Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 126 of 253
Found at i:39945323 original size:27 final size:30
Alignment explanation
Indices: 39945292--39945358 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
39945282 TTCATATTAT
* *
39945292 TTTATGTA-A-ATATTTTCTTTTAAATTTA
1 TTTATGTATATATATTCTCTTTAAAATTTA
39945320 -TTATGTATATATATTCTCTTTAAAATTTA
1 TTTATGTATATATATTCTCTTTAAAATTTA
39945349 TTTATGTATA
1 TTTATGTATA
39945359 ATTTGGGCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 7 0.21
28 1 0.03
29 17 0.50
30 9 0.26
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (30 bp):
TTTATGTATATATATTCTCTTTAAAATTTA
Found at i:39946119 original size:126 final size:127
Alignment explanation
Indices: 39945972--39946206 Score: 355
Period size: 130 Copynumber: 1.8 Consensus size: 127
39945962 ATTTTTGTCT
* * *
39945972 CGTGTTTTTGAAATCATGAGGTGATCTCA-TTTTTGGAGGCTTAAAATATCGTGTCCTAACGTGC
1 CGTGTTTTGGAAATCATGAGGTGATCTCATTTTTTAGAAGCTTAAAATATCGTGTCCTAACGTGC
* * * *
39946036 TGGATGTGGTATTTTATTCCTTTGGAACGAGTGAATCTTAAAATCCAACTTGAGTTGTTTCG
66 TGGATGTGGCATTTAACTCATTTGGAACGAGTGAATCTTAAAATCCAACTTGAGTTGTTTCG
* *
39946098 CGTGTTTTGGAAATCGTGAGGTGATCTCAGTTTTTTTTAGAAGTTTAAAATATCGTGTCCTAACG
1 CGTGTTTTGGAAATCATGAGGTGATCTCA---TTTTTTAGAAGCTTAAAATATCGTGTCCTAACG
39946163 TGCTGGATGTGGCATTTAACTCATTTGGAACGAGTGAATCTTAA
63 TGCTGGATGTGGCATTTAACTCATTTGGAACGAGTGAATCTTAA
39946207 CAAACTCGAA
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
126 27 0.28
130 69 0.72
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (127 bp):
CGTGTTTTGGAAATCATGAGGTGATCTCATTTTTTAGAAGCTTAAAATATCGTGTCCTAACGTGC
TGGATGTGGCATTTAACTCATTTGGAACGAGTGAATCTTAAAATCCAACTTGAGTTGTTTCG
Found at i:39947786 original size:3 final size:3
Alignment explanation
Indices: 39947778--39947966 Score: 63
Period size: 3 Copynumber: 62.7 Consensus size: 3
39947768 GGGGAGAGTG
* *
39947778 TTA TTA TTA TTA TTA TT- TTA TTA TTA CTT- TTA CCTTT TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA --TTA TTA TTA TTA
* * * ** * *
39947824 TTA TTA TTT TTA TTA ATA -TA ATA TTA TT- TCC TT- TTT TTA TATG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* ** * * *
39947867 TTG TTA TTA TTA TTA GCA CGTA -TA TTA TTA TTA TTAA TGTA TCA TTG
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A T-TA TTA TTA
* * *
39947914 TTA TTT TCTA TT- TTA GTA TTA CTT- TTA TTA TTA TTG TT- TCTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA
39947959 TTA TTA TT
1 TTA TTA TT
39947967 TTCATTACTT
Statistics
Matches: 142, Mismatches: 25, Indels: 38
0.69 0.12 0.19
Matches are distributed among these distances:
2 16 0.11
3 108 0.76
4 15 0.11
5 3 0.02
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:39947948 original size:15 final size:14
Alignment explanation
Indices: 39947930--39947973 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
39947920 TCTATTTTAG
39947930 TATTACTTTTATTAT
1 TATTA-TTTTATTAT
*
39947945 TATTGTTTCTATTAT
1 TATTATTT-TATTAT
39947960 TATTATTTTCATTA
1 TATTATTTT-ATTA
39947974 CTTCCATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:39948005 original size:16 final size:16
Alignment explanation
Indices: 39947950--39948008 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 16
39947940 ATTATTATTG
* *
39947950 TTTCTATTATTATTAT
1 TTTCTATTATCATCAT
*
39947966 TTTC-ATTA-CTTCCAT
1 TTTCTATTATCAT-CAT
*
39947981 TGT-TATTATCATCAT
1 TTTCTATTATCATCAT
39947996 TTTCTATTATCAT
1 TTTCTATTATCAT
39948009 TAATATGTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
14 1 0.03
15 17 0.52
16 15 0.45
ACGTcount: A:0.24, C:0.15, G:0.02, T:0.59
Consensus pattern (16 bp):
TTTCTATTATCATCAT
Found at i:39948075 original size:33 final size:30
Alignment explanation
Indices: 39948029--39948116 Score: 97
Period size: 33 Copynumber: 2.9 Consensus size: 30
39948019 TGTGTTCATT
* *
39948029 ATTAT-TATTTTTTTAATACTATTATCATC
1 ATTATATATTTTTTTATTACTATTATCACC
* * *
39948058 ATTATATATTTACTTTTTTTTAATATTATTACC
1 ATTATATA-TT--TTTTTATTACTATTATCACC
39948091 ATTATATATTTTTTTATTACTATTAT
1 ATTATATATTTTTTTATTACTATTAT
39948117 TTTTATTATC
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
29 5 0.10
30 16 0.33
31 2 0.04
32 2 0.04
33 23 0.48
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (30 bp):
ATTATATATTTTTTTATTACTATTATCACC
Found at i:39948079 original size:36 final size:33
Alignment explanation
Indices: 39948036--39948101 Score: 96
Period size: 36 Copynumber: 1.9 Consensus size: 33
39948026 ATTATTATTA
39948036 TTTTTTTAATACTATTATCATCATTATATATTTACT
1 TTTTTTTAATACTATTA-C--CATTATATATTTACT
*
39948072 TTTTTTTAATATTATTACCATTATATATTT
1 TTTTTTTAATACTATTACCATTATATATTT
39948102 TTTTATTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 12 0.41
35 1 0.03
36 16 0.55
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (33 bp):
TTTTTTTAATACTATTACCATTATATATTTACT
Found at i:39952437 original size:12 final size:12
Alignment explanation
Indices: 39952420--39952459 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
39952410 CCATAGAAAT
39952420 AATCATCCTTAG
1 AATCATCCTTAG
*
39952432 AATCAT--TTAT
1 AATCATCCTTAG
39952442 AATCATCCTTAG
1 AATCATCCTTAG
39952454 AATCAT
1 AATCAT
39952460 TTATTCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (12 bp):
AATCATCCTTAG
Found at i:39952443 original size:22 final size:22
Alignment explanation
Indices: 39952418--39952463 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
39952408 TACCATAGAA
39952418 ATAATCATCCTTAGAATCATTT
1 ATAATCATCCTTAGAATCATTT
39952440 ATAATCATCCTTAGAATCATTT
1 ATAATCATCCTTAGAATCATTT
39952462 AT
1 AT
39952464 TCTTTGGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (22 bp):
ATAATCATCCTTAGAATCATTT
Found at i:39954357 original size:42 final size:42
Alignment explanation
Indices: 39954298--39954463 Score: 197
Period size: 42 Copynumber: 4.0 Consensus size: 42
39954288 AAATATTTGA
* *
39954298 GATAGCTTCGACTATGCATTGGCACTTAGGGTGCGAGATCGG
1 GATAGCTTCGACTATGCATTGGCACTTAGTGTGCGAGATTGG
* *
39954340 GATAGCTTCGACTATGCATTAGCACTTAGTGTGCGAGATTAG
1 GATAGCTTCGACTATGCATTGGCACTTAGTGTGCGAGATTGG
* * * * *
39954382 GATAGCTCCGGCTATGCGTTGGCACTTAGTGTGCGTGATTGA
1 GATAGCTTCGACTATGCATTGGCACTTAGTGTGCGAGATTGG
* * * * * *
39954424 GTTAGCTTCGGCTACGTATTGGCATTTAGTGTGCAAGATT
1 GATAGCTTCGACTATGCATTGGCACTTAGTGTGCGAGATT
39954464 CCCGAGTAAC
Statistics
Matches: 105, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 105 1.00
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.31
Consensus pattern (42 bp):
GATAGCTTCGACTATGCATTGGCACTTAGTGTGCGAGATTGG
Found at i:39954569 original size:32 final size:32
Alignment explanation
Indices: 39954528--39954594 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
39954518 TGAGTATGAG
**
39954528 ATTGGTACGATATGGTACAGGTATGTACGAAA
1 ATTGGTACGATATGGTACAGACATGTACGAAA
*
39954560 ATTGGTACGATATGGTACAGACATGTACGGAA
1 ATTGGTACGATATGGTACAGACATGTACGAAA
39954592 ATT
1 ATT
39954595 CAATTGAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.28
Consensus pattern (32 bp):
ATTGGTACGATATGGTACAGACATGTACGAAA
Found at i:39957027 original size:6 final size:7
Alignment explanation
Indices: 39956985--39957026 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
39956975 AAAAAATAAG
39956985 GAAAAAA
1 GAAAAAA
*
39956992 CACAAAAA
1 GA-AAAAA
39957000 -AAGAAAA
1 GAA-AAAA
39957007 GAAAAAA
1 GAAAAAA
39957014 GAAAAAA
1 GAAAAAA
39957021 GAAAAA
1 GAAAAA
39957027 GGAGAGGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
6 1 0.03
7 23 0.74
8 7 0.23
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:39957910 original size:46 final size:46
Alignment explanation
Indices: 39957800--39957889 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 46
39957790 AGATCAATTG
*
39957800 ATTAAAGAAGCCACAAATCCTATACCCCTGAGTTGCAGTAGGATAA
1 ATTAAAGAAGCCACAAATTCTATACCCCTGAGTTGCAGTAGGATAA
* ** * *
39957846 ATTAAAGATGGTACAAATTCTATACCCCTTAGTTGCAGTGGGAT
1 ATTAAAGAAGCCACAAATTCTATACCCCTGAGTTGCAGTAGGAT
39957890 GGATAGAAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (46 bp):
ATTAAAGAAGCCACAAATTCTATACCCCTGAGTTGCAGTAGGATAA
Found at i:39958363 original size:44 final size:44
Alignment explanation
Indices: 39958315--39958721 Score: 128
Period size: 44 Copynumber: 9.2 Consensus size: 44
39958305 ATAGTGGCAA
* * * *
39958315 TGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGTAG
1 TGGAGCAGATTCAAGACACAAGCCTTATCTCCCTAAAGTTGCAG
* * *
39958359 TGGAGCAGCTTCAAGATACAAGTCTTATCTCCCTAAAGTTGCAG
1 TGGAGCAGATTCAAGACACAAGCCTTATCTCCCTAAAGTTGCAG
* * * * ** * * ** *
39958403 TGGAGTAGACTGAAAATTGC-AGATCTTATCTTCCT-AAGAAGTAG
1 TGGAGCAGATTCAAGA-CACAAG-CCTTATCTCCCTAAAGTTGCAG
** * ** ** *
39958447 TGGAGCAGA-TCGAAGACGGA-AAATCTTATCTCCATGTAGCGGCAA
1 TGGAGCAGATTC-AAGAC--ACAAGCCTTATCTCCCTAAAGTTGCAG
* * * * *
39958492 TGGAGCAGATTTAAGCCACCAGTCTTATCTCCCTGAAGTTGCAG
1 TGGAGCAGATTCAAGACACAAGCCTTATCTCCCTAAAGTTGCAG
* * * * * * ** *
39958536 TGGAGCAGACTAAAAATTAC-AGATCTTATCTTCCT-AAGCAGTAG
1 TGGAGCAGATTCAAGA-CACAAG-CCTTATCTCCCTAAAGTTGCAG
** * * ** ** *
39958580 TGGAGCAGA-TCGAAGACGGA-AAATCTTACCTCCATGTAGCGGCAA
1 TGGAGCAGATTC-AAGAC--ACAAGCCTTATCTCCCTAAAGTTGCAG
* * * *
39958625 TAGAGCAGATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGCAG
1 TGGAGCAGATTCAAGACACAAGCCTTATCTCCCTAAAGTTGCAG
* * * * * * *
39958669 CGGAGCAGGTTCAAGATACAAGTCTTATCACTCTGAAGTTGCAG
1 TGGAGCAGATTCAAGACACAAGCCTTATCTCCCTAAAGTTGCAG
39958713 TGGAGCAGA
1 TGGAGCAGA
39958722 CTGAAAATTG
Statistics
Matches: 260, Mismatches: 85, Indels: 36
0.68 0.22 0.09
Matches are distributed among these distances:
43 4 0.02
44 191 0.73
45 63 0.24
46 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (44 bp):
TGGAGCAGATTCAAGACACAAGCCTTATCTCCCTAAAGTTGCAG
Found at i:39958496 original size:133 final size:133
Alignment explanation
Indices: 39958379--39958676 Score: 515
Period size: 133 Copynumber: 2.2 Consensus size: 133
39958369 TCAAGATACA
* * *
39958379 AGTCTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAAATTGCAGATCTTATCTTCCTAAGAAG
1 AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAAATTACAGATCTTATCTTCCTAAGAAG
*
39958444 TAGTGGAGCAGATCGAAGACGGAAAATCTTATCTCCATGTAGCGGCAATGGAGCAGATTTAAGCC
66 TAGTGGAGCAGATCGAAGACGGAAAATCTTACCTCCATGTAGCGGCAATGGAGCAGATTTAAGCC
39958509 ACC
131 ACC
* *
39958512 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAATTACAGATCTTATCTTCCTAAGCAG
1 AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAAATTACAGATCTTATCTTCCTAAGAAG
*
39958577 TAGTGGAGCAGATCGAAGACGGAAAATCTTACCTCCATGTAGCGGCAATAGAGCAGATTTAAGCC
66 TAGTGGAGCAGATCGAAGACGGAAAATCTTACCTCCATGTAGCGGCAATGGAGCAGATTTAAGCC
39958642 ACC
131 ACC
* *
39958645 AGCCTTATCTCCCTAAAGTTGCAGCGGAGCAG
1 AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAG
39958677 GTTCAAGATA
Statistics
