Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold230
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: 2055625
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 6 of 14
Found at i:577244 original size:32 final size:30
Alignment explanation
Indices: 577201--577265 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 30
577191 GTTTTGTATG
577201 ATTTAATAATTTTAATTTATATTAAAT-TAA
1 ATTTAATAATTTTAATTTA-ATTAAATATAA
* *
577231 ATTTATATAAATTTTTATTTAATTTAATATAA
1 ATTTA-AT-AATTTTAATTTAATTAAATATAA
577263 ATT
1 ATT
577266 ATTATTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 5 0.17
31 8 0.27
32 17 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
ATTTAATAATTTTAATTTAATTAAATATAA
Found at i:577250 original size:16 final size:17
Alignment explanation
Indices: 577208--577251 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
577198 ATGATTTAAT
577208 AATTTTAATTTATATTA
1 AATTTTAATTTATATTA
*
577225 AA-TTAAATTTATA-TA
1 AATTTTAATTTATATTA
*
577240 AATTTTTATTTA
1 AATTTTAATTTA
577252 ATTTAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 17 0.74
17 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTTAATTTATATTA
Found at i:577252 original size:22 final size:23
Alignment explanation
Indices: 577227--577316 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 23
577217 TTATATTAAA
*
577227 TTAAATTT-ATATAAATTTTTAT
1 TTAAATTTAATATAAATTATTAT
577249 TT-AATTTAATATAAATTATTAT
1 TTAAATTTAATATAAATTATTAT
* *
577271 TT--ATATAATAAAAATTATTTTTAT
1 TTAAATTTAATATAAATTA---TTAT
*
577295 TTTAATTTAAT-TATAATTATTA
1 TTAAATTTAATATA-AATTATTA
577317 ATTTTAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
21 18 0.32
22 17 0.30
23 3 0.05
24 6 0.11
25 1 0.02
26 11 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTAAATTTAATATAAATTATTAT
Found at i:577273 original size:26 final size:26
Alignment explanation
Indices: 577244--577316 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 26
577234 TATATAAATT
577244 TTTATTTAATTTAATATAAATTATTA
1 TTTATTTAATTTAATATAAATTATTA
*
577270 TTTA--T-A--TAATAAAAATTATT-
1 TTTATTTAATTTAATATAAATTATTA
577290 TTTATTTTAATTTAAT-TATAATTATTA
1 TTTA-TTTAATTTAATATA-AATTATTA
577317 ATTTTAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
20 4 0.11
21 13 0.35
23 2 0.05
24 2 0.05
25 1 0.03
26 15 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTATTTAATTTAATATAAATTATTA
Found at i:577560 original size:25 final size:26
Alignment explanation
Indices: 577503--577561 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
577493 TTTATTTTTT
577503 TAAATATTTTAAACAAATATATTATA
1 TAAATATTTTAAACAAATATATTATA
** *
577529 TTTATATTTT-AATAAATAT-TTAATA
1 TAAATATTTTAAACAAATATATT-ATA
577554 TAAATATT
1 TAAATATT
577562 AAACATGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 2 0.07
25 17 0.63
26 8 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
TAAATATTTTAAACAAATATATTATA
Found at i:578005 original size:18 final size:17
Alignment explanation
Indices: 577978--578033 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
577968 TAAATTTAAA
577978 TAAAAATAATTTATTAT
1 TAAAAATAATTTATTAT
*
577995 TAAATAATAATTTAATAAT
1 TAAA-AATAATTT-ATTAT
* *
578014 TTAAAATATTTTATTAT
1 TAAAAATAATTTATTAT
578031 TAA
1 TAA
578034 TTTAAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 10 0.31
18 15 0.47
19 7 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAAATAATTTATTAT
Found at i:578020 original size:21 final size:19
Alignment explanation
Indices: 577994--578070 Score: 59
Period size: 21 Copynumber: 3.8 Consensus size: 19
577984 TAATTTATTA
577994 TTAAATAATAATTTAATAAT
1 TTAAAT-ATAATTTAATAAT
*
578014 TTAAA-ATATTTTATTATTAAT
1 TTAAATATAATTTA--A-TAAT
*
578035 TTAAATA-AATTTATTAATT
1 TTAAATATAATTTAATAA-T
*
578054 TTAATAAATAATTTAAT
1 TTAA-ATATAATTTAAT
578071 TTATAAACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
18 10 0.22
19 5 0.11
20 8 0.18
21 21 0.47
22 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAATATAATTTAATAAT
Found at i:578050 original size:18 final size:18
Alignment explanation
Indices: 578027--578062 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
578017 AAATATTTTA
578027 TTATTAATTTAAATAAAT
1 TTATTAATTTAAATAAAT
*
578045 TTATTAATTTTAATAAAT
1 TTATTAATTTAAATAAAT
578063 AATTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATTAATTTAAATAAAT
Found at i:578069 original size:18 final size:18
Alignment explanation
Indices: 578028--578073 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
578018 AATATTTTAT
*
578028 TATTAATTTAAATAAATT
1 TATTAATTTAAATAAATA
*
578046 TATTAATTTTAATAAATA
1 TATTAATTTAAATAAATA
578064 -ATTTAATTTA
1 TA-TTAATTTA
578074 TAAACATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTAATTTAAATAAATA
Found at i:578373 original size:16 final size:18
Alignment explanation
Indices: 578352--578385 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
578342 ATAATTAAAT
578352 TTAAATAA-AA-AATTTA
1 TTAAATAATAACAATTTA
578368 TTAAATAATAACAATTTA
1 TTAAATAATAACAATTTA
578386 AATTAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAATAATAACAATTTA
Found at i:578388 original size:15 final size:14
Alignment explanation
Indices: 578336--578413 Score: 61
Period size: 15 Copynumber: 5.4 Consensus size: 14
578326 ATGAATATAT
* *
578336 ATTTATATAATTAA
1 ATTTAAATAATAAA
578350 ATTTAAATAA-AAA
1 ATTTAAATAATAAA
578363 ATTTATTAAATAATAACA
1 A--T-TTAAATAATAA-A
**
578381 ATTTAAATTAATTTA
1 ATTTAAA-TAATAAA
578396 ATTTAAATAA-AAA
1 ATTTAAATAATAAA
578409 ATTTA
1 ATTTA
578414 CGTTTTATAC
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
13 9 0.17
14 12 0.23
15 14 0.27
16 13 0.25
17 2 0.04
18 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTTAAATAATAAA
Found at i:578529 original size:7 final size:7
Alignment explanation
Indices: 578517--578551 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
578507 CAATGGGCTT
578517 TGGCTAA
1 TGGCTAA
578524 TGGCTAA
1 TGGCTAA
578531 TGGCTAA
1 TGGCTAA
578538 TGGCTAA
1 TGGCTAA
578545 TGGCTAA
1 TGGCTAA
578552 GTAGAACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (7 bp):
TGGCTAA
Found at i:580339 original size:2 final size:2
Alignment explanation
Indices: 580332--580366 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
580322 CAGCTTAACA
*
580332 AT AT AT AT AT AA 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 A
580367 AGCCCCTACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:581926 original size:24 final size:23
Alignment explanation
Indices: 581880--582003 Score: 103
Period size: 24 Copynumber: 5.3 Consensus size: 23
581870 GGATTTAATT
* *
581880 AAATTAAATTT-TTAAAAATATA
1 AAATTTAATTTATTTAAAATATA
581902 AAATTTAATTTAATTTAAAATATA
1 AAATTTAATTT-ATTTAAAATATA
** ** *
581926 AAATTTAAATTTATTGGATTTAATT
1 AAATTT-AATTTATTTAAAAT-ATA
*
581951 AAATTTAA-TT-TTTACAAGTAT-
1 AAATTTAATTTATTTA-AAATATA
581972 AAATTTAATTTAATTTAAAATATA
1 AAATTTAATTT-ATTTAAAATATA
581996 AAATTTAA
1 AAATTTAA
582004 ATAATTTTAA
Statistics
Matches: 81, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
21 8 0.10
22 16 0.20
23 9 0.11
24 35 0.43
25 13 0.16
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATTTAATTTATTTAAAATATA
Found at i:581934 original size:71 final size:70
Alignment explanation
Indices: 581853--582009 Score: 262
Period size: 71 Copynumber: 2.2 Consensus size: 70
581843 GCTATTGTAC
581853 TAAAATTTAAATTAATTGGATTTAATTAAATTAAATTTTTAAAAATATAAAATTTAATTTAATTT
1 TAAAATTTAAATTAATTGGATTTAATTAAATTAAATTTTTAAAAATAT-AAATTTAATTTAATTT
581918 AAAATA
