Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 20 of 32
Found at i:3241020 original size:11 final size:11
Alignment explanation
Indices: 3241004--3241047 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
3240994 ATACGTAATT
3241004 ATATAAATATA
1 ATATAAATATA
*
3241015 ATATAAAAATA
1 ATATAAATATA
3241026 AGTA-AAATATA
1 A-TATAAATATA
3241037 ATATAAA-ATA
1 ATATAAATATA
3241047 A
1 A
3241048 AAGATAAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 6 0.21
11 21 0.72
12 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (11 bp):
ATATAAATATA
Found at i:3241308 original size:29 final size:29
Alignment explanation
Indices: 3241275--3241337 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
3241265 ATTAATTAAT
3241275 TATTAATAAAATAAAATATAAAAAAT-AAA
1 TATTAAT-AAATAAAATATAAAAAATCAAA
*** *
3241304 TATTAATTTTTAAAATATACAAAATCAAA
1 TATTAATAAATAAAATATAAAAAATCAAA
3241333 TATTA
1 TATTA
3241338 TTAATCTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
TATTAATAAATAAAATATAAAAAATCAAA
Found at i:3241434 original size:30 final size:32
Alignment explanation
Indices: 3241400--3241462 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
3241390 AAAATAATTT
3241400 TAATAT-AA-TATAAATATATTAAAATTTATA
1 TAATATAAATTATAAATATATTAAAATTTATA
**
3241430 TAATATAAATTATTCATATATTAAAATTTATA
1 TAATATAAATTATAAATATATTAAAATTTATA
3241462 T
1 T
3241463 CTAGAGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 6 0.21
31 2 0.07
32 21 0.72
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (32 bp):
TAATATAAATTATAAATATATTAAAATTTATA
Found at i:3241460 original size:18 final size:17
Alignment explanation
Indices: 3241413--3241460 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
3241403 TATAATATAA
3241413 ATATATTAAAATTTA-T
1 ATATATTAAAATTTATT
3241429 ATA-A-TATAAA-TTATT
1 ATATATTA-AAATTTATT
3241444 CATATATTAAAATTTAT
1 -ATATATTAAAATTTAT
3241461 ATCTAGAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
14 5 0.19
15 5 0.19
16 6 0.23
17 4 0.15
18 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATTAAAATTTATT
Found at i:3242364 original size:24 final size:24
Alignment explanation
Indices: 3242324--3242380 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
3242314 AATATCCTAT
3242324 AACCC-AAA-ACCTATAAACTGAA
1 AACCCAAAATACCTATAAACTGAA
3242346 AACCCAAAATACCTATAAACTGAA
1 AACCCAAAATACCTATAAACTGAA
3242370 AACCCAAAATA
1 AACCCAAAATA
3242381 AATTAACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 5 0.15
23 3 0.09
24 25 0.76
ACGTcount: A:0.56, C:0.26, G:0.04, T:0.14
Consensus pattern (24 bp):
AACCCAAAATACCTATAAACTGAA
Found at i:3243061 original size:17 final size:18
Alignment explanation
Indices: 3243028--3243062 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3243018 TTTATATTAA
*
3243028 TAAATTAAAATAATATAT
1 TAAATCAAAATAATATAT
3243046 TAAATCAAAA-AATATAT
1 TAAATCAAAATAATATAT
3243063 ATATATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAATCAAAATAATATAT
Found at i:3243084 original size:21 final size:20
Alignment explanation
Indices: 3243027--3243085 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
3243017 ATTTATATTA
*
3243027 ATAAAT-TAAAATAATATAT
1 ATAAATATAAAATTATATAT
*
3243046 -TAAATCAAAAAATATATATAT
1 ATAAAT-ATAAAAT-TATATAT
3243067 ATAAATATATAAATTATAT
1 ATAAATATA-AAATTATAT
3243086 TAAAAGGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 5 0.16
20 5 0.16
21 13 0.41
22 9 0.28
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAAATATAAAATTATATAT
Found at i:3244412 original size:18 final size:18
Alignment explanation
Indices: 3244386--3244426 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
3244376 AGATATTAAA
*
3244386 ATAAAATTAAAATATAAT
1 ATAAAATTAAAAAATAAT
*
3244404 ATAATATTAAAAAATAAT
1 ATAAAATTAAAAAATAAT
3244422 ATAAA
1 ATAAA
3244427 TATAATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAAATTAAAAAATAAT
Found at i:3246757 original size:24 final size:26
Alignment explanation
Indices: 3246730--3246785 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
3246720 TGCTACCCTT
*
3246730 TTATTGTTTAAAAAAAT-TA-ATATA
1 TTATTGTGTAAAAAAATATATATATA
*
3246754 TTATTGTGTAAAAATATATATATATA
1 TTATTGTGTAAAAAAATATATATATA
3246780 TATATT
1 T-TATT
3246786 ATATATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 15 0.56
25 2 0.07
26 6 0.22
27 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (26 bp):
TTATTGTGTAAAAAAATATATATATA
Found at i:3247931 original size:20 final size:20
Alignment explanation
Indices: 3247889--3247928 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3247879 TTATTTTTAT
* *
3247889 ATTATAAAAATTAAAAATTA
1 ATTATAAAAATAAAAAATAA
3247909 ATTA-AAAAATAAAAAATAA
1 ATTATAAAAATAAAAAATAA
3247928 A
1 A
3247929 ATTGGATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
ATTATAAAAATAAAAAATAA
Found at i:3248305 original size:16 final size:17
Alignment explanation
Indices: 3248274--3248320 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
3248264 AAATTATATT
*
3248274 TAAAATTATATAAAATA
1 TAAAATAATATAAAATA
3248291 TAAAATAAT-TAAAATA
1 TAAAATAATATAAAATA
*
3248307 TAATATAAATATAA
1 TAAAAT-AATATAA
3248321 TAAAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 12 0.46
17 11 0.42
18 3 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAATAATATAAAATA
Found at i:3248316 original size:11 final size:11
Alignment explanation
Indices: 3248287--3248340 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
3248277 AATTATATAA
3248287 AATATAAA-AT
1 AATATAAATAT
3248297 AAT-TAAAATAT
1 AATAT-AAATAT
3248308 AATATAAATAT
1 AATATAAATAT
3248319 AATA-AAATATT
1 AATATAAATA-T
*
3248330 AATATATATAT
1 AATATAAATAT
3248341 TTTTAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
9 1 0.03
10 11 0.29
11 21 0.55
12 5 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATAAATAT
Found at i:3248322 original size:16 final size:16
Alignment explanation
Indices: 3248287--3248339 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
3248277 AATTATATAA
* * *
3248287 AATATAAAATAATTAA
1 AATATAATATAAATAT
3248303 AATATAATATAAATAT
1 AATATAATATAAATAT
* *
3248319 AATAAAATATTAATAT
1 AATATAATATAAATAT
3248335 -ATATA
1 AATATA
3248340 TTTTTAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
15 4 0.13
16 27 0.87
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATATAATATAAATAT
Found at i:3248981 original size:2 final size:2
Alignment explanation
Indices: 3248976--3249011 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
3248966 ATATAGTTAG
3248976 TA TA TA TA TA TA TA TA TA TA TA TA TA GTA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
3249012 CGTTCATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3252987 original size:19 final size:19
Alignment explanation
Indices: 3252960--3252997 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3252950 AAATTATTTC
*
3252960 TTAAATTATCAATAAAATT
1 TTAAATTATAAATAAAATT
*
3252979 TTAATTTATAAATAAAATT
1 TTAAATTATAAATAAAATT
3252998 AATAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATTATAAATAAAATT
Found at i:3254759 original size:20 final size:21
Alignment explanation
Indices: 3254736--3254776 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
3254726 TTTCTAAAAA
3254736 AAATTATTTTT-AATTTGAAT
1 AAATTATTTTTGAATTTGAAT
*
3254756 AAATTTTTTTTGAATTTGAAT
1 AAATTATTTTTGAATTTGAAT
3254777 CAAAATTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (21 bp):
AAATTATTTTTGAATTTGAAT
Found at i:3255422 original size:24 final size:24
Alignment explanation
Indices: 3255392--3255439 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
3255382 TCGGTTTCAG
*
3255392 TTCTTTTCGCTCTTTCTTGTCATC
1 TTCTTTTCACTCTTTCTTGTCATC
3255416 TTCTTTTCACTCTTTCTTGTCATC
1 TTCTTTTCACTCTTTCTTGTCATC