Matches: 155, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 155 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (133 bp):
AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAAATTACAGATCTTATCTTCCTAAGAAG
TAGTGGAGCAGATCGAAGACGGAAAATCTTACCTCCATGTAGCGGCAATGGAGCAGATTTAAGCC
ACC
Found at i:39958584 original size:177 final size:177
Alignment explanation
Indices: 39958246--39958584 Score: 459
Period size: 177 Copynumber: 1.9 Consensus size: 177
39958236 GTGAATTTAT
* * * * * *
39958246 AGATCTTATCTCCCTAAGCAGTAGTGGAGCATATCAAAGACAGCAAATCTTATTTCTATATAGTG
1 AGATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCAAAGACAGAAAATCTTATCTCCATATAGCG
* * *
39958311 GCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGTAGTGGAGCAGCTTCAAGAT
66 GCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGCAGTGGAGCAGCTTAAAAAT
**
39958376 ACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAAATTGC
131 ACAAGTCTTATCTCCCTAAAGCAGCAGTGGAGTAGACTGAAAATTGC
* * * *
39958423 AGATCTTATCTTCCTAAGAAGTAGTGGAGCAGATCGAAGACGGAAAATCTTATCTCCATGTAGCG
1 AGATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCAAAGACAGAAAATCTTATCTCCATATAGCG
* *
39958488 GCAATGGAGCAGATTTAAGCCACCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC-TAAAAA
66 GCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGCAGTGGAGCAG-CTTAAAAA
* *
39958552 TTAC-AGATCTTATCTTCCT-AAGCAGTAGTGGAG
130 -TACAAG-TCTTATCTCCCTAAAGCAGCAGTGGAG
39958585 CAGATCGAAG
Statistics
Matches: 140, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
177 125 0.89
178 15 0.11
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (177 bp):
AGATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCAAAGACAGAAAATCTTATCTCCATATAGCG
GCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGCAGTGGAGCAGCTTAAAAAT
ACAAGTCTTATCTCCCTAAAGCAGCAGTGGAGTAGACTGAAAATTGC
Found at i:39958654 original size:177 final size:177
Alignment explanation
Indices: 39958471--39958833 Score: 483
Period size: 177 Copynumber: 2.1 Consensus size: 177
39958461 GACGGAAAAT
** * * * * *
39958471 CTTATCTCCATGTAGCGGCAATGGAGCAGATTTAAGCCACCAGTCTTATCTCCCTGAAGTTGCAG
1 CTTATCTCCATAAAGCGGCAACGGAGCAGATTCAAGACACAAGTCTTATCACCCTGAAGTTGCAG
*
39958536 TGGAGCAGACTAAAAATTACAGATCTTATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGACGGAA
66 TGGAGCAGACTAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGAA
* *
39958601 AATCTTACCTCCATGTAGCGGCAATAGAGCAGATTTAAGCCACCAGC
131 AATCTTACCTCCATGTAGCGACAATAGAGCAGACTTAAGCCACCAGC
* ** * * * *
39958648 CTTATCTCCCTAAAGTTGCAGCGGAGCAGGTTCAAGATACAAGTCTTATCACTCTGAAGTTGCAG
1 CTTATCTCCATAAAGCGGCAACGGAGCAGATTCAAGACACAAGTCTTATCACCCTGAAGTTGCAG
* * * * * *
39958713 TGGAGCAGACTGAAAATTGCAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCGAAGATGGCA
66 TGGAGCAGACTAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGAA
** * *
39958778 AATCTTATTTCCATGTAGCGACAATGGAGCAGACTTAAGCCACCATC
131 AATCTTACCTCCATGTAGCGACAATAGAGCAGACTTAAGCCACCAGC
39958825 CTTATCTCC
1 CTTATCTCC
39958834 TTGAGTAGTA
Statistics
Matches: 159, Mismatches: 27, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
177 159 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (177 bp):
CTTATCTCCATAAAGCGGCAACGGAGCAGATTCAAGACACAAGTCTTATCACCCTGAAGTTGCAG
TGGAGCAGACTAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGAA
AATCTTACCTCCATGTAGCGACAATAGAGCAGACTTAAGCCACCAGC
Found at i:39958806 original size:89 final size:88
Alignment explanation
Indices: 39958536--39958877 Score: 223
Period size: 88 Copynumber: 3.9 Consensus size: 88
39958526 GAAGTTGCAG
* * * *
39958536 TGGAGCAGACTAAAAATTACAGATCTTATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGACGGAA
1 TGGAGCAGACTAAAAATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGCA
*
39958601 AATCTTACCTCCATGTAGCGGCAA
66 AATCTTATCTCCATGTAGC-GCAA
* ** *** * * * * *
39958625 TAGAGCAGA-TTTAAGCCACCAG-CCTTATCTCCCTAAAGTTGCAGCGGAGCAGGTTC-AAGAT-
1 TGGAGCAGACTAAAAATTA-CAGATCTTATCTCCCT-AAGTAGTAGTGGAGCA-GATCGAAGATG
* * * * * *
39958686 ACAAGTCTTATCACTC-TGAAGTTGCAG
63 GCAAATCTTATCTC-CATGTAG-CGCAA
* * *
39958713 TGGAGCAGACTGAAAATTGCAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCGAAGATGGCA
1 TGGAGCAGACTAAAAATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGCA
*
39958778 AATCTTATTTCCATGTAGCGACAA
66 AATCTTATCTCCATGTAGCG-CAA
* *** * * * * **
39958802 TGGAGCAGACT-TAAGCCAC-CATCCTTATCTCCTTGAGTAGTAGTGGAGCAG-GCTGAAGATTA
1 TGGAGCAGACTAAAAATTACAGAT-CTTATCTCCCTAAGTAGTAGTGGAGCAGATC-GAAGATGG
39958864 CAAATCTTATCTCC
64 CAAATCTTATCTCC
39958878 CTAAGAAGTA
Statistics
Matches: 185, Mismatches: 55, Indels: 27
0.69 0.21 0.10
Matches are distributed among these distances:
87 6 0.03
88 107 0.58
89 69 0.37
90 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.25
Consensus pattern (88 bp):
TGGAGCAGACTAAAAATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGCA
AATCTTATCTCCATGTAGCGCAA
Found at i:39958808 original size:310 final size:309
Alignment explanation
Indices: 39958246--39958907 Score: 984
Period size: 310 Copynumber: 2.1 Consensus size: 309
39958236 GTGAATTTAT
* * * * ** * *
39958246 AGATCTTATCTCCCTAAGCAGTAGTGGAGCATATCAAAGACAGCAAATCTTATTTCTATATAGTG
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGAAAATCTTACCTCCATATAGCG
* * *
39958311 GCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGTAGTGGAGCAGCTTCAAGAT
66 GCAATAGAGCAGATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGCAGCGGAGCAGCTTCAAGAT
* * *
39958376 ACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAAATTGCAGATCTTATCTTCCTAAG
131 ACAAGTCTTATCACCCTAAAGTTGCAGTGGAGCAGACTGAAAATTGCAGATCTTATCTCCCTAAG
* *
39958441 AAGTAGTGGAGCAGATCGAAGACGGAAAATCTTATCTCCATGTAGCGGCAATGGAGCAGATTTAA
196 AAGTAGTGGAGCAGATCGAAGACGGAAAATCTTATCTCCATGTAGCGACAATGGAGCAGACTTAA
*
39958506 GCCACCAGT-CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAATTAC
261 GCCACCA-TCCTTATCTCCCTG-AGTAGCAGTGGAGCAGACTAAAAATTAC
* *
39958556 AGATCTTATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGACGGAAAATCTTACCTCCATGTAGCG
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGAAAATCTTACCTCCATATAGCG
*
39958621 GCAATAGAGCAGATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGCAGCGGAGCAGGTTCAAGAT
66 GCAATAGAGCAGATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGCAGCGGAGCAGCTTCAAGAT
* *
39958686 ACAAGTCTTATCACTCTGAAGTTGCAGTGGAGCAGACTGAAAATTGCAGATCTTATCTCCCTAAG
131 ACAAGTCTTATCACCCTAAAGTTGCAGTGGAGCAGACTGAAAATTGCAGATCTTATCTCCCTAAG
* * * * *
39958751 TAGTAGTGGAGTAGATCGAAGATGGCAAATCTTATTTCCATGTAGCGACAATGGAGCAGACTTAA
196 AAGTAGTGGAGCAGATCGAAGACGGAAAATCTTATCTCCATGTAGCGACAATGGAGCAGACTTAA
* * * * *
39958816 GCCACCATCCTTATCTCCTTGAGTAGTAGTGGAGCAGGCTGAAGATTAC
261 GCCACCATCCTTATCTCCCTGAGTAGCAGTGGAGCAGACTAAAAATTAC
* * *
39958865 AAATCTTATCTCCCTAAGAAGTAGTGGAGTAGATCGAAGACGG
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGG
39958908 TGAATCTCAT
Statistics
Matches: 315, Mismatches: 36, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
309 63 0.20
310 252 0.80
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (309 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGAAAATCTTACCTCCATATAGCG
GCAATAGAGCAGATTTAAGCCACCAGCCTTATCTCCCTAAAGTTGCAGCGGAGCAGCTTCAAGAT
ACAAGTCTTATCACCCTAAAGTTGCAGTGGAGCAGACTGAAAATTGCAGATCTTATCTCCCTAAG
AAGTAGTGGAGCAGATCGAAGACGGAAAATCTTATCTCCATGTAGCGACAATGGAGCAGACTTAA
GCCACCATCCTTATCTCCCTGAGTAGCAGTGGAGCAGACTAAAAATTAC
Found at i:39958874 original size:177 final size:177
Alignment explanation
Indices: 39958514--39958879 Score: 500
Period size: 177 Copynumber: 2.1 Consensus size: 177
39958504 AAGCCACCAG
* *
39958514 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAATTACAGATCTTATCTTCCTAAGCAGTA
1 TCTTATCACCCTGAAGTTGCAGTGGAGCAGACTAAAAATTACAGATCTTATCTCCCTAAGCAGTA
* *
39958579 GTGGAGCAGATCGAAGACGGAAAATCTTACCTCCATGTAGCGGCAATAGAGCAGATTTAAGCCAC
66 GTGGAGCAGATCGAAGACGGAAAATCTTACCTCCATGTAGCGACAATAGAGCAGACTTAAGCCAC
* * *
39958644 CAGCCTTATCTCCCTAAAGTTGCAGCGGAGCAGGTTCAAGATACAAG
131 CAGCCTTATCTCCCTAAAGTAGCAGCGGAGCAGGCTCAAGATACAAA
* * * *
39958691 TCTTATCACTCTGAAGTTGCAGTGGAGCAGACTGAAAATTGCAGATCTTATCTCCCTAAGTAGTA
1 TCTTATCACCCTGAAGTTGCAGTGGAGCAGACTAAAAATTACAGATCTTATCTCCCTAAGCAGTA
* * * ** *
39958756 GTGGAGTAGATCGAAGATGGCAAATCTTATTTCCATGTAGCGACAATGGAGCAGACTTAAGCCAC
66 GTGGAGCAGATCGAAGACGGAAAATCTTACCTCCATGTAGCGACAATAGAGCAGACTTAAGCCAC
* ** * * *
39958821 CATCCTTATCT-CCTTGAGTAGTAGTGGAGCAGGCTGAAGATTACAAA
131 CAGCCTTATCTCCCTAAAGTAGCAGCGGAGCAGGCTCAAGA-TACAAA
*
39958868 TCTTATCTCCCT
1 TCTTATCACCCT
39958880 AAGAAGTAGT
Statistics
Matches: 163, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
176 22 0.13
177 141 0.87
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (177 bp):
TCTTATCACCCTGAAGTTGCAGTGGAGCAGACTAAAAATTACAGATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATCGAAGACGGAAAATCTTACCTCCATGTAGCGACAATAGAGCAGACTTAAGCCAC
CAGCCTTATCTCCCTAAAGTAGCAGCGGAGCAGGCTCAAGATACAAA
Found at i:39958914 original size:44 final size:43
Alignment explanation
Indices: 39958866--39959038 Score: 102
Period size: 44 Copynumber: 4.0 Consensus size: 43
39958856 GAAGATTACA
39958866 AATCTTATCTCCCTAAGAAGTAGTGGAGTAGATCGAAGACGGT
1 AATCTTATCTCCCTAAGAAGTAGTGGAGTAGATCGAAGACGGT
* * * * ** * **
39958909 GAATCTCATCTTCCCGAGGTAGTAG-GGAAGTAGATTTAAGCCACT
1 -AATCTTATC-TCCCTAAGAAGTAGTGG-AGTAGATCGAAGACGGT
** ** * * **
39958954 AGCCTTATCTTTCTAAGCAGCAGT-GAGTAG-TCTGAAGATTGT
1 AATCTTATCTCCCTAAGAAGTAGTGGAGTAGATC-GAAGACGGT
*
39958996 AGATCTTATCTCCCTGAGCAA-TAGTGGAGTAGATCGAAGACGG
1 A-ATCTTATCTCCCTAAG-AAGTAGTGGAGTAGATCGAAGACGG
39959039 CGAATCTTCT
Statistics
Matches: 88, Mismatches: 33, Indels: 16
0.64 0.24 0.12
Matches are distributed among these distances:
41 1 0.01
42 10 0.11
43 23 0.26
44 29 0.33
45 25 0.28
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (43 bp):
AATCTTATCTCCCTAAGAAGTAGTGGAGTAGATCGAAGACGGT
Found at i:39958933 original size:177 final size:177
Alignment explanation
Indices: 39958514--39958943 Score: 422
Period size: 177 Copynumber: 2.4 Consensus size: 177
39958504 AAGCCACCAG
* ** * * * * * * *
39958514 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAATTACAGATCTTATCTTCCTAAGCAGTA
1 TCTTATCACCCTGAAGAAGCAGTGGAGCAGACTGAAAAGTGCAGATCTCATCTCCCGAAGTAGTA
* * *
39958579 GTGGAGCAGATCGAAGACGGAAAATCTTACCTCCATGTAGCGGCAATAGAGCAGATTTAAGCCAC
66 GTGGAGTAGATCGAAGACGGAAAATCTTACCTCCATGTAGCGACAATAGAGCAGACTTAAGCCAC
* * *
39958644 CAGCCTTATCTCCCTAAAGTTGCAGCGGAGCAGGTTCAAGATACAAG
131 CAGCCTTATCTCCCTAAAGTAGCAGCGGAGCAGGCTCAAGATACAAA
* ** * * *
39958691 TCTTATCACTCTGAAGTTGCAGTGGAGCAGACTGAAAATTGCAGATCTTATCTCCCTAAGTAGTA
1 TCTTATCACCCTGAAGAAGCAGTGGAGCAGACTGAAAAGTGCAGATCTCATCTCCCGAAGTAGTA
* * ** *
39958756 GTGGAGTAGATCGAAGATGGCAAATCTTATTTCCATGTAGCGACAATGGAGCAGACTTAAGCCAC
66 GTGGAGTAGATCGAAGACGGAAAATCTTACCTCCATGTAGCGACAATAGAGCAGACTTAAGCCAC
