Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 20 of 438
Found at i:5438315 original size:54 final size:55
Alignment explanation
Indices: 5438252--5438361 Score: 213
Period size: 54 Copynumber: 2.0 Consensus size: 55
5438242 GCATGCCCTG
5438252 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT-AAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAAA
5438306 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAAA
5438361 A
1 A
5438362 CAGAATTTGG
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 51 0.93
55 4 0.07
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (55 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAAA
Found at i:5438423 original size:142 final size:139
Alignment explanation
Indices: 5438167--5438430 Score: 392
Period size: 142 Copynumber: 1.9 Consensus size: 139
5438157 GCGTGTCCCG
5438167 AGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTGAAAACTAAATTAAAACAACAAGAATTGA
1 AGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTGAAAACTAAATTAAAACAACAAGAATTGA
*
5438232 AAATACCTTAGCATGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
66 AAATACCTTAGCATGCACTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
5438297 TAAATTAAA
131 TAAATTAAA
*
5438306 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT-GAA-AAC-AGAAT
1 AGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTG-AAAAC-TAAATTAAAACAACAAGAA-
* * *
5438368 TTGGAAATACC-TCGTCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
62 TTGAAAATACCTTAG-CATG-CACT-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
5438431 TTATTTTTTT
Statistics
Matches: 113, Mismatches: 5, Indels: 11
0.88 0.04 0.09
Matches are distributed among these distances:
139 18 0.16
140 42 0.37
141 9 0.08
142 44 0.39
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (139 bp):
AGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTGAAAACTAAATTAAAACAACAAGAATTGA
AAATACCTTAGCATGCACTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
TAAATTAAA
Found at i:5439359 original size:7 final size:7
Alignment explanation
Indices: 5439347--5439379 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
5439337 CCTTGATCCC
5439347 CTTTTTT
1 CTTTTTT
5439354 CTTTTTT
1 CTTTTTT
5439361 CTTTTTT
1 CTTTTTT
5439368 CTTGTTTT
1 CTT-TTTT
5439376 -TTTT
1 CTTTT
5439380 AGGATGCCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 2 0.08
7 19 0.76
8 4 0.16
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (7 bp):
CTTTTTT
Found at i:5450901 original size:2 final size:2
Alignment explanation
Indices: 5450894--5450928 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5450884 ATAAGTATTA
*
5450894 AT AT AT AT AT AT AT AT AT AT AT AT AC AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5450929 TTAAAATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5451488 original size:30 final size:30
Alignment explanation
Indices: 5451440--5451497 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 30
5451430 CTTCATAAAT
* *
5451440 ATATATACGTACTAAAAGTATACATAATAATA
1 ATATATACATAC-AAAAGTACAC-TAATAATA
5451472 ATATATACATAC-AAAGTACACTAATA
1 ATATATACATACAAAAGTACACTAATA
5451498 TTTAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 8 0.33
32 11 0.46
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.29
Consensus pattern (30 bp):
ATATATACATACAAAAGTACACTAATAATA
Found at i:5451544 original size:16 final size:16
Alignment explanation
Indices: 5451520--5451550 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5451510 AATAGTAAAC
*
5451520 ATAATATTAATATTAA
1 ATAAAATTAATATTAA
5451536 ATAAAATTAATATTA
1 ATAAAATTAATATTA
5451551 CAAATTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTAATATTAA
Found at i:5452626 original size:17 final size:18
Alignment explanation
Indices: 5452588--5452632 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
5452578 GGTTTACGTA
*
5452588 GGTTTGGGTAGTTAGTTG
1 GGTTTGGGTAGTTAGATG
5452606 GGTTTGGGTAGTTA-ATG
1 GGTTTGGGTAGTTAGATG
5452623 GGTTTTGGGT
1 GG-TTTGGGT
5452633 TATAATGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.11, C:0.00, G:0.44, T:0.44
Consensus pattern (18 bp):
GGTTTGGGTAGTTAGATG
Found at i:5456053 original size:19 final size:20
Alignment explanation
Indices: 5456023--5456060 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5456013 CAATTTGTAT
5456023 AATTTGTATATTAAAATTAG
1 AATTTGTATATTAAAATTAG
*
5456043 AATTT-TATATTCAAATTA
1 AATTTGTATATTAAAATTA
5456061 TCAAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
AATTTGTATATTAAAATTAG
Found at i:5456994 original size:19 final size:23
Alignment explanation
Indices: 5456953--5456996 Score: 67
Period size: 20 Copynumber: 2.0 Consensus size: 23
5456943 TTCTAACAGT
5456953 TTAATTAAATAAATCATTAAAAA
1 TTAATTAAATAAATCATTAAAAA
5456976 TTAA-TAAA-AAAT-ATTAAAAA
1 TTAATTAAATAAATCATTAAAAA
5456996 T
1 T
5456997 CTATTCAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 4 0.19
23 4 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
TTAATTAAATAAATCATTAAAAA
Found at i:5468022 original size:26 final size:26
Alignment explanation
Indices: 5467980--5468030 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5467970 ATTGAACTAT
*
5467980 TTTTTAATATTATTTTAATTCTTATA
1 TTTTTAATATTATTTTAATTATTATA
*
5468006 TTTTTATTA-TATATTTAATTATTAT
1 TTTTTAATATTAT-TTTAATTATTAT
5468031 TGTGCTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTTTAATATTATTTTAATTATTATA
Found at i:5472183 original size:15 final size:15
Alignment explanation
Indices: 5472163--5472200 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5472153 GTTTTCCAGA
5472163 GGAGTCAATGGTAGT
1 GGAGTCAATGGTAGT
*
5472178 GGAGTCAATTGTAGT
1 GGAGTCAATGGTAGT
*
5472193 GGACTCAA
1 GGAGTCAA
5472201 GGGGAGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (15 bp):
GGAGTCAATGGTAGT
Found at i:5475758 original size:54 final size:54
Alignment explanation
Indices: 5475676--5475783 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
5475666 AAAATATTAC
*
5475676 CTTAACCAGCCCAAAACAAGTTAGGTCAAGTGGAACACTTTACTTGTGAATAGA
1 CTTAACCAGCCCAAAACAAGTTAGGTCAAGTGGAACACTTTACTCGTGAATAGA
* *
5475730 CTTAATCAGCTCAAAACAAGTTAGGTCAAGTGGAACACTTTACTCGTGAATAGA
1 CTTAACCAGCCCAAAACAAGTTAGGTCAAGTGGAACACTTTACTCGTGAATAGA
5475784 TCTACTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (54 bp):
CTTAACCAGCCCAAAACAAGTTAGGTCAAGTGGAACACTTTACTCGTGAATAGA
Found at i:5477293 original size:10 final size:11
Alignment explanation
Indices: 5477240--5477290 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
5477230 CCTTCAAAAA
5477240 TCTATCAAATT
1 TCTATCAAATT
*
5477251 TC-ATTGAAATT
1 TCTA-TCAAATT
* *
5477262 T-TCTCAAAAT
1 TCTATCAAATT
5477272 TCTATCAAATT
1 TCTATCAAATT
5477283 TCTATCAA
1 TCTATCAA
5477291 TTTTATTTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
10 7 0.23
11 24 0.77
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (11 bp):
TCTATCAAATT
Found at i:5477492 original size:48 final size:46
Alignment explanation
Indices: 5477428--5477536 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 46
5477418 AGTGATAATT
5477428 TTAAATTTTCAATACTATTCAATATTTTCTTAATTTATGCAAATT-TAA
1 TTAAA-TTTCAATACTATTCAATATTTT-TTAATTTATGC-AATTATAA
** * *
5477476 TTAAATTTGCAATACTATTTGATGTTTTTTCATTTATGCAATTATAA
1 TTAAATTT-CAATACTATTCAATATTTTTTAATTTATGCAATTATAA
5477523 TTAAAATTTCAATA
1 TT-AAATTTCAATA
5477537 TTGCTTGATT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
46 4 0.07
47 23 0.43
48 27 0.50
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.50
Consensus pattern (46 bp):
TTAAATTTCAATACTATTCAATATTTTTTAATTTATGCAATTATAA
Found at i:5477527 original size:47 final size:46
Alignment explanation
Indices: 5477428--5477560 Score: 142
Period size: 47 Copynumber: 2.8 Consensus size: 46
5477418 AGTGATAATT
** *
5477428 TTAAATTTTCAATACTATTCAATATTTTCTTAATTTATGCAAATTTAA
1 TTAAA-TTTCAATACTATTTGATATTTT-TTCATTTATGCAAATTTAA
*
5477476 TTAAATTTGCAATACTATTTGATGTTTTTTCATTTATGC-AATTATAA
1 TTAAATTT-CAATACTATTTGATATTTTTTCATTTATGCAAATT-TAA
* ** *
5477523 TTAAAATTTCAATATTGCTTGATTTTTTTTCATTTATG
1 TT-AAATTTCAATACTATTTGATATTTTTTCATTTATG
5477561 ATGTTTGCAT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
46 4 0.05
47 43 0.58
48 27 0.36
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (46 bp):
TTAAATTTCAATACTATTTGATATTTTTTCATTTATGCAAATTTAA
Found at i:5478564 original size:7 final size:7
Alignment explanation
Indices: 5478554--5478578 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5478544 TTAGTATTTA
5478554 GTATTAT
1 GTATTAT
5478561 GTATTAT
1 GTATTAT
5478568 GTATTAT
1 GTATTAT
5478575 GTAT
1 GTAT
5478579 ATAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTAT
Found at i:5478564 original size:14 final size:15
Alignment explanation
Indices: 5478547--5478578 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5478537 TTCGTATTTA
5478547 GTATTTA-GTATTAT
1 GTATTTATGTATTAT
5478561 GTA-TTATGTATTAT
1 GTATTTATGTATTAT
5478575 GTAT
1 GTAT
5478579 ATAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.19
14 13 0.81
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (15 bp):
GTATTTATGTATTAT
Found at i:5482895 original size:7 final size:7
Alignment explanation
Indices: 5482863--5482894 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5482853 TTTTAGAACT
5482863 TTTAGGG
1 TTTAGGG
5482870 TTTAGGG
1 TTTAGGG
5482877 TTTAGGG
1 TTTAGGG
*
5482884 TTTAAGG
1 TTTAGGG
5482891 TTTA
1 TTTA
5482895 ACGTGAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:5483129 original size:126 final size:126
Alignment explanation
Indices: 5482895--5483231 Score: 455
Period size: 126 Copynumber: 2.7 Consensus size: 126
5482885 TTAAGGTTTA
* * * * *
5482895 ACGTGAAACCTTTTTTTAGAACTTTTGCCAACAGTGCATCCTGCTTAAAGCGTTTTTGACACTAT
1 ACGTGGAAGCTTTTTTCAGAACTTTTGCCGACAGTGCATCCTGCTTGAAGCGTTTTTGACACTAT
* *
5482960 TTGTTCAGAAACAT-TGACTCAGGCTCATTTTTCTACCAACTACTGCAGCAAAAGAGCGTCC
66 TTGTTCAGAAACGTCT-ACTCAGACTCATTTTTCTACCAACTACTGCAGCAAAAGAGCGTCC
* *
5483021 ACGTTGAAGCTTTTTTCAGAACTTTTGCCGACAGTGCATCCTGCTTGAAGCATTTTTGACACTAT
1 ACGTGGAAGCTTTTTTCAGAACTTTTGCCGACAGTGCATCCTGCTTGAAGCGTTTTTGACACTAT
* * * * *
5483086 CTGTTCAGAAACGTCTACTCAGATTTATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCC
66 TTGTTCAGAAACGTCTACTCAGACTCATTTTTCTACCAACTACTGCAGCAAAAGAGCGTCC
* * * * *
5483147 ACGTGGGAG-TTTTTTCCAGAAATTTT-CTGACACTGCATCCTGCTTGAAGCGTTTTCGACACTA
1 ACGTGGAAGCTTTTTT-CAGAACTTTTGCCGACAGTGCATCCTGCTTGAAGCGTTTTTGACACTA
*
5483210 TTTGTTCAGAAATGTCTACTCA
65 TTTGTTCAGAAACGTCTACTCA
5483232 AAATTATTCT
Statistics
Matches: 186, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
125 59 0.32
126 126 0.68
127 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (126 bp):
ACGTGGAAGCTTTTTTCAGAACTTTTGCCGACAGTGCATCCTGCTTGAAGCGTTTTTGACACTAT
TTGTTCAGAAACGTCTACTCAGACTCATTTTTCTACCAACTACTGCAGCAAAAGAGCGTCC
Found at i:5483922 original size:22 final size:23
Alignment explanation
Indices: 5483897--5483948 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
5483887 ACCCTAAAAA
*
5483897 CCTAAAACATAAAAACCA-TAAC
1 CCTAAAACATAAAAAACATTAAC
**
5483919 CCTAAATTATAAAAAACATTAAC
1 CCTAAAACATAAAAAACATTAAC
5483942 CCTAAAA
1 CCTAAAA
