Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
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 72 of 425
Found at i:20327114 original size:22 final size:23
Alignment explanation
Indices: 20327066--20327116 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
20327056 GAAAATCATG
*
20327066 TAATTAAGCATAATTTCACATAC
1 TAATTAAGCATAAATTCACATAC
* * *
20327089 TAATTAAGTA-AAATTCACTTAT
1 TAATTAAGCATAAATTCACATAC
20327111 TAATTA
1 TAATTA
20327117 CTCGAGATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (23 bp):
TAATTAAGCATAAATTCACATAC
Found at i:20329107 original size:17 final size:17
Alignment explanation
Indices: 20329067--20329109 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
20329057 ACTAAGAAAT
*
20329067 AAAAATAAACACCTAAA
1 AAAAATAAACAACTAAA
20329084 AAGAAATAAA-AACTAAA
1 AA-AAATAAACAACTAAA
20329101 GAAAAATAA
1 -AAAAATAA
20329110 TTTCTCCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.74, C:0.09, G:0.05, T:0.12
Consensus pattern (17 bp):
AAAAATAAACAACTAAA
Found at i:20329824 original size:34 final size:34
Alignment explanation
Indices: 20329781--20329846 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
20329771 ATCATAGATC
20329781 TCTTTAAGAATAATCTTCCCAATATTGATGGACT
1 TCTTTAAGAATAATCTTCCCAATATTGATGGACT
20329815 TCTTTAAGAATAATCTTCCCAATATTGATGGA
1 TCTTTAAGAATAATCTTCCCAATATTGATGGA
20329847 GCTTTCTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (34 bp):
TCTTTAAGAATAATCTTCCCAATATTGATGGACT
Found at i:20333939 original size:42 final size:42
Alignment explanation
Indices: 20333880--20334028 Score: 253
Period size: 42 Copynumber: 3.5 Consensus size: 42
20333870 TGTTGATTTC
20333880 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
20333922 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
* * * *
20333964 GACACTAAGTGTCCGAGTATAAATGGGCACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
*
20334006 GGCACTAAGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
20334029 ATTTGTACAG
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 99 1.00
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:20334094 original size:27 final size:28
Alignment explanation
Indices: 20334037--20334106 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
20334027 AAATTTGTAC
**
20334037 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
20334065 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
20334092 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
20334107 GACTCACTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:20340363 original size:28 final size:28
Alignment explanation
Indices: 20340298--20340398 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
20340288 ATAGTGAATC
*
20340298 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
20340327 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
20340355 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
20340385 CGCACACTTAGTGC
1 CGCACACTTAGTGC
20340399 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:20348316 original size:28 final size:28
Alignment explanation
Indices: 20348251--20348351 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
20348241 ATAGTGAATC
*
20348251 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
20348280 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
20348308 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
20348338 CGCACACTTAGTGC
1 CGCACACTTAGTGC
20348352 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:20352796 original size:40 final size:40
Alignment explanation
Indices: 20352752--20352965 Score: 127
Period size: 40 Copynumber: 5.7 Consensus size: 40
20352742 GCTACTCGTT
*
20352752 CAAATACCTTCGGGACATAGCCCGG-TTATAGTAGCTCGCA
1 CAAATACCTTCGGGACATAGCCCGGATT-TAGTAACTCGCA
* * *
20352792 CAAATGCCTTCGGGACTTATCCCGGATTTAGTAACTCG--
1 CAAATACCTTCGGGACATAGCCCGGATTTAGTAACTCGCA
* * *
20352830 C----GCCTTC--GA-TTAGTCCGGATTTAGTAACTCGCA
1 CAAATACCTTCGGGACATAGCCCGGATTTAGTAACTCGCA
* * *
20352863 CAAATGCCTTC-GGATCTTAGTCCGGA-TT-GTAACTCGCA
1 CAAATACCTTCGGGA-CATAGCCCGGATTTAGTAACTCGCA
* * * * *
20352901 CAAATGCCTTC-GGATCTTAGTCCGGA-TTAGTCACTTAGCA
1 CAAATACCTTCGGGA-CATAGCCCGGATTTAGTAAC-TCGCA
* *
20352941 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATACCTTCGGGACATAGCCCGGA
20352966 CATCATTCGA
Statistics
Matches: 152, Mismatches: 9, Indels: 27
0.81 0.05 0.14
Matches are distributed among these distances:
31 20 0.13
32 2 0.01
33 1 0.01
34 6 0.04
37 6 0.04
38 41 0.27
39 22 0.14
40 52 0.34
41 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
CAAATACCTTCGGGACATAGCCCGGATTTAGTAACTCGCA
Found at i:20352897 original size:38 final size:39
Alignment explanation
Indices: 20352839--20352965 Score: 179
Period size: 38 Copynumber: 3.3 Consensus size: 39
20352829 GCGCCTTCGA
20352839 TTAGTCCGGATTTAGTAACTCGCACAAATGCCTTCGGATC
1 TTAGTCCGGA-TTAGTAACTCGCACAAATGCCTTCGGATC
20352879 TTAGTCCGGATT-GTAACTCGCACAAATGCCTTCGGATC
1 TTAGTCCGGATTAGTAACTCGCACAAATGCCTTCGGATC
* *
20352917 TTAGTCCGGATTAGTCACTTAGCACAAA-GCCTTCGGGA-C
1 TTAGTCCGGATTAGTAAC-TCGCACAAATGCCTTC-GGATC
*
20352956 TTAGCCCGGA
1 TTAGTCCGGA
20352966 CATCATTCGA
Statistics
Matches: 81, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
38 38 0.47
39 22 0.27
40 21 0.26
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (39 bp):
TTAGTCCGGATTAGTAACTCGCACAAATGCCTTCGGATC
Found at i:20360919 original size:40 final size:41
Alignment explanation
Indices: 20360869--20361092 Score: 270
Period size: 40 Copynumber: 5.7 Consensus size: 41
20360859 AGCACTCGTT
* * * *
20360869 CAAATACCTTCGGGA-CATGGCCCGG-TTATAGTAGCTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATT-TAGTAACTCGCA
*
20360909 CAAATGCCTTCGGGA-CTTATCCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
*
20360949 C-AATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
*
20360988 CAAATGCCTTC-GGATCTTAG-TCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
* * *
20361027 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTCACTTAGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAAC-TCGCA
20361068 CAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CAAATGCCTTCGGGATCTTAGCCCGGA
20361093 CATCATTCGA
Statistics
Matches: 166, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
38 3 0.02
39 71 0.43
40 79 0.48
41 13 0.08
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (41 bp):
CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
Found at i:20360973 original size:39 final size:40
Alignment explanation
Indices: 20360897--20361092 Score: 278
Period size: 39 Copynumber: 5.0 Consensus size: 40
20360887 GGCCCGGTTA
*
20360897 TAGTAGCTCGCACAAATGCCTTCGGGA-CTTA-TCCCGGATT
1 TAGTAACTCGCACAAATGCCTTC-GGATCTTAGT-CCGGATT
20360937 TAGTAACTCGCAC-AATGCCTTCGGATCTTAGTCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATT
20360976 TAGTAACTCGCACAAATGCCTTCGGATCTTAGT-CGGATT
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATT
20361015 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATT
* * *
20361055 TAGTCACTTAGCACAAA-GCCTTCGGGA-CTTAGCCCGGA
1 TAGTAAC-TCGCACAAATGCCTTC-GGATCTTAGTCCGGA
20361093 CATCATTCGA
Statistics
Matches: 146, Mismatches: 4, Indels: 12
0.90 0.02 0.07
Matches are distributed among these distances:
38 3 0.02
39 72 0.49
40 60 0.41
41 11 0.08
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.28
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATT
Found at i:20360980 original size:79 final size:79
Alignment explanation
Indices: 20360897--20361092 Score: 285
Period size: 79 Copynumber: 2.5 Consensus size: 79
20360887 GGCCCGGTTA
20360897 TAGTAGCTCGCACAAATGCCTTCGGGACTTATCCCGGATTTAGTAACTCGCAC-AATGCCTTCGG
1 TAGTA-CTCGCACAAATGCCTTCGGGACTTATCCCGGATTTAGTAACTCGCACAAATGCCTTCGG
20360961 ATCTTAGTCCGGATT
65 ATCTTAGTCCGGATT
20360976 TAGTAACTCGCACAAATGCCTTC-GGATCTTAGT--CGGATTTAGTAACTCGCACAAATGCCTTC
1 TAGT-ACTCGCACAAATGCCTTCGGGA-CTTA-TCCCGGATTTAGTAACTCGCACAAATGCCTTC
20361038 GGATCTTAGTCCGGATT
63 GGATCTTAGTCCGGATT
* *
20361055 TAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TAGT-AC-TCGCACAAATGCCTTCGGGACTTATCCCGGA
20361093 CATCATTCGA
Statistics
Matches: 106, Mismatches: 3, Indels: 15
0.85 0.02 0.12
Matches are distributed among these distances:
78 22 0.21
79 67 0.63
80 17 0.16
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.28
Consensus pattern (79 bp):
TAGTACTCGCACAAATGCCTTCGGGACTTATCCCGGATTTAGTAACTCGCACAAATGCCTTCGGA
TCTTAGTCCGGATT
Found at i:20369688 original size:13 final size:13
Alignment explanation
Indices: 20369666--20369698 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
20369656 AAGGATTTGT
20369666 TTAT-TAAACTAA
1 TTATCTAAACTAA
20369678 TTATCTAAACTAA
1 TTATCTAAACTAA
*
20369691 TTAACTAA
1 TTATCTAA
20369699 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:20372603 original size:6 final size:5
Alignment explanation
Indices: 20372574--20372666 Score: 68
Period size: 6 Copynumber: 17.8 Consensus size: 5
20372564 TATGTCTTTC
* *
20372574 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAAAT CAAAAGA AAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT -AAAA-T AAAAT
20372622 AAAAAT AAAAT -AAAT AAAAT AAAAT AAAAAT AAGAAT -AAAT AAAA
1 -AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAA
20372667 AAAGGAGGAT
Statistics
Matches: 72, Mismatches: 6, Indels: 20
0.73 0.06 0.20
Matches are distributed among these distances:
3 3 0.04
4 7 0.10
5 28 0.39
6 34 0.47
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:20372669 original size:49 final size:49
Alignment explanation
Indices: 20372574--20372669 Score: 124
Period size: 49 Copynumber: 2.0 Consensus size: 49
20372564 TATGTCTTTC
* * *
20372574 AAAATAAAATAATAAAATTGAAATGAAAATAAAAATCAAAAGAAAAATA
1 AAAATAAAATAATAAAATTAAAATAAAAATAAAAATCAAAAAAAAAATA
*
20372623 AAAATAAAATAAATAAAA-TAAAATAAAAATAAGAAT-AAATAAAAAAA
1 AAAATAAAAT-AATAAAATTAAAATAAAAATAAAAATCAAA-AAAAAAA
20372670 GGAGGATTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
48 3 0.07
49 31 0.76
50 7 0.17
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (49 bp):
AAAATAAAATAATAAAATTAAAATAAAAATAAAAATCAAAAAAAAAATA
Found at i:20378063 original size:13 final size:13
Alignment explanation
Indices: 20378041--20378073 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
20378031 AAGGATTTGT
20378041 TTAT-TAAACTAA
1 TTATCTAAACTAA
20378053 TTATCTAAACTAA
1 TTATCTAAACTAA
*
20378066 TTAACTAA
1 TTATCTAA
20378074 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:20381840 original size:21 final size:21
Alignment explanation
Indices: 20381814--20381856 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
20381804 ACCCCTATTT
20381814 ATATATACTGTATACAATAGA
1 ATATATACTGTATACAATAGA
20381835 ATATATACTGTATACAATAGA
1 ATATATACTGTATACAATAGA
20381856 A
1 A
20381857 CCATGCACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (21 bp):
ATATATACTGTATACAATAGA
Found at i:20383429 original size:3 final size:3
Alignment explanation
Indices: 20383363--20383416 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
