Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 103 of 128
Found at i:34450015 original size:13 final size:13
Alignment explanation
Indices: 34449997--34450021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34449987 AAGCTTGAAT
34449997 TTGTTAAATAATA
1 TTGTTAAATAATA
34450010 TTGTTAAATAAT
1 TTGTTAAATAAT
34450022 TTTTTGGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TTGTTAAATAATA
Found at i:34455377 original size:38 final size:39
Alignment explanation
Indices: 34455325--34455452 Score: 125
Period size: 45 Copynumber: 3.2 Consensus size: 39
34455315 ATTTGCCGGC
*
34455325 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTAGGCACTTTATGTGCCGAATACTGTTACTG
* * *
34455363 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTAGGCACTTTATGTGCCGAATACTGTTACTG
* *
34455402 TTATTG-TTACCGACTCGGCACTTTATGTGTCGAATACTGTTACTG
1 TTACTGATT----A---GGCACTTTATGTGCCGAATACTGTTACTG
34455447 TTACTG
1 TTACTG
34455453 TTACCGACTC
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
38 16 0.22
39 25 0.34
45 33 0.45
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.40
Consensus pattern (39 bp):
TTACTGATTAGGCACTTTATGTGCCGAATACTGTTACTG
Found at i:34455420 original size:45 final size:45
Alignment explanation
Indices: 34455352--34455681 Score: 507
Period size: 45 Copynumber: 7.3 Consensus size: 45
34455342 ATGTGCCGAC
* *
34455352 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
* *
34455397 TACTGTTATTGTTACCGACTCGGCACTTTATGTGTCGAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
*
34455442 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCAAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
*
34455487 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATATTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
* *
34455532 TACTGTTACTGTTATCGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
* * * * *
34455577 TACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
* * *
34455622 TACTGCTACCGTTATCGACTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
*
34455667 TACCGTTACTGTTAC
1 TACTGTTACTGTTAC
34455682 AGATTCAGCA
Statistics
Matches: 256, Mismatches: 29, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 256 1.00
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
Found at i:34458219 original size:12 final size:12
Alignment explanation
Indices: 34458204--34458236 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
34458194 AACTGAACCG
34458204 TAAATATTTTTA
1 TAAATATTTTTA
34458216 TAAATATTTTTA
1 TAAATATTTTTA
34458228 TAAATATTT
1 TAAATATTT
34458237 ACTAAGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TAAATATTTTTA
Found at i:34459435 original size:21 final size:21
Alignment explanation
Indices: 34459411--34459569 Score: 115
Period size: 21 Copynumber: 7.6 Consensus size: 21
34459401 GTGTTTTACT
* *
34459411 TTCTGTTCGGCTCTTACAAGC
1 TTCTGTTCAGCTCTTACGAGC
* * *
34459432 TTCTGTTTAACTCTTATGAG-
1 TTCTGTTCAGCTCTTACGAGC
* *
34459452 TTTTCGTTCAGCTCTTTCGAGC
1 TTCT-GTTCAGCTCTTACGAGC
* * *
34459474 TTCTGTTCAACTCTTAAGAGT
1 TTCTGTTCAGCTCTTACGAGC
*
34459495 TTCTGTTTAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
* * * *
34459516 TTCTGTTCAACCCTTA-TAGGT
1 TTCTGTTCAGCTCTTACGA-GC
* * * *
34459537 TTCTATTTAGCTCTCATGAGC
1 TTCTGTTCAGCTCTTACGAGC
34459558 TTCTGTTCAGCT
1 TTCTGTTCAGCT
34459570 TTTAGGCTTT
Statistics
Matches: 101, Mismatches: 33, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
20 4 0.04
21 93 0.92
22 4 0.04
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.44
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTACGAGC
Found at i:34459467 original size:42 final size:42
Alignment explanation
Indices: 34459410--34459566 Score: 183
Period size: 42 Copynumber: 3.7 Consensus size: 42
34459400 CGTGTTTTAC
* * *
34459410 TTTCTGTTCGGCTCTTACAAGCTTCTGTTTAACTCTTATGAG
1 TTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACTCTTATGAG
* *
34459452 TTT-TCGTTCAGCTCTTTCGAGCTTCTGTTCAACTCTTAAGAG
1 TTTCT-GTTCAGCTCTTACGAGCTTCTGTTCAACTCTTATGAG
* *
34459494 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACCCTTAT-AGG
1 TTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACTCTTATGA-G
* * * *
34459536 TTTCTATTTAGCTCTCATGAGCTTCTGTTCA
1 TTTCTGTTCAGCTCTTACGAGCTTCTGTTCA
34459567 GCTTTTAGGC
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.02
42 97 0.97
43 1 0.01
ACGTcount: A:0.17, C:0.23, G:0.16, T:0.45
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACTCTTATGAG
Found at i:34473231 original size:20 final size:20
Alignment explanation
Indices: 34473208--34473247 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
34473198 CAAGGCCCTG
*
34473208 CATAT-ATTCACATGTATATA
1 CATATAATT-ACATCTATATA
34473228 CATATAATTACATCTATATA
1 CATATAATTACATCTATATA
34473248 TACACATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (20 bp):
CATATAATTACATCTATATA
Found at i:34475914 original size:41 final size:42
Alignment explanation
Indices: 34475857--34475936 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 42
34475847 TTGCAGGGGA
*
34475857 CACACGGCCAAATCACACGCCTATGTGT-TAGCCGTGTGTCT
1 CACACGGCCAAATCACACGCCCATGTGTCTAGCCGTGTGTCT
* *
34475898 CACACGGTCC-AATCACACGCCCGTGTGTCTGGCCGTGTG
1 CACACGG-CCAAATCACACGCCCATGTGTCTAGCCGTGTG
34475937 GACTCAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 23 0.68
42 11 0.32
ACGTcount: A:0.19, C:0.34, G:0.25, T:0.23
Consensus pattern (42 bp):
CACACGGCCAAATCACACGCCCATGTGTCTAGCCGTGTGTCT
Found at i:34481447 original size:19 final size:19
Alignment explanation
Indices: 34481419--34481455 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
34481409 CCGGAGTCTT
* *
34481419 AGCCTGTTTTCTTTTCCTA
1 AGCCTATTTTCTCTTCCTA
34481438 AGCCTATTTTCTCTTCCT
1 AGCCTATTTTCTCTTCCT
34481456 TCTAAAGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.08, T:0.51
Consensus pattern (19 bp):
AGCCTATTTTCTCTTCCTA
Found at i:34488240 original size:16 final size:15
Alignment explanation
Indices: 34488219--34488248 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
34488209 CATGTTTTTA
34488219 TAATCTTTACATATTT
1 TAATCTTTA-ATATTT
34488235 TAATCTTTAATATT
1 TAATCTTTAATATT
34488249 AACTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATCTTTAATATTT
Found at i:34489964 original size:11 final size:11
Alignment explanation
Indices: 34489948--34489972 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34489938 ACGTGCTGAC
34489948 TGCTGATATCG
1 TGCTGATATCG
34489959 TGCTGATATCG
1 TGCTGATATCG
34489970 TGC
1 TGC
34489973 CACCCCTGTT
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:0.16, C:0.20, G:0.28, T:0.36
Consensus pattern (11 bp):
TGCTGATATCG
Found at i:34490156 original size:31 final size:31
Alignment explanation
Indices: 34490099--34490157 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
34490089 CATAATAAGT
* * *
34490099 TGTAAAATTATTCATGAAATTTAATTTAATG
1 TGTAAAATAATACATGAAATTAAATTTAATG
34490130 TGTAAAATAATACAT-AAACTTAAATTTA
1 TGTAAAATAATACATGAAA-TTAAATTTA
34490158 GTGTAATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (31 bp):
TGTAAAATAATACATGAAATTAAATTTAATG
Found at i:34493421 original size:17 final size:16
Alignment explanation
Indices: 34493399--34493436 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
34493389 GCCGAATGCA
34493399 TATTTTAATCTAGATTT
1 TATTTTAATCTAGA-TT
*
34493416 TATTTTAGTCTAGATT
1 TATTTTAATCTAGATT
34493432 TATTT
1 TATTT
34493437 ATTCATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (16 bp):
TATTTTAATCTAGATT
Found at i:34494164 original size:61 final size:57
Alignment explanation
Indices: 34494071--34494226 Score: 194
Period size: 61 Copynumber: 2.7 Consensus size: 57
34494061 TGCCTGTTAG
* * *
34494071 GATATTATTATGGGAT-AT-TATCTTTTAGCAATTTGATTCATAATGAGATGTTATAG
1 GATATTATTATGGGATGATATATCTTTTAGCAATTTGATTC-TAATGAGATATCATAA
* *
34494127 GGTATTATTATGGGATGAGATACTATCTCTTAGCAATTTGATTTCTAATGAGATATCATAA
1 GATATTATTATGGGAT--GATA-TATCTTTTAGCAATTTGA-TTCTAATGAGATATCATAA
34494188 GATATTATTATGGGAT-AT-TATCTTTTAGCAATTTGATTC
1 GATATTATTATGGGATGATATATCTTTTAGCAATTTGATTC
34494227 CTACGTGACT
Statistics
Matches: 87, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
55 3 0.03
56 32 0.37
58 2 0.02
59 2 0.02
61 45 0.52
62 3 0.03
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (57 bp):
GATATTATTATGGGATGATATATCTTTTAGCAATTTGATTCTAATGAGATATCATAA
Found at i:34499351 original size:17 final size:16
Alignment explanation
Indices: 34499314--34499353 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
34499304 AAATTTAAAA
*
34499314 AAAAATTAAAAATTCT
1 AAAAATTAAAAAATCT
34499330 AAAAATATAAAAAATCT
1 AAAAAT-TAAAAAATCT
*
34499347 GAAAATT
1 AAAAATT
34499354 CATTCTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (16 bp):
AAAAATTAAAAAATCT
Found at i:34500987 original size:85 final size:87
Alignment explanation
Indices: 34500875--34501050 Score: 338
Period size: 85 Copynumber: 2.0 Consensus size: 87
34500865 TTGGAAAAGA
34500875 AAAATTTTAAAAGTGAAATGGATACCTTAAAAAAAATTTAATTTAATATTTTTTTGAATCCTTCA
1 AAAATTTTAAAAGTGAAATGGATACCTTAAAAAAAATTTAATTTAATATTTTTTTGAATCCTTCA
34500940 TATTTATGATTACAATGCAAAT
66 TATTTATGATTACAATGCAAAT
34500962 AAAA-TTTAAAAGTG-AATGGATACCTTAAAAAAAATTTAATTTAATATTTTTTTGAATCCTTCA
1 AAAATTTTAAAAGTGAAATGGATACCTTAAAAAAAATTTAATTTAATATTTTTTTGAATCCTTCA
34501025 TATTTATGATTACAATGCAAAT
66 TATTTATGATTACAATGCAAAT
34501047 AAAA
1 AAAA
34501051 ATGCCCATAA
Statistics
Matches: 89, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
85 75 0.84
86 10 0.11
87 4 0.04
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (87 bp):
AAAATTTTAAAAGTGAAATGGATACCTTAAAAAAAATTTAATTTAATATTTTTTTGAATCCTTCA
TATTTATGATTACAATGCAAAT
Found at i:34501412 original size:50 final size:50
Alignment explanation
Indices: 34501352--34501449 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 50
34501342 TTTTACATCA
* * *
34501352 AATTTTTAATATTTTTTTTAAAAATTTTAAAAATTTTTATAATCTTTTAG
1 AATTTCTAATATTTTTTTTAAAAATTTTAAAAATTTTTAAAATATTTTAG
* * * *
34501402 AATTTCTAATATTTTTTTTATAATTTTTTACAATTTTTAAAATATTTT
1 AATTTCTAATATTTTTTTTAAAAATTTTAAAAATTTTTAAAATATTTT
34501450 TAATTTTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (50 bp):
AATTTCTAATATTTTTTTTAAAAATTTTAAAAATTTTTAAAATATTTTAG
Found at i:34501460 original size:31 final size:31
Alignment explanation
Indices: 34501353--34501453 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 31
34501343 TTTACATCAA
* *
34501353 ATTTTTAATATTTTTTTTAAAAATTTTAAAA-
1 ATTTTTAATA-ATTTTTTAAAATTTTTAAAAT
* * * *
34501384 ATTTTT-ATAATCTTTTAGAATTTCTAATAT
1 ATTTTTAATAATTTTTTAAAATTTTTAAAAT
* * *
34501414 TTTTTTTATAATTTTTTACAATTTTTAAAAT
1 ATTTTTAATAATTTTTTAAAATTTTTAAAAT
34501445 ATTTTTAAT
1 ATTTTTAAT
34501454 TTTTTTTCCA
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 14 0.25
30 8 0.15
31 33 0.60
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (31 bp):
ATTTTTAATAATTTTTTAAAATTTTTAAAAT
Found at i:34520498 original size:20 final size:21
Alignment explanation
Indices: 34520473--34520513 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34520463 GGGAATGCTA
*
34520473 GGAGTT-GGAAGTATTAATAC
1 GGAGTTAGAAAGTATTAATAC
