTCTCATTTAAAACTTAAAG
*
4491567 ATTTTCATTTAAAAATATCTTAAAG
1 ATTCTCATTT--AAA-A-CTTAAAG
* *
4491592 ATTCTTATTTAAAACTCAAAG
1 ATTCTCATTTAAAACTTAAAG
4491613 ATTCTCATTTGAAAATATCTTAAAG
1 ATTCTCATTT--AAA-A-CTTAAAG
* *
4491638 ATTTTCATTTAAGACTTAAAG
1 ATTCTCATTTAAAACTTAAAG
4491659 ATTCTCATTTGAAAATGTCTTAAAG
1 ATTCTCATTT-AAAA---CTTAAAG
* * *
4491684 ATTTTCATTTAAGACTCAAAG
1 ATTCTCATTTAAAACTTAAAG
4491705 ATTCTCATTTAAAA
1 ATTCTCATTTAAAA
4491719 ATTTAAGACT
Statistics
Matches: 197, Mismatches: 27, Indels: 36
0.76 0.10 0.14
Matches are distributed among these distances:
21 97 0.49
22 9 0.05
23 12 0.06
24 12 0.06
25 67 0.34
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATTCTCATTTAAAACTTAAAG
Found at i:4491770 original size:159 final size:159
Alignment explanation
Indices: 4491447--4491752 Score: 424
Period size: 159 Copynumber: 1.9 Consensus size: 159
4491437 GGTTTTACAT
* * *
4491447 CTCAAATATTCTCATTTGAAAATGTCTTAAAGGTTCTCATTTAAGACTCAAAGATGCTCATTTGA
1 CTCAAAGATTCTCATTTGAAAATATCTTAAAGATTCTCATTTAAGACTCAAAGATGCTCATTTGA
* * *
4491512 AAACGTCGTAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTGAAACTCAAAGATTTTCATTT
66 AAACGTCGTAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTAAAAATCAAAGATCTTCATTT
*
4491577 AAAAATATCTTAAAGATTCTTATTTAAAA
131 AAAAATATCTCAAAGATTCTTATTTAAAA
* * *
4491606 CTCAAAGATTCTCATTTGAAAATATCTTAAAGATTTTCATTTAAGACTTAAAGATTCTCATTTGA
1 CTCAAAGATTCTCATTTGAAAATATCTTAAAGATTCTCATTTAAGACTCAAAGATGCTCATTTGA
* * * **
4491671 AAATGTCTTAAAGATTTTCATTT-AAGACTCAAAGATTCTCATTTAAAAATTTAAGA-CTTCA-T
66 AAACGTCGTAAAGATTCTCATTTGAA-ACTCAAAGATTCTCATTTAAAAATCAAAGATCTTCATT
*
4491733 T-AAAATAT-TCAAAGTTTCTT
130 TAAAAATATCTCAAAGATTCTT
4491753 TTCTAAATGG
Statistics
Matches: 130, Mismatches: 16, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
155 10 0.08
156 7 0.05
157 2 0.02
158 6 0.05
159 105 0.81
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (159 bp):
CTCAAAGATTCTCATTTGAAAATATCTTAAAGATTCTCATTTAAGACTCAAAGATGCTCATTTGA
AAACGTCGTAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTAAAAATCAAAGATCTTCATTT
AAAAATATCTCAAAGATTCTTATTTAAAA
Found at i:4493006 original size:8 final size:9
Alignment explanation
Indices: 4492988--4493048 Score: 79
Period size: 9 Copynumber: 6.4 Consensus size: 9
4492978 TTTTCTATCA
4492988 TTTTCATTT
1 TTTTCATTT
4492997 TTTTCATTTTT
1 TTTTCA--TTT
4493008 TTTTCATTTT
1 TTTTCA-TTT
4493018 TTTTCATTT
1 TTTTCATTT
4493027 TTTCTCA-TT
1 TTT-TCATTT
4493036 TTTTCATTT
1 TTTTCATTT
4493045 TTTT
1 TTTT
4493049 TCTTTTTCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
8 3 0.06
9 23 0.48
10 13 0.27
11 9 0.19
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCATTT
Found at i:4493008 original size:11 final size:10