20383353 AATCAATCTC
20383363 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20383411 TAT TAT
1 TAT TAT
20383417 GTCTCAATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20384092 original size:43 final size:43
Alignment explanation
Indices: 20384039--20384223 Score: 192
Period size: 43 Copynumber: 4.3 Consensus size: 43
20384029 TTATGTGAAA
* *
20384039 AAACGCCGCTATAGAACATGACTTTTAGCGGCACTTTCCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTCCCCAC
* * *
20384082 AAACACCGCTAAAGAACATGACCTTTAGTGGCACTTTCCCCAT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTCCCCAC
** * * ** *
20384125 AGGCGCTGCTAAAGAACATGACCTTTAACGGTGCTTTCTCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTCCCCAC
* * * * * *
20384168 AAGCGCCGCTAAAGAACCTAACTTTTAG-GGCACTTTTCCCAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTCCCCAC
*
20384210 AAACGCCACTAAAG
1 AAACGCCGCTAAAG
20384224 GTCATGAAAA
Statistics
Matches: 114, Mismatches: 28, Indels: 1
0.80 0.20 0.01
Matches are distributed among these distances:
42 21 0.18
43 93 0.82
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTCCCCAC
Found at i:20384875 original size:23 final size:23
Alignment explanation
Indices: 20384848--20384924 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 23
20384838 ATAAACTAAA
20384848 TTTCAGCAACTAAACAATTCAAT
1 TTTCAGCAACTAAACAATTCAAT
*
20384871 TTTCAG-TACTTAAA-AACTTCAAT
1 TTTCAGCAAC-TAAACAA-TTCAAT
* * ** *
20384894 TTACAACATTTAAACACTTCAAT
1 TTTCAGCAACTAAACAATTCAAT
*
20384917 TTGCAGCA
1 TTTCAGCA
20384925 CTTTAACACT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
22 4 0.10
23 36 0.88
24 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (23 bp):
TTTCAGCAACTAAACAATTCAAT
Found at i:20384908 original size:46 final size:46
Alignment explanation
Indices: 20384858--20384953 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 46
20384848 TTTCAGCAAC
* * *
20384858 TAAACAATTCAATTTTCAGTACTTAAAAACTTCAATTTACAACATT
1 TAAACAATTCAATTTGCAGCACTTAAAAACTTCAATTTACAACATG
* * * * *
20384904 TAAACACTTCAATTTGCAGCACTTTAACACTTTAATTTGCAACATG
1 TAAACAATTCAATTTGCAGCACTTAAAAACTTCAATTTACAACATG
20384950 TAAA
1 TAAA
20384954 AATAAAATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (46 bp):
TAAACAATTCAATTTGCAGCACTTAAAAACTTCAATTTACAACATG
Found at i:20384932 original size:23 final size:23
Alignment explanation
Indices: 20384860--20384944 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
20384850 TCAGCAACTA
* * * *
20384860 AACAATTCAATTTTCAGTACTTA
1 AACACTTCAATTTGCAGCACTTT
* * *
20384883 AAAACTTCAATTTACAACA-TTT
1 AACACTTCAATTTGCAGCACTTT
20384905 AAACACTTCAATTTGCAGCACTTT
1 -AACACTTCAATTTGCAGCACTTT
*
20384929 AACACTTTAATTTGCA
1 AACACTTCAATTTGCA
20384945 ACATGTAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
22 2 0.04
23 45 0.90
24 3 0.06
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (23 bp):
AACACTTCAATTTGCAGCACTTT
Found at i:20384962 original size:5 final size:5
Alignment explanation
Indices: 20384952--20384979 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
20384942 GCAACATGTA
20384952 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
20384980 GAGCACACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:20389561 original size:28 final size:28
Alignment explanation
Indices: 20389529--20389587 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
20389519 GCGTAGATCA
20389529 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
20389557 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
20389585 CGA
1 CGA
20389588 TATACCCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.46, C:0.25, G:0.12, T:0.17
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:20392301 original size:5 final size:5
Alignment explanation
Indices: 20392291--20392320 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
20392281 TACCAATTTG
20392291 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
20392321 AACACACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:20392664 original size:23 final size:22
Alignment explanation
Indices: 20392633--20393327 Score: 374
Period size: 23 Copynumber: 30.4 Consensus size: 22
20392623 TAATTCTAAC
20392633 ACAGCACTTTAACACTTCAATTT
1 ACAGCA-TTTAACACTTCAATTT
* *
20392656 ACAACACTTTAACA-TCTCAATTA
1 ACAGCA-TTTAACACT-TCAATTT
* *
20392679 ACAACATTTATACTCCTT-AA-TT
1 ACAGCATTTA-AC-ACTTCAATTT
**
20392701 ACAGCGATAAAACATCTT-AATTT
1 ACAGC-ATTTAACA-CTTCAATTT
* * * *
20392724 CCAGCAACTAAACATTTCAATTT
1 ACAGC-ATTTAACACTTCAATTT
* * *
20392747 GCAGTACTTAAACACTTCAATTT
1 ACAGCA-TTTAACACTTCAATTT
*
20392770 ACAACATTTAAACACTTCAATTT
1 ACAGCATTT-AACACTTCAATTT
* *
20392793 ACAACATTCAAACACTTCAATTT
1 ACAGCATT-TAACACTTCAATTT
* *
20392816 GCAGCACTATAACACTTCAATTT
1 ACAGCA-TTTAACACTTCAATTT
* *
20392839 ATAGCATTTAAATACTTCAATTT
1 ACAGCATTT-AACACTTCAATTT
** *
20392862 GTAGCACTTTAACA-TCTCAATTA
1 ACAGCA-TTTAACACT-TCAATTT
*
20392885 ACAACATTTATACAGC-TCAA-TT
1 ACAGCATTTA-ACA-CTTCAATTT
** *
20392907 ACAG-AGATAAAACATCTCAATTT
1 ACAGCATTTAACAC-T-TCAATTT
* * * *
20392930 CCAGCAACTAAACACTTAAATTT
1 ACAGC-ATTTAACACTTCAATTT
* * *
20392953 GCAGTACTTAAAACACTTCAATTT
1 ACAGCA-TT-TAACACTTCAATTT
*
20392977 ACAACATTTAAGCACTTCAATTT
1 ACAGCATTTAA-CACTTCAATTT
20393000 ACAGCATTTAAGCACTTCAATTT
1 ACAGCATTTAA-CACTTCAATTT
*
20393023 ATAGCATTTAACACTTCAATTT
1 ACAGCATTTAACACTTCAATTT
* *
20393045 GCAGCACTTTAACACTTTAATTT
1 ACAGCA-TTTAACACTTCAATTT
*
20393068 ACAGCATTTAAACACTGCAATTT
1 ACAGCATTT-AACACTTCAATTT
* * *
20393091 GCTGCACTTTAACA-TCTCAATTA
1 ACAGCA-TTTAACACT-TCAATTT
* *
20393114 ACAACATTTATACACCTCAA-TT
1 ACAGCATTTA-ACACTTCAATTT
**
20393136 ACAGCGATAAAACA-TCTCAATTT
1 ACAGC-ATTTAACACT-TCAATTT
*
20393159 CCAGCATTTAAACACTTCAATTT
1 ACAGCATTT-AACACTTCAATTT
* *
20393182 TCAGCACTTTAACA-TCTCAATTA
1 ACAGCA-TTTAACACT-TCAATTT
** *
20393205 ACAATATTTATACACCTCAA-TT
1 ACAGCATTTA-ACACTTCAATTT
* * *
20393227 ACATCA-ATAAAACATCTCAATTT
1 ACAGCATTTAACAC-T-TCAATTT
* * *
20393250 CCAGCAACTAAACACTTCAATTT
1 ACAGC-ATTTAACACTTCAATTT
* * *
20393273 GCAGTATTTAAACACTTCAACTT
1 ACAGCATTT-AACACTTCAATTT
*
20393296 ATAGCATTTAAACACTTCAATTT
1 ACAGCATTT-AACACTTCAATTT
20393319 ACAGCATTT
1 ACAGCATTT
20393328 CAATAGCAGC
Statistics
Matches: 518, Mismatches: 106, Indels: 96
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.00
20 5 0.01
21 5 0.01
22 93 0.18
23 373 0.72
24 31 0.06
25 10 0.02
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (22 bp):
ACAGCATTTAACACTTCAATTT
Found at i:20392782 original size:46 final size:46
Alignment explanation
Indices: 20392710--20393327 Score: 427
Period size: 46 Copynumber: 13.5 Consensus size: 46
20392700 TACAGCGATA
* ** * * *
20392710 AAACATCTT-AATTTCCAGCAACTAAACATTTCAATTTGCAGTACTT
1 AAACA-CTTCAATTTACAGCATTTAAACATTTCAATTTACAGCATTT
* * * *
20392756 AAACACTTCAATTTACAACATTTAAACACTTCAATTTACAACATTC
1 AAACACTTCAATTTACAGCATTTAAACATTTCAATTTACAGCATTT
* * * *
20392802 AAACACTTCAATTTGCAGCA-CTATAACACTTCAATTTATAGCATTT
1 AAACACTTCAATTTACAGCATTTA-AACATTTCAATTTACAGCATTT
* ** * * *
20392848 AAATACTTCAATTTGTAGCACTTT-AACATCTCAATTAACAACATTT
1 AAACACTTCAATTTACAGCA-TTTAAACATTTCAATTTACAGCATTT
* * * * * **
20392894 ATACAGC-TCAA-TTACAG-AGATAAAACATCTCAATTTCCAGCAACT
1 AAACA-CTTCAATTTACAGCA-TTTAAACATTTCAATTTACAGCATTT
* * * * * *
20392939 AAACACTTAAATTTGCAGTACTTAAAACACTTCAATTTACAACATTT
1 AAACACTTCAATTTACAGCA-TTTAAACATTTCAATTTACAGCATTT
* * * *
20392986 AAGCACTTCAATTTACAGCATTTAAGCACTTCAATTTATAGCATTT
1 AAACACTTCAATTTACAGCATTTAAACATTTCAATTTACAGCATTT
*
20393032 -AACACTTCAATTTGCAGCACTTT-AACACTTT-AATTTACAGCATTT
1 AAACACTTCAATTTACAGCA-TTTAAACA-TTTCAATTTACAGCATTT
* * * * * *
20393077 AAACACTGCAATTTGCTGCACTTT-AACATCTCAATTAACAACATTT
1 AAACACTTCAATTTACAGCA-TTTAAACATTTCAATTTACAGCATTT
* * * * *
20393123 ATACACCTCAA-TTACAGCGA-TAAAACATCTCAATTTCCAGCATTT
1 AAACACTTCAATTTACAGC-ATTTAAACATTTCAATTTACAGCATTT
* * * **
20393168 AAACACTTCAATTTTCAGCACTTT-AACATCTCAATTAACAATATTT
1 AAACACTTCAATTTACAGCA-TTTAAACATTTCAATTTACAGCATTT
* * * * * * * **
20393214 ATACACCTCAA-TTACATCAATAAAACATCTCAATTTCCAGCAACT
1 AAACACTTCAATTTACAGCATTTAAACATTTCAATTTACAGCATTT
* * * * *
20393259 AAACACTTCAATTTGCAGTATTTAAACACTTCAACTTATAGCATTT
1 AAACACTTCAATTTACAGCATTTAAACATTTCAATTTACAGCATTT
20393305 AAACACTTCAATTTACAGCATTT
1 AAACACTTCAATTTACAGCATTT
20393328 CAATAGCAGC
Statistics
Matches: 442, Mismatches: 110, Indels: 40
0.75 0.19 0.07
Matches are distributed among these distances:
44 5 0.01
45 133 0.30
46 265 0.60
47 38 0.09
48 1 0.00
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.33
Consensus pattern (46 bp):
AAACACTTCAATTTACAGCATTTAAACATTTCAATTTACAGCATTT
Found at i:20393037 original size:206 final size:206
Alignment explanation
Indices: 20392646--20393078 Score: 629
Period size: 206 Copynumber: 2.1 Consensus size: 206
20392636 GCACTTTAAC
* * *
20392646 ACTTCAATTTACAACACTTTAACATCTCAATTAACAACATTTATACTCCTTAATTACAGCGATAA
1 ACTTCAATTTACAACACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGAGATAA
* * *
20392711 AACATCTTAATTTCCAGCAACTAAACATTTCAATTTGCAGTACTTAAACACTTCAATTTACAACA
66 AACATCTCAATTTCCAGCAACTAAACACTTAAATTTGCAGTACTTAAACACTTCAATTTACAACA
*
20392776 TTTAAACACTTCAATTTACAACATTCAAACACTTCAATTTGCAGCACTATAACACTTCAATTTAT
131 TTTAAACACTTCAATTTACAACATTCAAACACTTCAATTTACAGCACTATAACACTTCAATTTAT
20392841 AGCATTTAAAT
196 AGCATTTAAAT
** * *
20392852 ACTTCAATTTGTAGCACTTTAACATCTCAATTAACAACATTTATACAGCTCAATTACAGAGATAA
1 ACTTCAATTTACAACACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGAGATAA
20392917 AACATCTCAATTTCCAGCAACTAAACACTTAAATTTGCAGTACTTAAAACACTTCAATTTACAAC
66 AACATCTCAATTTCCAGCAACTAAACACTTAAATTTGCAGTACTT-AAACACTTCAATTTACAAC
* * * * * * *
20392982 ATTTAAGCACTTCAATTTACAGCATTTAAGCACTTCAATTTATAGCA-TTTAACACTTCAATTTG
130 ATTTAAACACTTCAATTTACAACATTCAAACACTTCAATTTACAGCACTATAACACTTCAATTTA
* *
20393046 CAGCACTTT-AAC
195 TAGCA-TTTAAAT
* *
20393058 ACTTTAATTTACAGCA-TTTAA
1 ACTTCAATTTACAACACTTTAA
20393079 ACACTGCAAT
Statistics
Matches: 202, Mismatches: 23, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
205 5 0.02
206 134 0.66
207 63 0.31
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (206 bp):
ACTTCAATTTACAACACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGAGATAA
AACATCTCAATTTCCAGCAACTAAACACTTAAATTTGCAGTACTTAAACACTTCAATTTACAACA
TTTAAACACTTCAATTTACAACATTCAAACACTTCAATTTACAGCACTATAACACTTCAATTTAT
AGCATTTAAAT
Found at i:20393078 original size:91 final size:92
Alignment explanation
Indices: 20392634--20393324 Score: 433
Period size: 91 Copynumber: 7.6 Consensus size: 92
20392624 AATTCTAACA
* * * * *
20392634 CAGCACTTTAACACT-TCAATTTACAACACTTTAACA-TCTCAATTAACAACATTTATAC-TCCT
1 CAGCACTTTAACACTCTCAATTTACAGCA-TTTAACACT-TCAATTTACAGCACTTAAACAT-CT
* * * *
20392696 TAA-TTACAGCGA-TAAAACATCTT-AATTTC
63 CAATTTACAAC-ATTTAAACA-CTTCAATTTG
* * * * * * *
20392725 CAGCAAC-TAAACA-TTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAAACA-CTT
1 CAGC-ACTTTAACACTCTCAATTTACAGCA-TTTAACACTTCAATTTACAGCACTTAAACATC-T
*
20392787 CAATTTACAACATTCAAACACTTCAATTTG