* ** * * *
39958821 CATCCTTATCT-CCTTGAGTAGTAGTGGAGCAGGCTGAAGATTACAAA
131 CAGCCTTATCTCCCTAAAGTAGCAGCGGAGCAGGCTCAAGA-TACAAA
* * * * *
39958868 TCTTATCTCCCT-AAGAAGTAGTGGAGTAGA-TCGAAGACGGTG-A-ATCTCATCTTCCCGAGGT
1 TCTTATCACCCTGAAGAAGCAGTGGAGCAGACT-GAA-A-AGTGCAGATCTCATC-TCCCGAAGT
39958929 AGTAG-GGAAGTAGAT
62 AGTAGTGG-AGTAGAT
39958944 TTAAGCCACT
Statistics
Matches: 213, Mismatches: 34, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
175 1 0.00
176 48 0.23
177 162 0.76
178 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (177 bp):
TCTTATCACCCTGAAGAAGCAGTGGAGCAGACTGAAAAGTGCAGATCTCATCTCCCGAAGTAGTA
GTGGAGTAGATCGAAGACGGAAAATCTTACCTCCATGTAGCGACAATAGAGCAGACTTAAGCCAC
CAGCCTTATCTCCCTAAAGTAGCAGCGGAGCAGGCTCAAGATACAAA
Found at i:39959036 original size:131 final size:131
Alignment explanation
Indices: 39958709--39959296 Score: 643
Period size: 132 Copynumber: 4.5 Consensus size: 131
39958699 CTCTGAAGTT
* * ** * * *
39958709 GCAGTGGAGCAGACTGAAAATTGCAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCGAAGAT
1 GCAGT-GAGCAGGCTGAAGATTATAGATCTTATCTCCCTAAGCAATAGTGGAGTAGATCGAAGAC
** * * ** * * * *
39958774 GGCAAATCTTAT-TTCCATGTAGCG-ACAATGG-AGCAGACTTAAGCCACCATCCTTATCTC-CT
65 GGTGAATCTCATCTTCC-CG-AG-GTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTC-
*
39958835 TGAGTA
126 TGAGCA
* * *
39958841 GTAGTGGAGCAGGCTGAAGATTACAAATCTTATCTCCCTAAG-AAGTAGTGGAGTAGATCGAAGA
1 GCAGT-GAGCAGGCTGAAGATTATAGATCTTATCTCCCTAAGCAA-TAGTGGAGTAGATCGAAGA
* * *
39958905 CGGTGAATCTCATCTTCCCGAGGTAGTAGGGAAGTAGATTTAAGCCACTAGCCTTATCTTTCTAA
64 CGGTGAATCTCATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTGA
39958970 GCA
129 GCA
* * * *
39958973 GCAGTGAGTAGTCTGAAGATTGTAGATCTTATCTCCCTGAGCAATAGTGGAGTAGATCGAAGACG
1 GCAGTGAGCAGGCTGAAGATTATAGATCTTATCTCCCTAAGCAATAGTGGAGTAGATCGAAGACG
* * * * *
39959038 GCGAATCTTC-TCTTCCCGAGGTAGTAAGGAAGCAGATTTAAGCCA-TCAACGTTATCTCTATGA
66 GTGAATC-TCATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACT-AGCCTTATCTCTCTGA
39959101 GCA
129 GCA
* * * *
39959104 GCAGTGGAGCAGGCTGAAGATTACAAATCTTATTTCCCTAAGCAGTAGTGGAGTAGATCGAAGAC
1 GCAGT-GAGCAGGCTGAAGATTATAGATCTTATCTCCCTAAGCAATAGTGGAGTAGATCGAAGAC
* *
39959169 GGTGAATCTTATTTTCCC-AGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTGAG
65 GGTGAATCTCATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTGAG
39959233 CA
130 CA
* * * *
39959235 GCAGTGAGCAGGCCGAAGATTTTAGATCTTATCTCCCTAAGCATTAGCGGAGTAGATCGAAG
1 GCAGTGAGCAGGCTGAAGATTATAGATCTTATCTCCCTAAGCAATAGTGGAGTAGATCGAAG
39959297 CTACAAATCT
Statistics
Matches: 387, Mismatches: 58, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
130 52 0.13
131 164 0.42
132 166 0.43
133 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (131 bp):
GCAGTGAGCAGGCTGAAGATTATAGATCTTATCTCCCTAAGCAATAGTGGAGTAGATCGAAGACG
GTGAATCTCATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTGAGC
A
Found at i:39959312 original size:263 final size:263
Alignment explanation
Indices: 39958709--39959306 Score: 778
Period size: 263 Copynumber: 2.3 Consensus size: 263
39958699 CTCTGAAGTT
* * * * * * * *
39958709 GCAGTGGAGCAGACTGAAAATTGCAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCGAAGAT
1 GCAGT-GAGCAGGCCGAAGATTGTAGATCTTATCTCCCTAAGCAATAGCGGAGTAGATCGAAGAC
* * * * *
39958774 GGCAAATCTTAT-TT-CC-ATGTAGCGACAATGG-AGCAGACTTAAGCCACCATCCTTATCTCCT
65 GACAAATCTTCTCTTCCCGAGGTA--G-TAA-GGAAGCAGACTTAAGCCACCAACCTTATCTCCT
* *
39958835 TGAGTAGTAGTGGAGCAGGCTGAAGATTACAAATCTTATCTCCCTAAGAAGTAGTGGAGTAGATC
126 TGAGCAGCAGTGGAGCAGGCTGAAGATTACAAATCTTATCTCCCTAAGAAGTAGTGGAGTAGATC
* *
39958900 GAAGACGGTGAATCTCATCTTCCCGAGGTAGTAGGGAAGTAGATTTAAGCCACTAGCCTTATCTT
191 GAAGACGGTGAATCTCATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTC
39958965 TCTAAGCA
256 TCTAAGCA
* * * * *
39958973 GCAGTGAGTAGTCTGAAGATTGTAGATCTTATCTCCCTGAGCAATAGTGGAGTAGATCGAAGACG
1 GCAGTGAGCAGGCCGAAGATTGTAGATCTTATCTCCCTAAGCAATAGCGGAGTAGATCGAAGACG
* * * * *
39959038 GCGAATCTTCTCTTCCCGAGGTAGTAAGGAAGCAGATTTAAGCCATCAACGTTATCT-CTATGAG
66 ACAAATCTTCTCTTCCCGAGGTAGTAAGGAAGCAGACTTAAGCCACCAACCTTATCTCCT-TGAG
* *
39959102 CAGCAGTGGAGCAGGCTGAAGATTACAAATCTTATTTCCCTAAGCAGTAGTGGAGTAGATCGAAG
130 CAGCAGTGGAGCAGGCTGAAGATTACAAATCTTATCTCCCTAAGAAGTAGTGGAGTAGATCGAAG
* * *
39959167 ACGGTGAATCTTATTTTCCC-AGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTG
195 ACGGTGAATCTCATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTA
39959231 AGCA
260 AGCA
* * *
39959235 GCAGTGAGCAGGCCGAAGATTTTAGATCTTATCTCCCTAAGCATTAGCGGAGTAGATCGAAG-CT
1 GCAGTGAGCAGGCCGAAGATTGTAGATCTTATCTCCCTAAGCAATAGCGGAGTAGATCGAAGACG
39959299 ACAAATCT
66 ACAAATCT
39959307 CTTCTCCCTA
Statistics
Matches: 294, Mismatches: 35, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
261 7 0.02
262 104 0.35
263 169 0.57
264 8 0.03
265 2 0.01
266 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (263 bp):
GCAGTGAGCAGGCCGAAGATTGTAGATCTTATCTCCCTAAGCAATAGCGGAGTAGATCGAAGACG
ACAAATCTTCTCTTCCCGAGGTAGTAAGGAAGCAGACTTAAGCCACCAACCTTATCTCCTTGAGC
AGCAGTGGAGCAGGCTGAAGATTACAAATCTTATCTCCCTAAGAAGTAGTGGAGTAGATCGAAGA
CGGTGAATCTCATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTAA
GCA
Found at i:39959372 original size:262 final size:263
Alignment explanation
Indices: 39958843--39959346 Score: 687
Period size: 262 Copynumber: 1.9 Consensus size: 263
39958833 CTTGAGTAGT
39958843 AGTGGAGCAGGCTGAAGATTACAAATCTTATCTCCCTAAGAAGTAGTGGAGTAGATCGAAGACGG
1 AGTGGAGCAGGCTGAAGATTACAAATCTTATCTCCCTAAGAAGTAGTGGAGTAGATCGAAGACGG
* *
39958908 TGAATCTCATCTTCCCGAGGTAGTAGGGAAGTAGATTTAAGCCACTAGCCTTATCTTTCTAAGCA
66 TGAATCTCATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTAAGCA
* * * * *
39958973 GCAGTGAGTAGTCTGAAGATTGTAGATCTTATCTCCCTGAGCAATAGTGGAGTAGATCGAAGACG
131 GCAGTGAGCAGGCCGAAGATTGTAGATCTTATCTCCCTAAGCAATAGCGGAGTAGATCGAAGACG
* * * ** ** ** * * *
39959038 GCGAATCTTCTCTTCCCGAGGTAGTAAGGAAGCAGATTTAAGCCATCAACGTTATCTCTATGAGC
196 ACAAATCTTCTCTTCCCAAAATAACAAGGAAGCAGATCAAAGCCACCAACGCTAACTCTATGAGC
39959103 AGC
261 AGC
* *
39959106 AGTGGAGCAGGCTGAAGATTACAAATCTTATTTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGG
1 AGTGGAGCAGGCTGAAGATTACAAATCTTATCTCCCTAAGAAGTAGTGGAGTAGATCGAAGACGG
* * *
39959171 TGAATCTTATTTTCCC-AGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTGAGCA
66 TGAATCTCATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTAAGCA
* * *
39959235 GCAGTGAGCAGGCCGAAGATTTTAGATCTTATCTCCCTAAGCATTAGCGGAGTAGATCGAAG-CT
131 GCAGTGAGCAGGCCGAAGATTGTAGATCTTATCTCCCTAAGCAATAGCGGAGTAGATCGAAGACG
*
39959299 ACAAATC-TCT-TCTCCCTAAAATAACATTGG-AGCAGATCAAAG-CACCAA
196 ACAAATCTTCTCT-TCCC-AAAATAACA-AGGAAGCAGATCAAAGCCACCAA
39959347 TTCCTACACT
Statistics
Matches: 212, Mismatches: 26, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
259 1 0.00
260 12 0.06
261 20 0.09
262 102 0.48
263 77 0.36
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (263 bp):
AGTGGAGCAGGCTGAAGATTACAAATCTTATCTCCCTAAGAAGTAGTGGAGTAGATCGAAGACGG
TGAATCTCATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAGCCTTATCTCTCTAAGCA
GCAGTGAGCAGGCCGAAGATTGTAGATCTTATCTCCCTAAGCAATAGCGGAGTAGATCGAAGACG
ACAAATCTTCTCTTCCCAAAATAACAAGGAAGCAGATCAAAGCCACCAACGCTAACTCTATGAGC
AGC
Found at i:39959388 original size:25 final size:25
Alignment explanation
Indices: 39959354--39959405 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
39959344 CAATTCCTAC
39959354 ACTCCTGAAGATGCAGTGGTTTGGA
1 ACTCCTGAAGATGCAGTGGTTTGGA
39959379 ACTCCTGAAGATGCAGTGGTTTGGA
1 ACTCCTGAAGATGCAGTGGTTTGGA
39959404 AC
1 AC
39959406 AAGGCGGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (25 bp):
ACTCCTGAAGATGCAGTGGTTTGGA
Found at i:39959628 original size:25 final size:26
Alignment explanation
Indices: 39959598--39959646 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
39959588 GTCCTATTAA
39959598 CACCCCACTAAACCAAC-TACTAAAC
1 CACCCCACTAAACCAACTTACTAAAC
*
39959623 CACCCCACTAAACCACCTTACTAA
1 CACCCCACTAAACCAACTTACTAA
39959647 CTCCATCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.41, C:0.45, G:0.00, T:0.14
Consensus pattern (26 bp):
CACCCCACTAAACCAACTTACTAAAC
Found at i:39959634 original size:13 final size:13
Alignment explanation
Indices: 39959598--39959639 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
39959588 GTCCTATTAA
39959598 CACCCCACTAAAC
1 CACCCCACTAAAC
* *
39959611 CA-ACTACTAAAC
1 CACCCCACTAAAC
39959623 CACCCCACTAAAC
1 CACCCCACTAAAC
39959636 CACC
1 CACC
39959640 TTACTAACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.40, C:0.50, G:0.00, T:0.10
Consensus pattern (13 bp):
CACCCCACTAAAC
Found at i:39959645 original size:13 final size:12
Alignment explanation
Indices: 39959604--39959646 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
39959594 TTAACACCCC
*
39959604 ACTAAACCAACT
1 ACTAAACCACCT
*
39959616 ACTAAACCACCCC
1 ACTAAACCA-CCT
39959629 ACTAAACCACCTT
1 ACTAAACCACC-T
39959642 ACTAA
1 ACTAA
39959647 CTCCATCACC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (12 bp):
ACTAAACCACCT
Found at i:39959947 original size:3 final size:3
Alignment explanation
Indices: 39959941--39959987 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
39959931 GAGAGTGTTG
*
39959941 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TT- TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
39959986 TT
1 TT
39959988 CTATATACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:39960296 original size:25 final size:25
Alignment explanation
Indices: 39960258--39960305 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39960248 TATATTTACC
39960258 TTTTTTAATATTATTACCATTATAG
1 TTTTTTAATATTATTACCATTATAG
* * *
39960283 TTTTTTATTTTTATTACTATTAT
1 TTTTTTAATATTATTACCATTAT
39960306 TTTTATTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTTTTAATATTATTACCATTATAG
Found at i:39960809 original size:41 final size:40
Alignment explanation
Indices: 39960764--39960917 Score: 191
Period size: 41 Copynumber: 3.8 Consensus size: 40
39960754 CACGGATCAA
* *
39960764 TAGCGGCGTTTTACCAAAAACTCCGCTAAAAACCAGAGCAT
1 TAGCGGCGTTTT-CGAAAAACGCCGCTAAAAACCAGAGCAT
* **
39960805 TAGCGGCGTTTTTGGTGAAACGCCGCTAAAAACCAGAGCAT
1 TAGCGGCG-TTTTCGAAAAACGCCGCTAAAAACCAGAGCAT
* **
39960846 TAGCGGCGCTTTTGGTGAAACGCCGCTAAAAACCAGAGCAT
1 TAGCGGCG-TTTTCGAAAAACGCCGCTAAAAACCAGAGCAT
*
39960887 TAGCGGCGCTTTCGATAAAACGCCGCTAAAA
1 TAGCGGCGTTTTCGA-AAAACGCCGCTAAAA
39960918 GTCATATAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 4 0.04
41 93 0.92
42 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (40 bp):
TAGCGGCGTTTTCGAAAAACGCCGCTAAAAACCAGAGCAT
Found at i:39961002 original size:15 final size:16
Alignment explanation
Indices: 39960972--39961005 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39960962 ACTAATCTAT
39960972 AACCCCTAAAACACTA
