Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 134 of 143
Found at i:39736512 original size:15 final size:15
Alignment explanation
Indices: 39736406--39736537 Score: 63
Period size: 15 Copynumber: 8.8 Consensus size: 15
39736396 CCTGCCTTCA
39736406 TGTAAATGCAGCTCG
1 TGTAAATGCAGCTCG
* * *
39736421 TGTGATTGCA-CTTCA
1 TGTAAATGCAGC-TCG
* *
39736436 TGTAAATGCAACTTG
1 TGTAAATGCAGCTCG
* * *
39736451 TGTGATTGCA-CTTCA
1 TGTAAATGCAGC-TCG
39736466 TGTAAATGCAGCTCG
1 TGTAAATGCAGCTCG
** * *
39736481 TGCGACTGCA-ATCCG
1 TGTAAATGCAGCT-CG
39736496 TGTAAATGCAGCTCG
1 TGTAAATGCAGCTCG
* * * * *
39736511 TGTGACTGTAGTTCA
1 TGTAAATGCAGCTCG
39736526 TGTAAATGCAGC
1 TGTAAATGCAGC
39736538 AGTTTATGTG
Statistics
Matches: 80, Mismatches: 31, Indels: 12
0.65 0.25 0.10
Matches are distributed among these distances:
14 3 0.04
15 74 0.93
16 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (15 bp):
TGTAAATGCAGCTCG
Found at i:39736631 original size:15 final size:15
Alignment explanation
Indices: 39736599--39736725 Score: 101
Period size: 15 Copynumber: 8.3 Consensus size: 15
39736589 TGTAAATGCA
* *
39736599 GCAGTTTATGTGACT
1 GCAGTTCATGTAACT
*
39736614 GCAGTTCATGTAATT
1 GCAGTTCATGTAACT
* *
39736629 GCAGCTCATGCAACT
1 GCAGTTCATGTAACT
*
39736644 GCAGTTCATGTAAATGCA
1 GCAGTTCATGT-AA--CT
* **
39736662 GCAGTTTATGCGACT
1 GCAGTTCATGTAACT
* *
39736677 GCAGTTCTTGTAAAT
1 GCAGTTCATGTAACT
* *
39736692 GCAGCTCATGCAACT
1 GCAGTTCATGTAACT
*
39736707 GCAGTTCATGTAAAT
1 GCAGTTCATGTAACT
39736722 GCAG
1 GCAG
39736726 CAGTTTATGC
Statistics
Matches: 84, Mismatches: 25, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
15 71 0.85
16 2 0.02
17 1 0.01
18 10 0.12
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (15 bp):
GCAGTTCATGTAACT
Found at i:39736780 original size:30 final size:30
Alignment explanation
Indices: 39736369--39736772 Score: 351
Period size: 30 Copynumber: 13.1 Consensus size: 30
39736359 CATCGGAACA
* *
39736369 CAGTTCGTGCAAATGCAGCTCGTGTGACCTG
1 CAGTTCATGTAAATGCAGCTCGTGTGA-CTG
* *
39736400 C-CTTCATGTAAATGCAGCTCGTGTGATTG
1 CAGTTCATGTAAATGCAGCTCGTGTGACTG
* * * *
39736429 CACTTCATGTAAATGCAACTTGTGTGATTG
1 CAGTTCATGTAAATGCAGCTCGTGTGACTG
* *
39736459 CACTTCATGTAAATGCAGCTCGTGCGACTG
1 CAGTTCATGTAAATGCAGCTCGTGTGACTG
* * *
39736489 CAATCCGTGTAAATGCAGCTCGTGTGACTG
1 CAGTTCATGTAAATGCAGCTCGTGTGACTG
* **
39736519 TAGTTCATGTAAATGCAGCAGTTTATGTGACTG
1 CAGTTCATGTAAATGCAGC---TCGTGTGACTG
* * *
39736552 CAATCCGTGTAAATGCAGCTCGTGTGACTG
1 CAGTTCATGTAAATGCAGCTCGTGTGACTG
* **
39736582 TAGTTCATGTAAATGCAGCAGTTTATGTGACTG
1 CAGTTCATGTAAATGCAGC---TCGTGTGACTG
* * **
39736615 CAGTTCATGTAATTGCAGCTCATGCAACTG
1 CAGTTCATGTAAATGCAGCTCGTGTGACTG
** *
39736645 CAGTTCATGTAAATGCAGCAGTTTATGCGACTG
1 CAGTTCATGTAAATGCAGC---TCGTGTGACTG
* * **
39736678 CAGTTCTTGTAAATGCAGCTCATGCAACTG
1 CAGTTCATGTAAATGCAGCTCGTGTGACTG
** *
39736708 CAGTTCATGTAAATGCAGCAGTTTATGCGACTG
1 CAGTTCATGTAAATGCAGC---TCGTGTGACTG
*
39736741 CAGTTCATGTAAATGCTGCTCGTGTGACTG
1 CAGTTCATGTAAATGCAGCTCGTGTGACTG
39736771 CA
1 CA
39736773 AATCATGTTT
Statistics
Matches: 310, Mismatches: 50, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
29 3 0.01
30 202 0.65
31 1 0.00
33 104 0.34
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (30 bp):
CAGTTCATGTAAATGCAGCTCGTGTGACTG
Found at i:39736780 original size:63 final size:63
Alignment explanation
Indices: 39736369--39736772 Score: 453
Period size: 63 Copynumber: 6.5 Consensus size: 63
39736359 CATCGGAACA
* * * ** * *
39736369 CAGTTCGTGCAAATGCAGCTCGTGTGACCTGC-CTTCATGTAAATGCAGC---TCGTGTGATTG
1 CAGTTCATGTAAATGCAGCTCGTGTGA-CTGCAGTTCATGTAAATGCAGCAGTTTATGCGACTG
* * * * * **
39736429 CACTTCATGTAAATGCAACTTGTGTGATTGCACTTCATGTAAATGCAGC---TCGTGCGACTG
1 CAGTTCATGTAAATGCAGCTCGTGTGACTGCAGTTCATGTAAATGCAGCAGTTTATGCGACTG
* * * * *
39736489 CAATCCGTGTAAATGCAGCTCGTGTGACTGTAGTTCATGTAAATGCAGCAGTTTATGTGACTG
1 CAGTTCATGTAAATGCAGCTCGTGTGACTGCAGTTCATGTAAATGCAGCAGTTTATGCGACTG
* * * * *
39736552 CAATCCGTGTAAATGCAGCTCGTGTGACTGTAGTTCATGTAAATGCAGCAGTTTATGTGACTG
1 CAGTTCATGTAAATGCAGCTCGTGTGACTGCAGTTCATGTAAATGCAGCAGTTTATGCGACTG
* * **
39736615 CAGTTCATGTAATTGCAGCTCATGCAACTGCAGTTCATGTAAATGCAGCAGTTTATGCGACTG
1 CAGTTCATGTAAATGCAGCTCGTGTGACTGCAGTTCATGTAAATGCAGCAGTTTATGCGACTG
* * **
39736678 CAGTTCTTGTAAATGCAGCTCATGCAACTGCAGTTCATGTAAATGCAGCAGTTTATGCGACTG
1 CAGTTCATGTAAATGCAGCTCGTGTGACTGCAGTTCATGTAAATGCAGCAGTTTATGCGACTG
*
39736741 CAGTTCATGTAAATGCTGCTCGTGTGACTGCA
1 CAGTTCATGTAAATGCAGCTCGTGTGACTGCA
39736773 AATCATGTTT
Statistics
Matches: 305, Mismatches: 35, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
59 3 0.01
60 89 0.29
63 213 0.70
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (63 bp):
CAGTTCATGTAAATGCAGCTCGTGTGACTGCAGTTCATGTAAATGCAGCAGTTTATGCGACTG
Found at i:39742245 original size:22 final size:22
Alignment explanation
Indices: 39742220--39742262 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39742210 TGTATTTCAC
39742220 AATTT-AAATATAAAATTAAATA
1 AATTTAAAAT-TAAAATTAAATA
*
39742242 AATTTAAAATTAACATTAAAT
1 AATTTAAAATTAAAATTAAAT
39742263 TTATTCTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AATTTAAAATTAAAATTAAATA
Found at i:39742890 original size:18 final size:18
Alignment explanation
Indices: 39742836--39742890 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
39742826 ATTATTTTTT
* *
39742836 AAAATTTAAAAAATTCAA
1 AAAATTTAAATAATTAAA
* *
39742854 AAAATATAAATTATATAAA
1 AAAATTTAAATAAT-TAAA
*
39742873 AAAATTTAAATCATTAAA
1 AAAATTTAAATAATTAAA
39742891 TTATTAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATTTAAATAATTAAA
Found at i:39746881 original size:17 final size:18
Alignment explanation
Indices: 39746859--39746892 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
39746849 ATAAAAACAA
39746859 AAAATAAAT-TATTTTAT
1 AAAATAAATATATTTTAT
39746876 AAAATAAATATATTTTA
1 AAAATAAATATATTTTA
39746893 AATCATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATAAATATATTTTAT
Found at i:39755449 original size:5 final size:5
Alignment explanation
Indices: 39755439--39755465 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
39755429 GCCTAAATCT
39755439 AACCC AACCC AACCC AACCC AACCC AA
1 AACCC AACCC AACCC AACCC AACCC AA
39755466 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCC
Found at i:39765780 original size:51 final size:51
Alignment explanation
Indices: 39765719--39765842 Score: 135
Period size: 51 Copynumber: 2.4 Consensus size: 51
39765709 CTGTGTAAAT
* * * * *
39765719 ATTGAGAGAATGTGT-AAATATTACATGTTAAATTTGTTAAAT-AAAGACCAA
1 ATTGATAGAATATGTAAAAT-TTACAGGCTAAATTTATTAAATCAAA-ACCAA
* * *
39765770 ATTGATAGAATATGTAAAATTTTCGGGCTAAATTTATTAAATCAAAATCAA
1 ATTGATAGAATATGTAAAATTTACAGGCTAAATTTATTAAATCAAAACCAA
*
39765821 ATTGATAGAATATATAAAATTT
1 ATTGATAGAATATGTAAAATTT
39765843 GAGAGATAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
51 55 0.89
52 7 0.11
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (51 bp):
ATTGATAGAATATGTAAAATTTACAGGCTAAATTTATTAAATCAAAACCAA
Found at i:39765853 original size:51 final size:51
Alignment explanation
Indices: 39765747--39765853 Score: 135
Period size: 51 Copynumber: 2.1 Consensus size: 51
39765737 TATTACATGT
* * ** * *
39765747 TAAATTTGTTAAATAAAGACCAAATTGATAGAATATGTAAAATTTTCGGGC
1 TAAATTTATTAAATAAAGACCAAATTGATAGAATATATAAAATTTGAGAGA
*
39765798 TAAATTTATTAAATCAAA-ATCAAATTGATAGAATATATAAAATTTGAGAGA
1 TAAATTTATTAAAT-AAAGACCAAATTGATAGAATATATAAAATTTGAGAGA
39765849 TAAAT
1 TAAAT
39765854 ATTTCGGTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 45 0.94
52 3 0.06
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.34
Consensus pattern (51 bp):
TAAATTTATTAAATAAAGACCAAATTGATAGAATATATAAAATTTGAGAGA
Found at i:39766830 original size:3 final size:3
Alignment explanation
Indices: 39766822--39766851 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
39766812 TGATAGAAAT
*
39766822 TAA TAA TAA TAA TAA TAA TAA TAA TCA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39766852 GAAGAAGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39767216 original size:30 final size:31
Alignment explanation
Indices: 39767180--39767240 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
39767170 TATAGAATGA
*
39767180 TCATTAAATTATTTAAA-TTTTTTATTTAAG
1 TCATTAAATTAATTAAAGTTTTTTATTTAAG
39767210 TCATTAAATTAATTAAATGTTTTTTATTTAA
1 TCATTAAATTAATTAAA-GTTTTTTATTTAA
39767241 TTCACTGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 16 0.57
32 12 0.43
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (31 bp):
TCATTAAATTAATTAAAGTTTTTTATTTAAG
Found at i:39767979 original size:15 final size:16
Alignment explanation
Indices: 39767950--39767979 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39767940 TCATATAATA
39767950 TCGATTGAGTATTAGC
1 TCGATTGAGTATTAGC
39767966 TCGATTGA-TATTAG
1 TCGATTGAGTATTAG
39767980 TATTATTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (16 bp):
TCGATTGAGTATTAGC
