Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 108 of 127
Found at i:20100718 original size:42 final size:42
Alignment explanation
Indices: 20100593--20100764 Score: 276
Period size: 41 Copynumber: 4.1 Consensus size: 42
20100583 GATTGTCAAT
20100593 GAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
20100635 GAGCAATTTAC-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
*
20100676 GAGCAATTTA-TTTTTCAAAGTCGTGGGTGCTTCTGTTTAGAG
1 GAGCAATTTACTTTTTCAAAGTCGT-GGTGCCTCTGTTTAGAG
* * *
20100718 GAGCAATTTATGTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAG
1 GAGCAATTTA-CTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
20100761 GAGC
1 GAGC
20100765 TTTGGTAAAA
Statistics
Matches: 122, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
41 53 0.43
42 37 0.30
43 18 0.15
44 14 0.11
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (42 bp):
GAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
Found at i:20101072 original size:4 final size:4
Alignment explanation
Indices: 20101019--20101084 Score: 50
Period size: 4 Copynumber: 16.8 Consensus size: 4
20101009 TCTTTTGTAT
* * *
20101019 TTTA TGTA TTT- TATTA TTTA -TTA -TTA TTATA TGTA TATT- TTTA CTTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TT-TA TTTA T-TTA TTTA TTTA
20101066 TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTT
20101085 TTCTATTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
3 9 0.18
4 36 0.72
5 5 0.10
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:20101128 original size:21 final size:20
Alignment explanation
Indices: 20101020--20101156 Score: 62
Period size: 20 Copynumber: 7.1 Consensus size: 20
20101010 CTTTTGTATT
* *
20101020 TTATGTATTTTA-TTATTTA
1 TTATATATTTTATTTATATA
* *
20101039 TTAT-TATTATATGTATAT-
1 TTATATATTTTATTTATATA
* *
20101057 TTTTACT-TATTTATTTATTTA
1 TTATA-TAT-TTTATTTATATA
* *
20101078 TT-TATTTTTCTATTAATAT-
1 TTATATATTT-TATTTATATA
20101097 TTATAGGTATTTTATTTATATA
1 TTATA--TATTTTATTTATATA
*
20101119 GTTCTATA-TTTA-TTATATA
1 -TTATATATTTTATTTATATA
20101138 TTATA-ATTTT-TTTAT-TA
1 TTATATATTTTATTTATATA
20101155 TT
1 TT
20101157 TTTTTCTTGT
Statistics
Matches: 91, Mismatches: 13, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
17 5 0.05
18 20 0.22
19 21 0.23
20 25 0.27
21 12 0.13
22 4 0.04
23 4 0.04
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (20 bp):
TTATATATTTTATTTATATA
Found at i:20102271 original size:18 final size:17
Alignment explanation
Indices: 20102222--20102277 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
20102212 TTTAATATTC
20102222 TTTTTA-TTTTATTT-T
1 TTTTTACTTTTATTTAT
*
20102237 TGTTTTACTTTTCTTTAT
1 T-TTTTACTTTTATTTAT
*
20102255 TTTTTAATTTTTATTTAT
1 TTTTT-ACTTTTATTTAT
20102273 TTTTT
1 TTTTT
20102278 TATTATTCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 1 0.03
16 5 0.15
17 11 0.32
18 17 0.50
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTTACTTTTATTTAT
Found at i:20102463 original size:59 final size:58
Alignment explanation
Indices: 20102299--20102653 Score: 425
Period size: 58 Copynumber: 6.0 Consensus size: 58
20102289 TTTCTTTAAA
*
20102299 TGAAAATCAAAATTTTCAAAAAAATATTTTTAGGGAAAAGTTGAAAATATCAATTTTTCT
1 TGAAAAT-AAAATTTTCAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTCT
* * *
20102359 TAAAAAT-AAATTTTCAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATATTCCT
1 TGAAAATAAAATTTTCAAAAAAATATTTTTGG-GAAAAGTTGAAAGTATCAATTTTTCT
* *
20102417 TGAAAATCAAAATTTTC-GAAAAATATTTTTAGGGAAAAGTTAAAAGTATCAA-TTTTCTT
1 TGAAAAT-AAAATTTTCAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTC-T
* *
20102476 TGAAAATCAAAGTTTCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
1 TGAAAATAAAATTTTC--AAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTTCT
* *
20102537 TAAAAATAAAA-TTTCAAAAAAAGGTTTTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCT
1 TGAAAATAAAATTTTCAAAAAAA--TATTTTTG-GGAAAAGTTGAAAGTATCAATTTTTCT
* * *
20102596 TCG-AAATTAAAGTTTCAAAAAAACATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTC
1 T-GAAAATAAAATTTTCAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTC
20102654 CTGCACAAGA
Statistics
Matches: 259, Mismatches: 20, Indels: 33
0.83 0.06 0.11
Matches are distributed among these distances:
57 2 0.01
58 93 0.36
59 58 0.22
60 60 0.23
61 41 0.16
62 5 0.02
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (58 bp):
TGAAAATAAAATTTTCAAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTTCT
Found at i:20105028 original size:20 final size:21
Alignment explanation
Indices: 20104989--20105029 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20104979 AATACATTTT
20104989 TATTTTAAAAATATTAATATA
1 TATTTTAAAAATATTAATATA
20105010 TATTTATAAAAA-ATT-ATATA
1 TATTT-TAAAAATATTAATATA
20105030 AATATGCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 8 0.42
22 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTTTAAAAATATTAATATA
Found at i:20105034 original size:22 final size:21
Alignment explanation
Indices: 20104989--20105034 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
20104979 AATACATTTT
*
20104989 TATTTTAAAAATATTAATATA
1 TATTTTAAAAATATTAATAAA
20105010 TATTTATAAAAA-ATTATATAAA
1 TATTT-TAAAAATATTA-ATAAA
20105032 TAT
1 TAT
20105035 GCAGATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTTTAAAAATATTAATAAA
Found at i:20116929 original size:19 final size:19
Alignment explanation
Indices: 20116900--20116943 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
20116890 AGTGATATTG
20116900 AATAA-TCAAGAGTGAT-A
1 AATAATTCAAGAGTGATCA
20116917 AGATAATTCAAGAGTGATCA
1 A-ATAATTCAAGAGTGATCA
20116937 AATAATT
1 AATAATT
20116944 ATTTTGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.04
18 4 0.17
19 17 0.71
20 2 0.08
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (19 bp):
AATAATTCAAGAGTGATCA
Found at i:20119219 original size:14 final size:13
Alignment explanation
Indices: 20119193--20119240 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
20119183 CAAACTAACC
20119193 CCTAAA-TCTTAAA
1 CCTAAACTC-TAAA
20119206 CCTTAAACTCTAAAA
1 CC-TAAACTCT-AAA
*
20119221 CCTAAACTTTAAA
1 CCTAAACTCTAAA
20119234 CCTAAAC
1 CCTAAAC
20119241 CAAACTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 12 0.39
14 12 0.39
15 7 0.23
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (13 bp):
CCTAAACTCTAAA
Found at i:20119742 original size:31 final size:31
Alignment explanation
Indices: 20119707--20119767 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
20119697 TTAAAAATGT
20119707 TTTGTTTATAAAGAA-AAAAAAAGAGAAAAGA
1 TTTGTTTATAAAGAATAAAAAAAGA-AAAAGA
* **
20119738 TTTGTTTTTTTAGAATAAAAAAAGAAAAAG
1 TTTGTTTATAAAGAATAAAAAAAGAAAAAG
20119768 GAATTAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (31 bp):
TTTGTTTATAAAGAATAAAAAAAGAAAAAGA
Found at i:20123889 original size:19 final size:19
Alignment explanation
Indices: 20123865--20123916 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
20123855 AATAAAAGTG
20123865 AAATTGGGTTTAAAATTGA
1 AAATTGGGTTTAAAATTGA
**
20123884 AAATT-GGTTT-CCATTGA
1 AAATTGGGTTTAAAATTGA
20123901 AGAATTGGGCTTTAAA
1 A-AATTGGG-TTTAAA
20123917 GTTGGACTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
17 6 0.24
18 9 0.36
19 7 0.28
20 3 0.12
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.37
Consensus pattern (19 bp):
AAATTGGGTTTAAAATTGA
Found at i:20124659 original size:18 final size:19
Alignment explanation
Indices: 20124632--20124668 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20124622 TTAATAAAAA
20124632 TAAAAGTG-AAATTGGGTT
1 TAAAAGTGAAAATTGGGTT
*
20124650 TAAAATTGAAAATTGGGTT
1 TAAAAGTGAAAATTGGGTT
20124669 CCATTGGATT
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:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (19 bp):
TAAAAGTGAAAATTGGGTT
Found at i:20126254 original size:26 final size:26
Alignment explanation
Indices: 20126225--20126274 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
20126215 AGATTATGGA
*
20126225 AATTTTCAAGAAAATAATTCAATATT
1 AATTTTCAAGAAAATAACTCAATATT
20126251 AATTTTCAAGAAAATAACTCAATA
1 AATTTTCAAGAAAATAACTCAATA
20126275 CTAAAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.34
Consensus pattern (26 bp):
AATTTTCAAGAAAATAACTCAATATT
Found at i:20130215 original size:34 final size:33
Alignment explanation
Indices: 20130140--20130244 Score: 104
Period size: 34 Copynumber: 3.1 Consensus size: 33
20130130 CATATCTGAT
* * *
20130140 AAATTTTATAACTTATCAAAAATAGATTTCCGAA
1 AAATTATATAACTTATCGAAAATGGATTT-CGAA
* *
20130174 AAGTTATATAACTTATCGAAAATGGATTGTCAAA
1 AAATTATATAACTTATCGAAAATGGATT-TCGAA
* *
20130208 AAATTATA-AAATTTTCTGAAAATGGATTTTCGAA
1 AAATTATATAACTTATC-GAAAATGGA-TTTCGAA
20130242 AAA
1 AAA
20130245 GGAGAGAATT
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
33 6 0.10
34 50 0.85
35 3 0.05
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (33 bp):
AAATTATATAACTTATCGAAAATGGATTTCGAA
Found at i:20131471 original size:30 final size:31
Alignment explanation
Indices: 20131420--20131482 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 31
20131410 TCATAAATTG
20131420 TTTACTTTAATTTTTTAAAATATAAATAGTA
1 TTTACTTTAATTTTTTAAAATATAAATAGTA
20131451 TTTACTTTAATTTTTT-AAATATAAATAGTA
1 TTTACTTTAATTTTTTAAAATATAAATAGTA
20131481 TT
1 TT
20131483 AATCATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTACTTTAATTTTTTAAAATATAAATAGTA
Found at i:20132833 original size:9 final size:9
Alignment explanation
Indices: 20132819--20132893 Score: 60
Period size: 9 Copynumber: 8.3 Consensus size: 9
20132809 AGCGAAAGAA
*
20132819 CTGCTGCTT
1 CTGCTGCTG
*
20132828 CTGCTGCAG
1 CTGCTGCTG
20132837 CTGCTGCTG
1 CTGCTGCTG
*
20132846 CTGCTGGTG
1 CTGCTGCTG
** *
20132855 AAGCTGTTG
1 CTGCTGCTG
*
20132864 GTGCTGCTG
1 CTGCTGCTG
*
20132873 TTGCTGCTG
1 CTGCTGCTG
* *
20132882 TTGCTGATG
1 CTGCTGCTG
20132891 CTG
1 CTG
20132894 GTGGAGGAGG
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.05, C:0.24, G:0.35, T:0.36
Consensus pattern (9 bp):
CTGCTGCTG
Found at i:20132839 original size:6 final size:6
Alignment explanation
Indices: 20132819--20132893 Score: 60
Period size: 6 Copynumber: 12.5 Consensus size: 6
20132809 AGCGAAAGAA
* * * ** * *
20132819 CTGCTG CTTCTG CTGCAG CTGCTG CTGCTG CTGGTG AAGCTG TTGGTG
1 CTGCTG CTGCTG CTGCTG CTGCTG CTGCTG CTGCTG CTGCTG CTGCTG
* * *
20132867 CTGCTG TTGCTG CTGTTG CTGATG CTG
1 CTGCTG CTGCTG CTGCTG CTGCTG CTG
20132894 GTGGAGGAGG
Statistics
Matches: 52, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.05, C:0.24, G:0.35, T:0.36
Consensus pattern (6 bp):
CTGCTG
Found at i:20132859 original size:21 final size:21
Alignment explanation
Indices: 20132819--20132896 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
20132809 AGCGAAAGAA
* *
20132819 CTGCTGCTTCTGCTGCAGCTG
1 CTGCTGCTGCTGGTGCAGCTG
*
20132840 CTGCTGCTGCTGGTGAAGCTG
1 CTGCTGCTGCTGGTGCAGCTG
* * * *