65 AAAATA
* * * *
581924 TAAAATTTAAATTTATTGGATTTAATTAAATTTAATTTTTACAAGTATAAATTTAATTTAATTTA
1 TAAAATTTAAATTAATTGGATTTAATTAAATTAAATTTTTAAAAATATAAATTTAATTTAATTTA
581989 AAATA
66 AAATA
581994 TAAAATTTAAA-TAATT
1 TAAAATTTAAATTAATT
582010 TTAATTTATT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
69 4 0.05
70 33 0.41
71 44 0.54
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (70 bp):
TAAAATTTAAATTAATTGGATTTAATTAAATTAAATTTTTAAAAATATAAATTTAATTTAATTTA
AAATA
Found at i:582017 original size:70 final size:71
Alignment explanation
Indices: 581853--582017 Score: 230
Period size: 70 Copynumber: 2.3 Consensus size: 71
581843 GCTATTGTAC
*
581853 TAAAATTTAAATTAA-TTGGATTTAATTAAATTAAATTTTTAAAAATATAAAATTTAATTTAATT
1 TAAAATTTAAA-TAATTTTGATTTAATTAAATTAAATTTTTAAAAATATAAAATTTAATTTAATT
581917 TAAAATA
65 TAAAATA
* * *
581924 TAAAATTTAAAT--TTATTGGATTTAATTAAATTTAATTTTTACAAGTAT-AAATTTAATTTAAT
1 TAAAATTTAAATAATT-TT-GATTTAATTAAATTAAATTTTTAAAAATATAAAATTTAATTTAAT
581986 TTAAAATA
64 TTAAAATA
*
581994 TAAAATTTAAATAATTTTAATTTA
1 TAAAATTTAAATAATTTTGATTTA
582018 TTTATTTAAT
Statistics
Matches: 84, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
69 1 0.01
70 41 0.49
71 40 0.48
72 2 0.02
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (71 bp):
TAAAATTTAAATAATTTTGATTTAATTAAATTAAATTTTTAAAAATATAAAATTTAATTTAATTT
AAAATA
Found at i:582582 original size:12 final size:14
Alignment explanation
Indices: 582542--582583 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
582532 TATATCATTT
582542 ATAA-TAATTTAAAA
1 ATAATTAATTT-AAA
582556 ATAATTAATTTAAA
1 ATAATTAATTTAAA
582570 AT-ATTAA-TTAAA
1 ATAATTAATTTAAA
582582 AT
1 AT
582584 TTATAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.26
13 5 0.19
14 9 0.33
15 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATTAATTTAAA
Found at i:582609 original size:23 final size:23
Alignment explanation
Indices: 582583--582628 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
582573 TTAATTAAAA
582583 TTTAT-AATAAATAAATAATAATT
1 TTTATAAATAAATAAAT-ATAATT
*
582606 TTTATAAATTAATAAATATAATT
1 TTTATAAATAAATAAATATAATT
582629 AAAAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTATAAATAAATAAATATAATT
Found at i:582617 original size:41 final size:42
Alignment explanation
Indices: 582538--582618 Score: 103
Period size: 44 Copynumber: 1.9 Consensus size: 42
582528 AGAATATATC
*
582538 ATTTATAATAATTTAAAAATAATTAATTTAAAATATTAATTAAA
1 ATTTATAATAATATAAAAATAATT-ATTTAAAA-ATTAATTAAA
*
582582 ATTTATAATAA-ATAAATAATAATT-TTTATAAATTAAT
1 ATTTATAATAATATAAA-AATAATTATTTAAAAATTAAT
582619 AAATATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 6 0.18
42 6 0.18
43 4 0.12
44 18 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (42 bp):
ATTTATAATAATATAAAAATAATTATTTAAAAATTAATTAAA
Found at i:582635 original size:21 final size:22
Alignment explanation
Indices: 582611--582652 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
582601 TAATTTTTAT
*
582611 AAATTAATAAATA-TAATTAAA
1 AAATTAAAAAATATTAATTAAA
582632 AAATTAAAAAATATTAATTAA
1 AAATTAAAAAATATTAATTAA
582653 TATTTATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATTAAAAAATATTAATTAAA
Found at i:587860 original size:16 final size:17
Alignment explanation
Indices: 587841--587878 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
587831 ACATAATATG
*
587841 AATTTAATATATAAA-A
1 AATTTAATAAATAAATA
587857 AATTT-ATAAATAAATA
1 AATTTAATAAATAAATA
587873 AATTTA
1 AATTTA
587879 TCAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTTAATAAATAAATA
Found at i:587902 original size:15 final size:15
Alignment explanation
Indices: 587882--587929 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
587872 AAATTTATCA
587882 AAATTTATATAATAT
1 AAATTTATATAATAT
* *
587897 AAATTTTTAAAATAT
1 AAATTTATATAATAT
*
587912 AAAAATTATATAAATAT
1 -AAATTTATAT-AATAT
587929 A
1 A
587930 TAAAACTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 13 0.50
16 8 0.31
17 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATTTATATAATAT
Found at i:588730 original size:2 final size:2
Alignment explanation
Indices: 588723--588748 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
588713 GCTTCAATGA
588723 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
588749 GCCTCTGGTT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:589125 original size:28 final size:27
Alignment explanation
Indices: 589086--589138 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
589076 AATATCATGA
*
589086 TAAATTAAAAATA-TTAAAATATATATT
1 TAAAATAAAAATATTTAAAA-ATATATT
589113 TAAAATAATAAATATTTAAAAATATA
1 TAAAATAA-AAATATTTAAAAATATA
589139 AAAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 10 0.43
29 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
TAAAATAAAAATATTTAAAAATATATT
Found at i:589127 original size:16 final size:16
Alignment explanation
Indices: 589103--589151 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
589093 AAAATATTAA
*
589103 AATATATATTTAAAAT
1 AATAAATATTTAAAAT
589119 AATAAATATTTAAAA-
1 AATAAATATTTAAAAT
*
589134 ATATAAAAATATTAAAAT
1 A-ATAAATAT-TTAAAAT
589152 CATTCTATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 21 0.75
17 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATAAATATTTAAAAT
Found at i:589137 original size:10 final size:9
Alignment explanation
Indices: 589089--589150 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
589079 ATCATGATAA
589089 ATTAAAAAT
1 ATTAAAAAT
589098 ATTAAAATATAT
1 ATT-AAA-A-AT
*
589110 ATTTAAAAT
1 ATTAAAAAT
* *
589119 AATAAATAT
1 ATTAAAAAT
589128 -TTAAAAAT
1 ATTAAAAAT
589136 A-TAAAAAT
1 ATTAAAAAT
589144 ATTAAAA
1 ATTAAAA
589151 TCATTCTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
8 14 0.33
9 16 0.38
10 4 0.10
11 3 0.07
12 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:589433 original size:16 final size:18
Alignment explanation
Indices: 589412--589447 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
589402 TTATATTTAT
589412 ATTTAA-AATTTTA-ATA
1 ATTTAATAATTTTATATA
589428 ATTTAATAATTTTATATA
1 ATTTAATAATTTTATATA
589446 AT
1 AT
589448 GTTTATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAATAATTTTATATA
Found at i:591395 original size:15 final size:15
Alignment explanation
Indices: 591371--591406 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
591361 AAAATTTTAA
*
591371 AAATATTTTAAATTT
1 AAATAATTTAAATTT
591386 AAATAATTTAAATTT
1 AAATAATTTAAATTT
*
591401 ATATAA
1 AAATAA
591407 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATAATTTAAATTT
Found at i:592160 original size:19 final size:20
Alignment explanation
Indices: 592126--592165 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
592116 ATAAGAATAT
*
592126 AATATAAAAATTTAAT-TAA
1 AATATAAAAATATAATATAA
*
592145 AATATAAATATATAATATAA
1 AATATAAAAATATAATATAA
592165 A
1 A
592166 TTATTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AATATAAAAATATAATATAA
Found at i:592166 original size:19 final size:19
Alignment explanation
Indices: 592121--592166 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
592111 TGATTATAAG
*
592121 AATAT-AATATAAAAATTT
1 AATATAAATATAAAAATAT
*
592139 AAT-TAAAATATAAATATAT
1 AATAT-AAATATAAAAATAT
592158 AATATAAAT
1 AATATAAAT
592167 TATTATTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 1 0.04
18 3 0.13
19 18 0.78
20 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AATATAAATATAAAAATAT
Found at i:592368 original size:22 final size:22
Alignment explanation
