Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 112 of 190
Found at i:17489325 original size:6 final size:6
Alignment explanation
Indices: 17489316--17489403 Score: 81
Period size: 6 Copynumber: 15.0 Consensus size: 6
17489306 AAAACTAGGA
* * * * *
17489316 AAAATT AAAATC AAAATC AAAACT AAAATT AAAACT AAAATC AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
* * * *
17489364 AAAA-T CAAGTT AAAATC AAAATT AAAATT AAGA-T AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
17489404 TTAGCCCTTT
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
5 7 0.11
6 57 0.89
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (6 bp):
AAAATT
Found at i:17489331 original size:12 final size:12
Alignment explanation
Indices: 17489316--17489391 Score: 91
Period size: 12 Copynumber: 6.4 Consensus size: 12
17489306 AAAACTAGGA
* *
17489316 AAAATTAAAATC
1 AAAATCAAAATT
*
17489328 AAAATCAAAACT
1 AAAATCAAAATT
* *
17489340 AAAATTAAAACT
1 AAAATCAAAATT
17489352 AAAATCAAAATT
1 AAAATCAAAATT
*
17489364 AAAATC-AAGTT
1 AAAATCAAAATT
17489375 AAAATCAAAATT
1 AAAATCAAAATT
17489387 AAAAT
1 AAAAT
17489392 TAAGATAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
11 10 0.18
12 45 0.82
ACGTcount: A:0.66, C:0.09, G:0.01, T:0.24
Consensus pattern (12 bp):
AAAATCAAAATT
Found at i:17489381 original size:23 final size:23
Alignment explanation
Indices: 17489328--17489402 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 23
17489318 AATTAAAATC
*
17489328 AAAATCAAAACTAAAATTAAA-ACT
1 AAAATCAAAATTAAAA-TAAAGA-T
* *
17489352 AAAATCAAAATTAAAATCAAGTT
1 AAAATCAAAATTAAAATAAAGAT
*
17489375 AAAATCAAAATTAAAATTAAGAT
1 AAAATCAAAATTAAAATAAAGAT
17489398 AAAAT
1 AAAAT
17489403 TTTAGCCCTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 30 0.67
24 15 0.33
ACGTcount: A:0.65, C:0.08, G:0.03, T:0.24
Consensus pattern (23 bp):
AAAATCAAAATTAAAATAAAGAT
Found at i:17490147 original size:77 final size:77
Alignment explanation
Indices: 17490019--17490167 Score: 253
Period size: 77 Copynumber: 1.9 Consensus size: 77
17490009 TCATTTACTA
* *
17490019 ATTATCATGGTTATTCATTATTTAATAGATATGGTACTGTACCAATGGGCATTGGTTGAGTTGAT
1 ATTATCATGGCTATTCATTATTTAATAGATATGGTACTGTACCAATAGGCATTGGTTGAGTTGAT
17490084 AAGGATCGATTC
66 AAGGATCGATTC
* *
17490096 ATTATCATGGCTATTCATTCTTTAATAGATATGGTATTGTACCAATAGGCATTGGTTGAGTTGAT
1 ATTATCATGGCTATTCATTATTTAATAGATATGGTACTGTACCAATAGGCATTGGTTGAGTTGAT
*
17490161 AGGGATC
66 AAGGATC
17490168 AAATACTTCA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 67 1.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (77 bp):
ATTATCATGGCTATTCATTATTTAATAGATATGGTACTGTACCAATAGGCATTGGTTGAGTTGAT
AAGGATCGATTC
Found at i:17505944 original size:29 final size:29
Alignment explanation
Indices: 17505891--17505959 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
17505881 GAAAAAATTC
* *
17505891 ACATAATTTCTTTCAATACTATAAT-ATT
1 ACATAATTTCATTCAATAATATAATCATT
17505919 ACATAATTTACATTCAATGAAT-TAATCATT
1 ACATAATTT-CATTCAAT-AATATAATCATT
17505949 ACATAATTTCA
1 ACATAATTTCA
17505960 AAGTGAAGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 9 0.25
29 13 0.36
30 14 0.39
ACGTcount: A:0.42, C:0.14, G:0.01, T:0.42
Consensus pattern (29 bp):
ACATAATTTCATTCAATAATATAATCATT
Found at i:17506681 original size:18 final size:18
Alignment explanation
Indices: 17506658--17506692 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
17506648 TTAATATAAA
17506658 AATAA-TTATTTAATTTTT
1 AATAATTTA-TTAATTTTT
17506676 AATAATTTATTAATTTT
1 AATAATTTATTAATTTT
17506693 ATAAATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATAATTTATTAATTTTT
Found at i:17507783 original size:3 final size:3
Alignment explanation
Indices: 17507775--17507812 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
17507765 ATAAAAATTT
17507775 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
17507813 TACAATTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17509252 original size:2 final size:2
Alignment explanation
Indices: 17509245--17509282 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
17509235 CTGGTATGTA
17509245 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
17509283 CTTGTTAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:17510780 original size:18 final size:16
Alignment explanation
Indices: 17510748--17510782 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
17510738 TAATTTTTGC
17510748 TTTTATTTTCTTTCTT
1 TTTTATTTTCTTTCTT
17510764 TTTTATTTTTCCTTTCTT
1 TTTTA-TTTT-CTTTCTT
17510782 T
1 T
17510783 GTATATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 4 0.24
18 8 0.47
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTATTTTCTTTCTT
Found at i:17511286 original size:17 final size:18
Alignment explanation
Indices: 17511257--17511306 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
17511247 TTTAAAAAAA
*
17511257 AAAAAAAAAAAGAAAGG-
1 AAAAAAGAAAAGAAAGGT
*
17511274 AAGAAAGAAAAG-AAGGT
1 AAAAAAGAAAAGAAAGGT
*
17511291 AAAAAAGAAAATAAAG
1 AAAAAAGAAAAGAAAG
17511307 AAAATGAGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 4 0.15
17 20 0.74
18 3 0.11
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (18 bp):
AAAAAAGAAAAGAAAGGT
Found at i:17511369 original size:21 final size:21
Alignment explanation
Indices: 17511317--17511374 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
17511307 AAAATGAGGG
*
17511317 AAAGAAAGAAATAAAGAAATAG
1 AAAGAAA-AAATAAAGAAATAA
**
17511339 AGTGAAAAAATAAAGAAATAA
1 AAAGAAAAAATAAAGAAATAA
*
17511360 AAAGACAAAACTAAA
1 AAAGA-AAAAATAAA
17511375 AAAAGAAAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.72, C:0.03, G:0.14, T:0.10
Consensus pattern (21 bp):
AAAGAAAAAATAAAGAAATAA
Found at i:17512181 original size:2 final size:2
Alignment explanation
Indices: 17512174--17512207 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17512164 ACAATCTCTT
17512174 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17512208 GCTAACTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17515253 original size:15 final size:15
Alignment explanation
Indices: 17515233--17515272 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
17515223 TAATTGGTAG
17515233 GAAGCAAAATATGCC
1 GAAGCAAAATATGCC
17515248 GAAGCAAAATATGCC
1 GAAGCAAAATATGCC
* *
17515263 AAAACAAAAT
1 GAAGCAAAAT
17515273 TAGCATTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.55, C:0.17, G:0.15, T:0.12
Consensus pattern (15 bp):
GAAGCAAAATATGCC
Found at i:17516991 original size:66 final size:66
Alignment explanation
Indices: 17516850--17516993 Score: 202
Period size: 66 Copynumber: 2.2 Consensus size: 66
17516840 TCCAAATTCT
* * *
17516850 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATATAAATTTTAATTATAAAAATAAAA
1 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTAGAAAATAGAAATTTCAATTATAAAAATAAAA
17516915 A
66 A
**
17516916 TTTCAAGGAAAAGTTGAAAGTATCAATTTTCCTCAG-AAATAGAAATTTCAATTATAAAAA-AAA
1 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT-AGAAAATAGAAATTTCAATTATAAAAATAAA
*
17516979 ATG
65 A-A
17516982 TTTTGAGGAAAA
1 TTTTGAGGAAAA
17516994 TTCATGTGTC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
65 4 0.06
66 63 0.93
67 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (66 bp):
TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTAGAAAATAGAAATTTCAATTATAAAAATAAAA
A
Found at i:17517420 original size:58 final size:60
Alignment explanation
Indices: 17517351--17517505 Score: 172
Period size: 58 Copynumber: 2.6 Consensus size: 60
17517341 AAAAGTTTTC
* * * **
17517351 AAAAAGTATTTTGAGGAAAAGTTGAAAGGATCAATTTCCCTCAAAATTAAAA-T-TAAAA
1 AAAAAGCATTTTGAGGAAAAGTTGAAAGTATCAATTTCCCTAAAAACAAAAATTCTAAAA
* * * * *
17517409 AAAAAGCATTTTGAGAAAAAGTTGGAAGTATCAATTTTCCTTAAAAACAAAAATTCTCAAG
1 AAAAAGCATTTTGAGGAAAAGTTGAAAGTATCAA-TTTCCCTAAAAACAAAAATTCTAAAA
* *
17517470 AAAAA-CATTTTAAGGAAAAGTTAAAAGTATCAATTT
1 AAAAAGCATTTTGAGGAAAAGTTGAAAGTATCAATTT
17517506 TCCTTGTACA
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
58 30 0.38
59 17 0.21
60 25 0.31
61 8 0.10
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (60 bp):
AAAAAGCATTTTGAGGAAAAGTTGAAAGTATCAATTTCCCTAAAAACAAAAATTCTAAAA
Found at i:17517490 original size:60 final size:59
Alignment explanation
Indices: 17517351--17517510 Score: 180
Period size: 60 Copynumber: 2.7 Consensus size: 59
17517341 AAAAGTTTTC
* * * * **
17517351 AAAAAGTATTTTGAGGAAAAGTTGAAAGGATCAA-TTTCCCTCAAAATTAAAATTAAAA
1 AAAAAGCATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAAAATTAAAA
* * * *
17517409 AAAAAGCATTTTGAGAAAAAGTTGGAAGTATCAATTTTCCTTAAAAACAAAAATTCTCAAG
1 AAAAAGCATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAAAA-T-TAAAA
* *
17517470 AAAAA-CATTTTAAGGAAAAGTTAAAAGTATCAATTTTCCTT
1 AAAAAGCATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
17517511 GTACAACAGC
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
58 30 0.35
59 14 0.16
60 33 0.39
61 8 0.09
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.29
Consensus pattern (59 bp):
AAAAAGCATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAAAATTAAAA
Found at i:17529132 original size:86 final size:86
Alignment explanation
Indices: 17528987--17529433 Score: 368
Period size: 86 Copynumber: 5.2 Consensus size: 86
17528977 AGTCCAGATT
* * * * * *
17528987 ATTCATTTTAGGCTTCGGTTCAATCCAGGTCATTTTATTTTTAGATTTCGACCTATGCCAGATTC
1 ATTCATTTCAGACTTCAGTTTAATCCAGGTCATTTTATTTTTGGATTTTGACCTATGCCAGATTC
*
17529052 TTCTTTGACTCAGTCTAAGTC
66 TTCTTTGACTCAGTCCAAGTC
* * *
17529073 ATTCATTTTAGGCTTCAGTTTAATCCAGGTCATTTTATTTTTGGATTTTGACCTATGCCAGATCC
1 ATTCATTTCAGACTTCAGTTTAATCCAGGTCATTTTATTTTTGGATTTTGACCTATGCCAGATTC
* * *
17529138 TT-TTTCCATTCAGTCTAAGTC
66 TTCTTT-GACTCAGTCCAAGTC
* * * * * * * * *
17529159 ATTCATTTCATACTTTAGCTTAATCCAAGTCATTTTATTTTGGGATTTTGGCTTATGCTAGATCC
1 ATTCATTTCAGACTTCAGTTTAATCCAGGTCATTTTATTTTTGGATTTTGACCTATGCCAGATTC
* *
17529224 TTCTTCGGCTCAGTCCAAGTC
66 TTCTTTGACTCAGTCCAAGTC
* * * * * * *
17529245 ATTCATTTCAAACATT-GGTTTAATCTAAGTAATTTTATTTTTGGA-TTTCAGCCTATGCTAGA-
1 ATTCATTTCAGAC-TTCAGTTTAATCCAGGTCATTTTATTTTTGGATTTTGA-CCTATGCCAGAT
** * *
17529307 TCTTTCTTCAACTCAATCCAAGTT
64 TC-TTCTTTGACTCAGTCCAAGTC
* * * ** *
17529331 ATTCGTTTCAGACCTC-GATTTAATCTAGGTCATTTTGCTTTTGGATTTCGACCTATGCCAGA-T
1 ATTCATTTCAGACTTCAG-TTTAATCCAGGTCATTTTATTTTTGGATTTTGACCTATGCCAGATT
* *
17529394 CTTTCTTT-AGCTTAGTCCAAGTT
65 C-TTCTTTGA-CTCAGTCCAAGTC
* * *
17529417 GTTTATTTCAAACTTCA
1 ATTCATTTCAGACTTCA
17529434 ATTCAATATA
Statistics
Matches: 297, Mismatches: 54, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
85 10 0.03
86 280 0.94
87 7 0.02
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (86 bp):
ATTCATTTCAGACTTCAGTTTAATCCAGGTCATTTTATTTTTGGATTTTGACCTATGCCAGATTC
TTCTTTGACTCAGTCCAAGTC
Found at i:17529365 original size:172 final size:171
Alignment explanation
Indices: 17529008--17529433 Score: 428
Period size: 172 Copynumber: 2.5 Consensus size: 171
17528998 GCTTCGGTTC
* * * *
17529008 AATCCAGGTCATTTTATTTTTAGATTTCGACCTATGCCAGATTCTTCTTTGACTCAGTCTAAGTC
1 AATCCAGGTCATTTTA-TTTTGGATTTCGACCTATGCCAGATCCTTCTTTGGCTCAGTCCAAGTC
* ** * * *
17529073 ATTCATTTTAGGCTTCAGTTTAATCCAGGTCATTTTATTTTTGGATTTTGACCTATGCCAGATCC
65 ATTCATTTCAAACTTCAGTTTAATCCAAGTAATTTTATTTTTGGATTTAGACCTATGCCAGATCC
* * * * * **
17529138 TTTTTCCATTCAGTCTAAGTCATTCATTTCATACTTTAGCTT
130 TTTTTCAACTCAATCCAAGTCATTCATTTCAGACTCGAGCTT
* * * * * *
17529180 AATCCAAGTCATTTTATTTTGGGATTTTGGCTTATGCTAGATCCTTCTTCGGCTCAGTCCAAGTC
1 AATCCAGGTCATTTTATTTT-GGATTTCGACCTATGCCAGATCCTTCTTTGGCTCAGTCCAAGTC
* * *
17529245 ATTCATTTCAAACATT-GGTTTAATCTAAGTAATTTTATTTTTGGATTTCAG-CCTATGCTAGAT
65 ATTCATTTCAAAC-TTCAGTTTAATCCAAGTAATTTTATTTTTGGATTT-AGACCTATGCCAGAT
* * *
17529308 -CTTTCTTCAACTCAATCCAAGTTATTCGTTTCAGACCTCGA-TTT
128 CCTTT-TTCAACTCAATCCAAGTCATTCATTTCAGA-CTCGAGCTT
* * * * * *
17529352 AATCTAGGTCATTTTGCTTTTGGATTTCGACCTATGCCAGATCTTTCTTTAGCTTAGTCCAAGTT
1 AATCCAGGTCATTTT-ATTTTGGATTTCGACCTATGCCAGATCCTTCTTTGGCTCAGTCCAAGTC
* *
17529417 GTTTATTTCAAACTTCA
65 ATTCATTTCAAACTTCA
17529434 ATTCAATATA
Statistics
Matches: 203, Mismatches: 44, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
171 10 0.05
172 183 0.90
173 10 0.05
