Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 208 of 433
Found at i:65402863 original size:5 final size:5
Alignment explanation
Indices: 65402853--65402909 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
65402843 CTCTTGCCTC
*
65402853 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
65402900 TCTTT TCTTT
1 TCTTT TCTTT
65402910 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:65402893 original size:15 final size:14
Alignment explanation
Indices: 65402853--65402909 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
65402843 CTCTTGCCTC
*
65402853 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
65402868 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
65402883 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
65402900 TCTTTTCTTT
1 TCTTTTCTTT
65402910 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:65402910 original size:21 final size:21
Alignment explanation
Indices: 65402853--65402920 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
65402843 CTCTTGCCTC
* *
65402853 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
65402874 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
65402895 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
65402915 CTCTTT
1 -TCTTT
65402921 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:65405614 original size:30 final size:30
Alignment explanation
Indices: 65405529--65405625 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
65405519 TAAACTAAAA
* *
65405529 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
65405559 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
65405589 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
65405618 ATGAGCTA
1 -TGAGCTA
65405626 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:65407257 original size:30 final size:31
Alignment explanation
Indices: 65407208--65407267 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
65407198 ATAAAAAAAG
* *
65407208 AAACGAGCTGGAAAAAAGCTAAATTGAGCTC
1 AAACAAGCTGGAAAAAAGCTAAAGTGAGCTC
* *
65407239 AAACAAGCT-GAAACAAGCTCAAGTGAGCT
1 AAACAAGCTGGAAAAAAGCTAAAGTGAGCT
65407268 GATTGGAGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (31 bp):
AAACAAGCTGGAAAAAAGCTAAAGTGAGCTC
Found at i:65409059 original size:93 final size:92
Alignment explanation
Indices: 65408901--65409071 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 92
65408891 GGATGGTTGA
* *
65408901 GCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAATGTCCAAACTAGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCAAACTAGTTGAGTT
65408966 GAGTCCGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
* * *
65408993 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAACGCCCAAACTAGTTGAGT
65409058 TGAGTCCGAGTTCG
65 TGAGTCCGAGTTCG
65409072 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 24 0.33
93 49 0.67
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCAAACTAGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:65409067 original size:46 final size:46
Alignment explanation
Indices: 65408905--65409078 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
65408895 GGTTGAGCAT
* *
65408905 CCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * * * *
65408950 CCAAACTAGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
65408995 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
65409043 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
65409079 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 21 0.20
46 41 0.39
47 26 0.25
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:65413994 original size:30 final size:29
Alignment explanation
Indices: 65413949--65414033 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 29
65413939 TTCTTTTGTT
* *
65413949 TCAATTTGTTTTTCATCTTCTTTTTCACTC
1 TCAATTTCTTTTTCAT-TTCTTTTTCAATC
*
65413979 TCAAATTTC-TTTTCATTCTCTTTTTCAATT
1 TC-AATTTCTTTTTCATT-TCTTTTTCAATC
*
65414009 TCATTTTCTTTTTCATTTTCTTTTT
1 TCAATTTCTTTTTCA-TTTCTTTTT
65414034 GCTTTTCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
29 6 0.13
30 34 0.72
31 7 0.15
ACGTcount: A:0.14, C:0.20, G:0.01, T:0.65
Consensus pattern (29 bp):
TCAATTTCTTTTTCATTTCTTTTTCAATC
Found at i:65414033 original size:18 final size:18
Alignment explanation
Indices: 65413984--65414039 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
65413974 CACTCTCAAA
*
65413984 TTTC-TTTTCATTCTCTT
1 TTTCATTTTCATTTTCTT
*
65414001 TTTCAATTTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