Indices: 592336--592388 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
592326 GAACATATTT
*
592336 TCAAATTATTGCTAGAGAGCAA
1 TCAAATCATTGCTAGAGAGCAA
592358 TCAAATCATTGCTAGAGAGCAA
1 TCAAATCATTGCTAGAGAGCAA
592380 TCAAATCAT
1 TCAAATCAT
592389 GCTTCCTTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (22 bp):
TCAAATCATTGCTAGAGAGCAA
Found at i:594658 original size:19 final size:18
Alignment explanation
Indices: 594636--594703 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
594626 TATATATATA
594636 TAAATATAATATAAATTAT
1 TAAATATAATATAAATT-T
**
594655 TAAATATTTTA-AAATTT
1 TAAATATAATATAAATTT
* *
594672 TAAAAATAAATATAATTTT
1 TAAATAT-AATATAAATTT
594691 TATAATA-AATATA
1 TA-AATATAATATA
594704 TTACATTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
17 7 0.18
18 13 0.33
19 16 0.41
20 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATATAATATAAATTT
Found at i:594688 original size:18 final size:18
Alignment explanation
Indices: 594667--594703 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
594657 AATATTTTAA
594667 AATTTTAAAAATAAATAT
1 AATTTTAAAAATAAATAT
* *
594685 AATTTTTATAATAAATAT
1 AATTTTAAAAATAAATAT
594703 A
1 A
594704 TTACATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTTTAAAAATAAATAT
Found at i:595023 original size:21 final size:20
Alignment explanation
Indices: 594999--595057 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 20
594989 TTTTAATTAA
594999 ATATGATTATATAAATATGAT
1 ATAT-ATTATATAAATATGAT
595020 ATATAATTAT-TAAA-AT-AT
1 ATAT-ATTATATAAATATGAT
*
595038 A-ATATAATATAAAT-TGAT
1 ATATATTATATAAATATGAT
595056 AT
1 AT
595058 TTTAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
16 4 0.12
17 7 0.22
18 6 0.19
19 2 0.06
20 4 0.12
21 9 0.28
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
ATATATTATATAAATATGAT
Found at i:595024 original size:13 final size:14
Alignment explanation
Indices: 594951--595025 Score: 59
Period size: 14 Copynumber: 5.3 Consensus size: 14
594941 GATTTCAATG
594951 ATAAATATGATTAT
1 ATAAATATGATTAT
594965 ATAAATA--ATTAT
1 ATAAATATGATTAT
* *
594977 -TAAAATAATTAATTTT
1 AT-AAAT-A-TGATTAT
594993 AATTAAATATGATTAT
1 -A-TAAATATGATTAT
595009 ATAAATATGA-TAT
1 ATAAATATGATTAT
595022 ATAA
1 ATAA
595026 TTATTAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 17
0.71 0.04 0.24
Matches are distributed among these distances:
11 1 0.02
12 9 0.18
13 8 0.16
14 16 0.32
15 1 0.02
16 9 0.18
17 1 0.02
18 4 0.08
19 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (14 bp):
ATAAATATGATTAT
Found at i:595044 original size:19 final size:18
Alignment explanation
Indices: 594963--595045 Score: 77
Period size: 21 Copynumber: 4.7 Consensus size: 18
594953 AAATATGATT
594963 ATATAA-ATAATTATTAA
1 ATATAATATAATTATTAA
594980 A-ATAAT-TAATT-TTAA
1 ATATAATATAATTATTAA
* *
594995 TTA-AATATGATTATATAA
1 ATATAATATAATTAT-TAA
595013 ATATGATATATAATTATTAAA
1 ATAT-A-ATATAATTATT-AA
595034 ATATAATATAAT
1 ATATAATATAAT
595046 ATAAATTGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
15 7 0.13
16 14 0.26
17 2 0.04
18 5 0.09
19 7 0.13
20 3 0.06
21 15 0.28
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
ATATAATATAATTATTAA
Found at i:595095 original size:32 final size:30
Alignment explanation
Indices: 595027--595112 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 30
595017 GATATATAAT
*
595027 TATTAAAATATAATATAATATAAATTGATA
1 TATTAAAATATAATAAAATATAAATTGATA
*
595057 TTTTAAAATAT-ATAAAATATAAATT-ATTAACA
1 TATTAAAATATAATAAAATATAAATTGA-T---A
595089 TATTAAAAT-TAATAAAAATATAAA
1 TATTAAAATATAAT-AAAATATAAA
595113 AATATTTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
28 1 0.02
29 14 0.30
30 10 0.21
31 1 0.02
32 11 0.23
33 10 0.21
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (30 bp):
TATTAAAATATAATAAAATATAAATTGATA
Found at i:595177 original size:29 final size:28
Alignment explanation
Indices: 595018--595179 Score: 84
Period size: 28 Copynumber: 5.6 Consensus size: 28
595008 TATAAATATG
*
595018 ATATA-TAATTATTAAAATATAATATAA
1 ATATATTAATTTTTAAAATATAATATAA
* *
595045 TATAAATTGATATTTTAAAATATATAAAATATAA
1 -ATATATT-A-ATTTTTAAA-ATAT--AATATAA
* * *
595079 AT-TATTAACATATTAAAAT-TAATAAAA
1 ATATATTAA-TTTTTAAAATATAATATAA
** *
595106 ATATAAAAATATTTT-AAATATAAT-TATG
1 ATATATTAAT-TTTTAAAATATAATATA-A
**
595134 ATACTA-TAAAATTTATAAATATAATATAA
1 ATA-TATTAATTTTTA-AAATATAATATAA
595163 ATATATTAATTTTTAAA
1 ATATATTAATTTTTAAA
595180 TTTAAATTTA
Statistics
Matches: 98, Mismatches: 20, Indels: 32
0.65 0.13 0.21
Matches are distributed among these distances:
27 16 0.16
28 24 0.24
29 23 0.23
30 6 0.06
31 13 0.13
32 7 0.07
33 2 0.02
34 7 0.07
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
ATATATTAATTTTTAAAATATAATATAA
Found at i:595685 original size:17 final size:19
Alignment explanation
Indices: 595637--595687 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
595627 TTATGTCATA
595637 TTTTTAATAATTATTTTATT
1 TTTTTAAT-ATTATTTTATT
595657 TTTTAATAAATATTA-TTTA-T
1 TTTT--T-AATATTATTTTATT
595677 TTTTTAATATT
1 TTTTTAATATT
595688 TATTAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
17 6 0.21
18 1 0.04
20 9 0.32
21 4 0.14
22 5 0.18
23 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTAATATTATTTTATT
Found at i:595691 original size:21 final size:21
Alignment explanation
Indices: 595637--595697 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
595627 TTATGTCATA
595637 TTTTTAATAATTA-T-TTTAT
1 TTTTTAATAATTATTATTTAT
*
595656 TTTTTAATAAATATTATTTAT
1 TTTTTAATAATTATTATTTAT
*
595677 TTTTTAATATTTATTAATTTA
1 TTTTTAATAATTATT-ATTTA
595698 AATATCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.33
20 1 0.03
21 18 0.50
22 5 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTAATAATTATTATTTAT
Found at i:596589 original size:25 final size:25
Alignment explanation
Indices: 596542--596590 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
596532 CTAACTTTGC
596542 TTATTTTTTTATTATATAATATATA
1 TTATTTTTTTATTATATAATATATA
596567 TTATGTTTTTTA-TAT-TAAT-TATA
1 TTAT-TTTTTTATTATATAATATATA
596590 T
1 T
596591 GAAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 5 0.22
24 4 0.17
25 7 0.30
26 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
TTATTTTTTTATTATATAATATATA
Found at i:596789 original size:25 final size:23
Alignment explanation
Indices: 596761--596807 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
596751 AATATAAATA
596761 ATTTTAAATAAAATTTAAAATTTAT
1 ATTTTAAATAAAA-TT-AAATTTAT
*
596786 ATTTTAAATCAAATTAAATTTA
1 ATTTTAAATAAAATTAAATTTA
596808 AATAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 2 0.10
25 12 0.57
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTTAAATAAAATTAAATTTAT
Found at i:596809 original size:16 final size:16
Alignment explanation
Indices: 596788--596820 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
596778 AAATTTATAT
596788 TTTAAATCAAAT-TAAA
1 TTTAAAT-AAATATAAA
596804 TTTAAATAAATATAAA
1 TTTAAATAAATATAAA
596820 T
1 T
596821 AATATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TTTAAATAAATATAAA
Found at i:599684 original size:39 final size:39
Alignment explanation
Indices: 599635--599727 Score: 168
Period size: 39 Copynumber: 2.4 Consensus size: 39
599625 TATTGGACTT
599635 TGATCAAATTACATTATCTTCACTAGGTTCTTTTAAATG
1 TGATCAAATTACATTATCTTCACTAGGTTCTTTTAAATG
* *
599674 TGATTAAATTACTTTATCTTCACTAGGTTCTTTTAAATG
1 TGATCAAATTACATTATCTTCACTAGGTTCTTTTAAATG
599713 TGATCAAATTACATT
1 TGATCAAATTACATT
599728 GTTTTTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (39 bp):