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.44
Consensus pattern (171 bp):
AATCCAGGTCATTTTATTTTGGATTTCGACCTATGCCAGATCCTTCTTTGGCTCAGTCCAAGTCA
TTCATTTCAAACTTCAGTTTAATCCAAGTAATTTTATTTTTGGATTTAGACCTATGCCAGATCCT
TTTTCAACTCAATCCAAGTCATTCATTTCAGACTCGAGCTT
Found at i:17530686 original size:66 final size:65
Alignment explanation
Indices: 17530604--17530728 Score: 216
Period size: 66 Copynumber: 1.9 Consensus size: 65
17530594 ATTCTTTTTG
*
17530604 AGGAAAAGTTGAAAGTATCAATTTTCTTC-ATAAATAGAAATTTTAATTATAAAAATAAAAATTT
1 AGGAAAAGTTGAAAGTATCAATTTTCTTCGA-AAATAGAAATTTCAATTATAAAAA-AAAAATTT
17530668 CA
64 CA
17530670 AGGAAAAGTTGAAAGTATCAATTTTCTTCGAAAATAGAAATTTCAATTATAAAAAAAAA
1 AGGAAAAGTTGAAAGTATCAATTTTCTTCGAAAATAGAAATTTCAATTATAAAAAAAAA
17530729 TGTTTTAAAG
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
65 4 0.07
66 52 0.91
67 1 0.02
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.32
Consensus pattern (65 bp):
AGGAAAAGTTGAAAGTATCAATTTTCTTCGAAAATAGAAATTTCAATTATAAAAAAAAAATTTCA
Found at i:17530969 original size:60 final size:60
Alignment explanation
Indices: 17530898--17531118 Score: 251
Period size: 61 Copynumber: 3.7 Consensus size: 60
17530888 CGAAAAGTAT
*
17530898 TTTTTGA-GAAAAAGTTGAAAATATCAA-TTTTCCTTGAAAAATAATTTTTTAAAAAGATA
1 TTTTTGAGGAAAAAGTT-AAAATATCAATTTTTCCTTGAAAAATAATTTTTTAAAAAAATA
*
17530957 TTTTTGAGG-AAAAGTTAAAGTATCAATTTTT-CTT-AAAAATAATTTTTTTTAAAAAAAAATA
1 TTTTTGAGGAAAAAGTTAAAATATCAATTTTTCCTTGAAAAATAA--TTTTTT--AAAAAAATA
* * * *
17531018 TTTTTGAGGAAAAAGTTGAAAGTATCAATTTTTCCTTG-AAAATAAAATTGTTAAAAAAACA
1 TTTTTGAGGAAAAAGTT-AAAATATCAATTTTTCCTTGAAAAAT-AATTTTTTAAAAAAATA
*
17531079 TTTTT-AGGAAAAAGTTAAAAGTATGAATTTTTCC-TGAAAA
1 TTTTTGAGGAAAAAGTTAAAA-TATCAATTTTTCCTTGAAAA
17531119 CAAAATTTAT
Statistics
Matches: 142, Mismatches: 7, Indels: 25
0.82 0.04 0.14
Matches are distributed among these distances:
57 8 0.06
58 12 0.08
59 29 0.20
60 27 0.19
61 30 0.21
62 7 0.05
63 19 0.13
64 8 0.06
65 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.38
Consensus pattern (60 bp):
TTTTTGAGGAAAAAGTTAAAATATCAATTTTTCCTTGAAAAATAATTTTTTAAAAAAATA
Found at i:17531010 original size:15 final size:16
Alignment explanation
Indices: 17530981--17531011 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17530971 TTAAAGTATC
17530981 AATTTTTCTTAAAAAT
1 AATTTTTCTTAAAAAT
*
17530997 AATTTTTTTTAAAAA
1 AATTTTTCTTAAAAA
17531012 AAAATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTTTCTTAAAAAT
Found at i:17531132 original size:59 final size:61
Alignment explanation
Indices: 17530876--17531311 Score: 250
Period size: 58 Copynumber: 7.1 Consensus size: 61
17530866 TTTTTTCGTA
** **
17530876 AAAATAAAATTTCGAAAAGTAT-TTTTTGA-GAAAAAGTTGAAAA-TATCAA-TTTTCCTTG
1 AAAATAAAATTTATAAAAAAATATTTTTGAGGAAAAAGTT-AAAAGTATCAATTTTTCCTTG
* * * *
17530934 AAAA-ATAATTTTTTAAAAAGATATTTTTGAGG-AAAAGTT-AAAGTATCAATTTTT-CTTA
1 AAAATA-AAATTTATAAAAAAATATTTTTGAGGAAAAAGTTAAAAGTATCAATTTTTCCTTG
** * *
17530992 AAAATAATTTTTTTTAAAAAAAAATATTTTTGAGGAAAAAGTTGAAAGTATCAATTTTTCCTTG
1 AAAATAA---AATTTATAAAAAAATATTTTTGAGGAAAAAGTTAAAAGTATCAATTTTTCCTTG
* *
17531056 AAAATAAAATTGT-TAAAAAAACATTTTT-AGGAAAAAGTTAAAAGTATGAATTTTTCC-TG
1 AAAATAAAATT-TATAAAAAAATATTTTTGAGGAAAAAGTTAAAAGTATCAATTTTTCCTTG
* * *
17531115 AAAACAAAATTTATAAAATAAAAGTTTTCAAAAAGTATTTTGAGGAAAAA-TTGAAAGGATCAA-
1 AAAATAAAATTTAT-AAA-AAAA----T-----A-T-TTTTGAGGAAAAAGTTAAAAGTATCAAT
17531178 TTTTCCTTG
53 TTTTCCTTG
* * * * ** *
17531187 AAATTAAAATTAAAAAAAAAACA-TTTTGAGG-AAAAGTTGGAAGTA-CTAA-TTTTCCTTA
1 AAAATAAAATTTATAAAAAAATATTTTTGAGGAAAAAGTTAAAAGTATC-AATTTTTCCTTG
* * * * * *
17531245 AAAACAAAAATTCTCAAGAAAAACA-TTTTAAGG-AAAAGTTGAAAGTATCAA--TTTCCTT-
1 AAAATAAAATTTAT-AA-AAAAATATTTTTGAGGAAAAAGTTAAAAGTATCAATTTTTCCTTG
17531303 AAAATAAAA
1 AAAATAAAA
17531312 ACTCCCAAAT
Statistics
Matches: 305, Mismatches: 39, Indels: 68
0.74 0.09 0.17
Matches are distributed among these distances:
57 9 0.03
58 71 0.23
59 41 0.13
60 60 0.20
61 42 0.14
62 8 0.03
63 15 0.05
64 10 0.03
70 5 0.02
71 10 0.03
72 26 0.09
73 8 0.03
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.34
Consensus pattern (61 bp):
AAAATAAAATTTATAAAAAAATATTTTTGAGGAAAAAGTTAAAAGTATCAATTTTTCCTTG
Found at i:17532326 original size:15 final size:15
Alignment explanation
Indices: 17532306--17532341 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
17532296 GTTGTTTAGG
17532306 CTTTTATTTTCCATA
1 CTTTTATTTTCCATA
* *
17532321 CTTTTATTTTTCTTA
1 CTTTTATTTTCCATA
17532336 CTTTTA
1 CTTTTA
17532342 GTTCGATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTTTATTTTCCATA
Found at i:17532584 original size:35 final size:34
Alignment explanation
Indices: 17532521--17533524 Score: 401
Period size: 35 Copynumber: 28.8 Consensus size: 34
17532511 ACTAGTCATC
* * * *
17532521 GATTAAACCATAAGTTAAAAAATGAAAATGACTAG
1 GATTAAACCATGAGTCAGAAAATAAAAATGA-TAG
* * *
17532556 GATTAAACCATGAGTCAGAGAATAAAAATGACCAA
1 GATTAAACCATGAGTCAGAAAATAAAAATGA-TAG
* * *
17532591 GATTAAAGCACGAGTCAGAAAATAAAAATGATCGG
1 GATTAAACCATGAGTCAGAAAATAAAAATGAT-AG
* * *
17532626 GATTAAACCATAAATCAGAATATAAAAATGACTTA-
1 GATTAAACCATGAGTCAGAAAATAAAAATGA--TAG
** * * *
17532661 GATTAAATTATGAGTCAAAAAATGAAAATGACTGG
1 GATTAAACCATGAGTCAGAAAATAAAAATGA-TAG
* * * * * *
17532696 GATTAAATCATTAGTCAGAGAATAAAAACGGTCG
1 GATTAAACCATGAGTCAGAAAATAAAAATGATAG
* * * *
17532730 AGATTAAATCAT-AGTTAGAAGATGAAAATGATTAG
1 -GATTAAACCATGAGTCAGAAAATAAAAATGA-TAG
* * *
17532765 GATTAAA-CA--AGTTAG-AGA-AAAAATGACAACTGG
1 GATTAAACCATGAGTCAGAAAATAAAAATG---A-TAG
* * * * *
17532798 GATTAAACTATGAGTCAAAAAATGAAAACGATCGG
1 GATTAAACCATGAGTCAGAAAATAAAAATGAT-AG
* * *
17532833 GATTAAACCACGAGTCAAAAAATAAAAATAACT-G
1 GATTAAACCATGAGTCAGAAAATAAAAATGA-TAG
* * * ** * *
17532867 GAATAAAACCATGAATTAGAGGATGAAAATGATCAA
1 G-ATTAAACCATGAGTCAGAAAATAAAAATGAT-AG
* * * * *
17532903 GATTAAATCGTGAGTCAAAAAATGAAAATGATTGG
1 GATTAAACCATGAGTCAGAAAATAAAAATGA-TAG
** * *
17532938 GATTAAACCACAAGTCAGAGAATAAAAATGATCG
1 GATTAAACCATGAGTCAGAAAATAAAAATGATAG
* * * * *
17532972 AAATTAAATCATGTGTCAAAAAATAAAAATGATTG
1 -GATTAAACCATGAGTCAGAAAATAAAAATGATAG
* * * *
17533007 AAATTAAACCATGAGTCAGAGAAA-AAATGATAACTAA
1 -GATTAAACCATGAGTCAGA-AAATAAA-AATGA-TAG
* * *
17533044 AATTAAATCATGAGTC---AAA-AAAAATGATCG
1 GATTAAACCATGAGTCAGAAAATAAAAATGATAG
* * * *
17533074 AGATTAAATCATGAGTCAAAAAATGAAAATGATTG
1 -GATTAAACCATGAGTCAGAAAATAAAAATGATAG
* * * * * *
17533109 AAATTAAACCATGA-ACTAGAAGATGAAAATAATCG
1 -GATTAAACCATGAGTC-AGAAAATAAAAATGATAG
* * *
17533144 AGATTAAACCATAAGTCAGAAAATGAAAATGATTGG
1 -GATTAAACCATGAGTCAGAAAATAAAAATGA-TAG
** * * * *
17533180 GATTAAACCACAAGTTAGAAGATGAAAATGATTG
1 GATTAAACCATGAGTCAGAAAATAAAAATGATAG
* * * * *
17533214 AGATTAAACCACGAATTAG-AGA-AAAAATGACTGTTG
1 -GATTAAACCATGAGTCAGAAAATAAAAATGA---TAG
* * *
17533250 GCATTAAATCATGAGTCAAAAAATGACAAA-GATAG
1 G-ATTAAACCATGAGTCAGAAAAT-AAAAATGATAG
* * *
17533285 GAATTAAACCATGA-TTAGAGAAA-AAATGATGACTAA
1 G-ATTAAACCATGAGTCAGA-AAATAAA-AATGA-TAG
** * * * *
17533321 GATTAAACCACAAGTCAGAAATTGAAAATAACTAA
1 GATTAAACCATGAGTCAGAAAATAAAAATGA-TAG
** * * *
17533356 GACAAAACCACGAGTTAGAGAATAAAAATGACTAG
1 GATTAAACCATGAGTCAGAAAATAAAAATGA-TAG
*
17533391 GATTAAACCATGAGTCAAAAAATAAAAATGATCAG
1 GATTAAACCATGAGTCAGAAAATAAAAATGAT-AG
* * * * * *
17533426 TATTAAACCATAAGTCAAAAAACAAAAACGATCAA
1 GATTAAACCATGAGTCAGAAAATAAAAATGAT-AG
* *
17533461 GATTAAACCAT-AGATCTGAAAATAAAAATGATCG
1 GATTAAACCATGAG-TCAGAAAATAAAAATGATAG
* *
17533495 AGATTAAACCATGAGTTAAAAATATAAAAA
1 -GATTAAACCATGAGTCAGAAA-ATAAAAA
17533525 AAAAATTGAA
Statistics
Matches: 738, Mismatches: 180, Indels: 101
0.72 0.18 0.10
Matches are distributed among these distances:
30 7 0.01
31 21 0.03
32 12 0.02
33 21 0.03
34 46 0.06
35 550 0.75
36 64 0.09
37 6 0.01
38 7 0.01
39 4 0.01
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (34 bp):
GATTAAACCATGAGTCAGAAAATAAAAATGATAG
Found at i:17532980 original size:242 final size:242
Alignment explanation
Indices: 17532551--17533221 Score: 723
Period size: 242 Copynumber: 2.8 Consensus size: 242
17532541 AATGAAAATG
* * * * * *
17532551 ACTAGGATTAAACCATGAGTCAGAGAATAAAAATGACCAAGATTAAAGCACGAGTCAGAAAATAA
1 ACTAGGATTAAACTATGAGTCA-AAAAT-AAAATGATCGAGATTAAACCACGAGTCAAAAAATAA
* * * * * * *
17532616 AAATGATCGGGATTAAACCATAAATCAGAATATAAAAATGA-CTTAGATTAAATTATGAGTCAAA
64 AAATGAT-GGAATTAAACCATGAATTAGAAGATGAAAATGATC-AAGATTAAATCATGAGTCAAA
* * ** * *
17532680 AAATGAAAATGACTGGGATTAAATCATTAGTCAGAGAATAAAAACGGTCGAGATTAAATCATAGT
127 AAATGAAAATGATTGGGATTAAACCACAAGTCAGAGAATAAAAATGATCGAGATTAAATCAT-GT
* * * * *
17532745 -T-AGAAGATGAAAATGATT-AGGATTAAA-CA-AGTTAGAGAAAAAATGACA
191 GTCAAAAAATAAAAATGATTGA-AATTAAACCAGAGTCAGAGAAAAAATGACA
* * *
17532793 ACTGGGATTAAACTATGAGTCAAAAAATGAAAACGATCGGGATTAAACCACGAGTCAAAAAATAA
1 ACTAGGATTAAACTATGAGTC-AAAAAT-AAAATGATCGAGATTAAACCACGAGTCAAAAAATAA
* * * *
17532858 AAATAACTGGAATAAAACCATGAATTAGAGGATGAAAATGATCAAGATTAAATCGTGAGTCAAAA
64 AAATGA-TGGAATTAAACCATGAATTAGAAGATGAAAATGATCAAGATTAAATCATGAGTCAAAA
*
17532923 AATGAAAATGATTGGGATTAAACCACAAGTCAGAGAATAAAAATGATCGAAATTAAATCATGTGT
128 AATGAAAATGATTGGGATTAAACCACAAGTCAGAGAATAAAAATGATCGAGATTAAATCATGTGT
*
17532988 CAAAAAATAAAAATGATTGAAATTAAACCATGAGTCAGAGAAAAAATGATA
193 CAAAAAATAAAAATGATTGAAATTAAACCA-GAGTCAGAGAAAAAATGACA
** * * *
17533039 ACTAAAATTAAA-TCATGAGTC-AAAA-AAAATGATCGAGATTAAATCATGAGTCAAAAAATGAA
1 ACTAGGATTAAACT-ATGAGTCAAAAATAAAATGATCGAGATTAAACCACGAGTCAAAAAATAAA
* * * * * * *
17533101 AATGATTGAAATTAAACCATGAACTAGAAGATGAAAATAATCGAGATTAAACCATAAGTCAGAAA
65 AATGA-TGGAATTAAACCATGAATTAGAAGATGAAAATGATCAAGATTAAATCATGAGTCAAAAA
* * *
17533166 ATGAAAATGATTGGGATTAAACCACAAGTTAGA-AGATGAAAATGATTGAGATTAAA
129 ATGAAAATGATTGGGATTAAACCACAAGTCAGAGA-ATAAAAATGATCGAGATTAAA
17533222 CCACGAATTA
Statistics
Matches: 360, Mismatches: 58, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
241 3 0.01
242 293 0.81
243 23 0.06
244 7 0.02
245 1 0.00
246 33 0.09
ACGTcount: A:0.51, C:0.10, G:0.17, T:0.22
Consensus pattern (242 bp):
ACTAGGATTAAACTATGAGTCAAAAATAAAATGATCGAGATTAAACCACGAGTCAAAAAATAAAA
ATGATGGAATTAAACCATGAATTAGAAGATGAAAATGATCAAGATTAAATCATGAGTCAAAAAAT
GAAAATGATTGGGATTAAACCACAAGTCAGAGAATAAAAATGATCGAGATTAAATCATGTGTCAA
AAAATAAAAATGATTGAAATTAAACCAGAGTCAGAGAAAAAATGACA
Found at i:17533107 original size:29 final size:30
Alignment explanation
Indices: 17532996--17533112 Score: 78
Period size: 31 Copynumber: 3.7 Consensus size: 30
17532986 GTCAAAAAAT
* *
17532996 AAAAATGATTGAA-ATTAAACCATGAGTCAGAGA
1 AAAAATGA-TAAAGATTAAATCATGAGTC--A-A
*
17533029 AAAAATGATAACTAAAATTAAATCATGAGTCAAA
1 AAAAATGAT-A--AAGATTAAATCATGAGTC-AA
**
17533063 AAAAATGATCGAGATTAAATCATGAGTC-A
1 AAAAATGATAAAGATTAAATCATGAGTCAA
17533092 AAAAATGA-AAATGATTGAAAT
1 AAAAATGATAAA-GATT-AAAT
17533113 TAAACCATGA
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
28 1 0.01
29 13 0.19
30 4 0.06
31 16 0.23
32 1 0.01
33 8 0.11
34 10 0.14
35 3 0.04
36 14 0.20
ACGTcount: A:0.55, C:0.08, G:0.15, T:0.23
Consensus pattern (30 bp):
AAAAATGATAAAGATTAAATCATGAGTCAA
Found at i:17533292 original size:242 final size:239
Alignment explanation
Indices: 17532799--17533531 Score: 561
Period size: 242 Copynumber: 3.0 Consensus size: 239
17532789 GACAACTGGG
* *
17532799 ATTAAACTATGAGTCAAAAAATGAAAACGATCGGGATTAAACCACGAGTCAAAAAATAAAAATAA
1 ATTAAACCATGAGTC--AAAA--AAAACGATCGAGATTAAACCACGAGTCAAAAAATAAAAATAA
* * * * * * *
17532864 CTGGAATAAAACCATGAATTAGAGGATGAAAATGATCAAGATTAAATCGTGAGTCAAAAAATGAA
62 CTGAAATAAAACCATGAACTAGAAGATGAAAATAATCAAGATTAAACCATAAGTCAAAAAATGAA
* * **
17532929 AATGATTGGGATTAAACCACAAGTCAGAGAATAAAAATGATCGAAATTAAATCATGTGTCAAAAA
127 AATGATTGGGATTAAACCACAAGTCAGAGAATAAAAATGATCGAAATTAAACCACGAATCAAAAA
* *
17532994 ATAAAAATGATTGAAATTAAACCATGAGTCAGAGAAAAAATGATAACTAAA
192 ATAAAAATGATTGAAATTAAACCATGAGTC--A-AAAAAATGAAAAATAAA
* * * * * * *
17533045 ATTAAATCATGAGTCAAAAAAAATGATCGAGATTAAATCATGAGTCAAAAAATGAAAATGATTGA
1 ATTAAACCATGAGTCAAAAAAAACGATCGAGATTAAACCACGAGTCAAAAAATAAAAATAACTGA
* * *
17533110 AATTAAACCATGAACTAGAAGATGAAAATAATCGAGATTAAACCATAAGTCAGAAAATGAAAATG
66 AATAAAACCATGAACTAGAAGATGAAAATAATCAAGATTAAACCATAAGTCAAAAAATGAAAATG
* * * * * * *
17533175 ATTGGGATTAAACCACAAGTTAGA-AGATGAAAATGATTGAGATTAAACCACGAAT-TAGAGA-A