20132861 TTGGTGCTGCTGTTGCTGCTG
1 CTGCTGCTGCTGGTGCAGCTG
* *
20132882 TTGCTGATGCTGGTG
1 CTGCTGCTGCTGGTG
20132897 GAGGAGGCGG
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.05, C:0.23, G:0.36, T:0.36
Consensus pattern (21 bp):
CTGCTGCTGCTGGTGCAGCTG
Found at i:20134026 original size:16 final size:16
Alignment explanation
Indices: 20133991--20134028 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20133981 AGAACCGTAG
*
20133991 ATTCATGAATGACTAT
1 ATTCATGAATGACTAA
20134007 ATTCATGAAT-ACTCAA
1 ATTCATGAATGACT-AA
20134023 ATTCAT
1 ATTCAT
20134029 ACAATTTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (16 bp):
ATTCATGAATGACTAA
Found at i:20134272 original size:24 final size:23
Alignment explanation
Indices: 20134245--20134294 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
20134235 AGTGAATAGT
20134245 ATCTATGAATCTGATTAATTACAA
1 ATCTATGAATCT-ATTAATTACAA
* * * *
20134269 ATCTTTTAATCTTTTAATTATAA
1 ATCTATGAATCTATTAATTACAA
20134292 ATC
1 ATC
20134295 ATTTAACTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (23 bp):
ATCTATGAATCTATTAATTACAA
Found at i:20134538 original size:2 final size:2
Alignment explanation
Indices: 20134533--20134561 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20134523 ATATATGTGC
20134533 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20134562 AACACACACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20134706 original size:30 final size:27
Alignment explanation
Indices: 20134644--20134710 Score: 73
Period size: 30 Copynumber: 2.4 Consensus size: 27
20134634 TTATTAAAAT
*
20134644 AAAAATT-AAAAAAAAAAACAAATCAA
1 AAAAATTAAAAAAAAAAAAAAAATCAA
**
20134670 CTAAATTAAAAAAAAAAAGAAATAATCCAA
1 AAAAATTAAAAAAAAAAA-AAA-AAT-CAA
20134700 AAAAATTAAAA
1 AAAAATTAAAA
20134711 TAATAATCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
26 5 0.16
27 10 0.31
28 2 0.06
29 3 0.09
30 12 0.38
ACGTcount: A:0.76, C:0.07, G:0.01, T:0.15
Consensus pattern (27 bp):
AAAAATTAAAAAAAAAAAAAAAATCAA
Found at i:20136712 original size:31 final size:31
Alignment explanation
Indices: 20136648--20136713 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
20136638 AATCATAAAT
**
20136648 TATTTACTTTAATTTTTTAAAACATAAGTAG
1 TATTTACTTTAATTTTTTAAAACATAAACAG
* * *
20136679 TATTTAGTTTAATTTTTTTAAATATAAACAG
1 TATTTACTTTAATTTTTTAAAACATAAACAG
20136710 TATT
1 TATT
20136714 AATCATAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.52
Consensus pattern (31 bp):
TATTTACTTTAATTTTTTAAAACATAAACAG
Found at i:20137056 original size:12 final size:14
Alignment explanation
Indices: 20137027--20137055 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20137017 AAAATGAAAA
20137027 TTTAGTGGCTATTT
1 TTTAGTGGCTATTT
20137041 TTTAGTGG-TATTT
1 TTTAGTGGCTATTT
20137054 TT
1 TT
20137056 AAATAAACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.14, C:0.03, G:0.21, T:0.62
Consensus pattern (14 bp):
TTTAGTGGCTATTT
Found at i:20137804 original size:91 final size:90
Alignment explanation
Indices: 20137697--20137884 Score: 241
Period size: 91 Copynumber: 2.1 Consensus size: 90
20137687 TGTTCTTGGC
* * *
20137697 AAAAAATACCTTGAGTAATCACGTCATAAAAATTTATAAAGAGATTACTCAAGGTATTTTTGATG
1 AAAAAATACCTTGAGTAATCACATCATAAAAATTTATAAAGAGATTACTAAAGGTATTTTTGATC
*
20137762 AAAAATGCCTTCGATAACCCCATTA
66 AAAAATGCCTTCAATAACCCCATTA
* * * * * * * *
20137787 AAAATAATACCTTGAGTAATTACATCATAAAATTTTATGAGGGGATTATTAAATGTATTTTTTAT
1 AAAA-AATACCTTGAGTAATCACATCATAAAAATTTATAAAGAGATTACTAAAGGTATTTTTGAT
* *
20137852 CAGAAATGCCTTCAATAACCCTATTA
65 CAAAAATGCCTTCAATAACCCCATTA
20137878 AAAAAAT
1 AAAAAAT
20137885 TTTTAGAATT
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 7 0.08
91 76 0.92
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (90 bp):
AAAAAATACCTTGAGTAATCACATCATAAAAATTTATAAAGAGATTACTAAAGGTATTTTTGATC
AAAAATGCCTTCAATAACCCCATTA
Found at i:20138117 original size:126 final size:125
Alignment explanation
Indices: 20137786--20138256 Score: 407
Period size: 125 Copynumber: 3.7 Consensus size: 125
20137776 TAACCCCATT
* * * * **
20137786 AAAAATAATACCTTGAGTAATTACATCATAAAATTTTATGAGGGGATTATTAAATGTATTTTTTA
1 AAAAA-AATA-CTTGAGTAATCACATCATAAAAATTTATGAGGAGATTATTAAA-GTCTTTTTGG
* * ** * * * *
20137851 TCAGAAATGCCTTCAATAACCCTATTAAAAAAATTTTTAG-AATTATTCAAGGCGTTTTTAGTC
63 CCAAAAACACCTTCAATAACCCTATTAAAAAAATTTTTTGCAATTATTCAAGACATTTTT-GAC
* * * * * * *
20137914 AAAAACA-CCTTGAGTAATCACATCATAAAAATTTGTGAAGAGATTATTTATGGCATTTTTGGCC
1 AAAAAAATACTTGAGTAATCACATCATAAAAATTTATGAGGAGATTATTAAAGTC-TTTTTGGCC
* * * **** *
20137978 AGAAACGCTTTCAATAACCCTATTAAATTTTTTTTTTGCAATTATTCAAAACATTTTTGAC
65 AAAAACACCTTCAATAACCCTATTAAAAAAATTTTTTGCAATTATTCAAGACATTTTTGAC
* ** * *
20138039 AAAAAAATGACTTGAGTAATTATGTCATAAAAATTTATGAGGGGATTATTAAAGTCGTTTTGGCC
1 AAAAAAAT-ACTTGAGTAATCACATCATAAAAATTTATGAGGAGATTATTAAAGTCTTTTTGGCC
* * * **
20138104 AAAAATACCTTCAATAGCCCCATTAAAAAAA-TTTTT-CAATATTATTCAAGACATTTTTGGT
65 AAAAACACCTTCAATAACCCTATTAAAAAAATTTTTTGC-A-ATTATTCAAGACATTTTTGAC
* *
20138165 AAAAAAATACCTTGAGTAATCAC-TCTATAAAAATTTATGAGGAG-TTATTGAAGACTTTTTGGC
1 AAAAAAATA-CTTGAGTAATCACATC-ATAAAAATTTATGAGGAGATTATTAAAGTCTTTTTGGC
* *
20138228 CAAAAACACATTTAATAA-CCTAATTAAAA
64 CAAAAACACCTTCAATAACCCT-ATTAAAA
20138257 TTTTCTTTTA
Statistics
Matches: 273, Mismatches: 61, Indels: 21
0.77 0.17 0.06
Matches are distributed among these distances:
124 4 0.01
125 127 0.47
126 99 0.36
127 38 0.14
128 5 0.02
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (125 bp):
AAAAAAATACTTGAGTAATCACATCATAAAAATTTATGAGGAGATTATTAAAGTCTTTTTGGCCA
AAAACACCTTCAATAACCCTATTAAAAAAATTTTTTGCAATTATTCAAGACATTTTTGAC
Found at i:20138260 original size:252 final size:252
Alignment explanation
Indices: 20137797--20138265 Score: 601
Period size: 252 Copynumber: 1.9 Consensus size: 252
20137787 AAAATAATAC
* * * * * *
20137797 CTTGAGTAATTACATCATAAAATTTTATGAGGGGATTATTAAATGTATTTTTTATCAGAAATGCC
1 CTTGAGTAATTACATCATAAAAATTTATGAGGGGATTATTAAATGTAGTTTTGACCAAAAATACC
* * * *
20137862 TTCAATAACCCTATTAAAAAAATTTTTAGAATTATTCAAGGCGTTTTTAGTCAAAAACACCTTGA
66 TTCAATAACCCCATTAAAAAAATTTTTAGAATTATTCAAGACATTTTTAGTAAAAAACACCTTGA
* * * * * *
20137927 GTAATCACATCATAAAAATTTGTGAAGAGATTATTTATGGCATTTTTGGCCAGAAACGCTTTCAA
131 GTAATCACATCATAAAAATTTATGAAGAGATTATTGAAGACATTTTTGGCCAAAAACACTTTCAA
*
20137992 TAACCCTATTAAATTTTTTTTTTGCAATTATTCAAAACATTTTTGACAAAAAAATGA
196 TAACCCTATTAAATTTTCTTTTTGCAATTATTCAAAACATTTTTGACAAAAAAATGA
** * *
20138049 CTTGAGTAATTATGTCATAAAAATTTATGAGGGGATTATTAAA-GTCGTTTTGGCCAAAAATACC
1 CTTGAGTAATTACATCATAAAAATTTATGAGGGGATTATTAAATGTAGTTTTGACCAAAAATACC
* * *
20138113 TTCAATAGCCCCATTAAAAAAATTTTTCA-ATATTATTCAAGACATTTTTGGTAAAAAAATACCT
66 TTCAATAACCCCATTAAAAAAATTTTT-AGA-ATTATTCAAGACATTTTTAGT-AAAAAACACCT
*
20138177 TGAGTAATCAC-TCTATAAAAATTTATGAGGAG-TTATTGAAGAC-TTTTTGGCCAAAAACACAT
128 TGAGTAATCACATC-ATAAAAATTTATGAAGAGATTATTGAAGACATTTTTGGCCAAAAACAC-T
20138239 TT-AATAA-CCTAATTAAAATTTTCTTTT
191 TTCAATAACCCT-ATT-AAATTTTCTTTT
20138266 AGGATTATTT
Statistics
Matches: 185, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
250 3 0.02
251 63 0.34
252 83 0.45
253 36 0.19
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (252 bp):
CTTGAGTAATTACATCATAAAAATTTATGAGGGGATTATTAAATGTAGTTTTGACCAAAAATACC
TTCAATAACCCCATTAAAAAAATTTTTAGAATTATTCAAGACATTTTTAGTAAAAAACACCTTGA
GTAATCACATCATAAAAATTTATGAAGAGATTATTGAAGACATTTTTGGCCAAAAACACTTTCAA
TAACCCTATTAAATTTTCTTTTTGCAATTATTCAAAACATTTTTGACAAAAAAATGA
Found at i:20138477 original size:251 final size:250
Alignment explanation
Indices: 20138215--20138686 Score: 564
Period size: 251 Copynumber: 1.9 Consensus size: 250
20138205 GGAGTTATTG
* ** * * * *
20138215 AAGACTTTTTGGCCAAAAACACATTTAATAA-CCT-AATTAAAATTTT-CTTTTAGGATTATTTA
1 AAGACTTTTTGGCCAAAAACACATTGAATAATCCTAAAAAAAAATTTTAATTGT--G-TTAGTGA
* * * *
20138277 AGGTATTTTTGGTCAAAAATGCCTTCAATAATTCTCTT-ATAAAATTTTATAACGTGATTACTCA
63 AGGCATTTTTGGCCAAAAATACCTTCAATAA-TCCCTTCATAAAATTTTATAACGTGATTACTCA
* * ** *
20138341 ATG-TGTTTT-AGTCAAAAATGCTTTGAATAATCTTTAAAAAAAATTTTAAT-GGGATTATTGAA
127 AGGCTGTTTTCA-CCAAAAACACCTTGAATAATC-TTAAAAAAAATTTTAATAGGG-TTATTGAA
* *
20138403 GGCATTTTT-GACCAAAAATACTTTTAATAATCCATTTATAAATTTTTACAATGTGATTACTC
189 GGCATTTTTAG-CCAAAAACACATTTAATAATCCATTTATAAATTTTTACAATGTGATTACTC
** * *
20138465 AAGACGTTTTTGGCCAAAAATGCCTTGAATAATTCTAAAAAAAAATTTTAATTGTGTTAGTGAAG
1 AAGAC-TTTTTGGCCAAAAACACATTGAATAATCCTAAAAAAAAATTTTAATTGTGTTAGTGAAG
* *
20138530 GCATTTTTGGCCAAAAATACCTTCAATAATCCCTTCATAAATTTTTATGACGTGATTACTCAAGG
65 GCATTTTTGGCCAAAAATACCTTCAATAATCCCTTCATAAAATTTTATAACGTGATTACTCAAGG
* *
20138595 CTTTTTTCACCAAAAACACCTTGAATAATCTTAAAAAAAATTTTAATAGGGTTATTGAAGGTATT
130 CTGTTTTCACCAAAAACACCTTGAATAATCTTAAAAAAAATTTTAATAGGGTTATTGAAGGCATT
*
20138660 TTTAGTCAAAAACACATTTAATAATCC
195 TTTAGCCAAAAACACATTTAATAATCC
20138687 CATCATAAAT
Statistics
Matches: 186, Mismatches: 27, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
250 10 0.05
251 133 0.72
252 29 0.16
253 11 0.06
254 3 0.02
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (250 bp):
AAGACTTTTTGGCCAAAAACACATTGAATAATCCTAAAAAAAAATTTTAATTGTGTTAGTGAAGG
CATTTTTGGCCAAAAATACCTTCAATAATCCCTTCATAAAATTTTATAACGTGATTACTCAAGGC
TGTTTTCACCAAAAACACCTTGAATAATCTTAAAAAAAATTTTAATAGGGTTATTGAAGGCATTT
TTAGCCAAAAACACATTTAATAATCCATTTATAAATTTTTACAATGTGATTACTC
Found at i:20138483 original size:64 final size:62
Alignment explanation
Indices: 20138281--20138628 Score: 188
Period size: 62 Copynumber: 5.5 Consensus size: 62
20138271 TATTTAAGGT
* * * *
20138281 ATTTTTGGTCAAAAATGCCTTCAATAATTCTCTT-ATAAAATTTTATAACGTGATTACTCAATG-
1 ATTTTTGGCCAAAAATACCTTCAATAA-TC-CTTAATAAATTTTTA-AATGTGATTACTCAA-GA
20138344 -
62 C
* * * * * * * * * * * *
20138344 -TGTTTTAGTCAAAAATGCTTTGAATAATCTTTAAAAAAAATTTT-AATGGGATTATTGAAGGC
1 AT-TTTTGGCCAAAAATACCTTCAATAATCCTT-AATAAATTTTTAAATGTGATTACTCAAGAC
* * * *
20138406 ATTTTTGACCAAAAATACTTTTAATAATCCATTTATAAATTTTTACAATGTGATTACTCAAGAC
1 ATTTTTGGCCAAAAATACCTTCAATAATCC-TTAATAAATTTTTA-AATGTGATTACTCAAGAC
* * * * * * * * * * *
20138470 GTTTTTGGCCAAAAATGCCTTGAATAATTCTAAAAAAAAATTTTAATTGTG-TTAGTGAAGGC
1 ATTTTTGGCCAAAAATACCTTCAATAATCCT-TAATAAATTTTTAAATGTGATTACTCAAGAC
* * * *
20138532 ATTTTTGGCCAAAAATACCTTCAATAATCCCTTCATAAATTTTTATGACGTGATTACTCAAGGC
1 ATTTTTGGCCAAAAATACCTTCAATAAT-CCTTAATAAATTTTTA-AATGTGATTACTCAAGAC
* ** * *
20138596 TTTTTTCACCAAAAACACCTTGAATAAT-CTTAA
1 ATTTTTGGCCAAAAATACCTTCAATAATCCTTAA
20138629 AAAAAATTTT
Statistics
Matches: 217, Mismatches: 55, Indels: 27
0.73 0.18 0.09
Matches are distributed among these distances:
60 1 0.00
61 13 0.06
62 79 0.36
63 45 0.21
64 79 0.36
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (62 bp):
ATTTTTGGCCAAAAATACCTTCAATAATCCTTAATAAATTTTTAAATGTGATTACTCAAGAC
Found at i:20138544 original size:126 final size:124
Alignment explanation
Indices: 20138270--20138917 Score: 488
Period size: 126 Copynumber: 5.1 Consensus size: 124
