Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 6 of 31
Found at i:1432573 original size:18 final size:18
Alignment explanation
Indices: 1432550--1432601 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
1432540 AGACCTAATA
1432550 ATTTATATATTTATTTAT
1 ATTTATATATTTATTTAT
1432568 ATTTATATATTT-TATTAT
1 ATTTATATATTTAT-TTAT
1432586 A-TTATA-ATTATATTTA
1 ATTTATATATT-TATTTA
1432602 AAATATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.10
17 10 0.32
18 18 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTATATATTTATTTAT
Found at i:1432586 original size:30 final size:30
Alignment explanation
Indices: 1432546--1432619 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
1432536 TATTAGACCT
* *
1432546 AATAATTTA-TATATT-TATTTATATTT-A
1 AATATTTTATTATATTATAATTATATTTAA
*
1432573 TATATTTTATTATATTATAATTATATTTAA
1 AATATTTTATTATATTATAATTATATTTAA
1432603 AATATTTTA-TAT-TTATA
1 AATATTTTATTATATTATA
1432620 TAAATTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 7 0.17
28 11 0.28
29 13 0.32
30 9 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
AATATTTTATTATATTATAATTATATTTAA
Found at i:1432633 original size:20 final size:19
Alignment explanation
Indices: 1432606--1432673 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 19
1432596 TATTTAAAAT
1432606 ATTTT-ATAT-TTATATAA
1 ATTTTAATATATTATATAA
1432623 ATTTTAATATATTA-AT-A
1 ATTTTAATATATTATATAA
*
1432640 ATTTT--T-TA-CATATAA
1 ATTTTAATATATTATATAA
*
1432655 ATTTTAAAATATTTATATA
1 ATTTTAATATA-TTATATA
1432674 TTAATATTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 15
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.03
14 4 0.10
15 7 0.18
17 11 0.28
18 8 0.21
19 3 0.08
20 5 0.13
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTAATATATTATATAA
Found at i:1432640 original size:18 final size:16
Alignment explanation
Indices: 1432563--1432644 Score: 59
Period size: 17 Copynumber: 5.2 Consensus size: 16
1432553 TATATATTTA
1432563 TTTATATTTATAT-AT
1 TTTATATTTATATAAT
*
1432578 TTTAT-TATATTATAA-
1 TTTATATTTA-TATAAT
*
1432593 -TTATATTTA-AAATAT
1 TTTATATTTATATA-AT
1432608 TTTATATTTATATAAAT
1 TTTATATTTATAT-AAT
1432625 TTTAATATATTA-ATAAT
1 TTT-ATAT-TTATATAAT
1432642 TTT
1 TTT
1432645 TTACATATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
13 2 0.04
14 8 0.15
15 11 0.21
16 10 0.19
17 12 0.23
18 7 0.13
19 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATATTTATATAAT
Found at i:1433209 original size:12 final size:12
Alignment explanation
Indices: 1433194--1433218 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1433184 AATTTAAATA
1433194 ATTAAATATAAT
1 ATTAAATATAAT
1433206 ATTAAATATAAT
1 ATTAAATATAAT
1433218 A
1 A
1433219 ACTAATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTAAATATAAT
Found at i:1433249 original size:18 final size:18
Alignment explanation
Indices: 1433226--1433260 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1433216 ATAACTAATT
*
1433226 TATTTTTACTAAATAAAC
1 TATTTTAACTAAATAAAC
*
1433244 TATTTTAATTAAATAAA
1 TATTTTAACTAAATAAA
1433261 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTTTAACTAAATAAAC
Found at i:1433304 original size:23 final size:23
Alignment explanation
Indices: 1433261--1433304 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1433251 ATTAAATAAA
*
1433261 TTAAAATAATTTAATTTTTTATT
1 TTAAAATAATTTAATATTTTATT
1433284 TTAAAATAAATTTAA-ATTTTA
1 TTAAAAT-AATTTAATATTTTA
1433305 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAAATAATTTAATATTTTATT
Found at i:1433308 original size:19 final size:18
Alignment explanation
Indices: 1433281--1433319 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1433271 TTAATTTTTT
*
1433281 ATTTTAAAATAAATTTAA
1 ATTTTAAAATAAAATTAA
1433299 ATTTTAAAAATAAAATTAA
1 ATTTT-AAAATAAAATTAA
1433318 AT
1 AT
1433320 AAATATCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTTAAAATAAAATTAA
Found at i:1433800 original size:21 final size:21
Alignment explanation
Indices: 1433776--1433820 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1433766 AATATTATAT
1433776 AATTAAAAAAATTTATTAAAA
1 AATTAAAAAAATTTATTAAAA
* * *
1433797 AATTAATAATATTTATTTAAA
1 AATTAAAAAAATTTATTAAAA
1433818 AAT
1 AAT
1433821 AATTATAGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTAAAAAAATTTATTAAAA
Found at i:1437243 original size:5 final size:5
Alignment explanation
Indices: 1437217--1437257 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
1437207 AAAAATTTGA
1437217 TTAA- TTAAT TTAAAT TTAAAT TTAAT TTAAT TTAAT TTAAT
1 TTAAT TTAAT TT-AAT TT-AAT TTAAT TTAAT TTAAT TTAAT
1437258 AAAAAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.11
5 20 0.57
6 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TTAAT
Found at i:1437243 original size:21 final size:21
Alignment explanation
Indices: 1437217--1437256 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1437207 AAAAATTTGA
1437217 TTAA-TTAATTTAAATTTAAAT
1 TTAATTTAATTT-AATTTAAAT
1437238 TTAATTTAATTTAATTTAA
1 TTAATTTAATTTAATTTAA
1437257 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAATTTAATTTAATTTAAAT
Found at i:1437308 original size:16 final size:16
Alignment explanation
Indices: 1437289--1437351 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
1437279 CGAAATTAAT
1437289 TTAAATTCGAAATGAC
1 TTAAATTCGAAATGAC
*
1437305 TTAAA-TCTAAAATGAC
1 TTAAATTC-GAAATGAC
** *
1437321 TCGAACTCGAAATGAC
1 TTAAATTCGAAATGAC
* *
1437337 TTGAATCCGAAATGA
1 TTAAATTCGAAATGA
1437352 TCCGAACTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
15 2 0.05
16 34 0.89
17 2 0.05
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (16 bp):
TTAAATTCGAAATGAC
Found at i:1437350 original size:32 final size:32
Alignment explanation
Indices: 1437295--1437359 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
1437285 TAATTTAAAT
*
1437295 TCGAAATGACTTAAATCTAAAATGA-CTCGAAC
1 TCGAAATGACTTAAATCCAAAATGATC-CGAAC
* *
1437327 TCGAAATGACTTGAATCCGAAATGATCCGAAC
1 TCGAAATGACTTAAATCCAAAATGATCCGAAC
1437359 T
1 T
1437360 GAATTCGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (32 bp):
TCGAAATGACTTAAATCCAAAATGATCCGAAC
Found at i:1438042 original size:16 final size:16
Alignment explanation
Indices: 1438023--1438108 Score: 86
Period size: 16 Copynumber: 5.4 Consensus size: 16
1438013 TCAAATCTAG
1438023 AATGACTCGAATTCGA
1 AATGACTCGAATTCGA
* *
1438039 AATGACTTGAATCCGA
1 AATGACTCGAATTCGA
*
1438055 AATGAC-CTGAACTCGA
1 AATGACTC-GAATTCGA
*
1438071 AATGAC-CTGAATTCAA
1 AATGACTC-GAATTCGA
* *
1438087 AATGACTCAAACTCGA
1 AATGACTCGAATTCGA
1438103 AATGAC
1 AATGAC
1438109 ATGGAATAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
16 57 0.98
17 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (16 bp):
AATGACTCGAATTCGA
Found at i:1438059 original size:32 final size:32
Alignment explanation
Indices: 1438023--1438108 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
1438013 TCAAATCTAG
* * *
1438023 AATGACTCGAATTCGAAATGACTTGAATCCGA
1 AATGACTCGAACTCGAAATGACCTGAATCCAA
*
1438055 AATGAC-CTGAACTCGAAATGACCTGAATTCAA
1 AATGACTC-GAACTCGAAATGACCTGAATCCAA
*
1438087 AATGACTCAAACTCGAAATGAC
1 AATGACTCGAACTCGAAATGAC
1438109 ATGGAATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 1 0.02
32 45 0.96
33 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (32 bp):
AATGACTCGAACTCGAAATGACCTGAATCCAA
Found at i:1439189 original size:16 final size:17
Alignment explanation
Indices: 1439170--1439209 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1439160 ACCCGAATTT
1439170 GAAATGACT-TGAACCC
1 GAAATGACTCTGAACCC
*
1439186 GAAATGA-TCTGAATCC
1 GAAATGACTCTGAACCC
1439202 GAAATGAC
1 GAAATGAC
1439210 CCGAATCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (17 bp):
GAAATGACTCTGAACCC
Found at i:1439215 original size:16 final size:16
Alignment explanation
Indices: 1439158--1439216 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
1439148 TAAACCTGAT
**
1439158 TGACCCGAATTTGAAA
1 TGACCCGAATCCGAAA
** *
1439174 TGACTTGAACCCGAAA
1 TGACCCGAATCCGAAA
* *
1439190 TGATCTGAATCCGAAA
1 TGACCCGAATCCGAAA
1439206 TGACCCGAATC
1 TGACCCGAATC
1439217 TAAAATGATC
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (16 bp):
TGACCCGAATCCGAAA
Found at i:1439317 original size:16 final size:15
Alignment explanation
Indices: 1439270--1439323 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
1439260 GAACTCGAAA
*
1439270 CTAACTTAAAATAA-
1 CTAATTTAAAATAAT
*
1439284 CATAATCTAAAATAAT
1 C-TAATTTAAAATAAT
1439300 CTAATTTAAAATTAAT
1 CTAATTTAAAA-TAAT
*
1439316 CTGATTTA
1 CTAATTTA
1439324 CTCGATTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 1 0.03
15 20 0.61
16 12 0.36
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.37
Consensus pattern (15 bp):
CTAATTTAAAATAAT