131 ATTGGGATTAAACCACAAGTCAGAGA-ATAAAAATGATCGAAATTAAACCACGAATCAAAAAATA
** * *
17533237 AAAATGACTGTTGGCATTAAATCATGAGTC-AAAAAATGACAAAGATAGGA
195 AAAATGA---TTGAAATTAAACCATGAGTCAAAAAAATGA-AAA-ATA-AA
* * * * * * *
17533287 ATTAAACCATGA-TTAGAGAAAAAATGATGACTAAGATTAAACCACAAGTCAGAAATTGAAAATA
1 ATTAAACCATGAGTCA-A-AAAAAACGAT--C-GAGATTAAACCACGAGTCAAAAAATAAAAATA
* * ** * * * *
17533351 ACT-AAGACAAAACCACGAGTTAG-AGAATAAAAATGA-CTAGGATTAAACCATGAGTCAAAAAA
61 ACTGAA-ATAAAACCATGAACTAGAAG-ATGAAAATAATC-AAGATTAAACCATAAGTCAAAAAA
* ** * * * * * * *
17533413 TAAAAATGATCAGTATTAAACCATAAGTCAAAAAACAAAAACGATC-AAGATTAAACCA-TAGAT
123 TGAAAATGATTGGGATTAAACCACAAGTCAGAGAATAAAAATGATCGAA-ATTAAACCACGA-AT
** * * * * *
17533476 CTGAAAATAAAAATGATCGAGATTAAACCATGAGTTAAAAATAT-AAAAAAAAA
186 CAAAAAATAAAAATGATTGAAATTAAACCATGAGTCAAAAAAATGAAAAATAAA
17533529 ATT
1 ATT
17533532 GAAATTAAAC
Statistics
Matches: 385, Mismatches: 81, Indels: 46
0.75 0.16 0.09
Matches are distributed among these distances:
239 9 0.02
240 10 0.03
241 8 0.02
242 156 0.41
243 29 0.08
244 7 0.02
245 24 0.06
246 130 0.34
247 4 0.01
248 8 0.02
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.21
Consensus pattern (239 bp):
ATTAAACCATGAGTCAAAAAAAACGATCGAGATTAAACCACGAGTCAAAAAATAAAAATAACTGA
AATAAAACCATGAACTAGAAGATGAAAATAATCAAGATTAAACCATAAGTCAAAAAATGAAAATG
ATTGGGATTAAACCACAAGTCAGAGAATAAAAATGATCGAAATTAAACCACGAATCAAAAAATAA
AAATGATTGAAATTAAACCATGAGTCAAAAAAATGAAAAATAAA
Found at i:17533374 original size:176 final size:176
Alignment explanation
Indices: 17533076--17533400 Score: 401
Period size: 176 Copynumber: 1.8 Consensus size: 176
17533066 AATGATCGAG
* *
17533076 ATTAAATCATGAGTCAAAAAATGAAAATGATTGAAATTAAACCATGAACTAGAAGATGAAAATAA
1 ATTAAATCATGAGTCAAAAAATGAAAATGATAGAAATTAAACCATGAACTAGAAGATAAAAATAA
* * * * ** ** *
17533141 TCGAGATTAAACCATAAGTCAGAAAATGAAAATGATTGGGATTAAACCACAAGTTAGA-AGATGA
66 TCAAGATTAAACCACAAGTCAGAAAATGAAAATAACTAAGACAAAACCACAAGTTAGAGA-ATAA
*
17533205 AAATGA-TTGAGATTAAACCACGAATTAGAGAAAAAATGACTGTTGGC
130 AAATGACTAG-GATTAAACCACGAATTAGAGAAAAAATGACTGTTGGC
* * *
17533252 ATTAAATCATGAGTCAAAAAATGACAAA-GATAGGAATTAAACCATG-ATTAG-AGA-AAAAATG
1 ATTAAATCATGAGTCAAAAAATGA-AAATGATAGAAATTAAACCATGAACTAGAAGATAAAAATA
* *
17533313 ATGACTAAGATTAAACCACAAGTCAGAAATTGAAAATAACTAAGACAAAACCACGAGTTAGAGAA
65 AT--C-AAGATTAAACCACAAGTCAGAAAATGAAAATAACTAAGACAAAACCACAAGTTAGAGAA
17533378 TAAAAATGACTAGGATTAAACCA
127 TAAAAATGACTAGGATTAAACCA
17533401 TGAGTCAAAA
Statistics
Matches: 126, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
173 7 0.06
174 3 0.02
175 5 0.04
176 105 0.83
177 6 0.05
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21
Consensus pattern (176 bp):
ATTAAATCATGAGTCAAAAAATGAAAATGATAGAAATTAAACCATGAACTAGAAGATAAAAATAA
TCAAGATTAAACCACAAGTCAGAAAATGAAAATAACTAAGACAAAACCACAAGTTAGAGAATAAA
AATGACTAGGATTAAACCACGAATTAGAGAAAAAATGACTGTTGGC
Found at i:17533639 original size:35 final size:35
Alignment explanation
Indices: 17533569--17533698 Score: 120
Period size: 35 Copynumber: 3.7 Consensus size: 35
17533559 AAACAATCGG
* * * * *
17533569 GATTAAACCAC-AGTTAGAAAATGAAAAGGACTGA
1 GATTAAACCACAAATCAAAAAATGAAAATGATTGA
*
17533603 GATTAAACCACAAATCAAAAGATGAAAATGATTGA
1 GATTAAACCACAAATCAAAAAATGAAAATGATTGA
** * *
17533638 GATTAAAGTACGAGTCAAAAAATGAAAATGACTTGA
1 GATTAAACCACAAATCAAAAAATGAAAATGA-TTGA
** *
17533674 -ATTAAACCACGGATCAAAGAATGAA
1 GATTAAACCACAAATCAAAAAATGAA
17533699 TGTGACCAAG
Statistics
Matches: 78, Mismatches: 16, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
34 11 0.14
35 63 0.81
36 4 0.05
ACGTcount: A:0.52, C:0.12, G:0.18, T:0.19
Consensus pattern (35 bp):
GATTAAACCACAAATCAAAAAATGAAAATGATTGA
Found at i:17534624 original size:33 final size:33
Alignment explanation
Indices: 17534581--17534773 Score: 140
Period size: 33 Copynumber: 5.8 Consensus size: 33
17534571 ATTCATTGGT
* *
17534581 GGCCAACTAATCTAAGCTTAAATCTTCTTTGAA
1 GGCCAGCTAATCTAGGCTTAAATCTTCTTTGAA
* * * *
17534614 GGCCAGCTAATCTGGGATTAATTCTTTCTTAGAA
1 GGCCAGCTAATCTAGGCTTAAATC-TTCTTTGAA
* * *
17534648 GGCTAGCTAATTTAGGCTTAATAT-TTCATT-AA
1 GGCCAGCTAATCTAGGCTTAA-ATCTTCTTTGAA
* **
17534680 GGGCCAGCTAATCTAGGCTTAATAT-TTCATCAAA
1 -GGCCAGCTAATCTAGGCTTAA-ATCTTCTTTGAA
* ** * * * *
17534714 AGTTAGCTTATATGGGCTTAAATCTTTTCTTGAA
1 GGCCAGCTAATCTAGGCTTAAATCTTCT-TTGAA
*
17534748 GGCCAGCTAATTTAGGCTTAAATCTT
1 GGCCAGCTAATCTAGGCTTAAATCTT
17534774 GTATCATATC
Statistics
Matches: 122, Mismatches: 32, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
32 4 0.03
33 67 0.55
34 50 0.41
35 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (33 bp):
GGCCAGCTAATCTAGGCTTAAATCTTCTTTGAA
Found at i:17534667 original size:67 final size:66
Alignment explanation
Indices: 17534587--17534768 Score: 163
Period size: 67 Copynumber: 2.7 Consensus size: 66
17534577 TGGTGGCCAA
* * * * * *
17534587 CTAATCTAAGCTTAAATCTTCTTTGAAGGCCAGCTAATCTGGGATTAATTCTTTC-TTAGAAGGC
1 CTAATATAGGCTTAAATCTTCTTTGAAGGCCAGCTAATCTAGGATTAA-TATTTCATCA-AAAGC
17534651 TAG
64 TAG
* * * *
17534654 CTAATTTAGGCTTAATAT-TTCATT-AAGGGCCAGCTAATCTAGGCTTAATATTTCATCAAAAGT
1 CTAATATAGGCTTAA-ATCTTCTTTGAA-GGCCAGCTAATCTAGGATTAATATTTCATCAAAAGC
17534717 TAG
64 TAG
* * * * *
17534720 CTTATATGGGCTTAAATCTTTTCTTGAAGGCCAGCTAATTTAGGCTTAA
1 CTAATATAGGCTTAAATCTTCT-TTGAAGGCCAGCTAATCTAGGATTAA
17534769 ATCTTGTATC
Statistics
Matches: 94, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
65 2 0.02
66 27 0.29
67 61 0.65
68 4 0.04
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (66 bp):
CTAATATAGGCTTAAATCTTCTTTGAAGGCCAGCTAATCTAGGATTAATATTTCATCAAAAGCTA
G
Found at i:17536539 original size:10 final size:9
Alignment explanation
Indices: 17536520--17536581 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
17536510 ACCTATTCAA
17536520 TTTTTTTTC
1 TTTTTTTTC
17536529 TTTTTTCTTC
1 TTTTTT-TTC
*
17536539 -TTTTATTC
1 TTTTTTTTC
*
17536547 TTTTTTTCC
1 TTTTTTTTC
**
17536556 TTTCATTTC
1 TTTTTTTTC
17536565 ATTTTTTTTTC
1 --TTTTTTTTC
17536576 TTTTTT
1 TTTTTT
17536582 CCCTTTCACT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
8 3 0.07
9 28 0.68
10 3 0.07
11 7 0.17
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:17537452 original size:16 final size:16
Alignment explanation
Indices: 17537433--17537469 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
17537423 TGTTTTCATT
*
17537433 TTTTTCTTTTTTTTTG
1 TTTTTCTTTTTTTTTA
*
17537449 TTTTTGTTTTTTTTTA
1 TTTTTCTTTTTTTTTA
17537465 TTTTT
1 TTTTT
17537470 TTTGTTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.03, C:0.03, G:0.05, T:0.89
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTA
Found at i:17537453 original size:25 final size:24
Alignment explanation
Indices: 17537413--17537475 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
17537403 AAAAGGCTTC
* *
17537413 TCTTTCTTTTTGTTTTCATTTTTT
1 TCTTTTTTTTTGTTTTTATTTTTT
*
17537437 TCTTTTTTTTTGTTTTTGTTTTTT
1 TCTTTTTTTTTGTTTTTATTTTTT
*
17537461 TTTATTTTTTTTGTT
1 TCT-TTTTTTTTGTT
17537476 ACAACCCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 23 0.68
25 11 0.32
ACGTcount: A:0.03, C:0.06, G:0.06, T:0.84
Consensus pattern (24 bp):
TCTTTTTTTTTGTTTTTATTTTTT
Found at i:17537472 original size:19 final size:18
Alignment explanation
Indices: 17537439--17537475 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
17537429 CATTTTTTTC
17537439 TTTTTTTTTGTTTTTGTT
1 TTTTTTTTTGTTTTTGTT
*
17537457 TTTTTTTATTTTTTTTGTT
1 TTTTTTT-TTGTTTTTGTT
17537476 ACAACCCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.89
Consensus pattern (18 bp):
TTTTTTTTTGTTTTTGTT
Found at i:17541408 original size:23 final size:24
Alignment explanation
Indices: 17541369--17541414 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
17541359 AAGATTTACC
*
17541369 ATAACATTTCTTTTAAA-AATAAA
1 ATAACATTTCTTGTAAATAATAAA
17541392 ATAACATTAT-TTGTAAATAATAA
1 ATAACATT-TCTTGTAAATAATAA
17541415 TTATCGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (24 bp):
ATAACATTTCTTGTAAATAATAAA
Found at i:17543971 original size:144 final size:145
Alignment explanation
Indices: 17543751--17544319 Score: 482
Period size: 145 Copynumber: 3.9 Consensus size: 145
17543741 TAATTTTTGA
* * * * * * * *
17543751 GATTTTAAA-GCACCAAAAATTATAAAATATTAT-AGGATTGAGATTTGAAAAGTTTCATGAAAT
1 GATTTCAAACGCACCAAAAATCATGAAATATTATGA-AATTAAGATCTAAAAAGTTTCATGAAAA
* * * * * * *
17543814 TTCGAGCTTGAAAAAGTTAAAATATGAAAATACCTTTATAAGTGTATTTTGGTAATTTCATACTT
65 TCCAAGCTCGAAAAAGTTAAATTACGAAAATACCCTTATAAGGGTATTTTGGTAATTTCATACTT
* *
17543879 TCTAGGGTACTGCTAT
130 CCTAGGGTACTACTAT
* * * ** *
17543895 GATTTCAAA-GCACCAAAAATCATGAAATATTATGATATTGATATCTAAAAAGTTTTGTGAAATT
1 GATTTCAAACGCACCAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAAT
* * ** ***
17543959 CCAAGCTCGAAAAGGTTAAATTACGAAAATACCCCTTA-AAAGGTATTTTCATAATTTTGCACTT
66 CCAAGCTCGAAAAAGTTAAATTACGAAAATA-CCCTTATAAGGGTATTTTGGTAATTTCATACTT
* *
17544023 CCTCGGGTACTTCTAT
130 CCTAGGGTACTACTAT
* * * * * * **
17544039 GGTTTCAAACTCACTAAAAATCATGAAATATTATGAAATTAAAATATGAAAAGTTTCACAAAAAT
1 GATTTCAAACGCACCAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAAT
* * * * ** * * **
17544104 CTAAGGTTGGAAAAGCCAAATTACAAAAATACCTTTATAAGGGTATTTTGGTAATTTCACCCTT-
66 CCAAGCTCGAAAAAGTTAAATTACGAAAATACCCTTATAAGGGTATTTTGGTAATTTCATACTTC
* * *
17544168 CTCGAGGTACTATTGT
131 CTAG-GGTACTACTAT
* * * * * *
17544184 GATTTTAAATGCATCAAAAATCATGAAATATTATAAAATTAAGATCTACAATGTTTCATGAAAAT
1 GATTTCAAACGCACCAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAAT
* * ** * * *
17544249 CCAAGCTCGAAAAGGTTAATTTTTGAAAATACCCCTATAAGGGTATTTTGGTAATTTTATCCTTC
66 CCAAGCTCGAAAAAGTTAAATTACGAAAATACCCTTATAAGGGTATTTTGGTAATTTCATACTTC
17544314 CTAGGG
131 CTAGGG
17544320 CATGATGAAA
Statistics
Matches: 332, Mismatches: 87, Indels: 11
0.77 0.20 0.03
Matches are distributed among these distances:
144 127 0.38
145 202 0.61
146 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (145 bp):
GATTTCAAACGCACCAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAGTTTCATGAAAAT
CCAAGCTCGAAAAAGTTAAATTACGAAAATACCCTTATAAGGGTATTTTGGTAATTTCATACTTC
CTAGGGTACTACTAT
Found at i:17549357 original size:11 final size:11
Alignment explanation
Indices: 17549341--17549390 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
17549331 GTTTGGTAAA
17549341 AAAATAGAAGG
1 AAAATAGAAGG
*
17549352 AAAATAGAGGG
1 AAAATAGAAGG
17549363 AAGAAATA-AA-G
1 -A-AAATAGAAGG
17549374 AAAAT-GAAGG
1 AAAATAGAAGG
17549384 AAAATAG
1 AAAATAG
17549391 TTTTTCCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
9 6 0.19
10 7 0.22
11 12 0.38
12 2 0.06
13 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.26, T:0.10
Consensus pattern (11 bp):
AAAATAGAAGG
Found at i:17551011 original size:9 final size:9
Alignment explanation
Indices: 17550989--17551036 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
17550979 AAACGCTTTG
*
17550989 TATATATTG
1 TATATATTA
*
17550998 T-TATATAA
1 TATATATTA
17551006 TATATA-TA
1 TATATATTA
17551014 TATATATTA
1 TATATATTA
*
17551023 GATATATTA
1 TATATATTA
17551032 TATAT
1 TATAT
17551037 GTGATATACC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
8 13 0.41
9 19 0.59
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (9 bp):
TATATATTA
Found at i:17555632 original size:21 final size:20
Alignment explanation
Indices: 17555580--17555636 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
17555570 AAAGTGTAAT
17555580 TATTCAAAGTAAAATAAAAAA
1 TATTCAAA-TAAAATAAAAAA
* ** *
17555601 AATAAAAATAAAATGAATAAA
1 TATTCAAATAAAAT-AAAAAA
17555622 TATTCAAATAAAATA
1 TATTCAAATAAAATA
17555637 TAATTTATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (20 bp):
TATTCAAATAAAATAAAAAA
Found at i:17556006 original size:10 final size:9
Alignment explanation
Indices: 17555951--17556228 Score: 121
Period size: 9 Copynumber: 30.6 Consensus size: 9
17555941 AAATACAAAA
17555951 AAAAATTTTT
1 AAAAA-TTTT
* *
17555961 AAAAGTTCT
1 AAAAATTTT
*
17555970 AAAAATTCT
1 AAAAATTTT
17555979 AAAATAGTTTT
1 AAAA-A-TTTT
17555990 AAAAATTTT
1 AAAAATTTT
**
17555999 AGAAAATTCA
1 A-AAAATTTT
*
17556009 AAAAAATTT
1 AAAAATTTT
* *
17556018 AAATATTCT
1 AAAAATTTT
17556027 -AAAATGTTCT
1 AAAAAT-TT-T
17556037 AAAATATTTT
1 AAAA-ATTTT
* *
17556047 TAAAATTAT