20138260 TCTTTTAGGA
* * * * * *
20138270 TTATTTAAGGTATTTTTGGTCAAAAATGCCTTCAATAATTCTCTTATAAAATTTTATAACGTGAT
1 TTATTGAAGGCATTTTTGGCCAAAAATACCTTCAATAATCCT-TTATAAATTTTTATAACGTGAT
* * *
20138335 TACTC-A-ATGTGTTTTAGTCAAAAATGCTTTGAATAATCTTTAAAAAAAATTTTAA-TGGG
65 TACTCAAGACGT-TTTTAGCCAAAAATGCCTTGAATAATC-TTAAAAAAAATTTTAATTGGG
* * * * *
20138394 ATTATTGAAGGCATTTTTGACCAAAAATACTTTTAATAATCCATTTATAAATTTTTACAATGTGA
1 -TTATTGAAGGCATTTTTGGCCAAAAATACCTTCAATAATCC-TTTATAAATTTTTATAACGTGA
* * *
20138459 TTACTCAAGACGTTTTTGGCCAAAAATGCCTTGAATAATTCTAAAAAAAAATTTTAATTGTG
64 TTACTCAAGACGTTTTTAGCCAAAAATGCCTTGAATAA-TCTTAAAAAAAATTTTAATTGGG
* * *
20138521 TTAGTGAAGGCATTTTTGGCCAAAAATACCTTCAATAATCCCTTCATAAATTTTTATGACGTGAT
1 TTATTGAAGGCATTTTTGGCCAAAAATACCTTCAATAAT-CCTTTATAAATTTTTATAACGTGAT
* * ** *
20138586 TACTCAAGGCTTTTTTCA-CCAAAAACACCTTGAATAATCTTAAAAAAAATTTTAATAGGG
65 TACTCAAGACGTTTTT-AGCCAAAAATGCCTTGAATAATCTTAAAAAAAATTTTAATTGGG
* * * * * * * * * **
20138646 TTATTGAAGGTATTTTTAGTCAAAAACACATTTAATAATCCCATCATAAATTTCTT-TGATATGA
1 TTATTGAAGGCATTTTTGGCCAAAAATACCTTCAATAAT-CCTTTATAAATTT-TTATAACGTGA
* * * * *
20138710 TTACTTAAGGA-ATTTTT-GCCAAAAA--CCTTTTGAGTAATTTTTTAAAAAAAAAATTTTAATA
64 TTACTCAA-GACGTTTTTAGCCAAAAATGCC--TTGAATAA--TCTT--AAAAAAAATTTTAATT
20138771 GGG
122 GGG
* * * * ** * * * * * *
20138774 TTATTGAAAGCGTTTATGGCTAAAAATTTCTTCAATAATTCTCTCATAAATTTCTATGACATAAT
1 TTATTGAAGGCATTTTTGGCCAAAAATACCTTCAATAATCCT-TTATAAATTTTTATAACGTGAT
* * * * ** *
20138839 TACTTAA-AGCATTTTTAGCAAAAAAATGCCTTAAATAATCCCAAAAAAAATTTTAATGGGG
65 TACTCAAGA-CGTTTTTAGC-CAAAAATGCCTTGAATAATCTTAAAAAAAATTTTAATTGGG
* *
20138900 TTATTAAAGGTATTTTTG
1 TTATTGAAGGCATTTTTG
20138918 ATAAAAAAAA
Statistics
Matches: 422, Mismatches: 77, Indels: 47
0.77 0.14 0.09
Matches are distributed among these distances:
122 2 0.00
124 14 0.03
125 140 0.33
126 162 0.38
127 12 0.03
128 77 0.18
129 2 0.00
130 11 0.03
132 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (124 bp):
TTATTGAAGGCATTTTTGGCCAAAAATACCTTCAATAATCCTTTATAAATTTTTATAACGTGATT
ACTCAAGACGTTTTTAGCCAAAAATGCCTTGAATAATCTTAAAAAAAATTTTAATTGGG
Found at i:20138636 original size:64 final size:63
Alignment explanation
Indices: 20138353--20138641 Score: 216
Period size: 64 Copynumber: 4.6 Consensus size: 63
20138343 GTGTTTTAGT
* * * *
20138353 CAAAAATGCTTTGAATAATCTTTAAAAAAAATTTTAATG-G-GATTATTGAAGGCATTTTTGAC
1 CAAAAATACCTTGAATAATC-TTAAAAAAAATTTTAATGTGTGATTACTCAAGGCATTTTTGAC
* * * * * * * * *
20138415 CAAAAATACTTTTAATAATCCATT-TATAAATTTTTACA-ATGTGATTACTCAAGACGTTTTTGG
1 CAAAAATACCTTGAATAAT-C-TTAAAAAAAATTTTA-ATGTGTGATTACTCAAGGCATTTTTGA
20138478 C
63 C
* * * * *
20138479 CAAAAATGCCTTGAATAATTCTAAAAAAAAATTTTAAT-TGTG-TTAGTGAAGGCATTTTTGGC
1 CAAAAATACCTTGAATAA-TCTTAAAAAAAATTTTAATGTGTGATTACTCAAGGCATTTTTGAC
* * * * * * *
20138541 CAAAAATACCTTCAATAATCCCTT--CATAAATTTTTATGACGTGATTACTCAAGGCTTTTTTCA
1 CAAAAATACCTTGAATAAT--CTTAAAAAAAATTTTAATG-TGTGATTACTCAAGGCATTTTTGA
20138604 C
63 C
*
20138605 CAAAAACACCTTGAATAATCTTAAAAAAAATTTTAAT
1 CAAAAATACCTTGAATAATCTTAAAAAAAATTTTAAT
20138642 AGGGTTATTG
Statistics
Matches: 173, Mismatches: 40, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
61 11 0.06
62 61 0.35
63 16 0.09
64 84 0.49
65 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (63 bp):
CAAAAATACCTTGAATAATCTTAAAAAAAATTTTAATGTGTGATTACTCAAGGCATTTTTGAC
Found at i:20138693 original size:125 final size:125
Alignment explanation
Indices: 20138265--20138917 Score: 489
Period size: 125 Copynumber: 5.2 Consensus size: 125
20138255 AATTTTCTTT
* * * * * * * *
20138265 TAGGATTATTTAAGGTATTTTTGGTCAAAAATGCCTTCAATAATTCTC-TTATAAAATTTTATAA
1 TAGGGTTATTGAAGGCATTTTTGGCCAAAAATACCTTCAATAA-TCCCATCATAAATTTTTATAA
* * * * *
20138329 CGTGATTACTCAATG-TGTTTTAGTCAAAAATGCTTTGAATAA-TCTTTAAAAAAAATTTTAA
65 CGTGATTACTCAAGGCTTTTTTA-CCAAAAACGCCTTGAATAATTC-TTAAAAAAAATTTTAA
* * * * *
20138390 T-GGGATTATTGAAGGCATTTTTGACCAAAAATACTTTTAATAAT-CCATTTATAAATTTTTACA
1 TAGGG-TTATTGAAGGCATTTTTGGCCAAAAATACCTTCAATAATCCCA-TCATAAATTTTTATA
* * ** * *
20138453 ATGTGATTACTCAAGACGTTTTTGGCCAAAAATGCCTTGAATAATTCTAAAAAAAAATTTTAA
64 ACGTGATTACTCAAGGC-TTTTTTACCAAAAACGCCTTGAATAATTCTTAAAAAAAATTTTAA
* * * * *
20138516 TTGTGTTAGTGAAGGCATTTTTGGCCAAAAATACCTTCAATAATCCCTTCATAAATTTTTATGAC
1 TAGGGTTATTGAAGGCATTTTTGGCCAAAAATACCTTCAATAATCCCATCATAAATTTTTATAAC
*
20138581 GTGATTACTCAAGGCTTTTTTCACCAAAAACACCTTGAATAA-TCTTAAAAAAAATTTTAA
66 GTGATTACTCAAGGCTTTTTT-ACCAAAAACGCCTTGAATAATTCTTAAAAAAAATTTTAA
* * * * * * *
20138641 TAGGGTTATTGAAGGTATTTTTAGTCAAAAACACATTTAATAATCCCATCATAAATTTCTT-TGA
1 TAGGGTTATTGAAGGCATTTTTGGCCAAAAATACCTTCAATAATCCCATCATAAATTT-TTATAA
** * ** * * * *
20138705 TATGATTACTTAAGGAATTTTTGCCAAAAAC-CTTTTGAGTAATTTTTTAAAAAAAAAATTTTAA
65 CGTGATTACTCAAGGCTTTTTTACCAAAAACGC-CTTGAATAA-TTCTT--AAAAAAAATTTTAA
* * * * ** * * *
20138769 TAGGGTTATTGAAAGCGTTTATGGCTAAAAATTTCTTCAATAATTCTC-TCATAAATTTCTATGA
1 TAGGGTTATTGAAGGCATTTTTGGCCAAAAATACCTTCAATAA-TCCCATCATAAATTTTTATAA
* * * * * * * * **
20138833 CATAATTACTTAAAGCATTTTTAGCAAAAAAATGCCTTAAATAA-TCCCAAAAAAAATTTTAA
65 CGTGATTACTCAAGGCTTTTTTA-C-CAAAAACGCCTTGAATAATTCTTAAAAAAAATTTTAA
* * *
20138895 TGGGGTTATTAAAGGTATTTTTG
1 TAGGGTTATTGAAGGCATTTTTG
20138918 ATAAAAAAAA
Statistics
Matches: 420, Mismatches: 88, Indels: 39
0.77 0.16 0.07
Matches are distributed among these distances:
123 2 0.00
124 18 0.04
125 148 0.35
126 148 0.35
127 11 0.03
128 77 0.18
129 4 0.01
130 11 0.03
131 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (125 bp):
TAGGGTTATTGAAGGCATTTTTGGCCAAAAATACCTTCAATAATCCCATCATAAATTTTTATAAC
GTGATTACTCAAGGCTTTTTTACCAAAAACGCCTTGAATAATTCTTAAAAAAAATTTTAA
Found at i:20138697 original size:251 final size:249
Alignment explanation
Indices: 20138276--20138918 Score: 640
Period size: 251 Copynumber: 2.5 Consensus size: 249
20138266 AGGATTATTT
* * * * *
20138276 AAGGTATTTTTGGTCAAAAATGCCTTCAATAATTCTCTT-ATAAAATTTTATAACGTGATTACTC
1 AAGGCATTTTTGGCCAAAAATACCTTCAATAA-TCTCTTCATAAATTTTTATGACGTGATTACTC
* * * ** *
20138340 AATG-TGTTTTAGTCAAAAATGCTTTGAATAATCTTTAAAAAAAATTTTAATGGGATTATTGAAG
65 AAAGCTTTTTTA-CCAAAAAAACCTTGAATAATC-TTAAAAAAAATTTTAATGGG-TTATTGAAG
* * * * *
20138404 GCATTTTTGACCAAAAATACTTTTAATAATCCATTTATAAATTT-TTACAATGTGATTACTCAA-
127 GTATTTTTGACCAAAAACACATTTAATAATCCATTCATAAATTTCTT-CAATATGATTACTCAAG
* * *
20138467 GACGTTTTTGGCCAAAAATGCC-TTGAATAA-TTCT-AAAAAAAAATTTTAATTGTGTTAGTG
191 GA-ATTTTT-GCCAAAAA--CCTTTGAATAATTTCTAAAAAAAAAATTTTAATAGGGTTAGTG
*
20138527 AAGGCATTTTTGGCCAAAAATACCTTCAATAATCCCTTCATAAATTTTTATGACGTGATTACTCA
1 AAGGCATTTTTGGCCAAAAATACCTTCAATAATCTCTTCATAAATTTTTATGACGTGATTACTCA
* *
20138592 AGGCTTTTTTCACCAAAAACACCTTGAATAATCTTAAAAAAAATTTTAATAGGGTTATTGAAGGT
66 AAGCTTTTTT-ACCAAAAAAACCTTGAATAATCTTAAAAAAAATTTTAAT-GGGTTATTGAAGGT
* ** *
20138657 ATTTTT-AGTCAAAAACACATTTAATAATCCCA-TCATAAATTTCTTTGATATGATTACTTAAGG
129 ATTTTTGA-CCAAAAACACATTTAATAAT-CCATTCATAAATTTCTTCAATATGATTACTCAAGG
* * *
20138720 AATTTTTGCCAAAAACCTTTTGAGTAATTTTTTAAAAAAAAAATTTTAATAGGGTTATTG
192 AATTTTTGCCAAAAACC-TTTGAATAA-TTTCTAAAAAAAAAATTTTAATAGGGTTAGTG
* * * * ** * * * *
20138780 AAAGCGTTTATGGCTAAAAATTTCTTCAATAAT-TCTCTCATAAATTTCTATGACATAATTACTT
1 AAGGCATTTTTGGCCAAAAATACCTTCAATAATCTCT-TCATAAATTTTTATGACGTGATTACTC
* * * ** *
20138844 AAAGCATTTTTAGCAAAAAAATGCCTTAAATAATCCCAAAAAAAATTTTAATGGGGTTATTAAAG
65 AAAGCTTTTTTACCAAAAAAA--CCTTGAATAATCTTAAAAAAAATTTTAAT-GGGTTATTGAAG
20138909 GTATTTTTGA
127 GTATTTTTGA
20138919 TAAAAAAAAT
Statistics
Matches: 328, Mismatches: 47, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
248 2 0.01
250 21 0.06
251 131 0.40
252 45 0.14
253 83 0.25
254 45 0.14
255 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (249 bp):
AAGGCATTTTTGGCCAAAAATACCTTCAATAATCTCTTCATAAATTTTTATGACGTGATTACTCA
AAGCTTTTTTACCAAAAAAACCTTGAATAATCTTAAAAAAAATTTTAATGGGTTATTGAAGGTAT
TTTTGACCAAAAACACATTTAATAATCCATTCATAAATTTCTTCAATATGATTACTCAAGGAATT
TTTGCCAAAAACCTTTGAATAATTTCTAAAAAAAAAATTTTAATAGGGTTAGTG
Found at i:20140543 original size:61 final size:62
Alignment explanation
Indices: 20140430--20140570 Score: 180
Period size: 61 Copynumber: 2.3 Consensus size: 62
20140420 TTTAAGACAT
** *
20140430 TAAATGCCTTCAATAATCCTTTAAAAAAAATTGAAGGAGATTATTGAAGGCATTTTTTA-CCA
1 TAAATGCCTTCAATAATCCTAAAAAAAAAATTAAAGGAGATTATTGAAGGCA-TTTTTAGCCA
* *
20140492 TAAATGCCTTGAATAATCC-AAAAAAAAAATTAAAATG-GATTATTGAAGGCATTTTTAGCCA
1 TAAATGCCTTCAATAATCCTAAAAAAAAAATT-AAAGGAGATTATTGAAGGCATTTTTAGCCA
* *
20140553 AAAACGCCTTCAATAATC
1 TAAATGCCTTCAATAATC
20140571 GCACTTTTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
60 6 0.09
61 42 0.61
62 21 0.30
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (62 bp):
TAAATGCCTTCAATAATCCTAAAAAAAAAATTAAAGGAGATTATTGAAGGCATTTTTAGCCA
Found at i:20142559 original size:3 final size:3
Alignment explanation
Indices: 20142551--20142589 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
20142541 TAATAAATTG
20142551 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20142590 CAATTGCCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20144018 original size:41 final size:38
Alignment explanation
Indices: 20143957--20144041 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 38
20143947 TCGAATGGGC
**
20143957 TTTTATTTTTATTTTCATTATTTAATATATATATTTTTATT
1 TTTTATTAATATTTTCATTATTT-ATATAT-T-TTTTTATT
* *
20143998 TTTTATTAATATTTTTATTATTTATCTATTTTTTTATT
1 TTTTATTAATATTTTCATTATTTATATATTTTTTTATT
*
20144036 ATTTAT
1 TTTTAT
20144042 CTATTTCTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 13 0.33
39 1 0.03
40 5 0.13
41 20 0.51
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (38 bp):
TTTTATTAATATTTTCATTATTTATATATTTTTTTATT
Found at i:20144021 original size:19 final size:20
Alignment explanation
Indices: 20143966--20144041 Score: 84
Period size: 19 Copynumber: 3.8 Consensus size: 20
20143956 CTTTTATTTT
*
20143966 TATTTTCATTATTTAATATATA
1 TATTTTTATTATTT-ATATA-A
*
20143988 TATTTTTATTTTTTAT-TAA
1 TATTTTTATTATTTATATAA
*
20144007 TATTTTTATTATTTATCT-A
1 TATTTTTATTATTTATATAA
*
20144026 TTTTTTTATTATTTAT
1 TATTTTTATTATTTAT
20144042 CTATTTCTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 32 0.65
20 3 0.06
21 2 0.04
22 12 0.24
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTTTTATTATTTATATAA
Found at i:20144042 original size:19 final size:19
Alignment explanation
Indices: 20143990--20144082 Score: 97
Period size: 19 Copynumber: 5.0 Consensus size: 19
20143980 AATATATATA
* *
20143990 TTTTTATTTTTTAT-TAATA
1 TTTTTATTATTTATCT-ATT
20144009 TTTTTATTATTTATCTATT
1 TTTTTATTATTTATCTATT
20144028 TTTTTATTATTTATCTA-T
1 TTTTTATTATTTATCTATT
*
20144046 TTCTT-TTATTTATCTAATT
1 TTTTTATTATTTATCT-ATT
20144065 TTTTT-TT-TGTTATCTATT
1 TTTTTATTAT-TTATCTATT
20144083 AATATATTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
17 10 0.15
18 10 0.15
19 45 0.68
20 1 0.02
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.73