*
34520493 GGAGTTAGAAAGTATTCATAC
1 GGAGTTAGAAAGTATTAATAC
34520514 CGTGTATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.29
Consensus pattern (21 bp):
GGAGTTAGAAAGTATTAATAC
Found at i:34522184 original size:36 final size:36
Alignment explanation
Indices: 34522133--34522205 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
34522123 ATAGGCCCCT
*
34522133 GATATTGTATTTGACAGTATTTGATAATTCCATGGG
1 GATATTGTATCTGACAGTATTTGATAATTCCATGGG
34522169 GATATTGTATCTGACAGTATTTGATAATTCCATGGG
1 GATATTGTATCTGACAGTATTTGATAATTCCATGGG
34522205 G
1 G
34522206 TGTGTGCTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (36 bp):
GATATTGTATCTGACAGTATTTGATAATTCCATGGG
Found at i:34525423 original size:44 final size:43
Alignment explanation
Indices: 34525365--34525506 Score: 176
Period size: 44 Copynumber: 3.2 Consensus size: 43
34525355 TTGAAAAAAA
*
34525365 ACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
1 ACAGATCTTGTCTTCATGTACTGGAGTGAAGTAGATCAAAGAT
*** * * *
34525408 ACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAA
1 A-CAGATCTTGTCTTCATGTACTGG-AGTGAAGTAGATCAAAGAT
*
34525453 AGCAGATCTTGTCTTCATGTACTGGAGTGAAGTAGATCGAAGATT
1 A-CAGATCTTGTCTTCATGTACTGGAGTGAAGTAGATCAAAGA-T
34525498 ACAGATCTT
1 ACAGATCTT
34525507 ATCTCCCTAA
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
43 1 0.01
44 43 0.52
45 38 0.46
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (43 bp):
ACAGATCTTGTCTTCATGTACTGGAGTGAAGTAGATCAAAGAT
Found at i:34525459 original size:45 final size:45
Alignment explanation
Indices: 34525274--34525468 Score: 162
Period size: 44 Copynumber: 4.4 Consensus size: 45
34525264 GTTGAAAAGC
* * * * * * * *
34525274 AGCAGATCATGTCTTCCTATATTGGTAGCGAAGTGGATCGAATAT
1 AGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAA
* * * * *
34525319 A-CAGATCTTGTC-TCCCAATACTGGTGGTGGAGCAGATTGAAAAAA
1 AGCAGATCTTGTCTTCCC-ATACTGGTGGCGAAGTAGA-TCAAAGAA
* *** * * *
34525364 AACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAA
*
34525408 ACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAA
1 AGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAA
34525453 AGCAGATCTTGTCTTC
1 AGCAGATCTTGTCTTC
34525469 ATGTACTGGA
Statistics
Matches: 116, Mismatches: 29, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
43 3 0.03
44 49 0.42
45 45 0.39
46 17 0.15
47 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (45 bp):
AGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAA
Found at i:34525471 original size:89 final size:89
Alignment explanation
Indices: 34525276--34525513 Score: 282
Period size: 89 Copynumber: 2.7 Consensus size: 89
34525266 TGAAAAGCAG
* * * * * * *
34525276 CAGATCATGTCTTCCTATATTGGTAGCGAAGTGGATCGAATATACAGATCTTGTCTCCCAATACT
1 CAGATCTTGTCTTCATGTACTGG-AGTGAAGTAGATCGAAGATACAGATCTTGTCTCCCAATACT
* * *
34525341 GGTGGTGGAGCAGATTGAAAAAAAA
65 GGTGGCGAAGCAGATTCAAAAAAAA
* *
34525366 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCC-ATAC
1 CAGATCTTGTCTTCATGTACTGGAGTGAAGTAGATCGAAGATA-CAGATCTTGTC-TCCCAATAC
* * *
34525430 TGGTGGCGAAGTAGA-TCAAAGAAAG
64 TGGTGGCGAAGCAGATTCAAAAAAAA
*
34525455 CAGATCTTGTCTTCATGTACTGGAGTGAAGTAGATCGAAGATTACAGATCTTATCTCCC
1 CAGATCTTGTCTTCATGTACTGGAGTGAAGTAGATCGAAGA-TACAGATCTTGTCTCCC
34525514 TAAGCAGTAG
Statistics
Matches: 127, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
88 4 0.03
89 71 0.56
90 48 0.38
91 4 0.03
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (89 bp):
CAGATCTTGTCTTCATGTACTGGAGTGAAGTAGATCGAAGATACAGATCTTGTCTCCCAATACTG
GTGGCGAAGCAGATTCAAAAAAAA
Found at i:34525476 original size:45 final size:44
Alignment explanation
Indices: 34525366--34525495 Score: 170
Period size: 45 Copynumber: 2.9 Consensus size: 44
34525356 TGAAAAAAAA
* *
34525366 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAC
1 CAGATCTTGTCTTCATGTACTGGAGTGAAGTAGATCAAAGAAAC
*** * * *
34525410 CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAG
1 CAGATCTTGTCTTCATGTACTGG-AGTGAAGTAGATCAAAGAAAC
*
34525455 CAGATCTTGTCTTCATGTACTGGAGTGAAGTAGATCGAAGA
1 CAGATCTTGTCTTCATGTACTGGAGTGAAGTAGATCAAAGA
34525496 TTACAGATCT
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 35 0.49
45 37 0.51
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
CAGATCTTGTCTTCATGTACTGGAGTGAAGTAGATCAAAGAAAC
Found at i:34531818 original size:26 final size:27
Alignment explanation
Indices: 34531788--34531841 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
34531778 TACCTTTTAG
*
34531788 AAGTGTTTTTAAAAAATA-TTTTGAAA
1 AAGTGATTTTAAAAAATATTTTTGAAA
* *
34531814 AAGTGATTTTAAGAAGTATTTTTGAAA
1 AAGTGATTTTAAAAAATATTTTTGAAA
34531841 A
1 A
34531842 GTTTGTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (27 bp):
AAGTGATTTTAAAAAATATTTTTGAAA
Found at i:34533746 original size:50 final size:49
Alignment explanation
Indices: 34533659--34533919 Score: 128
Period size: 50 Copynumber: 5.2 Consensus size: 49
34533649 GAGTAGGGCT
* * * ** * * *
34533659 ATTATTACCACTTTCGATAAGTTTCTCTTTATGTGTCTTGGAGCAGGGCC
1 ATTATTACCACATTCTATAAGCTTC-CCCTATATGTCTAGGAGCAGGACC
* *
34533709 TTTATTACCATATTCTATAAGCCTTCCCCTATATGTCTAGGAGCAGGACC
1 ATTATTACCACATTCTATAAG-CTTCCCCTATATGTCTAGGAGCAGGACC
* * * ** * * *
34533759 ATTATTACCACCTTTTATAAGCTTCCCTCCATGCGTCTAGTAGTA-GAGTC
1 ATTATTACCACATTCTATAAGCTTCCC-CTATATGTCTAGGAGCAGGA-CC
* * * * * ** * * * *
34533809 TTTATTACTACCTTCTATAAGCCTCCCCCCATGCGTTTGGGAGCAAGATC
1 ATTATTACCACATTCTATAAG-CTTCCCCTATATGTCTAGGAGCAGGACC
* * * * * * * *
34533859 ATTATTACTAAATTCCATAAGCCTCCTCCCATGTGTCTAGGAGTAAGACC
1 ATTATTACCACATTCTATAAGCTTCC-CCTATATGTCTAGGAGCAGGACC
34533909 ATTATTACCAC
1 ATTATTACCAC
34533920 TTTTTGTGAG
Statistics
Matches: 164, Mismatches: 41, Indels: 12
0.76 0.19 0.06
Matches are distributed among these distances:
49 11 0.07
50 143 0.87
51 10 0.06
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (49 bp):
ATTATTACCACATTCTATAAGCTTCCCCTATATGTCTAGGAGCAGGACC
Found at i:34533852 original size:100 final size:97
Alignment explanation
Indices: 34533710--34534031 Score: 272
Period size: 100 Copynumber: 3.2 Consensus size: 97
34533700 AGCAGGGCCT
** * ** * * * * * *
34533710 TTATTACCATATTCTATAAGCCTTCCCCTATATGTCTAGGAGCAGGACCATTATTACCACCTTTT
1 TTATTACCACCTTCTATAAGCC-TCCCCCATGCGTTTGGGAGCAAGA-CATTATTACAAACTTTC
* *
34533775 ATAAGCTTCCCTCCATGCGTCTAGTAGTAGAGTCT
64 ATAAGCTTCCCTCCATGCGTCTAGGAGTA-AGTCA
* *
34533810 TTATTACTACCTTCTATAAGCCTCCCCCCATGCGTTTGGGAGCAAGATCATTATTACTAAA-TTC
1 TTATTACCACCTTCTATAAGCCT-CCCCCATGCGTTTGGGAGCAAGA-CATTATTAC-AAACTTT
* * *
34533874 CATAAGCCT-CCTCCCATGTGTCTAGGAGTAAGACCA
63 CATAAGCTTCCCT-CCATGCGTCTAGGAGTAAG-TCA
* * * * * * * *
34533910 TTATTACCACTTTTTGTGAGCATCCCCCATGCGTTTGGGAGCATGACATCTATTACAATCTTTCG
1 TTATTACCACCTTCTATAAGCCTCCCCCATGCGTTTGGGAGCAAGACAT-TATTACAAACTTTCA
* *
34533975 TAAGTCTTCTCT-CATGCGTCTAGGAGCAAAGTCA
65 TAAG-CTTCCCTCCATGCGTCTAGGAG-TAAGTCA
34534009 TTATTACCACCTTCTATAAGCCT
1 TTATTACCACCTTCTATAAGCCT
34534032 TCCTTGTGCA
Statistics
Matches: 174, Mismatches: 39, Indels: 19
0.75 0.17 0.08
Matches are distributed among these distances:
98 5 0.03
99 74 0.43
100 92 0.53
101 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (97 bp):
TTATTACCACCTTCTATAAGCCTCCCCCATGCGTTTGGGAGCAAGACATTATTACAAACTTTCAT
AAGCTTCCCTCCATGCGTCTAGGAGTAAGTCA
Found at i:34533996 original size:99 final size:99
Alignment explanation
Indices: 34533834--34534018 Score: 232
Period size: 99 Copynumber: 1.9 Consensus size: 99
34533824 TATAAGCCTC
*
34533834 CCCCCATGCGTTTGGGAGCAAGATCATTATTACTAAATTCCATAAGCCTCCTCCCATGTGTCTAG
1 CCCCCATGCGTTTGGGAGCAAGATCATTATTACTAAATTCCATAAGCCTCCTCCCATGCGTCTAG
*
34533899 GAG-TAAGACCATTATTACCACTTTTTGTGAGCAT
66 GAGCAAAG-CCATTATTACCACTTTTTGTGAGCAT
* * * * * * *
34533933 CCCCCATGCGTTTGGGAGCATGA-CATCTATTAC-AATCTTTCGTAAGTCTTCTCTCATGCGTCT
1 CCCCCATGCGTTTGGGAGCAAGATCAT-TATTACTAA-ATTCCATAAGCCTCCTCCCATGCGTCT
*
34533996 AGGAGCAAAGTCATTATTACCAC
64 AGGAGCAAAGCCATTATTACCAC
34534019 CTTCTATAAG
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
98 5 0.07
99 65 0.89
100 3 0.04
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (99 bp):
CCCCCATGCGTTTGGGAGCAAGATCATTATTACTAAATTCCATAAGCCTCCTCCCATGCGTCTAG
GAGCAAAGCCATTATTACCACTTTTTGTGAGCAT
Found at i:34534270 original size:58 final size:58
Alignment explanation
Indices: 34534163--34534289 Score: 150
Period size: 58 Copynumber: 2.2 Consensus size: 58
34534153 GTCACTTTAT
* *
34534163 TATCTTCA-T-TTCGGGCCCATCCATGAACCTTTTGGGCTCTCGATAGAGGTGAGACA
1 TATCTTCATTATTCGGGCCCATCCATGAACCCTTTGGGCTCTCAATAGAGGTGAGACA
* * ** * * * *
34534219 TATCTTTATTATTCGGGCCCCTCTTTGAACCCTTTGTGCTGTCAATGGAGGTGAGGCA
1 TATCTTCATTATTCGGGCCCATCCATGAACCCTTTGGGCTCTCAATAGAGGTGAGACA
34534277 TATCTTCATTATT
1 TATCTTCATTATT
34534290 TGAGTCCCTT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
56 7 0.12
57 1 0.02
58 50 0.86
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (58 bp):
TATCTTCATTATTCGGGCCCATCCATGAACCCTTTGGGCTCTCAATAGAGGTGAGACA
Found at i:34536323 original size:20 final size:20
Alignment explanation
Indices: 34536300--34536338 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
34536290 CGCTGCCAAC
34536300 GTCACGTCG-CCACCGCCACA
1 GTCACGTCGACCA-CGCCACA
34536320 GTCACGTCGACCACGCCAC
1 GTCACGTCGACCACGCCAC
34536339 TTGCGCCGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.21, C:0.49, G:0.21, T:0.10
Consensus pattern (20 bp):
GTCACGTCGACCACGCCACA
Found at i:34537456 original size:3 final size:3
Alignment explanation
Indices: 34537441--34537480 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
34537431 ATTTTTGTAA
34537441 TAT TAT TACT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34537481 AATTGTTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:34537841 original size:18 final size:17
Alignment explanation
Indices: 34537818--34537853 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
34537808 TTTAATTTTA
*
34537818 TATTTGTTTATTTACTTT
1 TATTTGTTGATTT-CTTT
34537836 TATTTGTTGATTTCTTT
1 TATTTGTTGATTTCTTT
34537853 T
1 T
34537854 CATTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (17 bp):
TATTTGTTGATTTCTTT
Found at i:34538477 original size:114 final size:114
Alignment explanation
Indices: 34538189--34538571 Score: 675
Period size: 114 Copynumber: 3.4 Consensus size: 114
34538179 TTTGGGTTTC
34538189 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGAT
* * * * *
34538254 TTTTTTCGTTCAACCTAATGGCTAAATATCCTTTT----AAAAACTTTA
66 TTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAGGAAAAAATTCA
34538299 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGAT
*
34538364 TTTTCTCATTCAACCAAATGGCTAAATATCATTTTAAGGAAAAAATTCA
66 TTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAGGAAAAAATTCA
34538413 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGAT
34538478 TTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAGGAAAAAATTCA
66 TTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAGGAAAAAATTCA
*
34538527 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCAAGAAAACGTGCC
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCC
34538572 AAATATCCTT
Statistics
Matches: 261, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