TGATCAAATTACATTATCTTCACTAGGTTCTTTTAAATG
Found at i:601851 original size:24 final size:26
Alignment explanation
Indices: 601824--601875 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
601814 AATATGACAT
601824 AATTA-CATAAATA-TAATA-TAAAAA
1 AATTATCA-AAATATTAATATTAAAAA
*
601848 AATTATCAAAATATTTATATTAAAAA
1 AATTATCAAAATATTAATATTAAAAA
601874 AA
1 AA
601876 AAAGACATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 10 0.42
25 6 0.25
26 8 0.33
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (26 bp):
AATTATCAAAATATTAATATTAAAAA
Found at i:620323 original size:2 final size:2
Alignment explanation
Indices: 620318--620345 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
620308 TTTTTTCTTC
620318 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
620346 GGTATAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:620480 original size:2 final size:2
Alignment explanation
Indices: 620473--620513 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
620463 TTTGCTTTGC
* * *
620473 AT AT AT AT AA AT AT AT AT AT AT AA AT AA 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 AT AT A
620514 AGTGACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:620492 original size:14 final size:14
Alignment explanation
Indices: 620473--620514 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
620463 TTTGCTTTGC
*
620473 ATATATATAAATAT
1 ATATATATAAATAA
620487 ATATATATAAATAA
1 ATATATATAAATAA
*
620501 ATATATATATATAA
1 ATATATATAAATAA
620515 GTGACTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATATATAAATAA
Found at i:620500 original size:18 final size:18
Alignment explanation
Indices: 620473--620514 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
620463 TTTGCTTTGC
*
620473 ATATATATAAATATATAT
1 ATATAAATAAATATATAT
620491 ATATAAATAAATATATAT
1 ATATAAATAAATATATAT
620509 ATATAA
1 ATATAA
620515 GTGACTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAAATAAATATATAT
Found at i:624889 original size:22 final size:22
Alignment explanation
Indices: 624862--624916 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
624852 ATTCAAGCAC
624862 TTTTAATATTAATAATTTTAAA
1 TTTTAATATTAATAATTTTAAA
* **
624884 TTTTAATATTTATAATTTTTTA
1 TTTTAATATTAATAATTTTAAA
624906 TTTTAA-ATTAA
1 TTTTAATATTAA
624917 ATTATTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAATATTAATAATTTTAAA
Found at i:625587 original size:16 final size:16
Alignment explanation
Indices: 625561--625613 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
625551 TAGTAATTTA
625561 ATTTAATTTAATTTATT
1 ATTT-ATTTAATTTATT
**
625578 ATTTATTTAATAAATT
1 ATTTATTTAATTTATT
*
625594 TTTTATTTAAATTTAATT
1 ATTTATTT-AATTT-ATT
625612 AT
1 AT
625614 AAAATATATA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 17 0.61
17 7 0.25
18 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTATTTAATTTATT
Found at i:625638 original size:21 final size:21
Alignment explanation
Indices: 625601--625640 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
625591 ATTTTTTATT
*
625601 TAAATTTAATTATAAAATATA
1 TAAATTTAATTAAAAAATATA
625622 TAAATATTAA-TAAAAAATA
1 TAAAT-TTAATTAAAAAATA
625641 ATTTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTTAATTAAAAAATATA
Found at i:626242 original size:16 final size:16
Alignment explanation
Indices: 626211--626263 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
626201 TTTATAATTA
*
626211 AATTATAATAAAATAAT
1 AATTTTAAT-AAATAAT
*
626228 ATTTTTAATAAATAAT
1 AATTTTAATAAATAAT
* * *
626244 AATTTGAATCAATAAG
1 AATTTTAATAAATAAT
626260 AATT
1 AATT
626264 CATAAAAACT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 23 0.77
17 7 0.23
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (16 bp):
AATTTTAATAAATAAT
Found at i:627354 original size:35 final size:34
Alignment explanation
Indices: 627314--627388 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 34
627304 TTAGAATTAC
** *
627314 AATAATTTTAAGTTTTAAATTATTATTTATAAAAT
1 AATAATTTTAAAATATAAA-TATTATTTATAAAAT
* *
627349 AATAA--TTAAAATATAAATATTTTTTATTAAAT
1 AATAATTTTAAAATATAAATATTATTTATAAAAT
627381 AATAATTT
1 AATAATTT
627389 AAATCGATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
32 18 0.55
33 9 0.27
34 1 0.03
35 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (34 bp):
AATAATTTTAAAATATAAATATTATTTATAAAAT
Found at i:627375 original size:32 final size:33
Alignment explanation
Indices: 627329--627392 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
627319 TTTTAAGTTT
627329 TAAATTATTATTTATAAAATAATAATTAAAATA
1 TAAATTATTATTTATAAAATAATAATTAAAATA
* * *
627362 TAAA-TATTTTTTATTAAATAATAATTTAAAT
1 TAAATTATTATTTATAAAATAATAATTAAAAT
627393 CGATTCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
TAAATTATTATTTATAAAATAATAATTAAAATA
Found at i:629196 original size:23 final size:23
Alignment explanation
Indices: 629142--629219 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
629132 TTATTTTTTT
*
629142 AATATTATATAT-AATTATATAA
1 AATATTATATATAAAATATATAA
* *
629164 ATATAATATATATAAAATATTTAA
1 A-ATATTATATATAAAATATATAA
629188 AATATTATATGATAAAGATATATAA
1 AATATTATAT-ATAAA-ATATATAA
*
629213 ATTATTA
1 AATATTA
629220 AATTTTAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
22 1 0.02
23 18 0.39
24 14 0.30
25 13 0.28
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (23 bp):
AATATTATATATAAAATATATAA
Found at i:629349 original size:17 final size:17
Alignment explanation
Indices: 629323--629362 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
629313 TTGAATTTAA
*
629323 AAATAAATATTAAATAT
1 AAATATATATTAAATAT
**
629340 AAATATATATTTGATAT
1 AAATATATATTAAATAT
629357 AAATAT
1 AAATAT
629363 TTTATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
AAATATATATTAAATAT
Found at i:629420 original size:24 final size:26
Alignment explanation
Indices: 629377--629427 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
629367 TTTTTAAAAT
*
629377 TTTTTTTATATATTTAAAATATATAA
1 TTTTATTATATATTTAAAATATATAA
629403 TTTTATTA-ATATTTAAATATATATA
1 TTTTATTATATATTTAAA-ATATATA
629428 GAATATGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTTATTATATATTTAAAATATATAA
Found at i:631026 original size:23 final size:23
Alignment explanation
Indices: 630983--631026 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
630973 GTAATTTTAT
**
630983 TAAATTATTTAAATTTAAATTAA
1 TAAATTATTTAAAAATAAATTAA
631006 TAAA-TATTTAAAAATAGAATT
1 TAAATTATTTAAAAATA-AATT
631027 TACATGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAATTATTTAAAAATAAATTAA
Found at i:631375 original size:107 final size:102
Alignment explanation
Indices: 630962--631540 Score: 499
Period size: 104 Copynumber: 5.6 Consensus size: 102
630952 AGAGTTATCT
* * *
630962 TATTTAAATGTGTAATTTTATTAAATT-ATTTAAATTTAAATTAATAAATATTTAAAAATAGAAT
1 TATTTAAATATGTAATTTTATT-TATTAATTTAAATTTAAATTAATAAATATTTAAAAATAGAGT
* * * *
631026 TTACATGATATTAATTTACTTTAAAATTAATAAAATTTT-
65 TCACAT-ATATTAA-ATAATTTAAAATTAATAAATTTTTC
* * *
631065 TATTTAAATCTGTAA---T-TTTATTAA-TT--ATTTAAATTAATAATTATTTAAAAATAAAG-T
1 TATTTAAATATGTAATTTTATTTATTAATTTAAATTTAAATTAATAAATATTTAAAAATAGAGTT
* * *
631122 CTACATTATATTAAATGATTGTAAAATGAATAAACTTTT-
66 C-ACA-TATATTAAATAATT-TAAAATTAATAAATTTTTC
* * * * *
631161 T-TTAAAATATGTATTTTTTATTAATTTA-TTAAATTTAAATGAACTAAATATTTAAAAATAGAG
1 TATTTAAATATGTA-ATTTTATTTATTAATTTAAATTTAAATTAA-TAAATATTTAAAAATAGAG
* * *
631224 TAT-ACATATATTAATCTACTTTAAAATTAATAAAATTTTCC
64 T-TCACATATATTAA-ATAATTTAAAATTAAT-AAATTTTTC
* * * *