Alignment explanation
Indices: 4492988--4493055 Score: 90
Period size: 10 Copynumber: 7.1 Consensus size: 10
4492978 TTTTCTATCA
4492988 TTTTCA-TTT
1 TTTTCATTTT
4492997 TTTTCATTTTT
1 TTTTCA-TTTT
4493008 TTTTCATTTT
1 TTTTCATTTT
4493018 TTTTCATTTT
1 TTTTCATTTT
*
4493028 TTCTCA--TT
1 TTTTCATTTT
4493036 TTTTCATTTT
1 TTTTCATTTT
4493046 TTTTC-TTTT
1 TTTTCATTTT
4493055 T
1 T
4493056 CTATCCATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
8 7 0.13
9 11 0.21
10 26 0.49
11 9 0.17
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTCATTTT
Found at i:4493012 original size:30 final size:31
Alignment explanation
Indices: 4492976--4493039 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
4492966 TTTGAGTCTC
4492976 TTTTTTC-TATCATTTTCATTTTTT-TCATTT
1 TTTTTTCAT-TCATTTTCATTTTTTCTCATTT
**
4493006 TTTTTTCATTTTTTTTCATTTTTTCTCATTT
1 TTTTTTCATTCATTTTCATTTTTTCTCATTT
4493037 TTT
1 TTT
4493040 CATTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (31 bp):
TTTTTTCATTCATTTTCATTTTTTCTCATTT
Found at i:4493040 original size:28 final size:28
Alignment explanation
Indices: 4492974--4493055 Score: 50
Period size: 31 Copynumber: 2.9 Consensus size: 28
4492964 AATTTGAGTC
4492974 TCTTTTTTCTATCA--TTTTCA-TTTTTT
1 TCTTTTTTCT-TCATTTTTTCATTTTTTT
* *
4493000 TCATTTTTTTTTCATTTTTTTTCATTTTTTC
1 TC-TTTTTTCTTCA--TTTTTTCATTTTTTT
4493031 TCATTTTTTCATT--TTTTTTC-TTTTT
1 TC-TTTTTTC-TTCATTTTTTCATTTTT
4493056 CTATCCATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
26 5 0.11
27 12 0.26
28 7 0.15
30 6 0.13
31 14 0.30
32 2 0.04
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (28 bp):
TCTTTTTTCTTCATTTTTTCATTTTTTT
Found at i:4497031 original size:32 final size:31
Alignment explanation
Indices: 4496939--4497031 Score: 84
Period size: 30 Copynumber: 3.0 Consensus size: 31
4496929 TTTTTTTAAC
* *
4496939 AATTTTATTTTCAAAAAAAATTGATACTTTTA
1 AATTTTATTTT-TAAAAAAATTGATACTTTCA
* * * * *
4496971 ACTTTT-TCTTTAAAAATATT-TTTC-TTCA
1 AATTTTATTTTTAAAAAAATTGATACTTTCA
4496999 AATTTTATTTTTAAGAAAAATTGATACTTTCA
1 AATTTTATTTTTAA-AAAAATTGATACTTTCA
4497031 A
1 A
4497032 CTCTTCCTTA
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
28 8 0.18
29 8 0.18
30 14 0.31
31 5 0.11
32 10 0.22
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (31 bp):
AATTTTATTTTTAAAAAAATTGATACTTTCA
Found at i:4497108 original size:61 final size:59
Alignment explanation
Indices: 4496895--4497129 Score: 260
Period size: 60 Copynumber: 3.9 Consensus size: 59
4496885 CTTTTATATA
* * *
4496895 AAAAATTTGACACTTTCAAC-TTTTCTTTAAAATA-TTTTTTTAACAATTTTATTTTCAAA
1 AAAAA-TTGATACTTTCAACTTTTTCTTAAAAATATTTTTTTTAA-AATTTTATTTTCAAG
* * * *