3255440 GGGATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.06, C:0.29, G:0.06, T:0.58
Consensus pattern (24 bp):
TTCTTTTCACTCTTTCTTGTCATC
Found at i:3256286 original size:36 final size:36
Alignment explanation
Indices: 3256234--3256387 Score: 157
Period size: 36 Copynumber: 4.3 Consensus size: 36
3256224 CACCATATAT
* * * *
3256234 TCCAGGATACCCTGCCGCTGGACATCCAGTACCT-C
1 TCCAGGTTACTCTGCCGCTGCACATCCACTACCTCC
* **
3256269 TGCCAGGTTACTTTGCCGCCACACATCCACTACCTCC
1 T-CCAGGTTACTCTGCCGCTGCACATCCACTACCTCC
* *
3256306 TCCAGGTTCCTCTGCCGCTGCACATCCTCTACCTCC
1 TCCAGGTTACTCTGCCGCTGCACATCCACTACCTCC
** * * *
3256342 AGCATGTTACTCAGCCGCTGCACATCCACTGCCTCC
1 TCCAGGTTACTCTGCCGCTGCACATCCACTACCTCC
*
3256378 TACAGGTTAC
1 TCCAGGTTAC
3256388 CCTGTTAATG
Statistics
Matches: 95, Mismatches: 22, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
35 1 0.01
36 92 0.97
37 2 0.02
ACGTcount: A:0.18, C:0.42, G:0.16, T:0.24
Consensus pattern (36 bp):
TCCAGGTTACTCTGCCGCTGCACATCCACTACCTCC
Found at i:3258015 original size:2 final size:2
Alignment explanation
Indices: 3258008--3258033 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3257998 AAACTTGCAG
3258008 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
3258034 TTACCCGAGG
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:3259007 original size:13 final size:13
Alignment explanation
Indices: 3258989--3259028 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
3258979 TTATGAATCG
*
3258989 TAAATTAAATTTT
1 TAAATTAAATTTA
*
3259002 TAAATTGAATTTA
1 TAAATTAAATTTA
*
3259015 TAAAATAAATTTA
1 TAAATTAAATTTA
3259028 T
1 T
3259029 TATCCAAACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
TAAATTAAATTTA
Found at i:3261458 original size:24 final size:24
Alignment explanation
Indices: 3261431--3261485 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
3261421 ATAAATACAA
* * *
3261431 TTAATAAAAATAATATTTATAACT
1 TTAATAAAAATAAAATATAAAACT
*
3261455 TTAA-ATATAATAAAATATAAAACT
1 TTAATA-AAAATAAAATATAAAACT
3261479 TTAATAA
1 TTAATAA
3261486 CTCGTAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.04
24 23 0.92
25 1 0.04
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAATAAAAATAAAATATAAAACT
Found at i:3261672 original size:15 final size:16
Alignment explanation
Indices: 3261641--3261673 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3261631 ATTCATTAGC
*
3261641 TTTTTTTTTAATAATA
1 TTTTTATTTAATAATA
3261657 TTTTTATTTAAT-ATA
1 TTTTTATTTAATAATA
3261672 TT
1 TT
3261674 AAAATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTATTTAATAATA
Found at i:3261694 original size:42 final size:41
Alignment explanation
Indices: 3261647--3261729 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 41
3261637 TAGCTTTTTT
*
3261647 TTTAATAATAT-TTTTATTTAATATATTAAA-ATTATAAATAAA
1 TTTAATAAT-TGTTGTATTTAATATA--AAATATTATAAATAAA
3261689 TTTAATAATTGTTGTATTTAATATAAAATTATTATAAATAA
1 TTTAATAATTGTTGTATTTAATATAAAA-TATTATAAATAA
3261730 TTAATTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
40 3 0.08
41 1 0.03
42 33 0.89
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (41 bp):
TTTAATAATTGTTGTATTTAATATAAAATATTATAAATAAA
Found at i:3261993 original size:26 final size:27
Alignment explanation
Indices: 3261935--3261993 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
3261925 ACTTATTAAT
*
3261935 AAAA-TTTTTAAAAATACTGTTATTTT
1 AAAATTTTTTAAAAATACTGTTATTTC
*
3261961 AAAATTTTTTAAAAATA-TTTTA-TTC
1 AAAATTTTTTAAAAATACTGTTATTTC
3261986 AAATATTT
1 AAA-ATTT
3261994 ATTTTTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 12 0.41
27 12 0.41
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (27 bp):
AAAATTTTTTAAAAATACTGTTATTTC
Found at i:3270441 original size:20 final size:20
Alignment explanation
Indices: 3270409--3270448 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3270399 TGATTTTTAA
3270409 TTTTTACAAATA-TTTATAT
1 TTTTTACAAATATTTTATAT
*
3270428 TTTTATACATATATTTTATAT
1 TTTT-TACAAATATTTTATAT
3270449 AATTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 7 0.39
21 7 0.39
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTACAAATATTTTATAT
Found at i:3278057 original size:7 final size:7
Alignment explanation
Indices: 3278042--3278072 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3278032 CTTGAACCAC
*
3278042 AACCGTG
1 AACCATG
3278049 AACCATG
1 AACCATG
3278056 AACCATG
1 AACCATG
3278063 AACCATG
1 AACCATG
3278070 AAC
1 AAC
3278073 ATTGAATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.42, C:0.29, G:0.16, T:0.13
Consensus pattern (7 bp):
AACCATG
Found at i:3278071 original size:21 final size:20
Alignment explanation
Indices: 3278034--3278072 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3278024 AAGAGGAACT
*
3278034 TGAACCACAACCGTGAACCA
1 TGAACCACAACCATGAACCA
*
3278054 TGAACCATGAACCATGAAC
1 TGAACCA-CAACCATGAAC
3278073 ATTGAATTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.41, C:0.31, G:0.15, T:0.13
Consensus pattern (20 bp):
TGAACCACAACCATGAACCA
Found at i:3278078 original size:21 final size:20
Alignment explanation
Indices: 3278029--3278078 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
3278019 GAAGGAAGAG
*
3278029 GAAC-TTGAACCACAACCGT
1 GAACATTGAACCACAACCAT
*
3278048 GAACCA-TGAACCATGAACCAT
1 GAA-CATTGAACCA-CAACCAT
3278069 GAACATTGAA
1 GAACATTGAA
3278079 TTGTTATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 3 0.12
20 10 0.40
21 12 0.48
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (20 bp):
GAACATTGAACCACAACCAT
Found at i:3289315 original size:2 final size:2
Alignment explanation
Indices: 3289308--3289336 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3289298 AGACAGTTAA
3289308 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
3289337 ATATATATAT
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:3289341 original size:2 final size:2
Alignment explanation
Indices: 3289336--3289372 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3289326 TCTCTCTCTC
3289336 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 T
3289373 TTCTATCAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3291560 original size:2 final size:2
Alignment explanation
Indices: 3291553--3291588 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3291543 TAAAACCAAA
3291553 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3291589 GCAGCTAATT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3291904 original size:18 final size:18
Alignment explanation
Indices: 3291881--3291915 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3291871 CCATAGCCAC
3291881 CTTCAC-CAATCACATTCT
1 CTTCACACAATC-CATTCT
3291899 CTTCACACAATCCATTC
1 CTTCACACAATCCATTC
3291916 GTAGCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.29, C:0.40, G:0.00, T:0.31
Consensus pattern (18 bp):
CTTCACACAATCCATTCT
Found at i:3293436 original size:28 final size:27
Alignment explanation
Indices: 3293405--3293473 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
3293395 TGTATTTTTA
*
3293405 TTATAATTAT-TTATTTTTTAATTATATT
1 TTATAATTATATTA-ATTTTAA-TATATT
*
3293433 TTATATTTATATTAATTTTAATATA-T
1 TTATAATTATATTAATTTTAATATATT
*
3293459 TAATAATTCATATTA
1 TTATAATT-ATATTA
3293474 TATAAAATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 7 0.20
27 10 0.29
28 15 0.43
29 3 0.09
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (27 bp):
TTATAATTATATTAATTTTAATATATT
Found at i:3293456 original size:18 final size:17
Alignment explanation
Indices: 3293397--3293462 Score: 52
Period size: 17 Copynumber: 3.9 Consensus size: 17
3293387 ATAATTCATG
3293397 TATTTT-TATTATAATTA
1 TATTTTATATT-TAATTA
3293414 T-TTATT-T-TTTAATTA
1 TATT-TTATATTTAATTA
3293429 TATTTTATATTTATATTA
1 TATTTTATATTTA-ATTA
3293447 -ATTTTAATATATTAAT