631265 TATTTAATTATG-AACTTTATTATTTTAAATTTTAAATCTAAATTAATAAATATTTAAAAATAGA
1 TATTTAAATATGTAATTTTATT-TATT-AA-TTTAAATTTAAATTAATAAATATTTAAAAATAGA
*
631329 GTTCACATAATATTAATATAATTTAAAATTAATAATTTTTTTC
63 GTTCACAT-ATATTAA-ATAATTTAAAATTAATAA-ATTTTTC
* * * * * *
631372 TATTTAAATATGTAATTTTATTTATTGATATAAATTTAAATTAA-AAATATTTTATAAGAGAGTC
1 TATTTAAATATGTAATTTTATTTATTAATTTAAATTTAAATTAATAAATATTTAAAAATAGAGTT
* * *
631436 CTCATGATATTAAATGACTTTAAAATTAATAAACTTTTC
66 CACAT-ATATTAAAT-AATTTAAAATTAATAAATTTTTC
* * *
631475 TTATTTAAATATGTAATTTTATTAATTTATTTAAATTTAAATGAACTAAAT-TTTAGAAAATAGA
1 -TATTTAAATATGTAATTTTATTTATTAATTTAAATTTAAATTAA-TAAATATTTA-AAAATAGA
631539 GT
63 GT
631541 CCATACACAA
Statistics
Matches: 385, Mismatches: 60, Indels: 59
0.76 0.12 0.12
Matches are distributed among these distances:
95 14 0.04
96 54 0.14
97 1 0.00
98 5 0.01
99 4 0.01
100 9 0.02
102 27 0.07
103 56 0.15
104 86 0.22
105 28 0.07
106 39 0.10
107 54 0.14
108 8 0.02
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (102 bp):
TATTTAAATATGTAATTTTATTTATTAATTTAAATTTAAATTAATAAATATTTAAAAATAGAGTT
CACATATATTAAATAATTTAAAATTAATAAATTTTTC
Found at i:634528 original size:22 final size:22
Alignment explanation
Indices: 634503--634544 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
634493 ATAACATAGT
*
634503 AATAAACACTTAATAATATAAC
1 AATAAACAATTAATAATATAAC
* *
634525 AATAAATAATTTATAATATA
1 AATAAACAATTAATAATATA
634545 TGAATAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAACAATTAATAATATAAC
Found at i:634875 original size:2 final size:2
Alignment explanation
Indices: 634864--634906 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
634854 ATGTACATAC
634864 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
634905 AT
1 AT
634907 GCAGGTAGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:635047 original size:17 final size:17
Alignment explanation
Indices: 635027--635084 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
635017 TTTATTATAA
*
635027 TTATTTTTTAAATAATT
1 TTATATTTTAAATAATT
*
635044 TTATATTTTATATAATTT
1 TTATATTTTAAATAA-TT
*
635062 TTAATATATT-AATAA-T
1 TT-ATATTTTAAATAATT
635078 TTATATT
1 TTATATT
635085 ATATTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 13 0.38
18 8 0.24
19 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATATTTTAAATAATT
Found at i:635062 original size:27 final size:29
Alignment explanation
Indices: 635050--635114 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 29
635040 AATTTTATAT
*
635050 TTTATA-TA-ATTTTTAATATATTAATAA
1 TTTATATTATATTTTAAATATATTAATAA
*
635077 TTTATATTATATTTTAAA-A-AAT-AT-A
1 TTTATATTATATTTTAAATATATTAATAA
635102 TTTATATTATATT
1 TTTATATTATATT
635115 ATAATTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 14 0.41
26 2 0.06
27 8 0.24
28 3 0.09
29 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTATATTATATTTTAAATATATTAATAA
Found at i:635123 original size:20 final size:20
Alignment explanation
Indices: 635043--635142 Score: 59
Period size: 20 Copynumber: 5.0 Consensus size: 20
635033 TTTAAATAAT
*
635043 TTTATATTTTA-TATAATT-
1 TTTATATTATATTATAATTA
635061 TTTA-A-TATATTAATAATTTA
1 TTTATATTATATT-ATAA-TTA
* * *
635081 TATTATATTTTA-AAAAATATA
1 T-TTATATTATATTATAAT-TA
635102 TTTATATTATATTATAATTA
1 TTTATATTATATTATAATTA
* *
635122 TTT-TATTTACATTATATTTA
1 TTTATA-TTATATTATAATTA
635142 T
1 T
635143 ATAATCGTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
16 3 0.05
17 2 0.03
18 8 0.13
19 4 0.06
20 29 0.46
21 13 0.21
22 1 0.02
23 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATATTATATTATAATTA
Found at i:635130 original size:25 final size:25
Alignment explanation
Indices: 635072--635118 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
635062 TTAATATATT
*
635072 AATA-ATTTATATTATATTTTAAAA
1 AATATATTTATATTATATTATAAAA
635096 AATATATTTATATTATATTATAA
1 AATATATTTATATTATATTATAA
635119 TTATTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AATATATTTATATTATATTATAAAA
Found at i:635383 original size:3 final size:3
Alignment explanation
Indices: 635375--635415 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
635365 GGAGAATGAG
*
635375 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
635416 TAATCAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:636072 original size:20 final size:21
Alignment explanation
Indices: 636042--636080 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
636032 TAAAAAAATA
636042 AATATAAATAATTTTATTTTT
1 AATATAAATAATTTTATTTTT
636063 AATA-AAATAATTTTATTT
1 AATATAAATAATTTTATTT
636081 GATTTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATATAAATAATTTTATTTTT
Found at i:636318 original size:17 final size:17
Alignment explanation
Indices: 636298--636331 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
636288 TATTACTGGT
636298 TTAAATTACAATCACAA
1 TTAAATTACAATCACAA
636315 TTAAATTACAATCACAA
1 TTAAATTACAATCACAA
636332 ATATATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAAATTACAATCACAA
Found at i:636339 original size:17 final size:17
Alignment explanation
Indices: 636299--636339 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
636289 ATTACTGGTT
*
636299 TAAATTACAATCACAAT
1 TAAATTACAATCACAAA
636316 TAAATTACAATCACAAA
1 TAAATTACAATCACAAA
*
636333 TATATTA
1 TAAATTA
636340 TATTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAATTACAATCACAAA
Found at i:636639 original size:2 final size:2
Alignment explanation
Indices: 636632--636661 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
636622 TCTTCATCCC
*
636632 CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
636662 TCATGTTCTA
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:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:637941 original size:2 final size:2
Alignment explanation
Indices: 637934--637964 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
637924 CCCTACCAAA
637934 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
637965 AGGTGGTCCA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:639231 original size:27 final size:29
Alignment explanation
Indices: 639201--639254 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
639191 AATTGATTTA
639201 ATTTATTAATAA-T-AAAAATT-TAATTAT
1 ATTTATTAA-AATTAAAAAATTATAATTAT
639228 ATTTATTAAAATTAAAAAATTATAATT
1 ATTTATTAAAATTAAAAAATTATAATT
639255 TACATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 2 0.08
27 10 0.42
28 7 0.29
29 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTTATTAAAATTAAAAAATTATAATTAT
Found at i:639769 original size:25 final size:22
Alignment explanation
Indices: 639730--639774 Score: 63
Period size: 25 Copynumber: 1.9 Consensus size: 22
639720 TAAATATTTA
639730 TTAAATTAATAATTATATAAAT
1 TTAAATTAATAATTATATAAAT
639752 TTAAATTATATTATATTATATAA
1 TTAAATTA-A-TA-ATTATATAA
639775 TTATTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 1 0.05
24 2 0.10
25 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAATTAATAATTATATAAAT
Found at i:640306 original size:20 final size:20
Alignment explanation
Indices: 640254--640308 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
640244 AAAATACTAC
640254 ATAA-AAAATA-ACATAAAT
1 ATAATAAAATATACATAAAT
*
640272 ATAATATAA-ATACATAAAT
1 ATAATAAAATATACATAAAT
**
640291 ATGTTAAAATATACATAA
1 ATAATAAAATATACATAA
640309 TAATAATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 5 0.17
19 17 0.57
20 8 0.27
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (20 bp):
ATAATAAAATATACATAAAT
Found at i:640807 original size:19 final size:18
