Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold42
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: 3911082
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 18191 characters in sequence are not A, C, G, or T
File 2 of 24
Found at i:220247 original size:8 final size:8
Alignment explanation
Indices: 220236--220295 Score: 61
Period size: 8 Copynumber: 7.4 Consensus size: 8
220226 TTAAATAAAT
220236 AAAATATA
1 AAAATATA
*
220244 AAAA-ATT
1 AAAATATA
220251 AAAATA-A
1 AAAATATA
220258 ATAAATATA
1 A-AAATATA
220267 AAAATATA
1 AAAATATA
220275 AAAATATGA
1 AAAATAT-A
*
220284 AATAATTTA
1 AA-AATATA
220293 AAA
1 AAA
220296 TTAAATTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
7 7 0.16
8 25 0.57
9 8 0.18
10 4 0.09
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (8 bp):
AAAATATA
Found at i:220263 original size:23 final size:24
Alignment explanation
Indices: 220223--220280 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
220213 TAACGTGCAT
*
220223 AATTTAAATAAATAAAATATAAAA
1 AATTAAAATAAATAAAATATAAAA
220247 AATTAAAATAAAT-AAATATAAAA
1 AATTAAAATAAATAAAATATAAAA
*
220270 ATATAAAAATA
1 A-ATTAAAATA
220281 TGAAATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 11 0.35
24 20 0.65
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (24 bp):
AATTAAAATAAATAAAATATAAAA
Found at i:220644 original size:11 final size:11
Alignment explanation
Indices: 220628--220656 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
220618 TTTATAATTT
220628 AGTTAATATTA
1 AGTTAATATTA
220639 AGTTAATATTA
1 AGTTAATATTA
220650 AGTTAAT
1 AGTTAAT
220657 TTATGATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (11 bp):
AGTTAATATTA
Found at i:222992 original size:3 final size:3
Alignment explanation
Indices: 222984--223033 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
222974 AAAAAATTAA
222984 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
223032 AA
1 AA
223034 AATTGGGATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:223698 original size:34 final size:33
Alignment explanation
Indices: 223650--223870 Score: 264
Period size: 34 Copynumber: 6.5 Consensus size: 33
223640 TGGTAAAAAC
*
223650 CACCATTTAATCAACAATGGTAA-CTTATCAAAT
1 CACCATTTAATCAACAATGGTAAGC-TACCAAAT
* *
223683 CTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
223717 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
** *
223751 TTCTCATTTAATCAACAATGGTAAGCTATCAAAT
1 CAC-CATTTAATCAACAATGGTAAGCTACCAAAT
* * * * *
223785 CTCCCATTTAGTCAACAATGGCAAACCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
223819 CACTCATTTAATCAACAATGGTAAACTACCAAAT
1 CAC-CATTTAATCAACAATGGTAAGCTACCAAAT
223853 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
223871 TCTCCCACTT
Statistics
Matches: 161, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
33 19 0.12
34 140 0.87
35 2 0.01
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAGCTACCAAAT
Found at i:223794 original size:102 final size:101
Alignment explanation
Indices: 223650--223870 Score: 345
Period size: 102 Copynumber: 2.2 Consensus size: 101
223640 TGGTAAAAAC
* *
223650 CACCATTTAATCAACAATGGTAACTTATCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGTAACTTATCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
223715 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** *
223751 TTCTCATTTAATCAACAATGGTAAGC-TATCAAATCTCCCATTTAGTCAACAATGGCAAACCACC
1 CAC-CATTTAATCAACAATGGTAA-CTTATCAAATCTACCATTTAGTCAACAATGGCAAACCACC
*
223815 AAATCACTCATTTAATCAACAATGGTAAACTACCAAAT
64 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
223853 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
223871 TCTCCCACTT
Statistics
Matches: 108, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
101 16 0.15
102 91 0.84
103 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGTAACTTATCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:228325 original size:34 final size:33
Alignment explanation
Indices: 228277--228495 Score: 262
Period size: 34 Copynumber: 6.5 Consensus size: 33
228267 TGGTAAAAAC
*
228277 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
228310 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
228344 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
228378 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
228412 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
228446 CACCTATTTAATCAACAATGGTAAACTACCAAAT
1 CACC-ATTTAATCAACAATGGTAACCTACCAAAT
228480 CACCATTTAATCAACA
1 CACCATTTAATCAACA
228496 GATTATTATT
Statistics
Matches: 160, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 21 0.13
34 133 0.83
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:228393 original size:68 final size:67
Alignment explanation
Indices: 228279--228495 Score: 292
Period size: 68 Copynumber: 3.2 Consensus size: 67
228269 GTAAAAACCA
* * *
228279 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
228344 CAC
65 CAC
* * * *
228347 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
228412 CTC
65 CAC
* * * *
228415 CCATTTAGTCAACAATGGCAAACCACCAAATCACCTATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTACC-ATTTAATCAACAATGGTAAGCTACCAAAT
228480 CA-
65 CAC
228482 CCATTTAATCAACA
1 CCATTTAATCAACA
228496 GATTATTATT
Statistics
Matches: 130, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
67 16 0.12
68 114 0.88
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:228456 original size:102 final size:101
Alignment explanation
Indices: 228277--228495 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
228267 TGGTAAAAAC
* *
228277 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
228342 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
228378 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
*
228443 AATCACCTATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
228480 CACCATTTAATCAACA
1 CACCATTTAATCAACA
228496 GATTATTATT
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 14 0.13
102 91 0.87
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:228593 original size:63 final size:63
Alignment explanation
Indices: 228525--228667 Score: 205
Period size: 63 Copynumber: 2.3 Consensus size: 63
228515 TATCTTATAG
* *
228525 CAAATAATAAAAATTATCCTCTCCATTATCAATCGAAAAGTAATTTTATATCTTATAAGATAA
1 CAAATAATAAAAATTATCCTCTCCATTATCAATCGAAAAGTAATTTTATATCTTACAACATAA
* * * * * *
228588 CAAATAATAAAAATTATCCTCTCGATTGTTAATCGAAAGGTAATTTTATATTTTACGACATAA
1 CAAATAATAAAAATTATCCTCTCCATTATCAATCGAAAAGTAATTTTATATCTTACAACATAA
*
228651 CAAATAATTAAAATTAT
1 CAAATAATAAAAATTAT
228668 TTTTTAATTG
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (63 bp):
CAAATAATAAAAATTATCCTCTCCATTATCAATCGAAAAGTAATTTTATATCTTACAACATAA
Found at i:228880 original size:38 final size:38
Alignment explanation
Indices: 228838--229011 Score: 190
Period size: 38 Copynumber: 4.6 Consensus size: 38
228828 TTGAATTGGC
* * * *
228838 TGACGATTAGAAAATTTAATTTGAAATTAACTGACGGT
1 TGACGATTAGAGAATTCAATTTGAAATTGACTGACGAT
* * *
228876 TGACGGTTAGAGAATTCAATTTGAAATTGATTGGC-AGT
1 TGACGATTAGAGAATTCAATTTGAAATTGACTGACGA-T
* * *
228914 TGACAACTAGAGAATTCAATTTGAAATTGACTGA-GCAC
1 TGACGATTAGAGAATTCAATTTGAAATTGACTGACG-AT
* *
228952 TGACGATTAGAGAATTCAATTTGGAATTGGCTGACGAT
1 TGACGATTAGAGAATTCAATTTGAAATTGACTGACGAT
* *
228990 TGACGAGTAGAGAATTTAATTT
1 TGACGATTAGAGAATTCAATTT
229012 AGAATTGGTC
Statistics
Matches: 112, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
38 110 0.98
39 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (38 bp):
TGACGATTAGAGAATTCAATTTGAAATTGACTGACGAT
Found at i:228987 original size:114 final size:114
Alignment explanation
Indices: 228837--229056 Score: 273
Period size: 114 Copynumber: 1.9 Consensus size: 114
228827 ATTGAATTGG
* *
228837 CTGACGATTAGAAAATTTAATTTGAAATTAACTGACGGTTGACG-GTTAGAGAATTCAATTT-GA
1 CTGACGATTAGAAAATTCAATTTGAAATTAACTGACGATTGACGAG-TAGAGAATTCAATTTAG-
* * *
228900 AATTGATTGGCAGTTGACAACTAGAGAATTCAATTTGAAATTGACTGAGCA
64 AATTGATCGGCAGCTAACAACTAGAGAATTCAATTTGAAATTGACTGAGCA
* * ** *
228951 CTGACGATTAGAGAATTCAATTTGGAATTGGCTGACGATTGACGAGTAGAGAATTTAATTTAGAA
1 CTGACGATTAGAAAATTCAATTTGAAATTAACTGACGATTGACGAGTAGAGAATTCAATTTAGAA
* ** * *
229016 TTGGTCGGTGGCTAACGACTAGAGAATTCAATTTGGAATTG
66 TTGATCGGCAGCTAACAACTAGAGAATTCAATTTGAAATTG
229057 GCTGGTGACT
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
114 87 0.98
115 2 0.02
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (114 bp):
CTGACGATTAGAAAATTCAATTTGAAATTAACTGACGATTGACGAGTAGAGAATTCAATTTAGAA
TTGATCGGCAGCTAACAACTAGAGAATTCAATTTGAAATTGACTGAGCA
Found at i:228993 original size:76 final size:76
Alignment explanation
Indices: 228845--229060 Score: 215
Period size: 76 Copynumber: 2.8 Consensus size: 76
228835 GGCTGACGAT
* * * * * **
228845 TAGAAAATTTAATTTGAAATTAACTGA-CGGTTGACGGTTAGAGAATTCAATTTGAAATTGATTG
1 TAGAGAATTTAATTTGAAATTGACTGAGC-GCTGACGATTAGAGAATTCAATTTGGAATTGGCTG
*
228909 GCAGTTGACAAC
65 ACAGTTGACAAC
* *
228921 TAGAGAATTCAATTTGAAATTGACTGAGCACTGACGATTAGAGAATTCAATTTGGAATTGGCTGA
1 TAGAGAATTTAATTTGAAATTGACTGAGCGCTGACGATTAGAGAATTCAATTTGGAATTGGCTGA
* *
228986 C-GATTGACGAG
66 CAG-TTGACAAC
* * * * *
228997 TAGAGAATTTAATTT-AGAATTGGTCGGTG-GCTAACGACTAGAGAATTCAATTTGGAATTGGCT
1 TAGAGAATTTAATTTGA-AATT-GACTGAGCGCTGACGATTAGAGAATTCAATTTGGAATTGGCT
229060 G
64 G
229061 GTGACTAGGG
Statistics
Matches: 117, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
75 2 0.02
76 110 0.94
77 5 0.04
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (76 bp):
TAGAGAATTTAATTTGAAATTGACTGAGCGCTGACGATTAGAGAATTCAATTTGGAATTGGCTGA
CAGTTGACAAC
Found at i:233418 original size:38 final size:37
Alignment explanation
Indices: 233274--233420 Score: 134
Period size: 38 Copynumber: 3.9 Consensus size: 37
233264 GGCTTACTGT
* * *
233274 TAAAGAATTCAATTTGAAATTAGCTGGCGGCTGACGG-T
1 TAAAGAATTCAATTTGGAATTGGCTGGCGGCT-A-GGAC
* * *
233312 TAGAGAATTCAATTTGGAATTGGCTGGCAGCTGACGAC
1 TAAAGAATTCAATTTGGAATTGGCTGGCGGCT-AGGAC
* * * ** *
233350 TAGAGAATTCAATTTAGAATAGGCCAGTGGCTAGTGAC
1 TAAAGAATTCAATTTGGAATTGGCTGGCGGCTAG-GAC
*
233388 TAAAGAATTCAATTTGGAATTGGCTGGTGGCTA
1 TAAAGAATTCAATTTGGAATTGGCTGGCGGCTA
233421 AGGAATTCCA
Statistics
Matches: 89, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
37 2 0.02
38 87 0.98
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (37 bp):
TAAAGAATTCAATTTGGAATTGGCTGGCGGCTAGGAC
Found at i:234627 original size:19 final size:18
Alignment explanation
Indices: 234603--234665 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
234593 AAACAGTAAC
234603 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
234622 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
234635 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
234654 TGTATCGATACA
1 TGTATCGATACA
234666 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:234640 original size:13 final size:13
Alignment explanation
Indices: 234622--234646 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234612 ACATAAGTGT
234622 TGTATCGATACAA
1 TGTATCGATACAA
234635 TGTATCGATACA
1 TGTATCGATACA
234647 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:234644 original size:32 final size:32
Alignment explanation
Indices: 234603--234673 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
234593 AAACAGTAAC
234603 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
234635 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
