Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 95 of 325
Found at i:31352528 original size:18 final size:17
Alignment explanation
Indices: 31352505--31352538 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31352495 AATGGAAAAT
31352505 TTATATTAAATTATTAAG
1 TTATATTAAA-TATTAAG
*
31352523 TTATATTCAATATTAA
1 TTATATTAAATATTAA
31352539 ATTTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TTATATTAAATATTAAG
Found at i:31352942 original size:23 final size:22
Alignment explanation
Indices: 31352915--31352963 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 22
31352905 TTTCAATTCC
31352915 TTTTAATTTAAT-T--T-AATT
1 TTTTAATTTAATATAATGAATT
31352933 TTTTAATTTAATATAATGAATT
1 TTTTAATTTAATATAATGAATT
*
31352955 TTTTTATTT
1 TTTTAATTT
31352964 TGAATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 12 0.46
19 1 0.04
21 1 0.04
22 12 0.46
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTAATTTAATATAATGAATT
Found at i:31353455 original size:25 final size:26
Alignment explanation
Indices: 31353406--31353455 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
31353396 TTAGTGCTAA
* *
31353406 ATTAAATAAAAAAGCTTAACCACCAG
1 ATTAAATAAAAAACCTTAAACACCAG
*
31353432 ATTAAA-AAAAAACCTTAAATACCA
1 ATTAAATAAAAAACCTTAAACACCA
31353456 AGAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.58, C:0.18, G:0.04, T:0.20
Consensus pattern (26 bp):
ATTAAATAAAAAACCTTAAACACCAG
Found at i:31357931 original size:24 final size:24
Alignment explanation
Indices: 31357868--31357919 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
31357858 TTTCTAAAAG
* * *
31357868 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
31357892 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
31357916 ATTT
1 ATTT
31357920 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:31362295 original size:24 final size:24
Alignment explanation
Indices: 31362267--31362319 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
31362257 TTTCTAAAAG
*
31362267 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGTATAATAT
*
31362291 ATTTAGCATTTATTAGTATAATAT
1 ATTTAGCATTTATGAGTATAATAT
31362315 ATTTA
1 ATTTA
31362320 ACTTTGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (24 bp):
ATTTAGCATTTATGAGTATAATAT
Found at i:31362329 original size:24 final size:24
Alignment explanation
Indices: 31362274--31362330 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
31362264 AAGATTTAGT
* *
31362274 ATTTATGAGTATAATATATTTAGC
1 ATTTATTAGTATAATATATTTAAC
31362298 ATTTATTAGTATAATATATTTAAC
1 ATTTATTAGTATAATATATTTAAC
31362322 -TTTGATTAG
1 ATTT-ATTAG
31362331 AATTAGGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.49
Consensus pattern (24 bp):
ATTTATTAGTATAATATATTTAAC
Found at i:31362750 original size:22 final size:23
Alignment explanation
Indices: 31362719--31362762 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
31362709 TTTATGAAGA
31362719 TTCATTAAAA-CATCATGCATTTC
1 TTCATTAAAAGCATCAT-CATTTC
31362742 TTCA-TAAAAGCATCATCATTT
1 TTCATTAAAAGCATCATCATTT
31362763 AATTAGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (23 bp):
TTCATTAAAAGCATCATCATTTC
Found at i:31363088 original size:13 final size:13
Alignment explanation
Indices: 31363070--31363096 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31363060 TCCTTTTTAC
31363070 AACTTAAAACCCA
1 AACTTAAAACCCA
31363083 AACTTAAAACCCA
1 AACTTAAAACCCA
31363096 A
1 A
31363097 TTACAAATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.30, G:0.00, T:0.15
Consensus pattern (13 bp):
AACTTAAAACCCA
Found at i:31365458 original size:14 final size:14
Alignment explanation
Indices: 31365439--31365492 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
31365429 TTCTTTTATG
31365439 TAAATATTTTCTTT
1 TAAATATTTTCTTT
* *
31365453 TAAATATTTATGTATA
1 TAAATATTT-TCT-TT
*
31365469 TATATATTTTCTTT
1 TAAATATTTTCTTT
31365483 TAAATATTTT
1 TAAATATTTT
31365493 TTGTGTATCT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 19 0.59
15 4 0.12
16 9 0.28
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (14 bp):
TAAATATTTTCTTT
Found at i:31365460 original size:30 final size:29
Alignment explanation
Indices: 31365426--31365499 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 29
31365416 TGTTGATTTT
31365426 ATATTCTTTTATGTAAATATTTTCTTTTAA
1 ATATT-TTTTATGTAAATATTTTCTTTTAA
* * *
31365456 ATATTTATGTATATATATATTTTCTTTTAA
1 ATATTT-TTTATGTAAATATTTTCTTTTAA
*
31365486 ATATTTTTTGTGTA
1 ATATTTTTTATGTA
31365500 TCTAATCTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 6 0.16
30 31 0.84
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (29 bp):
ATATTTTTTATGTAAATATTTTCTTTTAA
Found at i:31367455 original size:21 final size:21
Alignment explanation
Indices: 31367431--31367470 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31367421 TATTTTTGTA
*
31367431 TTTGTTTACTATTATTTTTAG
1 TTTGCTTACTATTATTTTTAG
* *
31367452 TTTGCTTATTATTCTTTTT
1 TTTGCTTACTATTATTTTT
31367471 CTTATTTGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTGCTTACTATTATTTTTAG
Found at i:31368017 original size:7 final size:6
Alignment explanation
Indices: 31367976--31368028 Score: 52
Period size: 6 Copynumber: 8.2 Consensus size: 6
31367966 GAAAATCCTA
* *
31367976 TTTTAT TTTATTT ATTTTAT TTTTAT TTTTAT TTTGAT TTTTGAT TTTATAT
1 TTTTAT TTT-TAT -TTTTAT TTTTAT TTTTAT TTTTAT TTTT-AT TTT-TAT
31368028 T
1 T
31368029 AAATTAGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 23 0.59
7 12 0.31
8 4 0.10
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:31368028 original size:26 final size:26
Alignment explanation
Indices: 31367976--31368028 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
31367966 GAAAATCCTA
*
31367976 TTTTATTTTATTTATTTTATTTTTAT
1 TTTTATTTTATTTATTTGATTTTTAT
31368002 TTTTATTTTGA-TT-TTTGATTTTATAT
1 TTTTATTTT-ATTTATTTGATTTT-TAT
31368028 T
1 T
31368029 AAATTAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.33
26 15 0.62
27 1 0.04
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (26 bp):
TTTTATTTTATTTATTTGATTTTTAT
Found at i:31382642 original size:25 final size:25
Alignment explanation
Indices: 31382594--31382642 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
31382584 TTAAAATATA
* * * *
31382594 AAAAATGACTGTTTTGCCCTTAGGT
1 AAAAATGACTATTATACCCCTAGGT
31382619 AAAAATGACTATTATACCCCTAGG
1 AAAAATGACTATTATACCCCTAGG
31382643 GTTTAATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (25 bp):
AAAAATGACTATTATACCCCTAGGT
Found at i:31382705 original size:11 final size:10
Alignment explanation
Indices: 31382673--31382728 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
31382663 CATGAGATTT
31382673 TGATAT-ACA
1 TGATATGACA
*
31382682 TGATTTGACA
1 TGATATGACA
31382692 TGATATGCACA
1 TGATATG-ACA
**
31382703 TGATATGTTA
1 TGATATGACA
*
31382713 TGAGATGCACA
1 TGATATG-ACA
31382724 TGATA
1 TGATA
31382729 CACTCATTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
9 5 0.14
10 16 0.44
11 15 0.42
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (10 bp):
TGATATGACA
Found at i:31382705 original size:21 final size:21
Alignment explanation
Indices: 31382679--31382728 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
31382669 ATTTTGATAT
* *
31382679 ACATGATTTGACATGATATGC
1 ACATGATATGACATGAGATGC
**
31382700 ACATGATATGTTATGAGATGC
1 ACATGATATGACATGAGATGC
31382721 ACATGATA
1 ACATGATA
31382729 CACTCATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (21 bp):
ACATGATATGACATGAGATGC
Found at i:31382830 original size:25 final size:24
Alignment explanation
Indices: 31382775--31382846 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 24
31382765 GGAGGAAGTG
*
31382775 CAAAAAGGGCTTTGCCCGAGTTTAC
1 CAAAAA-GGCTTTGCCCCAGTTTAC
* *
31382800 CGAAAAGGCCTTTGCCCCAGTTTAT
1 CAAAAAGG-CTTTGCCCCAGTTTAC
*
31382825 CAAAAAGAGCTTTACCCCAGTT
1 CAAAAAG-GCTTTGCCCCAGTT
31382847 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 2 0.05
25 37 0.93
26 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (24 bp):
CAAAAAGGCTTTGCCCCAGTTTAC
Found at i:31382869 original size:25 final size:25
Alignment explanation
Indices: 31382841--31382898 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
31382831 GAGCTTTACC
31382841 CCAGTTATTAAAAGAGGCTAGGCCT
1 CCAGTTATTAAAAGAGGCTAGGCCT
31382866 CCAGTTATTAAAAGAGGCTAGGCCT
1 CCAGTTATTAAAAGAGGCTAGGCCT
31382891 CCAGTTAT
1 CCAGTTAT
31382899 GCTGCCAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (25 bp):
CCAGTTATTAAAAGAGGCTAGGCCT
Found at i:31385085 original size:11 final size:11
Alignment explanation
Indices: 31385069--31385096 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
31385059 AACACATGCT
31385069 AATGGCTTCAC
1 AATGGCTTCAC
31385080 AATGGCTTCAC
1 AATGGCTTCAC
31385091 AATGGC
1 AATGGC
31385097 CAGGAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (11 bp):
AATGGCTTCAC
Found at i:31387371 original size:44 final size:44
Alignment explanation
Indices: 31387323--31387423 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 44
31387313 GTGGCCTTAC
* * * *
31387323 AGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTACAGTGG
1 AGCAGATTAAAGCAACAAATCCTATCTCCCTGAAATTACAGTGG
* * *
31387367 AGCAGATTGAAGCAACAAATCCTATCTCTCTGAAATTGCAGTGG
1 AGCAGATTAAAGCAACAAATCCTATCTCCCTGAAATTACAGTGG
31387411 AGCAGATTAAAGC
1 AGCAGATTAAAGC
31387424 GAGCTAATCC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (44 bp):
AGCAGATTAAAGCAACAAATCCTATCTCCCTGAAATTACAGTGG
Found at i:31387451 original size:45 final size:44
Alignment explanation
Indices: 31387323--31387453 Score: 138
Period size: 44 Copynumber: 3.0 Consensus size: 44
31387313 GTGGCCTTAC
* * ** * *
31387323 AGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTACAGTGG
1 AGCAGATTAAAGCAACAAATCCAATCTCTCTGAAGTTGCAGTGG
* * *
31387367 AGCAGATTGAAGCAACAAATCCTATCTCTCTGAAATTGCAGTGG
1 AGCAGATTAAAGCAACAAATCCAATCTCTCTGAAGTTGCAGTGG
* *
31387411 AGCAGATTAAAGCGAGCTAATCCAATAC-CTCTGAAGTTGCAGT
1 AGCAGATTAAAGC-AACAAATCCAAT-CTCTCTGAAGTTGCAGT
31387454 CGGTCGGATT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
44 49 0.67
45 23 0.32
46 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (44 bp):
AGCAGATTAAAGCAACAAATCCAATCTCTCTGAAGTTGCAGTGG
Found at i:31387838 original size:13 final size:13
Alignment explanation
Indices: 31387820--31387847 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31387810 CTTTTTTTAC
31387820 AACTTTAAACCCA
1 AACTTTAAACCCA
31387833 AACTTTAAACCCA
1 AACTTTAAACCCA
31387846 AA
1 AA
31387848 AACAAATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (13 bp):
AACTTTAAACCCA
Found at i:31389301 original size:22 final size:22
Alignment explanation
Indices: 31389275--31389326 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
31389265 TACATACCAT
*
31389275 TTATTTTTGAATTTGTTTATTA
1 TTATTTTTGAATTTGCTTATTA
* *
31389297 TTATTTTTTAGTTTGCTTATTA