Consensus pattern (19 bp):
TTTTTATTATTTATCTATT
Found at i:20144047 original size:36 final size:36
Alignment explanation
Indices: 20143959--20144109 Score: 107
Period size: 36 Copynumber: 4.1 Consensus size: 36
20143949 GAATGGGCTT
* *
20143959 TTATTT-T-TATTTTCATTATTTAATATATATATTTTTA
1 TTATTTATCTATTTTTATTATTT-ATCTAT-T-TTTTTA
* *
20143996 TTTTTTATTAATATTTTTATTATTTATCTATTTTTTTA
1 TTATTTA-T-CTATTTTTATTATTTATCTATTTTTTTA
20144034 TTATTTATCTATTTCTT-TTATTTATCTAATTTTTTT-
1 TTATTTATCTATTT-TTATTATTTATCT-ATTTTTTTA
** *
20144070 TT-TGTTATCTATTAATA-TATTTATCTTTTTATTTTGA
1 TTAT-TTATCTATTTTTATTATTTATCTATTT-TTTT-A
20144107 TTA
1 TTA
20144110 ATTTTTGGTT
Statistics
Matches: 94, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
34 3 0.03
35 15 0.16
36 26 0.28
37 18 0.19
38 12 0.13
39 2 0.02
40 5 0.05
41 13 0.14
ACGTcount: A:0.25, C:0.05, G:0.01, T:0.70
Consensus pattern (36 bp):
TTATTTATCTATTTTTATTATTTATCTATTTTTTTA
Found at i:20144442 original size:6 final size:6
Alignment explanation
Indices: 20144431--20144574 Score: 57
Period size: 6 Copynumber: 23.5 Consensus size: 6
20144421 TGTTCCCAAG
* *
20144431 TTTTAT TTTTA- -TTTAT TTTTAT ATTTATT TATTTAT TTATTAT TATTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T T-TTTAT TT-TTAT TTTTAT
* * ** * ** *
20144480 TATTAGA TTAGAT TTGT-T TAATAT TCTTTTAT TTTTAT CTTTA- TTTTATT
1 TTTTA-T TTTTAT TTTTAT TTTTAT T-TTT-AT TTTTAT TTTTAT TTTTA-T
* *
20144530 TTTTAT TTTTAT TTTCAC TTTTA- TTTTA- TTTTATT ATTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T -TTTTAT TTT
20144575 CTTTAAATAA
Statistics
Matches: 105, Mismatches: 19, Indels: 28
0.69 0.12 0.18
Matches are distributed among these distances:
4 4 0.04
5 17 0.16
6 52 0.50
7 20 0.19
8 12 0.11
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTAT
Found at i:20144447 original size:4 final size:4
Alignment explanation
Indices: 20144438--20144471 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
20144428 AAGTTTTATT
20144438 TTTA TTTA TTT- TTATA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TT
20144472 ATTATTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 2 0.07
4 24 0.86
5 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:20144527 original size:5 final size:5
Alignment explanation
Indices: 20144506--20144574 Score: 65
Period size: 5 Copynumber: 13.8 Consensus size: 5
20144496 TTTAATATTC
*
20144506 TTTTA TTTTTA TCTTTA TTTTA TTTT- TTAT- TTTTA TTTTCA CTTTTA
1 TTTTA -TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTT-A -TTTTA
20144553 TTTTA TTTTA --TTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTT
20144575 CTTTAAATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 30 0.55
6 12 0.22
7 4 0.07
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:20144534 original size:18 final size:16
Alignment explanation
Indices: 20144506--20144574 Score: 75
Period size: 18 Copynumber: 3.9 Consensus size: 16
20144496 TTTAATATTC
20144506 TTTTATTTTTATCTTTA
1 TTTTATTTTTAT-TTTA
20144523 TTTTATTTTTTATTTTTA
1 TTTTA-TTTTTA-TTTTA
*
20144541 TTTTCACTTTTATTTTA
1 TTTT-ATTTTTATTTTA
20144558 TTTTATTATTTTATTTT
1 TTTTA-T-TTTTATTTT
20144575 CTTTAAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.02
17 14 0.31
18 28 0.62
19 2 0.04
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTATTTTTATTTTA
Found at i:20144553 original size:30 final size:30
Alignment explanation
Indices: 20144501--20144575 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
20144491 ATTTGTTTAA
* *
20144501 TATTCTTTTATTTTTATCTTTATTTTATTT
1 TATTATTTTATTTTCATCTTTATTTTATTT
20144531 T-TTATTTTTATTTTCA-CTTTTATTTTATTT
1 TATTA-TTTTATTTTCATC-TTTATTTTATTT
20144561 TATTATTTTATTTTC
1 TATTATTTTATTTTC
20144576 TTTAAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
29 3 0.08
30 34 0.85
31 3 0.08
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (30 bp):
TATTATTTTATTTTCATCTTTATTTTATTT
Found at i:20144775 original size:59 final size:58
Alignment explanation
Indices: 20144674--20144903 Score: 295
Period size: 59 Copynumber: 3.9 Consensus size: 58
20144664 TAGGAAAAAT
* *
20144674 GAAATTAAAGTTTTCAAAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTT
1 GAAATTAAAGTTTTC-AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTC
* * *
20144733 AAAAATAAA-TTTTCAAAAAAGGTTTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTC
1 GAAATTAAAGTTTTCAAAAAA--TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTC
* * * *
20144792 GAAATTAAAGTTTCCAGAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTC
1 GAAATTAAAGTTTTCA-AAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTC
* *
20144851 GAAATTAAA-ATTTCTAAAAAATATTTTTGA-AAAAAGTTGAAAGTATTAATTTT
1 GAAATTAAAGTTTTC-AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTT
20144904 TCCTACACAA
Statistics
Matches: 149, Mismatches: 17, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
57 27 0.18
58 21 0.14
59 91 0.61
60 5 0.03
61 5 0.03
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (58 bp):
GAAATTAAAGTTTTCAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTC
Found at i:20146187 original size:26 final size:26
Alignment explanation
Indices: 20146157--20146209 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
20146147 CTAAAAGTAC
20146157 AAAAATGATAAAATAA-ATTAAAAAAAT
1 AAAAAT-A-AAAATAATATTAAAAAAAT
*
20146184 AAAAATAAAAATAATATTACAAAAAT
1 AAAAATAAAAATAATATTAAAAAAAT
20146210 TTATTTACGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 11 0.46
27 6 0.25
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (26 bp):
AAAAATAAAAATAATATTAAAAAAAT
Found at i:20146462 original size:3 final size:3
Alignment explanation
Indices: 20146454--20146505 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
20146444 ATTTGTCAAA
20146454 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20146502 ATT A
1 ATT A
20146506 CATCCTATCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:20147047 original size:24 final size:25
Alignment explanation
Indices: 20147019--20147076 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
20147009 TTAACATAAA
*
20147019 ATAAAATTAATCAC-ATATTAAATT
1 ATAAAATTAATCACGACATTAAATT
* * * *
20147043 ATAAAAATACTCTCGACATTAATTT
1 ATAAAATTAATCACGACATTAAATT
20147068 ATAAAATTA
1 ATAAAATTA
20147077 GGCATGTGGC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (25 bp):
ATAAAATTAATCACGACATTAAATT
Found at i:20149311 original size:11 final size:11
Alignment explanation
Indices: 20149295--20149336 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
20149285 AATTCCATAA
20149295 GAGATTTGTTT
1 GAGATTTGTTT
*
20149306 GAGATTTGTTA
1 GAGATTTGTTT
20149317 GAGATTTGTTT
1 GAGATTTGTTT
20149328 GAGATTTGT
1 GAGATTTGT
20149337 CAGATATTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:20149319 original size:22 final size:22
Alignment explanation
Indices: 20149294--20149336 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
20149284 AAATTCCATA
20149294 AGAGATTTGTTTGAGATTTGTT
1 AGAGATTTGTTTGAGATTTGTT
20149316 AGAGATTTGTTTGAGATTTGT
1 AGAGATTTGTTTGAGATTTGT
20149337 CAGATATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTGAGATTTGTT
Found at i:20149450 original size:52 final size:52
Alignment explanation
Indices: 20149362--20149516 Score: 152
Period size: 52 Copynumber: 3.0 Consensus size: 52
20149352 GGACAAAAAG
* * * * *
20149362 ACTTGCAAAAGAAGAATTCTAAGA-GAAAGAGAATTCTTAATAAGTAAGTTTG
1 ACTTACAAGAGAAGAATTCTAAAAGGAAAGAG-ATTCTTAATAAGCAAGTTTA
** * *
20149414 ACTTGTAAGAGAAGAATTTTAAAAGGAAATG-GATTCTTAATAGGCAAGTTTA
1 ACTTACAAGAGAAGAATTCTAAAAGGAAA-GAGATTCTTAATAAGCAAGTTTA
* * * **
20149466 ACTTACAGGAGAAGAATTCTAAGAGGAGAGAGATTCTTAATGGGCAAGTTT
1 ACTTACAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAAGCAAGTTT
20149517 GTATGGTTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
51 1 0.01
52 79 0.92
53 5 0.06
54 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.28
Consensus pattern (52 bp):
ACTTACAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAAGCAAGTTTA
Found at i:20156418 original size:5 final size:5
Alignment explanation
Indices: 20156408--20156432 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
20156398 CCTTTTTTTC
20156408 CCTTT CCTTT CCTTT CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT
20156433 ATAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CCTTT
Found at i:20157016 original size:56 final size:56
Alignment explanation
Indices: 20156955--20157067 Score: 183
Period size: 56 Copynumber: 2.0 Consensus size: 56
20156945 ATATGACATG
* *
20156955 AATCATGATCAATCTATTTAACAT-TAGTTCCATTAAAAAAATTAACAGAAAAATGA
1 AATCATGAACAATCTATTTAAC-TGAAGTTCCATTAAAAAAATTAACAGAAAAATGA
*
20157011 AATCATGAACAATCTATTTAACTGAAGTTCCATTAACAAAATTAACAGAAAAATGA
1 AATCATGAACAATCTATTTAACTGAAGTTCCATTAAAAAAATTAACAGAAAAATGA
20157067 A
1 A
20157068 GATTTTTCAC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
55 1 0.02
56 52 0.98
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.28
Consensus pattern (56 bp):
AATCATGAACAATCTATTTAACTGAAGTTCCATTAAAAAAATTAACAGAAAAATGA
Found at i:20178958 original size:2 final size:2
Alignment explanation
Indices: 20178945--20178988 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
20178935 TTGACACTTT
20178945 CA CA CA -A C- CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
20178985 CA CA
1 CA CA
20178989 GATATATACA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:20182466 original size:22 final size:23
Alignment explanation
Indices: 20182441--20182488 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
20182431 TTGGAAAGGG
*
20182441 AACTGATTTAGATGAG-CAACAA
1 AACTGATTTAGATGAGAAAACAA
* *
20182463 AACTGGTTTTGATGAGAAAACAA
1 AACTGATTTAGATGAGAAAACAA
20182486 AAC
1 AAC
20182489 AAAATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (23 bp):
AACTGATTTAGATGAGAAAACAA
Found at i:20184590 original size:12 final size:11
Alignment explanation
Indices: 20184562--20184595 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
20184552 TTTTAAAATT
20184562 TTAAAAATTAA
1 TTAAAAATTAA
*
20184573 TTAAAAATTTA
1 TTAAAAATTAA
20184584 TTAAAAA-TAA
1 TTAAAAATTAA
20184594 TT
1 TT
20184596 TATCTGTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAAAATTAA
Found at i:20185435 original size:41 final size:42
Alignment explanation
Indices: 20185364--20185453 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 42
20185354 TAACTTTATT
*
20185364 ATTAA-TTTTTAAAAATTATATAATAATATAATTATCTATAA
1 ATTAATTTTTTAAAAATTATATAATAATATAAATATCTATAA
* ** * *
20185405 ATTAATTTTTTAAAAA-TATATACTCTTATAAATATTTATAT
1 ATTAATTTTTTAAAAATTATATAATAATATAAATATCTATAA
20185446 ATT-ATTTT
1 ATTAATTTT
20185454 CATCTTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
40 5 0.12
41 27 0.64
42 10 0.24
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (42 bp):
ATTAATTTTTTAAAAATTATATAATAATATAAATATCTATAA
Found at i:20187553 original size:14 final size:15
