Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 162 of 168
Found at i:48674365 original size:22 final size:22
Alignment explanation
Indices: 48674340--48674385 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
48674330 TTTATATGAT
*
48674340 TTTTCTATTTATTGTTAC-ATTA
1 TTTTATATTTATT-TTACAATTA
*
48674362 TTTTATTTTTATTTTACAATTA
1 TTTTATATTTATTTTACAATTA
48674384 TT
1 TT
48674386 GTTGTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTATATTTATTTTACAATTA
Found at i:48674393 original size:22 final size:22
Alignment explanation
Indices: 48674347--48674393 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
48674337 GATTTTTCTA
*
48674347 TTTATTGTTACATTATTTTATT
1 TTTATTGTTACATTATTTTAGT
48674369 TTTATT-TTACAATTATTGTT-GT
1 TTTATTGTTAC-ATTATT-TTAGT
48674391 TTT
1 TTT
48674394 TAAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.18
22 16 0.73
23 2 0.09
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.68
Consensus pattern (22 bp):
TTTATTGTTACATTATTTTAGT
Found at i:48678737 original size:2 final size:2
Alignment explanation
Indices: 48678730--48678756 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48678720 ACTCATCAAC
48678730 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 T
48678757 TTCATGTTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48682578 original size:6 final size:6
Alignment explanation
Indices: 48682567--48682591 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
48682557 CTTCTTAGAA
48682567 GAAGAT GAAGAT GAAGAT GAAGAT G
1 GAAGAT GAAGAT GAAGAT GAAGAT G
48682592 GTGAATTACG
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:0.36, T:0.16
Consensus pattern (6 bp):
GAAGAT
Found at i:48685630 original size:17 final size:17
Alignment explanation
Indices: 48685609--48685645 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
48685599 TCAAATGCAC
48685609 ATTTTTATTAAAT-TTA
1 ATTTTTATTAAATATTA
*
48685625 ATTTTTATTTAATATTA
1 ATTTTTATTAAATATTA
48685642 ATTT
1 ATTT
48685646 ATTGTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTATTAAATATTA
Found at i:48688539 original size:23 final size:21
Alignment explanation
Indices: 48688513--48688580 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
48688503 TATAAATTAA
48688513 TTAAATCAAATATTATAATTTTT
1 TTAAAT-AAAT-TTATAATTTTT
*
48688536 TTAAATAAATTTTTAA-TTTT
1 TTAAATAAATTTATAATTTTT
* * *
48688556 ATAAAT-ACTTTAATAATTTAT
1 TTAAATAAATTT-ATAATTTTT
48688577 TTAA
1 TTAA
48688581 TTTAAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.11
20 12 0.32
21 11 0.30
22 4 0.11
23 6 0.16
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAATAAATTTATAATTTTT
Found at i:48688554 original size:21 final size:23
Alignment explanation
Indices: 48688513--48688555 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
48688503 TATAAATTAA
48688513 TTAAATCAAATATTATAATTTTT
1 TTAAATCAAATATTATAATTTTT
*
48688536 TTAAAT-AAAT-TTTTAATTTT
1 TTAAATCAAATATTATAATTTT
48688556 ATAAATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 4 0.21
23 6 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAAATCAAATATTATAATTTTT
Found at i:48688645 original size:2 final size:2
Alignment explanation
Indices: 48688638--48688671 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
48688628 AACATCATCA
48688638 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
48688672 GCAACTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48689179 original size:2 final size:2
Alignment explanation
Indices: 48689172--48689202 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
48689162 ACCTATTAAC
48689172 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 T
48689203 GCCCAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48701130 original size:16 final size:16
Alignment explanation
Indices: 48701109--48701141 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
48701099 TTCAAAAATA
48701109 AGAAACCAAAGCAACC
1 AGAAACCAAAGCAACC
48701125 AGAAACCAAAGCAACC
1 AGAAACCAAAGCAACC
48701141 A
1 A
48701142 TCTTTACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.30, G:0.12, T:0.00
Consensus pattern (16 bp):
AGAAACCAAAGCAACC
Found at i:48703024 original size:34 final size:35
Alignment explanation
Indices: 48702980--48703046 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
48702970 AAGTAAAATA
*
48702980 TTTTCAGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCAGTAAAATGATTTACGGGAAAATATTTTAC
* *
48703014 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCAGTAAAATGATTTACGGGAAAATATTTT
48703047 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCAGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:48707674 original size:6 final size:6
Alignment explanation
Indices: 48707640--48707665 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
48707630 ATCAAAATAT
48707640 ATCTAA ATCTAA ATCTAA ATCTAA AT
1 ATCTAA ATCTAA ATCTAA ATCTAA AT
48707666 AAATTTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
ATCTAA
Found at i:48713073 original size:17 final size:18
Alignment explanation
Indices: 48713053--48713098 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
48713043 ATTTTGTTTG
48713053 AAAAAT-AATTATTTTAT
1 AAAAATAAATTATTTTAT
48713070 -AAAATAAATTATTTTATAT
1 AAAAATAAATTA-TTT-TAT
48713089 AAAAATAAAT
1 AAAAATAAAT
48713099 GAATATGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.20
17 5 0.20
18 3 0.12
19 3 0.12
20 9 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAATAAATTATTTTAT
Found at i:48713075 original size:16 final size:17
Alignment explanation
Indices: 48713054--48713087 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
48713044 TTTTGTTTGA
48713054 AAAAT-AATTATTTTAT
1 AAAATAAATTATTTTAT
48713070 AAAATAAATTATTTTAT
1 AAAATAAATTATTTTAT
48713087 A
1 A
48713088 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATAAATTATTTTAT
Found at i:48713225 original size:13 final size:13
Alignment explanation
Indices: 48713207--48713233 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48713197 TCAAGTTCTC
48713207 TTTAGAATTTTTA
1 TTTAGAATTTTTA
48713220 TTTAGAATTTTTA
1 TTTAGAATTTTTA
48713233 T
1 T
48713234 AAGATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTAGAATTTTTA
Found at i:48713753 original size:20 final size:20
Alignment explanation
Indices: 48713716--48713753 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48713706 TAGCACTAGT
*
48713716 AATCTATATAACTTTATAGA
1 AATCTATATAACTATATAGA
*
48713736 AATCTATATACCTATATA
1 AATCTATATAACTATATA
48713754 TAAAAGGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
AATCTATATAACTATATAGA
Found at i:48716071 original size:16 final size:15
Alignment explanation
Indices: 48716044--48716075 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
48716034 AAATAAATTA
48716044 AATTAATAACTAACT
1 AATTAATAACTAACT
48716059 AATTAATTAACTAACT
1 AATTAA-TAACTAACT
48716075 A
1 A
48716076 TAAAATCCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTAATAACTAACT
Found at i:48718020 original size:62 final size:61
Alignment explanation
Indices: 48717867--48718048 Score: 201
Period size: 62 Copynumber: 3.0 Consensus size: 61
48717857 TTTATTTTTA
* * *
48717867 ATTTTTTTAGAATCAAGATTAAATAGATAGAA--TGCATAAATT-TAAGGGTTAAATTTGTTG
1 ATTTTTTTAGAATTAAGATCAAATTGATAGAATCTGCA-AAATTGT-AGGGTTAAATTTGTTG
* * *
48717927 A-ATTTTTAGAATTAGGATCAATTTGATAGAATCTGCAAACATTGTAGGGTTAAATTTGTTG