234667 TGTATCG
1 TGTATCG
234674 CTACGAATCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:238570 original size:15 final size:15
Alignment explanation
Indices: 238550--238599 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
238540 GAAAATCGAA
238550 TTTAATTTAAATTAT
1 TTTAATTTAAATTAT
**
238565 TTTAATTTTATTTTAT
1 TTTAA-TTTAAATTAT
*
238581 TTAAATTTAAATTAT
1 TTTAATTTAAATTAT
238596 TTTA
1 TTTA
238600 TTATGCATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAATTTAAATTAT
Found at i:239193 original size:106 final size:106
Alignment explanation
Indices: 239070--239281 Score: 379
Period size: 106 Copynumber: 2.0 Consensus size: 106
239060 GCTAATCTAT
* *
239070 CATCAAAACAACGTGTCGCTTAGTTTGAACACAAATTTAATATTATAGACATTAAATTTTTTAAA
1 CATCAAAACAACGTGTCGCTTAATTTGAACACAAATTTAATATTATAGACATTAAATTCTTTAAA
*
239135 ATTAAAATAAATTAAAATTATTTTTATTCATAAGTCGATCA
66 ATTAAAATAAATTAAAATTATTTTTATTCACAAGTCGATCA
* *
239176 CATCAAAATAACGTGTCGCTTAATTTGAACACAAATTTAATATTATAGAGATTAAATTCTTTAAA
1 CATCAAAACAACGTGTCGCTTAATTTGAACACAAATTTAATATTATAGACATTAAATTCTTTAAA
239241 ATTAAAATAAATTAAAATTATTTTTATTCACAAGTCGATCA
66 ATTAAAATAAATTAAAATTATTTTTATTCACAAGTCGATCA
239282 TTTAAATAGT
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 101 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (106 bp):
CATCAAAACAACGTGTCGCTTAATTTGAACACAAATTTAATATTATAGACATTAAATTCTTTAAA
ATTAAAATAAATTAAAATTATTTTTATTCACAAGTCGATCA
Found at i:240179 original size:2 final size:2
Alignment explanation
Indices: 240135--240169 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
240125 AATCTTTCCC
240135 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
240170 AAACTATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:240769 original size:22 final size:22
Alignment explanation
Indices: 240741--240784 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
240731 AATAAATATT
240741 AAATATA-ATTTATAATTAATAA
1 AAATATATATTTA-AATTAATAA
*
240763 AAATATATATTTAATTTAATAA
1 AAATATATATTTAAATTAATAA
240785 TATTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATATATATTTAAATTAATAA
Found at i:241318 original size:2 final size:2
Alignment explanation
Indices: 241306--241336 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
241296 ATAATTCTTC
*
241306 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
241337 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:242564 original size:2 final size:2
Alignment explanation
Indices: 242557--242594 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
242547 TGATTAGCAT
* *
242557 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
242595 AAAGAGAGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:243503 original size:20 final size:22
Alignment explanation
Indices: 243466--243507 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
243456 CCCATTGCTA
*
243466 TTATGACATATAGTTGTATATT
1 TTATGACATAAAGTTGTATATT
243488 TTATGA-ATAAAG-TGTATATT
1 TTATGACATAAAGTTGTATATT
243508 AATAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (22 bp):
TTATGACATAAAGTTGTATATT
Found at i:246008 original size:3 final size:3
Alignment explanation
Indices: 246002--246036 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
245992 GGTTTTTTTT
246002 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
246037 TTTAATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:246061 original size:14 final size:14
Alignment explanation
Indices: 246042--246088 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
246032 ATAATTTTAA
246042 TTTTAAAATAA-ATT
1 TTTTAAAA-AATATT
246056 TTTTAAAAAATATT
1 TTTTAAAAAATATT
246070 TTTTAAAAAATATT
1 TTTTAAAAAATATT
246084 TTTTA
1 TTTTA
246089 TGAATATATC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 2 0.06
14 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTAAAAAATATT
Found at i:246704 original size:22 final size:21
Alignment explanation
Indices: 246679--246735 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
246669 ATATTTAAAG
*
246679 TTATTTTATTTTAAGATATAAT
1 TTATTTTATTTTAAAAT-TAAT
246701 TTATTTTTATTTATAAAATTAAT
1 TTA-TTTTATTT-TAAAATTAAT
* *
246724 ATAATTTATTTT
1 TTATTTTATTTT
246736 TATTTGATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 1 0.03
22 10 0.33
23 14 0.47
24 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATTTTATTTTAAAATTAAT
Found at i:247127 original size:16 final size:17
Alignment explanation
Indices: 247106--247141 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
247096 TTTTAGATAG
247106 TTTAAAGT-TATTTTAT
1 TTTAAAGTATATTTTAT
*
247122 TTTAAAGTATGTTTTAT
1 TTTAAAGTATATTTTAT
247139 TTT
1 TTT
247142 TATTTATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (17 bp):
TTTAAAGTATATTTTAT
Found at i:247719 original size:15 final size:15
Alignment explanation
Indices: 247690--247718 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
247680 CTTTTGTTAT
247690 TTTTTTAATTTAAAA
1 TTTTTTAATTTAAAA
247705 TTTTTT-ATTTAAAA
1 TTTTTTAATTTAAAA
247719 AACATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTAATTTAAAA
Found at i:247879 original size:125 final size:125
Alignment explanation
Indices: 247686--248041 Score: 391
Period size: 132 Copynumber: 2.8 Consensus size: 125
247676 ATTTCTTTTG
* * * *
247686 TTATTTTTTTAATTTAAAATTTTTTATTTAAAAAACATAATAAATAATATTTTAA-TTGTTAATT
1 TTATTTTTTTAATTT-AAA-TTTTT-TTT-AAAAATATAATAATTAATATTTTAATTTATTAATA
* *
247750 TAAATTTTTTAAACTTAA-TAAATATTATGTTTTATTTCGGTAAAAAATTATAAT-AAAA-CCTT
62 TAAATTTTTTAAACTTAAGTAAATATTAT-TTTTATTTCAGTAAAAAATAATAATAAAAACCCTT
* *
247812 TTCATTTTTTTAATTTAAATTTTTTTTAAAAATATAAGAATTAATATTTTAAATTTTTTAATATA
1 TT-ATTTTTTTAATTTAAATTTTTTTTAAAAATATAATAATTAATATTTT-AATTTATTAATATA
* * *
247877 AATTTTTT-AACGTAAGTAAATATCTTATTTTTATTTTATTAAAAAATAATAATAAAAAAGCCCT
64 AATTTTTTAAACTTAAGTAAATA--TTATTTTTATTTCAGTAAAAAATAATAAT-AAAAA-CCCT
247941 T
125 T
** *
247942 TTATTTGTTAATTAAATTTTTA-TTTTTTTAAAAATATAATAATTAATATTTTAATTTATTAATG
1 TTATTT-TT--TT-AATTTAAATTTTTTTTAAAAATATAATAATTAATATTTTAATTTATTAATA
*
248006 TAAATTTTTTTAAACTTAATTAAATATTATTTTTAT
62 TAAA-TTTTTTAAACTTAAGTAAATATTATTTTTAT
248042 GAAAAAAATA
Statistics
Matches: 197, Mismatches: 17, Indels: 27
0.82 0.07 0.11
Matches are distributed among these distances:
123 20 0.10
124 11 0.06
125 28 0.14
126 26 0.13
127 17 0.09
128 4 0.02
129 4 0.02
130 8 0.04
131 24 0.12
132 37 0.19
133 18 0.09
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (125 bp):
TTATTTTTTTAATTTAAATTTTTTTTAAAAATATAATAATTAATATTTTAATTTATTAATATAAA
TTTTTTAAACTTAAGTAAATATTATTTTTATTTCAGTAAAAAATAATAATAAAAACCCTT
Found at i:248096 original size:27 final size:27
Alignment explanation
Indices: 248037--248099 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
248027 AAATATTATT
*
248037 TTTATGAAAAAAATAATTAATACATTA
1 TTTATTAAAAAAATAATTAATACATTA
248064 TTTATTAAAAAAATAATTAATACATTA
1 TTTATTAAAAAAATAATTAATACATTA
248091 TTTATTAAA
1 TTTATTAAA
248100 TTTTTTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (27 bp):
TTTATTAAAAAAATAATTAATACATTA
Found at i:248334 original size:9 final size:10
Alignment explanation
Indices: 248309--248362 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
248299 CTTACATAAT
*
248309 TAAATAAAAA
1 TAAATTAAAA
248319 TAAATTAAAA
1 TAAATTAAAA
248329 -AAATT-AAA
1 TAAATTAAAA
* *
248337 TTAATT-ATA
1 TAAATTAAAA
*
248346 TAAATAAAAA
1 TAAATTAAAA
248356 TAAATTA
1 TAAATTA
248363 TACCTTAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
8 3 0.09
9 15 0.43
10 17 0.49
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TAAATTAAAA
Found at i:248336 original size:14 final size:15
Alignment explanation
Indices: 248306--248340 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
248296 AAACTTACAT
248306 AATTAAATAAAAATA
1 AATTAAATAAAAATA
*
248321 AATTAAA-AAAATTA
1 AATTAAATAAAAATA
248335 AATTAA
1 AATTAA
248341 TTATATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATTAAATAAAAATA
Found at i:248361 original size:19 final size:19
Alignment explanation
Indices: 248309--248364 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
248299 CTTACATAAT
*
248309 TAAATAAAAATAAATTAAA
1 TAAATAAAAATAAATTATA
* * *
248328 AAAAT-TAAATTAATTATA
1 TAAATAAAAATAAATTATA
248346 TAAATAAAAATAAATTATA
1 TAAATAAAAATAAATTATA
248365 CCTTAAAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAATAAAAATAAATTATA
Found at i:248779 original size:22 final size:24
Alignment explanation
Indices: 248726--248786 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 24
248716 ATAATTACTA
*
248726 TTTTAAGTT-ATT-AATATATATT
1 TTTTAATTTAATTAAATATATATT
248748 TTTTAAATTTAATTAAATAT-TATT
1 TTTT-AATTTAATTAAATATATATT
*
248772 TTTT-ATTTTATTAAA
1 TTTTAATTTAATTAAA
248787 AAACTCAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 14 0.41
23 4 0.12
24 11 0.32
25 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTAATTTAATTAAATATATATT
Found at i:248781 original size:23 final size:24
Alignment explanation
Indices: 248724--248786 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 24
248714 TAATAATTAC
248724 TATTTTAAGTTATTAATATATATTTTT
1 TATTTTAA-TTA--AATATATATTTTT
*
248751 TAAATTTAATTAAATAT-TATTTTT
1 T-ATTTTAATTAAATATATATTTTT
248775 TATTTT-ATTAAA
1 TATTTTAATTAAA
248787 AAACTCAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 6 0.18
23 4 0.12
24 8 0.24
25 5 0.15
27 4 0.12
28 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TATTTTAATTAAATATATATTTTT
Found at i:249452 original size:13 final size:14
Alignment explanation
Indices: 249428--249461 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
249418 AACTTGCATA
249428 ATATTATTTATTTT
1 ATATTATTTATTTT
249442 ATATT-TTTATTTT
1 ATATTATTTATTTT
*
249455 ATTTTAT
1 ATATTAT
249462 ATTGATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
ATATTATTTATTTT
Found at i:252680 original size:15 final size:15
Alignment explanation
Indices: 252660--252694 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
252650 AACCATCAAA
252660 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
252675 GATGATGATGATAAT
1 GATGATGAAGATAAT
252690 GATGA
1 GATGA
252695 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:256656 original size:17 final size:17
Alignment explanation
Indices: 256636--256685 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
256626 TATTTTTACT
*
256636 TAACCTCTTAACAAAAC
1 TAACCTCTTGACAAAAC
* *
256653 TAACCTTTTGATAAAAC
1 TAACCTCTTGACAAAAC
256670 TAACCTCTTGACAAAA
1 TAACCTCTTGACAAAA
256686 GTAGGTTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.44, C:0.24, G:0.04, T:0.28
Consensus pattern (17 bp):
TAACCTCTTGACAAAAC
Found at i:259118 original size:13 final size:13
Alignment explanation
Indices: 259100--259126 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
259090 ATATTATGCT
259100 TTGTATCGATACA
1 TTGTATCGATACA
259113 TTGTATCGATACA
1 TTGTATCGATACA
259126 T
1 T
259127 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:259135 original size:19 final size:19
Alignment explanation
Indices: 259111--259167 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
259101 TGTATCGATA
*
259111 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGAT
*
259130 CATTGTATCGATACATAAT
1 CATTGTATCGATACATGAT
259149 CAATTGTATCGATACATGA
1 C-ATTGTATCGATACATGA
259168 AAATAGTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:261939 original size:22 final size:23
