Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold419
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: 303202
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.31
Warning! 24025 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:26296 original size:35 final size:34
Alignment explanation
Indices: 26216--26300 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 34
26206 AGGGATGGTA
* *
26216 AAAATTTAAAACTAAAAACTAAGTAAAAGGGATTT
1 AAAA-TTAAAACTAAAAACTAAGTAAAAGAGATGT
26251 AAAATTTAAAACTAAAAACTAAGTAAAAAGAGATGGT
1 AAAA-TTAAAACTAAAAACTAAGT-AAAAGAGAT-GT
26288 AAAA-TAAAA-TAAA
1 AAAATTAAAACTAAA
26301 TCAATGGGGG
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
34 4 0.09
35 29 0.63
36 8 0.17
37 5 0.11
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.22
Consensus pattern (34 bp):
AAAATTAAAACTAAAAACTAAGTAAAAGAGATGT
Found at i:28818 original size:51 final size:49
Alignment explanation
Indices: 28691--28870 Score: 207
Period size: 51 Copynumber: 3.6 Consensus size: 49
28681 AAAGTGATGG
* * * * * *
28691 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGGATAG-TTGA
* * *
28741 TCGCATGTGTAGTACCATGTGCAGGCTACTATATGTACCGGATAGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGGATAG-TT-GA
* *
28792 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTATCGGATAGTGATGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGGATAGT--TGA
*
28843 TCACATGTGTAGTACTATGTGTAGGCTA
1 TCACATGTGTAGTACTATGTGCAGGCTA
28871 TTATGTGAAC
Statistics
Matches: 110, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
50 40 0.36
51 69 0.63
52 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGGATAGTTGA
Found at i:29147 original size:37 final size:38
Alignment explanation
Indices: 29077--29150 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 38
29067 TATGTGTGGA
* * **
29077 ATTGAATTGAATATTTACTTGAAAATGGCAAAGTGAAT
1 ATTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAAT
*
29115 ATTGAATTGAATAGTGA-TTGAAAGTGAAAAAGTGAA
1 ATTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAA
29151 ATTATGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
37 16 0.52
38 15 0.48
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.31
Consensus pattern (38 bp):
ATTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAAT
Found at i:34938 original size:45 final size:44
Alignment explanation
Indices: 34879--34969 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
34869 TTTGGTTCGC
* * *
34879 TGTATTGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
34924 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
34968 TG
1 TG
34970 GAATAGAGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.30, C:0.05, G:0.29, T:0.36
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:35149 original size:15 final size:15
Alignment explanation
Indices: 35114--35166 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
35104 TTAATCATAT
* *
35114 TTAAACATAATTATTA
1 TTAAATATAATT-TAA
*
35130 TTAAATATATTTTAA
1 TTAAATATAATTTAA
35145 TTAAAATATAATTTAA
1 TT-AAATATAATTTAA
*
35161 TAAAAT
1 TTAAAT
35167 TCTTAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATAATTTAA
Found at i:35303 original size:155 final size:155
Alignment explanation
Indices: 35021--36633 Score: 3199
Period size: 155 Copynumber: 10.4 Consensus size: 155
35011 TAGAATACCC
* * *
35021 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
35086 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
35151 TATAATTTAATAAAATTCTTAATAA
131 TATAATTTAATAAAATTCTTAATAA
35176 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
35241 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
35306 TATAATTTAATAAAATTCTTAATAA
131 TATAATTTAATAAAATTCTTAATAA
35331 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
35396 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
35461 TATAATTTAATAAAATTCTTAATAA
131 TATAATTTAATAAAATTCTTAATAA
35486 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
35551 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
35616 TATAATTTAATAAAATTCTTAATAA
131 TATAATTTAATAAAATTCTTAATAA
35641 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
35706 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
35771 TATAATTTAATAAAATTCTTAATAA
131 TATAATTTAATAAAATTCTTAATAA
35796 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
35861 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
35926 TATAATTTAATAAAATTCTTAATAA
131 TATAATTTAATAAAATTCTTAATAA
35951 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
36016 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
36081 TATAATTTAATAAAATTCTTAATAA
131 TATAATTTAATAAAATTCTTAATAA
36106 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
36171 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
36236 TATAATTTAATAAAATTCTTAATAA
131 TATAATTTAATAAAATTCTTAATAA
36261 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
36326 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
36391 TATAATTTAATAAAATTCTTAATAA
131 TATAATTTAATAAAATTCTTAATAA
36416 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
36481 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
36546 TATAATTTAATAAAATTCTTAATAA
131 TATAATTTAATAAAATTCTTAATAA
36571 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTAT
1 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTAT
36634 AATAGCATTC
Statistics
Matches: 1455, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 1455 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (155 bp):
TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
TATAATTTAATAAAATTCTTAATAA
Found at i:35304 original size:15 final size:15
Alignment explanation
Indices: 35269--35321 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
35259 TTAATCATAT
* *
35269 TTAAACATAATTATTA
1 TTAAATATAATT-TAA
*
35285 TTAAATATATTTTAA
1 TTAAATATAATTTAA
35300 TTAAAATATAATTTAA
1 TT-AAATATAATTTAA
*
35316 TAAAAT
1 TTAAAT
35322 TCTTAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATAATTTAA
Found at i:35459 original size:15 final size:15
Alignment explanation
Indices: 35424--35476 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
35414 TTAATCATAT
* *
35424 TTAAACATAATTATTA
1 TTAAATATAATT-TAA
*
35440 TTAAATATATTTTAA
1 TTAAATATAATTTAA
35455 TTAAAATATAATTTAA
1 TT-AAATATAATTTAA
*
35471 TAAAAT
1 TTAAAT
35477 TCTTAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATAATTTAA
Found at i:35614 original size:15 final size:15
Alignment explanation
Indices: 35579--35631 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
35569 TTAATCATAT
* *
35579 TTAAACATAATTATTA
1 TTAAATATAATT-TAA
*
35595 TTAAATATATTTTAA
1 TTAAATATAATTTAA
35610 TTAAAATATAATTTAA
1 TT-AAATATAATTTAA
*
35626 TAAAAT
1 TTAAAT
35632 TCTTAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATAATTTAA
Found at i:35769 original size:15 final size:15
Alignment explanation
Indices: 35734--35786 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
35724 TTAATCATAT
* *
35734 TTAAACATAATTATTA
1 TTAAATATAATT-TAA
*
35750 TTAAATATATTTTAA
1 TTAAATATAATTTAA
35765 TTAAAATATAATTTAA
1 TT-AAATATAATTTAA
*
35781 TAAAAT
1 TTAAAT
35787 TCTTAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATAATTTAA
Found at i:35924 original size:15 final size:15
Alignment explanation
Indices: 35889--35941 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
35879 TTAATCATAT
* *
35889 TTAAACATAATTATTA
1 TTAAATATAATT-TAA
*
35905 TTAAATATATTTTAA
1 TTAAATATAATTTAA
35920 TTAAAATATAATTTAA
1 TT-AAATATAATTTAA
*
35936 TAAAAT
1 TTAAAT
35942 TCTTAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATAATTTAA
Found at i:36079 original size:15 final size:15
Alignment explanation
Indices: 36044--36096 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
36034 TTAATCATAT
* *
36044 TTAAACATAATTATTA
1 TTAAATATAATT-TAA
*
36060 TTAAATATATTTTAA
1 TTAAATATAATTTAA
36075 TTAAAATATAATTTAA
1 TT-AAATATAATTTAA
*
36091 TAAAAT
1 TTAAAT
36097 TCTTAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATAATTTAA
Found at i:36234 original size:15 final size:15
Alignment explanation
Indices: 36199--36251 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
36189 TTAATCATAT
* *
36199 TTAAACATAATTATTA
1 TTAAATATAATT-TAA
*
36215 TTAAATATATTTTAA
1 TTAAATATAATTTAA
36230 TTAAAATATAATTTAA
1 TT-AAATATAATTTAA
*
36246 TAAAAT
1 TTAAAT
36252 TCTTAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATAATTTAA
Found at i:36389 original size:15 final size:15
Alignment explanation
Indices: 36354--36406 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
36344 TTAATCATAT
* *
36354 TTAAACATAATTATTA
1 TTAAATATAATT-TAA
*
36370 TTAAATATATTTTAA
1 TTAAATATAATTTAA
36385 TTAAAATATAATTTAA
1 TT-AAATATAATTTAA
*
36401 TAAAAT
1 TTAAAT
36407 TCTTAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATAATTTAA
Found at i:36544 original size:15 final size:15
Alignment explanation
Indices: 36509--36561 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
36499 TTAATCATAT
* *
36509 TTAAACATAATTATTA
1 TTAAATATAATT-TAA
*
36525 TTAAATATATTTTAA
1 TTAAATATAATTTAA
36540 TTAAAATATAATTTAA
1 TT-AAATATAATTTAA
*
36556 TAAAAT
1 TTAAAT