1 ATTTTTTTAGAATTAAGATCAAATTGATAGAATCTGCAAA-ATTGTAGGGTTAAATTTGTTG
* * * * *
48717988 ATTTTTTTAGAATTAAGACCAAATTGATAGAATCTGTAATTATTGTAGAGCTAAATTTGTT
1 ATTTTTTTAGAATTAAGATCAAATTGATAGAATCTGCAA-AATTGTAGGGTTAAATTTGTT
48718049 ATTATGTAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
59 24 0.24
60 3 0.03
61 24 0.24
62 51 0.50
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (61 bp):
ATTTTTTTAGAATTAAGATCAAATTGATAGAATCTGCAAAATTGTAGGGTTAAATTTGTTG
Found at i:48724339 original size:3 final size:3
Alignment explanation
Indices: 48724331--48724368 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
48724321 TTCAAAGCAA
48724331 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
48724369 GATACTTGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:48724436 original size:18 final size:18
Alignment explanation
Indices: 48724415--48724467 Score: 79
Period size: 19 Copynumber: 2.9 Consensus size: 18
48724405 GTCTCTAAAA
* *
48724415 TTATTATTTTATAAAATT
1 TTATAATTTTTTAAAATT
48724433 TTATAATTTTTTAAAAATT
1 TTATAATTTTTT-AAAATT
48724452 TTATAATTTTTTAAAA
1 TTATAATTTTTTAAAA
48724468 AATATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 14 0.44
19 18 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATAATTTTTTAAAATT
Found at i:48724449 original size:19 final size:19
Alignment explanation
Indices: 48724421--48724468 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
48724411 AAAATTATTA
48724421 TTTTATAAAATTTTATAATT
1 TTTTA-AAAATTTTATAATT
48724441 TTTTAAAAATTTTATAATT
1 TTTTAAAAATTTTATAATT
48724460 TTTTAAAAA
1 TTTTAAAAA
48724469 ATATAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTTTATAATT
Found at i:48724464 original size:10 final size:10
Alignment explanation
Indices: 48724420--48724457 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
48724410 TAAAATTATT
48724420 ATTTTATAAA
1 ATTTTATAAA
*
48724430 ATTTTATAAT
1 ATTTTATAAA
*
48724440 TTTTTA-AAA
1 ATTTTATAAA
48724449 ATTTTATAA
1 ATTTTATAA
48724458 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
ATTTTATAAA
Found at i:48724478 original size:19 final size:19
Alignment explanation
Indices: 48724437--48724479 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
48724427 AAAATTTTAT
* * *
48724437 AATTTTTTAAAAATTTTAT
1 AATTTTTTAAAAAATATAA
48724456 AATTTTTTAAAAAATATAA
1 AATTTTTTAAAAAATATAA
48724475 AATTT
1 AATTT
48724480 GAAATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTTTTAAAAAATATAA
Found at i:48729976 original size:8 final size:8
Alignment explanation
Indices: 48729963--48729992 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
48729953 TCTTTTTTTA
48729963 AAAATAAT
1 AAAATAAT
48729971 AAAATAAT
1 AAAATAAT
48729979 AAAATAAT
1 AAAATAAT
48729987 AAAATA
1 AAAATA
48729993 TATTTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATAAT
Found at i:48731103 original size:9 final size:9
Alignment explanation
Indices: 48731089--48731113 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
48731079 TCTCCTTTCA
48731089 TCTTCTTGT
1 TCTTCTTGT
48731098 TCTTCTTGT
1 TCTTCTTGT
48731107 TCTTCTT
1 TCTTCTT
48731114 CCTCTCGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.24, G:0.08, T:0.68
Consensus pattern (9 bp):
TCTTCTTGT
Found at i:48733657 original size:20 final size:19
Alignment explanation
Indices: 48733613--48733657 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
48733603 TATATTAAAA
48733613 TAAATTTTAAAATTATTAT
1 TAAATTTTAAAATTATTAT
*
48733632 TGAAATTTTAAATTTATTCAT
1 T-AAATTTTAAAATTATT-AT
48733653 TAAAT
1 TAAAT
48733658 ATGTTAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TAAATTTTAAAATTATTAT
Found at i:48735991 original size:6 final size:6
Alignment explanation
Indices: 48735980--48736020 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
48735970 TCCTTTCCTC
* *
48735980 TTCTTG TTCTTG TTCTTG TTCTTC TTCTTG TTCTTC TTCTT
1 TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG TTCTT
48736021 CTTCATATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.22, G:0.10, T:0.68
Consensus pattern (6 bp):
TTCTTG
Found at i:48735997 original size:12 final size:12
Alignment explanation
Indices: 48735978--48736020 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
48735968 TCTCCTTTCC
48735978 TCTTCTTGTTCT
1 TCTTCTTGTTCT
*
48735990 TGTTCTTGTTCT
1 TCTTCTTGTTCT
48736002 TCTTCTTGTTCT
1 TCTTCTTGTTCT
48736014 TCTTCTT
1 TCTTCTT
48736021 CTTCATATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.00, C:0.23, G:0.09, T:0.67
Consensus pattern (12 bp):
TCTTCTTGTTCT
Found at i:48736006 original size:3 final size:3
Alignment explanation
Indices: 48735978--48736024 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
48735968 TCTCCTTTCC
* * * *
48735978 TCT TCT TGT TCT TGT TCT TGT TCT TCT TCT TGT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
48736025 ATATGAGCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.26, G:0.09, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:48736007 original size:18 final size:18
Alignment explanation
Indices: 48735978--48736024 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
48735968 TCTCCTTTCC
*
48735978 TCTTCTTGTTCTTGTTCT
1 TCTTCTTCTTCTTGTTCT
*
48735996 TGTTCTTCTTCTTGTTCT
1 TCTTCTTCTTCTTGTTCT
48736014 TCTTCTTCTTC
1 TCTTCTTCTTC
48736025 ATATGAGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.00, C:0.26, G:0.09, T:0.66
Consensus pattern (18 bp):
TCTTCTTCTTCTTGTTCT
Found at i:48738972 original size:20 final size:19
Alignment explanation
Indices: 48738947--48739007 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
48738937 AGACATACTT
48738947 TTTTAGTATTTTTTTATATA
1 TTTTAG-ATTTTTTTATATA
* *
48738967 TTTTAG-CTTTTTTATAACA
1 TTTTAGATTTTTTTAT-ATA
*
48738986 TATTAGA-TTTTTTATAT-
1 TTTTAGATTTTTTTATATA
48739003 TTTTA
1 TTTTA
48739008 TTATTATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 4 0.12
18 9 0.26
19 15 0.44
20 6 0.18
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTAGATTTTTTTATATA
Found at i:48738991 original size:19 final size:19
Alignment explanation
Indices: 48738956--48739001 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
48738946 TTTTTAGTAT
* * *
48738956 TTTTTTAT-ATATTTTAGC
1 TTTTTTATAACATATTAGA
48738974 TTTTTTATAACATATTAGA
1 TTTTTTATAACATATTAGA
48738993 TTTTTTATA
1 TTTTTTATA
48739002 TTTTTATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTTTATAACATATTAGA
Found at i:48739493 original size:9 final size:9
Alignment explanation
Indices: 48739479--48739503 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
48739469 AATATAAAGT
48739479 AAAGAAATA
1 AAAGAAATA
48739488 AAAGAAATA
1 AAAGAAATA
48739497 AAAGAAA
1 AAAGAAA
48739504 AAGAGAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (9 bp):
AAAGAAATA
Found at i:48740043 original size:2 final size:2
Alignment explanation
Indices: 48740036--48740065 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
48740026 TGAAGTATGA
*
48740036 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48740066 GAGCATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:48741339 original size:26 final size:25
Alignment explanation
Indices: 48741288--48741335 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
48741278 AATGTAATAT
* *
48741288 ACTTATCATTATAATTCTACATACA
1 ACTTATCATTAAAATTCTAAATACA
48741313 ACTTAGTCATTAAAATTC-AAATA
1 ACTTA-TCATTAAAATTCTAAATA