Found at i:39769423 original size:26 final size:26
Alignment explanation
Indices: 39769366--39769430 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
39769356 ACTCAAATGA
* *
39769366 AAATATTAAAAAAATATAAAATTATT
1 AAATATTAAAAAAATATAAAATAAAT
* *
39769392 AAATATTAAAATAATATAATATAAAT
1 AAATATTAAAAAAATATAAAATAAAT
* *
39769418 ATATATTTAAAAA
1 AAATATTAAAAAA
39769431 TTTAAAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AAATATTAAAAAAATATAAAATAAAT
Found at i:39770042 original size:5 final size:5
Alignment explanation
Indices: 39770026--39770057 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
39770016 GTTGGAACTA
39770026 AAAAG CAAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG A
39770058 TTGAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:39781126 original size:7 final size:7
Alignment explanation
Indices: 39781114--39781142 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
39781104 ATGCAAAAAC
39781114 AATATAA
1 AATATAA
39781121 AATATAA
1 AATATAA
39781128 AATATAA
1 AATATAA
39781135 AATATAA
1 AATATAA
39781142 A
1 A
39781143 TTTATAGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATATAA
Found at i:39781756 original size:12 final size:12
Alignment explanation
Indices: 39781739--39781768 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39781729 ACAGTCACAC
39781739 ACACATATACAT
1 ACACATATACAT
*
39781751 ATACATATACAT
1 ACACATATACAT
39781763 ACACAT
1 ACACAT
39781769 GTGTGTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (12 bp):
ACACATATACAT
Found at i:39783093 original size:22 final size:22
Alignment explanation
Indices: 39783055--39783096 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
39783045 AAAAGGAGTT
*
39783055 GTAATTTCAGTTTAAAGTAATA
1 GTAATTTCAGTTAAAAGTAATA
39783077 GTAATTTC-GATTAAAAGTAA
1 GTAATTTCAG-TTAAAAGTAA
39783097 CCTGTTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (22 bp):
GTAATTTCAGTTAAAAGTAATA
Found at i:39783835 original size:158 final size:159
Alignment explanation
Indices: 39783513--39783849 Score: 407
Period size: 162 Copynumber: 2.1 Consensus size: 159
39783503 TCTTTAATAT
* ** * * * * *
39783513 TTTTCATGCACTACTTCGTAACGAAATATGATACGTATGTTTAATTGAAAGAAGTCGTAAATACA
1 TTTTCATGCACTATTTTATAAAGAAATACGATACGTAGGTTTAATTGAAAGAAGTCATAAACACA
* *
39783578 CTACAAGTATTTAACTTAAGAAGGCGCGAAAATAACGAATTTTTGAAATGTAACTTCAATACCTC
66 CCACAAGTATTTAACTTAAGAA---GCGAAAATAACGAATTTTTGAAATGTAACTTCAATACATC
* *
39783643 TTTTCCCATATTCGAGATAATCTCTTTTTATA
128 TTTTCCCATATTCGAGATAATCTATTTGTATA
39783675 TTTTCATGCACTATTTTATAAAGAAATACGATACGTAGGTTTAATTGAAAGAAGAT-ATAAACAC
1 TTTTCATGCACTATTTTATAAAGAAATACGATACGTAGGTTTAATTGAAAGAAG-TCATAAACAC
* * *
39783739 GCCACGAA-TATTTAATTTAAGGAA-TGAAAATAACGAA-TTTTGAAATGTAACTTCAATACAAT
65 ACCAC-AAGTATTTAACTTAA-GAAGCGAAAATAACGAATTTTTGAAATGTAACTTCAATAC-AT
*
39783801 -TTTTCCCATATTCGAGGTAATCTATTTCGT-TA
127 CTTTTCCCATATTCGAGATAATCTATTT-GTATA
*
39783833 TTTTCATACACTATTTT
1 TTTTCATGCACTATTTT
39783850 GCAATGAAAA
Statistics
Matches: 153, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
158 65 0.42
159 14 0.09
162 68 0.44
163 6 0.04
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (159 bp):
TTTTCATGCACTATTTTATAAAGAAATACGATACGTAGGTTTAATTGAAAGAAGTCATAAACACA
CCACAAGTATTTAACTTAAGAAGCGAAAATAACGAATTTTTGAAATGTAACTTCAATACATCTTT
TCCCATATTCGAGATAATCTATTTGTATA
Found at i:39784715 original size:29 final size:29
Alignment explanation
Indices: 39784666--39784725 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
39784656 TTAAAAAAAA
*
39784666 TTTAGAAATTAAAATTAAATTATA-TATT
1 TTTAGAAATAAAAATTAAATTATATTATT
*
39784694 TTTACGAAATAAAAA-TATAATTTTATTATT
1 TTTA-GAAATAAAAATTA-AATTATATTATT
39784724 TT
1 TT
39784726 AATAGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 6 0.22
29 15 0.56
30 6 0.22
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTAGAAATAAAAATTAAATTATATTATT
Found at i:39786351 original size:22 final size:22
Alignment explanation
Indices: 39786307--39786356 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
39786297 AGGACACAGT
*
39786307 AAAAAA-CAACCCTACAGAGAC
1 AAAAAACCAACCCTACAGAAAC
39786328 AAAAAACCAAACCCTACA-AAAC
1 AAAAAACC-AACCCTACAGAAAC
*
39786350 AACAAAC
1 AAAAAAC
39786357 AGAAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.24
22 10 0.40
23 9 0.36
ACGTcount: A:0.62, C:0.30, G:0.04, T:0.04
Consensus pattern (22 bp):
AAAAAACCAACCCTACAGAAAC
Found at i:39787461 original size:16 final size:16
Alignment explanation
Indices: 39787437--39787467 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39787427 TGAGGCTCCC
*
39787437 CAAAGCTTGTAAAAAA
1 CAAACCTTGTAAAAAA
39787453 CAAACCTTGTAAAAA
1 CAAACCTTGTAAAAA
39787468 TAGGTATAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (16 bp):
CAAACCTTGTAAAAAA
Found at i:39789691 original size:21 final size:22
Alignment explanation
Indices: 39789665--39789710 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
39789655 CAAAACCATG
*
39789665 AAAACCCAAT-ACCCAAACCCT
1 AAAACCAAATCACCCAAACCCT
*
39789686 AAAACCAAATCACCCAAACCTT
1 AAAACCAAATCACCCAAACCCT
39789708 AAA
1 AAA
39789711 CCTAATTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.52, C:0.37, G:0.00, T:0.11
Consensus pattern (22 bp):
AAAACCAAATCACCCAAACCCT
Found at i:39797674 original size:15 final size:16
Alignment explanation
Indices: 39797643--39797682 Score: 64
Period size: 15 Copynumber: 2.5 Consensus size: 16
39797633 ATAATAAAAA
39797643 TATAATTTTATTATTTT
1 TATAA-TTTATTATTTT
39797660 TATAATTTA-TATTTT
1 TATAATTTATTATTTT
39797675 TATAATTT
1 TATAATTT
39797683 TTAAATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 14 0.61
16 4 0.17
17 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATAATTTATTATTTT
Found at i:39821254 original size:21 final size:19
Alignment explanation
Indices: 39821228--39821268 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
39821218 AAAAATACTC
39821228 AATATTATAATATTTTTATAA
1 AATATT-TAATA-TTTTATAA
*
39821249 AATATTTGATATTTTATAA
1 AATATTTAATATTTTATAA
39821268 A
1 A
39821269 TGGATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 4 0.21
21 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
AATATTTAATATTTTATAA
Found at i:39821795 original size:26 final size:26
Alignment explanation
Indices: 39821751--39821800 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
39821741 TTCTTAAATT
*
39821751 TAAAAAAAAAAAACTTATTTAACCAA
1 TAAAAAAAAAAAACCTATTTAACCAA
* *
39821777 TAAAAAAATATAACCTATTTAACC
1 TAAAAAAAAAAAACCTATTTAACC
39821801 GTAATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (26 bp):
TAAAAAAAAAAAACCTATTTAACCAA
Found at i:39822871 original size:13 final size:12
Alignment explanation
Indices: 39822841--39822878 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
39822831 TATAAAGATC
39822841 AATTTTTAAT-G
1 AATTTTTAATAG
39822852 AAATTTTTAATAG
1 -AATTTTTAATAG
39822865 AATTTTTAATAG
1 AATTTTTAATAG
39822877 AA
1 AA
39822879 AAAACAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 24 0.96
13 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (12 bp):
AATTTTTAATAG
Found at i:39824301 original size:8 final size:8
Alignment explanation
Indices: 39824285--39824326 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
39824275 GATAATACAA
39824285 TTATAATT
1 TTATAATT
*
39824293 TTATCATT
1 TTATAATT
39824301 TTAATAA-T
1 TT-ATAATT
*
39824309 TTATATTT
1 TTATAATT
39824317 TTATAATT
1 TTATAATT
39824325 TT
1 TT
39824327 TAAAAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 3 0.11
8 22 0.79
9 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (8 bp):
TTATAATT
Found at i:39824322 original size:15 final size:16
Alignment explanation
Indices: 39824285--39824325 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
39824275 GATAATACAA
39824285 TTATAATTTTATCATTT
1 TTATAA-TTTATCATTT
*
39824302 TAATAATTTAT-ATTT
1 TTATAATTTATCATTT
39824317 TTATAATTT
1 TTATAATTT
39824326 TTAAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 12 0.55
16 5 0.23
17 5 0.23
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATAATTTATCATTT
Found at i:39824338 original size:83 final size:83
Alignment explanation
Indices: 39824251--39824420 Score: 186
Period size: 81 Copynumber: 2.1 Consensus size: 83
39824241 TTTTATGAAG
* * * *
39824251 TTAAAATT-AAA-TTAGAATTTTTACGATAATACAATTATAATTTTATCATTTTAATAATTTATA
1 TTAAAATTAAAATTTAGAATTTTTAAGATAATA-AAGTATAATTTCA-C-TTTTAATAATTTAAA
*
39824314 TTTTTATAA-TTTTTAAAAAA
63 TTTTTAAAAGTTTTTAAAAAA
** * * *
39824334 TT-AAATTAAAATTTATCATTTTTAAGGTACTAAAGTATAATTTCACTTTTATTAATTTAAATTT
1 TTAAAATTAAAATTTAGAATTTTTAAGATAATAAAGTATAATTTCACTTTTAATAATTTAAATTT
*
39824398 TTAAAAGTTTTTTAAAAA
66 TTAAAAGTTTTTAAAAAA
39824416 TTAAA
1 TTAAA
39824421 TGAATTTTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
81 21 0.29
82 18 0.25
83 18 0.25
84 15 0.21
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (83 bp):
TTAAAATTAAAATTTAGAATTTTTAAGATAATAAAGTATAATTTCACTTTTAATAATTTAAATTT