4496954 AAAAATTGATACTTTTAACTTTTTCTTTAAAAATATTTTTCTTCAAATTTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTC-TTAAAAATATTTTTTTTAAAATTTTATTTTCAAG
* * *
4497014 AAAAATTGATACTTTCAACTCTTCCTTAGAAATATTTTTTTTTAAAGATTTTATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTTCTTAAAAATA-TTTTTTTTAAA-ATTTTATTTTCAAG
* * * **
4497075 AAAATTTGATACTTTTAACTTTTTCTCAAAAATATTTATTTGAAAAATTTT-TTTT
1 AAAAATTGATACTTTCAACTTTTTCTTAAAAATATTT-TTTTTAAAATTTTATTTT
4497130 ATTCATTTAT
Statistics
Matches: 148, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
58 12 0.08
59 22 0.15
60 60 0.41
61 54 0.36
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.51
Consensus pattern (59 bp):
AAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTTTAAAATTTTATTTTCAAG
Found at i:4497191 original size:18 final size:19
Alignment explanation
Indices: 4497154--4497197 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
4497144 TTTTACTCAT
4497154 TAAA-AAAATGACAAATAA
1 TAAACAAAATGACAAATAA
*
4497172 TAAACAAAATGATAAA-AA
1 TAAACAAAATGACAAATAA
4497190 TAAACAAA
1 TAAACAAA
4497198 GAATACCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.16
Consensus pattern (19 bp):
TAAACAAAATGACAAATAA
Found at i:4498859 original size:12 final size:13
Alignment explanation
Indices: 4498842--4498873 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
4498832 GAAAAGAAAG
4498842 AAAAAATAGA-TA
1 AAAAAATAGATTA
4498854 AAAAAATAGATTA
1 AAAAAATAGATTA
4498867 AAAAAAT
1 AAAAAAT
4498874 GAAAAAGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (13 bp):
AAAAAATAGATTA
Found at i:4499158 original size:12 final size:12
Alignment explanation
Indices: 4499141--4499172 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
4499131 ATTCTCTACT
4499141 CATACATGTATA
1 CATACATGTATA
4499153 CATACATGTATA
1 CATACATGTATA
4499165 CATACATG
1 CATACATG
4499173 CATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (12 bp):
CATACATGTATA
Found at i:4501180 original size:22 final size:23
Alignment explanation
Indices: 4501149--4501204 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
4501139 CAATTGGTGC
4501149 TTTTA-TATTTATATTT-TTG-T
1 TTTTATTATTTATATTTCTTGCT
*
4501169 TATTTATTATTTATTTTTCTTGCT
1 T-TTTATTATTTATATTTCTTGCT
4501193 TTTTATT-TTTAT
1 TTTTATTATTTAT
4501205 TAATAAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 1 0.03
21 4 0.13
22 15 0.48
23 9 0.29
24 2 0.06
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (23 bp):
TTTTATTATTTATATTTCTTGCT
Found at i:4509468 original size:119 final size:117
Alignment explanation
Indices: 4509107--4510008 Score: 572
Period size: 119 Copynumber: 7.7 Consensus size: 117
4509097 GCCTTTATTC
* * * *
4509107 AAGAAAAATTAATACTTTCAACTTTTCTTTAAAAAAATATTTTTT-AAAATTTTTTCTTTTAAAA