48741336 ACAAAACCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.38
Consensus pattern (25 bp):
ACTTATCATTAAAATTCTAAATACA
Found at i:48742502 original size:17 final size:16
Alignment explanation
Indices: 48742480--48742550 Score: 52
Period size: 16 Copynumber: 4.0 Consensus size: 16
48742470 AAAAAGTATT
*
48742480 TTAAAAATATTTTAAAA
1 TTAAAAA-AATTTAAAA
48742497 TTAAAAAAATTTAAAAAAGTA
1 TTAAAAAAATTT---AAA--A
*
48742518 TTTAAAAAAATTTAAAT
1 -TTAAAAAAATTTAAAA
*
48742535 TTTAAAAAATTTAAAA
1 TTAAAAAAATTTAAAA
48742551 AAAGTATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
16 18 0.41
17 7 0.16
19 6 0.14
21 1 0.02
22 12 0.27
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (16 bp):
TTAAAAAAATTTAAAA
Found at i:48742507 original size:39 final size:38
Alignment explanation
Indices: 48742462--48742598 Score: 168
Period size: 39 Copynumber: 3.5 Consensus size: 38
48742452 AATTTATTTT
48742462 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAAAAGTATTTTAAAAA-ATTTTAAAATTAA
* *
48742501 AAAAATTTAAAAAAGTA-TTTAAAAAAATTTAAATTTTAA
1 AAAAA-TTAAAAAAGTATTTTAAAAAATTTTAAA-ATTAA
* *
48742540 AAAATTTAAAAAAAGTATTTTAAAAGCATTTTAAAATTAA
1 AAAAATT-AAAAAAGTATTTTAAAA-AATTTTAAAATTAA
* *
48742580 AAAAATAAAAAAAATATTT
1 AAAAATTAAAAAAGTATTT
48742599 ATTATATTCT
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
38 9 0.11
39 41 0.49
40 27 0.32
41 7 0.08
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (38 bp):
AAAAATTAAAAAAGTATTTTAAAAAATTTTAAAATTAA
Found at i:48742520 original size:12 final size:10
Alignment explanation
Indices: 48742493--48742553 Score: 60
Period size: 10 Copynumber: 6.4 Consensus size: 10
48742483 AAAATATTTT
48742493 AAAA-TTAAA
1 AAAATTTAAA
48742502 AAAATTTAAA
1 AAAATTTAAA
48742512 AAAGTATTTAAA
1 AAA--ATTTAAA
48742524 AAAATTT---
1 AAAATTTAAA
*
48742531 -AAATTTTAA
1 AAAATTTAAA
48742540 AAAATTTAAA
1 AAAATTTAAA
48742550 AAAA
1 AAAA
48742554 GTATTTTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
6 6 0.14
9 4 0.09
10 24 0.55
12 10 0.23
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:48742574 original size:79 final size:73
Alignment explanation
Indices: 48742449--48742599 Score: 212
Period size: 79 Copynumber: 2.0 Consensus size: 73
48742439 AATAAATACC
* *
48742449 AAAAATTTATTTTAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAA
1 AAAAATTTATTTTAAAAATTAAAAAAGTATTTTAAAAACATTTTAAAATTAAAAAAA-TAAAAAA
*
48742514 AGTATTTAA
65 AATATTTAA
*
48742523 AAAAATTTAAATTTTAAAAAATTTAAAAAAAGTATTTTAAAAGCATTTTAAAATTAAAAAAATAA
1 AAAAATTT--ATTTT-AAAAA-TT-AAAAAAGTATTTTAAAAACATTTTAAAATTAAAAAAATAA
48742588 AAAAAATATTTA
61 AAAAAATATTTA
48742600 TTATATTCTG
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
74 8 0.12
76 5 0.07
77 5 0.07
78 15 0.22
79 35 0.51
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.36
Consensus pattern (73 bp):
AAAAATTTATTTTAAAAATTAAAAAAGTATTTTAAAAACATTTTAAAATTAAAAAAATAAAAAAA
ATATTTAA
Found at i:48742993 original size:18 final size:17
Alignment explanation
Indices: 48742972--48743006 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
48742962 ATCATAAGCC
*
48742972 TAAAAAATATTTTAAAAT
1 TAAAAAAT-TTTAAAAAT
48742990 TAAAAAATTTTAAAAAT
1 TAAAAAATTTTAAAAAT
48743007 ATTTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAAAATTTTAAAAAT
Found at i:48743031 original size:27 final size:27
Alignment explanation
Indices: 48742972--48743044 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 27
48742962 ATCATAAGCC
*
48742972 TAAAAAATATTTTAAAATTAAAAAATT
1 TAAAAAATATTTTAAAATTAAAAAATA
*
48742999 TTAAAAATATTTTAAAATT-AAAAATAA
1 TAAAAAATATTTTAAAATTAAAAAAT-A
48743026 TAAAAAATATATTTTAAAA
1 T-AAAAA-ATATTTTAAAA
48743045 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.15
27 19 0.47
28 4 0.10
29 11 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
TAAAAAATATTTTAAAATTAAAAAATA
Found at i:48743048 original size:11 final size:11
Alignment explanation
Indices: 48742989--48743055 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
48742979 TATTTTAAAA
48742989 TTAAAAA-ATT
1 TTAAAAATATT
48742999 TTAAAAATATT
1 TTAAAAATATT
48743010 TT--AAA-A--
1 TTAAAAATATT
*
48743016 TTAAAAATAAT
1 TTAAAAATATT
**
48743027 AAAAAATATATT
1 TTAAAA-ATATT
48743039 TTAAAAATATT
1 TTAAAAATATT
48743050 TTAAAA
1 TTAAAA
48743056 TTAAAAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
6 2 0.04
8 4 0.09
9 4 0.09
10 7 0.16
11 20 0.44
12 8 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:48744149 original size:65 final size:62
Alignment explanation
Indices: 48744015--48744151 Score: 154
Period size: 65 Copynumber: 2.2 Consensus size: 62
48744005 GCAAACAAAC
* ** *
48744015 ATTCGAACCACATATGTATAATTTACAACATTAAAATTCAGCTCAAAGAATTTGTAACCTAT
1 ATTCGAACCACATATGTATAAATTACAACATTAAAATTCAGCTCAAAGAATTTAAAACATAT
*
48744077 ATTCGAACCACATATGTATGTAAAATT-CATACATT-AAATTCAGCTC-AAGAACTTTAAATATA
1 ATTCGAACCACATATGTA--T-AAATTACA-ACATTAAAATTCAGCTCAAAGAA-TTTAAA-ACA
48744139 TAT
60 TAT
48744142 ATTCGAACCA
1 ATTCGAACCA
48744152 TATGTGCATA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
62 18 0.28
63 5 0.08
64 18 0.28
65 23 0.36
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (62 bp):
ATTCGAACCACATATGTATAAATTACAACATTAAAATTCAGCTCAAAGAATTTAAAACATAT
Found at i:48745332 original size:28 final size:28
Alignment explanation
Indices: 48745292--48745348 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
48745282 TATGTTTGTT
48745292 TTTATTATAATAA-CTTTATAATATATTA
1 TTTATTATAATAACCTTTATAAT-TATTA
*
48745320 TTTATTATTATAACCTTTATAATTATTA
1 TTTATTATAATAACCTTTATAATTATTA
48745348 T
1 T
48745349 AAAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTATTATAATAACCTTTATAATTATTA
Found at i:48745559 original size:14 final size:15
Alignment explanation
Indices: 48745540--48745568 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
48745530 TTACGAAACT
48745540 TTCACACAT-ATAAA
1 TTCACACATAATAAA
48745554 TTCACACATAATAAA
1 TTCACACATAATAAA
48745569 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:48746288 original size:29 final size:29
Alignment explanation
Indices: 48746256--48746353 Score: 67
Period size: 29 Copynumber: 3.3 Consensus size: 29
48746246 TTGAAAATGT
48746256 TAAA-ATTAGAATTAAATTGATAAATTTTG
1 TAAACATTAGAATTAAATTGAT-AATTTTG
* * * * *
48746285 TAAATGATGAGAGTTAAATTTATTAATTTTT
1 TAAA-CATTAGAATTAAATTGA-TAATTTTG
* *
48746316 TAGA-ATTCA-AACTAAATTGACTAATTTTG
1 TAAACATT-AGAATTAAATTGA-TAATTTTG
48746345 TAAACATTA
1 TAAACATTA
48746354 AGAGCTAAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
29 25 0.48
30 4 0.08
31 22 0.42
32 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (29 bp):
TAAACATTAGAATTAAATTGATAATTTTG
Found at i:48747910 original size:21 final size:21
Alignment explanation
Indices: 48747893--48747965 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
48747883 ACCAAAAATT
48747893 TATTTTAAAAATTTAAAAAAG
1 TATTTTAAAAATTTAAAAAAG
**
48747914 TATTTTAAAAATATT-TTAAA-
1 TATTTTAAAAAT-TTAAAAAAG
** *
48747934 -ATTAAAAAAATTTTAAAAAG
1 TATTTTAAAAATTTAAAAAAG
48747954 TATTTTAAAAAT
1 TATTTTAAAAAT
48747966 ATTTTAAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
18 2 0.05
19 12 0.30
21 24 0.60
22 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
TATTTTAAAAATTTAAAAAAG
Found at i:48747918 original size:12 final size:11
Alignment explanation
Indices: 48747899--48747996 Score: 61
Period size: 11 Copynumber: 9.6 Consensus size: 11
