Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 130 of 325
Found at i:39255111 original size:87 final size:89
Alignment explanation
Indices: 39254943--39255136 Score: 261
Period size: 87 Copynumber: 2.2 Consensus size: 89
39254933 AATATATATC
**
39254943 ATATCATAACTTACATAACTTACATAAATATATTTGATATCATAATTTATATAACTTACAAAACG
1 ATAT-ATAACTTACATAACTTACATAAATATATTAAATATCATAATTTATATAACTTACAAAACG
39255008 TACATAACTTATATAACTTAGATAA
65 TACATAACTTATATAACTTAGATAA
* * * *
39255033 ATATATAACTTACATAACTTACAT-AATA-CTTAAATAT-AT-TTTATATCATAATTTACATAAC
1 ATATATAACTTACATAACTTACATAAATATATTAAATATCATAATT-TAT-ATAACTTACAAAAC
*
39255094 TTACATAACTTATATAACTTAGATAA
64 GTACATAACTTATATAACTTAGATAA
*
39255120 ATATATAATTTACATAA
1 ATATATAACTTACATAA
39255137 ATATATATCA
Statistics
Matches: 94, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
85 2 0.02
86 5 0.05
87 59 0.63
88 4 0.04
89 20 0.21
90 4 0.04
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (89 bp):
ATATATAACTTACATAACTTACATAAATATATTAAATATCATAATTTATATAACTTACAAAACGT
ACATAACTTATATAACTTAGATAA
Found at i:39261108 original size:33 final size:33
Alignment explanation
Indices: 39261061--39261142 Score: 105
Period size: 31 Copynumber: 2.5 Consensus size: 33
39261051 TTAGAATTAA
*
39261061 TGTTTTTGGTTGTATTTTTTATGTTAAATTTGT
1 TGTTTTTGGTTGTATTTTTTATATTAAATTTGT
* *
39261094 TGTTTTTGGCTGTA--TTTTATATTATATTTGT
1 TGTTTTTGGTTGTATTTTTTATATTAAATTTGT
* *
39261125 TGTATTTGGTTGGATTTT
1 TGTTTTTGGTTGTATTTT
39261143 AATGCAGGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 26 0.63
33 15 0.37
ACGTcount: A:0.15, C:0.01, G:0.20, T:0.65
Consensus pattern (33 bp):
TGTTTTTGGTTGTATTTTTTATATTAAATTTGT
Found at i:39261267 original size:42 final size:42
Alignment explanation
Indices: 39261217--39261381 Score: 246
Period size: 42 Copynumber: 4.0 Consensus size: 42
39261207 GTAAGAAAAG
39261217 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCCAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCCAAA
*
39261259 CGCCGCTAAAAGCCTTGACCTTTTGC-GC-C-TTTCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCC-CAAA
* * *
39261299 CGCCGCTAAAAGACTTGACCTTTTGCGGCGCTTTTCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCCAAA
* *
39261341 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGTTTTTTCCCAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCCAA
39261382 TAAACGCCAC
Statistics
Matches: 111, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
39 6 0.05
40 30 0.27
41 4 0.04
42 66 0.59
43 5 0.05
ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26
Consensus pattern (42 bp):
CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCCAAA
Found at i:39262441 original size:21 final size:21
Alignment explanation
Indices: 39262411--39262456 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
39262401 CGAACGTGTG
*
39262411 GGCCCCCTTGGGCTGAGTATA
1 GGCCCCCTTGGGCCGAGTATA
* *
39262432 GGCCCTCTTGGGCCGAGTATG
1 GGCCCCCTTGGGCCGAGTATA
39262453 GGCC
1 GGCC
39262457 TTTGGTCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.30, G:0.37, T:0.22
Consensus pattern (21 bp):
GGCCCCCTTGGGCCGAGTATA
Found at i:39262687 original size:54 final size:54
Alignment explanation
Indices: 39262546--39262690 Score: 188
Period size: 54 Copynumber: 2.7 Consensus size: 54
39262536 TAAGACCTCG
*
39262546 ATTTGTAAAATTACTGAAATACCCTAG-ATTGTAAAATTATTAAAATATCCCTA
1 ATTTGTAAAATTACTGAAATACCCTAGTATTGTAAAATTATCAAAATATCCCTA
* * *
39262599 ATTTTTAAAATTACCGAAATACCCTCAGT-TTGTAAAATTATCGAAATA-CCCTCA
1 ATTTGTAAAATTACTGAAATACCCT-AGTATTGTAAAATTATCAAAATATCCCT-A
* * *
39262653 GTTTGTAAAATTACTGAAATACCCTTGTAGTGTAAAAT
1 ATTTGTAAAATTACTGAAATACCCTAGTATTGTAAAAT
39262691 GAACATAATG
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
53 29 0.37
54 50 0.63
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (54 bp):
ATTTGTAAAATTACTGAAATACCCTAGTATTGTAAAATTATCAAAATATCCCTA
Found at i:39262690 original size:27 final size:26
Alignment explanation
Indices: 39262547--39262677 Score: 165
Period size: 27 Copynumber: 4.9 Consensus size: 26
39262537 AAGACCTCGA
39262547 TTTGTAAAATTACTGAAATACCCTAG
1 TTTGTAAAATTACTGAAATACCCTAG
* * * *
39262573 ATTGTAAAATTATTAAAATATCCCTAA
1 TTTGTAAAATTACTGAAATA-CCCTAG
* *
39262600 TTTTTAAAATTACCGAAATACCCTCAG
1 TTTGTAAAATTACTGAAATACCCT-AG
39262627 TTTGTAAAATTA-TCGAAATACCCTCAG
1 TTTGTAAAATTACT-GAAATACCCT-AG
39262654 TTTGTAAAATTACTGAAATACCCT
1 TTTGTAAAATTACTGAAATACCCT
39262678 TGTAGTGTAA
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
26 21 0.24
27 67 0.75
28 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (26 bp):
TTTGTAAAATTACTGAAATACCCTAG
Found at i:39262747 original size:27 final size:27
Alignment explanation
Indices: 39262678--39262747 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
39262668 GAAATACCCT
* *
39262678 TGTAGTGTAAAATGAACATAATGCCCC
1 TGTAGGGTAAAATGACCATAATGCCCC
*
39262705 TGTAGGGTAAAATGACCGTAATGCCCC
1 TGTAGGGTAAAATGACCATAATGCCCC
*
39262732 TGTAGGGTAGAATGAC
1 TGTAGGGTAAAATGAC
39262748 GATTATGGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (27 bp):
TGTAGGGTAAAATGACCATAATGCCCC
Found at i:39262964 original size:26 final size:27
Alignment explanation
Indices: 39262916--39262966 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
39262906 ATTCACTCTT
*
39262916 ACTGGTGGTTGTGCCAAAATTACTGAC
1 ACTGGTGGCTGTGCCAAAATTACTGAC
* *
39262943 ACTGGTGGCT-TGCCACATTTACTG
1 ACTGGTGGCTGTGCCAAAATTACTG
39262967 TTTCTGAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (27 bp):
ACTGGTGGCTGTGCCAAAATTACTGAC
Found at i:39263185 original size:33 final size:34
Alignment explanation
Indices: 39263134--39263225 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 34
39263124 GCACTGTTAC
*
39263134 TGTATAGGGCTAAAGCCCAGACTGTTCT-ATTA-T
1 TGTATAGGGCTAAGGCCCAGACTGTTCTGA-TACT
* * *
39263167 TGTACAGGGCTAAGGCCCAAACTGTACTGATACT
1 TGTATAGGGCTAAGGCCCAGACTGTTCTGATACT
* *
39263201 TG-ATAGGGCTCAGGCCCAGATTGTT
1 TGTATAGGGCTAAGGCCCAGACTGTT
39263226 ACTACTTGCA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
33 44 0.92
34 4 0.08
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (34 bp):
TGTATAGGGCTAAGGCCCAGACTGTTCTGATACT
Found at i:39273351 original size:27 final size:26
Alignment explanation
Indices: 39273301--39273351 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
39273291 TAAGCACTTC
* * *
39273301 ATATAACCATTCATATATTTATTTTT
1 ATATAAACATTCATATAGTCATTTTT
39273327 ATATAAACATTTCATATAGTCATTT
1 ATATAAACA-TTCATATAGTCATTT
39273352 CATAAAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (26 bp):
ATATAAACATTCATATAGTCATTTTT
Found at i:39273963 original size:26 final size:26
Alignment explanation
Indices: 39273934--39274053 Score: 125
Period size: 26 Copynumber: 4.6 Consensus size: 26
39273924 ATATTCACCG
**
39273934 GCTCAAAGTATGCTAAATAAACACTA
1 GCTCAAAGCCTGCTAAATAAACACTA
*
39273960 GCTCAAAGCCTGCTAAGTAAACAACT-
1 GCTCAAAGCCTGCTAAATAAAC-ACTA
* *
39273986 GCTCAAAGCCTGCTAAATAATCACCA
1 GCTCAAAGCCTGCTAAATAAACACTA
* * * *
39274012 ACTCAAAGCTTACTAAATAAACACTG
1 GCTCAAAGCCTGCTAAATAAACACTA
* *
39274038 GCTCATATCCTGCTAA
1 GCTCAAAGCCTGCTAA
39274054 TCAGGTACAA
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
25 2 0.03
26 70 0.93
27 3 0.04
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.23
Consensus pattern (26 bp):
GCTCAAAGCCTGCTAAATAAACACTA
Found at i:39274017 original size:52 final size:52
Alignment explanation
Indices: 39273916--39274053 Score: 143
Period size: 52 Copynumber: 2.7 Consensus size: 52
39273906 GTACATACTA
** * ** * *
39273916 CCTACTAAATATTCACCGGCTCAAAGTATGCTAAATAAACACTAGCTCAAAG
1 CCTACTAAATAAACACTGGCTCAAAGCCTGCTAAATAAACACCAACTCAAAG
* * *
39273968 CCTGCTAAGTAAACAACT-GCTCAAAGCCTGCTAAATAATCACCAACTCAAAG
1 CCTACTAAATAAAC-ACTGGCTCAAAGCCTGCTAAATAAACACCAACTCAAAG
* * *
39274020 CTTACTAAATAAACACTGGCTCATATCCTGCTAA
1 CCTACTAAATAAACACTGGCTCAAAGCCTGCTAA
39274054 TCAGGTACAA
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
51 3 0.04
52 64 0.93
53 2 0.03
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (52 bp):
CCTACTAAATAAACACTGGCTCAAAGCCTGCTAAATAAACACCAACTCAAAG
Found at i:39274466 original size:21 final size:21
Alignment explanation
Indices: 39274442--39274482 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39274432 TTTTTATTTA
*
39274442 TTAAC-TAGTAAAACATATATT
1 TTAACATAATAAAACA-ATATT
39274463 TTAACATAATAAAACAATAT
1 TTAACATAATAAAACAATAT
39274483 CAGTAGTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (21 bp):
TTAACATAATAAAACAATATT
Found at i:39276096 original size:23 final size:23
Alignment explanation
Indices: 39276070--39276118 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
39276060 ACAGCTAACA
*
39276070 ATTTTGAGATCCAACAGGCAATG
1 ATTTTGAGATCAAACAGGCAATG
*
39276093 ATTTTGAGATCAAACTGGCAATG
1 ATTTTGAGATCAAACAGGCAATG
39276116 ATT
1 ATT
39276119 CAGATGATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (23 bp):
ATTTTGAGATCAAACAGGCAATG
Found at i:39280106 original size:12 final size:12
Alignment explanation
Indices: 39280089--39280115 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39280079 ACCTTAACAC
39280089 AAGAGAATGCAA
1 AAGAGAATGCAA
39280101 AAGAGAATGCAA
1 AAGAGAATGCAA
39280113 AAG
1 AAG
39280116 GTCCCCCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.26, T:0.07
Consensus pattern (12 bp):
AAGAGAATGCAA
Found at i:39294065 original size:40 final size:40
Alignment explanation
Indices: 39294021--39294223 Score: 196
Period size: 39 Copynumber: 5.2 Consensus size: 40
39294011 GTTCAAAACA
* * ***
39294021 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
* * *
39294061 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
* * * * * *
39294101 CCTTCGGG-CTTAGCCCGAATATCATAGCTCACACAATTG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
** *
39294140 CCTTCGGG-CTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
** * *
39294179 CCTTCGGG-CTTAGCCCGGATATCACAATTCGCACAATTA
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
39294218 CCTTCG
1 CCTTCG
39294224 CATCTTTGTT
Statistics
Matches: 144, Mismatches: 19, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 104 0.72
40 40 0.28
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
Found at i:39294136 original size:39 final size:39
Alignment explanation
Indices: 39294051--39294223 Score: 256
Period size: 39 Copynumber: 4.4 Consensus size: 39
39294041 TATGGTAACC
* *
39294051 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* * *
39294091 CGCACAATTGCCTTCGGGCTTAGCCCGAATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
* *
39294130 CACACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
39294169 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
39294208 CGCACAATTACCTTCG
1 CGCACAATTGCCTTCG
39294224 CATCTTTGTT
Statistics
Matches: 121, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 104 0.86
40 17 0.14
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:39300329 original size:40 final size:40