1 AACCCCTAAAACACTA
*
39960988 AACCCTTAAAA-ACTA
1 AACCCCTAAAACACTA
39961003 AAC
1 AAC
39961006 TATAACCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (16 bp):
AACCCCTAAAACACTA
Found at i:39961009 original size:37 final size:37
Alignment explanation
Indices: 39960957--39961027 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
39960947 CAAAAAATAA
* *
39960957 TAAACACTAATCTATAACCCCTAAAACACTAAACCCT
1 TAAAAACTAAACTATAACCCCTAAAACACTAAACCCT
*
39960994 TAAAAACTAAACTATAACCCCTAAAACCCTAAAC
1 TAAAAACTAAACTATAACCCCTAAAACACTAAAC
39961028 TCCAAAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (37 bp):
TAAAAACTAAACTATAACCCCTAAAACACTAAACCCT
Found at i:39961036 original size:37 final size:37
Alignment explanation
Indices: 39960962--39961037 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
39960952 AATAATAAAC
* *
39960962 ACTAATCTATAACCCCTAAAACACTAAACCCTTAAAA
1 ACTAAACTATAACCCCTAAAACACTAAACCCTAAAAA
*
39960999 ACTAAACTATAACCCCTAAAACCCTAAACTCC-AAAAA
1 ACTAAACTATAACCCCTAAAACACTAAAC-CCTAAAAA
39961036 AC
1 AC
39961038 ATCATATGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 33 0.94
38 2 0.06
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (37 bp):
ACTAAACTATAACCCCTAAAACACTAAACCCTAAAAA
Found at i:39961513 original size:17 final size:18
Alignment explanation
Indices: 39961488--39961523 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
39961478 CCTAAACTCT
*
39961488 TAAACCCCTAAAC-CTAA
1 TAAAACCCTAAACACTAA
39961505 TAAAACCCTAAACACTAA
1 TAAAACCCTAAACACTAA
39961523 T
1 T
39961524 CTATAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (18 bp):
TAAAACCCTAAACACTAA
Found at i:39962179 original size:19 final size:20
Alignment explanation
Indices: 39962132--39962179 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
39962122 ATATTAAATT
39962132 TAAA-AAAAACATTGATAAA
1 TAAATAAAAACATTGATAAA
39962151 TAAATAAAAACATTGAT-AA
1 TAAATAAAAACATTGATAAA
39962170 TAAATAAAAA
1 TAAATAAAAA
39962180 TAAAATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (20 bp):
TAAATAAAAACATTGATAAA
Found at i:39962182 original size:6 final size:6
Alignment explanation
Indices: 39962166--39962199 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
39962156 AAAAACATTG
39962166 ATAATAA ATAAAA ATAAAA TATAAAA ATAAAA AT
1 ATAA-AA ATAAAA ATAAAA -ATAAAA ATAAAA AT
39962200 GTATAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.62
7 10 0.38
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
ATAAAA
Found at i:39962189 original size:13 final size:13
Alignment explanation
Indices: 39962173--39962197 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39962163 TTGATAATAA
39962173 ATAAAAATAAAAT
1 ATAAAAATAAAAT
39962186 ATAAAAATAAAA
1 ATAAAAATAAAA
39962198 ATGTATAAAA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
ATAAAAATAAAAT
Found at i:39962412 original size:6 final size:6
Alignment explanation
Indices: 39962396--39962426 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
39962386 ACCCATACGA
*
39962396 TCCCTT CCCCTT TCCCTT TCCCTT TCCCTT T
1 TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT T
39962427 AGTTTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
TCCCTT
Found at i:39964641 original size:21 final size:22
Alignment explanation
Indices: 39964595--39964647 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
39964585 GAGAAACCAT
*
39964595 TTTATGTGTTAAATGCTGAAAA
1 TTTAGGTGTTAAATGCTGAAAA
*
39964617 TTTAGGTGTTAAATGCTG-CAA
1 TTTAGGTGTTAAATGCTGAAAA
39964638 TTTATGGTGT
1 TTTA-GGTGT
39964648 CTGAAAGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.43
Consensus pattern (22 bp):
TTTAGGTGTTAAATGCTGAAAA
Found at i:39966461 original size:43 final size:43
Alignment explanation
Indices: 39966399--39966632 Score: 267
Period size: 43 Copynumber: 5.5 Consensus size: 43
39966389 TTTTTGAAGT
*
39966399 TCATGATTTTTAGCAGCGTTTGTGAGAAAAGCGCCGCTAAAAG
1 TCATGATTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAG
* * * * * *
39966442 TCATGTTTTTTAGTGGCGTTTGTGGGAAAAGTGCCGTTAAAGG
1 TCATGATTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAG
39966485 TCATGATTTTTAGCGGCGTTT-TCGAGAAAAGCGCCGCTAAAAG
1 TCATGATTTTTAGCGGCGTTTGT-GAGAAAAGCGCCGCTAAAAG
* * *
39966528 T-ATGATCTTTAGCGGCGTTTTTG-GAAAAGCGCCGCTAAAGG
1 TCATGATTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAG
* * * * * * *
39966569 TCATGGTTTTTAGCGGTGTTTATAAAAAAAACGTCGCTAAAAG
1 TCATGATTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAG
* *
39966612 TCATGGTCTTTAGCGGCGTTT
1 TCATGATTTTTAGCGGCGTTT
39966633 TTTAAATAAA
Statistics
Matches: 161, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
41 18 0.11
42 37 0.23
43 106 0.66
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (43 bp):
TCATGATTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAG
Found at i:39966584 original size:84 final size:85
Alignment explanation
Indices: 39966399--39966634 Score: 305
Period size: 84 Copynumber: 2.8 Consensus size: 85
39966389 TTTTTGAAGT
* * * * *
39966399 TCATGATTTTTAGCAGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCATGTTTTTTAGTGGCGTTTG
1 TCATGATTTTTAGCGGCGTTTATGAGAAAAGCGCCGCTAAAAGTCATGATCTTTAGCGGCGTTT-
* * *
39966464 TGGGAAAAGTGCCGTTAAAGG
65 TTGGAAAAGCGCCGCTAAAGG
39966485 TCATGATTTTTAGCGGCGTTT-TCGAGAAAAGCGCCGCTAAAAGT-ATGATCTTTAGCGGCGTTT
1 TCATGATTTTTAGCGGCGTTTAT-GAGAAAAGCGCCGCTAAAAGTCATGATCTTTAGCGGCGTTT
39966548 TTGGAAAAGCGCCGCTAAAGG
65 TTGGAAAAGCGCCGCTAAAGG
* * * * * * *
39966569 TCATGGTTTTTAGCGGTGTTTATAAAAAAAACGTCGCTAAAAGTCATGGTCTTTAGCGGCGTTTT
1 TCATGATTTTTAGCGGCGTTTATGAGAAAAGCGCCGCTAAAAGTCATGATCTTTAGCGGCGTTTT
39966634 T
66 T
39966635 TAAATAAACA
Statistics
Matches: 133, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
84 54 0.41
85 38 0.29
86 41 0.31
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.33
Consensus pattern (85 bp):
TCATGATTTTTAGCGGCGTTTATGAGAAAAGCGCCGCTAAAAGTCATGATCTTTAGCGGCGTTTT
TGGAAAAGCGCCGCTAAAGG
Found at i:39966628 original size:127 final size:128
Alignment explanation
Indices: 39966401--39966633 Score: 297
Period size: 127 Copynumber: 1.8 Consensus size: 128
39966391 TTTGAAGTTC
* * * * *
39966401 ATGATTTTTAGCAGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCATGTTTTTTAGTGGCGTTTGTG
1 ATGATCTTTAGCAGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCATGGTTTTTAGCGGCGTTTATA
** ** * * *
39966466 GGAAAAGTGCCGTTAAAGGTCATGATTTTTAGCGGCGTTTTCGAGAAAAGCGCCGCTAAAAGT
66 AAAAAAACGCCGCTAAAAGTCATGATCTTTAGCGGCGTTTTCGAGAAAAGCGCCGCTAAAAGT
* * * *
39966529 ATGATCTTTAGCGGCGTTTTTG-GAAAAGCGCCGCTAAAGGTCATGGTTTTTAGCGGTGTTTATA
1 ATGATCTTTAGCAGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCATGGTTTTTAGCGGCGTTTATA
* *
39966593 AAAAAAACGTCGCTAAAAGTCATGGTCTTTAGCGGCGTTTT
66 AAAAAAACGCCGCTAAAAGTCATGATCTTTAGCGGCGTTTT
39966634 TTAAATAAAC
Statistics
Matches: 87, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
127 68 0.78
128 19 0.22
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (128 bp):
ATGATCTTTAGCAGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCATGGTTTTTAGCGGCGTTTATA
AAAAAAACGCCGCTAAAAGTCATGATCTTTAGCGGCGTTTTCGAGAAAAGCGCCGCTAAAAGT
Found at i:39973976 original size:18 final size:19
Alignment explanation
Indices: 39973953--39973990 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
39973943 TTGAAAAGTA
39973953 TATTATGTGA-TGTGATGT
1 TATTATGTGATTGTGATGT
*
39973971 TATTATTTGATTGTGATGT
1 TATTATGTGATTGTGATGT
39973990 T
1 T
39973991 TGTGCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (19 bp):
TATTATGTGATTGTGATGT
Found at i:39974257 original size:22 final size:22
Alignment explanation
Indices: 39974229--39974280 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
39974219 AGGATGAAGA
*
39974229 TATGTGG-CAGTTTATCTACAAT
1 TATGTGGTC-GTTTATCGACAAT
*
39974251 TATGTGGTCGTTTATCGATAAT
1 TATGTGGTCGTTTATCGACAAT
39974273 TATGTGGT
1 TATGTGGT
39974281 GGCTTGTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (22 bp):
TATGTGGTCGTTTATCGACAAT
Found at i:39974293 original size:22 final size:22
Alignment explanation
Indices: 39974248--39974294 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
39974238 GTTTATCTAC
* *
39974248 AATTATGTGGTCGTTTATCGAT
1 AATTATGTGGTCGCTTATCAAT
* *
39974270 AATTATGTGGTGGCTTGTCAAT
1 AATTATGTGGTCGCTTATCAAT
39974292 AAT
1 AAT
39974295 GTGCCATGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43
Consensus pattern (22 bp):
AATTATGTGGTCGCTTATCAAT
Found at i:39989206 original size:21 final size:21
Alignment explanation
Indices: 39989142--39989206 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
39989132 CAGAAGCAGT
*
39989142 ATACGACACATAAAGTGCCTG
1 ATACGACACATATAGTGCCTG
* * ** *
39989163 AAATGACACACGTGGTGCCTG
1 ATACGACACATATAGTGCCTG
39989184 ATACGACACATATAGTGCCTG
1 ATACGACACATATAGTGCCTG
39989205 AT
1 AT
39989207 CAGCAAAGCC
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (21 bp):
ATACGACACATATAGTGCCTG
Found at i:39990075 original size:12 final size:12
Alignment explanation
Indices: 39990058--39990091 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
39990048 AAAACCTTAG
39990058 TTTTTCCTTTTC
1 TTTTTCCTTTTC
39990070 TTTTT-CTTTTC
1 TTTTTCCTTTTC
39990081 TTCTTTCCTTT
1 TT-TTTCCTTT
39990092 CCCCCTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 8 0.40
13 4 0.20
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTCCTTTTC
Found at i:39990181 original size:3 final size:3
Alignment explanation
Indices: 39990173--39990215 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
39990163 ATGTATTAGT
*
39990173 TAA TAA TAA TAA TAA TACA TTA TAA TAA T-A TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TA
39990216 TTTAATTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.83
4 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:39990216 original size:13 final size:13
Alignment explanation
Indices: 39990175--39990216 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
39990165 GTATTAGTTA
39990175 ATAATAATAATAAT
1 ATAAT-ATAATAAT
* *
39990189 ACATTATAATAAT
1 ATAATATAATAAT
39990202 ATAATATAATAAT
1 ATAATATAATAAT
39990215 AT
1 AT
39990217 TTAATTCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 21 0.88
14 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:39992589 original size:45 final size:45
Alignment explanation
Indices: 39992524--39992614 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
39992514 CCAAAACATG
39992524 TGTCACATATATCACGAACTCAAACCACAACTCAATGAGTTCAGA
1 TGTCACATATATCACGAACTCAAACCACAACTCAATGAGTTCAGA
** * *
39992569 TGTCACATATATCATTAACTCATACCACAACTCAATGAGTTTAGA
1 TGTCACATATATCACGAACTCAAACCACAACTCAATGAGTTCAGA
39992614 T
1 T
39992615 CACATAGTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.27
Consensus pattern (45 bp):
TGTCACATATATCACGAACTCAAACCACAACTCAATGAGTTCAGA