1 TTATTTTTGAATTTGCTTATTA
*
31389319 TTCTTTTT
1 TTATTTTT
31389327 CTTATTTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.17, C:0.04, G:0.08, T:0.71
Consensus pattern (22 bp):
TTATTTTTGAATTTGCTTATTA
Found at i:31390368 original size:23 final size:23
Alignment explanation
Indices: 31390303--31390375 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
31390293 CTATCTCCTA
31390303 CCAAACACAACC-AATTTACCCT
1 CCAAACACAACCAAATTTACCCT
* **
31390325 CCAAACAGAACCAAACATACCCT
1 CCAAACACAACCAAATTTACCCT
* *
31390348 CCAAGCACAACCAAATTTACCCC
1 CCAAACACAACCAAATTTACCCT
31390371 CCAAA
1 CCAAA
31390376 TGCATCCACT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 11 0.27
23 30 0.73
ACGTcount: A:0.44, C:0.41, G:0.03, T:0.12
Consensus pattern (23 bp):
CCAAACACAACCAAATTTACCCT
Found at i:31405210 original size:30 final size:31
Alignment explanation
Indices: 31405147--31405216 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
31405137 AAATTACACC
* * * *
31405147 AACAATCACTCAACTTTGGAGTAACCGACAA
1 AACAATCACTCAACTTTCGAGAAAACAACAA
*
31405178 AACAATCACTCAACTTTCGA-AAAATAACAA
1 AACAATCACTCAACTTTCGAGAAAACAACAA
*
31405208 AACAGTCAC
1 AACAATCAC
31405217 CACTAACTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.47, C:0.26, G:0.09, T:0.19
Consensus pattern (31 bp):
AACAATCACTCAACTTTCGAGAAAACAACAA
Found at i:31405259 original size:30 final size:30
Alignment explanation
Indices: 31405225--31405297 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
31405215 ACCACTAACT
31405225 ATTTTTCATTACAAACATAACAGAGCTACC
1 ATTTTTCATTACAAACATAACAGAGCTACC
* * ** *
31405255 A-TTTTCTGTTACAAACGTAATGGAGGTACC
1 ATTTTTC-ATTACAAACATAACAGAGCTACC
31405285 ATTTTTCATTACA
1 ATTTTTCATTACA
31405298 GTTTCACTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 5 0.14
30 25 0.71
31 5 0.14
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (30 bp):
ATTTTTCATTACAAACATAACAGAGCTACC
Found at i:31411654 original size:22 final size:23
Alignment explanation
Indices: 31411624--31411672 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
31411614 AAAAAAGATT
31411624 TTTCGAAAAAATAAATAAAAAAC
1 TTTCGAAAAAATAAATAAAAAAC
*
31411647 TTTC-AAAAAATCAATAAAAAAC
1 TTTCGAAAAAATAAATAAAAAAC
31411669 TTTC
1 TTTC
31411673 CTTTCGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
TTTCGAAAAAATAAATAAAAAAC
Found at i:31415910 original size:3 final size:3
Alignment explanation
Indices: 31415902--31416022 Score: 81
Period size: 3 Copynumber: 40.7 Consensus size: 3
31415892 CATAAAAGAC
* * * *
31415902 AAT AAT AAT AAT AAT AAT -AT AAT ACCT -AT GAT ACT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* * * *
31415946 AAT AAT AAG AA- AATT AAT ATT AGT ATT AAT AAT AAT GGAA- AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT --AAT AAT AAT
* *
31415992 AAT AAC AAT AAT AAT -AT AGT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
31416023 AAGTGAAATT
Statistics
Matches: 93, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
2 9 0.10
3 79 0.85
4 3 0.03
5 2 0.02
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31430518 original size:73 final size:73
Alignment explanation
Indices: 31430412--31430836 Score: 503
Period size: 73 Copynumber: 5.9 Consensus size: 73
31430402 TAATTCATGT
** * ** **
31430412 TTTCAAAAATCAACTCATATTGTGAGAAATGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTC
1 TTTCAAAAATTGACTCATATTGCGAGAGGTGAGTCAAGCCTCAGGTCACACGCTGAGGTATTTTC
31430477 AGTTTATG
66 AGTTTATG
* *
31430485 TTTCAAAAATTGACTCATATTGCGAGAGGTGAGTCAAGCCTCAGGTCATACGCTGAGGTATTTTT
1 TTTCAAAAATTGACTCATATTGCGAGAGGTGAGTCAAGCCTCAGGTCACACGCTGAGGTATTTTC
*
31430550 AATTTATG
66 AGTTTATG
31430558 TTTCAAAAAATTGACTCATATTGCGAGAGGTGAGTCAAGCCTCAGGTCACACGCTGAGGTATTTT
1 TTTC-AAAAATTGACTCATATTGCGAGAGGTGAGTCAAGCCTCAGGTCACACGCTGAGGTATTTT
*
31430623 TAGTTTATG
65 CAGTTTATG
*
31430632 TTTCAAAAATTGACTCATATTGCGAGAGGTGAGTCAAGCCTCAGGT--CACGCTGAGGTATTTTA
1 TTTCAAAAATTGACTCATATTGCGAGAGGTGAGTCAAGCCTCAGGTCACACGCTGAGGTATTTTC
* *
31430695 ATTTCTTTTG
66 A-GT-TTATG
* * ** * **
31430705 TTTCAAAAA-TCAGCTCATATTGCGAGGGGTGAGTTGAGCC-CCGG-GGCACGCTGAGGTATTTT
1 TTTCAAAAATTGA-CTCATATTGCGAGAGGTGAGTCAAGCCTCAGGTCACACGCTGAGGTATTTT
31430767 -AGTTTATG
65 CAGTTTATG
* ** *
31430775 TTT-AGAAAA-T-ACTCATATTGTGAGAGGTGAGTCAAGCCTC-GG-GGCACGCTGAGGTCTTTT
1 TTTCA-AAAATTGACTCATATTGCGAGAGGTGAGTCAAGCCTCAGGTCACACGCTGAGGTATTTT
31430835 CA
65 CA
31430837 ATTTCTGCTT
Statistics
Matches: 316, Mismatches: 27, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
68 42 0.13
69 4 0.01
70 12 0.04
71 18 0.06
72 7 0.02
73 162 0.51
74 71 0.22
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (73 bp):
TTTCAAAAATTGACTCATATTGCGAGAGGTGAGTCAAGCCTCAGGTCACACGCTGAGGTATTTTC
AGTTTATG
Found at i:31430660 original size:147 final size:144
Alignment explanation
Indices: 31430393--31430840 Score: 577
Period size: 147 Copynumber: 3.1 Consensus size: 144
31430383 GGGTACTCTA
* * * * **
31430393 AGGTATCTTTAATTCATGTTTTCAAAAATCAACTCATATTGTGAGAAATGAGTTGAGCCTCAGGT
1 AGGTATTTTTAATTTATG-TTTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
*
31430458 CACACGCTGAGGTATTTTCAGTTTATGTTTCAAAAATTGACTCATATTGCGAGAGGTGAGTCAAG
65 CACACGCTGAGGTATTTTTAGTTTATGTTTCAAAAATTGACTCATATTGCGAGAGGTGAGTCAAG
31430523 CCTCAGGTCATACGCTG
130 CCTCAGGTC--ACGCTG
* **
31430540 AGGTATTTTTAATTTATGTTTCAAAAAATTGACTCATATTGCGAGAGGTGAGTCAAGCCTCAGGT
1 AGGTATTTTTAATTTATGTTTC-AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
31430605 CACACGCTGAGGTATTTTTAGTTTATGTTTCAAAAATTGACTCATATTGCGAGAGGTGAGTCAAG
65 CACACGCTGAGGTATTTTTAGTTTATGTTTCAAAAATTGACTCATATTGCGAGAGGTGAGTCAAG
31430670 CCTCAGGTCACGCTG
130 CCTCAGGTCACGCTG
* * * * *
31430685 AGGTA-TTTTAATTTCTTTTGTTTCAAAAATCAGCTCATATTGCGAGGGGTGAGTTGAGCC-CCG
1 AGGTATTTTTAA--T-TTATGTTTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
** *
31430748 G-GGCACGCTGAGGTA-TTTTAGTTTATGTTT-AGAAAA-T-ACTCATATTGTGAGAGGTGAGTC
63 GTCACACGCTGAGGTATTTTTAGTTTATGTTTCA-AAAATTGACTCATATTGCGAGAGGTGAGTC
* *
31430808 AAGCCTCGGGGCACGCTG
127 AAGCCTCAGGTCACGCTG
* *
31430826 AGGTCTTTTCAATTT
1 AGGTATTTTTAATTT
31430841 CTGCTTTTCA
Statistics
Matches: 270, Mismatches: 25, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
139 2 0.01
140 1 0.00
141 42 0.16
142 7 0.03
143 19 0.07
144 18 0.07
145 14 0.05
146 35 0.13
147 132 0.49
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33
Consensus pattern (144 bp):
AGGTATTTTTAATTTATGTTTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
ACACGCTGAGGTATTTTTAGTTTATGTTTCAAAAATTGACTCATATTGCGAGAGGTGAGTCAAGC
CTCAGGTCACGCTG
Found at i:31430849 original size:14 final size:14
Alignment explanation
Indices: 31430830--31430865 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
31430820 ACGCTGAGGT
* *
31430830 CTTTTCAATTTCTG
1 CTTTTCAATTCCTA
31430844 CTTTTCAATTCCTA
1 CTTTTCAATTCCTA
31430858 CTTTTCAA
1 CTTTTCAA
31430866 AAAAATCAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.19, C:0.25, G:0.03, T:0.53
Consensus pattern (14 bp):
CTTTTCAATTCCTA
Found at i:31430936 original size:13 final size:13
Alignment explanation
Indices: 31430918--31430942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31430908 CACGCTGAGG
31430918 TATTTTCAATTTC
1 TATTTTCAATTTC
31430931 TATTTTCAATTT
1 TATTTTCAATTT
31430943 ATGTTGTTCA
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:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTCAATTTC
Found at i:31433148 original size:10 final size:9
Alignment explanation
Indices: 31433119--31433176 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
31433109 TTTCTTTTTC
31433119 ATATTAT-T
1 ATATTATAT
*
31433127 ATTTTA-AT
1 ATATTATAT
31433135 ATATGTATAT
1 ATAT-TATAT
31433145 ATATTATAT
1 ATATTATAT
* *
31433154 TTGTGTATAT
1 ATAT-TATAT
31433164 -TATTATAT
1 ATATTATAT
31433172 ATATT
1 ATATT
31433177 TTTAATGTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
8 14 0.35
9 15 0.38
10 11 0.28
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (9 bp):
ATATTATAT
Found at i:31434798 original size:3 final size:3
Alignment explanation
Indices: 31434790--31434847 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
31434780 GGATTAAAAT
* *
31434790 ATA ATA ATA ATA ATA GTA ATA ATA ATA GA-C ATA ATA ATA GA-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA ATA
31434835 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
31434848 AGTAAAGAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:31434809 original size:12 final size:12
Alignment explanation
Indices: 31434794--31434847 Score: 74
Period size: 12 Copynumber: 4.5 Consensus size: 12
31434784 TAAAATATAA
31434794 TAATAATAATAG
1 TAATAATAATAG
31434806 TAATAATAATAG
1 TAATAATAATAG
31434818 -ACATAATAATAG
1 TA-ATAATAATAG
* *
31434830 AAATAATAATAA
1 TAATAATAATAG
31434842 TAATAA
1 TAATAA
31434848 AGTAAAGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
11 1 0.03
12 36 0.95
13 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (12 bp):
TAATAATAATAG
Found at i:31434883 original size:26 final size:24
Alignment explanation
Indices: 31434808--31434894 Score: 68
Period size: 26 Copynumber: 3.4 Consensus size: 24
31434798 AATAATAGTA
*
31434808 ATAATAATAG-ACATAATAATAGAAATA
1 ATAATAATAGTA-A-AATAA-AG-AATC
* *
31434835 ATAATAATAATAAAGTAAAGAATAC
1 ATAATAATAGTAAAATAAAGAAT-C
* *
31434860 ATTAATAATAGTAAAATCAGGAATC
1 A-TAATAATAGTAAAATAAAGAATC
31434885 ATAATAATAG
1 ATAATAATAG
31434895 CAGCAATAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
24 12 0.24
25 5 0.10
26 22 0.44
27 10 0.20
28 1 0.02
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (24 bp):
ATAATAATAGTAAAATAAAGAATC
Found at i:31435969 original size:22 final size:23
Alignment explanation
Indices: 31435927--31435970 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
31435917 CACTATTGAT
*
31435927 TATTTTTTTTTGTATGCTTGAATC
1 TATTTTTTTTCGTAT-CTTGAATC
31435951 TATTTTTTTTCGTAT-TTGAA
1 TATTTTTTTTCGTATCTTGAA
31435971 AAAAAATGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
24 14 0.74
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.64
Consensus pattern (23 bp):
TATTTTTTTTCGTATCTTGAATC
Found at i:31437808 original size:230 final size:231
Alignment explanation
Indices: 31437340--31437814 Score: 918
Period size: 230 Copynumber: 2.1 Consensus size: 231
31437330 GATTAAATAA
*
31437340 GTTATTATATGATATGATCTGATATTGCTATATTTTTACCAAAATCCTCTCATTTATTAGGCAAT
1 GTTA-TATATGATATGATCTGATATTGCTATATTTTTACCAAAATCCTCTCACTTATTAGGCAAT
31437405 CTTTCGGACCTGGTGACCCAACCCATAAACAGGTCTAACCTTGTATTATTTTTATTATTATTTTA
65 CTTTCGGACCTGGTGACCCAACCCATAAACAGGTCTAACCTTGTATTATTTTTATTATTATTTTA
31437470 AAACAATACATTAACACGCGCAATCATATGATTTGACTTCTCCTACTGTTGCTTTATCATTTTTC
130 AAACAATACATTAACACGCGCAATCATATGATTTGACTTCTCCTACTGTTGCTTTATCATTTTTC
31437535 ATAGAAAAAAAAATTATTATGTTCTAACAATAACAAT
195 ATAGAAAAAAAAATTATTATGTTCTAACAATAACAAT