36562 TCTTAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATAATTTAA
Found at i:38037 original size:40 final size:40
Alignment explanation
Indices: 37961--38038 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
37951 GGTTTAAGTT
* *
37961 TCAAGGTTCAAGTTCAGGTTTGGGGTTTAGGATTCAAGAG
1 TCAAGGTTCAAGTTCAGGTTTGAGATTTAGGATTCAAGAG
*
38001 TCAAGGTTCAGAGTTGA-GTTTGAGATTTATGG-TTCAAG
1 TCAAGGTTCA-AGTTCAGGTTTGAGATTTA-GGATTCAAG
38039 GTTCAGAGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 26 0.79
41 7 0.21
ACGTcount: A:0.26, C:0.09, G:0.31, T:0.35
Consensus pattern (40 bp):
TCAAGGTTCAAGTTCAGGTTTGAGATTTAGGATTCAAGAG
Found at i:42076 original size:19 final size:19
Alignment explanation
Indices: 42002--42112 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 19
41992 AAAATTTAAA
*
42002 ATTTT-AATTTTTAAATTT
1 ATTTTGAATTTTTAAAATT
*
42020 TTTTTAGAATTTTTAAAAATAT
1 ATTTT-GAATTTTT-AAAAT-T
*
42042 AAATTTTGATTTTTTTTATAAA-T
1 --ATTTTGA--ATTTTTA-AAATT
42065 ATTTTGAA-TTTTAAAATTT
1 ATTTTGAATTTTTAAAA-TT
42084 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTT-AAAATT
42104 ATTTT-AATT
1 ATTTTGAATT
42113 GATTTTGTAA
Statistics
Matches: 75, Mismatches: 5, Indels: 25
0.71 0.05 0.24
Matches are distributed among these distances:
17 3 0.04
18 9 0.12
19 13 0.17
20 18 0.24
21 15 0.20
22 1 0.01
23 3 0.04
24 5 0.07
25 8 0.11
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:53927 original size:30 final size:30
Alignment explanation
Indices: 53891--53949 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
53881 TTATTTATTG
*
53891 TTAATTTTGTTATTATTTTAAAGACATTTA
1 TTAATTTTGCTATTATTTTAAAGACATTTA
* *
53921 TTAATTTTGCTATTATTTTAGAGGCATTT
1 TTAATTTTGCTATTATTTTAAAGACATTT
53950 GCTTGTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (30 bp):
TTAATTTTGCTATTATTTTAAAGACATTTA
Found at i:54057 original size:18 final size:18
Alignment explanation
Indices: 54034--54073 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
54024 AAATATTTTA
54034 TTTTGATGTATT-TAGTAT
1 TTTTGATGTATTATA-TAT
54052 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
54070 TTTT
1 TTTT
54074 TAAAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:54135 original size:125 final size:126
Alignment explanation
Indices: 53980--54230 Score: 495
Period size: 125 Copynumber: 2.0 Consensus size: 126
53970 TTTAGTGTTA
53980 TTTAAGTATACATATTTTTTAAAATTTATTTTCAATTTGTTGGGAAATATTTTATTTTGATGTAT
1 TTTAAGTATACATATTTTTTAAAATTTATTTTCAATTTGTTGGGAAATATTTTATTTTGATGTAT
54045 TTAGTATTTTTGATGTATTATATATTTTTTAAAATAATATAAAAAATAATATGGGTGGGCC
66 TTAGTATTTTTGATGTATTATATATTTTTTAAAATAATATAAAAAATAATATGGGTGGGCC
54106 TTTAAGTATA-ATATTTTTTAAAATTTATTTTCAATTTGTTGGGAAATATTTTATTTTGATGTAT
1 TTTAAGTATACATATTTTTTAAAATTTATTTTCAATTTGTTGGGAAATATTTTATTTTGATGTAT
54170 TTAGTATTTTTGATGTATTATATATTTTTTAAAATAATATAAAAAATAATATGGGTGGGCC
66 TTAGTATTTTTGATGTATTATATATTTTTTAAAATAATATAAAAAATAATATGGGTGGGCC
54231 GGGTTGTGCC
Statistics
Matches: 125, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
125 115 0.92
126 10 0.08
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (126 bp):
TTTAAGTATACATATTTTTTAAAATTTATTTTCAATTTGTTGGGAAATATTTTATTTTGATGTAT
TTAGTATTTTTGATGTATTATATATTTTTTAAAATAATATAAAAAATAATATGGGTGGGCC
Found at i:54182 original size:18 final size:18
Alignment explanation
Indices: 54159--54198 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
54149 AAATATTTTA
54159 TTTTGATGTATT-TAGTAT
1 TTTTGATGTATTATA-TAT
54177 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
54195 TTTT
1 TTTT
54199 TAAAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:70474 original size:19 final size:20
Alignment explanation
Indices: 70450--70487 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
70440 CCCAACAATT
70450 AAAAATAAT-TTTAAATATC
1 AAAAATAATATTTAAATATC
*
70469 AAAAATCATATTTAAATAT
1 AAAAATAATATTTAAATAT
70488 TATTCCTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATAATATTTAAATATC
Found at i:71895 original size:44 final size:43
Alignment explanation
Indices: 71850--72120 Score: 305
Period size: 43 Copynumber: 6.3 Consensus size: 43
71840 TTATGTGAAA
* * * *
71850 AAACGACGCTATAGAACATGACCTTTAGCGGCGCTTTTATAAAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAT-CAC
*
71894 AAACGCCGCTAAAGAACATGACCTTTAGCGGCG-TTTTACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTA-TCAC
* * * *
71937 GAACACCACTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAC
*
71980 AAACGCCGCTGAAGAACATGACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAC
* * * * * *
72023 AAACGCCGCTATAGAGA-ATGACTTTTAACAGC-TTTTTTTCAC
1 AAACGCCGCTAAAGA-ACATGACCTTTAGCGGCGCTTTTATCAC
* * * *
72065 AAACGTCGCTAAAGAACATGATCTTTAGCAGCACTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAC
*
72108 AAACGCTGCTAAA
1 AAACGCCGCTAAA
72121 AGTACCATTC
Statistics
Matches: 191, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.01
42 33 0.17
43 120 0.63
44 37 0.19
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAC
Found at i:72091 original size:85 final size:86
Alignment explanation
Indices: 71850--72120 Score: 280
Period size: 85 Copynumber: 3.2 Consensus size: 86
71840 TTATGTGAAA
* * * * * * *
71850 AAACGACGCTATAGAACATGACCTTTAGCGGCGCTTTTATAAAAAAACGCCGCTAAAGAACATGA
1 AAACGCCGCTAAAGAACATGATCTTTAACAGCGCTTTTAT-CACAAACGCCGCTAAAGAACATGA
*
71915 CCTTTAGCGGCG-TTTTACCCAC
65 CCTTTAGCGGCGCTTTTA-TCAC
* * * * * *
71937 GAACACCACTAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAACGCCGCTGAAGAACATGAC
1 AAACGCCGCTAAAGAACATGATCTTTAACAGCGCTTTTATCACAAACGCCGCTAAAGAACATGAC
72002 CTTTAGCGGCGCTTTTATCAC
66 CTTTAGCGGCGCTTTTATCAC
* * * *
72023 AAACGCCGCTATAGAGA-ATGA-CTTTTAACAGC-TTTTTTTCACAAACGTCGCTAAAGAACATG
1 AAACGCCGCTAAAGA-ACATGATC-TTTAACAGCGCTTTTATCACAAACGCCGCTAAAGAACATG
* * *
72085 ATCTTTAGCAGCACTTTTATCAC
64 ACCTTTAGCGGCGCTTTTATCAC
*
72108 AAACGCTGCTAAA
1 AAACGCCGCTAAA
72121 AGTACCATTC
Statistics
Matches: 156, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
85 58 0.37
86 58 0.37
87 40 0.26
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGATCTTTAACAGCGCTTTTATCACAAACGCCGCTAAAGAACATGAC
CTTTAGCGGCGCTTTTATCAC
Found at i:76785 original size:7 final size:7
Alignment explanation
Indices: 76773--76919 Score: 63
Period size: 7 Copynumber: 20.9 Consensus size: 7
76763 ACTTGGACCC
76773 TAAACCT
1 TAAACCT
76780 TAAACCT
1 TAAACCT
76787 TAAACTCT
1 TAAAC-CT
*
76795 ATAACCCT
1 -TAAACCT
*
76803 TAAACCA
1 TAAACCT
*
76810 TAAATAC-
1 TAAA-CCT
*
76817 TAAACTT
1 TAAACCT
*
76824 TAAACCC
1 TAAACCT
*
76831 TAAACCC
1 TAAACCT
*
76838 TAAACCA
1 TAAACCT
76845 TAAACAC-
1 TAAAC-CT
* *
76852 TAAGCCA
1 TAAACCT
76859 TAAA-CT
1 TAAACCT
* *
76865 TACACCC
1 TAAACCT
*
76872 TAAACCG
1 TAAACCT
76879 TAAACAC-
1 TAAAC-CT
76886 TAAACTCT
1 TAAAC-CT
76894 T-AACAC-
1 TAAAC-CT
* *
76900 TAAATCA
1 TAAACCT
76907 TAAACCT
1 TAAACCT
76914 TAAACC
1 TAAACC
76920 CCAAACCATA
Statistics
Matches: 108, Mismatches: 21, Indels: 22
0.72 0.14 0.15
Matches are distributed among these distances:
6 7 0.06
7 89 0.82
8 8 0.07
9 4 0.04
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.23
Consensus pattern (7 bp):
TAAACCT
Found at i:76833 original size:14 final size:14
Alignment explanation
Indices: 76769--76919 Score: 85
Period size: 14 Copynumber: 10.7 Consensus size: 14
76759 GGCCACTTGG
76769 ACCCTAAACCTTAA
1 ACCCTAAACCTTAA
*
76783 ACCTTAAA-CTCTATA
1 ACCCTAAACCT-TA-A
*
76798 ACCCTTAAACCATAA
1 ACCC-TAAACCTTAA
** *
76813 ATACTAAACTTTAA
1 ACCCTAAACCTTAA
*
76827 ACCCTAAACCCTAA
1 ACCCTAAACCTTAA
*
76841 ACCATAAACAC-TAA
1 ACCCTAAAC-CTTAA
* * *
76855 GCCATAAA-CTTAC
1 ACCCTAAACCTTAA
*
76868 ACCCTAAACCGTAA
1 ACCCTAAACCTTAA
*
76882 ACACTAAACTCTT-A
1 ACCCTAAAC-CTTAA
* * *
76896 ACACTAAATCATAA
1 ACCCTAAACCTTAA
*
76910 ACCTTAAACC
1 ACCCTAAACC
76920 CCAAACCATA
Statistics
Matches: 103, Mismatches: 25, Indels: 18
0.71 0.17 0.12
Matches are distributed among these distances:
12 1 0.01
13 12 0.12
14 73 0.71
15 10 0.10
16 6 0.06
17 1 0.01
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (14 bp):
ACCCTAAACCTTAA
Found at i:76840 original size:21 final size:21
Alignment explanation
Indices: 76769--76931 Score: 105
Period size: 21 Copynumber: 7.7 Consensus size: 21
76759 GGCCACTTGG
*
76769 ACCCTAAACCTTAAACCTTAA
1 ACCCTAAACCTTAAACCCTAA
* *
76790 ACTCTATAACCCTTAAACCATAA
1 ACCCTA-AA-CCTTAAACCCTAA
** *
76813 ATACTAAACTTTAAACCCTAA
1 ACCCTAAACCTTAAACCCTAA
* *
76834 ACCCTAAACCATAAACACTAA
1 ACCCTAAACCTTAAACCCTAA
* * *
76855 GCCATAAA-CTTACACCCTAA
1 ACCCTAAACCTTAAACCCTAA
* * *
76875 ACCGTAAACAC-TAAACTCTTA
1 ACCCTAAAC-CTTAAACCCTAA
* * * *
76896 ACACTAAATCATAAACCTTAA
1 ACCCTAAACCTTAAACCCTAA
* *
76917 ACCCCAAACCATAAA
1 ACCCTAAACCTTAAA
76932 AATATACCTT
Statistics
Matches: 107, Mismatches: 30, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
20 16 0.15
21 70 0.65
22 5 0.05
23 16 0.15
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.21
Consensus pattern (21 bp):
ACCCTAAACCTTAAACCCTAA
Found at i:76945 original size:69 final size:69
Alignment explanation
Indices: 76800--76951 Score: 162
Period size: 69 Copynumber: 2.2 Consensus size: 69
76790 ACTCTATAAC
* * * * * **