Found at i:1443078 original size:4 final size:4
Alignment explanation
Indices: 1443069--1443093 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1443059 TGTGAAGTCA
1443069 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
1443094 TCTTTGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:1443616 original size:15 final size:16
Alignment explanation
Indices: 1443588--1443622 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1443578 TATATATTTT
1443588 TTATAATTAAATTTTAA
1 TTATAATT-AATTTTAA
1443605 TTATAATT-ATTTTAA
1 TTATAATTAATTTTAA
1443620 TTA
1 TTA
1443623 ATTAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
17 8 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATAATTAATTTTAA
Found at i:1443641 original size:19 final size:19
Alignment explanation
Indices: 1443592--1443642 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1443582 TATTTTTTAT
*
1443592 AATTAAA-TT-TTAATTAT
1 AATTAAATTTATTAATTAA
*
1443609 AATT-ATTTTAATTAATTAA
1 AATTAAATTT-ATTAATTAA
1443628 AATTAAATTTATTAA
1 AATTAAATTTATTAA
1443643 ATTAGATAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.04
17 6 0.22
19 16 0.59
20 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTAAATTTATTAATTAA
Found at i:1454065 original size:175 final size:175
Alignment explanation
Indices: 1453774--1454109 Score: 539
Period size: 175 Copynumber: 1.9 Consensus size: 175
1453764 AATAAAAAAT
* * *
1453774 AAAACAAAAAGAAACAAGGAAAAAACAGAGCAGATTCAACTTCTCATGATCATATAGGGAATACA
1 AAAACAAAAAGAAACAAGGAAAAAACAGAGCAAAGTCAACTTCTCATGATCATATAGGAAATACA
* * * *
1453839 TTTACCAAATGAAAAGAGATTCGATAGAAAAAGAAGATAAATCCAAGAGGAAATCGCTATTGTAG
66 CTTACCAAATGAAAAGAGATTCAATAGAAAAAGAAGATAAACCCAAGAGGAAATCGCCATTGTAG
1453904 CTTTGTGAGGAAGAAGAGAATTGAGAAAAAAAAATGGGGAGGAAA
131 CTTTGTGAGGAAGAAGAGAATTGAGAAAAAAAAATGGGGAGGAAA
* * * *
1453949 AAAACAAAAAGAAACAAGGGAAAAACAGAGTAAAGTCAACTTCTCGTGCTCAT-TAAGGAAATAC
1 AAAACAAAAAGAAACAAGGAAAAAACAGAGCAAAGTCAACTTCTCATGATCATAT-AGGAAATAC
*
1454013 ACTTACCAAATGAAAAGAGATTCAATAGAAAAAGAAGATAAACCCCAGAGGAAATCGCCATTGTA
65 ACTTACCAAATGAAAAGAGATTCAATAGAAAAAGAAGATAAACCCAAGAGGAAATCGCCATTGTA
*
1454078 GCTTTGTGATGAAGAAGAGAATTGAGAAAAAA
130 GCTTTGTGAGGAAGAAGAGAATTGAGAAAAAA
1454110 TGAGGAGGAT
Statistics
Matches: 147, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
174 1 0.01
175 146 0.99
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (175 bp):
AAAACAAAAAGAAACAAGGAAAAAACAGAGCAAAGTCAACTTCTCATGATCATATAGGAAATACA
CTTACCAAATGAAAAGAGATTCAATAGAAAAAGAAGATAAACCCAAGAGGAAATCGCCATTGTAG
CTTTGTGAGGAAGAAGAGAATTGAGAAAAAAAAATGGGGAGGAAA
Found at i:1454815 original size:21 final size:21
Alignment explanation
Indices: 1454790--1454838 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
1454780 ATAAATTTAT
1454790 TTATTAATAAA-ATATTTAAAA
1 TTATTAATAAATAT-TTTAAAA
1454811 TTATTGAATAAATATTTTAAAA
1 TTATT-AATAAATATTTTAAAA
1454833 -TATTAA
1 TTATTAA
1454839 ACTTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 2 0.08
21 9 0.35
22 13 0.50
23 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TTATTAATAAATATTTTAAAA
Found at i:1454829 original size:22 final size:21
Alignment explanation
Indices: 1454790--1454838 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
1454780 ATAAATTTAT
1454790 TTATTAATAAAATATTTAAAA
1 TTATTAATAAAATATTTAAAA
1454811 TTATTGAAT-AAATATTTTAAAA
1 TTATT-AATAAAATA-TTTAAAA
1454833 -TATTAA
1 TTATTAA
1454839 ACTTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 2 0.08
21 14 0.54
22 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TTATTAATAAAATATTTAAAA
Found at i:1455096 original size:153 final size:152
Alignment explanation
Indices: 1454933--1455240 Score: 383
Period size: 153 Copynumber: 2.0 Consensus size: 152
1454923 ACTCACTATT
* *
1454933 TTTAAATTTTTAAC-TCGATAAATATATTTTATTGTTAAAATATCTAAAATTATCT-TATAAATA
1 TTTAAATTTTTAACAT-GATAAATATATTTTATTATTAAAATATCTAAAATTATATGT-TAAATA
** * *
1454996 -TTAAAAAATTTTTA-AAATAAAAAATAATATAAAATAATTTTTTTA-CTCTTAAGAAACTATCG
64 TTTAAAAAAAATTTATAAAT--AAAATAATATAAAATAATTTTTTTAGCT-TGAA-AAACTATCA
1455058 TATTTTAATACAAAAGCATTAATTTATA
125 TATTTTAATACAAAAGCATTAATTTATA
* * *
1455086 TTTAATTTTTTAACATGATAAATGTATTTTATTATTAAAATATTTAAAATTATATGTTAAATATT
1 TTTAAATTTTTAACATGATAAATATATTTTATTATTAAAATATCTAAAATTATATGTTAAATATT
** *
1455151 TAAAAAAAATTTATAGCTAAAATGATATAAAATAATTTTTTTAGCTTGAAAAACTATCATATTTT
66 TAAAAAAAATTTATAAATAAAATAATATAAAATAATTTTTTTAGCTTGAAAAACTATCATATTTT
** **
1455216 AATATGAAAGTTTTAATTTATA
131 AATACAAAAGCATTAATTTATA
1455238 TTT
1 TTT
1455241 TTCTTTTAAA
Statistics
Matches: 134, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
152 35 0.26
153 81 0.60
154 16 0.12
155 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (152 bp):
TTTAAATTTTTAACATGATAAATATATTTTATTATTAAAATATCTAAAATTATATGTTAAATATT
TAAAAAAAATTTATAAATAAAATAATATAAAATAATTTTTTTAGCTTGAAAAACTATCATATTTT
AATACAAAAGCATTAATTTATA
Found at i:1456412 original size:30 final size:30
Alignment explanation
Indices: 1456378--1456440 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1456368 CTGGTTTATA
1456378 TTATATGGAGATA-AATTAAATTTAA-AATAT
1 TTATATGGA-ATATAATTAAATTTAATAA-AT
**
1456408 TTATATTTAATATAATTAAATTTAATAAAT
1 TTATATGGAATATAATTAAATTTAATAAAT
1456438 TTA
1 TTA
1456441 AATATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 3 0.10
30 24 0.83
31 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (30 bp):
TTATATGGAATATAATTAAATTTAATAAAT
Found at i:1456492 original size:31 final size:32
Alignment explanation
Indices: 1456457--1456533 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
1456447 AAATTTTATT
* * *
1456457 AATTTAAATTTGATT-AAATTTCATTAATTTA
1 AATTTAAATTTAATTAAAATTTAATTAATATA
*
1456488 AATTTAAA-ATAATTAAAATTTAATTAATATA
1 AATTTAAATTTAATTAAAATTTAATTAATATA
1456519 AATATTAAATTTAAT
1 AAT-TTAAATTTAAT
1456534 AGATCTAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
30 4 0.11
31 25 0.66
32 5 0.13
33 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (32 bp):
AATTTAAATTTAATTAAAATTTAATTAATATA
Found at i:1456501 original size:25 final size:26
Alignment explanation
Indices: 1456433--1456499 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 26
1456423 TTAAATTTAA
*
1456433 TAAATTTAAATATTAAATTTTATTAATT
1 TAAATTTAAA-A-TAAATTTCATTAATT
* *
1456461 TAAATTT-GATTAAATTTCATTAATT
1 TAAATTTAAAATAAATTTCATTAATT
1456486 TAAATTTAAAATAA
1 TAAATTTAAAATAA
1456500 TTAAAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 21 0.64
26 4 0.12
27 1 0.03
28 7 0.21
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (26 bp):
TAAATTTAAAATAAATTTCATTAATT
Found at i:1456508 original size:47 final size:46
Alignment explanation
Indices: 1456388--1456547 Score: 128
Period size: 47 Copynumber: 3.3 Consensus size: 46
1456378 TTATATGGAG
* *
1456388 ATAAA-TTAAATTTAAAATATTTATATTT-AATATAATTAAATTTA
1 ATAAATTTAAATTTAAAATATTAAAATTTAAATATAATTAAATTTA
* * * * *
1456432 ATAAATTTAAATATT-AAATTTTATTAATTTAAATTTGATTAAATTTC
1 ATAAATTTAAAT-TTAAAATATTA-AAATTTAAATATAATTAAATTTA
*
1456479 ATTAATTTAAATTTAAAATAATTAAAATTTAATTAATATAAATATTAAATTTA
1 ATAAATTTAAATTTAAAAT-ATTAAAATTT-A--AATAT--A-ATTAAATTTA
* *
1456532 ATAGATCTAAATTTAA
1 ATAAATTTAAATTTAA
1456548 GATGATTTAA
Statistics
Matches: 88, Mismatches: 16, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
44 5 0.06
45 12 0.14
46 8 0.09
47 33 0.38
48 4 0.05
50 4 0.05
53 22 0.25
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (46 bp):
ATAAATTTAAATTTAAAATATTAAAATTTAAATATAATTAAATTTA
Found at i:1456521 original size:15 final size:14
Alignment explanation
Indices: 1456391--1456526 Score: 76
Period size: 15 Copynumber: 8.9 Consensus size: 14
1456381 TATGGAGATA
*
1456391 AATTAAATTTAAAAT
1 AATTAAATTT-AATT
* *
1456406 ATTTATATTTAATAT
1 AATTAAATTTAAT-T
*
1456421 AATTAAATTTAATA
1 AATTAAATTTAATT
1456435 AATTTAAATATTAAATTT
1 AA-TTAAAT-TT-AA-TT
*
1456453 TATT-AATTTAAATTT
1 AATTAAATTT-AA-TT
* *
1456468 GATTAAATTTCATT
1 AATTAAATTTAATT
*
1456482 AATTTAAATTTAAAAT
1 AA-TTAAATTT-AATT
1456498 AATTAAAATTTAATT
1 AATT-AAATTTAATT
1456513 AATATAAATATTAA
1 AAT-TAAAT-TTAA
1456527 ATTTAATAGA
Statistics
Matches: 96, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
14 7 0.07
15 58 0.60
16 25 0.26
17 4 0.04
18 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (14 bp):
AATTAAATTTAATT
Found at i:1456527 original size:53 final size:53
Alignment explanation
Indices: 1456433--1456547 Score: 130
Period size: 53 Copynumber: 2.2 Consensus size: 53
1456423 TTAAATTTAA
* * * *
1456433 TAAATTT-AAATATTAAATTTTATTAATTTAAATTTGATTAAATTTCATTA-ATT
1 TAAATTTAAAATATTAAATTTAATTAATATAAA-TTGATTAAATTT-AATAGATC
1456486 TAAATTTAAAATAATTAAAATTTAATTAATATAAA-T-ATTAAATTTAATAGATC
1 TAAATTTAAAAT-ATT-AAATTTAATTAATATAAATTGATTAAATTTAATAGATC