110 96 0.37
114 165 0.63
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGAT
TTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAGGAAAAAATTCA
Found at i:34539079 original size:22 final size:22
Alignment explanation
Indices: 34539023--34539080 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
34539013 AATTAATTTT
*
34539023 TTAAAATTTTATAATTTCAAAAA
1 TTAAAATTAT-TAATTTCAAAAA
* * *
34539046 TTATAAA-AATTACTTTTAAAAA
1 TTA-AAATTATTAATTTCAAAAA
34539068 TTAAAATTATTAA
1 TTAAAATTATTAA
34539081 AAAATTTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
21 3 0.11
22 17 0.63
23 4 0.15
24 3 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAAATTATTAATTTCAAAAA
Found at i:34539085 original size:17 final size:16
Alignment explanation
Indices: 34539059--34539104 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
34539049 TAAAAATTAC
34539059 TTTT-AAAAATTAAAA
1 TTTTAAAAAATTAAAA
*
34539074 TTATTAAAAAATTTAAA
1 TT-TTAAAAAATTAAAA
34539091 TTTTAAAAAATTAA
1 TTTTAAAAAATTAA
34539105 TTAAATGCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 2 0.07
16 13 0.48
17 12 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTTAAAAAATTAAAA
Found at i:34551007 original size:19 final size:17
Alignment explanation
Indices: 34550971--34551009 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
34550961 TTTGAGGACT
*
34550971 AATTTAAAACATTTTAA
1 AATTTAAAACAATTTAA
34550988 AATTTAAATACCAATTTAA
1 AATTTAAA-A-CAATTTAA
34551007 AAT
1 AAT
34551010 CAGACCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 10 0.53
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTTAAAACAATTTAA
Found at i:34555618 original size:13 final size:14
Alignment explanation
Indices: 34555600--34555628 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
34555590 ATTTCACTAT
34555600 CAATTATAATA-AA
1 CAATTATAATACAA
34555613 CAATTATAATACAA
1 CAATTATAATACAA
34555627 CA
1 CA
34555629 TTTCCTGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (14 bp):
CAATTATAATACAA
Found at i:34555886 original size:46 final size:45
Alignment explanation
Indices: 34555816--34555954 Score: 208
Period size: 46 Copynumber: 3.0 Consensus size: 45
34555806 ACAATGCTAT
*
34555816 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTT-ACTGAAATACCATACCTACGTTTCAC
*
34555862 AACTCAATATGGTTTTCGTTACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTC-TTACTGAAATACCATACCTACGTTTCAC
*
34555908 AACTCAGTATGGTTTTCTTTACT-AAATTACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTC-TTACTGAAA-TACCATACCTACGTTTCAC
34555954 A
1 A
34555955 CTTTGCCATG
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
45 3 0.03
46 81 0.94
47 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.36
Consensus pattern (45 bp):
AACTCAGTATGGTTTTCTTACTGAAATACCATACCTACGTTTCAC
Found at i:34567513 original size:35 final size:35
Alignment explanation
Indices: 34567462--34567532 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
34567452 GAATAGAAGA
34567462 TAAGATGAATGGCAAAGCATACACATGTTTTGTAC
1 TAAGATGAATGGCAAAGCATACACATGTTTTGTAC
*
34567497 TAAGTTGAATGGCAAAGCATACACATGTTTTGTAC
1 TAAGATGAATGGCAAAGCATACACATGTTTTGTAC
34567532 T
1 T
34567533 TAAATGGGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (35 bp):
TAAGATGAATGGCAAAGCATACACATGTTTTGTAC
Found at i:34569888 original size:42 final size:42
Alignment explanation
Indices: 34569843--34570080 Score: 377
Period size: 42 Copynumber: 5.7 Consensus size: 42
34569833 TGTTAAACAA
* * * ** * *
34569843 AAACCCATAAGGGTTGAACAGAAGCTCGTAAGAGCTGAACGA
1 AAACCCATTAGGGTTAAACTGAAGCTCAAAAAAGCTGAACGG
* *
34569885 AAACCCATAAGGGTTAAATTGAAGCTCAAAAAAGCTGAACGG
1 AAACCCATTAGGGTTAAACTGAAGCTCAAAAAAGCTGAACGG
34569927 AAACCCATTAGGGTTAAACTGAAGCTCAAAAAAGCTGAACGG
1 AAACCCATTAGGGTTAAACTGAAGCTCAAAAAAGCTGAACGG
34569969 AAACCCATTAGGGTTAAACTGAAGCTCAAAAAAGCTGAACGG
1 AAACCCATTAGGGTTAAACTGAAGCTCAAAAAAGCTGAACGG
34570011 AAACCCATTAGGGTTAAACTGAAGCTCAAAAAAGCTGAACGG
1 AAACCCATTAGGGTTAAACTGAAGCTCAAAAAAGCTGAACGG
* *
34570053 AAACCCATTAGGGTTAAACAGAAACTCA
1 AAACCCATTAGGGTTAAACTGAAGCTCA
34570081 TATAAGTTAA
Statistics
Matches: 185, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 185 1.00
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.16
Consensus pattern (42 bp):
AAACCCATTAGGGTTAAACTGAAGCTCAAAAAAGCTGAACGG
Found at i:34574579 original size:2 final size:2
Alignment explanation
Indices: 34574572--34574598 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34574562 TGATTAAATC
34574572 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 T
34574599 CTGAGCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34575154 original size:13 final size:13
Alignment explanation
Indices: 34575136--34575160 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34575126 CATGTTTAGG
34575136 TATGTTTAATGTA
1 TATGTTTAATGTA
34575149 TATGTTTAATGT
1 TATGTTTAATGT
34575161 GCCTATATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (13 bp):
TATGTTTAATGTA
Found at i:34577243 original size:16 final size:16
Alignment explanation
Indices: 34577222--34577252 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
34577212 AGAAAGAGTA
34577222 CAATATGAAGATAATG
1 CAATATGAAGATAATG
34577238 CAATATGAAGATAAT
1 CAATATGAAGATAAT
34577253 CTCAACGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (16 bp):
CAATATGAAGATAATG
Found at i:34588182 original size:20 final size:20
Alignment explanation
Indices: 34588159--34588201 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
34588149 GTTATTTTGG
*
34588159 TGTATATAAGTGTTTTTTTA
1 TGTATATAAGTGTTTTGTTA
34588179 TGTATATAAGTGTTTTGTTA
1 TGTATATAAGTGTTTTGTTA
34588199 TGT
1 TGT
34588202 TATCCTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (20 bp):
TGTATATAAGTGTTTTGTTA
Found at i:34588483 original size:7 final size:7
Alignment explanation
Indices: 34588471--34588519 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
34588461 AAAAGTTAGA
34588471 TTTTATT
1 TTTTATT
34588478 TTTTATT
1 TTTTATT
34588485 TTTTATT
1 TTTTATT
*
34588492 TGTT-TT
1 TTTTATT
*
34588498 TCTTA-T
1 TTTTATT
34588504 TTTTA-T
1 TTTTATT
34588510 TTTTATT
1 TTTTATT
34588517 TTT
1 TTT
34588520 GATAAGGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 16 0.43
7 21 0.57
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.84
Consensus pattern (7 bp):
TTTTATT
Found at i:34588486 original size:6 final size:6
Alignment explanation
Indices: 34588471--34588519 Score: 55
Period size: 6 Copynumber: 7.7 Consensus size: 6
34588461 AAAAGTTAGA
34588471 TTTTATT TTTTATT TTTTAT TTGTT-T TTCTTAT TTTTAT TTTTAT TTTT
1 TTTTA-T TTTTA-T TTTTAT TT-TTAT TT-TTAT TTTTAT TTTTAT TTTT
34588520 GATAAGGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
6 22 0.56
7 17 0.44
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:34590662 original size:369 final size:368
Alignment explanation
Indices: 34589963--34590698 Score: 1310
Period size: 369 Copynumber: 2.0 Consensus size: 368
34589953 CTTTTGGGGT
34589963 TTGGTTGTGAAGAGAAGGAAGACTGTTCTGATCTGGCAGTTAAACTCCAACCTATCTGTACAACG
1 TTGGTTGTGAAGAGAAGGAAGACTGTTCTGATCTGGCAGTTAAACTCCAACCTATCTGTACAACG
* *
34590028 ATTTACTACACTGTACCGCATATACATCAACTTTGCTGCATATTATTATCTGATCTGGCAACTTA
66 ATTTACCACACTATACCGCATATACATCAACTTTGCTGCATATTATTATCTGATCTGGCAACTTA
* *
34590093 AATCGCAACATATCTGTACAACGGTTTACCACAATGCACTGTACTGTATATACGCCAGCTTTGCT
131 AACCGCAACATATCTATACAACGGTTTACCACAATGCACTGTACTGTATATACGCCAGCTTTGCT
34590158 ACATATTATTATCTGAGTGGCTTAGTCCACATATATGGTGTGTAAGGTTGGATGGGCCTTTCGAG
196 ACATATTATTATCTGAGTGGCTTAGTCCACATATATGGTGTGTAAGGTTGGATGGGCCTTTCGAG
* *
34590223 GTCCTATATGGTGTGTTTGGTTGGATGATCTTAAACAGCTCTTTTGGGGTCTGATCGGGAGACGG
261 GTCCTATATGGTGTGTTTGGTTGGATGACCTTAAACAGCTCTTTTGGGGTCTGATCGGGAGACAG
34590288 AGAGGTATTTTAGCTGGATGGGTGAGTTTTTACTACTTGATTGG
326 AGAGGTATTTTAGCTGGAT-GGTGAGTTTTTACTACTTGATTGG
*
34590332 TTGGTTGTGAAGAGAAGGAAGACTGTTCTGATCTGGCAGTTAAACTGCAACCTATCTGTACAACG
1 TTGGTTGTGAAGAGAAGGAAGACTGTTCTGATCTGGCAGTTAAACTCCAACCTATCTGTACAACG
* * * *
34590397 GTTTACCGCACTATACCGCATATACATCAACTTTGCTGCATATTGTTATCTGATCTGGCAATTTA
66 ATTTACCACACTATACCGCATATACATCAACTTTGCTGCATATTATTATCTGATCTGGCAACTTA
*
34590462 AACCGTAACATATCTATACAACGGTTTACCACAATGCACTGTACTGTATATACGCCAGCTTTGCT
131 AACCGCAACATATCTATACAACGGTTTACCACAATGCACTGTACTGTATATACGCCAGCTTTGCT
*
34590527 ACATATTATTATCTGAGTGGCTTAGTCCACATATATGGTGTGTAAGGTTGGATGGGTCTTTCGAG
196 ACATATTATTATCTGAGTGGCTTAGTCCACATATATGGTGTGTAAGGTTGGATGGGCCTTTCGAG
* * *
34590592 GTCCTATATGGTGTGTTTGGTTGGATGACCTTAAACAGCTCTTTTGGGGTGTGATTGGGGGACAG
261 GTCCTATATGGTGTGTTTGGTTGGATGACCTTAAACAGCTCTTTTGGGGTCTGATCGGGAGACAG
*
34590657 AGAGGTGTTTTAGCTGGATGGTGAGTTTTTACTACTTGATTG
326 AGAGGTATTTTAGCTGGATGGTGAGTTTTTACTACTTGATTG
34590699 CATTCATACG
Statistics
Matches: 350, Mismatches: 17, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
368 23 0.07
369 327 0.93
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (368 bp):
TTGGTTGTGAAGAGAAGGAAGACTGTTCTGATCTGGCAGTTAAACTCCAACCTATCTGTACAACG
ATTTACCACACTATACCGCATATACATCAACTTTGCTGCATATTATTATCTGATCTGGCAACTTA
AACCGCAACATATCTATACAACGGTTTACCACAATGCACTGTACTGTATATACGCCAGCTTTGCT
ACATATTATTATCTGAGTGGCTTAGTCCACATATATGGTGTGTAAGGTTGGATGGGCCTTTCGAG
GTCCTATATGGTGTGTTTGGTTGGATGACCTTAAACAGCTCTTTTGGGGTCTGATCGGGAGACAG
AGAGGTATTTTAGCTGGATGGTGAGTTTTTACTACTTGATTGG
Found at i:34604820 original size:15 final size:15
Alignment explanation
Indices: 34604800--34604830 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34604790 CAAACATCAC
34604800 TCATAGCAACTTTAT
1 TCATAGCAACTTTAT
*
34604815 TCATAGCAATTTTAT
1 TCATAGCAACTTTAT
34604830 T
1 T
34604831 TAATTTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.45
Consensus pattern (15 bp):
TCATAGCAACTTTAT
Found at i:34605630 original size:18 final size:18
Alignment explanation
Indices: 34605615--34605649 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34605605 AAGCCCAACA
34605615 CCATC-ATTCGGCCCAAAG
1 CCATCAATT-GGCCCAAAG
34605633 CCATCAATTGGCCCAAA
1 CCATCAATTGGCCCAAA
34605650 CTTGCTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.31, C:0.37, G:0.14, T:0.17
Consensus pattern (18 bp):
CCATCAATTGGCCCAAAG
Found at i:34605682 original size:15 final size:15
Alignment explanation
Indices: 34605662--34605691 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34605652 TGCTAGTAAT
34605662 TCCACCATTAGGCCC
1 TCCACCATTAGGCCC
*
34605677 TCCACCATTCGGCCC
1 TCCACCATTAGGCCC
34605692 ACTTGTTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.50, G:0.13, T:0.20
Consensus pattern (15 bp):
TCCACCATTAGGCCC
Found at i:34605808 original size:63 final size:63
Alignment explanation
Indices: 34605670--34605817 Score: 156
Period size: 63 Copynumber: 2.3 Consensus size: 63
34605660 ATTCCACCAT
*** * * *
34605670 TAGGCCCTCCACCATTCGGCCCACTTGTTTGTGGCCTATACACATGATTCTCAAAATTCGGCC
1 TAGGCCCTCCACCATTCGGCCCAAACGTGTGTGGCCTATACACATGATTCTCAAAATCCGACC
* * * *
34605733 T-GACCCCTCCACCATTCGGCCCAAACGTGTGTGGCCTATACGCATGGTTCTC-AACTCCTGACC
1 TAG-GCCCTCCACCATTCGGCCCAAACGTGTGTGGCCTATACACATGATTCTCAAAATCC-GACC
* *
34605796 TAGGCCCACCACCAATCGGCCC
1 TAGGCCCTCCACCATTCGGCCC
34605818 TGCATACTGA