Found at i:39999741 original size:9 final size:9
Alignment explanation
Indices: 39999727--39999751 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
39999717 AAAGCCAAGC
39999727 AAATCGACT
1 AAATCGACT
39999736 AAATCGACT
1 AAATCGACT
39999745 AAATCGA
1 AAATCGA
39999752 TTAATCGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (9 bp):
AAATCGACT
Found at i:40000145 original size:44 final size:43
Alignment explanation
Indices: 40000064--40000174 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 43
40000054 CAAGTGCTTA
* *
40000064 TGTAAGACATGTCTGGGACATGCATCAGCCTCAAGATGTAAGACAG
1 TGTAAGACA-GTCTGGGACATGCAACAGCCACAAGATGT--GACAG
* * *
40000110 TGTAAGACA-TCTGGGACATGCAACGGCCACGAGATGTGTCAG
1 TGTAAGACAGTCTGGGACATGCAACAGCCACAAGATGTGACAG
*
40000152 TGTAAGACCATGTCCGGGACATG
1 TGTAAGA-CA-GTCTGGGACATG
40000175 GCATTGGCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
42 11 0.20
43 2 0.04
44 24 0.43
45 10 0.18
46 9 0.16
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.21
Consensus pattern (43 bp):
TGTAAGACAGTCTGGGACATGCAACAGCCACAAGATGTGACAG
Found at i:40002011 original size:17 final size:18
Alignment explanation
Indices: 40001977--40002013 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40001967 CAATTAACCC
40001977 CTCAATTAAGATAATTTT
1 CTCAATTAAGATAATTTT
*
40001995 CTCAATTAATA-AATTTT
1 CTCAATTAAGATAATTTT
40002012 CT
1 CT
40002014 AGACATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.46
Consensus pattern (18 bp):
CTCAATTAAGATAATTTT
Found at i:40007233 original size:34 final size:38
Alignment explanation
Indices: 40007160--40007243 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 38
40007150 TAAAAGTTAC
*
40007160 ATTAATAGTTATAAAATATATTACTATGTTATATCTAT
1 ATTAATAGTTATAAAATATATTACTATGTTATATATAT
**
40007198 ATTAATAGTTAT-AGTTATA-TA-TATG-TATATATAT
1 ATTAATAGTTATAAAATATATTACTATGTTATATATAT
*
40007232 ATTAACAGTTAT
1 ATTAATAGTTAT
40007244 GTTGTTAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 19 0.45
35 4 0.10
36 2 0.05
37 5 0.12
38 12 0.29
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.48
Consensus pattern (38 bp):
ATTAATAGTTATAAAATATATTACTATGTTATATATAT
Found at i:40007743 original size:20 final size:19
Alignment explanation
Indices: 40007705--40007743 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
40007695 GATTATTATA
* *
40007705 TATGTGTAGTTTATTATAT
1 TATGTGTAGTATATAATAT
40007724 TATGTAGTAGTATATAATAT
1 TATGT-GTAGTATATAATAT
40007744 ATTACAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (19 bp):
TATGTGTAGTATATAATAT
Found at i:40008686 original size:23 final size:23
Alignment explanation
Indices: 40008636--40008686 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
40008626 GTCGAGAGAT
* *
40008636 AAAATCTCAACTTAAGATAGTAC
1 AAAATCTCAACTTAAAATAATAC
40008659 AAAATCTCAACTTAAAATAATAC
1 AAAATCTCAACTTAAAATAATAC
*
40008682 CAAAT
1 AAAAT
40008687 ATATTAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.53, C:0.18, G:0.04, T:0.25
Consensus pattern (23 bp):
AAAATCTCAACTTAAAATAATAC
Found at i:40009380 original size:22 final size:21
Alignment explanation
Indices: 40009350--40009391 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40009340 CTAAAGTCCC
40009350 TTCCCTTCTCATTTTCCTTTCT
1 TTCCCTTCTC-TTTTCCTTTCT
*
40009372 TTCCTTTCTCTTTTCCTTTC
1 TTCCCTTCTCTTTTCCTTTC
40009392 CAAAAACTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCCCTTCTCTTTTCCTTTCT
Found at i:40015181 original size:12 final size:12
Alignment explanation
Indices: 40015164--40015205 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
40015154 GGGACATGCC
40015164 CGTGTTGGAGGT
1 CGTGTTGGAGGT
* **
40015176 CGTGTTCGAGCC
1 CGTGTTGGAGGT
40015188 CGTGTTGGAGGT
1 CGTGTTGGAGGT
40015200 CGTGTT
1 CGTGTT
40015206 CGACCCCGTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.07, C:0.17, G:0.43, T:0.33
Consensus pattern (12 bp):
CGTGTTGGAGGT
Found at i:40015193 original size:24 final size:24
Alignment explanation
Indices: 40015161--40015216 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
40015151 CTTGGGACAT
40015161 GCCCGTGTTGGAGGTCGTGTTCGA
1 GCCCGTGTTGGAGGTCGTGTTCGA
40015185 GCCCGTGTTGGAGGTCGTGTTCGA
1 GCCCGTGTTGGAGGTCGTGTTCGA
*
40015209 CCCCGTGT
1 GCCCGTGT
40015217 AACTCTCTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.07, C:0.25, G:0.39, T:0.29
Consensus pattern (24 bp):
GCCCGTGTTGGAGGTCGTGTTCGA
Found at i:40015541 original size:43 final size:43
Alignment explanation
Indices: 40015441--40015566 Score: 148
Period size: 43 Copynumber: 3.0 Consensus size: 43
40015431 ACATACGGCC
* * * * **
40015441 TAACCACGTGCCCATGTTACCAGG-TTTATGTCATACATTG-T
1 TAACCACATGCCCATGTTACCAGGCTATGTGTCACACACGGTT
* * *
40015482 CAACCACAAGCCCATGTTACCAGGCTGTGTGTCACACACGGTT
1 TAACCACATGCCCATGTTACCAGGCTATGTGTCACACACGGTT
*
40015525 TAACCACATGCCCATGTTACCAGGCCATGTGTCACACACGGT
1 TAACCACATGCCCATGTTACCAGGCTATGTGTCACACACGGT
40015567 CTAGATACAT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 21 0.30
42 11 0.15
43 39 0.55
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (43 bp):
TAACCACATGCCCATGTTACCAGGCTATGTGTCACACACGGTT
Found at i:40016301 original size:19 final size:20
Alignment explanation
Indices: 40016269--40016306 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
40016259 TCATATCATC
40016269 TCAAGACTTCCATG-CCATG
1 TCAAGACTTCCATGTCCATG
* *
40016288 TCAAGAGTTTCATGTCCAT
1 TCAAGACTTCCATGTCCAT
40016307 TGAATCATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (20 bp):
TCAAGACTTCCATGTCCATG
Found at i:40018219 original size:13 final size:14
Alignment explanation
Indices: 40018192--40018224 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
40018182 AGGCGAAATT
40018192 ATATACATGGAATA
1 ATATACATGGAATA
40018206 ATATACAT-GAATA
1 ATATACATGGAATA
*
40018219 AAATAC
1 ATATAC
40018225 TCTACAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (14 bp):
ATATACATGGAATA
Found at i:40018857 original size:32 final size:34
Alignment explanation
Indices: 40018821--40018899 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 34
40018811 AATAGGGTCC
*
40018821 TTAAAAGAAACAA-AT-TATATACATAAATAAAT
1 TTAAAAGAAAAAATATATATATACATAAATAAAT
*
40018853 TTAAAAGAAAAAAAATATATATATACATAAATAGAT
1 TTAAAAG--AAAAAATATATATATACATAAATAAAT
40018889 TTAAAAGAAAA
1 TTAAAAGAAAA
40018900 TATTTACATA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
32 7 0.17
34 9 0.22
35 2 0.05
36 23 0.56
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.27
Consensus pattern (34 bp):
TTAAAAGAAAAAATATATATATACATAAATAAAT
Found at i:40019898 original size:14 final size:14
Alignment explanation
Indices: 40019878--40019912 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40019868 GCAACAAGAT
*
40019878 AAAAAATTAAAGGA
1 AAAAAATGAAAGGA
*
40019892 GAAAAATGAAAGGA
1 AAAAAATGAAAGGA
40019906 AAAAAAT
1 AAAAAAT
40019913 AGCCATATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.11
Consensus pattern (14 bp):
AAAAAATGAAAGGA
Found at i:40021053 original size:177 final size:177
Alignment explanation
Indices: 40020728--40021154 Score: 477
Period size: 177 Copynumber: 2.4 Consensus size: 177
40020718 GGCTTGGTAT
* ** *
40020728 CTAAAATCTGCTCCCCCGCTACCT-TGGGAAGATAAGATTCGCTGTCTT-TGATCTGCTCCACTG
1 CTAAAATCTGCTCCCCTGCTACCTCT-GGAAGATAAGATTCGCCATCTTCT-ATCTGCTCCACTA
* * * ** * *
40020791 CTATCTCAGGGAGATAAGATCTACAATCTTTAATCAGCTTCCTTGCTACCACAGGAAGATAAAAC
64 CT-GCTTAGGAAGATAAGAAATACAACCTTCAATCAGCTTCCTTGCTACCACAGGAAGATAAAAC
**
40020856 TACAATCTTCAACCTGTTCTCTTACTACCTCTAA-A-AGATAAGGTTGGTGG
128 TACAATCTTCAACCTGTTCTCTTACTA-C-CTAAGAGAGATAAGACTGGTGG
*
40020906 CTAAAATCTGCTCCCCTGCTACCTCTGGAAGATAAGAGTCGCCATCTTCTATCTGCTCCACTACT
1 CTAAAATCTGCTCCCCTGCTACCTCTGGAAGATAAGATTCGCCATCTTCTATCTGCTCCACTACT
* ** * * * *
40020971 GCTTAGGAAGATAATAAATATGACCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTAC
66 GCTTAGGAAGATAAGAAATACAACCTTCAATCAGCTTCCTTGCTACCACAGGAAGATAAAACTAC
* *
40021036 AATCTTCAACTTGTTCTCTTGCTACCTAAGAGAGATAAGACTGGTGG
131 AATCTTCAACCTGTTCTCTTACTACCTAAGAGAGATAAGACTGGTGG
* * * * * * * * *
40021083 CTAAAATCTACTCTCATGTTACCTC-GAGAAGATAAGATTTGCCATCTTCGATCTGCTCTATTAA
1 CTAAAATCTGCTCCCCTGCTACCTCTG-GAAGATAAGATTCGCCATCTTCTATCTGCTCCACTAC
40021147 TGCTTAGG
65 TGCTTAGG
40021155 GAGGCAAAAT
Statistics
Matches: 211, Mismatches: 33, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
175 4 0.02
176 3 0.01
177 146 0.69
178 56 0.27
179 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (177 bp):
CTAAAATCTGCTCCCCTGCTACCTCTGGAAGATAAGATTCGCCATCTTCTATCTGCTCCACTACT
GCTTAGGAAGATAAGAAATACAACCTTCAATCAGCTTCCTTGCTACCACAGGAAGATAAAACTAC
AATCTTCAACCTGTTCTCTTACTACCTAAGAGAGATAAGACTGGTGG
Found at i:40034685 original size:50 final size:50
Alignment explanation
Indices: 40034610--40034717 Score: 180
Period size: 50 Copynumber: 2.2 Consensus size: 50
40034600 TAAATGACCA
*
40034610 TGTATATTTGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
1 TGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
* *
40034660 TGTATATTCGGCCATATAGGTATGTATATATGTGATGTTATATTTGATCT
1 TGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
*
40034710 TGTGTATT
1 TGTATATT
40034718 TGGCTAAATG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.46
Consensus pattern (50 bp):
TGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
Found at i:40038129 original size:32 final size:34
Alignment explanation
Indices: 40038093--40038173 Score: 94
Period size: 38 Copynumber: 2.3 Consensus size: 34
40038083 GATAAGGCCC
*
40038093 TTAAAAGAAACAA-AT-TATATACATAAATAAAT
1 TTAAAAGAAAAAATATATATATACATAAATAAAT
*
40038125 TTAAAAGAAAAAAAAAATATATATATACATAAATAGAT
1 TTAAAAG----AAAAAATATATATATACATAAATAAAT
40038163 TTAAAAGAAAA
1 TTAAAAGAAAA
40038174 TATTTACATA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
32 7 0.17
34 4 0.10
36 5 0.12
37 2 0.05
38 23 0.56
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (34 bp):
TTAAAAGAAAAAATATATATATACATAAATAAAT
Found at i:40038455 original size:22 final size:21
Alignment explanation
Indices: 40038430--40038483 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
40038420 AATTACAAAG
40038430 AAAAAAAACAT-AAGCTGAAATA
1 AAAAAAAAC-TCAA-CTGAAATA
*
40038452 AAAAAAATACTCAATTGAAATA
1 AAAAAAA-ACTCAACTGAAATA
40038474 AAAATAAAAC
1 AAAA-AAAAC
40038484 CAAAGAGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.17
Consensus pattern (21 bp):
AAAAAAAACTCAACTGAAATA
Found at i:40040388 original size:3 final size:3
Alignment explanation
Indices: 40040380--40040408 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40040370 GAAGTTGAAG
40040380 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40040409 TTTGATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40043458 original size:23 final size:27