76800 CCTTAAACCATAAATACTAAACTTTAAACCCTAAACCCTAAACCATAAACACTAAGCCATAAACT
1 CCTTAAACCATAAACACTAAACTTTAAACACTAAACCATAAACCATAAACACCAAACCATAAAAA
76865 TACA
66 TACA
* * * * *
76869 CCCTAAACCGTAAACACTAAACTCTT-AACACTAAATCATAAACCTTAAACCCCAAACCATAAAA
1 CCTTAAACCATAAACACTAAACT-TTAAACACTAAACCATAAACCATAAACACCAAACCATAAAA
*
76933 ATATA
65 ATACA
*
76938 CCTTAAACCCTAAA
1 CCTTAAACCATAAA
76952 TATATATATT
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
69 65 0.97
70 2 0.03
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.21
Consensus pattern (69 bp):
CCTTAAACCATAAACACTAAACTTTAAACACTAAACCATAAACCATAAACACCAAACCATAAAAA
TACA
Found at i:77127 original size:14 final size:14
Alignment explanation
Indices: 77110--77153 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
77100 CCTAACTATA
*
77110 AAATAATAAACCCT
1 AAATCATAAACCCT
*
77124 AAATCCTAAACCCT
1 AAATCATAAACCCT
*
77138 AAATCATAAACACT
1 AAATCATAAACCCT
77152 AA
1 AA
77154 TCCCAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATCATAAACCCT
Found at i:77153 original size:21 final size:21
Alignment explanation
Indices: 77129--77170 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
77119 ACCCTAAATC
* *
77129 CTAAACCCTAAATCATAAACA
1 CTAAACCCAAAATAATAAACA
*
77150 CTAATCCCAAAATAATAAACA
1 CTAAACCCAAAATAATAAACA
77171 TTATATCTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (21 bp):
CTAAACCCAAAATAATAAACA
Found at i:77373 original size:19 final size:20
Alignment explanation
Indices: 77339--77377 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
77329 CAGCATTTTG
77339 TGAAAAGCGCCGCTAATGCT
1 TGAAAAGCGCCGCTAATGCT
77359 TGAAAAGCG-CGCTAATGCT
1 TGAAAAGCGCCGCTAATGCT
77378 CGATCTATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.21
Consensus pattern (20 bp):
TGAAAAGCGCCGCTAATGCT
Found at i:77618 original size:40 final size:41
Alignment explanation
Indices: 77526--77620 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
77516 GAAAAGCACT
77526 GCTAATGCTCGATCTATAGCGACGTTTTTCGATAAAGCGCC
1 GCTAATGCTCGATCTATAGCGACGTTTTTCGATAAAGCGCC
** *
77567 GCTAATGCTCGATCTATAGCGGTGTTTTTC-A-AATATCGCC
1 GCTAATGCTCGATCTATAGCGACGTTTTTCGATAA-AGCGCC
*
77607 GTTAATGCTCGATC
1 GCTAATGCTCGATC
77621 AATTGTGGCG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.04
40 19 0.39
41 28 0.57
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (41 bp):
GCTAATGCTCGATCTATAGCGACGTTTTTCGATAAAGCGCC
Found at i:77634 original size:40 final size:41
Alignment explanation
Indices: 77526--77654 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 41
77516 GAAAAGCACT
*
77526 GCTAATGCTCGATCTATAGCGACGTTTTTCGATAAAGCGCC
1 GCTAATGCTCGATCTATAGCGGCGTTTTTCGATAAAGCGCC
* *
77567 GCTAATGCTCGATCTATAGCGGTGTTTTTC-A-AATATCGCC
1 GCTAATGCTCGATCTATAGCGGCGTTTTTCGATAA-AGCGCC
* * * * * * *
77607 GTTAATGCTCGATCAATTGTGGCGTTTTT-TAAAAAGTGCC
1 GCTAATGCTCGATCTATAGCGGCGTTTTTCGATAAAGCGCC
77647 GCTAATGC
1 GCTAATGC
77655 CACTAAAGCT
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
39 2 0.03
40 42 0.57
41 30 0.41
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (41 bp):
GCTAATGCTCGATCTATAGCGGCGTTTTTCGATAAAGCGCC
Found at i:77842 original size:41 final size:40
Alignment explanation
Indices: 77698--77863 Score: 188
Period size: 40 Copynumber: 4.1 Consensus size: 40
77688 TTTTGCAACG
* * *
77698 TTTTCAAAAAAACGCAGCTAATGCTCGATCTATAGCGGCGT
1 TTTTC-AAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGT
* * * *
77739 TTTTCAAAAAGCGTCACTAATGCTTGATCTATAGCGGCGT
1 TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGT
*
77779 TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGACGT
1 TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGT
** * * * *
77819 TTGTTTTATAAGCGCCGCTAATGCTTGACCTTTTGCGGCGT
1 TT-TTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGT
77860 TTTT
1 TTTT
77864 GTCATAAACA
Statistics
Matches: 107, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
40 69 0.64
41 38 0.36
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (40 bp):
TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGT
Found at i:77857 original size:81 final size:81
Alignment explanation
Indices: 77698--77863 Score: 208
Period size: 81 Copynumber: 2.0 Consensus size: 81
77688 TTTTGCAACG
* * *
77698 TTTTCAAAAAAACGCAGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGTCACTAATGCT
1 TTTTCAAAAAAACGCAGCTAATGCTCGACCTATAGCGACGTTTTTCAAAAAGCGCCACTAATGCT
*
77763 TGATCTATAGCGGCGT
66 TGACCTATAGCGGCGT
* * ** * *
77779 TTTTC-AAAAAGCGCCGCTAATGCTCGACCTATAGCGACGTTTGTTTTATAAGCGCCGCTAATGC
1 TTTTCAAAAAAACGCAGCTAATGCTCGACCTATAGCGACGTTT-TTCAAAAAGCGCCACTAATGC
* *
77843 TTGACCTTTTGCGGCGT
65 TTGACCTATAGCGGCGT
77860 TTTT
1 TTTT
77864 GTCATAAACA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 33 0.46
81 39 0.54
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (81 bp):
TTTTCAAAAAAACGCAGCTAATGCTCGACCTATAGCGACGTTTTTCAAAAAGCGCCACTAATGCT
TGACCTATAGCGGCGT
Found at i:78973 original size:5 final size:5
Alignment explanation
Indices: 78900--78959 Score: 120
Period size: 5 Copynumber: 12.0 Consensus size: 5
78890 TTACAAGTCA
78900 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
78950 AATAT AATAT
1 AATAT AATAT
78960 TAAATTTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 55 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:79172 original size:7 final size:7
Alignment explanation
Indices: 79160--79306 Score: 63
Period size: 7 Copynumber: 20.9 Consensus size: 7
79150 ACTTGGACCC
79160 TAAACCT
1 TAAACCT
79167 TAAACCT
1 TAAACCT
79174 TAAACTCT
1 TAAAC-CT
*
79182 ATAACCCT
1 -TAAACCT
*
79190 TAAACCA
1 TAAACCT
*
79197 TAAATAC-
1 TAAA-CCT
*
79204 TAAACTT
1 TAAACCT
*
79211 TAAACCC
1 TAAACCT
*
79218 TAAACCC
1 TAAACCT
*
79225 TAAACCA
1 TAAACCT
79232 TAAACAC-
1 TAAAC-CT
* *
79239 TAAGCCA
1 TAAACCT
79246 TAAA-CT
1 TAAACCT
* *
79252 TACACCC
1 TAAACCT
*
79259 TAAACCG
1 TAAACCT
79266 TAAACAC-
1 TAAAC-CT
79273 TAAACTCT
1 TAAAC-CT
79281 T-AACAC-
1 TAAAC-CT
* *
79287 TAAATCA
1 TAAACCT
79294 TAAACCT
1 TAAACCT
79301 TAAACC
1 TAAACC
79307 CCAAACCATA
Statistics
Matches: 108, Mismatches: 21, Indels: 22
0.72 0.14 0.15
Matches are distributed among these distances:
6 7 0.06
7 89 0.82
8 8 0.07
9 4 0.04
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.23
Consensus pattern (7 bp):
TAAACCT
Found at i:79220 original size:14 final size:14
Alignment explanation
Indices: 79156--79306 Score: 85
Period size: 14 Copynumber: 10.7 Consensus size: 14
79146 GGCCACTTGG
79156 ACCCTAAACCTTAA
1 ACCCTAAACCTTAA
*
79170 ACCTTAAA-CTCTATA
1 ACCCTAAACCT-TA-A
*
79185 ACCCTTAAACCATAA
1 ACCC-TAAACCTTAA
** *
79200 ATACTAAACTTTAA
1 ACCCTAAACCTTAA
*
79214 ACCCTAAACCCTAA
1 ACCCTAAACCTTAA
*
79228 ACCATAAACAC-TAA
1 ACCCTAAAC-CTTAA
* * *
79242 GCCATAAA-CTTAC
1 ACCCTAAACCTTAA
*
79255 ACCCTAAACCGTAA
1 ACCCTAAACCTTAA
*
79269 ACACTAAACTCTT-A
1 ACCCTAAAC-CTTAA
* * *
79283 ACACTAAATCATAA
1 ACCCTAAACCTTAA
*
79297 ACCTTAAACC
1 ACCCTAAACC
79307 CCAAACCATA
Statistics
Matches: 103, Mismatches: 25, Indels: 18
0.71 0.17 0.12
Matches are distributed among these distances:
12 1 0.01
13 12 0.12
14 73 0.71
15 10 0.10
16 6 0.06
17 1 0.01
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (14 bp):
ACCCTAAACCTTAA
Found at i:79227 original size:21 final size:21
Alignment explanation
Indices: 79156--79318 Score: 105
Period size: 21 Copynumber: 7.7 Consensus size: 21
79146 GGCCACTTGG
*
79156 ACCCTAAACCTTAAACCTTAA
1 ACCCTAAACCTTAAACCCTAA
* *
79177 ACTCTATAACCCTTAAACCATAA
1 ACCCTA-AA-CCTTAAACCCTAA
** *
79200 ATACTAAACTTTAAACCCTAA
1 ACCCTAAACCTTAAACCCTAA
* *
79221 ACCCTAAACCATAAACACTAA
1 ACCCTAAACCTTAAACCCTAA
* * *
79242 GCCATAAA-CTTACACCCTAA
1 ACCCTAAACCTTAAACCCTAA
* * *
79262 ACCGTAAACAC-TAAACTCTTA
1 ACCCTAAAC-CTTAAACCCTAA
* * * *
79283 ACACTAAATCATAAACCTTAA
1 ACCCTAAACCTTAAACCCTAA
* *
79304 ACCCCAAACCATAAA
1 ACCCTAAACCTTAAA
79319 AATATACCTT
Statistics
Matches: 107, Mismatches: 30, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
20 16 0.15
21 70 0.65
22 5 0.05
23 16 0.15
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.21
Consensus pattern (21 bp):
ACCCTAAACCTTAAACCCTAA
Found at i:79332 original size:69 final size:69
Alignment explanation
Indices: 79187--79338 Score: 162
Period size: 69 Copynumber: 2.2 Consensus size: 69
79177 ACTCTATAAC
* * * * * **
79187 CCTTAAACCATAAATACTAAACTTTAAACCCTAAACCCTAAACCATAAACACTAAGCCATAAACT
1 CCTTAAACCATAAACACTAAACTTTAAACACTAAACCATAAACCATAAACACCAAACCATAAAAA
79252 TACA
66 TACA
* * * * *
79256 CCCTAAACCGTAAACACTAAACTCTT-AACACTAAATCATAAACCTTAAACCCCAAACCATAAAA
1 CCTTAAACCATAAACACTAAACT-TTAAACACTAAACCATAAACCATAAACACCAAACCATAAAA
*
79320 ATATA
65 ATACA
*
79325 CCTTAAACCCTAAA
1 CCTTAAACCATAAA
79339 TATATATATT
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
69 65 0.97
70 2 0.03
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.21
Consensus pattern (69 bp):
CCTTAAACCATAAACACTAAACTTTAAACACTAAACCATAAACCATAAACACCAAACCATAAAAA
TACA
Found at i:79514 original size:14 final size:14
Alignment explanation
Indices: 79497--79540 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
79487 CCTAACTATA
*
79497 AAATAATAAACCCT
1 AAATCATAAACCCT
*
79511 AAATCCTAAACCCT
1 AAATCATAAACCCT