1 AAAAATTTT
17556056 AAATAATTTT
1 AAA-AATTTT
* *
17556066 TAAAATTAT
1 AAAAATTTT
17556075 -AAAA--TT
1 AAAAATTTT
17556081 AAAAA----
1 AAAAATTTT
* **
17556086 AAAAACTAA
1 AAAAATTTT
17556095 AAAAATTTT
1 AAAAATTTT
17556104 -AAAATTTT
1 AAAAATTTT
*
17556112 AAAAATTCT
1 AAAAATTTT
17556121 AAAAATATTT
1 AAAAAT-TTT
* *
17556131 CAAATTTTAT
1 AAAAATTT-T
*
17556141 AAAAATTAT
1 AAAAATTTT
*
17556150 -AAAATAATT
1 AAAAAT-TTT
17556159 AAAAATTTT
1 AAAAATTTT
**
17556168 AGAAAATTCAA
1 A-AAAATT-TT
17556179 AAAAATTTT
1 AAAAATTTT
17556188 --AAATTTT
1 AAAAATTTT
*
17556195 AAAAATTCTA
1 AAAAATT-TT
*
17556205 AAAAATTAT
1 AAAAATTTT
17556214 AAAAGATTTT
1 AAAA-ATTTT
17556224 AAAAA
1 AAAAA
17556229 ATTATAAAGA
Statistics
Matches: 202, Mismatches: 42, Indels: 49
0.69 0.14 0.17
Matches are distributed among these distances:
5 5 0.02
6 1 0.00
7 11 0.05
8 21 0.10
9 79 0.39
10 70 0.35
11 13 0.06
12 2 0.01
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (9 bp):
AAAAATTTT
Found at i:17556058 original size:19 final size:20
Alignment explanation
Indices: 17556036--17556079 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
17556026 TAAAATGTTC
17556036 TAAAAT-ATTTTTAAAATTA
1 TAAAATAATTTTTAAAATTA
17556055 T-AAATAATTTTTAAAATTA
1 TAAAATAATTTTTAAAATTA
17556074 TAAAAT
1 TAAAAT
17556080 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.17
19 15 0.65
20 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAATAATTTTTAAAATTA
Found at i:17556107 original size:9 final size:9
Alignment explanation
Indices: 17556095--17556228 Score: 96
Period size: 10 Copynumber: 14.6 Consensus size: 9
17556085 AAAAAACTAA
17556095 AAAAATTTT
1 AAAAATTTT
17556104 -AAAATTTT
1 AAAAATTTT
*
17556112 AAAAATTCT
1 AAAAATTTT
17556121 AAAAATATTT
1 AAAAAT-TTT
* *
17556131 CAAATTTTAT
1 AAAAATTT-T
*
17556141 AAAAATTAT
1 AAAAATTTT
*
17556150 -AAAATAATT
1 AAAAAT-TTT
17556159 AAAAATTTT
1 AAAAATTTT
**
17556168 AGAAAATTCAA
1 A-AAAATT-TT
17556179 AAAAATTTT
1 AAAAATTTT
17556188 --AAATTTT
1 AAAAATTTT
*
17556195 AAAAATTCTA
1 AAAAATT-TT
*
17556205 AAAAATTAT
1 AAAAATTTT
17556214 AAAAGATTTT
1 AAAA-ATTTT
17556224 AAAAA
1 AAAAA
17556229 ATTATAAAGA
Statistics
Matches: 96, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
7 7 0.07
8 13 0.14
9 30 0.31
10 45 0.47
11 1 0.01
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (9 bp):
AAAAATTTT
Found at i:17556193 original size:56 final size:54
Alignment explanation
Indices: 17555949--17556228 Score: 190
Period size: 57 Copynumber: 4.9 Consensus size: 54
17555939 AAAAATACAA
* *
17555949 AAAAAAATTTTTAAAAGTTCTAAAAATTCTAAAATAGTTTTAAAAATTTTAGAAAATTC
1 AAAAAAA-TTTTAAAA-TTATAAAAATTCTAAAATA--ATTAAAAATTTTA-AAAATTC
* * * * *
17556008 AAAAAAA-TTTAAATATTCTAAAATGTTCTAAAATATTTTTAAAATTATAAATAATT-
1 AAAAAAATTTTAAA-ATTATAAAA-ATTCTAAAATA-ATTAAAAATTTTAAA-AATTC
*** * * ** * *
17556064 TTTAAAATTATAAAATTAAAAAAAAAACTAAAAAAATTTTAAAATTTTAAAAATTC
1 AAAAAAATTTTAAAATT-ATAAAAATTCTAAAATAA-TTAAAAATTTTAAAAATTC
* * * *
17556120 TAAAAATATTTCAAATTTTATAAAAATTATAAAATAATTAAAAATTTTAGAAAATTC
1 -AAAAAAATTTTAAA-ATTATAAAAATTCTAAAATAATTAAAAATTTTA-AAAATTC
*
17556177 AAAAAAATTTT-AAATTTTAAAAATTCTAAAA-AATTATAAAAGATTTTAAAAA
1 AAAAAAATTTTAAAATTATAAAAATTCTAAAATAA-T-TAAAA-ATTTTAAAAA
17556229 ATTATAAAGA
Statistics
Matches: 175, Mismatches: 33, Indels: 30
0.74 0.14 0.13
Matches are distributed among these distances:
53 2 0.01
54 16 0.09
55 15 0.09
56 55 0.31
57 67 0.38
58 13 0.07
59 7 0.04
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (54 bp):
AAAAAAATTTTAAAATTATAAAAATTCTAAAATAATTAAAAATTTTAAAAATTC
Found at i:17556229 original size:20 final size:19
Alignment explanation
Indices: 17556094--17556241 Score: 112
Period size: 20 Copynumber: 7.9 Consensus size: 19
17556084 AAAAAAACTA
*
17556094 AAAAAATT-TTAAAATTTT
1 AAAAAATTATAAAAATTTT
*
17556112 -AAAAATTCTAAAAATATTT
1 AAAAAATTATAAAAAT-TTT
* ** *
17556131 CAAATTTTATAAAAATTAT
1 AAAAAATTATAAAAATTTT
17556150 AAAATAA-T-TAAAAATTTT
1 AAAA-AATTATAAAAATTTT
* *
17556168 AGAAAATTCAAAAAAATTTT
1 AAAAAATT-ATAAAAATTTT
* *
17556188 ---AAATTTTAAAAATTCT
1 AAAAAATTATAAAAATTTT
17556204 AAAAAATTATAAAAGATTTT
1 AAAAAATTATAAAA-ATTTT
17556224 AAAAAATTATAAAGAATT
1 AAAAAATTATAAA-AATT
17556242 AAGGAAGCTT
Statistics
Matches: 102, Mismatches: 16, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
16 8 0.08
17 14 0.14
18 19 0.19
19 19 0.19
20 41 0.40
21 1 0.01
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAAATTATAAAAATTTT
Found at i:17556230 original size:56 final size:54
Alignment explanation
Indices: 17555930--17556231 Score: 189
Period size: 56 Copynumber: 5.3 Consensus size: 54
17555920 ATTTTTTTTC
* * * *
17555930 AAAATTATAAAAAATACAAAAAAAAATTTTTAAAAGTTCTAAAAATTCTAAAATAGTTTTA
1 AAAATTTTAAAAAATTC--AAAAAAA-TTTT-AAA-TTTTAAAAATTCTAAAA-A-ATTTA
* * * *
17555991 AAAATTTTAGAAAATTCAAAAAAA-TTTAAATATTCTAAAATGTTCTAAAATATTTTT
1 AAAATTTTAAAAAATTCAAAAAAATTTTAAAT-TT-TAAAA-ATTCTAAAA-AATTTA
* * *** * ** ** *
17556048 AAAATTATAAATAATT-TTTAAAATTATAAAATTAAAAAAAAAACTAAAAAAATTTT
1 AAAATTTTAAAAAATTCAAAAAAATT-TTAAATT-TTAAAAATTCT-AAAAAATTTA
* * *
17556104 AAAATTTT-AAAAATTCTAAAAATATTTCAAATTTTATAAAAATTATAAAATAA-TTA
1 AAAATTTTAAAAAATTC-AAAAAAATTTTAAA-TTT-TAAAAATTCTAAAA-AATTTA
*
17556160 AAAATTTTAGAAAATTCAAAAAAATTTTAAATTTTAAAAATTCTAAAAAATTATA
1 AAAATTTTAAAAAATTCAAAAAAATTTTAAATTTTAAAAATTCTAAAAAATT-TA
17556215 AAAGATTTTAAAAAATT
1 AAA-ATTTTAAAAAATT
17556232 ATAAAGAATT
Statistics
Matches: 188, Mismatches: 37, Indels: 37
0.72 0.14 0.14
Matches are distributed among these distances:
53 2 0.01
54 14 0.07
55 15 0.08
56 64 0.34
57 57 0.30
58 15 0.08
59 7 0.04
61 14 0.07
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (54 bp):
AAAATTTTAAAAAATTCAAAAAAATTTTAAATTTTAAAAATTCTAAAAAATTTA
Found at i:17556236 original size:10 final size:10
Alignment explanation
Indices: 17556195--17556242 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
17556185 TTTAAATTTT
*
17556195 AAAAATTCTA
1 AAAAATTATA
17556205 AAAAATTATA
1 AAAAATTATA
* *
17556215 AAAGATTTTA
1 AAAAATTATA
17556225 AAAAATTATA
1 AAAAATTATA
*
17556235 AAGAATTA
1 AAAAATTA
17556243 AGGAAGCTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (10 bp):
AAAAATTATA
Found at i:17556266 original size:84 final size:83
Alignment explanation
Indices: 17556093--17556284 Score: 212
Period size: 84 Copynumber: 2.3 Consensus size: 83
17556083 AAAAAAAACT
* *
17556093 AAAAAAATTTTAAAATTTTAAAAATTCTAAAAATATTTCAAATTTTATAAAAATTATAAAATAAT
1 AAAAAAATTTT-AAATTTTAAAAATTCTAAAAATATTTAAAATTTTATAAAAATTATAAAAGAAT
**
17556158 TAAAAATTTTAGAAAATTC
65 TAAAAAGCTTAGAAAATTC
17556177 AAAAAAATTTTAAATTTTAAAAATTCTAAAAA-ATTATAAAAGATTTTA-AAAAATTAT-AAAGA
1 AAAAAAATTTTAAATTTTAAAAATTCTAAAAATATT-T-AAA-ATTTTATAAAAATTATAAAAGA
* * *
17556239 ATTAAGGAAGCTTATAAATTTTC
63 ATTAA-AAAGCTTAGAAA-ATTC
* *
17556262 -AAAAAATCTTACAATTTAAAAAA
1 AAAAAAATTTTA-AATTTTAAAAA
17556285 AATTAAAAAT
Statistics
Matches: 93, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
82 3 0.03
83 31 0.33
84 40 0.43
85 19 0.20
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.35
Consensus pattern (83 bp):
AAAAAAATTTTAAATTTTAAAAATTCTAAAAATATTTAAAATTTTATAAAAATTATAAAAGAATT
AAAAAGCTTAGAAAATTC
Found at i:17556615 original size:16 final size:16
Alignment explanation
Indices: 17556594--17556643 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 16
17556584 ATTTAAAAAA
17556594 AATTTTAGATTTTTTT
1 AATTTTAGATTTTTTT
*
17556610 AATTTTAG--TTTTTA
1 AATTTTAGATTTTTTT
17556624 AATTGTTATGATTTTTTT
1 AATT-TTA-GATTTTTTT
17556642 AA
1 AA
17556644 ACTTTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 9 0.32
15 3 0.11
16 9 0.32
18 7 0.25
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (16 bp):
AATTTTAGATTTTTTT
Found at i:17556675 original size:15 final size:15
Alignment explanation
Indices: 17556657--17556696 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
17556647 TTAAAAAAAA
17556657 ATTTATTAAATTTTT
1 ATTTATTAAATTTTT
*
17556672 ATTT-TTTAA-TTTT
1 ATTTATTAAATTTTT
17556685 -TTTATTAAATTT
1 ATTTATTAAATTT
17556697 CTTACAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
12 3 0.14
13 8 0.38
14 6 0.29
15 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTATTAAATTTTT
Found at i:17556708 original size:30 final size:27
Alignment explanation
Indices: 17556658--17556712 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 27
17556648 TAAAAAAAAA
*
17556658 TTTATTAAATTTTTATTTTTTAATTTT
1 TTTATTAAATTTTTAATTTTTAATTTT
17556685 TTTATTAAATTTCTTACAATTTTTAATT
1 TTTATTAAATTT-TT--AATTTTTAATT
17556713 CTTCAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 12 0.50
28 2 0.08
30 10 0.42
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTATTAAATTTTTAATTTTTAATTTT
Found at i:17556779 original size:11 final size:10
Alignment explanation
Indices: 17556761--17556844 Score: 68
Period size: 10 Copynumber: 8.8 Consensus size: 10
17556751 TTTTTTAATT
17556761 TTTTAAAAAA
1 TTTTAAAAAA
17556771 TTTTAAAAAA
1 TTTTAAAAAA
17556781 TTTT--AAAA
1 TTTTAAAAAA
*
17556789 TTTT-AAAAT
1 TTTTAAAAAA
** *
17556798 TTTTTTAGAA
1 TTTTAAAAAA
17556808 TTTT-AAAAA
1 TTTTAAAAAA
***
17556817 TTTTTTGAAA
1 TTTTAAAAAA
*
17556827 TTTCAAAAAA
1 TTTTAAAAAA
17556837 TTTTAAAA
1 TTTTAAAA
17556845 TGTCTTATAA
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
8 8 0.14
9 14 0.24
10 36 0.62
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:17556788 original size:18 final size:18
Alignment explanation
Indices: 17556767--17556845 Score: 86
Period size: 19 Copynumber: 4.3 Consensus size: 18
17556757 AATTTTTTAA
17556767 AAAATTTTAAAAAATTTT
1 AAAATTTTAAAAAATTTT
**
17556785 AAAATTTTAAAATTTTTTT
1 AAAATTTTAAAA-AATTTT
* *
17556804 AGAATTTTAAAAATTTTTT
1 AAAATTTTAAAAA-ATTTT
* *
17556823 GAAATTTCAAAAAATTTT
1 AAAATTTTAAAAAATTTT
17556841 AAAAT
1 AAAAT
17556846 GTCTTATAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
18 20 0.40
19 30 0.60
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (18 bp):
AAAATTTTAAAAAATTTT
Found at i:17556812 original size:8 final size:8
Alignment explanation
Indices: 17556767--17556800 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
17556757 AATTTTTTAA
17556767 AAAATTTT
1 AAAATTTT
17556775 AAAAAATTTT
1 --AAAATTTT
17556785 AAAATTTT
1 AAAATTTT
17556793 AAAATTTT
1 AAAATTTT
17556801 TTTAGAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
AAAATTTT
Found at i:17556949 original size:9 final size:9
Alignment explanation
Indices: 17556937--17556979 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
17556927 TTTTTTGAAG
17556937 TTTTTAAAA
1 TTTTTAAAA
*
17556946 TTTTTTAGTAA
1 -TTTTTA-AAA
17556957 TTTTTAAAA
1 TTTTTAAAA
*
17556966 TTTTTAGAA
1 TTTTTAAAA
17556975 TTTTT
1 TTTTT
17556980 TTAATCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 15 0.52
10 12 0.41
11 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:17557033 original size:9 final size:10
Alignment explanation
Indices: 17556884--17557036 Score: 83
Period size: 10 Copynumber: 15.9 Consensus size: 10
17556874 AAAAATTAAT
17556884 AATTTTTTAG
1 AATTTTTTAG
17556894 AATTGTTTTA-
1 AATT-TTTTAG
17556904 AATTATTTT-G
1 AATT-TTTTAG
* * *
17556914 AAGTTTTAAA
1 AATTTTTTAG
*
17556924 AATTTTTTTG
1 AATTTTTTAG
* *
17556934 AAGTTTTTAA
1 AATTTTTTAG
17556944 AATTTTTTAG
1 AATTTTTTAG
17556954 TAA-TTTTTA-
1 -AATTTTTTAG
*
17556963 AAATTTTTAG
1 AATTTTTTAG
*
17556973 AATTTTTT-T
1 AATTTTTTAG
*
17556982 AA--TCTT--
1 AATTTTTTAG
*
17556988 AATTTTTT-T
1 AATTTTTTAG
* *
17556997 AATTTTTAAAA
1 AATTTTT-TAG
*
17557008 AACTTTTTAG
1 AATTTTTTAG
17557018 AATTTTTTAG
1 AATTTTTTAG
17557028 AATTTTTTA
1 AATTTTTTA
17557037 TATGTTTGTG
Statistics
Matches: 109, Mismatches: 23, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
6 2 0.02
7 3 0.03
8 5 0.05
9 18 0.17
10 68 0.62
11 13 0.12
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.59
Consensus pattern (10 bp):
AATTTTTTAG
Found at i:17557035 original size:20 final size:19
Alignment explanation
Indices: 17556884--17557036 Score: 102
Period size: 20 Copynumber: 8.0 Consensus size: 19
17556874 AAAAATTAAT
17556884 AATTTTTTAGAATTGTTTTA
1 AATTTTTTAGAATT-TTTTA
**
17556904 AATTATTTT-GAAGTTTTAAA
1 AATT-TTTTAGAA-TTTTTTA
* *