1 TATTTT-ATAT-TTAAT
3293463 AATTCATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
15 9 0.21
16 7 0.17
17 13 0.31
18 10 0.24
19 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTTATATTTAATTA
Found at i:3293540 original size:20 final size:19
Alignment explanation
Indices: 3293497--3293549 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
3293487 ACATATTCAT
3293497 ATTATATTATATCATATTTA
1 ATTATATTATAT-ATATTTA
*
3293517 ATTACT-TTATATATATTTTT
1 ATTA-TATTATATATA-TTTA
3293537 ATTATATTATATA
1 ATTATATTATATA
3293550 AGTTTGGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 24 0.83
21 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTATATTATATATATTTA
Found at i:3294065 original size:71 final size:70
Alignment explanation
Indices: 3293928--3294072 Score: 202
Period size: 73 Copynumber: 2.0 Consensus size: 70
3293918 ACACTTCGTG
*
3293928 AAAACTAGAAAGGATTTAATAGCAGCACCATAAATAACATTAAAGCTATGCATGCAGCTCTTGAA
1 AAAACTAGAAAGGATTTAATAGCAGCACCATAAATAACATTAAAGCTATG-ATGCAGCTATTGAA
*
3293993 AATGGA
65 AAAGGA
* * * *
3293999 AAAACTAGAACAGGAATTTAATGGCAGTACCCTAAATAGCATTAAAGCTATG-TGCAGCTATTGA
1 AAAACTAGAA-AGG-ATTTAATAGCAGCACCATAAATAACATTAAAGCTATGATGCAGCTATTGA
3294063 AAAAGGA
64 AAAAGGA
3294070 AAA
1 AAA
3294073 CCACTCACAG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
71 30 0.45
72 3 0.05
73 33 0.50
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.22
Consensus pattern (70 bp):
AAAACTAGAAAGGATTTAATAGCAGCACCATAAATAACATTAAAGCTATGATGCAGCTATTGAAA
AAGGA
Found at i:3294222 original size:24 final size:24
Alignment explanation
Indices: 3294166--3294243 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
3294156 TAATTTAATG
*
3294166 ATTTAT-T-TTATTATTTAAAAAAT
1 ATTTATATATTATT-TTTAATAAAT
* *
3294189 ATTAAAATATTATTTTTAATAAAT
1 ATTTATATATTATTTTTAATAAAT
* *
3294213 ATTTATATATT-TTTATAATTAA-
1 ATTTATATATTATTTTTAATAAAT
3294235 ATTTATATA
1 ATTTATATA
3294244 AAAAATTATT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 9 0.20
23 13 0.28
24 19 0.41
25 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTATATATTATTTTTAATAAAT
Found at i:3294238 original size:22 final size:24
Alignment explanation
Indices: 3294174--3294243 Score: 76
Period size: 22 Copynumber: 3.1 Consensus size: 24
3294164 TGATTTATTT
* *
3294174 TATTATTTA-AA-AAATATTAAAA
1 TATTATTTATAATAAATATTTATA
*
3294196 TATTATTTTTAATAAATATTTATA
1 TATTATTTATAATAAATATTTATA
*
3294220 TATT-TTTATAATTAA-ATTTATA
1 TATTATTTATAATAAATATTTATA
3294242 TA
1 TA
3294244 AAAAATTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 17 0.41
23 11 0.27
24 13 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTATTTATAATAAATATTTATA
Found at i:3296448 original size:4 final size:4
Alignment explanation
Indices: 3296441--3296473 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
3296431 TTGCATGCAC
*
3296441 ACAT ACAT ACAT ACAT ATAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
3296474 TATATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:3296460 original size:2 final size:2
Alignment explanation
Indices: 3296455--3296498 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
3296445 ACATACATAC
* * *
3296455 AT AT AT AC AT AC AT AC 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
3296497 AT
1 AT
3296499 GATTGTAAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3296462 original size:12 final size:12
Alignment explanation
Indices: 3296441--3296497 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
3296431 TTGCATGCAC
*
3296441 ACATACATACAT
1 ACATATATACAT
3296453 ACATATATACAT
1 ACATATATACAT
* *
3296465 ACATACATATAT
1 ACATATATACAT
* *
3296477 ATATATATATAT
1 ACATATATACAT
*
3296489 ATATATATA
1 ACATATATA
3296498 TGATTGTAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (12 bp):
ACATATATACAT
Found at i:3296464 original size:16 final size:16
Alignment explanation
Indices: 3296443--3296493 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
3296433 GCATGCACAC
3296443 ATACATACATACATAT
1 ATACATACATACATAT
3296459 ATACATACATACATAT
1 ATACATACATACATAT
* * *
3296475 ATATATATATATATAT
1 ATACATACATACATAT
3296491 ATA
1 ATA
3296494 TATATGATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (16 bp):
ATACATACATACATAT
Found at i:3299249 original size:6 final size:6
Alignment explanation
Indices: 3299233--3299357 Score: 59
Period size: 6 Copynumber: 21.2 Consensus size: 6
3299223 AAAGTATCAC
* *
3299233 AAATA- AAATAT AAATAT ATGAATATTTT AAATTT A-ATAT -AATAT AATTAT
1 AAATAT AAATAT AAATAT A--AATA---T AAATAT AAATAT AAATAT AAATAT
* ** * * *
3299283 AAAAAT TTATAT AAATAT AAGT-T -AATTT AAATAT AATTAT -AATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
*
3299328 -AATAA AATATAT AAATAT -AATAT AAATAT A
1 AAATAT AA-ATAT AAATAT AAATAT AAATAT A
3299358 TAAATTATTA
Statistics
Matches: 90, Mismatches: 17, Indels: 25
0.68 0.13 0.19
Matches are distributed among these distances:
4 2 0.02
5 27 0.30
6 47 0.52
7 5 0.06
8 4 0.04
9 3 0.03
11 2 0.02
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (6 bp):
AAATAT
Found at i:3299301 original size:29 final size:28
Alignment explanation
Indices: 3299267--3299365 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
3299257 TTTTAAATTT
*
3299267 AATATAATATAATTATAAAAATTTATATA
1 AATATAATA-AATTATAAAAATTAATATA
* *
3299296 AATATAAGTTAATT-TAAATA-TAAT-TA
1 AATATAA-TAAATTATAAAAATTAATATA
* *
3299322 TAATATAATAAAATATATAAATATAATATA
1 -AATATAATAAATTATAAAAAT-TAATATA
3299352 AATAT-ATAAATTAT
1 AATATAATAAATTAT
3299366 TAGATATATC
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
26 6 0.11
27 14 0.25
28 13 0.23
29 20 0.36
30 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (28 bp):
AATATAATAAATTATAAAAATTAATATA
Found at i:3299316 original size:45 final size:44
Alignment explanation
Indices: 3299262--3299347 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 44
3299252 GAATATTTTA
*
3299262 AATTTAATATAA-TATAATTATAA-AAATTTATATAAATATAAGTT
1 AATTTAATATAATTATAA-TATAATAAA-ATATATAAATATAAGTT
3299306 AATTTAAATATAATTATAATATAATAAAATATATAAATATAA
1 AATTT-AATATAATTATAATATAATAAAATATATAAATATAA
3299348 TATAAATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
44 5 0.13
45 25 0.66
46 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (44 bp):
AATTTAATATAATTATAATATAATAAAATATATAAATATAAGTT
Found at i:3299346 original size:51 final size:51
Alignment explanation
Indices: 3299233--3299352 Score: 122
Period size: 51 Copynumber: 2.4 Consensus size: 51
3299223 AAAGTATCAC
* * *
3299233 AAATAAAATATAAATATATGAATATTTTAAATTTAATATAATATAATTATAA
1 AAAT-AAATATAAATATAAGAATAATTTAAATATAATATAATATAATTATAA
** *
3299285 AAATTTATATAAATATAAG-TTAATTTAAATATAATTATAATATAA-TA-AA
1 AAATAAATATAAATATAAGAATAATTTAAATATAA-TATAATATAATTATAA
3299334 ATATATAAATAT-AATATAA
1 A-A-ATAAATATAAATATAA
3299353 ATATATAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
49 3 0.05
50 22 0.39
51 28 0.49
52 4 0.07
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (51 bp):
AAATAAATATAAATATAAGAATAATTTAAATATAATATAATATAATTATAA
Found at i:3299354 original size:40 final size:40
Alignment explanation
Indices: 3299260--3299357 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 40
3299250 ATGAATATTT
* *
3299260 TAAATTTAATAT-AATATAATTATAAAAATTTATATAAATA
1 TAAA-TTAATATAAATATAATTATAAAAATTAATAAAAATA
* * *
3299300 TAAGTTAATTTAAATATAATTAT-AATA-TAATAAAATATA
1 TAAATTAATATAAATATAATTATAAAAATTAATAAAA-ATA
3299339 TAAATATAATATAAATATA
1 TAAAT-TAATATAAATATA
3299358 TAAATTATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
38 6 0.12
39 16 0.33
40 26 0.54
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (40 bp):
TAAATTAATATAAATATAATTATAAAAATTAATAAAAATA
Found at i:3299373 original size:56 final size:53
Alignment explanation