TTAAAAGTTTTTAAAAAA
Found at i:39825305 original size:18 final size:18
Alignment explanation
Indices: 39825282--39825319 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
39825272 TGAATTTTCA
39825282 AATTCGAATA-ACTCGAAT
1 AATTCGAATAGAC-CGAAT
39825300 AATTCGAATAGACCGAAT
1 AATTCGAATAGACCGAAT
39825318 AA
1 AA
39825320 AATTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (18 bp):
AATTCGAATAGACCGAAT
Found at i:39832226 original size:64 final size:64
Alignment explanation
Indices: 39832147--39832274 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
39832137 CAATCAACTC
39832147 ATGGTTAAAGAACTAAGCCAAAATGCTAGCACCCTGACGCTAGATTTAGGATTCGACATATCTT
1 ATGGTTAAAGAACTAAGCCAAAATGCTAGCACCCTGACGCTAGATTTAGGATTCGACATATCTT
39832211 ATGGTTAAAGAACTAAGCCAAAATGCTAGCACCCTGACGCTAGATTTAGGATTCGACATATCTT
1 ATGGTTAAAGAACTAAGCCAAAATGCTAGCACCCTGACGCTAGATTTAGGATTCGACATATCTT
39832275 TTTAGCTCGG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (64 bp):
ATGGTTAAAGAACTAAGCCAAAATGCTAGCACCCTGACGCTAGATTTAGGATTCGACATATCTT
Found at i:39834794 original size:3 final size:3
Alignment explanation
Indices: 39834786--39834838 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
39834776 TCCACCAGTA
39834786 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39834834 T-T TAT
1 TAT TAT
39834839 AATATATAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:39841784 original size:15 final size:14
Alignment explanation
Indices: 39841761--39841804 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
39841751 ATGATTTTAC
39841761 TTCTTTTAAGTAAA
1 TTCTTTTAAGTAAA
* *
39841775 TTCTTTTTAAAT-AT
1 TTC-TTTTAAGTAAA
39841789 TTCTTTTAAGTAAA
1 TTCTTTTAAGTAAA
39841803 TT
1 TT
39841805 TTAACTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 7 0.29
14 10 0.42
15 7 0.29
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.57
Consensus pattern (14 bp):
TTCTTTTAAGTAAA
Found at i:39843146 original size:21 final size:22
Alignment explanation
Indices: 39843120--39843163 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
39843110 GTTTATATTT
* *
39843120 GAAGATTT-ATTCAAAATTTAA
1 GAAGATTTGATTAAAAAATTAA
39843141 GAAGATTTGATTAAAAAATTAA
1 GAAGATTTGATTAAAAAATTAA
39843163 G
1 G
39843164 TTTAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (22 bp):
GAAGATTTGATTAAAAAATTAA
Found at i:39845434 original size:22 final size:23
Alignment explanation
Indices: 39845409--39845454 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
39845399 ATTAATGATA
*
39845409 TAAAAAAATATAAAAATT-TTAT
1 TAAAAAAATAAAAAAATTATTAT
* *
39845431 TAAATAATTAAAAAAATTATTAT
1 TAAAAAAATAAAAAAATTATTAT
39845454 T
1 T
39845455 GATACGGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAAAAAATAAAAAAATTATTAT
Found at i:39852328 original size:13 final size:13
Alignment explanation
Indices: 39852300--39852345 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
39852290 CAAAAAACTT
*
39852300 AAATATT-AAATT
1 AAATATTAAAATC
39852312 AAATATTAAAATC
1 AAATATTAAAATC
*
39852325 AAAT-TCAAATATC
1 AAATATTAAA-ATC
39852338 AAATATTA
1 AAATATTA
39852346 TATTAAGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 11 0.39
13 15 0.54
14 2 0.07
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATATTAAAATC
Found at i:39852676 original size:21 final size:18
Alignment explanation
Indices: 39852622--39852679 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 18
39852612 TAATAAAAAT
39852622 ATAA-TTTTATTATTTTA
1 ATAATTTTTATTATTTTA
39852639 ATAATTTATATATTTATTTTAA
1 ATAATTT-T-TA-TTATTTT-A
39852661 ATTAAATTTTTATTATTTT
1 A-T-AATTTTTATTATTTT
39852680 CGTGATCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 4 0.12
18 2 0.06
19 1 0.03
20 2 0.06
21 14 0.41
22 4 0.12
23 2 0.06
24 5 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATAATTTTTATTATTTTA
Found at i:39853059 original size:30 final size:30
Alignment explanation
Indices: 39852997--39853062 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
39852987 TAGCTTTTAT
*
39852997 TTTTATAATTTTTAAAGAATTAAATCAAAA
1 TTTTATAATTTTTAAAGAATAAAATCAAAA
* * *
39853027 TTTTATCATTTTTATAGAATCAAAAT-ATAA
1 TTTTATAATTTTTAAAGAAT-AAAATCAAAA
39853057 TTTTAT
1 TTTTAT
39853063 TTTTATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTTATAATTTTTAAAGAATAAAATCAAAA
Found at i:39853536 original size:165 final size:165
Alignment explanation
Indices: 39853264--39853594 Score: 617
Period size: 165 Copynumber: 2.0 Consensus size: 165
39853254 TTAAATACTA
39853264 CCAATTCAGCTATTGCCTATTAACAGCATTTTCTTTTTTATAATTGATAAAAAATTACTTCTTCT
1 CCAATTCAGCTATTGCCTATTAACAGCATTTTCTTTTTTATAATTGATAAAAAATTACTTCTTCT
* *
39853329 TAAAGACAAATAAAATAAAACCAGAAAACAATTATTAATCATAAATGAACAACTAATTGGACAGG
66 TAAAGAAAAATAAAATAAAACCAGAAAACAATTATTAATCATAAATGAACAACTAATCGGACAGG
*
39853394 TCAAAAGGCAAACTTAAGAAAACTCTTCTCTAGAG
131 TCAAAAGGCAAACTTAACAAAACTCTTCTCTAGAG
*
39853429 CCAATTCAGCTATTGCCTATTAACAGCATTTTCTTTTTTATAATTGATAAAAAATTACTTCTTTT
1 CCAATTCAGCTATTGCCTATTAACAGCATTTTCTTTTTTATAATTGATAAAAAATTACTTCTTCT
*
39853494 TAAAGAAAAATAAAATAAAACTAGAAAACAATTATTAATCATAAATGAACAACTAATCGGACAGG
66 TAAAGAAAAATAAAATAAAACCAGAAAACAATTATTAATCATAAATGAACAACTAATCGGACAGG
39853559 TCAAAAGGCAAACTTAACAAAACTCTTCTCTAGAG
131 TCAAAAGGCAAACTTAACAAAACTCTTCTCTAGAG
39853594 C
1 C
39853595 AACAGACAAT
Statistics
Matches: 161, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
165 161 1.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (165 bp):
CCAATTCAGCTATTGCCTATTAACAGCATTTTCTTTTTTATAATTGATAAAAAATTACTTCTTCT
TAAAGAAAAATAAAATAAAACCAGAAAACAATTATTAATCATAAATGAACAACTAATCGGACAGG
TCAAAAGGCAAACTTAACAAAACTCTTCTCTAGAG
Found at i:39866576 original size:132 final size:132
Alignment explanation
Indices: 39866325--39866721 Score: 625
Period size: 132 Copynumber: 3.0 Consensus size: 132
39866315 CACGAGCATA
* * *
39866325 TCTCCTTGATTGGAGGGATTAAGCTGAGAACATTCTTCAAAATTTTCTCCCACACCAGGATTAAT
1 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCACGCCAGGATTAAT
* * * * *
39866390 TTCATCTACTTGTGGGGTTTCTACGGTTGATAAAGTAGCCGCAAGGGAAACTTCCTCCGACCTAG
66 TTCATCAACTTGTGGGTTTTCTACGGTTGATAAAGTAGCCACGAGGGTAACTTCCTCCGACCTAG
39866455 CC
131 CC
39866457 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCACGCCAGGATTAAT
1 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCACGCCAGGATTAAT
* * * *
39866522 TTCATAAACTTGTGGGTTTTCTACGGTTGATAAAGTAGGCACGGGGGTACCTTCCTCCGACCTAG
66 TTCATCAACTTGTGGGTTTTCTACGGTTGATAAAGTAGCCACGAGGGTAACTTCCTCCGACCTAG
39866587 CC
131 CC
* *
39866589 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTACTCCCATGCCAGGATTAAT
1 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCACGCCAGGATTAAT
* * *
39866654 TTCGA-CAACTTGAGGGTTTTCTATGGTTGATAAAGTAGCCACGAAGGTAACTTCCTCCGACCTA
66 TTC-ATCAACTTGTGGGTTTTCTACGGTTGATAAAGTAGCCACGAGGGTAACTTCCTCCGACCTA
39866718 GCC
130 GCC
39866721 T
1 T
39866722 GTTCTTCCAA
Statistics
Matches: 243, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
132 242 1.00
133 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (132 bp):
TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCACGCCAGGATTAAT
TTCATCAACTTGTGGGTTTTCTACGGTTGATAAAGTAGCCACGAGGGTAACTTCCTCCGACCTAG
CC
Found at i:39871797 original size:33 final size:33
Alignment explanation
Indices: 39871755--39871819 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
39871745 CAAGTGGCGA
*
39871755 AAACGAAGGAGATGTTGTCCAAACAAGCGGTTC
1 AAACGAAGGAAATGTTGTCCAAACAAGCGGTTC
*
39871788 AAACGAAGGAAATGTTGTCGAAACAAGCGGTT
1 AAACGAAGGAAATGTTGTCCAAACAAGCGGTT
39871820 AAGATCGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.18
Consensus pattern (33 bp):
AAACGAAGGAAATGTTGTCCAAACAAGCGGTTC
Found at i:39889196 original size:3 final size:3
Alignment explanation
Indices: 39889182--39889223 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
39889172 AGTCATTTTC
*
39889182 ATA ATA AAA ATA ATA ATA ATA ATA ATAA ATAA ATA A-A ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A ATA ATA ATA AT
39889224 TAACCAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 26 0.74
4 7 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:39889398 original size:13 final size:13
Alignment explanation
Indices: 39889377--39889418 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
39889367 AAATTTAATT
39889377 ATATAAATATAAA
1 ATATAAATATAAA
*
39889390 ATATTAATATAAA
1 ATATAAATATAAA
* *
39889403 A-ATAATTTTAAA
1 ATATAAATATAAA
39889415 ATAT
1 ATAT
39889419 TTTATTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATAAATATAAA
Found at i:39889936 original size:25 final size:24
Alignment explanation
Indices: 39889888--39889936 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
39889878 TAAAATAAAC
*
39889888 AATAAAAAATCATCTCATACATTA
1 AATAAAAAATCATCTCATAAATTA
* *
39889912 AATAATAAATTCATCTTATAAATTA
1 AATAA-AAAATCATCTCATAAATTA
39889937 TTTAGGTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (24 bp):
AATAAAAAATCATCTCATAAATTA
Found at i:39892516 original size:19 final size:19