63 CAATTTACAACATTTAAACACTTCAATTTG
* * * ** *
20392817 CAGCACTATAACACT-TCAATTTATAGCATTTAAATACTTCAATTTGTAGCACTTTAACATCTCA
1 CAGCACTTTAACACTCTCAATTTACAGCATTT-AACACTTCAATTTACAGCACTTAAACATCTCA
* * *
20392881 ATTAACAACATTTATACAGC-TCAA-TTA
65 ATTTACAACATTTAAACA-CTTCAATTTG
** * * * * * * *
20392908 CAG-A-GATAAAACATCTCAATTTCCAGCAACTAAACACTTAAATTTGCAGTACTTAAAACA-CT
1 CAGCACTTTAACAC-TCTCAATTTACAGC-ATTTAACACTTCAATTTACAGCACTT-AAACATC-
* *
20392970 TCAATTTACAACATTTAAGCACTTCAATTTA
62 TCAATTTACAACATTTAAACACTTCAATTTG
* * * *
20393001 CAGCA-TTTAAGCACT-TCAATTTATAGCATTTAACACTTCAATTTGCAGCACTTTAACA-CTTT
1 CAGCACTTTAA-CACTCTCAATTTACAGCATTTAACACTTCAATTTACAGCACTTAAACATC-TC
* *
20393063 AATTTACAGCATTTAAACACTGCAATTTG
64 AATTTACAACATTTAAACACTTCAATTTG
* * * * *
20393092 CTGCACTTTAACA-TCTCAATTAACAACATTTATACACCTCAA-TTACAGCGA-TAAAACATCTC
1 CAGCACTTTAACACTCTCAATTTACAGCATTTA-ACACTTCAATTTACAGC-ACTTAAACATCTC
* * *
20393154 AATTTCCAGCATTTAAACACTTCAATTTT
64 AATTTACAACATTTAAACACTTCAATTTG
* ** * * * *
20393183 CAGCACTTTAACA-TCTCAATTAACAATATTTATACACCTCAA-TTACATCAATAAAACATCTCA
1 CAGCACTTTAACACTCTCAATTTACAGCATTTA-ACACTTCAATTTACAGCACTTAAACATCTCA
* * **
20393246 ATTTCCAGCAACTAAACACTTCAATTTG
65 ATTTACAACATTTAAACACTTCAATTTG
* * *
20393274 CAGTA-TTTAAACACT-TCAACTTATAGCATTTAAACACTTCAATTTACAGCA
1 CAGCACTTT-AACACTCTCAATTTACAGCATTT-AACACTTCAATTTACAGCA
20393325 TTTCAATAGC
Statistics
Matches: 486, Mismatches: 82, Indels: 63
0.77 0.13 0.10
Matches are distributed among these distances:
89 6 0.01
90 9 0.02
91 290 0.60
92 155 0.32
93 19 0.04
94 5 0.01
95 2 0.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (92 bp):
CAGCACTTTAACACTCTCAATTTACAGCATTTAACACTTCAATTTACAGCACTTAAACATCTCAA
TTTACAACATTTAAACACTTCAATTTG
Found at i:20394409 original size:2 final size:2
Alignment explanation
Indices: 20394402--20394433 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20394392 GCTCTTGTAC
20394402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20394434 GTTTGCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20395240 original size:29 final size:29
Alignment explanation
Indices: 20395109--20395241 Score: 171
Period size: 29 Copynumber: 4.6 Consensus size: 29
20395099 GTGACAAGAT
* *
20395109 TGGCACTAAATGTGCAAGCTTGAAATATA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
*
20395138 TGGCACTAAGTGTGCAAGCTTGAAATATA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* *
20395167 TGGCACTAAGTGTGCGAACTT-AAATTGTA
1 TGGCACTAAGTGTGCGAGCTTGAAA-TATA
* *
20395196 TGGCACTATGTGTGCGAGCTT-AAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAAT-ATA
20395225 TGGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
20395242 AATCGATTAT
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
28 4 0.04
29 89 0.96
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATATA
Found at i:20397852 original size:37 final size:37
Alignment explanation
Indices: 20397797--20397878 Score: 114
Period size: 37 Copynumber: 2.2 Consensus size: 37
20397787 TAAAACTATT
*
20397797 AGAAAAGATAATGTACAGAACATTATTTAAC-AAAAG
1 AGAAAAGATAATATACAGAACATTATTTAACTAAAAG
*
20397833 AGAAAATGATATTATACAGAACATTATTTAACTAAAA-
1 AGAAAA-GATAATATACAGAACATTATTTAACTAAAAG
*
20397870 AGATAAGAT
1 AGAAAAGAT
20397879 TTTCCAGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
36 9 0.22
37 28 0.68
38 4 0.10
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.26
Consensus pattern (37 bp):
AGAAAAGATAATATACAGAACATTATTTAACTAAAAG
Found at i:20399432 original size:3 final size:3
Alignment explanation
Indices: 20399426--20399490 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
20399416 TTTTTCTCTT
20399426 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20399474 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
20399491 TACTAAAATG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20399919 original size:29 final size:29
Alignment explanation
Indices: 20399799--20399919 Score: 79
Period size: 29 Copynumber: 4.1 Consensus size: 29
20399789 ATTTTTATGT
20399799 TTTAGAGTTTTAGGATTTAGGATTTTGTA
1 TTTAGAGTTTTAGGATTTAGGATTTTGTA
* * * * *
20399828 TTTAAGGGTTTAAGGGTTTA-G-TGTCTATA
1 TTT-AGAGTTTTAGGATTTAGGAT-TTTGTA
* ** * *
20399857 GTTTAGGGTTTTATGG-TTTAAAATTTAAG-G
1 -TTTAGAGTTTTA-GGATTTAGGATTT-TGTA
20399887 TTTAGAGTTTTAGGATTTAGGATTTTGTA
1 TTTAGAGTTTTAGGATTTAGGATTTTGTA
20399916 TTTA
1 TTTA
20399920 AGGGCTTAAG
Statistics
Matches: 67, Mismatches: 16, Indels: 18
0.66 0.16 0.18
Matches are distributed among these distances:
28 4 0.06
29 43 0.64
30 19 0.28
31 1 0.01
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.50
Consensus pattern (29 bp):
TTTAGAGTTTTAGGATTTAGGATTTTGTA
Found at i:20400348 original size:40 final size:40
Alignment explanation
Indices: 20400258--20400534 Score: 384
Period size: 40 Copynumber: 7.0 Consensus size: 40
20400248 AATGTTTTTT
* * *
20400258 GCGGTGTTTTTCAGAAAGCGCCGCTAATGCTCGAATCTATA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCG-ATCTATA
* *
20400299 GCGGCGTTTTTTAAAAAGTGCTGCTAATGCTCGATCTATA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATA
*
20400339 GCGGTGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATA
* *
20400379 GC-GCGTTTTTT-AAAAGCACCGCTAATGCTCGACCTATA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATA
*
20400417 GCGACGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATA
* * * *
20400457 GCGGTGTATTTT--AAAGTGCTGCTAATGCTCGATCTATA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATA
*
20400495 GCGGCGTTTTTT-AAAAGCGCCGCTAATGCTTGATCTATA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATA
20400534 G
1 G
20400535 TGGTATTTTT
Statistics
Matches: 209, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
38 61 0.29
39 40 0.19
40 80 0.38
41 28 0.13
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (40 bp):
GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATA
Found at i:20400426 original size:78 final size:78
Alignment explanation
Indices: 20400258--20400534 Score: 398
Period size: 78 Copynumber: 3.5 Consensus size: 78
20400248 AATGTTTTTT
* * *
20400258 GCGGTGTTTTTCAGAAAGCGCCGCTAATGCTCGAATCTATAGCGGCGTTTTTTAAAAAGTGCTGC
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCG-ATCTATAGC-GCGTTTTTT-AAAAGTGCTGC
20400323 TAATGCTCGATCTATA
63 TAATGCTCGATCTATA
* ** *
20400339 GCGGTGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCGCGTTTTTTAAAAGCACCGCTAA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCGCGTTTTTTAAAAGTGCTGCTAA
*
20400404 TGCTCGACCTATA
66 TGCTCGATCTATA
*
20400417 GCGACGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCG-GTGTATTTT-AAAGTGCTGCT
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCGCGT-T-TTTTAAAAGTGCTGCT
20400480 AATGCTCGATCTATA
64 AATGCTCGATCTATA
*
20400495 GCGGCGTTTTTT-AAAAGCGCCGCTAATGCTTGATCTATAG
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAG
20400535 TGGTATTTTT
Statistics
Matches: 180, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
77 29 0.16
78 98 0.54
79 13 0.07
80 9 0.05
81 31 0.17
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (78 bp):
GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCGCGTTTTTTAAAAGTGCTGCTAA
TGCTCGATCTATA
Found at i:20403211 original size:3 final size:3
Alignment explanation
Indices: 20403203--20403227 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20403193 TGGGGTTTGA
20403203 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
20403228 CGTGAATGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:20407774 original size:12 final size:12
Alignment explanation
Indices: 20407755--20407791 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
20407745 TAAAATATAT
20407755 AATGTATAATAA
1 AATGTATAATAA
*
20407767 AATTTATAAATAA
1 AATGTAT-AATAA
20407780 AATGTATAATAA
1 AATGTATAATAA
20407792 TATAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (12 bp):
AATGTATAATAA
Found at i:20407780 original size:13 final size:13
Alignment explanation
Indices: 20407755--20407788 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
20407745 TAAAATATAT
20407755 AATGTAT-AATAA
1 AATGTATAAATAA
*
20407767 AATTTATAAATAA
1 AATGTATAAATAA
20407780 AATGTATAA
1 AATGTATAA
20407789 TAATATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (13 bp):
AATGTATAAATAA
Found at i:20407800 original size:25 final size:26
Alignment explanation
Indices: 20407748--20407805 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
20407738 TATATAGTAA
* **
20407748 AATATATAATGTATAATAAAATTTAT
1 AATATAAAATGTATAATAAAATAAAT
*
20407774 AA-ATAAAATGTATAATAATATAAAT
1 AATATAAAATGTATAATAAAATAAAT
20407799 AATATAA
1 AATATAA
20407806 TAATAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 21 0.78
26 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (26 bp):
AATATAAAATGTATAATAAAATAAAT
Found at i:20407804 original size:17 final size:17
Alignment explanation
Indices: 20407784--20407819 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
20407774 AAATAAAATG
20407784 TATAATAAT-ATAAATAA
1 TATAATAATAATAAA-AA
20407801 TATAATAATAATAAAAA
1 TATAATAATAATAAAAA
20407818 TA
1 TA
20407820 ATTTGATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TATAATAATAATAAAAA
Found at i:20409459 original size:44 final size:44
Alignment explanation
Indices: 20409394--20409768 Score: 466
Period size: 44 Copynumber: 8.6 Consensus size: 44
20409384 CCCCACCAAC
* * *
20409394 ACAGAGACGTCAAATCAACTATCTTCGATCTGCTCTCTGACAAT
1 ACAGAGATGCCAAATCTACTATCTTCGATCTGCTCTCTGACAAT
* * *
20409438 ACAGAGACGCCAAATCTACTATCTTCGATTTGCTCTCTAACAAT
1 ACAGAGATGCCAAATCTACTATCTTCGATCTGCTCTCTGACAAT
* * * * * *
20409482 ATAGAGATGTCAAATCTGCTATCTTCGATCTGCTTTCCGTCAAT
1 ACAGAGATGCCAAATCTACTATCTTCGATCTGCTCTCTGACAAT
*
20409526 ACAGAGATGCCAAATCTACTATCTGCGATCTGCTCTCTGACAAT
1 ACAGAGATGCCAAATCTACTATCTTCGATCTGCTCTCTGACAAT
* * *
20409570 ATAGAGATGCCAAATCTGCTATCTTTGATCTGCTCTCTGACAAT
1 ACAGAGATGCCAAATCTACTATCTTCGATCTGCTCTCTGACAAT
*
20409614 ACAGAGACGCCAAATCTACTATCTTCGATCTGCTCTCTGACAAT
1 ACAGAGATGCCAAATCTACTATCTTCGATCTGCTCTCTGACAAT
* * * *
20409658 ACAGAGACGCCAAATCTGCTATCCTCGATCTGCTCTCTGTCAAT
1 ACAGAGATGCCAAATCTACTATCTTCGATCTGCTCTCTGACAAT
* * * * * *
20409702 TCAGAGATGCCAGATGT-C-ATCTTCGATCTACTCTCTGTCACT
1 ACAGAGATGCCAAATCTACTATCTTCGATCTGCTCTCTGACAAT
* * *
20409744 ACAAAGATGCCAAATTTGCTATCTT
1 ACAGAGATGCCAAATCTACTATCTT
20409769 TAGAGATGCC
Statistics
Matches: 287, Mismatches: 42, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
42 34 0.12
43 2 0.01
44 251 0.87
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (44 bp):
ACAGAGATGCCAAATCTACTATCTTCGATCTGCTCTCTGACAAT
Found at i:20409822 original size:68 final size:66
Alignment explanation
Indices: 20409704--20409837 Score: 171
Period size: 68 Copynumber: 2.0 Consensus size: 66
20409694 CTGTCAATTC
* * * * *
20409704 AGAGATGCCAGATGTCATCTTCGATCTACTCTCTGTCACTACAAAGATGCCAAATTTGCTATCTT
1 AGAGATGCCAAATCTCATCTTCGATCTACTCTCTGACAATACAAAGATGCCAAATCTGCTATCTT
20409769 T
66 T
**
20409770 AGAGATGCCAAATCTACTATCTTCGATCTGTTCTCTGACAATACAGAA-ATGCCAAATCTGCTAT