Alignment explanation
Indices: 40043428--40043490 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
40043418 AATACCCTTA
40043428 CTCATTCTCT-AT-T-TCAATCATC-T
1 CTCATTCTCTCATCTCTCAATCATCAT
40043451 CTCATTCTTCTCATCTCTCAATCATCAT
1 CTCATTC-TCTCATCTCTCAATCATCAT
40043479 -TCATTCTCTCAT
1 CTCATTCTCTCAT
40043491 TCCCTCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
23 7 0.20
24 3 0.09
25 2 0.06
26 7 0.20
27 15 0.43
28 1 0.03
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.46
Consensus pattern (27 bp):
CTCATTCTCTCATCTCTCAATCATCAT
Found at i:40057208 original size:54 final size:54
Alignment explanation
Indices: 40057126--40057234 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
40057116 TTTGAAGCTT
40057126 ACAGTAGCACGTACTCTATTCATCGGGGTAGCACGAAGATGTATTTCGATTTTA
1 ACAGTAGCACGTACTCTATTCATCGGGGTAGCACGAAGATGTATTTCGATTTTA
40057180 ACAGTAGCACGTACTCTATTCATCGGGGTAGCACGAAGATGTATTTCGATTTTA
1 ACAGTAGCACGTACTCTATTCATCGGGGTAGCACGAAGATGTATTTCGATTTTA
40057234 A
1 A
40057235 ACGAATGTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (54 bp):
ACAGTAGCACGTACTCTATTCATCGGGGTAGCACGAAGATGTATTTCGATTTTA
Found at i:40057597 original size:12 final size:12
Alignment explanation
Indices: 40057580--40057612 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
40057570 AGATTGAGAT
40057580 TCGAGATTTACA
1 TCGAGATTTACA
40057592 TCGAGATTTACA
1 TCGAGATTTACA
40057604 TCGAGATTT
1 TCGAGATTT
40057613 TGGAGAAAAC
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:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (12 bp):
TCGAGATTTACA
Found at i:40059868 original size:21 final size:21
Alignment explanation
Indices: 40059844--40059908 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
40059834 TTTTATTTTT
40059844 TGTTCAGCTCTTATGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
** * *
40059865 TGTTCAATTCTTACGAGCTTT
1 TGTTCAGCTCTTATGAGCTTC
*
40059886 TGTTCAGCT-TT-TAAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
40059905 TGTT
1 TGTT
40059909 GGCGTATTCG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 9 0.26
20 2 0.06
21 24 0.69
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (21 bp):
TGTTCAGCTCTTATGAGCTTC
Found at i:40062469 original size:32 final size:32
Alignment explanation
Indices: 40062432--40062495 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
40062422 GACCTTGGAA
*
40062432 ATCAAAATGATGGACAAGGAAATAGAGCCAAT
1 ATCAAAATGACGGACAAGGAAATAGAGCCAAT
*
40062464 ATCAAATTGACGGACAAGGAAATAGAGCCAAT
1 ATCAAAATGACGGACAAGGAAATAGAGCCAAT
40062496 CATATGCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.48, C:0.14, G:0.22, T:0.16
Consensus pattern (32 bp):
ATCAAAATGACGGACAAGGAAATAGAGCCAAT
Found at i:40066100 original size:85 final size:85
Alignment explanation
Indices: 40065944--40066109 Score: 190
Period size: 85 Copynumber: 2.0 Consensus size: 85
40065934 CTACTCGCTT
* *** * * ** * *
40065944 TTTTTTTACATTCAATTGGATACTTGAACTTTCAAAATGTATCAAAAAGGCCCTCAAAATTTTCA
1 TTTTTTTACACTCAATTGGATACTTGAACAACCAAAATGCATAAAAAAGAACCTCAAAACTTTAA
*
40066009 TAAAAAAGCAATTAAGTCCA
66 AAAAAAAGCAATTAAGTCCA
* *
40066029 TTTTTTTGCACTCAATTGGGTACTTGAACAACCAAAATGCATAAAAAAGAACCTC-AAACTTTAA
1 TTTTTTTACACTCAATTGGATACTTGAACAACCAAAATGCATAAAAAAGAACCTCAAAACTTTAA
*
40066093 AAGAAAAATCAATTAAG
66 AA-AAAAAGCAATTAAG
40066110 CCACTGCCCC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
84 8 0.12
85 58 0.88
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (85 bp):
TTTTTTTACACTCAATTGGATACTTGAACAACCAAAATGCATAAAAAAGAACCTCAAAACTTTAA
AAAAAAAGCAATTAAGTCCA
Found at i:40066323 original size:23 final size:22
Alignment explanation
Indices: 40066297--40066340 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40066287 AAATTATAAA
40066297 AATTATGAAATTTTAATAAAAAG
1 AATT-TGAAATTTTAATAAAAAG
**
40066320 AATTTTTAATTTTAATAAAAA
1 AATTTGAAATTTTAATAAAAA
40066341 AGATGATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (22 bp):
AATTTGAAATTTTAATAAAAAG
Found at i:40068306 original size:27 final size:27
Alignment explanation
Indices: 40068274--40068325 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
40068264 TGTTAAATTT
*
40068274 ATTTAAGGA-ATAAAAAGTACATATTAA
1 ATTTAA-GATATAAAAAATACATATTAA
40068301 ATTTAAGATATAAAAAATACATATT
1 ATTTAAGATATAAAAAATACATATT
40068326 TAAAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.33
Consensus pattern (27 bp):
ATTTAAGATATAAAAAATACATATTAA
Found at i:40072211 original size:42 final size:42
Alignment explanation
Indices: 40072094--40072257 Score: 202
Period size: 42 Copynumber: 3.9 Consensus size: 42
40072084 TACCATACCA
* * * * *
40072094 ATGCCATTTCCCAGATATGGTCTTACATGTAATCTCGTGTCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
40072136 ATGCCAATAGCCCAGCTATGATCTTACACGAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * * *
40072179 TTGCCATATCCCAGATATGGTTTTACAAGAAATCTCATATAG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
*
40072221 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCA
40072258 GTAACCCTAA
Statistics
Matches: 102, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 69 0.68
43 33 0.32
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:40078822 original size:46 final size:44
Alignment explanation
Indices: 40078679--40078894 Score: 177
Period size: 46 Copynumber: 4.7 Consensus size: 44
40078669 TGTGTGAGCC
** * *
40078679 AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGA-GAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-C-TACGA-GACGTGCT
* * * *
40078725 ATTGTAAGACCATGTCTAGGACATAGTATCGGC-ATTGAGACGAGTGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CGAGAC--GTGCT
*
40078773 AGTGTAAGACATGTCTGGGACATGCTTCGGGCT-CGAGACGTAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCTACGAGACGT--GCT
* * *
40078819 AGTGTAAGACATGTCTGGGACATGCATCGGCTATGAGATGTGTT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGACGTGCT
*
40078863 AGTGTAAGACCATGTCTAGGACATGGCATCGG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG
40078895 TACAGATATG
Statistics
Matches: 141, Mismatches: 16, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
44 13 0.09
45 20 0.14
46 61 0.43
47 30 0.21
48 17 0.12
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGACGTGCT
Found at i:40083632 original size:39 final size:40
Alignment explanation
Indices: 40083587--40083697 Score: 98
Period size: 40 Copynumber: 2.8 Consensus size: 40
40083577 CGGGGTTTAG
* * *
40083587 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
40083626 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * *
40083666 CCGGATATAGTCGCTAGCACAAATGCCTTCGG
1 CCGGATATAACCACTAGCATAAAGGCCTTCGG
40083698 ATCTTAGTCC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
39 15 0.25
40 45 0.75
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:40083657 original size:40 final size:40
Alignment explanation
Indices: 40083610--40083753 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
40083600 CTCGCACAAG
* * * * *
40083610 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
40083650 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
40083690 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
40083731 GCCTTC-GGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
40083754 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
39 3 0.03
40 71 0.77
41 18 0.20
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:40322327 original size:79 final size:82
Alignment explanation
Indices: 40322216--40322400 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
40322206 GCTACTCGTT
* *
40322216 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
40322279 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
40322296 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
40322359 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
40322376 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40322401 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:40322400 original size:40 final size:40
Alignment explanation
Indices: 40322197--40322400 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
40322187 CGGAATTTAA
** *
40322197 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40322237 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
40322277 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40322316 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
40322356 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40322396 CCGGA
1 CCGGA
40322401 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40328162 original size:32 final size:34
Alignment explanation
Indices: 40328126--40328218 Score: 109
Period size: 34 Copynumber: 2.8 Consensus size: 34
40328116 ACATATATAT
*
40328126 ATACACCTTGAG-AT-AATATATATATCATACCA
1 ATACACCATGAGAATAAATATATATATCATACCA
* *
40328158 ATACATCATGGGAATAAATATATATATCATACCA
1 ATACACCATGAGAATAAATATATATATCATACCA
* * * *
40328192 ACACATCATGTGCATAAATATATATAT
1 ATACACCATGAGAATAAATATATATAT
40328219 GTGCAAGTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 9 0.17
33 2 0.04
34 42 0.79
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (34 bp):
ATACACCATGAGAATAAATATATATATCATACCA
Found at i:40328178 original size:34 final size:34
Alignment explanation
Indices: 40328140--40328218 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 34
40328130 ACCTTGAGAT
*
40328140 AATATATATATCATACCAATACATCATGGGAATA
1 AATATATATATCATACCAACACATCATGGGAATA
* *
40328174 AATATATATATCATACCAACACATCATGTGCATA
1 AATATATATATCATACCAACACATCATGGGAATA
40328208 AATATATATAT
1 AATATATATAT
40328219 GTGCAAGTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (34 bp):
AATATATATATCATACCAACACATCATGGGAATA
Found at i:40330693 original size:27 final size:27
Alignment explanation
Indices: 40330663--40330860 Score: 261
Period size: 27 Copynumber: 7.3 Consensus size: 27
40330653 TATTGAAATG
* *
40330663 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
*
40330690 CCCTCGATTTATAGAATTACCGTTTCA
1 CCCTCGATTTATAGAATTACCGTTTTA
* * *
40330717 CCCTCGATTTACAAAATTATCGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
*
40330744 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
*
40330771 CCCTCGATTTATAGAATTACTGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* * *
40330798 CCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* * * *
40330825 CCCTCAATTTAAAAAATTATCGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
40330852 CCCTCGATT
1 CCCTCGATT
40330861 GTGAAATTAC
Statistics
Matches: 149, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 149 1.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCGTTTTA
Found at i:40330778 original size:81 final size:81
Alignment explanation
Indices: 40330663--40330860 Score: 306