5483949 ACCCTAACGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (23 bp):
CCTAAAACATAAAAAACATTAAC
Found at i:5483941 original size:23 final size:22
Alignment explanation
Indices: 5483905--5483947 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
5483895 AACCTAAAAC
*
5483905 ATAAAAACCATAACCCTAAATT
1 ATAAAAAACATAACCCTAAATT
5483927 ATAAAAAACATTAACCCTAAA
1 ATAAAAAACA-TAACCCTAAA
5483948 AACCCTAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (22 bp):
ATAAAAAACATAACCCTAAATT
Found at i:5485032 original size:40 final size:39
Alignment explanation
Indices: 5484988--5485101 Score: 111
Period size: 39 Copynumber: 2.9 Consensus size: 39
5484978 TAGATAGAGA
*
5484988 ATTAGCGGCGCTTTTTAGAAAACGCCGCTAAAAAACAAAC
1 ATTAGCGGCG-TTTTTCGAAAACGCCGCTAAAAAACAAAC
* * * * * * *
5485028 ATTAGCGGTGTTTTCCGAAAATGCCACTAAAGATCAAGC
1 ATTAGCGGCGTTTTTCGAAAACGCCGCTAAAAAACAAAC
* * *
5485067 CTTAGCTGCGTTTTTCGAAAAGCGCCGCAAAAAAA
1 ATTAGCGGCGTTTTTCGAAAA-CGCCGCTAAAAAA
5485102 GTTGACTAAA
Statistics
Matches: 56, Mismatches: 17, Indels: 2
0.75 0.23 0.03
Matches are distributed among these distances:
39 39 0.70
40 17 0.30
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (39 bp):
ATTAGCGGCGTTTTTCGAAAACGCCGCTAAAAAACAAAC
Found at i:5485244 original size:40 final size:40
Alignment explanation
Indices: 5485133--5485270 Score: 127
Period size: 40 Copynumber: 3.5 Consensus size: 40
5485123 CTTTGTTGAG
* * * *
5485133 AAGATCGATCTTTAGCGGCGCTTTTTGAAAAACGCCGTTA
1 AAGATCGAGCATTAGCGGCGCCTTTTGAAAAACGCCGCTA
* * * * * *
5485173 AAAATCAAGCATTAGCGACG-CTTTCCGAAAAACACAGCTA
1 AAGATCGAGCATTAGCGGCGCCTTT-TGAAAAACGCCGCTA
* *
5485213 AAGATCGAGCATTAGCGGCGCCTTTTAAAAAATGCCGCTA
1 AAGATCGAGCATTAGCGGCGCCTTTTGAAAAACGCCGCTA
* *
5485253 AAGAT-TAGTATTAGCGGC
1 AAGATCGAGCATTAGCGGC
5485271 ATTTTTCAAA
Statistics
Matches: 76, Mismatches: 20, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
39 14 0.18
40 58 0.76
41 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (40 bp):
AAGATCGAGCATTAGCGGCGCCTTTTGAAAAACGCCGCTA
Found at i:5485444 original size:72 final size:73
Alignment explanation
Indices: 5485297--5485470 Score: 253
Period size: 72 Copynumber: 2.4 Consensus size: 73
5485287 CGCAAAAAAG
* * *
5485297 TTGAGCTTTAGTGGCATTAACGGCGCTTTTTAGAAAACGCCACAAAAAAGTTGACCAAAACGGCA
1 TTGAGCTTTAGTGGCATTAGCGGCGCTTTTTAAAAAACACCACAAAAAAGTTGACCAAAACGGCA
5485362 TCGTTTTA
66 TCGTTTTA
* ** *
5485370 TTGAGCTTTAGTGGCATTAGCGGTG-TTTTCTAAAAAACACCGTAAAAAA-TTGACCAAAATGGC
1 TTGAGCTTTAGTGGCATTAGCGGCGCTTTT-TAAAAAACACCACAAAAAAGTTGACCAAAACGGC
5485433 ATCGTTTTA
65 ATCGTTTTA
*
5485442 TTGAGCTTTAGTGGCATTAGCAGCGCTTT
1 TTGAGCTTTAGTGGCATTAGCGGCGCTTT
5485471 CGGAAAACAC
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
72 49 0.54
73 41 0.46
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (73 bp):
TTGAGCTTTAGTGGCATTAGCGGCGCTTTTTAAAAAACACCACAAAAAAGTTGACCAAAACGGCA
TCGTTTTA
Found at i:5485641 original size:14 final size:15
Alignment explanation
Indices: 5485624--5485663 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
5485614 TAGAGTTTTG
5485624 AGTTTATGGTTTA-T
1 AGTTTATGGTTTATT
*
5485638 AGTTTAGGGTTTATT
1 AGTTTATGGTTTATT
*
5485653 ATTTTATGGTT
1 AGTTTATGGTT
5485664 ATGGTCTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
AGTTTATGGTTTATT
Found at i:5487779 original size:131 final size:131
Alignment explanation
Indices: 5487619--5488091 Score: 449
Period size: 131 Copynumber: 3.6 Consensus size: 131
5487609 AAACCGAAAC
* *** * *
5487619 CCAGCAC-AGTAGGGCACGATTCCTCGAATTTTTAAACATCGAGTATTGCCTT-ATTTT-TAGAA
1 CCAGCACGA-TAGGGCACGATTCCCCGAATTGCCAAACATCGAGTATTACCTTCGTTTTATAGAA
* * *
5487681 TTTTTAAGAAACATGAGTGAAATTTTAAAGGGGATATTCTATTATTTTGAACCAATGGGAAATCG
65 TTTTTAAGAAACATGAGTGAAATTTCAAA-GGGATATTCTATTATTTTGAACAAACGGGAAATCG
5487746 CAA
129 CAA
** *
5487749 GCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATCACCTTCGTTTTATAGAA
1 -CCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAGTATTACCTTCGTTTTATAGAA
* * * * * * * *
5487814 TCTTTAA-AGACATGGGTGAAATTCCAAAAGAATATT-TGATTGTTTTGAACGAACGGGAAATCG
65 TTTTTAAGAAACATGAGTGAAATTTCAAAGGGATATTCT-ATTATTTTGAACAAACGGGAAATCG
5487877 CAA
129 CAA
* * *
5487880 CCTAGCACGATAGGGCACGATT-CCTGAATTGCCAAACATCGAGTATTACCTTCGTTTTAAAGAG
1 CC-AGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAGTATTACCTTCGTTTTATAGAA
* * * * * *
5487944 TTTTT-AGAAAACATGAATGAAATTTCAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTG
65 TTTTTAAG-AAACATGAGTGAAATTTCAAAGGGATATTCTATTATTTTGAACAAACGGGAAATCG
*
5488008 TAA
129 CAA
* *** * ** ** * *
5488011 CCCAGCACGTTAGGGCACGATTCTGAGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGGA
1 -CCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAGTATTACCTTCGTTTTATAGAA
5488076 TTTTT-AGAAAACATGA
65 TTTTTAAG-AAACATGA
5488092 ATGATTATAA
Statistics
Matches: 281, Mismatches: 51, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
129 1 0.00
130 43 0.15
131 154 0.55
132 72 0.26
133 11 0.04
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (131 bp):
CCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAGTATTACCTTCGTTTTATAGAAT
TTTTAAGAAACATGAGTGAAATTTCAAAGGGATATTCTATTATTTTGAACAAACGGGAAATCGCA
A
Found at i:5488087 original size:132 final size:129
Alignment explanation
Indices: 5487680--5488095 Score: 456
Period size: 131 Copynumber: 3.2 Consensus size: 129
5487670 TATTTTTAGA
* * * * *
5487680 ATTTTTAAGAAACATGAGTGAAATTTTAAAGGGGATATTCTATTATTTTGAACCAATGGGAAATC
1 ATTTTTAA-AAACATGAATGAAATTTCAAA-GGGATATTCGATTATTTTGAACAAACGGGAAATC
* * *
5487745 GCAAGCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATCACCTTCGTTTTAT
64 GCAACCCAGCACGATAGGGCACGATT--CTGAATTGCCAAACATCGAACATCACCTTCGTTTTAA
*
5487810 AGA
127 AGG
* * ** * * * * * *
5487813 ATCTTTAAAGACATGGGTGAAATTCCAAAAGAATATTTGATTGTTTTGAACGAACGGGAAATCGC
1 ATTTTTAAAAACATGAATGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACGGGAAATCGC
* ** *
5487878 AACCTAGCACGATAGGGCACGATTCCTGAATTGCCAAACATCGAGTATTACCTTCGTTTTAAA-G
66 AACCCAGCACGATAGGGCACGATT-CTGAATTGCCAAACATCGAACATCACCTTCGTTTTAAAGG
* * * *
5487942 AGTTTTTAGAAAACATGAATGAAATTTCAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATT
1 A-TTTTTA-AAAACATGAATGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACGGGAAATC
* * * *
5488007 GTAACCCAGCACGTTAGGGCACGATTCTGAGAATTGCCAAATATCGAACATCGCCTTCGTTTTAA
64 GCAACCCAGCACGATAGGGCACGATTCT--GAATTGCCAAACATCGAACATCACCTTCGTTTTAA
5488072 AGG
127 AGG
5488075 ATTTTTAGAAAACATGAATGA
1 ATTTTTA-AAAACATGAATGA
5488096 TTATAAAACT
Statistics
Matches: 236, Mismatches: 42, Indels: 11
0.82 0.15 0.04
Matches are distributed among these distances:
129 1 0.00
130 41 0.17
131 117 0.50
132 68 0.29
133 9 0.04
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (129 bp):
ATTTTTAAAAACATGAATGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACGGGAAATCGC
AACCCAGCACGATAGGGCACGATTCTGAATTGCCAAACATCGAACATCACCTTCGTTTTAAAGG
Found at i:5490756 original size:22 final size:21
Alignment explanation
Indices: 5490724--5490768 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
5490714 ATGGTATATA
*
5490724 TTTTTTGTTTTGTTTTTGTTGT
1 TTTTTTGTTTTGGTTTTG-TGT
*
5490746 TTTTTTTTTTTGGTTTTGTGT
1 TTTTTTGTTTTGGTTTTGTGT
5490767 TT
1 TT
5490769 GCACGGGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (21 bp):
TTTTTTGTTTTGGTTTTGTGT
Found at i:5494156 original size:21 final size:21
Alignment explanation
Indices: 5494118--5494170 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5494108 ACTTAGAGTG
*
5494118 GAGGCAGCAGAGAAGGAGGCA
1 GAGGCAGCAGCGAAGGAGGCA
* * * *
5494139 GCGGTAGCAGCGAGGGAGTCA
1 GAGGCAGCAGCGAAGGAGGCA
5494160 GAGGCAGCAGC
1 GAGGCAGCAGC
5494171 AATGGCAGCA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.19, G:0.47, T:0.04
Consensus pattern (21 bp):
GAGGCAGCAGCGAAGGAGGCA
Found at i:5496850 original size:31 final size:31
Alignment explanation
Indices: 5496780--5496865 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
5496770 TTAGATTTAA
* * *
5496780 TGTTTTTTGTTGTATTTTTTATGTTACATTTGC
1 TGTTTTTGGTTGTA--TTTAATGCTACATTTGC
* * *
5496813 TATTTTTGGTTGTATTTGATGCTATATTTGC
1 TGTTTTTGGTTGTATTTAATGCTACATTTGC
*
5496844 TGTTTTTGGTTGGATTTAATGC
1 TGTTTTTGGTTGTATTTAATGC
5496866 AGGAAGGGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
31 33 0.73
33 12 0.27
ACGTcount: A:0.14, C:0.06, G:0.20, T:0.60
Consensus pattern (31 bp):
TGTTTTTGGTTGTATTTAATGCTACATTTGC
Found at i:5497013 original size:45 final size:44
Alignment explanation
Indices: 5496946--5497099 Score: 129
Period size: 43 Copynumber: 3.5 Consensus size: 44
5496936 GTAGCGACGC
5496946 TTTTCTCAC--AAACGCCGCTAAAAGTCTTGATCTTTTGTGGTAT
1 TTTTCTCACATAAACGCCGCTAAAAGTCTTGATCTTTTGTGG-AT
* * * * * **
5496989 TTTTCTCATATAAACGCCGTTAAAAGCCATGA-CTTTTAGCGGCG
1 TTTTCTCACATAAACGCCGCTAAAAGTCTTGATCTTTT-GTGGAT
* * * *
5497033 CTTTC-CCCATAAACGCCGCTAAAAGTCTTGATATTTTGTGGCGT
1 TTTTCTCACATAAACGCCGCTAAAAGTCTTGATCTTTTGTGG-AT
* *
5497077 TTTTCTCAGATAAACACCG-TAAA
1 TTTTCTCACATAAACGCCGCTAAA
5497100 TTTTTACGAC
Statistics
Matches: 84, Mismatches: 21, Indels: 11
0.72 0.18 0.09
Matches are distributed among these distances:
43 32 0.38
44 21 0.25
45 31 0.37
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (44 bp):
TTTTCTCACATAAACGCCGCTAAAAGTCTTGATCTTTTGTGGAT
Found at i:5500128 original size:18 final size:19
Alignment explanation
Indices: 5500107--5500148 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
5500097 AAAAATTATA
5500107 TTTAATTCAAAAT-A-AAAT
1 TTTAATT-AAAATAATAAAT
5500125 TTTAATTAAAATAATAAAT
1 TTTAATTAAAATAATAAAT
5500144 TTTAA
1 TTTAA
5500149 AATTTAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.23
18 8 0.36
19 9 0.41
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAATTAAAATAATAAAT
Found at i:5500909 original size:137 final size:139
Alignment explanation
Indices: 5500756--5501033 Score: 461
Period size: 138 Copynumber: 2.0 Consensus size: 139
5500746 TTTCTGATTG
* *
5500756 TTTTAGGGTTAAGGTTTTAATAGTTTAAG-GTTTTAGAGTTTTTTAAGGGAGAAATTAATGAACA
1 TTTTAGGGTTAAGGTTTTAATAGTTTAAGAATTTTAGAGTTTTTTAAGGGAAAAATTAATGAACA
* * *
5500820 CTTAGAGTTGAGGGTTAATTAATTAAAATAACTATGAAGATAAGAAAAAATCAATTAAATTAGGG
66 CTTAGAGTTGAGGGTTAATTAATTAAAATAACTATGAAAATAAGAAAAAATAAATTAAACTAGGG
5500885 TTT-ATGGT
131 TTTAATGGT
* * *
5500893 TTTTAGGGTTAGGGTTTTAATGGTTTAAGAATTTTAGTGTTTTTTAAGGGAAAAATTAATGAACA
1 TTTTAGGGTTAAGGTTTTAATAGTTTAAGAATTTTAGAGTTTTTTAAGGGAAAAATTAATGAACA
*
5500958 CTTAGAGTTGAGGGTTAATTAATTAAATTAACTATGAAAATAAGAAAAAATAAATTAAACTAGGG
66 CTTAGAGTTGAGGGTTAATTAATTAAAATAACTATGAAAATAAGAAAAAATAAATTAAACTAGGG
5501023 TTTAATGGT
131 TTTAATGGT
5501032 TT
1 TT
5501034 AGGATTTAAT
Statistics
Matches: 130, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
137 27 0.21
138 96 0.74
139 7 0.05
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.38
Consensus pattern (139 bp):
TTTTAGGGTTAAGGTTTTAATAGTTTAAGAATTTTAGAGTTTTTTAAGGGAAAAATTAATGAACA
CTTAGAGTTGAGGGTTAATTAATTAAAATAACTATGAAAATAAGAAAAAATAAATTAAACTAGGG
TTTAATGGT
Found at i:5501056 original size:15 final size:15
Alignment explanation
Indices: 5501021--5501072 Score: 70
Period size: 15 Copynumber: 3.3 Consensus size: 15