Alignment explanation
Indices: 261914--261963 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
261904 TATTCTCTAC
*
261914 TTATTTAATTGTACTTTAT-TTT
1 TTATTTAATTATACTTTATATTT
* * *
261936 TTATATATTTATATTTTATATTT
1 TTATTTAATTATACTTTATATTT
261959 TTATT
1 TTATT
261964 ACGATAAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (23 bp):
TTATTTAATTATACTTTATATTT
Found at i:261946 original size:15 final size:15
Alignment explanation
Indices: 261928--261963 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
261918 TTAATTGTAC
261928 TTTATTTTTTATATA
1 TTTATTTTTTATATA
* *
261943 TTTATATTTTATATT
1 TTTATTTTTTATATA
261958 TTTATT
1 TTTATT
261964 ACGATAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTTTTTATATA
Found at i:262018 original size:6 final size:7
Alignment explanation
Indices: 262000--262026 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
261990 ATAAATTTAA
262000 TAAAAAT
1 TAAAAAT
262007 TAAAAAT
1 TAAAAAT
262014 TAAAAAT
1 TAAAAAT
262021 TAAAAA
1 TAAAAA
262027 GCATTTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
TAAAAAT
Found at i:263141 original size:32 final size:32
Alignment explanation
Indices: 263093--263153 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
263083 AGTCAACAAC
* * *
263093 CTGAATCCGAACTGACTCAAACTCGAAATGAT
1 CTGAATCCAAAATGACTCAAACCCGAAATGAT
*
263125 CTGAATCCAAAATGACTCGAACCCGAAAT
1 CTGAATCCAAAATGACTCAAACCCGAAAT
263154 AATTTGAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20
Consensus pattern (32 bp):
CTGAATCCAAAATGACTCAAACCCGAAATGAT
Found at i:263153 original size:16 final size:16
Alignment explanation
Indices: 263099--263222 Score: 56
Period size: 16 Copynumber: 7.8 Consensus size: 16
263089 CAACCTGAAT
* *
263099 CCGAACTGACTCAAAC
1 CCGAAATGACTCGAAC
* *
263115 TCGAAATGA-TCTGAAT
1 CCGAAATGACTC-GAAC
*
263131 CCAAAATGACTCGAAC
1 CCGAAATGACTCGAAC
* * *
263147 CCGAAATAATTTGAAC
1 CCGAAATGACTCGAAC
** *
263163 TTGAAATAAC-CTGAAC
1 CCGAAATGACTC-GAAC
* * *
263179 CCGAAATGACCCAAAT
1 CCGAAATGACTCGAAC
* *
263195 TCGAAATGAC-CTAAAC
1 CCGAAATGACTC-GAAC
263211 CCGAAATGACTC
1 CCGAAATGACTC
263223 AAATAATTAA
Statistics
Matches: 79, Mismatches: 23, Indels: 11
0.70 0.20 0.10
Matches are distributed among these distances:
15 3 0.04
16 72 0.91
17 4 0.05
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.19
Consensus pattern (16 bp):
CCGAAATGACTCGAAC
Found at i:263201 original size:32 final size:32
Alignment explanation
Indices: 263165--263226 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
263155 ATTTGAACTT
*
263165 GAAATAACCTGAACCCGAAATGACCCAAATTC
1 GAAATAACCTAAACCCGAAATGACCCAAATTC
* *
263197 GAAATGACCTAAACCCGAAATGACTCAAAT
1 GAAATAACCTAAACCCGAAATGACCCAAAT
263227 AATTAACCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.45, C:0.26, G:0.13, T:0.16
Consensus pattern (32 bp):
GAAATAACCTAAACCCGAAATGACCCAAATTC
Found at i:264346 original size:15 final size:15
Alignment explanation
Indices: 264324--264364 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
264314 GAAAATTTTA
264324 TAACTTAAAATAACC
1 TAACTTAAAATAACC
* *
264339 TAATTTAAAATAATC
1 TAACTTAAAATAACC
264354 TAACTTAAAAT
1 TAACTTAAAAT
264365 CAACTTGACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (15 bp):
TAACTTAAAATAACC
Found at i:265146 original size:23 final size:24
Alignment explanation
Indices: 265120--265167 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
265110 AAAATTATTT
*
265120 AATTAATT-AAATCAATAGATTAA
1 AATTAATTAAAATCAACAGATTAA
*
265143 AATTAATTAAAATCAACCGATTAA
1 AATTAATTAAAATCAACAGATTAA
265167 A
1 A
265168 TAAAGCCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.31
Consensus pattern (24 bp):
AATTAATTAAAATCAACAGATTAA
Found at i:266253 original size:31 final size:31
Alignment explanation
Indices: 266218--266288 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
266208 CAAATTATCC
*
266218 AAAATCAATA-TTAAGTGATAAAATTAAATTA
1 AAAATCAA-AGTTAAGAGATAAAATTAAATTA
*
266249 AAAATCAAAGTTAAGAGATAAAATTTAATTA
1 AAAATCAAAGTTAAGAGATAAAATTAAATTA
*
266280 GAAATCAAA
1 AAAATCAAA
266289 TTTTAGTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.28
Consensus pattern (31 bp):
AAAATCAAAGTTAAGAGATAAAATTAAATTA
Found at i:268017 original size:14 final size:14
Alignment explanation
Indices: 267998--268032 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
267988 TAGATTGAGA
*
267998 TTTTATATATTATT
1 TTTTATATATAATT
*
268012 TTTTATTTATAATT
1 TTTTATATATAATT
268026 TTTTATA
1 TTTTATA
268033 CGTTAATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATATATAATT
Found at i:268053 original size:2 final size:2
Alignment explanation
Indices: 268046--268086 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
268036 TAATAATTAT
* *
268046 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA GA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
268087 AATTATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 33 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:268126 original size:25 final size:25
Alignment explanation
Indices: 268078--268142 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
268068 TATATGAGAT
*
268078 TTATATATAAATTATGAAAATTATAA
1 TTATAAAT-AATTATGAAAATTATAA
* * *
268104 TTATAAATAATTATTAAATTTATAT
1 TTATAAATAATTATGAAAATTATAA
268129 TTA-ATAATAATTAT
1 TTATA-AATAATTAT
268143 AATAATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.03
25 26 0.76
26 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
TTATAAATAATTATGAAAATTATAA
Found at i:269430 original size:121 final size:123
Alignment explanation
Indices: 269271--269530 Score: 380
Period size: 136 Copynumber: 2.0 Consensus size: 123
269261 TATATATATA
269271 TATATAAAACTAACATCACCTCTATTTGCAGC-TATATATATATAACTAACAT-AAGATGTTATT
1 TATATAAAACTAACATCACCTCTATTTGCAGCATATATATATATAACTAACATAAAGATGTTATT
269334 TCTATAAGAAATTAATTAAATAAATCATAAAATTGTTGAGTTATAACGTTCTAACATG
66 TCTATAAGAAATTAATTAAATAAATCATAAAATTGTTGAGTTATAACGTTCTAACATG
269392 TATATAAAACTAACATCACCTCTATTTGCAGCTATATATATATATATATATATATATAACTAACA
1 TATATAAAACTAACATCACCTCTATTTGCAGC-------------ATATATATATATAACTAACA
*
269457 TAAAGATGTTATTTCTATAAGAAATTAATTAAATAAATCATAAAATTGTTTAGTTATAACGTTCT
53 TAAAGATGTTATTTCTATAAGAAATTAATTAAATAAATCATAAAATTGTTGAGTTATAACGTTCT
269522 AACATG
118 AACATG
269528 TAT
1 TAT
269531 GGAGAATATA
Statistics
Matches: 123, Mismatches: 1, Indels: 15
0.88 0.01 0.11
Matches are distributed among these distances:
121 32 0.26
135 20 0.16
136 71 0.58
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (123 bp):
TATATAAAACTAACATCACCTCTATTTGCAGCATATATATATATAACTAACATAAAGATGTTATT
TCTATAAGAAATTAATTAAATAAATCATAAAATTGTTGAGTTATAACGTTCTAACATG
Found at i:269431 original size:2 final size:2
Alignment explanation
Indices: 269424--269449 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
269414 TATTTGCAGC
269424 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
269450 ACTAACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:272317 original size:2 final size:2
Alignment explanation
Indices: 272310--272343 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
272300 GGTGAGATCA
*
272310 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
272344 TTAAACAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:272521 original size:21 final size:21
Alignment explanation
Indices: 272495--272548 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
272485 TTTTTGTATA
272495 CATGTATCGATACATGCCTTC
1 CATGTATCGATACATGCCTTC
272516 CATGTATCGATACATGCCTTC
1 CATGTATCGATACATGCCTTC
272537 CATGTATCGATA
1 CATGTATCGATA
272549 TAAGGTCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (21 bp):
CATGTATCGATACATGCCTTC
Found at i:272612 original size:21 final size:21
Alignment explanation
Indices: 272588--272640 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
272578 TTTTATAATT
*
272588 TGTATTGATACAATAAGTTAA
1 TGTATTGATACAATAAGTGAA
*
272609 TGTATCGATAC-ATAAGTGAA
1 TGTATTGATACAATAAGTGAA
* *
272629 TATATTGGTACA
1 TGTATTGATACA
272641 TGCTTGTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.36
Consensus pattern (21 bp):
TGTATTGATACAATAAGTGAA
Found at i:274865 original size:166 final size:165
Alignment explanation
Indices: 274685--275079 Score: 399
Period size: 165 Copynumber: 2.4 Consensus size: 165
274675 TTCAAACATC
* * * * *
274685 AAAATTCTTCAAATATTATCATTTAACTCCCA-TCAAATCATTTTTGAAAAATTCCTT-TTATTT
1 AAAATTCATCAAATATTATTATTTAACTCACAGT-AAATCATTTTTGAAAAATTCATTCAT-TTT
* * * * * * * *
274748 C-TTAAGTTATTGATTTTTTTTTGGAATTCTTCATGTTTTCAAATTACGGGGTTTTCTTCTTCGT
64 CATTAA-TTATTCATTTTTCTTTGAAATTC-TCATATTTTCAAAATACAGAGTTTTCTACTTCGT
* * *
274812 AAATTTTTTTGGGAGG-CT-TTTCATAGGTTTTTAAG-TTTT
127 AAATTTTTTCGGG-GGAATATTTC-TAGGCTTTT-AGTTTTT
** * *
274851 AAAATTCATCAAATATTATTATTTATTTCATAGTAAATCATTTTTTAAAAATTCATTCATTTTCA
1 AAAATTCATCAAATATTATTATTTAACTCACAGTAAATCATTTTTGAAAAATTCATTCATTTTCA
* * * * *
274916 TTCATTTTTCATTTTTCTTTGAAATTCTCTTATTTTCAAAATATAGAGTTTTCTACTTTGTAAAT
66 TTAATTATTCATTTTTCTTTGAAATTCTCATATTTTCAAAATACAGAGTTTTCTACTTCGTAAAT
*
274981 TTTTTCGGGGGAATATTTCTTGGCTTTTAGTTTTT
131 TTTTTCGGGGGAATATTTCTAGGCTTTTAGTTTTT
** * *
275016 AAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTT-AAAAATTCATTCATTTTC
1 AAAATTCATCAAATATTATTATTTAACTCACAGTAAATCA-TTTTTGAAAAATTCATTCATTTTC
275080 TTTTTTTTCC
Statistics
Matches: 195, Mismatches: 27, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
164 4 0.02
165 107 0.55
166 79 0.41
167 5 0.03
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (165 bp):
AAAATTCATCAAATATTATTATTTAACTCACAGTAAATCATTTTTGAAAAATTCATTCATTTTCA
TTAATTATTCATTTTTCTTTGAAATTCTCATATTTTCAAAATACAGAGTTTTCTACTTCGTAAAT
TTTTTCGGGGGAATATTTCTAGGCTTTTAGTTTTT
Found at i:275134 original size:155 final size:160
Alignment explanation
Indices: 274847--275210 Score: 402
Period size: 155 Copynumber: 2.3 Consensus size: 160
274837 GGTTTTTAAG
* *
274847 TTTTAAAATTCATCAAATATTATTATTTATTTCATAGTAAATCATTTTTTAAAAATTCATTCATT
1 TTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTTAAAAATTCATTCA-T
* * * * * **
274912 TTCATTCATTTTTCATTTTTCTTTGAAATTCTCTTATTTTCAAAATATAGAGTTTTCTACTTTGT
65 TT-ATTC--TTTT-ATTTTTCCTTGAAATTCTCCTATTTCCAAAAAATAGAGTTTTCTAATCCGT
* * *
274977 AAAT-TTTTTCG-GGGGAATATTTCTTGGCTTT-TAGT
126 AAATATTTTT-GAGGGG-ATATTTCTTAG-TTTAAAAT
275012 TTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTTAAAAATTCATTCA-T
1 TTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTTAAAAATTCATTCATT
* *
275076 T-TTC-TTT-TTTTTCCTTGAAATTTTCCTATTTCCAAAAAATCGA-TTTTCTAATCCGTAAATA
66 TATTCTTTTATTTTTCCTTGAAATTCTCCTATTTCCAAAAAATAGAGTTTTCTAATCCGTAAATA
* *
275137 TTTTTGAGGGGATTTTTTTTAGTTTAAAAT
131 TTTTTGAGGGGATATTTCTTAGTTTAAAAT
* * * * * *
275167 TTTTAAAATTCATCTACTATTGTTATTAAATTCACATTAAATCA
1 TTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATCA
275211 AATTTGAAAA
Statistics
Matches: 174, Mismatches: 22, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
154 3 0.02
155 63 0.36
156 39 0.22
158 3 0.02
161 3 0.02
163 2 0.01
165 61 0.35
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (160 bp):
TTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTTAAAAATTCATTCATT
TATTCTTTTATTTTTCCTTGAAATTCTCCTATTTCCAAAAAATAGAGTTTTCTAATCCGTAAATA
TTTTTGAGGGGATATTTCTTAGTTTAAAAT
Found at i:275408 original size:13 final size:15
Alignment explanation
Indices: 275390--275421 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