65414019 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
65414038 TT
1 TT
65414040 CAAAGGCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 4 0.12
18 24 0.73
19 5 0.15
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:65414040 original size:12 final size:12
Alignment explanation
Indices: 65414007--65414033 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
65413997 TCTTTTTCAA
65414007 TTTCATTTTCTT
1 TTTCATTTTCTT
65414019 TTTCATTTTCTT
1 TTTCATTTTCTT
65414031 TTT
1 TTT
65414034 GCTTTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:65414112 original size:5 final size:5
Alignment explanation
Indices: 65414102--65414148 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
65414092 CTTTTGCCTC
*
65414102 TCTTT TCTTT T-TATT TCGTTT TCTTTT TTTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TCTTT TCTTT TCTTT
65414149 GTTTTCGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 1 0.03
5 26 0.72
6 8 0.22
7 1 0.03
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:65414123 original size:16 final size:15
Alignment explanation
Indices: 65414102--65414144 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
65414092 CTTTTGCCTC
65414102 TCTTTTCTTTTTATT
1 TCTTTTCTTTTTATT
*
65414117 TCGTTTTCTTTTTTTTT
1 TC-TTTTC-TTTTTATT
65414134 TCTTTTCTTTT
1 TCTTTTCTTTT
65414145 CTTTGTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 6 0.24
16 10 0.40
17 9 0.36
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (15 bp):
TCTTTTCTTTTTATT
Found at i:65414128 original size:21 final size:21
Alignment explanation
Indices: 65414102--65414148 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
65414092 CTTTTGCCTC
65414102 TCTTTTCTTTTT-ATTTCGTTT
1 TCTTTTCTTTTTCATTTC-TTT
* *
65414123 TCTTTTTTTTTTCTTTTCTTT
1 TCTTTTCTTTTTCATTTCTTT
65414144 TCTTT
1 TCTTT
65414149 GTTTTCGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (21 bp):
TCTTTTCTTTTTCATTTCTTT
Found at i:65414159 original size:21 final size:20
Alignment explanation
Indices: 65414102--65414159 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 20
65414092 CTTTTGCCTC
65414102 TCTTTTCTTTTTATTTCG-TTT
1 TCTTTTC-TTTT-TTTCGCTTT
65414123 TC-TTT-TTTTTTT--CTTT
1 TCTTTTCTTTTTTTCGCTTT
65414139 TCTTTTCTTTGTTTTCGCTTT
1 TCTTTTCTTT-TTTTCGCTTT
65414160 ACAAGAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
16 5 0.16
17 6 0.19
18 7 0.23
19 4 0.13
20 3 0.10
21 6 0.19
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.78
Consensus pattern (20 bp):
TCTTTTCTTTTTTTCGCTTT
Found at i:65416720 original size:30 final size:30
Alignment explanation
Indices: 65416686--65416782 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
65416676 TAAACTAAAA
*
65416686 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGATAAAGT
* * * * * *
65416716 TGAGCTGAGGC-TAAACTCCTAAGATGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGATAAAGT
* *
65416746 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGAT-AAAGT
65416776 TGAGCTA
1 TGAGCTA
65416783 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGATAAAGT
Found at i:65426022 original size:13 final size:13
Alignment explanation
Indices: 65426001--65426032 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
65425991 GAATGGTCAT
*
65426001 CATGGTGTGAACA
1 CATGATGTGAACA
65426014 CATGATGTGAACA
1 CATGATGTGAACA
65426027 CATGAT
1 CATGAT
65426033 CAATACATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (13 bp):
CATGATGTGAACA
Found at i:65427065 original size:16 final size:16
Alignment explanation
Indices: 65427041--65427076 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
65427031 CGAAGCCAAA
* *
65427041 ATTTTAGCTTTTTGGC
1 ATTTAAGCTTTTTGAC
65427057 ATTTAAGCTTTTTGAC
1 ATTTAAGCTTTTTGAC
65427073 ATTT
1 ATTT
65427077 TGGCATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (16 bp):
ATTTAAGCTTTTTGAC
Found at i:65429218 original size:13 final size:13
Alignment explanation
Indices: 65429200--65429224 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65429190 GTATTGATCA
65429200 TGTGTTCACACCT
1 TGTGTTCACACCT
65429213 TGTGTTCACACC
1 TGTGTTCACACC
65429225 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:65431751 original size:77 final size:77
Alignment explanation
Indices: 65431591--65431751 Score: 209
Period size: 77 Copynumber: 2.1 Consensus size: 77
65431581 AGTAAAAAAG
* * * *
65431591 AAAAAAAATTTGCTTCGTAAAATTCAAGTATTATATTGTATTTACCATTTTAGTGGTTTATAAAC
1 AAAAAAAAATTACTTCGTAAAATTCAAGTATTATATTGTAATTACCATTTTAGTAGTTTATAAAC
65431656 AAAAAAAAATAT