Indices: 3299233--3299373 Score: 114
Period size: 56 Copynumber: 2.6 Consensus size: 53
3299223 AAAGTATCAC
* *
3299233 AAATAAAATATAAATATATGAATATT-TTAA-A---TTTAATATAATATAATTAT
1 AAATATAATATAAATATAT-AA-ATTATTAATATAATTTAATATAATAAAATTAT
* * * *
3299283 AAAAATTTATATAAATATAAGTTAATT-TAAATATAATTATAATATAATAAAATATAT
1 AAATA-TAATATAAATAT-A-TAAATTATTAATATAATT-TAATATAATAAAAT-TAT
3299340 AAATATAATATAAATATATAAATTATTAGATATA
1 AAATATAATATAAATATATAAATTATTA-ATATA
3299374 TCGATGTATA
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
50 4 0.06
51 16 0.23
52 3 0.04
53 1 0.01
54 5 0.07
55 5 0.07
56 29 0.41
57 7 0.10
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (53 bp):
AAATATAATATAAATATATAAATTATTAATATAATTTAATATAATAAAATTAT
Found at i:3302510 original size:21 final size:20
Alignment explanation
Indices: 3302484--3302533 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
3302474 TTAATGTTTA
3302484 AATAATTTTTTTAATACTGTT
1 AATAATTTTTTTAAT-CTGTT
* *
3302505 AATAATTATTTTTTATTTGTT
1 AATAATT-TTTTTAATCTGTT
3302526 AAT-ATTTT
1 AATAATTTT
3302534 AAAAGTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 14 0.54
22 7 0.27
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (20 bp):
AATAATTTTTTTAATCTGTT
Found at i:3302580 original size:14 final size:14
Alignment explanation
Indices: 3302539--3302581 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3302529 ATTTTAAAAG
3302539 TATAAAAATTATAA
1 TATAAAAATTATAA
**
3302553 TAT-TGAATTAATAA
1 TATAAAAATT-ATAA
3302567 TATAAAAATTATAA
1 TATAAAAATTATAA
3302581 T
1 T
3302582 TTTTTACGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 4 0.17
14 15 0.65
15 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
TATAAAAATTATAA
Found at i:3303277 original size:22 final size:23
Alignment explanation
Indices: 3303225--3303281 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
3303215 AATATTTTTA
*
3303225 AATTATTATTTAAAATTAATTAAT
1 AATT-TTATTTATAATTAATTAAT
*
3303249 -ATATTATTTATAA-TAATTAAT
1 AATTTTATTTATAATTAATTAAT
3303270 AATTTTATTTAT
1 AATTTTATTTAT
3303282 TATTTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 8 0.28
22 19 0.66
23 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTTTATTTATAATTAATTAAT
Found at i:3303378 original size:17 final size:16
Alignment explanation
Indices: 3303355--3303396 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
3303345 ATTTTAAAAA
*
3303355 AATTTTATATATTTTT
1 AATTTTATATATATTT
*
3303371 AATATTTATTTATATTT
1 AAT-TTTATATATATTT
3303388 AATTTTATA
1 AATTTTATA
3303397 AAAATAATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AATTTTATATATATTT
Found at i:3303892 original size:10 final size:11
Alignment explanation
Indices: 3303877--3303906 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3303867 TCTCTTTCCC
3303877 GAAAAAAAAAG
1 GAAAAAAAAAG
*
3303888 AAAAAAAAAAG
1 GAAAAAAAAAG
3303899 GAAAAAAA
1 GAAAAAAA
3303907 GGGAAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAG
Found at i:3309275 original size:2 final size:2
Alignment explanation
Indices: 3309268--3309294 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3309258 AAAGTAGTTA
3309268 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3309295 GCTTGTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3310632 original size:22 final size:25
Alignment explanation
Indices: 3310588--3310636 Score: 77
Period size: 22 Copynumber: 2.1 Consensus size: 25
3310578 TGAAGTAAAA
3310588 TTATTTTTAAATATTCATAATTTTT
1 TTATTTTTAAATATTCATAATTTTT
3310613 TTATTTTT-AA-ATT-ATAATTTTT
1 TTATTTTTAAATATTCATAATTTTT
3310635 TT
1 TT
3310637 TAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 11 0.46
23 3 0.12
24 2 0.08
25 8 0.33
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (25 bp):
TTATTTTTAAATATTCATAATTTTT
Found at i:3314255 original size:30 final size:30
Alignment explanation
Indices: 3314221--3314309 Score: 112
Period size: 30 Copynumber: 2.9 Consensus size: 30
3314211 TATAATTATT
*
3314221 TTAAAATTTATTTAGATATAAAATTAAAA-A
1 TTAAAATTTATTTAGA-ATAAAAATAAAAGA
3314251 TTAAAATTTATTT-GAATAAAAATAAAAGA
1 TTAAAATTTATTTAGAATAAAAATAAAAGA
3314280 TTAAGAATTTATTTA-AAGTTAAAAATAAAA
1 TTAA-AATTTATTTAGAA--TAAAAATAAAA
3314310 AAATTATTTG
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
28 11 0.21
29 7 0.13
30 24 0.45
32 11 0.21
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (30 bp):
TTAAAATTTATTTAGAATAAAAATAAAAGA
Found at i:3319188 original size:9 final size:10
Alignment explanation
Indices: 3319159--3319217 Score: 72
Period size: 9 Copynumber: 6.2 Consensus size: 10
3319149 AATACATGAC
*
3319159 ATAAAAAATA
1 ATAATAAATA
3319169 A-AATAAAATA
1 ATAAT-AAATA
3319179 A-AATAAATA
1 ATAATAAATA
3319188 ATAAT-AATA
1 ATAATAAATA
3319197 ATAAT-AATA
1 ATAATAAATA
3319206 ATAATAAATA
1 ATAATAAATA
3319216 AT
1 AT
3319218 TATGTTTTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
9 26 0.58
10 19 0.42
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
ATAATAAATA
Found at i:3319192 original size:3 final size:3
Alignment explanation
Indices: 3319165--3319217 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
3319155 TGACATAAAA
3319165 AAT AA- AAT AA- AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
3319208 AAT AAAT AAT
1 AAT -AAT AAT
3319218 TATGTTTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.13
3 33 0.73
4 6 0.13
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:3324173 original size:181 final size:183
Alignment explanation
Indices: 3323910--3324246 Score: 554
Period size: 181 Copynumber: 1.8 Consensus size: 183
3323900 GAAAAAGTTG
3323910 AAAAAAATCTTTTATTACATGAAAATATGCATTATTGCATATTACTAGTTTTTTTTTTTCATCTA
1 AAAAAAATCTTTTATTACATGAAAATATGC--TA-T-CATATTACTAGTTTTTTTTTTTCATCTA
3323975 ACCACTGCTGAGGATTGCTTAGCCTTACACTCTACGCCCTAAAAGCGTAAGAATTAAACTAATGC
62 ACCACTGCTGAGGATTGCTTAGCCTTACACTCTACGCCCTAAAAGCGTAAGAATTAAACTAATGC
** *
3324040 CTAGAAGTCTGTAAAGTACAGCTTTTCGAGGTGTAAGATAGGTACATAGATAACTTA
127 CTAGAAGTCTAAAAAATACAGCTTTTCGAGGTGTAAGATAGGTACATAGATAACTTA
3324097 AAAAATAATCTTTTATTACATGAAAATATGC-A-CA-ATTACTAGTTTTTTTTTTTCATCTAACC
1 AAAAA-AATCTTTTATTACATGAAAATATGCTATCATATTACTAGTTTTTTTTTTTCATCTAACC
* * *
3324159 ACTGCTGAGGATTGCTTAGCCTTACACTCTACGCCCTAAAAGCGTAGGAATTAAACTAATGCTTG
65 ACTGCTGAGGATTGCTTAGCCTTACACTCTACGCCCTAAAAGCGTAAGAATTAAACTAATGCCTA
3324224 GAAGTCTAAAAAATACAGCTTTT
130 GAAGTCTAAAAAATACAGCTTTT
3324247 ACTCTAAAAC
Statistics
Matches: 143, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
181 110 0.77
182 2 0.01
185 1 0.01
187 5 0.03
188 25 0.17
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (183 bp):
AAAAAAATCTTTTATTACATGAAAATATGCTATCATATTACTAGTTTTTTTTTTTCATCTAACCA
CTGCTGAGGATTGCTTAGCCTTACACTCTACGCCCTAAAAGCGTAAGAATTAAACTAATGCCTAG
AAGTCTAAAAAATACAGCTTTTCGAGGTGTAAGATAGGTACATAGATAACTTA
Found at i:3326442 original size:21 final size:21
Alignment explanation
Indices: 3326418--3326457 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3326408 ATAATTTATT
3326418 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
3326439 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
3326458 AATTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:3327387 original size:1 final size:1
Alignment explanation
Indices: 3327381--3327410 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
3327371 ATTCTTGACT
*
3327381 CCCCCCCCCCCCCCCCCCCCCCCGCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
3327411 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.97, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:3331437 original size:25 final size:25
Alignment explanation
Indices: 3331389--3331437 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
3331379 TAAATTTGAG
***
3331389 TTTAAAATTAAATTAATTTTTTAAA