275380 TTTAATTTTA
275390 AATTTATTT-TA-TT
1 AATTTATTTATATTT
275403 AATTTATTTATATTT
1 AATTTATTTATATTT
275418 AATT
1 AATT
275422 GGCTAAGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATTTATTTATATTT
Found at i:275772 original size:21 final size:21
Alignment explanation
Indices: 275748--275789 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
275738 GAGAAACAGA
275748 GAGAAAGAAA-AGAAAGAAAAT
1 GAGAAA-AAATAGAAAGAAAAT
*
275769 GAGAAAAAATAGAGAGAAAAT
1 GAGAAAAAATAGAAAGAAAAT
275790 TGAAAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (21 bp):
GAGAAAAAATAGAAAGAAAAT
Found at i:279998 original size:13 final size:13
Alignment explanation
Indices: 279980--280004 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
279970 CTATTTATGA
279980 TGTATCGATACAC
1 TGTATCGATACAC
279993 TGTATCGATACA
1 TGTATCGATACA
280005 TGAATAGTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:280056 original size:14 final size:14
Alignment explanation
Indices: 280033--280063 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
280023 GATTTTTAAC
280033 GATACATGAATAGT
1 GATACATGAATAGT
*
280047 GATACGTGAATAGT
1 GATACATGAATAGT
280061 GAT
1 GAT
280064 GAACAGTGAA
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:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (14 bp):
GATACATGAATAGT
Found at i:280160 original size:53 final size:53
Alignment explanation
Indices: 280096--280232 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
280086 CTACTACCAA
280096 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
280149 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCTAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
280202 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
280233 TATGCAATCT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:280265 original size:20 final size:20
Alignment explanation
Indices: 280202--280272 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
280192 GCTAATGTCC
**
280202 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
280222 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
280242 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
280262 TGTATCGATAC
1 TGTATCGATAC
280273 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:280338 original size:21 final size:21
Alignment explanation
Indices: 280312--280352 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
280302 GTCAACCTTG
280312 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
280333 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
280353 TTTTACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:286615 original size:20 final size:20
Alignment explanation
Indices: 286590--286734 Score: 103
Period size: 20 Copynumber: 6.8 Consensus size: 20
286580 TTTTCACAAT
286590 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
286610 TTGTATCGATACATTCTGGGTTTTACCCA
1 TTGTATCGATACA-T-T--G--TT---CA
* *
286639 GATGTATCGATACATGGTTCA
1 -TTGTATCGATACATTGTTCA
* *
286660 TTATATCGATACATTTTTCA
1 TTGTATCGATACATTGTTCA
* * *
286680 ATGTATTGATACATGGTTCA
1 TTGTATCGATACATTGTTCA
*
286700 TTATATCGATACAATT-TTCA
1 TTGTATCGATAC-ATTGTTCA
*
286720 ATGTATCGATACATT
1 TTGTATCGATACATT
286735 CAGGCATTTT
Statistics
Matches: 97, Mismatches: 17, Indels: 23
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.03
20 67 0.69
21 5 0.05
22 1 0.01
24 3 0.03
26 3 0.03
29 3 0.03
30 12 0.12
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:286695 original size:40 final size:40
Alignment explanation
Indices: 286640--286733 Score: 170
Period size: 40 Copynumber: 2.4 Consensus size: 40
286630 TTTTACCCAG
*
286640 ATGTATCGATACATGGTTCATTATATCGATACATTTTTCA
1 ATGTATCGATACATGGTTCATTATATCGATACAATTTTCA
*
286680 ATGTATTGATACATGGTTCATTATATCGATACAATTTTCA
1 ATGTATCGATACATGGTTCATTATATCGATACAATTTTCA
286720 ATGTATCGATACAT
1 ATGTATCGATACAT
286734 TCAGGCATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (40 bp):
ATGTATCGATACATGGTTCATTATATCGATACAATTTTCA
Found at i:289173 original size:47 final size:48
Alignment explanation
Indices: 289096--289194 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 48
289086 AATCCCGTTA
* * * *
289096 TTTCTGAGGGGATACTCAAACCTCGGTTTTATTTCTAAAACACCAATT
1 TTTCTGAGGGGATACTCAAACCCCGATTTTATTCCCAAAACACCAATT
* *
289144 TTTC-GAGGGGATACTCCAACCCCGATTTTATTCCCAAAACATCAATT
1 TTTCTGAGGGGATACTCAAACCCCGATTTTATTCCCAAAACACCAATT
289191 TTTC
1 TTTC
289195 ACAATCGGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
47 41 0.91
48 4 0.09
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (48 bp):
TTTCTGAGGGGATACTCAAACCCCGATTTTATTCCCAAAACACCAATT
Found at i:289249 original size:126 final size:128
Alignment explanation
Indices: 289023--289355 Score: 492
Period size: 126 Copynumber: 2.6 Consensus size: 128
289013 TTTTTCATCT
* * * *
289023 CGGGGATACTCCAACCCC-AGTTTTATTCTCAAAACACCAAATTTTCATAATCGGGGATACTCAA
1 CGGGGATACTCCAACCCCGA-TTTTATTCCCAAAACACCAATTTTTCACAATCGGGGATACTCCA
* * *
289087 ATCCCGTTATTTCTGAGGGGATACTCAAACCTCGGTTTTATTTCTAAAACACCAATTTTTCG-A
65 ACCCCGTTATTTCTGAGGGGATAATCAAACCCCGGTTTTATTTCTAAAACACCAATTTTTCGAA
* *
289150 -GGGGATACTCCAACCCCGATTTTATTCCCAAAACATCAATTTTTCACAATCGGGGATGCTCCAA
1 CGGGGATACTCCAACCCCGATTTTATTCCCAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* *
289214 CCCCGTTATTTCTGAGGGGATAATCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCGCAA
66 CCCCGTTATTTCTGAGGGGATAATCAAACCCCGGTTTTATTTCTAAAACACCAATTTTTCG-AA
* * *
289278 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTTCA
1 -CGGGGATACTCCAACCCCGATTTTATTCCCAAAACACCAATTTTTCACAATCGGGGATACTCCA
289343 ACCCCGTTATTTC
65 ACCCCGTTATTTC
289356 ATCGGAGATA
Statistics
Matches: 185, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
126 112 0.61
127 1 0.01
128 1 0.01
130 71 0.38
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (128 bp):
CGGGGATACTCCAACCCCGATTTTATTCCCAAAACACCAATTTTTCACAATCGGGGATACTCCAA
CCCCGTTATTTCTGAGGGGATAATCAAACCCCGGTTTTATTTCTAAAACACCAATTTTTCGAA
Found at i:289305 original size:51 final size:51
Alignment explanation
Indices: 289229--289455 Score: 210
Period size: 51 Copynumber: 4.4 Consensus size: 51
289219 TTATTTCTGA
* * * * *
289229 GGGGATAATCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCGCAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
*
289280 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
* * * * * *** *
289331 GGGGATACTTCAACCCCG---TTATTTCATCGGAGATACTCCAACCCTGTT-ATTTTT
1 GGGGATACTCCAACCCCGATTTTATTTC--C--A-AAACACCAA--TTTTTCACAATC
289385 GAGAGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
1 G-G-GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
289438 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
289456 TTATTTCTGA
Statistics
Matches: 138, Mismatches: 25, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
48 7 0.05
50 1 0.01
51 77 0.56
52 5 0.04
53 10 0.07
54 10 0.07
55 5 0.04
56 15 0.11
57 1 0.01
59 7 0.05
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
Found at i:289365 original size:28 final size:28
Alignment explanation
Indices: 289328--289404 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
289318 ATTTTTCACA
* *
289328 ATCGGGGATACTTCAACCCCGTTATTTC
1 ATCGGAGATACTCCAACCCCGTTATTTC
*
289356 ATCGGAGATACTCCAACCCTGTTATTT-
1 ATCGGAGATACTCCAACCCCGTTATTTC
*
289383 -TTGAGAGGATACTCCAACCCCG
1 ATCG-GA-GATACTCCAACCCCG
289405 ATTTTATTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
27 2 0.05
28 38 0.90
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (28 bp):
ATCGGAGATACTCCAACCCCGTTATTTC
Found at i:289473 original size:107 final size:107
Alignment explanation
Indices: 289282--289478 Score: 342
Period size: 107 Copynumber: 1.8 Consensus size: 107
289272 TCGCAATCGG
* *
289282 GGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTTCAACCC
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCC
*
289347 CGTTATTTCATCGGAGATACTCCAACCCTGTTATTTTTGAGA
66 CGTTATTTCATAGGAGATACTCCAACCCTGTTATTTTTGAGA
289389 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCC
*
289454 CGTTATTTC-TGAGGGGATACTCCAA
66 CGTTATTTCAT-AGGAGATACTCCAA
289479 TCTGAGTTTT
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
106 1 0.01
107 84 0.99
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (107 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCC
CGTTATTTCATAGGAGATACTCCAACCCTGTTATTTTTGAGA
Found at i:289581 original size:79 final size:79
Alignment explanation
Indices: 289143--289587 Score: 383
Period size: 79 Copynumber: 5.6 Consensus size: 79
289133 AAACACCAAT
* * * *
289143 TTTTCGAGGGGATACTCCAACCCCGATTTTATTCCCAAAACATCAATTTTTCACAATCGGGGATG
1 TTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATA
289208 CTCCAACCCCGTTA
66 CTCCAACCCCGTTA
* * * *
289222 -TTTCTGAGGGGATAATCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCGCAATCGGGGAT
1 TTTTC-GAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGAT
* *
289286 ACTCCAACTCCGATTT
65 ACTCCAACCCCG-TTA
* * * * * * *** * ** **
289302 TATTTCCA----AAACACCAATTTTTCACAATCGGGGA-TACTTCAAC-CCCGTTATTT--C-AT
1 T-TTTCGAGGGGATACTCCAA----CCCCGAT--TTTATTTCTAAAACACCAATT-TTTCACAAT
* *
289358 CGGAGATACTCCAACCCTGTTA
58 CGGGGATACTCCAACCCCGTTA
* * *
289380 TTTTTGAGAGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATA
1 TTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATA
289445 CTCCAACCCCGTTA
66 CTCCAACCCCGTTA
* * *
289459 -TTTCTGAGGGGATACTCCAA-TCTGAGTTTTATTTCTAAAACACCGATTTTTCACAATCGGGGA
1 TTTTC-GAGGGGATACTCCAACCCCGA-TTTTATTTCTAAAACACCAATTTTTCACAATCGGGGA
289522 TACTCCAACCCCGTTA
64 TACTCCAACCCCGTTA
* * *
289538 TTTTCAAGGGGATACTCCAACCCCGATTTTATTTCTAGAACACCGATTTT
1 TTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTT
289588 CCATAGTCAG
Statistics
Matches: 283, Mismatches: 59, Indels: 48
0.73 0.15 0.12
Matches are distributed among these distances:
75 1 0.00
76 8 0.03
77 18 0.06
78 14 0.05
79 204 0.72
80 10 0.04
81 14 0.05
82 13 0.05
83 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (79 bp):
TTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATA
CTCCAACCCCGTTA
Found at i:303657 original size:22 final size:23
Alignment explanation
Indices: 303625--303680 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 23
303615 TGGACATGTT
*
303625 AAAAATACATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
303647 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
303670 AAAAATGCATG
1 AAAAATGCATG
303681 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 19 0.59
23 13 0.41
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:304638 original size:20 final size:20
Alignment explanation
Indices: 304615--304665 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
304605 TTGTAGAATA
* *
304615 TATCGATACATTCATACATG
1 TATCGATACATTCAAAAATG
* *
304635 TATCGATATATTGAAAAATG
1 TATCGATACATTCAAAAATG
304655 TATCGATACAT
1 TATCGATACAT
304666 CAGGGTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (20 bp):
TATCGATACATTCAAAAATG
Found at i:305234 original size:32 final size:32
Alignment explanation
Indices: 305193--306106 Score: 1614
Period size: 32 Copynumber: 28.6 Consensus size: 32
305183 GATTTGAAAA
* ** **
305193 GGGTTGCCACTGACTTGCATGGGCTTTTAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305225 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* *
305257 GGGTTGCCACCGACTTGTGTGGGTTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