48747889 AATTTATTTT
48747899 AAAA-ATTTAA
1 AAAATATTTAA
*
48747909 AAAAGTATTTTA
1 AAAA-TATTTAA
48747921 AAAATATTT--
1 AAAATATTTAA
* *
48747930 TAAA-ATTAAA
1 AAAATATTTAA
48747940 AAAAT-TTTAA
1 AAAATATTTAA
* *
48747950 AAAGTATTTTA
1 AAAATATTTAA
48747961 AAAATATTT--
1 AAAATATTTAA
*
48747970 TAAA-A-TTAA
1 AAAATATTTAA
*
48747979 AAAATTTTTAA
1 AAAATATTTAA
48747990 AAAATAT
1 AAAATAT
48747997 ATATTTATTA
Statistics
Matches: 66, Mismatches: 12, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 9 0.14
10 15 0.23
11 27 0.41
12 9 0.14
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAATATTTAA
Found at i:48747928 original size:11 final size:11
Alignment explanation
Indices: 48747893--48747974 Score: 79
Period size: 11 Copynumber: 7.9 Consensus size: 11
48747883 ACCAAAAATT
48747893 TATTTT-AAAA
1 TATTTTAAAAA
*
48747903 -ATTTAAAAAA
1 TATTTTAAAAA
48747913 GTATTTTAAAAA
1 -TATTTTAAAAA
48747925 TATTTT--AAA
1 TATTTTAAAAA
48747934 -A--TTAAAAA
1 TATTTTAAAAA
*
48747942 AATTTTAAAAA
1 TATTTTAAAAA
48747953 GTATTTTAAAAA
1 -TATTTTAAAAA
48747965 TATTTTAAAA
1 TATTTTAAAA
48747975 TTAAAAAATT
Statistics
Matches: 60, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
6 2 0.03
8 4 0.07
9 8 0.13
10 4 0.07
11 23 0.38
12 19 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:48747952 original size:40 final size:40
Alignment explanation
Indices: 48747899--48747992 Score: 170
Period size: 40 Copynumber: 2.4 Consensus size: 40
48747889 AATTTATTTT
*
48747899 AAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTTTAAAAAGTATTTTAAAAATATTTTAAAATTAA
48747939 AAAAATTTTAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTTTAAAAAGTATTTTAAAAATATTTTAAAATTAA
*
48747979 AAAATTTTTAAAAA
1 AAAAATTTTAAAAA
48747993 ATATATATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (40 bp):
AAAAATTTTAAAAAGTATTTTAAAAATATTTTAAAATTAA
Found at i:48748346 original size:3 final size:3
Alignment explanation
Indices: 48748340--48748364 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
48748330 TGTACATTAT
48748340 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
48748365 TCTGTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:48753643 original size:18 final size:18
Alignment explanation
Indices: 48753620--48753671 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
48753610 ACCCCATCTG
* *
48753620 GAGTAATCACTAGGTCTA
1 GAGTAATCACTAGGCCGA
* *
48753638 GAGTAATCGCTAGGCCGG
1 GAGTAATCACTAGGCCGA
*
48753656 GAGTAATCACTGGGCC
1 GAGTAATCACTAGGCC
48753672 TATTACCCCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (18 bp):
GAGTAATCACTAGGCCGA
Found at i:48759423 original size:2 final size:2
Alignment explanation
Indices: 48759416--48759451 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
48759406 CCCTTTCCAC
48759416 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48759452 NNNNNNNNNN
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):
TA
Found at i:48774221 original size:28 final size:29
Alignment explanation
Indices: 48774160--48774230 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
48774150 AAAAATAAAA
*
48774160 ATTTACTAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
48774189 ATTTACCAAAATATATA-AAC-TTTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTTT
*
48774217 ATTTATCAAAATAT
1 ATTTACCAAAATAT
48774231 GTCAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
28 21 0.54
29 16 0.41
30 2 0.05
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTTACCAAAATATTACAACTTTTTTTTT
Found at i:48774321 original size:27 final size:27
Alignment explanation
Indices: 48774282--48774340 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
48774272 TACTGGTGAC
*
48774282 GCCAATGGAATTGGCGGCACCAAAGGT
1 GCCAATGCAATTGGCGGCACCAAAGGT
* *
48774309 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATGCAATTGGCGGCACCAAAGGT
48774336 GCCAA
1 GCCAA
48774341 ACTAATTGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.31, T:0.15
Consensus pattern (27 bp):
GCCAATGCAATTGGCGGCACCAAAGGT
Found at i:48774348 original size:27 final size:27
Alignment explanation
Indices: 48774290--48774355 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
48774280 ACGCCAATGG
*
48774290 AATTGGCGGCACCAAAGGTGCCAATGC
1 AATTGGCGGCACCAAAGGTGCCAATAC
* *
48774317 CATTGGCGGCACCAATGGTGCCAA-AC
1 AATTGGCGGCACCAAAGGTGCCAATAC
*
48774343 TAATTGGTGGCAC
1 -AATTGGCGGCAC
48774356 TACTCGTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.27, C:0.26, G:0.29, T:0.18
Consensus pattern (27 bp):
AATTGGCGGCACCAAAGGTGCCAATAC
Found at i:48774527 original size:19 final size:21
Alignment explanation
Indices: 48774489--48774527 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
48774479 AATAATTGAT
*
48774489 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
48774510 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
48774528 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:48774600 original size:3 final size:3
Alignment explanation
Indices: 48774594--48774652 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
48774584 ATTATTATTA
48774594 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
48774642 TTG TTG TTG TT
1 TTG TTG TTG TT
48774653 AGTATGAAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:48775518 original size:18 final size:18
Alignment explanation
Indices: 48775475--48775519 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
48775465 TTGACATGGT
*
48775475 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
***
48775493 TACCGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
48775511 TGGTGGCGA
1 TGGTGGCGA
48775520 TCATTGGGAT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.47, T:0.13
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:48782201 original size:16 final size:16
Alignment explanation
Indices: 48782180--48782210 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48782170 TAGTCTGATT
48782180 TTTTTTTTTGGTTTTG
1 TTTTTTTTTGGTTTTG
*
48782196 TTTTTTTTTTGTTTT
1 TTTTTTTTTGGTTTT
48782211 TTTGATATAT
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:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (16 bp):
TTTTTTTTTGGTTTTG
Found at i:48782211 original size:17 final size:17
Alignment explanation
Indices: 48782179--48782210 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
48782169 TTAGTCTGAT
48782179 TTTTTTTTTTGGTTTTG
1 TTTTTTTTTTGGTTTTG
48782196 TTTTTTTTTT-GTTTT
1 TTTTTTTTTTGGTTTT
48782211 TTTGATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (17 bp):
TTTTTTTTTTGGTTTTG
Found at i:48784351 original size:13 final size:13
Alignment explanation
Indices: 48784335--48784400 Score: 96
Period size: 13 Copynumber: 5.1 Consensus size: 13
48784325 TTTAAACCAA
48784335 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
48784348 ACTTATCAAAAGC
1 ACTTTTCAAAAGC
* * *
48784361 ATTTTTCCACAGC
1 ACTTTTCAAAAGC
48784374 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
48784387 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
48784400 A
1 A
48784401 ATGAAGAGCT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:48789780 original size:31 final size:32
Alignment explanation
Indices: 48789745--48789809 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
48789735 AACGTGAATA
* * *
48789745 AAAAAATCGACAATCTTCTTAAT-TAATAATT
1 AAAAAATCCAAAATCCTCTTAATCTAATAATT
*