66 AAAAAAAAATAT
* * *
65431668 ATAAAAAAATTACTTCGTGAAATTCAAGTATTATATTGTAATTATCATTTTAGTAG-TTATAGAA
1 AAAAAAAAATTACTTCGTAAAATTCAAGTATTATATTGTAATTACCATTTTAGTAGTTTATA-AA
* *
65431732 -AAAAAGAGAGTAT
65 CAAAAA-AAAATAT
65431745 AAAAAAA
1 AAAAAAA
65431752 TTCAAAAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
76 10 0.14
77 62 0.86
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (77 bp):
AAAAAAAAATTACTTCGTAAAATTCAAGTATTATATTGTAATTACCATTTTAGTAGTTTATAAAC
AAAAAAAAATAT
Found at i:65431789 original size:8 final size:9
Alignment explanation
Indices: 65431743--65431800 Score: 62
Period size: 11 Copynumber: 5.9 Consensus size: 9
65431733 AAAAGAGAGT
65431743 ATAAAAAAA
1 ATAAAAAAA
*
65431752 TTCAAAAAAA
1 AT-AAAAAAA
65431762 ATTCAAAAAAA
1 A-T-AAAAAAA
65431773 ATTCAAAAAAA
1 A-T-AAAAAAA
65431784 ATAAAAAAA
1 ATAAAAAAA
65431793 ATAAAAAA
1 ATAAAAAA
65431801 GGAGGTGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
9 16 0.36
10 8 0.18
11 21 0.47
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:65431800 original size:11 final size:11
Alignment explanation
Indices: 65431745--65431794 Score: 86
Period size: 11 Copynumber: 4.7 Consensus size: 11
65431735 AAGAGAGTAT
65431745 AAAAAAATTCA
1 AAAAAAATTCA
65431756 AAAAAAATTCA
1 AAAAAAATTCA
65431767 AAAAAAATTCA
1 AAAAAAATTCA
65431778 AAAAAAA-T-A
1 AAAAAAATTCA
65431787 AAAAAAAT
1 AAAAAAAT
65431795 AAAAAAGGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
9 8 0.21
10 1 0.03
11 29 0.76
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:65433050 original size:17 final size:17
Alignment explanation
Indices: 65433018--65433053 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
65433008 GGTTCATGTT
**
65433018 GCAATTAAAGTTGAAAA
1 GCAATTAAAGAAGAAAA
65433035 GCAATTAAAGAAGAAAA
1 GCAATTAAAGAAGAAAA
65433052 GC
1 GC
65433054 TCTGTTCGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.08, G:0.19, T:0.17
Consensus pattern (17 bp):
GCAATTAAAGAAGAAAA
Found at i:65433927 original size:12 final size:12
Alignment explanation
Indices: 65433908--65433940 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
65433898 AGAAAGAAAA
65433908 GAGTGAAAAGGT
1 GAGTGAAAAGGT
*
65433920 GTGTGAAAA-GT
1 GAGTGAAAAGGT
65433931 GAGTGAAAAG
1 GAGTGAAAAG
65433941 AAACGAGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.39, T:0.18
Consensus pattern (12 bp):
GAGTGAAAAGGT
Found at i:65435636 original size:51 final size:49
Alignment explanation
Indices: 65435511--65435706 Score: 248
Period size: 49 Copynumber: 4.0 Consensus size: 49
65435501 GTAGCTGAAG
* * *
65435511 CTATCTGGTACGCATAGTAGCCTGCACTTAGTAATACACATGTGACCAA
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAA
* * * *
65435560 TTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAA
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA
* * * * *
65435610 GTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 -CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAA
* *
65435660 CAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
65435707 TCACAATAGC
Statistics
Matches: 125, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 79 0.63
50 6 0.05
51 40 0.32
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (49 bp):
CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAA
Found at i:65435690 original size:100 final size:100
Alignment explanation
Indices: 65435507--65435704 Score: 333
Period size: 100 Copynumber: 2.0 Consensus size: 100
65435497 ACTTGTAGCT
* * **
65435507 GAAGCTATCTGGTACGCATAGTAGCCTGCACTTAGTAATACACATGTGACCAATTATCCGGTACA
1 GAAGCTATCAGGTACGCATAGTAGCCTGCACTTAGTAATACACATGCGACCAACAATCCGGTACA
65435572 CGTAGTAGCCTGCACTTAGTACTACACACGTGATC
66 CGTAGTAGCCTGCACTTAGTACTACACACGTGATC
* * *
65435607 GAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTGGTACA
1 GAAGCTATCAGGTACGCATAGTAGCCTGCACTTAGTAATACACATGCGACCAACAATCCGGTACA
65435672 CGTAGTAGCCTGCACTTAGTACTACACACGTGA
66 CGTAGTAGCCTGCACTTAGTACTACACACGTGA
65435705 CCTCACAATA
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 91 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (100 bp):
GAAGCTATCAGGTACGCATAGTAGCCTGCACTTAGTAATACACATGCGACCAACAATCCGGTACA
CGTAGTAGCCTGCACTTAGTACTACACACGTGATC
Found at i:65436083 original size:35 final size:35
Alignment explanation
Indices: 65436027--65436093 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
65436017 ATATTTCATA
*
65436027 ATAACAATCTTCATATCATATAAATAACATTAATG
1 ATAACAATCATCATATCATATAAATAACATTAATG
* *
65436062 ATAATAATCATCATGTCATATAAATAACATTA