*
79525 AAATCATAAACACT
1 AAATCATAAACCCT
79539 AA
1 AA
79541 TCCCAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATCATAAACCCT
Found at i:79540 original size:21 final size:21
Alignment explanation
Indices: 79516--79557 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
79506 ACCCTAAATC
* *
79516 CTAAACCCTAAATCATAAACA
1 CTAAACCCAAAATAATAAACA
*
79537 CTAATCCCAAAATAATAAACA
1 CTAAACCCAAAATAATAAACA
79558 TTATATCTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (21 bp):
CTAAACCCAAAATAATAAACA
Found at i:79986 original size:40 final size:41
Alignment explanation
Indices: 79894--79988 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
79884 GAAAAGCACT
79894 GCTAATGCTCGATCTATAGCGACGTTTTTCGATAAAGCGCC
1 GCTAATGCTCGATCTATAGCGACGTTTTTCGATAAAGCGCC
** *
79935 GCTAATGCTCGATCTATAGCGGTGTTTTTC-A-AATATCGCC
1 GCTAATGCTCGATCTATAGCGACGTTTTTCGATAA-AGCGCC
*
79975 GTTAATGCTCGATC
1 GCTAATGCTCGATC
79989 AATTGTGGCG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.04
40 19 0.39
41 28 0.57
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (41 bp):
GCTAATGCTCGATCTATAGCGACGTTTTTCGATAAAGCGCC
Found at i:80002 original size:40 final size:41
Alignment explanation
Indices: 79894--80022 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 41
79884 GAAAAGCACT
*
79894 GCTAATGCTCGATCTATAGCGACGTTTTTCGATAAAGCGCC
1 GCTAATGCTCGATCTATAGCGGCGTTTTTCGATAAAGCGCC
* *
79935 GCTAATGCTCGATCTATAGCGGTGTTTTTC-A-AATATCGCC
1 GCTAATGCTCGATCTATAGCGGCGTTTTTCGATAA-AGCGCC
* * * * * * *
79975 GTTAATGCTCGATCAATTGTGGCGTTTTT-TAAAAAGTGCC
1 GCTAATGCTCGATCTATAGCGGCGTTTTTCGATAAAGCGCC
80015 GCTAATGC
1 GCTAATGC
80023 CACTAAAGCT
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
39 2 0.03
40 42 0.57
41 30 0.41
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (41 bp):
GCTAATGCTCGATCTATAGCGGCGTTTTTCGATAAAGCGCC
Found at i:80210 original size:41 final size:40
Alignment explanation
Indices: 80066--80231 Score: 188
Period size: 40 Copynumber: 4.1 Consensus size: 40
80056 TTTTGCAACG
* * *
80066 TTTTCAAAAAAACGCAGCTAATGCTCGATCTATAGCGGCGT
1 TTTTC-AAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGT
* * * *
80107 TTTTCAAAAAGCGTCACTAATGCTTGATCTATAGCGGCGT
1 TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGT
*
80147 TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGACGT
1 TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGT
** * * * *
80187 TTGTTTTATAAGCGCCGCTAATGCTTGACCTTTTGCGGCGT
1 TT-TTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGT
80228 TTTT
1 TTTT
80232 GTCATAAACA
Statistics
Matches: 107, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
40 69 0.64
41 38 0.36
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (40 bp):
TTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGT
Found at i:80225 original size:81 final size:81
Alignment explanation
Indices: 80066--80231 Score: 208
Period size: 81 Copynumber: 2.0 Consensus size: 81
80056 TTTTGCAACG
* * *
80066 TTTTCAAAAAAACGCAGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGTCACTAATGCT
1 TTTTCAAAAAAACGCAGCTAATGCTCGACCTATAGCGACGTTTTTCAAAAAGCGCCACTAATGCT
*
80131 TGATCTATAGCGGCGT
66 TGACCTATAGCGGCGT
* * ** * *
80147 TTTTC-AAAAAGCGCCGCTAATGCTCGACCTATAGCGACGTTTGTTTTATAAGCGCCGCTAATGC
1 TTTTCAAAAAAACGCAGCTAATGCTCGACCTATAGCGACGTTT-TTCAAAAAGCGCCACTAATGC
* *
80211 TTGACCTTTTGCGGCGT
65 TTGACCTATAGCGGCGT
80228 TTTT
1 TTTT
80232 GTCATAAACA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 33 0.46
81 39 0.54
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (81 bp):
TTTTCAAAAAAACGCAGCTAATGCTCGACCTATAGCGACGTTTTTCAAAAAGCGCCACTAATGCT
TGACCTATAGCGGCGT
Found at i:81343 original size:5 final size:5
Alignment explanation
Indices: 81268--81327 Score: 120
Period size: 5 Copynumber: 12.0 Consensus size: 5
81258 TTACAAGTCA
81268 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
81318 AATAT AATAT
1 AATAT AATAT
81328 TAAATTTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 55 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:82450 original size:20 final size:20
Alignment explanation
Indices: 82409--82452 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
82399 TCATAATATT
* *
82409 TAATTTAGTATAATTTGCAA
1 TAATTTAGTATAATATGAAA
82429 TAATTTAGTAT-ATAATGAAA
1 TAATTTAGTATAAT-ATGAAA
82449 TAAT
1 TAAT
82453 CATAAAGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (20 bp):
TAATTTAGTATAATATGAAA
Found at i:88206 original size:35 final size:35
Alignment explanation
Indices: 88160--88234 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
88150 ATGTTGCCAT
88160 AGAATGGAAAAATGTTCAACATGTCATAAAACATA
1 AGAATGGAAAAATGTTCAACATGTCATAAAACATA
88195 AGAATGGAAAAATGTTCAACATGTCATAAAACATA
1 AGAATGGAAAAATGTTCAACATGTCATAAAACATA
88230 AGAAT
1 AGAAT
88235 AAGGGATGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.23
Consensus pattern (35 bp):
AGAATGGAAAAATGTTCAACATGTCATAAAACATA
Found at i:88764 original size:50 final size:50
Alignment explanation
Indices: 88706--88837 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 50
88696 TATTGAGGTT
* * *
88706 ATGAGAGGTCCCATGTAAGACCTTATCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATGGGCACCGAG
* * *
88756 ATGAGAGGTCCTC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCC-CATGTAAGACCATATCTGGGACATGGCATGGGCACCGAG
** *
88806 ATGAGAACTCCCATGTAAGACCATATTTGGGA
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGA
88838 TATGACATTG
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
49 1 0.01
50 67 0.97
51 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATGGGCACCGAG
Found at i:90368 original size:34 final size:34
Alignment explanation
Indices: 90325--90392 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
90315 GTTTTTCATC
90325 TTCTCATTTTTTAGTAAAATAATACTATGATAGG
1 TTCTCATTTTTTAGTAAAATAATACTATGATAGG
90359 TTCTCATTTTTTAGTAAAATAATACTATGATAGG
1 TTCTCATTTTTTAGTAAAATAATACTATGATAGG
90393 ATATTTGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (34 bp):
TTCTCATTTTTTAGTAAAATAATACTATGATAGG
Found at i:92173 original size:21 final size:21
Alignment explanation
Indices: 92118--92176 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
92108 AATAAAATTT
* *
92118 TATTTT-TAATTGATATTTATA
1 TATTTTATAATT-AAATTTAAA
92139 TATTTTATAATTAAATTTAAA
1 TATTTTATAATTAAATTTAAA
*
92160 T-TTTTATTATTTAAATT
1 TATTTTA-TAATTAAATT
92177 GAATTCAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 5 0.15
21 23 0.70
22 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TATTTTATAATTAAATTTAAA
Found at i:93040 original size:8 final size:9
Alignment explanation
Indices: 93017--93041 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
93007 TTTTTGAAAT
93017 AATTTTTTG
1 AATTTTTTG
93026 AATTTTTTG
1 AATTTTTTG
93035 AATTTTT
1 AATTTTT
93042 AAAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
AATTTTTTG
Found at i:96300 original size:113 final size:113
Alignment explanation
Indices: 96146--96360 Score: 285
Period size: 113 Copynumber: 1.9 Consensus size: 113
96136 CCAAGTATTG
* * *
96146 ATACCAATTTGAGCTTCAAAGTTCAGAAAAATCGAGCAAAAATCAAAAGTATCGATACCTTTAAC
1 ATACCAATTTGAGCTTCAAAGTTCAGAAAAATCGAACAAAAATCAAAAGTACCGATACCCTTAAC
*
96211 AACA-TAT-TGATACCTTGCAAAAATTATCAATACCCTTGCCTGGTATCA
66 AA-AGTATCAG-TACCTTGCAAAAATTATCAATACCCTTGCCTGGTATCA
* *
96259 ATACCAATTTGAGCTTCAATTTGTT-AG-AAAATTGAACAAAAATCAAAAGTACCGATACCCTTA
1 ATACCAATTTGAGCTTCAA--AGTTCAGAAAAATCGAACAAAAATCAAAAGTACCGATACCCTTA
* * *
96322 ACAAAGTATCAGTACCTTTCAAAATTTATCGATACCCTT
64 ACAAAGTATCAGTACCTTGCAAAAATTATCAATACCCTT
96361 CTTGATATCG
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
112 1 0.01
113 82 0.92
114 3 0.03
115 3 0.03
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (113 bp):
ATACCAATTTGAGCTTCAAAGTTCAGAAAAATCGAACAAAAATCAAAAGTACCGATACCCTTAAC
AAAGTATCAGTACCTTGCAAAAATTATCAATACCCTTGCCTGGTATCA
Found at i:111125 original size:632 final size:632
Alignment explanation
Indices: 109920--111183 Score: 2519
Period size: 632 Copynumber: 2.0 Consensus size: 632
109910 ATTTAAAAAA
*
109920 TGCTTTTTAATTAATAAATAATAATTAAGACTAGATTAAGGATGGATTGGATGGGCAGTGGGTAC
1 TGCTTTTTAATTAATAAATAAAAATTAAGACTAGATTAAGGATGGATTGGATGGGCAGTGGGTAC
109985 GTTTAGCTTACTTTTTGTTTTATACTATGGTATCTAATTTCACCGTTATTGTTGTTTTTATATAA
66 GTTTAGCTTACTTTTTGTTTTATACTATGGTATCTAATTTCACCGTTATTGTTGTTTTTATATAA
110050 TCGCAGATAAACGTATCGTTCATCTAAACCCACCCAAAATCGAAAGAGTAAGAATTGAATATAAG
131 TCGCAGATAAACGTATCGTTCATCTAAACCCACCCAAAATCGAAAGAGTAAGAATTGAATATAAG
110115 ATGCATTGTTGGTGGGGAATGAAGAAGAGAAACAAAAATGAACACATTTATCAAAACATGTCATA
196 ATGCATTGTTGGTGGGGAATGAAGAAGAGAAACAAAAATGAACACATTTATCAAAACATGTCATA
110180 ATTTGTGGCAGTCTCGTCGGTGACAGCTTACACACACTACCATTTCCCCTATTTATTCTAACATT
261 ATTTGTGGCAGTCTCGTCGGTGACAGCTTACACACACTACCATTTCCCCTATTTATTCTAACATT
110245 GATCCATTGAACACCCACGTGCTTTACCCCCCACTCCTTCATCTCTCTTGTTATAATTTATCGTT
326 GATCCATTGAACACCCACGTGCTTTACCCCCCACTCCTTCATCTCTCTTGTTATAATTTATCGTT
110310 TTGGTTTCAGTATTTGTCCCGACGAGATGAGATCTACCCCTGATAATCCGTGAAGATCAACTGTT
391 TTGGTTTCAGTATTTGTCCCGACGAGATGAGATCTACCCCTGATAATCCGTGAAGATCAACTGTT
110375 AACCACTCAATCAACCCTCCAAGTTCAACACTCAAACTACGAATCCAACGTGGCACCAATCTATT