5501011 ATTAAACTAG
5501021 GGTTTAATGGTTT-A
1 GGTTTAATGGTTTAA
5501035 GGATTTAATGGTTTAA
1 GG-TTTAATGGTTTAA
5501051 GGTTTATAGTGGTTTAA
1 GGTTTA-A-TGGTTTAA
5501068 GGTTT
1 GGTTT
5501073 TTTGGTGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.06
15 15 0.44
16 4 0.12
17 13 0.38
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (15 bp):
GGTTTAATGGTTTAA
Found at i:5501082 original size:18 final size:18
Alignment explanation
Indices: 5501038--5501092 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
5501028 TGGTTTAGGA
*
5501038 TTTAATGGTTTAAGG-TT
1 TTTAGTGGTTTAAGGTTT
*
5501055 TATAGTGGTTTAAGGTTT
1 TTTAGTGGTTTAAGGTTT
* *
5501073 TTTGGTGGTTTAGGGTTT
1 TTTAGTGGTTTAAGGTTT
5501091 TT
1 TT
5501093 AATGTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.55
Consensus pattern (18 bp):
TTTAGTGGTTTAAGGTTT
Found at i:5501091 original size:17 final size:17
Alignment explanation
Indices: 5501038--5501093 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
5501028 TGGTTTAGGA
* *
5501038 TTTAATGGTTTAAGGTT
1 TTTAGTGGTTTAGGGTT
* *
5501055 TATAGTGGTTTAAGGTTT
1 TTTAGTGGTTT-AGGGTT
*
5501073 TTTGGTGGTTTAGGGTT
1 TTTAGTGGTTTAGGGTT
5501090 TTTA
1 TTTA
5501094 ATGTTTTTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.54
Consensus pattern (17 bp):
TTTAGTGGTTTAGGGTT
Found at i:5501457 original size:127 final size:127
Alignment explanation
Indices: 5501223--5501533 Score: 511
Period size: 127 Copynumber: 2.5 Consensus size: 127
5501213 ATTAACTATT
* * *
5501223 AATTACGG-AAAAAAGC-TCTCATGTGGACGCTCTTTTACTACAGTGGTATCTAATAAAATAATT
1 AATTTCGGAAAAAAAGCTTC-CACGTGGACGCTCTTTTACTACAGTGGTATCTGATAAAATAATT
* *
5501286 TTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTTTTAGCAA
65 TTGAGAAGATATTTCTAAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTTTCAGCAA
5501349 AATTTCGGAAAAAAAGCTTCCACGTGGACGCTCTTTTACTACAGTGGTATCTGATAAAATAATTT
1 AATTTCGGAAAAAAAGCTTCCACGTGGACGCTCTTTTACTACAGTGGTATCTGATAAAATAATTT
5501414 TGAGAAGATATTTCTAAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTTTCAGCAA
66 TGAGAAGATATTTCTAAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTTTCAGCAA
* * * *
5501476 AATTTTGGAAAAAAAGCTTCCACGTAGACACTCTTTTGCTACAGTGGTATCTGA-AAAA
1 AATTTCGGAAAAAAAGCTTCCACGTGGACGCTCTTTTACTACAGTGGTATCTGATAAAA
5501534 GCCTTAGACT
Statistics
Matches: 174, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
126 11 0.06
127 161 0.93
128 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (127 bp):
AATTTCGGAAAAAAAGCTTCCACGTGGACGCTCTTTTACTACAGTGGTATCTGATAAAATAATTT
TGAGAAGATATTTCTAAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTTTCAGCAA
Found at i:5503560 original size:7 final size:7
Alignment explanation
Indices: 5503548--5503632 Score: 152
Period size: 7 Copynumber: 12.0 Consensus size: 7
5503538 TTATATAGGT
5503548 AATACTA
1 AATACTA
5503555 AATACTA
1 AATACTA
5503562 AATACTA
1 AATACTA
5503569 AATACTA
1 AATACTA
5503576 AATACTA
1 AATACTA
5503583 AATACTA
1 AATACTA
5503590 AATACTA
1 AATACTA
5503597 AATACTA
1 AATACTA
5503604 AATACTA
1 AATACTA
5503611 AATACTA
1 AATACTA
*
5503618 AATACGA
1 AATACTA
5503625 AACTACTA
1 AA-TACTA
5503633 TTTTATTATG
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
7 71 0.95
8 4 0.05
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:5504800 original size:20 final size:21
Alignment explanation
Indices: 5504771--5504820 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
5504761 ACACAAATTT
*
5504771 TTTG-CAAAAATT-AGAGAAC
1 TTTGACAAAAATTGAGAGAAA
5504790 TTTGACAAAAATTGAGAGAAA
1 TTTGACAAAAATTGAGAGAAA
*
5504811 TTTGAGAAAA
1 TTTGACAAAA
5504821 TTTGGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 4 0.15
20 8 0.30
21 15 0.56
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (21 bp):
TTTGACAAAAATTGAGAGAAA
Found at i:5506133 original size:174 final size:174
Alignment explanation
Indices: 5505843--5506188 Score: 692
Period size: 174 Copynumber: 2.0 Consensus size: 174
5505833 GGAGAATAAT
5505843 AGACCATTTGGGACTTAGCCTTTTGTACATTAATGATGCGGTGGGTCTATTGAGACTTTTCAAAA
1 AGACCATTTGGGACTTAGCCTTTTGTACATTAATGATGCGGTGGGTCTATTGAGACTTTTCAAAA
5505908 TATTTTATTGGTTAATCGGTGTTCATTGTTAGGTTAATTTGATGATAACTACGTTAGGACACAAA
66 TATTTTATTGGTTAATCGGTGTTCATTGTTAGGTTAATTTGATGATAACTACGTTAGGACACAAA
5505973 ATTCAACGGTTTTATCAAGTTCAAATATTTATGGTTTTTTTTGA
131 ATTCAACGGTTTTATCAAGTTCAAATATTTATGGTTTTTTTTGA
5506017 AGACCATTTGGGACTTAGCCTTTTGTACATTAATGATGCGGTGGGTCTATTGAGACTTTTCAAAA
1 AGACCATTTGGGACTTAGCCTTTTGTACATTAATGATGCGGTGGGTCTATTGAGACTTTTCAAAA
5506082 TATTTTATTGGTTAATCGGTGTTCATTGTTAGGTTAATTTGATGATAACTACGTTAGGACACAAA
66 TATTTTATTGGTTAATCGGTGTTCATTGTTAGGTTAATTTGATGATAACTACGTTAGGACACAAA
5506147 ATTCAACGGTTTTATCAAGTTCAAATATTTATGGTTTTTTTT
131 ATTCAACGGTTTTATCAAGTTCAAATATTTATGGTTTTTTTT
5506189 TGAATTATTC
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 172 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (174 bp):
AGACCATTTGGGACTTAGCCTTTTGTACATTAATGATGCGGTGGGTCTATTGAGACTTTTCAAAA
TATTTTATTGGTTAATCGGTGTTCATTGTTAGGTTAATTTGATGATAACTACGTTAGGACACAAA
ATTCAACGGTTTTATCAAGTTCAAATATTTATGGTTTTTTTTGA
Found at i:5510900 original size:25 final size:24
Alignment explanation
Indices: 5510839--5510900 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 24
5510829 AAGCAGTAAG
**
5510839 AAACTTGAGCTTGAGCTCAACTCA
1 AAACTTGAGCTTGAGCTCAAAGCA
* *
5510863 AAATTTGAGGCTTGAGACTCAAAGCT
1 AAACTTGA-GCTTGAG-CTCAAAGCA
*
5510889 AGACTTGAGCTT
1 AAACTTGAGCTT
5510901 AATGGAGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 7 0.23
25 11 0.37
26 12 0.40
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (24 bp):
AAACTTGAGCTTGAGCTCAAAGCA
Found at i:5516171 original size:10 final size:11
Alignment explanation
Indices: 5516142--5516171 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5516132 AATGTTTTTT
5516142 AATAAATTTAA
1 AATAAATTTAA
5516153 AATAAATTTAA
1 AATAAATTTAA
5516164 AA-AAATTT
1 AATAAATTT
5516172 TGAACTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATAAATTTAA
Found at i:5519505 original size:23 final size:23
Alignment explanation
Indices: 5519476--5519521 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5519466 TAGAGTCACT
5519476 AAACTAAATTTTATGGTATGATA
1 AAACTAAATTTTATGGTATGATA
5519499 AAACTAAATTTTATGGTATGATA
1 AAACTAAATTTTATGGTATGATA
5519522 CATGGGGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (23 bp):
AAACTAAATTTTATGGTATGATA
Found at i:5521388 original size:26 final size:27
Alignment explanation
Indices: 5521344--5521415 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 27
5521334 TTATTAATTT
5521344 TTTTATAATTAAT-TATTAAAT-TATTA
1 TTTTATAATTAATAT-TTAAATATATTA
5521370 TTTTAT-ATTAATATGTT-AATATATTA
1 TTTTATAATTAATAT-TTAAATATATTA
5521396 -TTTATAATTAA-ATTTAAATA
1 TTTTATAATTAATATTTAAATA
5521416 AAAATATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
24 2 0.05
25 20 0.49
26 19 0.46
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (27 bp):
TTTTATAATTAATATTTAAATATATTA
Found at i:5522054 original size:20 final size:20
Alignment explanation
Indices: 5522029--5522069 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5522019 TTATGGGTTT
5522029 ACTTTTGATAAACATATTTA
1 ACTTTTGATAAACATATTTA
* *
5522049 ACTTTTGGTAAACATTTTTA
1 ACTTTTGATAAACATATTTA
5522069 A
1 A
5522070 TAGGGTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (20 bp):
ACTTTTGATAAACATATTTA
Found at i:5522567 original size:30 final size:30
Alignment explanation
Indices: 5522533--5522595 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
5522523 ACTTATTTTA
5522533 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
5522563 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
5522593 TTG
1 TTG
5522596 CTTGTTTGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:5528467 original size:44 final size:44
Alignment explanation
Indices: 5528410--5528533 Score: 194
Period size: 44 Copynumber: 2.8 Consensus size: 44
5528400 CGGTAATTAT
* * *
5528410 AATACAATACACTTAATCACCAAAAGTCAACAAATGATGATTCC
1 AATACAATGCACTTAGTCACCAAAAGTCAGCAAATGATGATTCC
* *
5528454 AATACAGTGCACTTAGTCACCAAAAGTCAGCAAATGATGATTTC
1 AATACAATGCACTTAGTCACCAAAAGTCAGCAAATGATGATTCC
*
5528498 AATACAATGCGCTTAGTCACCAAAAGTCAGCAAATG
1 AATACAATGCACTTAGTCACCAAAAGTCAGCAAATG
5528534 GTTATGTGCA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 73 1.00
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.23
Consensus pattern (44 bp):
AATACAATGCACTTAGTCACCAAAAGTCAGCAAATGATGATTCC
Found at i:5533882 original size:16 final size:15
Alignment explanation
Indices: 5533855--5533884 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5533845 ATTTGTAAAA
5533855 TTTTAATAATTTATT
1 TTTTAATAATTTATT
5533870 TTTTAATTAATTTAT
1 TTTTAA-TAATTTAT
5533885 AAATTAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTAATAATTTATT
Found at i:5534701 original size:28 final size:28
Alignment explanation
Indices: 5534670--5534726 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
5534660 GGGAAAAAAG
5534670 AAAGAAAGAATAGTTTGATTTCTTCACC
1 AAAGAAAGAATAGTTTGATTTCTTCACC
*
5534698 AAAGAAAGAATAGTTTGCTTTCTTCACC
1 AAAGAAAGAATAGTTTGATTTCTTCACC
5534726 A
1 A
5534727 TTCATTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (28 bp):
AAAGAAAGAATAGTTTGATTTCTTCACC
Found at i:5542016 original size:52 final size:52
Alignment explanation
Indices: 5541933--5542033 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
5541923 GTATCGATAA
*
5541933 ATACTATATACAAGTCATTAACTGAGATAGTGTTAGTGAGCACTAACTCTAT
1 ATACTATATACAAGTCATTAACTGAGATAGTGTTAGTGAGAACTAACTCTAT
* * * *
5541985 ATACTCTATATAAGTCATTGACTGAGCTAGTGTTAGTGAGAACTAACTC
1 ATACTATATACAAGTCATTAACTGAGATAGTGTTAGTGAGAACTAACTC
5542034 AGTTGGTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (52 bp):
ATACTATATACAAGTCATTAACTGAGATAGTGTTAGTGAGAACTAACTCTAT
Found at i:5542835 original size:14 final size:16
Alignment explanation
Indices: 5542816--5542853 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
5542806 AAATGAAGTA
5542816 CTAAATTTT-T-ACTG
1 CTAAATTTTATAACTG
*
5542830 CTAAATTTTATAAGTG
1 CTAAATTTTATAACTG
5542846 CTAAATTT
1 CTAAATTT
5542854 ATATTAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 11 0.52
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (16 bp):
CTAAATTTTATAACTG
Found at i:5542849 original size:16 final size:15
Alignment explanation
Indices: 5542811--5542853 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
5542801 CTAATAAATG
*
5542811 AAGTACTAAATTTTT
1 AAGTGCTAAATTTTT
*
5542826 -ACTGCTAAATTTTAT
1 AAGTGCTAAATTTT-T
5542841 AAGTGCTAAATTT
1 AAGTGCTAAATTT
5542854 ATATTAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 11 0.48
15 1 0.04
16 11 0.48
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (15 bp):
AAGTGCTAAATTTTT
Found at i:5547717 original size:19 final size:19
Alignment explanation
Indices: 5547681--5547719 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5547671 ATACAAATAA
* **
5547681 TTTTAAACATTTTTTTAAT
1 TTTTAAAAATTTAATTAAT
5547700 TTTTAAAAATTTAATTAAT
1 TTTTAAAAATTTAATTAAT
5547719 T
1 T
5547720 GCTAACGTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAAAATTTAATTAAT
Found at i:5548749 original size:23 final size:22