Alignment explanation
Indices: 20187526--20187554 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20187516 TAATGCTTCA
20187526 AAACACTGAAAGACT
1 AAACACTGAAAGACT
20187541 AAACACT-AAAGACT
1 AAACACTGAAAGACT
20187555 CTAACCAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.21, G:0.10, T:0.14
Consensus pattern (15 bp):
AAACACTGAAAGACT
Found at i:20193796 original size:12 final size:12
Alignment explanation
Indices: 20193779--20193805 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20193769 TATTGCCTAT
20193779 AAAAAAAAAGAA
1 AAAAAAAAAGAA
20193791 AAAAAAAAAGAA
1 AAAAAAAAAGAA
20193803 AAA
1 AAA
20193806 GAGCGGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:20194089 original size:3 final size:3
Alignment explanation
Indices: 20194081--20194110 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
20194071 TCACTTTTTA
20194081 TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
20194111 TATATTGACG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:20195589 original size:16 final size:16
Alignment explanation
Indices: 20195546--20195597 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
20195536 ATAAATATGC
** *
20195546 ATATAAATATACATAC
1 ATATAAATATATGTAA
*
20195562 ATATATATATATGTAA
1 ATATAAATATATGTAA
*
20195578 ATATAAATATATGTAT
1 ATATAAATATATGTAA
20195594 ATAT
1 ATAT
20195598 GAATTTAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (16 bp):
ATATAAATATATGTAA
Found at i:20196229 original size:10 final size:9
Alignment explanation
Indices: 20196194--20196238 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
20196184 TTTTAATTTT
*
20196194 TTTTTATAA
1 TTTTTAAAA
*
20196203 TTTATAAAA
1 TTTTTAAAA
20196212 TTTGTTAAAA
1 TTT-TTAAAA
20196222 GTTTTTAAAA
1 -TTTTTAAAA
20196232 TTTTTAA
1 TTTTTAA
20196239 TTTGTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 17 0.55
10 11 0.35
11 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:20196702 original size:19 final size:18
Alignment explanation
Indices: 20196659--20196711 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
20196649 AGGTATAATA
20196659 TTTTAAAATTATAAA-ATT
1 TTTTAAAATTA-AAATATT
*
20196677 TGATTAAAATTAAAATTATT
1 T-TTTAAAATTAAAA-TATT
*
20196697 TTTTAAAATCAAAAT
1 TTTTAAAATTAAAAT
20196712 GATTCAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 5 0.17
19 20 0.69
20 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
TTTTAAAATTAAAATATT
Found at i:20199000 original size:13 final size:14
Alignment explanation
Indices: 20198979--20199007 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20198969 AAGTAAAAAA
20198979 AATTATTAAAATAT
1 AATTATTAAAATAT
20198993 AATT-TTAAAATAT
1 AATTATTAAAATAT
20199006 AA
1 AA
20199008 AAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTATTAAAATAT
Found at i:20199049 original size:24 final size:22
Alignment explanation
Indices: 20198986--20199058 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 22
20198976 AAAAATTATT
*
20198986 AAAATATAATTTTA-AAATATAA
1 AAAATATAATTTTAGATATA-AA
*
20199008 AAAATAAAAATTTTAGATATTAAA
1 AAAAT-ATAATTTTAGATA-TAAA
20199032 AAAATATAATTTTGAGATATAAA
1 AAAATATAATTTT-AGATATAAA
20199055 AAAA
1 AAAA
20199059 GACAAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 5 0.11
23 23 0.52
24 14 0.32
25 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
AAAATATAATTTTAGATATAAA
Found at i:20217909 original size:59 final size:59
Alignment explanation
Indices: 20217811--20217928 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
20217801 TTCAAACCAT
* * * *
20217811 TAATGACAACCCAATTGGAATGCCAATCCATTGACTAGTCATTGTTATGTATACTCTGC
1 TAATGACAACCCAATTGGAATGCCAATCCATCGACTAGTCATTATCATGGATACTCTGC
*
20217870 TAATGACAACCCAATTGGAATGCCAATCCATCGATTAGTCATTATCATGGATACTCTGC
1 TAATGACAACCCAATTGGAATGCCAATCCATCGACTAGTCATTATCATGGATACTCTGC
20217929 ATCCAAACTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (59 bp):
TAATGACAACCCAATTGGAATGCCAATCCATCGACTAGTCATTATCATGGATACTCTGC
Found at i:20219115 original size:25 final size:26
Alignment explanation
Indices: 20219082--20219132 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
20219072 AAAATTTTAA
20219082 ATTTAAATT-TTATAAATGAT-TATTT
1 ATTTAAATTATTATAAAT-ATATATTT
*
20219107 ATTTAAATTATTTTAAATATATATTT
1 ATTTAAATTATTATAAATATATATTT
20219133 TATAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
ATTTAAATTATTATAAATATATATTT
Found at i:20222382 original size:10 final size:10
Alignment explanation
Indices: 20222367--20222404 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
20222357 TAAATTTATA
20222367 TTCTAAATGT
1 TTCTAAATGT
*
20222377 TTCTAAAAGT
1 TTCTAAATGT
20222387 TTCTTAAA-GT
1 TTC-TAAATGT
20222397 TTCTAAAT
1 TTCTAAAT
20222405 TTTATTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 4 0.16
10 17 0.68
11 4 0.16
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (10 bp):
TTCTAAATGT
Found at i:20230695 original size:34 final size:33
Alignment explanation
Indices: 20230648--20230713 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
20230638 ATAATTAAAA
*
20230648 TACATATCGAATATACATATTTGATAATATTAT
1 TACATATCGAATATACATATTTGATAACATTAT
**
20230681 TACATTATCGAATATATTTATTTGATAACATTA
1 TACA-TATCGAATATACATATTTGATAACATTA
20230714 AGAATTTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 4 0.14
34 25 0.86
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (33 bp):
TACATATCGAATATACATATTTGATAACATTAT
Found at i:20234932 original size:14 final size:15
Alignment explanation
Indices: 20234913--20234945 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
20234903 ATTTTTTATA
*
20234913 AAAATTTAT-TTCTT
1 AAAATTTATATTCAT
20234927 AAAATTTATATTCAT
1 AAAATTTATATTCAT
20234942 AAAA
1 AAAA
20234946 AATGTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTTATATTCAT
Found at i:20239343 original size:51 final size:51
Alignment explanation
Indices: 20239270--20239381 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 51
20239260 ATATGCCTGG
** ** **
20239270 TTCTTATTCTTTGCATGCTAAGTTCCCACTTTGAATGCTTCAAAGT-TGTTA
1 TTCTTATTCTTTGCACACTAAGTTCCCACAGTGAATGCTTCAAA-TCTGAGA
* * *
20239321 TTCTTATTCTTTGCACATTAAGTTGCCACAGTGAGTGCTTCAAATCTGAGA
1 TTCTTATTCTTTGCACACTAAGTTCCCACAGTGAATGCTTCAAATCTGAGA
20239372 TTCTTATTCT
1 TTCTTATTCT
20239382 GTTCACTTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 1 0.02
51 50 0.98
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (51 bp):
TTCTTATTCTTTGCACACTAAGTTCCCACAGTGAATGCTTCAAATCTGAGA
Found at i:20252349 original size:14 final size:13
Alignment explanation
Indices: 20252319--20252347 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20252309 ATGCACGCTC
20252319 AAAA-CCTAAGAA
1 AAAAGCCTAAGAA
20252331 AAAAGCCTAAGAA
1 AAAAGCCTAAGAA
20252344 AAAA
1 AAAA
20252348 AGGATTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.69, C:0.14, G:0.10, T:0.07
Consensus pattern (13 bp):
AAAAGCCTAAGAA
Found at i:20256763 original size:3 final size:3
Alignment explanation
Indices: 20256755--20256780 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20256745 AAAAGGTCAA
20256755 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
20256781 GAACTTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20261375 original size:31 final size:29
Alignment explanation
Indices: 20261340--20261401 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 29
20261330 AAAAAAAACC
* *
20261340 AAATAGTAAGAAAATATTTGAGTAGATCAAG
1 AAATAGCAAGAAAACATTT--GTAGATCAAG
20261371 AAATAGCAAGAAAACATTTGTAGATCAAG
1 AAATAGCAAGAAAACATTTGTAGATCAAG
20261400 AA
1 AA
20261402 CAAACAACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.41
31 17 0.59
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.23
Consensus pattern (29 bp):
AAATAGCAAGAAAACATTTGTAGATCAAG
Found at i:20264704 original size:62 final size:62
Alignment explanation
Indices: 20264630--20264751 Score: 156
Period size: 62 Copynumber: 2.0 Consensus size: 62
20264620 TTGTATAAGG
* * * *
20264630 AAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTTTTGACAAAATTTT-TTTAAAAAAGA
1 AAAATTGATACTTCCAACTTTTCCCTAAAATATATTTTTT-AAAAAATTTTATTTAAAAAAGA
* * * *
20264692 AAAATTGGTACTTCCAACTTTTCCCTAAACTGTATTTTTTAAAAAATTTTATTTTAAAAA
1 AAAATTGATACTTCCAACTTTTCCCTAAAATATATTTTTTAAAAAATTTTATTTAAAAAA
20264752 TTTTACTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 9 0.18
62 42 0.82
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.44
Consensus pattern (62 bp):
AAAATTGATACTTCCAACTTTTCCCTAAAATATATTTTTTAAAAAATTTTATTTAAAAAAGA
Found at i:20264750 original size:14 final size:14
Alignment explanation
Indices: 20264728--20264835 Score: 60
Period size: 14 Copynumber: 7.4 Consensus size: 14
20264718 AAACTGTATT
20264728 TTTTAAAAAATTTTA
1 TTTT-AAAAATTTTA
20264743 TTTTAAAAATTTTA
1 TTTTAAAAATTTTA
* *
20264757 CTTTAAGAAAAATTGATA
1 -TTT--TAAAAATT-TTA
*
20264775 CTTTT--AACTTTT-
1 -TTTTAAAAATTTTA
* * *
20264787 CTTCAAAATATTTTT
1 TTTTAAAA-ATTTTA
*
20264802 TTTTGAAAATTTTA
1 TTTTAAAAATTTTA
*
20264816 TTTTAGAAATTTTA
1 TTTTAAAAATTTTA
20264830 TTTTAA
1 TTTTAA
20264836 GAAAAATTGA
Statistics
Matches: 70, Mismatches: 15, Indels: 17
0.69 0.15 0.17
Matches are distributed among these distances:
11 2 0.03
13 3 0.04
14 40 0.57
15 12 0.17
17 7 0.10
18 6 0.09
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.54
Consensus pattern (14 bp):
TTTTAAAAATTTTA
Found at i:20264819 original size:15 final size:14
Alignment explanation
Indices: 20264808--20264839 Score: 55
Period size: 14 Copynumber: 2.2 Consensus size: 14
20264798 TTTTTTTTGA
20264808 AAATTTTATTTTAG
1 AAATTTTATTTTAG
20264822 AAATTTTATTTTAAG
1 AAATTTTATTTT-AG
20264837 AAA
1 AAA
20264840 AATTGATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
AAATTTTATTTTAG
Found at i:20264874 original size:73 final size:72
Alignment explanation
Indices: 20264688--20264892 Score: 252
Period size: 73 Copynumber: 2.8 Consensus size: 72
20264678 TTTTTTAAAA
* * * * * * **
20264688 AAGAAAAATTGGTACTTCCAACTTTTCCCTAAACTGTATTTTTTAAAAAATTTTATTTTAAAAAT
1 AAGAAAAATTGATACTTTCAAC-TTTCTCTAAAATATTTTTTTTTGAAAATTTTATTTTAAAAAT
20264753 TTTACTTT
65 TTTACTTT
* *
20264761 AAGAAAAATTGATACTTTTAACTTT-TCTTCAAAATATTTTTTTTTGAAAATTTTATTTTAGAAA
1 AAGAAAAATTGATACTTTCAACTTTCTC-T-AAAATATTTTTTTTTGAAAATTTTATTTTAAAAA
*
20264825 TTTTATTTT
64 TTTTACTTT
20264834 AAGAAAAATTGATACTTTCAACTTTCTCTAAAATACTTTTTTTCTTG-AAATTTTATTTT
1 AAGAAAAATTGATACTTTCAACTTTCTCTAAAATA-TTTTTTT-TTGAAAATTTTATTTT
20264893 CAAGAAAAAT
Statistics
Matches: 115, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
71 1 0.01
72 10 0.09
73 99 0.86
74 5 0.04
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (72 bp):
AAGAAAAATTGATACTTTCAACTTTCTCTAAAATATTTTTTTTTGAAAATTTTATTTTAAAAATT
TTACTTT
Found at i:20265025 original size:60 final size:60
Alignment explanation
Indices: 20264822--20265011 Score: 250
Period size: 60 Copynumber: 3.2 Consensus size: 60