Alignment explanation
Indices: 39300285--39300469 Score: 205
Period size: 39 Copynumber: 4.7 Consensus size: 40
39300275 GTTCAAAACA
* * ***
39300285 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
* * *
39300325 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
* * * * *
39300365 CCTTCGGG-CTTAGCCCGGATATCATAGCTCACACAATTG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
** *
39300404 CCTTCGGG-CTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
39300443 CCTTCGGG-CTTAGCCCGGATATCACAA
1 CCTTCGGGACTTAGCCCGGATATCACAA
39300470 TTCGCACATT
Statistics
Matches: 129, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 89 0.69
40 40 0.31
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATCACAACCCGCACAAATG
Found at i:39300400 original size:39 final size:39
Alignment explanation
Indices: 39300315--39300477 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
39300305 TATGGTAACC
* *
39300315 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
39300355 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
* *
39300394 CACACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
39300433 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
39300472 CGCACA
1 CGCACA
39300478 TTATTCGCAT
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 97 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:39305140 original size:11 final size:11
Alignment explanation
Indices: 39305124--39305148 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39305114 GAATTTAAGG
39305124 TAGAAATTGAA
1 TAGAAATTGAA
39305135 TAGAAATTGAA
1 TAGAAATTGAA
39305146 TAG
1 TAG
39305149 GAAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (11 bp):
TAGAAATTGAA
Found at i:39305862 original size:34 final size:34
Alignment explanation
Indices: 39305801--39305867 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
39305791 TTAGAAAATG
* ***
39305801 GAAAGTGAATTTAAATTGAATTGTGA-TTGAATT
1 GAAAGTGAATTTAAATAGAAAAATGATTTGAATT
39305834 GAAAGTGAACTTTAAATAGAAAAATGATTTGAAT
1 GAAAGTGAA-TTTAAATAGAAAAATGATTTGAAT
39305868 ACCTTATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 9 0.32
34 13 0.46
35 6 0.21
ACGTcount: A:0.45, C:0.01, G:0.19, T:0.34
Consensus pattern (34 bp):
GAAAGTGAATTTAAATAGAAAAATGATTTGAATT
Found at i:39305979 original size:21 final size:21
Alignment explanation
Indices: 39305953--39306016 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
39305943 GCTATGCCGA
39305953 TCAGGCACTATATGTGTCGTAT
1 TCAGGCACT-TATGTGTCGTAT
**
39305975 T-AGGCACCTCGTGTGTCGT-T
1 TCAGGCA-CTTATGTGTCGTAT
39305995 TCAGGCACTTTATGTGTCGTAT
1 TCAGGCAC-TTATGTGTCGTAT
39306017 ACTATTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 3 0.09
21 27 0.79
22 4 0.12
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (21 bp):
TCAGGCACTTATGTGTCGTAT
Found at i:39312009 original size:43 final size:42
Alignment explanation
Indices: 39311946--39312057 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 42
39311936 TACCGTACCA
* **
39311946 ATGCCATATCCCAGATATGGTCTTACAT-GTGATCTCATATCG
1 ATGCCATAGCCCAGATATGGTCTTACATAAAG-TCTCATATCG
39311988 ATGCCAATAGCCCA-ATTATGGTCTTACATAAAGTCTCATATCG
1 ATGCC-ATAGCCCAGA-TATGGTCTTACATAAAGTCTCATATCG
* *
39312031 ATGCCATATCCTAGATATGGTCTTACA
1 ATGCCATAGCCCAGATATGGTCTTACA
39312058 CGTAAATCTG
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
42 24 0.39
43 36 0.59
44 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGCCATAGCCCAGATATGGTCTTACATAAAGTCTCATATCG
Found at i:39321751 original size:43 final size:42
Alignment explanation
Indices: 39321682--39321802 Score: 122
Period size: 42 Copynumber: 2.8 Consensus size: 42
39321672 ATCAAGTACA
* * *
39321682 ATGCTGACGTCCCAGAC-GTGGTCTTACATGTAATTCA-ATATCG
1 ATGCTGATGTCCCAGACAG-GGTCTTACACG-AAATCAGATA-CG
*
39321725 ATGCCT-CTGTCCCAGACAGGGTCTTACACGAAATCAGATACG
1 ATG-CTGATGTCCCAGACAGGGTCTTACACGAAATCAGATACG
* *
39321767 ATGCTGATGTCCCAGACATGGTCTTATACGTAAATC
1 ATGCTGATGTCCCAGACAGGGTCTTACACG-AAATC
39321803 TCAATCGAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
41 2 0.03
42 31 0.47
43 30 0.45
44 3 0.05
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (42 bp):
ATGCTGATGTCCCAGACAGGGTCTTACACGAAATCAGATACG
Found at i:39321782 original size:42 final size:43
Alignment explanation
Indices: 39321682--39321838 Score: 135
Period size: 43 Copynumber: 3.7 Consensus size: 43
39321672 ATCAAGTACA
* * *
39321682 ATGCTGACGTCCCAGAC-GTGGTCTTACATGTAATTCAATATCG
1 ATGCTGATGTCCCAGACAG-GGTCTTACACGTAAATCAATATCG
*
39321725 ATGCCT-CTGTCCCAGACAGGGTCTTACACG-AAATCAGATA-CG
1 ATG-CTGATGTCCCAGACAGGGTCTTACACGTAAATCA-ATATCG
* * *
39321767 ATGCTGATGTCCCAGACATGGTCTTATACGTAAATCTCA-ATCG
1 ATGCTGATGTCCCAGACAGGGTCTTACACGTAAATC-AATATCG
* ** * *
39321810 AGGCTTTTGTCCTAGACACGGTCTTACAC
1 ATGCTGATGTCCCAGACAGGGTCTTACAC
39321839 AATGTCACAT
Statistics
Matches: 93, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
41 2 0.02
42 32 0.34
43 56 0.60
44 3 0.03
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (43 bp):
ATGCTGATGTCCCAGACAGGGTCTTACACGTAAATCAATATCG
Found at i:39321821 original size:85 final size:85
Alignment explanation
Indices: 39321682--39321838 Score: 201
Period size: 85 Copynumber: 1.8 Consensus size: 85
39321672 ATCAAGTACA
* * * *
39321682 ATGCTGACGTCCCAGACGTGGTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAGACAGGGT
1 ATGCTGACGTCCCAGACATGGTCTTACACGTAATTCAATATCGAGGCCTCTGTCCCAGACACGGT
39321747 CTTACACGAAATCAGATACG
66 CTTACACGAAATCAGATACG
* * * * *
39321767 ATGCTGATGTCCCAGACATGGTCTTATACGTAAATCTC-A-ATCGAGGCTTTTGTCCTAGACACG
1 ATGCTGACGTCCCAGACATGGTCTTACACGT-AAT-TCAATATCGAGGCCTCTGTCCCAGACACG
39321830 GTCTTACAC
64 GTCTTACAC
39321839 AATGTCACAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
85 55 0.90
86 4 0.07
87 2 0.03
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (85 bp):
ATGCTGACGTCCCAGACATGGTCTTACACGTAATTCAATATCGAGGCCTCTGTCCCAGACACGGT
CTTACACGAAATCAGATACG
Found at i:39322685 original size:29 final size:29
Alignment explanation
Indices: 39322643--39322701 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
39322633 AATCGGCCAA
39322643 GAGAACGGTAAAAATGAATACCATTTTAT
1 GAGAACGGTAAAAATGAATACCATTTTAT
*
39322672 GAGAATGGTAAAAATGAATACCATTTTAT
1 GAGAACGGTAAAAATGAATACCATTTTAT
39322701 G
1 G
39322702 TTATAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (29 bp):
GAGAACGGTAAAAATGAATACCATTTTAT
Found at i:39325827 original size:49 final size:49
Alignment explanation
Indices: 39325774--39325878 Score: 165
Period size: 49 Copynumber: 2.1 Consensus size: 49
39325764 TAGGCAGGTT
**
39325774 TTACACTGGCTCTCATCTATTGGTGTCAATGCCATGTCCCAGACAAGTC
1 TTACACTGGCTCTCATCTATCAGTGTCAATGCCATGTCCCAGACAAGTC
* * *
39325823 TTACATTGGTTCTCATCTATCAGTGTCAATGCCATGTCCCAGACAGGTC
1 TTACACTGGCTCTCATCTATCAGTGTCAATGCCATGTCCCAGACAAGTC
39325872 TTACACT
1 TTACACT
39325879 AATACACAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (49 bp):
TTACACTGGCTCTCATCTATCAGTGTCAATGCCATGTCCCAGACAAGTC
Found at i:39325995 original size:46 final size:48
Alignment explanation
Indices: 39325930--39326072 Score: 168
Period size: 48 Copynumber: 3.0 Consensus size: 48
39325920 ACCAACTTGT
* * *
39325930 ATATCTCGAGGTC-GATGCATGTCCTAGACATGTCTTACACTAGCTCTC
1 ATATCTCAAGG-CAGATGCATGTCCCAGACATGTCTTACACTGGCTCTC
* * * *
39325978 GT-T-TCAATGCAGATGCATGTCCCAAACATGTCTTACACTGGCTGGT-
1 ATATCTCAAGGCAGATGCATGTCCCAGACATGTCTTACACTGGCT-CTC
*
39326024 ATATCTCAAGGCTGATGCATGTCCCAGACATGTCTTACACTGGCTCTC
1 ATATCTCAAGGCAGATGCATGTCCCAGACATGTCTTACACTGGCTCTC
39326072 A
1 A
39326073 ATATGTGGCC
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
45 1 0.01
46 34 0.44
47 4 0.05
48 39 0.50
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.30
Consensus pattern (48 bp):
ATATCTCAAGGCAGATGCATGTCCCAGACATGTCTTACACTGGCTCTC
Found at i:39326041 original size:94 final size:94
Alignment explanation
Indices: 39325899--39326071 Score: 249
Period size: 94 Copynumber: 1.8 Consensus size: 94
39325889 AAGCTAACGC
* * *
39325899 CATGTCCCAAACAAGTCTAACACCAACTTGTATATCTCGAGGTCGATGCATGTCCTAGACATGTC
1 CATGTCCCAAACAAGTCTAACACCAACTGGTATATCTCAAGGTCGATGCATGTCCCAGACATGTC
39325964 TTACACTAGCTCTCGTTTCAATGCAGATG
66 TTACACTAGCTCTCGTTTCAATGCAGATG
* * ***
39325993 CATGTCCCAAACATGTCTTACACTGGCTGGTATATCTCAAGG-CTGATGCATGTCCCAGACATGT
1 CATGTCCCAAACAAGTCTAACACCAACTGGTATATCTCAAGGTC-GATGCATGTCCCAGACATGT
*
39326057 CTTACACTGGCTCTC
65 CTTACACTAGCTCTC
39326072 AATATGTGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
93 1 0.01
94 68 0.99
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (94 bp):
CATGTCCCAAACAAGTCTAACACCAACTGGTATATCTCAAGGTCGATGCATGTCCCAGACATGTC
TTACACTAGCTCTCGTTTCAATGCAGATG
Found at i:39327608 original size:80 final size:80
Alignment explanation
Indices: 39327524--39327672 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
39327514 TATGGTAACC
* * * *
39327524 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
39327588 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
39327604 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
39327669 CCGG
66 CCGG
39327673 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:39327614 original size:40 final size:38
Alignment explanation
Indices: 39327565--39327672 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
39327555 ATCACGATTT
*
39327565 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
39327605 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
39327645 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
39327673 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:39335348 original size:42 final size:40
Alignment explanation
Indices: 39335269--39335416 Score: 278
Period size: 40 Copynumber: 3.6 Consensus size: 40
39335259 CGGTTGCACG
39335269 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
39335309 GCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGG--ATATATCAACTCGCACGAAT
39335351 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
39335391 GCCTTCGGGTCTTAGCCCGGATATAT
1 GCCTTCGGGTCTTAGCCCGGATATAT
39335417 TTCCAATGTT
Statistics
Matches: 106, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
40 66 0.62
42 40 0.38
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAAT
Found at i:39340546 original size:48 final size:49
Alignment explanation
Indices: 39340450--39340944 Score: 729
Period size: 48 Copynumber: 10.2 Consensus size: 49
39340440 TGTAGTGAAT
*
39340450 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATG-ATATATGTGGTAAAGCCGAATGGCTA
* *
39340500 ATGTGAAATATGTATGAGATATG-TATATGTGGCAAAGCCGACTGGCTA
1 ATGTGAAATATGTATGAGATATGATATATGTGGTAAAGCCGAATGGCTA
* *
39340548 CTGTGAAATATATATGAGATATG-TATATGT-GTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGATATATGTGGTAAAGCCGAATGGCTA
* *
39340595 ATGTGAAATATGCATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATG-ATATATGTGGTAAAGCCGAATGGCTA
* *
39340645 ATGTGAAATATGCATGAGA-ATGTATATATGTGGTAAAAG-CGAATGACTA