Alignment explanation
Indices: 5548711--5548773 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
5548701 AAAATGAAAA
*
5548711 TTTATATTAAAAATTTAATTTAAT
1 TTTATATT--AAATTTAATATAAT
* *
5548735 TTTATATTAATATTTTATATATT
1 TTTATATTAA-ATTTAATATAAT
5548758 TTTATAATTAAATTTA
1 TTTAT-ATTAAATTTA
5548774 TAATTAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
22 2 0.06
23 18 0.55
24 13 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTATATTAAATTTAATATAAT
Found at i:5548751 original size:24 final size:23
Alignment explanation
Indices: 5548711--5548784 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 23
5548701 AAAATGAAAA
*
5548711 TTTATATTAAAAATTTAATTTAAT
1 TTTATATT-AAATTTTAATTTAAT
* *
5548735 TTTATATTAATATTTT-ATATATT
1 TTTATATTAA-ATTTTAATTTAAT
*
5548758 TTTATAATTAAATTTATAATTAAAT
1 TTTAT-ATTAAATTT-TAATTTAAT
5548783 TT
1 TT
5548785 ATTATTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
23 16 0.40
24 18 0.45
25 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTATATTAAATTTTAATTTAAT
Found at i:5548775 original size:12 final size:12
Alignment explanation
Indices: 5548758--5548786 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5548748 TTTATATATT
5548758 TTTATAATTAAA
1 TTTATAATTAAA
5548770 TTTATAATTAAA
1 TTTATAATTAAA
5548782 TTTAT
1 TTTAT
5548787 TATTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTATAATTAAA
Found at i:5549235 original size:28 final size:27
Alignment explanation
Indices: 5549200--5549252 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
5549190 ACCCAAATAA
*
5549200 TATAAAAAT-AATTAATTACGAAAAAGG
1 TATAAAAATAAAATAATTAC-AAAAAGG
5549227 TATAGAAAATAAAATAATTACAAAAA
1 TATA-AAAATAAAATAATTACAAAAA
5549253 TAAGCATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 10 0.43
29 9 0.39
ACGTcount: A:0.64, C:0.04, G:0.08, T:0.25
Consensus pattern (27 bp):
TATAAAAATAAAATAATTACAAAAAGG
Found at i:5552924 original size:78 final size:78
Alignment explanation
Indices: 5552794--5553012 Score: 268
Period size: 78 Copynumber: 2.9 Consensus size: 78
5552784 AAAGTTTGTT
* * * * * *
5552794 TATTTAAATTGC--AAAAAACTAC-TAAAATTAATAACTGAAATAGCGACAAAGTCATTACATAA
1 TATTTAAATTGCAAAAAAAACCACATAAAATTGATAAATAAAATAGCAAAAAAGTCATTACATAA
*
5552856 ATACAAAGTTTAC
66 ATACAAAGTTGAC
* * *
5552869 TATTTAAATTGCAAAAAAAACCCCATAAAATTGATAAATAAAATGGCAAAAAAGTCATTGCATAA
1 TATTTAAATTGCAAAAAAAACCACATAAAATTGATAAATAAAATAGCAAAAAAGTCATTACATAA
*
5552934 ATACAAAGTTGAT
66 ATACAAAGTTGAC
* * * *
5552947 TATTTAAATTG-AAAAAAAAACACATAAAATTGATAAATAAAA-CGAAAAAAAATCATTACATAA
1 TATTTAAATTGCAAAAAAAACCACATAAAATTGATAAATAAAATAGCAAAAAAGTCATTACATAA
5553010 ATA
66 ATA
5553013 TGAAGTTATT
Statistics
Matches: 124, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
75 12 0.10
76 20 0.16
77 37 0.30
78 55 0.44
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (78 bp):
TATTTAAATTGCAAAAAAAACCACATAAAATTGATAAATAAAATAGCAAAAAAGTCATTACATAA
ATACAAAGTTGAC
Found at i:5553276 original size:33 final size:33
Alignment explanation
Indices: 5553211--5553338 Score: 118
Period size: 33 Copynumber: 3.9 Consensus size: 33
5553201 AGCCGGAAGT
* * * *
5553211 AGTGGAGTACGGCGGTGGATACAGG-TAGGGAGG
1 AGTGGAGTACGACGGTAGATACGGGCCA-GGAGG
*
5553244 AGTGGAGTACGACGGTAGATATGGGCCAGGAGG
1 AGTGGAGTACGACGGTAGATACGGGCCAGGAGG
* * * *
5553277 AATAGAGTACGGCGGTAGATACGGACC-GAGAGG
1 AGTGGAGTACGACGGTAGATACGGGCCAG-GAGG
*
5553310 AGTGGAGTAC-AGCGTTAGATACGGGCCAG
1 AGTGGAGTACGA-CGGTAGATACGGGCCAG
5553339 AAAGAGCGAA
Statistics
Matches: 76, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
32 1 0.01
33 73 0.96
34 2 0.03
ACGTcount: A:0.28, C:0.13, G:0.44, T:0.15
Consensus pattern (33 bp):
AGTGGAGTACGACGGTAGATACGGGCCAGGAGG
Found at i:5553329 original size:66 final size:66
Alignment explanation
Indices: 5553215--5553338 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 66
5553205 GGAAGTAGTG
* * *
5553215 GAGTACGGCGGTGGATACAGGTAGGGAGGAGTGGAGTACGACGGTAGATATGGGCCAGGAGGAAT
1 GAGTACGGCGGTAGATACAGGTAGAGAGGAGTGGAGTACGACGGTAGATACGGGCCAGGAGGAAT
5553280 A
66 A
*
5553281 GAGTACGGCGGTAGATAC-GG-ACCGAGAGGAGTGGAGTAC-AGCGTTAGATACGGGCCAG
1 GAGTACGGCGGTAGATACAGGTA--GAGAGGAGTGGAGTACGA-CGGTAGATACGGGCCAG
5553339 AAAGAGCGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
64 1 0.02
65 3 0.06
66 47 0.92
ACGTcount: A:0.28, C:0.14, G:0.44, T:0.15
Consensus pattern (66 bp):
GAGTACGGCGGTAGATACAGGTAGAGAGGAGTGGAGTACGACGGTAGATACGGGCCAGGAGGAAT
A
Found at i:5555366 original size:16 final size:15
Alignment explanation
Indices: 5555342--5555371 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5555332 TAAAAATCAA
5555342 ATAAAATTACATTAT
1 ATAAAATTACATTAT
5555357 ATAAACATTACATTA
1 ATAAA-ATTACATTA
5555372 AAAAAATCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAAATTACATTAT
Found at i:5555647 original size:106 final size:106
Alignment explanation
Indices: 5555361--5555652 Score: 405
Period size: 104 Copynumber: 2.8 Consensus size: 106
5555351 CATTATATAA
*
5555361 ACATTACATTAAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACCTAATCATA
1 ACATTAC-TTAAAAAAATCACAAAACACTATACTAAACACTAACAATTTATATAACCTAATCATA
5555426 AATTACTAACAAAATAACTATAAAATTATTTTTAAAAAAAAT
65 AATTACTAACAAAATAACTATAAAATTATTTTTAAAAAAAAT
* *
5555468 ACATTA-AT-AAAAAATCACAAAACAC-ATAACTAAACACTAACAATTTATATAACCTAATCATG
1 ACATTACTTAAAAAAATCACAAAACACTAT-ACTAAACACTAACAATTTATATAACCTAATCATA
* * * *
5555530 AATTACTAACAAAATATCTATAAAATTGTTTTTTAAAAAATT
65 AATTACTAACAAAATAACTATAAAATTATTTTTAAAAAAAAT
* * * *
5555572 ACATTACTTAAAAAAATCACAAAACCCTATACTAAATACTAACAA-AT-TGTAACCTAATCTCAT
1 ACATTACTTAAAAAAATCACAAAACACTATACTAAACACTAACAATTTATATAACCTAA--TCAT
*
5555635 AAATCACTAACAAAATAA
64 AAATTACTAACAAAATAA
5555653 ATAACTATAA
Statistics
Matches: 164, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
103 1 0.01
104 103 0.63
105 3 0.02
106 49 0.30
107 8 0.05
ACGTcount: A:0.54, C:0.16, G:0.01, T:0.28
Consensus pattern (106 bp):
ACATTACTTAAAAAAATCACAAAACACTATACTAAACACTAACAATTTATATAACCTAATCATAA
ATTACTAACAAAATAACTATAAAATTATTTTTAAAAAAAAT
Found at i:5555908 original size:60 final size:60
Alignment explanation
Indices: 5555835--5555953 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
5555825 ATACTAAACT
* * * *
5555835 AAACACAAAAATTTATAATATAATCTTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAAACATAAATTACTAACAAATTAATTTTAAAATAATTAC
*
5555895 AAACACAACAATTTATAACATAAACATAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAAAAATTTATAACATAAACATAAATTACTAACAAATTAATTTTAAAATAATTA
5555954 TAAAAAAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAAACATAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:5559905 original size:2 final size:2
Alignment explanation
Indices: 5559898--5559936 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5559888 ACTACAAATC
5559898 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5559937 TACATAACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5560775 original size:24 final size:25
Alignment explanation
Indices: 5560729--5560776 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
5560719 ATTATTATTC
* *
5560729 TTTAATATATATGTTATGCATATAT
1 TTTAATATATATATTATACATATAT
*
5560754 TTTAATAT-TATATTATATATATA
1 TTTAATATATATATTATACATATA
5560777 CATTTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (25 bp):
TTTAATATATATATTATACATATAT
Found at i:5560843 original size:27 final size:27
Alignment explanation
Indices: 5560799--5560850 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
5560789 CTATGCATAC
* ** *
5560799 ATACTTTTAACATTATATTTTATATGT
1 ATACTCTTAACACCATATTATATATGT
5560826 ATACTCTTAACACCATATTATATAT
1 ATACTCTTAACACCATATTATATAT
5560851 ATATCTTGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.37, C:0.13, G:0.02, T:0.48
Consensus pattern (27 bp):
ATACTCTTAACACCATATTATATATGT
Found at i:5561027 original size:23 final size:23
Alignment explanation
Indices: 5560968--5561017 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 23
5560958 GTATATTATC
5560968 ATATTTTATTATATAATTAGTATAT
1 ATATTTTA-T-TATAATTAGTATAT
*
5560993 ATATTTTATTATACTTA-TATAT
1 ATATTTTATTATAATTAGTATAT
5561015 ATA
1 ATA
5561018 CCTTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 8 0.33
23 7 0.29
24 1 0.04
25 8 0.33
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATTTTATTATAATTAGTATAT
Found at i:5562291 original size:39 final size:37
Alignment explanation
Indices: 5562194--5562291 Score: 99
Period size: 39 Copynumber: 2.6 Consensus size: 37
5562184 TATGGTATTT
* * * *
5562194 AAAATATATATAT-ATATATGTATATAATAGTATTTA
1 AAAATATATACATAATATATATATATAATAGCATTAA
* * * *
5562230 AGAATATATACATAAGAAATATATAACTAATGGCATTAA
1 AAAATATATACATAATATATATAT-A-TAATAGCATTAA
5562269 AAAATATATACATAATATATATA
1 AAAATATATACATAATATATATA
5562292 AAATACCTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
36 11 0.23
37 7 0.15
38 1 0.02
39 29 0.60
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (37 bp):
AAAATATATACATAATATATATATATAATAGCATTAA
Found at i:5563583 original size:88 final size:84
Alignment explanation
Indices: 5563475--5563898 Score: 264
Period size: 88 Copynumber: 5.0 Consensus size: 84
5563465 AAAAACAGAC
* * *
5563475 ATTAAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
1 ATTAAAAGCAGATATTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
5563540 GAGTTGATTTTTTGAAACTTAA
65 GAGTTGATTTTTTGAAAC--AA
* * ** * * *
5563562 CTTGAAAAGCAGATTTTGAAAATACCTCG-ATATGCGACTGAAGGTTCAACTCACCTCTCGCAAT
1 ATT-AAAAGCAGATATTGAAAATACCTCGCACGTGAG-C-CAAGGCTCAACTCACCTCTCGCAAT
5563626 ATGAGTTGA-TTTTTGAAAAACACAA
63 ATGAGTTGATTTTTTG---AA-ACAA
** * * * ** *** *
5563651 ATTAAAAGACTCA-ACT-CAACT--CTCGCA-GAAATTAAAAAGCTCAACTCACCTCTCGCAATA
1 ATTAAAAG-CAGATATTGAAAATACCTCGCACGTGA-GCCAAGGCTCAACTCACCTCTCGCAATA
5563711 TGAGTTGAATTTTTTTG--A-AA
64 TGAGTTG-A-TTTTTTGAAACAA
* * * *
5563731 A--AAAA-CAGAAATTGAAAATAGCTCAGCACGTGAGCTAAGGCTCAACTCACTTCTCGCAATAT
1 ATTAAAAGCAGATATTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
5563793 GAGTTGA-TTTTTGAAAACAGA
65 GAGTTGATTTTTTG-AAACA-A
** * * * * *
5563814 ATCTGAAAAATAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATCTCGCAAT
1 AT-T-AAAAGCAGATATTGAAAATACCTCG-CACGTGAGCCAAGGCTCAACTCACCTCTCGCAAT
*
5563879 GTGAGTTGATTTTTTTGAAA
63 ATGAGTTGA-TTTTTTGAAA
5563899 AATATAAATT
Statistics
Matches: 257, Mismatches: 48, Indels: 62
0.70 0.13 0.17
Matches are distributed among these distances:
76 2 0.01
77 2 0.01
78 13 0.05
80 7 0.03
81 35 0.14
82 3 0.01
83 2 0.01
84 30 0.12
85 5 0.02
86 5 0.02
87 24 0.09
88 110 0.43
89 9 0.04
90 8 0.03
91 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (84 bp):
ATTAAAAGCAGATATTGAAAATACCTCGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTTGAAACAA
Found at i:5563685 original size:30 final size:30
Alignment explanation
Indices: 5563649--5563707 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
5563639 TGAAAAACAC
5563649 AAATT-AAAAGACTCAACTCAACTCTCGCAG
1 AAATTAAAAAG-CTCAACTCAACTCTCGCAG
*
5563679 AAATTAAAAAGCTCAACTCACCTCTCGCA
1 AAATTAAAAAGCTCAACTCAACTCTCGCA
5563708 ATATGAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.42, C:0.29, G:0.08, T:0.20