1456539 TAAATTTAA
1 TAAATTTAA
1456548 GATGATTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
52 3 0.06
53 27 0.50
54 5 0.09
55 3 0.06
56 16 0.30
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (53 bp):
TAAATTTAAAATATTAAATTTAATTAATATAAATTGATTAAATTTAATAGATC
Found at i:1456686 original size:16 final size:16
Alignment explanation
Indices: 1456661--1456868 Score: 107
Period size: 16 Copynumber: 13.5 Consensus size: 16
1456651 AAAACCAATC
1456661 AATTTAAATCTAAAAT
1 AATTTAAATCTAAAAT
*
1456677 AATTTGAATCTAAAAT
1 AATTTAAATCTAAAAT
*
1456693 AATTTAAATTTAAAAT
1 AATTTAAATCTAAAAT
*
1456709 AAATTAAATC---AA-
1 AATTTAAATCTAAAAT
* * *
1456721 ACTTTAACTC-GAAAT
1 AATTTAAATCTAAAAT
* * *
1456736 AACTCAAATATAAAAT
1 AATTTAAATCTAAAAT
*
1456752 AA--TCAATACTCAAAAT
1 AATTTAAAT-CT-AAAAT
*
1456768 AATTTAAATTTAAAAT
1 AATTTAAATCTAAAAT
*
1456784 AATTTAAAAT-TAAATT
1 AATTT-AAATCTAAAAT
* *
1456800 AATATAAAT-AAAAAT
1 AATTTAAATCTAAAAT
* * ** *
1456815 AATATAAATATTTATT
1 AATTTAAATCTAAAAT
**
1456831 AATTTTAAA-CTATCA-
1 AA-TTTAAATCTAAAAT
1456846 AATTTAAAT-TAAAAT
1 AATTTAAATCTAAAAT
1456861 AATTTAAA
1 AATTTAAA
1456869 ATCAATTAAT
Statistics
Matches: 145, Mismatches: 34, Indels: 27
0.70 0.17 0.13
Matches are distributed among these distances:
12 7 0.05
13 2 0.01
14 14 0.10
15 33 0.23
16 75 0.52
17 10 0.07
18 4 0.03
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.37
Consensus pattern (16 bp):
AATTTAAATCTAAAAT
Found at i:1460757 original size:173 final size:171
Alignment explanation
Indices: 1460431--1460772 Score: 596
Period size: 173 Copynumber: 2.0 Consensus size: 171
1460421 AATAAAAAAT
1460431 AAAACAAAAAGAAACAAGGAAAAACAGAGCAGATTCAACTTCTCATGATCATAAAGGGAATACAT
1 AAAACAAAAAGAAACAAGGAAAAACAGAGCAGATTCAACTTCTCATGATCATAAAGGGAATACAT
* * *
1460496 TTACCAAATGAAAAGAGATTCGATAGAAAAAGAAGATAAATCCCAGAGGAAATCGCCATTGTAGC
66 TTACCAAATGAAAAGAAATTCAATAGAAAAAGAAGATAAACCCCAGAGGAAATCGCCATTGTAGC
*
1460561 TTTGTGAGGAAGAAGAGAATTGAGAAAAAAATGGGGAGGAAA
131 TTTGTGAGGAAGAAGAAAATTGAG-AAAAAATGGGGAGGAAA
*
1460603 AAAACAAAAAGAAACAAGGAAAAAAACAGAGCAGATTCAACTTCTCATGCTCATAAAGGGAATAC
1 AAAACAAAAAGAAACAAGG--AAAAACAGAGCAGATTCAACTTCTCATGATCATAAAGGGAATAC
1460668 ATTTACCAAATGAAAA-AAATTCAATAGAAAAAGAAGATAAACCCCAGAGGAAATCGCCATTGTA
64 ATTTACCAAATGAAAAGAAATTCAATAGAAAAAGAAGATAAACCCCAGAGGAAATCGCCATTGTA
*
1460732 GCTTTGTGAGGAAGAGGAAAATTGAGAAAAAATGGGGAGGA
129 GCTTTGTGAGGAAGAAGAAAATTGAGAAAAAATGGGGAGGA
1460773 TTTGGAGTGA
Statistics
Matches: 162, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
172 34 0.21
173 69 0.43
174 59 0.36
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.17
Consensus pattern (171 bp):
AAAACAAAAAGAAACAAGGAAAAACAGAGCAGATTCAACTTCTCATGATCATAAAGGGAATACAT
TTACCAAATGAAAAGAAATTCAATAGAAAAAGAAGATAAACCCCAGAGGAAATCGCCATTGTAGC
TTTGTGAGGAAGAAGAAAATTGAGAAAAAATGGGGAGGAAA
Found at i:1460881 original size:29 final size:29
Alignment explanation
Indices: 1460841--1460906 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
1460831 AGGATAGTGC
*
1460841 TTATTTTAAAATAAATTATCAATATAATA
1 TTATTTTAAAATAAATTATCAAAATAATA
* *
1460870 TTATTTTAAAATTACTTATCAAAATAATA
1 TTATTTTAAAATAAATTATCAAAATAATA
1460899 TTATTTTA
1 TTATTTTA
1460907 TTTGTATGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (29 bp):
TTATTTTAAAATAAATTATCAAAATAATA
Found at i:1461358 original size:172 final size:169
Alignment explanation
Indices: 1461020--1461467 Score: 499
Period size: 172 Copynumber: 2.7 Consensus size: 169
1461010 ATAATTATTA
* *
1461020 TTTATTATTAAAATATTTAAAATTATTTGATAAATATTTTAAAAATATTAAAATTTAAAATTATG
1 TTTATTATTAAAATATTCAAAATTATTTGATAAATA-TTTAAAAATATTAAAATCTAAAATTATG
* * * * * ** * *
1461085 AAAAACAAA--ATTTATACTTAAGAAACGTCATATTTTAATA-AGAAAATATTAATATATATTTT
65 TAAAATAAATTTTTTATGCTTAAAAAATATCATATTTTAATATA-AAAATATCAATATATAATTT
*
1461147 TTAAGCTTATTATTTTTAAATTTTTTATTTGATAAATATAT
129 TTAAGCTTATTATTTTTAAATTTTTAATTTGATAAATATAT
* *
1461188 TTTAATATTAAAATATTCAAAATTACTTTG-T-AATATTTAAAAATTTTCAAAATCTAAAATTAT
1 TTTATTATTAAAATATTCAAAATTA-TTTGATAAATATTTAAAAATATT-AAAATCTAAAATTAT
*
1461251 GTAAAATAAATTTTTTATGCTTAAAAAATTATCATATTTTAATATAAAAGTATCAATTTATATAA
64 GTAAAATAAATTTTTTATGCTTAAAAAA-TATCATATTTTAATATAAAAATATCAA--TATATAA
* *
1461316 TTTTT-AGATTTATTATTTTGT-CATTTTTAATATT-ATAAATATAT
126 TTTTTAAG-CTTATTATTTT-TAAATTTTTAAT-TTGATAAATATAT
* *
1461360 TTTATTATTAAAATA-TCTAAAATTA-TTGTTAAATATTTAAAAAAATT-AAATCTAAAATTATG
1 TTTATTATTAAAATATTC-AAAATTATTTGATAAATATTTAAAAATATTAAAATCTAAAATTATG
* *
1461422 T-AAAT-AATTTTTTTTAGCTTGAAAAACTATCATATTTTAATATAAA
65 TAAAATAAATTTTTTAT-GCTT-AAAAAATATCATATTTTAATATAAA
1461468 GGTTTCAACT
Statistics
Matches: 242, Mismatches: 22, Indels: 31
0.82 0.07 0.11
Matches are distributed among these distances:
166 11 0.05
167 26 0.11
168 33 0.14
169 44 0.18
170 45 0.19
171 6 0.02
172 74 0.31
173 3 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (169 bp):
TTTATTATTAAAATATTCAAAATTATTTGATAAATATTTAAAAATATTAAAATCTAAAATTATGT
AAAATAAATTTTTTATGCTTAAAAAATATCATATTTTAATATAAAAATATCAATATATAATTTTT
AAGCTTATTATTTTTAAATTTTTAATTTGATAAATATAT
Found at i:1461375 original size:18 final size:19
Alignment explanation
Indices: 1461340--1461375 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1461330 ATTTTGTCAT
1461340 TTTTAATATTATAAATATA
1 TTTTAATATTATAAATATA
*
1461359 TTTTATTATTA-AAATAT
1 TTTTAATATTATAAATAT
1461376 CTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATATTATAAATATA
Found at i:1461402 original size:21 final size:21
Alignment explanation
Indices: 1461361--1461401 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1461351 TAAATATATT
1461361 TTATTATTAAAATATCTAAAA
1 TTATTATTAAAATATCTAAAA
* *
1461382 TTATTGTT-AAATATTTAAAA
1 TTATTATTAAAATATCTAAAA
1461402 AAATTAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
TTATTATTAAAATATCTAAAA
Found at i:1461535 original size:170 final size:170
Alignment explanation
Indices: 1461020--1461555 Score: 463
Period size: 170 Copynumber: 3.2 Consensus size: 170
1461010 ATAATTATTA
* * *
1461020 TTTATTATTAAAATATTTAAAATTA-TTTGATAAATATTTTAAAAATATTAAAATTTAAAATTAT
1 TTTATTATTAAAATATCTAAAATTACTTTG-T-AATA-TTTAAAAAAATTAAAATCTAAAATTAT
* * * * * * * *
1461084 GAAAAACAAA--ATTTATACTTAAGAAAC-GTCATATTTTAATA-AGAAAATATTAA--TATATA
63 GTAAAATAAATTTTTTATGCTTAAAAAACTATCATATTTTAATATA-AAAGTATCAACTTATATA
* * * * ** *
1461143 TTTTTTAAGCTTATTATTTT-TAAATTTTTTATTTGATAAATATAT
127 ATTTTTAAACTTAATATTTTCTCAA--CATTAATTGATAAATATAT
* **
1461188 TTTAATATTAAAATAT-TCAAAATTACTTTGTAATATTTAAAAATTTTCAAAATCTAAAATTATG
1 TTTATTATTAAAATATCT-AAAATTACTTTGTAATATTTAAAAAAATT-AAAATCTAAAATTATG
* *
1461252 TAAAATAAATTTTTTATGCTTAAAAAATTATCATATTTTAATATAAAAGTATCAATTTATATAAT
64 TAAAATAAATTTTTTATGCTTAAAAAACTATCATATTTTAATATAAAAGTATCAACTTATATAAT
* * * * *** *
1461317 TTTTAGATTTATTATTTTGTCATTTTTAATATTATAAATATAT
129 TTTTAAACTTAATATTTTCTCAACATTAAT-TGATAAATATAT
1461360 TTTATTATTAAAATATCTAAAATTA--TTGTTAAATATTTAAAAAAATT-AAATCTAAAATTATG
1 TTTATTATTAAAATATCTAAAATTACTTTG-T-AATATTTAAAAAAATTAAAATCTAAAATTATG
* * * * * *
1461422 T-AAAT-AATTTTTTTTAGCTTGAAAAACTATCATATTTTAATATAAAGGTTTCAACTTATGCTT
64 TAAAATAAATTTTTTAT-GCTTAAAAAACTATCATATTTTAATATAAAAGTATCAACTTAT-ATA
* * *
1461485 TTCTTTTAAACTTAATA-TTTCTCAACATTAACTTGAAAAATACAT
127 AT-TTTTAAACTTAATATTTTCTCAACATTAA-TTGATAAATATAT
*
1461530 TTTATTATTAACATATCTAAAATTAC
1 TTTATTATTAAAATATCTAAAATTAC
1461556 ATAAAAATTT
Statistics
Matches: 306, Mismatches: 43, Indels: 35
0.80 0.11 0.09
Matches are distributed among these distances:
166 11 0.04
167 27 0.09
168 32 0.10
169 59 0.19
170 85 0.28
171 20 0.07
172 69 0.23
173 3 0.01
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (170 bp):
TTTATTATTAAAATATCTAAAATTACTTTGTAATATTTAAAAAAATTAAAATCTAAAATTATGTA
AAATAAATTTTTTATGCTTAAAAAACTATCATATTTTAATATAAAAGTATCAACTTATATAATTT
TTAAACTTAATATTTTCTCAACATTAATTGATAAATATAT
Found at i:1461754 original size:21 final size:21
Alignment explanation
Indices: 1461707--1461751 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1461697 TGTTAGATTT
1461707 TAAA-AATTTTAAATATTTAA
1 TAAATAATTTTAAATATTTAA
*
1461727 TAAATAATTTTAGATATATTAA
1 TAAATAATTTTAAATAT-TTAA
1461749 TAA
1 TAA
1461752 TAAAATGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 11 0.50
22 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TAAATAATTTTAAATATTTAA
Found at i:1461929 original size:21 final size:21
Alignment explanation
Indices: 1461888--1461929 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1461878 TTTTAGAAAT
*
1461888 TTTTAAATATTTTTAAGATAA
1 TTTTAAATATTTTTAAAATAA
*
1461909 TTTTAGATA-TTTTAATAATAA
1 TTTTAAATATTTTTAA-AATAA
1461930 ATTATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (21 bp):
TTTTAAATATTTTTAAAATAA
Found at i:1462004 original size:175 final size:169