1 ATGTGAAATATGTATGAGATATG-ATATATGTGGT-AAAGCCGAATGGCTA
* * *
39340694 CTGTGAAATATATATGAGATATG-TATATGCGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGATATATGTGGTAAAGCCGAATGGCTA
*
39340742 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATG-ATATATGTGGTAAAGCCGAATGGCTA
*
39340792 ATGTGAAATATGTATGAGATATG-TATATGTGGTAAAGTCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGATATATGTGGTAAAGCCGAATGGCTA
*
39340840 ATGTGAAATATGCATGAGATATG-TATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGATATATGTGGTAAAGCCGAATGGCTA
*
39340888 ATGTGAAATATGCATGAGA-ATGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATG-ATATATGTGGTAAAGCCGAATGGCTA
39340937 ATGTGAAA
1 ATGTGAAA
39340945 AGCCGAATGG
Statistics
Matches: 410, Mismatches: 25, Indels: 21
0.90 0.05 0.05
Matches are distributed among these distances:
47 41 0.10
48 178 0.43
49 80 0.20
50 111 0.27
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (49 bp):
ATGTGAAATATGTATGAGATATGATATATGTGGTAAAGCCGAATGGCTA
Found at i:39340947 original size:21 final size:21
Alignment explanation
Indices: 39340922--39340965 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
39340912 TATATGTGGT
39340922 AAAGCCGAATGGCTAATGTGA
1 AAAGCCGAATGGCTAATGTGA
39340943 AAAGCCGAATGGCTAATGTGA
1 AAAGCCGAATGGCTAATGTGA
39340964 AA
1 AA
39340966 TATGTATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.18
Consensus pattern (21 bp):
AAAGCCGAATGGCTAATGTGA
Found at i:39340947 original size:70 final size:70
Alignment explanation
Indices: 39340873--39341014 Score: 259
Period size: 70 Copynumber: 2.0 Consensus size: 70
39340863 TATATGTGGT
39340873 AAAGCCGAATGGCTAATGTGAAATATGCATGAG-AATGTATATATGTGGTAAAGCCGAATGGCTA
1 AAAGCCGAATGGCTAATGTGAAATATGCATGAGAAAT-TATATATGTGGTAAAGCCGAATGGCTA
39340937 ATGTGA
65 ATGTGA
*
39340943 AAAGCCGAATGGCTAATGTGAAATATGTATGAGAAATTATATATGTGGTAAAGCCGAATGGCTAA
1 AAAGCCGAATGGCTAATGTGAAATATGCATGAGAAATTATATATGTGGTAAAGCCGAATGGCTAA
39341008 TGTGA
66 TGTGA
39341013 AA
1 AA
39341015 TATGTATGAG
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
70 67 0.96
71 3 0.04
ACGTcount: A:0.39, C:0.09, G:0.26, T:0.26
Consensus pattern (70 bp):
AAAGCCGAATGGCTAATGTGAAATATGCATGAGAAATTATATATGTGGTAAAGCCGAATGGCTAA
TGTGA
Found at i:39342731 original size:40 final size:40
Alignment explanation
Indices: 39342672--39342877 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 40
39342662 CAATTGAATG
* * * *
39342672 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * *
39342712 ATATCCGGGTTAAGACCCGAAGGCA-TTGTGCTAGTGA-C
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
39342750 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
39342790 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
39342830 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
39342870 ATATCCGG
1 ATATCCGG
39342878 TTGTATTCCG
Statistics
Matches: 140, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
38 23 0.16
39 18 0.13
40 99 0.71
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:39342808 original size:78 final size:80
Alignment explanation
Indices: 39342674--39342877 Score: 243
Period size: 78 Copynumber: 2.6 Consensus size: 80
39342664 ATTGAATGAT
* * ** * * *
39342674 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCA-T
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
*
39342738 TGTGCTAGT-G-ACAC
66 TGTGCAAGTCGTAC-C
* * *
39342752 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
* *
39342817 TGTGCAAGTCGTTCT
66 TGTGCAAGTCGTACC
* *
39342832 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
39342878 TTGTATTCCG
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
78 53 0.50
79 9 0.08
80 44 0.41
81 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
TGTGCAAGTCGTACC
Found at i:39350739 original size:40 final size:40
Alignment explanation
Indices: 39350680--39350885 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 40
39350670 CAATTGAATG
* * * *
39350680 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * *
39350720 ATATCCGGGTTAAGACCCGAAGGCA-TTGTGCTAGTGA-C
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
39350758 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
39350798 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
39350838 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
39350878 ATATCCGG
1 ATATCCGG
39350886 TTGTATTCCG
Statistics
Matches: 140, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
38 23 0.16
39 18 0.13
40 99 0.71
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:39350816 original size:78 final size:80
Alignment explanation
Indices: 39350682--39350885 Score: 243
Period size: 78 Copynumber: 2.6 Consensus size: 80
39350672 ATTGAATGAT
* * ** * * *
39350682 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCA-T
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
*
39350746 TGTGCTAGT-G-ACAC
66 TGTGCAAGTCGTAC-C
* * *
39350760 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
* *
39350825 TGTGCAAGTCGTTCT
66 TGTGCAAGTCGTACC
* *
39350840 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
39350886 TTGTATTCCG
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
78 53 0.50
79 9 0.08
80 44 0.41
81 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
TGTGCAAGTCGTACC
Found at i:39352379 original size:50 final size:48
Alignment explanation
Indices: 39352249--39352446 Score: 324
Period size: 48 Copynumber: 4.1 Consensus size: 48
39352239 GGGTGTTACA
* *
39352249 AGATATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
*
39352297 AGATATGTATATGCGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
*
39352345 AGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
1 AGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* *
39352395 AGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
39352443 AGAT
1 AGAT
39352447 GTGTGTATAT
Statistics
Matches: 140, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
48 94 0.67
50 46 0.33
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.30
Consensus pattern (48 bp):
AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
Found at i:39352425 original size:98 final size:98
Alignment explanation
Indices: 39352256--39352445 Score: 335
Period size: 98 Copynumber: 1.9 Consensus size: 98
39352246 ACAAGATATG
*
39352256 TATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGCGGTAAAGCCG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGCGGTAAAGCCG
*
39352321 AATGGCTAATGTGAAATATGTATGAGAAATGTA
66 AATGGCTAATGTGAAATATGTAGGAGAAATGTA
* *
39352354 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGCGGTAAAGCCG
*
39352419 AATGGCTAGTGTGAAATATGTAGGAGA
66 AATGGCTAATGTGAAATATGTAGGAGA
39352446 TGTGTGTATA
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.29
Consensus pattern (98 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGCGGTAAAGCCG
AATGGCTAATGTGAAATATGTAGGAGAAATGTA
Found at i:39354077 original size:23 final size:23
Alignment explanation
Indices: 39354045--39354117 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 23
39354035 CTGATGTTAT
39354045 ATTCGGGCTAAGTTCCAAAGAGC
1 ATTCGGGCTAAGTTCCAAAGAGC
* * *
39354068 ATTCGTGCT-AG-T---AA-TGT
1 ATTCGGGCTAAGTTCCAAAGAGC
*
39354085 ATCCGGGCTAAGTTCCAAAGAGC
1 ATTCGGGCTAAGTTCCAAAGAGC
*
39354108 ATTCGTGCTA
1 ATTCGGGCTA
39354118 GTGATGTATT
Statistics
Matches: 35, Mismatches: 9, Indels: 12
0.62 0.16 0.21
Matches are distributed among these distances:
17 8 0.23
18 4 0.11
19 1 0.03
21 1 0.03
22 4 0.11
23 17 0.49
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (23 bp):
ATTCGGGCTAAGTTCCAAAGAGC
Found at i:39354264 original size:40 final size:40
Alignment explanation
Indices: 39353928--39354248 Score: 477
Period size: 40 Copynumber: 8.1 Consensus size: 40
39353918 AGTTATATAG
* * *
39353928 CCGGGCTAAG-TCCGAAGAGCATTCGTGCT-GATGTTATAG
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAG-TGATGTAT
*
39353967 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
39354007 CCGGGCTAAGTTCCGAAGAGCATTCGTGCT-GATGTTATAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAG-TGATGTAT
* * *
39354047 TCGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTAATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
*
39354087 CCGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
39354127 TCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
*
39354167 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
*
39354207 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
39354247 CC
1 CC
39354249 AAGCTAAACC
Statistics
Matches: 258, Mismatches: 20, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
39 11 0.04
40 245 0.95
41 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
Found at i:39354368 original size:29 final size:29
Alignment explanation
Indices: 39354283--39354383 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 29
39354273 GCTGGAGTTA
* * * *
39354283 TGAGGCACTGTGTGTGCAAGTTCTTCAAC
1 TGAGGCACTATGTGTGCGAGTTCTTTAAT
**
39354312 TGA-GCACTATGTGTGCGAGATT-GGTAAT
1 TGAGGCACTATGTGTGCGAG-TTCTTTAAT
*
39354340 TGAGGCACTATGTATGCGAGTTCTTTAAT
1 TGAGGCACTATGTGTGCGAGTTCTTTAAT
* *
39354369 CGA-GCGCTATGTGTG
1 TGAGGCACTATGTGTG
39354384 TGAAATCAGT
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
28 31 0.54
29 26 0.46
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.33
Consensus pattern (29 bp):
TGAGGCACTATGTGTGCGAGTTCTTTAAT
Found at i:39356548 original size:48 final size:48
Alignment explanation
Indices: 39356452--39357203 Score: 1191
Period size: 48 Copynumber: 15.4 Consensus size: 48
39356442 TGTAGTGAAT
*
39356452 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTA
39356502 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* *
39356550 CTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
*
39356598 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTA
*
39356648 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGTCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* *
39356696 ATGTGAAATATGCATGAGAAATGTATATATGTGGTAAAGCC-AATTGGCTA
1 ATGTGAAATATGTATGAGATATG--TATATGTGGTAAAGCCGAA-TGGCTA
* * *
39356746 ATGTGAAATATGCATGATAAATGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTA
* *
39356796 ATGTGAAATATGTATGAGATATGTGTATGTGGTAAAGTCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* *
39356844 CTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
*
39356892 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTA
39356942 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* * *
39356990 CTGTGAAATATATATGAGATATGTATATGCGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
*
39357038 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTA
39357088 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
39357136 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* *
39357184 GTGTGAAATATGTAGGAGAT
1 ATGTGAAATATGTATGAGAT
39357204 GTGTGTATAT
Statistics
Matches: 657, Mismatches: 35, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