48789776 AAAAAATCCAAAATCCTCTTGATCTAATAATT
1 AAAAAATCCAAAATCCTCTTAATCTAATAATT
48789808 AA
1 AA
48789810 GAAGAGTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.32
Consensus pattern (32 bp):
AAAAAATCCAAAATCCTCTTAATCTAATAATT
Found at i:48792750 original size:18 final size:18
Alignment explanation
Indices: 48792727--48792764 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
48792717 AGAACTACCA
48792727 TAGCCCCTCCTTAACTCT
1 TAGCCCCTCCTTAACTCT
48792745 TAGCCCCTCCTTAACTCT
1 TAGCCCCTCCTTAACTCT
48792763 TA
1 TA
48792765 TAATGCGCTT
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:0.18, C:0.42, G:0.05, T:0.34
Consensus pattern (18 bp):
TAGCCCCTCCTTAACTCT
Found at i:48792973 original size:19 final size:18
Alignment explanation
Indices: 48792971--48793036 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
48792961 TTTAAAATAT
48792971 TTTTAAAATACTTTTTTTAA
1 TTTTAAAATA--TTTTTTAA
**
48792991 TTGTTTTAAT--TTTTTAA
1 TT-TTAAAATATTTTTTAA
48793008 TTTTAAAATATTTTTTAA
1 TTTTAAAATATTTTTTAA
48793026 TTTTTAAAATA
1 -TTTTAAAATA
48793037 AATTTTTTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
16 5 0.13
17 9 0.24
18 7 0.18
19 10 0.26
20 2 0.05
21 5 0.13
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTAAAATATTTTTTAA
Found at i:48793005 original size:18 final size:17
Alignment explanation
Indices: 48792982--48793035 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
48792972 TTTAAAATAC
**
48792982 TTTTTTTAATTGTTTTAA
1 TTTTTTTAATT-TTAAAA
48793000 -TTTTTTAATTTTAAAA
1 TTTTTTTAATTTTAAAA
48793016 TATTTTTTAATTTTTAAAA
1 T-TTTTTTAA-TTTTAAAA
48793035 T
1 T
48793036 AAATTTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 4 0.13
17 10 0.32
18 8 0.26
19 9 0.29
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTTTTAATTTTAAAA
Found at i:48793007 original size:8 final size:8
Alignment explanation
Indices: 48792983--48793030 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
48792973 TTAAAATACT
48792983 TTTTTTAA
1 TTTTTTAA
48792991 TTGTTTTAA
1 TT-TTTTAA
48793000 TTTTTTAA
1 TTTTTTAA
**
48793008 TTTTAAAATA
1 TTTT-TTA-A
48793018 TTTTTTAA
1 TTTTTTAA
48793026 TTTTT
1 TTTTT
48793031 AAAATAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 18 0.55
9 10 0.30
10 5 0.15
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (8 bp):
TTTTTTAA
Found at i:48793042 original size:19 final size:18
Alignment explanation
Indices: 48793002--48793042 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
48792992 TGTTTTAATT
**
48793002 TTTTAATTTTAAAATATT
1 TTTTAATTTTAAAATAAA
48793020 TTTTAATTTTTAAAATAAA
1 TTTTAA-TTTTAAAATAAA
48793039 TTTT
1 TTTT
48793043 TTGTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAATTTTAAAATAAA
Found at i:48793044 original size:23 final size:23
Alignment explanation
Indices: 48793013--48793057 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
48793003 TTTAATTTTA
*
48793013 AAATATTTTTTAATTT-TTAAAAT
1 AAATATTTTGT-ATTTATTAAAAT
*
48793036 AAATTTTTTGTATTTATTAAAA
1 AAATATTTTGTATTTATTAAAA
48793058 AATGGGCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
AAATATTTTGTATTTATTAAAAT
Found at i:48793060 original size:21 final size:19
Alignment explanation
Indices: 48792998--48793060 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 19
48792988 TAATTGTTTT
48792998 AATTTTTTAA-TTTTAAAA
1 AATTTTTTAATTTTTAAAA
*
48793016 TATTTTTTAATTTTTAAAATA
1 AATTTTTTAATTTTT-AAA-A
*
48793037 AATTTTTTGTATTTATTAAAA
1 AATTTTTT-AATTT-TTAAAA
48793058 AAT
1 AAT
48793061 GGGCTGGCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 9 0.24
19 4 0.11
20 3 0.08
21 12 0.32
22 7 0.19
23 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
AATTTTTTAATTTTTAAAA
Found at i:48794005 original size:27 final size:28
Alignment explanation
Indices: 48793944--48794007 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
48793934 CATTTGCTTT
* *
48793944 CTGAAAATAATTTCTATTTTTTATTTTA
1 CTGAAAATGATTTCTATTTTCTATTTTA
* * *
48793972 -AGGAAATGATTTTTATTTTCTA-TTTA
1 CTGAAAATGATTTCTATTTTCTATTTTA
48793998 CTGAAAATGA
1 CTGAAAATGA
48794008 CAAAACATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (28 bp):
CTGAAAATGATTTCTATTTTCTATTTTA
Found at i:48810777 original size:28 final size:24
Alignment explanation
Indices: 48810746--48810804 Score: 57
Period size: 28 Copynumber: 2.3 Consensus size: 24
48810736 TTTATGTTTT
48810746 TTTAAAATTTATGATAATATAATTTATC
1 TTTAAAATTTATG-TAA-A-AATTTA-C
**
48810774 TTTATGATTTATGTAAAAATTTAC
1 TTTAAAATTTATGTAAAAATTTAC
48810798 -TTAAAAT
1 TTTAAAAT
48810805 AGAATTTATC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
23 5 0.19
24 1 0.04
25 6 0.22
26 1 0.04
27 3 0.11
28 11 0.41
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (24 bp):
TTTAAAATTTATGTAAAAATTTAC
Found at i:48828508 original size:21 final size:22
Alignment explanation
Indices: 48828465--48828509 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
48828455 TTACCGAGTT
48828465 GAGAAAGAGTGGAAGCAAATAA
1 GAGAAAGAGTGGAAGCAAATAA
*
48828487 GAGAAAG-GT-GAAGGCAACTAA
1 GAGAAAGAGTGGAA-GCAAATAA
48828508 GA
1 GA
48828510 TGTGGTGGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 11 0.52
22 7 0.33
ACGTcount: A:0.51, C:0.07, G:0.33, T:0.09
Consensus pattern (22 bp):
GAGAAAGAGTGGAAGCAAATAA
Found at i:48829527 original size:30 final size:30
Alignment explanation
Indices: 48829493--48829555 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
48829483 ACTTAACAAG
*
48829493 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* * *
48829523 CAAATACCTTTAAAATATTAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
48829553 CAA
1 CAA
48829556 TAAAATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:48829613 original size:14 final size:14
Alignment explanation
Indices: 48829589--48829615 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48829579 CAAATAATAA
48829589 CAACATAATAGTAG
1 CAACATAATAGTAG
48829603 CAACATAATAGTA
1 CAACATAATAGTA
48829616 AAATAGTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (14 bp):
CAACATAATAGTAG
Found at i:48832623 original size:12 final size:12
Alignment explanation
Indices: 48832591--48832624 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
48832581 GGCGGCAGTA
48832591 GTGGTGGTGGAG
1 GTGGTGGTGGAG
* *
48832603 GAGGAGGTGGAG
1 GTGGTGGTGGAG
48832615 GTGGTGGTGG
1 GTGGTGGTGG
48832625 GTAGCAGTTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.68, T:0.21
Consensus pattern (12 bp):
GTGGTGGTGGAG
Found at i:48839292 original size:16 final size:16
Alignment explanation
Indices: 48839273--48839307 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
48839263 ATTTCGTGAC
48839273 TTTTTTTA-TTAAATA
1 TTTTTTTATTTAAATA
*
48839288 TTTTTTTATTTTAATA
1 TTTTTTTATTTAAATA
48839304 TTTT
1 TTTT
48839308 ACTATATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTTATTTAAATA
Found at i:48843115 original size:19 final size:21
Alignment explanation
Indices: 48843091--48843129 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
48843081 TTACGTAAAT
48843091 TTAATT-CTA-AAAAATAATA
1 TTAATTACTATAAAAATAATA
*
48843110 TTAATTATTATAAAAATAAT
1 TTAATTACTATAAAAATAAT
48843130 GAATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAATTACTATAAAAATAATA
Found at i:48844289 original size:11 final size:11
Alignment explanation
Indices: 48844273--48844304 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
48844263 ATTTTTTTTA