Alignment explanation
Indices: 1461625--1462152 Score: 487
Period size: 175 Copynumber: 3.0 Consensus size: 169
1461615 TAATAAGCTT
* * * * * * *
1461625 AAAAAATATATAAATTAATACTTTCATATTAAAATATGTTAG--TTTTAAGTATAAAAAATTTGT
1 AAAAAATACACAAATTAATATTTTCGTATTAAAATACGATAGTTTTTTAAGCA-AAAAAA-TTGT
* * * *
1461688 TTTATATAATGTTAGATTTTAAAAATTTTAAATATTTAATAA-ATAATTTTAGATATATTAATAA
64 TTTATATAATTTTA-ATTTTAAAATTTTTAAATATTT-TTAAGATAATTTTAGATATTTTAATAA
* * *
1461752 TAAAATGTATTTGCTTAACT-AAAAATTAT-AAAATAATAAGTTTC
127 TAAAATATATTT-ATTAA-TAAAAAATTATAAAAATAATAA-ATTC
* * * * *
1461796 AAAGAAAAACCCAAATTGATATTTTCGTATTAAAATATGATATTTTTTTAAATGCAAAAAAATTC
1 AAA-AAATACACAAATTAATATTTTCGTATTAAAATACGATAGTTTTTT-AA-GCAAAAAAATT-
* *
1461861 GTTTTATCTAATTTTTATTTTAGAAATTTTTAAATATTTTTAAGATAATTTTAGATATTTTAATA
62 GTTTTATATAATTTTAATTTTA-AAATTTTTAAATATTTTTAAGATAATTTTAGATATTTTAATA
*
1461926 ATAAATTATATTTATTAAGTTAAAAAATTATAAAAATAATAAATCTC
126 ATAAAATATATTTATTAA--TAAAAAATTATAAAAATAATAAAT-TC
* * * ** * * *
1461973 AAAAAATATATATATTAAT-TTTTTTTATTAAACTACGATAGTTTTTTAAGTATAAAAATT-TTA
1 AAAAAATACACAAATTAATATTTTCGTATTAAAATACGATAGTTTTTTAAGCAAAAAAATTGTT-
* * * *
1462036 TTTTATAATTTTAAATTTTAATATTTTTAAAATATTTTTATCGAATAATTTTAAATATTTTAATA
65 TTATATAATTTT-AATTTTAAAATTTTT-AAATATTTTTA-AG-ATAATTTTAGATATTTTAATA
*
1462101 ATAAAATATATTTATTGAATAAAATAATTA-AAAAATAATAAATTA
126 ATAAAATATATTTATT-AATAAAA-AATTATAAAAATAATAAATTC
1462146 AAAAAAT
1 AAAAAAT
1462153 TTAAAAGAGA
Statistics
Matches: 296, Mismatches: 42, Indels: 36
0.79 0.11 0.10
Matches are distributed among these distances:
171 5 0.02
172 47 0.16
173 34 0.11
174 40 0.14
175 131 0.44
176 24 0.08
177 15 0.05
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (169 bp):
AAAAAATACACAAATTAATATTTTCGTATTAAAATACGATAGTTTTTTAAGCAAAAAAATTGTTT
TATATAATTTTAATTTTAAAATTTTTAAATATTTTTAAGATAATTTTAGATATTTTAATAATAAA
ATATATTTATTAATAAAAAATTATAAAAATAATAAATTC
Found at i:1462111 original size:18 final size:18
Alignment explanation
Indices: 1462088--1462126 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1462078 GAATAATTTT
1462088 AAATAT-TTTAAT-AATA
1 AAATATATTTAATGAATA
*
1462104 AAATATATTTATTGAATA
1 AAATATATTTAATGAATA
1462122 AAATA
1 AAATA
1462127 ATTAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 5 0.25
18 9 0.45
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
AAATATATTTAATGAATA
Found at i:1462688 original size:5 final size:5
Alignment explanation
Indices: 1462667--1462796 Score: 59
Period size: 5 Copynumber: 25.6 Consensus size: 5
1462657 GTGAGTTCAT
* * * * * * *
1462667 ATTAT ATTAA AATAA ATTAA ATTTAA AAT-A TTTAA ATTCAA AATAA TTTAT
1 ATTAA ATTAA ATTAA ATTAA A-TTAA ATTAA ATTAA ATT-AA ATTAA ATTAA
** * * * *
1462718 ATTTT ATATAA -TTAA ATTTA A-TAA ATTTA ATTAA TTTAA ATTCA ATTAA
1 ATTAA AT-TAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
* *
1462767 ATTAAA TATTAA ATTTA ATTAA TTTAA ATT
1 ATT-AA -ATTAA ATTAA ATTAA ATTAA ATT
1462797 TAAAATGATT
Statistics
Matches: 90, Mismatches: 27, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
4 8 0.09
5 65 0.72
6 14 0.16
7 3 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (5 bp):
ATTAA
Found at i:1462701 original size:15 final size:16
Alignment explanation
Indices: 1462673--1462815 Score: 97
Period size: 16 Copynumber: 9.2 Consensus size: 16
1462663 TCATATTATA
*
1462673 TTAAAATAAATTAAAT
1 TTAAAATAATTTAAAT
1462689 TTAAAAT-ATTTAAAT
1 TTAAAATAATTTAAAT
* *
1462704 TCAAAATAATTTATAT
1 TTAAAATAATTTAAAT
* *
1462720 TTTATATAA-TTAAAT
1 TTAAAATAATTTAAAT
*
1462735 TTAATA-AATTTAATTAAT
1 TTAAAATAATTT-A--AAT
*
1462753 TTAAATTCAA-TTAAA-
1 TTAAAAT-AATTTAAAT
1462768 TT-AAAT-A-TTAAAT
1 TTAAAATAATTTAAAT
*
1462781 TT-AATTAATTTAAAT
1 TTAAAATAATTTAAAT
* *
1462796 TTAAAATGATTAAAAT
1 TTAAAATAATTTAAAT
1462812 TTAA
1 TTAA
1462816 TTAATATGAA
Statistics
Matches: 101, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
12 6 0.06
13 5 0.05
14 6 0.06
15 35 0.35
16 37 0.37
18 8 0.08
19 2 0.02
20 2 0.02
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (16 bp):
TTAAAATAATTTAAAT
Found at i:1462712 original size:31 final size:31
Alignment explanation
Indices: 1462667--1462841 Score: 80
Period size: 31 Copynumber: 5.7 Consensus size: 31
1462657 GTGAGTTCAT
*
1462667 ATTATATT-AAAATAAATTAAATTTAAAATA
1 ATTAAATTCAAAATAAATTAAATTTAAAATA
* * * * *
1462697 TTTAAATTCAAAATAATTTATATTTTATATA
1 ATTAAATTCAAAATAAATTAAATTTAAAATA
* * *
1462728 ATTAAATTTAATAAATTTAATT-AATTTAAATTCA
1 ATTAAA-TTCA-AAA-TAAATTAAATTTAAAAT-A
*
1462762 ATTAAATT--AAAT--ATTAAATTT-AATTA
1 ATTAAATTCAAAATAAATTAAATTTAAAATA
* * *
1462788 ATTTAAATTTAAAAT-GATTAAAATTT-AATTA
1 A-TTAAATTCAAAATAAATT-AAATTTAAAATA
* * *
1462819 ATATGAATTCAAGATAATTTAAA
1 AT-TAAATTCAAAATAAATTAAA
1462842 AATTAAAAAA
Statistics
Matches: 113, Mismatches: 19, Indels: 25
0.72 0.12 0.16
Matches are distributed among these distances:
26 2 0.02
27 14 0.12
28 5 0.04
29 5 0.04
30 13 0.12
31 47 0.42
32 5 0.04
33 11 0.10
34 11 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (31 bp):
ATTAAATTCAAAATAAATTAAATTTAAAATA
Found at i:1462792 original size:9 final size:9
Alignment explanation
Indices: 1462726--1462793 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
1462716 ATATTTTATA
1462726 TAATTAAATT
1 TAATT-AATT
*
1462736 TAATAAATT
1 TAATTAATT
1462745 TAATTAATT
1 TAATTAATT
1462754 TAAATTCAATT
1 T-AATT-AATT
* *
1462765 AAATTAA-A
1 TAATTAATT
1462773 T-ATTAAATT
1 TAATT-AATT
1462782 TAATTAATT
1 TAATTAATT
1462791 TAA
1 TAA
1462794 ATTTAAAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
7 3 0.06
8 2 0.04
9 23 0.49
10 15 0.32
11 4 0.09
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (9 bp):
TAATTAATT
Found at i:1462918 original size:14 final size:15
Alignment explanation
Indices: 1462901--1462933 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1462891 TCAGAATAAT
1462901 TTAAT-AATTCAAAA
1 TTAATCAATTCAAAA
*
1462915 TTAATCAATTCAAAT
1 TTAATCAATTCAAAA
1462930 TTAA
1 TTAA
1462934 AATAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAATCAATTCAAAA
Found at i:1462946 original size:16 final size:16
Alignment explanation
Indices: 1462921--1462978 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
1462911 AAAATTAATC
*
1462921 AATTCAAATTTAAAAT
1 AATTTAAATTTAAAAT
*
1462937 AATTTTAATTTAAAAT
1 AATTTAAATTTAAAAT
*
1462953 AATTTAAATTCAAAAT
1 AATTTAAATTTAAAAT
1462969 ACA-TTAAATT
1 A-ATTTAAATT
1462979 CAAATTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
16 36 0.97
17 1 0.03
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:1467513 original size:14 final size:15
Alignment explanation
Indices: 1467483--1467539 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 15
1467473 ACATATTTAA
1467483 ATATTATTAATATAAT
1 ATATT-TTAATATAAT
1467499 ATATTTTAATA-AAT
1 ATATTTTAATATAAT
*
1467513 AT-TATTTAAAATTAA-
1 ATAT-TTTAATA-TAAT
1467528 A-ATTTTAATATA
1 ATATTTTAATATA
1467540 TTTGATAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
13 3 0.09
14 17 0.49
15 8 0.23
16 7 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTTTAATATAAT
Found at i:1467532 original size:28 final size:28
Alignment explanation
Indices: 1467480--1467537 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1467470 ATAACATATT
*
1467480 TAAATATTATTAATATAATATATTTTAA
1 TAAATATTATTAAAATAATATATTTTAA
1467508 TAAATATTATTTAAAATTAA-A-ATTTTAA
1 TAAATATTA-TTAAAA-TAATATATTTTAA
1467536 TA
1 TA
1467538 TATTTGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 18 0.67
29 6 0.22
30 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TAAATATTATTAAAATAATATATTTTAA
Found at i:1468263 original size:2 final size:2
Alignment explanation
Indices: 1468256--1468292 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1468246 GAGATTTAGA
1468256 AT AT AT AT AT 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 AT AT AT AT AT A
1468293 AATCATTATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1468503 original size:50 final size:50
Alignment explanation
Indices: 1468429--1468532 Score: 192
Period size: 50 Copynumber: 2.1 Consensus size: 50
1468419 ATGGTCAGGA
1468429 TTGT-AGTCAAAGTGAGCTCAAGGATCCTTCTCCATTCCATTGTTTAGCT
1 TTGTAAGTCAAAGTGAGCTCAAGGATCCTTCTCCATTCCATTGTTTAGCT
*
1468478 TTGTAAGTCAGAGTGAGCTCAAGGATCCTTCTCCATTCCATTGTTTAGCT
1 TTGTAAGTCAAAGTGAGCTCAAGGATCCTTCTCCATTCCATTGTTTAGCT
1468528 TTGTA
1 TTGTA
1468533 TAGGACACAA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 4 0.08
50 49 0.92
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (50 bp):
TTGTAAGTCAAAGTGAGCTCAAGGATCCTTCTCCATTCCATTGTTTAGCT
Found at i:1477785 original size:32 final size:27
Alignment explanation
Indices: 1477738--1477795 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 27
1477728 AAAAATAACT