48 404 0.61
49 2 0.00
50 249 0.38
51 2 0.00
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (48 bp):
ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
Found at i:39356635 original size:98 final size:96
Alignment explanation
Indices: 39356452--39357203 Score: 1191
Period size: 98 Copynumber: 7.7 Consensus size: 96
39356442 TGTAGTGAAT
*
39356452 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
1 ATGTGAAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
39356517 GAGATATGTATATGTGGTAAAGCCGAATGGCTA
64 GAGATATGTATATGTGGTAAAGCCGAATGGCTA
* *
39356550 CTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
*
39356615 GAAATGTATATATGTGGTAAAGCCGAATGGCTA
66 GATATG--TATATGTGGTAAAGCCGAATGGCTA
* *
39356648 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGTCGAATGGCTAATGTGAAATATGCATGA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
*
39356713 GAAATGTATATATGTGGTAAAGCC-AATTGGCTA
66 GATATG--TATATGTGGTAAAGCCGAA-TGGCTA
* * *
39356746 ATGTGAAATATGCATGATAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
1 ATGTGAAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
* *
39356811 GAGATATGTGTATGTGGTAAAGTCGAATGGCTA
64 GAGATATGTATATGTGGTAAAGCCGAATGGCTA
* *
39356844 CTGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
*
39356909 GAAATGTATATATGTGGTAAAGCCGAATGGCTA
66 GATATG--TATATGTGGTAAAGCCGAATGGCTA
* *
39356942 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
*
39357007 GATATGTATATGCGGTAAAGCCGAATGGCTA
66 GATATGTATATGTGGTAAAGCCGAATGGCTA
*
39357038 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
1 ATGTGAAATATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
39357103 GAGATATGTATATGTGGTAAAGCCGAATGGCTA
64 GAGATATGTATATGTGGTAAAGCCGAATGGCTA
* *
39357136 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
39357201 GAT
66 GAT
39357204 GTGTGTATAT
Statistics
Matches: 607, Mismatches: 37, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
96 183 0.30
97 2 0.00
98 375 0.62
99 2 0.00
100 45 0.07
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (96 bp):
ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
GATATGTATATGTGGTAAAGCCGAATGGCTA
Found at i:39357213 original size:146 final size:146
Alignment explanation
Indices: 39356452--39357202 Score: 1342
Period size: 146 Copynumber: 5.1 Consensus size: 146
39356442 TGTAGTGAAT
39356452 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
1 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
39356517 GAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGG
66 GAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGG
39356582 TAAAGCCGAATGGCTA
131 TAAAGCCGAATGGCTA
39356598 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
1 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
* * ** *
39356663 GAGATATGTATATGTGGTAAAGTCGAATGGCTAATGTGAAATATGCATGAGAAATGTATATATGT
66 GAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATG--TATATGT
39356728 GGTAAAGCC-AATTGGCTA
129 GGTAAAGCCGAA-TGGCTA
* *
39356746 ATGTGAAATATGCATGATAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
1 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
* *
39356811 GAGATATGTGTATGTGGTAAAGTCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGG
66 GAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGG
39356876 TAAAGCCGAATGGCTA
131 TAAAGCCGAATGGCTA
39356892 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
1 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
*
39356957 GAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGCGG
66 GAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGG
39357022 TAAAGCCGAATGGCTA
131 TAAAGCCGAATGGCTA
39357038 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
1 ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
* *
39357103 GAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGG
66 GAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGG
39357168 TAAAGCCGAATGGCTA
131 TAAAGCCGAATGGCTA
* *
39357184 GTGTGAAATATGTAGGAGA
1 ATGTGAAATATGTATGAGA
39357203 TGTGTGTATA
Statistics
Matches: 579, Mismatches: 22, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
146 439 0.76
147 4 0.01
148 136 0.23
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (146 bp):
ATGTGAAATATGTATGAGAAATGTATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
GAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATATATGAGATATGTATATGTGG
TAAAGCCGAATGGCTA
Found at i:39361118 original size:27 final size:27
Alignment explanation
Indices: 39361088--39361146 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
39361078 TTAACACCCT
39361088 AGGGGCAAAAT-GGTAATTCTACCCTAC
1 AGGGG-AAAATCGGTAATTCTACCCTAC
* ** *
39361115 AGGGGTATTTCGGTAATTTTACCCTAC
1 AGGGGAAAATCGGTAATTCTACCCTAC
39361142 AGGGG
1 AGGGG
39361147 TATTTTAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (27 bp):
AGGGGAAAATCGGTAATTCTACCCTAC
Found at i:39361147 original size:27 final size:28
Alignment explanation
Indices: 39361114--39361296 Score: 225
Period size: 27 Copynumber: 6.8 Consensus size: 28
39361104 TTCTACCCTA
* **
39361114 CAGGGGTATTTCGGTAATTTTACCCTA-
1 CAGGGGTATTTTGGTAATTTTACCAAAC
* *
39361141 CAGGGGTATTTTAGTAATTTT-GCAAAC
1 CAGGGGTATTTTGGTAATTTTACCAAAC
*
39361168 CATGGGTATTTTGGTAATTTTA-CAAAC
1 CAGGGGTATTTTGGTAATTTTACCAAAC
*
39361195 CAGGGGTATTTTGGTAATTTT-GCAAAC
1 CAGGGGTATTTTGGTAATTTTACCAAAC
* *
39361222 CAGGGATATTTTGGTAATTTT-GCAAAC
1 CAGGGGTATTTTGGTAATTTTACCAAAC
* *
39361249 CAGGGGTATTTTGGTAGTTTTA-CAACC
1 CAGGGGTATTTTGGTAATTTTACCAAAC
39361276 CAGGGGTATTTTGGTAATTTT
1 CAGGGGTATTTTGGTAATTTT
39361297 GTAAATCGAG
Statistics
Matches: 139, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
26 2 0.01
27 137 0.99
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (28 bp):
CAGGGGTATTTTGGTAATTTTACCAAAC
Found at i:39361233 original size:81 final size:80
Alignment explanation
Indices: 39361114--39361297 Score: 269
Period size: 81 Copynumber: 2.3 Consensus size: 80
39361104 TTCTACCCTA
* * ** * *
39361114 CAGGGGTATTTCGGTAATTTTACCCTACAGGGGTATTTTAGTAATTTTGCAAACCATGGGTATTT
1 CAGGGGTATTTTGGTAATTTT-GCAAACAGGGATATTTTAGTAATTTTGCAAACCAGGGGTATTT
39361179 TGGTAATTTTACAAAC
65 TGGTAATTTTACAAAC
*
39361195 CAGGGGTATTTTGGTAATTTTGCAAACCAGGGATATTTTGGTAATTTTGCAAACCAGGGGTATTT
1 CAGGGGTATTTTGGTAATTTTGCAAA-CAGGGATATTTTAGTAATTTTGCAAACCAGGGGTATTT
* *
39361260 TGGTAGTTTTACAACC
65 TGGTAATTTTACAAAC
39361276 CAGGGGTATTTTGGTAATTTTG
1 CAGGGGTATTTTGGTAATTTTG
39361298 TAAATCGAGG
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 2 0.02
81 91 0.98
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.39
Consensus pattern (80 bp):
CAGGGGTATTTTGGTAATTTTGCAAACAGGGATATTTTAGTAATTTTGCAAACCAGGGGTATTTT
GGTAATTTTACAAAC
Found at i:39361310 original size:54 final size:54
Alignment explanation
Indices: 39361114--39361297 Score: 253
Period size: 54 Copynumber: 3.4 Consensus size: 54
39361104 TTCTACCCTA
* * ** *
39361114 CAGGGGTATTTCGGTAATTTTACCCTA-CAGGGGTATTTTAGTAATTTTGCAAAC
1 CAGGGGTATTTTGGTAATTTT-GCAAACCAGGGGTATTTTGGTAATTTTGCAAAC
* *
39361168 CATGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGCAAAC
1 CAGGGGTATTTTGGTAATTTTGCAAACCAGGGGTATTTTGGTAATTTTGCAAAC
* * * *
39361222 CAGGGATATTTTGGTAATTTTGCAAACCAGGGGTATTTTGGTAGTTTTACAACC
1 CAGGGGTATTTTGGTAATTTTGCAAACCAGGGGTATTTTGGTAATTTTGCAAAC
39361276 CAGGGGTATTTTGGTAATTTTG
1 CAGGGGTATTTTGGTAATTTTG
39361298 TAAATCGAGG
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
53 2 0.02
54 114 0.98
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.39
Consensus pattern (54 bp):
CAGGGGTATTTTGGTAATTTTGCAAACCAGGGGTATTTTGGTAATTTTGCAAAC
Found at i:39361319 original size:81 final size:81
Alignment explanation
Indices: 39361154--39361321 Score: 239
Period size: 81 Copynumber: 2.1 Consensus size: 81
39361144 GGGTATTTTA
*
39361154 GTAATTTTGCAAACCATGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGCA
1 GTAATTTTGCAAACCAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGCA
****
39361219 AACCAGGGATATTTTG
66 AACCAGGGATAAAACG
* * *
39361235 GTAATTTTGCAAACCAGGGGTATTTTGGTAGTTTTACAACCCAGGGGTATTTTGGTAATTTTGTA
1 GTAATTTTGCAAACCAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGCA
*
39361300 AATCGAGGG-TAAAACG
66 AA-CCAGGGATAAAACG
39361316 GTAATT
1 GTAATT
39361322 CTATAAATTG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 72 0.94
82 5 0.06
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (81 bp):
GTAATTTTGCAAACCAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGCA
AACCAGGGATAAAACG
Found at i:39361337 original size:81 final size:80
Alignment explanation
Indices: 39361171--39361418 Score: 214
Period size: 81 Copynumber: 3.1 Consensus size: 80
39361161 TGCAAACCAT
* * * ***
39361171 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGCAAA-CCAGGGATATTTTG
1 GGGTATTTTGGTAATTTTACAACCCAGGGGTATTTTGGTAATTTTGTAAATCGAGGG-TAAAATG
* * **
39361235 GTAATTTTGCAAACCA
65 GTAATTCTGTAAATGA
* *
39361251 GGGGTATTTTGGTAGTTTTACAACCCAGGGGTATTTTGGTAATTTTGTAAATCGAGGGTAAAACG
1 -GGGTATTTTGGTAATTTTACAACCCAGGGGTATTTTGGTAATTTTGTAAATCGAGGGTAAAATG
*
39361316 GTAATTCTATAAATTGA
65 GTAATTCTGTAAA-TGA
*** * ** *** *
39361333 GGGTAAAATAGTAATTCTGTA-AACTGA-GGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAAT
1 GGGTATTTTGGTAATT-T-TACAACCCAGGGGTATTTTGGTAATTTTGTAAATCGAGGGTAAAAT
39361396 GGTAATTCTGTAAACTGA
64 GGTAATTCTGTAAA-TGA
39361414 GGGTA
1 GGGTA
39361419 AAACGGTAAT
Statistics
Matches: 136, Mismatches: 27, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
81 123 0.90
82 11 0.08
83 2 0.01
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (80 bp):
GGGTATTTTGGTAATTTTACAACCCAGGGGTATTTTGGTAATTTTGTAAATCGAGGGTAAAATGG
TAATTCTGTAAATGA
Found at i:39361535 original size:81 final size:81
Alignment explanation
Indices: 39361287--39361551 Score: 338
Period size: 81 Copynumber: 3.3 Consensus size: 81
39361277 AGGGGTATTT
* * * *
39361287 TGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAATAGTAATTCTG
1 TGGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTG
39361352 TAAA-CTGAGGGTAAAA
66 TAAATC-GAGGGTAAAA
* * * *
39361368 TGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCT
1 TGGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATC-GAGGGTAAAATGGTAATTCT
39361432 GTAAATCGAGGGTAAAA
65 GTAAATCGAGGGTAAAA
* * *
39361449 CGGTAATTTTAAAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAATGGTAATTCTG
1 TGGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTG
***
39361514 TAAATCG-GGAGTACTT
66 TAAATCGAGG-GTAAAA
* *
39361530 TGGTAATTTTACAAGTCGAGGG
1 TGGTAATTTTATAAATCGAGGG
39361552 CATTTCAGTA
Statistics
Matches: 161, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
80 2 0.01
81 157 0.98
82 2 0.01
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (81 bp):
TGGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTG
TAAATCGAGGGTAAAA
Found at i:39361537 original size:27 final size:27
Alignment explanation
Indices: 39361287--39361520 Score: 328