1 AGAGATGCCAAATCT-C-ATCTTCGATCTACTCTCTGACAATACA-AAGATGCCAAATCTGCTAT
20409834 CTTT
63 CTTT
20409838 GATCTGCTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 13 0.22
67 1 0.02
68 42 0.72
69 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (66 bp):
AGAGATGCCAAATCTCATCTTCGATCTACTCTCTGACAATACAAAGATGCCAAATCTGCTATCTT
T
Found at i:20409842 original size:44 final size:44
Alignment explanation
Indices: 20409770--20410129 Score: 501
Period size: 44 Copynumber: 8.2 Consensus size: 44
20409760 TGCTATCTTT
* *
20409770 AGAGATGCCAAATCTACTATCTTCGATCTGTTCTCTGACAATAC
1 AGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* * *
20409814 AGAAATGCCAAATCTGCTATCTTTGATCTGCTCTCTTACAATAC
1 AGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* *
20409858 AGAGAGGCCAAATCTGCTATCTTCAATCTGCTCTCTGACAATAC
1 AGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
*
20409902 AGAGATGCCAAATCTGCTATCTTGGATCTGCTCTCTGACAATAC
1 AGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
** * *
20409946 AGAGACACCAAATCTACTATCTTCGATCTACTCTCTGACAATAC
1 AGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* * *
20409990 AGAGATGCCAAATCTGCTATCATCGATCTGCTCTCCGTCAATAC
1 AGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* * *
20410034 AGAGATG-CAAGATGT-C-ATCTTCAATCTGCTCTCTGTCAATAC
1 AGAGATGCCAA-ATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* *
20410076 AGAGATGCCAAATCTGCTATCTTCAATCTGTTCTCTGACAATAC
1 AGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
*
20410120 AGAGACGCCA
1 AGAGATGCCA
20410130 GATGTCACTG
Statistics
Matches: 279, Mismatches: 33, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
42 33 0.12
43 8 0.03
44 238 0.85
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (44 bp):
AGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
Found at i:20410049 original size:330 final size:330
Alignment explanation
Indices: 20409440--20410098 Score: 1050
Period size: 330 Copynumber: 2.0 Consensus size: 330
20409430 CTGACAATAC
* * * *
20409440 AGAGACGCCAAATCTACTATCTTCGATTTGCTCTCTAACAATATAGAGATGTCAAATCTGCTATC
1 AGAGACGCCAAATCTACTATCTTCGATCTGCTCTCTAACAATACAGAAATGCCAAATCTGCTATC
* * *
20409505 TTCGATCTGCTTTCCGTCAATACAGAGATGCCAAATCTACTATCTGCGATCTGCTCTCTGACAAT
66 TTCGATCTGCTCTCCGTCAATACAGAGAGGCCAAATCTACTATCTGCAATCTGCTCTCTGACAAT
* * *
20409570 ATAGAGATGCCAAATCTGCTATCTTTGATCTGCTCTCTGACAATACAGAGACGCCAAATCTACTA
131 ACAGAGATGCCAAATCTGCTATCTTGGATCTGCTCTCTGACAATACAGAGACACCAAATCTACTA
* * *
20409635 TCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGCTATCCTCGATCTGCTCTCTGTCA
196 TCTTCGATCTACTCTCTGACAATACAGAGACGCCAAATCTGCTATCATCGATCTGCTCTCCGTCA
* * * * *
20409700 ATTCAGAGATGCCAGATGTCATCTTCGATCTACTCTCTGTCACTACAAAGATGCCAAATTTGCTA
261 ATACAGAGATGCAAGATGTCATCTTCAATCTACTCTCTGTCAATACAAAGATGCCAAATCTGCTA
20409765 TCTTT
326 TCTTT
* * *
20409770 AGAGATGCCAAATCTACTATCTTCGATCTGTTCTCTGACAATACAGAAATGCCAAATCTGCTATC
1 AGAGACGCCAAATCTACTATCTTCGATCTGCTCTCTAACAATACAGAAATGCCAAATCTGCTATC
* * * *
20409835 TTTGATCTGCTCT-CTTACAATACAGAGAGGCCAAATCTGCTATCTTCAATCTGCTCTCTGACAA
66 TTCGATCTGCTCTCCGT-CAATACAGAGAGGCCAAATCTACTATCTGCAATCTGCTCTCTGACAA
20409899 TACAGAGATGCCAAATCTGCTATCTTGGATCTGCTCTCTGACAATACAGAGACACCAAATCTACT
130 TACAGAGATGCCAAATCTGCTATCTTGGATCTGCTCTCTGACAATACAGAGACACCAAATCTACT
*
20409964 ATCTTCGATCTACTCTCTGACAATACAGAGATGCCAAATCTGCTATCATCGATCTGCTCTCCGTC
195 ATCTTCGATCTACTCTCTGACAATACAGAGACGCCAAATCTGCTATCATCGATCTGCTCTCCGTC
* *
20410029 AATACAGAGATGCAAGATGTCATCTTCAATCTGCTCTCTGTCAATACAGAGATGCCAAATCTGCT
260 AATACAGAGATGCAAGATGTCATCTTCAATCTACTCTCTGTCAATACAAAGATGCCAAATCTGCT
20410094 ATCTT
325 ATCTT
20410099 CAATCTGTTC
Statistics
Matches: 300, Mismatches: 28, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
329 2 0.01
330 298 0.99
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (330 bp):
AGAGACGCCAAATCTACTATCTTCGATCTGCTCTCTAACAATACAGAAATGCCAAATCTGCTATC
TTCGATCTGCTCTCCGTCAATACAGAGAGGCCAAATCTACTATCTGCAATCTGCTCTCTGACAAT
ACAGAGATGCCAAATCTGCTATCTTGGATCTGCTCTCTGACAATACAGAGACACCAAATCTACTA
TCTTCGATCTACTCTCTGACAATACAGAGACGCCAAATCTGCTATCATCGATCTGCTCTCCGTCA
ATACAGAGATGCAAGATGTCATCTTCAATCTACTCTCTGTCAATACAAAGATGCCAAATCTGCTA
TCTTT
Found at i:20418562 original size:27 final size:29
Alignment explanation
Indices: 20418499--20418562 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 29
20418489 AAAAAATAAT
*
20418499 ATAAATATATTATATGATATAATAGCTTA
1 ATAAATATATTATATGAAATAATAGCTTA
*
20418528 ATATATAT-TTATAT-AAATAATA-CTATA
1 ATAAATATATTATATGAAATAATAGCT-TA
*
20418555 TTAAATAT
1 ATAAATAT
20418563 GTGTGAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 2 0.07
27 15 0.50
28 6 0.20
29 7 0.23
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (29 bp):
ATAAATATATTATATGAAATAATAGCTTA
Found at i:20418759 original size:12 final size:12
Alignment explanation
Indices: 20418740--20418776 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
20418730 TAAAATATAT
20418740 AATGTATAATAA
1 AATGTATAATAA
*
20418752 AATTTATAAATAA
1 AATGTAT-AATAA
20418765 AATGTATAATAA
1 AATGTATAATAA
20418777 TATAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (12 bp):
AATGTATAATAA
Found at i:20418765 original size:13 final size:13
Alignment explanation
Indices: 20418740--20418773 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
20418730 TAAAATATAT
20418740 AATGTAT-AATAA
1 AATGTATAAATAA
*
20418752 AATTTATAAATAA
1 AATGTATAAATAA
20418765 AATGTATAA
1 AATGTATAA
20418774 TAATATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (13 bp):
AATGTATAAATAA
Found at i:20418788 original size:46 final size:47
Alignment explanation
Indices: 20418672--20418788 Score: 116
Period size: 46 Copynumber: 2.5 Consensus size: 47
20418662 TTACACAATT
* *
20418672 AATGAATAATAAAATAATACATAATTTATAATAAAAATGTAAGGAATAA
1 AATGTATAATAAAATAATA-ATAATGTATAATAAAAATGTAA-GAATAA
* * * *
20418721 TATATATAGTAAAAT-AT-ATAATGTATAAT-AAAATTTATA-AATAA
1 AATGTATAATAAAATAATAATAATGTATAATAAAAATGTA-AGAATAA
*
20418765 AATGTATAATAATATAATAATAAT
1 AATGTATAATAAAATAATAATAAT
20418789 AAAAATAATT
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
44 16 0.29
45 9 0.16
46 17 0.31
48 2 0.04
49 11 0.20
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.34
Consensus pattern (47 bp):
AATGTATAATAAAATAATAATAATGTATAATAAAAATGTAAGAATAA
Found at i:20421485 original size:31 final size:29
Alignment explanation
Indices: 20421428--20421488 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 29
20421418 TTTTTTAAAT
20421428 ATGTATAATAAAATTAAAATTAAAATTTC
1 ATGTATAATAAAATTAAAATTAAAATTTC
* *
20421457 ATGTATACATATAAATTATAATTTAAATTTC
1 ATGTATA-ATA-AAATTAAAATTAAAATTTC
20421488 A
1 A
20421489 AATGTCTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.25
30 3 0.11
31 18 0.64
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (29 bp):
ATGTATAATAAAATTAAAATTAAAATTTC
Found at i:20421986 original size:25 final size:25
Alignment explanation
Indices: 20421952--20422014 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 25
20421942 ATTTTATGTC
20421952 TTTTTTTAAATTTACATAATT-AAA-T
1 TTTTTTTAAATTT--ATAATTCAAATT
*
20421977 TTTTTTTAAAATTATAATTCAAATT
1 TTTTTTTAAATTTATAATTCAAATT
20422002 TTTTTTTAAATTT
1 TTTTTTTAAATTT
20422015 TCAGTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 6 0.18
24 3 0.09
25 25 0.74
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTTTTAAATTTATAATTCAAATT
Found at i:20422000 original size:24 final size:24
Alignment explanation
Indices: 20421952--20422013 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 24
20421942 ATTTTATGTC
*
20421952 TTTTTTTAAATTTACATAATTAAAT
1 TTTTTTTAAAATTA-ATAATTAAAT
20421977 TTTTTTTAAAATT-ATAATTCAAAT
1 TTTTTTTAAAATTAATAATT-AAAT
*
20422001 TTTTTTTTAAATT
1 TTTTTTTAAAATT
20422014 TTCAGTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 6 0.18
24 16 0.47
25 12 0.35
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTTTTAAAATTAATAATTAAAT
Found at i:20434003 original size:36 final size:33
Alignment explanation
Indices: 20433953--20434020 Score: 82
Period size: 36 Copynumber: 2.0 Consensus size: 33
20433943 TTTAATCATC
* *
20433953 AAATTTTTTTTAAAAAATTGAATTATTTTTTAATAG
1 AAATATTTATTAAAAAATT-AA--ATTTTTTAATAG
*
20433989 AAATATTTATTAAAATATTAAATTTTTTAATA
1 AAATATTTATTAAAAAATTAAATTTTTTAATA
20434021 TAGTACTCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 11 0.38
35 2 0.07
36 16 0.55
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (33 bp):
AAATATTTATTAAAAAATTAAATTTTTTAATAG
Found at i:20436192 original size:47 final size:47
Alignment explanation
Indices: 20436127--20436233 Score: 153
Period size: 47 Copynumber: 2.3 Consensus size: 47
20436117 GCATTCTATT
* *
20436127 TAGCCTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCA-TACTCTGA
1 TAGCCTTTGTGGCATATTCTGTATGTTGCCTTTGTGG-AGTACTCTAA
* **
20436174 TAGCATTTGTGGCATATTCTGTATGTTTTCTTTGTGGAGTACTCTAA
1 TAGCCTTTGTGGCATATTCTGTATGTTGCCTTTGTGGAGTACTCTAA
20436221 TAGCCTTTGTGGC
1 TAGCCTTTGTGGC
20436234 GTATCTATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
46 1 0.02
47 52 0.98
ACGTcount: A:0.15, C:0.17, G:0.24, T:0.44
Consensus pattern (47 bp):
TAGCCTTTGTGGCATATTCTGTATGTTGCCTTTGTGGAGTACTCTAA
Found at i:20436249 original size:21 final size:21
Alignment explanation
Indices: 20436203--20436259 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
20436193 TGTATGTTTT
*
20436203 CTTTGTGGAGTACTCTAATAGC
1 CTTTGTGGCGTA-TCTAATAGC
*
20436225 CTTTGTGGCGTATCTATTTAGC
1 CTTTGTGGCGTATCTA-ATAGC
*
20436247 TTTTGTGGCGTAT
1 CTTTGTGGCGTAT
20436260 TCTGATAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.44
Consensus pattern (21 bp):
CTTTGTGGCGTATCTAATAGC
Found at i:20442876 original size:77 final size:77
Alignment explanation
Indices: 20442749--20442903 Score: 292
Period size: 77 Copynumber: 2.0 Consensus size: 77
20442739 CAGATGCGGT
20442749 TCACTTGACCGTTTTCTCAGGGATTGTCCCAAAAGAATTGAAAAGGAGATATTACCAGCTCTAAA
1 TCACTTGACCGTTTTCTCAGGGATTGTCCCAAAAGAATTGAAAAGGAGATATTACCAGCTCTAAA
20442814 GCCAAGCAATCC
66 GCCAAGCAATCC
*
20442826 TCACTTGACTGTTTTCTCAGGGATTGTCCCAAAAGAATTGAAAAGGAGATATTACCAGCTCTAAA
1 TCACTTGACCGTTTTCTCAGGGATTGTCCCAAAAGAATTGAAAAGGAGATATTACCAGCTCTAAA
*
20442891 GCCGAGCAATCC
66 GCCAAGCAATCC
20442903 T
1 T
20442904 ATGGGAAGAG
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (77 bp):
TCACTTGACCGTTTTCTCAGGGATTGTCCCAAAAGAATTGAAAAGGAGATATTACCAGCTCTAAA
GCCAAGCAATCC
Found at i:20448899 original size:22 final size:22
Alignment explanation
Indices: 20448869--20448922 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
20448859 ATATCCATTT
*
20448869 TTTTTAAATTAATAAAAAACT-A
1 TTTTAAAATTAATAAAAAA-TAA
* *
20448891 TTTTAAAATTAATAGAAGATAA
1 TTTTAAAATTAATAAAAAATAA
20448913 TTTTAAAATT
1 TTTTAAAATT
20448923 TTAATAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (22 bp):
TTTTAAAATTAATAAAAAATAA
Found at i:20453865 original size:46 final size:48
Alignment explanation
Indices: 20453815--20453937 Score: 153
Period size: 48 Copynumber: 2.6 Consensus size: 48
20453805 TGTGCACTAG
20453815 TGTAAGATATGTCTGGGACATGCATCGGCCAC-A-AT-TTGAGAGCCAA