1477738 ATTTATTAAATAAATTTAATGATTAAATA
1 ATTTATTAAATAAATTTAA--ATTAAATA
1477767 ATTTATTATCAATAAAATTTAAATTAAAT
1 ATTTATTA--AAT-AAATTTAAATTAAAT
1477796 TTGTAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 8 0.31
30 7 0.27
31 3 0.12
32 8 0.31
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
ATTTATTAAATAAATTTAAATTAAATA
Found at i:1482349 original size:18 final size:18
Alignment explanation
Indices: 1482304--1482351 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1482294 TTTCTTATAA
1482304 AAATTAAATTTAAATTAAT
1 AAATT-AATTTAAATTAAT
** *
1482323 AAAAAAATTTAAATTCAT
1 AAATTAATTTAAATTAAT
*
1482341 TAATTAATTTA
1 AAATTAATTTA
1482352 TTTATTAAGT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTAATTTAAATTAAT
Found at i:1487682 original size:2 final size:2
Alignment explanation
Indices: 1487675--1487710 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1487665 CCACAGATTC
1487675 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
1487711 TATGGCGGTG
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:1488395 original size:3 final size:3
Alignment explanation
Indices: 1488381--1488415 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1488371 AATAAATTAC
*
1488381 TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1488416 TTAAAACATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1496163 original size:13 final size:12
Alignment explanation
Indices: 1496145--1496190 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1496135 CCCTCTGACC
1496145 CTTTTCTTCTTTT
1 CTTTTCTT-TTTT
1496158 CTTTTCTTTTTT
1 CTTTTCTTTTTT
1496170 -TTTT-TTTTTT
1 CTTTTCTTTTTT
**
1496180 GGTTTCTTTTT
1 CTTTTCTTTTT
1496191 CAATCTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 6 0.20
11 7 0.23
12 9 0.30
13 8 0.27
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (12 bp):
CTTTTCTTTTTT
Found at i:1496171 original size:22 final size:22
Alignment explanation
Indices: 1496146--1496190 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1496136 CCTCTGACCC
*
1496146 TTTTCTTCTTTTCTTTTCTTTT
1 TTTTCTTCTTTTCGTTTCTTTT
* * *
1496168 TTTTTTTTTTTTGGTTTCTTTT
1 TTTTCTTCTTTTCGTTTCTTTT
1496190 T
1 T
1496191 CAATCTTTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.84
Consensus pattern (22 bp):
TTTTCTTCTTTTCGTTTCTTTT
Found at i:1506925 original size:2 final size:2
Alignment explanation
Indices: 1506911--1506946 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1506901 CACATTTCTT
*
1506911 TC TC TC GC T- 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 TC TC TC TC T
1506947 TGGATATTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1516641 original size:2 final size:2
Alignment explanation
Indices: 1516634--1516666 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1516624 GTAAACAGGC
1516634 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1516667 CGCTGTGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1519298 original size:2 final size:2
Alignment explanation
Indices: 1519291--1519342 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
1519281 ATTTTGGCAT
* * *
1519291 TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1519333 TA TA TA TA TA
1 TA TA TA TA TA
1519343 AAAAAGATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1519320 original size:16 final size:16
Alignment explanation
Indices: 1519291--1519342 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
1519281 ATTTTGGCAT
*
1519291 TATATATATATATATA
1 TATATATGTATATATA
*
1519307 TATGTATGTATATATA
1 TATATATGTATATATA
1519323 TATATATGTATATATA
1 TATATATGTATATATA
1519339 TATA
1 TATA
1519343 AAAAAGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
TATATATGTATATATA
Found at i:1523441 original size:22 final size:22
Alignment explanation
Indices: 1523413--1523456 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1523403 AACTGATTGG
1523413 CTGAGCAAATCTGTTATTCTAA
1 CTGAGCAAATCTGTTATTCTAA
1523435 CTGAGCAAATCTGTTATTCTAA
1 CTGAGCAAATCTGTTATTCTAA
1523457 GTTTGTCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (22 bp):
CTGAGCAAATCTGTTATTCTAA
Found at i:1532579 original size:21 final size:20
Alignment explanation
Indices: 1532555--1532595 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1532545 TTTGTTATAT
1532555 AAATTA-TATCAAATAATATTA
1 AAATTATTAT-AAAT-ATATTA
1532576 AAATTATTATAAATATATTA
1 AAATTATTATAAATATATTA
1532596 TCAAAGGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 10 0.53
22 3 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTATTATAAATATATTA
Found at i:1532685 original size:28 final size:26
Alignment explanation
Indices: 1532649--1532703 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 26
1532639 ATTATCTAAA
1532649 AAATTATTAT-ATTAAATATTAAATATT
1 AAATTATTATAATT-AATATTAAA-ATT
1532676 AAATTAATTATAATTAATATTAAAATT
1 AAATT-ATTATAATTAATATTAAAATT
1532703 A
1 A
1532704 TTAAAACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 9 0.35
28 14 0.54
29 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATTATTATAATTAATATTAAAATT
Found at i:1533051 original size:27 final size:27
Alignment explanation
Indices: 1533005--1533074 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
1532995 CGAAAATTTT
*
1533005 ATTTATATTTATATAAAATTAAAT-TA
1 ATTTATATTTATTTAAAATTAAATATA
* * **
1533031 ATTTTATATTTTTTTATAATTTTATATA
1 A-TTTATATTTATTTAAAATTAAATATA
1533059 ATTTATATTTATTTAA
1 ATTTATATTTATTTAA
1533075 TTTTACTATC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
26 1 0.03
27 31 0.89
28 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
ATTTATATTTATTTAAAATTAAATATA
Found at i:1533094 original size:27 final size:23
Alignment explanation
Indices: 1533035--1533094 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
1533025 AAATTAATTT
1533035 TATATTTT-TTTATAATTTTATA
1 TATATTTTATTTATAATTTTATA
1533057 TA-ATTTATATTTATTTAATTTTACTA
1 TATATTT-TATTTA--TAATTTTA-TA
1533083 TCATATTTTATT
1 T-ATATTTTATT
1533095 ATCTATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
21 4 0.13
22 3 0.10
23 4 0.13
25 8 0.26
26 3 0.10
27 5 0.16
28 4 0.13
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (23 bp):
TATATTTTATTTATAATTTTATA
Found at i:1542584 original size:15 final size:16
Alignment explanation
Indices: 1542564--1542593 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1542554 TATACTTTTG
1542564 ATATATTTAT-TTATA
1 ATATATTTATATTATA
1542579 ATATATTTATATTAT
1 ATATATTTATATTAT
1542594 TTTATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATATTTATATTATA
Found at i:1542604 original size:28 final size:29
Alignment explanation
Indices: 1542567--1542621 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
1542557 ACTTTTGATA
1542567 TATTTATTTATAATA-TATTTATATTATTT
1 TATTTATTTA-AATATTATTTATATTATTT
* *
1542596 TATTT-TTTAATTATTTTTTATATTAT
1 TATTTATTTAAATATTATTTATATTAT
1542622 CTTCACTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.13
28 15 0.65
29 5 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (29 bp):
TATTTATTTAAATATTATTTATATTATTT
Found at i:1542732 original size:13 final size:13
Alignment explanation
Indices: 1542714--1542738 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1542704 ATGTTAATAT
1542714 AAATATTTTATCC
1 AAATATTTTATCC
1542727 AAATATTTTATC
1 AAATATTTTATC
1542739 TTAATCTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATATTTTATCC
Found at i:1546439 original size:227 final size:223
Alignment explanation
Indices: 1546034--1546486 Score: 780
Period size: 227 Copynumber: 2.0 Consensus size: 223
1546024 GTTTCATGTC
* *
1546034 CAAGCTGATTACACTTGATGCACTTTGCATCTGGTCTCTTCCAGCATTTGAATGTTAGATGGCCT
1 CAAGCTGATTACACTTAATGCACTTTGCATCTGGTCTCTTCCAGCATTTAAATGTTAGATGGCCT
1546099 ATTTTGCTGCAATACTAACAAGGTGGATAGTTTCACTTTGAATTTGTACCCTTGCTTTGGATTTG
66 ATTTTGCTGCAATACTAACAAGGTGGATAGTTTCACTTTGAATTTGTACCCTTGCTTTGGATTTG
* * *
1546164 GTTATTTGCAGTGTTTCGTTGCTTGACACTTGAATCTTTCTGTAATTTTTCTTTTTATTCCTACC
131 GTTATTTGCAGTATTTCGCTGCTTGACACTTGAATCTTTCTATAATTTTTCTTTTTATTCCT---
*
1546229 AACTTCCTAATGCTTGGTTGGTAAGGCTCTTT
193 -ACTTCCTAATGCTTGGTTGGTAAGGCTCCTT
* * *
1546261 CAAGTTGATTACACTTAATGCACTTTGCATCTGGTCTCTTCGAGCATTTAAATGTTGGATGGCCT
1 CAAGCTGATTACACTTAATGCACTTTGCATCTGGTCTCTTCCAGCATTTAAATGTTAGATGGCCT
1546326 ATTTTGCTGCAATACTAACAAGGTGGATAGTTTCACTTTGAATTTGTACCCTTGCTTTGGATTTG
66 ATTTTGCTGCAATACTAACAAGGTGGATAGTTTCACTTTGAATTTGTACCCTTGCTTTGGATTTG
1546391 GTTATTTGCAGTATTTCGCTGCTTGACACTTGAATCTTTCTATAATTTTTCTTTTTATTCCTACT
131 GTTATTTGCAGTATTTCGCTGCTTGACACTTGAATCTTTCTATAATTTTTCTTTTTATTCCTACT
*
1546456 TCCTGATGCTTGGTTGGTAAGGCTCCTT
196 TCCTAATGCTTGGTTGGTAAGGCTCCTT
1546484 CAA
1 CAA
1546487 CAATACGTTC
Statistics
Matches: 216, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
223 32 0.15
227 184 0.85