1 ATAACAATCATCATATCATATAAATAACATTA
65436094 TATTACTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.34
Consensus pattern (35 bp):
ATAACAATCATCATATCATATAAATAACATTAATG
Found at i:65436320 original size:30 final size:30
Alignment explanation
Indices: 65436286--65436344 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
65436276 CTTTAATATG
65436286 AACTTTGGAAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGAAAAATTACAC-TTTTGCCCCTA
* * *
65436316 AACTTTTGCATAATTACACTTTTGCCCCT
1 AACTTTGGAAAAATTACACTTTTGCCCCT
65436345 GGCTCGAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:65445071 original size:24 final size:23
Alignment explanation
Indices: 65445035--65445088 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
65445025 ATTAAGACCT
*
65445035 AATTAACTAATTTAACTAACAGCA
1 AATTAAATAATTTAA-TAACAGCA
* * **
65445059 AATTAAATGATTTTATTCCAGCA
1 AATTAAATAATTTAATAACAGCA
65445082 AATTAAA
1 AATTAAA
65445089 CGTAAAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (23 bp):
AATTAAATAATTTAATAACAGCA
Found at i:65446479 original size:19 final size:19
Alignment explanation
Indices: 65446455--65446494 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
65446445 AGCTCCCATG
65446455 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
65446474 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
65446493 TA
1 TA
65446495 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:65447093 original size:31 final size:32
Alignment explanation
Indices: 65447040--65447099 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
65447030 AATTCATTCA
*
65447040 CACCTATGTTCACATGGCAAGACTATTCAGTT
1 CACCTATGTTCACATAGCAAGACTATTCAGTT
*
65447072 CACCT-TGTTCACACTAG-AAGACTCTTCA
1 CACCTATGTTCACA-TAGCAAGACTATTCA
65447100 ACATTCGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (32 bp):
CACCTATGTTCACATAGCAAGACTATTCAGTT
Found at i:65451791 original size:18 final size:18
Alignment explanation
Indices: 65451768--65451805 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
65451758 CATGCACCTA
65451768 ATTAAATGTTGTTCATTC
1 ATTAAATGTTGTTCATTC
65451786 ATTAAATGTTGTTCATTC
1 ATTAAATGTTGTTCATTC
65451804 AT
1 AT
65451806 GCATGTGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
ATTAAATGTTGTTCATTC
Found at i:65452148 original size:30 final size:30
Alignment explanation
Indices: 65452062--65452159 Score: 106
Period size: 30 Copynumber: 3.3 Consensus size: 30
65452052 TTAAACTAAA
* *
65452062 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * *
65452092 TTGAGCTGAGATTAAGCTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
65452122 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
65452152 ATGAGCTA
1 ATGAGCTA
65452160 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:65454332 original size:30 final size:30
Alignment explanation
Indices: 65454261--65454343 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
65454251 CTTTTGTTTC
* *
65454261 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
65454292 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
65454321 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
65454344 GATTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:65454334 original size:12 final size:12
Alignment explanation
Indices: 65454319--65454350 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
65454309 TTTTTCAATC
65454319 TCATTTTCTTTT
1 TCATTTTCTTTT
65454331 TCATTTTCTTTT
1 TCATTTTCTTTT
*
65454343 TGATTTTC
1 TCATTTTC
65454351 AAAGGCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.16, G:0.03, T:0.72
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:65454452 original size:15 final size:14
Alignment explanation
Indices: 65454412--65454457 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
65454402 CTCTTGCCTC
*
65454412 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
65454427 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
65454442 TCTTTTGCTTTTTCT
1 TCTTTT-CTTTTTCT
65454457 T
1 T
65454458 TTCTTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
15 14 0.50
16 10 0.36
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.76
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:65454464 original size:16 final size:16
Alignment explanation
Indices: 65454412--65454474 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 16
65454402 CTCTTGCCTC
* *
65454412 TCTTTTCTTTTT-ATT
1 TCTTTGCTTTTTCTTT
* *
65454427 TCATTTTCTTTTTCTTC
1 TC-TTTGCTTTTTCTTT
65454444 T-TTTGCTTTTTCTTT
1 TCTTTGCTTTTTCTTT