Alignment explanation
Indices: 39892460--39892516 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
39892450 CTAACCCTAG
* *
39892460 GTTCAAGGTTCATGATTCGA
1 GTTCAAGGTTCAAGGTT-GA
*
39892480 GTTCTA-GTTC-AGGTTTGA
1 GTTCAAGGTTCAAGG-TTGA
39892498 GTTCAAGGTTCAAGGTTGA
1 GTTCAAGGTTCAAGGTTGA
39892517 ATATTCGAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
18 8 0.27
19 14 0.47
20 8 0.27
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (19 bp):
GTTCAAGGTTCAAGGTTGA
Found at i:39895472 original size:16 final size:17
Alignment explanation
Indices: 39895448--39895487 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
39895438 TTAAATTGAT
39895448 TTTAAATTTA-TTTAAA
1 TTTAAATTTATTTTAAA
*
39895464 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
39895481 TTTAAAT
1 TTTAAAT
39895488 AAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:39895515 original size:7 final size:6
Alignment explanation
Indices: 39895448--39895518 Score: 58
Period size: 6 Copynumber: 12.0 Consensus size: 6
39895438 TTAAATTGAT
* * **
39895448 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA TAAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
39895493 TTAAAA TATTAAA TTTAACA TTTAAA
1 TTTAAA T-TTAAA TTTAA-A TTTAAA
39895519 AGTCCAAATG
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
4 4 0.08
5 3 0.06
6 34 0.65
7 11 0.21
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:39895549 original size:7 final size:7
Alignment explanation
Indices: 39895537--39895566 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
39895527 TGTCCATTTA
39895537 CATGGCC
1 CATGGCC
39895544 CATGGCC
1 CATGGCC
39895551 CATGGCC
1 CATGGCC
*
39895558 CAGGGCC
1 CATGGCC
39895565 CA
1 CA
39895567 ATTACAAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.43, G:0.30, T:0.10
Consensus pattern (7 bp):
CATGGCC
Found at i:39895578 original size:14 final size:14
Alignment explanation
Indices: 39895561--39895599 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
39895551 CATGGCCCAG
39895561 GGCCCAATTACAAA
1 GGCCCAATTACAAA
*
39895575 GGCCCAATTAC--G
1 GGCCCAATTACAAA
39895587 GGCCCAATTACAA
1 GGCCCAATTACAA
39895600 TAGTCCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 11 0.50
14 11 0.50
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.15
Consensus pattern (14 bp):
GGCCCAATTACAAA
Found at i:39895592 original size:12 final size:13
Alignment explanation
Indices: 39895558--39895598 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 13
39895548 GCCCATGGCC
39895558 CAGGGCCCAATTA
1 CAGGGCCCAATTA
*
39895571 CAAAGGCCCAATTA
1 C-AGGGCCCAATTA
39895585 C-GGGCCCAATTA
1 CAGGGCCCAATTA
39895597 CA
1 CA
39895599 ATAGTCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 11 0.46
13 1 0.04
14 12 0.50
ACGTcount: A:0.34, C:0.32, G:0.20, T:0.15
Consensus pattern (13 bp):
CAGGGCCCAATTA
Found at i:39895669 original size:20 final size:20
Alignment explanation
Indices: 39895644--39895703 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
39895634 GTGCCTACTG
*
39895644 CTGCTGGCCACCAGCTCCAT
1 CTGCTGACCACCAGCTCCAT
39895664 CTGCTGACCACCAGCTCCAT
1 CTGCTGACCACCAGCTCCAT
39895684 CTGCTGACCACCAAGCTCCA
1 CTGCTGACCACC-AGCTCCA
39895704 CCATGCCCTG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 31 0.82
21 7 0.18
ACGTcount: A:0.20, C:0.45, G:0.17, T:0.18
Consensus pattern (20 bp):
CTGCTGACCACCAGCTCCAT
Found at i:39897300 original size:161 final size:163
Alignment explanation
Indices: 39897121--39897434 Score: 476
Period size: 162 Copynumber: 1.9 Consensus size: 163
39897111 CTTTTCAATT
** *
39897121 TAGTCCTTTGACTGTTTGACTGTGCCATAGGCTGCCACGTGTCA-CTTTTTGGATTATTTATGCA
1 TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTATGCA
*
39897185 TTTAGT-CTTTCTTATTTTTTATTTGTTTTAATTTAATCC-CAAATCAAC-TTTATTTTAATTAC
66 TTTAGTCCTTT-TTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTA-TTTAATTAC
*
39897247 GAAATTGGCCCAATAA-TTTTTCAAGGTTTATAAAC
129 AAAATTGGCCCAA-AATTTTTTCAAGGTTTATAAAC
* *
39897282 TAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATCTTTTTGGATTATTTCTGCA
1 TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTATGCA
* *
39897347 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACAA
66 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAA
*
39897412 AATTGGTCCAAAATTTTTTCAAG
131 AATTGGCCCAAAATTTTTTCAAG
39897435 ATTTTCAAAT
Statistics
Matches: 138, Mismatches: 10, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
161 40 0.29
162 54 0.39
163 40 0.29
164 4 0.03
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (163 bp):
TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTATGCA
TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAA
AATTGGCCCAAAATTTTTTCAAGGTTTATAAAC
Found at i:39897487 original size:162 final size:160
Alignment explanation
Indices: 39897149--39897456 Score: 408
Period size: 163 Copynumber: 1.9 Consensus size: 160
39897139 ACTGTGCCAT
*
39897149 AGGCTGCCACGTGTCACTTTTTGGATTATTTATGCATTTAGTCTTTCTTATTTTTTATTTGTTTT
1 AGGCTGCCACGTGTCACTTTTTGGATTATTTATGCATTTAGTCTTTCTTATTTTTAATTTGTTTT
* *
39897214 AATTTAATCCCAAATCAACTTTATTTTAATTACGAAATTGGCCCAATAATTTTTCAAGGTTTATA
66 AATTTAATCCCAAATCAACTTTATTTTAATTACAAAATTGGCCCAATAATTTTTCAAGATTTATA
* * *
39897279 AACTAGTCCTTTGACTGTTTGACTGCACCAG
131 AACTAGTCCCTTGACTGCTGGACT-CACCAG
* *
39897310 AGGTTGCCACGTGTCATCTTTTTGGATTATTTCTGCATTTAGTCCTTT-TTATTTTTAATTTGTT
1 AGGCTGCCACGTGTCA-CTTTTTGGATTATTTATGCATTTAGT-CTTTCTTATTTTTAATTTGTT
* * *
39897374 TTAATTTAATCCTTAAATCGACTTT-TATTTAATTACAAAATTGGTCCAA-AATTTTTTCAAGAT
64 TTAATTTAATCC-CAAATCAACTTTAT-TTTAATTACAAAATTGGCCCAATAA-TTTTTCAAGAT
* *
39897437 TT-TCAAATTGGTCCCTTGAC
126 TTAT-AAACTAGTCCCTTGAC
39897457 CTCTGGATAC
Statistics
Matches: 130, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
161 15 0.12
162 56 0.43
163 59 0.45
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.46
Consensus pattern (160 bp):
AGGCTGCCACGTGTCACTTTTTGGATTATTTATGCATTTAGTCTTTCTTATTTTTAATTTGTTTT
AATTTAATCCCAAATCAACTTTATTTTAATTACAAAATTGGCCCAATAATTTTTCAAGATTTATA
AACTAGTCCCTTGACTGCTGGACTCACCAG
Found at i:39897567 original size:30 final size:30
Alignment explanation
Indices: 39897528--39897641 Score: 192
Period size: 30 Copynumber: 3.7 Consensus size: 30
39897518 CCCTAAATTG
39897528 TCCAGAAATTATATTTTGACCCCAAAACTTT
1 TCCA-AAATTATATTTTGACCCCAAAACTTT
*
39897559 TCCAAAATTAAATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
39897589 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
39897619 TCCAAAATTATATTTTTGACCCC
1 TCCAAAATTATA-TTTTGACCCC
39897642 GATTTCATCG
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
30 65 0.82
31 14 0.18
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (30 bp):
TCCAAAATTATATTTTGACCCCAAAACTTT
Found at i:39897656 original size:30 final size:29
Alignment explanation
Indices: 39897622--39897729 Score: 100
Period size: 30 Copynumber: 3.7 Consensus size: 29
39897612 AAACTTTTCC
*
39897622 AAAATTATATTTTTGACCCCGATTTCATCG
1 AAAATTACATTTTT-ACCCCGATTTCATCG
39897652 AAAATTACCA-TTTTACCCCCGAATCTT--TC-
1 AAAATTA-CATTTTTA-CCCCG-AT-TTCATCG
*
39897681 AAAATTCCATTTTTAACCCCGATTTCATCG
1 AAAATTACATTTTT-ACCCCGATTTCATCG
39897711 AAAATTACCA-TTTTACCCC
1 AAAATTA-CATTTTTACCCC
39897730 TGAATCTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
27 2 0.03
28 4 0.06
29 23 0.35
30 29 0.45
31 5 0.08
32 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCGATTTCATCG
Found at i:39897656 original size:60 final size:59
Alignment explanation
Indices: 39897540--39897840 Score: 262
Period size: 59 Copynumber: 5.1 Consensus size: 59
39897530 CAGAAATTAT
* * * *
39897540 ATTTTGACCCCAAAACTTTTCCAAAATTA-AATTTTGACCCCAAAACTTT--TCCAAAATTA-C
1 ATTTT-ACCCCAAAACTTTT-CAAAATTATATTTTTAACCCC--GA-TTTCATCGAAAATTACC
*
39897600 ATTTTGACCCCAAAACTTTTCCAAAATTATATTTTTGACCCCGATTTCATCGAAAATTACC
1 ATTTT-ACCCCAAAACTTTT-CAAAATTATATTTTTAACCCCGATTTCATCGAAAATTACC
** **
39897661 ATTTTACCCCCGAA-TCTTTCAAAATTCCATTTTTAACCCCGATTTCATCGAAAATTACC
1 ATTTTACCCCAAAACT-TTTCAAAATTATATTTTTAACCCCGATTTCATCGAAAATTACC
* * * *
39897720 ATTTTACCCCTGAATCTTTT-AAAATT-TAGTTTTTAACCCCGATTTCACCGAAAATCACC
1 ATTTTACCCC-AAAACTTTTCAAAATTATA-TTTTTAACCCCGATTTCATCGAAAATTACC
* * ** * *
39897779 ATTTTACCCCCGAATCTTTT-AAAATTCCA-TTTTAACCCCGATTTTA-CCAAAATTACC
1 ATTTTA-CCCCAAAACTTTTCAAAATTATATTTTTAACCCCGATTTCATCGAAAATTACC
39897836 ATTTT
1 ATTTT
39897841 GCCCTCGGGT
Statistics
Matches: 213, Mismatches: 18, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
57 14 0.07
58 20 0.09
59 104 0.49
60 57 0.27
61 18 0.08
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (59 bp):
ATTTTACCCCAAAACTTTTCAAAATTATATTTTTAACCCCGATTTCATCGAAAATTACC
Found at i:39897684 original size:29 final size:27
Alignment explanation
Indices: 39897632--39897840 Score: 129
Period size: 29 Copynumber: 7.1 Consensus size: 27
39897622 AAAATTATAT
*
39897632 TTTTGACCCCGATTTCATCGAAAATTACCA
1 TTTTAACCCCGATTT--TC-AAAATTACCA
*