17556924 AATTTTTTTGAAGTTTTTAA
1 AATTTTTTAGAA-TTTTTTA
17556944 AATTTTTTAGTAA-TTTTTA
1 AATTTTTTAG-AATTTTTTA
* *
17556963 AAATTTTTAGAATTTTTTT
1 AATTTTTTAGAATTTTTTA
* *
17556982 AA--TCTT--AATTTTTTT
1 AATTTTTTAGAATTTTTTA
* * *
17556997 AATTTTTAAAAAACTTTTTA
1 AATTTTT-TAGAATTTTTTA
17557017 GAATTTTTTAGAATTTTTTA
1 -AATTTTTTAGAATTTTTTA
17557037 TATGTTTGTG
Statistics
Matches: 107, Mismatches: 15, Indels: 22
0.74 0.10 0.15
Matches are distributed among these distances:
15 11 0.10
17 5 0.05
18 2 0.02
19 25 0.23
20 49 0.46
21 15 0.14
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.59
Consensus pattern (19 bp):
AATTTTTTAGAATTTTTTA
Found at i:17561492 original size:17 final size:18
Alignment explanation
Indices: 17561472--17561513 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
17561462 AGTTTAAAAA
17561472 TTAAAAAATTGGATT-TT
1 TTAAAAAATTGGATTATT
* **
17561489 TTAAACAATTTTATTATT
1 TTAAAAAATTGGATTATT
17561507 TTAAAAA
1 TTAAAAA
17561514 GAAAAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (18 bp):
TTAAAAAATTGGATTATT
Found at i:17565818 original size:13 final size:14
Alignment explanation
Indices: 17565802--17565841 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
17565792 ATAATATGAA
17565802 TAAATAACATAAT-
1 TAAATAACATAATG
17565815 TAAATAACATACATG
1 TAAATAACATA-ATG
17565830 TAAATAA-ATAAT
1 TAAATAACATAAT
17565842 ATAAGCAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.52
14 5 0.20
15 7 0.28
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (14 bp):
TAAATAACATAATG
Found at i:17568971 original size:37 final size:36
Alignment explanation
Indices: 17568929--17569008 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 36
17568919 AAGGGTACAA
** *
17568929 ATTTTATATGTTATAATATTAAGTAAAT-ATATTTTAG
1 ATTTTATATGAAATAATATTAAGT-AATGATA-TTTAC
17568966 ATTTTATATGAAATAATATTAAGTAATGATATTTAC
1 ATTTTATATGAAATAATATTAAGTAATGATATTTAC
17569002 ATTTTAT
1 ATTTTAT
17569009 TTTAATTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
36 14 0.36
37 25 0.64
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.50
Consensus pattern (36 bp):
ATTTTATATGAAATAATATTAAGTAATGATATTTAC
Found at i:17569237 original size:71 final size:71
Alignment explanation
Indices: 17569043--17569417 Score: 298
Period size: 71 Copynumber: 5.3 Consensus size: 71
17569033 AAAGACTACA
* * * * **
17569043 TTTTTTATATTAAAAACATGATCTTTGTTAAAATTTTGGAATTTTGAAAAAAAAAATT-AACATT
1 TTTTTTATCTTAAAAACATGGTCTTTGTTAAAATTTTAGAATTTTGAAAATAAAGTTTCAACA-T
*
17569107 CAATACA-
65 CCATA-AT
* * * * * *
17569114 -TTTTTATATTAAAAACCTAAG-CTTTATTAAAATTTTAGAA-TTTCAAACATAAAGTTTTAACA
1 TTTTTTATCTTAAAAACAT-GGTCTTTGTTAAAATTTTAGAATTTTGAAA-ATAAAGTTTCAACA
17569176 TCCATAAT
64 TCCATAAT
* ** * *
17569184 TTTTTTATTTTAAAAACATGGTCTTCATTAAAATTTTAGAATTTTGCAAATAAAGATTCAACATC
1 TTTTTTATCTTAAAAACATGGTCTTTGTTAAAATTTTAGAATTTTGAAAATAAAGTTTCAACATC
*
17569249 GATTATAT
66 CA-TA-AT
* ** *
17569257 TTTTTAATCTTAAAAACACAGTCTTTGTTTGTTAAAATTTTAGAATTTTGAAAATAAAATTTCAA
1 TTTTTTATCTTAAAAACATGGTC----TTTGTTAAAATTTTAGAATTTTGAAAATAAAGTTTCAA
*
17569322 CAT-C-T-AC
62 CATCCATAAT
* * * ** * *
17569329 TTTTTTATCTTAAAAATATGATTTTTGTTAAAATTCAAGAATTTTGAAAATATAGTTTCAATATC
1 TTTTTTATCTTAAAAACATGGTCTTTGTTAAAATTTTAGAATTTTGAAAATAAAGTTTCAACATC
**
17569394 CATTGT
66 CATAAT
*
17569400 GTTTTTATCTTAAAAACA
1 TTTTTTATCTTAAAAACA
17569418 CAACACTTGT
Statistics
Matches: 243, Mismatches: 45, Indels: 32
0.76 0.14 0.10
Matches are distributed among these distances:
68 36 0.15
69 8 0.03
70 47 0.19
71 69 0.28
72 25 0.10
73 21 0.09
74 1 0.00
77 36 0.15
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.43
Consensus pattern (71 bp):
TTTTTTATCTTAAAAACATGGTCTTTGTTAAAATTTTAGAATTTTGAAAATAAAGTTTCAACATC
CATAAT
Found at i:17569370 original size:145 final size:146
Alignment explanation
Indices: 17569043--17569419 Score: 335
Period size: 145 Copynumber: 2.6 Consensus size: 146
17569033 AAAGACTACA
* ** *** * * *
17569043 TTTTTTATATTAAAAACATGATCTTTGTTAAAATTTTGGAATTTTGAAAAAAAAAATT-AACATT
1 TTTTTTATCTTAAAAACATGATCTTCATTAAAATTCAAGAATTTTGAAAATAAAGATTCAACATC
* ** * *
17569107 CAATACATTTTTATATTAAAAAC-CTAAG-C----TTTATTAAAATTTTAGAATTTCAAACATAA
66 CATTATGTTTTTATCTTAAAAACAC--AGTCTTTGTTTGTTAAAATTTTAGAATTTCAAACATAA
* * *
17569166 AGTTTTAACATCCATAAT
129 AATTTCAACATCCATAAC
* * ** *
17569184 TTTTTTATTTTAAAAACATGGTCTTCATTAAAATTTTAGAATTTTGCAAATAAAGATTCAACATC
1 TTTTTTATCTTAAAAACATGATCTTCATTAAAATTCAAGAATTTTGAAAATAAAGATTCAACATC
* * *
17569249 GATTATATTTTTTAATCTTAAAAACACAGTCTTTGTTTGTTAAAATTTTAGAATTTTGAAA-ATA
66 CATTAT-GTTTTT-ATCTTAAAAACACAGTCTTTGTTTGTTAAAATTTTAGAA-TTTCAAACATA
17569313 AAATTTCAACAT-C-T-AC
128 AAATTTCAACATCCATAAC
* * ** * * *
17569329 TTTTTTATCTTAAAAATATGATTTTTGTTAAAATTCAAGAATTTTGAAAATATAGTTTCAATATC
1 TTTTTTATCTTAAAAACATGATCTTCATTAAAATTCAAGAATTTTGAAAATAAAGATTCAACATC
*
17569394 CATTGTGTTTTTATCTTAAAAACACA
66 CATTATGTTTTTATCTTAAAAACACA
17569420 ACACTTGTTG
Statistics
Matches: 192, Mismatches: 34, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
141 50 0.26
142 8 0.04
143 21 0.11
144 16 0.08
145 59 0.31
146 1 0.01
147 1 0.01
148 30 0.16
149 6 0.03
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (146 bp):
TTTTTTATCTTAAAAACATGATCTTCATTAAAATTCAAGAATTTTGAAAATAAAGATTCAACATC
CATTATGTTTTTATCTTAAAAACACAGTCTTTGTTTGTTAAAATTTTAGAATTTCAAACATAAAA
TTTCAACATCCATAAC
Found at i:17570487 original size:128 final size:128
Alignment explanation
Indices: 17570259--17570504 Score: 431
Period size: 128 Copynumber: 1.9 Consensus size: 128
17570249 GCATTAATTA
* * *
17570259 AATAAATAATAAGTATTTAACATATTATTAATTAAAAAGGTAGTTGGCACTTGGACACGTGGCAT
1 AATAAATAATAAGAATTTAACATATTATTAATTAAAAAAGTAGTTGGCACTTGGACACATGGCAT
17570324 GTATAGTATTGTAAATATAATATTATTTATTTAAAATTTAACTTTTTATAATTTATTCATTTG
66 GTATAGTATTGTAAATATAATATTATTTATTTAAAATTTAACTTTTTATAATTTATTCATTTG
*
17570387 AATAAATAATATA-AATTTAATATATTATTAATTAAAAAAGTAGTTGGCACTTGGACACATGGCA
1 AATAAATAATA-AGAATTTAACATATTATTAATTAAAAAAGTAGTTGGCACTTGGACACATGGCA
*
17570451 TGTGTAGTATTGTAAATATAATATTATTTATTTAAAATTTAACTTTTTATAATT
65 TGTATAGTATTGTAAATATAATATTATTTATTTAAAATTTAACTTTTTATAATT
17570505 GTAATTAAAT
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
128 111 0.99
129 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.43
Consensus pattern (128 bp):
AATAAATAATAAGAATTTAACATATTATTAATTAAAAAAGTAGTTGGCACTTGGACACATGGCAT
GTATAGTATTGTAAATATAATATTATTTATTTAAAATTTAACTTTTTATAATTTATTCATTTG
Found at i:17570631 original size:48 final size:47
Alignment explanation
Indices: 17570535--17570632 Score: 108
Period size: 48 Copynumber: 2.1 Consensus size: 47
17570525 AAGTCTATTG
* * *
17570535 AAAACAAATAGTTATGTTTGTACAAAATAGACAGATAAGTTTGTTAA
1 AAAACAAATAGTTATATTTATACAAAATAGACAGATAAGTTAGTTAA
* * * *
17570582 AAAATAAATAGCTTATATTTATTCAAAATAGACTGTTAAGTCTAG-TAA
1 AAAACAAATAG-TTATATTTATACAAAATAGACAGATAAGT-TAGTTAA
17570630 AAA
1 AAA
17570633 TAAGACAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
47 10 0.24
48 30 0.71
49 2 0.05
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (47 bp):
AAAACAAATAGTTATATTTATACAAAATAGACAGATAAGTTAGTTAA
Found at i:17572741 original size:19 final size:20
Alignment explanation
Indices: 17572717--17572767 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
17572707 GCCACCAATG
*
17572717 CAAACCCTAAACCTCTATA-
1 CAAACCCTAAACCTCTAAAC
*
17572736 CAAACCTTAAA-CTCTAAAC
1 CAAACCCTAAACCTCTAAAC
17572755 CAAACCCTAAACC
1 CAAACCCTAAACC
17572768 ACCATTGCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.22
19 20 0.74
20 1 0.04
ACGTcount: A:0.45, C:0.37, G:0.00, T:0.18
Consensus pattern (20 bp):
CAAACCCTAAACCTCTAAAC
Found at i:17572792 original size:39 final size:38
Alignment explanation
Indices: 17572717--17572874 Score: 100
Period size: 38 Copynumber: 4.3 Consensus size: 38
17572707 GCCACCAATG
* * * *
17572717 CAAACCCTAAACCTCTATACAAACCTTAAACTCTAAAC
1 CAAACCCTAAACCACCATACAAACATTAAACCCTAAAC
*
17572755 CAAACCCTAAACCACCATTGCAAACATTAAACCCTAAA-
1 CAAACCCTAAACCACCA-TACAAACATTAAACCCTAAAC
* * *
17572793 C-TA----AAACC-CCATGCAAACCTTAAACCCTCAAA-
1 CAAACCCTAAACCACCATACAAACATTAAACCCT-AAAC
* * * * **
17572825 CAGACACTAAACCATCACACAAACCCTAAACCCT-AAC
1 CAAACCCTAAACCACCATACAAACATTAAACCCTAAAC
*
17572862 CAAACCCCAAACC
1 CAAACCCTAAACC
17572875 CTTAAACTTA
Statistics
Matches: 96, Mismatches: 15, Indels: 19
0.74 0.12 0.15
Matches are distributed among these distances:
31 16 0.17
32 7 0.07
33 6 0.06
36 2 0.02
37 16 0.17
38 32 0.33
39 17 0.18
ACGTcount: A:0.46, C:0.38, G:0.02, T:0.15
Consensus pattern (38 bp):
CAAACCCTAAACCACCATACAAACATTAAACCCTAAAC
Found at i:17572816 original size:31 final size:34
Alignment explanation
Indices: 17572763--17572825 Score: 96
Period size: 31 Copynumber: 1.9 Consensus size: 34
17572753 ACCAAACCCT
17572763 AAACCACCATTGCAAACATTAAACCCT-AAACTA
1 AAACCACCATTGCAAACATTAAACCCTCAAACTA
*
17572796 AAACC-CCA-TGCAAACCTTAAACCCTCAAAC
1 AAACCACCATTGCAAACATTAAACCCTCAAAC
17572826 AGACACTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 16 0.57
32 7 0.25
33 5 0.18
ACGTcount: A:0.46, C:0.35, G:0.03, T:0.16
Consensus pattern (34 bp):
AAACCACCATTGCAAACATTAAACCCTCAAACTA
Found at i:17572835 original size:19 final size:19
Alignment explanation
Indices: 17572813--17572881 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
17572803 ATGCAAACCT
*
17572813 TAAACCCTCAAACAGACAC
1 TAAACCCTCAAACAAACAC
* * *
17572832 TAAACCATCACACAAACCC
1 TAAACCCTCAAACAAACAC
* *
17572851 TAAACCCT-AACCAAACCC
1 TAAACCCTCAAACAAACAC
* *
17572869 CAAACCCTTAAAC
1 TAAACCCTCAAAC
17572882 TTATCCAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
18 15 0.38
19 25 0.62
ACGTcount: A:0.46, C:0.41, G:0.01, T:0.12
Consensus pattern (19 bp):
TAAACCCTCAAACAAACAC
Found at i:17572889 original size:18 final size:19
Alignment explanation
Indices: 17572868--17572920 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
17572858 TAACCAAACC
*
17572868 CCAAACCCTTAAACTTAT-
1 CCAAACCCTTAAACCTATG
*
17572886 CCAAAACCATTAAACCTATG
1 CC-AAACCCTTAAACCTATG
*
17572906 CTAAACCC-TAAACCT
1 CCAAACCCTTAAACCT
17572921 TTATACCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 9 0.31
19 19 0.66
20 1 0.03
ACGTcount: A:0.42, C:0.34, G:0.02, T:0.23
Consensus pattern (19 bp):
CCAAACCCTTAAACCTATG
Found at i:17572918 original size:26 final size:26
Alignment explanation
Indices: 17572889--17572944 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
17572879 AACTTATCCA
*
17572889 AAACCATTAAACCTATGCTAAACCCT
1 AAACCATTAAACCTATCCTAAACCCT
* *
17572915 AAACCTTTATACCTATCCTAAACCCT
1 AAACCATTAAACCTATCCTAAACCCT
17572941 AAAC
1 AAAC
17572945 TATCATACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.32, G:0.02, T:0.25
Consensus pattern (26 bp):
AAACCATTAAACCTATCCTAAACCCT
Found at i:17572952 original size:26 final size:26
Alignment explanation
Indices: 17572899--17572953 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
17572889 AAACCATTAA
* *
17572899 ACCTATGCTAAACCCTAAACCTTTAT
1 ACCTATCCTAAACCCTAAACCTTCAT
17572925 ACCTATCCTAAACCCTAAA-CTATCAT
1 ACCTATCCTAAACCCTAAACCT-TCAT
17572951 ACC
1 ACC
17572954 AGAACCTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.36, C:0.35, G:0.02, T:0.27
Consensus pattern (26 bp):
ACCTATCCTAAACCCTAAACCTTCAT
Found at i:17573031 original size:16 final size:16
Alignment explanation
Indices: 17573010--17573048 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17573000 TTAACCTAAG
*
17573010 CCAAACCCTAACCAAA
1 CCAAACCCAAACCAAA
* *
17573026 CCAAACTCAAACTAAA
1 CCAAACCCAAACCAAA
17573042 CCAAACC
1 CCAAACC
17573049 AACCCTAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.41, G:0.00, T:0.08
Consensus pattern (16 bp):
CCAAACCCAAACCAAA
Found at i:17576596 original size:16 final size:17
Alignment explanation
Indices: 17576575--17576608 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17576565 TAGTTTTAAG
17576575 TTTTTGCAC-TTTATTT
1 TTTTTGCACTTTTATTT
*
17576591 TTTTTGTACTTTTATTT
1 TTTTTGCACTTTTATTT
17576608 T
1 T
17576609 CTTGCTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTTGCACTTTTATTT
Found at i:17578658 original size:22 final size:25
Alignment explanation
Indices: 17578631--17578676 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