456 AACCACTCAATCAACCCTCCAAGTTCAACACTCAAACTACGAATCCAACGTGGCACCAATCTATT
110440 GGACCCTTTATCTATGAAAAGCCCTTTTGGCTCTCTTTATATCTTCCTTCATTGGAGACCATTTT
521 GGACCCTTTATCTATGAAAAGCCCTTTTGGCTCTCTTTATATCTTCCTTCATTGGAGACCATTTT
110505 AGCACTAAACCAAAAATGAAAATGGGGTCTCTTTTTACTCCTCTGCT
586 AGCACTAAACCAAAAATGAAAATGGGGTCTCTTTTTACTCCTCTGCT
110552 TGCTTTTTAATTAATAAATAAAAATTAAGACTAGATTAAGGATGGATTGGATGGGCAGTGGGTAC
1 TGCTTTTTAATTAATAAATAAAAATTAAGACTAGATTAAGGATGGATTGGATGGGCAGTGGGTAC
110617 GTTTAGCTTACTTTTTGTTTTATACTATGGTATCTAATTTCACCGTTATTGTTGTTTTTATATAA
66 GTTTAGCTTACTTTTTGTTTTATACTATGGTATCTAATTTCACCGTTATTGTTGTTTTTATATAA
110682 TCGCAGATAAACGTATCGTTCATCTAAACCCACCCAAAATCGAAAGAGTAAGAATTGAATATAAG
131 TCGCAGATAAACGTATCGTTCATCTAAACCCACCCAAAATCGAAAGAGTAAGAATTGAATATAAG
110747 ATGCATTGTTGGTGGGGAATGAAGAAGAGAAACAAAAATGAACACATTTATCAAAACATGTCATA
196 ATGCATTGTTGGTGGGGAATGAAGAAGAGAAACAAAAATGAACACATTTATCAAAACATGTCATA
110812 ATTTGTGGCAGTCTCGTCGGTGACAGCTTACACACACTACCATTTCCCCTATTTATTCTAACATT
261 ATTTGTGGCAGTCTCGTCGGTGACAGCTTACACACACTACCATTTCCCCTATTTATTCTAACATT
110877 GATCCATTGAACACCCACGTGCTTTACCCCCCACTCCTTCATCTCTCTTGTTATAATTTATCGTT
326 GATCCATTGAACACCCACGTGCTTTACCCCCCACTCCTTCATCTCTCTTGTTATAATTTATCGTT
110942 TTGGTTTCAGTATTTGTCCCGACGAGATGAGATCTACCCCTGATAATCCGTGAAGATCAACTGTT
391 TTGGTTTCAGTATTTGTCCCGACGAGATGAGATCTACCCCTGATAATCCGTGAAGATCAACTGTT
111007 AACCACTCAATCAACCCTCCAAGTTCAACACTCAAACTACGAATCCAACGTGGCACCAATCTATT
456 AACCACTCAATCAACCCTCCAAGTTCAACACTCAAACTACGAATCCAACGTGGCACCAATCTATT
111072 GGACCCTTTATCTATGAAAAGCCCTTTTGGCTCTCTTTATATCTTCCTTCATTGGAGACCATTTT
521 GGACCCTTTATCTATGAAAAGCCCTTTTGGCTCTCTTTATATCTTCCTTCATTGGAGACCATTTT
111137 AGCACTAAACCAAAAATGAAAATGGGGTCTCTTTTTACTCCTCTGCT
586 AGCACTAAACCAAAAATGAAAATGGGGTCTCTTTTTACTCCTCTGCT
111184 CCTTCCACTC
Statistics
Matches: 631, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
632 631 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (632 bp):
TGCTTTTTAATTAATAAATAAAAATTAAGACTAGATTAAGGATGGATTGGATGGGCAGTGGGTAC
GTTTAGCTTACTTTTTGTTTTATACTATGGTATCTAATTTCACCGTTATTGTTGTTTTTATATAA
TCGCAGATAAACGTATCGTTCATCTAAACCCACCCAAAATCGAAAGAGTAAGAATTGAATATAAG
ATGCATTGTTGGTGGGGAATGAAGAAGAGAAACAAAAATGAACACATTTATCAAAACATGTCATA
ATTTGTGGCAGTCTCGTCGGTGACAGCTTACACACACTACCATTTCCCCTATTTATTCTAACATT
GATCCATTGAACACCCACGTGCTTTACCCCCCACTCCTTCATCTCTCTTGTTATAATTTATCGTT
TTGGTTTCAGTATTTGTCCCGACGAGATGAGATCTACCCCTGATAATCCGTGAAGATCAACTGTT
AACCACTCAATCAACCCTCCAAGTTCAACACTCAAACTACGAATCCAACGTGGCACCAATCTATT
GGACCCTTTATCTATGAAAAGCCCTTTTGGCTCTCTTTATATCTTCCTTCATTGGAGACCATTTT
AGCACTAAACCAAAAATGAAAATGGGGTCTCTTTTTACTCCTCTGCT
Found at i:115315 original size:14 final size:14
Alignment explanation
Indices: 115298--115328 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
115288 AACTTTGAAC
115298 TTGGGATTCGAGGT
1 TTGGGATTCGAGGT
*
115312 TTGGGGTTCGAGGT
1 TTGGGATTCGAGGT
115326 TTG
1 TTG
115329 ATGTTTAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.06, G:0.45, T:0.39
Consensus pattern (14 bp):
TTGGGATTCGAGGT
Found at i:115326 original size:7 final size:7
Alignment explanation
Indices: 115307--115364 Score: 80
Period size: 7 Copynumber: 8.3 Consensus size: 7
115297 CTTGGGATTC
115307 GAGGTTT
1 GAGGTTT
* *
115314 GGGGTTC
1 GAGGTTT
115321 GAGGTTT
1 GAGGTTT
*
115328 GATGTTT
1 GAGGTTT
*
115335 AAGGTTT
1 GAGGTTT
115342 GAGGTTT
1 GAGGTTT
115349 GAGGTTT
1 GAGGTTT
115356 GAGGTTT
1 GAGGTTT
115363 GA
1 GA
115365 CATTCAAGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (7 bp):
GAGGTTT
Found at i:118756 original size:22 final size:23
Alignment explanation
Indices: 118725--118775 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
118715 TTGCAAAAGT
*
118725 AAGACTAAAAATCTATAAAAGAC
1 AAGACTAAAAATCTATAAAAGAA
* *
118748 AAGAC-AAAAATTTCTAAAAGAA
1 AAGACTAAAAATCTATAAAAGAA
118770 AAGACT
1 AAGACT
118776 TATGAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.18
Consensus pattern (23 bp):
AAGACTAAAAATCTATAAAAGAA
Found at i:119621 original size:30 final size:30
Alignment explanation
Indices: 119581--119647 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
119571 GTAATTTGAT
*
119581 ACAT-AAACTTTGATT-TGATGCAATTATAA
1 ACATGAAACTTTGATTGTG-TGCAAATATAA
* *
119610 AGATGAAACTTTGATTGTGTTCAAATATAA
1 ACATGAAACTTTGATTGTGTGCAAATATAA
119640 ACATGAAA
1 ACATGAAA
119648 TATTCATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 27 0.84
31 2 0.06
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.34
Consensus pattern (30 bp):
ACATGAAACTTTGATTGTGTGCAAATATAA
Found at i:137355 original size:13 final size:14
Alignment explanation
Indices: 137337--137365 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
137327 CTTTTGTTAT
137337 AAAAAGAAAA-AAG
1 AAAAAGAAAAGAAG
137350 AAAAAGAAAAGAAG
1 AAAAAGAAAAGAAG
137364 AA
1 AA
137366 GGAGATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAGAAG
Found at i:142096 original size:27 final size:26
Alignment explanation
Indices: 142055--142105 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
142045 AATACTCATA
142055 TTTATATAATTAAAATAT-TCATATT
1 TTTATATAATTAAAATATGTCATATT
142080 TTTATACTAAGTTAAAATATGTCATA
1 TTTATA-TAA-TTAAAATATGTCATA
142106 AGTCCTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 3 0.13
27 9 0.39
28 5 0.22
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (26 bp):
TTTATATAATTAAAATATGTCATATT
Found at i:143866 original size:15 final size:15
Alignment explanation
Indices: 143846--143897 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
143836 ACTACAAAAC
143846 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
143861 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
143880 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
143895 ATT
1 ATT
143898 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:144739 original size:13 final size:14
Alignment explanation
Indices: 144721--144753 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
144711 TATTTATTTA
144721 TTTTAAAAATAT-T
1 TTTTAAAAATATAT
*
144734 TTTTAAAGATATAT
1 TTTTAAAAATATAT
144748 TTTTAA
1 TTTTAA
144754 TCCCAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
TTTTAAAAATATAT
Found at i:153252 original size:13 final size:14
Alignment explanation
Indices: 153234--153262 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
153224 GTCCCTATAA
153234 TTTTATTT-TTTAT
1 TTTTATTTCTTTAT
153247 TTTTATTTCTTTAT
1 TTTTATTTCTTTAT
153261 TT
1 TT
153263 GTTAAAGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTATTTCTTTAT
Found at i:155904 original size:42 final size:38
Alignment explanation
Indices: 155857--155949 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 38
155847 AGACAAGCTT
155857 TTAGCGGCGTTTGGACAAAAAAACGCCGCTAAAAATAGAGCA
1 TTAGCGGCGTTT--AC-AAAAAACGCCGCTAAAAAT-GAGCA
**
155899 TTAGCGGCGCTTTACGTAAAACGCCGCTAAAAATGAGCA
1 TTAGCGGCG-TTTACAAAAAACGCCGCTAAAAATGAGCA
155938 TTAGCGGCGTTT
1 TTAGCGGCGTTT
155950 TTTGGAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
38 3 0.06
39 14 0.29
40 17 0.35
41 2 0.04
42 9 0.19
43 3 0.06
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (38 bp):
TTAGCGGCGTTTACAAAAAACGCCGCTAAAAATGAGCA
Found at i:155924 original size:40 final size:40
Alignment explanation
Indices: 155875--155971 Score: 142
Period size: 40 Copynumber: 2.4 Consensus size: 40
155865 GTTTGGACAA
155875 AAAAACGCCGCTAAAAATAGAGCATTAGCGGCG-CTTTACG
1 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGTCTTTACG
* * **
155915 TAAAACGCCGCTAAAAATGAGCATTAGCGGCGTTTTTTGG
1 AAAAACGCCGCTAAAAATGAGCATTAGCGGCGTCTTTACG
155955 AAAAACGCCGCTAAAAA
1 AAAAACGCCGCTAAAAA
155972 CCTAAGCACA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 14 0.27
40 37 0.73
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.20
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCGGCGTCTTTACG
Found at i:156078 original size:41 final size:41
Alignment explanation
Indices: 156026--156162 Score: 238
Period size: 41 Copynumber: 3.3 Consensus size: 41
156016 CGTTTTTAAA
*
156026 AAAAGCACCGCTAATGCTCAGATCTTGAGAGGCGTTTTTGG
1 AAAAGCGCCGCTAATGCTCAGATCTTGAGAGGCGTTTTTGG
156067 AAAAGCGCCGCTAATGCTCAGATCTTGAGAGGCGTTTTTGG
1 AAAAGCGCCGCTAATGCTCAGATCTTGAGAGGCGTTTTTGG
* *
156108 AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGG
1 AAAAGCGCCGCTAATGCTCAGATCTTGAGAGGCGTTTTTGG
*
156149 GAAAGCGCCGCTAA
1 AAAAGCGCCGCTAA
156163 AGCCCCGAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (41 bp):
AAAAGCGCCGCTAATGCTCAGATCTTGAGAGGCGTTTTTGG
Found at i:156303 original size:14 final size:15
Alignment explanation
Indices: 156274--156307 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
156264 TAAGGTTTAT
156274 AGATTATGGAATTAG
1 AGATTATGGAATTAG
156289 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
156303 AGATT
1 AGATT
156308 CTGATTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:156561 original size:7 final size:7
Alignment explanation
Indices: 156546--156598 Score: 88
Period size: 7 Copynumber: 7.6 Consensus size: 7
156536 AAGGTGTAGA
*
156546 GGTTAGG
1 GGTTTGG
156553 GGTTTGG
1 GGTTTGG
156560 GGTTTGG
1 GGTTTGG
156567 GGTTTGG
1 GGTTTGG
156574 GGTTTGG
1 GGTTTGG
156581 GGTTTGG
1 GGTTTGG
*
156588 AGTTTGG
1 GGTTTGG
156595 GGTT
1 GGTT