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (223 bp):
CAAGCTGATTACACTTAATGCACTTTGCATCTGGTCTCTTCCAGCATTTAAATGTTAGATGGCCT
ATTTTGCTGCAATACTAACAAGGTGGATAGTTTCACTTTGAATTTGTACCCTTGCTTTGGATTTG
GTTATTTGCAGTATTTCGCTGCTTGACACTTGAATCTTTCTATAATTTTTCTTTTTATTCCTACT
TCCTAATGCTTGGTTGGTAAGGCTCCTT
Found at i:1554600 original size:50 final size:50
Alignment explanation
Indices: 1554525--1554784 Score: 391
Period size: 50 Copynumber: 5.2 Consensus size: 50
1554515 AGTTGTTGTT
*
1554525 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
1554575 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* *
1554625 ATTGTTGACAATTCTTCACTAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * *
1554675 ATTGTTAGACGATTCTTCACCAACCTGTGACAATAGA-ATGAGTTGGCCATA
1 ATTGTT-GACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
*
1554726 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1554776 ATTGTTGAC
1 ATTGTTGAC
1554785 TCTAAGTATA
Statistics
Matches: 191, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
49 1 0.01
50 144 0.75
51 46 0.24
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:1554733 original size:101 final size:100
Alignment explanation
Indices: 1554525--1554784 Score: 441
Period size: 101 Copynumber: 2.6 Consensus size: 100
1554515 AGTTGTTGTT
* *
1554525 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTC
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTC
*
1554589 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
65 TTCACCAACCTGTGACAATAGAAGGAGGTGGCCATA
*
1554625 ATTGTTGACAATTCTTCACTAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTAGACGATTC
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTT-GACGATTC
* *
1554690 TTCACCAACCTGTGACAATAGAATGAGTTGGCCATA
65 TTCACCAACCTGTGACAATAGAAGGAGGTGGCCATA
1554726 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGAC
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGAC
1554785 TCTAAGTATA
Statistics
Matches: 151, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
100 53 0.35
101 98 0.65
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (100 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
TCACCAACCTGTGACAATAGAAGGAGGTGGCCATA
Found at i:1559255 original size:50 final size:50
Alignment explanation
Indices: 1559177--1559435 Score: 389
Period size: 50 Copynumber: 5.2 Consensus size: 50
1559167 AGTTGTTGTC
*
1559177 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
1559227 ATTGTTGACGATTCTTCACCAACTTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* *
1559277 ATTGTTGATAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
1559327 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-ATGAGGTAGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* *
1559377 ATTGTTGACAATTCTTCACCAACCTTTGACAATAAAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1559427 ATTGTTGAC
1 ATTGTTGAC
1559436 TCTAAGTATA
Statistics
Matches: 190, Mismatches: 14, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
49 1 0.01
50 187 0.98
51 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:1559355 original size:100 final size:100
Alignment explanation
Indices: 1559177--1559435 Score: 439
Period size: 100 Copynumber: 2.6 Consensus size: 100
1559167 AGTTGTTGTC
* *
1559177 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTC
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTC
* *
1559241 TTCACCAACTTTTGACAATAGAAGGAGGTGGCCATA
65 TTCACCAACCTTTGACAATAGAAGGAGGTAGCCATA
*
1559277 ATTGTTGATAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
*
1559342 TCACCAACCTTTGACAATAGAATGAGGTAGCCATA
66 TCACCAACCTTTGACAATAGAAGGAGGTAGCCATA
*
1559377 ATTGTTGACAATTCTTCACCAACCTTTGACAATAAAGGGAGGTGGCCATAATTGTTGAC
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGAC
1559436 TCTAAGTATA
Statistics
Matches: 150, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
100 148 0.99
101 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (100 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCT
TCACCAACCTTTGACAATAGAAGGAGGTAGCCATA
Found at i:1560073 original size:27 final size:27
Alignment explanation
Indices: 1560043--1560140 Score: 70
Period size: 29 Copynumber: 3.3 Consensus size: 27
1560033 AATTTGATTT
1560043 TATTTAAAATATTTTTAATAATAAAAA
1 TATTTAAAATATTTTTAATAATAAAAA
* *
1560070 TATTTTATTTAAATTTAATTTTTAAGATATATAAA
1 TA-TTTA---AAA--T-ATTTTTAATA-ATAAAAA
*
1560105 TATTTAATAATATTTTAAATAATAAAATA
1 TATTTAA-AATATTTTTAATAATAAAA-A
*
1560134 AATTTAA
1 TATTTAA
1560141 TTAATTTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
27 2 0.04
28 9 0.16
29 15 0.27
30 1 0.02
31 4 0.07
32 2 0.04
33 1 0.02
34 13 0.24
35 8 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (27 bp):
TATTTAAAATATTTTTAATAATAAAAA
Found at i:1560144 original size:4 final size:5
Alignment explanation
Indices: 1560134--1560163 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1560124 TAATAAAATA
1560134 AATTT AA-TT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT AATTT A
1560164 TGAATAGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:1560636 original size:2 final size:2
Alignment explanation
Indices: 1560629--1560674 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1560619 CCTTTCATGG
* * *
1560629 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1560671 AT AT
1 AT AT
1560675 CAATTGATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1561602 original size:19 final size:18
Alignment explanation
Indices: 1561572--1561618 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
1561562 CCATTATTTT
*
1561572 AAAAAATAT-AAAGATAA
1 AAAAAATATAAAACATAA
1561589 AAAAAATAATTAAAACATAA
1 AAAAAAT-A-TAAAACATAA
*
1561609 AAAAATTATA
1 AAAAAATATA
1561619 TTTTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 7 0.28
18 3 0.12
19 2 0.08
20 13 0.52
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAAAATATAAAACATAA
Found at i:1561803 original size:20 final size:22
Alignment explanation
Indices: 1561761--1561804 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1561751 TCATTAAATT
1561761 TTTAAATAATAAAAATTAATTAA
1 TTTAAATAATAAAAATT-ATTAA
*
1561784 TTTAAATAA-AAATATT-TTAA
1 TTTAAATAATAAAAATTATTAA
1561804 T
1 T
1561805 AAATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
22 6 0.30
23 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAAATAATAAAAATTATTAA
Found at i:1562153 original size:18 final size:19
Alignment explanation
Indices: 1562130--1562169 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1562120 TTTATTTTTT
*
1562130 ATAAAAATT-TAAAAATAA
1 ATAAAAATTAAAAAAATAA
1562148 ATAAAAATTAAAAAAATAA
1 ATAAAAATTAAAAAAATAA
1562167 ATA
1 ATA
1562170 TATTTCCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
ATAAAAATTAAAAAAATAA
Found at i:1562183 original size:47 final size:48
Alignment explanation
Indices: 1562107--1562197 Score: 148
Period size: 47 Copynumber: 1.9 Consensus size: 48
1562097 TTTTAAAATT
* **
1562107 TTAAAAAAATAAATTTATTTTTTATAAAAATTTAAAAATAAATAAAAA
1 TTAAAAAAATAAATATATTTTCCATAAAAATTTAAAAATAAATAAAAA
1562155 TTAAAAAAATAAATATA-TTTCCATAAAAATTTAAAAATAAATA
1 TTAAAAAAATAAATATATTTTCCATAAAAATTTAAAAATAAATA
1562198 TCTTTTACCT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 24 0.60
48 16 0.40
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (48 bp):
TTAAAAAAATAAATATATTTTCCATAAAAATTTAAAAATAAATAAAAA
Found at i:1562425 original size:13 final size:14
Alignment explanation
Indices: 1562407--1562435 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1562397 ATATGTAGTA
1562407 AAAAC-TAAAATAT
1 AAAACTTAAAATAT
1562420 AAAACTTAAAATAT
1 AAAACTTAAAATAT
1562434 AA
1 AA
1562436 TACATAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAACTTAAAATAT
Found at i:1562802 original size:18 final size:18
Alignment explanation
Indices: 1562781--1562824 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1562771 ATTATGCTTG
1562781 AAATATAAATTTAAATAA
1 AAATATAAATTTAAATAA
**
1562799 AAATA-AAATTTATTTAA
1 AAATATAAATTTAAATAA
1562816 AAA-ATAAAT
1 AAATATAAAT
1562825 CAGACTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 1 0.04
17 17 0.74
18 5 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATATAAATTTAAATAA
Found at i:1562816 original size:17 final size:18
Alignment explanation
Indices: 1562781--1562823 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1562771 ATTATGCTTG
1562781 AAATATAAATTTAAAT-AA
1 AAATA-AAATTTAAATAAA
**
1562799 AAATAAAATTTATTTAAA
1 AAATAAAATTTAAATAAA
1562817 AAATAAA
1 AAATAAA
1562824 TCAGACTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAAATTTAAATAAA
Found at i:1565873 original size:8 final size:8
Alignment explanation
Indices: 1565833--1565911 Score: 65
Period size: 8 Copynumber: 9.9 Consensus size: 8
1565823 TCAATTCATG
*