48844273 TTTTAAAATAT
1 TTTTAAAATAT
48844284 TTTTAAAATAT
1 TTTTAAAATAT
48844295 TTTTAAAATA
1 TTTTAAAATA
48844305 AATTTTAAGT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:48848696 original size:82 final size:82
Alignment explanation
Indices: 48848601--48848758 Score: 255
Period size: 82 Copynumber: 1.9 Consensus size: 82
48848591 ATTGAATATA
* * *
48848601 ATTTCTAACAATGTCGTATCCAAACATTATACTCAAAA-TCTGTTGATATGCCTAATTTTCTTTT
1 ATTTCTAACAATGTCGTATCCAAACATAAAACTCAAAACT-TGTTGATATGCCTAATTTTCTTTC
48848665 AAATAACTTTAATCAGTT
65 AAATAACTTTAATCAGTT
* *
48848683 ATTTCTAACAATGTCGTCTCCAAACATAAAACTCAAAACTTGTTGGTATGCCTAATTTTCTTTCA
1 ATTTCTAACAATGTCGTATCCAAACATAAAACTCAAAACTTGTTGATATGCCTAATTTTCTTTCA
48848748 AATAACTTTAA
66 AATAACTTTAA
48848759 GCATCTGGCT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
82 69 0.99
83 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (82 bp):
ATTTCTAACAATGTCGTATCCAAACATAAAACTCAAAACTTGTTGATATGCCTAATTTTCTTTCA
AATAACTTTAATCAGTT
Found at i:48851020 original size:10 final size:10
Alignment explanation
Indices: 48851007--48851046 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
48850997 TTTTAGGAAC
48851007 TTTTTATATA
1 TTTTTATATA
48851017 TTTTTAT-T-
1 TTTTTATATA
48851025 TTTTTA-ATA
1 TTTTTATATA
*
48851034 TTTTTGTATA
1 TTTTTATATA
48851044 TTT
1 TTT
48851047 AGTTAGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
8 7 0.27
9 6 0.23
10 13 0.50
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (10 bp):
TTTTTATATA
Found at i:48855832 original size:22 final size:22
Alignment explanation
Indices: 48855807--48855848 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
48855797 ATTAAAAATT
48855807 TCAATAAAAATATATAAAAAAA
1 TCAATAAAAATATATAAAAAAA
*
48855829 TCAATACAAATATATAAAAA
1 TCAATAAAAATATATAAAAA
48855849 TCAAACTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
TCAATAAAAATATATAAAAAAA
Found at i:48862320 original size:16 final size:16
Alignment explanation
Indices: 48862299--48862331 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
48862289 GTGAACATCT
48862299 ATTGAGGAAATAATTA
1 ATTGAGGAAATAATTA
48862315 ATTGAGGAAATAATTA
1 ATTGAGGAAATAATTA
48862331 A
1 A
48862332 ATATTAGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (16 bp):
ATTGAGGAAATAATTA
Found at i:48870634 original size:16 final size:17
Alignment explanation
Indices: 48870602--48870635 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
48870592 AATGTTTTAA
48870602 TTATATTCAATAAATTT
1 TTATATTCAATAAATTT
*
48870619 TTATATT-AATATATTT
1 TTATATTCAATAAATTT
48870635 T
1 T
48870636 AATCATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATTCAATAAATTT
Found at i:48870698 original size:23 final size:22
Alignment explanation
Indices: 48870672--48870714 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
48870662 AATATTATTT
*
48870672 TATACTAATTATTATAATTAAAA
1 TATACTAATTA-TAAAATTAAAA
*
48870695 TATACTATTTATAAAATTAA
1 TATACTAATTATAAAATTAA
48870715 TTAAATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (22 bp):
TATACTAATTATAAAATTAAAA
Found at i:48870713 original size:31 final size:30
Alignment explanation
Indices: 48870645--48870720 Score: 75
Period size: 32 Copynumber: 2.5 Consensus size: 30
48870635 TAATCATATT
*
48870645 TAAAATT-TTAAATGAAAAATATTATTTTA
1 TAAAATTATTAAATGAAAAATACTATTTTA
* *
48870674 TACTAATTATTATAATTAAAATATACTA-TTTA
1 TA-AAATTATTA-AATGAAAA-ATACTATTTTA
48870706 TAAAATTAATTAAAT
1 TAAAATT-ATTAAAT
48870721 ATTAAATACA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
29 2 0.05
30 4 0.11
31 10 0.26
32 17 0.45
33 5 0.13
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (30 bp):
TAAAATTATTAAATGAAAAATACTATTTTA
Found at i:48870975 original size:45 final size:45
Alignment explanation
Indices: 48870926--48871012 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 45
48870916 ACTTTTTGTA
48870926 AAAATATATTCAAATAATATAAT-TTATTTTAATTATAAAAAAATT
1 AAAATATATTCAAATAATAT-ATCTTATTTTAATTATAAAAAAATT
* *
48870971 AAAATATCTTTAAATAATATATCTTATTTTAATTATAAAAAA
1 AAAATATATTCAAATAATATATCTTATTTTAATTATAAAAAA
48871013 TATTTTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 2 0.05
45 37 0.95
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (45 bp):
AAAATATATTCAAATAATATATCTTATTTTAATTATAAAAAAATT
Found at i:48873088 original size:61 final size:61
Alignment explanation
Indices: 48872958--48873080 Score: 219
Period size: 61 Copynumber: 2.0 Consensus size: 61
48872948 AGTGGGAACT
**
48872958 TACTTTTCCTAGGCTTAGAGGAACTTATGTGCCCAACATGGATATACCCCCGAGTTTTCTA
1 TACTTTTCCTAGGCTTAGAGGAACTTATGTGCCCAACATGGATATACCCCAAAGTTTTCTA
*
48873019 TACTTTTCCTAGGCTTAGAGGAACTTATGTGCCCAACATGGATATACCCTAAAGTTTTCTA
1 TACTTTTCCTAGGCTTAGAGGAACTTATGTGCCCAACATGGATATACCCCAAAGTTTTCTA
48873080 T
1 T
48873081 GTTTTTCCAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (61 bp):
TACTTTTCCTAGGCTTAGAGGAACTTATGTGCCCAACATGGATATACCCCAAAGTTTTCTA
Found at i:48874586 original size:4 final size:4
Alignment explanation
Indices: 48874577--48874606 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
48874567 CAATAACTGC
48874577 AACA AACA AACA AACA AACA AACA AACA AA
1 AACA AACA AACA AACA AACA AACA AACA AA
48874607 GCACCCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AACA
Found at i:48886825 original size:23 final size:22
Alignment explanation
Indices: 48886799--48886847 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
48886789 TTTTGAGAGG
*
48886799 TTAAAACATAATTTTATCATTT
1 TTAAAACATAATTTCATCATTT
***
48886821 ATTAATTTATAATTTCATCATTT
1 -TTAAAACATAATTTCATCATTT
48886844 TTAA
1 TTAA
48886848 GGGATTAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAACATAATTTCATCATTT
Found at i:48887517 original size:29 final size:29
Alignment explanation
Indices: 48887454--48887516 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
48887444 ATTAATAAGG
* * *
48887454 TTAAAAT-TTTAAATTAGGGTCAAACATT
1 TTAAAATGGTTAAATAAAGGTCAAACATT
*
48887482 TTAAAATGGTTAAATAAAGGTCAAATCTTT
1 TTAAAATGGTTAAATAAAGGTCAAA-CATT
48887512 TTAAA
1 TTAAA
48887517 TAAGGGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 7 0.24
29 14 0.48
30 8 0.28
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.38
Consensus pattern (29 bp):
TTAAAATGGTTAAATAAAGGTCAAACATT
Found at i:48902354 original size:31 final size:31
Alignment explanation
Indices: 48902302--48902453 Score: 129
Period size: 31 Copynumber: 4.9 Consensus size: 31
48902292 ATTGTAAGAT
*
48902302 TAAAATTATACTTTAAGTTATTAAATTATTAA
1 TAAATTTATA-TTTAAGTTATTAAATTATTAA
*
48902334 TAAATTTATATTTTAA-TTATTTAATT-TTAA
1 TAAATTTATA-TTTAAGTTATTAAATTATTAA
* **
48902364 -AAATTTGTAAAATAA-TTATTAAATTATTTAA
1 TAAATTTAT-ATTTAAGTTATTAAATTA-TTAA
* *
48902395 -AAGTTTTTATTTAAGTTATTAAATTATT--
1 TAAATTTATATTTAAGTTATTAAATTATTAA
*
48902423 TGAAAGTTTTTATTTAAGTTATTAAATTATT
1 T-AAA-TTTATATTTAAGTTATTAAATTATT
48902454 TGAAAGTTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
29 19 0.19
30 13 0.13
31 55 0.54
32 14 0.14
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.53
Consensus pattern (31 bp):
TAAATTTATATTTAAGTTATTAAATTATTAA
Found at i:48902454 original size:31 final size:31
Alignment explanation
Indices: 48902379--48902472 Score: 179
Period size: 31 Copynumber: 3.0 Consensus size: 31
48902369 TGTAAAATAA
*
48902379 TTATTAAATTATTTAAAAGTTTTTATTTAAG
1 TTATTAAATTATTTGAAAGTTTTTATTTAAG