31437572 GTTATATATGATATGATCTGATATTGCTATATTTTTACCAAAATCCTCTCACTTATTAGGCAATC
1 GTTATATATGATATGATCTGATATTGCTATATTTTTACCAAAATCCTCTCACTTATTAGGCAATC
31437637 TTTCGGACCTGGTGACCCAACCCATAAACAGGTCTAACCTTGTATTATTTTT-TTATTATTTTAA
66 TTTCGGACCTGGTGACCCAACCCATAAACAGGTCTAACCTTGTATTATTTTTATTATTATTTTAA
31437701 AACAATACATTAACACGCGCAATCATATGATTTGACTTCTCCTACTGTTGCTTTATCATTTTTCA
131 AACAATACATTAACACGCGCAATCATATGATTTGACTTCTCCTACTGTTGCTTTATCATTTTTCA
31437766 TAGAAAAAAAAATTATTATGTTCTAACAATAACAAT
196 TAGAAAAAAAAATTATTATGTTCTAACAATAACAAT
31437802 GTTATATAT-ATAT
1 GTTATATATGATAT
31437815 AGAGTAAACT
Statistics
Matches: 242, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
229 4 0.02
230 122 0.50
231 112 0.46
232 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.39
Consensus pattern (231 bp):
GTTATATATGATATGATCTGATATTGCTATATTTTTACCAAAATCCTCTCACTTATTAGGCAATC
TTTCGGACCTGGTGACCCAACCCATAAACAGGTCTAACCTTGTATTATTTTTATTATTATTTTAA
AACAATACATTAACACGCGCAATCATATGATTTGACTTCTCCTACTGTTGCTTTATCATTTTTCA
TAGAAAAAAAAATTATTATGTTCTAACAATAACAAT
Found at i:31437874 original size:21 final size:21
Alignment explanation
Indices: 31437836--31437877 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31437826 CAATGCAAAC
***
31437836 CACTCAATTATTGTTTTTTTT
1 CACTCAATTATAAATTTTTTT
31437857 CACTCAATTATAAATTTTTTT
1 CACTCAATTATAAATTTTTTT
31437878 ATTTTGGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.14, G:0.02, T:0.57
Consensus pattern (21 bp):
CACTCAATTATAAATTTTTTT
Found at i:31437970 original size:30 final size:28
Alignment explanation
Indices: 31437903--31437973 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 28
31437893 TTATTGTCTT
*
31437903 TTTTTTTG-TCACCCAACTATTAAATTT
1 TTTTTTTGTTCACCCAACTATTAAATTA
*
31437930 TTTTAATTTGTTCACCCAACTAATCTAGATTA
1 TTTT--TTTGTTCACCCAACT-AT-TAAATTA
31437962 TTTTTTTGTTCA
1 TTTTTTTGTTCA
31437974 TTTCTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 4 0.11
29 4 0.11
30 18 0.49
31 2 0.05
32 9 0.24
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.52
Consensus pattern (28 bp):
TTTTTTTGTTCACCCAACTATTAAATTA
Found at i:31439572 original size:42 final size:42
Alignment explanation
Indices: 31439509--31439669 Score: 162
Period size: 42 Copynumber: 3.7 Consensus size: 42
31439499 CTTCGTTTTC
** * * *
31439509 TCGATGCCATAGTTCAACTATGGTTTTACACCTCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTTTTACACATATTCACAT-A
* *
31439552 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTTTTACACATATTCACATA
*
31439593 TCGATGCCATAGCCTAGCTATGGTTTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTTTTACAC---AT---AT-TCACATA
*
31439642 TCGATGCCATAGCCCAGATATGGTTTTA
1 TCGATGCCATAGCCCAGCTATGGTTTTA
31439670 TACGAAAATC
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.02
42 59 0.60
43 1 0.01
45 2 0.02
48 2 0.02
49 32 0.33
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTTTTACACATATTCACATA
Found at i:31439734 original size:31 final size:31
Alignment explanation
Indices: 31439691--31439839 Score: 237
Period size: 31 Copynumber: 4.8 Consensus size: 31
31439681 TTTGTCACTT
*
31439691 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
31439722 GTAGCC-AGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
31439753 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
31439784 GTAGCAGAAGCTATCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
31439815 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
31439840 TGTCATTTGT
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
30 1 0.01
31 106 0.99
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:31439924 original size:50 final size:51
Alignment explanation
Indices: 31439815--31439943 Score: 188
Period size: 50 Copynumber: 2.5 Consensus size: 51
31439805 CACTGATCAG
* * * * * *
31439815 GTAGCCGAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATTAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTAATCAGATAAGT
31439866 GTAGCCGAAGCTATCACTTATCACTT-TCACTTATCCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTAATCAGATAAGT
*
31439916 GTAGCCGAAGCTATCACTTATCTCTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
31439944 TGCCATAGTC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 45 0.64
51 25 0.36
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTAATCAGATAAGT
Found at i:31456375 original size:14 final size:14
Alignment explanation
Indices: 31456356--31456385 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31456346 TTATATCGAG
31456356 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
31456370 ACCAATCCAATTCA
1 ACCAATCCAAATCA
31456384 AC
1 AC
31456386 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:31464109 original size:14 final size:14
Alignment explanation
Indices: 31464090--31464119 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31464080 TATTATCGAG
31464090 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
31464104 ACCAATCCAATTCA
1 ACCAATCCAAATCA
31464118 AC
1 AC
31464120 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:31466770 original size:25 final size:27
Alignment explanation
Indices: 31466736--31466786 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
31466726 ATCGGTAAAA
*
31466736 TTTTTCTATCA-AT-ATTTTCATACGG
1 TTTTCCTATCATATAATTTTCATACGG
31466761 TTTTCCTATCATATCAATTTTCATAC
1 TTTTCCTATCATAT-AATTTTCATAC
31466787 AAAAATATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 2 0.09
28 10 0.45
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.51
Consensus pattern (27 bp):
TTTTCCTATCATATAATTTTCATACGG
Found at i:31476238 original size:17 final size:18
Alignment explanation
Indices: 31476212--31476250 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
31476202 CTAAAGTGGA
31476212 CAAAAAAAATATAA-TAC
1 CAAAAAAAATATAATTAC
* *
31476229 CAAAATAAATCTAATTAC
1 CAAAAAAAATATAATTAC
31476247 CAAA
1 CAAA
31476251 TTCAAGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (18 bp):
CAAAAAAAATATAATTAC
Found at i:31479891 original size:27 final size:27
Alignment explanation
Indices: 31479834--31479904 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
31479824 TACAGATTGC
* * * *
31479834 GCCTATGTCAGAGGCGCGGCTAGTTGA
1 GCCTATCTCAGAGGCGCGACTAATCGA
* * *
31479861 GCCTTTTTCAGAGGCGCGACTAATCGT
1 GCCTATCTCAGAGGCGCGACTAATCGA
31479888 GCCTATCTCAGAGGCGC
1 GCCTATCTCAGAGGCGC
31479905 AAATGGTAGG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.31, T:0.24
Consensus pattern (27 bp):
GCCTATCTCAGAGGCGCGACTAATCGA
Found at i:31485066 original size:3 final size:3
Alignment explanation
Indices: 31485058--31485267 Score: 207
Period size: 3 Copynumber: 70.3 Consensus size: 3
31485048 TTAATTAATT
* *
31485058 TTA TTA TTA TTA TTT TTA CTA TTA TT- TATA TTCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT-A TTA TTA TTA TTA
* * * *
31485104 TTA TTTA TTA TCA TCA TTA TTA TTA ATA TTA TTA TT- TT- TTA CTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
31485148 TTA TTA TTTA TTA TCA TTA TTA TTA TTA CTA CTA TTA CTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
31485194 TTA TTA TTA TTAA TTA TTA TCA TTA TTA TCA TTA TTA TTA CTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
31485240 TT- TTA TT- TT- TTA CTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
31485268 CATTTTTTAT
Statistics
Matches: 174, Mismatches: 24, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
2 11 0.06
3 150 0.86
4 13 0.07
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:31485094 original size:25 final size:26
Alignment explanation
Indices: 31485057--31485265 Score: 138
Period size: 25 Copynumber: 8.3 Consensus size: 26
31485047 ATTAATTAAT
* *
31485057 TTTATTATT-ATTATTTTTACTATTA
1 TTTATTATTCATTATTATTAATATTA
*
31485082 TTTA-TATTCATTATTATTATTATTA
1 TTTATTATTCATTATTATTAATATTA
31485107 TTTATTATCATCATTATTATTAATATTA
1 TTTATTAT--TCATTATTATTAATATTA
* * *
31485135 -TTATTTTTTACTATTATT-AT-TTA
1 TTTATTATTCATTATTATTAATATTA
* * *
31485158 -TTATCATT-ATTATTATTACTACTA
1 TTTATTATTCATTATTATTAATATTA
* *
31485182 -TTACTATT-ATTATTATTATTATTA
1 TTTATTATTCATTATTATTAATATTA
* * *
31485206 ATTATTA-TCATTATTATCATTATTA
1 TTTATTATTCATTATTATTAATATTA
* *
31485231 TTACTATTATT--TTATTTTTTACTATTA
1 TT--TATTATTCATTA-TTATTAATATTA
31485258 -TTATTATT
1 TTTATTATT
31485266 ATCATTTTTT
Statistics
Matches: 151, Mismatches: 21, Indels: 25
0.77 0.11 0.13
Matches are distributed among these distances:
22 8 0.05
23 10 0.07
24 36 0.24
25 52 0.34
26 7 0.05
27 20 0.13
28 18 0.12
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTATTATTCATTATTATTAATATTA
Found at i:31487003 original size:38 final size:38
Alignment explanation
Indices: 31486952--31487028 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
31486942 TACATGCCAG
*
31486952 AGTTGTAGGATTTCACTCGTATCAGCATAAGCCAAAAT
1 AGTTGTAAGATTTCACTCGTATCAGCATAAGCCAAAAT
**
31486990 AGTTGTAAGATTTCACTCGTATTGGCATAAGCCAAAAT
1 AGTTGTAAGATTTCACTCGTATCAGCATAAGCCAAAAT
31487028 A
1 A
31487029 ATCTTCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (38 bp):
AGTTGTAAGATTTCACTCGTATCAGCATAAGCCAAAAT
Found at i:31489411 original size:16 final size:16
Alignment explanation
Indices: 31489390--31489422 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31489380 TAAAAGATTA
31489390 AAAGTAA-ATAATACAC
1 AAAGTAATAT-ATACAC
31489406 AAAGTAATATATACAC
1 AAAGTAATATATACAC
31489422 A
1 A
31489423 GGAAAAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAGTAATATATACAC
Found at i:31490672 original size:15 final size:16
Alignment explanation
Indices: 31490654--31490683 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31490644 GGTTTTGGGC
31490654 TGTTGGG-TTTTTAGA
1 TGTTGGGCTTTTTAGA
31490669 TGTTGGGCTTTTTAG
1 TGTTGGGCTTTTTAG
31490684 CCCGGGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.03, G:0.33, T:0.53
Consensus pattern (16 bp):
TGTTGGGCTTTTTAGA
Found at i:31491455 original size:205 final size:205
Alignment explanation
Indices: 31491055--31492011 Score: 1484
Period size: 205 Copynumber: 4.7 Consensus size: 205
31491045 AAATCTGCTT
* * *
31491055 CTTCGATTTGTTCCCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* * * *
31491120 GTGAAAGCCAAATCAGCTATGTCTTTGATTTGCTCCTTATAAGCACAAGGATGCCAAATCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* * *
31491185 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTA-CTGCTCTCCATCGAAATG
131 GGATC-TACTTCAGTAAAAACATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCATCGAAATG
31491249 GAGATGCCAGA
195 GAGATGCCAGA
*
31491260 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGTGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* * *
31491325 GCGAAAACCAAATCAGCTATGTCTTTGATTTGCTCTTTGTAAGCACAAGGATGCCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
** * * * * *
31491390 GGATCTACTTCAGTAAAAACATCTGAAGTTTGGATCTGCTATGTGTCTGCCCTCCGTCAAAATGG
131 GGATCTACTTCAGTAAAAACATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCATCGAAATGG
*
31491455 AGATGCCAGG
196 AGATGCCAGA
* *
31491465 CTTCGACTTGTTCTCTGACAATACAGAGATGCCAATTCATCTTAGACTTGCTTTAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
*
31491530 ACGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* * * * *
31491595 AGATCTACTTCAGTGAAATCATCTTGAAGGCTAAATCTGCTATGTATTTGCTCTCCATCGAAATG
131 GGATCTACTTCAGTAAAAACATC-TGAAGGCTAGATCTGCTATGTATCTGCTCTCCATCGAAATG
31491660 GAGATGCCAGA
195 GAGATGCCAGA
*
31491671 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* *
31491736 GCGAAAACCAAATCAGTTATGTCTTCGATTTGCTCCTTGTAAGCACAATGATGCCAAATCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* * * * *
31491801 AGATCTACTTCAGTGAAATCATCTGAAGGCTAGATCTACTATGCATCTGCTCTCCATCGAAATGG
131 GGATCTACTTCAGTAAAAACATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCATCGAAATGG
31491866 AGATGCCAGA
196 AGATGCCAGA
* * * * *
31491876 CTTCGACTTGTTCTCTGACAATACAGAGTTTCCAAATCATCTTAGATTTGCTTTAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* *
31491941 GCGAAAATCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
31492006 GGATCT
131 GGATCT
31492012 GCTTTAGCCA
Statistics
Matches: 689, Mismatches: 61, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
204 33 0.05
205 467 0.68
206 189 0.27
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (205 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
GGATCTACTTCAGTAAAAACATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCATCGAAATGG
AGATGCCAGA
Found at i:31491866 original size:411 final size:409
Alignment explanation
Indices: 31491055--31492011 Score: 1511
Period size: 411 Copynumber: 2.3 Consensus size: 409
31491045 AAATCTGCTT
* *
31491055 CTTCGATTTGTTCCCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTAACGTAAGCAC
1 CTTCGACTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTAACGTAAGCAC
* * * *
31491120 GTGAAAGCCAAATCAGCTATGTCTTTGATTTGCTCCTTATAAGCACAAGGATGCCAAATCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* *
31491185 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTACTGCTCTCCATCGAAATGG
131 GGATC-TACTTCAGTATAAACATCTGAAGGCCAAATCTGCTATGTACTGCTCTCCATCGAAATGG
31491250 AGATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTA
195 AGATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTA
* * * *
31491315 GTGTAAGCACGCGAAAACCAAATCAGCTATGTCTTTGATTTGCTCTTTGTAAGCACAAGGATGCC
260 GCGTAAACACGCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCC
* ** * * **
31491380 AAACCATCTTGGATCTACTTCAGTAAAAACATCTGAAGTTTGGATCTGCTATGTGTCTGCCCTCC
325 AAACCATCTTAGATCTACTTCAGTAAAAACATCTGAAGGCTAGATCTACTATGCATCTGCCCTCC
* *
31491445 GTCAAAATGGAGATGCCAGG
390 ATCAAAATGGAGATGCCAGA
* * *
31491465 CTTCGACTTGTTCTCTGACAATACAGAGATGCCAATTCATCTTAGACTTGCTTTAGCGTAAGCAC
1 CTTCGACTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTAACGTAAGCAC
*
31491530 ACGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* * * *
31491595 AGATCTACTTCAGTGA-AATCATCTTGAAGGCTAAATCTGCTATGTATTTGCTCTCCATCGAAAT
131 GGATCTACTTCAGT-ATAAACATC-TGAAGGCCAAATCTGCTATGTA-CTGCTCTCCATCGAAAT
31491659 GGAGATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTT
193 GGAGATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTT
* *
31491724 TAGCGTAAACACGCGAAAACCAAATCAGTTATGTCTTCGATTTGCTCCTTGTAAGCACAATGATG
258 TAGCGTAAACACGCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATG
* * * *
31491789 CCAAATCATCTTAGATCTACTTCAGTGAAATCATCTGAAGGCTAGATCTACTATGCATCTGCTCT
323 CCAAACCATCTTAGATCTACTTCAGTAAAAACATCTGAAGGCTAGATCTACTATGCATCTGCCCT
*
31491854 CCATCGAAATGGAGATGCCAGA
388 CCATCAAAATGGAGATGCCAGA
* *
31491876 CTTCGACTTGTTCTCTGACAATACAGAGTTTCCAAATCATCTTAGATTTGCTTTAACGTAAGCAC
1 CTTCGACTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTAACGTAAGCAC
* *
31491941 GCGAAAATCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
31492006 GGATCT
131 GGATCT
31492012 GCTTTAGCCA
Statistics
Matches: 499, Mismatches: 45, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
409 14 0.03
410 145 0.29
411 340 0.68
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (409 bp):
CTTCGACTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTAACGTAAGCAC
GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
GGATCTACTTCAGTATAAACATCTGAAGGCCAAATCTGCTATGTACTGCTCTCCATCGAAATGGA
GATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAG
CGTAAACACGCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCA
AACCATCTTAGATCTACTTCAGTAAAAACATCTGAAGGCTAGATCTACTATGCATCTGCCCTCCA
TCAAAATGGAGATGCCAGA
Found at i:31496511 original size:23 final size:24
Alignment explanation
Indices: 31496436--31496649 Score: 310
Period size: 24 Copynumber: 9.0 Consensus size: 24
31496426 GCTTTATCAT
*
31496436 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
31496461 ATAACTGGGGAAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
31496485 ATAACTGGGGCATAAGTCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31496508 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
31496532 ATAACTGGGGCATAAGTCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31496555 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
31496578 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
31496602 ATAACTGGGGCGTAAGCCCTTTTTA
1 ATAACTGGGGCATAAGCCC-TTTTA
31496627 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
31496650 GCACTTCCTC
Statistics
Matches: 172, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
23 67 0.39
24 71 0.41
25 34 0.20
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:31496511 original size:47 final size:47
Alignment explanation
Indices: 31496457--31496648 Score: 305
Period size: 47 Copynumber: 4.1 Consensus size: 47
31496447 CCTAGCCTCT
* * *
31496457 TTTAATAACTGGGGAAAAAGCCCTTTTAATAACTGGGGCATAAGTCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
*
31496504 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGTCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
31496551 TTTAATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
* *
31496597 TTTTGATAACTGGGGCGTAAGCCCTTTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC-TTTTAATAACTGGGGCATAAGCCC
31496646 TTT
1 TTT
31496649 TGCACTTCCT
Statistics
Matches: 137, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
46 22 0.16
47 89 0.65
48 3 0.02
49 23 0.17
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (47 bp):
TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
Found at i:31496828 original size:25 final size:25
Alignment explanation
Indices: 31496782--31496829 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
31496772 ATATTTAAGC
* * * *
31496782 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
31496807 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
31496830 CATTTTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:31505559 original size:16 final size:16
Alignment explanation
Indices: 31505538--31505570 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31505528 TAAAAGATTA
31505538 AAAGTAA-ATAATACAC
1 AAAGTAATAT-ATACAC
31505554 AAAGTAATATATACAC
1 AAAGTAATATATACAC
31505570 A
1 A
31505571 GGAAAAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAGTAATATATACAC
Found at i:31510993 original size:45 final size:43
Alignment explanation
Indices: 31510896--31511012 Score: 126
Period size: 45 Copynumber: 2.7 Consensus size: 43
31510886 ATCTCATCCC
* * * *
31510896 CCTGAAGTAGTAGTGGAACAGATTGAAGTTGTAGATCTTATCT
1 CCTGAAGTTGTAGTGGAGCAGATTGAAGTGGCAGATCTTATCT
* * *
31510939 CCTTAAAGTTGTAGTGGAGTAGATCGAAGATGGCAGATCTTATCTT
1 CC-TGAAGTTGTAGTGGAGCAGATTGAAG-TGGCAGATCTTATC-T
* *
31510985 CCTGAAGTTGCAGTAGAGCAGATTGAAG
1 CCTGAAGTTGTAGTGGAGCAGATTGAAG
31511013 CCACTAGCCT
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
43 2 0.03
44 21 0.36
45 33 0.56
46 3 0.05
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (43 bp):
CCTGAAGTTGTAGTGGAGCAGATTGAAGTGGCAGATCTTATCT
Found at i:31511170 original size:44 final size:45
Alignment explanation
Indices: 31511120--31511244 Score: 112
Period size: 44 Copynumber: 2.8 Consensus size: 45
31511110 TATGGCGAAT
* * *
31511120 CTTATCTTCCTGAATTTGCAGTGGAGCAAATTGAAGCCA-CCAGC
1 CTTATCTTCCTGAATTTGCAGTGGAGCAAATTGAAGACAGCAAAC
* * * * * * *
31511164 CTTATCTCCCTGAAGTTGTAATGGAGCAGACTGAAGACAGCAAAT
1 CTTATCTTCCTGAATTTGCAGTGGAGCAAATTGAAGACAGCAAAC
*
31511209 CTTAT-TTCCCTG-ATGTTGCAGTGGAACAAATTGAAG
1 CTTATCTT-CCTGAAT-TTGCAGTGGAGCAAATTGAAG
31511245 TTACAAATTA
Statistics
Matches: 61, Mismatches: 17, Indels: 5
0.73 0.20 0.06
Matches are distributed among these distances:
44 34 0.56
45 27 0.44
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (45 bp):
CTTATCTTCCTGAATTTGCAGTGGAGCAAATTGAAGACAGCAAAC
Found at i:31511669 original size:143 final size:143
Alignment explanation
Indices: 31510975--31511662 Score: 930
Period size: 143 Copynumber: 4.8 Consensus size: 143
31510965 AAGATGGCAG
* * * * *
31510975 ATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACTAGCCTTATCTCTCTAAAGTTAT
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
* * * *
31511040 AGTGGAGCAGACTAAAGACAGCGAATCTTATTTCCAC-GACGTTGCAGTGGAACAGATT-AATGC
66 AGTGGAGCAGACTGAAGACAACAAATCTTATTTCC-CTGATGTTGCAGTGGAACAGATTGAA-GC
*
31511103 TATAAATTATGGCGA
129 TACAAATTATGGCGA
* *
31511118 ATCTTATCTTCCTGAATTTGCAGTGGAGCAAATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
* * * *
31511183 AATGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTGATGTTGCAGTGGAACAAATTGAAGTTA
66 AGTGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGATGTTGCAGTGGAACAGATTGAAGCTA
31511248 CAAATTATGGCGA
131 CAAATTATGGCGA
* * *
31511261 ATCTTATCTTCCTGAAGTTGCATTGGAACAGATTGAAACCACCAGCCTTATCTCCCTGAAGTTGT
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
* *
31511326 AGTGGAGCAAACTAAAGACAACAAATCTTATTTCCCTGATGTTGCAGTGGAACAGATTGAAGCTA
66 AGTGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGATGTTGCAGTGGAACAGATTGAAGCTA
* *
31511391 CAAATTATGACAA
131 CAAATTATGGCGA
* * * *
31511404 ATTTTATCTTTCTGAAGTTGCAGTGGAGCAGATAGAAGCCACCAGCCTTATCTCCCTGAAGTTGC
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
* * * * * *
31511469 AGCGGAGCAGACTGAAAACATCAAATCTTATTTCCTTGATGATGCAATGGAACAGATTGAAGCTA
66 AGTGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGATGTTGCAGTGGAACAGATTGAAGCTA
* *
31511534 AAAATTTTGGCGA
131 CAAATTATGGCGA
* ** * *
31511547 ATCTTATATTCCTGAAGTTGCAGTAAAGCAGATTGAAGCCACCAGCCTTATCTCTCTGAAGTTGC
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
* * * * * *
31511612 AGCGGAGCAGACTGAAGATAACAGATTTTATTTCCTTGAAGTTGCAGTGGA
66 AGTGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGATGTTGCAGTGGA
31511663 GTAGATTAAA
Statistics
Matches: 482, Mismatches: 61, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
142 1 0.00
143 479 0.99
144 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (143 bp):
ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGT
AGTGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGATGTTGCAGTGGAACAGATTGAAGCTA
CAAATTATGGCGA
Found at i:31513229 original size:15 final size:15
Alignment explanation
Indices: 31513203--31513259 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
31513193 CATATATATT
31513203 ATATAA-TTCAATCA
1 ATATAATTTCAATCA
31513217 ATATAATTTCAATCA
1 ATATAATTTCAATCA
*
31513232 AAATAATTTCAATCA
1 ATATAATTTCAATCA
*
31513247 ATATAAATTCAAT
1 ATATAATTTCAAT
31513260 AAATTCATCG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 6 0.15
15 33 0.85
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAATTTCAATCA
Found at i:31514493 original size:10 final size:10
Alignment explanation
Indices: 31514478--31514542 Score: 67
Period size: 8 Copynumber: 7.4 Consensus size: 10
31514468 TTCTTTAGTT
31514478 TATATATATA
1 TATATATATA
31514488 TATATATATA
1 TATATATATA
31514498 -ATATA-ATA
1 TATATATATA
31514506 TA-ATATA-A
1 TATATATATA
31514514 TATA-ATATA
1 TATATATATA
31514523 -ATATA-ATA
1 TATATATATA
31514531 TA-ATATA-A
1 TATATATATA
31514539 TATA
1 TATA
31514543 ATTAAAACAT
Statistics
Matches: 47, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
8 24 0.51
9 13 0.28
10 10 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATATATA
Found at i:31514503 original size:5 final size:5
Alignment explanation
Indices: 31514481--31514544 Score: 110
Period size: 5 Copynumber: 12.4 Consensus size: 5
31514471 TTTAGTTTAT
31514481 ATATA TATATA TATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA -ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
31514533 ATATA ATATA AT
1 ATATA ATATA AT
31514545 TAAAACATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 47 0.81
6 11 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:31515115 original size:44 final size:43
Alignment explanation
Indices: 31514995--31515249 Score: 125
Period size: 44 Copynumber: 5.5 Consensus size: 43
31514985 TCATAGTTTT
** *
31514995 AATCTGCTCCACTGCAACTTCAAGGAAATAAAATCTGCTATCTTC
1 AATCTGCTCCACTGCAACTTC-AGGAAAT-AAGGCTGCTAGCTTC
* * * * *
31515040 AGTCTGCTCCGCTGCAACTTCAGAGAGATAAGGCTGGTGGCTTC
1 AATCTGCTCCACTGCAACTTCAG-GAAATAAGGCTGCTAGCTTC
* **
31515084 AATCTGCTCTACTGCAACTTCAGGAATATAAGATTCGCCATAATTTTTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGAA-ATAAG----G-C-----TGCTAGCTTC
* * * * ** * *
31515138 AATCTGTTCCATTGCATCATCAAGGAAATAAGATTTGAT-GTTTTC
1 AATCTGCTCCACTGCAACTTC-AGGAAATAAG-GCTGCTAG-CTTC
* * * * *
31515183 AGTCTGCTCCGCTGCAACTTCAGAGAGATAAGGCTGGTGGCTTC
1 AATCTGCTCCACTGCAACTTCAG-GAAATAAGGCTGCTAGCTTC
31515227 AATCTGCTCCACTGCAACTTCAG
1 AATCTGCTCCACTGCAACTTCAG
31515250 AAAGATAAAA
Statistics
Matches: 155, Mismatches: 39, Indels: 33
0.68 0.17 0.15
Matches are distributed among these distances:
43 2 0.01
44 67 0.43
45 51 0.33
48 1 0.01
49 1 0.01
54 28 0.18
55 5 0.03
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (43 bp):
AATCTGCTCCACTGCAACTTCAGGAAATAAGGCTGCTAGCTTC
Found at i:31515184 original size:143 final size:143
Alignment explanation
Indices: 31514995--31515689 Score: 919
Period size: 143 Copynumber: 4.9 Consensus size: 143
31514985 TCATAGTTTT
* * * * * * * *
31514995 AATCTGCTCCACTGCAACTTCAAGGAAATAAAATCTGCTATCTTCAGTCTGCTCCGCTGCAACTT
1 AATCTGTTCCACTGCAACATCAAGGAAATAAGATTTGATGTTTTCAGTCTGCTCCACTGCAACTT
* * *
31515060 CAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCTACTGCAACTTCAGGAATATAAGATTCGCCAT
66 CAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCAT
*
31515125 AATTTTTAGCTTC
131 AATTTGTAGCTTC
* * *
31515138 AATCTGTTCCATTGCATCATCAAGGAAATAAGATTTGATGTTTTCAGTCTGCTCCGCTGCAACTT
1 AATCTGTTCCACTGCAACATCAAGGAAATAAGATTTGATGTTTTCAGTCTGCTCCACTGCAACTT
* * * *
31515203 CAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGAAAGATAAAATTCGTCAT
66 CAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCAT
31515268 AATTTGTAGCTTC
131 AATTTGTAGCTTC
* * * *
31515281 AATCTGTTCCACTGCAACATCAGGGAAATAAGATTTGTTGTCTTT-AGTTTGCTCCACTACAACT
1 AATCTGTTCCACTGCAACATCAAGGAAATAAGATTTGATGT-TTTCAGTCTGCTCCACTGCAACT
* * * *
31515345 TCAGGGAGATAAGGCTAGTGGCTTCAATCTGTTCCAATGCAACTTCAGGAAGATAAGATTCTCCA
65 TCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCA
*
31515410 TAATTTGTAACTTC
130 TAATTTGTAGCTTC
* * * * * *
31515424 AATTTGTTCCACTGCAACATCAGGGAAATAAGATTTGCTGTCTTCAGTTTGCTCCATTGCAACTT
1 AATCTGTTCCACTGCAACATCAAGGAAATAAGATTTGATGTTTTCAGTCTGCTCCACTGCAACTT
* *
31515489 CAGGGAGATAAGGCTGGTGGCTTCAATTTGCTCGACTGCAACTTCAGGAAGATAAGATTCGCCAT
66 CAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCAT
* *
31515554 AATTTATAGCTTT
131 AATTTGTAGCTTC
* ** * *
31515567 AATCTGTTCCACTGCAACGTCGTGGAAATAAGA-TTCACTGTCTTT-AGTCTGCTCCACTACAAC
1 AATCTGTTCCACTGCAACATCAAGGAAATAAGATTTGA-TGT-TTTCAGTCTGCTCCACTGCAAC
* * * *
31515630 TTTAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCTACTGCAACTTCAAGAAGATAAGAT
64 TTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGAT
31515690 CTGCCATCTT
Statistics
Matches: 488, Mismatches: 60, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
142 4 0.01
143 479 0.98
144 5 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (143 bp):
AATCTGTTCCACTGCAACATCAAGGAAATAAGATTTGATGTTTTCAGTCTGCTCCACTGCAACTT
CAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCAT
AATTTGTAGCTTC
Found at i:31515250 original size:44 final size:44
Alignment explanation
Indices: 31515180--31515544 Score: 163
Period size: 44 Copynumber: 7.8 Consensus size: 44
31515170 ATTTGATGTT
* * *
31515180 TTCAGTCTGCTCCGCTGCAACTTCAGAGAGATAAGGCTGGTGGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGC
** * * *
31515224 TTCAATCTGCTCCACTGCAACTTCAGAAAGATAAAATTCGTCATAATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGAT--AA---GGC-----TGGTGGC
* * * ** * *
31515278 TTCAATCTGTTCCACTGCAACATCAGGGAAATAAGATTTGTTGTC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG-GCTGGTGGC
* * * * *
31515323 TTTAGTTTGCTCCACTACAACTTCAGGGAGATAAGGCTAGTGGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGC
* * * * * **
31515367 TTCAATCTGTTCCAATGCAACTTCAGGAAGATAAGATTCTCCATAATTTGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG-----GC-----TGGTGGC
* * * * ** * *
31515421 TTCAATTTGTTCCACTGCAACATCAGGGAAATAAGATTTGCTGTC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG-GCTGGTGGC
* * *
31515466 TTCAGTTTGCTCCATTGCAACTTCAGGGAGATAAGGCTGGTGGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGC
* * *
31515510 TTCAATTTGCTCGACTGCAACTTCAGGAAGATAAG
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
31515545 ATTCGCCATA
Statistics
Matches: 236, Mismatches: 64, Indels: 42
0.69 0.19 0.12
Matches are distributed among these distances:
44 97 0.41
45 64 0.27
46 2 0.01
49 4 0.02
50 1 0.00
52 2 0.01
54 66 0.28
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (44 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGC
Found at i:31515338 original size:45 final size:45
Alignment explanation
Indices: 31515269--31515547 Score: 181
Period size: 44 Copynumber: 6.1 Consensus size: 45
31515259 ATTCGTCATA
* * * *
31515269 ATTTGTAG-CTTCAATCTGTTCCACTGCAACATCAGGGAAATAAG
1 ATTTGTTGTCTTCAATTTGCTCCACTGCAACTTCAGGGAAATAAG
* * * *
31515313 ATTTGTTGTCTTTAGTTTGCTCCACTACAACTTCAGGGAGATAAG
1 ATTTGTTGTCTTCAATTTGCTCCACTGCAACTTCAGGGAAATAAG
** * * * * *
31515358 GCTAG-TGGCTTCAATCTGTTCCAATGCAACTTCA-GGAAGATAAG
1 ATTTGTTGTCTTCAATTTGCTCCACTGCAACTTCAGGGAA-ATAAG
* * *
31515402 ATTCTCCATAATTTGTAACTTCAATTTGTTCCACTGCAACATCAGGGAAATAAG
1 A-T-T---T--GTTGT--CTTCAATTTGCTCCACTGCAACTTCAGGGAAATAAG
* * * *
31515456 ATTTGCTGTCTTCAGTTTGCTCCATTGCAACTTCAGGGAGATAAG
1 ATTTGTTGTCTTCAATTTGCTCCACTGCAACTTCAGGGAAATAAG
** * * *
31515501 -GCTGGTGGCTTCAATTTGCTCGACTGCAACTTCA-GGAAGATAAG
1 ATTTGTTGTCTTCAATTTGCTCCACTGCAACTTCAGGGAA-ATAAG
31515545 ATT
1 ATT
31515548 CGCCATAATT
Statistics
Matches: 176, Mismatches: 44, Indels: 29
0.71 0.18 0.12
Matches are distributed among these distances:
43 6 0.03
44 66 0.38
45 62 0.35
46 1 0.01
47 3 0.02
49 1 0.01
52 3 0.02
53 1 0.01
54 29 0.16
55 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (45 bp):
ATTTGTTGTCTTCAATTTGCTCCACTGCAACTTCAGGGAAATAAG
Found at i:31523100 original size:21 final size:21
Alignment explanation
Indices: 31523074--31523114 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31523064 CCTATTTGCT
31523074 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTCGTGTGTCGTATC
*
31523095 AGGCACCTCGTGTGTTGTAT
1 AGGCACCTCGTGTGTCGTAT
31523115 ATTGATCAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.32
Consensus pattern (21 bp):
AGGCACCTCGTGTGTCGTATC
Found at i:31524511 original size:27 final size:27
Alignment explanation
Indices: 31524478--31524537 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
31524468 AAAAACCATC
*
31524478 AACCCAAACTAAACCCAATCCCAACCA
1 AACCCAAACTAAACCCAATCCCAAACA
31524505 AACCCAAACTAAACCCAATCCCAAACA
1 AACCCAAACTAAACCCAATCCCAAACA
31524532 AACCCA
1 AACCCA
31524538 CTTAACCCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (27 bp):
AACCCAAACTAAACCCAATCCCAAACA
Found at i:31524536 original size:16 final size:17
Alignment explanation
Indices: 31524502--31524537 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
31524492 CCAATCCCAA
31524502 CCAAACCCAAACTAAAC
1 CCAAACCCAAACTAAAC
*
31524519 CCAATCCCAAAC-AAAC
1 CCAAACCCAAACTAAAC
31524535 CCA
1 CCA
31524538 CTTAACCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.50, C:0.44, G:0.00, T:0.06
Consensus pattern (17 bp):
CCAAACCCAAACTAAAC
Found at i:31525096 original size:13 final size:13
Alignment explanation
Indices: 31525080--31525105 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31525070 TATATCTTTG
31525080 CTCATATTACTGT
1 CTCATATTACTGT
31525093 CTCATATTACTGT
1 CTCATATTACTGT
31525106 TGTTAGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
CTCATATTACTGT
Found at i:31534688 original size:10 final size:10
Alignment explanation
Indices: 31534669--31534707 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
31534659 TTAAATTCTA
31534669 AAAGATAAAT
1 AAAGATAAAT
31534679 ACAA-ATAAAT
1 A-AAGATAAAT
31534689 AAAGATAAAT
1 AAAGATAAAT
*
31534699 GAAGATAAA
1 AAAGATAAA
31534708 AACTAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 22 0.85
11 2 0.08
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:31537100 original size:23 final size:23
Alignment explanation
Indices: 31537072--31537120 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
31537062 TCAAATAGAG
*
31537072 TAAAAAGTGAAATGAAAATGAAAT
1 TAAAATGTGAAATG-AAATGAAAT
* *
31537096 TAAAATTTGGAATGAAATGAAAT
1 TAAAATGTGAAATGAAATGAAAT
31537119 TA
1 TA
31537121 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.27
Consensus pattern (23 bp):
TAAAATGTGAAATGAAATGAAAT
Found at i:31537209 original size:22 final size:21
Alignment explanation
Indices: 31537184--31537239 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
31537174 GAAATGAAGT
31537184 TGAAATTAAATTAAAATTGGAA