Consensus pattern (30 bp):
AAATTAAAAAGCTCAACTCAACTCTCGCAG
Found at i:5563946 original size:79 final size:77
Alignment explanation
Indices: 5563830--5564336 Score: 305
Period size: 79 Copynumber: 6.5 Consensus size: 77
5563820 AAAATAGATT
* * * *
5563830 TTGAAAATACCTC-GACATGTGACCCGAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTT
1 TTGAAAATACCTCAG-CGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
* *
5563894 TGAAAAATATAAA
65 TGAAAAACAGAAA
* * *
5563907 TTGAAAAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 TTG--AAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*
5563972 TTGAAAGACAGAAA
64 TTGAAAAACAGAAA
* * * *
5563986 TTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTT
1 TTGAAAATACCTCAGCGTGTGA-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTT
**
5564050 TTTGAAAGGCAGAAA
63 TTTGAAAAACAGAAA
** *** * * * * * **
5564065 TTGAAAA-A-CGGAAATTGAAAAT-ACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAA
1 TTGAAAATACCTCAGCGTG----TGACCT----GAG-G--CTCA-ACTC-AC-C-TCTCGCAATA
* *
5564127 T-A--CGAGTTGATTTTTTTG-ACAACAGAAA
51 TGAGTTGA-TT--TTTT--TGAAAAACAGAAA
*
5564155 TTGAAATTACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-TTTTTTT
1 TTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
5564217 GAAAAACAGAAA
66 GAAAAACAGAAA
* * ** *
5564229 TTGAAAATACCTCAGCATGT--CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTT
1 TTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
5564290 G-AAAACAGAAA
66 GAAAAACAGAAA
* *
5564301 TTGAAATTACCTCAGCGTGT--CTTGAGGCTCAACTCA
1 TTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCA
5564337 TTTTGAACAG
Statistics
Matches: 336, Mismatches: 61, Indels: 71
0.72 0.13 0.15
Matches are distributed among these distances:
72 44 0.13
73 7 0.02
74 59 0.18
75 4 0.01
76 7 0.02
77 56 0.17
78 4 0.01
79 96 0.29
80 5 0.01
81 1 0.00
82 1 0.00
83 2 0.01
84 1 0.00
85 1 0.00
87 8 0.02
88 5 0.01
89 6 0.02
90 15 0.04
91 10 0.03
92 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (77 bp):
TTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
GAAAAACAGAAA
Found at i:5564134 original size:93 final size:93
Alignment explanation
Indices: 5563972--5564143 Score: 238
Period size: 93 Copynumber: 1.8 Consensus size: 93
5563962 GTTGATTTTT
* * * *
5563972 TTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCACAATAC
5564037 GAGTTAATTTTTTTTTGAAAGGCAGAAA
66 GAGTTAATTTTTTTTTGAAAGGCAGAAA
* * * * *
5564065 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGA-CCTGAGGCTCAACTCGCCTCTCACAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCACAATA
*
5564129 CGAGTTGATTTTTTT
65 CGAGTTAATTTTTTT
5564144 GACAACAGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
92 2 0.03
93 66 0.97
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (93 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCACAATAC
GAGTTAATTTTTTTTTGAAAGGCAGAAA
Found at i:5564136 original size:170 final size:164
Alignment explanation
Indices: 5563912--5564235 Score: 443
Period size: 170 Copynumber: 1.9 Consensus size: 164
5563902 ATAAATTGAA
* * * *
5563912 AAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTGAA
*
5563977 AGACAGAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGT
66 A-ACAGAAATTGAAAATACCTCA--GCGTG-GCCTAAGGCTCAACTCACCTCTCGCAATATGAG-
* **
5564041 TAATTTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
126 T--TGTTTTTTTGAAAAACAGAAATTGAAAAACGGAAATTG
* * * *
5564082 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATACGAGTTGATTTTTTTGAC
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTGAA
* * *
5564147 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTT
66 AACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGTT
5564212 TTTTTGAAAAACAGAAATTGAAAA
131 TTTTTGAAAAACAGAAATTGAAAA
5564236 TACCTCAGCA
Statistics
Matches: 138, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
164 25 0.18
166 3 0.02
167 33 0.24
169 19 0.14
170 58 0.42
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (164 bp):
AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTGAA
AACAGAAATTGAAAATACCTCAGCGTGGCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGTT
TTTTTGAAAAACAGAAATTGAAAAACGGAAATTG
Found at i:5564187 original size:244 final size:242
Alignment explanation
Indices: 5563478--5564299 Score: 828
Period size: 253 Copynumber: 3.3 Consensus size: 242
5563468 AACAGACATT
5563478 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
* ** * ** * * *
5563543 TTGATTTTTTG-AAACTTAA-CTTGAAAAGCAGATTTTGAAAATACCTCGATATGCGA-CTGAAG
66 TT-AATTTTTGAAAACAGAATC-TGAAAAACAGAAATTGAAAATACCTCGACATGTGACCCG-AG
* * * * * *
5563605 GTTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACACAAATT-AAAAGACTCAACT
128 GCTCAACTCACATCTCACAATACGAGTTGATTTTTTTGAAAAACAGAAATTGAAAA-A-T-ACCT
* * * ** *
5563667 CAACTCTCGCAGAAATTAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTG
190 C-A---GCG-TGTACCT--GAAGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTTG
* *
5563728 AAAAAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCTAAGGCTCAACTCACTTCTCGCAATAT
1 ---AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
* * **
5563793 GAGTTGATTTTTGAAAACAGAATCTGAAAAATAGATTTTGAAAATACCTCGACATGTGACCCGAG
63 GAGTTAATTTTTGAAAACAGAATCTGAAAAACAGAAATTGAAAATACCTCGACATGTGACCCGAG
* ** * *
5563858 GCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCTCA
128 GCTCAACTCACATCTCACAATACGAGTTGATTTTTTTGAAAAACAGAAATTG-AAAAATACCTCA
* *
5563923 GTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
192 GCGTGT-ACCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* *
5563975 AAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
* * * * *
5564040 TTAATTTTTTTTTGAAAGGCAGAAAT-TGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCT
66 TTAA----TTTTTGAAA-ACAG-AATCTGAAAAACAGAAATTGAAAATACCTCGACATGTGACCC
* * * *
5564104 GAGGCTCAACTCGCCTCTCACAATACGAGTTGATTTTTTTG-ACAACAGAAATTG-AAATTACCT
125 GAGGCTCAACTCACATCTCACAATACGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCT
*
5564167 CAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-TTTTTTTG
190 CAGCGTGTACCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* * ** **
5564218 AAAAACAGAAATTGAAAATACCTCAGCA--TG-TCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
5564280 GTTGAA-TTTTGAAAACAGAA
65 GTT-AATTTTTGAAAACAGAA
5564300 ATTGAAATTA
Statistics
Matches: 495, Mismatches: 58, Indels: 50
0.82 0.10 0.08
Matches are distributed among these distances:
235 2 0.00
236 3 0.01
237 8 0.02
240 1 0.00
241 30 0.06
242 2 0.00
243 33 0.07
244 97 0.20
246 15 0.03
247 9 0.02
248 50 0.10
249 71 0.14
250 6 0.01
252 6 0.01
253 132 0.27
254 7 0.01
255 18 0.04
256 1 0.00
257 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (242 bp):
AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
TTAATTTTTGAAAACAGAATCTGAAAAACAGAAATTGAAAATACCTCGACATGTGACCCGAGGCT
CAACTCACATCTCACAATACGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGT
GTACCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
Found at i:5564202 original size:74 final size:74
Alignment explanation
Indices: 5564069--5564336 Score: 362
Period size: 74 Copynumber: 3.6 Consensus size: 74
5564059 CAGAAATTGA
* * * * *
5564069 AAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATACGAGT
1 AAAACAGAAATTGAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGT
5564134 TGATTTTTTTG
64 TGATTTTTTTG
* *
5564145 ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
5564210 -TTTTTTTG
66 ATTTTTTTG
* * **
5564218 AAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
1 -AAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
5564283 GA--ATTTTG
65 GATTTTTTTG
* *
5564291 AAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCA
1 AAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCA
5564337 TTTTGAACAG
Statistics
Matches: 174, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
72 44 0.25
73 13 0.07
74 91 0.52
76 26 0.15
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (74 bp):
AAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTTTG
Found at i:5564333 original size:146 final size:148
Alignment explanation
Indices: 5564065--5564336 Score: 404
Period size: 146 Copynumber: 1.8 Consensus size: 148
5564055 AAGGCAGAAA
* * * *
5564065 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATAC
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGT-ACCTGAGGCTCAACTCACCTCTCACAATAC
* *
5564130 GAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
65 GAGTTGA-TATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
5564195 TCGCAATATGAGTTGTTTTT
129 TCGCAATATGAGTTGTTTTT
* ** * *
5564215 TTGAAAAACAGAAATTGAAAATACCTCAGCATGT-CTTGAGGCTCAACTCATTTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTACCTGAGGCTCAACTCACCTCTCACAATACG
*
5564279 AGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCA
66 AGTTGATATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCA
5564337 TTTTGAACAG
Statistics
Matches: 110, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
146 49 0.45
148 30 0.27
150 31 0.28
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (148 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCATGTACCTGAGGCTCAACTCACCTCTCACAATACG
AGTTGATATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTC
GCAATATGAGTTGTTTTT
Found at i:5564359 original size:49 final size:49
Alignment explanation
Indices: 5564293--5564388 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
5564283 GAATTTTGAA
*
5564293 AACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
5564342 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
5564389 CTCGCAATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (49 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:5564422 original size:72 final size:72
Alignment explanation
Indices: 5564342--5564565 Score: 299
Period size: 72 Copynumber: 3.0 Consensus size: 72
5564332 ACTCATTTTG
5564342 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
5564407 TTTTGAA
66 TTTTGAA
5564414 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
5564479 TTTTTTTTGAA
66 ----TTTTGAA
* * * * ** *
5564490 AGACAGAAATTGAAAATACCTCAGCATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATATGAGC
1 A-ACAGAAATTGAAATTACCTCA--ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
5564554 TG-ATTTTGAA
62 TGAATTTTGAA
5564564 AA
1 AA
5564566 AGTAGAAATT
Statistics
Matches: 137, Mismatches: 7, Indels: 15
0.86 0.04 0.09
Matches are distributed among these distances:
72 65 0.47
73 1 0.01
74 8 0.06
76 8 0.06
77 20 0.15
78 1 0.01
79 33 0.24
80 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (72 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
TTTTGAA
Found at i:5564435 original size:121 final size:121
Alignment explanation
Indices: 5564221--5564460 Score: 444
Period size: 121 Copynumber: 2.0 Consensus size: 121
5564211 TTTTTTGAAA
*
5564221 AACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
*
5564286 TTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTTG
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
* *
5564342 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