17578621 CTAGCAAGCG
17578631 ATAAAG-AAA-AAT-ACTTAGGAAC
1 ATAAAGAAAACAATCACTTAGGAAC
17578653 ATAAAGAAAACAATCACTTAGGAA
1 ATAAAGAAAACAATCACTTAGGAA
17578677 TTATGTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.29
23 3 0.14
24 3 0.14
25 9 0.43
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.17
Consensus pattern (25 bp):
ATAAAGAAAACAATCACTTAGGAAC
Found at i:17579912 original size:18 final size:17
Alignment explanation
Indices: 17579885--17579918 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17579875 AGTAGTGTAA
*
17579885 ATTTACTTTTCTCTGCAC
1 ATTTAATTTTCT-TGCAC
17579903 ATTTAATTTTCTTGCA
1 ATTTAATTTTCTTGCA
17579919 TTTTCTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTTAATTTTCTTGCAC
Found at i:17583008 original size:59 final size:59
Alignment explanation
Indices: 17582911--17583247 Score: 414
Period size: 59 Copynumber: 5.7 Consensus size: 59
17582901 TTGTGCAGGA
*
17582911 AAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTGAAACTTTGATTTTCAAAG
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGG
* * * *
17582970 AAAATTGATACTTTCAACTTTTCCTCAAAAATTCTTTTTTTTGAGA-TTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA-T-ATTTTTTTGAAACTTTGATTTTCAAGG
* * * *
17583030 AAAATTGACACTTTCAACTTTTCCCCAGAAATATTTTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGG
* * * ** * *
17583089 AAAATTGATATTTTCGACTTTTCCT-AAAAAAACCCATTTTTGAAA-TTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTTTGAAACTTTGATTTTCAAGG
17583148 AAAATTGATACTTTCAACTTTT-CTCCAAAAATATTTTTTTTGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAATA-TTTTTTTGAAACTTTGATTTTCAAGG
* *
17583208 AAAATTGATATTTTCAACTTTTCCCCAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
17583248 TTATTTTTGT
Statistics
Matches: 234, Mismatches: 34, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
58 22 0.09
59 106 0.45
60 95 0.41
61 11 0.05
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.45
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGG
Found at i:17583037 original size:60 final size:59
Alignment explanation
Indices: 17582911--17583248 Score: 396
Period size: 60 Copynumber: 5.7 Consensus size: 59
17582901 TTGTGCAGGA
* *
17582911 AAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTGAAACTTTGATTTTCAAAG
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATTTTTTTTTGAAACTTTGATTTTCAAGG
* * *
17582970 AAAATTGATACTTTCAACTTTTCCTCAAAAATTCTTTTTTTTGAGA-TTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA-T-TTTTTTTTGAAACTTTGATTTTCAAGG
* * * * *
17583030 AAAATTGACACTTTCAACTTTTCCCCAGAAATATTTTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTGAAACTTTGATTTTCAAGG
* * * **** * *
17583089 AAAATTGATATTTTCGACTTTTCCTAAAAAAACCCATTTTTGAAA-TTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAATTTTTTTTTGAAACTTTGATTTTCAAGG
17583148 AAAATTGATACTTTCAACTTTT-CTCCAAAAATATTTTTTTTGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAAT-TTTTTTTTGAAACTTTGATTTTCAAGG
* *
17583208 AAAATTGATATTTTCAACTTTTCCCCAAAAATATTTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTTTT
17583249 TATTTTTGTT
Statistics
Matches: 233, Mismatches: 38, Indels: 15
0.81 0.13 0.05
Matches are distributed among these distances:
58 22 0.09
59 99 0.42
60 101 0.43
61 11 0.05
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTGAAACTTTGATTTTCAAGG
Found at i:17583062 original size:119 final size:119
Alignment explanation
Indices: 17582911--17583249 Score: 511
Period size: 119 Copynumber: 2.8 Consensus size: 119
17582901 TTGTGCAGGA
* *
17582911 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAACTTTGATTTTCAAAGAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAACTTTGATTTTCAAGGAAAATT
* *
17582976 GATACTTTCAACTTTTCCTCAAAAATTCTTTTTTTTGAGATTTTATTTTTAAGG
66 GATATTTTCAACTTTTCCTCAAAAATTCTTTTTTTTGAAATTTTATTTTTAAGG
* * *
17583030 AAAATTGACACTTTCAACTTTTCCCCAGAAATATTTTTTGGAAACTTTGATTTTCAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAACTTTGATTTTCAAGGAAAATT
* ** ***
17583095 GATATTTTCGACTTTTCCT-AAAAAAACCCATTTTTGAAATTTTATTTTTAAGG
66 GATATTTTCAACTTTTCCTCAAAAATTCTTTTTTTTGAAATTTTATTTTTAAGG
*
17583148 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTTGAAACTTTGATTTTCAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGAAACTTTGATTTTCAAGGAAAAT
*
17583213 TGATATTTTCAACTTTTCCCCAAAAATAT-TTTTTTTT
65 TGATATTTTCAACTTTTCCTCAAAAAT-TCTTTTTTTT
17583250 ATTTTTGTTT
Statistics
Matches: 193, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
118 58 0.30
119 125 0.65
120 10 0.05
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (119 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAACTTTGATTTTCAAGGAAAATT
GATATTTTCAACTTTTCCTCAAAAATTCTTTTTTTTGAAATTTTATTTTTAAGG
Found at i:17583301 original size:15 final size:14
Alignment explanation
Indices: 17583260--17583344 Score: 70
Period size: 15 Copynumber: 6.1 Consensus size: 14
17583250 ATTTTTGTTT
17583260 AAAG-AAAATAAAA
1 AAAGTAAAATAAAA
* *
17583273 CAA-TAAAACAAAAA
1 AAAGTAAAA-TAAAA
17583287 AAAGTGAAAATAAAA
1 AAAGT-AAAATAAAA
*
17583302 AAAATAAAATAAAGA
1 AAAGTAAAATAAA-A
*
17583317 AAAGTAAAACAAAA
1 AAAGTAAAATAAAA
*
17583331 ATA--AAAATAAAA
1 AAAGTAAAATAAAA
17583343 AA
1 AA
17583345 TAAAATATAG
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
12 9 0.16
13 6 0.11
14 17 0.30
15 21 0.37
16 4 0.07
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.11
Consensus pattern (14 bp):
AAAGTAAAATAAAA
Found at i:17583310 original size:30 final size:30
Alignment explanation
Indices: 17583263--17583342 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
17583253 TTTGTTTAAA
*
17583263 GAAAAT-AAAACAATAAAACAAAAAAAAGT
1 GAAAATAAAAAAAATAAAACAAAAAAAAGT
* *
17583292 GAAAATAAAAAAAATAAAATAAAGAAAAGT
1 GAAAATAAAAAAAATAAAACAAAAAAAAGT
* *
17583322 AAAACAAAAATAAAAATAAAA
1 GAAA-ATAAA-AAAAATAAAA
17583343 AATAAAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 6 0.14
30 23 0.53
31 4 0.09
32 10 0.23
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.11
Consensus pattern (30 bp):
GAAAATAAAAAAAATAAAACAAAAAAAAGT
Found at i:17584299 original size:17 final size:18
Alignment explanation
Indices: 17584279--17584312 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17584269 ATAATCAGAT
17584279 AAATAAA-AAAAATTAAC
1 AAATAAATAAAAATTAAC
*
17584296 AAATAAATTAAAATTAA
1 AAATAAATAAAAATTAA
17584313 ATAACAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATAAATAAAAATTAAC
Found at i:17584317 original size:22 final size:20
Alignment explanation
Indices: 17584231--17584323 Score: 80
Period size: 22 Copynumber: 4.3 Consensus size: 20
17584221 AATTTTTAGC
17584231 CAGATAAAT-AAAAAAATAA
1 CAGATAAATAAAAAAAATAA
* *
17584250 AAGAAAAAATCAAACAAAAATAA
1 CAG-ATAAAT-AAA-AAAAATAA
17584273 TCAGATAAATAAAAAAAATTAA
1 -CAGATAAATAAAAAAAA-TAA
* *
17584295 CAAATAAATTAAAATTAAATAA
1 CAGATAAA-TAAAA-AAAATAA
17584317 CAGATAA
1 CAGATAA
17584324 TACATAACTA
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
19 2 0.03
20 5 0.08
21 12 0.20
22 22 0.37
23 16 0.27
24 2 0.03
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.18
Consensus pattern (20 bp):
CAGATAAATAAAAAAAATAA
Found at i:17584497 original size:25 final size:25
Alignment explanation
Indices: 17584447--17584516 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
17584437 ATATACATAT
* *
17584447 ATAAAATAATAATAATAAAAATAAA
1 ATAAAATAAAAATAATAAAAACAAA
*
17584472 ATAAAATAAAAAT-GTAAAATACAAA
1 ATAAAATAAAAATAATAAAA-ACAAA
* *
17584497 A-AAATTTAAAAAAAATAAAA
1 ATAAA-ATAAAAATAATAAAA
17584517 TGAAGAGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
24 8 0.22
25 23 0.64
26 5 0.14
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (25 bp):
ATAAAATAAAAATAATAAAAACAAA
Found at i:17584780 original size:43 final size:42
Alignment explanation
Indices: 17584719--17584950 Score: 306
Period size: 41 Copynumber: 5.5 Consensus size: 42
17584709 TTTTATCAAA
* *** * *
17584719 GCTCCTCTAAGCAGAGGCTTAATGACTTTGAGAAACATAAATG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAA-ATAAATT
* * * * *
17584762 GCTCCTCTAATCAGAGGCTCAACAACTTTGAAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AGAAAATAAATT
* *
17584805 GCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAATAAATT
17584847 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAATAAATT
*
17584888 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAATAAATT
17584929 GCTCCTCTAAACAGAGGCACCA
1 GCTCCTCTAAACAGAGGCACCA
17584951 AATTGCTCCT
Statistics
Matches: 171, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
41 70 0.41
42 39 0.23
43 58 0.34
44 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAATAAATT
Found at i:17584909 original size:83 final size:84
Alignment explanation
Indices: 17584719--17584950 Score: 324
Period size: 83 Copynumber: 2.8 Consensus size: 84
17584709 TTTTATCAAA
* *** * * * * * * *
17584719 GCTCCTCTAAGCAGAGGCTTAATGACTTTGAGAAACATAAATGGCTCCTCTAATCAGAGGCTCAA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGGAAA-GTAAATTGCTCCTCTAAACAGAGGCACCA
17584784 CAACTTTGAAAAAAATAAATT
65 CAACTTTG-AAAAAATAAATT
17584805 GCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
17584870 GACTTTG-AAAAATAAATT
66 AACTTTGAAAAAATAAATT
17584888 GCTCCTCTAAACAGAGGCACCACGACTTT-GGAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
17584951 AATTGCTCCT
Statistics
Matches: 134, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
82 34 0.25
83 40 0.30
85 31 0.23
86 29 0.22
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (84 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
AACTTTGAAAAAATAAATT
Found at i:17584953 original size:26 final size:26
Alignment explanation
Indices: 17584924--17584976 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
17584914 TTTGGAAAGT
17584924 AAATTGCTCCTCTAAACAGAGGCACC
1 AAATTGCTCCTCTAAACAGAGGCACC
17584950 AAATTGCTCCTCTAAACAGAGGCACC
1 AAATTGCTCCTCTAAACAGAGGCACC
17584976 A
1 A
17584977 CGACTTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.30, G:0.15, T:0.19
Consensus pattern (26 bp):
AAATTGCTCCTCTAAACAGAGGCACC
Found at i:17584991 original size:67 final size:67
Alignment explanation
Indices: 17584883--17585017 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
17584873 TTTGAAAAAT
*
17584883 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCA
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA
17584948 CC
66 CC
*
17584950 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCA
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA
17585015 CC
66 CC
17585017 A
1 A
17585018 CGAATTTGGA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (67 bp):
AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA
CC
Found at i:17585012 original size:41 final size:41
Alignment explanation
Indices: 17584950--17585124 Score: 296
Period size: 41 Copynumber: 4.3 Consensus size: 41
17584940 CAGAGGCACC
17584950 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGT
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGT
* * *
17584991 AAATTGCTCCTCTAAATAGAGGCACCACGAATTTGGAAAGT
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGT
* *
17585032 AAATTGCTCCTCTAAACAGAAGCACCACGACTTTGGAAAGT
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGT
*
17585073 AAATTGCTCATCTAAACAGAGGCACCACGACTTTGAAAAGT
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGT
17585114 AAATTGCTCCT
1 AAATTGCTCCT
17585125 TGACAATCAT
Statistics
Matches: 124, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 124 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (41 bp):
AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGT
Found at i:17585031 original size:108 final size:108
Alignment explanation
Indices: 17584842--17585058 Score: 398
Period size: 108 Copynumber: 2.0 Consensus size: 108
17584832 TTGGGAAAGT
17584842 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCA
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCA
* *
17584907 CCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACC
66 CCACGAATTTGGAAAGTAAATTGCTCCTCTAAACAGAAGCACC
* *
17584950 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCA
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCA
17585015 CCACGAATTTGGAAAGTAAATTGCTCCTCTAAACAGAAGCACC