Period size: 27 Copynumber: 8.7 Consensus size: 27
39361277 AGGGGTATTT
*
39361287 TGGTAATTTTGTAAATCGAGGGTAAAA
1 TGGTAATTCTGTAAATCGAGGGTAAAA
* * *
39361314 CGGTAATTCTATAAATTGAGGGTAAAA
1 TGGTAATTCTGTAAATCGAGGGTAAAA
*
39361341 TAGTAATTCTGTAAA-CTGAGGGTAAAA
1 TGGTAATTCTGTAAATC-GAGGGTAAAA
39361368 TGGTAATTCTGTAAATCGAGGGTAAAA
1 TGGTAATTCTGTAAATCGAGGGTAAAA
39361395 TGGTAATTCTGTAAA-CTGAGGGTAAAA
1 TGGTAATTCTGTAAATC-GAGGGTAAAA
*
39361422 CGGTAATTCTGTAAATCGAGGGTAAAA
1 TGGTAATTCTGTAAATCGAGGGTAAAA
* * **
39361449 CGGTAATTTTAAAAATCGAGGGTAAAA
1 TGGTAATTCTGTAAATCGAGGGTAAAA
* *
39361476 CGATAATTCTGTAAATCGAGGGTAAAA
1 TGGTAATTCTGTAAATCGAGGGTAAAA
39361503 TGGTAATTCTGTAAATCG
1 TGGTAATTCTGTAAATCG
39361521 GGAGTACTTT
Statistics
Matches: 184, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
26 1 0.01
27 181 0.98
28 2 0.01
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.29
Consensus pattern (27 bp):
TGGTAATTCTGTAAATCGAGGGTAAAA
Found at i:39366109 original size:23 final size:24
Alignment explanation
Indices: 39366068--39366112 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
39366058 TTTGCTCTTC
*
39366068 TAGCATGAACTTGTCTTACCTTTT
1 TAGCATGAACTCGTCTTACCTTTT
*
39366092 TAGCAT-AACTCGTTTTACCTT
1 TAGCATGAACTCGTCTTACCTT
39366113 ACCTTACCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (24 bp):
TAGCATGAACTCGTCTTACCTTTT
Found at i:39366310 original size:53 final size:53
Alignment explanation
Indices: 39366181--39366433 Score: 236
Period size: 53 Copynumber: 4.8 Consensus size: 53
39366171 ACACGGGTAC
* * * * *
39366181 CTTACCATTGCCATGACTTGTCATGTTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
* *
39366230 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
* *
39366283 CTCACCAATGCCATGCCTTTG-CATGGTCTTACATGG-A-CTTTTGCCTTATAGAA
1 CTTACCAATGCCATGCC-TTGACATGGTCTTACATGGTATC-CTTGCCTTAT-GAA
* * * * *
39366336 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTAGCCTTA-GAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
* *
39366389 CCTTACCAATTCCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
39366434 AAACCCTAAT
Statistics
Matches: 168, Mismatches: 22, Indels: 22
0.79 0.10 0.10
Matches are distributed among these distances:
49 37 0.22
50 1 0.01
51 1 0.01
52 14 0.08
53 66 0.39
54 19 0.11
55 30 0.18
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (53 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
Found at i:39366370 original size:106 final size:108
Alignment explanation
Indices: 39366228--39366426 Score: 296
Period size: 106 Copynumber: 1.9 Consensus size: 108
39366218 ATCCTTTTGA
* * *
39366228 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTAGCCTTA-GAAACCTCACCAA
* *
39366291 -TGCCATGCCTTTGCATGGTCTTACATGGACTTTTGCCTTATAG
65 TTCCCATGCCTTGGCATGGTCTTACATGGACTTTTGCCTTATAG
* * *
39366334 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTAGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTAGCCTTAGAAACCTCACCAAT
39366399 TCCCATGCCTTGGCATGGTCTTACATGG
66 TCCCATGCCTTGGCATGGTCTTACATGG
39366427 TATCCTTAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
105 1 0.01
106 48 0.59
107 7 0.09
108 26 0.32
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.35
Consensus pattern (108 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTAGCCTTAGAAACCTCACCAAT
TCCCATGCCTTGGCATGGTCTTACATGGACTTTTGCCTTATAG
Found at i:39373074 original size:43 final size:42
Alignment explanation
Indices: 39373027--39373123 Score: 106
Period size: 44 Copynumber: 2.3 Consensus size: 42
39373017 GTCATACAAA
* * *
39373027 AAATCATATATGATGCCAATGTCCCAGACATGGTCTTACACG
1 AAATCATATATGATGCCAACGTCCCAAACATGGTCCTACACG
* *
39373069 TAAATC-TCAAATTGATGCCAACGTCCCAAACGTGGTCCTACACG
1 -AAATCAT-ATA-TGATGCCAACGTCCCAAACATGGTCCTACACG
*
39373113 AAATCACATAT
1 AAATCATATAT
39373124 CAAAGTTCTA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
42 2 0.05
43 14 0.32
44 28 0.64
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (42 bp):
AAATCATATATGATGCCAACGTCCCAAACATGGTCCTACACG
Found at i:39373565 original size:14 final size:14
Alignment explanation
Indices: 39373546--39373583 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
39373536 GTTTGCCAGT
*
39373546 AAAATGTTTTCCGG
1 AAAATGATTTCCGG
*
39373560 AAAATGATTTCTGG
1 AAAATGATTTCCGG
39373574 AAAATGATTT
1 AAAATGATTT
39373584 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCCGG
Found at i:39373609 original size:20 final size:20
Alignment explanation
Indices: 39373567--39373608 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
39373557 CGGAAAATGA
39373567 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
*
39373587 TTTCTGG-AATTGATTTACT
1 TTTCTGGAAAATGATTTACT
39373606 TTT
1 TTT
39373609 TTAGTGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:39375499 original size:58 final size:59
Alignment explanation
Indices: 39375398--39375588 Score: 312
Period size: 58 Copynumber: 3.2 Consensus size: 59
39375388 GACAAGATTG
* * * * * *
39375398 GCACTAAGTGTGCGGGTTTAAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
39375458 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
39375516 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
39375575 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39375589 GATTCACTAT
Statistics
Matches: 124, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
58 55 0.44
59 54 0.44
60 15 0.12
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (59 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
Found at i:39375558 original size:88 final size:87
Alignment explanation
Indices: 39375428--39375588 Score: 304
Period size: 88 Copynumber: 1.8 Consensus size: 87
39375418 AAAATTGTAC
39375428 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACTA
1 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACTA
39375493 AGTGTGCGAGCTGAAAATATAT
66 AGTGTGCGAGCTGAAAATATAT
*
39375515 AGCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACT
1 AGCACTAAGTGTGCGAACTGAAAA-TATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACT
39375580 AAGTGTGCG
65 AAGTGTGCG
39375589 GATTCACTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
87 23 0.32
88 49 0.68
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (87 bp):
AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACTA
AGTGTGCGAGCTGAAAATATAT
Found at i:39375600 original size:29 final size:29
Alignment explanation
Indices: 39375428--39375588 Score: 304
Period size: 29 Copynumber: 5.5 Consensus size: 29
39375418 AAAATTGTAC
*
39375428 AGCACTAAGTGTGCGAACTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
39375457 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
39375486 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
39375515 AGCACTAAGTGTGCGAGCTGAAAATTATAT
1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT
39375545 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
39375574 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
39375589 GATTCACTAT
Statistics
Matches: 130, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
29 101 0.78
30 29 0.22
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:39386620 original size:10 final size:10
Alignment explanation
Indices: 39386605--39386629 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
39386595 AATAAGAATA
39386605 ATTATTTATT
1 ATTATTTATT
39386615 ATTATTTATT
1 ATTATTTATT
39386625 ATTAT
1 ATTAT
39386630 AAAATGTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTATTTATT
Found at i:39390479 original size:29 final size:29
Alignment explanation
Indices: 39390447--39390505 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
39390437 TGCTTGTCTT
39390447 TTAAGGTTTATAATACAATCCTCGAATGC
1 TTAAGGTTTATAATACAATCCTCGAATGC
*
39390476 TTAAGGTTTGTAATACAATCCTCGAATGC
1 TTAAGGTTTATAATACAATCCTCGAATGC
39390505 T
1 T
39390506 CGACATGCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (29 bp):
TTAAGGTTTATAATACAATCCTCGAATGC
Found at i:39399624 original size:6 final size:6
Alignment explanation
Indices: 39399601--39399637 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
39399591 ATAAGTCCTC
* *
39399601 AAAAAT AAATAG AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
39399638 GTAATAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:39404609 original size:17 final size:18
Alignment explanation
Indices: 39404567--39404615 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
39404557 AGTTGAAAAG
39404567 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
39404586 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
39404603 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
39404616 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:39405503 original size:40 final size:40
Alignment explanation
Indices: 39405437--39405603 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
39405427 AAATTGAATG
* * *
39405437 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
39405476 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
39405516 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
39405556 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
39405596 ATATCCGG
1 ATATCCGG
39405604 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:39412989 original size:40 final size:39
Alignment explanation
Indices: 39412944--39413151 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 39
39412934 CGGAATACAA
*
39412944 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
39412984 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
39413024 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* *** *
39413064 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC
** * * *
39413104 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
39413144 CCGGATAT
1 CCGGATAT
39413152 CATTCAATTG
Statistics
Matches: 141, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 4 0.03
40 134 0.95
41 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:39413084 original size:80 final size:80
Alignment explanation
Indices: 39412944--39413150 Score: 238
Period size: 80 Copynumber: 2.6 Consensus size: 80
39412934 CGGAATACAA
* * *
39412944 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT-
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG
*
39413008 GCCTTCGGGTATTAGC
65 GCCTTCGGGTATTAAC
* * **
39413024 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG
*
39413088 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
39413104 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
39413151 TCATTCAATT
Statistics
Matches: 107, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
79 3 0.03
80 102 0.95
81 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG
CCTTCGGGTATTAAC
Found at i:39420999 original size:40 final size:39
Alignment explanation
Indices: 39420954--39421161 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 39
39420944 CGGAATACAA
*
39420954 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