5564407 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
5564461 CTCGCAATAT
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 115 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (121 bp):
AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:5564478 original size:193 final size:197
Alignment explanation
Indices: 5564147--5564514 Score: 591
Period size: 193 Copynumber: 1.9 Consensus size: 197
5564137 TTTTTTTGAC
* *
5564147 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTT
1 AACAGAAATTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTA
* *
5564212 TTTTTGAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATA
66 ATTTTGAAAAACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATA
*
5564277 TGAGTTGAA-TTTTGAAA-ACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTT
131 TGAGTTGAATTTTTGAAAGACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTT
5564340 TG
196 TG
* **
5564342 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-A
1 AACAGAAATTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTA
* *
5564406 ATTTTG-AAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATA
66 ATTTTGAAAAACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATA
5564470 TGAGTTGAATTTTTTTTGAAAGACAGAAATTGAAAATACCTCAGC
131 TGAGTTGAA---TTTTTGAAAGACAGAAATTGAAAATACCTCAGC
5564515 ATGTGAACCG
Statistics
Matches: 158, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
193 64 0.41
194 5 0.03
195 59 0.37
197 8 0.05
198 22 0.14
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (197 bp):
AACAGAAATTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGTA
ATTTTGAAAAACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATA
TGAGTTGAATTTTTGAAAGACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTT
TG
Found at i:5564641 original size:13 final size:13
Alignment explanation
Indices: 5564614--5564647 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5564604 GAGTTGATTC
*
5564614 TTGAACAACATAAA
1 TTGAA-AACAAAAA
5564628 TTGAAAACAAAAA
1 TTGAAAACAAAAA
5564641 TTGAAAA
1 TTGAAAA
5564648 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.21
Consensus pattern (13 bp):
TTGAAAACAAAAA
Found at i:5564859 original size:279 final size:280
Alignment explanation
Indices: 5564485--5565111 Score: 1107
Period size: 279 Copynumber: 2.2 Consensus size: 280
5564475 TGAATTTTTT
5564485 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAA-ACAGAAATTGAAAATACCTCAGC--GTG-ACCTGAGGCTCAACTCACCTCTCGCAATA
*
5564549 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTTAACCCACCTCTCGCAATATGAGTTGATTC
62 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
*
5564614 TTGAACAACATAAATTGAAAACAAAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACC
127 TTGAACAACATAAATTGAAAACAAAAATTAAAAATACCTCAGCGTGACCTGAGGCTCAACTCACC
5564679 TCTCGCAATATGAGCTG-TTTTGAAAAACTAGAAATTAAAAGGTTCAACCCA-CTTCTCGCAATA
192 TCTCGCAATATGAGCTGATTTTGAAAAACTAGAAATTAAAAGGTTCAACCCACCTT-TCGCAATA
5564742 TGAGTTGATTCTTGAACAACGTAAA
256 TGAGTTGATTCTTGAACAACGTAAA
*
5564767 TTGAAAACAGAAATTGAAAATACCTTAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
5564832 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
* * *
5564897 ACAACGTAAATTGAAAACAGAAATTAAAAATACCTTAGCGTGACCTGAGGCTCAACTCACCTCTC
131 ACAACATAAATTGAAAACAAAAATTAAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTC
* * *
5564962 GCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCGACCTTTTGCAATATGAGT
196 GCAATATGAGCTGATTTTGAAAAACTAGAAATTAAAAGGTTCAACCCACCTTTCGCAATATGAGT
5565027 TGATTCTTGAACAACGTAAA
261 TGATTCTTGAACAACGTAAA
5565047 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
5565112 TTGAACTTAA
Statistics
Matches: 332, Mismatches: 10, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
278 3 0.01
279 170 0.51
280 128 0.39
281 25 0.08
282 6 0.02
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (280 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
ACAACATAAATTGAAAACAAAAATTAAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTC
GCAATATGAGCTGATTTTGAAAAACTAGAAATTAAAAGGTTCAACCCACCTTTCGCAATATGAGT
TGATTCTTGAACAACGTAAA
Found at i:5564907 original size:140 final size:140
Alignment explanation
Indices: 5564485--5565111 Score: 1105
Period size: 140 Copynumber: 4.5 Consensus size: 140
5564475 TGAATTTTTT
5564485 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAA-ACAGAAATTGAAAATACCTCAGC--GTG-ACCTGAGGCTCAACTCACCTCTCGCAATA
*
5564549 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTTAACCCACCTCTCGCAATATGAGTTGATTC
62 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
*
5564614 TTGAACAACATAAA
127 TTGAACAACGTAAA
*
5564628 TTGAAAACAAAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
5564693 CTG-TTTTGAAAAACTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
5564757 ACAACGTAAA
131 ACAACGTAAA
*
5564767 TTGAAAACAGAAATTGAAAATACCTTAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
5564832 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
5564897 ACAACGTAAA
131 ACAACGTAAA
* *
5564907 TTGAAAACAGAAATTAAAAATACCTTAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
* * *
5564972 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCGACCTTTTGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
5565037 ACAACGTAAA
131 ACAACGTAAA
5565047 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
5565112 TTGAACTTAA
Statistics
Matches: 467, Mismatches: 15, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
139 136 0.29
140 303 0.65
142 22 0.05
143 6 0.01
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (140 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
ACAACGTAAA
Found at i:5564908 original size:54 final size:54
Alignment explanation
Indices: 5564808--5564913 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
5564798 GACCTGAGGC
*
5564808 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
5564862 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
5564914 CAGAAATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:5565201 original size:72 final size:71
Alignment explanation
Indices: 5565050--5565209 Score: 232
Period size: 72 Copynumber: 2.2 Consensus size: 71
5565040 ACGTAAATTG
* * *
5565050 AAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTG
5565115 AACTTA
66 AACTTA
*
5565121 AAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTT
1 AAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTT
***
5565186 GTTTTTGA
65 GAACTT-A
5565194 AAAACAAAAATT-AAAA
1 AAAACAAAAATTGAAAA
5565210 GGCTTAACTC
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
71 7 0.09
72 69 0.86
73 4 0.05
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (71 bp):
AAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTG
AACTTA
Found at i:5565302 original size:120 final size:124
Alignment explanation
Indices: 5565084--5565328 Score: 374
Period size: 120 Copynumber: 2.0 Consensus size: 124
5565074 GCGTGACCTG
* *
5565084 AGGCTCAACTCACCTCTCGCAATATGAGTTGAACTTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAACTTAAAACACAAAAACTGAAAATACCTCAGCG
*
5565149 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGTTTTTGAAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG-AAAACAAAAATTAAA
* * *
5565209 AGGCTTAACTCACCTCTCGC-ATATGAG-TCAA-TTTAAA-ACATAAACT-AAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAACTTAAAACACAAAAACTGAAAATACCTCAGCG
* *
5565269 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
5565328 A
1 A
5565329 ATACCTCAAC
Statistics
Matches: 112, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
119 16 0.14
120 55 0.49
121 7 0.06
122 5 0.04
123 3 0.03
124 7 0.06
125 19 0.17
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTCAACTTAAAACACAAAAACTGAAAATACCTCAGCG
TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
Found at i:5565350 original size:71 final size:69
Alignment explanation
Indices: 5565209--5565381 Score: 208
Period size: 71 Copynumber: 2.5 Consensus size: 69
5565199 AAAAATTAAA
* * * * * *
5565209 AGGCTTAACTCACCTCTCGC-ATATGAG-TCAATTTAAAACATAAACTAAAATACCTCAGCGTGC
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAATACCTCAACGTGC
5565272 CCCG
66 CCCG
*
5565276 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAACT-AAAATACCTCAACGT
* **
5565341 GTCTTG
64 GCCCCG
5565347 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTT
5565382 CCTTGAAAAG
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
67 18 0.20
68 7 0.08
69 5 0.05
70 11 0.12
71 50 0.55
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (69 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAATACCTCAACGTGC
CCCG
Found at i:5566920 original size:37 final size:37
Alignment explanation
Indices: 5566879--5566954 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
5566869 GGAATTACTC
5566879 GCATACTTCCTTCATCATCTTATTATTCAGATTCATG
1 GCATACTTCCTTCATCATCTTATTATTCAGATTCATG
*
5566916 GCATACTTCCTTCATCATCTTGTTATTCAGATTCATG
1 GCATACTTCCTTCATCATCTTATTATTCAGATTCATG
5566953 GC
1 GC
5566955 GTTATCTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.22, C:0.25, G:0.11, T:0.42
Consensus pattern (37 bp):
GCATACTTCCTTCATCATCTTATTATTCAGATTCATG
Found at i:5575399 original size:23 final size:23
Alignment explanation
Indices: 5575369--5575418 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
5575359 GGTTTTTTGG
5575369 TTTTTTTTGGGGGGTTAGGTTTT
1 TTTTTTTTGGGGGGTTAGGTTTT
***
5575392 TTTTTTTTTTTGGGTTAGGTTTT
1 TTTTTTTTGGGGGGTTAGGTTTT
5575415 TTTT
1 TTTT
5575419 GGGGGGCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.04, C:0.00, G:0.26, T:0.70
Consensus pattern (23 bp):
TTTTTTTTGGGGGGTTAGGTTTT
Found at i:5576783 original size:40 final size:39
Alignment explanation
Indices: 5576704--5576785 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 39
5576694 CAAAATTTTT
* *
5576704 TCACCTTCTTTTCCCTAACAAGATAATGGCGGGAAGTAA
1 TCACCTTCTTTTCCCTAACAAGACAATGGCCGGAAGTAA
*
5576743 TCACCTTCTTTTCCTCT-ACGAAGACGATGGCCGGAAGTAA
1 TCACCTTCTTTTCC-CTAAC-AAGACAATGGCCGGAAGTAA
5576783 TCA
1 TCA
5576786 TCAGATCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 16 0.42
40 22 0.58
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (39 bp):
TCACCTTCTTTTCCCTAACAAGACAATGGCCGGAAGTAA
Found at i:5579431 original size:2 final size:2
Alignment explanation
Indices: 5579424--5579488 Score: 55
Period size: 2 Copynumber: 33.5 Consensus size: 2
5579414 ATAATATTAA
* * * *
5579424 AT AT AT AT AT AC AT A- AT AT TT AT A- AA AT AT AT AT ACT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
5579465 AT AT AT AT AT AC AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5579489 AAATGAACAT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
1 3 0.06
2 45 0.90
3 2 0.04
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:5579442 original size:13 final size:13
Alignment explanation
Indices: 5579406--5579488 Score: 75
Period size: 13 Copynumber: 6.3 Consensus size: 13
5579396 ATGAAAAGTG
5579406 TATACATAATA-A
1 TATACATAATATA
*
5579418 TATTAAAT-ATATA
1 TA-TACATAATATA
*
5579431 TATACATAATATT
1 TATACATAATATA
5579444 TATA-A-AATATA
1 TATACATAATATA
5579455 TATACTAAATATATATA
1 TATAC---ATA-ATATA
5579472 TATACATAATATA
1 TATACATAATATA