39897662 TTTTACCCCCGAATCTTTCAAAATT-CCA
1 TTTTAACCCCG-AT-TTTCAAAATTACCA
39897690 TTTTTAACCCCGATTTCATCGAAAATTACCA
1 -TTTTAACCCCGATTT--TC-AAAATTACCA
* **
39897721 TTTT-ACCCCTGAATCTTTTAAAATTTA-GT
1 TTTTAACCCC-G-AT-TTTCAAAA-TTACCA
* *
39897750 TTTTAACCCCGATTTCACCGAAAATCACCA
1 TTTTAACCCCGATTT--TC-AAAATTACCA
* *
39897780 TTTTACCCCCGAATCTTTTAAAATT-CCA
1 TTTTAACCCCG-AT-TTTCAAAATTACCA
39897808 TTTTAACCCCGATTTTACCAAAATTACCA
1 TTTTAACCCCGATTTT--CAAAATTACCA
39897837 TTTT
1 TTTT
39897841 GCCCTCGGGT
Statistics
Matches: 141, Mismatches: 17, Indels: 43
0.70 0.08 0.21
Matches are distributed among these distances:
26 3 0.02
27 6 0.04
28 26 0.18
29 46 0.33
30 45 0.32
31 9 0.06
32 6 0.04
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.37
Consensus pattern (27 bp):
TTTTAACCCCGATTTTCAAAATTACCA
Found at i:39897700 original size:59 final size:59
Alignment explanation
Indices: 39897621--39897840 Score: 311
Period size: 59 Copynumber: 3.8 Consensus size: 59
39897611 AAAACTTTTC
** *
39897621 CAAAATTATATTTTTGACCCCGATTTCATCGAAAATTACCATTTTACCCCCGAATCTTT
1 CAAAATTCCATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCCGAATCTTT
*
39897680 CAAAATTCCATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCTGAATCTTT
1 CAAAATTCCATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCCGAATCTTT
* * * *
39897739 TAAAATT-TAGTTTTTAACCCCGATTTCACCGAAAATCACCATTTTACCCCCGAATCTTT
1 CAAAATTCCA-TTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCCGAATCTTT
* * *
39897798 TAAAATTCCA-TTTTAACCCCGATTTTA-CCAAAATTACCATTTT
1 CAAAATTCCATTTTTAACCCCGATTTCATCGAAAATTACCATTTT
39897841 GCCCTCGGGT
Statistics
Matches: 146, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
57 14 0.10
58 17 0.12
59 114 0.78
60 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.37
Consensus pattern (59 bp):
CAAAATTCCATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCCGAATCTTT
Found at i:39897772 original size:118 final size:117
Alignment explanation
Indices: 39897590--39897841 Score: 359
Period size: 118 Copynumber: 2.1 Consensus size: 117
39897580 CAAAACTTTT
* *
39897590 CCAAAATTA-CATTTTGACCCCAAAACTTTTCCAAAATTATATTTTTGACCCCGATTTCATCGAA
1 CCAAAATTACCATTTTGACCCCAAAACTTTT-CAAAATTATATTTTTAACCCCGATTTCACCGAA
*
39897654 AATTACCATTTTACCCCCGAATCTTTCAAAATTCCATTTTTAACCCCGATTTCA
65 AATCACCATTTTACCCCCGAATCTTTCAAAATTCCA-TTTTAACCCCGATTTCA
* * *
39897708 TCGAAAATTACCATTTT-ACCCCTGAATCTTTT-AAAATT-TAGTTTTTAACCCCGATTTCACCG
1 -CCAAAATTACCATTTTGACCCC-AAAACTTTTCAAAATTATA-TTTTTAACCCCGATTTCACCG
* *
39897770 AAAATCACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTAACCCCGATTTTA
63 AAAATCACCATTTTACCCCCGAATCTTTCAAAATTCCATTTTAACCCCGATTTCA
39897825 CCAAAATTACCATTTTG
1 CCAAAATTACCATTTTG
39897842 CCCTCGGGTA
Statistics
Matches: 120, Mismatches: 9, Indels: 10
0.86 0.06 0.07
Matches are distributed among these distances:
116 15 0.12
117 18 0.15
118 61 0.51
119 13 0.11
120 13 0.11
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.37
Consensus pattern (117 bp):
CCAAAATTACCATTTTGACCCCAAAACTTTTCAAAATTATATTTTTAACCCCGATTTCACCGAAA
ATCACCATTTTACCCCCGAATCTTTCAAAATTCCATTTTAACCCCGATTTCA
Found at i:39899652 original size:26 final size:26
Alignment explanation
Indices: 39899602--39899652 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
39899592 TTTTCTGTTA
*
39899602 TTTTTTCACTATTTTGCTTTTGTTTT
1 TTTTTTCACTATTTTGCTTTCGTTTT
*
39899628 TTTTTTCATTATTTTG-TTATCGTTT
1 TTTTTTCACTATTTTGCTT-TCGTTT
39899653 CACTATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.10, C:0.10, G:0.08, T:0.73
Consensus pattern (26 bp):
TTTTTTCACTATTTTGCTTTCGTTTT
Found at i:39907200 original size:11 final size:11
Alignment explanation
Indices: 39907184--39907253 Score: 50
Period size: 11 Copynumber: 6.4 Consensus size: 11
39907174 ATTTACTCAC
39907184 TATTTTGCTAT
1 TATTTTGCTAT
* *
39907195 TGTTTTTCTAT
1 TATTTTGCTAT
* *
39907206 TATTTTGTTCT
1 TATTTTGCTAT
* **
39907217 CATTTCACTAT
1 TATTTTGCTAT
* *
39907228 TATATTACTAT
1 TATTTTGCTAT
*
39907239 TATTTTGTTAT
1 TATTTTGCTAT
39907250 TATT
1 TATT
39907254 ATTTGAATAT
Statistics
Matches: 42, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
11 42 1.00
ACGTcount: A:0.20, C:0.10, G:0.06, T:0.64
Consensus pattern (11 bp):
TATTTTGCTAT
Found at i:39908029 original size:2 final size:2
Alignment explanation
Indices: 39908022--39908072 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
39908012 GCATATACAA
39908022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
39908064 AT AT TT AT A
1 AT AT AT AT A
39908073 CGTGTACGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:39920796 original size:14 final size:14
Alignment explanation
Indices: 39920777--39920824 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
39920767 TCATCTCCTC
39920777 TCTTTTTTTAGTTT
1 TCTTTTTTTAGTTT
* *
39920791 TCTTTTTGTA-TCT
1 TCTTTTTTTAGTTT
39920804 TCTTTTTTTAGTTT
1 TCTTTTTTTAGTTT
39920818 TCTTTTT
1 TCTTTTT
39920825 CCTTTGACCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.06, C:0.10, G:0.06, T:0.77
Consensus pattern (14 bp):
TCTTTTTTTAGTTT
Found at i:39921093 original size:14 final size:14
Alignment explanation
Indices: 39921074--39921121 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
39921064 AATCAAATGT
39921074 AAAAGAAAACTAAA
1 AAAAGAAAACTAAA
* **
39921088 AAAAGAAGA-TACG
1 AAAAGAAAACTAAA
39921101 AAAAGAAAACTAAA
1 AAAAGAAAACTAAA
39921115 AAAAGAA
1 AAAAGAA
39921122 GAGAGATGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.75, C:0.06, G:0.12, T:0.06
Consensus pattern (14 bp):
AAAAGAAAACTAAA
Found at i:39930290 original size:43 final size:43
Alignment explanation
Indices: 39930080--39930288 Score: 221
Period size: 42 Copynumber: 4.9 Consensus size: 43
39930070 TTTTTCAAAT
* * * *
39930080 ATAA-TCTCACGCTCATTCCGAAACATGAGTTTTCCTTTAAAC
1 ATAATTCTCATGCTCATCCCGAGACATGAGTCTTCCTTTAAAC
* * *
39930122 ATAATT-TCATTCTCATCCCGAGACATGAGTCTTCTTTTAAAT
1 ATAATTCTCATGCTCATCCCGAGACATGAGTCTTCCTTTAAAC
* * *
39930164 ATAA-TCTCATTCTCGTCCCGAGACATGAGTCTTTCTTTAAAC
1 ATAATTCTCATGCTCATCCCGAGACATGAGTCTTCCTTTAAAC
* * * *
39930206 AT-ATTCTCATGCTCATTCCGAGTCACGAGTCTTCCATTTATAC
1 ATAATTCTCATGCTCATCCCGAGACATGAGTCTTCC-TTTAAAC
* *
39930249 A-AATTCTCATGCTCAACCTGAGACATGAGTCTTCCATTTA
1 ATAATTCTCATGCTCATCCCGAGACATGAGTCTTCC-TTTA
39930289 TATATCAAGT
Statistics
Matches: 139, Mismatches: 23, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
41 2 0.01
42 96 0.69
43 41 0.29
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (43 bp):
ATAATTCTCATGCTCATCCCGAGACATGAGTCTTCCTTTAAAC
Found at i:39931120 original size:22 final size:19
Alignment explanation
Indices: 39931084--39931127 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
39931074 ACTTTCATAA
*
39931084 TTAACTTAATTAATCATCTTT
1 TTAACTTAATCAATC-T-TTT
39931105 TTAACTTTAATCAATCTTTT
1 TTAAC-TTAATCAATCTTTT
39931125 TTA
1 TTA
39931128 TAATAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 6 0.29
22 9 0.43
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAACTTAATCAATCTTTT
Found at i:39932743 original size:23 final size:24
Alignment explanation
Indices: 39932717--39932798 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 24
39932707 CAAATACCTC
39932717 TAAAATAGTTA-AAAATTTAACTA
1 TAAAATAGTTAGAAAATTTAACTA
* *
39932740 TAAAATAAGAGTTATACAATATCTAACTA
1 TAAAAT---AGTTAGA-AA-ATTTAACTA
*
39932769 TAAAATAG-TAGAAAAATTAACT-
1 TAAAATAGTTAGAAAATTTAACTA
39932791 TAACAATA
1 TAA-AATA
39932799 TAATAGTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
22 3 0.06
23 16 0.33
24 2 0.04
25 3 0.06
26 7 0.15
27 1 0.02
28 2 0.04
29 14 0.29
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.30
Consensus pattern (24 bp):
TAAAATAGTTAGAAAATTTAACTA
Found at i:39938692 original size:13 final size:14
Alignment explanation
Indices: 39938674--39938721 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
39938664 TTAAAATTTA
39938674 AAGTTTGAG-TTCG
1 AAGTTTGAGATTCG
39938687 AAGTTTGAGATTC-
1 AAGTTTGAGATTCG
* *
39938700 ATGTTCGAGATTCG
1 AAGTTTGAGATTCG
39938714 -AGTTTGAG
1 AAGTTTGAG
39938722 GAATTTAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 26 0.90
14 3 0.10
ACGTcount: A:0.25, C:0.08, G:0.29, T:0.38
Consensus pattern (14 bp):
AAGTTTGAGATTCG
Found at i:39947468 original size:16 final size:16
Alignment explanation
Indices: 39947447--39947479 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39947437 TGTTAGGAGG
39947447 TCCTTAAATTGCATAT
1 TCCTTAAATTGCATAT
39947463 TCCTTAAATTGCATAT
1 TCCTTAAATTGCATAT
39947479 T
1 T
39947480 TTTACGATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (16 bp):
TCCTTAAATTGCATAT
Found at i:39947612 original size:16 final size:17
Alignment explanation
Indices: 39947591--39947624 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
39947581 GTGTAAATTT
*
39947591 ATTTTTAT-TAATTTAA
1 ATTTTTATAAAATTTAA
39947607 ATTTTTATAAAATTTAA
1 ATTTTTATAAAATTTAA
39947624 A
1 A