1565833 TATATTAA
1 TATATTTA
1565841 TA-ATTTA
1 TATATTTA
*
1565848 TTATATATA
1 -TATATTTA
1565857 TATATTTTA
1 TATA-TTTA
1565866 TATATTTA
1 TATATTTA
*
1565874 TTTATTTA
1 TATATTTA
* *
1565882 TTTA-TAA
1 TATATTTA
1565889 TATATTTA
1 TATATTTA
1565897 TATTATTT-
1 TA-TATTTA
1565905 TATATTT
1 TATATTT
1565912 TAATTATTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
7 14 0.24
8 29 0.49
9 16 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATATTTA
Found at i:1565910 original size:27 final size:27
Alignment explanation
Indices: 1565846--1565937 Score: 72
Period size: 27 Copynumber: 3.5 Consensus size: 27
1565836 ATTAATAATT
*
1565846 TATTATATATATATATT-TTATATATTTA
1 TATTAT-TTTATAT-TTATTATATATTTA
*
1565874 T-TTA--TT-TATTTATAATATATTTA
1 TATTATTTTATATTTATTATATATTTA
1565897 TATTATTTTATATTTTAATTAT-T-TTTA
1 TATTATTTTATA-TTT-ATTATATATTTA
1565924 TATTATTTTCATAT
1 TATTATTTT-ATAT
1565938 CATATCATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
22 2 0.04
23 14 0.26
24 4 0.08
26 2 0.04
27 19 0.36
28 8 0.15
29 4 0.08
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (27 bp):
TATTATTTTATATTTATTATATATTTA
Found at i:1569976 original size:25 final size:26
Alignment explanation
Indices: 1569948--1570001 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
1569938 AATGTAAAAG
*
1569948 TAATTTTAATTTTT-TTTATTTTA-TA
1 TAATTTT-ATTTTTATTTAATTTATTA
1569973 TAA-TTTATTTTTATTTAATTTATTA
1 TAATTTTATTTTTATTTAATTTATTA
1569998 TAAT
1 TAAT
1570002 ATTTTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 6 0.24
24 11 0.44
25 8 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (26 bp):
TAATTTTATTTTTATTTAATTTATTA
Found at i:1569984 original size:15 final size:15
Alignment explanation
Indices: 1569962--1569996 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1569952 TTTAATTTTT
1569962 TTTA-TTTTATATAA
1 TTTATTTTTATATAA
*
1569976 TTTATTTTTATTTAA
1 TTTATTTTTATATAA
1569991 TTTATT
1 TTTATT
1569997 ATAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTTTTATATAA
Found at i:1570004 original size:23 final size:23
Alignment explanation
Indices: 1569956--1570014 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
1569946 AGTAATTTTA
*
1569956 ATTTTT-TTTATTTTATATAATTT
1 ATTTTTATTTAATTTATATAA-TT
1569979 ATTTTTATTTAATTTATTATAA-T
1 ATTTTTATTTAATTTA-TATAATT
1570002 ATTTTTA-TTAATT
1 ATTTTTATTTAATT
1570015 ATTCGTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
22 6 0.18
23 14 0.42
24 8 0.24
25 5 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
ATTTTTATTTAATTTATATAATT
Found at i:1570098 original size:43 final size:44
Alignment explanation
Indices: 1570026--1570108 Score: 100
Period size: 43 Copynumber: 1.9 Consensus size: 44
1570016 TTCGTTTAAA
1570026 TTATTTATATCAAATTTTAAATTTATTAAAAATAT-TTAATAAT
1 TTATTTATATCAAATTTTAAATTTATTAAAAATATATTAATAAT
** *
1570069 TTATTTAATAT-AAATTTTTTATCTT-TTAAATATATATTAA
1 TTATTT-ATATCAAATTTTAAAT-TTATTAAAAATATATTAA
1570109 AAATAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
43 24 0.71
44 10 0.29
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (44 bp):
TTATTTATATCAAATTTTAAATTTATTAAAAATATATTAATAAT
Found at i:1570736 original size:16 final size:16
Alignment explanation
Indices: 1570715--1570756 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1570705 AATTTATTTA
1570715 AAAATATATATTAAAT
1 AAAATATATATTAAAT
**
1570731 AAAATATATATTTGAT
1 AAAATATATATTAAAT
1570747 ATAAATATAT
1 A-AAATATAT
1570757 TTAGATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAAATATATATTAAAT
Found at i:1571135 original size:2 final size:2
Alignment explanation
Indices: 1571128--1571153 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1571118 AATTTTCTAT
1571128 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
1571154 TCTAAACGCC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1571571 original size:16 final size:16
Alignment explanation
Indices: 1571550--1571580 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1571540 AATATTATAA
*
1571550 TAATTTAATTTTAATT
1 TAATTTAATTCTAATT
1571566 TAATTTAATTCTAAT
1 TAATTTAATTCTAAT
1571581 AGATAATATA
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:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTAATTCTAATT
Found at i:1572130 original size:22 final size:22
Alignment explanation
Indices: 1572102--1572150 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
1572092 TTATTATATT
1572102 ATCATTTATCCATTTTGT-ATAA
1 ATCATTTATCCATTTT-TAATAA
1572124 ATCATTTATCCATTTTTAATAA
1 ATCATTTATCCATTTTTAATAA
1572146 ATCAT
1 ATCAT
1572151 AGATATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.35, C:0.14, G:0.02, T:0.49
Consensus pattern (22 bp):
ATCATTTATCCATTTTTAATAA
Found at i:1573994 original size:14 final size:14
Alignment explanation
Indices: 1573956--1573994 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1573946 TTTCGTTAAC
1573956 TAAAATTTTAAAATA
1 TAAAA-TTTAAAATA
*
1573971 TAAAAATTAAAATA
1 TAAAATTTAAAATA
*
1573985 TTAAATTTAA
1 TAAAATTTAA
1573995 TCGAATTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAATTTAAAATA
Found at i:1575908 original size:76 final size:77
Alignment explanation
Indices: 1575828--1575990 Score: 208
Period size: 76 Copynumber: 2.1 Consensus size: 77
1575818 AAAGAGAGAA
*
1575828 ATATTTTGGACAGTGAT-TCATGATGCTATTAAATATTTTTAAAC-TTTTAATAAGTTT-TCAAA
1 ATATTTTGGACAGGGATAT-ATGATGCTATTAAATATTTTTAAACGTTTTAATAAGTTTCT-AAA
1575890 GATT-TTTGAATTTG
64 G-TTCTTTGAATTTG
* * * *
1575904 ATATTTTAGACCGGGGTATATGATGCTATTAAATATTTTTAAACGTTTTATTAAGTTTCTAAAGT
1 ATATTTTGGACAGGGATATATGATGCTATTAAATATTTTTAAACGTTTTAATAAGTTTCTAAAGT
1575969 TCTTTGAATTTG
66 TCTTTGAATTTG
**
1575981 GCATTTTGGA
1 ATATTTTGGA
1575991 TGCTACATGG
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
76 40 0.53
77 34 0.45
78 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (77 bp):
ATATTTTGGACAGGGATATATGATGCTATTAAATATTTTTAAACGTTTTAATAAGTTTCTAAAGT
TCTTTGAATTTG
Found at i:1579733 original size:86 final size:83
Alignment explanation
Indices: 1579611--1579778 Score: 264
Period size: 86 Copynumber: 2.0 Consensus size: 83
1579601 TTTTTTTTTA
* * *
1579611 AAGATGGTTTGTCCTCACAGTCTCGAATATCAATATTATAACAGCACTAATTTCAAAAGTATATA
1 AAGATGGTTGGTCCTCACAGTCTCGAACATCAATATTATAACAGCACTAATTTCAAAAG--CATA
1579676 AATAGTGGACGATATTATCCC
64 AATAGTGGACGATA-TATCCC
*
1579697 AAGATTGTTGGTCCTCACAGTCTCGAACATCAATATTATAACAGCACTAATTTCAAAAGCATAAA
1 AAGATGGTTGGTCCTCACAGTCTCGAACATCAATATTATAACAGCACTAATTTCAAAAGCATAAA
*
1579762 TAGTGGACTATATATCC
66 TAGTGGACGATATATCC
1579779 TAAATAATTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
83 5 0.06
84 16 0.21
86 56 0.73
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (83 bp):
AAGATGGTTGGTCCTCACAGTCTCGAACATCAATATTATAACAGCACTAATTTCAAAAGCATAAA
TAGTGGACGATATATCCC
Found at i:1579992 original size:21 final size:21
Alignment explanation
Indices: 1579933--1579994 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
1579923 ATGTTTTAAA
* *
1579933 CTTTTGATATATTTTTCATAAC
1 CTTTT-ATATAATTTTGATAAC
**
1579955 CTTTTATATAAAATTGATAATC
1 CTTTTATATAATTTTGATAA-C
1579977 C-TTTATATAATTTTGATA
1 CTTTTATATAATTTTGATA
1579995 TAATTTTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 26 0.79
22 7 0.21
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.52
Consensus pattern (21 bp):
CTTTTATATAATTTTGATAAC
Found at i:1580456 original size:30 final size:30
Alignment explanation
Indices: 1580398--1580456 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1580388 CATAACTTAA
* *
1580398 ATCATATCTTTATGATTTAATTAGTTATAG
1 ATCATATCTTTATGATATAATTAATTATAG
* *
1580428 ATCATATCTTTGTGATATGATTAATTATA
1 ATCATATCTTTATGATATAATTAATTATA
1580457 AACTTTAGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (30 bp):
ATCATATCTTTATGATATAATTAATTATAG
Found at i:1580598 original size:23 final size:24
Alignment explanation
Indices: 1580566--1580616 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
1580556 TATAAGCTTG
*
1580566 TTTTCTTCTATTATT-TCTTTAGT
1 TTTTCCTCTATTATTATCTTTAGT
* *
1580589 TTTTCCTCTATTTTTATTTTTAGT
1 TTTTCCTCTATTATTATCTTTAGT
1580613 TTTT
1 TTTT
1580617 TTACCTCCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.12, C:0.12, G:0.04, T:0.73
Consensus pattern (24 bp):
TTTTCCTCTATTATTATCTTTAGT
Found at i:1581262 original size:114 final size:110
Alignment explanation
Indices: 1581037--1581313 Score: 310
Period size: 114 Copynumber: 2.5 Consensus size: 110
1581027 ACACAGGCTT
* ** * *
1581037 ATAAAAAATAAAATTTTAAACTAAAAAATTTATT-GTTTTAAAATTTAAAATAATAATTATCCTA
1 ATAAAAAATAAAATTATAAACTAATCAATTTATTATTTTTAAAATTTAAAATAACAATTATCCTA
* **
1581101 AAATCATGATTTTTTAAAGTATTTTTCACTTGGATTACAACGATTA
66 AAATCATGATTTTTT-AAGTATCTTTCACTTAAATTACAACGATTA
* *