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
62 5 0.07
63 63 0.91
64 1 0.01
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.24
Consensus pattern (63 bp):
TAGGCCCTCCACCATTCGGCCCAAACGTGTGTGGCCTATACACATGATTCTCAAAATCCGACC
Found at i:34608666 original size:14 final size:15
Alignment explanation
Indices: 34608637--34608668 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
34608627 AAAAACATCA
34608637 TAATTTTATCTATTT
1 TAATTTTATCTATTT
34608652 TAATTTTAT-TATTT
1 TAATTTTATCTATTT
34608666 TAA
1 TAA
34608669 CTATAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTATCTATTT
Found at i:34610216 original size:136 final size:137
Alignment explanation
Indices: 34609961--34610233 Score: 539
Period size: 136 Copynumber: 2.0 Consensus size: 137
34609951 AGTAAACAAA
34609961 AAGAATTAAATTGAAAATAGATTTGTTCTACAATCTTCTCTATTTTTACCTAGTTTCTTTCAAAC
1 AAGAATTAAATTGAAAATAGATTTGTTCTACAATCTTCTCTATTTTTACCTAGTTTCTTTCAAAC
34610026 ACCAACTAAGAATTGAAAACAAAATAATGATAAATAATTATATTAATTTAATATTCTTAATATGA
66 ACCAACTAAGAATTGAAAACAAAATAATGATAAATAATTATATTAATTTAATATTCTTAATATGA
34610091 TGTATTT
131 TGTATTT
34610098 AAGAATTAAA-TGAAAATAGATTTGTTCTACAATCTTCTCTATTTTTACCTAGTTTCTTTCAAAC
1 AAGAATTAAATTGAAAATAGATTTGTTCTACAATCTTCTCTATTTTTACCTAGTTTCTTTCAAAC
34610162 ACCAACTAAGAATTGAAAACAAAATAATGATAAATAATTATATTAATTTAATATTCTTAATATGA
66 ACCAACTAAGAATTGAAAACAAAATAATGATAAATAATTATATTAATTTAATATTCTTAATATGA
34610227 TGTATTT
131 TGTATTT
34610234 TATGTTTAAA
Statistics
Matches: 136, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
136 126 0.93
137 10 0.07
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (137 bp):
AAGAATTAAATTGAAAATAGATTTGTTCTACAATCTTCTCTATTTTTACCTAGTTTCTTTCAAAC
ACCAACTAAGAATTGAAAACAAAATAATGATAAATAATTATATTAATTTAATATTCTTAATATGA
TGTATTT
Found at i:34610269 original size:5 final size:5
Alignment explanation
Indices: 34610259--34610283 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
34610249 TTTTACTCAA
34610259 AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT
34610284 TAATATCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:34612355 original size:15 final size:15
Alignment explanation
Indices: 34612335--34612365 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
34612325 ATGTTTACAA
34612335 GTCGGATCAAGTTTT
1 GTCGGATCAAGTTTT
34612350 GTCGGATCAAGTTTT
1 GTCGGATCAAGTTTT
34612365 G
1 G
34612366 GTTTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.39
Consensus pattern (15 bp):
GTCGGATCAAGTTTT
Found at i:34612843 original size:21 final size:21
Alignment explanation
Indices: 34612817--34612872 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
34612807 AACAGTAATG
*
34612817 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
34612838 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
34612859 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
34612873 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:34616579 original size:39 final size:39
Alignment explanation
Indices: 34616525--34616601 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
34616515 AATCGATTTG
34616525 TTCATCTTTAAAGCTTTACTTGAACTATTGTTTTCTTTA
1 TTCATCTTTAAAGCTTTACTTGAACTATTGTTTTCTTTA
*
34616564 TTCATCTTTAAAGCTTTACTTGAACTATTTTTTTCTTT
1 TTCATCTTTAAAGCTTTACTTGAACTATTGTTTTCTTT
34616602 TCACTTTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56
Consensus pattern (39 bp):
TTCATCTTTAAAGCTTTACTTGAACTATTGTTTTCTTTA
Found at i:34616948 original size:30 final size:30
Alignment explanation
Indices: 34616912--34616978 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
34616902 GAATAAACCG
34616912 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
34616942 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
34616972 AATACAC
1 AATACAC
34616979 AAATACAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (30 bp):
AATACACTACATATATTTTTTTATTTTTAA
Found at i:34618000 original size:273 final size:273
Alignment explanation
Indices: 34617505--34618046 Score: 1021
Period size: 273 Copynumber: 2.0 Consensus size: 273
34617495 TTTGTTTTGT
34617505 TTTTTCTAAGTGAATAAAATCTTGATTTTAAGCTGATAACTTTGTGGTGCATAAATTATCACTTC
1 TTTTTCTAAGTGAATAAAATCTTGATTTTAAGCTGATAACTTTGTGGTGCATAAATTATCACTTC
*
34617570 TACTTCACTCAGATACCTCCTTTCTTTCTTTTTTTCCCACTGTTCTCTTCATCTTTTTTTCCTGT
66 TACTTCACTCAAATACCTCCTTTCTTTCTTTTTTTCCCACTGTTCTCTTCATCTTTTTTTCCTGT
*
34617635 TCAACTGCTTTTGATGTTTTCTTAGAAAGCTCACATCAGCCAATTAAGCTTAATGCAAATGAAAA
131 TCAACTGCTTTTGATGTTTTCTTAGAAAGCTCACATCAGCCAATTAACCTTAATGCAAATGAAAA
34617700 TGGCTTCTGTGCTGAGCTACCATTCAGGATTGGACTAAATAATTTAGCTTGATGGTGCCTAAAAC
196 TGGCTTCTGTGCTGAGCTACCATTCAGGATTGGACTAAATAATTTAGCTTGATGGTGCCTAAAAC
34617765 AAGGCTTTTGTAC
261 AAGGCTTTTGTAC
*
34617778 TTTTTCTATGTGAATAAAATCTTGATTTTAAGCTGATAACTTTGTGGTGCATAAATTATCACTTC
1 TTTTTCTAAGTGAATAAAATCTTGATTTTAAGCTGATAACTTTGTGGTGCATAAATTATCACTTC
*
34617843 TACTTCACTCAAATACTTCCTTTCTTTCTTTTTTTCCCACTGTTCTCTTCATCTTTTTTTCCTGT
66 TACTTCACTCAAATACCTCCTTTCTTTCTTTTTTTCCCACTGTTCTCTTCATCTTTTTTTCCTGT
34617908 TCAACTGCTTTTGATGTTTTCTTAGAAAGCTCACATCAGCCAATTAACCTTAATGCAAATGAAAA
131 TCAACTGCTTTTGATGTTTTCTTAGAAAGCTCACATCAGCCAATTAACCTTAATGCAAATGAAAA
* * *
34617973 TGGCTTCTGTGCTGAGCTGCTATTCAGGATTGGAGTAAATAATTTAGCTTGATGGTGCCTAAAAC
196 TGGCTTCTGTGCTGAGCTACCATTCAGGATTGGACTAAATAATTTAGCTTGATGGTGCCTAAAAC
34618038 AAGGCTTTT
261 AAGGCTTTT
34618047 ATACAAGATG
Statistics
Matches: 262, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
273 262 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.41
Consensus pattern (273 bp):
TTTTTCTAAGTGAATAAAATCTTGATTTTAAGCTGATAACTTTGTGGTGCATAAATTATCACTTC
TACTTCACTCAAATACCTCCTTTCTTTCTTTTTTTCCCACTGTTCTCTTCATCTTTTTTTCCTGT
TCAACTGCTTTTGATGTTTTCTTAGAAAGCTCACATCAGCCAATTAACCTTAATGCAAATGAAAA
TGGCTTCTGTGCTGAGCTACCATTCAGGATTGGACTAAATAATTTAGCTTGATGGTGCCTAAAAC
AAGGCTTTTGTAC
Found at i:34620533 original size:21 final size:20
Alignment explanation
Indices: 34620501--34620559 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
34620491 GAACAAAGCA
34620501 AAAAAGAGGGGAGAAACCAGC
1 AAAAAGA-GGGAGAAACCAGC
* *
34620522 AAAAATGAGGGACAAACCAGT
1 AAAAA-GAGGGAGAAACCAGC
*
34620543 AAGAAAAAGGGAGAAAC
1 AA-AAAGAGGGAGAAAC
34620560 TGTTGTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 27 0.84
22 5 0.16
ACGTcount: A:0.56, C:0.12, G:0.29, T:0.03
Consensus pattern (20 bp):
AAAAAGAGGGAGAAACCAGC
Found at i:34624111 original size:23 final size:23
Alignment explanation
Indices: 34624085--34624152 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
34624075 GGACTCACCA
34624085 CAGCTTGTATGAGCTTACCGTTT
1 CAGCTTGTATGAGCTTACCGTTT
* *
34624108 CAGC-TCTACAGAGCTTACCG-TT
1 CAGCTTGTA-TGAGCTTACCGTTT
*
34624130 CAGCTCG-ATAGAGCTTACCGTTT
1 CAGCTTGTAT-GAGCTTACCGTTT
34624153 ACCAGCTTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (23 bp):
CAGCTTGTATGAGCTTACCGTTT
Found at i:34624134 original size:22 final size:22
Alignment explanation
Indices: 34624095--34624151 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
34624085 CAGCTTGTAT
*
34624095 GAGCTTACCGTTTCAGCTCTACA
1 GAGCTTACCG-TTCAGCTCGACA
*
34624118 GAGCTTACCGTTCAGCTCGATA
1 GAGCTTACCGTTCAGCTCGACA
34624140 GAGCTTACCGTT
1 GAGCTTACCGTT
34624152 TACCAGCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (22 bp):
GAGCTTACCGTTCAGCTCGACA
Found at i:34634163 original size:25 final size:25
Alignment explanation
Indices: 34634135--34634191 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
34634125 CCCTACTCCT
* *
34634135 AACTAAAAGATGAAAGGAACCTTAA
1 AACTAAAACATGAAAGAAACCTTAA
34634160 AACTAAAACATGAAAGAAACCTTAA
1 AACTAAAACATGAAAGAAACCTTAA
34634185 AACTAAA
1 AACTAAA
34634192 GAGCTTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.60, C:0.14, G:0.11, T:0.16
Consensus pattern (25 bp):
AACTAAAACATGAAAGAAACCTTAA
Found at i:34636356 original size:42 final size:42
Alignment explanation
Indices: 34636219--34636364 Score: 161
Period size: 42 Copynumber: 3.5 Consensus size: 42
34636209 GTTACTCGGT
* * * *
34636219 GGAATCAACACTTAGCAACCAAC-TTATATTCAATGATACGG
1 GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG
* * *
34636260 GGAATCAGCACATAGCAACC-CCTTTCACAATTAAGGATACGG
1 GGAATCAGCACTTAGCAACCACCTTT-ACAATCAATGATACGG
* * **
34636302 TGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTTGG
1 -GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG
34636345 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
34636365 CCTCGGACAA
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
40 1 0.01
41 20 0.23
42 32 0.37
43 29 0.33
44 5 0.06
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG
Found at i:34636375 original size:85 final size:84
Alignment explanation
Indices: 34636215--34636375 Score: 214
Period size: 85 Copynumber: 1.9 Consensus size: 84
34636205 AATCGTTACT
* * *
34636215 CGGTGGAATCAACACTTAGCAACCAACTTATATTCAATGATACGGGGAATCAGCACATAGCAACC
1 CGGTGGAATCAACACTTAGCAACCAACTTAGAATCAATAATACGGGGAATCAGCACATAGCAACC
**
34636280 CCTTTCACAATTAAGGATA
66 CCTCGCACAATTAAGGATA
* * ** *
34636299 CGGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTTGGGGAATCAGCACTTAGCAAC
1 CGGTGGAATCAACACTTAGCAACCAAC-TTAGAATCAATAATACGGGGAATCAGCACATAGCAAC
*
34636364 CCCTCGGACAAT
65 CCCTCGCACAAT
34636376 CTGCACTTAG
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
84 25 0.38
85 40 0.62
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (84 bp):
CGGTGGAATCAACACTTAGCAACCAACTTAGAATCAATAATACGGGGAATCAGCACATAGCAACC
CCTCGCACAATTAAGGATA
Found at i:34637031 original size:14 final size:14
Alignment explanation
Indices: 34637014--34637058 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
34637004 ATTAAATTTA
34637014 AAAATATAAAAATT
1 AAAATATAAAAATT
*
34637028 AAAATA-ACTAAATT
1 AAAATATA-AAAATT
34637042 AAAATATAAAAATT
1 AAAATATAAAAATT
34637056 AAA
1 AAA
34637059 TCCAAAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:34637539 original size:6 final size:6
Alignment explanation
Indices: 34637528--34637561 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
34637518 TGCCACACTT
* *
34637528 GCAACA GCAACA GCAGCA GCGACA GCAACA GCAA
1 GCAACA GCAACA GCAACA GCAACA GCAACA GCAA
34637562 GGGACTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.44, C:0.32, G:0.24, T:0.00
Consensus pattern (6 bp):
GCAACA
Found at i:34644659 original size:32 final size:32
Alignment explanation
Indices: 34644622--34644684 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
34644612 GAGCTGGGTC
34644622 ACTCATACAGGCTCAACTCATTAAGAAACACT
1 ACTCATACAGGCTCAACTCATTAAGAAACACT
**
34644654 ACTCATACAGGCTCAACTTGTTAAGAAACAC
1 ACTCATACAGGCTCAACTCATTAAGAAACAC
34644685 CACTTCAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.27, G:0.11, T:0.22
Consensus pattern (32 bp):
ACTCATACAGGCTCAACTCATTAAGAAACACT
Found at i:34656958 original size:14 final size:14
Alignment explanation
Indices: 34656939--34656967 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
34656929 TTTCATCCTA
34656939 ATCAAGGTTGGAAT
1 ATCAAGGTTGGAAT
34656953 ATCAAGGTTGGAAT
1 ATCAAGGTTGGAAT
34656967 A
1 A
34656968 ATTTTGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (14 bp):
ATCAAGGTTGGAAT