Alignment explanation
Indices: 640757--640807 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
640747 CATAACATAA
640757 AAATA-TAAAAAATTTAT
1 AAATATTAAAAAATTTAT
*
640774 AAATATTATATAAATTTAT
1 AAATATTA-AAAAATTTAT
*
640793 AATATTTTAAAAAAT
1 AA-ATATTAAAAAAT
640808 AAAATCTACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 5 0.18
18 2 0.07
19 16 0.57
20 5 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATTAAAAAATTTAT
Found at i:645879 original size:13 final size:11
Alignment explanation
Indices: 645842--645870 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
645832 AAAGTCAGTC
645842 AAAAAAAA-TA
1 AAAAAAAATTA
645852 AAAAAAAATTA
1 AAAAAAAATTA
645863 AAAAAAAA
1 AAAAAAAA
645871 GGTTAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAAAAATTA
Found at i:646164 original size:17 final size:18
Alignment explanation
Indices: 646089--646181 Score: 62
Period size: 19 Copynumber: 4.9 Consensus size: 18
646079 TTATTTATAT
* *
646089 AATAAAAAAATTTAAATTT
1 AATAAAAAATTTTAAA-TA
* * *
646108 AATTATAAATATTAATATA
1 AATAAAAAATTTTAA-ATA
* **
646127 AATATATTATTTTAAAT-
1 AATAAAAAATTTTAAATA
646144 AATAAAATAAATTTTTAAATA
1 AAT-AAA-AAA-TTTTAAATA
646165 AATAAAAAATTTTAAAT
1 AATAAAAAATTTTAAAT
646182 TAAGATATGA
Statistics
Matches: 55, Mismatches: 14, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
17 3 0.05
18 12 0.22
19 25 0.45
20 12 0.22
21 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATAAAAAATTTTAAATA
Found at i:647960 original size:30 final size:30
Alignment explanation
Indices: 647924--647984 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
647914 AAAAAGATAA
*
647924 AAAAATAATATAAA-ATAATATAATATAAAT
1 AAAAAT-ATATAAATATAATAAAATATAAAT
* *
647954 AAAAATATATAAATATATTAAAATTTAAAT
1 AAAAATATATAAATATAATAAAATATAAAT
647984 A
1 A
647985 TAATATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (30 bp):
AAAAATATATAAATATAATAAAATATAAAT
Found at i:647991 original size:5 final size:5
Alignment explanation
Indices: 647928--647992 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
647918 AGATAAAAAA
* *
647928 ATAAT ATAAA ATAAT ATAAT ATAA- ATAA- A-AAT AT-AT A-AAT ATATT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
647973 AAAAT TTAAAT ATAAT ATAA
1 ATAAT AT-AAT ATAAT ATAA
647993 ATGCCAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
3 2 0.04
4 12 0.26
5 29 0.62
6 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:648352 original size:20 final size:19
Alignment explanation
Indices: 648327--648376 Score: 68
Period size: 17 Copynumber: 2.7 Consensus size: 19
648317 ATTTATTTTT
648327 ATATTATAATTATATTTAAA
1 ATATTAT-ATTATATTTAAA
648347 ATATTATA-TAT-TTTAAA
1 ATATTATATTATATTTAAA
*
648364 AAATTATATTATA
1 ATATTATATTATA
648377 AAATTTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 13 0.48
18 6 0.22
19 1 0.04
20 7 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATTATATTATATTTAAA
Found at i:648361 original size:17 final size:18
Alignment explanation
Indices: 648327--648393 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 18
648317 ATTTATTTTT
648327 ATATTATAATTATATTTAAA
1 ATATTAT-A-TATATTTAAA
648347 ATATTATATAT-TTTAAA
1 ATATTATATATATTTAAA
*
648364 AAATTATAT-TA--TAAA
1 ATATTATATATATTTAAA
*
648379 ATTTTA-ATATATTTA
1 ATATTATATATATTTA
648394 TATTTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
14 2 0.05
15 10 0.25
16 1 0.03
17 16 0.40
18 3 0.08
19 1 0.03
20 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTATATATATTTAAA
Found at i:648402 original size:24 final size:23
Alignment explanation
Indices: 648367--648424 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 23
648357 TTTTAAAAAA
648367 TTATATTATAAAATTTTAATATAT
1 TTATATTATAAAATTTTAAT-TAT
*
648391 TTATATTTTAAAATTTTAATTATT
1 TTATATTATAAAATTTTAATTA-T
*
648415 TTTTATTATA
1 TTATATTATA
648425 TTTAAAATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 28 0.93
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTATATTATAAAATTTTAATTAT
Found at i:648402 original size:39 final size:42
Alignment explanation
Indices: 648325--648403 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 42
648315 CAATTTATTT
*
648325 TTATATTATAATTATATTTAAAATATTATATATTTTAAAAAA
1 TTATATTATAATAATATTTAAAATATTATATATTTTAAAAAA
*
648367 TTATATTATAA-AAT-TTTAATATATT-TATATTTTAAAA
1 TTATATTATAATAATATTTAAAATATTATATATTTTAAAA
648404 TTTTAATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
39 12 0.34
40 10 0.29
41 2 0.06
42 11 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (42 bp):
TTATATTATAATAATATTTAAAATATTATATATTTTAAAAAA
Found at i:649168 original size:54 final size:53
Alignment explanation
Indices: 649137--649258 Score: 208
Period size: 54 Copynumber: 2.3 Consensus size: 53
649127 TTTTATTTTA
649137 TAAACTTTAAATTTATGTAATTATTTTTAAAAAATAATATATATTTAATAATTT
1 TAAACTTTAAATTTATGTAATTATTTTTAAAAAATAATATATATTT-ATAATTT
*
649191 TAAATTTTAAATTTATGTAATTATTTTTAAAAAATAATATATATTTAATAATTT
1 TAAACTTTAAATTTATGTAATTATTTTTAAAAAATAATATATATTT-ATAATTT
*
649245 TAAATTTTAAATTT
1 TAAACTTTAAATTT
649259 TTATATTTAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.52
Consensus pattern (53 bp):
TAAACTTTAAATTTATGTAATTATTTTTAAAAAATAATATATATTTATAATTT
Found at i:649185 original size:28 final size:28
Alignment explanation
Indices: 649154--649245 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 28
649144 TAAATTTATG
649154 TAATTATTTTTAAAAAATAATATATATT
1 TAATTATTTTTAAAAAATAATATATATT
* *** * *
649182 TAA-TAATTTTAAATTTTAA-ATTTATG
1 TAATTATTTTTAAAAAATAATATATATT
649208 TAATTATTTTTAAAAAATAATATATATT
1 TAATTATTTTTAAAAAATAATATATATT
*
649236 TAATAATTTT
1 TAATTATTTT
649246 AAATTTTAAA
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
26 8 0.16
27 24 0.49
28 17 0.35
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (28 bp):
TAATTATTTTTAAAAAATAATATATATT
Found at i:649260 original size:15 final size:16
Alignment explanation
Indices: 649233--649281 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
649223 AATAATATAT
*
649233 ATTTAATAA-TTTTAA
1 ATTTTATAATTTTTAA
*
649248 ATTTTA-AATTTTTAT
1 ATTTTATAATTTTTAA
*
649263 A-TTTATAATCTTTAA
1 ATTTTATAATTTTTAA
649278 ATTT
1 ATTT
649282 GATTCATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 6 0.22
15 19 0.70
16 2 0.07
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTATAATTTTTAA
Found at i:650042 original size:23 final size:23
Alignment explanation
Indices: 650016--650083 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 23
650006 CACTAGATCC
650016 AATCATTCTCAATAAAATATAAA
1 AATCATTCTCAATAAAATATAAA
*
650039 AATC-TATCTCATTAAAATATAAA
1 AATCAT-TCTCAATAAAATATAAA
* * *
650062 AATCTAATGTAAATAAAATATA
1 AATC-ATTCTCAATAAAATATA
650084 TTTAAATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 1 0.03
23 24 0.65
24 12 0.32
ACGTcount: A:0.56, C:0.10, G:0.01, T:0.32
Consensus pattern (23 bp):
AATCATTCTCAATAAAATATAAA
Found at i:650078 original size:24 final size:23
Alignment explanation
Indices: 650026--650083 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
650016 AATCATTCTC
*
650026 AATAAAATATAAAAATCTATCTC
1 AATAAAATATAAAAATCTATCTA
* *
650049 ATTAAAATATAAAAATCTAATGTA
1 AATAAAATATAAAAATCT-ATCTA
650073 AATAAAATATA
1 AATAAAATATA
650084 TTTAAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (23 bp):
AATAAAATATAAAAATCTATCTA
Found at i:650579 original size:4 final size:4
Alignment explanation
Indices: 650570--650609 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
650560 AATATATGCT