156599 AAGAGTTAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.04, C:0.00, G:0.55, T:0.42
Consensus pattern (7 bp):
GGTTTGG
Found at i:156569 original size:89 final size:89
Alignment explanation
Indices: 156394--156556 Score: 256
Period size: 89 Copynumber: 1.8 Consensus size: 89
156384 TTCAGTGTTA
* *
156394 GGTTAGGGGTTAAGGTTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAATGATTAGTGG
1 GGTTAGGGGTTAAGATTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAATGATTAGAGG
156459 TTAGGGGTTAGGGATTCGGGGTCG
66 TTAGGGGTTAGGGATTCGGGGTCG
* * * *
156483 GGTTAGGGTTTATGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAA-GGTGTAGAG
1 GGTTAGGGGTTAAGATTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAATGAT-TAGAG
156547 GTTAGGGGTT
65 GTTAGGGGTT
156557 TGGGGTTTGG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
88 2 0.03
89 65 0.97
ACGTcount: A:0.27, C:0.01, G:0.29, T:0.43
Consensus pattern (89 bp):
GGTTAGGGGTTAAGATTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAATGATTAGAGG
TTAGGGGTTAGGGATTCGGGGTCG
Found at i:157022 original size:17 final size:16
Alignment explanation
Indices: 156989--157022 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
156979 ATATTAGATT
*
156989 TAAAAAAATTAATAAA
1 TAAAAAAATTAACAAA
157005 TAAAAAAATGTAACAAA
1 TAAAAAAAT-TAACAAA
157022 T
1 T
157023 TGATACGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAAAATTAACAAA
Found at i:157406 original size:22 final size:23
Alignment explanation
Indices: 157374--157439 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
157364 TAAAATCCCC
157374 TCCCCCC--AAAATCCCCAACTT
1 TCCCCCCTTAAAATCCCCAACTT
* *
157395 TCCCGCC-TAAAATCCCTAA-TT
1 TCCCCCCTTAAAATCCCCAACTT
* *
157416 TCCCCCCTTGAAACCCCCAACTT
1 TCCCCCCTTAAAATCCCCAACTT
157439 T
1 T
157440 ACAAACATAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 14 0.39
22 19 0.53
23 3 0.08
ACGTcount: A:0.26, C:0.47, G:0.03, T:0.24
Consensus pattern (23 bp):
TCCCCCCTTAAAATCCCCAACTT
Found at i:161940 original size:44 final size:43
Alignment explanation
Indices: 161724--161950 Score: 287
Period size: 43 Copynumber: 5.3 Consensus size: 43
161714 AGATTATGTT
** * *
161724 TTTAGCGGCGTTT-TGCTAGAAGCGCCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* ** *
161765 TTTAGCGGCGTTTATGATAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * **
161808 TATAGCGGCGTTTGTGGGGAAAGCGTTGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
161851 TTTAGCGGTGTTTGTGGGGAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
161894 TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCTTGATC
1 TTTAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTCTTGGTC
161938 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
161951 TTTCCGGCGC
Statistics
Matches: 162, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
41 13 0.08
42 20 0.12
43 94 0.58
44 35 0.22
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:162682 original size:68 final size:64
Alignment explanation
Indices: 162531--162688 Score: 192
Period size: 64 Copynumber: 2.4 Consensus size: 64
162521 TATATATTTT
* * *
162531 AAAGTTCTTGAGCTGAAATTAATGTACGAATTTTATATACATATGTGATTCAAATATAGGTTAT
1 AAAGTTCTTGAGCTGAATTTAATGTACGAATTTTACATACATATGTGATTCAAATATAGGTTAC
* * *
162595 AAAGTTCTTGAGCTGAATTTAATTTATGAATTTTACATACATATGTGTATGGTTCGAATATAGGT
1 AAAGTTCTTGAGCTGAATTTAATGTACGAATTTTACATACATATGTG-A---TTCAAATATAGGT
162660 TAC
62 TAC
*
162663 AAA-TTCTTTGAACTGAATTTTAATGT
1 AAAGTTC-TTGAGCTGAA-TTTAATGT
162689 TGTAAATTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
64 43 0.54
65 1 0.01
67 3 0.04
68 26 0.32
69 7 0.09
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (64 bp):
AAAGTTCTTGAGCTGAATTTAATGTACGAATTTTACATACATATGTGATTCAAATATAGGTTAC
Found at i:162772 original size:41 final size:42
Alignment explanation
Indices: 162727--162843 Score: 134
Period size: 41 Copynumber: 2.8 Consensus size: 42
162717 ATCTGAGATT
*
162727 TTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTG-AAT-TAA
1 TTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAAATGT-A
* *
162768 TTCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAAATGTA
1 TTCAGGCTTTATGCCTAGCAGGC-TTGATGCCGGTGAAATGTA
* * *
162810 -TCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 TTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTG
162844 TTTTATACAA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
40 2 0.03
41 54 0.84
42 7 0.11
43 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.32
Consensus pattern (42 bp):
TTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAAATGTA
Found at i:164684 original size:13 final size:13
Alignment explanation
Indices: 164662--164723 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
164652 TTTGGCAATA
164662 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
164675 CTTTTAAAAAGTG
1 CTTTTGAAAAGTG
*
164688 -TTGTGGAAAAGTG
1 CTT-TTGAAAAGTG
*
164701 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
164714 CTTTTGAAAA
1 CTTTTGAAAA
164724 TTTTGAGTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
12 2 0.05
13 37 0.90
14 2 0.05
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:165050 original size:17 final size:18
Alignment explanation
Indices: 165030--165079 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 18
165020 ATATTGACAC
165030 AATTGTATTATTTTAA-A
1 AATTGTATTATTTTAACA
*
165047 AA-T-TATTGCTTTTAACA
1 AATTGTATT-ATTTTAACA
165064 AATTTGTATTATTTTA
1 AA-TTGTATTATTTTA
165080 TTTTAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
15 4 0.15
16 7 0.27
17 5 0.19
19 6 0.23
20 4 0.15
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (18 bp):
AATTGTATTATTTTAACA
Found at i:166082 original size:17 final size:18
Alignment explanation
Indices: 166060--166093 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
166050 TTCTTTATTG
166060 CTTTTT-AGGGAAAAACA
1 CTTTTTAAGGGAAAAACA
*
166077 CTTTTTAATGGAAAAAC
1 CTTTTTAAGGGAAAAAC
166094 TCATCTGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (18 bp):
CTTTTTAAGGGAAAAACA
Found at i:166944 original size:19 final size:18
Alignment explanation
Indices: 166916--166951 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
166906 AAATAAATTA
166916 ATTTTCAAAAATTCAAAAT
1 ATTTTC-AAAATTCAAAAT
*
166935 ATTTTGAAAATTCAAAA
1 ATTTTCAAAATTCAAAA
166952 AATTATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (18 bp):
ATTTTCAAAATTCAAAAT
Found at i:170161 original size:16 final size:18
Alignment explanation
Indices: 170142--170175 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
170132 TTAAATGTAA
170142 AATTAA-AC-AAATTCAC
1 AATTAACACAAAATTCAC
170158 AATTAACACAAAATTCAC
1 AATTAACACAAAATTCAC
170176 CCTATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.24
Consensus pattern (18 bp):
AATTAACACAAAATTCAC
Found at i:170874 original size:21 final size:22
Alignment explanation
Indices: 170850--170903 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
170840 GCAATACATC
170850 AATTATATAATTTTTTA-AATA
1 AATTATATAATTTTTTATAATA
*
170871 AATTATAT-ATTTTTTATAGTA
1 AATTATATAATTTTTTATAATA
*
170892 AA-AATATAATTT
1 AATTATATAATTT
170904 CATCATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AATTATATAATTTTTTATAATA
Found at i:171284 original size:14 final size:14
Alignment explanation
Indices: 171267--171325 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
171257 AATAAACACC
171267 AAAATTTAAAAAAA
1 AAAATTTAAAAAAA
171281 AAAA--T-AAAAAA
1 AAAATTTAAAAAAA
** *
171292 AGTATTTTAAAAAA
1 AAAATTTAAAAAAA
*
171306 AAATTTTAAAAATAA
1 AAAATTTAAAAA-AA
171321 AAAAT
1 AAAAT
171326 AAAAATATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
11 8 0.24
12 1 0.03
13 1 0.03
14 18 0.53
15 6 0.18
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
AAAATTTAAAAAAA
Found at i:171303 original size:13 final size:13
Alignment explanation
Indices: 171267--171322 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 13
171257 AATAAACACC
171267 AAAA-TTTAAAAA
1 AAAATTTTAAAAA
**
171279 AAAA-AATAAAAA
1 AAAATTTTAAAAA
*
171291 AAGTATTTTAAAAA
1 AA-AATTTTAAAAA
171305 AAAATTTTAAAAA
1 AAAATTTTAAAAA
171318 TAAAA
1 -AAAA
171323 AATAAAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
12 12 0.34
13 11 0.31
14 12 0.34
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (13 bp):
AAAATTTTAAAAA
Found at i:176119 original size:20 final size:20
Alignment explanation
Indices: 176094--176149 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
176084 TATGGGTTTG
*
176094 CACTTTGGTGCCTCTGTTCA
1 CACTTTAGTGCCTCTGTTCA
* **
176114 CACTTTAGTGTCTCTGTTTG
1 CACTTTAGTGCCTCTGTTCA
*
176134 CACTTTAATGCCTCTG
1 CACTTTAGTGCCTCTG
176150 ACTGCACAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.27, G:0.18, T:0.43
Consensus pattern (20 bp):
CACTTTAGTGCCTCTGTTCA
Found at i:179952 original size:27 final size:27
Alignment explanation
Indices: 179914--179968 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
179904 ACTCATTAAG
179914 CCTTTCTATGATACATAGTGATATTGC
1 CCTTTCTATGATACATAGTGATATTGC
179941 CCTTTCTATGATACATAGTGATATTGC
1 CCTTTCTATGATACATAGTGATATTGC
179968 C
1 C
179969 GAGAGTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (27 bp):
CCTTTCTATGATACATAGTGATATTGC