1 TGAAATTAAATTAAAATT-GAA
* *
31537206 TGAAATGAAATTCAAATTGAA
1 TGAAATTAAATTAAAATTGAA
31537227 TAGAAATTGAAAT
1 T-GAAATT-AAAT
31537240 GAATATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.14, T:0.30
Consensus pattern (21 bp):
TGAAATTAAATTAAAATTGAA
Found at i:31537211 original size:33 final size:33
Alignment explanation
Indices: 31537173--31537242 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
31537163 ACTTTTTGAT
* * *
31537173 TGAAATGAAGTTGAAATTAAATTA-AAATTGGAA
1 TGAAATGAAATTCAAATTAAA-TAGAAATTGAAA
*
31537206 TGAAATGAAATTCAAATTGAATAGAAATTGAAA
1 TGAAATGAAATTCAAATTAAATAGAAATTGAAA
31537239 TGAA
1 TGAA
31537243 TATATAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.53, C:0.01, G:0.17, T:0.29
Consensus pattern (33 bp):
TGAAATGAAATTCAAATTAAATAGAAATTGAAA
Found at i:31537244 original size:16 final size:17
Alignment explanation
Indices: 31537197--31537245 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
31537187 AATTAAATTA
*
31537197 AAATTGGAATGAA-ATG
1 AAATTGAAATGAATATG
*
31537213 AAATTCAAATTGAATA-G
1 AAATTGAAA-TGAATATG
31537230 AAATTGAAATGAATAT
1 AAATTGAAATGAATAT
31537246 ATAATTAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 13 0.48
17 13 0.48
18 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.16, T:0.29
Consensus pattern (17 bp):
AAATTGAAATGAATATG
Found at i:31537491 original size:28 final size:28
Alignment explanation
Indices: 31537432--31537490 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
31537422 AAAAAAGGTG
* *
31537432 AAATGAATATGGAATGAAATGAAATTTA
1 AAATGAATATGGAATGAAATAAAATATA
31537460 AAATGAATAT-GAGATGAAATTAAAATATA
1 AAATGAATATGGA-ATGAAA-TAAAATATA
31537489 AA
1 AA
31537491 TTTAAATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 16 0.59
29 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (28 bp):
AAATGAATATGGAATGAAATAAAATATA
Found at i:31537516 original size:17 final size:16
Alignment explanation
Indices: 31537496--31537559 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 16
31537486 ATAAATTTAA
31537496 ATGAGAAAAAAATGAAT
1 ATGA-AAAAAAATGAAT
*
31537513 ATGAAAAAAGAATAAATT
1 ATGAAAAAA-AATGAA-T
31537531 GAAATGAGAAAAAAATGAAT
1 ---ATGA-AAAAAAATGAAT
31537551 ATGAAAAAA
1 ATGAAAAAA
31537560 GAATAAATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
16 10 0.26
17 13 0.33
18 1 0.03
20 1 0.03
21 9 0.23
22 5 0.13
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.17
Consensus pattern (16 bp):
ATGAAAAAAAATGAAT
Found at i:31537533 original size:16 final size:16
Alignment explanation
Indices: 31537496--31537567 Score: 54
Period size: 17 Copynumber: 4.0 Consensus size: 16
31537486 ATAAATTTAA
*
31537496 ATGAGAAAAAAATGAAT
1 ATGA-AAAAAAATAAAT
31537513 ATGAAAAAAGAATAAATT
1 ATGAAAAAA-AATAAA-T
*
31537531 GAAATGAGAAAAAAATGAAT
1 ---ATGA-AAAAAAATAAAT
31537551 ATGAAAAAAGAATAAAT
1 ATGAAAAAA-AATAAAT
31537568 TGGAATGAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
16 10 0.22
17 19 0.42
18 1 0.02
20 1 0.02
21 9 0.20
22 5 0.11
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (16 bp):
ATGAAAAAAAATAAAT
Found at i:31537536 original size:38 final size:38
Alignment explanation
Indices: 31537486--31537593 Score: 173
Period size: 38 Copynumber: 2.9 Consensus size: 38
31537476 AAATTAAAAT
*
31537486 ATAAATTTAAATGAGAAAAAAATGAATATGAAAAAAGA
1 ATAAATTGAAATGAGAAAAAAATGAATATGAAAAAAGA
31537524 ATAAATTGAAATGAGAAAAAAATGAATATGAAAAAAGA
1 ATAAATTGAAATGAGAAAAAAATGAATATGAAAAAAGA
* * *
31537562 ATAAATTGGAATGAGAGAAAAATAAAT-TGAAA
1 ATAAATTGAAATGAGAAAAAAATGAATATGAAA
31537594 TGAGATTAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
37 5 0.08
38 61 0.92
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (38 bp):
ATAAATTGAAATGAGAAAAAAATGAATATGAAAAAAGA
Found at i:31537537 original size:21 final size:20
Alignment explanation
Indices: 31537508--31537803 Score: 133
Period size: 21 Copynumber: 13.9 Consensus size: 20
31537498 GAGAAAAAAA
31537508 TGAATATGAAAAAAGAATAAAT
1 TGAA-ATGAAAAAA-AATAAAT
*
31537530 TGAAATG--AGAAAA-AAA-
1 TGAAATGAAAAAAAATAAAT
31537546 TGAATATGAAAAAAGAATAAAT
1 TGAA-ATGAAAAAA-AATAAAT
* *
31537568 TGGAATGAGAGAAAAATAAAT
1 TGAAATGA-AAAAAAATAAAT
*
31537589 TGAAATGAGATTAAAATGTGAAATGAAT
1 TGAAAT--GA--AAAA----AAATAAAT
*
31537617 ATGAAATTAAATTAAAATATAAAT
1 -TGAAATGAAA--AAAA-ATAAAT
31537641 TGAAATGAAAAAATAATAAAT
1 TGAAATGAAAAAA-AATAAAT
*
31537662 TGAAATGAGAAAATAATAAAT
1 TGAAATGA-AAAAAAATAAAT
*
31537683 TTAAATG-AAAAAAATAAAT
1 TGAAATGAAAAAAAATAAAT
* ** *
31537702 TTAAATGAAATGAAATGAATTT
1 TGAAATGAAAAAAAAT-AA-AT
*
31537724 TGAAATGAAAATGAAATGAAA-
1 TGAAATGAAAA-AAAAT-AAAT
* * *
31537745 TGAATTTTGAAATGAAAATGACA-
1 TGAA--ATGAAA-AAAAAT-AAAT
* *
31537768 TGAAAT--TAAAATATAAAT
1 TGAAATGAAAAAAAATAAAT
31537786 TGAAATGAAAAAAAATAA
1 TGAAATGAAAAAAAATAA
31537804 CAAGACTTAT
Statistics
Matches: 213, Mismatches: 31, Indels: 62
0.70 0.10 0.20
Matches are distributed among these distances:
16 4 0.02
17 8 0.04
18 12 0.06
19 25 0.12
20 16 0.08
21 59 0.28
22 26 0.12
23 37 0.17
24 8 0.04
25 2 0.01
27 3 0.01
28 7 0.03
29 6 0.03
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.25
Consensus pattern (20 bp):
TGAAATGAAAAAAAATAAAT
Found at i:31537622 original size:29 final size:28
Alignment explanation
Indices: 31537581--31537650 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
31537571 AATGAGAGAA
* * *
31537581 AAATAAAT-TGAAATGAGATTAAAATGT
1 AAATGAATATGAAATGAAATTAAAATAT
*
31537608 GAAATGAATATGAAATTAAATTAAAATAT
1 -AAATGAATATGAAATGAAATTAAAATAT
31537637 AAATTGAA-ATGAAA
1 AAA-TGAATATGAAA
31537651 AAATAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 16 0.44
29 20 0.56
ACGTcount: A:0.59, C:0.00, G:0.13, T:0.29
Consensus pattern (28 bp):
AAATGAATATGAAATGAAATTAAAATAT
Found at i:31537635 original size:18 final size:18
Alignment explanation
Indices: 31537474--31537796 Score: 110
Period size: 21 Copynumber: 17.6 Consensus size: 18
31537464 GAATATGAGA
*
31537474 TGAAATTAAAATATAAAT
1 TGAAATGAAAATATAAAT
*
31537492 TTAAATGAGAAA-A-AAA-
1 TGAAATGA-AAATATAAAT
*
31537508 TGAATATGAAAAAAGAATAAAT
1 TGAA-ATG--AAAA-TATAAAT
31537530 TGAAATGAGAAA-A-AAA-
1 TGAAATGA-AAATATAAAT
*
31537546 TGAATATGAAAAAAGAATAAAT
1 TGAA-ATG--AAAA-TATAAAT
* *
31537568 TGGAATGAGAGAAAAATAAAT
1 TGAAAT--GA-AAATATAAAT
* *
31537589 TGAAATGAGATTA-AAAT
1 TGAAATGAAAATATAAAT
31537606 GTGAAATG--AATATGAAAT
1 -TGAAATGAAAATAT-AAAT
*
31537624 T-AAATTAAAATATAAAT
1 TGAAATGAAAATATAAAT
31537641 TGAAATGAAAAAATAATAAAT
1 TGAAATG--AAAAT-ATAAAT
31537662 TGAAATGAGAAAATAATAAAT
1 TGAAAT--GAAAAT-ATAAAT
* *
31537683 TTAAATGAAAAAAATAAAT
1 TGAAATG-AAAATATAAAT
* * *
31537702 TTAAATGAAATGAAATGAATTT
1 TGAAATGAAA--ATAT-AA-AT
*
31537724 TGAAATGAAAAT-GAAA-
1 TGAAATGAAAATATAAAT
31537740 TGAAATG--AAT-T---T
1 TGAAATGAAAATATAAAT
* *
31537752 TGAAATGAAAAT-GACA-
1 TGAAATGAAAATATAAAT
*
31537768 TGAAATTAAAATATAAAT
1 TGAAATGAAAATATAAAT
31537786 TGAAATGAAAA
1 TGAAATGAAAA
31537797 AAAATAACAA
Statistics
Matches: 238, Mismatches: 24, Indels: 86
0.68 0.07 0.25
Matches are distributed among these distances:
12 7 0.03
14 6 0.03
16 32 0.13
17 24 0.10
18 51 0.21
19 22 0.09
20 19 0.08
21 55 0.23
22 20 0.08
23 2 0.01
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (18 bp):
TGAAATGAAAATATAAAT
Found at i:31537714 original size:5 final size:5
Alignment explanation
Indices: 31537704--31537773 Score: 59
Period size: 5 Copynumber: 12.8 Consensus size: 5
31537694 AAATAAATTT
* *
31537704 AAATG AAATG AAATG AATTTTG AAATG AAAATG AAATG AAATG AATTTTG
1 AAATG AAATG AAATG AA--ATG AAATG -AAATG AAATG AAATG AA--ATG
*
31537754 AAATG AAAATG ACATG AAAT
1 AAATG -AAATG AAATG AAAT
31537774 TAAAATATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
5 35 0.66
6 10 0.19
7 8 0.15
ACGTcount: A:0.54, C:0.01, G:0.17, T:0.27
Consensus pattern (5 bp):
AAATG
Found at i:31537715 original size:94 final size:95
Alignment explanation
Indices: 31537546--31537717 Score: 226
Period size: 94 Copynumber: 1.8 Consensus size: 95
31537536 GAGAAAAAAA
* * **
31537546 TGAATATGAAAAAAGAATAAATTGGAATGAGAGAAAAATAAATTGAAATGAGATTAAAATGTGAA
1 TGAATATGAAAAAAGAATAAATTGAAATGAGAGAAAAATAAATTGAAATGAAAAAAAAATGTGAA
31537611 ATGAATATGAAATTAAATTAAAATATAAAT
66 ATGAATATGAAATTAAATTAAAATATAAAT
* *
31537641 TGAA-ATGAAAAAATAATAAATTGAAATGAGA-AAATAATAAATTTAAATGAAAAAAATAAAT-T
1 TGAATATGAAAAAAGAATAAATTGAAATGAGAGAAA-AATAAATTGAAATG-AAAAAA-AAATGT
*
31537703 TAAATGAA-ATGAAAT
63 GAAATGAATATGAAAT
31537718 GAATTTTGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
93 3 0.04
94 45 0.67
95 15 0.22
96 4 0.06
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.26
Consensus pattern (95 bp):
TGAATATGAAAAAAGAATAAATTGAAATGAGAGAAAAATAAATTGAAATGAAAAAAAAATGTGAA
ATGAATATGAAATTAAATTAAAATATAAAT
Found at i:31537729 original size:17 final size:17
Alignment explanation
Indices: 31537707--31537761 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
31537697 TAAATTTAAA
31537707 TGAAATGAAATGAATTT
1 TGAAATGAAATGAATTT
31537724 TGAAATG-AA--AA---
1 TGAAATGAAATGAATTT
31537735 TGAAATGAAATGAATTT
1 TGAAATGAAATGAATTT
31537752 TGAAATGAAA
1 TGAAATGAAA
31537762 ATGACATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
11 7 0.22
12 2 0.06
14 4 0.12
16 2 0.06
17 17 0.53
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (17 bp):
TGAAATGAAATGAATTT
Found at i:31537735 original size:28 final size:28
Alignment explanation
Indices: 31537704--31537773 Score: 131
Period size: 28 Copynumber: 2.5 Consensus size: 28
31537694 AAATAAATTT
31537704 AAATGAAATGAAATGAATTTTGAAATGA
1 AAATGAAATGAAATGAATTTTGAAATGA
31537732 AAATGAAATGAAATGAATTTTGAAATGA
1 AAATGAAATGAAATGAATTTTGAAATGA
*
31537760 AAATGACATGAAAT
1 AAATGAAATGAAAT
31537774 TAAAATATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.54, C:0.01, G:0.17, T:0.27
Consensus pattern (28 bp):
AAATGAAATGAAATGAATTTTGAAATGA
Found at i:31537739 original size:23 final size:23
Alignment explanation
Indices: 31537685--31537771 Score: 76
Period size: 28 Copynumber: 3.8 Consensus size: 23
31537675 TAATAAATTT
*
31537685 AAATGAAAA--AAAT-AAATTT-
1 AAATGAAAATGAAATGAATTTTG
31537704 AAATG-AAATGAAATGAATTTTG
1 AAATGAAAATGAAATGAATTTTG
31537726 AAATGAAAATGAAATGAAATGAATTTTG
1 AAATG---A--AAATGAAATGAATTTTG
*
31537754 AAATGAAAATGACATGAA
1 AAATGAAAATGAAATGAA
31537772 ATTAAAATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
18 3 0.05
19 5 0.09
20 4 0.07
21 5 0.09
22 5 0.09
23 11 0.20
25 1 0.02
28 22 0.39
ACGTcount: A:0.57, C:0.01, G:0.15, T:0.26
Consensus pattern (23 bp):
AAATGAAAATGAAATGAATTTTG
Found at i:31537739 original size:94 final size:92
Alignment explanation
Indices: 31537542--31537744 Score: 223
Period size: 94 Copynumber: 2.2 Consensus size: 92
31537532 AAATGAGAAA
* * **
31537542 AAAATGAATATGAAAAAAGAATAAATTGGAATGAGAGAAAAATAAATTGAAATGAGATTAAAATG
1 AAAATGAA-ATGAAAAAAGAATAAATTGAAATGAGAGAAAAATAAATTGAAATGAAAAAAAAATG