Period size: 81 Copynumber: 2.4 Consensus size: 81
40330653 TATTGAAATG
*
40330663 CCCTCGATTTGTAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTCACCCTCGATTTA
1 CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTCACCCTCGATTTA
* *
40330728 CAAAATTATCGTTTTA
66 CAAAATTACCATTTTA
* *
40330744 CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTCGATTTA
1 CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTCACCCTCGATTTA
40330809 CAAAATTACCATTTTA
66 CAAAATTACCATTTTA
* * * * *
40330825 CCCTCAATTTAAAAAATTATCGTTTTACCCTCGATT
1 CCCTCGATTTATAGAATTACCATTTTACCCTCGATT
40330861 GTGAAATTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 107 1.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (81 bp):
CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTCACCCTCGATTTA
CAAAATTACCATTTTA
Found at i:40330907 original size:53 final size:52
Alignment explanation
Indices: 40330850--40331041 Score: 172
Period size: 54 Copynumber: 3.6 Consensus size: 52
40330840 ATTATCGTTT
* * ** *
40330850 TACCCTCGATTGTGAAATTACTGAAATACCCTTA-TAGGATAGAATTACCAAAA
1 TACCCTAGATTGTAAAATTACCAAAATACCC-TAGTAGG-TAAAATTACCAAAA
* **
40330903 TACCCCTAGTTTGTAAAATTACCAAAATACCCTAGTTTGTAAAATTACCAAAA
1 TA-CCCTAGATTGTAAAATTACCAAAATACCCTAGTAGGTAAAATTACCAAAA
* * * ** * *
40330956 TACCCTAGTTTGTAAAATTTCCAAAATACCACTGGTTTGTGAAATTACCGAAA
1 TACCCTAGATTGTAAAATTACCAAAATACC-CTAGTAGGTAAAATTACCAAAA
*
40331009 CACCCTCA-ATTTGTAAAATTACCAAAATACCCT
1 TACCCT-AGA-TTGTAAAATTACCAAAATACCCT
40331042 TGATTTACAA
Statistics
Matches: 119, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
52 27 0.23
53 45 0.38
54 47 0.39
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (52 bp):
TACCCTAGATTGTAAAATTACCAAAATACCCTAGTAGGTAAAATTACCAAAA
Found at i:40330942 original size:26 final size:26
Alignment explanation
Indices: 40330892--40331068 Score: 221
Period size: 27 Copynumber: 6.7 Consensus size: 26
40330882 TATAGGATAG
40330892 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATA-CCCTAGTTTGTAA
40330919 AATTACCAAAATACCCTAGTTTGTAA
1 AATTACCAAAATACCCTAGTTTGTAA
40330945 AATTACCAAAATACCCTAGTTTGTAA
1 AATTACCAAAATACCCTAGTTTGTAA
* * *
40330971 AATTTCCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACC-CTAGTTTGTAA
* * *
40330998 AATTACCGAAACACCCTCAATTTGTAA
1 AATTACCAAAATACCCT-AGTTTGTAA
* **
40331025 AATTACCAAAATACCCTTGATTTACAA
1 AATTACCAAAATACCCTAG-TTTGTAA
40331052 AATTA-CAGAAATACCCT
1 AATTACCA-AAATACCCT
40331069 TGACTTTCTA
Statistics
Matches: 131, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
26 57 0.44
27 74 0.56
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.29
Consensus pattern (26 bp):
AATTACCAAAATACCCTAGTTTGTAA
Found at i:40331055 original size:54 final size:53
Alignment explanation
Indices: 40330892--40331124 Score: 202
Period size: 54 Copynumber: 4.3 Consensus size: 53
40330882 TATAGGATAG
* * * **
40330892 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCC-TAGTTTGTAA
1 AATTACCGAAATA-CCCTAATTTGTAAAATTACCAAAATACCCTTGGTTTACAA
* * * ***
40330945 AATTACCAAAATACCCTAGTTTGTAAAATTTCCAAAATACCAC-TGGTTTGTGA
1 AATTACCGAAATACCCTAATTTGTAAAATTACCAAAATACC-CTTGGTTTACAA
* *
40330998 AATTACCGAAACACCCTCAATTTGTAAAATTACCAAAATACCCTTGATTTACAA
1 AATTACCGAAATACCCT-AATTTGTAAAATTACCAAAATACCCTTGGTTTACAA
* * * * *
40331052 AATTACAGAAATACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGGTTTACAA
1 AATTACCGAAATACCC-T-AATTTGT-AAAATTACCA-AAATACCCTTGGTTTACAA
**
40331108 AATTATTGAAATACCCT
1 AATTACCGAAATACCCT
40331125 TGGTTTTTAG
Statistics
Matches: 153, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
52 27 0.18
53 38 0.25
54 42 0.27
55 8 0.05
56 38 0.25
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (53 bp):
AATTACCGAAATACCCTAATTTGTAAAATTACCAAAATACCCTTGGTTTACAA
Found at i:40331091 original size:29 final size:27
Alignment explanation
Indices: 40331033--40331126 Score: 118
Period size: 27 Copynumber: 3.4 Consensus size: 27
40331023 AAAATTACCA
*
40331033 AAATACCCTTGATTTACAAAATTACAG
1 AAATACCCTTGATTTACAAAATTATAG
40331060 AAATACCCTTGACTTT-CTAAAAATTATAG
1 AAATACCCTTGA-TTTAC--AAAATTATAG
* * *
40331089 AAATACCATTGGTTTACAAAATTATTG
1 AAATACCCTTGATTTACAAAATTATAG
40331116 AAATACCCTTG
1 AAATACCCTTG
40331127 GTTTTTAGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
27 32 0.55
28 6 0.10
29 20 0.34
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATACCCTTGATTTACAAAATTATAG
Found at i:40332150 original size:25 final size:26
Alignment explanation
Indices: 40332050--40332223 Score: 264
Period size: 26 Copynumber: 6.8 Consensus size: 26
40332040 GAGGAAGTGC
*
40332050 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
40332076 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
40332102 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
40332128 AAAAGGGCTTATG-CCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
**
40332153 AAAAGGGCTTATGCCCCAGTTTATTA
1 AAAAGGGCTTATGCCCCAGTTTATCG
* *
40332179 AAAAGGGCTT-TGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTATCG
40332204 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
40332224 ATTAAAGAGG
Statistics
Matches: 138, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
25 57 0.41
26 81 0.59
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATCG
Found at i:40332166 original size:51 final size:52
Alignment explanation
Indices: 40332050--40332223 Score: 300
Period size: 51 Copynumber: 3.4 Consensus size: 52
40332040 GAGGAAGTGC
40332050 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
40332102 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATG-CCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
* *
40332153 AAAAGGGCTTATGCCCCAGTTTATTAAAAAGGGCTT-TGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
40332204 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
40332224 ATTAAAGAGG
Statistics
Matches: 117, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
50 12 0.10
51 66 0.56
52 39 0.33
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
Found at i:40332433 original size:42 final size:42
Alignment explanation
Indices: 40332368--40332459 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
40332358 TAGTCTCCCT
* * ** *
40332368 AAATAGGCTTGCATACATTCATTGTTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
40332410 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
40332452 AAATGGGC
1 AAATGGGC
40332460 CTAAGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:40332518 original size:31 final size:31
Alignment explanation
Indices: 40332483--40332557 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
40332473 CGTTTACAGT
40332483 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
* *
40332514 AAAGGATTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
40332545 AAAGGCTTCGGCC
1 AAAGGCTTCGGCC
40332558 TAGTAACCGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATGATATGATTTATGA
Found at i:40333428 original size:21 final size:22
Alignment explanation
Indices: 40333398--40333438 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
40333388 ATCATTTTAC
* *
40333398 ATATATAACCTTTAT-TAATTA
1 ATATAAAACCATTATATAATTA
40333419 ATATAAAACCATTATATAAT
1 ATATAAAACCATTATATAAT
40333439 AAGGTCATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATAAAACCATTATATAATTA
Found at i:40340461 original size:31 final size:31
Alignment explanation
Indices: 40340423--40340484 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
40340413 TCAAGAAAAC
40340423 AACTTGACCAGAACATAAGTAAATATGAAAT
1 AACTTGACCAGAACATAAGTAAATATGAAAT
40340454 AACTTGACCAGAACATAAGTAAATATGAAAT
1 AACTTGACCAGAACATAAGTAAATATGAAAT
40340485 TATGATTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.23
Consensus pattern (31 bp):
AACTTGACCAGAACATAAGTAAATATGAAAT
Found at i:40348116 original size:79 final size:81
Alignment explanation
Indices: 40347980--40348164 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
40347970 TTGAATGATG
*
40347980 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
40348044 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
40348059 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
40348121 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
40348139 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40348165 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:40348178 original size:40 final size:40
Alignment explanation
Indices: 40347981--40348164 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
40347971 TGAATGATGT
* * * *
40347981 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
40348021 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
40348061 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
40348099 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
40348140 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
40348165 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:40348186 original size:79 final size:79
Alignment explanation
Indices: 40348033--40348197 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
40348023 GGACTAAGAT
* **
40348033 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
40348098 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
40348112 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
40348175 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
40348191 CCGAAGG
1 CCGAAGG
40348198 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:40356073 original size:79 final size:81
Alignment explanation
Indices: 40355937--40356121 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
40355927 TTGAATGATG
*
40355937 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
40356001 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
40356016 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
40356078 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
40356096 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40356122 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:40356135 original size:40 final size:40
Alignment explanation
Indices: 40355938--40356121 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
40355928 TGAATGATGT
* * * *
40355938 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
40355978 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
40356018 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
40356056 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
40356097 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
40356122 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:40356143 original size:79 final size:79
Alignment explanation
Indices: 40355990--40356154 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
40355980 GGACTAAGAT
* **
40355990 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