305289 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
305321 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
305353 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305385 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305417 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305449 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305481 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
305513 GGGCTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* *
305545 GGGCTGCCACCGACTTATGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305577 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305609 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305641 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305673 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305705 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305737 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305769 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305801 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305833 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
305865 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
305897 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* *
305929 GGGTTGCCACCGACTTGTATGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
305961 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
305993 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
306025 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* *
306057 GGGTTGCCACTGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* *
306089 GGG-TGCCACGGAGTTGTG
1 GGGTTGCCACCGACTTGTG
306107 GATTTAAAAG
Statistics
Matches: 861, Mismatches: 21, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
31 13 0.02
32 848 0.98
ACGTcount: A:0.14, C:0.19, G:0.36, T:0.31
Consensus pattern (32 bp):
GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
Found at i:306123 original size:27 final size:27
Alignment explanation
Indices: 306089--306771 Score: 1089
Period size: 27 Copynumber: 25.0 Consensus size: 27
306079 GCTTTGAAAT
*
306089 GGGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
306116 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
306143 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
306170 GGGTGCCACAGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
306197 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
306225 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
306252 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
306279 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
306306 GAGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
306333 AGGTGCTACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
306360 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
306387 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
306414 GAGATGCCACGGAGTTGTGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
306442 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
306470 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
306497 GGGTGCCACGGAGTTGTGGACTTTGAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
306525 -GGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
306551 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* * **
306579 GAGTGCCACAGAGTTGTGGACTTTGAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
306606 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
306633 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* *
306661 GAGTGCCTCGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* *
306689 GAGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
306716 GGGTGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
306744 GGATGCCACGGAGTTGTGGACTTCAAAA
1 GGGTGCCACGGAGTTGTGGACTT-AAAA
306772 AGAAATGCCA
Statistics
Matches: 609, Mismatches: 38, Indels: 17
0.92 0.06 0.03
Matches are distributed among these distances:
26 5 0.01
27 416 0.68
28 188 0.31
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:306223 original size:82 final size:81
Alignment explanation
Indices: 306089--306771 Score: 1089
Period size: 82 Copynumber: 8.3 Consensus size: 81
306079 GCTTTGAAAT
* *
306089 GGGTGCCACGGAGTTGTGGATTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
306154 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
* *
306170 GGGTGCCACAGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
306235 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
*
306252 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
306317 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
* * *
306333 AGGTGCTACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
306398 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
*
306414 GAGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
306479 GGAGTTGTGGACTTAAAA
64 GGAGTTGTGGACTTAAAA
* *
306497 GGGTGCCACGGAGTTGTGGACTTTGAAA-GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
306561 GAGTTGTGGACTTTAAAA
65 GAGTTGTGGAC-TTAAAA
* * **
306579 GAGTGCCACAGAGTTGTGGACTTTGAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
306644 AGTTGTGGACTTTAAAA
66 AGTTGTGGAC-TTAAAA
* * * * *
306661 GAGTGCCTCGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGATTTAAAAGGGTGCCACA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
306726 GAGTTGTGGACTTTAAAA
65 GAGTTGTGGAC-TTAAAA
*
306744 GGATGCCACGGAGTTGTGGACTTCAAAA
1 GGGTGCCACGGAGTTGTGGACTT-AAAA
306772 AGAAATGCCA
Statistics
Matches: 561, Mismatches: 33, Indels: 14
0.92 0.05 0.02
Matches are distributed among these distances:
81 201 0.36
82 226 0.40
83 134 0.24
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (81 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAA
Found at i:308063 original size:197 final size:197
Alignment explanation
Indices: 307723--308119 Score: 769
Period size: 197 Copynumber: 2.0 Consensus size: 197
307713 GATTGGGATG
307723 AGTCAACCTTTGAAGACCCTTAAGATTTTTCCAAGTTGTTTTGAGTTGCCCCTTGTTTAGGTGTT
1 AGTCAACCTTTGAAGACCCTTAAGATTTTTCCAAGTTGTTTTGAGTTGCCCCTTGTTTAGGTGTT
307788 TAAGAGGTTTTTGACTAGCTTTAGGGTGAAAAAGGTTTTTTTATTTTTTTTGTAGGATTGGGTGA
66 TAAGAGGTTTTTGACTAGCTTTAGGGTGAAAAAGGTTTTTTTATTTTTTTTGTAGGATTGGGTGA
307853 GTTTCAAAGCTTGTGTCTCACCAAGTTTTTTGCTAAAAAGAACATTTCCCTAAAAAACAGGTTCA
131 GTTTCAAAGCTTGTGTCTCACCAAGTTTTTTGCTAAAAAGAACATTTCCCTAAAAAACAGGTTCA
307918 TC
196 TC
*
307920 AGTCGACCTTTGAAGACCCTTAAGATTTTTCCAAGTTGTTTTGAGTTGCCCCTTGTTTAGGTGTT
1 AGTCAACCTTTGAAGACCCTTAAGATTTTTCCAAGTTGTTTTGAGTTGCCCCTTGTTTAGGTGTT
307985 TAAGAGGTTTTTGACTAGCTTTAGGGTGAAAAAGG-TTTTTTATTTTTTTTTGTAGGATTGGGTG
66 TAAGAGGTTTTTGACTAGCTTTAGGGTGAAAAAGGTTTTTTTA-TTTTTTTTGTAGGATTGGGTG
308049 AGTTTCAAAGCTTGTGTCTCACCAAGTTTTTTGCTAAAAAGAACATTTCCCTAAAAAACAGGTTC
130 AGTTTCAAAGCTTGTGTCTCACCAAGTTTTTTGCTAAAAAGAACATTTCCCTAAAAAACAGGTTC
308114 ATC
195 ATC
308117 AGT
1 AGT
308120 TCACATGACA
Statistics
Matches: 198, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
196 7 0.04
197 191 0.96
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (197 bp):
AGTCAACCTTTGAAGACCCTTAAGATTTTTCCAAGTTGTTTTGAGTTGCCCCTTGTTTAGGTGTT
TAAGAGGTTTTTGACTAGCTTTAGGGTGAAAAAGGTTTTTTTATTTTTTTTGTAGGATTGGGTGA
GTTTCAAAGCTTGTGTCTCACCAAGTTTTTTGCTAAAAAGAACATTTCCCTAAAAAACAGGTTCA
TC
Found at i:314240 original size:22 final size:23
Alignment explanation
Indices: 314208--314263 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 23
314198 TGGACATGTT
*
314208 AAAAATACATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
314230 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
314253 AAAAATGCATG
1 AAAAATGCATG
314264 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 19 0.59
23 13 0.41
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:315221 original size:20 final size:20
Alignment explanation
Indices: 315198--315248 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
315188 TTGTAGAATA
* *
315198 TATCGATACATTCATACATG
1 TATCGATACATTCAAAAATG
* *
315218 TATCGATATATTGAAAAATG
1 TATCGATACATTCAAAAATG
315238 TATCGATACAT
1 TATCGATACAT
315249 CAGGGTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (20 bp):
TATCGATACATTCAAAAATG
Found at i:316147 original size:1 final size:1
Alignment explanation
Indices: 316143--316222 Score: 52
Period size: 1 Copynumber: 80.0 Consensus size: 1
316133 GATTTTTTTT
* * * * * * ** * *
316143 AAAAAAAAAACAACAAGAAAACAAAAAAAAAAACAAAGAAAAAATCAAAACAAAAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
316208 ACAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAA
316223 GAGAGAAAAG
Statistics
Matches: 56, Mismatches: 23, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.85, C:0.10, G:0.04, T:0.01
Consensus pattern (1 bp):
A
Found at i:316184 original size:16 final size:16
Alignment explanation
Indices: 316165--316222 Score: 82
Period size: 16 Copynumber: 3.6 Consensus size: 16
316155 ACAAGAAAAC
316165 AAAAAAAAAAACAAAG
1 AAAAAAAAAAACAAAG
*
316181 AAAAAATCAAAACAAA-
1 AAAAAA-AAAAACAAAG
316197 AAAAAAACAAAACAAAG
1 AAAAAAA-AAAACAAAG
316214 AAAAAAAAA
1 AAAAAAAAA
316223 GAGAGAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
16 22 0.59
17 15 0.41
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAAACAAAG
Found at i:316185 original size:33 final size:33
Alignment explanation
Indices: 316146--316219 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
316136 TTTTTTTAAA
* *
316146 AAAAAAACAACAAGAAAACAAAAAAAAAAACAAAG
1 AAAAAATCAA-AACAAAA-AAAAAAAAAAACAAAG
*
316181 AAAAAATCAAAACAAAAAAAAAACAAAACAAAG
1 AAAAAATCAAAACAAAAAAAAAAAAAAACAAAG
316214 AAAAAA
1 AAAAAA
316220 AAAGAGAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 21 0.58
34 6 0.17
35 9 0.25
ACGTcount: A:0.84, C:0.11, G:0.04, T:0.01
Consensus pattern (33 bp):
AAAAAATCAAAACAAAAAAAAAAAAAAACAAAG
Found at i:316222 original size:21 final size:21
Alignment explanation
Indices: 316143--316220 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 21
316133 GATTTTTTTT
*
316143 AAAAAAAAAACAACAAGAAAAC
1 AAAAAAAAAACAA-AAAAAAAC
316165 AAAAAAAAAAACAAAGAAAAAATC
1 -AAAAAAAAAACAAA-AAAAAA-C
*
316189 AAAACAAAAAA-AAAACAAAAC
1 AAAA-AAAAAACAAAAAAAAAC
316210 AAAGAAAAAAA
1 AAA-AAAAAAA
316221 AAGAGAGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
21 10 0.20
22 7 0.14
23 25 0.51
24 7 0.14
ACGTcount: A:0.85, C:0.10, G:0.04, T:0.01
Consensus pattern (21 bp):
AAAAAAAAAACAAAAAAAAAC
Found at i:317462 original size:61 final size:61
Alignment explanation
Indices: 317334--318499 Score: 1166
Period size: 61 Copynumber: 19.5 Consensus size: 61
317324 GCAGGACGTA
* *
317334 TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGTAAGACG------CC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCC
* * * *
317389 TTTCAAAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGTAGGATGCCTTTTCC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC
317450 TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG------CC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCC
* * * ** *
317505 TTTCAAAGCCCACACAAGCTGGTGGCAC-CTTCAGTCCTCAAAGAGTAGGACGTTTTTTTC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC
* * * * *
317565 TTGCAAAGCCCACACAAGTTGGTGACACTTTTCTAGTCCTCAAAGAGTAGGATGCCTCTTCC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCC
* * *