1 TTTAAAATTAAATTAATAAATTAAA
*
3331414 TTTAAATTTAAATTAATAAATTAA
1 TTTAAAATTAAATTAATAAATTAA
3331438 TTATAATCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTAAAATTAAATTAATAAATTAAA
Found at i:3342320 original size:14 final size:14
Alignment explanation
Indices: 3342301--3342346 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
3342291 TAAAGATAAA
*
3342301 AAAATATAAGTATT
1 AAAATATAAATATT
*
3342315 AAAATATAAATTTT
1 AAAATATAAATATT
3342329 AAAATTATTAAATATT
1 AAAA-TA-TAAATATT
3342345 AA
1 AA
3342347 TTAAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 16 0.59
15 2 0.07
16 9 0.33
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (14 bp):
AAAATATAAATATT
Found at i:3345382 original size:494 final size:494
Alignment explanation
Indices: 3344455--3345442 Score: 1877
Period size: 494 Copynumber: 2.0 Consensus size: 494
3344445 AACTATGACG
3344455 TGGGTGCTGCATTTTCAGTACTCATATAGCAGTCACAAAACATCTCTCTCCTCTTGAGACTTCCA
1 TGGGTGCTGCATTTTCAGTACTCATATAGCAGTCACAAAACATCTCTCTCCTCTTGAGACTTCCA
3344520 TTAACGTTATGCAGAGTTCCTATACATTTACATGGGATCAAAAGATAATTTGACAGAAAACTTGG
66 TTAACGTTATGCAGAGTTCCTATACATTTACATGGGATCAAAAGATAATTTGACAGAAAACTTGG
* *
3344585 ATACTTTTTGACTTTTGAGCCTTAAAATTAAACTGCTTTATTCACCAATTAATACTGCTATTTTC
131 ATACTTTTTGACTTCTGAGCCTTAAAATGAAACTGCTTTATTCACCAATTAATACTGCTATTTTC
*
3344650 TGTTTCCCGTGACCGTCTTTGTCCGAGAAAAGACAAGCACTAACAATATGCTAAAGCAGAGAAGA
196 TGTTTCCCGTGACCGTCTTTGTCCGAGAAAAGACAAGCACGAACAATATGCTAAAGCAGAGAAGA
*
3344715 GAAGTAAACGAAAAATAAGTGTGGTTTTATCTTCTTTTTTCCAGGCAGCTGCATCTGGCTGTGAG
261 GAAGTAAAAGAAAAATAAGTGTGGTTTTATCTTCTTTTTTCCAGGCAGCTGCATCTGGCTGTGAG
3344780 GAGAAAGGGACAAATTGTTTGATTTAGTCAATCAGCATTTAATATCCTTTGCCATTTAATCAATA
326 GAGAAAGGGACAAATTGTTTGATTTAGTCAATCAGCATTTAATATCCTTTGCCATTTAATCAATA
3344845 TTCATACTTGACACTGTCTGGATACTTGAATTGTGGGAGCCTAGATTCTTTCTGGAGCAGGCTTG
391 TTCATACTTGACACTGTCTGGATACTTGAATTGTGGGAGCCTAGATTCTTTCTGGAGCAGGCTTG
3344910 AGTTGAGTACTTACCTCAAAGCCAAAAAAGTATAAAAAA
456 AGTTGAGTACTTACCTCAAAGCCAAAAAAGTATAAAAAA
3344949 TGGGTGCTGCATTTTCAGTACTCATATAGCAGTCACAAAACATCTCTCTCCTCTTGAGACTTCCA
1 TGGGTGCTGCATTTTCAGTACTCATATAGCAGTCACAAAACATCTCTCTCCTCTTGAGACTTCCA
3345014 TTAACGTTATGCAGAGTTCCTATACATTTACATGGGATCAAAAGATAATTTGACAGAAAACTTGG
66 TTAACGTTATGCAGAGTTCCTATACATTTACATGGGATCAAAAGATAATTTGACAGAAAACTTGG
* *
3345079 ATACTTTTTGACTTCTGAGCCTTAAACTGAAACTGCTTTATTCGCCAATTAATACTGCTATTTTC
131 ATACTTTTTGACTTCTGAGCCTTAAAATGAAACTGCTTTATTCACCAATTAATACTGCTATTTTC
*
3345144 TGTTTCCCGTGACCGTCTTTGTCCGAGAAAAGACAAGCACGAACAATATGTTAAAGCAGAGAAGA
196 TGTTTCCCGTGACCGTCTTTGTCCGAGAAAAGACAAGCACGAACAATATGCTAAAGCAGAGAAGA
*
3345209 GAAGTAAAAGAGAAATAAGTGTGGTTTTATCTTCTTTTTTCCAGGCAGCTGCATCTGGCTGTGAG
261 GAAGTAAAAGAAAAATAAGTGTGGTTTTATCTTCTTTTTTCCAGGCAGCTGCATCTGGCTGTGAG
*
3345274 GAGAAGGGGACAAATTGTTTGATTTAGTCAATCAGCATTTAATATCCTTTGCCATTTAATCAATA
326 GAGAAAGGGACAAATTGTTTGATTTAGTCAATCAGCATTTAATATCCTTTGCCATTTAATCAATA
**
3345339 TTCATACTTGATTCTGTCTGGATACTTGAATTGTGGGAGCCTAGATTCTTTCTGGAGCAGGCTTG
391 TTCATACTTGACACTGTCTGGATACTTGAATTGTGGGAGCCTAGATTCTTTCTGGAGCAGGCTTG
3345404 AGTTGAGTACTTACCTCAAAGCCAAAAAAGTATAAAAAA
456 AGTTGAGTACTTACCTCAAAGCCAAAAAAGTATAAAAAA
3345443 AATGGAGATG
Statistics
Matches: 483, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
494 483 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (494 bp):
TGGGTGCTGCATTTTCAGTACTCATATAGCAGTCACAAAACATCTCTCTCCTCTTGAGACTTCCA
TTAACGTTATGCAGAGTTCCTATACATTTACATGGGATCAAAAGATAATTTGACAGAAAACTTGG
ATACTTTTTGACTTCTGAGCCTTAAAATGAAACTGCTTTATTCACCAATTAATACTGCTATTTTC
TGTTTCCCGTGACCGTCTTTGTCCGAGAAAAGACAAGCACGAACAATATGCTAAAGCAGAGAAGA
GAAGTAAAAGAAAAATAAGTGTGGTTTTATCTTCTTTTTTCCAGGCAGCTGCATCTGGCTGTGAG
GAGAAAGGGACAAATTGTTTGATTTAGTCAATCAGCATTTAATATCCTTTGCCATTTAATCAATA
TTCATACTTGACACTGTCTGGATACTTGAATTGTGGGAGCCTAGATTCTTTCTGGAGCAGGCTTG
AGTTGAGTACTTACCTCAAAGCCAAAAAAGTATAAAAAA
Found at i:3347827 original size:15 final size:15
Alignment explanation
Indices: 3347802--3347831 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3347792 AAAATAATGA
3347802 TTAAAAAAATTATTT
1 TTAAAAAAATTATTT
3347817 TTAAAAAAATTATTT
1 TTAAAAAAATTATTT
3347832 AAAAGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAAAAAATTATTT
Found at i:3347832 original size:13 final size:14
Alignment explanation
Indices: 3347802--3347841 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
3347792 AAAATAATGA
3347802 TTAAAAAAATTATTT
1 TTAAAAAAATTA-TT
3347817 TTAAAAAAATTATT
1 TTAAAAAAATTATT
*
3347831 TAAAAGAAAAT
1 TTAAA-AAAAT
3347842 AGATGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TTAAAAAAATTATT
Found at i:3349318 original size:2 final size:2
Alignment explanation
Indices: 3349311--3349336 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3349301 AATTTTAGGA
3349311 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
3349337 TGTTTGTTTG
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:3354346 original size:12 final size:12
Alignment explanation
Indices: 3354326--3354357 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3354316 GAAAACAAAG
3354326 GCCGCCAACTGT
1 GCCGCCAACTGT
*
3354338 GCTGCCAACTGT
1 GCCGCCAACTGT
3354350 GCCGCCAA
1 GCCGCCAA
3354358 TTTTGAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.41, G:0.25, T:0.16
Consensus pattern (12 bp):
GCCGCCAACTGT
Found at i:3354374 original size:12 final size:12
Alignment explanation
Indices: 3354359--3354404 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
3354349 TGCCGCCAAT
3354359 TTTGAAATTCAA
1 TTTGAAATTCAA
*
3354371 TTTGAAATAGTAAA
1 TTTGAAAT--TCAA
3354385 TGTTGAAATTCAA
1 T-TTGAAATTCAA
3354398 TTTGAAA
1 TTTGAAA
3354405 CAGTGAAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 14 0.48
13 4 0.14
14 4 0.14
15 7 0.24
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (12 bp):
TTTGAAATTCAA
Found at i:3354416 original size:27 final size:27
Alignment explanation
Indices: 3354360--3354416 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
3354350 GCCGCCAATT
* *
3354360 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
3354387 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
3354414 TTG
1 TTG
3354417 CACAGTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:3355822 original size:26 final size:25
Alignment explanation
Indices: 3355768--3355818 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
3355758 TTCATTTATG
* *
3355768 ATTTTTAAAATTATAAAATAAAGCT
1 ATTTTTAAAATTATAAAATAAAACA
*
3355793 ATTTTTAAAAGTTA-AAATTAAAACA
1 ATTTTTAAAA-TTATAAAATAAAACA
3355818 A
1 A
3355819 ATTTAGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (25 bp):
ATTTTTAAAATTATAAAATAAAACA
Found at i:3361940 original size:15 final size:15
Alignment explanation
Indices: 3361920--3362003 Score: 60
Period size: 15 Copynumber: 5.4 Consensus size: 15
3361910 GTGGCTGTGG
3361920 CTTCTTCTCTTCTTC
1 CTTCTTCTCTTCTTC
*
3361935 CTTCTTCTCTTCCTC
1 CTTCTTCTCTTCTTC
* ***
3361950 TTTCTTGGGTTCTTC
1 CTTCTTCTCTTCTTC
* *
3361965 TTTCTTTGGCTCTTCTTT
1 CTTC-TT--CTCTTCTTC
* *
3361983 CTTCTGCTCCTCTTC
1 CTTCTTCTCTTCTTC
3361998 CTTCTT
1 CTTCTT
3362004 GGGTTCTTCT
Statistics
Matches: 51, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
15 40 0.78
16 2 0.04
17 1 0.02
18 8 0.16
ACGTcount: A:0.00, C:0.35, G:0.07, T:0.58
Consensus pattern (15 bp):
CTTCTTCTCTTCTTC
Found at i:3361997 original size:33 final size:33
Alignment explanation
Indices: 3361960--3362051 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
3361950 TTTCTTGGGT
* *
3361960 TCTTCTTTCTTTGGCTCTTCTTTCTTCTGCTCC
1 TCTTCTTTCTTGGGTTCTTCTTTCTTCTGCTCC
* * *
3361993 TCTTCCTTCTTGGGTTCTTCTTTCTTTTGGTCC
1 TCTTCTTTCTTGGGTTCTTCTTTCTTCTGCTCC
* *
3362026 TCCTCTTTCTTGGGTTCTTCCTTCTT
1 TCTTCTTTCTTGGGTTCTTCTTTCTT