Found at i:34663172 original size:16 final size:16
Alignment explanation
Indices: 34663151--34663186 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
34663141 TTTGGTTCGC
34663151 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
34663167 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
34663183 TGTA
1 TGTA
34663187 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:34668353 original size:91 final size:91
Alignment explanation
Indices: 34668198--34668773 Score: 1152
Period size: 91 Copynumber: 6.3 Consensus size: 91
34668188 NNNNNNNNNN
34668198 AAATTGAAACTTGATTGTTTATACATAATTTACAGCATTTACAGCATTTCATTTCATTTTAAATT
1 AAATTGAAACTTGATTGTTTATACATAATTTACAGCATTTACAGCATTTCATTTCATTTTAAATT
34668263 TGGACATTATATAACCATCGAAATCG
66 TGGACATTATATAACCATCGAAATCG
34668289 AAATTGAAACTTGATTGTTTATACATAATTTACAGCATTTACAGCATTTCATTTCATTTTAAATT
1 AAATTGAAACTTGATTGTTTATACATAATTTACAGCATTTACAGCATTTCATTTCATTTTAAATT
34668354 TGGACATTATATAACCATCGAAATCG
66 TGGACATTATATAACCATCGAAATCG
34668380 AAATTGAAACTTGATTGTTTATACATAATTTACAGCATTTACAGCATTTCATTTCATTTTAAATT
1 AAATTGAAACTTGATTGTTTATACATAATTTACAGCATTTACAGCATTTCATTTCATTTTAAATT
34668445 TGGACATTATATAACCATCGAAATCG
66 TGGACATTATATAACCATCGAAATCG
34668471 AAATTGAAACTTGATTGTTTATACATAATTTACAGCATTTACAGCATTTCATTTCATTTTAAATT
1 AAATTGAAACTTGATTGTTTATACATAATTTACAGCATTTACAGCATTTCATTTCATTTTAAATT
34668536 TGGACATTATATAACCATCGAAATCG
66 TGGACATTATATAACCATCGAAATCG
34668562 AAATTGAAACTTGATTGTTTATACATAATTTACAGCATTTACAGCATTTCATTTCATTTTAAATT
1 AAATTGAAACTTGATTGTTTATACATAATTTACAGCATTTACAGCATTTCATTTCATTTTAAATT
34668627 TGGACATTATATAACCATCGAAATCG
66 TGGACATTATATAACCATCGAAATCG
34668653 AAATTGAAACTTGATTGTTTATACATAATTTACAGCATTTACAGCATTTCATTTCATTTTAAATT
1 AAATTGAAACTTGATTGTTTATACATAATTTACAGCATTTACAGCATTTCATTTCATTTTAAATT
34668718 TGGACATTATATAACCATCGAAATCG
66 TGGACATTATATAACCATCGAAATCG
34668744 AAATTGAAACTTGATTGTTTATACATAATT
1 AAATTGAAACTTGATTGTTTATACATAATT
34668774 AACCCTTAAT
Statistics
Matches: 485, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 485 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (91 bp):
AAATTGAAACTTGATTGTTTATACATAATTTACAGCATTTACAGCATTTCATTTCATTTTAAATT
TGGACATTATATAACCATCGAAATCG
Found at i:34670106 original size:188 final size:188
Alignment explanation
Indices: 34669789--34670164 Score: 727
Period size: 188 Copynumber: 2.0 Consensus size: 188
34669779 TTACCCGGTG
34669789 ACAGCAAATCGGGGAAGAGTGCGATGAAGAAGGTGTCTGAAACGAGAAAAGGGAAATCGATTTGG
1 ACAGCAAATCGGGGAAGAGTGCGATGAAGAAGGTGTCTGAAACGAGAAAAGGGAAATCGATTTGG
34669854 GTTAGTGAACAGTGAAAATAAAACAGCAAATCGGTTCCTCCTTCTTGATAAAATGAAGAAAATCA
66 GTTAGTGAACAGTGAAAATAAAACAGCAAATCGGTTCCTCCTTCTTGATAAAATGAAGAAAATCA
34669919 AAGAAACCCTAAACTTAAATCAATGACGGACTGCTGGGAAGGGCAAAAAATATTACCT
131 AAGAAACCCTAAACTTAAATCAATGACGGACTGCTGGGAAGGGCAAAAAATATTACCT
34669977 ACAGCAAATCGGGGAAGAGTGCGATGGAAGAAGGTG-CTGAAACGAGAAAAGGGAAATCGATTTG
1 ACAGCAAATCGGGGAAGAGTGCGAT-GAAGAAGGTGTCTGAAACGAGAAAAGGGAAATCGATTTG
*
34670041 GGTTAGTGAACAGTGAAAATAAAACAGTAAATCGGTTCCTCCTTCTTGATAAAATGAAGAAAATC
65 GGTTAGTGAACAGTGAAAATAAAACAGCAAATCGGTTCCTCCTTCTTGATAAAATGAAGAAAATC
34670106 AAAGAAACCCTAAACTTAAATCAATGACGGACTGCTGGGAAGGGCAAAAAATATTACCT
130 AAAGAAACCCTAAACTTAAATCAATGACGGACTGCTGGGAAGGGCAAAAAATATTACCT
34670165 GTGCAAGGAG
Statistics
Matches: 186, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
188 176 0.95
189 10 0.05
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (188 bp):
ACAGCAAATCGGGGAAGAGTGCGATGAAGAAGGTGTCTGAAACGAGAAAAGGGAAATCGATTTGG
GTTAGTGAACAGTGAAAATAAAACAGCAAATCGGTTCCTCCTTCTTGATAAAATGAAGAAAATCA
AAGAAACCCTAAACTTAAATCAATGACGGACTGCTGGGAAGGGCAAAAAATATTACCT
Found at i:34671340 original size:24 final size:23
Alignment explanation
Indices: 34671308--34671356 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
34671298 TTAGAATGGG
* *
34671308 AAAAAGAAGTAAAGATGATGGGGA
1 AAAAAGAAGGAAAGATG-TAGGGA
34671332 AAAAAGAAGGAAAGATGTAGGGA
1 AAAAAGAAGGAAAGATGTAGGGA
34671355 AA
1 AA
34671357 TGAGTATGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.57, C:0.00, G:0.33, T:0.10
Consensus pattern (23 bp):
AAAAAGAAGGAAAGATGTAGGGA
Found at i:34671796 original size:15 final size:16
Alignment explanation
Indices: 34671772--34671804 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
34671762 CAATTTTTTG
*
34671772 AATTACAAAAA-AAAA
1 AATTAAAAAAATAAAA
34671787 AATTAAAAAAATAAAA
1 AATTAAAAAAATAAAA
34671803 AA
1 AA
34671805 ATATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (16 bp):
AATTAAAAAAATAAAA
Found at i:34671962 original size:13 final size:13
Alignment explanation
Indices: 34671944--34671970 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34671934 ATGACATCTA
34671944 TGCTAAACAAATT
1 TGCTAAACAAATT
34671957 TGCTAAACAAATT
1 TGCTAAACAAATT
34671970 T
1 T
34671971 ATTATTACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (13 bp):
TGCTAAACAAATT
Found at i:34672332 original size:23 final size:22
Alignment explanation
Indices: 34672276--34672333 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
34672266 AATTTTCAAG
34672276 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
34672295 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
34672317 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
34672334 TATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:34672955 original size:16 final size:16
Alignment explanation
Indices: 34672931--34672966 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
34672921 AATTGCAAAT
* *
34672931 TTTTTTATACTATTTA
1 TTTTATATACCATTTA
34672947 TTTTATATACCATTTA
1 TTTTATATACCATTTA
34672963 TTTT
1 TTTT
34672967 TTAAGATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTATATACCATTTA
Found at i:34675834 original size:14 final size:14
Alignment explanation
Indices: 34675815--34675844 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
34675805 AATACAAGAT
34675815 TATGTAAGTATATA
1 TATGTAAGTATATA
*
34675829 TATGTATGTATATA
1 TATGTAAGTATATA
34675843 TA
1 TA
34675845 ATAATAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TATGTAAGTATATA
Found at i:34675977 original size:3 final size:3
Alignment explanation
Indices: 34675911--34675962 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
34675901 AAAATAAAAC
* * *
34675911 TAA TAA TAA TAAA TAG TAA TAA TAG TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34675957 TAA TAA
1 TAA TAA
34675963 ATGTAATGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:34680633 original size:16 final size:16
Alignment explanation
Indices: 34680612--34680666 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
34680602 TGAATTACTG
* *
34680612 ATTACAACTTTATTCC
1 ATTACAGCTCTATTCC
34680628 ATTACAGCTCTATT-C
1 ATTACAGCTCTATTCC
34680643 ATTTACAGCTCTATTCC
1 A-TTACAGCTCTATTCC
34680660 ATTACAG
1 ATTACAG
34680667 TGAACCAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 2 0.06
16 31 0.89
17 2 0.06
ACGTcount: A:0.29, C:0.25, G:0.05, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:34680882 original size:19 final size:21
Alignment explanation
Indices: 34680844--34680884 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
34680834 AATTAATATT
*
34680844 TTATATTTAAAATTATAAAAA
1 TTATATTTAAAATTAGAAAAA
34680865 TTAT-TTTAAAATT-GAAAAA
1 TTATATTTAAAATTAGAAAAA
34680884 T
1 T
34680885 GTTAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTATATTTAAAATTAGAAAAA
Found at i:34680900 original size:18 final size:19
Alignment explanation
Indices: 34680846--34680917 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 19
34680836 TTAATATTTT
34680846 ATATTTAAAATTATA-AAAA
1 ATATTTAAAA-TATACAAAA
* *
34680865 TTATTTTAAAAT-T-GAAAA
1 ATA-TTTAAAATATACAAAA
*
34680883 AT-GTTAAAATA-ACAAAA
1 ATATTTAAAATATACAAAA
34680900 ATATTTAAAATATACAAA
1 ATATTTAAAATATACAAA
34680918 TTATGAAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
16 7 0.17
17 6 0.14
18 14 0.33
19 8 0.19
20 7 0.17
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
ATATTTAAAATATACAAAA
Found at i:34687719 original size:21 final size:21
Alignment explanation
Indices: 34687693--34687796 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
34687683 AGGGTTAATA
34687693 TGAAGCTCAGAAGAGCTAAAC
1 TGAAGCTCAGAAGAGCTAAAC
* *
34687714 TGAAGCTCAAAAGAGCTGAAC
1 TGAAGCTCAGAAGAGCTAAAC
* * * * *
34687735 TGAAACCCAGAAGGGTTAATC
1 TGAAGCTCAGAAGAGCTAAAC
* * * *
34687756 TGAAACTCATATGAG-TTAAC
1 TGAAGCTCAGAAGAGCTAAAC
34687776 TGAAGCTCATG-AGAGCTAAAC
1 TGAAGCTCA-GAAGAGCTAAAC
34687797 AGAAAGCAAA
Statistics
Matches: 62, Mismatches: 19, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 14 0.23
21 48 0.77
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.19
Consensus pattern (21 bp):
TGAAGCTCAGAAGAGCTAAAC
Found at i:34731308 original size:5 final size:5
Alignment explanation
Indices: 34731298--34731323 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34731288 CCAGACCTAC
34731298 ACTAG ACTAG ACTAG ACTAG ACTAG A
1 ACTAG ACTAG ACTAG ACTAG ACTAG A
34731324 GAAAGCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ACTAG
Found at i:34737537 original size:78 final size:75
Alignment explanation
Indices: 34737469--34737633 Score: 249
Period size: 78 Copynumber: 2.1 Consensus size: 75
34737459 ATTTTATATA
* *
34737469 AAATTAAAATTTAAATATATTAAAATATTTTATTCTCTTGTGTGATGGTTTAATCTGATTTAACT
1 AAATTAAAATTTAAAGA-A-AAAAATATTTT-TTCTCTTGTGTGATGGTTTAATCTGATTTAACT
34737534 TTAAATTTAATTG
63 TTAAATTTAATTG
*
34737547 AAATTAAAAGAATTTAGAGAAAAAAATATTTTTTCTCTTGTGTGATGGTTTAATCTGATTTAACT
1 AAATT--AA-AATTTAAAGAAAAAAATATTTTTTCTCTTGTGTGATGGTTTAATCTGATTTAACT
34737612 TTAAATTTAATTG
63 TTAAATTTAATTG
34737625 AAATTAAAA
1 AAATTAAAA
34737634 GAATTTAGAG
Statistics
Matches: 81, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
75 2 0.02
76 2 0.02
78 56 0.69
79 10 0.12
80 3 0.04
81 8 0.10
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (75 bp):
AAATTAAAATTTAAAGAAAAAAATATTTTTTCTCTTGTGTGATGGTTTAATCTGATTTAACTTTA
AATTTAATTG
Found at i:34737634 original size:78 final size:79
Alignment explanation
Indices: 34737490--34737650 Score: 315
Period size: 78 Copynumber: 2.1 Consensus size: 79
34737480 TAAATATATT
34737490 AAAATATTTTATTCTCTTGTGTGATGGTTTAATCTGATTTAACTTTAAATTTAATTGAAATTAAA
1 AAAATATTTTATTCTCTTGTGTGATGGTTTAATCTGATTTAACTTTAAATTTAATTGAAATTAAA
34737555 AGAATTTAGAGAAA
66 AGAATTTAGAGAAA
34737569 AAAATATTTT-TTCTCTTGTGTGATGGTTTAATCTGATTTAACTTTAAATTTAATTGAAATTAAA
1 AAAATATTTTATTCTCTTGTGTGATGGTTTAATCTGATTTAACTTTAAATTTAATTGAAATTAAA
34737633 AGAATTTAGAGAAA
66 AGAATTTAGAGAAA
34737647 AAAA
1 AAAA
34737651 ACAATTATAG
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 72 0.88
79 10 0.12
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.42
Consensus pattern (79 bp):
AAAATATTTTATTCTCTTGTGTGATGGTTTAATCTGATTTAACTTTAAATTTAATTGAAATTAAA
AGAATTTAGAGAAA
Found at i:34740170 original size:57 final size:56
Alignment explanation
Indices: 34740082--34740196 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 56
34740072 AATTTCATAT
*
34740082 CATCAAACACAAGTGAATTCTCAATTTATGAGAAAAGTTAAAGGGAATTCTATCCAC
1 CATCAAACACAAATGAATTCTCAATTTATGAGAAAAGTT-AAGGGAATTCTATCCAC