5579485 TATA
1 TATA
5579489 AAATGAACAT
Statistics
Matches: 58, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
11 9 0.16
12 10 0.17
13 24 0.41
14 3 0.05
15 1 0.02
16 1 0.02
17 10 0.17
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (13 bp):
TATACATAATATA
Found at i:5579472 original size:17 final size:17
Alignment explanation
Indices: 5579450--5579488 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
5579440 TATTTATAAA
5579450 ATATATATAC-TAAATAT
1 ATATATATACAT-AATAT
5579467 ATATATATACATAATAT
1 ATATATATACATAATAT
5579484 ATATA
1 ATATA
5579489 AAATGAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATATATACATAATAT
Found at i:5579507 original size:41 final size:40
Alignment explanation
Indices: 5579424--5579511 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 40
5579414 ATAATATTAA
* *
5579424 ATATATATATACATAATATTTATAAAATATATATACTAAAT
1 ATATATATATACATAATATATATAAAATACATATAC-AAAT
5579465 ATATATATATACATAATATATATAAAATGAACATATAC-AAT
1 ATATATATATACATAATATATATAAAAT--ACATATACAAAT
5579506 ATATAT
1 ATATAT
5579512 TAGAAATACT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 36 0.84
43 7 0.16
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.39
Consensus pattern (40 bp):
ATATATATATACATAATATATATAAAATACATATACAAAT
Found at i:5579579 original size:20 final size:21
Alignment explanation
Indices: 5579556--5579674 Score: 73
Period size: 22 Copynumber: 5.2 Consensus size: 21
5579546 AATACTACAT
*
5579556 AAATATGTACATAT-ATATTA
1 AAATATATACATATAATATTA
*
5579576 AAATAAATACATAATAATATTA
1 AAATATATACAT-ATAATATTA
*
5579598 AAAGTATATACATAAAATAGTGTTAA
1 AAA-TATATACATATAATA---TT-A
*
5579624 AAATACATACATAATATAGTTATTA
1 AAATATATACAT-ATA-A--TATTA
5579649 AAATATAT--ATATACATATTA
1 AAATATATACATATA-ATATTA
5579669 GAAATA
1 -AAATA
5579675 ATAATAATGT
Statistics
Matches: 79, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
20 15 0.19
21 7 0.09
22 18 0.23
23 10 0.13
25 18 0.23
26 8 0.10
27 1 0.01
29 2 0.03
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATATATACATATAATATTA
Found at i:5579612 original size:23 final size:22
Alignment explanation
Indices: 5579406--5579492 Score: 58
Period size: 21 Copynumber: 4.0 Consensus size: 22
5579396 ATGAAAAGTG
5579406 TATACATAATAATATT-AAATA
1 TATACATAATAATATTAAAATA
*
5579427 TATATATACATAATATTTATAAA-A
1 TATACATA-ATAATA-TTA-AAATA
* * *
5579451 TATATATACTAA-A-TATATATA
1 TATACATAATAATATTA-AAATA
5579472 TATACATAAT-ATATATAAAAT
1 TATACATAATAATAT-TAAAAT
5579493 GAACATATAC
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
20 6 0.12
21 17 0.33
22 10 0.19
23 7 0.13
24 9 0.17
25 3 0.06
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
TATACATAATAATATTAAAATA
Found at i:5579616 original size:22 final size:22
Alignment explanation
Indices: 5579579--5579653 Score: 53
Period size: 25 Copynumber: 3.1 Consensus size: 22
5579569 TATATTAAAA
5579579 TAAATACATAATAATATTAAAA
1 TAAATACATAATAATATTAAAA
*
5579601 GTATATACATAA-AATAGTGTTAAAAA
1 -TAAATACATAATAATA---TT-AAAA
*
5579627 TACATACATAATATAGTTATTAAAA
1 TAAATACATAATA-A--TATTAAAA
5579652 TA
1 TA
5579654 TATATATACA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
22 4 0.10
23 10 0.24
25 18 0.43
26 7 0.17
27 1 0.02
29 2 0.05
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (22 bp):
TAAATACATAATAATATTAAAA
Found at i:5579645 original size:23 final size:22
Alignment explanation
Indices: 5579563--5579641 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 22
5579553 CATAAATATG
5579563 TACAT-ATATATT-AAAATAAA
1 TACATAATATATTAAAAATAAA
* *
5579583 TACATAATAATATTAAAAGTATA
1 TACATAAT-ATATTAAAAATAAA
* *
5579606 TACATAAAATAGTGTTAAAAATACA
1 TACAT--AATA-TATTAAAAATAAA
5579631 TACATAATATA
1 TACATAATATA
5579642 GTTATTAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 5 0.11
21 2 0.04
22 6 0.13
23 15 0.32
24 1 0.02
25 18 0.38
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (22 bp):
TACATAATATATTAAAAATAAA
Found at i:5579860 original size:12 final size:12
Alignment explanation
Indices: 5579845--5579994 Score: 59
Period size: 12 Copynumber: 12.6 Consensus size: 12
5579835 CAATAGTGAA
*
5579845 AATAATAAGTAT
1 AATAATAAATAT
5579857 AATAATAAATAT
1 AATAATAAATAT
*
5579869 AATGAT--ATAT
1 AATAATAAATAT
*
5579879 AAAAATAACACTAT
1 AATAATAA-A-TAT
*
5579893 ATATAAAAAATAT
1 A-ATAATAAATAT
*
5579906 -ATATATACACGTAT
1 AATA-ATA-A-ATAT
5579920 AAT-A-AAATAT
1 AATAATAAATAT
*
5579930 -AT-ATTAATATT
1 AATAATAAATA-T
5579941 AATAATAAATAT
1 AATAATAAATAT
****
5579953 AAT-AGGGGTA-
1 AATAATAAATAT
5579963 AA-AATAAATAT
1 AATAATAAATAT
5579974 AATAATAACATAT
1 AATAATAA-ATAT
5579987 ACATAATA
1 A-ATAATA
5579995 CGGTATTAAA
Statistics
Matches: 101, Mismatches: 19, Indels: 34
0.66 0.12 0.22
Matches are distributed among these distances:
9 3 0.03
10 20 0.20
11 10 0.10
12 30 0.30
13 17 0.17
14 14 0.14
15 7 0.07
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:5580014 original size:22 final size:22
Alignment explanation
Indices: 5579989--5580032 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5579979 TAACATATAC
*
5579989 ATAATACGGTATTAAAAAAAAT
1 ATAATACAGTATTAAAAAAAAT
* *
5580011 ATAATATAGTATTTAAAAAAAT
1 ATAATACAGTATTAAAAAAAAT
5580033 GTATACATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (22 bp):
ATAATACAGTATTAAAAAAAAT
Found at i:5580042 original size:23 final size:22
Alignment explanation
Indices: 5579997--5580045 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5579987 ACATAATACG
*
5579997 GTATTAAAAAAAATATAATATA
1 GTATTAAAAAAAATATAACATA
* *
5580019 GTATTTAAAAAAATGTATACATA
1 GTATTAAAAAAAATATA-ACATA
5580042 GTAT
1 GTAT
5580046 ATATACTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (22 bp):
GTATTAAAAAAAATATAACATA
Found at i:5580201 original size:40 final size:38
Alignment explanation
Indices: 5580104--5580208 Score: 106
Period size: 38 Copynumber: 2.7 Consensus size: 38
5580094 CTACATAAAT
* * *
5580104 AGATATATA-GTAATAGTATATACATAATATAGTATTAA
1 AGATATATACGTAATA-TATATACAAAATACAATATTAA
* *
5580142 AGATATATACATAACATATATA-AAAATACAATATTAAA
1 AGATATATACGTAATATATATACAAAATACAATATT-AA
*
5580180 AGATACATATACGTAATATATATATAAAA
1 AGAT--ATATACGTAATATATATACAAAA
5580209 AATGTATACA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
37 10 0.18
38 21 0.38
39 4 0.07
40 16 0.29
41 4 0.07
ACGTcount: A:0.55, C:0.06, G:0.07, T:0.32
Consensus pattern (38 bp):
AGATATATACGTAATATATATACAAAATACAATATTAA
Found at i:5580234 original size:23 final size:22
Alignment explanation
Indices: 5580199--5580250 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
5580189 TACGTAATAT
*
5580199 ATATATAAAAAATGTATACATA
1 ATATATAAAAAATATATACATA
*
5580221 ATATAGTAAAAAATATTTACATA
1 ATATA-TAAAAAATATATACATA
5580244 ATATATA
1 ATATATA
5580251 CATATTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATATAAAAAATATATACATA
Found at i:5580278 original size:18 final size:20
Alignment explanation
Indices: 5580241--5580279 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
5580231 AAATATTTAC
5580241 ATAATATATACATATTAGAA
1 ATAATATATACATATTAGAA
*
5580261 ATAATA-ATA-ATGTTAGAA
1 ATAATATATACATATTAGAA
5580279 A
1 A
5580280 CACCTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (20 bp):
ATAATATATACATATTAGAA
Found at i:5580354 original size:2 final size:2
Alignment explanation
Indices: 5580304--5580343 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5580294 ACTACATAAA
*
5580304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5580344 TAAAGATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5580404 original size:12 final size:11
Alignment explanation
Indices: 5580384--5580464 Score: 54
Period size: 12 Copynumber: 6.7 Consensus size: 11
5580374 TACTACTATT
5580384 AATAATAATAA
1 AATAATAATAA
*
5580395 TAAGAATAATATA
1 -AATAATAATA-A
*
5580408 AATAATAGTAA
1 AATAATAATAA
5580419 ATATAATAATATTA
1 A-ATAATAATA--A
*
5580433 AATAATATTAA
1 AATAATAATAA
**
5580444 AAGTAATTAATTT
1 AA-TAA-TAATAA
5580457 AATAATAA
1 AATAATAA
5580465 AGAAATGAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
11 8 0.15
12 31 0.56
13 14 0.25
14 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
AATAATAATAA
Found at i:5580426 original size:15 final size:15
Alignment explanation
Indices: 5580388--5580436 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
5580378 ACTATTAATA
*
5580388 ATAATAATAAGAATAAT
1 ATAATAAT-AGTA-AAT
5580405 ATAAATAATAGTAAAT
1 AT-AATAATAGTAAAT
*
5580421 ATAATAATATTAAAT
1 ATAATAATAGTAAAT
5580436 A
1 A
5580437 ATATTAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 13 0.45
16 5 0.17
17 5 0.17
18 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (15 bp):
ATAATAATAGTAAAT
Found at i:5582430 original size:15 final size:15
Alignment explanation
Indices: 5582387--5582454 Score: 63
Period size: 15 Copynumber: 4.6 Consensus size: 15
5582377 AGTTATGATA
*
5582387 TTTAATCTTTAT-AT
1 TTTAATTTTTATAAT
*
5582401 TTTAA-TTTGATTAAT
1 TTTAATTTTTA-TAAT
5582416 TTTAATTTTTATAATT
1 TTTAATTTTTATAA-T
5582432 TTTAAATTTTTA-AAT
1 TTT-AATTTTTATAAT
5582447 TTT-ATTTT
1 TTTAATTTT
5582455 AGATCTAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
13 8 0.17
14 6 0.13
15 14 0.30
16 10 0.22
17 8 0.17
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (15 bp):
TTTAATTTTTATAAT
Found at i:5582439 original size:8 final size:8
Alignment explanation
Indices: 5582415--5582449 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
5582405 ATTTGATTAA
5582415 TTTT-AAT
1 TTTTAAAT
5582422 TTTTATAAT
1 TTTTA-AAT
5582431 TTTTAAAT
1 TTTTAAAT
5582439 TTTTAAAT
1 TTTTAAAT
5582447 TTT
1 TTT
5582450 ATTTTAGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 4 0.15
8 14 0.54
9 8 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTTAAAT
Found at i:5585663 original size:137 final size:136
Alignment explanation
Indices: 5585463--5585736 Score: 539
Period size: 137 Copynumber: 2.0 Consensus size: 136
5585453 AGCCCATTCA
5585463 GTAACAGTGGTACTGGGCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCA
1 GTAACAGTGGTACTGGGCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCA
5585528 GATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCC
66 GATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCC
5585593 ATTTGG
131 ATTTGG
5585599 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
1 GTAACAGTGGTACTGGG-CAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
5585664 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCC
65 AGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCC
5585729 CATTTGG
130 CATTTGG
5585736 G
1 G
5585737 GAGACTACTC
Statistics
Matches: 137, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
136 17 0.12
137 120 0.88
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (136 bp):
GTAACAGTGGTACTGGGCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCA
GATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCC
ATTTGG
Found at i:5585694 original size:64 final size:64
Alignment explanation
Indices: 5585484--5585694 Score: 151
Period size: 64 Copynumber: 3.2 Consensus size: 64
5585474 ACTGGGCAGA
*
5585484 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