20264812 TTTATTTTAG
* *
20264822 AAATTTTATTTT-AAGAAAAATTGATACTTTCAAC-TTT-CTCTAAAATACTTTTTTTCTTG-
1 AAATTTTATTTTCAAGAAAAATTGATACTTTTAACTTTTCCTCTAAAA-A-TATTTTT-TTGA
*
20264881 AAATTTTATTTTCAAGAAAAATTTATACTTTTAACTTTTCC-CTAAAAATATTTTTTT-A
1 AAATTTTATTTTCAAGAAAAATTGATACTTTTAACTTTTCCTCTAAAAATATTTTTTTGA
*
20264939 AACCTTTTTATTTTCAAGAAAAATTGATACTTTTAACTTTTCCTC-AAAAATATTTTTTTGA
1 AA--ATTTTATTTTCAAGAAAAATTGATACTTTTAACTTTTCCTCTAAAAATATTTTTTTGA
20265000 AAATTTTATTTT
1 AAATTTTATTTT
20265012 AGGAAAATCA
Statistics
Matches: 117, Mismatches: 6, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
58 4 0.03
59 27 0.23
60 72 0.62
61 13 0.11
62 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (60 bp):
AAATTTTATTTTCAAGAAAAATTGATACTTTTAACTTTTCCTCTAAAAATATTTTTTTGA
Found at i:20265042 original size:14 final size:15
Alignment explanation
Indices: 20265025--20265062 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
20265015 AAAATCATTG
20265025 AAAAAAAAGAAT-AT
1 AAAAAAAAGAATAAT
*
20265039 AAAAATAAGAATAAT
1 AAAAAAAAGAATAAT
20265054 AAAATAAAA
1 AAAA-AAAA
20265063 AATTAAGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 11 0.55
15 6 0.30
16 3 0.15
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (15 bp):
AAAAAAAAGAATAAT
Found at i:20265111 original size:12 final size:12
Alignment explanation
Indices: 20265094--20265136 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 12
20265084 TTTAATTTAG
20265094 AAATAATAATAA
1 AAATAATAATAA
20265106 AAATAATAATAA
1 AAATAATAATAA
20265118 TAAATTAATTAATTAA
1 -AAA-TAA-TAA-TAA
20265134 AAA
1 AAA
20265137 AAACTTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.44
13 3 0.11
14 3 0.11
15 6 0.22
16 3 0.11
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATAATAATAA
Found at i:20265502 original size:21 final size:20
Alignment explanation
Indices: 20265462--20265501 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20265452 TTATTAATTT
*
20265462 CTGGGTTTTTCCATCGAAAA
1 CTGGGTTTTTCCACCGAAAA
20265482 CTGGGTTTTT-CACCAGAAAA
1 CTGGGTTTTTCCACC-GAAAA
20265502 ATCACTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (20 bp):
CTGGGTTTTTCCACCGAAAA
Found at i:20266162 original size:45 final size:44
Alignment explanation
Indices: 20266007--20266200 Score: 220
Period size: 44 Copynumber: 4.4 Consensus size: 44
20265997 ACAATTCTTG
* * * *
20266007 GAAAAA-AAACAAAGCTCCTCTAAACAAAAGTTCAACGACTTTT
1 GAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTT
* *
20266050 GAAAAATAAACAAAGCTCCTCTAAGCAGAGGCTTAACGACTTTT
1 GAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTT
*
20266094 GAAAAATAAACAAAGCTCTTCTAATCAGAGGCTCAACGAC-TTT
1 GAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTT
20266137 GAAAAACATAAACAAAGCTCCTCTAAAT-AGAGG--CAACAGAAC-TTT
1 G-AAAA-ATAAACAAAGCTCCTCT-AATCAGAGGCTCAAC-G-ACTTTT
*
20266182 GAGAAAATAAATAAAGCTC
1 GA-AAAATAAACAAAGCTC
20266201 ATATGAATAG
Statistics
Matches: 134, Mismatches: 10, Indels: 13
0.85 0.06 0.08
Matches are distributed among these distances:
43 14 0.10
44 87 0.65
45 30 0.22
46 3 0.02
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (44 bp):
GAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTT
Found at i:20266183 original size:88 final size:85
Alignment explanation
Indices: 20266007--20266280 Score: 270
Period size: 88 Copynumber: 3.1 Consensus size: 85
20265997 ACAATTCTTG
* * * *
20266007 GAAAAA-AAACAAAGCTCCTCTAAACAAAAGTTCAACGACTTTTGAAAAATAAACAAAGCTCCTC
1 GAAAAATAAACAAAGCTCATCTAATC-AGAGGTCAACGAC-TTTGAAAAATAAACAAAGCTCCTC
**
20266071 TAAGCAGAGGCTTAAC-G-ACTTTT
64 TAAATAGAGGC--AACAGAAC-TTT
*
20266094 GAAAAATAAACAAAGCTCTTCTAATCAGAGGCTCAACGACTTTGAAAAACATAAACAAAGCTCCT
1 GAAAAATAAACAAAGCTCATCTAATCAGAGG-TCAACGACTTTG-AAAA-ATAAACAAAGCTCCT
20266159 CTAAATAGAGGCAACAGAACTTT
63 CTAAATAGAGGCAACAGAACTTT
* * * *
20266182 GAGAAAATAAATAAAGCTCATATGAAT-AGAGG-CAACAGAACTTTGGAAAAATAAATAAATCTC
1 GA-AAAATAAACAAAGCTCATCT-AATCAGAGGTCAAC-G-ACTTT-GAAAAATAAACAAAGCTC
* *
20266245 CTATAAATTGAGGCAACAGAACTTT
61 CTCTAAATAGAGGCAACAGAACTTT
20266270 GGAAAAATAAA
1 -GAAAAATAAA
20266281 TTGCTCATTG
Statistics
Matches: 162, Mismatches: 13, Indels: 23
0.82 0.07 0.12
Matches are distributed among these distances:
87 20 0.12
88 78 0.48
89 60 0.37
90 4 0.02
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.21
Consensus pattern (85 bp):
GAAAAATAAACAAAGCTCATCTAATCAGAGGTCAACGACTTTGAAAAATAAACAAAGCTCCTCTA
AATAGAGGCAACAGAACTTT
Found at i:20266210 original size:44 final size:44
Alignment explanation
Indices: 20266047--20266281 Score: 200
Period size: 44 Copynumber: 5.3 Consensus size: 44
20266037 TTCAACGACT
* * **
20266047 TTTGA-AAAATAAACAAAGCTCCTCTAAGCAGAGGCTTAAC-G-AC
1 TTTGAGAAAATAAATAAAGCTCCTATAAATAGAGGC--AACAGAAC
* * *
20266090 TTTTGA-AAAATAAACAAAGCTCTTCT-AATCAGAGGCTCAAC-G-AC
1 -TTTGAGAAAATAAATAAAGCTCCTATAAAT-AGAGG--CAACAGAAC
* * *
20266134 TTTGAAAAACATAAACAAAGCTCCTCTAAATAGAGGCAACAGAAC
1 TTTGAGAAA-ATAAATAAAGCTCCTATAAATAGAGGCAACAGAAC
* *
20266179 TTTGAGAAAATAAATAAAGCTCATATGAATAGAGGCAACAGAAC
1 TTTGAGAAAATAAATAAAGCTCCTATAAATAGAGGCAACAGAAC
* *
20266223 TTTG-GAAAAATAAATAAATCTCCTATAAATTGAGGCAACAGAAC
1 TTTGAG-AAAATAAATAAAGCTCCTATAAATAGAGGCAACAGAAC
20266267 TTTG-GAAAAATAAAT
1 TTTGAG-AAAATAAAT
20266282 TGCTCATTGA
Statistics
Matches: 169, Mismatches: 13, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
43 11 0.07
44 123 0.73
45 31 0.18
46 4 0.02
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.23
Consensus pattern (44 bp):
TTTGAGAAAATAAATAAAGCTCCTATAAATAGAGGCAACAGAAC
Found at i:20267273 original size:8 final size:8
Alignment explanation
Indices: 20267262--20267301 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
20267252 TCTTTTTTCA
20267262 TTTTTATTT
1 TTTTTA-TT
20267271 TTTTTATT
1 TTTTTATT
*
20267279 TTTTCATT
1 TTTTTATT
20267287 TTTTTCATT
1 TTTTT-ATT
20267296 TTTTTA
1 TTTTTA
20267302 AGCATAGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 14 0.50
9 14 0.50
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTATT
Found at i:20267274 original size:9 final size:9
Alignment explanation
Indices: 20267249--20267300 Score: 58
Period size: 9 Copynumber: 6.1 Consensus size: 9
20267239 TCACTTTGAA
20267249 TCATCTTTTT
1 TCAT-TTTTT
20267259 TCA--TTTT
1 TCATTTTTT
20267266 T-ATTTTTT
1 TCATTTTTT
*
20267274 TTA-TTTTT
1 TCATTTTTT
20267282 TCATTTTTT
1 TCATTTTTT
20267291 TCATTTTTT
1 TCATTTTTT
20267300 T
1 T
20267301 AAGCATAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
6 1 0.03
7 5 0.14
8 12 0.32
9 16 0.43
10 3 0.08
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.79
Consensus pattern (9 bp):
TCATTTTTT
Found at i:20267282 original size:17 final size:17
Alignment explanation
Indices: 20267254--20267301 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
20267244 TTGAATCATC
20267254 TTTTTTCA--TTTTTAT
1 TTTTTTCATTTTTTTAT
* *
20267269 TTTTTTTATTTTTTCAT
1 TTTTTTCATTTTTTTAT
20267286 TTTTTTCATTTTTTTA
1 TTTTTTCATTTTTTTA
20267302 AGCATAGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 7 0.26
17 20 0.74
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTCATTTTTTTAT
Found at i:20271236 original size:62 final size:62
Alignment explanation
Indices: 20271167--20271288 Score: 158
Period size: 62 Copynumber: 2.0 Consensus size: 62
20271157 TTTTTTAAGA
* * *
20271167 AAAATTGATATTTTCAACTTTTCTTTAAAACGT-TTTTCTTGACAAAATTTT-TTTAAGAAAAG
1 AAAATTGATACTTCCAACTTTTCTTCAAAACGTATTTTCTTG--AAAATTTTATTTAAGAAAAG
* * *
20271229 AAAATTGATACTTCCAACTTTTCTTCAAAATGTATTTTTTTGAAAATTTTATTTTAGAAA
1 AAAATTGATACTTCCAACTTTTCTTCAAAACGTATTTTCTTGAAAATTTTATTTAAGAAA
20271289 TTTTGCTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
61 8 0.15
62 37 0.71
63 7 0.13
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (62 bp):
AAAATTGATACTTCCAACTTTTCTTCAAAACGTATTTTCTTGAAAATTTTATTTAAGAAAAG
Found at i:20271356 original size:15 final size:14
Alignment explanation
Indices: 20271345--20271376 Score: 55
Period size: 14 Copynumber: 2.2 Consensus size: 14
20271335 TTTTTTTTGA
20271345 AAATTTTATTTTAG
1 AAATTTTATTTTAG
20271359 AAATTTTATTTTAAG
1 AAATTTTATTTT-AG
20271374 AAA
1 AAA
20271377 AATTGATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
AAATTTTATTTTAG
Found at i:20271406 original size:58 final size:57
Alignment explanation
Indices: 20271344--20271603 Score: 346
Period size: 57 Copynumber: 4.5 Consensus size: 57
20271334 TTTTTTTTTG
*
20271344 AAAATTTTATTTTAGAAATTTTATTTT-AAGAAAAATTGATACTTTCAACTTTTCCTCA
1 AAAATATT-TTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCC-CA
*
20271402 AAAATATTTTTTAGAAGTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCCTA
1 AAAATATTTTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCC-A
*
20271460 AAAATATTTTTTA-AAACCTTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTCCCCCA
1 AAAATATTTTTTAGAAA---TTTTATTTTCAAGAAAAATTGATACTTTCAACTTT-TCCCA
* * * *
20271520 AAGATATTTTTTA-AAATTTTATTTTCAAGAAAAGTTGATACTTTTAACTTTTTCACA
1 AAAATATTTTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAAC-TTTTCCCA
*
20271577 AAAATATTTTTTTGAGAATTTTATTTT
1 AAAATATTTTTTAGA-AATTTTATTTT
20271604 AGAAAATCAT
Statistics
Matches: 182, Mismatches: 11, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
57 64 0.35
58 53 0.29
59 11 0.06
60 51 0.28
61 3 0.02
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.47
Consensus pattern (57 bp):
AAAATATTTTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCCA
Found at i:20271434 original size:73 final size:73
Alignment explanation
Indices: 20271229--20271427 Score: 303
Period size: 73 Copynumber: 2.8 Consensus size: 73
20271219 TTAAGAAAAG
* * * *
20271229 AAAATTGATACTTCCAACTTTTCTTCAAAATGTATTTTTTTGAAAATTTTATTTTAGAAATTTTG
1 AAAATTGATACTTTCAACTTTTCCTCAAAATATATTTTTTTGAAAATTTTATTTTAGAAATTTTA
20271294 CTTTAAGA
66 CTTTAAGA
* *
20271302 AAAATTGATACTTTCAACTTTTTCTCAAAATATTTTTTTTTGAAAATTTTATTTTAGAAATTTTA
1 AAAATTGATACTTTCAACTTTTCCTCAAAATATATTTTTTTGAAAATTTTATTTTAGAAATTTTA
*
20271367 TTTTAAGA
66 CTTTAAGA
* *
20271375 AAAATTGATACTTTCAACTTTTCCTCAAAA-ATATTTTTTAG-AAGTTTTATTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAATATATTTTTTTGAAAATTTTATTTT
20271428 CAAGAAAAAT
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
71 11 0.10
72 9 0.08
73 95 0.83
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.50
Consensus pattern (73 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAATATATTTTTTTGAAAATTTTATTTTAGAAATTTTA
CTTTAAGA
Found at i:20271558 original size:117 final size:117
Alignment explanation
Indices: 20271362--20271588 Score: 359
Period size: 117 Copynumber: 1.9 Consensus size: 117
20271352 ATTTTAGAAA
* * *
20271362 TTTTATTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAGTTTTATTT
1 TTTTATTTTAAGAAAAATTGATACTTTCAACTTTCCCCCAAAAATATTTTTTAGAAATTTTATTT
*
20271427 TCAAGAAAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTAAAACCT
66 TCAAGAAAAATTGATACTTTCAACTTTTTCAC-AAAAATATTTTTTAAAACCT
*
20271479 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTCCCCCAAAGATATTTTTTA-AAATTTTATT
1 TTTTATTTT-AAGAAAAATTGATACTTTCAACTTTCCCCCAAAAATATTTTTTAGAAATTTTATT
* *
20271543 TTCAAGAAAAGTTGATACTTTTAACTTTTTCACAAAAATATTTTTT
65 TTCAAGAAAAATTGATACTTTCAACTTTTTCACAAAAATATTTTTT
20271589 TGAGAATTTT
Statistics
Matches: 101, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
117 54 0.53
118 47 0.47
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (117 bp):
TTTTATTTTAAGAAAAATTGATACTTTCAACTTTCCCCCAAAAATATTTTTTAGAAATTTTATTT
TCAAGAAAAATTGATACTTTCAACTTTTTCACAAAAATATTTTTTAAAACCT
Found at i:20271608 original size:57 final size:56
Alignment explanation
Indices: 20271424--20271609 Score: 212
Period size: 60 Copynumber: 3.2 Consensus size: 56
20271414 AGAAGTTTTA
* *
20271424 TTTTCAAGAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTAAAACCTTTTTA
1 TTTT-AAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTAGAA---TTTTA
* * *
20271484 TTTTCAAGAAAAATTGATACTTTCAACTTTCCCCCAAAGATATTTTTTAAAATTTTA
1 TTTT-AAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTAGAATTTTA
* * * *
20271541 TTTTCAAGAAAAGTTGATACTTTTAACTTTTTCACAAAAATATTTTTTTGAGAATTTTA
1 TTTT-AAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTT-AGAATTTTA
20271600 TTTT-AGAAAA
1 TTTTAAGAAAA
20271610 TCATTGAAAA
Statistics
Matches: 114, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
57 47 0.41
58 6 0.05
59 12 0.11
60 49 0.43
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (56 bp):
TTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTAGAATTTTA
Found at i:20271644 original size:16 final size:15
Alignment explanation
Indices: 20271616--20271652 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
20271606 AAAATCATTG
20271616 AAAAAAAAGAAAAAT
1 AAAAAAAAGAAAAAT
*
20271631 AAAATAAAATAAAAAT
1 AAAA-AAAAGAAAAAT
20271647 AAAAAA
1 AAAAAA
20271653 TTAAGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (15 bp):
AAAAAAAAGAAAAAT
Found at i:20271691 original size:3 final size:3
Alignment explanation
Indices: 20271683--20271717 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
20271673 CTAATTTAGA
*
20271683 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20271718 ATAAAGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:20275017 original size:8 final size:8
Alignment explanation
Indices: 20274932--20275017 Score: 50
Period size: 8 Copynumber: 10.5 Consensus size: 8
20274922 ATAATAATAC
20274932 AAAAAATAT
1 AAAAAA-AT
20274941 AAAAAAACT
1 AAAAAAA-T
20274950 AAAAAAA-
1 AAAAAAAT
* * *
20274957 CAAGAAAG
1 AAAAAAAT
*
20274965 GAAAAAAT
1 AAAAAAAT
*
20274973 GAAAAAAT
1 AAAAAAAT
*
20274981 ATAAAATAT
1 A-AAAAAAT
20274990 AAACAAAA-
1 AAA-AAAAT
* *
20274998 AAATACAT
1 AAAAAAAT
20275006 AAAAAAAT
1 AAAAAAAT
20275014 AAAA
1 AAAA
20275018 CAAAAGCTAA
Statistics
Matches: 60, Mismatches: 12, Indels: 11
0.72 0.14 0.13
Matches are distributed among these distances:
7 7 0.12
8 29 0.48
9 24 0.40
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.13
Consensus pattern (8 bp):
AAAAAAAT
Found at i:20276024 original size:4 final size:4
Alignment explanation
Indices: 20276015--20276039 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
20276005 GTAAAAAAAT
20276015 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
20276040 AATATTTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:20276156 original size:13 final size:13
Alignment explanation
Indices: 20276140--20276164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20276130 CAAACTCTAA
20276140 AAAATAAAAAATT
1 AAAATAAAAAATT
20276153 AAAATAAAAAAT
1 AAAATAAAAAAT
20276165 AAACTTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAAAATT
Found at i:20281406 original size:11 final size:11
Alignment explanation
Indices: 20281374--20281408 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
20281364 TGAAATTGTC
*
20281374 AAAAAAAAAAA
1 AAAAAAAAAAG
20281385 AAAAAAAAAAG
1 AAAAAAAAAAG
*
20281396 AAAAATAAAAG
1 AAAAAAAAAAG
20281407 AA
1 AA
20281409 TGAAGCTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:20282374 original size:61 final size:61
Alignment explanation
Indices: 20282291--20282405 Score: 176
Period size: 61 Copynumber: 1.9 Consensus size: 61
20282281 TTTATAAAAG
* * * *
20282291 AGATATTTGCATTTCATGTGCATCATTTTAAGAAAAGACATTTGTATTTTATTTTAAGAAA
1 AGATATTTGCATATCATATGCATCATTTTAAGAAAAGACATTTGCATTTAATTTTAAGAAA
* *
20282352 AGATATTTGCCTATCATATGCATCATTTTAAGAAAAGATATTTGCATTTAATTT
1 AGATATTTGCATATCATATGCATCATTTTAAGAAAAGACATTTGCATTTAATTT
20282406 GCATCATCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (61 bp):
AGATATTTGCATATCATATGCATCATTTTAAGAAAAGACATTTGCATTTAATTTTAAGAAA
Found at i:20282409 original size:35 final size:35
Alignment explanation
Indices: 20282341--20282444 Score: 109
Period size: 35 Copynumber: 2.9 Consensus size: 35
20282331 TTTGTATTTT
* *
20282341 ATTTTAAGAAAAGATATTTGCCTATCATATGCATC
1 ATTTTAAGAAAAGATATTTGCATATAATATGCATC
* *
20282376 ATTTTAAGAAAAGATATTTGCATTTAATTTGCATC
1 ATTTTAAGAAAAGATATTTGCATATAATATGCATC
* * *
20282411 ATCATTTAAAGAGAAGACATTTGTATCATAATAT
1 AT--TTT-AAGAAAAGATATTTGCAT-ATAATAT
20282445 TGTTCACCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
35 33 0.59
37 3 0.05
38 15 0.27
39 5 0.09
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (35 bp):
ATTTTAAGAAAAGATATTTGCATATAATATGCATC
Found at i:20282792 original size:42 final size:40
Alignment explanation
Indices: 20282733--20282811 Score: 113
Period size: 42 Copynumber: 1.9 Consensus size: 40
20282723 AAAAAGTCAT
* * *
20282733 TTGCATTTTTTTGATGGTGATATCTAAGTATTAAGATTTGAA
1 TTGCATCTTCTTGATGGTGATATCCAAGT-TTAA-ATTTGAA
20282775 TTGCATCTTCTTGATGGTGATATCCAAGTTTAAATTT
1 TTGCATCTTCTTGATGGTGATATCCAAGTTTAAATTT
20282812 TAAATTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 4 0.12
41 4 0.12
42 26 0.76
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.47
Consensus pattern (40 bp):
TTGCATCTTCTTGATGGTGATATCCAAGTTTAAATTTGAA
Found at i:20283019 original size:48 final size:48
Alignment explanation
Indices: 20282918--20283019 Score: 109
Period size: 48 Copynumber: 2.1 Consensus size: 48
20282908 ATATCCGAAG
* * **
20282918 ACATTTGCATCTTCTTAGTGGTGATATCCAAGTTTAAATTTTGAATTT
1 ACATTTGCATCTTCTCAGTAGTGATATCCAAGTTTAAAGCTTGAATTT
* * *
20282966 GCATTTGCAT-TCTCTCAGTAGTGATATTCGAGTATTAAAGCTTGAA-TT
1 ACATTTGCATCT-TCTCAGTAGTGATATCCAAGT-TTAAAGCTTGAATTT
20283014 ACATTT
1 ACATTT
20283020 TCTCGATGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
47 1 0.02
48 33 0.75
49 10 0.23
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (48 bp):
ACATTTGCATCTTCTCAGTAGTGATATCCAAGTTTAAAGCTTGAATTT
Found at i:20283042 original size:147 final size:147
Alignment explanation
Indices: 20282778--20283336 Score: 703
Period size: 147 Copynumber: 3.8 Consensus size: 147
20282768 ATTTGAATTG
* * * *
20282778 CATCTTCTTGATGGTGATATCCAAGTTTAAATTTTAAATTTTCATTTGCATTCTCTCGGTGGTGA
1 CATCTTCTTGATGGTGATATCCAAGTTTAAAGTTTGAATTTGCATTTGCATTCTCTCGATGGTGA
* ** * * *
20282843 TATTCGAGTATTAAAGCATGAATTGTATTTTTTCGATGGTGATGTTCGAGTTTCCTTTGGTGGCA
66 TATTCGAGTATTAAAGCTTGAATTACATTTTCTCGATGGTGATATTCGAGTTTCCTTCGGTGGCA
* *
20282908 ATATCCGAAGACATTTG
131 ATATCCGAAGTCATTTA
* *
20282925 CATCTTCTT-AGTGGTGATATCCAAGTTTAAATTTTGAATTTGCATTTGCATTCTCTC-AGTAGT
1 CATCTTCTTGA-TGGTGATATCCAAGTTTAAAGTTTGAATTTGCATTTGCATTCTCTCGA-TGGT
* *
20282988 GATATTCGAGTATTAAAGCTTGAATTACATTTTCTCGATGGTGATATTTGAGTTTCCTTCAGTGG
64 GATATTCGAGTATTAAAGCTTGAATTACATTTTCTCGATGGTGATATTCGAGTTTCCTTCGGTGG
* *
20283053 CGATATCCGAAGTCATTCA
129 CAATATCCGAAGTCATTTA
* * * * *
20283072 TATCTTCTCGACGGTGATATCCGAGTTTAAAGTTTGAATTTACATTTGCATTCTCTCGATGGTGA
1 CATCTTCTTGATGGTGATATCCAAGTTTAAAGTTTGAATTTGCATTTGCATTCTCTCGATGGTGA
* * * ** * *
20283137 TA-TCAGAGTATTAAAGCTTAAATTATATTTTTTTTATGGTGATATTCGAGTTCCCTTGGGTGGC
66 TATTC-GAGTATTAAAGCTTGAATTACATTTTCTCGATGGTGATATTCGAGTTTCCTTCGGTGGC
*
20283201 AATATTCGAAGTCATTTA
130 AATATCCGAAGTCATTTA
* * * *
20283219 CATCTTCTCGGTGGTAATATTCAAGTTTAAAGTTTGAATTTGCATTTGCATTCTCTCGATGGTGA
1 CATCTTCTTGATGGTGATATCCAAGTTTAAAGTTTGAATTTGCATTTGCATTCTCTCGATGGTGA
* * * *
20283284 TATCCGAGTATTAAAGCTTGAATTACATATTCTCGGTGGTAATA-TCTGAGTTT
66 TATTCGAGTATTAAAGCTTGAATTACATTTTCTCGATGGTGATATTC-GAGTTT
20283337 AAAGTTTGAA
Statistics
Matches: 353, Mismatches: 52, Indels: 14
0.84 0.12 0.03
Matches are distributed among these distances:
146 5 0.01
147 345 0.98
148 3 0.01
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.41
Consensus pattern (147 bp):
CATCTTCTTGATGGTGATATCCAAGTTTAAAGTTTGAATTTGCATTTGCATTCTCTCGATGGTGA
TATTCGAGTATTAAAGCTTGAATTACATTTTCTCGATGGTGATATTCGAGTTTCCTTCGGTGGCA
ATATCCGAAGTCATTTA
Found at i:20283305 original size:49 final size:49
Alignment explanation
Indices: 20283224--20283397 Score: 179
Period size: 48 Copynumber: 3.7 Consensus size: 49
20283214 ATTTACATCT
* * * *
20283224 TCTCGGTGGTAATAT-TCAAGT-TTAAAGTTTGAATTTGCATTTGCATTC
1 TCTCGGTGGTGATATCT-GAGTATTAAAGCTTGAATTTACATTTGCATTC
* *
20283272 TCTCGATGGTGATATCCGAGTATTAAAGCTTGAA-TTACA--T--A-T-
1 TCTCGGTGGTGATATCTGAGTATTAAAGCTTGAATTTACATTTGCATTC
* *
20283314 TCTCGGTGGTAATATCTGAGT-TTAAAGTTTGAATTTACATTTGCATTC
1 TCTCGGTGGTGATATCTGAGTATTAAAGCTTGAATTTACATTTGCATTC
* *
20283362 TTTCGGTGGTGATATTTGAGTATTAAAGCTTGAATT
1 TCTCGGTGGTGATATCTGAGTATTAAAGCTTGAATT
20283398 GTATTTTTTC
Statistics
Matches: 102, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
41 11 0.11
42 23 0.23
43 1 0.01
44 2 0.02
46 2 0.02
47 1 0.01
48 38 0.37
49 24 0.24
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.42
Consensus pattern (49 bp):
TCTCGGTGGTGATATCTGAGTATTAAAGCTTGAATTTACATTTGCATTC
Found at i:20283308 original size:294 final size:294
Alignment explanation
Indices: 20282779--20283336 Score: 823
Period size: 294 Copynumber: 1.9 Consensus size: 294
20282769 TTTGAATTGC
* * * * *
20282779 ATCTTCTTGATGGTGATATCCAAGTTTAAATTTTAAATTTTCATTTGCATTCTCTCGGTGGTGAT
1 ATCTTCTCGACGGTGATATCCAAGTTTAAAGTTTAAATTTACATTTGCATTCTCTCGATGGTGAT
* * * * *
20282844 ATTCGAGTATTAAAGCATGAATTGTATTTTTTCGATGGTGATGTTCGAGTTTCCTTTGGTGGCAA
66 ATTCGAGTATTAAAGCATAAATTATATTTTTTCGATGGTGATATTCGAGTTCCCTTGGGTGGCAA
* * * *
20282909 TATCCGAAGACATTTGCATCTTCTTAGTGGTGATATCCAAGTTTAAATTTTGAATTTGCATTTGC
131 TATCCGAAGACATTTACATCTTCTCAGTGGTAATATCCAAGTTTAAAGTTTGAATTTGCATTTGC
* * * *
20282974 ATTCTCTCAGTAGTGATATTCGAGTATTAAAGCTTGAATTACATTTTCTCGATGGTGATATTTGA
196 ATTCTCTCAGTAGTGATATCCGAGTATTAAAGCTTGAATTACATATTCTCGATGGTAATATCTGA
20283039 GTTTCCTTCAGTGGCGATATCCGAAGTCATTCAT
261 GTTTCCTTCAGTGGCGATATCCGAAGTCATTCAT
* *
20283073 ATCTTCTCGACGGTGATATCCGAGTTTAAAGTTTGAATTTACATTTGCATTCTCTCGATGGTGAT
1 ATCTTCTCGACGGTGATATCCAAGTTTAAAGTTTAAATTTACATTTGCATTCTCTCGATGGTGAT
* **
20283138 A-TCAGAGTATTAAAGCTTAAATTATATTTTTTTTATGGTGATATTCGAGTTCCCTTGGGTGGCA
66 ATTC-GAGTATTAAAGCATAAATTATATTTTTTCGATGGTGATATTCGAGTTCCCTTGGGTGGCA
* * * *