3362052 TGGTTCTTCC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.00, C:0.30, G:0.12, T:0.58
Consensus pattern (33 bp):
TCTTCTTTCTTGGGTTCTTCTTTCTTCTGCTCC
Found at i:3362003 original size:48 final size:48
Alignment explanation
Indices: 3361926--3362066 Score: 144
Period size: 48 Copynumber: 2.9 Consensus size: 48
3361916 GTGGCTTCTT
* * * *
3361926 CTCTTCTTCCTTCTTCTCTTCCTCTTTCTTGGGTTCTTCTTTCTTTGG-
1 CTCTTCTTTCTTCTGCTC-TCTTCCTTCTTGGGTTCTTCTTTCTTTGGC
3361974 CTCTTCTTTCTTCTGCTCCTCTTCCTTCTTGGGTTCTTCTTTCTTTTGGTC
1 CTCTTCTTTCTTCTGCT-CTCTTCCTTCTTGGGTTCTTCTTTC-TTTGG-C
* * * * *
3362025 CTCCTCTTTCTT-GGGT-TCTTCCTTCTTTGGTTCTTCCTTCTT
1 CTCTTCTTTCTTCTGCTCTCTTCCTTCTTGGGTTCTTCTTTCTT
3362067 CTCTGGCTCT
Statistics
Matches: 80, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
47 2 0.03
48 59 0.74
49 6 0.08
50 2 0.03
51 11 0.14
ACGTcount: A:0.00, C:0.31, G:0.11, T:0.57
Consensus pattern (48 bp):
CTCTTCTTTCTTCTGCTCTCTTCCTTCTTGGGTTCTTCTTTCTTTGGC
Found at i:3362011 original size:15 final size:15
Alignment explanation
Indices: 3361993--3362066 Score: 67
Period size: 15 Copynumber: 4.7 Consensus size: 15
3361983 CTTCTGCTCC
* *
3361993 TCTTCCTTCTTGGGT
1 TCTTCTTTCTTTGGT
3362008 TCTTCTTTCTTTTGGT
1 TCTTCTTTC-TTTGGT
* *
3362024 CCTCCTCTTTCTTGGGT
1 --TCTTCTTTCTTTGGT
*
3362041 TCTTCCTTCTTTGGT
1 TCTTCTTTCTTTGGT
*
3362056 TCTTCCTTCTT
1 TCTTCTTTCTT
3362067 CTCTGGCTCT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
15 31 0.63
16 5 0.10
17 5 0.10
18 8 0.16
ACGTcount: A:0.00, C:0.28, G:0.14, T:0.58
Consensus pattern (15 bp):
TCTTCTTTCTTTGGT
Found at i:3362509 original size:2 final size:2
Alignment explanation
Indices: 3362502--3362531 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3362492 ACAAATACAA
3362502 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
3362532 TAAGCAGTCC
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:3363833 original size:2 final size:2
Alignment explanation
Indices: 3363826--3363854 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3363816 GTAAACGAAC
3363826 AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3363855 CACTCAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3364301 original size:24 final size:24
Alignment explanation
Indices: 3364269--3364314 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3364259 CACTAAATTT
*
3364269 AATTATAAATTAATAAA-AATATTA
1 AATTATAAAATAA-AAATAATATTA
*
3364293 AATTTTAAAATAAAAATAATAT
1 AATTATAAAATAAAAATAATAT
3364315 ATTTAACAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AATTATAAAATAAAAATAATATTA
Found at i:3365109 original size:22 final size:22
Alignment explanation
Indices: 3365054--3365109 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
3365044 TAAATTTGAT
* *
3365054 ATAAAATATAT-TTATTTTTAA
1 ATAAAATAAATATTAATTTTAA
* * *
3365075 A-ATATTAATTATTAATTTTAA
1 ATAAAATAAATATTAATTTTAA
3365096 ATAAAATAAATATT
1 ATAAAATAAATATT
3365110 TTTTTATTAA
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
20 5 0.20
21 11 0.44
22 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAAATAAATATTAATTTTAA
Found at i:3365421 original size:25 final size:23
Alignment explanation
Indices: 3365370--3365440 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
3365360 TTCAATTATA
* * *
3365370 TATTAATTTTATATTAATAT-AT
1 TATTTATTTTATTTTAAAATAAT
3365392 TATTTTATTTTATTTTAAAATAAT
1 TA-TTTATTTTATTTTAAAATAAT
*
3365416 TGATTTACTATTATTTTAAAA-AAT
1 T-ATTTA-TTTTATTTTAAAATAAT
3365440 T
1 T
3365441 TTAAAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 2 0.05
23 15 0.37
24 11 0.27
25 13 0.32
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (23 bp):
TATTTATTTTATTTTAAAATAAT
Found at i:3366759 original size:18 final size:18
Alignment explanation
Indices: 3366728--3366780 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
3366718 TAAATTTATT
*
3366728 TTTTTATAATTAAAAATAA
1 TTTTAATAA-TAAAAATAA
*
3366747 TTTTAATAATAAAATTAA
1 TTTTAATAATAAAAATAA
3366765 TTATTAATATATAAAA
1 TT-TTAATA-ATAAAA
3366781 TTAGATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 10 0.33
19 14 0.47
20 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTTAATAATAAAAATAA
Found at i:3366789 original size:20 final size:19
Alignment explanation
Indices: 3366733--3366783 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
3366723 TTATTTTTTT
*
3366733 ATAATTAAAAATAATT-TTA
1 ATAA-TAAAATTAATTATTA
3366752 ATAATAAAATTAATTATTA
1 ATAATAAAATTAATTATTA
3366771 ATATATAAAATTA
1 ATA-ATAAAATTA
3366784 GATATTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 10 0.34
19 10 0.34
20 9 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAATAAAATTAATTATTA
Found at i:3366940 original size:25 final size:25
Alignment explanation
Indices: 3366912--3366966 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
3366902 AATTATTTTT
3366912 ATATATATTTTA-ATAATATTTAAAA
1 ATAT-TATTTTATATAATATTTAAAA
**
3366937 ATATTATTTTATATTTTATTTAAAA
1 ATATTATTTTATATAATATTTAAAA
3366962 ATATT
1 ATATT
3366967 GATAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATTATTTTATATAATATTTAAAA
Found at i:3366982 original size:17 final size:17
Alignment explanation
Indices: 3366957--3366999 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3366947 ATATTTTATT
* *
3366957 TAAAAATATTGATAATA
1 TAAATATATTAATAATA
*
3366974 TAAATATATTAATTATA
1 TAAATATATTAATAATA
*
3366991 TAAGTATAT
1 TAAATATAT
3367000 AAAATTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
TAAATATATTAATAATA
Found at i:3367128 original size:15 final size:15
Alignment explanation
Indices: 3367085--3367131 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
3367075 ATAATAATTC
*
3367085 AAAACTTTCAAATAA
1 AAAACTTTAAAATAA
3367100 AAAA--TTAATTAATAA
1 AAAACTTTAA--AATAA
3367115 AAAACTTTAAAATAA
1 AAAACTTTAAAATAA
3367130 AA
1 AA
3367132 GTAAGATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
13 3 0.11
15 20 0.74
17 4 0.15
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAACTTTAAAATAA
Found at i:3368115 original size:11 final size:11
Alignment explanation
Indices: 3368099--3368198 Score: 91
Period size: 11 Copynumber: 9.1 Consensus size: 11
3368089 GTCGTCTAAA
*
3368099 TATATTTATTT
1 TATATTTATAT
3368110 TATATTTATAT
1 TATATTTATAT
*
3368121 TATTATTTAAAT
1 TA-TATTTATAT
*
3368133 TATGTATTTATTT
1 TA--TATTTATAT
3368146 TATATTTATAT
1 TATATTTATAT
*
3368157 TATTTTTATAT
1 TATATTTATAT
3368168 TATAATTT-TAT
1 TAT-ATTTATAT
*
3368179 T-TAATTA-A-
1 TATATTTATAT
3368187 TATATTTATAT
1 TATATTTATAT
3368198 T
1 T
3368199 TTAATAAATT
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
8 1 0.01
9 9 0.12
10 2 0.03
11 38 0.53
12 13 0.18
13 9 0.12
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (11 bp):
TATATTTATAT
Found at i:3368143 original size:36 final size:35
Alignment explanation
Indices: 3368101--3368170 Score: 122
Period size: 36 Copynumber: 2.0 Consensus size: 35
3368091 CGTCTAAATA
3368101 TATTTATTTTATATTTATATTATTATTTAAATTATG
1 TATTTATTTTATATTTATATTATT-TTTAAATTATG
*
3368137 TATTTATTTTATATTTATATTATTTTTATATTAT
1 TATTTATTTTATATTTATATTATTTTTAAATTAT
3368171 AATTTTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 9 0.27
36 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (35 bp):
TATTTATTTTATATTTATATTATTTTTAAATTATG
Found at i:3368190 original size:24 final size:23
Alignment explanation
Indices: 3368110--3368226 Score: 67
Period size: 24 Copynumber: 4.7 Consensus size: 23
3368100 ATATTTATTT
3368110 TATATTTATATTATTATTTAAATT-A
1 TATATTTA-ATT-TTATTT-AATTAA
* * *
3368135 TGTATTTATTTTATATTTATATTATTTT
1 TATATTTAATTT-TATTTA-ATTA---A
3368163 TATATTATAATTTTATTTAATTAA
1 TATATT-TAATTTTATTTAATTAA
* * *
3368187 TATATTTATATTTTAATAAATTTA
1 TATATTTA-ATTTTATTTAATTAA
*
3368211 TTTATTT-ATTTTATTT