*
31537607 TGAAATGAATATGAAATTAAATTAAAAT
65 TGAAATGAATATGAAATGAAATTAAAAT
* *
31537635 ATAAATTGAAATGAAAAAATAATAAATTGAAATGAGA-AAATAATAAATTTAAATGAAAAAAATA
1 A-AAA-TGAAATGAAAAAAGAATAAATTGAAATGAGAGAAA-AATAAATTGAAATG-AAAAAA-A
* * *
31537699 AAT-TTAAATGAA-ATGAAATGAATTTTGAAAT
61 AATGTGAAATGAATATGAAATGAA-ATTAAAAT
31537730 GAAAATGAAATGAAA
1 -AAAATGAAATGAAA
31537745 TGAATTTTGA
Statistics
Matches: 93, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
93 4 0.04
94 60 0.65
95 24 0.26
96 5 0.05
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.26
Consensus pattern (92 bp):
AAAATGAAATGAAAAAAGAATAAATTGAAATGAGAGAAAAATAAATTGAAATGAAAAAAAAATGT
GAAATGAATATGAAATGAAATTAAAAT
Found at i:31537785 original size:28 final size:28
Alignment explanation
Indices: 31537704--31537795 Score: 89
Period size: 28 Copynumber: 3.3 Consensus size: 28
31537694 AAATAAATTT
* * *
31537704 AAATGAAATGAAATGAATTTTGAAATGA
1 AAATGAAATGAAATAAAATATGAAATGA
* * *
31537732 AAATGAAATGAAATGAATTTTGAAATGA
1 AAATGAAATGAAATAAAATATGAAATGA
*
31537760 AAATGACATGAAATTAAAATAT-AAATTG-
1 AAATGAAATGAAA-TAAAATATGAAA-TGA
31537788 AAATGAAA
1 AAATGAAA
31537796 AAAAATAACA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 50 0.88
29 7 0.12
ACGTcount: A:0.57, C:0.01, G:0.15, T:0.27
Consensus pattern (28 bp):
AAATGAAATGAAATAAAATATGAAATGA
Found at i:31538052 original size:23 final size:21
Alignment explanation
Indices: 31538017--31538081 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 21
31538007 ACTTGAAATG
31538017 AATATGAAA-TGAAATGAAATTAA
1 AATAT-AAATTGAAATGAAA--AA
31538040 AATATAAATTGAAAT-AAAAA
1 AATATAAATTGAAATGAAAAA
31538060 AAT-T-AATTGAAATGAGAAAA
1 AATATAAATTGAAATGA-AAAA
31538080 AA
1 AA
31538082 ATTGAAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
18 9 0.23
19 2 0.05
20 11 0.28
22 6 0.15
23 11 0.28
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.25
Consensus pattern (21 bp):
AATATAAATTGAAATGAAAAA
Found at i:31538057 original size:17 final size:17
Alignment explanation
Indices: 31538031--31538090 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
31538021 TGAAATGAAA
*
31538031 TGAAATTAAAATATAAAT
1 TGAAA-TAAAAAATAAAT
*
31538049 TGAAATAAAAAAATTAAT
1 TGAAAT-AAAAAATAAAT
*
31538067 TGAAATGAGAAAA-AAAT
1 TGAAAT-AAAAAATAAAT
31538084 TGAAATA
1 TGAAATA
31538091 TTAAATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 1 0.03
17 10 0.28
18 25 0.69
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (17 bp):
TGAAATAAAAAATAAAT
Found at i:31538073 original size:41 final size:42
Alignment explanation
Indices: 31538045--31538417 Score: 141
Period size: 42 Copynumber: 9.3 Consensus size: 42
31538035 ATTAAAATAT
31538045 AAAT-TGAAATAAAAAAATTAATTGAAATGAGAAAAAAATTG
1 AAATATGAAATAAAAAAATTAATTGAAATGAGAAAAAAATTG
* * * * * **
31538086 AAATATTAAATAAAAAAATT-GTTAAAAAGTTGAAATGCAA-TG
1 AAATATGAAATAAAAAAATTAATTGAAATG-AGAAA-AAAATTG
* *
31538128 AAATATGAAAT---GAAATGTAATTTGAAATGA-ATATAAAATT-
1 AAATATGAAATAAAAAAAT-TAA-TTGAAATGAGA-AAAAAATTG
*
31538168 -AA-ATGAAAGTTGAAATAAA-T-A-TGAAATGA-AAATAAAATAT-
1 AAATATGAAA--T-AAAAAAATTAATTGAAATGAGAAA-AAAAT-TG
* * *
31538208 AAAT-TGCAAT--TAAAA--AATTGAAATCAGACAAAAAA-T-
1 AAATATGAAATAAAAAAATTAATTGAAATGAGA-AAAAAATTG
* *
31538244 -AATATG-AA-AAAAGAATAAATTGAAATGAGAAAAAAATTG
1 AAATATGAAATAAAAAAATTAATTGAAATGAGAAAAAAATTG
31538283 AAATATGAAAT---AAAATGTAATTTGAAATGA-AAATAAAATAT-
1 AAATATGAAATAAAAAAAT-TAA-TTGAAATGAGAAA-AAAAT-TG
* * *
31538324 AAAT-TGAAATGAAAAACACTAAATTGAAATGGGACAAAAAATT-
1 AAATATGAAAT-AAAAA-AATTAATTGAAATGAGA-AAAAAATTG
** *
31538367 -AATAT-AAA-AAAAAGAAAAAATTGAAATGAGAAAAAATTTG
1 AAATATGAAATAAAAA-AATTAATTGAAATGAGAAAAAAATTG
31538407 AAATATGAAAT
1 AAATATGAAAT
31538418 GAAATGAAAA
Statistics
Matches: 249, Mismatches: 35, Indels: 94
0.66 0.09 0.25
Matches are distributed among these distances:
35 5 0.02
36 10 0.04
37 13 0.05
38 25 0.10
39 34 0.14
40 42 0.17
41 44 0.18
42 47 0.19
43 12 0.05
44 13 0.05
45 4 0.02
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.25
Consensus pattern (42 bp):
AAATATGAAATAAAAAAATTAATTGAAATGAGAAAAAAATTG
Found at i:31538136 original size:17 final size:17
Alignment explanation
Indices: 31538116--31538211 Score: 70
Period size: 17 Copynumber: 5.4 Consensus size: 17
31538106 GTTAAAAAGT
*
31538116 TGAAATGCAATGAAATA
1 TGAAATGAAATGAAATA
* *
31538133 TGAAATGAAATGTAATT
1 TGAAATGAAATGAAATA
*
31538150 TGAAATGAATATAAAATTAAA
1 TGAAATGAA-ATGAAA-T--A
31538171 TGAAAGTTGAAAT-AAATA
1 TGAAA--TGAAATGAAATA
*
31538189 TGAAATGAAAATAAAATA
1 TGAAATG-AAATGAAATA
31538207 T-AAAT
1 TGAAAT
31538212 TGCAATTAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
16 2 0.03
17 31 0.48
18 16 0.25
19 1 0.02
20 1 0.02
21 8 0.12
22 2 0.03
23 4 0.06
ACGTcount: A:0.57, C:0.01, G:0.14, T:0.28
Consensus pattern (17 bp):
TGAAATGAAATGAAATA
Found at i:31538166 original size:28 final size:28
Alignment explanation
Indices: 31538124--31538198 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
31538114 GTTGAAATGC
* *
31538124 AATGAAATATGAAATGAAATGTAATTTGA
1 AATG-AATATGAAATGAAATGAAAGTTGA
* *
31538153 AATGAATATAAAATTAAATGAAAGTTGA
1 AATGAATATGAAATGAAATGAAAGTTGA
*
31538181 AATAAATATGAAATGAAA
1 AATGAATATGAAATGAAA
31538199 ATAAAATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 35 0.90
29 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (28 bp):
AATGAATATGAAATGAAATGAAAGTTGA
Found at i:31538181 original size:23 final size:23
Alignment explanation
Indices: 31538155--31538198 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
31538145 TAATTTGAAA
*
31538155 TGAATATAAA-ATTAAATGAAAGT
1 TGAA-ATAAATATGAAATGAAAGT
31538178 TGAAATAAATATGAAATGAAA
1 TGAAATAAATATGAAATGAAA
31538199 ATAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (23 bp):
TGAAATAAATATGAAATGAAAGT
Found at i:31538292 original size:17 final size:18
Alignment explanation
Indices: 31538260--31538298 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
31538250 AAAAAAGAAT
31538260 AAATTGAAATGAGAAA-A
1 AAATTGAAATGAGAAATA
31538277 AAATTGAAAT-ATGAAATA
1 AAATTGAAATGA-GAAATA
31538295 AAAT
1 AAAT
31538299 GTAATTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (18 bp):
AAATTGAAATGAGAAATA
Found at i:31538407 original size:17 final size:16
Alignment explanation
Indices: 31538379--31538438 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
31538369 TATAAAAAAA
31538379 AGAAAAAATTGAAATG
1 AGAAAAAATTGAAATG
31538395 AGAAAAAATTTGAAAT-
1 AGAAAAAA-TTGAAATG
31538411 ATG---AAA-TGAAATG
1 A-GAAAAAATTGAAATG
31538424 A-AAAAAATTGAAATG
1 AGAAAAAATTGAAATG
31538439 CAATGAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
12 6 0.16
13 1 0.03
14 6 0.16
15 7 0.19
16 9 0.24
17 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.22
Consensus pattern (16 bp):
AGAAAAAATTGAAATG
Found at i:31538408 original size:124 final size:116
Alignment explanation
Indices: 31538189--31538423 Score: 326
Period size: 124 Copynumber: 2.0 Consensus size: 116
31538179 GAAATAAATA
* * *
31538189 TGAAATGAAAATAAAATATAAATTGCAATTAAAAAATTGAAATCAGACAAAAAATAATATGAAAA
1 TGAAATGAAAATAAAATATAAATTGAAATAAAAAAATTGAAATCAGACAAAAAATAATATAAAAA
*
31538254 AAGAATAAATTGAAATGAGAAAAAAATTGAAATATGAAATAAAATGTAATT
66 AAGAAAAAATTGAAATGAGAAAAAAATTGAAATATGAAATAAAATGTAATT
**
31538305 TGAAATGAAAATAAAATATAAATTGAAATGAAAAACACTAAATTGAAATGGGACAAAAAATTAAT
1 TGAAATGAAAATAAAATATAAATTGAAAT---AAA-A--AAATTGAAATCAGACAAAAAA-TAAT
* *
31538370 ATAAAAAAAAGAAAAAATTGAAATGAGAAAAAATTTGAAATATGAAATGAAATG
59 AT-AAAAAAAGAAAAAATTGAAATGAGAAAAAAATTGAAATATGAAATAAAATG
31538424 AAAAAAATTG
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
116 28 0.27
119 2 0.02
120 1 0.01
122 19 0.18
123 6 0.06
124 47 0.46
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.23
Consensus pattern (116 bp):
TGAAATGAAAATAAAATATAAATTGAAATAAAAAAATTGAAATCAGACAAAAAATAATATAAAAA
AAGAAAAAATTGAAATGAGAAAAAAATTGAAATATGAAATAAAATGTAATT
Found at i:31538421 original size:5 final size:5
Alignment explanation
Indices: 31538411--31538514 Score: 59
Period size: 5 Copynumber: 19.2 Consensus size: 5
31538401 AATTTGAAAT
* * *
31538411 ATGAA ATGAA ATGAA A-AAA ATTGAA ATGCA ATGAAA TATGAA TTGAA
1 ATGAA ATGAA ATGAA ATGAA A-TGAA ATGAA ATG-AA -ATGAA ATGAA
* *
31538458 TATGGA ATGGAA TAT-AA TTTGAA ATGAA ATGAA AGTTGAA ATGAA TATGAA
1 -ATGAA AT-GAA -ATGAA -ATGAA ATGAA ATGAA A--TGAA ATGAA -ATGAA
31538509 ATGAA A
1 ATGAA A
31538515 ATAAAACATA
Statistics
Matches: 78, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
4 3 0.04
5 47 0.60
6 18 0.23
7 10 0.13
ACGTcount: A:0.54, C:0.01, G:0.19, T:0.26
Consensus pattern (5 bp):
ATGAA
Found at i:31538422 original size:12 final size:12
Alignment explanation
Indices: 31538405--31538514 Score: 56
Period size: 11 Copynumber: 9.4 Consensus size: 12
31538395 AGAAAAAATT
31538405 TGAAATATGAAA
1 TGAAATATGAAA
**
31538417 TGAAATGAAAAAAA
1 TGAAAT--ATGAAA
*
31538431 TTG-AA-ATGCAA
1 -TGAAATATGAAA
*
31538442 TGAAATATGAAT
1 TGAAATATGAAA
*
31538454 TG-AATATGGAA
1 TGAAATATGAAA
* *
31538465 TGGAATAT-AATT
1 TGAAATATGAA-A
31538477 TG-AA-ATGAAA
1 TGAAATATGAAA
31538487 TGAAAGT-TGAAA
1 TGAAA-TATGAAA
31538499 TG-AATATGAAA
1 TGAAATATGAAA
31538510 TGAAA
1 TGAAA
31538515 ATAAAACATA
Statistics
Matches: 73, Mismatches: 12, Indels: 26
0.66 0.11 0.23
Matches are distributed among these distances:
10 7 0.10
11 30 0.41
12 28 0.38
14 6 0.08
15 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.19, T:0.26
Consensus pattern (12 bp):
TGAAATATGAAA
Found at i:31538451 original size:27 final size:29
Alignment explanation
Indices: 31538388--31538452 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 29
31538378 AAGAAAAAAT
*
31538388 TGAAATGA-GAAAAAATTTGAAATATGAAA
1 TGAAAT-ATGAAAAAAATTGAAATATGAAA
*
31538417 TG-AA-ATGAAAAAAATTG-AA-ATGCAA
1 TGAAATATGAAAAAAATTGAAATATGAAA
31538442 TGAAATATGAA
1 TGAAATATGAA
31538453 TTGAATATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
25 7 0.23
26 5 0.16
27 15 0.48
28 2 0.06
29 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.17, T:0.23
Consensus pattern (29 bp):
TGAAATATGAAAAAAATTGAAATATGAAA
Found at i:31538516 original size:17 final size:15
Alignment explanation
Indices: 31538411--31538514 Score: 59
Period size: 17 Copynumber: 6.4 Consensus size: 15
31538401 AATTTGAAAT
31538411 ATGAAATGAAATGAA
1 ATGAAATGAAATGAA
* *
31538426 A-AAAATTGAAATGCA
1 ATGAAA-TGAAATGAA
*
31538441 ATGAAATATGAATTGAA
1 ATG-AA-ATGAAATGAA
*
31538458 TATGGAATGGAATAT-AA
1 -ATGAAAT-GAA-ATGAA
*
31538475 TTTGAAATGAAATGAA
1 -ATGAAATGAAATGAA
31538491 AGTTGAAATGAATATGAA
1 A--TGAAATGAA-ATGAA
31538509 ATGAAA
1 ATGAAA
31538515 ATAAAACATA
Statistics
Matches: 68, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
14 3 0.04
15 12 0.18
16 12 0.18
17 30 0.44
18 11 0.16
ACGTcount: A:0.54, C:0.01, G:0.19, T:0.26
Consensus pattern (15 bp):
ATGAAATGAAATGAA