Found at i:183021 original size:141 final size:142
Alignment explanation
Indices: 182755--183039 Score: 563
Period size: 141 Copynumber: 2.0 Consensus size: 142
182745 TATATAAACA
182755 TATATTAACTATATAAGAAAATCACATCACATTAAAGCAAATCAAATCAAAGTCATTAATTTGCT
1 TATATTAACTATATAAGAAAATCACATCACATTAAAGCAAATCAAATCAAAGTCATTAATTTGCT
182820 ACCTCTTTCCTCAGAAATATTTTAATTGATCATCTCTCGTGACTTGAAATCCTAGCTAGTAGTTA
66 ACCTCTTTCCTCAGAAATATTTTAATTGATCATCTCTCGTGACTTGAAATCCTAGCTAGTAGTTA
182885 GATTGGTCCAAG
131 GATTGGTCCAAG
182897 TATATTAACTA-ATAAGAAAATCACATCACATTAAAGCAAATCAAATCAAAGTCATTAATTTGCT
1 TATATTAACTATATAAGAAAATCACATCACATTAAAGCAAATCAAATCAAAGTCATTAATTTGCT
182961 ACCTCTTTCCTCAGAAATATTTTAATTGATCATCTCTCGTGACTTGAAATCCTAGCTAGTAGTTA
66 ACCTCTTTCCTCAGAAATATTTTAATTGATCATCTCTCGTGACTTGAAATCCTAGCTAGTAGTTA
183026 GATTGGTCCAAG
131 GATTGGTCCAAG
183038 TA
1 TA
183040 CCTACTCGAA
Statistics
Matches: 143, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
141 132 0.92
142 11 0.08
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (142 bp):
TATATTAACTATATAAGAAAATCACATCACATTAAAGCAAATCAAATCAAAGTCATTAATTTGCT
ACCTCTTTCCTCAGAAATATTTTAATTGATCATCTCTCGTGACTTGAAATCCTAGCTAGTAGTTA
GATTGGTCCAAG
Found at i:188165 original size:2 final size:2
Alignment explanation
Indices: 188158--188187 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
188148 TTTGTCAAGA
188158 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
188188 GTGTGTGTGT
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:190478 original size:22 final size:21
Alignment explanation
Indices: 190453--190494 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
190443 ATTACTCAGG
*
190453 TTTTTAAAGGAAAAACTTGAA
1 TTTTTAAAGGAAAAACCTGAA
*
190474 TTTTTACAGGAAAAACCTGAA
1 TTTTTAAAGGAAAAACCTGAA
190495 GTTTGATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (21 bp):
TTTTTAAAGGAAAAACCTGAA
Found at i:190771 original size:18 final size:19
Alignment explanation
Indices: 190750--190785 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
190740 GAAAAACCAT
190750 TTTATTT-TTTTAATTTTC
1 TTTATTTATTTTAATTTTC
*
190768 TTTATTTATTTTCATTTT
1 TTTATTTATTTTAATTTT
190786 TTAGAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTATTTATTTTAATTTTC
Found at i:200905 original size:9 final size:9
Alignment explanation
Indices: 200887--200986 Score: 51
Period size: 9 Copynumber: 10.6 Consensus size: 9
200877 CCTGATATAA
200887 TAAATATTTT
1 TAAAT-TTTT
200897 TAAA-TTTT
1 TAAATTTTT
200905 TAAATTTTT
1 TAAATTTTT
* *
200914 TTAATTTTA
1 TAAATTTTT
*
200923 AAATATTTTT
1 TAA-ATTTTT
*
200933 TTAA-TTTT
1 TAAATTTTT
*
200941 AAAATATTTT
1 TAAAT-TTTT
200951 TAAAATACTTTTT
1 T--AA-A-TTTTT
*
200964 TTAATTTTT
1 TAAATTTTT
*
200973 TTAATTTTT
1 TAAATTTTT
*
200982 AAAAT
1 TAAAT
200987 AATTTTTTGG
Statistics
Matches: 69, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
8 14 0.20
9 30 0.43
10 15 0.22
11 1 0.01
12 2 0.03
13 6 0.09
14 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (9 bp):
TAAATTTTT
Found at i:200914 original size:18 final size:18
Alignment explanation
Indices: 200888--200954 Score: 91
Period size: 19 Copynumber: 3.7 Consensus size: 18
200878 CTGATATAAT
*
200888 AAATATTTTTAAATTTTT
1 AAATATTTTTAAATTTTA
*
200906 AAAT-TTTTTTAATTTTA
1 AAATATTTTTAAATTTTA
*
200923 AAATATTTTTTTAATTTTA
1 AAATA-TTTTTAAATTTTA
200942 AAATATTTTTAAA
1 AAATATTTTTAAA
200955 ATACTTTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 15 0.34
18 11 0.25
19 18 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AAATATTTTTAAATTTTA
Found at i:200919 original size:17 final size:17
Alignment explanation
Indices: 200888--200953 Score: 78
Period size: 17 Copynumber: 3.7 Consensus size: 17
200878 CTGATATAAT
* *
200888 AAATATTTTTAAATTTTT
1 AAAT-TTTTTTAATTTTA
200906 AAATTTTTTTAATTTTAA
1 AAATTTTTTTAATTTT-A
200924 AATATTTTTTTAATTTTA
1 AA-ATTTTTTTAATTTTA
*
200942 AAATATTTTTAA
1 AAATTTTTTTAA
200954 AATACTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
17 20 0.47
18 9 0.21
19 14 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATTTTTTTAATTTTA
Found at i:200966 original size:31 final size:29
Alignment explanation
Indices: 200918--200994 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
200908 ATTTTTTTAA
200918 TTTTAAAATATTTTTTTAATTTTAAAATAT
1 TTTTAAAATATTTTTTTAATTTTAAAA-AT
***
200948 TTTTAAAATACTTTTTTTAATTTTTTTAAT
1 TTTTAAAATA-TTTTTTTAATTTTAAAAAT
*
200978 TTTTAAAATAATTTTTT
1 TTTTAAAATATTTTTTT
200995 GGCATTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 6 0.14
30 22 0.52
31 14 0.33
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTTAAAATATTTTTTTAATTTTAAAAAT
Found at i:201444 original size:25 final size:25
Alignment explanation
Indices: 201382--201463 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
201372 CGGACACACC
* *
201382 ATAGCTCGCAAGAGCATCCCGTTAT
1 ATAGCTCTCATGAGCATCCCGTTAT
* * * *
201407 TTAGCTTTTATGAGCATCTCGTTAT
1 ATAGCTCTCATGAGCATCCCGTTAT
* *
201432 ATGGCTCTCATGAGCTTCCCGATTA-
1 ATAGCTCTCATGAGCATCCCG-TTAT
201457 ATAGCTC
1 ATAGCTC
201464 ACTTGAGCTT
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
25 40 0.93
26 3 0.07
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.34
Consensus pattern (25 bp):
ATAGCTCTCATGAGCATCCCGTTAT
Found at i:201470 original size:25 final size:25
Alignment explanation
Indices: 201432--201589 Score: 110
Period size: 25 Copynumber: 6.3 Consensus size: 25
201422 ATCTCGTTAT
* *
201432 ATGGCTCTCATGAGCTTCCCGATTA
1 ATGGCTCACTTGAGCTTCCCGATTA
* * *
201457 ATAGCTCACTTGAGCTTCCCAATAA
1 ATGGCTCACTTGAGCTTCCCGATTA
* * **
201482 AAGGCTCTCTCATGAGCTTTTCGA-TA
1 ATGGCTCACT--TGAGCTTCCCGATTA
* *
201508 ATGGCTCTCATGAGCTTCCCGATT-
1 ATGGCTCACTTGAGCTTCCCGATTA
* * *
201532 ACGGCTC-TTATGAGCTT-CCTATTA
1 ATGGCTCACT-TGAGCTTCCCGATTA
201556 CATGGCTCACTTGAGCTTCCCG-TTA
1 -ATGGCTCACTTGAGCTTCCCGATTA
201581 TATGGCTCA
1 -ATGGCTCA
201590 AAAGAGCTTC
Statistics
Matches: 101, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
23 5 0.05
24 23 0.23
25 52 0.51
26 12 0.12
27 9 0.09
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (25 bp):
ATGGCTCACTTGAGCTTCCCGATTA
Found at i:201520 original size:24 final size:24
Alignment explanation
Indices: 201434--201550 Score: 99
Period size: 24 Copynumber: 4.7 Consensus size: 24
201424 CTCGTTATAT
*
201434 GGCTCTCATGAGCTTCCCGATTAAT
1 GGCTCTCATGAGCTTCCCGA-TAAC
* * * * *
201459 AGCTCACTTGAGCTTCCCAATAAAA
1 GGCTCTCATGAGCTTCCCGAT-AAC
** *
201484 GGCTCTCTCATGAGCTTTTCGATAAT
1 GG--CTCTCATGAGCTTCCCGATAAC
*
201510 GGCTCTCATGAGCTTCCCGATTAC
1 GGCTCTCATGAGCTTCCCGATAAC
*
201534 GGCTCTTATGAGCTTCC
1 GGCTCTCATGAGCTTCC
201551 TATTACATGG
Statistics
Matches: 72, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
24 35 0.49
25 19 0.26
26 4 0.06
27 14 0.19
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (24 bp):
GGCTCTCATGAGCTTCCCGATAAC
Found at i:201613 original size:25 final size:26
Alignment explanation
Indices: 201543--201610 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
201533 CGGCTCTTAT
***
201543 GAGCTTCCT-ATTACATGGCTCACTT
1 GAGCTTCCTGATTACATGGCTCAAAA
* *
201568 GAGCTTCCCG-TTATATGGCTCAAAA
1 GAGCTTCCTGATTACATGGCTCAAAA
201593 GAGCTTCCTGATTACATG
1 GAGCTTCCTGATTACATG
201611 CTCGCATGGG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
25 28 0.82
26 6 0.18
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (26 bp):
GAGCTTCCTGATTACATGGCTCAAAA
Found at i:207715 original size:6 final size:6
Alignment explanation
Indices: 207692--207724 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
207682 GAAATAGGGG
207692 AAAAGA AAGAAG- AAAAGA AAAAGA AAAAGA AAA
1 AAAAGA AA-AAGA AAAAGA AAAAGA AAAAGA AAA
207725 GGAAGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 3 0.12
6 19 0.76
7 3 0.12
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:207721 original size:17 final size:18
Alignment explanation
Indices: 207692--207725 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
207682 GAAATAGGGG
207692 AAAAGAAAGAAGAAAAGA
1 AAAAGAAAGAAGAAAAGA
207710 AAAAGAAA-AAGAAAAG
1 AAAAGAAAGAAGAAAAG
207726 GAAGGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAGAAAGAAGAAAAGA
Found at i:208785 original size:23 final size:23
Alignment explanation
Indices: 208755--208809 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
208745 GGCTTTTTCG
*
208755 ATCAGGCACTTGATGTGTTGCAT
1 ATCAGGCACTTGATGTGTCGCAT
* *
208778 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTGATGTGTCGCAT
*
208801 TTCAGGCAC
1 ATCAGGCAC
208810 CTCGTATGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (23 bp):
ATCAGGCACTTGATGTGTCGCAT
Found at i:212296 original size:45 final size:45
Alignment explanation
Indices: 212240--212332 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
212230 TACTATGTGA
* *
212240 ACCAAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCAAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
* *
212285 ACCAGACATCATTGATTAATAAGGTGGTTGCTTTGTGCTGAATCC
1 ACCAAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
212330 ACC
1 ACC
212333 GAGTATCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (45 bp):
ACCAAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:214431 original size:24 final size:23