20283202 ATATTCGAAGTCATTTACATCTTCTCGGTGGTAATATTCAAGTTTAAAGTTTGAATTTGCATTTG
130 ATATCCGAAGACATTTACATCTTCTCAGTGGTAATATCCAAGTTTAAAGTTTGAATTTGCATTTG
* *
20283267 CATTCTCTC-GATGGTGATATCCGAGTATTAAAGCTTGAATTACATATTCTCGGTGGTAATATCT
195 CATTCTCTCAG-TAGTGATATCCGAGTATTAAAGCTTGAATTACATATTCTCGATGGTAATATCT
20283331 GAGTTT
259 GAGTTT
20283337 AAAGTTTGAA
Statistics
Matches: 233, Mismatches: 29, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
293 3 0.01
294 230 0.99
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.41
Consensus pattern (294 bp):
ATCTTCTCGACGGTGATATCCAAGTTTAAAGTTTAAATTTACATTTGCATTCTCTCGATGGTGAT
ATTCGAGTATTAAAGCATAAATTATATTTTTTCGATGGTGATATTCGAGTTCCCTTGGGTGGCAA
TATCCGAAGACATTTACATCTTCTCAGTGGTAATATCCAAGTTTAAAGTTTGAATTTGCATTTGC
ATTCTCTCAGTAGTGATATCCGAGTATTAAAGCTTGAATTACATATTCTCGATGGTAATATCTGA
GTTTCCTTCAGTGGCGATATCCGAAGTCATTCAT
Found at i:20283329 original size:42 final size:44
Alignment explanation
Indices: 20283272--20283397 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 44
20283262 ATTTGCATTC
* *
20283272 TCTCGATGGTGATATCCGAGTATTAAAGCTTGAATTACA-T-AT
1 TCTCGGTGGTGATATCTGAGTATTAAAGCTTGAATTACATTCAT
* *
20283314 TCTCGGTGGTAATATCTGAGT-TTAAAGTTTGAATTTACATTTGCAT
1 TCTCGGTGGTGATATCTGAGTATTAAAGCTTGAA-TTACA-TT-CAT
*
20283360 TCTTTCGGTGGTGATATTTGAGTATTAAAGCTTGAATT
1 TC--TCGGTGGTGATATCTGAGTATTAAAGCTTGAATT
20283398 GTATTTTTTC
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
41 11 0.16
42 23 0.33
44 1 0.01
46 4 0.06
48 19 0.28
49 11 0.16
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (44 bp):
TCTCGGTGGTGATATCTGAGTATTAAAGCTTGAATTACATTCAT
Found at i:20283346 original size:41 final size:43
Alignment explanation
Indices: 20283214--20283353 Score: 115
Period size: 42 Copynumber: 3.2 Consensus size: 43
20283204 ATTCGAAGTC
* * * * *
20283214 ATTTACATCTTCTCGGTGGTAATATTCAAGT-TTAAAGTTTGA
1 ATTTACATATTCTCGATGGTAATATCCGAGTATTAAAGCTTGA
* *
20283256 ATTTGCATTTGCATTCTCTCGATGGTGATATCCGAGTATTAAAGCTTGA
1 ATTTACA--T--A-T-TCTCGATGGTAATATCCGAGTATTAAAGCTTGA
* * *
20283305 A-TTACATATTCTCGGTGGTAATATCTGAGT-TTAAAGTTTGA
1 ATTTACATATTCTCGATGGTAATATCCGAGTATTAAAGCTTGA
20283346 ATTTACAT
1 ATTTACAT
20283354 TTGCATTCTT
Statistics
Matches: 78, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
41 11 0.14
42 30 0.38
43 1 0.01
44 2 0.03
46 1 0.01
47 1 0.01
48 21 0.27
49 11 0.14
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (43 bp):
ATTTACATATTCTCGATGGTAATATCCGAGTATTAAAGCTTGA
Found at i:20283372 original size:90 final size:90
Alignment explanation
Indices: 20283216--20283397 Score: 285
Period size: 90 Copynumber: 2.0 Consensus size: 90
20283206 TCGAAGTCAT
* *
20283216 TTACATCTTCTCGGTGGTAATATTCAAGTTTAAAGTTTGAATTTGCATTTGCATTCTCTCGATGG
1 TTACATATTCTCGGTGGTAATATTCAAGTTTAAAGTTTGAATTTACATTTGCATTCTCTCGATGG
20283281 TGATATCCGAGTATTAAAGCTTGAA
66 TGATATCCGAGTATTAAAGCTTGAA
* * *
20283306 TTACATATTCTCGGTGGTAATA-TCTGAGTTTAAAGTTTGAATTTACATTTGCATTCTTTCGGTG
1 TTACATATTCTCGGTGGTAATATTC-AAGTTTAAAGTTTGAATTTACATTTGCATTCTCTCGATG
**
20283370 GTGATATTTGAGTATTAAAGCTTGAA
65 GTGATATCCGAGTATTAAAGCTTGAA
20283396 TT
1 TT
20283398 GTATTTTTTC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
89 2 0.02
90 82 0.98
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.42
Consensus pattern (90 bp):
TTACATATTCTCGGTGGTAATATTCAAGTTTAAAGTTTGAATTTACATTTGCATTCTCTCGATGG
TGATATCCGAGTATTAAAGCTTGAA
Found at i:20283391 original size:237 final size:236
Alignment explanation
Indices: 20283088--20283572 Score: 675
Period size: 237 Copynumber: 2.1 Consensus size: 236
20283078 CTCGACGGTG
20283088 ATATCCGAGTTTAAAGTTTGAATTTACATTTGCATTCTCTCGATGGTGATATCAGAGTATTAAAG
1 ATATCCGAGTTTAAAGTTTGAATTTACATTTGCATTCTCTCGATGGTGATATCAGAGTATTAAAG
** * * ** *
20283153 CTTAAATTATATTTTTTTTATGGTGATATTCGAG-TTCCCTTGGGTGGCAATATTCGAAGTCATT
66 CTTAAATTATATTTTTTCAATGATGATATTCGAGCTT-CATTCAGTGGCAATATCCGAAGTCATT
*
20283217 TACATCTTCTCGGTGGTAATATTCAAGTTTAAAGTTTGAATTTGCATTTGCATTCTCTCGATGGT
130 TACATCTTCTCGGTAGTAATATTCAAGTTTAAAGTTTGAATTTGCATTTGCATTCTCTCGATGGT
20283282 GATATCCGAGTATTAAAGCTTGAATTACATATTCTCGGTGGTA
195 GATAT-CGAGTATTAAAGCTTGAATTACATATTCTCGGTGGTA
* * * **
20283325 ATATCTGAGTTTAAAGTTTGAATTTACATTTGCATTCTTTCGGTGGTGATATTTGAGTATTAAAG
1 ATATCCGAGTTTAAAGTTTGAATTTACATTTGCATTCTCTCGATGGTGATATCAGAGTATTAAAG
* * *
20283390 CTTGAATTGTATTTTTTCAATGATGATATTCGAGCTTCATTCAGTGGCGATATCCGAAGTCATTT
66 CTTAAATTATATTTTTTCAATGATGATATTCGAGCTTCATTCAGTGGCAATATCCGAAGTCATTT
* * * * * *
20283455 GCATCTTTTCGGTAGTGATATTCGAGTTTAAAGTTTGAATTTGCATTTGCATTTTCTTGATGGTG
131 ACATCTTCTCGGTAGTAATATTCAAGTTTAAAGTTTGAATTTGCATTTGCATTCTCTCGATGGTG
* * * * * * *
20283520 ATATTGAGTATTAAAGTTTGAATTATATTTTTTCGATGGTG
196 ATATCGAGTATTAAAGCTTGAATTACATATTCTCGGTGGTA
*
20283561 ATATTCGAGTTT
1 ATATCCGAGTTT
20283573 CTTTTAGTGA
Statistics
Matches: 216, Mismatches: 31, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
236 40 0.19
237 174 0.81
238 2 0.01
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.43
Consensus pattern (236 bp):
ATATCCGAGTTTAAAGTTTGAATTTACATTTGCATTCTCTCGATGGTGATATCAGAGTATTAAAG
CTTAAATTATATTTTTTCAATGATGATATTCGAGCTTCATTCAGTGGCAATATCCGAAGTCATTT
ACATCTTCTCGGTAGTAATATTCAAGTTTAAAGTTTGAATTTGCATTTGCATTCTCTCGATGGTG
ATATCGAGTATTAAAGCTTGAATTACATATTCTCGGTGGTA
Found at i:20283619 original size:146 final size:148
Alignment explanation
Indices: 20283306--20283621 Score: 442
Period size: 146 Copynumber: 2.2 Consensus size: 148
20283296 AAAGCTTGAA
* *
20283306 TTACATATTCTCGGTGGTAATA-TCTGAGTTTAAAGTTTGAATTTACATTTGCATTCTTTCGGTG
1 TTACATATTCTCGGTGGTGATATTCTGAGTTTAAAGTTTGAATTTACATTTGCATTCTTTCGATG
*
20283370 GTGATATTTGAGTATTAAAGCTTGAATTGTATTTTTTCAATGATGATATTCGAGCTTCATTCAGT
66 GTGATATTTGAGTATTAAAGCTTGAATTATATTTTTTCAATGATGATATTCGAGCTTCATTCAGT
*
20283435 GGCGATATCCGAAGTCAT
131 GACGATATCCGAAGTCAT
* * * * * *
20283453 TTGCATCTTTTCGGTAGTGATATTC-GAGTTTAAAGTTTGAATTTGCATTTGCATT-TTCTTGAT
1 TTACATATTCTCGGTGGTGATATTCTGAGTTTAAAGTTTGAATTTACATTTGCATTCTT-TCGAT
* * * * * *
20283516 GGTGATA-TTGAGTATTAAAGTTTGAATTATATTTTTTCGATGGTGATATTCGAGTTTCTTTTAG
65 GGTGATATTTGAGTATTAAAGCTTGAATTATATTTTTTCAATGATGATATTCGAGCTTCATTCAG
20283580 TGACGATATCCGAAGTCAT
130 TGACGATATCCGAAGTCAT
*
20283599 TTACATATTCTCAGTGGTGATAT
1 TTACATATTCTCGGTGGTGATAT
20283622 CTAAGATTAT
Statistics
Matches: 146, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
146 88 0.60
147 56 0.38
148 2 0.01
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (148 bp):
TTACATATTCTCGGTGGTGATATTCTGAGTTTAAAGTTTGAATTTACATTTGCATTCTTTCGATG
GTGATATTTGAGTATTAAAGCTTGAATTATATTTTTTCAATGATGATATTCGAGCTTCATTCAGT
GACGATATCCGAAGTCAT
Found at i:20283765 original size:50 final size:49
Alignment explanation
Indices: 20283675--20283817 Score: 115
Period size: 50 Copynumber: 2.8 Consensus size: 49
20283665 TTAATGGTTT
* * * * ***
20283675 AATTTAAGGTTGTTGAGCCTCTGCTGAGAAGCGTTTTTTTTCAAGATAAG
1 AATTTAAAGTTGTTGAGCCTCTACTAAGAAGAGCCCTTTTT-AAGATAAG
* * *
20283725 AATTTAAAGTTGTTGAGCCTCTACTAAGAGGAGCCCTTTTTTAGATGAG
1 AATTTAAAGTTGTTGAGCCTCTACTAAGAAGAGCCCTTTTTAAGATAAG
* * * * *
20283774 AATTTTTTAAAGTTATTGAGCTTTTACTGAGAAGAGCCGTTTTT
1 AA---TTTAAAGTTGTTGAGCCTCTACTAAGAAGAGCCCTTTTT
20283818 TTATTTTAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
49 8 0.11
50 33 0.45
52 33 0.45
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (49 bp):
AATTTAAAGTTGTTGAGCCTCTACTAAGAAGAGCCCTTTTTAAGATAAG
Found at i:20284122 original size:15 final size:16
Alignment explanation
Indices: 20284104--20284140 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
20284094 ACAAGAAAGG
20284104 AAAAAAAATACA-AAC
1 AAAAAAAATACACAAC
*
20284119 AAAAAAAATATACAAC
1 AAAAAAAATACACAAC
20284135 AAAAAA
1 AAAAAA
20284141 TAAAAGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (16 bp):
AAAAAAAATACACAAC
Found at i:20284123 original size:16 final size:16
Alignment explanation
Indices: 20284104--20284140 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
20284094 ACAAGAAAGG
20284104 AAAAAAA-ATACAAACA
1 AAAAAAATATAC-AACA
20284120 AAAAAAATATACAACA
1 AAAAAAATATACAACA
20284136 AAAAA
1 AAAAA
20284141 TAAAAGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (16 bp):
AAAAAAATATACAACA
Found at i:20284124 original size:17 final size:16
Alignment explanation
Indices: 20284104--20284145 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
20284094 ACAAGAAAGG
20284104 AAAAAAAATACAAACAA
1 AAAAAAAATAC-AACAA
*
20284121 AAAAAATATACAACAA
1 AAAAAAAATACAACAA
20284137 AAAATAAAA
1 AAAA-AAAA
20284146 GCTAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAAAAATACAACAA
Found at i:20288722 original size:5 final size:5
Alignment explanation
Indices: 20288712--20288787 Score: 50
Period size: 5 Copynumber: 14.0 Consensus size: 5
20288702 TAAAAATTAG
20288712 TAAAA TAAAA T-AAA TAAAA -AAAA CTAAAAA TAAAA TCAAAATA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA -T-AAAA TAAAA T--AAA-A TAAAA
20288760 TGAATCAA -AAAA TAAAA TTAAAA TAAAA
1 T-AA--AA TAAAA TAAAA -TAAAA TAAAA
20288788 AAACCTGTGA
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
4 10 0.17
5 25 0.42
6 13 0.22
7 7 0.12
8 4 0.07
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:20288724 original size:27 final size:25
Alignment explanation
Indices: 20288694--20288760 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
20288684 ATAAAAGTCT
20288694 ATAAATAATAAAAATTAGTAAAATAAA
1 ATAAATAATAAAAATTA--AAAATAAA
* *
20288721 ATAAATAAAAAAAACTAAAAATAAA
1 ATAAATAATAAAAATTAAAAATAAA
*
20288746 ATCAA-AATATAAAAT
1 ATAAATAATA-AAAAT
20288761 GAATCAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
24 3 0.09
25 16 0.47
27 15 0.44
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.22
Consensus pattern (25 bp):
ATAAATAATAAAAATTAAAAATAAA
Found at i:20288733 original size:17 final size:18
Alignment explanation
Indices: 20288713--20288790 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 18
20288703 AAAAATTAGT
20288713 AAAATAAAAT-AAATAAAA
1 AAAATAAAATAAAAT-AAA
*
20288731 AAAACTAAAAATAAAATCAA
1 AAAA-T-AAAATAAAATAAA
* * *
20288751 AATATAAAAT-GAATCAA
1 AAAATAAAATAAAATAAA
20288768 AAAATAAAATTAAAATAAA
1 AAAATAAAA-TAAAATAAA
20288787 AAAA
1 AAAA
20288791 CCTGTGATTG
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
17 14 0.29
18 10 0.20
19 11 0.22
20 10 0.20
21 4 0.08
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.18
Consensus pattern (18 bp):
AAAATAAAATAAAATAAA
Found at i:20289243 original size:20 final size:20
Alignment explanation
Indices: 20289220--20289266 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
20289210 TAACCTTAAT
20289220 CCTAGAAAC-CCAAATCCAAA
1 CCTAGAAACTCCAAA-CCAAA
*
20289240 CCTAGAAACTTCAAACCAAA
1 CCTAGAAACTCCAAACCAAA
20289260 CCTAGAA
1 CCTAGAA
20289267 GTCTAAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.49, C:0.32, G:0.06, T:0.13
Consensus pattern (20 bp):
CCTAGAAACTCCAAACCAAA
Done.