39420994 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
39421034 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* *** *
39421074 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC
** * * *
39421114 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
39421154 CCGGATAT
1 CCGGATAT
39421162 CATTCAATTG
Statistics
Matches: 141, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 4 0.03
40 134 0.95
41 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:39421094 original size:80 final size:80
Alignment explanation
Indices: 39420954--39421160 Score: 238
Period size: 80 Copynumber: 2.6 Consensus size: 80
39420944 CGGAATACAA
* * *
39420954 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT-
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG
*
39421018 GCCTTCGGGTATTAGC
65 GCCTTCGGGTATTAAC
* * **
39421034 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG
*
39421098 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
39421114 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
39421161 TCATTCAATT
Statistics
Matches: 107, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
79 3 0.03
80 102 0.95
81 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG
CCTTCGGGTATTAAC
Found at i:39422909 original size:21 final size:21
Alignment explanation
Indices: 39422884--39422927 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
39422874 CTCATACATA
39422884 TTTCACATTAGCCATTCGGCT
1 TTTCACATTAGCCATTCGGCT
39422905 TTTCACATTAGCCATTCGGCT
1 TTTCACATTAGCCATTCGGCT
39422926 TT
1 TT
39422928 ACCACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (21 bp):
TTTCACATTAGCCATTCGGCT
Found at i:39423006 original size:48 final size:49
Alignment explanation
Indices: 39422905--39423402 Score: 754
Period size: 48 Copynumber: 10.2 Consensus size: 49
39422895 CCATTCGGCT
* *
39422905 TTTCACATTAGCCATTCGGCTTTACCACATATATACATCTCTCATGCATA
1 TTTCACATTAGCCATTCGGCTTTACCACA-ATATACATATCTCATACATA
*
39422955 TTTCACATTAGCCATTCGGCTTTACCAC-ATATACATATCTCATGCATA
1 TTTCACATTAGCCATTCGGCTTTACCACAATATACATATCTCATACATA
*
39423003 TTTCACATTAGCCATTCGACTTTACCAC-ATATACATATCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACAATATACATATCTCATACATA
*
39423051 TTTCACATTAGCCATTCGGCTTTACCACATATATACATTTCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACA-ATATACATATCTCATACATA
* *
39423101 TTTCACATTAGCCATTCGGCTTTACCGC-ATATACATATCTCATATATA
1 TTTCACATTAGCCATTCGGCTTTACCACAATATACATATCTCATACATA
* * * *
39423149 TTTCACAGTAGTCATTCGGCTTTACCACATATATACATTTCTCATGCATA
1 TTTCACATTAGCCATTCGGCTTTACCACA-ATATACATATCTCATACATA
* *
39423199 TTTCACATTAGCCATTCGGCTTTACCACATATATACATTTCTCATGCATA
1 TTTCACATTAGCCATTCGGCTTTACCACA-ATATACATATCTCATACATA
*
39423249 TTTCACATTAGCCATTCGGCTTTACCAC-ATATACATATCTCATATATA
1 TTTCACATTAGCCATTCGGCTTTACCACAATATACATATCTCATACATA
* * *
39423297 TTTCACAGTAGCCAGTCGGCTTTGCCAC-ATATACATATCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACAATATACATATCTCATACATA
*
39423345 TTTCACATTAGCCATTCGGCTTTACCACATATATACATTTCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACA-ATATACATATCTCATACATA
39423395 TTTCACAT
1 TTTCACAT
39423403 ATTCACTACA
Statistics
Matches: 415, Mismatches: 27, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
48 221 0.53
50 194 0.47
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.37
Consensus pattern (49 bp):
TTTCACATTAGCCATTCGGCTTTACCACAATATACATATCTCATACATA
Found at i:39423026 original size:98 final size:97
Alignment explanation
Indices: 39422905--39423402 Score: 766
Period size: 98 Copynumber: 5.1 Consensus size: 97
39422895 CCATTCGGCT
* *
39422905 TTTCACATTAGCCATTCGGCTTTACCACATATATACATCTCTCATGCATATTTCACATTAGCCAT
1 TTTCACATTAGCCATTCGGCTTTACCAC--ATATACATATCTCATACATATTTCACATTAGCCAT
* *
39422970 TCGGCTTTACCAC-ATATACATATCTCATGCATA
64 TCGGCTTTACCACAATATACATTTCTCATACATA
*
39423003 TTTCACATTAGCCATTCGACTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTC
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTC
39423068 GGCTTTACCACATATATACATTTCTCATACATA
66 GGCTTTACCACA-ATATACATTTCTCATACATA
* * * *
39423101 TTTCACATTAGCCATTCGGCTTTACCGCATATACATATCTCATATATATTTCACAGTAGTCATTC
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTC
*
39423166 GGCTTTACCACATATATACATTTCTCATGCATA
66 GGCTTTACCACA-ATATACATTTCTCATACATA
* *
39423199 TTTCACATTAGCCATTCGGCTTTACCACATATATACATTTCTCATGCATATTTCACATTAGCCAT
1 TTTCACATTAGCCATTCGGCTTTACCAC--ATATACATATCTCATACATATTTCACATTAGCCAT
* *
39423264 TCGGCTTTACCAC-ATATACATATCTCATATATA
64 TCGGCTTTACCACAATATACATTTCTCATACATA
* * *
39423297 TTTCACAGTAGCCAGTCGGCTTTGCCACATATACATATCTCATACATATTTCACATTAGCCATTC
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTC
39423362 GGCTTTACCACATATATACATTTCTCATACATA
66 GGCTTTACCACA-ATATACATTTCTCATACATA
39423395 TTTCACAT
1 TTTCACAT
39423403 ATTCACTACA
Statistics
Matches: 366, Mismatches: 28, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
96 92 0.25
98 231 0.63
100 43 0.12
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.37
Consensus pattern (97 bp):
TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTC
GGCTTTACCACAATATACATTTCTCATACATA
Found at i:39427427 original size:54 final size:53
Alignment explanation
Indices: 39427286--39427531 Score: 229
Period size: 54 Copynumber: 4.7 Consensus size: 53
39427276 ATTAGGGTTT
* * * * *
39427286 AAGGATACCATGTAAGACCATGGCAAGTCATGGAAATTGGTAAGGTTTC-TAAGGA
1 AAGGATACCATGTAAGACCATGTCAAGACATGG-CATTGATAA-G-TTCATAAGGC
* *
39427341 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTT-C-ATAAGGC
* * * *
39427396 AAAGG-T-CCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCATAAGGC
* *
39427448 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGATTC--AA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAG-TTCATAAGGC
* * *
39427497 AAGGATACCACGTAAGACCATGACAAGTCATGGCA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCA
39427532 ATGGTAAGGT
Statistics
Matches: 164, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
49 32 0.20
51 4 0.02
52 12 0.07
53 35 0.21
54 43 0.26
55 34 0.21
56 4 0.02
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCATAAGGC
Found at i:39427738 original size:16 final size:16
Alignment explanation
Indices: 39427717--39427747 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39427707 ATAAATTTGA
39427717 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
39427733 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
39427748 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:39429011 original size:27 final size:27
Alignment explanation
Indices: 39428981--39429033 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
39428971 GTCATTCTAT
*
39428981 ACTACAAACGTATTTTGATAATTTTAC
1 ACTACAAACGTATTTCGATAATTTTAC
**
39429008 ACTACAAGGGTATTTCGATAATTTTA
1 ACTACAAACGTATTTCGATAATTTTA
39429034 TAAATCGGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (27 bp):
ACTACAAACGTATTTCGATAATTTTAC
Found at i:39429045 original size:27 final size:27
Alignment explanation
Indices: 39428990--39429290 Score: 274
Period size: 27 Copynumber: 11.2 Consensus size: 27
39428980 TACTACAAAC
* * *
39428990 GTATTTTGATAATTTTAC-ACTACAAGG
1 GTATTTCGATAATTTTACAAAT-CGAGG
* *
39429017 GTATTTCGATAATTTTATAAATCGGGG
1 GTATTTCGATAATTTTACAAATCGAGG
* * *
39429044 GTGTTTCGGA-AATTTTACAAATTGAAG
1 GTATTTC-GATAATTTTACAAATCGAGG
39429071 GTATTTC-AGTAATTTTACAAATCGAGG
1 GTATTTCGA-TAATTTTACAAATCGAGG
* * *
39429098 GTGTTTCTATAATTTCACAAATCGAGG
1 GTATTTCGATAATTTTACAAATCGAGG
* *
39429125 GTATTTCGATAATTTTAGAAATTGAGG
1 GTATTTCGATAATTTTACAAATCGAGG
* *
39429152 GTATTTC-AGTAATTTCAC-AATCGAGT
1 GTATTTCGA-TAATTTTACAAATCGAGG
* *
39429178 GTATTTCGGTAATTTTGCAAATCGAGG
1 GTATTTCGATAATTTTACAAATCGAGG
* * *
39429205 GTATTTTGGTAATTTTACAAATCAAGG
1 GTATTTCGATAATTTTACAAATCGAGG
* *
39429232 GTATTT-TAGTAATTTCAC-AATCGAGG
1 GTATTTCGA-TAATTTTACAAATCGAGG
** * *
39429258 AAATTTTGATAATTTTACAAATCAAGG
1 GTATTTCGATAATTTTACAAATCGAGG
39429285 GTATTT
1 GTATTT
39429291 TAGTAATTTC
Statistics
Matches: 221, Mismatches: 42, Indels: 22
0.78 0.15 0.08
Matches are distributed among these distances:
25 1 0.00
26 40 0.18
27 175 0.79
28 5 0.02
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
GTATTTCGATAATTTTACAAATCGAGG
Found at i:39429218 original size:80 final size:79
Alignment explanation
Indices: 39429016--39429299 Score: 334
Period size: 80 Copynumber: 3.5 Consensus size: 79
39429006 ACACTACAAG
* * * * *
39429016 GGTATTTCGATAATTTTATAAATCGGGGGTGTTTCGGAAATTTTACAAATTGAAGGTATTTCAGT
1 GGTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTGAGGGTATTTCAGT
*
39429081 AATTTTACAAATCGA
66 AATTTCAC-AATCGA
* * * * *
39429096 GGGTGTTTCTATAATTTCACAAATCGAGGGTATTTCGATAATTTTAGAAATTGAGGGTATTTCAG
1 -GGTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTGAGGGTATTTCAG
39429161 TAATTTCACAATCGA
65 TAATTTCACAATCGA
* * * ** *
39429176 GTGTATTTCGGTAATTTTGCAAATCGAGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTAG
1 G-GTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTGAGGGTATTTCAG
39429241 TAATTTCACAATCGA
65 TAATTTCACAATCGA
* * * **
39429256 GGAAATTTTGATAATTTTACAAATCAAGGGTATTTTAGTAATTT
1 GG-TATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTT
39429300 CTCTTTATTA
Statistics
Matches: 173, Mismatches: 28, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
79 2 0.01
80 109 0.63
81 62 0.36
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.39
Consensus pattern (79 bp):
GGTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATTGAGGGTATTTCAGT
AATTTCACAATCGA
Found at i:39429660 original size:28 final size:28
Alignment explanation
Indices: 39429618--39429704 Score: 120
Period size: 28 Copynumber: 3.1 Consensus size: 28
39429608 GCCTATTTAG
* * * *
39429618 GCCCAATCTCGTTCACATGGCCCATCAG
1 GCCCAATCACATTCATATGGCCCATCAA
*
39429646 GTCCAATCACATTCATATGGCCCATCAA
1 GCCCAATCACATTCATATGGCCCATCAA
*
39429674 GCCCAATCACATTTATATGGCCCATCAA
1 GCCCAATCACATTCATATGGCCCATCAA
39429702 GCC
1 GCC
39429705 TAACTACTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.28, C:0.36, G:0.14, T:0.23
Consensus pattern (28 bp):
GCCCAATCACATTCATATGGCCCATCAA
Found at i:39433882 original size:43 final size:43
Alignment explanation
Indices: 39433787--39433955 Score: 141
Period size: 43 Copynumber: 4.0 Consensus size: 43
39433777 TAGGACTCTG
* * *
39433787 ATATGTGATTTCGTGTAAGACCATGTCTGGGA-TTTAGCATCGA
1 ATATATGATTTCGTGTAAGACCATGTCTGGGACATTGGCATC-A
* *
39433830 CT-TGA-GATTTACGTGTAAGACCATGTTTGGGACATTGGCATC-
1 ATAT-ATGATTT-CGTGTAAGACCATGTCTGGGACATTGGCATCA
* * * *
39433872 ATATATGATTTCGTGTAAGACCCTGTCTAGGATAGTGGCATCA
1 ATATATGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCA
* * * * *
39433915 ATATTTGATTACATGTAAGACC-TAGTTTGGGACGTTGGCAT
1 ATATATGATTTCGTGTAAGACCAT-GTCTGGGACATTGGCAT
39433956 TTTATGAGCT
Statistics
Matches: 100, Mismatches: 19, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
42 35 0.35
43 58 0.58
44 7 0.07