Alignment explanation
Indices: 214353--214435 Score: 67
Period size: 25 Copynumber: 3.4 Consensus size: 23
214343 TTTTGCTTTA
* *
214353 ATGAGCATCCCGTTATATGACTCT
1 ATGAGCTTCCCGTT-TATGGCTCT
* * *
214377 CACGAGCTTCCTGATTAATGGCTCTT
1 -ATGAGCTTCCCG-TTTATGGCTC-T
*
214403 TTGAGCTTCCCGTTTATGGCTCAT
1 ATGAGCTTCCCGTTTATGGCTC-T
214427 ATGAGCTTC
1 ATGAGCTTC
214436 TTGATAATTG
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
24 18 0.40
25 24 0.53
26 3 0.07
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (23 bp):
ATGAGCTTCCCGTTTATGGCTCT
Found at i:214448 original size:49 final size:50
Alignment explanation
Indices: 214354--214450 Score: 119
Period size: 49 Copynumber: 2.0 Consensus size: 50
214344 TTTGCTTTAA
214354 TGAGCATCCCGTTATATGACTCTCACGAGCTTCCTGATTAATGGCTCTTT
1 TGAGCATCCCGTTATATGACTCTCACGAGCTTCCTGATTAATGGCTCTTT
* * * *
214404 TGAGCTTCCCGTT-TATGGCTCAT-ATGAGCTTCTTGA-TAATTGGCTCT
1 TGAGCATCCCGTTATATGACTC-TCACGAGCTTCCTGATTAA-TGGCTCT
214451 CCAAAGCTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
48 3 0.07
49 25 0.61
50 13 0.32
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.38
Consensus pattern (50 bp):
TGAGCATCCCGTTATATGACTCTCACGAGCTTCCTGATTAATGGCTCTTT
Found at i:214523 original size:24 final size:24
Alignment explanation
Indices: 214479--214534 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
214469 AGGATCTCTC
*
214479 ATGAGCTTCCCGATATTGGCTCAA
1 ATGAGCTTCCCGATATAGGCTCAA
**
214503 ATGAGCTTCCCGAT-TAAGGCTCTT
1 ATGAGCTTCCCGATAT-AGGCTCAA
214527 ATGAGCTT
1 ATGAGCTT
214535 TCTGTGACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (24 bp):
ATGAGCTTCCCGATATAGGCTCAA
Found at i:221218 original size:4 final size:4
Alignment explanation
Indices: 221209--221255 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
221199 TATTTCCCTT
* ** *
221209 TTTA TTTA TTTA TTTA TTTA TATA TTTA TACA TTTA TCTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
221256 CCTTTTTATT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:221402 original size:4 final size:4
Alignment explanation
Indices: 221393--221422 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
221383 TTTTCCTCTA
*
221393 TATT TATT TATG TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TATT TA
221423 CTTGTCCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:221512 original size:12 final size:12
Alignment explanation
Indices: 221482--221522 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
221472 TTTGTCACTA
221482 TTATTATTATCATT
1 TTATTATT-T-ATT
221496 GTTATTATTTATT
1 -TTATTATTTATT
221509 TTATTATTTATT
1 TTATTATTTATT
221521 TT
1 TT
221523 TTTCTTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.54
13 3 0.12
14 1 0.04
15 8 0.31
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (12 bp):
TTATTATTTATT
Found at i:222169 original size:21 final size:21
Alignment explanation
Indices: 222119--222163 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
222109 AGCATCCTAG
* *
222119 CAACCCCAGCCTCTAACCCAT
1 CAACCCTAGCATCTAACCCAT
222140 CAACCCTAGCATCTAACCCAT
1 CAACCCTAGCATCTAACCCAT
222161 CAA
1 CAA
222164 GGCTAGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.47, G:0.04, T:0.16
Consensus pattern (21 bp):
CAACCCTAGCATCTAACCCAT
Found at i:224587 original size:2 final size:2
Alignment explanation
Indices: 224580--224619 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
224570 ATCTAGTTAA
224580 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
224620 TACATTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:225147 original size:17 final size:18
Alignment explanation
Indices: 225117--225159 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
225107 TATATTCTTT
225117 TAATTTTTTAAAAAAATA
1 TAATTTTTTAAAAAAATA
225135 TAATTTTTT-AAAAAATA
1 TAATTTTTTAAAAAAATA
225152 TAAATTTT
1 T-AATTTT
225160 AGAATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTTTTTAAAAAAATA
Found at i:225389 original size:47 final size:47
Alignment explanation
Indices: 225332--225521 Score: 371
Period size: 47 Copynumber: 4.0 Consensus size: 47
225322 CACTGACCAA
*
225332 AAAGGAATTTACACTAATATGTTATTCGAATTGTGAAATTCAACTCG
1 AAAGGTATTTACACTAATATGTTATTCGAATTGTGAAATTCAACTCG
225379 AAAGGTATTTACACTAATATGTTATTCGAATTGTGAAATTCAACTCG
1 AAAGGTATTTACACTAATATGTTATTCGAATTGTGAAATTCAACTCG
225426 AAAGGTATTTACACTAATATGTTATTCGAATTGTGAAATTCAACTCG
1 AAAGGTATTTACACTAATATGTTATTCGAATTGTGAAATTCAACTCG
225473 AAAGGTATTTACACTAATATGTTATTCGAATTGTGAAATTCAACTCG
1 AAAGGTATTTACACTAATATGTTATTCGAATTGTGAAATTCAACTCG
225520 AA
1 AA
225522 TTGAGTTAGT
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 142 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (47 bp):
AAAGGTATTTACACTAATATGTTATTCGAATTGTGAAATTCAACTCG
Found at i:226325 original size:18 final size:19
Alignment explanation
Indices: 226297--226346 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
226287 TAAACTATTT
*
226297 AAAATTTTAAAAAATA-AA
1 AAAAATTTAAAAAATACAA
* *
226315 AATAATTTAAAATATACAA
1 AAAAATTTAAAAAATACAA
*
226334 AAAAATATAAAAA
1 AAAAATTTAAAAA
226347 TTTCGAAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATTTAAAAAATACAA
Found at i:227507 original size:6 final size:6
Alignment explanation
Indices: 227496--227524 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
227486 TTTACATGGA
227496 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
227525 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:228273 original size:19 final size:20
Alignment explanation
Indices: 228237--228289 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
228227 AATTACAAAA
*
228237 AAAAAATCAAAATAATTT-T
1 AAAAATTCAAAATAATTTAT
228256 CAAAAATTCAAAAT-ATTTAT
1 -AAAAATTCAAAATAATTTAT
228276 AAAAATTTCAAAAT
1 AAAAA-TTCAAAAT
228290 TTATATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTAT
Found at i:230889 original size:9 final size:9
Alignment explanation
Indices: 230875--230900 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
230865 CCATAAGCTT
230875 TGTACAACG
1 TGTACAACG
230884 TGTACAACG
1 TGTACAACG
230893 TGTACAAC
1 TGTACAAC
230901 CACGTATTCC
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:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (9 bp):
TGTACAACG
Found at i:237071 original size:14 final size:14
Alignment explanation
Indices: 237039--237071 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
237029 AGAACTGTTA
237039 TGAAAAATTAATTT
1 TGAAAAATTAATTT
*
237053 T-AAAAATTACTTT
1 TGAAAAATTAATTT
237066 TGAAAA
1 TGAAAA
237072 GCTTGATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (14 bp):
TGAAAAATTAATTT
Found at i:246101 original size:20 final size:19
Alignment explanation
Indices: 246076--246141 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 19
246066 TAACGGAAAG
246076 AAATCAAAGGATTGTGAATC
1 AAATCAAAGGATTG-GAATC
* * * **
246096 AAATCAATGTAATGGAAAG
1 AAATCAAAGGATTGGAATC
*
246115 AAATCAAAAGATTGAGAATC
1 AAATCAAAGGATTG-GAATC
246135 AAATCAA
1 AAATCAA
246142 TGTAAACAAG
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
19 13 0.38
20 21 0.62
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
AAATCAAAGGATTGGAATC
Found at i:246128 original size:39 final size:39
Alignment explanation
Indices: 246065--246146 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
246055 AAGCAAAACA
* *
246065 GTAACGGAAAGAAATCAAAGGATTGTGAATCAAATCAAT
1 GTAACGGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
*
246104 GTAATGGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
1 GTAACGGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
246143 GTAA
1 GTAA
246147 ACAAGATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.21
Consensus pattern (39 bp):
GTAACGGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
Found at i:248894 original size:52 final size:52
Alignment explanation
Indices: 248816--248918 Score: 206
Period size: 52 Copynumber: 2.0 Consensus size: 52
248806 CCGTGTAGCC
248816 ATAGGAAAATGTATTCCCCCGAACTGAACTCGGTCCATATGAGCCTATAATA
1 ATAGGAAAATGTATTCCCCCGAACTGAACTCGGTCCATATGAGCCTATAATA
248868 ATAGGAAAATGTATTCCCCCGAACTGAACTCGGTCCATATGAGCCTATAAT
1 ATAGGAAAATGTATTCCCCCGAACTGAACTCGGTCCATATGAGCCTATAAT
248919 GGGTGGAGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (52 bp):
ATAGGAAAATGTATTCCCCCGAACTGAACTCGGTCCATATGAGCCTATAATA
Found at i:256718 original size:44 final size:44
Alignment explanation
Indices: 256658--256817 Score: 250
Period size: 44 Copynumber: 3.6 Consensus size: 44
256648 TAATTCTACT
*
256658 TCCCTAGGT-AGCAGTGGAATAGATTGAAGATTGTGAATCCTATC
1 TCCCT-GGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATC
* *
256702 TCCCTTGTCAGTAGTGGAATAGGTTGAAGATTGTGAATCCTATC
1 TCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATC
* *
256746 TCCCTGGTCAGCAGTGGAATAGGCTGAAGATTGAGAATCCTATC
1 TCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATC
*
256790 TCCCTGGTTAGCAGTGGAATAGGTTGAA
1 TCCCTGGTCAGCAGTGGAATAGGTTGAA
256818 AGTAAACAAA
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
43 2 0.02
44 104 0.98
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (44 bp):
TCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATC
Done.