1 TATATTTAATTTTATTT
3368227 TTTATTTCGT
Statistics
Matches: 72, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
22 7 0.10
23 4 0.06
24 34 0.47
25 7 0.10
27 4 0.06
28 11 0.15
29 5 0.07
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (23 bp):
TATATTTAATTTTATTTAATTAA
Found at i:3368195 original size:47 final size:47
Alignment explanation
Indices: 3368099--3368215 Score: 114
Period size: 47 Copynumber: 2.5 Consensus size: 47
3368089 GTCGTCTAAA
* * * *
3368099 TATATTTATTTTATATTTATATTATTATTTAAATTATGTATTTATTT
1 TATATTTATATTATATTTATATTATAATTTAAATTAAGTATATATTT
* * * *
3368146 TATATTTATATTATTTTTATATTATAATTTTATTTAATTA-ATATATT
1 TATATTTATATTATATTTATATTATAATTTAAATTAAGTATATAT-TT
* *
3368193 TATATTT-TAATAAATTTAT-TTAT
1 TATATTTATATTATATTTATATTAT
3368216 TTATTTTATT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
45 4 0.07
46 12 0.21
47 42 0.72
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (47 bp):
TATATTTATATTATATTTATATTATAATTTAAATTAAGTATATATTT
Found at i:3368212 original size:52 final size:51
Alignment explanation
Indices: 3368097--3368225 Score: 126
Period size: 52 Copynumber: 2.5 Consensus size: 51
3368087 CTGTCGTCTA
*
3368097 AATATATTTA-TTTTATATTTATATTATTATTTAAATTATGTATTTATTTT
1 AATATATTTATTTTTATATTTATATTATTATTTAAATTATATATTTATTTT
*
3368147 ATATTTATATTATTTTTATA-TTATAATT-TTATTT-AATTAATATATTTATATTTT
1 A-ATATAT-TTATTTTTATATTTAT-ATTATTATTTAAATT-ATATA-TT-TATTTT
*
3368201 AATAAATTTATTTATT-TATTT-TATT
1 AATATATTTATTT-TTATATTTATATT
3368226 TTTTATTTCG
Statistics
Matches: 66, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
50 1 0.02
51 12 0.18
52 26 0.39
53 20 0.30
54 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (51 bp):
AATATATTTATTTTTATATTTATATTATTATTTAAATTATATATTTATTTT
Found at i:3368226 original size:33 final size:32
Alignment explanation
Indices: 3368148--3368226 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
3368138 ATTTATTTTA
* * *
3368148 TATTTATATTATTTTTATATTATAATTTTATT
1 TATTTATTTTATTTATATATTATAAATTTATT
* * * *
3368180 TAATTAATATATTTATATTTTAATAAATTTATT
1 TATTTATTTTATTTATATATT-ATAAATTTATT
3368213 TATTTATTTTATTT
1 TATTTATTTTATTT
3368227 TTTATTTCGT
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
32 15 0.42
33 21 0.58
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (32 bp):
TATTTATTTTATTTATATATTATAAATTTATT
Found at i:3368230 original size:12 final size:13
Alignment explanation
Indices: 3368101--3368233 Score: 59
Period size: 13 Copynumber: 10.7 Consensus size: 13
3368091 CGTCTAAATA
3368101 TATTTATTTTA--
1 TATTTATTTTATT
*
3368112 TATTTATATTA-T
1 TATTTATTTTATT
** *
3368124 TATTTAAATTATG
1 TATTTATTTTATT
3368137 TATTTATTTTA--
1 TATTTATTTTATT
*
3368148 TATTTATATTA-T
1 TATTTATTTTATT
*
3368160 T-TTTATATTA-T
1 TATTTATTTTATT
* *
3368171 AATTTTATTTAATT
1 TA-TTTATTTTATT
* *
3368185 AATATATTTATATTT
1 TATTTATTT-TA-TT
* * *
3368200 TAATAAATTTATT
1 TATTTATTTTATT
3368213 TATTTATTTTATT
1 TATTTATTTTATT
3368226 T-TTTATTT
1 TATTTATTT
3368234 CGTATGGAAA
Statistics
Matches: 95, Mismatches: 19, Indels: 15
0.74 0.15 0.12
Matches are distributed among these distances:
11 30 0.32
12 18 0.19
13 35 0.37
14 6 0.06
15 6 0.06
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (13 bp):
TATTTATTTTATT
Found at i:3371766 original size:1 final size:1
Alignment explanation
Indices: 3371756--3371785 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
3371746 CAAATCAGTT
*
3371756 GGGGGTGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
3371786 AATGGCTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:3376417 original size:1 final size:1
Alignment explanation
Indices: 3376411--3376437 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
3376401 TACATGATAG
3376411 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
3376438 AACTCAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3385580 original size:2 final size:2
Alignment explanation
Indices: 3385573--3385606 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3385563 TTGATTTCCA
* *
3385573 CT CT CT CT CT CT CT CT GT CT CT CT GT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3385607 TTAATTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.44, G:0.06, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3389571 original size:15 final size:15
Alignment explanation
Indices: 3389526--3389571 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3389516 TTTTAAAAAA
*
3389526 TAATATTTAATAAATT
1 TAATATTT-ATAATTT
3389542 T-ATAGTTTA-AATTT
1 TAATA-TTTATAATTT
3389556 TAATATTTATAATTT
1 TAATATTTATAATTT
3389571 T
1 T
3389572 TTATATATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 9 0.35
15 13 0.50
16 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TAATATTTATAATTT
Found at i:3391791 original size:21 final size:21
Alignment explanation
Indices: 3391765--3391806 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3391755 AATAATCAAA
3391765 TTAAAT-TAATAATAAATAAAT
1 TTAAATATAATAA-AAATAAAT
*
3391786 TTAAATATCATAAAAATAAAT
1 TTAAATATAATAAAAATAAAT
3391807 CGAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TTAAATATAATAAAAATAAAT
Found at i:3391792 original size:17 final size:17
Alignment explanation
Indices: 3391755--3391786 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3391745 TTTGGATAAC
3391755 AATAATCAAATTAAATT
1 AATAATCAAATTAAATT
3391772 AATAAT-AAA-TAAATT
1 AATAATCAAATTAAATT
3391787 TAAATATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAATCAAATTAAATT
Found at i:3394167 original size:45 final size:45
Alignment explanation
Indices: 3394103--3394191 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
3394093 AATGATTATC
*
3394103 CAATTTGTTTTAGGGACAAGATGTTTACGGTAATTT-TAGTAGATG
1 CAATTTGTTTTAGGGACAAGATGTTTAAGG-AATTTGTAGTAGATG
*
3394148 CAATTTGTTTTAGGGACAAGATGTTTAAGGCATTTGTAGTAGAT
1 CAATTTGTTTTAGGGACAAGATGTTTAAGGAATTTGTAGTAGAT
3394192 TTTGCTTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 4 0.10
45 37 0.90
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.39
Consensus pattern (45 bp):
CAATTTGTTTTAGGGACAAGATGTTTAAGGAATTTGTAGTAGATG
Found at i:3396337 original size:12 final size:12
Alignment explanation
Indices: 3396312--3396345 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3396302 AAATTATAAA
*
3396312 AATAAAAAAATT
1 AATAAAAAATTT
*
3396324 AATTAAAAATTT
1 AATAAAAAATTT
3396336 AATAAAAAAT
1 AATAAAAAAT
3396346 AAAATTAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAAAAAATTT
Found at i:3397071 original size:26 final size:26
Alignment explanation
Indices: 3397026--3397077 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3397016 TTTAAAAAAG
*
3397026 TTTATATATTTAAATAATTTTTAAAT
1 TTTATATATTTAAATAATTTTCAAAT
* * *
3397052 TTTATATTTTTAATTTATTTTCAAAT
1 TTTATATATTTAAATAATTTTCAAAT
3397078 ATATTAGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTATATATTTAAATAATTTTCAAAT
Found at i:3397271 original size:14 final size:14
Alignment explanation
Indices: 3397252--3397294 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
3397242 TTAATATATT
3397252 TTATAATATTTATA
1 TTATAATATTTATA
3397266 TTATAATATTCTATA
1 TTATAATATT-TATA
*
3397281 TT-TACTATTTATA
1 TTATAATATTTATA
3397294 T
1 T
3397295 AAGATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 5 0.19
14 16 0.59
15 6 0.22
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATAATATTTATA
Found at i:3397337 original size:24 final size:22
Alignment explanation
Indices: 3397310--3397354 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
3397300 AAATTACATA
3397310 ATATATATTAATATAAAATAATGT
1 ATATATATTAATA-AAAA-AATGT
* *
3397334 ATATTTTTTAATAAAAAAATG
1 ATATATATTAATAAAAAAATG
3397355 ATCAAGCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 4 0.21