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (43 bp):
ATATATGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCA
Found at i:39433911 original size:42 final size:43
Alignment explanation
Indices: 39433787--39433936 Score: 146
Period size: 43 Copynumber: 3.5 Consensus size: 43
39433777 TAGGACTCTG
* *
39433787 ATATGTGATTTCGTGTAAGACCATGTCTGGGAT-TTAGCATCGA
1 ATATATGATTTCGTGTAAGACCATGTCTGGGATATTGGCATC-A
* * *
39433830 CT-TGA-GATTTACGTGTAAGACCATGTTTGGGACATTGGCATC-
1 ATAT-ATGATTT-CGTGTAAGACCATGTCTGGGATATTGGCATCA
* * *
39433872 ATATATGATTTCGTGTAAGACCCTGTCTAGGATAGTGGCATCA
1 ATATATGATTTCGTGTAAGACCATGTCTGGGATATTGGCATCA
* * *
39433915 ATATTTGATTACATGTAAGACC
1 ATATATGATTTCGTGTAAGACC
39433937 TAGTTTGGGA
Statistics
Matches: 87, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
42 34 0.39
43 46 0.53
44 7 0.08
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (43 bp):
ATATATGATTTCGTGTAAGACCATGTCTGGGATATTGGCATCA
Found at i:39435051 original size:32 final size:32
Alignment explanation
Indices: 39435010--39435080 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
39435000 TGGCTTCAAG
* *
39435010 CCTTGATATCGGCACTTTGGGTACGAATAATA
1 CCTTGATATCGGCACTTCGAGTACGAATAATA
*
39435042 CCTTGATATCGGCACTTCGAGTGCGAATAATA
1 CCTTGATATCGGCACTTCGAGTACGAATAATA
39435074 CCTTGAT
1 CCTTGAT
39435081 TTGGCTACGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (32 bp):
CCTTGATATCGGCACTTCGAGTACGAATAATA
Found at i:39444205 original size:13 final size:13
Alignment explanation
Indices: 39444183--39444215 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39444173 AAGGGTTTGT
39444183 TTAT-TAAACTAA
1 TTATCTAAACTAA
39444195 TTATCTAAACTAA
1 TTATCTAAACTAA
*
39444208 TTAACTAA
1 TTATCTAA
39444216 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:39449120 original size:5 final size:5
Alignment explanation
Indices: 39449110--39449198 Score: 76
Period size: 5 Copynumber: 16.8 Consensus size: 5
39449100 TATGTCTTTC
*
39449110 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAA- ATAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT AAAAT A-AAAT AAAAT
39449155 AAAAT AAGAAT AAAAT AAGAAT AAAAAT AAGAAT AAGAAT AAAA
1 AAAAT AA-AAT AAAAT AA-AAT -AAAAT AA-AAT AA-AAT AAAA
39449199 AATAGGAGGA
Statistics
Matches: 72, Mismatches: 2, Indels: 20
0.77 0.02 0.21
Matches are distributed among these distances:
3 3 0.04
4 1 0.01
5 35 0.49
6 31 0.43
7 2 0.03
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:39449139 original size:6 final size:6
Alignment explanation
Indices: 39449130--39449199 Score: 61
Period size: 6 Copynumber: 11.5 Consensus size: 6
39449120 AATAAAATTG
* * * *
39449130 AAATGA AAATAA AAATAA ATAAAATA AAATAA GAAT-A AAATAA GAATAA
1 AAATAA AAATAA AAATAA A-AATA-A AAATAA AAATAA AAATAA AAATAA
* *
39449179 AAATAA GAATAA GAATAA AAA
1 AAATAA AAATAA AAATAA AAA
39449200 ATAGGAGGAT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
5 4 0.08
6 40 0.77
7 6 0.12
8 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:39449145 original size:12 final size:11
Alignment explanation
Indices: 39449110--39449199 Score: 76
Period size: 12 Copynumber: 7.9 Consensus size: 11
39449100 TATGTCTTTC
39449110 AAAATAAAATAAT
1 AAAAT-AAA-AAT
**
39449123 AAAATTGAAAT
1 AAAATAAAAAT
39449134 GAAAATAAAAAT
1 -AAAATAAAAAT
39449146 -AAAT-AAAAT
1 AAAATAAAAAT
*
39449155 AAAATAAGAAT
1 AAAATAAAAAT
*
39449166 AAAATAAGAAT
1 AAAATAAAAAT
*
39449177 AAAAATAAGAAT
1 -AAAATAAAAAT
39449189 AAGAATAAAAA
1 AA-AATAAAAA
39449200 ATAGGAGGAT
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
9 5 0.08
10 8 0.12
11 20 0.30
12 28 0.42
13 5 0.08
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:39449146 original size:31 final size:30
Alignment explanation
Indices: 39449110--39449198 Score: 94
Period size: 31 Copynumber: 2.9 Consensus size: 30
39449100 TATGTCTTTC
* *
39449110 AAAATAAAATAATAAAAT-TGAAATGAAAATA
1 AAAATAAAAAAATAAAATAAG-AAT-AAAATA
39449141 AAAATAAATAAAATAAAATAAGAATAAAATA
1 AAAATAAA-AAAATAAAATAAGAATAAAATA
*
39449172 AGAAT--AAAAATAAGAATAAGAATAAAA
1 AAAATAAAAAAATAA-AATAAGAATAAAA
39449199 AATAGGAGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
28 7 0.13
29 14 0.27
31 18 0.35
32 12 0.23
33 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (30 bp):
AAAATAAAAAAATAAAATAAGAATAAAATA
Found at i:39449168 original size:11 final size:11
Alignment explanation
Indices: 39449135--39449196 Score: 83
Period size: 11 Copynumber: 5.6 Consensus size: 11
39449125 AATTGAAATG
*
39449135 AAAATAAAAAT
1 AAAATAAGAAT
39449146 -AAATAA-AAT
1 AAAATAAGAAT
39449155 AAAATAAGAAT
1 AAAATAAGAAT
39449166 AAAATAAGAAT
1 AAAATAAGAAT
39449177 AAAAATAAGAAT
1 -AAAATAAGAAT
39449189 AAGAATAA
1 AA-AATAA
39449197 AAAATAGGAG
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
9 3 0.06
10 12 0.26
11 16 0.34
12 16 0.34
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (11 bp):
AAAATAAGAAT
Found at i:39459057 original size:46 final size:43
Alignment explanation
Indices: 39458921--39459092 Score: 125
Period size: 46 Copynumber: 3.7 Consensus size: 43
39458911 GTTATCATGG
* *
39458921 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGA-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-GCCTC--GA-GACGA
* *
39458967 GCCTA-TGTAGGATCATGTCTGGGACATGGCATCGACATCGAGACGA
1 G-CTAGTGTAAGA-CATGTCTGGGACAT-GCATCG-CCTCGAGACGA
*
39459013 GTTCTAGTGTAAGACCTGTCTGGGACATGCATCAGCCTCGAGACGTAA
1 G--CTAGTGTAAGACATGTCTGGGACATGCATC-GCCTCGAGACG--A
* * *
39459061 GCCAGTGTAAAACCTG-CTTGGGACATGCATCG
1 GCTAGTGTAAGACATGTC-TGGGACATGCATCG
39459093 ACTATGAGAT
Statistics
Matches: 105, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
45 4 0.04
46 51 0.49
47 35 0.33
48 15 0.14
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (43 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGCCTCGAGACGA
Found at i:39473418 original size:17 final size:18
Alignment explanation
Indices: 39473376--39473424 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
39473366 AGTTGAAAAG
39473376 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
39473395 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
39473412 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
39473425 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:39474312 original size:40 final size:40
Alignment explanation
Indices: 39474246--39474412 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
39474236 AAATTGAATG
* * *
39474246 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
39474285 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
39474325 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
39474365 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
39474405 ATATCCGG
1 ATATCCGG
39474413 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:39481405 original size:17 final size:18
Alignment explanation
Indices: 39481363--39481411 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
39481353 AGTTGAAAAG
39481363 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
39481382 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
39481399 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
39481412 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:39482298 original size:40 final size:39
Alignment explanation
Indices: 39482232--39482397 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 39
39482222 AAATTGAATG
* * *
39482232 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGG-TATT
* * **
39482271 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTATT
*
39482310 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-G-TATT
* * **
39482350 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGT-ATT
39482390 ATATCCGG
1 ATATCCGG
39482398 TTATATTCCG
Statistics
Matches: 103, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
38 3 0.03
39 42 0.41
40 56 0.54
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTATT
Found at i:39483959 original size:15 final size:16
Alignment explanation
Indices: 39483939--39483968 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39483929 TAATCATCAT
39483939 CTTTCCTTTT-TTTTC
1 CTTTCCTTTTATTTTC
39483954 CTTTCCTTTTATTTT
1 CTTTCCTTTTATTTT
39483969 ATTGTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (16 bp):
CTTTCCTTTTATTTTC
Found at i:39486399 original size:51 final size:51
Alignment explanation
Indices: 39486323--39486423 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
39486313 GATTTTTGCA
39486323 TATTATATGATTATGTCATATTGTAACTTAGATTAGTGAATTAGAAAAGGC
1 TATTATATGATTATGTCATATTGTAACTTAGATTAGTGAATTAGAAAAGGC
*
39486374 TATTATATGATTATGTCTTATTGTAACTTAGATTAGTGAATTAGAAAAGG
1 TATTATATGATTATGTCATATTGTAACTTAGATTAGTGAATTAGAAAAGG
39486424 TCAAATGGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.41
Consensus pattern (51 bp):
TATTATATGATTATGTCATATTGTAACTTAGATTAGTGAATTAGAAAAGGC
Found at i:39488321 original size:2 final size:2
Alignment explanation
Indices: 39488314--39488344 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39488304 TCATTACTTT
39488314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39488345 TTTATTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39490466 original size:29 final size:29
Alignment explanation
Indices: 39490424--39490482 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
39490414 TTGACTGTCT
39490424 TAATATTTATTATGTAGGG-TTTTCAATTA
1 TAATATTTATTATGT-GGGATTTTCAATTA
*
39490453 TAATATTTATTATGTGGGATTTTTAATTA
1 TAATATTTATTATGTGGGATTTTCAATTA
39490482 T
1 T
39490483 GTTTCTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 3 0.11
29 25 0.89
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.54
Consensus pattern (29 bp):
TAATATTTATTATGTGGGATTTTCAATTA
Found at i:39492505 original size:42 final size:38
Alignment explanation
Indices: 39492385--39492534 Score: 167
Period size: 42 Copynumber: 3.7 Consensus size: 38
39492375 CGAATAATAC
*
39492385 CCGGGCTAAGT-CCGAAGGCATTTATGCTATTGATATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-ATTGATATAT
* *
39492423 CCGGGCTAAGTCCCGAAGGCATTCGTGCTTTGTTATATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCATTG--ATATAT
*
39492463 CCGGGCTAAGATCCCGAAAGGCATTTGTGCAGTTGACCATAT
1 CCGGGCTAAG-TCCCG-AAGGCATTTGTGCA-TTGA-TATAT
*
39492505 CCGGGTCTAAGACCCGAAGGCAATTTGTGC
1 CCGGG-CTAAGTCCCGAAGGC-ATTTGTGC
39492535 GGTTCTATAT
Statistics
Matches: 96, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
38 14 0.15
39 14 0.15
40 16 0.17
41 11 0.11
42 33 0.34
43 8 0.08
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (38 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCATTGATATAT
Found at i:39492545 original size:82 final size:77
Alignment explanation
Indices: 39492385--39492548 Score: 188
Period size: 82 Copynumber: 2.1 Consensus size: 77
39492375 CGAATAATAC
* *
39492385 CCGGGCTAAGTCCGAAGGCATTTATGCTATTGATATATCCGGGCTAAGTCCCGAAGGCATTCGTG
1 CCGGGCTAAGTCCGAAGGCATTTATGCTATTGACATATCCGGGCTAAGACCCGAAGGCATTCGTG