1581147 ATAAAAGATAAAATTATAAACTAATCAATTTGATTATTTTTAAAATTTAAAATAACAATTATCTT
1 ATAAAAAATAAAATTATAAACTAATCAATTT-ATTATTTTTAAAATTTAAAATAACAATTATCCT
* * *
1581212 GAAATTCTTGATAACTTTTT-ATTATCTTTCACTTAAATTACAAC-AGTTA
65 -AAAATCATGAT---TTTTTAAGTATCTTTCACTTAAATTACAACGA-TTA
* *
1581261 ATAAAATATAAAATTATAAACTTATCAATTTTATTATATTTT-AAATTTAAAAT
1 ATAAAAAATAAAATTATAAACTAATCAA-TTTATTAT-TTTTAAAATTTAAAAT
1581314 TTAAAATCAT
Statistics
Matches: 143, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
110 27 0.19
111 3 0.02
112 26 0.18
113 10 0.07
114 65 0.45
115 7 0.05
116 5 0.03
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (110 bp):
ATAAAAAATAAAATTATAAACTAATCAATTTATTATTTTTAAAATTTAAAATAACAATTATCCTA
AAATCATGATTTTTTAAGTATCTTTCACTTAAATTACAACGATTA
Found at i:1585205 original size:22 final size:22
Alignment explanation
Indices: 1585180--1585221 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1585170 GAAATTTATA
1585180 GCCGTGGATTGCACTTGAAGGT
1 GCCGTGGATTGCACTTGAAGGT
1585202 GCCGTGGATTGCACTTGAAG
1 GCCGTGGATTGCACTTGAAG
1585222 ATGATTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (22 bp):
GCCGTGGATTGCACTTGAAGGT
Found at i:1591432 original size:2 final size:2
Alignment explanation
Indices: 1591425--1591455 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1591415 TTTACAGGAT
1591425 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
1591456 GTAATGATAA
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:1591891 original size:6 final size:6
Alignment explanation
Indices: 1591880--1591909 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1591870 AAAATGTGCA
1591880 GGCAGG GGCAGG GGCAGG GGCAGG GGCAGG
1 GGCAGG GGCAGG GGCAGG GGCAGG GGCAGG
1591910 AACAGGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.67, T:0.00
Consensus pattern (6 bp):
GGCAGG
Found at i:1591915 original size:18 final size:18
Alignment explanation
Indices: 1591880--1591915 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1591870 AAAATGTGCA
**
1591880 GGCAGGGGCAGGGGCAGG
1 GGCAGGGGCAGGAACAGG
1591898 GGCAGGGGCAGGAACAGG
1 GGCAGGGGCAGGAACAGG
1591916 AATTGAAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.17, G:0.61, T:0.00
Consensus pattern (18 bp):
GGCAGGGGCAGGAACAGG
Found at i:1599983 original size:2 final size:2
Alignment explanation
Indices: 1599976--1600005 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1599966 TGAAATTTGA
*
1599976 AT AT AT AT AC 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
1600006 GTCACCTTCT
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:1600803 original size:2 final size:2
Alignment explanation
Indices: 1600796--1600834 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1600786 ATCTTATCTT
*
1600796 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1600835 TTATTTTCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1601392 original size:12 final size:12
Alignment explanation
Indices: 1601372--1601401 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1601362 GCCCCCTGCC
*
1601372 CTCTCTCTCTCT
1 CTCTATCTCTCT
1601384 CTCTATCTCTCT
1 CTCTATCTCTCT
1601396 CTCTAT
1 CTCTAT
1601402 GTATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.43, G:0.00, T:0.50
Consensus pattern (12 bp):
CTCTATCTCTCT
Found at i:1601425 original size:14 final size:14
Alignment explanation
Indices: 1601403--1601443 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1601393 TCTCTCTATG
*
1601403 TATATATATATATA
1 TATACATATATATA
1601417 TATACATATATATA
1 TATACATATATATA
*
1601431 TATACACATATAT
1 TATACATATATAT
1601444 CGATGTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
TATACATATATATA
Found at i:1601427 original size:16 final size:16
Alignment explanation
Indices: 1601406--1601443 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1601396 CTCTATGTAT
*
1601406 ATATATATATATATAC
1 ATATATATATATACAC
1601422 ATATATATATATACAC
1 ATATATATATATACAC
1601438 ATATAT
1 ATATAT
1601444 CGATGTCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATATATATACAC
Found at i:1601443 original size:2 final size:2
Alignment explanation
Indices: 1601403--1601434 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1601393 TCTCTCTATG
*
1601403 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1601435 CACATATATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1602522 original size:19 final size:19
Alignment explanation
Indices: 1602498--1602534 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1602488 AAAAAAAAAA
1602498 AGAAAATAT-ATATTTTTTT
1 AGAAAAT-TGATATTTTTTT
1602517 AGAAAATTGATATTTTTT
1 AGAAAATTGATATTTTTT
1602535 AAATTGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (19 bp):
AGAAAATTGATATTTTTTT
Found at i:1613195 original size:195 final size:195
Alignment explanation
Indices: 1612863--1613250 Score: 731
Period size: 195 Copynumber: 2.0 Consensus size: 195
1612853 ATCCGACTCT
1612863 AAAATTGCATTCGTTGCCTGTCGCCAACTCTAAGCTCTTCCTGAGAACGGTGATTTTACTGATGA
1 AAAATTGCATTCGTTGCCTGTCGCCAACTCTAAGCTCTTCCTGAGAACGGTGATTTTACTGATGA
1612928 TTACGAATATTGAATATTGTGTGAAGCCTAATCTCGCGTTTGAGAATCCAGGCTTAGGAGTGCTT
66 TTACGAATATTGAATATTGTGTGAAGCCTAATCTCGCGTTTGAGAATCCAGGCTTAGGAGTGCTT
*
1612993 ACATTGCACTCCAAGCCTGGAAACATGCGGTATATCCGGCCCTTTAAAAGCCACTCAGCAGTGGG
131 ACATTGCACTCCAAGCCTGGAAACATGCGGTATATCCGGCCCTTTAAAAACCACTCAGCAGTGGG
* *
1613058 AAAATTGCATTCGTTGCCTGTCGCCGACTCTAAGCTCTTCCTGAGAGCGGTGATTTTACTGATGA
1 AAAATTGCATTCGTTGCCTGTCGCCAACTCTAAGCTCTTCCTGAGAACGGTGATTTTACTGATGA
1613123 TTACGAATATTGAATATTGTGTGAAGCCTAATCTCGCGTTTGAGAATCCAGGCTTAGGAGTGCTT
66 TTACGAATATTGAATATTGTGTGAAGCCTAATCTCGCGTTTGAGAATCCAGGCTTAGGAGTGCTT
* *
1613188 ACATTGCACTCCAAGCCTGGAAACATGCGGTATATCTGGGCCTTTAAAAACCACTCAGCAGTG
131 ACATTGCACTCCAAGCCTGGAAACATGCGGTATATCCGGCCCTTTAAAAACCACTCAGCAGTG
1613251 AGAAGGCCCG
Statistics
Matches: 188, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
195 188 1.00
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (195 bp):
AAAATTGCATTCGTTGCCTGTCGCCAACTCTAAGCTCTTCCTGAGAACGGTGATTTTACTGATGA
TTACGAATATTGAATATTGTGTGAAGCCTAATCTCGCGTTTGAGAATCCAGGCTTAGGAGTGCTT
ACATTGCACTCCAAGCCTGGAAACATGCGGTATATCCGGCCCTTTAAAAACCACTCAGCAGTGGG
Found at i:1613601 original size:12 final size:12
Alignment explanation
Indices: 1613578--1613609 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1613568 CAAAATACTG
1613578 TTATTT-TTAAA
1 TTATTTATTAAA
1613589 TTATTTATTAAA
1 TTATTTATTAAA
1613601 TTA-TTATTA
1 TTATTTATTA
1613610 TTTTAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTATTAAA
Found at i:1614134 original size:18 final size:17
Alignment explanation
Indices: 1614113--1614164 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
1614103 ATTATTAATA
1614113 TATTAAATAATATTATTT
1 TATTAAATAATATTA-TT
*
1614131 TATTAAAAATAAAATTATT
1 TATT--AAATAATATTATT
*
1614150 TATATAAATTATATT
1 TAT-TAAATAATATT
1614165 TGATATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 12 0.43
19 5 0.18
20 11 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTAAATAATATTATT
Found at i:1614157 original size:20 final size:20
Alignment explanation
Indices: 1614103--1614157 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
1614093 TAATCTATAT
* * *
1614103 ATTATTAATATATTAAATAAT
1 ATTATTTATATA-AAAATAAA
1614124 ATTATTT-TATTAAAAATAAA
1 ATTATTTATA-TAAAAATAAA
1614144 ATTATTTATATAAA
1 ATTATTTATATAAA
1614158 TTATATTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTATTTATATAAAAATAAA
Found at i:1615110 original size:29 final size:29
Alignment explanation
Indices: 1615062--1615118 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1615052 TTTCTCAATC
1615062 AAAACAATAATAGTTCGATAAATAATTTA
1 AAAACAATAATAGTTCGATAAATAATTTA
* * * *
1615091 AAAATAATAATATTTTGATAATTAATTT
1 AAAACAATAATAGTTCGATAAATAATTT
1615119 TTATTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.39
Consensus pattern (29 bp):
AAAACAATAATAGTTCGATAAATAATTTA
Found at i:1616492 original size:20 final size:19
Alignment explanation
Indices: 1616467--1616506 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1616457 ATTAAATTAA
*
1616467 TTTTATATATTTATATAATT
1 TTTTATATAATTA-ATAATT
1616487 TTTTATATAATTAATAATT
1 TTTTATATAATTAATAATT
1616506 T
1 T
1616507 ATAATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTATATAATTAATAATT
Found at i:1624848 original size:15 final size:14
Alignment explanation
Indices: 1624816--1624859 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1624806 ATTACCTTAG
1624816 TTTATTAAAAAATAT
1 TTTA-TAAAAAATAT
*
1624831 TTTATAAAAGATAT
1 TTTATAAAAAATAT
*
1624845 TTT-TAAAAATTAT
1 TTTATAAAAAATAT
1624858 TT
1 TT
1624860 AAATAGGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 10 0.38
14 12 0.46
15 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TTTATAAAAAATAT
Done.