40356055 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
40356069 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
40356132 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
40356148 CCGAAGG
1 CCGAAGG
40356155 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:40358071 original size:54 final size:54
Alignment explanation
Indices: 40358007--40358116 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
40357997 CATACATGTT
*
40358007 CATGCATACATCTCAATACATCCAATCATATTTATAGATAATTTGCATAGAAAC
1 CATGCATACATCTCAATACATACAATCATATTTATAGATAATTTGCATAGAAAC
*
40358061 CATGCATACATCTCAATACATACAATCATATTTATAGATAATTTGCATAGCAAC
1 CATGCATACATCTCAATACATACAATCATATTTATAGATAATTTGCATAGAAAC
40358115 CA
1 CA
40358117 CATACTCATT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (54 bp):
CATGCATACATCTCAATACATACAATCATATTTATAGATAATTTGCATAGAAAC
Found at i:40366586 original size:16 final size:15
Alignment explanation
Indices: 40366547--40366594 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
40366537 CTTTTGCAAG
*
40366547 TTTACATTTTTACCC
1 TTTACATTTTAACCC
* *
40366562 TTAACATTTTAACTTC
1 TTTACATTTTAAC-CC
*
40366578 TTTACATTTTAATCC
1 TTTACATTTTAACCC
40366593 TT
1 TT
40366595 AAGCTCGTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTACATTTTAACCC
Found at i:40370448 original size:29 final size:28
Alignment explanation
Indices: 40370415--40370570 Score: 170
Period size: 29 Copynumber: 5.4 Consensus size: 28
40370405 GGGTTACAAA
40370415 GCCTTTGTGGCTATCTCAGTTAAAAGAAT
1 GCCTTTGTGGCTATCTCA-TTAAAAGAAT
* * * *
40370444 GCCTTTGTGGCGATCTCTATTATAGGGAT
1 GCCTTTGTGGCTATCTC-ATTAAAAGAAT
*
40370473 GCATTTGTGGCTATCTCAGTTAAAAGAAT
1 GCCTTTGTGGCTATCTCA-TTAAAAGAAT
*
40370502 GCCTTTGTGGTTATCTCTATTAAAA-AGAT
1 GCCTTTGTGGCTATCTC-ATTAAAAGA-AT
* *
40370531 GCCTTTGTGGCTATCTCCATTAAAAGGAC
1 GCCTTTGTGGCTATCT-CATTAAAAGAAT
*
40370560 GCCTTCGTGGC
1 GCCTTTGTGGC
40370571 CATTTTTAGA
Statistics
Matches: 106, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
28 2 0.02
29 101 0.95
30 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (28 bp):
GCCTTTGTGGCTATCTCATTAAAAGAAT
Found at i:40370488 original size:58 final size:58
Alignment explanation
Indices: 40370418--40370570 Score: 209
Period size: 58 Copynumber: 2.6 Consensus size: 58
40370408 TTACAAAGCC
* **
40370418 TTTGTGGCTATCTCAGTTAAAAGAATGCCTTTGTGGCGATCTCTATTATAGGGATGCA
1 TTTGTGGCTATCTCAGTTAAAAGAATGCCTTTGTGGCGATCTCTATTAAAAAGATGCA
** *
40370476 TTTGTGGCTATCTCAGTTAAAAGAATGCCTTTGTGGTTATCTCTATTAAAAAGATGCC
1 TTTGTGGCTATCTCAGTTAAAAGAATGCCTTTGTGGCGATCTCTATTAAAAAGATGCA
* * *
40370534 TTTGTGGCTATCTCCA-TTAAAAGGACGCCTTCGTGGC
1 TTTGTGGCTATCT-CAGTTAAAAGAATGCCTTTGTGGC
40370571 CATTTTTAGA
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
58 82 0.98
59 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (58 bp):
TTTGTGGCTATCTCAGTTAAAAGAATGCCTTTGTGGCGATCTCTATTAAAAAGATGCA
Found at i:40372773 original size:34 final size:34
Alignment explanation
Indices: 40372727--40372791 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
40372717 AGATGCAGTT
* *
40372727 TGGGCCTAAGCCCGTTACAGTATCAGTATCAATA
1 TGGGCCTAAGCCCATTACAGTAACAGTATCAATA
*
40372761 TGGGCCTTAGCCCATTACAGTAACAGTATCA
1 TGGGCCTAAGCCCATTACAGTAACAGTATCA
40372792 GTGCAGTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (34 bp):
TGGGCCTAAGCCCATTACAGTAACAGTATCAATA
Found at i:40373227 original size:27 final size:26
Alignment explanation
Indices: 40373197--40373368 Score: 119
Period size: 27 Copynumber: 6.4 Consensus size: 26
40373187 AATCAATCGT
* * *
40373197 TTTTACCTTATAAGGGTATTATAGTTA
1 TTTTACCCTA-AAGGGTATTACAGTCA
*
40373224 TTTTACCCTACAGAGGTATTACAGTCA
1 TTTTACCCTAAAG-GGTATTACAGTCA
*
40373251 TTTTACCCTACAGGGGTATTACAGTCA
1 TTTTACCCTA-AAGGGTATTACAGTCA
* * * *
40373278 TTTTACCGTACAGGGGTATTTCGGTCA
1 TTTTACCCTA-AAGGGTATTACAGTCA
* * * ***
40373305 TTTTACCATATGAGGATATTTTTGTCA
1 TTTTACCCTA-AAGGGTATTACAGTCA
** * *
40373332 TTTTACCCTATGGGGATATTTCGGTCA
1 TTTTACCCTAAAGGG-TATTACAGTCA
40373359 TTTTACCCTA
1 TTTTACCCTA
40373369 TGGGGGTATT
Statistics
Matches: 120, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
26 4 0.03
27 115 0.96
28 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (26 bp):
TTTTACCCTAAAGGGTATTACAGTCA
Found at i:40373309 original size:81 final size:80
Alignment explanation
Indices: 40373223--40373405 Score: 197
Period size: 81 Copynumber: 2.2 Consensus size: 80
40373213 TATTATAGTT
*
40373223 ATTTTACCCTACAGAGGTATTACAGTCATTTTACCCTACAGGGG-TATTACAGTCATTTTACCGT
1 ATTTTACCCTA-AGAGGTATTACAGTCATTTTACCCTA-AGGGGATATTACAGTCATTTTACCCT
*
40373287 ACAGGGGTATTTCGGTC
64 ACAGGGGTATTTCGATC
* * *** * * *
40373304 ATTTTACCATATGAGGATATTTTTGTCATTTTACCCTATGGGGATATTTCGGTCATTTTACCCTA
1 ATTTTACCCTAAGAGG-TATTACAGTCATTTTACCCTAAGGGGATATTACAGTCATTTTACCCTA
**
40373369 TGGGGGTATTTCGATC
65 CAGGGGTATTTCGATC
* *
40373385 ATTTTATCCTATAGGGGTATT
1 ATTTTACCCTA-AGAGGTATT
40373406 TTGGTCACCA
Statistics
Matches: 83, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
80 8 0.10
81 72 0.87
82 3 0.04
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (80 bp):
ATTTTACCCTAAGAGGTATTACAGTCATTTTACCCTAAGGGGATATTACAGTCATTTTACCCTAC
AGGGGTATTTCGATC
Found at i:40373369 original size:27 final size:26
Alignment explanation
Indices: 40373223--40373412 Score: 173
Period size: 27 Copynumber: 7.0 Consensus size: 26
40373213 TATTATAGTT
* * * *
40373223 ATTTTACCCTACAGAGGTATTACAGTC
1 ATTTTACCCTA-TGGGGTATTTCGGTC
* * *
40373250 ATTTTACCCTACAGGGGTATTACAGTC
1 ATTTTACCCTA-TGGGGTATTTCGGTC
* *
40373277 ATTTTACCGTACAGGGGTATTTCGGTC
1 ATTTTACCCTA-TGGGGTATTTCGGTC
* * **
40373304 ATTTTACCATATGAGGATATTTTTGTC
1 ATTTTACCCTATG-GGGTATTTCGGTC
40373331 ATTTTACCCTATGGGGATATTTCGGTC
1 ATTTTACCCTATGGGG-TATTTCGGTC
*
40373358 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
* *
40373385 ATTTTATCCTATAGGGGTATTTTGGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
40373412 A
1 A
40373413 CCATTTCGAC
Statistics
Matches: 142, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
26 3 0.02
27 135 0.95
28 4 0.03
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (26 bp):
ATTTTACCCTATGGGGTATTTCGGTC
Found at i:40373406 original size:81 final size:81
Alignment explanation
Indices: 40373247--40373412 Score: 203
Period size: 81 Copynumber: 2.0 Consensus size: 81
40373237 AGGTATTACA
* *
40373247 GTCATTTTACCCTACAGGGGTATTACAGTCATTTTACCGTACAGGGGTATTTCGGTCATTTTACC
1 GTCATTTTACCCTACAGGGGTATTACAGTCATTTTACCCTACAGGGGTATTTCGATCATTTTACC
*
40373312 ATATGAGGATATTTTT
66 ATATGAGGATATTTTG
* * * **
40373328 GTCATTTTACCCTA-TGGGGATATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTAT
1 GTCATTTTACCCTACAGGGG-TATTACAGTCATTTTACCCTACAGGGGTATTTCGATCATTTTA-
*
40373392 CC-TAT-AGGGGTATTTTG
64 CCATATGA-GGATATTTTG
40373409 GTCA
1 GTCA
40373413 CCATTTCGAC
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
80 5 0.07
81 66 0.90
82 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (81 bp):
GTCATTTTACCCTACAGGGGTATTACAGTCATTTTACCCTACAGGGGTATTTCGATCATTTTACC
ATATGAGGATATTTTG
Found at i:40386826 original size:43 final size:43
Alignment explanation
Indices: 40386669--40386827 Score: 139
Period size: 43 Copynumber: 3.7 Consensus size: 43
40386659 TATGTGTTTT
* * * *
40386669 CGTGTAAGACCACCTTTGGAACGTTGGCATCGACT-TATGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGA-TTA
* * * *
40386713 CGTGTAAGACCATGTCTGGGACATCGGCATCG-TATTTGATTT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
*
40386755 CGTGTAAGACC-CTGT-TAGGGACAG-TGGCATCGATATTTGGTTA
1 CGTGTAAGACCAC-GTCT-GGGAC-GTTGGCATCGATATTTGATTA
* *
40386798 CATGTAAGACCACGTCTGAGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
40386828 TGTACGAGCT
Statistics
Matches: 92, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
41 1 0.01
42 29 0.32
43 34 0.37
44 28 0.30
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
Found at i:40392163 original size:46 final size:44
Alignment explanation
Indices: 40392113--40392284 Score: 186
Period size: 46 Copynumber: 3.8 Consensus size: 44
40392103 TGGTTGAGCA
40392113 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAA-G
*** * *
40392159 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GGAAG
*
40392206 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAA-G
*
40392252 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTT
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTT
40392285 CTGGGCGGGT
Statistics
Matches: 107, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 3 0.03
46 63 0.59
47 32 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (44 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAG
Found at i:40392269 original size:93 final size:93
Alignment explanation
Indices: 40392110--40392280 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
40392100 GGATGGTTGA
*
40392110 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
40392175 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * *
40392203 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
40392267 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
40392281 ACTTCTGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:40395252 original size:15 final size:15
Alignment explanation
Indices: 40395214--40395263 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
40395204 GTATCTTGGG
*
40395214 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
40395229 -TTCTCTTATTCTGGA
1 TTTCT-TTATTCTGGA
*
40395244 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
40395258 TTTCTT
1 TTTCTT
40395264 GTTATCTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 12 0.39
15 15 0.48
16 4 0.13
ACGTcount: A:0.10, C:0.18, G:0.12, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:40397694 original size:46 final size:45
Alignment explanation
Indices: 40397644--40397819 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
40397634 TGGTTGAGCA
40397644 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
40397690 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
40397737 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
40397783 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40397820 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:40397800 original size:93 final size:93
Alignment explanation
Indices: 40397641--40397811 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
40397631 GGATGGTTGA
* *
40397641 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40397706 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
40397734 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40397799 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
40397812 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Done.