*
650570 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTT TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
650610 AACGTGCCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:650856 original size:27 final size:27
Alignment explanation
Indices: 650792--650848 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
650782 TTAATCAAAT
**
650792 ATAAATAATAATTATTTAAATTTATTTT
1 ATAAA-AATAATTATTTAAATTTATTAA
650820 ATAAAAATAATT-TTTAAATTT-TTAA
1 ATAAAAATAATTATTTAAATTTATTAA
650845 ATAA
1 ATAA
650849 TAAAATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 6 0.22
26 9 0.33
27 7 0.26
28 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATAAAAATAATTATTTAAATTTATTAA
Found at i:652799 original size:23 final size:24
Alignment explanation
Indices: 652761--652833 Score: 80
Period size: 23 Copynumber: 3.1 Consensus size: 24
652751 TATTGACTTT
* *
652761 TTATAAGTAATTTATATATT-TATA
1 TTATAATTAATATATAT-TTATATA
652785 TTAT-ATTAATATATATTTATATA
1 TTATAATTAATATATATTTATATA
* *
652808 TTATAATTAA-ATTTATTTAAATA
1 TTATAATTAATATATATTTATATA
652831 TTA
1 TTA
652834 GGTTAATTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
22 2 0.05
23 32 0.74
24 9 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (24 bp):
TTATAATTAATATATATTTATATA
Found at i:652905 original size:21 final size:20
Alignment explanation
Indices: 652858--652907 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
652848 CTCATATGAG
*
652858 TTTAATTTTAAATAAAATTT
1 TTTAAATTTAAATAAAATTT
652878 TTATAAATTTAAAT-AAATTT
1 TT-TAAATTTAAATAAAATTT
652898 AATTTAAATT
1 --TTTAAATT
652908 ACTATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 8 0.31
21 16 0.62
22 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTAAATTTAAATAAAATTT
Found at i:653096 original size:10 final size:10
Alignment explanation
Indices: 653081--653132 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
653071 ATATTTAAAA
*
653081 TTATATGTAT
1 TTATATATAT
*
653091 TTATATAAAT
1 TTATATATAT
*
653101 TTTTATATA-
1 TTATATATAT
653110 TT-TATATAT
1 TTATATATAT
653119 TTATATTATAT
1 TTATA-TATAT
653130 TTA
1 TTA
653133 AAATTATAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.17
9 4 0.11
10 17 0.49
11 8 0.23
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TTATATATAT
Found at i:653726 original size:14 final size:15
Alignment explanation
Indices: 653689--653739 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
653679 TTTAAATTAT
* *
653689 ATTAAAATAAATTTA
1 ATTAAAATTATTTTA
653704 ATATAAAATT-TTTTA
1 AT-TAAAATTATTTTA
653719 ATTAAAATTATTTTA
1 ATTAAAATTATTTTA
653734 ACTTAA
1 A-TTAA
653740 TTAAATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 7 0.23
15 14 0.45
16 10 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAAAATTATTTTA
Found at i:653834 original size:20 final size:20
Alignment explanation
Indices: 653811--653868 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
653801 ATAAAAATGT
653811 ATTAAAATATATATAATTTA
1 ATTAAAATATATATAATTTA
*
653831 ATTAATAATATAT-TAATTTTT
1 ATTAA-AATATATATAA-TTTA
*
653852 ATAAAAATA-ATATAATT
1 ATTAAAATATATATAATT
653869 ACAATAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 4 0.12
20 15 0.45
21 14 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTAAAATATATATAATTTA
Found at i:657265 original size:11 final size:10
Alignment explanation
Indices: 657185--657279 Score: 72
Period size: 10 Copynumber: 9.3 Consensus size: 10
657175 CAACAGCTCT
657185 AATAATACTAA
1 AATAATA-TAA
657196 ACATAATATAA
1 A-ATAATATAA
*
657207 AAAAATAATTAA
1 AATAAT-A-TAA
*
657219 AATAACATAA
1 AATAATATAA
657229 AAT-ATGAT-A
1 AATAAT-ATAA
* *
657238 TATGATATAA
1 AATAATATAA
657248 AATAATATAA
1 AATAATATAA
657258 ACATAATAT-A
1 A-ATAATATAA
657268 AAT-ATATAA
1 AATAATATAA
657277 AAT
1 AAT
657280 TTATGTAATG
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
8 4 0.06
9 12 0.17
10 26 0.38
11 14 0.20
12 13 0.19
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (10 bp):
AATAATATAA
Found at i:657708 original size:9 final size:9
Alignment explanation
Indices: 657694--657719 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
657684 TAAATTTAAT
657694 TATAAAATA
1 TATAAAATA
657703 TATAAAATA
1 TATAAAATA
657712 TATAAAAT
1 TATAAAAT
657720 TTTTATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TATAAAATA
Found at i:658561 original size:3 final size:3
Alignment explanation
Indices: 658555--658589 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
658545 ATATATGAAG
658555 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA GTAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA T
658590 TATATAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:664198 original size:17 final size:17
Alignment explanation
Indices: 664160--664198 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
664150 TTAATTTATC
664160 TTTAAATAAATCATTAA
1 TTTAAATAAATCATTAA
*
664177 ATTAAATAAAAT-ATTAA
1 TTTAAAT-AAATCATTAA
664194 TTTAA
1 TTTAA
664199 TTTAAGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAATAAATCATTAA
Found at i:664248 original size:20 final size:20
Alignment explanation
Indices: 664220--664258 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
664210 ATTTAGATAT
*
664220 AAATTAAAACTTAAAAATTC
1 AAATAAAAACTTAAAAATTC
* *
664240 AAATAAAAATTTATAAATT
1 AAATAAAAACTTAAAAATT
664259 AATAATTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAAAAACTTAAAAATTC
Found at i:667101 original size:6 final size:6
Alignment explanation
Indices: 667090--667167 Score: 102
Period size: 6 Copynumber: 13.0 Consensus size: 6
667080 GCTAACTGTA
* * *
667090 ATATAT ATATAT ATATAT ATTTAT ATCTAT ATATAT GTATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * *
667138 ATATTT ATATCT ATATAT ATGTAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT
667168 TCAAGATCAT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
ATATAT
Found at i:667105 original size:10 final size:10
Alignment explanation
Indices: 667090--667167 Score: 102
Period size: 10 Copynumber: 7.8 Consensus size: 10
667080 GCTAACTGTA
667090 ATATATATAT
1 ATATATATAT
667100 ATATATATAT
1 ATATATATAT
* *
667110 TTATATCTAT
1 ATATATATAT
*
667120 ATATATGTAT
1 ATATATATAT
667130 ATATATATAT
1 ATATATATAT
* *
667140 ATTTATATCT
1 ATATATATAT
*
667150 ATATATATGT
1 ATATATATAT
667160 ATATATAT
1 ATATATAT
667168 TCAAGATCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 59 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (10 bp):
ATATATATAT
Found at i:667136 original size:32 final size:32
Alignment explanation
Indices: 667090--667167 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
667080 GCTAACTGTA
*
667090 ATATATATATATATATATATTTATATCTATAT
1 ATATGTATATATATATATATTTATATCTATAT
667122 ATATGTATATATATATATATTTATATCTATAT
1 ATATGTATATATATATATATTTATATCTATAT
667154 ATATGTATATATAT
1 ATATGTATATATAT
667168 TCAAGATCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (32 bp):
ATATGTATATATATATATATTTATATCTATAT
Found at i:667520 original size:36 final size:36
Alignment explanation
Indices: 667480--667555 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
667470 TTACGGTCAA
* *
667480 TTGTAGAAGAAGATTTCATAGAATTGGATGATCTTG
1 TTGTAGAAGAAGACTTCATAGAATTGGATGATCTCG
667516 TTGTAGAAGAAGACTTCATAGAATTGGATGATCTCG
1 TTGTAGAAGAAGACTTCATAGAATTGGATGATCTCG
667552 TTGT
1 TTGT
667556 TTGATTTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.36
Consensus pattern (36 bp):
TTGTAGAAGAAGACTTCATAGAATTGGATGATCTCG
Found at i:667657 original size:30 final size:30