*
39492450 CTTTGTTATATAT
66 C-TGGTTATATAT
*
39492463 CCGGGCTAAGATCCCGAAAGGCATTTGTGC-AGTTGACCATATCCGGGTCTAAGACCCGAAGGCA
1 CCGGGCTAAG-T-CCG-AAGGCATTTATGCTA-TTGA-CATATCCGGG-CTAAGACCCGAAGGC-
* *
39492527 ATTTGTGC-GGTTCTATAT
59 ATTCGTGCTGGTTATATAT
39492545 CCGG
1 CCGG
39492549 TTAAATTCCG
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
78 10 0.14
79 1 0.01
80 4 0.05
81 16 0.22
82 21 0.29
83 14 0.19
84 7 0.10
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (77 bp):
CCGGGCTAAGTCCGAAGGCATTTATGCTATTGACATATCCGGGCTAAGACCCGAAGGCATTCGTG
CTGGTTATATAT
Found at i:39494628 original size:37 final size:36
Alignment explanation
Indices: 39494579--39494684 Score: 158
Period size: 37 Copynumber: 2.9 Consensus size: 36
39494569 CCCGACGGTT
39494579 TGCACAATGCCTTCGGGTCTTAGCCCGGATAAACAC
1 TGCACAATGCCTTCGGGTCTTAGCCCGGATAAACAC
* *
39494615 TGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGCAC
1 TGCAC-AATGCCTTCGGGTCTTAGCCCGGATAAACAC
*
39494652 TAGCACAATTGCCTTCGGGTCTTAACCCGGATA
1 T-GCACAA-TGCCTTCGGGTCTTAGCCCGGATA
39494685 TAATTTCAGC
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
36 5 0.08
37 32 0.51
38 26 0.41
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.25
Consensus pattern (36 bp):
TGCACAATGCCTTCGGGTCTTAGCCCGGATAAACAC
Found at i:39500714 original size:40 final size:40
Alignment explanation
Indices: 39500655--39500823 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
39500645 CGGGACTTTA
* * *
39500655 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
39500695 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
39500735 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
39500775 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
39500815 CCCGGATAT
1 CCCGGATAT
39500824 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:39508745 original size:40 final size:40
Alignment explanation
Indices: 39508686--39508854 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
39508676 CGGGACTTTA
* * *
39508686 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
39508726 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
39508766 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
39508806 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
39508846 CCCGGATAT
1 CCCGGATAT
39508855 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:39512243 original size:52 final size:52
Alignment explanation
Indices: 39512161--39512284 Score: 221
Period size: 52 Copynumber: 2.4 Consensus size: 52
39512151 GATGATGAAA
*
39512161 AAAGAAAAAGAAAGAAAAAAAAAGCTCTCATGTTGTTCTTGGTCGAATAGAAG
1 AAAGAAAAAG-AAGAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
39512214 AAAGAAAAAGAAGAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
1 AAAGAAAAAGAAGAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
*
39512266 AAAGAAAAAGAAGGAAAAA
1 AAAGAAAAAGAAGAAAAAA
39512285 GAGCTTTGAG
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 59 0.86
53 10 0.14
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.17
Consensus pattern (52 bp):
AAAGAAAAAGAAGAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
Found at i:39513592 original size:39 final size:40
Alignment explanation
Indices: 39513529--39513782 Score: 315
Period size: 39 Copynumber: 6.5 Consensus size: 40
39513519 TGGATGATAA
* * *
39513529 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
* *
39513569 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
39513608 CCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
39513648 CCGGGATAAGT-CCGAAGGCATTGGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
39513687 CCGGGCTAAGT-CCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39513726 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
39513765 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
39513783 TACTTGGCTT
Statistics
Matches: 190, Mismatches: 20, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
38 15 0.08
39 120 0.63
40 55 0.29
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39513660 original size:79 final size:79
Alignment explanation
Indices: 39513529--39513782 Score: 311
Period size: 79 Copynumber: 3.2 Consensus size: 79
39513519 TGGATGATAA
* * *
39513529 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TCCGGGCTAAGTCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCGGGCTAAGTCCGAAGGCATTTG
*
39513593 TGCGAGTTATTACAT
65 TGCGAGTTACTACAT
* * *
39513608 CCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATATCCGGGATAAGTCCGAAGGCATTGGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGT
* *
39513673 GTGAGTTACTATAT
66 GCGAGTTACTACAT
* *
39513687 CCGGGCTAAGT-CCGAAGGCATTGGTGCGAGTTACTATATCCGGGCTATGTCCCGAAGGCA-TTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGT-CCGAAGGCATTTG
* *
39513750 AGCGAG-TAGCTATAT
65 TGCGAGTTA-CTACAT
* *
39513765 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
39513783 TACTTGGCTT
Statistics
Matches: 153, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
77 8 0.05
78 57 0.37
79 88 0.58
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGT
GCGAGTTACTACAT
Found at i:39515399 original size:28 final size:27
Alignment explanation
Indices: 39515336--39515405 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
39515326 ATAGTGAGTC
39515336 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
39515363 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
39515391 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39515406 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:39523393 original size:40 final size:39
Alignment explanation
Indices: 39523349--39523530 Score: 238
Period size: 39 Copynumber: 4.6 Consensus size: 39
39523339 GTTCAAAACA
* * ** * *
39523349 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
39523389 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* * *
39523429 CCTTCGGGCTTAGCCCGGGTATCATAGCTCGGACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
*
39523468 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
39523507 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
39523531 CTCGAACATT
Statistics
Matches: 127, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 87 0.69
40 40 0.31
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:39523465 original size:39 final size:39
Alignment explanation
Indices: 39523379--39523530 Score: 241
Period size: 39 Copynumber: 3.9 Consensus size: 39
39523369 TATGGTAACC
* * * *
39523379 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCT
*
39523419 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
*
39523458 CGGACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
39523497 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
39523531 CTCGAACATT
Statistics
Matches: 104, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 87 0.84
40 17 0.16
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
Found at i:39526646 original size:28 final size:27
Alignment explanation
Indices: 39526583--39526652 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
39526573 ATAGTGAGTC
39526583 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
39526610 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
39526638 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39526653 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:39529799 original size:6 final size:6
Alignment explanation
Indices: 39529788--39529813 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39529778 CCTTGTATCT
39529788 GGTCTC GGTCTC GGTCTC GGTCTC GG
1 GGTCTC GGTCTC GGTCTC GGTCTC GG
39529814 GTAAGGGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.38, T:0.31
Consensus pattern (6 bp):
GGTCTC
Found at i:39535315 original size:28 final size:27
Alignment explanation
Indices: 39535252--39535321 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
39535242 ATAGTGAGTC
*
39535252 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
39535279 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
39535307 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39535322 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:39548993 original size:20 final size:22
Alignment explanation
Indices: 39548953--39548993 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
39548943 TTTCTTTACT
*
39548953 TTTAGTTGATATTCTATTATTG
1 TTTAGTTGATATTCTAATATTG
39548975 TTTAGTTG-T-TTCTAATATT
1 TTTAGTTGATATTCTAATATT
39548994 TTATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.22, C:0.05, G:0.12, T:0.61
Consensus pattern (22 bp):
TTTAGTTGATATTCTAATATTG
Found at i:39553959 original size:17 final size:15
Alignment explanation
Indices: 39553935--39553971 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
39553925 CAGGCCATGT
*
39553935 GTCACACATAACTGA
1 GTCACACACAACTGA
39553950 GTCACACACAACTGA
1 GTCACACACAACTGA
39553965 GTCACAC
1 GTCACAC
39553972 GCCCGTGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.32, G:0.14, T:0.16
Consensus pattern (15 bp):
GTCACACACAACTGA
Found at i:39556205 original size:25 final size:25
Alignment explanation
Indices: 39556177--39556226 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
39556167 ACCATTGAAG
* *
39556177 AACATTCATGGTAAGTCCCTAAACA
1 AACATTCAAGGCAAGTCCCTAAACA
39556202 AACATTCAAGGCAAGTCCCTAAACA
1 AACATTCAAGGCAAGTCCCTAAACA
39556227 TTTAACACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20
Consensus pattern (25 bp):
AACATTCAAGGCAAGTCCCTAAACA
Found at i:39558921 original size:24 final size:23
Alignment explanation
Indices: 39558869--39558921 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 23
39558859 GGCCTAGCAT
39558869 CTTTTAATAACTGGGGCAAAGCC
1 CTTTTAATAACTGGGGCAAAGCC
*
39558892 CTTTTTAGTAAACTGGGGCAAAGCC
1 C-TTTTAAT-AACTGGGGCAAAGCC
39558917 CTTTT
1 CTTTT
39558922 CGCACTTCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 1 0.04
24 10 0.37
25 16 0.59
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (23 bp):
CTTTTAATAACTGGGGCAAAGCC
Found at i:39561421 original size:47 final size:46
Alignment explanation
Indices: 39561355--39561571 Score: 176
Period size: 47 Copynumber: 4.6 Consensus size: 46
39561345 ATTGTGGGCT
39561355 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGA-TATGAGAGCC
* * * *
39561401 AGTGTAAGACTATGTCTGGGACATGGCATCGG-CATCGAAACGAGTGCT
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCCA-CGATATGAGAGCC
* * * * *
39561449 AGTGTAAGACACGTCTGGTACATGCATCGGCTACGATATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGATATGAGAGCC
* * * *
39561495 AGTGTAAGACCATGTCCT-GGATATGGCATCGACTTGA-GATAT--GAGCA
1 AGTGTAAGA-CATGT-CTGGGACAT-GCATCGGC--CACGATATGAGAGCC
39561542 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
39561572 AACATTCTAC
Statistics
Matches: 138, Mismatches: 22, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
46 35 0.25
47 63 0.46
48 33 0.24
49 6 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACGATATGAGAGCC
Done.