317627 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATG-CTTTCTCC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTT-TCC
* * * * *
317688 TTTCGAAGCCCACACAAGCTGGTGGCACCTTT-AGTCCTCAAAAAGCAGGATGCCTTTTCC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC
* * * *
317748 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTTTAGTCCTTAAAGAGTAGGACGCCTTTTCC
1 TTTCAAAGCCCACACAAGTTGGTGGCAC-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC
* * *
317810 TTTTAAAGCCCACACAAGTTGTTGGCACTTTTCAGTCCTCAAAGAGCAGGATG-CTTTCTCC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTT-TCC
* * * * * * *
317871 TTTCGAAGCCCACACAAGTTTGTGGCACCTTTCTAGTCCTCAGAGAACAGGACACCTTTTTCT
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCC-TTTTCC
* ** *
317934 TTTCAAAGCCCACACAAGTTGGTGGCACCTCTT-AGTCCTCAAAGAATAGGACGCCTTTTTC
1 TTTCAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC
* * * * *
317995 TCTTCAAAGCCCACCCGAGTTGGTGGCACCTTTT-AGTCTTCAAAGAGCAGGACACCTTTTCT
1 T-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC
* *
318057 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACACCTTTTCC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCC
* * * * *
318119 TTTTAAAGCCTACATAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACACCTTTTTC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCC
* * * *
318181 TTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCTAGTCCTTAAAGAGCAAGACGCCTTTTCC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCC
* * *
318242 TTT-AAAGCTCACACAAGCTGGTGGCAC-CTTCAGTCCTC-AA-AG-A-GA-------T-C
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC
* * * * *
318289 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCTGGACGCCTTCTCA
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC
* * * * *
318350 TTTTAAAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGACACCTTCTCC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC
* * * * * * * * *
318411 TTTTAAAGCCCAAACAAGTTAGTCGCAC-CTTCTAGTCCTTAAAAAGCATGATG-C-TTTCTC
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC-C
* *
318471 TTTGCAAAGCCTATACAAGTTGGTGGCAC
1 TTT-CAAAGCCCACACAAGTTGGTGGCAC
318500 CTACTAGTCC
Statistics
Matches: 948, Mismatches: 117, Indels: 86
0.82 0.10 0.07
Matches are distributed among these distances:
47 4 0.00
48 23 0.02
49 10 0.01
50 1 0.00
51 2 0.00
53 2 0.00
54 20 0.02
55 76 0.08
56 5 0.01
57 2 0.00
58 2 0.00
59 9 0.01
60 124 0.13
61 333 0.35
62 301 0.32
63 28 0.03
64 6 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (61 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC
Found at i:317635 original size:62 final size:62
Alignment explanation
Indices: 317338--318499 Score: 1192
Period size: 62 Copynumber: 19.4 Consensus size: 62
317328 GACGTATTTC
* * *
317338 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGTAAGACGCC-TTT-C----
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * * * *
317393 AAAGCCCACATAAGTTGGTGGCACTTTTC-AGTCCTCAAGGAGTAGGATGCCTTTTCCTTTC
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
*
317454 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCC-TTT-C----
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * * ** * **
317509 AAAGCCCACACAAGCTGGTGGCAC-CTTC-AGTCCTCAAAGAGTAGGACGTTTTTTTCTTGC
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * * *
317569 AAAGCCCACACAAGTTGGTGACACTTTTCTAGTCCTCAAAGAGTAGGATGCCTCTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * *
317631 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGATG-CTTTCTCCTTTC
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTT-TCCTTTT
* * * * *
317692 GAAGCCCACACAAGCTGGTGGCAC-CTT-TAGTCCTCAAAAAGCAGGATGCCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * *
317752 AAAGCCCACACAAGTTGGTGGCACTTTTTTAGTCCTTAAAGAGTAGGACGCCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * *
317814 AAAGCCCACACAAGTTGTTGGCACTTTTC-AGTCCTCAAAGAGCAGGATG-CTTTCTCCTTTC
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTT-TCCTTTT
* * * * * * *
317875 GAAGCCCACACAAGTTTGTGGCACCTTTCTAGTCCTCAGAGAACAGGACACCTTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * ** * *
317937 CAAAGCCCACACAAGTTGGTGGCACCTCT-TAGTCCTCAAAGAATAGGACGCCTTTTTCTCTTC
1 -AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCT-TTT
* * * * * *
318000 AAAGCCCACCCGAGTTGGTGGCACCTTT-TAGTCTTCAAAGAGCAGGACACCTTTTCTTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
*
318061 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * * *
318123 AAAGCCTACATAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * *
318185 AAAGCCCACACAAGTTGGTGGCAC-CTTCTAGTCCTTAAAGAGCAAGACGCCTTTTCC-TTT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * *
318245 AAAGCTCACACAAGCTGGTGGCAC-CTTC-AGTCCTC-AA-AG-A-GA-------T-CTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * * *
318293 AAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAGGAGCTGGACGCCTTCTCATTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * * *
318354 AAAGCCCACATAAGTTGGTGGCACTTTTC-AGTCCTCAAGGAGCAGGACACCTTCTCCTTTT
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
* * * * * * * * *
318415 AAAGCCCAAACAAGTTAGTCGCAC-CTTCTAGTCCTTAAAAAGCATGATG-C-TTTCTCTTTGC
1 AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTC-CTTT-T
* *
318476 AAAGCCTATACAAGTTGGTGGCAC
1 AAAGCCCACACAAGTTGGTGGCAC
318500 CTACTAGTCC
Statistics
Matches: 944, Mismatches: 118, Indels: 84
0.82 0.10 0.07
Matches are distributed among these distances:
47 1 0.00
48 26 0.03
49 10 0.01
50 1 0.00
51 2 0.00
53 2 0.00
54 19 0.02
55 71 0.08
56 10 0.01
57 3 0.00
58 2 0.00
59 10 0.01
60 124 0.13
61 315 0.33
62 317 0.34
63 31 0.03
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (62 bp):
AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
Found at i:319217 original size:62 final size:63
Alignment explanation
Indices: 319098--319226 Score: 188
Period size: 62 Copynumber: 2.1 Consensus size: 63
319088 ATACATTATT
* * * * *
319098 CATTGTATCGATACATTCTGGGTTTTACGCAGATGTATCGATATATGGTTCATTGTATTGATA
1 CATTGTATCGATACATACTGGGTTTTACCCAGATGTATCGATACATGGTTCAATGTATCGATA
**
319161 CATTGTATCGATACATACTGGG-TTTACCCAGATGTATCGATACATTTTTCAATGTATCGATA
1 CATTGTATCGATACATACTGGGTTTTACCCAGATGTATCGATACATGGTTCAATGTATCGATA
319223 CATT
1 CATT
319227 CATGCATTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
62 38 0.64
63 21 0.36
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (63 bp):
CATTGTATCGATACATACTGGGTTTTACCCAGATGTATCGATACATGGTTCAATGTATCGATA
Found at i:321679 original size:46 final size:46
Alignment explanation
Indices: 321611--321700 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 46
321601 TATTTCTGAG
* * *
321611 GGGATACTCAAACCCCGGTTTTATTTCTAAAACACCAATTTTTCGA
1 GGGATACTCAAACCCCGATTTTATTCCCAAAACACCAATTTTTCGA
* * *
321657 GGGATACTCCAACCTCGATTTTATTCCCAAAACATCAATTTTTC
1 GGGATACTCAAACCCCGATTTTATTCCCAAAACACCAATTTTTC
321701 ACAATCGGGG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (46 bp):
GGGATACTCAAACCCCGATTTTATTCCCAAAACACCAATTTTTCGA
Found at i:321754 original size:125 final size:127
Alignment explanation
Indices: 321532--321861 Score: 452
Period size: 125 Copynumber: 2.6 Consensus size: 127
321522 TTTCTTCTCG
* * * * * *
321532 GGGATACTCCAACCAC-AGTTTTATTCTCAAAACACCAAATTTTCATAATCGGGGATACTCAAAT
1 GGGATACTCCAACCTCGA-TTTTATTCCCAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
* *
321596 CCTGATATTTCTGAGGGGATACTCAAACCCCGGTTTTATTTCTAAAACACCAATTTTTCG-A-
65 CCTGTTATTTCTGAGGGGATAATCAAACCCCGGTTTTATTTCTAAAACACCAATTTTTCGAAC
* *
321657 GGGATACTCCAACCTCGATTTTATTCCCAAAACATCAATTTTTCACAATCGGGGATGCTCCAACC
1 GGGATACTCCAACCTCGATTTTATTCCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACC
* * *
321722 CCGTTATTTCTGAGGGGATAATCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCGCAATC
66 CTGTTATTTCTGAGGGGATAATCAAACCCCGGTTTTATTTCTAAAACACCAATTTTTCG-AA-C
* *
321786 GGGGATACTCCAA-CTCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTTCAA
1 -GGGATACTCCAACCT-CGATTTTATTCCCAAAACACCAATTTTTCACAATCGGGGATACTCCAA
321850 CCCTGTTATTTC
64 CCCTGTTATTTC
321862 ATCGAAGATA
Statistics
Matches: 180, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
125 109 0.61
126 1 0.01
127 1 0.01
129 2 0.01
130 67 0.37
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (127 bp):
GGGATACTCCAACCTCGATTTTATTCCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACC
CTGTTATTTCTGAGGGGATAATCAAACCCCGGTTTTATTTCTAAAACACCAATTTTTCGAAC
Found at i:321811 original size:51 final size:51
Alignment explanation
Indices: 321735--321852 Score: 173
Period size: 51 Copynumber: 2.3 Consensus size: 51
321725 TTATTTCTGA
* * * * *
321735 GGGGATAATCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCGCAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
*
321786 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
*
321837 GGGGATACTTCAACCC
1 GGGGATACTCCAACCC
321853 TGTTATTTCA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
Found at i:321899 original size:28 final size:28
Alignment explanation
Indices: 321839--321905 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
321829 TCACAATCGG
*
321839 GGATACTTCAACCCTGTTATTTCATCGAA
1 GGATACTCCAACCCTGTTATTT-ATCGAA
*
321868 -GATACTCCAACCCTGTTATTT-TTGAGA
1 GGATACTCCAACCCTGTTATTTATCGA-A
321895 GGATACTCCAA
1 GGATACTCCAA
321906 GATGACATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 3 0.09
27 1 0.03
28 30 0.88
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (28 bp):
GGATACTCCAACCCTGTTATTTATCGAA
Found at i:323450 original size:47 final size:47
Alignment explanation
Indices: 323383--323505 Score: 131
Period size: 47 Copynumber: 2.5 Consensus size: 47
323373 AATCCCGTTA
* * * *
323383 TTTTCGAGGGAATA-TCCCAACCCCGGTTTTATTTCTAAAACACCAAT
1 TTTTCGAGGGGATACT-CCAACCCCGATTTTATTCCCAAAACACCAAT
* *
323430 TTTTCGAGGGGATACTCCAACCCCGATTTTATTCCCAAAACTCTAAT
1 TTTTCGAGGGGATACTCCAACCCCGATTTTATTCCCAAAACACCAAT
*
323477 TTTTCACAATCGGGGATACTCCAACCCCG
1 TTTT--CGA--GGGGATACTCCAACCCCG
323506 TTATTTCATC
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
47 43 0.67
48 1 0.02
49 2 0.03
51 18 0.28
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (47 bp):
TTTTCGAGGGGATACTCCAACCCCGATTTTATTCCCAAAACACCAAT
Found at i:323521 original size:28 final size:28
Alignment explanation
Indices: 323489--323561 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
323479 TTCACAATCG
**
323489 GGGATACTCCAACCCCGTTATTTCATCA
1 GGGATACTCCAACCCCGTTATTTCAGAA
* * *
323517 GGGATACTCCAATCCTGTTATTTCCGAA
1 GGGATACTCCAACCCCGTTATTTCAGAA
*
323545 GGGATATTCCAACCCCG
1 GGGATACTCCAACCCCG
323562 ATTTTATTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCAGAA
Found at i:323602 original size:79 final size:78
Alignment explanation
Indices: 323513--323744 Score: 315
Period size: 79 Copynumber: 2.9 Consensus size: 78
323503 CCGTTATTTC
* * * * *
323513 ATCAGGGATACTCCAATCCTGTTATTTCCGAAGGGATATTCCAACCCCGATTTTATTTCCAAAAC
1 ATCAGGGATACTCCAACCCCGTTATTTTC-AAGGGATACTCCAACCCCGATTTTATTTCTAAAAC
323578 ACCAATTTTTCACA
65 ACCAATTTTTCACA
323592 ATC-GGTGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCC-AGTTTTATTTCTAAA
1 ATCAGG-GATACTCCAACCCCGTTATTTTCAA-GGGATACTCCAACCCCGA-TTTTATTTCTAAA
* *
323655 ACATCGATTTTTCACA
63 ACACCAATTTTTCACA
* * *
323671 ATCAGGGATACTCCAACCCCATTATTTTCAAGGAGATACTCCAACCTCGATTTTATTTCTAGAAC
1 ATCAGGGATACTCCAACCCCGTTATTTTCAAGG-GATACTCCAACCCCGATTTTATTTCTAAAAC
323736 ACCAATTTT
65 ACCAATTTT
323745 CCATAGTCAG
Statistics