Found at i:31538549 original size:38 final size:36
Alignment explanation
Indices: 31538505--31538627 Score: 122
Period size: 38 Copynumber: 3.2 Consensus size: 36
31538495 GAAATGAATA
*
31538505 TGAAATGAAAATAAAACATAAATTGAAATAAAAAAACT
1 TGAAATGAAAA-AAAA-ATAAATTGAAATAAAAAAAAT
* *
31538543 TGAAATGAGACAAAAAATTAATATGAAA-AAAAACGTAAAT
1 TGAAATGA-AAAAAAAATAAAT-TGAAATAAAAA---AAAT
31538583 TGAAATGAAAAAAAAATAAATTGAAATGAAAAAAAAAT
1 TGAAATGAAAAAAAAATAAATTGAAAT--AAAAAAAAT
*
31538621 TTAAATG
1 TGAAATG
31538628 CAATGAAATA
Statistics
Matches: 71, Mismatches: 6, Indels: 16
0.76 0.06 0.17
Matches are distributed among these distances:
37 10 0.14
38 32 0.45
39 13 0.18
40 11 0.15
41 5 0.07
ACGTcount: A:0.65, C:0.03, G:0.11, T:0.21
Consensus pattern (36 bp):
TGAAATGAAAAAAAAATAAATTGAAATAAAAAAAAT
Found at i:31538599 original size:17 final size:17
Alignment explanation
Indices: 31538476--31538627 Score: 62
Period size: 17 Copynumber: 8.5 Consensus size: 17
31538466 GGAATATAAT
** *
31538476 TTGAAATGAAATGAAAG
1 TTGAAATGAAAAAAAAA
* **
31538493 TTGAAATGAATATGAAA
1 TTGAAATGAAAAAAAAA
*
31538510 -TGAAAAT-AAAACATAAA
1 TTG-AAATGAAAA-AAAAA
*
31538527 TTGAAAT--AAAAAAAC
1 TTGAAATGAAAAAAAAA
*
31538542 TTGAAATGAGACAAAAAA
1 TTGAAATGA-AAAAAAAA
31538560 TT-AATATGAAAAAAAACGTAAA
1 TTGAA-ATG--AAAAAA---AAA
31538582 TTGAAATGAAAAAAAAATAAA
1 TTGAAATG---AAAAAA-AAA
31538603 TTGAAATGAAAAAAAAA
1 TTGAAATGAAAAAAAAA
*
31538620 TTTAAATG
1 TTGAAATG
31538628 CAATGAAATA
Statistics
Matches: 107, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
15 10 0.09
16 8 0.07
17 35 0.33
18 19 0.18
19 4 0.04
20 1 0.01
21 12 0.11
22 8 0.07
23 10 0.09
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.22
Consensus pattern (17 bp):
TTGAAATGAAAAAAAAA
Found at i:31538633 original size:22 final size:21
Alignment explanation
Indices: 31538247--31538620 Score: 131
Period size: 21 Copynumber: 17.6 Consensus size: 21
31538237 AAAAAATAAT
*
31538247 ATGAAAAAAGAATAAATTGAA
1 ATGAAAAAAAAATAAATTGAA
*
31538268 ATG---AGAAAA-AAATTGAAA
1 ATGAAAAAAAAATAAATTG-AA
** *
31538286 TATGAAATAAAATGTAATTTGAA
1 -ATGAAA-AAAAAATAAATTGAA
31538309 ATGAAAATAAAATATAAATTGAA
1 ATGAAAA-AAAA-ATAAATTGAA
* *
31538332 ATG-AAAAACACTAAATTGAA
1 ATGAAAAAAAAATAAATTGAA
* * *
31538352 ATGGGACAAAAAATTAATAT-AA
1 AT-GAAAAAAAAATAAAT-TGAA
*
31538374 A--AAAAAGAAA-AAATTGAA
1 ATGAAAAAAAAATAAATTGAA
**
31538392 ATGAGAAAAAATTTGAAATATGAA
1 ATGA-AAAAAAAAT-AAAT-TGAA
**
31538416 ATGAAATGAAAA-AAATTGAA
1 ATGAAAAAAAAATAAATTGAA
** * *
31538436 ATGCAATGAAATATGAATTGAA
1 ATG-AAAAAAAAATAAATTGAA
*** * *
31538458 TATGGAATGGAATATAATTTGAA
1 -AT-GAAAAAAAAATAAATTGAA
*
31538481 ATGAAATGAAAGTTGAAATGAATATGAA
1 ATGAAA--AAA----AAATAAAT-TGAA
31538509 ATGAAAATAAAACATAAATTGAA
1 ATGAAAA-AAAA-ATAAATTGAA
*
31538532 AT-----AAAAA-AACTTGAA
1 ATGAAAAAAAAATAAATTGAA
* *
31538547 ATGAGACAAAAAATTAA-T---
1 ATGA-AAAAAAAATAAATTGAA
*
31538565 ATGAAAAAAAACGTAAATTGAA
1 ATGAAAAAAAA-ATAAATTGAA
31538587 ATGAAAAAAAAATAAATTGAA
1 ATGAAAAAAAAATAAATTGAA
31538608 ATGAAAAAAAAAT
1 ATGAAAAAAAAAT
31538621 TTAAATGCAA
Statistics
Matches: 261, Mismatches: 48, Indels: 88
0.66 0.12 0.22
Matches are distributed among these distances:
15 9 0.03
16 1 0.00
17 17 0.07
18 19 0.07
19 10 0.04
20 19 0.07
21 53 0.20
22 45 0.17
23 51 0.20
24 19 0.07
26 1 0.00
27 7 0.03
28 10 0.04
ACGTcount: A:0.61, C:0.02, G:0.14, T:0.23
Consensus pattern (21 bp):
ATGAAAAAAAAATAAATTGAA
Found at i:31538643 original size:17 final size:17
Alignment explanation
Indices: 31538623--31538799 Score: 106
Period size: 17 Copynumber: 10.5 Consensus size: 17
31538613 AAAAAAATTT
*
31538623 AAATGCAATGAAATATG
1 AAATGAAATGAAATATG
* *
31538640 AAATGAAATGTAATTTG
1 AAATGAAATGAAATATG
31538657 AAATGAATATG-AA-ATG
1 AAATGAA-ATGAAATATG
*
31538673 AAAGCTGAAATG-AATACG
1 AAA--TGAAATGAAATATG
*
31538691 AAATGAAAATAAAATAT-
1 AAATG-AAATGAAATATG
* *
31538708 AAAT----TAAAATGTG
1 AAATGAAATGAAATATG
*
31538721 GAATGAAAATGAAATTAAGTG
1 AAATG-AAATGAAA-T-A-TG
31538742 AAATTTGAAATGAAA-ATG
1 AAA--TGAAATGAAATATG
*
31538760 AAATTAAATGAAAT-T-
1 AAATGAAATGAAATATG
31538775 AAATGAAATGAAATATG
1 AAATGAAATGAAATATG
31538792 AAATGAAA
1 AAATGAAA
31538800 AAAAAATGAC
Statistics
Matches: 126, Mismatches: 14, Indels: 40
0.70 0.08 0.22
Matches are distributed among these distances:
12 7 0.06
13 3 0.02
15 13 0.10
16 18 0.14
17 44 0.35
18 25 0.20
19 2 0.02
21 4 0.03
22 8 0.06
23 2 0.02
ACGTcount: A:0.56, C:0.02, G:0.16, T:0.25
Consensus pattern (17 bp):
AAATGAAATGAAATATG
Found at i:31538645 original size:5 final size:5
Alignment explanation
Indices: 31538623--31538799 Score: 84
Period size: 5 Copynumber: 31.6 Consensus size: 5
31538613 AAAAAAATTT
* *
31538623 AAATG CAATG AAATATG AAATG AAATG TAATTTG AAATG AATATG AAATG
1 AAATG AAATG -AA-ATG AAATG AAATG -AA-ATG AAATG AA-ATG AAATG
* * * * *
31538673 AAAGCTG AAATG AATACG AAATG AAAATA AAATAT AAATTA AAATGTG GAATG
1 AAA--TG AAATG AA-ATG AAATG -AAATG AAAT-G AAA-TG AAA--TG AAATG
* * * *
31538726 AAAATG AAATT AAGTG AAATTTG AAATG AAAATG AAATT AAATG AAATT
1 -AAATG AAATG AAATG AAA--TG AAATG -AAATG AAATG AAATG AAATG
31538775 AAATG AAATG AAATATG AAATG AAA
1 AAATG AAATG -AA-ATG AAATG AAA
31538800 AAAAAATGAC
Statistics
Matches: 133, Mismatches: 21, Indels: 36
0.70 0.11 0.19
Matches are distributed among these distances:
5 72 0.54
6 39 0.29
7 22 0.17
ACGTcount: A:0.56, C:0.02, G:0.16, T:0.25
Consensus pattern (5 bp):
AAATG
Found at i:31538671 original size:23 final size:23
Alignment explanation
Indices: 31538637--31538698 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
31538627 GCAATGAAAT
* **
31538637 ATGAA-ATGAAATGTAATTTGAA
1 ATGAATATGAAATGAAAGCTGAA
31538659 ATGAATATGAAATGAAAGCTGAA
1 ATGAATATGAAATGAAAGCTGAA
*
31538682 ATGAATACGAAATGAAA
1 ATGAATATGAAATGAAA
31538699 ATAAAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 5 0.14
23 30 0.86
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.24
Consensus pattern (23 bp):
ATGAATATGAAATGAAAGCTGAA
Found at i:31538711 original size:28 final size:27
Alignment explanation
Indices: 31538629--31538798 Score: 111
Period size: 28 Copynumber: 6.2 Consensus size: 27
31538619 ATTTAAATGC
*
31538629 AATGAAATATGAAATG-AAATGTAATTTGA
1 AATG-AATATGAAATGAAAATG-AAATT-A
* *
31538658 AATGAATATGAAATG-AAA-G--CTGA
1 AATGAATATGAAATGAAAATGAAATTA
* *
31538681 AATGAATACGAAATGAAAATAAAATATA
1 AATGAATATGAAATGAAAATGAAAT-TA
* * *
31538709 AATTAAAATGTGGAATGAAAATGAAATTA
1 AA-T-GAATATGAAATGAAAATGAAATTA
* *
31538738 AGTGAAATTTGAAATGAAAATGAAATTA
1 AATG-AATATGAAATGAAAATGAAATTA
*
31538766 AATGAA-ATTAAATG-AAATGAAATATGA
1 AATGAATATGAAATGAAAATGAAAT-T-A
31538793 AATGAA
1 AATGAA
31538799 AAAAAAATGA
Statistics
Matches: 113, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
23 15 0.13
24 4 0.04
25 9 0.08
26 7 0.06
27 11 0.10
28 42 0.37
29 8 0.07
30 17 0.15
ACGTcount: A:0.56, C:0.01, G:0.16, T:0.26
Consensus pattern (27 bp):
AATGAATATGAAATGAAAATGAAATTA
Found at i:31543050 original size:18 final size:17
Alignment explanation
Indices: 31543012--31543054 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
31543002 AGTCTAAATA
31543012 TTTTATTTATTCATTTAT
1 TTTTATTTATT-ATTTAT
31543030 TTTTATTTATT-TTTAGT
1 TTTTATTTATTATTTA-T
31543047 TTTT-TTTA
1 TTTTATTTA
31543055 AAGAGGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.33
17 5 0.21
18 11 0.46
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTATTTATTATTTAT
Found at i:31543053 original size:11 final size:10
Alignment explanation
Indices: 31543013--31543054 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
31543003 GTCTAAATAT
31543013 TTTATTTATTCA
1 TTTATTT-TT-A
31543025 TTTATTTTTA
1 TTTATTTTTA
31543035 TTTATTTTTA
1 TTTATTTTTA
31543045 GTTT-TTTTTA
1 -TTTATTTTTA
31543055 AAGAGGCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 17 0.59
11 5 0.17
12 7 0.24
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:31544744 original size:26 final size:27
Alignment explanation
Indices: 31544683--31544751 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
31544673 AGTATAAAGA
* *
31544683 GTATAACAGTCATTTCACCCTACAGGG
1 GTATTACAGTCATTTTACCCTACAGGG
31544710 GTATTACAGTCATTTTACCCTACA-GG
1 GTATTACAGTCATTTTACCCTACAGGG
31544736 GTATTACAGTCATTTT
1 GTATTACAGTCATTTT
31544752 CATCAGAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 18 0.45
27 22 0.55
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (27 bp):
GTATTACAGTCATTTTACCCTACAGGG
Found at i:31551760 original size:29 final size:30
Alignment explanation
Indices: 31551727--31551793 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
31551717 AATATATAAC
**
31551727 AAAATTTCTGTAATTAAAAGTAGA-ATGACT
1 AAAATTTCTAAAATTAAAAGTAGAGAT-ACT
*
31551757 -AAATTTTTAAAATTAAAAGTAGAGATACT
1 AAAATTTCTAAAATTAAAAGTAGAGATACT
31551786 AAAATTTC
1 AAAATTTC
31551794 AATTGTGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.34
Consensus pattern (30 bp):
AAAATTTCTAAAATTAAAAGTAGAGATACT
Found at i:31556707 original size:48 final size:49
Alignment explanation
Indices: 31556650--31556755 Score: 196
Period size: 48 Copynumber: 2.2 Consensus size: 49
31556640 ACATTTGGTA
31556650 CAAGTTTCATACTTCTAACCATTAACCTATATTTCATTTATGCATTTG-
1 CAAGTTTCATACTTCTAACCATTAACCTATATTTCATTTATGCATTTGC
31556698 CAAGTTTCATACTTCTAACCATTAACCTATATTTCATTTATGCATTTGC
1 CAAGTTTCATACTTCTAACCATTAACCTATATTTCATTTATGCATTTGC
31556747 CAAGATTTC
1 CAAG-TTTC
31556756 CAATTCCAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
48 48 0.86
49 4 0.07
50 4 0.07
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (49 bp):
CAAGTTTCATACTTCTAACCATTAACCTATATTTCATTTATGCATTTGC
Found at i:31559317 original size:18 final size:19
Alignment explanation
Indices: 31559283--31559318 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
31559273 GAAATTTAAA
*
31559283 GAAAATCGTTCGTGTTTAG
1 GAAAAACGTTCGTGTTTAG
31559302 GAAAAACGTT-GTGTTTA
1 GAAAAACGTTCGTGTTTA
31559319 TTATAACCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (19 bp):
GAAAAACGTTCGTGTTTAG
Found at i:31570071 original size:18 final size:18
Alignment explanation
Indices: 31570048--31570097 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
31570038 TCAATAATAT
*
31570048 TCATTTATTCAGTATCAG
1 TCATTTATTCAGTAACAG
*
31570066 TCATTTATTCTGTAACAG
1 TCATTTATTCAGTAACAG
*
31570084 TCAATTATTCAGTA
1 TCATTTATTCAGTA
31570098 GCAGACAGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (18 bp):
TCATTTATTCAGTAACAG
Found at i:31570342 original size:16 final size:16
Alignment explanation
Indices: 31570321--31570351 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31570311 GGTACGAAGT
31570321 ACCTGTAACACCCCTC
1 ACCTGTAACACCCCTC
31570337 ACCTGTAACACCCCT
1 ACCTGTAACACCCCT
31570352 AACCCGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.48, G:0.06, T:0.19
Consensus pattern (16 bp):
ACCTGTAACACCCCTC
Done.