1 AAGAAAAATTGATACTTTCAACTTTTC-TCAAAAAAATATTTTTTGAAAATTTTAT-TTTTAAGA
** * ** * * * *
4509171 AAAATTGATACACTCAACTTTTCCTCCAAAAATATCTATTGAAAA-TTTTATCTTT
64 AAAATTGATACTTTTAACTTTT--TCTTAAAATGTTTTTTGAAAATTTTTATTTTT
*
4509226 AA-AGAAAATTGATACTTTCAACTTTTCTTCAAAAAAATATTTTTTGAAATTTTTATTTCTTAA-
1 AAGA-AAAATTGATACTTTCAACTTTTC-TCAAAAAAATATTTTTTGAAAATTTTATTT-TTAAG
* ** * * * ** *
4509289 AAAAATTTATACTCCTAACTTTTTCTCAAAAAATATCTTTTGAAAA-TTTTATCATC
63 AAAAATTGATACTTTTAACTTTTTCT--TAAAATGTTTTTTGAAAATTTTTATTTTT
* * *
4509345 AAGAAAAATTCATACTTTCAACTTTTTCTCAAAAAAATATTTTTTTAAAATTTTATTTTTGAGAA
1 AAGAAAAATTGATACTTTCAAC-TTTTCTCAAAAAAATATTTTTTGAAAATTTTATTTTTAAGAA
*
4509410 AAATTGATACTTTTAACTTTATT-TTAAAATGTTTTTTCAAAATTTTTATTTTT
65 AAATTGATACTTTTAACTTT-TTCTTAAAATGTTTTTTGAAAATTTTTATTTTT
* * * ** *
4509463 AA-AGAAAATTAATATTTTCAACTTTT-TCCTAAAGCAT-TTTTTTGAAATTTTTATTTTTAAGA
1 AAGA-AAAATTGATACTTTCAACTTTTCT-CAAAAAAATATTTTTTGAAAATTTTATTTTTAAGA
* * * **
4509525 AAAATTTATGCTTTCAACTTTTTCTTAAAGCGTTTTTT-----TTTTTATTTTT
64 AAAATTGATACTTTTAACTTTTTCTTAAAATGTTTTTTGAAAATTTTTATTTTT
* *** * * *
4509574 AAGAAAAATTGATACTTTTAACTTTTCT--TTGAAATGTTTTTCTGAAATTTTTATATTTAAGAA
1 AAGAAAAATTGATACTTTCAACTTTTCTCAAAAAAATATTTTT-TGAAAATTTTATTTTTAAGAA
*
4509637 AAATTGATACTTTTAAC-TTCTCATTAAAATGTTTTTTTTG-AAATTTTTATTTTT
65 AAATTGATACTTTTAACTTTTTC-TTAAAATG--TTTTTTGAAAATTTTTATTTTT
* *** *
4509691 AAGAAAAATTGATACTTTCAACTTTT-TCCTAAAGTTTTTTTTTTGAAAATTTTATTTTTAACG-
1 AAGAAAAATTGATACTTTCAACTTTTCT-CAAAAAAATATTTTTTGAAAATTTTATTTTTAA-GA
* * * *
4509754 AAAATTGATAC-TTCAACTTTTGCTTAAATGGTGTTTTTTTTTTTTTTTG-AAATTTTTATTTTC
64 AAAATTGATACTTTTAACTTTTTCTTAAA--ATG---------TTTTTTGAAAATTTTTATTTTT
* ** * * *
4509817 AA-AGTAAATTGATACTTTCAACTTTT-TC-CTAAAATTTTTTTTCAAAATTTTTATTTTTAAGG
1 AAGA-AAAATTGATACTTTCAACTTTTCTCAAAAAAATATTTTTTGAAAA-TTTTATTTTTAAGA
* * * *
4509879 AAAATTGATACTTTCAACTTTTCCTTAAGGTAAT-TTTTTT---TATTTTTATTTTA
64 AAAATTGATACTTTTAACTTTTTCTTAA---AATGTTTTTTGAAAATTTTTATTTTT
* * * * ** * *
4509932 AAG-AAATTTTATATTTTTAACTTTTC-CTAAAAATGTTTTTTTTG-AAATTTTAATTTTTCACG
1 AAGAAAAATTGATACTTTCAACTTTTCTC-AAAAAAATATTTTTTGAAAATTTT-ATTTTT-AAG
*
4509994 AAAAATTAATACTTT
63 AAAAATTGATACTTT
4510009 CAGTTTTTCC
Statistics
Matches: 639, Mismatches: 93, Indels: 105
0.76 0.11 0.13
Matches are distributed among these distances:
109 2 0.00
110 9 0.01
111 72 0.11
112 2 0.00
113 6 0.01
114 22 0.03
115 24 0.04
116 79 0.12
117 79 0.12
118 59 0.09
119 163 0.26
120 20 0.03
124 14 0.02
125 25 0.04
126 61 0.10
127 1 0.00
129 1 0.00
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (117 bp):
AAGAAAAATTGATACTTTCAACTTTTCTCAAAAAAATATTTTTTGAAAATTTTATTTTTAAGAAA
AATTGATACTTTTAACTTTTTCTTAAAATGTTTTTTGAAAATTTTTATTTTT
Done.