66 CCACGAATTTGGAAAGTAAATTGCTCCTCTAAACAGAAGCACC
17585058 A
1 A
17585059 CGACTTTGGA
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 105 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (108 bp):
AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCA
CCACGAATTTGGAAAGTAAATTGCTCCTCTAAACAGAAGCACC
Found at i:17585071 original size:149 final size:150
Alignment explanation
Indices: 17584800--17585099 Score: 530
Period size: 149 Copynumber: 2.0 Consensus size: 150
17584790 TGAAAAAAAT
*
17584800 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGGAAAGTAAATTGCTCCTCTAAACAGAGGC
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGC
* *
17584865 ACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTG
66 ACCACGAATTTGAAAAATAAATTGCTCCTCTAAACAGAAGCACCACGACTTTGGAAAGTAAATTG
*
17584930 CTCCTCTAAACAGAGGCACC
131 CTCATCTAAACAGAGGCACC
*
17584950 AAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAATAGAGGC
1 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGC
* *
17585014 ACCACGAATTTGGAAAGTAAATTGCTCCTCTAAACAGAAGCACCACGACTTTGGAAAGTAAATTG
66 ACCACGAATTTGAAAAATAAATTGCTCCTCTAAACAGAAGCACCACGACTTTGGAAAGTAAATTG
17585079 CTCATCTAAACAGAGGCACC
131 CTCATCTAAACAGAGGCACC
17585099 A
1 A
17585100 CGACTTTGAA
Statistics
Matches: 143, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
149 109 0.76
150 34 0.24
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (150 bp):
AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGC
ACCACGAATTTGAAAAATAAATTGCTCCTCTAAACAGAAGCACCACGACTTTGGAAAGTAAATTG
CTCATCTAAACAGAGGCACC
Found at i:17586131 original size:8 final size:8
Alignment explanation
Indices: 17586119--17586194 Score: 73
Period size: 8 Copynumber: 8.8 Consensus size: 8
17586109 TTGAGTCCTT
17586119 TTTTTTCA
1 TTTTTTCA
*
17586127 CTTTTTC-
1 TTTTTTCA
17586134 TTTTTTCA
1 TTTTTTCA
17586142 TTTTTTTCA
1 -TTTTTTCA
17586151 TTTTTTCA
1 TTTTTTCA
17586159 TTTTTTCTTCA
1 --TTTT-TTCA
17586170 TTTTTTTCA
1 -TTTTTTCA
17586179 TTTTTTTTCA
1 --TTTTTTCA
17586189 TTTTTT
1 TTTTTT
17586195 TTAAGCATAG
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
7 6 0.10
8 20 0.33
9 12 0.20
10 18 0.30
11 4 0.07
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:17586136 original size:17 final size:16
Alignment explanation
Indices: 17586128--17586193 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 16
17586118 TTTTTTTCAC
* *
17586128 TTTTTCTTTTTTCATT
1 TTTTTCATTTTTCTTT
17586144 TTTTTCATTTTTTCATTT
1 TTTTTCA-TTTTTC-TTT
17586162 TTTCTTCATTTTTTTCATTT
1 TTT-TTCA--TTTTTC-TTT
17586182 TTTTTCATTTTT
1 TTTTTCATTTTT
17586194 TTTAAGCATA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
16 6 0.14
17 11 0.25
18 5 0.11
19 8 0.18
20 14 0.32
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTCATTTTTCTTT
Found at i:17586146 original size:9 final size:9
Alignment explanation
Indices: 17586118--17586195 Score: 92
Period size: 9 Copynumber: 8.8 Consensus size: 9
17586108 CTTGAGTCCT
17586118 TTTTTTTCA
1 TTTTTTTCA
*
17586127 -CTTTTTC-
1 TTTTTTTCA
17586134 -TTTTTTCA
1 TTTTTTTCA
17586142 TTTTTTTCA
1 TTTTTTTCA
17586151 -TTTTTTCA
1 TTTTTTTCA
17586159 TTTTTTCTTCA
1 -TTTTT-TTCA
17586170 TTTTTTTCA
1 TTTTTTTCA
17586179 TTTTTTTTCA
1 -TTTTTTTCA
17586189 TTTTTTT
1 TTTTTTT
17586196 TAAGCATAGT
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
7 6 0.10
8 14 0.23
9 19 0.31
10 18 0.30
11 4 0.07
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:17586156 original size:19 final size:19
Alignment explanation
Indices: 17586134--17586195 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
17586124 TCACTTTTTC
17586134 TTTTTTCA-TTTTTTTCA-
1 TTTTTTCATTTTTTTTCAT
17586151 TTTTTTCATTTTTTCTTCAT
1 TTTTTTCATTTTTT-TTCAT
17586171 TTTTTTCATTTTTTTTCAT
1 TTTTTTCATTTTTTTTCAT
17586190 TTTTTT
1 TTTTTT
17586196 TAAGCATAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.19
18 5 0.12
19 15 0.36
20 14 0.33
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTCATTTTTTTTCAT
Found at i:17592303 original size:15 final size:16
Alignment explanation
Indices: 17592283--17592314 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
17592273 TGTTAAGTGT
17592283 AATGAATG-AAAATGC
1 AATGAATGAAAAATGC
17592298 AATGAATGAAAAATGC
1 AATGAATGAAAAATGC
17592314 A
1 A
17592315 TGTATGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (16 bp):
AATGAATGAAAAATGC
Found at i:17595623 original size:94 final size:96
Alignment explanation
Indices: 17595496--17595673 Score: 308
Period size: 95 Copynumber: 1.9 Consensus size: 96
17595486 TACTTTCAAC
17595496 TTTTCCCCAAAAAAATTTTTTTGGAAACTTTGA-TTTCAAAGAAAATTGATACTTTCAAC-TTTC
1 TTTTCCCCAAAAAAATTTTTTTGGAAACTTTGATTTTCAAAGAAAATTGATACTTTCAACTTTTC
*
17595559 CTCAAAAAATTCTTTTTTTTGAGATTTTTTAA
66 CTC-AAAAATCCTTTTTTTTGAGATTTTTTAA
*
17595591 TTTTCCCCAAAAATATTTTTTT-GAAACTTTGATTTTCAAAGAAAATTGATACTTTCAACTTTTC
1 TTTTCCCCAAAAAAATTTTTTTGGAAACTTTGATTTTCAAAGAAAATTGATACTTTCAACTTTTC
17595655 CTCAAAAATCCTTTTTTTT
66 CTCAAAAATCCTTTTTTTT
17595674 TAAATTTTAT
Statistics
Matches: 79, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
94 10 0.13
95 62 0.78
96 7 0.09
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (96 bp):
TTTTCCCCAAAAAAATTTTTTTGGAAACTTTGATTTTCAAAGAAAATTGATACTTTCAACTTTTC
CTCAAAAATCCTTTTTTTTGAGATTTTTTAA
Found at i:17595816 original size:58 final size:58
Alignment explanation
Indices: 17595591--17595971 Score: 475
Period size: 59 Copynumber: 6.5 Consensus size: 58
17595581 GATTTTTTAA
* * * *
17595591 TTTTCCCCAAAAATATTTTTTTGAAACTTTGATTTTCAAAGAAAATTGATACTTTCAAC
1 TTTTCCTCAAAAATATTTTTTTGAAA-TTTTATTTTTAAGGAAAATTGATACTTTCAAC
* * *
17595650 TTTTCCTCAAAAATCCTTTTTTTTTAAATTTTATTTTTAAGAAAAATTGATACTTTCAA-
1 TTTTCCTCAAAAAT--ATTTTTTTGAAATTTTATTTTTAAGGAAAATTGATACTTTCAAC
* * *
17595709 TGTTT-CTCCAAAAATATTTTTTTGAAACTTTGATTTTCAAAGAAAATTGATACTTTCAAC
1 T-TTTCCT-CAAAAATATTTTTTTGAAA-TTTTATTTTTAAGGAAAATTGATACTTTCAAC
**
17595769 TTTTCCTCAAAAACCTTTTTTTGAAATTTTATTTTTAAGGAAAATTGATACTTTCAAC
1 TTTTCCTCAAAAATATTTTTTTGAAATTTTATTTTTAAGGAAAATTGATACTTTCAAC
*
17595827 TTTTCCCCAAAAATATTTTTTTGGAAA-TTTATTTTTAAGGAAAATTGATACTTTCAAC
1 TTTTCCTCAAAAATATTTTTTT-GAAATTTTATTTTTAAGGAAAATTGATACTTTCAAC
* * *
17595885 -TTTGCTCCAAAAATAATTTTTTTGGAAA-TTTATTTTTAAGAAAAATTGATACTTTTAAC
1 TTTTCCT-CAAAAAT-ATTTTTTT-GAAATTTTATTTTTAAGGAAAATTGATACTTTCAAC
* *
17595944 TTTTCCCCAAAAATATTTTTTGGAAATT
1 TTTTCCTCAAAAATATTTTTTTGAAATT
17595972 GATACTTTCA
Statistics
Matches: 282, Mismatches: 28, Indels: 25
0.84 0.08 0.07
Matches are distributed among these distances:
57 8 0.03
58 104 0.37
59 116 0.41
60 44 0.16
61 10 0.04
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.46
Consensus pattern (58 bp):
TTTTCCTCAAAAATATTTTTTTGAAATTTTATTTTTAAGGAAAATTGATACTTTCAAC
Found at i:17595837 original size:117 final size:118
Alignment explanation
Indices: 17595591--17595969 Score: 581
Period size: 117 Copynumber: 3.2 Consensus size: 118
17595581 GATTTTTTAA
17595591 TTTTCCCCAAAAATATTTTTTTGAAACTTTGATTTTCAAAGAAAATTGATACTTTCAACTTTTCC
1 TTTTCCCCAAAAATATTTTTTTGAAACTTTGATTTTCAAAGAAAATTGATACTTTCAACTTTTCC
*
17595656 TCAAAAATCCTTTTTTTTTAAATTTTATTTTTAAGAAAAATTGATACTTTCAA-
66 TCAAAAATCC-TTTTTTTGAAATTTTATTTTTAAGAAAAATTGATACTTTCAAC
*
17595709 TGTTTCTCCAAAAATATTTTTTTGAAACTTTGATTTTCAAAGAAAATTGATACTTTCAACTTTTC
1 T-TTTCCCCAAAAATATTTTTTTGAAACTTTGATTTTCAAAGAAAATTGATACTTTCAACTTTTC
*
17595774 CTCAAAAA-CCTTTTTTTGAAATTTTATTTTTAAGGAAAATTGATACTTTCAAC
65 CTCAAAAATCCTTTTTTTGAAATTTTATTTTTAAGAAAAATTGATACTTTCAAC
* * *
17595827 TTTTCCCCAAAAATATTTTTTTGGAAA-TTT-ATTTTTAAGGAAAATTGATACTTTCAAC-TTTG
1 TTTTCCCCAAAAATATTTTTTT-GAAACTTTGATTTTCAAAGAAAATTGATACTTTCAACTTTTC
** *
17595889 CTCCAAAAATAATTTTTTTGGAAA-TTTATTTTTAAGAAAAATTGATACTTTTAAC
65 CT-CAAAAATCCTTTTTTT-GAAATTTTATTTTTAAGAAAAATTGATACTTTCAAC
*
17595944 TTTTCCCCAAAAATATTTTTTGGAAA
1 TTTTCCCCAAAAATATTTTTTTGAAA
17595970 TTGATACTTT
Statistics
Matches: 243, Mismatches: 12, Indels: 14
0.90 0.04 0.05
Matches are distributed among these distances:
115 5 0.02
116 36 0.15
117 120 0.49
118 12 0.05
119 70 0.29
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (118 bp):
TTTTCCCCAAAAATATTTTTTTGAAACTTTGATTTTCAAAGAAAATTGATACTTTCAACTTTTCC
TCAAAAATCCTTTTTTTGAAATTTTATTTTTAAGAAAAATTGATACTTTCAAC
Found at i:17595996 original size:157 final size:160
Alignment explanation
Indices: 17595810--17596124 Score: 444
Period size: 157 Copynumber: 2.0 Consensus size: 160
17595800 TTTTTAAGGA
* * * *
17595810 AAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAA-TTTATTTTTAAGGAAAATTG
1 AAATTGATACTTTCAACTTTTCCCAAAAAACACTTTTTT-GAAATTTTATTTTTAAGAAAAATTG
*
17595874 ATACTTTCAACTTTGCTCC-AAAAA-TAATTTTTTTGGAAA-TTT-ATTTTTAAGAAAAATTGAT
65 ATACTTTCAACTTTGC-CCAAAAAATTAATTTTTTTGGAAACTTTGATTTTCAAGAAAAATTGAT
17595935 ACTTTT-AACTTTTCCCCAAAAATATTTTTTGG
129 A-TTTTCAACTTTTCCCCAAAAATATTTTTTGG
* *
17595967 AAATTGATACTTTCAACTTTTCCTAAAAAACCCTTTTTTGAAATTTTATTTTTAAGAAAAATTGA
1 AAATTGATACTTTCAACTTTTCCCAAAAAACACTTTTTTGAAATTTTATTTTTAAGAAAAATTGA
* ** * *
17596032 TACTTTCAACTTTTCCCAAAAAATTTTTTTTTTTTGAAACTTTGATTTTCAAGGAAAATTGATAT
66 TACTTTCAACTTTGCCCAAAAAATTAATTTTTTTGGAAACTTTGATTTTCAAGAAAAATTGATAT
*
17596097 TTTCAACTTTTTCCCAAAAATATTTTTT
131 TTTCAACTTTTCCCCAAAAATATTTTTT
17596125 TTATTTTTAT
Statistics
Matches: 139, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
156 6 0.04
157 73 0.53
158 12 0.09
159 7 0.05
160 41 0.29
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.46
Consensus pattern (160 bp):
AAATTGATACTTTCAACTTTTCCCAAAAAACACTTTTTTGAAATTTTATTTTTAAGAAAAATTGA
TACTTTCAACTTTGCCCAAAAAATTAATTTTTTTGGAAACTTTGATTTTCAAGAAAAATTGATAT
TTTCAACTTTTCCCCAAAAATATTTTTTGG
Found at i:17596004 original size:40 final size:40
Alignment explanation
Indices: 17595927--17596011 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
17595917 TTTTTAAGAA
* * * *
17595927 AAATTGATACTTTTAACTTTTCCCCAAAAATATTTTTTGG
1 AAATTGATACTTTCAACTTTTCCCAAAAAACACTTTTTGG
* * *
17595967 AAATTGATACTTTCAACTTTTCCTAAAAAACCCTTTTTTG
1 AAATTGATACTTTCAACTTTTCCCAAAAAACACTTTTTGG
17596007 AAATT
1 AAATT
17596012 TTATTTTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (40 bp):
AAATTGATACTTTCAACTTTTCCCAAAAAACACTTTTTGG
Found at i:17596043 original size:98 final size:98
Alignment explanation
Indices: 17595868--17596062 Score: 288
Period size: 98 Copynumber: 2.0 Consensus size: 98
17595858 TTTTTAAGGA
*
17595868 AAATTGATACTTTCAACTTTGCTCCAAAAATAATTTTTTTGGAAATTTATTTTTAAGAAAAATTG
1 AAATTGATACTTTCAACTTT-CTCCAAAAATAACTTTTTTGGAAATTTATTTTTAAGAAAAATTG
* *
17595933 ATACTTTTAACTTTTCCCCAAAAATATTTTTTGG
65 ATACTTTCAACTTTTCCCAAAAAATATTTTTTGG
*
17595967 AAATTGATACTTTCAACTTT-TCCTAAAAA-ACCCTTTTTT-GAAATTTTATTTTTAAGAAAAAT
1 AAATTGATACTTTCAACTTTCTCC-AAAAATA-ACTTTTTTGGAAA-TTTATTTTTAAGAAAAAT
*
17596029 TGATACTTTCAACTTTTCCCAAAAAATTTTTTTT
63 TGATACTTTCAACTTTTCCCAAAAAATATTTTTT
17596063 TTTTGAAACT
Statistics
Matches: 88, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
97 8 0.09
98 60 0.68
99 20 0.23
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (98 bp):
AAATTGATACTTTCAACTTTCTCCAAAAATAACTTTTTTGGAAATTTATTTTTAAGAAAAATTGA
TACTTTCAACTTTTCCCAAAAAATATTTTTTGG
Found at i:17596101 original size:62 final size:61
Alignment explanation
Indices: 17595967--17596131 Score: 201
Period size: 58 Copynumber: 2.7 Consensus size: 61
17595957 TATTTTTTGG
* *** * *
17595967 AAATTGATACTTTCAACTTTTCCTAAAAAA---CCCTTTTTTGAAATTTTATTTTTAAGAA
1 AAATTGATACTTTCAACTTTTCCCAAAAAATTTTTTTTTTTTGAAATTTGATTTTCAAGAA
*
17596025 AAATTGATACTTTCAACTTTTCCCAAAAAATTTTTTTTTTTTGAAACTTTGATTTTCAAGGA
1 AAATTGATACTTTCAACTTTTCCCAAAAAATTTTTTTTTTTTGAAA-TTTGATTTTCAAGAA
*
17596087 AAATTGATATTTTCAACTTTTTCCCAAAAATATTTTTTTTATTTT
1 AAATTGATACTTTCAAC-TTTTCCCAAAAA-ATTTTTTTT-TTTT
17596132 TATTTAAAGA
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
58 29 0.32
61 10 0.11
62 28 0.30
63 12 0.13
64 9 0.10
65 4 0.04
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.48
Consensus pattern (61 bp):
AAATTGATACTTTCAACTTTTCCCAAAAAATTTTTTTTTTTTGAAATTTGATTTTCAAGAA
Found at i:17596149 original size:5 final size:5
Alignment explanation
Indices: 17596141--17596281 Score: 83
Period size: 5 Copynumber: 26.8 Consensus size: 5
17596131 TTATTTAAAG