24 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
ATATATATTAATAAAAAAATGT
Found at i:3398515 original size:6 final size:6
Alignment explanation
Indices: 3398504--3398530 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3398494 AGTTATGAGT
3398504 ATTAAA ATTAAA ATTAAA ATTAAA ATT
1 ATTAAA ATTAAA ATTAAA ATTAAA ATT
3398531 TATTAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTAAA
Found at i:3401173 original size:32 final size:31
Alignment explanation
Indices: 3401131--3401190 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3401121 CTCAATAACG
* * *
3401131 ATTAATTTATATTTTAAATTATTAAATTTAGT
1 ATTAAATTATA-TATAAATTATAAAATTTAGT
3401163 ATTAAATTATATATAAATTATAAAATTT
1 ATTAAATTATATATAAATTATAAAATTT
3401191 TAATTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (31 bp):
ATTAAATTATATATAAATTATAAAATTTAGT
Found at i:3401199 original size:16 final size:18
Alignment explanation
Indices: 3401180--3401213 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3401170 TATATATAAA
3401180 TTAT-AAAATTT-TAATT
1 TTATAAAAATTTATAATT
3401196 TTATAAAAATTTATAATT
1 TTATAAAAATTTATAATT
3401214 AAATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATAAAAATTTATAATT
Found at i:3403679 original size:20 final size:20
Alignment explanation
Indices: 3403649--3403717 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
3403639 AATCATTTTT
3403649 TTTATTATTATTATTCATATA
1 TTTA-TATTATTATTCATATA
* *
3403670 TTTATATTA-TATTAATAATT
1 TTTATATTATTATTCAT-ATA
* *
3403690 TTTAAAATATT-TTCATA-A
1 TTTATATTATTATTCATATA
3403708 TTTATATTAT
1 TTTATATTAT
3403718 ATAAATTTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
18 8 0.21
19 7 0.18
20 18 0.47
21 5 0.13
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATATTATTATTCATATA
Found at i:3408766 original size:2 final size:2
Alignment explanation
Indices: 3408759--3408794 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3408749 GTTTATATTA
3408759 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
3408795 TTTACAGAAA
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:3411067 original size:191 final size:191
Alignment explanation
Indices: 3410743--3411118 Score: 680
Period size: 191 Copynumber: 2.0 Consensus size: 191
3410733 GCAGGTATTT
3410743 ACTTTCAAGTCCTTCAGACCAAAATACTAAGATCGAATGGCATAACTTTGTTTCATGAGATCTAA
1 ACTTTCAAGTCCTTCAGACCAAAATACTAAGATCGAATGGCATAACTTTGTTTCATGAGATCTAA
*
3410808 TATATATGCCATTTTTCCATAGATTGAAATGCAGAAGAGACATTGGTTCACAATTTTTGATTCCT
66 TATATATGCCATTTTTCCATAGATTGAAATGCAGAAGAGACATTGGTTCACAATGTTTGATTCCT
*
3410873 TTAATCAAACGATAATAAACAATTAGGATTACATGTTTCAAAAGCTCTTCTTTTTGGCATA
131 TTAATCAAAAGATAATAAACAATTAGGATTACATGTTTCAAAAGCTCTTCTTTTTGGCATA
* * * *
3410934 ACTTTCAAGTCCTTCAGATCAGAATACTAAGATTGATTGGCATAACTTTGTTTCATGAGATCTAA
1 ACTTTCAAGTCCTTCAGACCAAAATACTAAGATCGAATGGCATAACTTTGTTTCATGAGATCTAA
* *
3410999 TATATATGCCATTTTTCCATAGTTTGAAATGCAGAAGAGACATTGGTTCTCAATGTTTGATTCCT
66 TATATATGCCATTTTTCCATAGATTGAAATGCAGAAGAGACATTGGTTCACAATGTTTGATTCCT
3411064 TTAATCAAAAGATAATAAACAATTAGGATTACATGTTTCAAAAGCTCTTCTTTTT
131 TTAATCAAAAGATAATAAACAATTAGGATTACATGTTTCAAAAGCTCTTCTTTTT
3411119 TGGTTCTGTT
Statistics
Matches: 177, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
191 177 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (191 bp):
ACTTTCAAGTCCTTCAGACCAAAATACTAAGATCGAATGGCATAACTTTGTTTCATGAGATCTAA
TATATATGCCATTTTTCCATAGATTGAAATGCAGAAGAGACATTGGTTCACAATGTTTGATTCCT
TTAATCAAAAGATAATAAACAATTAGGATTACATGTTTCAAAAGCTCTTCTTTTTGGCATA
Found at i:3417314 original size:15 final size:16
Alignment explanation
Indices: 3417294--3417323 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3417284 AATTTAATTT
3417294 TTTTAAAAA-AAAATA
1 TTTTAAAAATAAAATA
3417309 TTTTAAAAATAAAAT
1 TTTTAAAAATAAAAT
3417324 TTAAAATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTTTAAAAATAAAATA
Found at i:3421332 original size:4 final size:4
Alignment explanation
Indices: 3421317--3421348 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
3421307 TAATATTTGA
3421317 AATT AA-T AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT AATT A
3421349 TATAATTCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:3421642 original size:16 final size:15
Alignment explanation
Indices: 3421585--3421644 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
3421575 ATTATATAAT
*
3421585 AAATTGAATA-TTTA
1 AAATTTAATATTTTA
*
3421599 AATTTTAATATTTTAA
1 AAATTTAATATTTT-A
*
3421615 ATAATTT-TTATTTTCA
1 A-AATTTAATATTTT-A
3421631 AAATTTAATATTTT
1 AAATTTAATATTTT
3421645 TTAAAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
14 8 0.22
15 8 0.22
16 16 0.44
17 4 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
AAATTTAATATTTTA
Found at i:3421877 original size:20 final size:18
Alignment explanation
Indices: 3421822--3421859 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3421812 TTTAACACTT
3421822 AGAATCAATTATTTTAAA
1 AGAATCAATTATTTTAAA
3421840 AGAATCAATTATTTTAAA
1 AGAATCAATTATTTTAAA
3421858 AG
1 AG
3421860 GATGACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (18 bp):
AGAATCAATTATTTTAAA
Found at i:3424832 original size:14 final size:15
Alignment explanation
Indices: 3424795--3424839 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
3424785 ATTTATTTTT
*
3424795 TAAATTTAATATTAAA
1 TAAATTTAATATT-TA
3424811 TAAATTTAA-ATTTA
1 TAAATTTAATATTTA
*
3424825 TAATTTTAATATTTA
1 TAAATTTAATATTTA
3424840 ATTTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 9 0.35
15 8 0.31
16 9 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TAAATTTAATATTTA
Found at i:3426129 original size:17 final size:19
Alignment explanation
Indices: 3426091--3426126 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3426081 TTATATTTAA
3426091 ATATTAAAATTTTATTTTT
1 ATATTAAAATTTTATTTTT
*
3426110 ATATTAATA-TTTATTTT
1 ATATTAAAATTTTATTTT
3426127 ATAATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATATTAAAATTTTATTTTT
Found at i:3430017 original size:2 final size:2
Alignment explanation
Indices: 3430010--3430036 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3430000 AAGTAGACTG
3430010 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3430037 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3430484 original size:17 final size:17
Alignment explanation
Indices: 3430464--3430497 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3430454 CTATCTTCTT
*
3430464 TTAAAAAAGATTTTTTA
1 TTAAAAAAGAATTTTTA
*
3430481 TTAAAAATGAATTTTTA
1 TTAAAAAAGAATTTTTA
3430498 AGAAACATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TTAAAAAAGAATTTTTA
Found at i:3430950 original size:29 final size:29
Alignment explanation
Indices: 3430896--3430952 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3430886 GAAACAATTT
*
3430896 TCATAATTTAATAGAATAAGTCAATTTTA
1 TCATAATTTAATAGAATAAGTAAATTTTA
* *
3430925 TCATTATTTAATATAATATA-TAAATTTT
1 TCATAATTTAATAGAATA-AGTAAATTTT
3430953 TTATATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (29 bp):
TCATAATTTAATAGAATAAGTAAATTTTA
Found at i:3431986 original size:21 final size:21
Alignment explanation
Indices: 3431961--3432009 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3431951 GGATGCTACT
*
3431961 TATAAAAAAATTTAAGTATTA
1 TATAAAAAAATTTAAATATTA
*** *
3431982 TATAATTTAATTTAAATATTT
1 TATAAAAAAATTTAAATATTA
3432003 TATAAAA
1 TATAAAA
3432010 GTAAGGTATT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TATAAAAAAATTTAAATATTA
Found at i:3433133 original size:2 final size:2
Alignment explanation
Indices: 3433126--3433155 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3433116 GTTTGATTCC
3433126 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3433156 TTCTGTTTTA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.