39947625 AAGGTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTTATAAAATTTAA
Found at i:39949215 original size:3 final size:3
Alignment explanation
Indices: 39949207--39949250 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
39949197 TATTATATAA
* * *
39949207 ATG ATG ATG ATG ATG GTG ATG GTG ATG GTG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
39949251 CACCGTTTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.27, C:0.00, G:0.39, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:39950086 original size:31 final size:31
Alignment explanation
Indices: 39950041--39950107 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
39950031 TTGCAAGATC
* *
39950041 AACGGCTCTAATATCCTT-GTGATGGACATCT
1 AACGGCTCTAATAT-CTTCATGATGGACATCA
* *
39950072 AACGGCTTTGATATCTTCATGATGGACATCA
1 AACGGCTCTAATATCTTCATGATGGACATCA
39950103 AACGG
1 AACGG
39950108 GTTATAATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 3 0.10
31 28 0.90
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (31 bp):
AACGGCTCTAATATCTTCATGATGGACATCA
Found at i:39950941 original size:24 final size:24
Alignment explanation
Indices: 39950896--39950942 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
39950886 TGTATTTTAT
* *
39950896 TACTATGATTATCCTTATTATTAC
1 TACTATGATTATCATTAGTATTAC
39950920 TACTATGATTAGT-ATTAGTATTA
1 TACTATGATTA-TCATTAGTATTA
39950943 TTATTATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (24 bp):
TACTATGATTATCATTAGTATTAC
Found at i:39956613 original size:2 final size:2
Alignment explanation
Indices: 39956608--39956638 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
39956598 TATCATTTTA
*
39956608 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39956639 ATTATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:39958351 original size:7 final size:6
Alignment explanation
Indices: 39958323--39958347 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39958313 AAAATTAATA
39958323 TAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT T
39958348 TAATACTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TAATTT
Found at i:39964298 original size:16 final size:17
Alignment explanation
Indices: 39964277--39964324 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
39964267 GACCCGACTC
39964277 ATTTTTAAGT-TTATA-T
1 ATTTTTAA-TATTATATT
*
39964293 ATTTTTTATATTATATT
1 ATTTTTAATATTATATT
39964310 ATTTTTATATATTAT
1 ATTTTTA-ATATTAT
39964325 GTATTTTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 12 0.44
17 7 0.26
18 7 0.26
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
ATTTTTAATATTATATT
Found at i:39964331 original size:16 final size:16
Alignment explanation
Indices: 39964287--39964332 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
39964277 ATTTTTAAGT
*
39964287 TTATATATTTTTTATA
1 TTATATATTTTATATA
39964303 TTATATTATTTTTATATA
1 TTATA-TA-TTTTATATA
*
39964321 TTATGTATTTTA
1 TTATATATTTTA
39964333 GAACACATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 10 0.38
17 4 0.15
18 12 0.46
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTATATATTTTATATA
Found at i:39967250 original size:7 final size:7
Alignment explanation
Indices: 39967238--39967265 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
39967228 AAGGAATATG
39967238 ATTTTAA
1 ATTTTAA
39967245 ATTTTAA
1 ATTTTAA
39967252 ATTTTAA
1 ATTTTAA
39967259 ATTTTAA
1 ATTTTAA
39967266 TTTAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTTAA
Found at i:39969849 original size:21 final size:20
Alignment explanation
Indices: 39969820--39969858 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39969810 TTTTTAAATT
39969820 AATTGTTAAATTTAATTTTAA
1 AATTGTT-AATTTAATTTTAA
*
39969841 AATTTTTAATTTAATTTT
1 AATTGTTAATTTAATTTT
39969859 TTTTAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
AATTGTTAATTTAATTTTAA
Found at i:39974960 original size:12 final size:12
Alignment explanation
Indices: 39974927--39974960 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39974917 TGAGTCTCTG
*
39974927 TTCTTTCTTCTT
1 TTCTTTCTTTTT
*
39974939 TTGTTTCTTTTT
1 TTCTTTCTTTTT
39974951 TTCTTTCTTT
1 TTCTTTCTTT
39974961 ATTCTTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (12 bp):
TTCTTTCTTTTT
Found at i:39975021 original size:14 final size:14
Alignment explanation
Indices: 39974998--39975032 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
39974988 AGATATTAGT
39974998 TAATAATAATAAAA
1 TAATAATAATAAAA
* *
39975012 TAATACTAATTAAA
1 TAATAATAATAAAA
39975026 TAATAAT
1 TAATAAT
39975033 TTATATTATT
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:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:39978550 original size:21 final size:23
Alignment explanation
Indices: 39978520--39978561 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
39978510 AATGCTAACA
*
39978520 AAAGTTAAAAT-TTTTAAATTAT
1 AAAGTTAAAATAATTTAAATTAT
39978542 AAAG-TAAAATAATTTAAATT
1 AAAGTTAAAATAATTTAAATT
39978562 TTAACTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (23 bp):
AAAGTTAAAATAATTTAAATTAT
Found at i:39983750 original size:31 final size:31
Alignment explanation
Indices: 39983713--39983782 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
39983703 TCATATTTAC
** *
39983713 CATATTTATATATTATTACATATATCATATT
1 CATATTTATATAAAAATACATATATCATATT
* * *
39983744 CATATTTTTCTAAAAATATATATATCATATT
1 CATATTTATATAAAAATACATATATCATATT
39983775 CATATTTA
1 CATATTTA
39983783 ATTTAATCAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (31 bp):
CATATTTATATAAAAATACATATATCATATT
Found at i:39989492 original size:30 final size:32
Alignment explanation
Indices: 39989415--39989493 Score: 101
Period size: 30 Copynumber: 2.6 Consensus size: 32
39989405 AGATCCCAAA
*
39989415 AAATTTAAGTAC-CAATTTAAAAAAGAGTGTC
1 AAATTTAAGTACTAAATTTAAAAAAGAGTGTC
* *
39989446 AAATTTATGTATTAAATTTAAAAAA-A-TGTC
1 AAATTTAAGTACTAAATTTAAAAAAGAGTGTC
*
39989476 AAATTTAAATACTAAATT
1 AAATTTAAGTACTAAATT
39989494 ATATTAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 19 0.46
31 11 0.27
32 11 0.27
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (32 bp):
AAATTTAAGTACTAAATTTAAAAAAGAGTGTC
Found at i:39989505 original size:55 final size:57
Alignment explanation
Indices: 39989463--39989571 Score: 150
Period size: 55 Copynumber: 1.9 Consensus size: 57
39989453 TGTATTAAAT
39989463 TTAAAAAAATGTCAAATTTAAATACT-AA-ATTATATTAAAAATTTTAAATATCAAA
1 TTAAAAAAATGTCAAATTTAAATACTAAATATTATATTAAAAATTTTAAATATCAAA
* * * *
39989518 TTAATAAAATGTTAAATTTAATTATTAAATATTATATTAAACCAATTTTAAATA
1 TTAAAAAAATGTCAAATTTAAATACTAAATATTATATTAAA--AATTTTAAATA
39989572 ATGAAATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
55 22 0.48
56 2 0.04
57 11 0.24
59 11 0.24
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (57 bp):
TTAAAAAAATGTCAAATTTAAATACTAAATATTATATTAAAAATTTTAAATATCAAA
Found at i:39995533 original size:40 final size:40
Alignment explanation
Indices: 39995478--39995556 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
39995468 ATGCCTAGTT
*
39995478 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTGACTTG
1 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTTG
* *
39995518 TGATGTAATTTTGTTTGTGATTTAAAAATATGTTAACTT
1 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTT
39995557 CCTACTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.48
Consensus pattern (40 bp):
TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTTG
Found at i:39997514 original size:33 final size:33
Alignment explanation
Indices: 39997477--39997556 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
39997467 AGGAGAGAGC
*
39997477 CTCCGTTCAGACAGCGGTAAGCAAAGTAATAGT
1 CTCCGCTCAGACAGCGGTAAGCAAAGTAATAGT
*
39997510 CTCCGCTCAGACGGCGGTAAGCAAAGTAATAGT
1 CTCCGCTCAGACAGCGGTAAGCAAAGTAATAGT
*
39997543 CTCCGCTCGGACAG
1 CTCCGCTCAGACAG
39997557 TGCAAAACGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (33 bp):
CTCCGCTCAGACAGCGGTAAGCAAAGTAATAGT
Found at i:40004373 original size:16 final size:16
Alignment explanation
Indices: 40004352--40004386 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40004342 GGTTGGCTAG
*
40004352 CATACAAATATGCATA
1 CATACAAATATACATA
*
40004368 CATACATATATACATA
1 CATACAAATATACATA
40004384 CAT
1 CAT
40004387 CATACATGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.29
Consensus pattern (16 bp):
CATACAAATATACATA
Found at i:40006971 original size:15 final size:14
Alignment explanation
Indices: 40006951--40006980 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
40006941 GATAGATTCC
40006951 TAAAGAGAAGAGAGA
1 TAAAGAGAAGA-AGA
40006966 TAAAGAGAAGAAGA
1 TAAAGAGAAGAAGA
40006980 T
1 T
40006981 TTAATTGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.10
Consensus pattern (14 bp):
TAAAGAGAAGAAGA
Found at i:40009335 original size:14 final size:15
Alignment explanation
Indices: 40009296--40009336 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
40009286 TTTTTGTACA
40009296 TTTT-AAAATTTAGT
1 TTTTAAAAATTTAGT