5585548 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
5585610 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
5585621 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
5585685 GCCCATTTCA
1 GCCCATTTCA
5585695 AAATACATGC
Statistics
Matches: 103, Mismatches: 27, Indels: 34
0.63 0.16 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.24
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 16 0.16
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:5587554 original size:26 final size:26
Alignment explanation
Indices: 5587518--5587653 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
5587508 CATGAAATTC
5587518 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5587544 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5587570 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5587596 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5587622 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5587648 TTATCA
1 TTATCA
5587654 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5591502 original size:64 final size:64
Alignment explanation
Indices: 5591429--5591639 Score: 151
Period size: 64 Copynumber: 3.2 Consensus size: 64
5591419 CTGGGCCAGA
*
5591429 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
5591493 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
5591555 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
5591566 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
5591630 GCCCATTTCA
1 GCCCATTTCA
5591640 AAATACATGC
Statistics
Matches: 103, Mismatches: 27, Indels: 34
0.63 0.16 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.24
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 16 0.16
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:5591641 original size:137 final size:137
Alignment explanation
Indices: 5591395--5591681 Score: 556
Period size: 137 Copynumber: 2.1 Consensus size: 137
5591385 TATTGGGCCT
**
5591395 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
5591460 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
5591525 CATATGC
131 CATATGC
5591532 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
5591597 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
5591662 CATATGC
131 CATATGC
5591669 AAGCCCATTTGGG
1 AAGCCCATTTGGG
5591682 GAGACTACTC
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 148 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:5593501 original size:26 final size:26
Alignment explanation
Indices: 5593465--5593600 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
5593455 CATGAAATTC
5593465 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5593491 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5593517 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5593543 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5593569 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5593595 TTATCA
1 TTATCA
5593601 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5597970 original size:32 final size:32
Alignment explanation
Indices: 5597933--5598099 Score: 84
Period size: 32 Copynumber: 5.2 Consensus size: 32
5597923 TAGTTAGGAG
5597933 TATTTGATTCATTTCGATCATAGCATCCTAAT
1 TATTTGATTCATTTCGATCATAGCATCCTAAT
** * * *
5597965 TATTTGA--CA-TAAGCATCACATCTAGT--TAGGAG
1 TATTTGATTCATTTCG-ATCATAGC-A-TCCTA--AT
5597997 TATTTGATTCATTTCGATCATAGCATCCTAAT
1 TATTTGATTCATTTCGATCATAGCATCCTAAT
** * *
5598029 TATTTGA--CA-TAAGCATCATATCTAGT--TAGGAG
1 TATTTGATTCATTTCG-ATCATAGC-A-TCCTA--AT
*
5598061 CATTTGATTCATTTCGATCATAGCATCCTAAT
1 TATTTGATTCATTTCGATCATAGCATCCTAAT
5598093 TATTTGA
1 TATTTGA
5598100 CATAAGCATC
Statistics
Matches: 95, Mismatches: 20, Indels: 40
0.61 0.13 0.26
Matches are distributed among these distances:
29 4 0.04
30 21 0.22
31 2 0.02
32 41 0.43
33 2 0.02
34 21 0.22
35 4 0.04
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.40
Consensus pattern (32 bp):
TATTTGATTCATTTCGATCATAGCATCCTAAT
Found at i:5597994 original size:64 final size:64
Alignment explanation
Indices: 5597920--5598232 Score: 509
Period size: 64 Copynumber: 4.9 Consensus size: 64
5597910 TTCATAACAT
*
5597920 ATCTAGTTAGGAGTATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCAC
1 ATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCAC
* *
5597984 ATCTAGTTAGGAGTATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCAT
1 ATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCAC
5598048 ATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCAC
1 ATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCAC
* *
5598112 ATCTAGTTAGGGGCATTTCATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCAC
1 ATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCAC
* * * * * * * *
5598176 ATCTAGTTGGGAGCATTTAATTTATTTTGATCATAGCATTCTAGTCATTTGGCATAA
1 ATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAA
5598233 ACATAGGCAT
Statistics
Matches: 235, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 235 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (64 bp):
ATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCAC
Found at i:5598541 original size:87 final size:86
Alignment explanation
Indices: 5598335--5599119 Score: 1052
Period size: 87 Copynumber: 9.0 Consensus size: 86
5598325 ATCAAAGACG
* * * *
5598335 GCAAGCCTTAACCCCCTAAGTAGTAAGGTAACAGGTTGAAGATTGCAGATCTTGTCTCCATGAAG
1 GCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCT-AAA
** * *
5598400 TTGCAGTGGAACAGATCGAAGAA
65 CAGTAGTGGAGCAGATCGAAG-A
* * * *
5598423 GTAAGCCTTAACCCCTTAAGTAGTAGGGTAACAGGATGAAGATTGTAGATCTTGTCTCCCTAAAC
1 GCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCTAAAC
* *
5598488 AGTAGTAGAGCAAATCGAAGTA
66 AGTAGTGGAGCAGATCGAAG-A
*
5598510 GCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTATCCCTAAAC
1 GCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCTAAAC
*
5598575 AGTAGTGGAGCAGATCAAAGA
66 AGTAGTGGAGCAGATCGAAGA
* *
5598596 CGGCAAGCCTTAA-CCCCTAAGTAGTAAGGTAACAGGCTGAAGATTGCAGATCTTGTATCCCTAA
1 --GCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCTAA
*
5598660 ACAGTAGTGGAGCAGATCAAAGA
64 ACAGTAGTGGAGCAGATCGAAGA
* *
5598683 CGGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTATCCTTAA
1 --GCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCTAA
* *
5598748 ACAGTAATGGAGCAGATCAAAGA
64 ACAGTAGTGGAGCAGATCGAAGA
* *
5598771 CGACAAGCCTTAACCCTCTAAGTAGTAGGGTAACAGGGTGAAGATTGCAGATCTTGTCTCCCTGA
1 -G-CAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCT-A
*** * * *
5598836 AGTTGCAGTGGAACAGATTGAAGAA
63 AACAGTAGTGGAGCAGATCGAAG-A
*
5598861 GCAAGCCTTAA-CCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGTAGATCTTGTCTCCCTAAAC
1 GCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCTAAAC
* *
5598925 AGCAGTGGAACAGATCGAAGAA
66 AGTAGTGGAGCAGATCGAAG-A
* * *
5598947 GCAAGCCTTAACCCTCTAAGTAGTAAGGTAACAGGCTGAAGATTGTAGATCTTGTCTCCCTAAAC
1 GCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCTAAAC
*
5599012 AGTAGTGGAGCAAATCGAAGAA
66 AGTAGTGGAGCAGATCGAAG-A
* * * *
5599034 GCAAGCCTTAACCCCCTAAGTAGTAGTGTAATAGGCTAAAGATTGCAGATCTTGTCTCCCTAAGC
1 GCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCTAAAC
*
5599099 AGTAGTGGAGCAAATCGAAGA
66 AGTAGTGGAGCAGATCGAAGA
5599120 TAAGCAGTAG
Statistics
Matches: 632, Mismatches: 58, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
86 35 0.06
87 376 0.59
88 203 0.32
89 17 0.03
90 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (86 bp):
GCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCTAAAC
AGTAGTGGAGCAGATCGAAGA
Found at i:5598606 original size:175 final size:173
Alignment explanation
Indices: 5598282--5599119 Score: 1088
Period size: 175 Copynumber: 4.8 Consensus size: 173
5598272 GCGATATCGG
* * ** * * * *
5598282 TGAAAATTGTAGATCTTATCTCCCTAAAGTTGCAGTAGAACAAATCAAAGACGGCAAGCCTTAAC
1 TGAAGATTGTAGATCTTGTCTCCCTAAA-CAGTAGTGGAGCAAATCGAAGA--GCAAGCCTTAAC
* * * *** * *
5598347 CCCCTAAGTAGTAAGGTAACAGGTTGAAGATTGCAGATCTTGTCTCCATGAAGTTGCAGTGGAAC
63 CCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCT-AAACAGTAGTGGAGC
* * *
5598412 AGATCGAAGAAGTAAGCCTTAACCC-CTTAAGTAGTAGGGTAACAGGA
127 AGATCGAAGAAGCAAGCCTTAACCCTC-TAAGTAGTAAGGTAACAGGC
*
5598459 TGAAGATTGTAGATCTTGTCTCCCTAAACAGTAGTAGAGCAAATCGAAGTAGCAAGCCTTAACCC
1 TGAAGATTGTAGATCTTGTCTCCCTAAACAGTAGTGGAGCAAATCGAAG-AGCAAGCCTTAACCC
*
5598524 CCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTATCCCTAAACAGTAGTGGAGCAGA
65 CCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCTAAACAGTAGTGGAGCAGA
* *
5598589 TCAAAGACGGCAAGCCTTAACCC-CTAAGTAGTAAGGTAACAGGC
130 TCGAAGA-AGCAAGCCTTAACCCTCTAAGTAGTAAGGTAACAGGC
* * * *
5598633 TGAAGATTGCAGATCTTGTATCCCTAAACAGTAGTGGAGCAGATCAAAGACGGCAAGCCTTAACC
1 TGAAGATTGTAGATCTTGTCTCCCTAAACAGTAGTGGAGCAAATCGAAGA--GCAAGCCTTAACC
* * *
5598698 CCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTATCCTTAAACAGTAATGGAGCAG
64 CCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCTAAACAGTAGTGGAGCAG
* * * *
5598763 ATCAAAGACGACAAGCCTTAACCCTCTAAGTAGTAGGGTAACAGGG
129 ATCGAAGAAG-CAAGCCTTAACCCTCTAAGTAGTAAGGTAACAGGC
* *** * * * *
5598809 TGAAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAAGCAAGCCTTAA-C
1 TGAAGATTGTAGATCTTGTCTCCCT-AAACAGTAGTGGAGCAAATCGAAG-AGCAAGCCTTAACC
* * *
5598873 CCCTAAGTAGTAGGGTAACAGGCTGAAGATTGTAGATCTTGTCTCCCTAAACAGCAGTGGAACAG
64 CCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCTAAACAGTAGTGGAGCAG
5598938 ATCGAAGAAGCAAGCCTTAACCCTCTAAGTAGTAAGGTAACAGGC
129 ATCGAAGAAGCAAGCCTTAACCCTCTAAGTAGTAAGGTAACAGGC
5598983 TGAAGATTGTAGATCTTGTCTCCCTAAACAGTAGTGGAGCAAATCGAAGAAGCAAGCCTTAACCC
1 TGAAGATTGTAGATCTTGTCTCCCTAAACAGTAGTGGAGCAAATCGAAG-AGCAAGCCTTAACCC
* * * * *
5599048 CCTAAGTAGTAGTGTAATAGGCTAAAGATTGCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAA
65 CCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCTAAACAGTAGTGGAGCAGA
5599113 TCGAAGA
130 TCGAAGA
5599120 TAAGCAGTAG
Statistics
Matches: 587, Mismatches: 65, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
173 31 0.05
174 205 0.35
175 236 0.40
176 70 0.12
177 44 0.07
178 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (173 bp):
TGAAGATTGTAGATCTTGTCTCCCTAAACAGTAGTGGAGCAAATCGAAGAGCAAGCCTTAACCCC
CTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTCTCCCTAAACAGTAGTGGAGCAGAT
CGAAGAAGCAAGCCTTAACCCTCTAAGTAGTAAGGTAACAGGC
Found at i:5598659 original size:44 final size:44
Alignment explanation
Indices: 5598523--5598659 Score: 111
Period size: 44 Copynumber: 3.1 Consensus size: 44
5598513 AGCCTTAACC
*
5598523 CCCTAAGTAGTAGGGTAACAGGCTGAAGATTGCAGATCTTGTAT
1 CCCTAAGTAGTAAGGTAACAGGCTGAAGATTGCAGATCTTGTAT
** * * * * ** * * *
5598567 CCCTAAACAGT-AGTGGAGCA-GATCAAAGACGGCA-AGCCTT-AAC
1 CCCTAAGTAGTAAG-GTAACAGGCT-GAAGATTGCAGA-TCTTGTAT
5598610 CCCTAAGTAGTAAGGTAACAGGCTGAAGATTGCAGATCTTGTAT
1 CCCTAAGTAGTAAGGTAACAGGCTGAAGATTGCAGATCTTGTAT
5598654 CCCTAA
1 CCCTAA
5598660 ACAGTAGTGG
Statistics
Matches: 63, Mismatches: 23, Indels: 14
0.63 0.23 0.14
Matches are distributed among these distances:
43 28 0.44
44 35 0.56
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (44 bp):
CCCTAAGTAGTAAGGTAACAGGCTGAAGATTGCAGATCTTGTAT
Done.