1 TGTAAGATATGTCTGGGACATGCATCGGCCACGAGATATTGA-AGCCAA
* * * * *
20453861 TGTAAGATATGTCTGGGACATGCTTTGGCCTCGAGATATTTAAGCCAG
1 TGTAAGATATGTCTGGGACATGCATCGGCCACGAGATATTGAAGCCAA
* *
20453909 TGTAAGACATGTTTGGGACATGCATCGGC
1 TGTAAGATATGTCTGGGACATGCATCGGC
20453938 ATTGAGACGA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 29 0.45
47 1 0.02
48 32 0.49
49 3 0.05
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.28
Consensus pattern (48 bp):
TGTAAGATATGTCTGGGACATGCATCGGCCACGAGATATTGAAGCCAA
Found at i:20453926 original size:48 final size:46
Alignment explanation
Indices: 20453813--20453980 Score: 160
Period size: 46 Copynumber: 3.6 Consensus size: 46
20453803 TTTGTGCACT
20453813 AGTGTAAGATATGTCTGGGACATGCATCGGCCACAATTTGAGAGCC
1 AGTGTAAGATATGTCTGGGACATGCATCGGCCACAATTTGAGAGCC
* * * * *
20453859 AATGTAAGATATGTCTGGGACATGCTTTGGCCTCGAGATATTTA-AGCC
1 AGTGTAAGATATGTCTGGGACATGCATCGGCCAC-A-AT-TTGAGAGCC
* * ** *** *
20453907 AGTGTAAGACATGTTTGGGACATGCATCGG-CATTGAGACGAGAGCT
1 AGTGTAAGATATGTCTGGGACATGCATCGGCCA-CAATTTGAGAGCC
*
20453953 AGTGTAAGACATGTCTGGGACATGCATC
1 AGTGTAAGATATGTCTGGGACATGCATC
20453981 AGCCTCGCGA
Statistics
Matches: 98, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
45 1 0.01
46 61 0.62
47 2 0.02
48 31 0.32
49 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (46 bp):
AGTGTAAGATATGTCTGGGACATGCATCGGCCACAATTTGAGAGCC
Found at i:20454005 original size:94 final size:94
Alignment explanation
Indices: 20453811--20454024 Score: 232
Period size: 94 Copynumber: 2.3 Consensus size: 94
20453801 CATTTGTGCA
* *** *
20453811 CTAGTGTAAGATATGTCTGGGACATGCATCGGCCACAATTTGAGAGCCAATGTAAGATATGTCTG
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGACGAGAGCCAATGTAAGACATGTCTG
* ** **
20453876 GGACATGCTTTGGCCTCGAGATATTTAAG
66 GGACATGCATCAGCCTCGAGATATACAAG
* * ** * *
20453905 CCAGTGTAAGACATGTTTGGGACATGCATCGG-CATTGAGACGAGAGCTAGTGTAAGACATGTCT
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCA-CAAGACGAGAGCCAATGTAAGACATGTCT
*
20453969 GGGACATGCATCAGCCTCGCGATATACAAG
65 GGGACATGCATCAGCCTCGAGATATACAAG
* * *
20453999 CTAGTGTACGACCTATCTGGGACATG
1 CTAGTGTAAGACATGTCTGGGACATG
20454025 GCGTCAGCTT
Statistics
Matches: 97, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
93 2 0.02
94 95 0.98
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (94 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGACGAGAGCCAATGTAAGACATGTCTG
GGACATGCATCAGCCTCGAGATATACAAG
Found at i:20454556 original size:22 final size:21
Alignment explanation
Indices: 20454531--20454578 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
20454521 AGCACGGCCA
*
20454531 TGTTATAATGACCATACGGGCG
1 TGTT-TAACGACCATACGGGCG
*
20454553 TGTTTCACGACCATACGGGCG
1 TGTTTAACGACCATACGGGCG
20454574 TGTTT
1 TGTTT
20454579 CCCTTCCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (21 bp):
TGTTTAACGACCATACGGGCG
Found at i:20454566 original size:21 final size:21
Alignment explanation
Indices: 20454540--20454579 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
20454530 ATGTTATAAT
20454540 GACCATACGGGCGTGTTTCAC
1 GACCATACGGGCGTGTTTCAC
20454561 GACCATACGGGCGTGTTTC
1 GACCATACGGGCGTGTTTC
20454580 CCTTCCACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (21 bp):
GACCATACGGGCGTGTTTCAC
Found at i:20454591 original size:21 final size:21
Alignment explanation
Indices: 20454540--20454593 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
20454530 ATGTTATAAT
*
20454540 GACCATACGGGCGTGTTTCAC
1 GACCACACGGGCGTGTTTCAC
* *
20454561 GACCATACGGGCGTGTTTCCC
1 GACCACACGGGCGTGTTTCAC
**
20454582 TTCCACACGGGC
1 GACCACACGGGC
20454594 ATGTGCCCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.33, G:0.28, T:0.22
Consensus pattern (21 bp):
GACCACACGGGCGTGTTTCAC
Found at i:20461164 original size:49 final size:49
Alignment explanation
Indices: 20461061--20461186 Score: 146
Period size: 49 Copynumber: 2.6 Consensus size: 49
20461051 TGTTGTGTGT
* * * *
20461061 CAGTGTAAGACCTACCTGGGACATGACATCGACACTGATAGATGAGAGC
1 CAGTGTAAGACCTGCCTGGGACATGGCATCGACACTCATAGATGAAAGC
* *
20461110 CAGTGTAAGACCTGCCTGGGACATGGCATCGGC-CTCACTATATGAAAGC
1 CAGTGTAAGACCTGCCTGGGACATGGCATCGACACTCA-TAGATGAAAGC
* * *
20461159 TAGTGTAAGATCATGTCTGGGACATGGC
1 CAGTGTAAGA-CCTGCCTGGGACATGGC
20461187 GTCAGTATCT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
48 3 0.05
49 48 0.73
50 15 0.23
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (49 bp):
CAGTGTAAGACCTGCCTGGGACATGGCATCGACACTCATAGATGAAAGC
Found at i:20462428 original size:20 final size:21
Alignment explanation
Indices: 20462389--20462428 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20462379 GTTATAATGA
**
20462389 CCACACGGGTGTGTTGCCCTT
1 CCACACGGGCATGTTGCCCTT
20462410 CCACACGGGCATG-TGCCCT
1 CCACACGGGCATGTTGCCCT
20462429 ATTTTAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.38, G:0.28, T:0.23
Consensus pattern (21 bp):
CCACACGGGCATGTTGCCCTT
Found at i:20469489 original size:39 final size:40
Alignment explanation
Indices: 20469442--20469570 Score: 131
Period size: 40 Copynumber: 3.3 Consensus size: 40
20469432 GGACTAGGAT
**
20469442 CCGAAGGCATTCGTGCGGGTTAATAAATCC-GGGCTAAG-C
1 CCGAAGGCATTCGTGCAAGTTAATAAA-CCTGGGCTAAGTC
* *
20469481 CCGAAGGCATT-GTGCAAGTTACTAAACCTGGGTTAAGTC
1 CCGAAGGCATTCGTGCAAGTTAATAAACCTGGGCTAAGTC
*** **
20469520 CCGAAGGCATTCGTGCAAGTCGCTATAACC-GGGCTTCGTC
1 CCGAAGGCATTCGTGCAAGTTAATA-AACCTGGGCTAAGTC
20469560 CCGAAGGCATT
1 CCGAAGGCATT
20469571 TGAGCGAGTC
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
37 2 0.03
38 19 0.25
39 23 0.30
40 29 0.38
41 4 0.05
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCAAGTTAATAAACCTGGGCTAAGTC
Found at i:20469534 original size:78 final size:80
Alignment explanation
Indices: 20469389--20469535 Score: 194
Period size: 78 Copynumber: 1.9 Consensus size: 80
20469379 TCGAATGATG
* * *
20469389 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTATAACCGGACTAAGATCCGAAGGCATTC
20469454 GTGCGGGTTAATAAA
66 GTGCGGGTTAATAAA
* **
20469469 TCCGGGCTAAG-CCCGAAGGCATTGTGC-AAGTTACTA-AACCTGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTATAACC-GGACTAAGAT-CCGAAGGCAT
20469530 TCGTGC
64 TCGTGC
20469536 AAGTCGCTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
77 4 0.07
78 29 0.49
79 15 0.25
80 11 0.19
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTATAACCGGACTAAGATCCGAAGGCATTC
GTGCGGGTTAATAAA
Found at i:20477525 original size:39 final size:40
Alignment explanation
Indices: 20477425--20477606 Score: 185
Period size: 40 Copynumber: 4.6 Consensus size: 40
20477415 TCGAATGATG
* * *
20477425 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
20477465 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
20477505 TCCGGGCTAAG-CCCGAAGGCATT-GTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * **
20477543 CCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTCGCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
**
20477584 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
20477607 TGAGCGAGTC
Statistics
Matches: 118, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
38 22 0.19
39 23 0.19
40 64 0.54
41 9 0.08
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:20477570 original size:78 final size:80
Alignment explanation
Indices: 20477425--20477606 Score: 201
Period size: 78 Copynumber: 2.3 Consensus size: 80
20477415 TCGAATGATG
* * * *
20477425 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
20477490 GTGCGAGTTAATAAA
66 GTGCGAGTTAATAAA
* **
20477505 TCCGGGCTAAG-CCCGAAGGCATTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
* ***
20477567 CGTGCAAGTCGCTATAA
65 CGTGCGAGTTAATA-AA
**
20477584 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
20477607 TGAGCGAGTC
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
77 1 0.01
78 45 0.52
79 29 0.34
80 11 0.13
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTTAATAAA
Found at i:20484710 original size:27 final size:27
Alignment explanation
Indices: 20484672--20484726 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
20484662 AGCTCTGAAC
20484672 TTTTCAGCCCTGTGTTTACGGATCTTA
1 TTTTCAGCCCTGTGTTTACGGATCTTA
20484699 TTTTCAGCCCTGTGTTTACGGATCTTA
1 TTTTCAGCCCTGTGTTTACGGATCTTA
20484726 T
1 T
20484727 CTACTGGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (27 bp):
TTTTCAGCCCTGTGTTTACGGATCTTA
Found at i:20486151 original size:74 final size:74
Alignment explanation
Indices: 20486030--20486176 Score: 258
Period size: 74 Copynumber: 2.0 Consensus size: 74
20486020 ATATATCTTC
*
20486030 ATTGTGACAGCCCAAAATTGACCCTAGTCGGGAGGTGGTTTCGGGACCACAAAACCGAAGCATAA
1 ATTGTGACAGCCCAAAATTGACCCTAGTCGGAAGGTGGTTTCGGGACCACAAAACCGAAGCATAA
20486095 AAATAATTT
66 AAATAATTT
* **
20486104 ATTGTGACAGCCCAAAATTGACCCTAGTCGGAATGTGGTTTCGGGACCACAAAACCGGGGCATAA
1 ATTGTGACAGCCCAAAATTGACCCTAGTCGGAAGGTGGTTTCGGGACCACAAAACCGAAGCATAA
20486169 AAATAATT
66 AAATAATT
20486177 AAAAATTTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (74 bp):
ATTGTGACAGCCCAAAATTGACCCTAGTCGGAAGGTGGTTTCGGGACCACAAAACCGAAGCATAA
AAATAATTT
Found at i:20487983 original size:40 final size:39
Alignment explanation
Indices: 20487856--20487985 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
20487846 ATGCTGGAAA
*
20487856 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-AGTGG
* * **
20487896 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGC-AGTGG
*
20487936 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA-GTGG
20487976 TTATATCCGG
1 TTATATCCGG
20487986 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.24
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAGTGG
Found at i:20496037 original size:40 final size:39
Alignment explanation
Indices: 20495910--20496039 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
20495900 ATGCTGGAAA
*
20495910 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-AGTGG
* * **
20495950 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGC-AGTGG
*
20495990 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA-GTGG
20496030 TTATATCCGG
1 TTATATCCGG
20496040 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.24
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAGTGG
Found at i:20496038 original size:80 final size:79
Alignment explanation
Indices: 20495873--20496039 Score: 194
Period size: 80 Copynumber: 2.1 Consensus size: 79
20495863 AAATTGAATG
* ** *
20495873 ATATCCGGGCTAAGCCCCGAAGACATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAA
1 ATATCCGGGCTAAGACCCGAAGACATTATGCAAGAAATTATATCCGGGCTAAGACCCGAAGGCAA
20495938 TTGTGCTAGTGGCT
66 TTGTGCTAGTGGCT
* * * ** *
20495952 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCATTCTATCCGGGCTAAGACCCGAAGGC-
1 ATATCCGGGCTAAGACCCGAAGACATT-ATGCAAGAAATTATATCCGGGCTAAGACCCGAAGGCA
*
20496016 ATTCGTGC-ACGTGGTT
65 ATT-GTGCTA-GTGGCT
20496032 ATATCCGG
1 ATATCCGG
20496040 TTGTATTCCG
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
79 28 0.38
80 45 0.62
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.23