Matches: 135, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
78 7 0.05
79 125 0.93
80 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (78 bp):
ATCAGGGATACTCCAACCCCGTTATTTTCAAGGGATACTCCAACCCCGATTTTATTTCTAAAACA
CCAATTTTTCACA
Found at i:323628 original size:107 final size:106
Alignment explanation
Indices: 323438--323635 Score: 317
Period size: 107 Copynumber: 1.8 Consensus size: 106
323428 ATTTTTCGAG
* *
323438 GGGATACTCCAACCCCGATTTTATTCCCAAAACTCTAATTTTTCACAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTCCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACC
323503 CCGTTATTTCATCAGGGATACTCCAATCCTGTTATTTCCGAA
66 CCGTTATTTCA-CAGGGATACTCCAATCCTGTTATTTCCGAA
* * *
323545 GGGATATTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGTGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTCCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACC
323610 CCGTTATTTTCA-AGGGGATACTCCAA
66 CCGTTA-TTTCACA-GGGATACTCCAA
323636 CCCCAGTTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
106 1 0.01
107 78 0.93
108 5 0.06
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (106 bp):
GGGATACTCCAACCCCGATTTTATTCCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTCACAGGGATACTCCAATCCTGTTATTTCCGAA
Found at i:325899 original size:2 final size:2
Alignment explanation
Indices: 325892--325933 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
325882 TTTTGTATTC
*
325892 AT AT AT AT AT AT AT AT AT AT AT AT GT 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
325934 CACTATTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:327225 original size:28 final size:28
Alignment explanation
Indices: 327154--327316 Score: 166
Period size: 28 Copynumber: 5.7 Consensus size: 28
327144 TACCACAGTT
* * ** *
327154 CTTAGACTTTTCAAAATTATGCATTGACC
1 CTTAAACTTTTTAAAATTACACTTTGA-C
*
327183 CTTAAACTTTTTAAAATTACACTTTTAC
1 CTTAAACTTTTTAAAATTACACTTTGAC
* * * *
327211 CCTAAACATTTTAAAATTACATTTTTAC
1 CTTAAACTTTTTAAAATTACACTTTGAC
*
327239 CTTAAACTTTTTAAAATTGCACTTTGAC
1 CTTAAACTTTTTAAAATTACACTTTGAC
*
327267 CTTTTAAACTTTTCAAAATTACA-TATTGAGC
1 C--TTAAACTTTTTAAAATTACACT-TTGA-C
327298 CTTAAACTTTTTAAAATTA
1 CTTAAACTTTTTAAAATTA
327317 TACTCGGACC
Statistics
Matches: 113, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 50 0.44
29 39 0.35
30 22 0.19
31 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.43
Consensus pattern (28 bp):
CTTAAACTTTTTAAAATTACACTTTGAC
Found at i:329198 original size:25 final size:22
Alignment explanation
Indices: 329161--329214 Score: 54
Period size: 25 Copynumber: 2.3 Consensus size: 22
329151 AAATATAAAT
**
329161 TGAATTTTCTAAAACTGATTTACTA
1 TGAATTTAATAAAA-TGATTTA--A
*
329186 TGAATTTAATAAAATTATTTAA
1 TGAATTTAATAAAATGATTTAA
329208 TGAATTT
1 TGAATTT
329215 TAAAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 8 0.31
24 6 0.23
25 12 0.46
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (22 bp):
TGAATTTAATAAAATGATTTAA
Found at i:329495 original size:17 final size:15
Alignment explanation
Indices: 329473--329508 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
329463 AAATGCATCA
329473 AAAATAATATATTATCT
1 AAAATAATA-ATTAT-T
329490 AAAATAATAATTATT
1 AAAATAATAATTATT
329505 AAAA
1 AAAA
329509 GTTGTAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 5 0.26
17 9 0.47
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATAATAATTATT
Found at i:329902 original size:20 final size:21
Alignment explanation
Indices: 329877--329931 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
329867 CATGCTTACA
329877 ATTGTATCGATACATTTC-TC
1 ATTGTATCGATACATTTCTTC
329897 ATTGTATCGATACA-TTCTTC
1 ATTGTATCGATACATTTCTTC
*
329917 AATGTATCGATACAT
1 ATTGTATCGATACAT
329932 GCAGGCAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (21 bp):
ATTGTATCGATACATTTCTTC
Found at i:333217 original size:79 final size:79
Alignment explanation
Indices: 333061--333282 Score: 236
Period size: 79 Copynumber: 2.8 Consensus size: 79
333051 TGAGAAATTT
* * * * *
333061 AATATTTTGGAGATAATAA-CGA-GTTGGAGTATCCCTTTGAAAATAACGGGGTTAGAGTATCCC
1 AATATTTAGGAAATAA-AACCGAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
** *
333124 CGGTTGTGAAAAATC
65 CAATTATGAAAAATC
* * *
333139 GATGA-TTAGGAAATAAAATCG-GGATTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCC
1 AAT-ATTTAGGAAATAAAACCGAGG-TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCC
*
333202 CCAATTATGAGAAATC
64 CCAATTATGAAAAATC
* * * **
333218 AATATTTTGGAAATAAAGCCGAGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCC
1 AATATTTAGGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
333283 GATGAAATAA
Statistics
Matches: 119, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
77 2 0.02
78 15 0.13
79 100 0.84
80 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (79 bp):
AATATTTAGGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
AATTATGAAAAATC
Found at i:333366 original size:52 final size:51
Alignment explanation
Indices: 333297--333902 Score: 312
Period size: 52 Copynumber: 11.6 Consensus size: 51
333287 AAATAACAAG
* *
333297 GTTGGAGTATCCTCGATTGTAAAAAATTGGTGTTTTTGGGAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAAAAAATTGGTG-TTTTGGAAATAAAATCGGA
** * * *
333349 GTTGGAGTATCCCCGATTAAAGAAAAATTGGTATTTTGAAAATAAAACTAGG-
1 GTTGGAGTATCCCCGATTGTA-AAAAATTGGTGTTTTGGAAATAAAA-TCGGA
* * * *
333401 GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAA-CCGA
1 GTTGGAGTATCCCCGATTGTAAAAAATTGGTGTTTTGGAAATAAAATCGGA
* *** * * ***** *
333451 GGTTGGAGTATCTCCTCGGA-GGTAAAGGGGTTGGAGTATCCCCGATGAAATAAC-GA
1 -GTTGGAGTATC-CC-C-GATTGTAAA-AAATTGGTGTTTTGGAAAT-AAA-ATCGGA
* * *
333507 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATTGGA
1 -GTTGGAGTATCCCCGATTGTAAAAAATTGGTG-TTTTGGAAATAAAATCGGA
* * *
333560 GTTGGAGTATCCCCGATT-AAAGGAAAATTGGTGTTTTGAAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTGTAA--AAAATTGGTGTTTTGGAAATAAAATCGGA
** * * *
333612 GTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAAAT-GGG
1 GTTGGAGTATCCCCGATTGTAAAAAATTGGTGTTTTGGAAAT-AAAATCGGA
* * * * *** * ** *
333663 GTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGG
1 GTTGGAGTATCCCCGATTGTAAAAAATTGGTGTTTTGGAAATAAAATCGGA
* **** * ****** *
333714 GTTGGAGTATCCCCTCGGA-GGTAACGGGGTTGGAGTACCCCCAATGAAATAAC-GA
1 GTTGGAGTAT-CCC-C-GATTGTAA-AAAATTGGTGTTTTGGAAAT-AAA-ATCGGA
* * *
333769 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCAGA
1 -GTTGGAGTATCCCCGATTGTAAAAAATTGGTG-TTTTGGAAATAAAATCGGA
* * * * *
333822 GTTGGAGTATCCCCAATT-AAAGGAAAATTGGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTAA--AAAATTGGTGTTTTGGAAATAAAATCGGA
* *
333874 GTTGGAGTATCCCCGATTATGAAAAATTG
1 GTTGGAGTATCCCCGATTGTAAAAAATTG
333903 AGAAACTTAA
Statistics
Matches: 409, Mismatches: 113, Indels: 65
0.70 0.19 0.11
Matches are distributed among these distances:
49 1 0.00
50 3 0.01
51 108 0.26
52 160 0.39
53 66 0.16
54 34 0.08
55 10 0.02
56 26 0.06
57 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTAAAAAATTGGTGTTTTGGAAATAAAATCGGA
Found at i:333446 original size:51 final size:51
Alignment explanation
Indices: 333296--333727 Score: 270
Period size: 51 Copynumber: 8.3 Consensus size: 51
333286 GAAATAACAA
* * * * *
333296 GGTTGGAGTATCCTCGATTGTAAAAAATTGGTGTTTTTGGGAATAAAA-TCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTG-TTTTAGAAATAAAACT-GG
* ** * * *
333348 AGTTGGAGTATCCCCGATTAAAGAAAAATTGGTATTTT-GAAAATAAAACTAG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTAGTGTTTTAG-AAATAAAACTGG
* *
333400 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGA
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACTGG
* ** * *** *
333451 GGTTGGAGTATCTCCTCGGA-GGT-AAAGGGGTTGGAGTATCCCCGATGAAAT--AAC-GA
1 GGTTGGAGTATC-CC-C-GATTGTGAAA--AATT--AGTGT--TTTA-GAAATAAAACTGG
* * * *
333507 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATTGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTG-TTTTAGAAATAAAACTGG
* ** * *
333559 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTT-GAAAATAAAA-TCGG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTAGTGTTTTAG-AAATAAAACT-GG
* *
333611 GGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAAATGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACTGG
* * * * * * * * *
333662 GGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACTGG
333713 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
333728 TCGGAGGTAA
Statistics
Matches: 300, Mismatches: 55, Indels: 51
0.74 0.14 0.13
Matches are distributed among these distances:
49 5 0.02
51 122 0.41
52 106 0.35
53 29 0.10
54 7 0.02
55 4 0.01
56 18 0.06
57 3 0.01
58 1 0.00
59 5 0.02
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACTGG
Found at i:333453 original size:211 final size:211
Alignment explanation
Indices: 333188--333676 Score: 773
Period size: 211 Copynumber: 2.3 Consensus size: 211
333178 GAAAATAATG
* * * * * * * *
333188 GGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGAGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCC
*
333253 CCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGATTGTA
66 CCTCGGAGGTAAAGGGGTTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGATTGTA
*
333318 AAAAATTGGTGTTTTTGGGAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAATTGGTAT
131 AAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAATTGGTAT
333383 TTTGAAAATAAAA-CTA
196 TTTGAAAATAAAATC-A
*
333399 GGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCT
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCC
* *
333464 CCTCGGAGGTAAAGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTG
66 CCTCGGAGGTAAAGGGGTTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGATTGTA
* * *
333529 AAAAATTGGTGTTTTTGGAAATAAAATTGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGT
131 AAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAATTGGTAT
*
333594 TTTGAAAATAAAATCG
196 TTTGAAAATAAAATCA
* ** *
333610 GGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAAATGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCC
333675 CC
66 CC
333677 AATTATGAGA
Statistics
Matches: 255, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
211 254 1.00
212 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (211 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCC
CCTCGGAGGTAAAGGGGTTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGATTGTA
AAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAATTGGTAT
TTTGAAAATAAAATCA
Found at i:333525 original size:107 final size:107
Alignment explanation
Indices: 333163--333572 Score: 362
Period size: 107 Copynumber: 3.9 Consensus size: 107
333153 AAAATCGGGA
* * * * * * * *
333163 TTGGAGTATCCCC--TCGAAAATAATGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTT
1 TTGGAGTATCCCCGAT-G-AAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTT
* *
333225 TGGAAATAAAGCCGAGGTTGGAGTATCCCCTCGGAGGTAACGGGG
64 TGGAAATAAAACCGAGGTTGGAGTAT-CCCTCGGAGGTAAAGGGG
* * * *
333270 TTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGATTGTAAAAAATTGGTGTTTTTG
1 TTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTTG
* * * ***
333335 GGAATAAAATCG-GAGTTGGAGTATCCC-C-GA-TTAAAGAAAAA
66 GAAATAAAACCGAG-GTTGGAGTATCCCTCGGAGGTAAAG--GGG
*** *
333376 TT-G-GTAT-TTTGA--AAATAAAACTAGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTG-TT
1 TTGGAGTATCCCCGATGAAAT--AACGA-GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTT
*
333435 TTAGAAATAAAACCGAGGTTGGAGTATCTCCTCGGAGGTAAAGGGG
63 TTGGAAATAAAACCGAGGTTGGAGTATC-CCTCGGAGGTAAAGGGG
* *
333481 TTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTG
1 TTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTTG
**
333546 GAAATAAAATTG-GAGTTGGAGTATCCC
66 GAAATAAAACCGAG-GTTGGAGTATCCC
333573 CGATTAAAGG
Statistics
Matches: 239, Mismatches: 43, Indels: 42
0.74 0.13 0.13
Matches are distributed among these distances:
101 4 0.02
103 31 0.13
104 41 0.17
105 6 0.03
106 6 0.03
107 90 0.38
108 56 0.23
109 1 0.00
110 4 0.02
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (107 bp):
TTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTTG
GAAATAAAACCGAGGTTGGAGTATCCCTCGGAGGTAAAGGGG
Found at i:333706 original size:262 final size:262
Alignment explanation
Indices: 333297--333901 Score: 892
Period size: 262 Copynumber: 2.3 Consensus size: 262
333287 AAATAACAAG
* * ** *
333297 GTTGGAGTATCCTCGATTGTAA--AAAATTGGTGTTTTTGGGAATAAAATCGGAGTTGGAGTATC
1 GTTGGAGTATCCCCGATT-AAAGGAAAATTGGTG-TTTTGAAAATAAAATCGGGGTTGGAGTATC
* * * * *
333360 CCCGATTAAAGAAAAATTGGTATTTTGAAAATAAAACTAGGGTTGGAGTATCCCCGATTGTGAAA
64 CCCGATT-ATGAAAAATTAGTATTTTGAAAATAAAAATAGGGTTGGAGTATCCCCAATTATGAAA
* * * * *
333425 AATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCTCCTCGGAGGTAAAGGGGTTGGAGTAT
128 AATCAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGGAGGTAAAGGGGTTGGAGTAC
*
333490 CCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAA
193 CCCCAATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAA
**
333555 TTGGA
258 TCAGA
333560 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCC
* * * * *
333625 CGATTGTGGAAAATTAGTGTTTT-AGAAATAAAAATGGGGTTGGAGTATCCCCAATTATGAGAAA
66 CGATTATGAAAAATTAGTATTTTGA-AAATAAAAATAGGGTTGGAGTATCCCCAATTATGAAAAA
* * * *
333689 TCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTACCC
130 TCAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGGAGGTAAAGGGGTTGGAGTACCC
333754 CCAATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATC
195 CCAATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATC
333819 AGA
260 AGA
* *
333822 GTTGGAGTATCCCCAATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCC
333887 CGATTATGAAAAATT
66 CGATTATGAAAAATT
333902 GAGAAACTTA
Statistics
Matches: 308, Mismatches: 31, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
261 1 0.00
262 246 0.80
263 51 0.17
264 10 0.03
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.29
Consensus pattern (262 bp):
GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCC
CGATTATGAAAAATTAGTATTTTGAAAATAAAAATAGGGTTGGAGTATCCCCAATTATGAAAAAT
CAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGGAGGTAAAGGGGTTGGAGTACCCC
CAATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCA
GA
Found at i:336275 original size:13 final size:13
Alignment explanation
Indices: 336257--336282 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
336247 ACAAAGATTG
336257 ATGTATCGATACA
1 ATGTATCGATACA
336270 ATGTATCGATACA
1 ATGTATCGATACA
336283 TTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:336295 original size:21 final size:21
Alignment explanation
Indices: 336269--336310 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
336259 GTATCGATAC
336269 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
*
336290 AATGTATCGATATATTTCCTT
1 AATGTATCGATACATTTCCTT
336311 GGCAGTCGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:336359 original size:19 final size:19
Alignment explanation
Indices: 336335--336384 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
336325 AGTGATACAT
*
336335 TGTATCGATACAAAACTTG
1 TGTATCGATACAAAACTTA
*
336354 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
336373 TGTATCGATACA
1 TGTATCGATACA
336385 TTTACGGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:338030 original size:21 final size:21
Alignment explanation
Indices: 338006--338058 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
337996 TTCTACAATT
*
338006 TGTATCGATACAAAAATTGAA
1 TGTATCGATACAAAAAGTGAA
* *
338027 TGTATTGATAC-ATAAGTGAA
1 TGTATCGATACAAAAAGTGAA
*
338047 TGTATCAATACA
1 TGTATCGATACA
338059 TGCTTGTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (21 bp):
TGTATCGATACAAAAAGTGAA
Found at i:339018 original size:33 final size:33
Alignment explanation
Indices: 338981--339052 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
338971 AATATCCCTC
338981 ATGATTGGTGATTTCTATGGCATGATAAAAGGT
1 ATGATTGGTGATTTCTATGGCATGATAAAAGGT
339014 ATGATTGGTGATTTCTATGGCATGATAAAAGGT
1 ATGATTGGTGATTTCTATGGCATGATAAAAGGT
339047 AT-ATTG
1 ATGATTG
339053 ATTGAAGTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
32 4 0.10
33 35 0.90
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.38
Consensus pattern (33 bp):
ATGATTGGTGATTTCTATGGCATGATAAAAGGT
Found at i:342373 original size:51 final size:53
Alignment explanation
Indices: 342317--342455 Score: 162
Period size: 52 Copynumber: 2.7 Consensus size: 53
342307 AATGGACTGC
*
342317 ATGTATCGATACATTGAA-AAA-TGTATCGATACATTTCGATCAA-AAACCAGA
1 ATGTATCGATACA-TAAACAAATTGTATCGATACATTTCGATCAAGAAACCAGA
* * * *
342368 ATGTATCAATACA-AAACAAATTATATCGATACATTTGGATCAAGAACCCAGA
1 ATGTATCGATACATAAACAAATTGTATCGATACATTTCGATCAAGAAACCAGA
* * *
342420 ATATATAGATATA-AAACAAATTGTATCGATACATTT
1 ATGTATCGATACATAAACAAATTGTATCGATACATTT
342456 AGAAATGTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
49 2 0.03
50 3 0.04
51 32 0.43
52 38 0.51
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (53 bp):
ATGTATCGATACATAAACAAATTGTATCGATACATTTCGATCAAGAAACCAGA
Found at i:343345 original size:52 final size:52
Alignment explanation
Indices: 343260--343799 Score: 283
Period size: 52 Copynumber: 10.2 Consensus size: 52
343250 TTAAAGATAA
* * * ** * *
343260 TAAAGATGAGAAGAGTGCAAATGAACGGATTCAAAGCCAACGACATTGGACT
1 TAAAAATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACT
* * * * *
343312 TGAATATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAATGATATTAGACT
1 TAAAAATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACT
* * ** * * *
343364 TAAAAAAGACAAGGGTGTCAATGTGTTGATTCAAGGCCAACAACATTGGGA-T
1 TAAAAATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAACGACATT-GGACT
* * * * * * *
343416 TAAAAATGACAA-AAGTGCCTATGTGCTAATTCAAGGCCAATGACGTTGCAGT
1 TAAAAATGAGAAGAA-TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACT
* * * * * * *
343468 TAGAAA-GAGATA-AAGGTGCTGATATGT-C-GATTCAAGGTCAATGATGACT-CACT
1 TAAAAATGAGA-AGAA--TGC-CA-ATGTGCTGATTCAAGGCCAACGA-CATTGGACT
* * * * * **
343521 TAAAGATGATAAGGGTGAGAAGAGTTCCAATGTGCTGATTCATGACCAGCGACATTAAACT
1 T--A-A--A-AA---TGAGAAGAATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACT
* *
343582 TAAAGATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAACGACATTGGATT
1 TAAAAATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACT
* * *
343634 TAAAAATTAGAAGAATGCCAATATGCTGATTCAAGGCCAATGACATTAGG-CT
1 TAAAAATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAACGACATT-GGACT
* * * * * ** * **
343686 TAGAAATGATAA-AGATGCCAATATGTTAATTCAAGGCCAGTGATATCAGACT
1 TAAAAATGAGAAGA-ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACT
* * * *
343738 TAAAGATGATAA-AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACT
1 TAAAAATGAGAAGA-ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACT
*
343790 TAGAAA-GAGA
1 TAAAAATGAGA
343800 TGGTTTGACA
Statistics
Matches: 371, Mismatches: 92, Indels: 51
0.72 0.18 0.10
Matches are distributed among these distances:
51 10 0.03
52 290 0.78
53 26 0.07
54 2 0.01
55 6 0.02
56 1 0.00
58 2 0.01
59 7 0.02
60 4 0.01
61 17 0.05
62 1 0.00
63 5 0.01
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (52 bp):
TAAAAATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACT
Found at i:343896 original size:33 final size:33
Alignment explanation
Indices: 343859--343927 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
343849 TAGAAGGAGA
* * *
343859 TGCCACCGACTTGTGTGGGTTTTTGAAGGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAAGGGGT
*
343892 TGCCACTGACTTGTGTGGGCTTTAGAAAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAAGGGGT
343925 TGC
1 TGC
343928 TACTTTAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.14, C:0.16, G:0.38, T:0.32
Consensus pattern (33 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAAGGGGT
Found at i:343979 original size:33 final size:33
Alignment explanation
Indices: 343930--344137 Score: 192
Period size: 33 Copynumber: 6.4 Consensus size: 33
343920 GGGGTTGCTA
* ***
343930 CTTTAGAAAGGGGTTGCCATTGACTTGTGTGGG
1 CTTTAGAAAGGAGTTGCCACCAACTTGTGTGGG
* * *
343963 CTTTCGAAAGGAGTTGCCCCCAACTTGTGTAGG
1 CTTTAGAAAGGAGTTGCCACCAACTTGTGTGGG
* *
343996 CTTTAGAAA-GAGTTGCCACCGACTTGTGTGGA
1 CTTTAGAAAGGAGTTGCCACCAACTTGTGTGGG
* *
344028 TTTTA-AAAGG-GTTGCCACTAACTTGTGTGGG
1 CTTTAGAAAGGAGTTGCCACCAACTTGTGTGGG
* * * **
344059 CTTTAGAAA-AAGGTTGCCATCGACTTGTGTTAG
1 CTTTAGAAAGGA-GTTGCCACCAACTTGTGTGGG
* *
344092 CTTTCAAAAAAG-GTTGCCACCAACTTGTGTGGG
1 CTTT-AGAAAGGAGTTGCCACCAACTTGTGTGGG
344125 CTTTAGAGAAGGA
1 CTTTAGA-AAGGA
344138 TGCCACGAAG
Statistics
Matches: 136, Mismatches: 31, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
31 25 0.18
32 29 0.21
33 78 0.57
34 4 0.03
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (33 bp):
CTTTAGAAAGGAGTTGCCACCAACTTGTGTGGG
Found at i:344225 original size:33 final size:32
Alignment explanation
Indices: 344133--344477 Score: 208
Period size: 33 Copynumber: 10.9 Consensus size: 32
344123 GGCTTTAGAG
** *
344133 AAGGATGCCAC-GAAGTTGTGGACTTTGAAGAAA
1 AAGG-TGCCACAG-AGTTGTGGACTTAAAAGGAA
*
344166 AAGGTACCAC-GAAGTTGTGGACTTAAAAGGAA
1 AAGGTGCCACAG-AGTTGTGGACTTAAAAGGAA
* * *
344198 AATGTGGCACAGAGTTATGGACTTTAAAA-GAA
1 AAGGTGCCACAGAGTTGTGGAC-TTAAAAGGAA
*
344230 ACAGGTGCCACAGAGATGTGGACTTAAAAGGAAA
1 A-AGGTGCCACAGAGTTGTGGACTTAAAAGG-AA
* *
344264 AAGGTGCCATAGAGTTGTGGA-TT--TA--AA
1 AAGGTGCCACAGAGTTGTGGACTTAAAAGGAA
* *
344291 AAGGTGCAAC-GAAGTTGTGGACTTAAAAGCAAA
1 AAGGTGCCACAG-AGTTGTGGACTTAAAAG-GAA
* * *
344324 AAGGGTGACACAGAGTTTTTGACTTAAAA-G--
1 AA-GGTGCCACAGAGTTGTGGACTTAAAAGGAA
*
344354 --GGTGCCATAGAGTTGTGGACTTTAAAAGGAA
1 AAGGTGCCACAGAGTTGTGGAC-TTAAAAGGAA
* *
344385 AAGGGTGCCACAGAGTTATAGACTTTAAAA-GAA
1 AA-GGTGCCACAGAGTTGTGGAC-TTAAAAGGAA
* *
344418 AGAGGTACGAC-GAAGTTGTGGACTTTAATAAGG--
1 A-AGGTGCCACAG-AGTTGTGGAC-TTAA-AAGGAA
*
344451 --GGTGCCACAGAGTTGTAGACTTTAAAA
1 AAGGTGCCACAGAGTTGTGGAC-TTAAAA
344478 AGGGTGCTAC
Statistics
Matches: 249, Mismatches: 37, Indels: 56
0.73 0.11 0.16
Matches are distributed among these distances:
26 1 0.00
27 35 0.14
28 8 0.03
29 3 0.01
30 22 0.09
31 1 0.00
32 53 0.21
33 74 0.30
34 50 0.20
35 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.23
Consensus pattern (32 bp):
AAGGTGCCACAGAGTTGTGGACTTAAAAGGAA
Found at i:344365 original size:27 final size:28
Alignment explanation
Indices: 344322--344382 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
344312 CTTAAAAGCA
* *
344322 AAAAGGGTGACACAGAGTTTTTGAC-TT
1 AAAAGGGTGACACAGAGTTGTGGACTTT
* *
344349 AAAAGGGTGCCATAGAGTTGTGGACTTT
1 AAAAGGGTGACACAGAGTTGTGGACTTT
344377 AAAAGG
1 AAAAGG
344383 AAAAGGGTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 21 0.72
28 8 0.28
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.26
Consensus pattern (28 bp):
AAAAGGGTGACACAGAGTTGTGGACTTT
Done.