* *
17596141 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT AAAAA AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAAT
* * * *
17596191 AAAGT AAAAA AAAATT AAAA- AAAAT AAAAT AAAGGT AAAA- AGAAT ACTAAAT
1 AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT A--AAAT
* *
17596243 AAACCT AATCTAAT AAATAA AAAAT AAAAT AAAAT AAAA
1 AAA-AT AA---AAT AAA-AT AAAAT AAAAT AAAAT AAAA
17596282 AACCTAAAGT
Statistics
Matches: 105, Mismatches: 16, Indels: 30
0.70 0.11 0.20
Matches are distributed among these distances:
3 3 0.03
4 7 0.07
5 66 0.63
6 17 0.16
7 8 0.08
8 3 0.03
9 1 0.01
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:17596175 original size:30 final size:28
Alignment explanation
Indices: 17596140--17596219 Score: 96
Period size: 25 Copynumber: 2.9 Consensus size: 28
17596130 TTTATTTAAA
17596140 GAAAATAAAATAATAAAACAAAATAAAAGT
1 GAAAATAAAA-AATAAAA-AAAATAAAAGT
*
17596170 GAAAATAAAAAA-AAATAAAAT-AAAGT
1 GAAAATAAAAAATAAAAAAAATAAAAGT
*
17596196 -AAAA-AAAAATTAAAAAAAATAAAA
1 GAAAATAAAAAATAAAAAAAATAAAA
17596220 TAAAGGTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
24 5 0.11
25 12 0.27
26 8 0.18
27 5 0.11
28 3 0.07
29 2 0.04
30 10 0.22
ACGTcount: A:0.79, C:0.01, G:0.05, T:0.15
Consensus pattern (28 bp):
GAAAATAAAAAATAAAAAAAATAAAAGT
Found at i:17596179 original size:22 final size:20
Alignment explanation
Indices: 17596141--17596283 Score: 96
Period size: 20 Copynumber: 7.0 Consensus size: 20
17596131 TTATTTAAAG
*
17596141 AAAATAAAAT--AATAAAAC
1 AAAATAAAATAAAATAAAAA
17596159 AAAATAAAAGTGAAAATAAAAA
1 AAAATAAAA-T-AAAATAAAAA
*
17596181 AAAATAAAATAAAGTAAAAA
1 AAAATAAAATAAAATAAAAA
17596201 AAAATTAAAA-AAAATAAAATA
1 AAAA-TAAAATAAAATAAAA-A
** * *
17596222 AAGGTAAAA-AGAATACTAAA
1 AAAATAAAATAAAATA-AAAA
* *** **
17596242 TAAACCTAATCTAATAAATAA
1 AAAATAAAATAAAATAAA-AA
17596263 AAAATAAAATAAAATAAAAA
1 AAAATAAAATAAAATAAAAA
17596283 A
1 A
17596284 CCTAAAGTGG
Statistics
Matches: 94, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
18 9 0.10
19 1 0.01
20 39 0.41
21 29 0.31
22 16 0.17
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.17
Consensus pattern (20 bp):
AAAATAAAATAAAATAAAAA
Found at i:17596220 original size:30 final size:31
Alignment explanation
Indices: 17596171--17596231 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
17596161 AATAAAAGTG
17596171 AAAATAAAAAAAAATAAAATAAA-GTAAAAA
1 AAAATAAAAAAAAATAAAATAAAGGTAAAAA
*
17596201 AAAATTAAAAAAAATAAAATAAAGGTAAAAA
1 AAAATAAAAAAAAATAAAATAAAGGTAAAAA
17596232 GAATACTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (31 bp):
AAAATAAAAAAAAATAAAATAAAGGTAAAAA
Found at i:17597178 original size:22 final size:21
Alignment explanation
Indices: 17597088--17597181 Score: 68
Period size: 22 Copynumber: 4.3 Consensus size: 21
17597078 AATTTTCAGC
*
17597088 CAGATAAAT-AAAAAAAATAA
1 CAGATAAATCAGAAAAAATAA
* *
17597108 AAGAAAAAATCA-AACGAAAATAA
1 CAG-ATAAATCAGAA--AAAATAA
*
17597131 TCAGATAAATCAGAAAAATTAA
1 -CAGATAAATCAGAAAAAATAA
*
17597153 CAGATAAATTA-AAATTAAATAA
1 CAGATAAATCAGAAA--AAATAA
17597175 CAGATAA
1 CAGATAA
17597182 TACATAAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
20 5 0.08
21 17 0.29
22 19 0.32
23 14 0.24
24 4 0.07
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.18
Consensus pattern (21 bp):
CAGATAAATCAGAAAAAATAA
Found at i:17597331 original size:5 final size:5
Alignment explanation
Indices: 17597306--17597378 Score: 58
Period size: 5 Copynumber: 13.4 Consensus size: 5
17597296 ATATACATAT
*
17597306 ATAAA ATAATA ATAAT A-AAA ATAAA ATAAA ATAAA ATTGTAAA ATACAA
1 ATAAA ATAA-A ATAAA ATAAA ATAAA ATAAA ATAAA A---TAAA ATA-AA
*
17597355 AAAAA ATAAAA ATAAAA ATAAA AT
1 ATAAA AT-AAA AT-AAA ATAAA AT
17597379 GAAGAGAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
4 3 0.05
5 29 0.51
6 20 0.35
8 5 0.09
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:17597341 original size:30 final size:30
Alignment explanation
Indices: 17597306--17597378 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
17597296 ATATACATAT
17597306 ATAAAATAATAATAATA-AAAATAAAAT-AAA
1 ATAAAATAATAA-AATACAAAA-AAAATAAAA
**
17597336 ATAAAATTGTAAAATACAAAAAAAATAAAA
1 ATAAAATAATAAAATACAAAAAAAATAAAA
17597366 AT-AAA-AATAAAAT
1 ATAAAATAATAAAAT
17597379 GAAGAGAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
28 6 0.16
29 12 0.32
30 19 0.51
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (30 bp):
ATAAAATAATAAAATACAAAAAAAATAAAA
Found at i:17597362 original size:11 final size:12
Alignment explanation
Indices: 17597313--17597377 Score: 64
Period size: 11 Copynumber: 5.6 Consensus size: 12
17597303 TATATAAAAT
*
17597313 AATAATAATAAA
1 AATAAAAATAAA
17597325 AAT-AAAAT-AA
1 AATAAAAATAAA
* *
17597335 AATAAAATTGTAA
1 AATAAAAAT-AAA
*
17597348 AATACAAA-AAA
1 AATAAAAATAAA
17597359 AATAAAAATAAA
1 AATAAAAATAAA
17597371 AATAAAA
1 AATAAAA
17597378 TGAAGAGAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
10 5 0.12
11 17 0.40
12 13 0.30
13 8 0.19
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (12 bp):
AATAAAAATAAA
Found at i:17597366 original size:17 final size:17
Alignment explanation
Indices: 17597264--17597377 Score: 65
Period size: 18 Copynumber: 6.6 Consensus size: 17
17597254 CCTAAGATAA
* *
17597264 AAAAATAATAATAAAAG
1 AAAAATAAAAATAAAAT
* *
17597281 AAAAGAAAAAAATATATAT
1 AAAA-ATAAAAATA-AAAT
* *
17597300 ACATATATAAAAT--AAT
1 AAAAATA-AAAATAAAAT
*
17597316 AATAATAAAAATAAAAT
1 AAAAATAAAAATAAAAT
*
17597333 -AAAATAAAATTGTAAAAT
1 AAAAATAAAA--ATAAAAT
*
17597351 ACAAA-AAAAATAAAAAT
1 AAAAATAAAAAT-AAAAT
17597368 AAAAATAAAA
1 AAAAATAAAA
17597378 TGAAGAGAAT
Statistics
Matches: 71, Mismatches: 16, Indels: 19
0.67 0.15 0.18
Matches are distributed among these distances:
15 5 0.07
16 15 0.21
17 16 0.23
18 23 0.32
19 12 0.17
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAATAAAAATAAAAT
Found at i:17597367 original size:6 final size:6
Alignment explanation
Indices: 17597313--17597377 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
17597303 TATATAAAAT
* * * *
17597313 AATAAT AATAAA AAT-AA AAT-AA AATAAA ATTGTAA AATACA AA-AAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AAT-AAA AATAAA AATAAA
17597359 AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA A
17597378 TGAAGAGAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
5 14 0.29
6 31 0.63
7 4 0.08
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (6 bp):
AATAAA
Found at i:17601103 original size:104 final size:104
Alignment explanation
Indices: 17600912--17601190 Score: 314
Period size: 104 Copynumber: 2.7 Consensus size: 104
17600902 GTCCAGAGAT
* *
17600912 CTTACAAATCT-AGATATGCATGAAAGCTCCTCTAATTAGAGG-TAATGAAACTTTAAAATTTCA
1 CTTACAAATCTCA-ATATGCATGAAAGCTCCTCTAATTAGAGGCT-TTGAAACTTTAAAATTTTA
* * *
17600975 AAATATTTTGCTCAAAGGTCTTAGAGATTATG-CTAGAAGGT
64 AAATGTTTTACTCAAAGGTCTTAGAGATTATGCCT-GAAGGC
* * * * * *
17601016 TTTACAAATCTCAATATGTATGAAAGCTCCTCGAATCAAAGGCTTTGAAACTTCAAAATTTTAAA
1 CTTACAAATCTCAATATGCATGAAAGCTCCTCTAATTAGAGGCTTTGAAACTTTAAAATTTTAAA
*
17601081 ATGTTTTAC-CAAACGGTTTTAGAGATTATGCCTGAAGGC
66 ATGTTTTACTCAAA-GGTCTTAGAGATTATGCCTGAAGGC
* * * * * * *
17601120 CTTACAAATCTCGACATGCAAGAAAGCTCTTTTAATTAGAGGCTTTGAAATTTTTAAAAATTTAA
1 CTTACAAATCTCAATATGCATGAAAGCTCCTCTAATTAGAGGCTTTGAAA-CTTTAAAATTTTAA
17601185 AATGTT
65 AATGTT
17601191 CTATCCGGAA
Statistics
Matches: 145, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
103 4 0.03
104 120 0.83
105 21 0.14
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (104 bp):
CTTACAAATCTCAATATGCATGAAAGCTCCTCTAATTAGAGGCTTTGAAACTTTAAAATTTTAAA
ATGTTTTACTCAAAGGTCTTAGAGATTATGCCTGAAGGC
Found at i:17601488 original size:41 final size:41
Alignment explanation
Indices: 17601416--17601523 Score: 119
Period size: 41 Copynumber: 2.6 Consensus size: 41
17601406 AATATGAGGT
* *
17601416 TTACTTAGAGGTATTAGGAAATCAT-TCAAAAATCAAAGATC
1 TTACCTAGAGGTCTT-GGAAATCATGTCAAAAATCAAAGATC
* * ** *
17601457 TTACCTGGAGGTCTTGGAAATCATGTGAAAAATCTGAGATT
1 TTACCTAGAGGTCTTGGAAATCATGTCAAAAATCAAAGATC
* *
17601498 TTACCTAAAGGTCTTGAAAATCATGT
1 TTACCTAGAGGTCTTGGAAATCATGT
17601524 AGTCATTCTC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 9 0.16
41 47 0.84
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (41 bp):
TTACCTAGAGGTCTTGGAAATCATGTCAAAAATCAAAGATC
Found at i:17603067 original size:25 final size:24
Alignment explanation
Indices: 17603033--17603083 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
17603023 CATTCATCTT
17603033 TTCTTCGTTTCTTTTCTTTTCTTTC
1 TTCTTCGTTTCTTTT-TTTTCTTTC
* * *
17603058 TTCTTTGTTTGTTTTTTTTTTTTC
1 TTCTTCGTTTCTTTTTTTTCTTTC
17603082 TT
1 TT
17603084 ATTATTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (24 bp):
TTCTTCGTTTCTTTTTTTTCTTTC
Found at i:17603555 original size:47 final size:48
Alignment explanation
Indices: 17603498--17603601 Score: 120
Period size: 47 Copynumber: 2.2 Consensus size: 48
17603488 TTTTTTTCTT
* * * *
17603498 TCTTTCTTCTTTTTTTTTATTCTCCTTCCT-TTTCATTTTATCTTTTA
1 TCTTTTTTCTTTGTATTTATTCTCCTTACTCTTTCATTTTATCTTTTA
* * * *
17603545 TCTTTTTTCTTTGTATTTGTTCTCCTTATTCTTTCATTTTCTCTTTTT
1 TCTTTTTTCTTTGTATTTATTCTCCTTACTCTTTCATTTTATCTTTTA
*
17603593 TTTTTTTTC
1 TCTTTTTTC
17603602 CATTTTCTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 24 0.51
48 23 0.49
ACGTcount: A:0.07, C:0.19, G:0.02, T:0.72
Consensus pattern (48 bp):
TCTTTTTTCTTTGTATTTATTCTCCTTACTCTTTCATTTTATCTTTTA
Found at i:17603637 original size:25 final size:24
Alignment explanation
Indices: 17603581--17603657 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 24
17603571 TATTCTTTCA
* *
17603581 TTTTCTCTTTTTTTTTTTTTCCATTT
1 TTTTCACTTTTCTTTTTTTTCC--TT
*
17603607 TCTTTCCCTTTTCTTATTTTTTCCTT
1 T-TTTCACTTTTCTT-TTTTTTCCTT
17603633 TTTTCACTTTTCTTTTTCTTTCCTT
1 TTTTCACTTTTCTTTTT-TTTCCTT
17603658 CAAATGGATT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
24 3 0.07
25 19 0.42
26 4 0.09
27 11 0.24
28 8 0.18
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTCACTTTTCTTTTTTTTCCTT
Found at i:17604103 original size:17 final size:16
Alignment explanation
Indices: 17604083--17604184 Score: 53
Period size: 18 Copynumber: 5.6 Consensus size: 16
17604073 TATTTTTCCC
*
17604083 TTTTTTTTTCTTTTCA
1 TTTTTTTTTTTTTTCA
*
17604099 TTTTTTTTTTGGCTTTTCTTC
1 TTTTTTTTTT---TTTTC--A
17604120 TTTTCTCTTTTTTTTTC-
1 TTTT-T-TTTTTTTTTCA
17604137 TCTCTTTCTTTTTTTCTTCTA
1 T-T-TTT-TTTTTTT-TTC-A
*
17604158 TTTTTTTTTGTTTTTTA
1 TTTTTTTTT-TTTTTCA
17604175 TTTTTTTTTT
1 TTTTTTTTTT
17604185 GCAGGCCCCC
Statistics
Matches: 70, Mismatches: 3, Indels: 26
0.71 0.03 0.26
Matches are distributed among these distances:
16 10 0.14
17 11 0.16
18 16 0.23
19 16 0.23
20 6 0.09
21 5 0.07
22 1 0.01
23 5 0.07
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTTTTTTCA
Found at i:17604142 original size:14 final size:13
Alignment explanation
Indices: 17604084--17604179 Score: 68
Period size: 15 Copynumber: 6.8 Consensus size: 13
17604074 ATTTTTCCCT
*
17604084 TTTTTTTTCTTTTC
1 TTTTTTTT-TTCTC
**
17604098 ATTTTTTTTTTGGC
1 -TTTTTTTTTTCTC
17604112 TTTTCTTCTTTTCTC
1 TTTT-TT-TTTTCTC
17604127 TTTTTTTTTCTCTC
1 TTTTTTTTT-TCTC
17604141 TTTCTTTTTTTCTTC
1 TTT-TTTTTTTC-TC
*
17604156 TATTTTTTTTTGT-
1 T-TTTTTTTTTCTC
17604169 TTTTTATTTTT
1 TTTTT-TTTTT
17604180 TTTTTGCAGG
Statistics
Matches: 69, Mismatches: 5, Indels: 16
0.77 0.06 0.18
Matches are distributed among these distances:
12 4 0.06
13 13 0.19
14 17 0.25
15 33 0.48
16 2 0.03
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (13 bp):
TTTTTTTTTTCTC
Found at i:17604144 original size:28 final size:28
Alignment explanation
Indices: 17604085--17604165 Score: 85
Period size: 27 Copynumber: 2.9 Consensus size: 28
17604075 TTTTTCCCTT
* *
17604085 TTTTTTTCTTTTCAT-TTTTTTTTTGGC
1 TTTTCTTCTTTTCATCTTTTTTTTTCGC
*
17604112 TTTTCTTCTTTTC-TCTTTTTTTTTCTC
1 TTTTCTTCTTTTCATCTTTTTTTTTCGC
* *
17604139 TCTTTCTTTTTTTCTTCTATTTTTTTT
1 T-TTTCTTCTTTTCATCT-TTTTTTTT
17604166 TGTTTTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 23 0.50
28 11 0.24
29 3 0.07
30 8 0.17
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (28 bp):
TTTTCTTCTTTTCATCTTTTTTTTTCGC
Done.