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGACATTATGCAAGAAATTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCTAGTGGCT
Found at i:20499051 original size:41 final size:41
Alignment explanation
Indices: 20498994--20499149 Score: 237
Period size: 41 Copynumber: 3.8 Consensus size: 41
20498984 AATGTTCGAG
20498994 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAAAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAAAGTTA
20499035 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCG-AAGTGTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAAAGT-TA
*
20499076 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGC-AAA-TTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAAAGTTA
* **
20499115 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCG
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
20499150 GGTTACCATA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 16 0.15
40 20 0.19
41 71 0.66
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.24
Consensus pattern (41 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAAAGTTA
Found at i:20501579 original size:53 final size:54
Alignment explanation
Indices: 20501515--20501721 Score: 191
Period size: 53 Copynumber: 3.8 Consensus size: 54
20501505 TTCCTTTTTA
* *
20501515 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * * *
20501568 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATCG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * * * * * * *
20501622 TAGTTTATCAATGCCAGGTCTTGACATGTTATTACATGATTTCTTTGCCTTTTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * *
20501677 AACTTGCCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
20501722 AAACCCTAAT
Statistics
Matches: 118, Mismatches: 34, Indels: 3
0.76 0.22 0.02
Matches are distributed among these distances:
53 47 0.40
54 33 0.28
55 38 0.32
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:20503372 original size:71 final size:71
Alignment explanation
Indices: 20503288--20503451 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
20503278 CGATTTGTCT
20503288 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
20503353 CTTTCA
66 CTTTCA
20503359 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
20503424 CTTTCA
66 CTTTCA
20503430 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
20503452 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:20503489 original size:71 final size:70
Alignment explanation
Indices: 20503288--20503485 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
20503278 CGATTTGTCT
* * * *
20503288 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
20503353 CTTTCA
65 CTTTCA
* * * *
20503359 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
20503424 CTTTCA
65 CTTTCA
* *
20503430 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
20503486 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:20508963 original size:32 final size:32
Alignment explanation
Indices: 20508924--20508990 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
20508914 TATGACATTT
* *
20508924 ATACAATTCACAGCATAACATGTAATTCAAGC
1 ATACAATTCAAAACATAACATGTAATTCAAGC
** *
20508956 ATACAATTCAAAATGTAACATTTAATTCAAGC
1 ATACAATTCAAAACATAACATGTAATTCAAGC
20508988 ATA
1 ATA
20508991 TAAACATACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.28
Consensus pattern (32 bp):
ATACAATTCAAAACATAACATGTAATTCAAGC
Found at i:20511361 original size:31 final size:31
Alignment explanation
Indices: 20511326--20511392 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
20511316 CTTCCTGCAT
* *
20511326 TAAAATCCAACCAAATAC-AAAAATTATAGTA
1 TAAAATCCAACCAAAAACAAAAAATT-TAGCA
* *
20511357 TAAAATGCAGCCAAAAACAAAAAATTTAGCA
1 TAAAATCCAACCAAAAACAAAAAATTTAGCA
20511388 TAAAA
1 TAAAA
20511393 AATACAACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 24 0.77
32 7 0.23
ACGTcount: A:0.60, C:0.15, G:0.06, T:0.19
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAAAAAATTTAGCA
Found at i:20511664 original size:21 final size:21
Alignment explanation
Indices: 20511640--20511736 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
20511630 TCTACTGCCA
*
20511640 TCGCTGCTACCTCTGCCTCCC
1 TCGCTGCTGCCTCTGCCTCCC
*
20511661 TCGCT-CGTGCCTCTGCCTCTC
1 TCGCTGC-TGCCTCTGCCTCCC
* * * *
20511682 TCACTGATGCCACTACCTCCC
1 TCGCTGCTGCCTCTGCCTCCC
* *
20511703 TCGCTGCTGTCGCTGCCTCCC
1 TCGCTGCTGCCTCTGCCTCCC
* *
20511724 TCTCTACTGCCTC
1 TCGCTGCTGCCTC
20511737 GGTTCTAAGT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
20 1 0.02
21 57 0.98
ACGTcount: A:0.06, C:0.48, G:0.15, T:0.30
Consensus pattern (21 bp):
TCGCTGCTGCCTCTGCCTCCC
Found at i:20517368 original size:9 final size:9
Alignment explanation
Indices: 20517354--20517593 Score: 186
Period size: 9 Copynumber: 27.1 Consensus size: 9
20517344 TATTTAAGTA
20517354 TTATGTAAG
1 TTATGTAAG
20517363 TTATGTAAG
1 TTATGTAAG
*
20517372 TTATGATATG
1 TTATG-TAAG
* * *
20517382 ATATAT-AT
1 TTATGTAAG
20517390 TTATGTAAG
1 TTATGTAAG
* *
20517399 TTATAT-AT
1 TTATGTAAG
*
20517407 TTATCTAAG
1 TTATGTAAG
*
20517416 TTATATAAG
1 TTATGTAAG
*
20517425 TTATGTGAG
1 TTATGTAAG
20517434 TTATGTAAG
1 TTATGTAAG
* *
20517443 TTATAT-AT
1 TTATGTAAG
*
20517451 TTATCTAAG
1 TTATGTAAG
*
20517460 TTATATAAG
1 TTATGTAAG
*
20517469 TTATCTAAG
1 TTATGTAAG
20517478 TTATGTAAG
1 TTATGTAAG
* *
20517487 TTATAT-AT
1 TTATGTAAG
*
20517495 TTATCTAAG
1 TTATGTAAG
20517504 TTATGTAAG
1 TTATGTAAG
* *
20517513 TTATAT-AT
1 TTATGTAAG
*
20517521 TTATCTAAG
1 TTATGTAAG
*
20517530 TTATATAAG
1 TTATGTAAG
* *
20517539 TTATAT-AT
1 TTATGTAAG
*
20517547 TTATCTAAG
1 TTATGTAAG
*
20517556 TTATATAAG
1 TTATGTAAG
20517565 TTATGTAAG
1 TTATGTAAG
*
20517574 TTTTGTAAG
1 TTATGTAAG
20517583 TTATGTTAAG
1 TTATG-TAAG
20517593 T
1 T
20517594 ATTTATCAAA
Statistics
Matches: 183, Mismatches: 40, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
8 34 0.19
9 138 0.75
10 11 0.06
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:20517419 original size:26 final size:27
Alignment explanation
Indices: 20517354--20517586 Score: 208
Period size: 26 Copynumber: 8.8 Consensus size: 27
20517344 TATTTAAGTA
* * *
20517354 TTATGTAAGTTATGTAAGTTATGATATG
1 TTATATAAGTTATCTAAGTTAT-ATAAG
* * * *
20517382 ATATAT-ATTTATGTAAGTTATAT-AT
1 TTATATAAGTTATCTAAGTTATATAAG
* * * *
20517407 TTATCTAAGTTATATAAGTTATGTGAG
1 TTATATAAGTTATCTAAGTTATATAAG
* * * *
20517434 TTATGTAAGTTATAT-ATTTATCTAAG
1 TTATATAAGTTATCTAAGTTATATAAG
*
20517460 TTATATAAGTTATCTAAGTTATGTAAG
1 TTATATAAGTTATCTAAGTTATATAAG
* *
20517487 TTATAT-ATTTATCTAAGTTATGTAAG
1 TTATATAAGTTATCTAAGTTATATAAG
*
20517513 TTATAT-ATTTATCTAAGTTATATAAG
1 TTATATAAGTTATCTAAGTTATATAAG
*
20517539 TTATAT-ATTTATCTAAGTTATATAAG
1 TTATATAAGTTATCTAAGTTATATAAG
* * *
20517565 TTATGTAAGTTTTGTAAGTTAT
1 TTATATAAGTTATCTAAGTTAT
20517587 GTTAAGTATT
Statistics
Matches: 176, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.02
26 112 0.64
27 56 0.32
28 4 0.02
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (27 bp):
TTATATAAGTTATCTAAGTTATATAAG
Found at i:20517420 original size:15 final size:17
Alignment explanation
Indices: 20517383--20517562 Score: 103
Period size: 17 Copynumber: 10.4 Consensus size: 17
20517373 TATGATATGA
*
20517383 TATATATTTATGTAAGT
1 TATATATTTATCTAAGT
20517400 TATATATTTATCTAAGT
1 TATATATTTATCTAAGT
* * *
20517417 TATATAAGTTATGTGAGT
1 TATAT-ATTTATCTAAGT
* * * *
20517435 TATGTAAGTTATAT-ATT
1 TATAT-ATTTATCTAAGT
* * *
20517452 TATCTAAGTTATATAAGT
1 TATAT-ATTTATCTAAGT
* * *
20517470 TATCTAAGTTATGTAAGT
1 TATAT-ATTTATCTAAGT
20517488 TATATATTTATCTAAGT
1 TATATATTTATCTAAGT
* * * *
20517505 TATGTAAGTTATAT-ATT
1 TATAT-ATTTATCTAAGT
* * *
20517522 TATCTAAGTTATATAAGT
1 TATAT-ATTTATCTAAGT
20517540 TATATATTTATCTAAGT
1 TATATATTTATCTAAGT
20517557 TATATA
1 TATATA
20517563 AGTTATGTAA
Statistics
Matches: 137, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
17 81 0.59
18 56 0.41
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.49
Consensus pattern (17 bp):
TATATATTTATCTAAGT
Found at i:20517438 original size:44 final size:44
Alignment explanation
Indices: 20517390--20517586 Score: 268
Period size: 44 Copynumber: 4.3 Consensus size: 44
20517380 TGATATATAT
* *
20517390 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTGAG
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATCTAAG
20517434 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATCTAAG
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATCTAAG
*
20517478 TTATGTAAGTTATATATTTATCTAAGTTATGTAAGTTATATATTTATCTAAG
1 TTATGTAAGTTATATATTTATCTAAG---T-T-A--TATA-AGTTATCTAAG
* *
20517530 TTATATAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATCTAAG
*
20517574 TTTTGTAAGTTAT
1 TTATGTAAGTTAT
20517587 GTTAAGTATT
Statistics
Matches: 137, Mismatches: 8, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
44 88 0.64
45 4 0.03
47 2 0.01
48 2 0.01
49 2 0.01
51 4 0.03
52 35 0.26
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (44 bp):
TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATCTAAG
Found at i:20517718 original size:15 final size:15
Alignment explanation
Indices: 20517698--20517753 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
20517688 GTAAGTTGCG
20517698 AATTAAATAATATTT
1 AATTAAATAATATTT
20517713 AATTAAATAATATTT
1 AATTAAATAATATTT
* *
20517728 -A-TAAAAAAAATTTT
1 AATTAAATAATA-TTT
20517742 AATTAAATAATA
1 AATTAAATAATA
20517754 CTGAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 16 0.47
16 7 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTAAATAATATTT
Found at i:20517746 original size:29 final size:29
Alignment explanation
Indices: 20517702--20517783 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
20517692 GTTGCGAATT
*
20517702 AAATAATATTTAATTAAATAATATTTATAAA
1 AAATAAT-TTTAATTAAATAATATTGA-AAA
*
20517733 AAA-AATTTTAATTAAATAATACTGAAAA
1 AAATAATTTTAATTAAATAATATTGAAAA
* *
20517761 AAATTATTTTAATTCAATAATAT
1 AAATAATTTTAATTAAATAATAT
20517784 ACATGTCGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
28 6 0.13
29 33 0.73
30 3 0.07
31 3 0.07
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (29 bp):
AAATAATTTTAATTAAATAATATTGAAAA
Found at i:20517998 original size:24 final size:24
Alignment explanation
Indices: 20517957--20518027 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
20517947 TTAACTTAAA
* *
20517957 TGATAAAATGGGCGATAATATTTG
1 TGATAAAACGGACGATAATATTTG
*
20517981 TGATAAAACGGACAATAATATTTG
1 TGATAAAACGGACGATAATATTTG
* *
20518005 TGATAAAACAGACGAGAATATTT
1 TGATAAAACGGACGATAATATTT
20518028 CAATAATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.30
Consensus pattern (24 bp):
TGATAAAACGGACGATAATATTTG
Found at i:20518144 original size:64 final size:64
Alignment explanation
Indices: 20518075--20518209 Score: 252
Period size: 64 Copynumber: 2.1 Consensus size: 64
20518065 ATATTTTATT
* *
20518075 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATAAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