*
34740139 CATCAAACACAAATGAATTCTCAATTTATGAGAACAGTTAAGGGAATTCTATCCAC
1 CATCAAACACAAATGAATTCTCAATTTATGAGAAAAGTTAAGGGAATTCTATCCAC
34740195 CA
1 CA
34740197 AAAGTAAAAG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 19 0.34
57 37 0.66
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (56 bp):
CATCAAACACAAATGAATTCTCAATTTATGAGAAAAGTTAAGGGAATTCTATCCAC
Found at i:34746550 original size:44 final size:44
Alignment explanation
Indices: 34746468--34746897 Score: 286
Period size: 44 Copynumber: 9.7 Consensus size: 44
34746458 TCAATCTGCC
* * *
34746468 TCACTGCCAATATAAGAAGACAGGATCTACTATT-TTCGATCCACT
1 TCAC-GCCAATATATGAAGACAAGATCTGCT-TTCTTCGATCCACT
* * * *
34746513 TTACGCCAATACATGAAGACAAGATATGCTTTCTTCGATCTACT
1 TCACGCCAATATATGAAGACAAGATCTGCTTTCTTCGATCCACT
* * * ** * *
34746557 CCGCCACCAATATGGGAAGACAAGATATGC-ATCTTCGATCCACT
1 TC-ACGCCAATATATGAAGACAAGATCTGCTTTCTTCGATCCACT
* * * *
34746601 TCGCTACCAATATAGGAAGACAGGATCTG-TTATCTTCGATCCACT
1 TCAC-GCCAATATATGAAGACAAGATCTGCTT-TCTTCGATCCACT
* * * *
34746646 TCATGACAATACATGAAGACAAGATCTGCTTTCTTCGATCTACT
1 TCACGCCAATATATGAAGACAAGATCTGCTTTCTTCGATCCACT
* * *
34746690 T--TGCCACTAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACT
1 TCACGCCAATA-TAT--GAAGACAAGATCTGCTTTCTTCGATCCACT
* * *
34746734 TCACTACCAATATAGGAAGAC-AGAATCTG-TTATCTTCGATCTACT
1 TCAC-GCCAATATATGAAGACAAG-ATCTGCTT-TCTTCGATCCACT
* * * *
34746779 TCACGCCAAGACATGAAGACAAGATCTGCTTTCTTCAATCTACT
1 TCACGCCAATATATGAAGACAAGATCTGCTTTCTTCGATCCACT
* * ** * * *
34746823 TCGCCACCAATATGGGAAGACAAGATCTGC-ATATTCGATTCACT
1 TC-ACGCCAATATATGAAGACAAGATCTGCTTTCTTCGATCCACT
* * *
34746867 TCGCTACCAATATA-GAAAGACAGGATCTGCT
1 TCAC-GCCAATATATG-AAGACAAGATCTGCT
34746898 ATCTGTGAAA
Statistics
Matches: 304, Mismatches: 60, Indels: 42
0.75 0.15 0.10
Matches are distributed among these distances:
42 6 0.02
43 9 0.03
44 184 0.61
45 98 0.32
46 2 0.01
47 5 0.02
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (44 bp):
TCACGCCAATATATGAAGACAAGATCTGCTTTCTTCGATCCACT
Found at i:34746611 original size:89 final size:89
Alignment explanation
Indices: 34746474--34746897 Score: 356
Period size: 89 Copynumber: 4.8 Consensus size: 89
34746464 TGCCTCACTG
* * * * ** * *
34746474 CCAATATAAGAAGACAGGATCTACTATTTTCGATCCACTTTAC-GCCAATACATGAAGACAAGAT
1 CCAATATAGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATACAGGAAGACAAGAT
* * * *
34746538 ATGCTTTCTTCGATCTACTCCGCCA
65 CTGCTTTCTTCGATCCACTTCACCA
* * * *
34746563 CCAATATGGGAAGACAAGATATGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATC
1 CCAATATAGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATACAGGAAGACAAGATC
**
34746628 TG-TTATCTTCGATCCACTTCATGA
66 TGCTT-TCTTCGATCCACTTCACCA
* * * * * * * * **
34746652 -CAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTTGCCACTAGTATGGGAAGACAAGAT
1 CCAATATAGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATACAGGAAGACAAGAT
* *
34746716 CTGC-ATCTTCGATCCACTTCACTA
65 CTGCTTTCTTCGATCCACTTCACCA
* * * * * *
34746740 CCAATATAGGAAGAC-AGAATCTGTTATCTTCGATCTACTTCAC-GCCAAGACATGAAGACAAGA
1 CCAATATAGGAAGACAAG-ATCTG-CATCTTCGATCCACTTCGCTACCAATACAGGAAGACAAGA
* * *
34746803 TCTGCTTTCTTCAATCTACTTCGCCA
64 TCTGCTTTCTTCGATCCACTTCACCA
* * * * * *
34746829 CCAATATGGGAAGACAAGATCTGCATATTCGATTCACTTCGCTACCAATATAGAAAGACAGGATC
1 CCAATATAGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATACAGGAAGACAAGATC
34746894 TGCT
66 TGCT
34746898 ATCTGTGAAA
Statistics
Matches: 262, Mismatches: 63, Indels: 20
0.76 0.18 0.06
Matches are distributed among these distances:
88 87 0.33
89 173 0.66
90 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (89 bp):
CCAATATAGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATACAGGAAGACAAGATC
TGCTTTCTTCGATCCACTTCACCA
Found at i:34746712 original size:133 final size:133
Alignment explanation
Indices: 34746474--34746901 Score: 658
Period size: 133 Copynumber: 3.2 Consensus size: 133
34746464 TGCCTCACTG
* * * * *
34746474 CCAATATAAGAAGACAGGATCTACTATTTTCGATCCACTTTACGCCAATACATGAAGACAAGATA
1 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCCACTTCACGCCAATACATGAAGACAAGATC
* *
34746539 TGCTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATATGCATCTTCGATCCACTTCG
66 TGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCG
34746604 CTA
131 CTA
* * *
34746607 CCAATATAGGAAGACAGGATCTGTTATCTTCGATCCACTTCATGACAATACATGAAGACAAGATC
1 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCCACTTCACGCCAATACATGAAGACAAGATC
* * * *
34746672 TGCTTTCTTCGATCTACTTTGCCACTAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCA
66 TGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCG
34746737 CTA
131 CTA
* * * *
34746740 CCAATATAGGAAGACAGAATCTGTTATCTTCGATCTACTTCACGCCAAGACATGAAGACAAGATC
1 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCCACTTCACGCCAATACATGAAGACAAGATC
* * *
34746805 TGCTTTCTTCAATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATATTCGATTCACTTCG
66 TGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCG
34746870 CTA
131 CTA
*
34746873 CCAATATAGAAAGACAGGATCTGCTATCT
1 CCAATATAGGAAGACAGGATCTGCTATCT
34746902 GTGAAACATG
Statistics
Matches: 266, Mismatches: 29, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
133 266 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (133 bp):
CCAATATAGGAAGACAGGATCTGCTATCTTCGATCCACTTCACGCCAATACATGAAGACAAGATC
TGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCG
CTA
Found at i:34771715 original size:42 final size:42
Alignment explanation
Indices: 34771634--34771715 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
34771624 TAACCCTATT
* *
34771634 GGGTTTCTGTTTAGCTCTTATGAGCTTCCGTTCAACCTTTAC
1 GGGTTTCTGTTTAGCACTTATGAGCTTCCGTGCAACCTTTAC
* * *
34771676 GGGTTTCTGTTTAGCACTTATGTGCTTCTGTGCAGCCTTT
1 GGGTTTCTGTTTAGCACTTATGAGCTTCCGTGCAACCTTT
34771716 GGTCTTCTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (42 bp):
GGGTTTCTGTTTAGCACTTATGAGCTTCCGTGCAACCTTTAC
Found at i:34774074 original size:25 final size:25
Alignment explanation
Indices: 34774030--34774095 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
34774020 TTCATGATAC
* *
34774030 ATATCATCTTTTAC-TGTTT-CTTCA
1 ATATCATCCTTTACAT-TTTCCGTCA
34774054 TATATCATCCTTTACATTTTCCGTCA
1 -ATATCATCCTTTACATTTTCCGTCA
34774080 AT-TCATCCTTTACATT
1 ATATCATCCTTTACATT
34774096 CGTAGTGCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
24 14 0.38
25 18 0.49
26 5 0.14
ACGTcount: A:0.23, C:0.24, G:0.03, T:0.50
Consensus pattern (25 bp):
ATATCATCCTTTACATTTTCCGTCA
Found at i:34774146 original size:33 final size:34
Alignment explanation
Indices: 34774101--34774259 Score: 130
Period size: 33 Copynumber: 4.7 Consensus size: 34
34774091 ACATTCGTAG
*
34774101 TGCCATAACCCAGTTATGGTCTTA-TTATTAGAA
1 TGCCATAGCCCAGTTATGGTCTTACTTATTAGAA
* * * *
34774134 TGCCATAGCCCAGCTATGGTCTTACATATAAAAA
1 TGCCATAGCCCAGTTATGGTCTTACTTATTAGAA
* * * ***
34774168 TTACCATGGTCCAACCATGGTCTTACGTTCA-TAG--
1 -TGCCATAGCCCAGTTATGGTCTTAC-TT-ATTAGAA
* *
34774202 TGCCATAGCCCAGTTATGGTCTTA-TGATCAGAA
1 TGCCATAGCCCAGTTATGGTCTTACTTATTAGAA
*
34774235 TGTCATAGCCCAGTTATGGTCTTAC
1 TGCCATAGCCCAGTTATGGTCTTAC
34774260 ATATAAACAC
Statistics
Matches: 96, Mismatches: 22, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
30 1 0.01
31 3 0.03
33 63 0.66
34 6 0.06
35 20 0.21
36 2 0.02
37 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (34 bp):
TGCCATAGCCCAGTTATGGTCTTACTTATTAGAA
Found at i:34774277 original size:101 final size:100
Alignment explanation
Indices: 34774089--34774394 Score: 391
Period size: 101 Copynumber: 3.0 Consensus size: 100
34774079 AATTCATCCT
* * *
34774089 TTACATTCGTAGTGCCATAACCCAGTTATGGTCTTATTATTAGAATGCCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAGCCCAGCTATGGT
*
34774154 CTTACATATAAAAAT-TACCATGGTCCAACCATGGTC
66 CTTACATATAAACATCT--CATGGTCCAACCATGGTC
* * * * *
34774190 TTACGTTCATAGTGCCATAGCCCAGTTATGGTCTTATGATCAGAATGTCATAGCCCAGTTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAGCCCAGCTATGGT
*
34774255 CTTACATATAAACACTCTCATGGTTCAACCATGGTC
66 CTTACATATAAACA-TCTCATGGTCCAACCATGGTC
* * * * * * *
34774291 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTTTCATTAAAATGCCACAGCTCAACCATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAGCCCAGCTATGGT
*
34774356 CTTACAGT-TAAACATTTCCATGGTCCAACCATGGTC
66 CTTACA-TATAAACATCT-CATGGTCCAACCATGGTC
34774392 TTA
1 TTA
34774395 TCCGTCAATT
Statistics
Matches: 178, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
100 2 0.01
101 173 0.97
102 2 0.01
103 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (100 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAGCCCAGCTATGGT
CTTACATATAAACATCTCATGGTCCAACCATGGTC
Found at i:34776331 original size:11 final size:11
Alignment explanation
Indices: 34776315--34776358 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
34776305 TTATATACTA
34776315 AATAAAATATT
1 AATAAAATATT
34776326 AATAAAATATTTT
1 AATAAAATA--TT
*
34776339 ATTAAAATATT
1 AATAAAATATT
34776350 AATAAAATA
1 AATAAAATA
34776359 ATATTTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 19 0.66
13 10 0.34
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATAAAATATT
Found at i:34779152 original size:22 final size:21
Alignment explanation
Indices: 34779115--34779157 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
34779105 GAAAAATTAT
**
34779115 ATAAATAAATGCAATTATTTAA
1 ATAAATAAATAAAATT-TTTAA
34779137 ATAAATAAATAAAATTTTTAA
1 ATAAATAAATAAAATTTTTAA
34779158 CTTCAACCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAAATAAATAAAATTTTTAA
Found at i:34780016 original size:19 final size:19
Alignment explanation
Indices: 34779965--34780025 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
34779955 AAAAATTAAA
* * *
34779965 AAAAATCAAAGTAATTTTC
1 AAAATTCAAAATAATTTTT
*
34779984 AAAATTTGAAAATAATTTTT
1 AAAA-TTCAAAATAATTTTT
*
34780004 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTTT
34780022 AAAA
1 AAAA
34780026 ATTATAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
18 9 0.26
19 11 0.31
20 15 0.43
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:34781045 original size:26 final size:25
Alignment explanation
Indices: 34780994--34781048 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
34780984 AATTTAGCTC
* *
34780994 TTAATATTTATATTTTTTTATCAAT
1 TTAATATTTATATTTTTTAATAAAT
* *
34781019 TTAATTTTTATCTTTTTTAATTAAAT
1 TTAATATTTATATTTTTTAA-TAAAT
34781045 TTAA
1 TTAA
34781049 CCCTTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (25 bp):
TTAATATTTATATTTTTTAATAAAT
Found at i:34783860 original size:97 final size:95
Alignment explanation
Indices: 34783438--34783986 Score: 489
Period size: 98 Copynumber: 5.5 Consensus size: 95
34783428 TTTTTTTTCT
*
34783438 TTTTTTTCATGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTT-GGTGCTGGC
1 TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTTGGGTGCTGG-
34783502 TTGCCAATGGCCGGCACCCAGTACAATTTTAAAAAAAAAA
65 -T--C-ATGGCCGGCACCCAGTACAA-TTT----AAAAAA
34783542 TTCTTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAAT--AAAAAAAATTT-GGTGC
1 ----TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTTGGGTGC
* **
34783604 TGGCCTGTCAATGGCCGACACCCAGTACAATATTAAAATTT
62 T-G---GTC-ATGGCCGGCACCCAGTACAAT-TTAAAA-AA
* * * *
34783645 TTTTTTTCATGTCAGAATCAAATATCAGTATACGAAAAAAAT--AAAAAAAATTTGGGTGCTGGC
1 TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTTGGGTGCTGG-
* *
34783708 CTATCAATGGCCGGCACCTAGTACAATTAAAAAAA
65 ---TC-ATGGCCGGCACCCAGTACAATTTAAAAAA
*** *
34783743 AAATTTTCTTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTT-GG-G-T-G-
1 TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTTGGGTGCTGGT
34783803 C-T-GCCGGCACCCAGTACAATTTAAAAAAAAA
66 CATGGCCGGCACCCAGTACAATTT---AAAAAA
**
34783834 TTCTTTTTTTTTTCGTGTCAGAATCAGATATAAATATAC-AAAAAAA-ATTAAAAAAATTTGGGT
1 ------TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTTGGGT
34783897 GCTGGCCTTTCAATGGCCGGCACCCAGTACAATTTAAAAAA
60 GCTGG----TC-ATGGCCGGCACCCAGTACAATTTAAAAAA
34783938 TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAA
1 TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAA
34783987 TTTTTGAGTG
Statistics
Matches: 375, Mismatches: 30, Indels: 80
0.77 0.06 0.16
Matches are distributed among these distances:
88 18 0.05
89 1 0.00
91 7 0.02
95 11 0.03
96 11 0.03
97 31 0.08
98 70 0.19
99 65 0.17
100 44 0.12
102 4 0.01
104 7 0.02
105 1 0.00
106 41 0.11
107 21 0.06
108 42 0.11
110 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (95 bp):
TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTTGGGTGCTGGT
CATGGCCGGCACCCAGTACAATTTAAAAAA
Found at i:34783901 original size:195 final size:194
Alignment explanation
Indices: 34783437--34784035 Score: 676
Period size: 195 Copynumber: 3.0 Consensus size: 194
34783427 TTTTTTTTTC
*
34783437 TTTTTTTTCATGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTT-GGTGCTGG
1 TTTTTTTTCATGTCAGAATCAGATATAAATATAC-AAAAAAA-ATAAAAAAAATTTGGGTGCTGG
* **
34783501 CTTGCCAATGGCCGGCACCCAGTACAATTTTAAAAAAAAAATTCTTTTTTTTCGTGTCAGAATCA
64 CCTATCAATGGCCGGCACCCAGTACAA--TTAAAAAAAAAA-------TTTTCGTGTCAGAATCA
*
34783566 GATATAAATATACGAAAAAAAT-AAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGACACCCAGT
120 GATATAAATATACGAAAAAAATAAAAAAAAAATT-GTGC-GG-CTGTC-ATGGCCGACACCCAGT
34783630 ACAATATTAAAATT
181 ACAATATTAAAATT
* * * *
34783644 TTTTTTTTCATGTCAGAATCAAATATCAGTATACGAAAAAAATAAAAAAAATTTGGGTGCTGGCC
1 TTTTTTTTCATGTCAGAATCAGATATAAATATACAAAAAAAATAAAAAAAATTTGGGTGCTGGCC
* *
34783709 TATCAATGGCCGGCACCTAGTACAATTAAAAAAAAAATTTTCTTGTCAGAATCAGATATAAATAT
66 TATCAATGGCCGGCACCCAGTACAATTAAAAAAAAAATTTTCGTGTCAGAATCAGATATAAATAT
*
34783774 ACGAAAAAAATAAAAAAAAAATT-TG-GG-TG-C-T-GCCGGCACCCAGTACAAT-TTAAAAAAA
131 ACGAAAAAAATAAAAAAAAAATTGTGCGGCTGTCATGGCCGACACCCAGTACAATATT-----AA
34783832 AATTCTT
191 AA---TT
* *
34783839 TTTTTTTTCGTGTCAGAATCAGATATAAATATACAAAAAAAATTAAAAAAATTTGGGTGCTGGCC
1 TTTTTTTTCATGTCAGAATCAGATATAAATATACAAAAAAAATAAAAAAAATTTGGGTGCTGGCC
* * ***
34783904 TTTCAATGGCCGGCACCCAGTACAATTTAAAAAATTTTTTTCGTGTCAGAATCAGATATAAATAT
66 TATCAATGGCCGGCACCCAGTACAATTAAAAAAAAAATTTTCGTGTCAGAATCAGATATAAATAT
*** *
34783969 ACGAAAAAAATAAAAAAATTTTTGAGTGCTGGTCTGTCAATGGGCGACACCCAGTACAATATTAA
131 ACGAAAAAAATAAAAAAAAAATT--GTGC-GG-CTGTC-ATGGCCGACACCCAGTACAATATTAA
34784034 AA
191 AA
34784036 AAAATTCTTT
Statistics
Matches: 340, Mismatches: 30, Indels: 49
0.81 0.07 0.12
Matches are distributed among these distances:
187 2 0.01
188 17 0.05
189 1 0.00
191 1 0.00
192 6 0.02
194 2 0.01
195 139 0.41
196 2 0.01
197 38 0.11
198 12 0.04
200 2 0.01
202 6 0.02
203 1 0.00
204 12 0.04
205 13 0.04
206 53 0.16
207 33 0.10
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (194 bp):
TTTTTTTTCATGTCAGAATCAGATATAAATATACAAAAAAAATAAAAAAAATTTGGGTGCTGGCC
TATCAATGGCCGGCACCCAGTACAATTAAAAAAAAAATTTTCGTGTCAGAATCAGATATAAATAT
ACGAAAAAAATAAAAAAAAAATTGTGCGGCTGTCATGGCCGACACCCAGTACAATATTAAAATT
Found at i:34784000 original size:294 final size:302
Alignment explanation
Indices: 34783441--34784039 Score: 871
Period size: 294 Copynumber: 2.0 Consensus size: 302
34783431 TTTTTCTTTT
34783441 TTTTCATGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTTGGTGCTGGCTTGC
1 TTTTCATGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTT-GTGC-GGC-TGC
34783506 CAATGGCCGGCACCCAGTACAATTTTAAAAAAAAAATTCTTTTTTTTCGTGTCAGAATCAGATAT
63 C-ATGGCCGGCACCCAGTACAATTTTAAAAAAAAAATTCTTTTTTTTCGTGTCAGAATCAGATAT
*
34783571 AAATATACGAAAAAAATAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGACACCCAGTACAATA
127 AAATATACAAAAAAAATAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGACACCCAGTACAATA
** * * *
34783636 TTAAAATTTTTTTTTTCATGTCAGAATCAAATATCAGTATACGAAAAAAATAAAAAAAATTTGGG
192 TTAAAATAATTTTTTTCATGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAATTTGAG
* *
34783701 TGCTGGCCTATCAATGGCCGGCACCTAGTACAAT-TAAAAAAAAAA
257 TGCTGGCCTATCAATGGCCGACACCCAGTACAATATAAAAAAAAAA
*
34783746 TTTTCTTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAA-TT-TG-GG-TG-C-T
1 TTTTCATGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTTGTGCGGCTGCCAT
34783805 -GCCGGCACCCAGTACAA-TTT-AAAAAAAAATTCTTTTTTTTTTCGTGTCAGAATCAGATATAA
66 GGCCGGCACCCAGTACAATTTTAAAAAAAAAATTC--TTTTTTTTCGTGTCAGAATCAGATATAA
* * *
34783867 ATATACAAAAAAAATTAAAAAAATTTGGGTGCTGGCCTTTCAATGGCCGGCACCCAGTACAAT-T
129 ATATACAAAAAAAATAAAAAAAATTT-GGTGCTGGCCTGTCAATGGCCGACACCCAGTACAATAT
* * *
34783931 TAAAA-AATTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAATTTTTGAG
193 TAAAATAATTTTTTTCATGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAA-ATTTGAG
* * * *
34783995 TGCTGGTCTGTCAATGGGCGACACCCAGTACAATATTAAAAAAAA
257 TGCTGGCCTATCAATGGCCGACACCCAGTACAATATAAAAAAAAA
34784040 TTCTTTTTTG
Statistics
Matches: 270, Mismatches: 19, Indels: 20
0.87 0.06 0.06
Matches are distributed among these distances:
292 12 0.04
293 48 0.18
294 109 0.40
295 44 0.16
297 1 0.00
298 2 0.01
300 2 0.01
302 2 0.01
304 2 0.01
305 48 0.18
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (302 bp):
TTTTCATGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTTGTGCGGCTGCCAT
GGCCGGCACCCAGTACAATTTTAAAAAAAAAATTCTTTTTTTTCGTGTCAGAATCAGATATAAAT
ATACAAAAAAAATAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGACACCCAGTACAATATTAA
AATAATTTTTTTCATGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAATTTGAGTGCT
GGCCTATCAATGGCCGACACCCAGTACAATATAAAAAAAAAA
Found at i:34784036 original size:99 final size:98
Alignment explanation
Indices: 34783438--34784036 Score: 593
Period size: 99 Copynumber: 6.0 Consensus size: 98
34783428 TTTTTTTTCT
*
34783438 TTTTTTTCATGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTT-GGTGCTGGC
1 TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAAT--AAAAAAAATTTGGGTGCTGGC
* * * *
34783502 TTGCCAATGGCCGGCACCCAGTACAATTTTAAAAAAAAAA
64 CTGTCAATGGCCGACACCCAGTACAATATT-----AAAAA
34783542 TTCTTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATTT-GGTGCTG
1 ----TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATTTGGGTGCTG
*
34783606 GCCTGTCAATGGCCGACACCCAGTACAATATTAAAATTT
62 GCCTGTCAATGGCCGACACCCAGTACAATATTAAAA--A
* * * *
34783645 TTTTTTTCATGTCAGAATCAAATATCAGTATACGAAAAAAATAAAAAAAATTTGGGTGCTGGCCT
1 TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATTTGGGTGCTGGCCT
* * * *
34783710 ATCAATGGCCGGCACCTAGTACAAT-TAAAAAAA
66 GTCAATGGCCGACACCCAGTACAATAT-TAAAAA
*** *
34783743 AAATTTTCTTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAAATTTGGGTGCT-G-
1 TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAAT--AAAAAAAATTTGGGTGCTGGC
34783806 C---C----G--G-CACCCAGTACAAT-TTAAAAAAAAA
64 CTGTCAATGGCCGACACCCAGTACAATATT----AAAAA
* *
34783834 TTCTTTTTTTTTTCGTGTCAGAATCAGATATAAATATACAAAAAAAATTAAAAAAATTTGGGTGC
1 ------TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATTTGGGTGC
* *
34783899 TGGCCTTTCAATGGCCGGCACCCAGTACAAT-TTAAAAAA
60 TGGCCTGTCAATGGCCGACACCCAGTACAATATT-AAAAA
* * *
34783938 TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAATTTTTGAGTGCTGGTC
1 TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAA-ATTTGGGTGCTGGCC
*
34784003 TGTCAATGGGCGACACCCAGTACAATATTAAAAA
65 TGTCAATGGCCGACACCCAGTACAATATTAAAAA
34784037 AAATTCTTTT
Statistics
Matches: 423, Mismatches: 38, Indels: 69
0.80 0.07 0.13
Matches are distributed among these distances:
88 13 0.03
89 1 0.00
91 6 0.01
95 18 0.04
96 1 0.00
97 38 0.09
98 83 0.20
99 91 0.22
100 58 0.14
101 4 0.01
104 7 0.02
106 47 0.11
107 15 0.04
108 41 0.10
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (98 bp):
TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATTTGGGTGCTGGCCT
GTCAATGGCCGACACCCAGTACAATATTAAAAA
Found at i:34786088 original size:29 final size:29
Alignment explanation
Indices: 34786022--34786088 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
34786012 ACTTCGTAAT
*
34786022 ATTTAAAAATATAAGGACTAAATTCTTAA
1 ATTTAAAAATATAAGAACTAAATTCTTAA
**
34786051 AAATAAAAATATACA-AACTAAATTC-TAA
1 ATTTAAAAATATA-AGAACTAAATTCTTAA
34786079 ATTTACAAAA
1 ATTTA-AAAA
34786089 AATATATAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 6 0.19
29 24 0.77
30 1 0.03
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (29 bp):
ATTTAAAAATATAAGAACTAAATTCTTAA
Found at i:34786652 original size:96 final size:99
Alignment explanation
Indices: 34786485--34786798 Score: 339
Period size: 96 Copynumber: 3.0 Consensus size: 99
34786475 TATAATTATG
* *
34786485 TTTATTTTTTTCGTATATTTATATTTGATTTAGACACGAAAAAAAAAGATTTTTTTTAAAAATTG
1 TTTATTTTTTTCATATATTTATATTTGATTTTGACAC----AAAAAA-A--TTTTTTAAAAATTG
*
34786550 TACTGGGTGTCAGCCATTGACAGGCCAGCACCC-AATTTTT
59 TACTGGGTGCCAGCCATTGACAGGCCAGCACCCAAATTTTT
34786590 TTTATTTTTTTCATATATTTATATTTGATTTTGACACAAAAAAA-TTTTT-AAAATTGTACTGGG
1 TTTATTTTTTTCATATATTTATATTTGATTTTGACACAAAAAAATTTTTTAAAAATTGTACTGGG
* *
34786653 TGCCGGCCATTGACAGGTCAGCACCCAAATTTTT
66 TGCCAGCCATTGACAGGCCAGCACCCAAATTTTT
* *
34786687 TTTA-TTTTTTCATATATTTATATCTGATTCTGACACAAAAAAAAAGAATTTTTTTAAAAAAAAA
1 TTTATTTTTTTCATATATTTATATTTGATTTTGACAC----AAAAA-AA-TTTTTT----AAAAA
* * * *
34786751 TTGTACTGGGTGTCGGCTATTGACAGGCCAACACCCAAAATTTTT
56 TTGTACTGGGTGCCAGCCATTGACAGGCCAGCACCC-AAATTTTT
34786796 TTT
1 TTT
34786799 TCGTTTTTCT
Statistics
Matches: 184, Mismatches: 11, Indels: 24
0.84 0.05 0.11
Matches are distributed among these distances:
96 67 0.36
97 16 0.09
100 6 0.03
101 8 0.04
103 5 0.03
105 35 0.19
108 36 0.20
109 11 0.06
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (99 bp):
TTTATTTTTTTCATATATTTATATTTGATTTTGACACAAAAAAATTTTTTAAAAATTGTACTGGG
TGCCAGCCATTGACAGGCCAGCACCCAAATTTTT
Found at i:34792077 original size:25 final size:25
Alignment explanation
Indices: 34792043--34792231 Score: 168
Period size: 25 Copynumber: 7.9 Consensus size: 25
34792033 TGAGTATTTT
34792043 GAAGTTTATTTGATGTAATAAAATA
1 GAAGTTTATTTGATGTAATAAAATA
34792068 GAAGTTTATTTGATGTAATAAAAATA
1 GAAGTTTATTTGATGTAAT-AAAATA
* * ** *
34792094 GAAATTTTTTTGA-GT--T-ATTTT
1 GAAGTTTATTTGATGTAATAAAATA
34792115 G-A-TATTATTTGATGTAATAAAATA
1 GAAGT-TTATTTGATGTAATAAAATA
34792139 GAAGTTTATTTGATGTAATAAAAATA
1 GAAGTTTATTTGATGTAAT-AAAATA
* * ***
34792165 GAAATTT-TTTGA-GTTAT-TTTTA
1 GAAGTTTATTTGATGTAATAAAATA
*
34792187 -TA--TTATTTGATGTAATAAAATA
1 GAAGTTTATTTGATGTAATAAAATA
34792209 GAAGTTTATTTGATGTAATAAAA
1 GAAGTTTATTTGATGTAATAAAA
34792232 NNNNNNNNNN