48902410 TTATTAAATTATTTGAAAGTTTTTATTTAAG
1 TTATTAAATTATTTGAAAGTTTTTATTTAAG
48902441 TTATTAAATTATTTGAAAGTTTTTATTTAAG
1 TTATTAAATTATTTGAAAGTTTTTATTTAAG
48902472 T
1 T
48902473 CATCGAGTTG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (31 bp):
TTATTAAATTATTTGAAAGTTTTTATTTAAG
Found at i:48905048 original size:19 final size:18
Alignment explanation
Indices: 48905014--48905051 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
48905004 AACACTTGTC
48905014 TTTTTAATTTTATAATTA
1 TTTTTAATTTTATAATTA
48905032 TTTTTACATCTTT-TAATTA
1 TTTTTA-AT-TTTATAATTA
48905051 T
1 T
48905052 AAATTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 9 0.50
20 3 0.17
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTAATTTTATAATTA
Found at i:48910275 original size:14 final size:14
Alignment explanation
Indices: 48910258--48910287 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
48910248 CGTTGATGGT
*
48910258 GGGAGGGGGAGAGG
1 GGGAGAGGGAGAGG
48910272 GGGAGAGGGAGAGG
1 GGGAGAGGGAGAGG
48910286 GG
1 GG
48910288 TGACAGGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.77, T:0.00
Consensus pattern (14 bp):
GGGAGAGGGAGAGG
Found at i:48911286 original size:17 final size:17
Alignment explanation
Indices: 48911264--48911298 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
48911254 TAAATTAATT
*
48911264 TGAATTGAATTAAAAGA
1 TGAATTAAATTAAAAGA
*
48911281 TGAATTAAATTAATAGA
1 TGAATTAAATTAAAAGA
48911298 T
1 T
48911299 AACACAATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (17 bp):
TGAATTAAATTAAAAGA
Found at i:48914985 original size:19 final size:19
Alignment explanation
Indices: 48914940--48914977 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
48914930 ACTGTTAAAT
*
48914940 TATATTATTGCCCTTAGTA
1 TATATTATTGCCCTAAGTA
48914959 TATATTATTAGCCCTAAGT
1 TATATTATT-GCCCTAAGT
48914978 TTAATTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (19 bp):
TATATTATTGCCCTAAGTA
Found at i:48926408 original size:22 final size:22
Alignment explanation
Indices: 48926383--48926429 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
48926373 TTGATTTTCC
*
48926383 TTAAAATTATTTAAATAATTTA
1 TTAAAATTATTAAAATAATTTA
48926405 TTAAAATTATTAAAATAATTTA
1 TTAAAATTATTAAAATAATTTA
48926427 TTA
1 TTA
48926430 TACTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAAATTATTAAAATAATTTA
Found at i:48927201 original size:8 final size:8
Alignment explanation
Indices: 48927190--48927220 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
48927180 AATTTTATTA
48927190 TTTTTAAT
1 TTTTTAAT
48927198 TTTTTAAT
1 TTTTTAAT
48927206 TTTTTAAT
1 TTTTTAAT
48927214 TTTTTAA
1 TTTTTAA
48927221 AATTAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTAAT
Found at i:48929319 original size:26 final size:26
Alignment explanation
Indices: 48929289--48929350 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
48929279 TAAAAAAATA
48929289 ACCAAAATATTATAACTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTATTT
* *
48929315 ACCAAATTATTATAATTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTATTT
*
48929341 ATCAAAATAT
1 ACCAAAATAT
48929351 ACAAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (26 bp):
ACCAAAATATTATAACTTTTTTATTT
Found at i:48943185 original size:28 final size:27
Alignment explanation
Indices: 48943123--48943185 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
48943113 AATTACATTT
**
48943123 AAAATTAAAATATAAAAATTAAGTCTC
1 AAAATTAAAATATAAAAATTAAAACTC
* * *
48943150 AAATTTAAACATATTAAAATTAAAACTG
1 AAAATTAAA-ATATAAAAATTAAAACTC
48943178 AAAATTAA
1 AAAATTAA
48943186 CCATTTTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.30
Consensus pattern (27 bp):
AAAATTAAAATATAAAAATTAAAACTC
Found at i:48943472 original size:20 final size:21
Alignment explanation
Indices: 48943435--48943488 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
48943425 CCCGACCTAT
**
48943435 TTTTAATAAATACTAAAAATTTA
1 TTTTAA-AAATAC-AAAAAAGTA
48943458 TTTTAAAAATA-AAAAAAGTA
1 TTTTAAAAATACAAAAAAGTA
48943478 TTTTAAAAATA
1 TTTTAAAAATA
48943489 TTTTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 18 0.62
22 5 0.17
23 6 0.21
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
TTTTAAAAATACAAAAAAGTA
Found at i:48944005 original size:14 final size:14
Alignment explanation
Indices: 48943986--48944019 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
48943976 CATGATATAA
*
48943986 TTAAAAAATAGAAT
1 TTAAAAAATAAAAT
48944000 TTAAAAAATAAAAT
1 TTAAAAAATAAAAT
48944014 TCTAAA
1 T-TAAA
48944020 TGAAGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (14 bp):
TTAAAAAATAAAAT
Found at i:48952826 original size:24 final size:24
Alignment explanation
Indices: 48952790--48952840 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
48952780 AACGAAGGAT
*
48952790 GGACCTTTCGGTGATGGAATATCA
1 GGACCTTTAGGTGATGGAATATCA
* *
48952814 GGACTTTTAGGTGGTGGAATATCA
1 GGACCTTTAGGTGATGGAATATCA
48952838 GGA
1 GGA
48952841 GGGATGCTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.29
Consensus pattern (24 bp):
GGACCTTTAGGTGATGGAATATCA
Found at i:48953867 original size:26 final size:27
Alignment explanation
Indices: 48953838--48953890 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
48953828 TATTCTTTAT
*
48953838 ATATG-AAATTTTTATAATTTTT-TAAA
1 ATATGTAAATTTTGA-AATTTTTATAAA
48953864 ATATGTAAATTTTGAAATTTTTATAAA
1 ATATGTAAATTTTGAAATTTTTATAAA
48953891 TATTTTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (27 bp):
ATATGTAAATTTTGAAATTTTTATAAA
Found at i:48957080 original size:20 final size:20
Alignment explanation
Indices: 48957039--48957080 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
48957029 ATTTTTGGAC
* *
48957039 AAAAATCTATTTTATTATTT
1 AAAAATATATTTTATTAATT
48957059 AAAAATATA-TTTATATAATT
1 AAAAATATATTTTAT-TAATT
48957079 AA
1 AA
48957081 TTTTTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAAATATATTTTATTAATT
Found at i:48962931 original size:216 final size:208
Alignment explanation
Indices: 48962538--48962934 Score: 455
Period size: 216 Copynumber: 1.9 Consensus size: 208
48962528 GCCTTGAGAT
* *
48962538 TTTAGGGGGATTTGGATAGGAGGTTGTCATTGGTGAAGTTCAATATGAATTTAATGGTTTTTGTA
1 TTTAGGGGGATTTGGATAGGAGGTTGTCATTGATGAAGTTCAATATGAATTTAATGCTTTTTGTA
* * * * *
48962603 TTGGAGTTCCAAAAATGAATTATCAACAGGTGATCAGAGAAAGTGGCAGTGGACATCTCCCTAGG
66 TTGGAGTTCCAAAAATCAATTACCAACAGGTGATCAAAGAAAGTGGCAGCGGACATCTCCCCAGG
* ** **
48962668 CATTTGGACTGAATTTGAATCTAGGAGTCATCACTATTGGGAGGGCTTTACCTGAATACCACTCT
131 CATTTAGACTGAATTCAAATCTAGGAGTCATCACTATTGAAAGGGCTTTACCTGAATACCACTCT
48962733 GGCCTGAACAAGA
196 GGCCTGAACAAGA
* * *
48962746 TTTAGGGGGATTTGGATATGAGGGGTTGTCATTGATGAAGTTTATATTTGAATTTAATGCTTTTT
1 TTTAGGGGGATTTGGATA-G-GAGGTTGTCATTGATGAAGTTCA-ATATGAATTTAATGCTTTTT
* *
48962811 GTATTGGTGAAGTT-CAGAAGA-CAATTTACCAACAGGTGATCAAA-AGAAGTGGC-GCGGTACT
63 GTATT-G-G-AGTTCCA-AAAATCAA-TTACCAACAGGTGATCAAAGA-AAGTGGCAGCGG-ACA
* *
48962872 TCTTCCCCCGGGCATTTAGA-TTAAGTTCAAATCTTA-GAGTCATCACTATTGAAAGGGCTTTAC
121 TC-T-CCCCAGGCATTTAGACTGAA-TTCAAATC-TAGGAGTCATCACTATTGAAAGGGCTTTAC
48962935 TAAATACTAC
Statistics
Matches: 156, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
208 18 0.12
209 1 0.01
210 20 0.13
211 23 0.15
212 1 0.01
213 9 0.06
214 35 0.22
215 4 0.03
216 43 0.28
217 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.32
Consensus pattern (208 bp):