Alignment explanation
Indices: 667621--667739 Score: 184
Period size: 30 Copynumber: 4.0 Consensus size: 30
667611 TCAATTGTAG
667621 AAGCAGTTACCTCCAGAGATAGGAAGAGTT
1 AAGCAGTTACCTCCAGAGATAGGAAGAGTT
* *
667651 AAGCAGTTACCTCCAGAGACAGAAAGAGTT
1 AAGCAGTTACCTCCAGAGATAGGAAGAGTT
*
667681 AAGCAGTTACCTCAAGAGATAGGAAGAGTT
1 AAGCAGTTACCTCCAGAGATAGGAAGAGTT
* * *
667711 ACGCAGTTACCTCCTGAGTTAGGAAGAGT
1 AAGCAGTTACCTCCAGAGATAGGAAGAGT
667740 ATGATTTATA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (30 bp):
AAGCAGTTACCTCCAGAGATAGGAAGAGTT
Found at i:667784 original size:61 final size:61
Alignment explanation
Indices: 667705--667828 Score: 203
Period size: 61 Copynumber: 2.0 Consensus size: 61
667695 AGAGATAGGA
* ** *
667705 AGAGTTACGCAGTTACCTCCTGAGTTAGGAAGAGTATGATTTATATATTCAGGAACCTAAT
1 AGAGTTAAGCAGTTACCTCCACAGATAGGAAGAGTATGATTTATATATTCAGGAACCTAAT
*
667766 AGAGTTAAGCATTTACCTCCACAGATAGGAAGAGTATGATTTATATATTCAGGAACCTAAT
1 AGAGTTAAGCAGTTACCTCCACAGATAGGAAGAGTATGATTTATATATTCAGGAACCTAAT
667827 AG
1 AG
667829 GAAACAAGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (61 bp):
AGAGTTAAGCAGTTACCTCCACAGATAGGAAGAGTATGATTTATATATTCAGGAACCTAAT
Found at i:668037 original size:31 final size:32
Alignment explanation
Indices: 667999--668058 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
667989 ATGTGCCTAA
667999 TATCAGGAAT-TTTGCTT-CAGAAGAATTAAGT
1 TATCAGGAATATTTG-TTGCAGAAGAATTAAGT
*
668030 TATCAGGATTATTTGTTGCAGAAGAATTA
1 TATCAGGAATATTTGTTGCAGAAGAATTA
668059 TCAGACAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (32 bp):
TATCAGGAATATTTGTTGCAGAAGAATTAAGT
Found at i:675411 original size:2 final size:2
Alignment explanation
Indices: 675404--675433 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
675394 CAAACAAGCG
675404 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
675434 TTTTTTTTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:676986 original size:21 final size:22
Alignment explanation
Indices: 676952--677000 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 22
676942 TTTGATTATT
*
676952 ATTTGAATTAAAATAAAAT-AAA
1 ATTT-AATAAAAATAAAATCAAA
676974 ATTTAATAAAAATAAAATCAAA
1 ATTTAATAAAAATAAAATCAAA
676996 ATTTA
1 ATTTA
677001 TTCAAATACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
ATTTAATAAAAATAAAATCAAA
Found at i:677040 original size:99 final size:99
Alignment explanation
Indices: 676915--677096 Score: 285
Period size: 99 Copynumber: 1.8 Consensus size: 99
676905 ATTTGATAAA
* * * *
676915 AATTGAATGAAATCAATATTTTATATATTTGATTATTATTTGAATTAAAATAAAATAAAATTTAA
1 AATTGAATCAAATCAATATTTTATATATTTAATTATTATTTAAATTAAAATAAAATAAAATTAAA
676980 TAAAAATAAAATCAAAATTTATTCAAATACTTTG
66 TAAAAATAAAATCAAAATTTATTCAAATACTTTG
* *
677014 AATTGAATCAAATCAAT-TTTTAATATATTTAATTATTATTTAAATTAAAATTAAATTAAATTAA
1 AATTGAATCAAATCAATATTTT-ATATATTTAATTATTATTTAAATTAAAATAAAATAAAATTAA
*
677078 ATAAAAATTAAATCAAAAT
65 ATAAAAATAAAATCAAAAT
677097 CTGCAGAAAC
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
98 4 0.05
99 71 0.95
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (99 bp):
AATTGAATCAAATCAATATTTTATATATTTAATTATTATTTAAATTAAAATAAAATAAAATTAAA
TAAAAATAAAATCAAAATTTATTCAAATACTTTG
Found at i:677067 original size:11 final size:11
Alignment explanation
Indices: 677053--677096 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
677043 TAATTATTAT
677053 TTAAATTAAAA
1 TTAAATTAAAA
677064 TTAAATT-AAA
1 TTAAATTAAAA
*
677074 TTAAATAAAAA
1 TTAAATTAAAA
*
677085 TTAAATCAAAA
1 TTAAATTAAAA
677096 T
1 T
677097 CTGCAGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
TTAAATTAAAA
Found at i:677072 original size:16 final size:17
Alignment explanation
Indices: 677053--677096 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
677043 TAATTATTAT
*
677053 TTAAATTAAAAT-TAAA
1 TTAAATTAAAATAAAAA
677069 TTAAATT-AAATAAAAA
1 TTAAATTAAAATAAAAA
*
677085 TTAAATCAAAAT
1 TTAAATTAAAAT
677097 CTGCAGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.17
16 16 0.67
17 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAAATTAAAATAAAAA
Found at i:677879 original size:33 final size:34
Alignment explanation
Indices: 677824--677902 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 34
677814 TATTAAAATA
** *
677824 TTTAA-AAATTATTTTTATATAAATATT-TATATAT
1 TTTAATAAATTAAATTTAAATAAA-ATTATAT-TAT
677858 TTT-AT-AATTAAATTTAAATAAAATTATATTAT
1 TTTAATAAATTAAATTTAAATAAAATTATATTAT
677890 TTTAATAAATTAA
1 TTTAATAAATTAA
677903 TAATAATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
32 9 0.24
33 20 0.53
34 9 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TTTAATAAATTAAATTTAAATAAAATTATATTAT
Found at i:677913 original size:29 final size:33
Alignment explanation
Indices: 677837--677915 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 33
677827 AAAAATTATT
*
677837 TTTATATAAATATTTATA-TATTTTATAATTAAA
1 TTTAAATAAA-ATTTATATTATTTTATAATTAAA
677870 TTTAAATAAAA-TTATATTA-TTT-TAA-TAAA
1 TTTAAATAAAATTTATATTATTTTATAATTAAA
677899 -TT-AATAATAATTTATAT
1 TTTAAATAA-AATTTATAT
677916 CAAATCAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
27 5 0.12
28 4 0.10
29 10 0.24
30 3 0.07
31 8 0.19
32 3 0.07
33 9 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
TTTAAATAAAATTTATATTATTTTATAATTAAA
Found at i:682591 original size:2 final size:2
Alignment explanation
Indices: 682584--682610 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
682574 TAATTAATAG
682584 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
682611 AATTGTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:682841 original size:14 final size:14
Alignment explanation
Indices: 682802--682841 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
682792 TTCATTTAAA
682802 ATAAATATGATAAT
1 ATAAATATGATAAT
*
682816 ATTAAATATGATTAT
1 A-TAAATATGATAAT
*
682831 ATAAATGTGAT
1 ATAAATATGAT
682842 GCATTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (14 bp):
ATAAATATGATAAT
Found at i:683055 original size:37 final size:37
Alignment explanation
Indices: 683014--683100 Score: 106
Period size: 35 Copynumber: 2.4 Consensus size: 37
683004 GACACTCATA
* * * *
683014 TAGAATTTGGGTAACTATATATTTGGTGACATTCGTT
1 TAGAATTTGAGTAACTAGACATTTGATGACATTCGTT
* *
683051 TAGAATTTGTGT--TTAGACATTTGATGACATTCGTT
1 TAGAATTTGAGTAACTAGACATTTGATGACATTCGTT
683086 TAGAATTTGAGTAAC
1 TAGAATTTGAGTAAC
683101 ATTGGTTATA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
35 30 0.73
37 11 0.27
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.43
Consensus pattern (37 bp):
TAGAATTTGAGTAACTAGACATTTGATGACATTCGTT
Found at i:683102 original size:22 final size:22
Alignment explanation
Indices: 683061--683103 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
683051 TAGAATTTGT
*
683061 GTTTAGACATTTGATGACATTC
1 GTTTAGACATTTGATAACATTC
683083 GTTTAGA-ATTTGAGTAACATT
1 GTTTAGACATTTGA-TAACATT
683104 GGTTATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (22 bp):
GTTTAGACATTTGATAACATTC
Found at i:683260 original size:31 final size:29
Alignment explanation
Indices: 683202--683264 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
683192 CTAGATTTAT
683202 TTAATATTTAAAAAAAATTAAATAAAAATA
1 TTAATATTTAAAAAAAATTAAATAAAAA-A
*
683232 TTAA-ATTTAAAAATAAATTTGAATAAAAAA
1 TTAATATTTAAAAA-AAA-TTAAATAAAAAA
683262 TTA
1 TTA
683265 TGTTCATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 9 0.30
30 11 0.37
31 10 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (29 bp):
TTAATATTTAAAAAAAATTAAATAAAAAA
Done.