Statistics
Matches: 129, Mismatches: 20, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
19 3 0.02
20 13 0.10
21 10 0.08
22 4 0.03
23 3 0.02
24 7 0.05
25 59 0.46
26 30 0.23
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (25 bp):
GAAGTTTATTTGATGTAATAAAATA
Found at i:34792212 original size:70 final size:71
Alignment explanation
Indices: 34792030--34792231 Score: 356
Period size: 70 Copynumber: 2.9 Consensus size: 71
34792020 TGTACAAATA
34792030 TTTTGAG-TATTTTGA-AGTTTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAAAT
1 TTTTGAGTTATTTTGATA--TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAAAT
34792093 AGAAATTT
64 AGAAATTT
34792101 TTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAAATAG
1 TTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAAATAG
34792166 AAA-TT
66 AAATTT
*
34792171 TTTTGAGTTATTTTTATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAA
1 TTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAA
34792232 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 1, Indels: 5
0.96 0.01 0.04
Matches are distributed among these distances:
70 62 0.48
71 57 0.45
72 8 0.06
73 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (71 bp):
TTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAAATAG
AAATTT
Found at i:34792439 original size:23 final size:23
Alignment explanation
Indices: 34792408--34792768 Score: 284
Period size: 23 Copynumber: 14.7 Consensus size: 23
34792398 NNNNNTATTG
34792408 AATTGAAAAACCCTAACCTAATTA
1 AATT-AAAAACCCTAACCTAATTA
*
34792432 AATTAAAAACCCTAACCTAACCCTAA
1 AATTAAAAACCCTAACCTAA---TTA
34792458 CCTAATTAAATTAAAAACCCTAACCTAATTA
1 ---AATT-AA----AAACCCTAACCTAATTA
*
34792489 AATTAAAAATCCTAACCTAATTA
1 AATTAAAAACCCTAACCTAATTA
34792512 AACCTT--AAACCCTAACCTAATTA
1 AA--TTAAAAACCCTAACCTAATTA
34792535 AATTAAAAACCCTAACCTAATTA
1 AATTAAAAACCCTAACCTAATTA
* *
34792558 AATTGAAAAGAAAACCCTAGCCAAATTA
1 AATT----A-AAAACCCTAACCTAATTA
34792586 AATTGAAAAA-CCTAACCTAATTA
1 AATT-AAAAACCCTAACCTAATTA
*
34792609 AA-AAGAAAACCCTAACCTAATTA
1 AATTA-AAAACCCTAACCTAATTA
*
34792632 AATTGAAAAGAAAACCCTAGCCTAATTA
1 AATT----A-AAAACCCTAACCTAATTA
34792660 AATTGAAAAA-CCTAACCTAATTA
1 AATT-AAAAACCCTAACCTAATTA
* *
34792683 AA-AAGAAAACCTTAACCTAATTA
1 AATTA-AAAACCCTAACCTAATTA
****
34792706 AACCCTAAACCCTAACCTAATTA
1 AATTAAAAACCCTAACCTAATTA
* * *
34792729 AATTGAAAATCCAAACCTAATTA
1 AATTAAAAACCCTAACCTAATTA
*
34792752 AATTGAAAACCCTAACC
1 AATTAAAAACCCTAACC
34792769 CTAAACCCTT
Statistics
Matches: 279, Mismatches: 28, Indels: 61
0.76 0.08 0.17
Matches are distributed among these distances:
21 4 0.01
22 8 0.03
23 177 0.63
24 12 0.04
25 4 0.01
26 2 0.01
27 3 0.01
28 47 0.17
29 4 0.01
30 2 0.01
31 2 0.01
34 14 0.05
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.24
Consensus pattern (23 bp):
AATTAAAAACCCTAACCTAATTA
Found at i:34792459 original size:34 final size:34
Alignment explanation
Indices: 34792416--34792485 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
34792406 TGAATTGAAA
34792416 AACCCTAACCTAATTAAATTAAAAACCCTAACCT
1 AACCCTAACCTAATTAAATTAAAAACCCTAACCT
34792450 AACCCTAACCTAATTAAATTAAAAACCCTAACCT
1 AACCCTAACCTAATTAAATTAAAAACCCTAACCT
34792484 AA
1 AA
34792486 TTAAATTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.23
Consensus pattern (34 bp):
AACCCTAACCTAATTAAATTAAAAACCCTAACCT
Found at i:34792600 original size:74 final size:73
Alignment explanation
Indices: 34792453--34792768 Score: 359
Period size: 74 Copynumber: 4.4 Consensus size: 73
34792443 CTAACCTAAC
*
34792453 CCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATT---A-AAAATCCTAACCTAATTAAA
1 CCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAGAAAACCCTAACCTAATTAAA
*
34792514 CCTT--AAAC
66 --TTGAAAAA
* *
34792522 CCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTGAAAAGAAAACCCTAGCCAAATTAA
1 CCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATT-AAAAGAAAACCCTAACCTAATTAA
34792587 ATTGAAAAA
65 ATTGAAAAA
* *
34792596 CCTAACCTAATTAAA-AAGAAAACCCTAACCTAATTAAATTGAAAAGAAAACCCTAGCCTAATTA
1 CCTAACCTAATTAAATTA-AAAACCCTAACCTAATTAAATT-AAAAGAAAACCCTAACCTAATTA
34792660 AATTGAAAAA
64 AATTGAAAAA
* * ****
34792670 CCTAACCTAATTAAA-AAGAAAACCTTAACCTAATT--A--AACCCTAAACCCTAACCTAATTAA
1 CCTAACCTAATTAAATTA-AAAACCCTAACCTAATTAAATTAAAAGAAAACCCTAACCTAATTAA
*
34792730 ATTGAAAAT
65 ATTGAAAAA
* *
34792739 CCAAACCTAATTAAATTGAAAACCCTAACC
1 CCTAACCTAATTAAATTAAAAACCCTAACC
34792769 CTAAACCCTT
Statistics
Matches: 221, Mismatches: 17, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
69 92 0.42
72 3 0.01
73 2 0.01
74 124 0.56
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.24
Consensus pattern (73 bp):
CCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAGAAAACCCTAACCTAATTAAA
TTGAAAAA
Found at i:34792974 original size:115 final size:116
Alignment explanation
Indices: 34792796--34793013 Score: 361
Period size: 115 Copynumber: 1.9 Consensus size: 116
34792786 CTAACCCTTA
*
34792796 ACATTCACATAATGTTAGATTTGGAAAAAATGTTTTTTCCTGGTACTAACAATTAATAATTTTAT
1 ACATTCACATAATGTTAGATTTGGAAAAAATG-TTTTTCCTGGTACTAACAAATAATAATTTTAT
*
34792861 ATAATTTGATAA-TTTTACTAACAATTAATACAATTTATTGGATAATAATTTT
65 ATAAATTGA-AATTTTTACTAACAATTAATACAATTTATTGGATAATAATTTT
34792913 ACATTCACATAATGTTAGATTTGG-AAAAATG-TTTTCACTGGTACTAACAAATAATAATTTTAT
1 ACATTCACATAATGTTAGATTTGGAAAAAATGTTTTTC-CTGGTACTAACAAATAATAATTTTAT
*
34792976 ATAAATTGAAATTTTTACTAACCATTAATACAATTTAT
65 ATAAATTGAAATTTTTACTAACAATTAATACAATTTAT
34793014 CAATTAATAA
Statistics
Matches: 96, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
114 7 0.07
115 58 0.60
116 7 0.07
117 24 0.25
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (116 bp):
ACATTCACATAATGTTAGATTTGGAAAAAATGTTTTTCCTGGTACTAACAAATAATAATTTTATA
TAAATTGAAATTTTTACTAACAATTAATACAATTTATTGGATAATAATTTT
Found at i:34796223 original size:123 final size:124
Alignment explanation
Indices: 34796004--34796242 Score: 419
Period size: 123 Copynumber: 1.9 Consensus size: 124
34795994 CCCAAACATG
34796004 CTACTGTAGCAAAAGCGCGTCCACGAAGGCTCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAAGGCTCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
34796069 TAGAAGCGATTTTATACTATTTACTCAGAAACGTCAA-AAAAATTATTTCATCCATGAC
66 TAAAAGCGATTTTATACTATTTACTCAGAAACGTCAACAAAAATTATTTCATCCATGAC
*
34796127 CTACTGTAGCAAAAGCGCGTCCACGAAGGCTCGATTTCACAAATTCTTCTCAAATAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAAGGCTCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
34796192 TAAAAGCGATTTTATACTATTTGA-TCAGAAACGTCAACTCAAAATTATTTC
66 TAAAAGCGATTTTATACTATTT-ACTCAGAAACGTCAAC-AAAAATTATTTC
34796243 TTCCCGGACC
Statistics
Matches: 110, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
123 98 0.89
124 1 0.01
125 11 0.10
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAAGGCTCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAAAAGCGATTTTATACTATTTACTCAGAAACGTCAACAAAAATTATTTCATCCATGAC
Found at i:34799369 original size:15 final size:15
Alignment explanation
Indices: 34799335--34799363 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34799325 ATAGGTGAAA
34799335 AAATAATTACATTTG
1 AAATAATTACATTTG
34799350 AAATAATTACATTT
1 AAATAATTACATTT
34799364 ATAATATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (15 bp):
AAATAATTACATTTG
Found at i:34799588 original size:14 final size:15
Alignment explanation
Indices: 34799564--34799592 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
34799554 AGTTTTTAAT
34799564 TAAAAAGCTTAAAAA
1 TAAAAAGCTTAAAAA
34799579 TAAAAA-CTTAAAAA
1 TAAAAAGCTTAAAAA
34799593 CATGTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21
Consensus pattern (15 bp):
TAAAAAGCTTAAAAA
Found at i:34801770 original size:10 final size:10
Alignment explanation
Indices: 34801738--34801799 Score: 58
Period size: 10 Copynumber: 6.4 Consensus size: 10
34801728 ATAGTAGTAA
34801738 TTTTAA-AAT
1 TTTTAATAAT
*
34801747 TTTT-ATAAG
1 TTTTAATAAT
*
34801756 ATTTAATAAT
1 TTTTAATAAT
34801766 TTTT-ATAAT
1 TTTTAATAAT
34801775 ATTTTAATAAT
1 -TTTTAATAAT
* *
34801786 TTCTAATAGT
1 TTTTAATAAT
34801796 TTTT
1 TTTT
34801800 GCTTTCTCTC
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
8 1 0.02
9 14 0.33
10 22 0.52
11 5 0.12
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:34801780 original size:20 final size:20
Alignment explanation
Indices: 34801737--34801787 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
34801727 AATAGTAGTA
34801737 ATTTTAA-AATTTTTATAAG
1 ATTTTAATAATTTTTATAAG
*
34801756 A-TTTAATAATTTTTATAAT
1 ATTTTAATAATTTTTATAAG
34801775 ATTTTAATAATTT
1 ATTTTAATAATTT
34801788 CTAATAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 5 0.17
19 13 0.45
20 11 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTTAATAATTTTTATAAG
Found at i:34801799 original size:20 final size:20
Alignment explanation
Indices: 34801737--34801793 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
34801727 AATAGTAGTA
* *
34801737 ATTTTAA-AATTTTTATAAG
1 ATTTTAATAATTTTAATAAT
*
34801756 A-TTTAATAATTTTTATAAT
1 ATTTTAATAATTTTAATAAT
34801775 ATTTTAATAATTTCTAATA
1 ATTTTAATAATTT-TAATA
34801794 GTTTTTGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.15
19 13 0.39
20 11 0.33
21 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTTTAATAATTTTAATAAT
Found at i:34802200 original size:27 final size:28
Alignment explanation
Indices: 34802166--34802222 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
34802156 NNNNNNCATA
34802166 TTAATAATATTCTATA-TTTTT-TAATAT
1 TTAATAATATT-TATAGTTTTTCTAATAT
*
34802193 TTAATAATATTTATAGTTTTTCTATTAT
1 TTAATAATATTTATAGTTTTTCTAATAT
34802221 TT
1 TT
34802223 TTATGTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 4 0.15
27 16 0.59
28 7 0.26
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (28 bp):
TTAATAATATTTATAGTTTTTCTAATAT
Found at i:34802903 original size:20 final size:20
Alignment explanation
Indices: 34802854--34802906 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
34802844 AGATGTCAAC
**
34802854 TTTA-AAATTATAATTATTA
1 TTTATAAATTATAATTAAAA
*
34802873 TATTAT-GATTATAATTAAAA
1 T-TTATAAATTATAATTAAAA
34802893 TTTATAAATTATAA
1 TTTATAAATTATAA
34802907 ATTATAGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTATAAATTATAATTAAAA
Found at i:34807373 original size:9 final size:9
Alignment explanation
Indices: 34807359--34807399 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
34807349 AACCAATCAA
34807359 TTTTAATAT
1 TTTTAATAT
34807368 TTTTAAATAT
1 TTTT-AATAT
34807378 TTTT-A-AT
1 TTTTAATAT
34807385 TTTTAATAAT
1 TTTTAAT-AT
34807395 TTTTA
1 TTTTA
34807400 TAATTTCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
7 6 0.21
8 2 0.07
9 4 0.14
10 16 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTAATAT
Found at i:34807388 original size:17 final size:17
Alignment explanation
Indices: 34807366--34807399 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
34807356 CAATTTTAAT
34807366 ATTTTTAA-ATATTTTTA
1 ATTTTTAATA-ATTTTTA
34807383 ATTTTTAATAATTTTTA
1 ATTTTTAATAATTTTTA
34807400 TAATTTCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTAATAATTTTTA
Done.