20518139 AAATATTTGTATATAAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATAAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
20518203 AAATATT
1 AAATATT
20518210 AAATCACAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 69 1.00
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.38
Consensus pattern (64 bp):
AAATATTTGTATATAAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
Found at i:20519002 original size:6 final size:7
Alignment explanation
Indices: 20518983--20519008 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20518973 ACTTATAAAC
20518983 GCAAAAA
1 GCAAAAA
20518990 GCAAAAA
1 GCAAAAA
20518997 GCAAAAA
1 GCAAAAA
20519004 GCAAA
1 GCAAA
20519009 TCTATAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (7 bp):
GCAAAAA
Found at i:20520864 original size:19 final size:20
Alignment explanation
Indices: 20520830--20520876 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
20520820 ATTTTGATCC
*
20520830 GGGGAAATATTTAGGGATTA
1 GGGGAAATAGTTAGGGATTA
*
20520850 GGGGAAA-AGTTAGGGATTT
1 GGGGAAATAGTTAGGGATTA
20520869 GGGGAAAT
1 GGGGAAAT
20520877 TTGGGTGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.34, C:0.00, G:0.40, T:0.26
Consensus pattern (20 bp):
GGGGAAATAGTTAGGGATTA
Found at i:20521360 original size:147 final size:148
Alignment explanation
Indices: 20521151--20521467 Score: 367
Period size: 147 Copynumber: 2.1 Consensus size: 148
20521141 AATGAAACCT
* * * *
20521151 TAATACAAATTTGCGGCGTTTTATATAAAGTGCCACTAAAAACAAAGAATAAAACGGCGCCGTTT
1 TAATACACATTTGTGGCGTTTTGTACAAAGTGCCACTAAAAACAAAGAATAAAACGGCGCCGTTT
* * *
20521216 AGAAAAC-ACATAACATAA-AT-TTGCGGCGTTTTAGTCAAAGCGCCACCAATAACAAGGATAA-
66 AG-AAACTA-AT-ACATAACATATTGCGGCGTTTT-GGCAAAACGCCACCAACAACAAGGATAAT
20521277 ACGGTGTCATTTCTTGAACTCG
127 ACGGTGTCATTTCTTGAACTCG
** * *
20521299 TAATACATTTTTGTGGC-TTTTGTACAAAGTGCCACTAAAAACAAA-ACATAGAACGGTGCCGTT
1 TAATACACATTTGTGGCGTTTTGTACAAAGTGCCACTAAAAACAAAGA-ATAAAACGGCGCCGTT
* *** * * *
20521362 TTGCTGCTAATACATAACCTATTGCGGCGTTTTGGGAAAACGCCACTAACAACAAGGATAATACG
65 TAGAAACTAATACATAACATATTGCGGCGTTTTGGCAAAACGCCACCAACAACAAGGATAATACG
* *
20521427 GTGTCATTTTTTGGACTCG
130 GTGTCATTTCTTGAACTCG
20521446 TAATACACATTTGTGGCGTTTT
1 TAATACACATTTGTGGCGTTTT
20521468 AAATGAAAAT
Statistics
Matches: 142, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
145 6 0.04
146 28 0.20
147 90 0.63
148 18 0.13
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (148 bp):
TAATACACATTTGTGGCGTTTTGTACAAAGTGCCACTAAAAACAAAGAATAAAACGGCGCCGTTT
AGAAACTAATACATAACATATTGCGGCGTTTTGGCAAAACGCCACCAACAACAAGGATAATACGG
TGTCATTTCTTGAACTCG
Found at i:20522023 original size:103 final size:105
Alignment explanation
Indices: 20521909--20522119 Score: 245
Period size: 108 Copynumber: 2.0 Consensus size: 105
20521899 TAAGGCCAGA
*
20521909 TTTATAATTTAGGGTATAAGG-GTTTAAGGATTTA-G-T-T-TTTAGAGTTTAGAGTTT-TAGGG
1 TTTATAATTTAGGGTATAAGGAGTTTAAGGATTTAGGATATCTTTAGAGTTTAGAGTTTAAAGGG
* *
20521968 TTTAAAAGATTTATAGGTCATGGGTTATGATTTAGGAGTTAGGC
66 TTT---AGAGTT-TAGATCATGGGTTATGATTTAGGAGTTAGGC
* * *
20522012 TTTATATTTTAGGGTTTAAGGCAGTTTAAGGTTTTAGGATATCGCTTTAGAGTTTAGAGTTTAAA
1 TTTATAATTTAGGGTATAAGG-AGTTTAAGGATTTAGGATAT--CTTTAGAGTTTAGAGTTTAAA
* *
20522077 TGGTTTAGAGTTTAGATCATGGGTTATGATTTAGGGGTTAGGC
63 GGGTTTAGAGTTTAGATCATGGGTTATGATTTAGGAGTTAGGC
20522120 AATCATGGGT
Statistics
Matches: 91, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
103 19 0.21
105 12 0.13
106 1 0.01
107 1 0.01
108 30 0.33
109 5 0.05
111 17 0.19
112 6 0.07
ACGTcount: A:0.27, C:0.03, G:0.27, T:0.43
Consensus pattern (105 bp):
TTTATAATTTAGGGTATAAGGAGTTTAAGGATTTAGGATATCTTTAGAGTTTAGAGTTTAAAGGG
TTTAGAGTTTAGATCATGGGTTATGATTTAGGAGTTAGGC
Found at i:20522116 original size:14 final size:14
Alignment explanation
Indices: 20522097--20522145 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
20522087 TTTAGATCAT
20522097 GGGTTATGATTTAG
1 GGGTTATGATTTAG
* * * *
20522111 GGGTTAGGCAATCAT
1 GGGTTATG-ATTTAG
20522126 GGGTTATGATTTAG
1 GGGTTATGATTTAG
20522140 GGGTTA
1 GGGTTA
20522146 GGCTTCATAT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.22, C:0.04, G:0.37, T:0.37
Consensus pattern (14 bp):
GGGTTATGATTTAG
Found at i:20522129 original size:29 final size:29
Alignment explanation
Indices: 20522092--20522148 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
20522082 TAGAGTTTAG
20522092 ATCATGGGTTATGATTTAGGGGTTAGGCA
1 ATCATGGGTTATGATTTAGGGGTTAGGCA
20522121 ATCATGGGTTATGATTTAGGGGTTAGGC
1 ATCATGGGTTATGATTTAGGGGTTAGGC
20522149 TTCATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.23, C:0.07, G:0.35, T:0.35
Consensus pattern (29 bp):
ATCATGGGTTATGATTTAGGGGTTAGGCA
Found at i:20522786 original size:39 final size:40
Alignment explanation
Indices: 20522727--20522868 Score: 135
Period size: 41 Copynumber: 3.5 Consensus size: 40
20522717 GGAACTAAAG
* ** *
20522727 CGCCACTATATCTCCTTTTTTTGCGATGTTTTGA-AAAAA
1 CGCCACTATTTCTCAGTTTTTTGCGATGTTTGGATAAAAA
* *
20522766 CGCCACTATTTCTCAATTTTTTGCGGCAT-TTTGGATGAAAA
1 CGCCACTATTTCTCAGTTTTTTGC-G-ATGTTTGGATAAAAA
* * **
20522807 CGCCACTATTACTCAGTTTTTAGCGGCGTTATGGATAAAAA
1 CGCCACTATTTCTCAGTTTTTTGCGATGTT-TGGATAAAAA
* *
20522848 TGCCACTATTGCTCAGTTTTT
1 CGCCACTATTTCTCAGTTTTT
20522869 ACCGGCGTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
39 21 0.25
40 9 0.11
41 55 0.65
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (40 bp):
CGCCACTATTTCTCAGTTTTTTGCGATGTTTGGATAAAAA
Found at i:20522875 original size:41 final size:41
Alignment explanation
Indices: 20522761--20522877 Score: 153
Period size: 41 Copynumber: 2.9 Consensus size: 41
20522751 GATGTTTTGA
* * * * *
20522761 AAAAACGCCACTATTTCTCAATTTTTTGCGGCATTTTGGAT
1 AAAAACGCCACTATTACTCAGTTTTTAGCGGCGTTATGGAT
*
20522802 GAAAACGCCACTATTACTCAGTTTTTAGCGGCGTTATGGAT
1 AAAAACGCCACTATTACTCAGTTTTTAGCGGCGTTATGGAT
* * *
20522843 AAAAATGCCACTATTGCTCAGTTTTTACCGGCGTT
1 AAAAACGCCACTATTACTCAGTTTTTAGCGGCGTT
20522878 TTGTTTCAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (41 bp):
AAAAACGCCACTATTACTCAGTTTTTAGCGGCGTTATGGAT
Found at i:20522942 original size:12 final size:12
Alignment explanation
Indices: 20522925--20522950 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20522915 TTTTTCATTC
20522925 AAACGCCACTAA
1 AAACGCCACTAA
20522937 AAACGCCACTAA
1 AAACGCCACTAA
20522949 AA
1 AA
20522951 GTCTGTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.31, G:0.08, T:0.08
Consensus pattern (12 bp):
AAACGCCACTAA
Found at i:20525354 original size:6 final size:6
Alignment explanation
Indices: 20525343--20525383 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
20525333 ATAATTTAAT
20525343 AAATAA AAATAA AAATATA AAACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATA-A AAA-TAA AAATAA AAATAA AAA
20525384 ACATATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 23 0.70
7 8 0.24
8 2 0.06
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:20525371 original size:20 final size:20
Alignment explanation
Indices: 20525346--20525385 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
20525336 ATTTAATAAA
*
20525346 TAAAAATAAAAATATAAAAC
1 TAAAAATAAAAATAAAAAAC
20525366 TAAAAATAAAAATAAAAAAC
1 TAAAAATAAAAATAAAAAAC
20525386 ATATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:20525417 original size:9 final size:9
Alignment explanation
Indices: 20525403--20525479 Score: 111
Period size: 9 Copynumber: 8.6 Consensus size: 9
20525393 TTTATACAAA
20525403 TAATTCGGT
1 TAATTCGGT
20525412 TAATTCGGT
1 TAATTCGGT
20525421 TAATTCAGG-
1 TAATTC-GGT
*
20525430 TAATTCGGG
1 TAATTCGGT
20525439 TAATTCGGT
1 TAATTCGGT
* *
20525448 TAATTTGAT
1 TAATTCGGT
20525457 TAATTCGGT
1 TAATTCGGT
20525466 TAATTCGGT
1 TAATTCGGT
20525475 TAATT
1 TAATT
20525480 TTACACTTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
8 2 0.03
9 57 0.93
10 2 0.03
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:20532721 original size:45 final size:46
Alignment explanation
Indices: 20532624--20532732 Score: 132
Period size: 45 Copynumber: 2.3 Consensus size: 46
20532614 AGATTAAGAT
* *
20532624 CGAATGGCTAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGC
1 CGAATGGCCAATGTGATGAATGTGAAAG-GTGAATATGTGATAAGGC
*
20532671 CGAATGGCCAATGTGAT-ATATGTGTAA-GTGAATATGTGATAAGGC
1 CGAATGGCCAATGTGATGA-ATGTGAAAGGTGAATATGTGATAAGGC
* *
20532716 TGAATGACCAATTGTGA
1 CGAATGGCCAA-TGTGA
20532733 AAAGTGTGCA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
45 26 0.47
46 6 0.11
47 23 0.42
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (46 bp):
CGAATGGCCAATGTGATGAATGTGAAAGGTGAATATGTGATAAGGC
Found at i:20533441 original size:38 final size:38
Alignment explanation
Indices: 20533390--20533467 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
20533380 CAAGGGAAGG
20533390 ATTGTATTTTGTCAACCTACGTATATGTGATAAGGTTT
1 ATTGTATTTTGTCAACCTACGTATATGTGATAAGGTTT
20533428 ATTGTATTTTGTCAACCTACGTATATGTGATAAGGTTT
1 ATTGTATTTTGTCAACCTACGTATATGTGATAAGGTTT
20533466 AT
1 AT
20533468 GTTTGGTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (38 bp):
ATTGTATTTTGTCAACCTACGTATATGTGATAAGGTTT
Found at i:20533570 original size:2 final size:2
Alignment explanation
Indices: 20533563--20533593 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20533553 AATTAAGTTT
20533563 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 T
20533594 TCATGTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20540668 original size:40 final size:40
Alignment explanation
Indices: 20540608--20540842 Score: 373
Period size: 40 Copynumber: 5.9 Consensus size: 40
20540598 CTCGCCGATG
* *
20540608 ATCCAGGCTAAGTCCCGAAGAGCATTCGTGCTGGAGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
20540648 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
*
20540688 ATCCGGGCTAATTCCCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
* * *
20540728 ATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAG-ATTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
* *
20540767 ATCAGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
* *
20540807 ATCCGGGCTAGGTCCCGAAGAGCATTCATGCTGGTG
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
20540843 ATGTGTATTC
Statistics
Matches: 178, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
39 34 0.19
40 144 0.81
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAT
Found at i:20540807 original size:79 final size:80
Alignment explanation
Indices: 20540613--20540838 Score: 364
Period size: 79 Copynumber: 2.8 Consensus size: 80
20540603 CGATGATCCA
*
20540613 GGCTAAGTCCCGAAGAGCATTCGTGCTGGAGTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTG
1 GGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTG
* * *
20540678 CTGGTGTTATATCCG
66 CTAGTATTATATCAG
* *
20540693 GGCTAATTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCTCGAAGAGCATTCGTG
1 GGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTG
20540758 CTAG-ATTATATCAG
66 CTAGTATTATATCAG
* * *
20540772 GGTTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGCATTCATG
1 GGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTG
20540837 CT
66 CT
20540839 GGTGATGTGT
Statistics
Matches: 135, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 70 0.52
80 65 0.48
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (80 bp):
GGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTG
CTAGTATTATATCAG
Found at i:20540825 original size:119 final size:120
Alignment explanation
Indices: 20540608--20540842 Score: 391
Period size: 119 Copynumber: 2.0 Consensus size: 120
20540598 CTCGCCGATG
* *
20540608 ATCCAGGCTAAGTCCCGAAGAGCATTCGTGCTGGAGTTATATCCGGGCTAAGTCCCGAAGAGCAT
1 ATCCAGGCTAAGTCCCGAAGAGCATTCGTGCTAGAGTTATATCAGGGCTAAGTCCCGAAGAGCAT
* *
20540673 TCGTGCTGGTGTTATATCCGGGCTAATTCCCGAAGAGCATTCGTGCTGGTGTTAT
66 TCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTGTTAT
* * *
20540728 ATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGA-TTATATCAGGGTTAAGTCCCGAAGAGCAT
1 ATCCAGGCTAAGTCCCGAAGAGCATTCGTGCTAGAGTTATATCAGGGCTAAGTCCCGAAGAGCAT
*
20540792 TCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGCATTCATGCTGGTG
66 TCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTG
20540843 ATGTGTATTC
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
119 75 0.70
120 32 0.30
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (120 bp):
ATCCAGGCTAAGTCCCGAAGAGCATTCGTGCTAGAGTTATATCAGGGCTAAGTCCCGAAGAGCAT
TCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTGTTAT
Found at i:20544758 original size:45 final size:46
Alignment explanation
Indices: 20544661--20544769 Score: 150
Period size: 45 Copynumber: 2.3 Consensus size: 46
20544651 AGCTTAAGAT
*
20544661 CGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGC
1 CGAATGGCCAATGTGATGAATGTGAAAG-GTGAATATGTGATAAGGC
*
20544708 CGAATGGCCAATGTGAT-ATATGTGTAA-GTGAATATGTGATAAGGC
1 CGAATGGCCAATGTGATGA-ATGTGAAAGGTGAATATGTGATAAGGC
*
20544753 CGAATGACCAATTGTGA
1 CGAATGGCCAA-TGTGA
20544770 AAAGTGTGCA
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
45 27 0.47
46 6 0.11
47 24 0.42
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (46 bp):
CGAATGGCCAATGTGATGAATGTGAAAGGTGAATATGTGATAAGGC
Found at i:20544895 original size:39 final size:40
Alignment explanation
Indices: 20544840--20544924 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
20544830 AAATGAATTG
* * * *
20544840 TGCTGAGATTGCATCCGGG-TTAGAGACCCGCTGGCTTCA
1 TGCTGGGATTGCATCCGGGTTTAAAGACCCGCAGGCTTAA
* *
20544879 TGCTGGGATTGTATCCGGGTTTAAAGTCCCGCAGGCTTAA
1 TGCTGGGATTGCATCCGGGTTTAAAGACCCGCAGGCTTAA
20544919 TGCTGG
1 TGCTGG
20544925 TGAATTAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 17 0.44
40 22 0.56
ACGTcount: A:0.18, C:0.22, G:0.32, T:0.28
Consensus pattern (40 bp):
TGCTGGGATTGCATCCGGGTTTAAAGACCCGCAGGCTTAA
Found at i:20553783 original size:21 final size:22
Alignment explanation
Indices: 20553757--20553798 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20553747 CACTTAACAC
*
20553757 AGGGGC-ACACGCCTGTGTGAG
1 AGGGGCAACACGCCCGTGTGAG
20553778 AGGGGCAACACGCCCGTGTGA
1 AGGGGCAACACGCCCGTGTGA
20553799 CCATTTAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.21, C:0.26, G:0.40, T:0.12
Consensus pattern (22 bp):
AGGGGCAACACGCCCGTGTGAG
Found at i:20556626 original size:48 final size:48
Alignment explanation
Indices: 20556523--20556794 Score: 244
Period size: 48 Copynumber: 5.7 Consensus size: 48
20556513 GGTGAATTGC
* * * * * *
20556523 CGATGCCATGTTCCA-AGCATGGTCTTACACT-GTTTCACATGTCGAGGT
1 CGATGCCATGTCCCAGA-CATGGTCTTACACTAG-CTCTCATATCAATGT
* * *
20556571 CGATGCCATGTCCCAGATATGGTCTTACACTAGCTCTCGTCTCAATGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGT
* * * *
20556619 CGTTGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGT
* * * * *
20556667 CGATGCCATGTCCCAGACATGGTCTTACAATGGCTCTCACATCATTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGT
* * * * * * *
20556715 CGATGCCATGTTCCAAACATGGTCTTACAATGGCTCTCCTATC-GTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAAT-GT
* * *
20556763 CGACGCCATGTCCCAAACACGGTCTTACACTA
1 CGATGCCATGTCCCAGACATGGTCTTACACTA
20556795 ATGCACATAT
Statistics
Matches: 189, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
47 1 0.01
48 186 0.98
49 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGT
Found at i:20562386 original size:25 final size:25
Alignment explanation
Indices: 20562357--20562407 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
20562347 GGCTCCCTGC
*
20562357 TTCCTAATTCTGTCAACTAGAGGTT
1 TTCCTAATTCTATCAACTAGAGGTT
20562382 TTCCTAATTCTATCAACTAGAGGTT
1 TTCCTAATTCTATCAACTAGAGGTT
20562407 T
1 T
20562408 CTCCCTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (25 bp):
TTCCTAATTCTATCAACTAGAGGTT
Found at i:20565304 original size:144 final size:142
Alignment explanation
Indices: 20564977--20565354 Score: 447
Period size: 144 Copynumber: 2.6 Consensus size: 142
20564967 GTGAATTACT
* *
20564977 GATGCCATGTTCCAAACATGGTCTTACACTAGCACACATGTCGTGGCCGATGCCATGTCCCAGAC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCGT-GCCGATGCCATGTCCCAGAC
* * ** *
20565042 ATGGTCTTACACTA--GCTATCGTCTCAATGCCGATGCCATGTCCAGACATGGTCTTACACTGGC
65 ATGGTCTTACACTAGTGC-A-CATATCAATGCCGACACCATGTCCAGACATGGTCTTACACTAGC
* **
20565105 TCTCATAATGTGGCC
128 TCTCACAACATGGCC
* * * * *
20565120 GATGCTATGTCCCAGACATGGTCTTACACTAG-TGCACATATCAATGTCGATGCCATGTCCCAGA
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCT-CACATATC-GTGCCGATGCCATGTCCCAGA
* * *
20565184 CATGGTCTTACACGAGTGCACATATTAATGTCGACACCATGTCCCAGACATGGTCTTACACTAGC
64 CATGGTCTTACACTAGTGCACATATCAATGCCGACACCATGT-CCAGACATGGTCTTACACTAGC
*
20565249 TCTCACAACATTGCC
128 TCTCACAACATGGCC
* * * * *
20565264 GATGCCATATTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGCTGACGCCATGTCCCAGAC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCGT-GCCGATGCCATGTCCCAGAC
*
20565329 ATGGTCTTATACTAGTGCACATATCA
65 ATGGTCTTACACTAGTGCACATATCA
20565355 CCCAAATGTT
Statistics
Matches: 196, Mismatches: 32, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
143 85 0.43
144 108 0.55
145 3 0.02
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (142 bp):
GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCGTGCCGATGCCATGTCCCAGACA
TGGTCTTACACTAGTGCACATATCAATGCCGACACCATGTCCAGACATGGTCTTACACTAGCTCT
CACAACATGGCC
Found at i:20565352 original size:48 final size:48
Alignment explanation
Indices: 20564977--20565354 Score: 328
Period size: 48 Copynumber: 7.9 Consensus size: 48
20564967 GTGAATTACT
* * ** * *
20564977 GATGCCATGTTCCAAACATGGTCTTACACTAGCACACATGTCGTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGTGCACATATCATGGCC
* *
20565025 GATGCCATGTCCCAGACATGGTCTTACACTA--GCTATCGTCTCAAT-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGTGC-A-CATATC-ATGGCC
* * *
20565073 GATGCCATGT-CCAGACATGGTCTTACACTGGCT-CTCATAAT-GTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAG-TGCACAT-ATCATGGCC
* *
20565120 GATGCTATGTCCCAGACATGGTCTTACACTAGTGCACATATCAAT-GTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGTGCACATATC-ATGGCC
* * *
20565168 GATGCCATGTCCCAGACATGGTCTTACACGAGTGCACATATTAAT-GTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGTGCACATA-TCATGGCC
** * *
20565216 GACACCATGTCCCAGACATGGTCTTACACTAGCTCTCACA-A-CATTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAG-T-GCACATATCATGGCC
* * * * * * *
20565264 GATGCCATATTCCAAACATGGTCTTACACTGGCT-CTCATATCGTGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAG-TGCACATATCATGGCC
* *
20565312 GACGCCATGTCCCAGACATGGTCTTATACTAGTGCACATATCA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGTGCACATATCA
20565355 CCCAAATGTT
Statistics
Matches: 268, Mismatches: 43, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
46 5 0.02
47 41 0.15
48 212 0.79
49 6 0.02
50 4 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGTGCACATATCATGGCC
Found at i:20570736 original size:19 final size:20
Alignment explanation
Indices: 20570709--20570747 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20570699 AAACCGAATT
*
20570709 TAGTCT-AAAATCCCATAAA
1 TAGTCTAAAAATCCAATAAA
*
20570728 TAGTTTAAAAATCCAATAAA
1 TAGTCTAAAAATCCAATAAA
20570748 GTCCATAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.28
Consensus pattern (20 bp):
TAGTCTAAAAATCCAATAAA
Found at i:20571565 original size:16 final size:17
Alignment explanation
Indices: 20571544--20571575 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20571534 GTGGCCAGCC
20571544 CTTGTG-GGCCCACACA
1 CTTGTGTGGCCCACACA
20571560 CTTGTGTGGCCCACAC
1 CTTGTGTGGCCCACAC
20571576 GGCCCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.16, C:0.38, G:0.25, T:0.22
Consensus pattern (17 bp):
CTTGTGTGGCCCACACA
Found at i:20571853 original size:91 final size:91
Alignment explanation
Indices: 20571695--20571883 Score: 263
Period size: 91 Copynumber: 2.1 Consensus size: 91
20571685 GATCACATGA
*
20571695 CCTCACCAGCCAACACACGGTCGTGTCATGCGCCCGTGTCTCGCGCGCACGGCCTAGCTCGTCGA
1 CCTCACCAGCCAACACACGGTCGTGTCATGCGCCCGTGTCTCGCGCACACGGCCTAGCTCGTCGA
*
20571760 TCACACGCCCATCTATTGCCACACAG
66 TCACACACCCATCTATTGCCACACAG
* * * * * * *
20571786 CCTCACCAGCCATCACATGGTCGTGTCTTGCGCCCGTGTCTCGTGCACACGGCCTGGTTCGTTGA
1 CCTCACCAGCCAACACACGGTCGTGTCATGCGCCCGTGTCTCGCGCACACGGCCTAGCTCGTCGA
* * *
20571851 TCACACACCCGTGTATTGCCACACGG
66 TCACACACCCATCTATTGCCACACAG
20571877 CCT-ACCA
1 CCTCACCA
20571884 CACAGGCGAC
Statistics
Matches: 86, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 4 0.05
91 82 0.95
ACGTcount: A:0.17, C:0.40, G:0.22, T:0.21
Consensus pattern (91 bp):
CCTCACCAGCCAACACACGGTCGTGTCATGCGCCCGTGTCTCGCGCACACGGCCTAGCTCGTCGA
TCACACACCCATCTATTGCCACACAG
Found at i:20578064 original size:19 final size:20
Alignment explanation
Indices: 20578037--20578075 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20578027 AAATCGAGTT
*
20578037 TAGTCT-AAAATCCCATAAA
1 TAGTCTAAAAATCCAATAAA
*
20578056 TAGTTTAAAAATCCAATAAA
1 TAGTCTAAAAATCCAATAAA
20578076 GTCCATAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.28
Consensus pattern (20 bp):
TAGTCTAAAAATCCAATAAA
Found at i:20582096 original size:22 final size:23
Alignment explanation
Indices: 20582047--20582096 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 23
20582037 TGTCTTACAA
20582047 GCTATAATGATTTACTATATTAT
1 GCTATAATGATTTACTATATTAT
20582070 G---TAAT-ATTATACTATA-TAT
1 GCTATAATGATT-TACTATATTAT
20582089 GCTATAAT
1 GCTATAAT
20582097 CTATAACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 9
0.72 0.00 0.28
Matches are distributed among these distances:
19 7 0.30
20 11 0.48
22 4 0.17
23 1 0.04
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (23 bp):
GCTATAATGATTTACTATATTAT
Found at i:20582687 original size:14 final size:13
Alignment explanation
Indices: 20582663--20582701 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
20582653 AATTTATTTT
20582663 TAATATATTAATA
1 TAATATATTAATA
*
20582676 TAAATATTTTAA-A
1 T-AATATATTAATA
20582689 TAATATATTAATA
1 TAATATATTAATA
20582702 ATATTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 9 0.41
13 4 0.18
14 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATATATTAATA
Done.