TTTAGGGGGATTTGGATAGGAGGTTGTCATTGATGAAGTTCAATATGAATTTAATGCTTTTTGTA
TTGGAGTTCCAAAAATCAATTACCAACAGGTGATCAAAGAAAGTGGCAGCGGACATCTCCCCAGG
CATTTAGACTGAATTCAAATCTAGGAGTCATCACTATTGAAAGGGCTTTACCTGAATACCACTCT
GGCCTGAACAAGA
Found at i:48965278 original size:21 final size:20
Alignment explanation
Indices: 48965254--48965296 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
48965244 ATCATTTCTT
* *
48965254 ATTTAATTATTTCATATTAAA
1 ATTTAAATATTT-AAATTAAA
48965275 ATTTAAATATTTAAATTAAA
1 ATTTAAATATTTAAATTAAA
48965295 AT
1 AT
48965297 AAACTAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTAAATATTTAAATTAAA
Found at i:48974397 original size:35 final size:35
Alignment explanation
Indices: 48974351--48974419 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
48974341 GGAAAAAAAG
48974351 TTTACCGCCACCGGAAAACAGAGGAGCTTCAACCT
1 TTTACCGCCACCGGAAAACAGAGGAGCTTCAACCT
*
48974386 TTTACCGCCACCGGAAAACAGAGGAGTTTCAACC
1 TTTACCGCCACCGGAAAACAGAGGAGCTTCAACC
48974420 AGTGTCACTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.17
Consensus pattern (35 bp):
TTTACCGCCACCGGAAAACAGAGGAGCTTCAACCT
Found at i:48976450 original size:17 final size:17
Alignment explanation
Indices: 48976396--48976455 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
48976386 AGAAATTTAT
48976396 AAATATATATTATAAAA
1 AAATATATATTATAAAA
* **
48976413 AATTAT-TAATATATATTA
1 AAATATAT-AT-TATAAAA
48976431 AAATATATATTATAAAA
1 AAATATATATTATAAAA
48976448 AAATATAT
1 AAATATAT
48976456 TTTAATGGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 1 0.03
17 20 0.59
18 12 0.35
19 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATATATTATAAAA
Found at i:48978641 original size:20 final size:20
Alignment explanation
Indices: 48978613--48978685 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 20
48978603 AGTTTTTTAT
48978613 TTTCTTATAATTTTTTAATAA
1 TTTC-TATAATTTTTTAATAA
48978634 TTTCTAT-A--TTTTAAT-A
1 TTTCTATAATTTTTTAATAA
*
48978650 TTT-TATAATAAATTTTAATAA
1 TTTCTATAAT--TTTTTAATAA
*
48978671 TTTTCTAAAATTTTT
1 -TTTCTATAATTTTT
48978686 ATATATGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
15 3 0.07
16 5 0.12
17 7 0.17
19 1 0.02
20 10 0.24
21 8 0.19
22 3 0.07
23 5 0.12
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTCTATAATTTTTTAATAA
Found at i:48978668 original size:10 final size:9
Alignment explanation
Indices: 48978625--48978674 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
48978615 TCTTATAATT
48978625 TTTTAATAA
1 TTTTAATAA
48978634 TTTCT-AT-A
1 TTT-TAATAA
*
48978642 TTTTAATAT
1 TTTTAATAA
48978651 TTTATAATAAA
1 TTT-TAAT-AA
48978662 TTTTAATAA
1 TTTTAATAA
48978671 TTTT
1 TTTT
48978675 CTAAAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
7 1 0.03
8 6 0.18
9 14 0.41
10 9 0.26
11 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTAATAA
Found at i:48978686 original size:20 final size:20
Alignment explanation
Indices: 48978624--48978686 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
48978614 TTCTTATAAT
*
48978624 TTTTTAATAA-TTTCT-ATA
1 TTTTTAATAATTTTCTAAAA
*
48978642 -TTTTAAT-ATTTTATAATAA
1 TTTTTAATAATTTTCTAA-AA
*
48978661 ATTTTAATAATTTTCTAAAA
1 TTTTTAATAATTTTCTAAAA
48978681 TTTTTA
1 TTTTTA
48978687 TATATGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.03
17 11 0.31
18 1 0.03
19 1 0.03
20 14 0.39
21 8 0.22
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTAATAATTTTCTAAAA
Found at i:48979003 original size:30 final size:32
Alignment explanation
Indices: 48978965--48979039 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
48978955 CTCTTTTATA
48978965 ATAAATTTTAACAAATG-TTT-T-TA-TGTTTT
1 ATAAATTTTAA-AAATGATTTCTATATTGTTTT
*
48978994 TTAATATTTTAAAAATGATTTCTATATTGTTTT
1 ATAA-ATTTTAAAAATGATTTCTATATTGTTTT
48979027 ATAAATTTTAAAA
1 ATAAATTTTAAAA
48979040 TTTTTCTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 8 0.21
30 10 0.26
31 1 0.03
32 11 0.28
33 9 0.23
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (32 bp):
ATAAATTTTAAAAATGATTTCTATATTGTTTT
Found at i:48979036 original size:32 final size:28
Alignment explanation
Indices: 48978965--48979062 Score: 103
Period size: 26 Copynumber: 3.4 Consensus size: 28
48978955 CTCTTTTATA
48978965 ATAAATTTTAACAAATGTTTTTATGTTTT
1 ATAAATTTTAA-AAATGTTTTTATGTTTT
*
48978994 TTAATATTTTAAAAATGATTTCTATATTGTTTT
1 ATAA-ATTTTAAAAATG-TTT-T-TA-TGTTTT
48979027 ATAAATTTT-AAAAT-TTTTCTAT-TTTT
1 ATAAATTTTAAAAATGTTTT-TATGTTTT
48979053 ATAAATTTTA
1 ATAAATTTTA
48979063 TATTTTATAA
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
26 13 0.22
27 1 0.02
28 3 0.05
29 11 0.18
30 10 0.17
31 6 0.10
32 7 0.12
33 9 0.15
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (28 bp):
ATAAATTTTAAAAATGTTTTTATGTTTT
Found at i:48979066 original size:17 final size:17
Alignment explanation
Indices: 48979032--48979090 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
48979022 GTTTTATAAA
*
48979032 TTTTA-AAATTTTTCTAT
1 TTTTATAAA-TTTTATAT
48979049 TTTTATAAATTTTATAT
1 TTTTATAAATTTTATAT
*
48979066 TTTATAATAAATTTTGT-T
1 TTT-T-ATAAATTTTATAT
48979084 TTTTATA
1 TTTTATA
48979091 TCTCTAACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
16 3 0.08
17 16 0.43
18 8 0.22
19 10 0.27
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTATAAATTTTATAT
Found at i:48979075 original size:19 final size:19
Alignment explanation
Indices: 48979041--48979090 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
48979031 ATTTTAAAAT
*
48979041 TTTTCTATTTT-T-ATAAA
1 TTTTATATTTTATAATAAA
48979058 TTTTATATTTTATAATAAA
1 TTTTATATTTTATAATAAA
* *
48979077 TTTTGTTTTTTATA
1 TTTTATATTTTATA
48979091 TCTCTAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 10 0.36
18 1 0.04
19 17 0.61
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTATATTTTATAATAAA
Found at i:48979115 original size:10 final size:10
Alignment explanation
Indices: 48979100--48979176 Score: 54
Period size: 10 Copynumber: 8.0 Consensus size: 10
48979090 ATCTCTAACA
48979100 AATTTTTAAT
1 AATTTTTAAT
48979110 AATTTTT-A-
1 AATTTTTAAT
*
48979118 AATGTTTTTAT
1 AAT-TTTTAAT
*
48979129 AAATTTTAA-
1 AATTTTTAAT
*
48979138 AATTTTTTAT
1 AATTTTTAAT
*
48979148 AATTTTTTAT
1 AATTTTTAAT
**
48979158 -ATTTCAAAT
1 AATTTTTAAT
*
48979167 ATTTTTTAAT
1 AATTTTTAAT
48979177 TTTTATAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
8 3 0.06
9 18 0.35
10 29 0.56
11 2 0.04
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:48979156 original size:20 final size:19
Alignment explanation
Indices: 48979099--48979154 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
48979089 TATCTCTAAC
*
48979099 AAATTTTTAATAATTTTT-
1 AAATTTTTTATAATTTTTA
*
48979117 AAATGTTTTTATAAATTTTA
1 AAAT-TTTTTATAATTTTTA
48979137 AAATTTTTTATAATTTTT
1 AAATTTTTTATAATTTTT
48979155 TATATTTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.12
19 25 0.76
20 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
AAATTTTTTATAATTTTTA
Found at i:48979324 original size:36 final size:36
Alignment explanation
Indices: 48979283--48979352 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
48979273 TGAAGCTCAT
*
48979283 AATAACAAATAAAATACGGCTTGGACGGCTTGGCAA
1 AATAACAAATAAAATACGGCTTGGACAGCTTGGCAA
48979319 AATAACAAATAAAATACGGCTTGGACAGCTTGGC
1 AATAACAAATAAAATACGGCTTGGACAGCTTGGC
48979353 TCGGAAAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.20
Consensus pattern (36 bp):
AATAACAAATAAAATACGGCTTGGACAGCTTGGCAA
Done.