* *
40009310 TTTTATACATTTA-T
1 TTTTAAAAATTTAGT
40009324 TTTTAAAAATTTA
1 TTTTAAAAATTTA
40009337 ATCCCTCCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (15 bp):
TTTTAAAAATTTAGT
Found at i:40010128 original size:28 final size:28
Alignment explanation
Indices: 40010088--40010141 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
40010078 AAGCAAAGGT
40010088 TTATAGATCGTATAACGACGAATCGGGC
1 TTATAGATCGTATAACGACGAATCGGGC
* *
40010116 TTATATATGGTATAACGACGAATCGG
1 TTATAGATCGTATAACGACGAATCGG
40010142 CGATAGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (28 bp):
TTATAGATCGTATAACGACGAATCGGGC
Found at i:40022931 original size:18 final size:19
Alignment explanation
Indices: 40022908--40022955 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
40022898 TTTACAATTT
40022908 TTTTAAAATTAT-TATAAA
1 TTTTAAAATTATATATAAA
*
40022926 TTTTAAAAGATATATATAAA
1 TTTTAAAA-TTATATATAAA
*
40022946 TTTTGAAATT
1 TTTTAAAATT
40022956 TTTAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 8 0.32
19 4 0.16
20 13 0.52
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (19 bp):
TTTTAAAATTATATATAAA
Found at i:40023809 original size:2 final size:2
Alignment explanation
Indices: 40023802--40023827 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40023792 AATATTTTAA
40023802 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
40023828 TGTCTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40027027 original size:20 final size:19
Alignment explanation
Indices: 40027002--40027041 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
40026992 AGGGAGAAAT
*
40027002 TTAACCATGGTTAAGTTAAA
1 TTAACCATAGTT-AGTTAAA
40027022 TTAACCATAGTTAGTTAAA
1 TTAACCATAGTTAGTTAAA
40027041 T
1 T
40027042 AATCAAGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (19 bp):
TTAACCATAGTTAGTTAAA
Found at i:40029737 original size:16 final size:16
Alignment explanation
Indices: 40029692--40029741 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
40029682 TAAACCTAGC
*
40029692 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
40029708 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
40029722 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
40029738 TAAT
1 TAAT
40029742 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:40044561 original size:67 final size:67
Alignment explanation
Indices: 40044453--40044586 Score: 250
Period size: 67 Copynumber: 2.0 Consensus size: 67
40044443 GTTTAACTCC
* *
40044453 AAATCAACACTATTGGTAGCCATTTGGGATGACACAAAAATATGTTCCCCATAAAGACTGTCGAT
1 AAATCAACACTATTGGTAGCCATTTGGGATGACACAAAAATATGTTCCCCACAAAAACTGTCGAT
40044518 TT
66 TT
40044520 AAATCAACACTATTGGTAGCCATTTGGGATGACACAAAAATATGTTCCCCACAAAAACTGTCGAT
1 AAATCAACACTATTGGTAGCCATTTGGGATGACACAAAAATATGTTCCCCACAAAAACTGTCGAT
40044585 TT
66 TT
40044587 GGGTAATAGA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (67 bp):
AAATCAACACTATTGGTAGCCATTTGGGATGACACAAAAATATGTTCCCCACAAAAACTGTCGAT
TT
Found at i:40044926 original size:11 final size:11
Alignment explanation
Indices: 40044910--40045011 Score: 62
Period size: 11 Copynumber: 9.0 Consensus size: 11
40044900 AAGCAACCTC
*
40044910 TAAAATAATAG
1 TAAAATAATAA
40044921 TAAAATTAATAA
1 TAAAA-TAATAA
*
40044933 TAAAATAAAAA
1 TAAAATAATAA
* * *
40044944 TTATATAATATCC
1 TAAAATAATA--A
*
40044957 TAACAAT-ACAA
1 TAA-AATAATAA
*
40044968 CAAAATAATAA
1 TAAAATAATAA
*
40044979 TAATATAATAA
1 TAAAATAATAA
*
40044990 TAAAATGATAA
1 TAAAATAATAA
* *
40045001 CAAAACAATAA
1 TAAAATAATAA
40045012 ATGAGAAAAA
Statistics
Matches: 67, Mismatches: 19, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
10 3 0.04
11 48 0.72
12 10 0.15
13 4 0.06
14 2 0.03
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:40046368 original size:30 final size:31
Alignment explanation
Indices: 40046332--40046435 Score: 97
Period size: 32 Copynumber: 3.3 Consensus size: 31
40046322 TATTCCTATA
*
40046332 TTAATTTTATAATAATTT-ATAAGATATTTT
1 TTAATTTTATAATAATTTCATAATATATTTT
* *
40046362 TTAATTTTATAAATATATTTCATTATA-ATTTG
1 TTAATTTTAT-AATA-ATTTCATAATATATTTT
* *
40046394 TTAATTTTTATAAT-ATTTGATCATATATTTGAT
1 TTAA-TTTTATAATAATTTCATAATATATTT--T
40046427 TTAATTTTA
1 TTAATTTTA
40046436 AAATTTTAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
30 19 0.31
31 8 0.13
32 20 0.33
33 14 0.23
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (31 bp):
TTAATTTTATAATAATTTCATAATATATTTT
Found at i:40046431 original size:33 final size:31
Alignment explanation
Indices: 40046332--40046450 Score: 92
Period size: 32 Copynumber: 3.9 Consensus size: 31
40046322 TATTCCTATA
*
40046332 TTAA-TTTTATAATAATTTATAAGATATTT-T
1 TTAATTTTTATAAT-ATTTATAATATATTTGT
* *
40046362 TTAATTTTATAAATATATTTCATTATA-ATTTG-
1 TTAATTTT-TATA-ATATTT-ATAATATATTTGT
*
40046394 TTAATTTTTATAATATTTGATCATATATTTGAT
1 TTAATTTTTATAATATTT-ATAATATATTTG-T
40046427 TTAA-TTTTA-AA-ATTT-TAATATATT
1 TTAATTTTTATAATATTTATAATATATT
40046451 ATAAAATATT
Statistics
Matches: 74, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
28 8 0.11
30 19 0.26
31 13 0.18
32 24 0.32
33 10 0.14
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (31 bp):
TTAATTTTTATAATATTTATAATATATTTGT
Found at i:40047100 original size:21 final size:22
Alignment explanation
Indices: 40047067--40047110 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
40047057 AAATGATTTT
* *
40047067 AAAATCATTAAATT-TTTTAAA
1 AAAAACATAAAATTATTTTAAA
40047088 AAAAACATAAAATTATTTTAAA
1 AAAAACATAAAATTATTTTAAA
40047110 A
1 A
40047111 TTAATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAACATAAAATTATTTTAAA
Found at i:40047109 original size:11 final size:11
Alignment explanation
Indices: 40047095--40047126 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
40047085 AAAAAAAACA
40047095 TAAAATTATTT
1 TAAAATTATTT
*
40047106 TAAAATTAATT
1 TAAAATTATTT
40047117 TAAAATTATT
1 TAAAATTATT
40047127 AAAATCATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:40047997 original size:9 final size:9
Alignment explanation
Indices: 40047983--40048024 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
40047973 GATGATGATG
40047983 ATTTTAATA
1 ATTTTAATA
40047992 ATTTT-AT-
1 ATTTTAATA
40047999 ATTTTAAAATA
1 ATTTT--AATA
40048010 ATTTTAATA
1 ATTTTAATA
40048019 ATTTTA
1 ATTTTA
40048025 TATTTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
7 5 0.17
8 2 0.07
9 15 0.52
10 2 0.07
11 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTTTAATA
Found at i:40048013 original size:27 final size:29
Alignment explanation
Indices: 40047983--40048053 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 29
40047973 GATGATGATG
40047983 ATTTTAATAATTTTATA-TTTT-AAAATA
1 ATTTTAATAATTTTATATTTTTAAAAATA
40048010 ATTTTAATAATTTTATATTTTTTAAAAAATA
1 ATTTTAATAATTTTATA-TTTTT-AAAAATA
40048041 ATTTTAATAATTT
1 ATTTTAATAATTT
40048054 CAAAATCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
27 17 0.43
29 4 0.10
31 19 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
ATTTTAATAATTTTATATTTTTAAAAATA
Found at i:40048058 original size:22 final size:22
Alignment explanation
Indices: 40048015--40048058 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
40048005 AAATAATTTT
* *
40048015 AATAATTTTATATTTTTTAAAA
1 AATAATTTTATATATTTCAAAA
40048037 AATAATTTTA-ATAATTTCAAAA
1 AATAATTTTATAT-ATTTCAAAA
40048059 TCATTTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTATATATTTCAAAA
Found at i:40056899 original size:31 final size:30
Alignment explanation
Indices: 40056841--40056899 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
40056831 TATCTATTTA
*
40056841 TTTATTTTATATTTGAATTCAATAATTAAG
1 TTTATTTTATATTTGAATTCAAAAATTAAG
*
40056871 TTTATTTTAATTTTTGAACTT-AAAAATTA
1 TTTATTTT-ATATTTGAA-TTCAAAAATTA
40056900 TAGAAGTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.32
31 15 0.60
32 2 0.08
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.54
Consensus pattern (30 bp):
TTTATTTTATATTTGAATTCAAAAATTAAG
Found at i:40074347 original size:6 final size:6
Alignment explanation
Indices: 40074336--40074421 Score: 72
Period size: 6 Copynumber: 14.7 Consensus size: 6
40074326 ATTTGTTTTA
** *
40074336 AAATTT AAATTT ATTTTT AAATTT AAATTT -AATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * *
40074383 -ATTTT CAAATTT AAAATT --ATTAT AAATTT AAATTC AAAT
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAATTT AAAT
40074422 GTCCAAATTA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
4 2 0.03
5 10 0.16
6 44 0.70
7 7 0.11
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:40074377 original size:17 final size:17
Alignment explanation
Indices: 40074336--40074416 Score: 92
Period size: 17 Copynumber: 4.6 Consensus size: 17
40074326 ATTTGTTTTA
*
40074336 AAATTTAAATTTATTTTT
1 AAATTTAAATTTA-ATTT
40074354 AAATTTAAATTTAATTT
1 AAATTTAAATTTAATTT
* *
40074371 AAGTTTAAATTTATTTT
1 AAATTTAAATTTAATTT
*
40074388 CAAATTTAAAATT-ATTAT
1 -AAATTTAAATTTAATT-T
40074406 AAATTTAAATT
1 AAATTTAAATT
40074417 CAAATGTCCA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
17 30 0.56
18 24 0.44
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTAATTT
Found at i:40074377 original size:23 final size:24
Alignment explanation
Indices: 40074336--40074396 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
40074326 ATTTGTTTTA
**
40074336 AAATTTAAATTTATTTTTAAATTT
1 AAATTTAAATTTAAGTTTAAATTT
40074360 AAATTT-AATTTAAGTTTAAATTT
1 AAATTTAAATTTAAGTTTAAATTT
*
40074383 -ATTTTCAAATTTAA
1 AAATTT-AAATTTAA
40074397 AATTATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 4 0.12
23 15 0.47
24 13 0.41
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
AAATTTAAATTTAAGTTTAAATTT
Found at i:40074378 original size:35 final size:35
Alignment explanation
Indices: 40074336--40074416 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 35
40074326 ATTTGTTTTA
* *
40074336 AAATTTAAATTTATTTTTAAATTTAAATTTAATT-T
1 AAATTTAAATTTATTTTCAAATTTAAAATT-ATTAT
*
40074371 AAGTTTAAATTTATTTTCAAATTTAAAATTATTAT
1 AAATTTAAATTTATTTTCAAATTTAAAATTATTAT
40074406 AAATTTAAATT
1 AAATTTAAATT
40074417 CAAATGTCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 3 0.07
35 38 0.93
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (35 bp):
AAATTTAAATTTATTTTCAAATTTAAAATTATTAT
Found at i:40074383 original size:29 final size:29
Alignment explanation
Indices: 40074337--40074421 Score: 68
Period size: 29 Copynumber: 2.9 Consensus size: 29
40074327 TTTGTTTTAA
**
40074337 AATTTAAATTTATTTTTAAATTTAAATTT
1 AATTTAAATTTAAATTTAAATTTAAATTT
* *
40074366 AATTTAAGTTTAAATTT-ATTTTCAAATTT
1 AATTTAAATTTAAATTTAAATTT-AAATTT
* *
40074395 AAAATT--ATTATAAATTTAAATTCAAAT
1 -AATTTAAATT-TAAATTTAAATTTAAAT
40074422 GTCCAAATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
28 6 0.14
29 31 0.70
30 7 0.16
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (29 bp):
AATTTAAATTTAAATTTAAATTTAAATTT
Found at i:40074393 original size:53 final size:52
Alignment explanation
Indices: 40074304--40074416 Score: 147
Period size: 53 Copynumber: 2.2 Consensus size: 52
40074294 CCAAACCCAT
* * * *
40074304 TTTAAATTTATCTTAAGATTATATTTGTTTTAAAATTTAAATTTATTTTTAAA
1 TTTAAATTTATCTTAAGATTAAATTTATTTTAAAATTTAAAATTA-TTATAAA
* *
40074357 TTTAAATTTAAT-TTAAGTTTAAATTTATTTTCAAATTTAAAATTATTATAAA
1 TTTAAATTT-ATCTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
40074409 TTTAAATT
1 TTTAAATT
40074417 CAAATGTCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
52 14 0.26
53 37 0.70
54 2 0.04
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (52 bp):
TTTAAATTTATCTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
Found at i:40075037 original size:12 final size:13
Alignment explanation
Indices: 40075020--40075095 Score: 59
Period size: 15 Copynumber: 5.6 Consensus size: 13
40075010 AACATGTATC
40075020 TAATAA-ATATAG
1 TAATAATATATAG
*
40075032 TAATAAATATATAT
1 TAAT-AATATATAG
40075046 TAATAATCATAATCA-
1 TAATAAT-AT-AT-AG
40075061 TAATAA-ATATAG
1 TAATAATATATAG
*
40075073 TAATAATGATAGTAT
1 TAATAAT-ATA-TAG
40075088 TAATAATA
1 TAATAATA
40075096 ATTTTTTTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
11 1 0.02
12 12 0.23
13 7 0.13
14 15 0.28
15 17 0.32
16 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (13 bp):
TAATAATATATAG
Found at i:40076275 original size:30 final size:30
Alignment explanation
Indices: 40076240--40076525 Score: 298
Period size: 30 Copynumber: 9.6 Consensus size: 30
40076230 GGACTGTTCA
*
40076240 AAAATTACATTTTGACCCCTAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
40076270 AAAATTATATTTTGACCCCAAAACTTCTT-A
1 AAAATTACATTTTGACCCCAAAACTT-TTCC
40076300 AAAATTACATTTTGACCACC-AAACTTTTCC
1 AAAATTACATTTTGACC-CCAAAACTTTTCC
* * * * *
40076330 AAAATAATATTTTAACCTCAAAAC-TTTCTA
1 AAAATTACATTTTGACCCCAAAACTTTTC-C
* **
40076360 AAAATTATATTTTGACCCCTTAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * * *
40076390 AAAATTATATTTTAACCCAAAAAC-TTTCTA
1 AAAATTACATTTTGACCCCAAAACTTTTC-C
*
40076420 AAAATTACATTTTGACCCCTAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
40076450 AAAATTAGATTTTGACCCCAAAAC-TTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
40076479 AAAATTACCATTTT-ACCCCCAAAC-TTCCC
1 AAAATTA-CATTTTGACCCCAAAACTTTTCC
*
40076508 AAAATTTCATTTTGACCC
1 AAAATTACATTTTGACCC
40076526 TAATTTTACC
Statistics
Matches: 214, Mismatches: 32, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
28 6 0.03
29 46 0.21
30 150 0.70
31 12 0.06
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:40076312 original size:60 final size:60
Alignment explanation
Indices: 40076239--40076525 Score: 397
Period size: 60 Copynumber: 4.8 Consensus size: 60
40076229 TGGACTGTTC
40076239 AAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAAC-TTCTT
1 AAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTC-T
* * *
40076299 AAAAATTACATTTTGACCACC-AAACTTTTCCAAAATAATATTTTAACCTCAAAACTTTCT
1 AAAAATTACATTTTGACC-CCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTCT
* * * *
40076359 AAAAATTATATTTTGACCCCTTAACTTTTCCAAAATTATATTTTAACCCAAAAACTTTCT
1 AAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTCT
*
40076419 AAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTAGATTTTGACCCCAAAACTTTC-
1 AAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTCT
* * *
40076478 CAAAATTACCATTTT-ACCCCCAAAC-TTCCCAAAATT-TCATTTTGACCC
1 AAAAATTA-CATTTTGACCCCTAAACTTTTCCAAAATTAT-ATTTTGACCC
40076526 TAATTTTACC
Statistics
Matches: 205, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
58 20 0.10
59 18 0.09
60 162 0.79
61 5 0.02
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.36
Consensus pattern (60 bp):
AAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTCT
Found at i:40076585 original size:59 final size:58
Alignment explanation
Indices: 40076477--40076623 Score: 177
Period size: 59 Copynumber: 2.5 Consensus size: 58
40076467 CCAAAACTTT
** * *
40076477 CCAAAATTACCATTTTACCCCCAAACTTCCCAAAATTTCATTTTGACCCTAATTTTAC
1 CCAAAATTACCATTTTACCCCCAAACTTCCCAAAATCCCATTTTAACCCTAATTTCAC
* * * * * *
40076535 CCAAAATTACTATTTTACGTCTCGAACTTTCCAAAATCCCATTTTAACCCTGATTTCAC
1 CCAAAATTACCATTTTAC-CCCCAAACTTCCCAAAATCCCATTTTAACCCTAATTTCAC
* *
40076594 CAAAAATTACCATTTTACCCCCAAAATTCC
1 CCAAAATTACCATTTTACCCCCAAACTTCC
40076624 ATTTTTGACC
Statistics
Matches: 71, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
58 24 0.34
59 47 0.66
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (58 bp):
CCAAAATTACCATTTTACCCCCAAACTTCCCAAAATCCCATTTTAACCCTAATTTCAC
Found at i:40076654 original size:50 final size:49
Alignment explanation
Indices: 40076565--40076663 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 49
40076555 CTCGAACTTT
40076565 CCAAAATCCCATTTTAACCCTGATTTCACCAAAAATTACCATTTTACCC
1 CCAAAATCCCATTTTAACCCTGATTTCACCAAAAATTACCATTTTACCC
* * * *
40076614 CCAAAATTCCATTTTTGA-CCTCGATTTTACCCAAAATTACCATTTTACCC
1 CCAAAATCCCA-TTTTAACCCT-GATTTCACCAAAAATTACCATTTTACCC
40076664 TCTAACCTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
49 13 0.30
50 31 0.70
ACGTcount: A:0.32, C:0.31, G:0.03, T:0.33
Consensus pattern (49 bp):
CCAAAATCCCATTTTAACCCTGATTTCACCAAAAATTACCATTTTACCC
Found at i:40076723 original size:108 final size:108
Alignment explanation
Indices: 40076505--40076723 Score: 257
Period size: 108 Copynumber: 2.0 Consensus size: 108
40076495 CCCCAAACTT
* * * *
40076505 CCCAAAATTTCATTTTGACCCTAATTTTACCCAAAATTACTATTTTACGTCTCGAACTTTCCAAA
1 CCCAAAATTCCATTTTGACCCTAATTTTACCCAAAATTACCATTTTACGCCTCGAACCTTCCAAA
* *
40076570 ATCCCATTTTAACCCTGATTTCACCAAAAATTACCATTTTACC
66 ATCCCATTTTAACCCTAATTTAACCAAAAATTACCATTTTACC
* *
40076613 CCCAAAATTCCATTTTTGA-CCTCGATTTTACCCAAAATTACCATTTTAC-CCTCTAACCTTCCA
1 CCCAAAATTCCA-TTTTGACCCT-AATTTTACCCAAAATTACCATTTTACGCCTCGAACCTTCCA
* * * * *
40076676 AAATCCCCGTTTTGACCC-AATTTTAACC-AATATTACCGTTTTGCC
64 AAAT-CCCATTTTAACCCTAA-TTTAACCAAAAATTACCATTTTACC
40076721 CCC
1 CCC
40076724 GGGTATCCAA
Statistics
Matches: 94, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
108 47 0.50
109 47 0.50
ACGTcount: A:0.30, C:0.31, G:0.05, T:0.35
Consensus pattern (108 bp):
CCCAAAATTCCATTTTGACCCTAATTTTACCCAAAATTACCATTTTACGCCTCGAACCTTCCAAA
ATCCCATTTTAACCCTAATTTAACCAAAAATTACCATTTTACC
Found at i:40077897 original size:18 final size:18
Alignment explanation
Indices: 40077874--40077909 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
40077864 GAATAAATCT
*
40077874 TTAATTAAATAAATTTAA
1 TTAATTAAAAAAATTTAA
40077892 TTAATTAAAAAAATTTAA
1 TTAATTAAAAAAATTTAA
40077910 CCCTAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAATTAAAAAAATTTAA
Found at i:40078258 original size:18 final size:18
Alignment explanation
Indices: 40078235--40078270 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
40078225 AGATTTAAGG
*
40078235 TTAAATTTTTTTAATTAA
1 TTAAATTTATTTAATTAA
40078253 TTAAATTTATTTAATTAA
1 TTAAATTTATTTAATTAA
40078271 AGATTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAAATTTATTTAATTAA
Done.