65454459 TCTTTG-TTTTCTCTTT
1 TCTTTGCTTTT-TCTTT
65454475 ACAAGAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 19 0.47
16 19 0.47
17 2 0.05
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.76
Consensus pattern (16 bp):
TCTTTGCTTTTTCTTT
Found at i:65455511 original size:15 final size:15
Alignment explanation
Indices: 65455491--65455520 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
65455481 GAAGTAGTTT
65455491 TTTTTTTTGTATATA
1 TTTTTTTTGTATATA
*
65455506 TTTTTTTTGTTTATA
1 TTTTTTTTGTATATA
65455521 AACTACTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTTTTTTGTATATA
Found at i:65457147 original size:30 final size:30
Alignment explanation
Indices: 65457061--65457158 Score: 115
Period size: 30 Copynumber: 3.3 Consensus size: 30
65457051 TTAAACTACA
* *
65457061 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * *
65457091 TTGAGCTGAGATTAAGCTCCTGAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
65457121 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
65457151 ATGAGCTA
1 ATGAGCTA
65457159 GGAGTGAGCT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:65457169 original size:30 final size:29
Alignment explanation
Indices: 65457075--65457170 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 29
65457065 GCTAAGCTTT
*
65457075 AGCTCGTGAGCTAAAGTTGAGCT-GAGATTA
1 AGCTCGTGAGCTGAA-TTGAGCTAG-GATTA
* * *
65457105 AGCTCCTGAGCTGAAGCTGAGCTAAGG-TTT
1 AGCTCGTGAGCTGAA-TTGAGCT-AGGATTA
* *
65457135 AGCTCGTGAGCTGAATATGAGCTAGGAGTG
1 AGCTCGTGAGCTGAAT-TGAGCTAGGATTA
65457165 AGCTCG
1 AGCTCG
65457171 GTTTAGCTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
29 3 0.06
30 49 0.91
31 1 0.02
32 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (29 bp):
AGCTCGTGAGCTGAATTGAGCTAGGATTA
Found at i:65458071 original size:21 final size:20
Alignment explanation
Indices: 65458047--65458101 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
65458037 ACATTCTTGT
65458047 AAAGAGAAAACAAAGAAAAGA
1 AAAGAGAAAACAAA-AAAAGA
*
65458068 AAAGA-AAAAGCAAAAGAAGA
1 AAAGAGAAAA-CAAAAAAAGA
65458088 AAA-AGAAAACAAAA
1 AAAGAGAAAACAAAA
65458102 TAAAAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 6 0.19
20 16 0.52
21 9 0.29
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAGAGAAAACAAAAAAAGA
Found at i:65458089 original size:15 final size:14
Alignment explanation
Indices: 65458058--65458096 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
65458048 AAGAGAAAAC
65458058 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
65458074 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
65458089 AAAGAAAA
1 AAAGAAAA
65458097 CAAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 4 0.18
17 5 0.23
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:65458229 original size:30 final size:29
Alignment explanation
Indices: 65458195--65458275 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
65458185 TTTGGAAAAC
*
65458195 AAAAAGGAAATGAAAAAGAAAATGAGATTG
1 AAAAA-GAAATGAAAAAGAAAATGAGAGTG
***
65458225 AAAAAGAGAATGAAAAAGAGTTTGAGAGTG
1 AAAAAGA-AATGAAAAAGAAAATGAGAGTG
65458255 AAAAAGAAGATGAAAAAGAAA
1 AAAAAGAA-ATGAAAAAGAAA
65458276 TTGAAACAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
29 3 0.07
30 40 0.93
ACGTcount: A:0.63, C:0.00, G:0.25, T:0.12
Consensus pattern (29 bp):
AAAAAGAAATGAAAAAGAAAATGAGAGTG
Found at i:65461056 original size:30 final size:30
Alignment explanation
Indices: 65461022--65461118 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
65461012 TAAACTAAAA
*
65461022 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGATAAAGT
* * * * * *
65461052 TGAGCTGAGGC-TAAACTCCTAAGATGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGATAAAGT
* *
65461082 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGAT-AAAGT
65461112 TGAGCTA
1 TGAGCTA
65461119 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGATAAAGT
Found at i:65462598 original size:13 final size:13
Alignment explanation
Indices: 65462580--65462604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65462570 TAACCTACAA
65462580 AATTAAATAACAT
1 AATTAAATAACAT
65462593 AATTAAATAACA
1 AATTAAATAACA
65462605 CACAACTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:65462859 original size:10 final size:10
Alignment explanation
Indices: 65462826--65462874 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
65462816 AAAAAGGAAT
*
65462826 GAGCTGAAAC
1 GAGCTCAAAC
65462836 GAGCT-AAATTC
1 GAGCTCAAA--C
65462847 GAGCTCAAAC
1 GAGCTCAAAC
*
65462857 GAGCTAAAAC
1 GAGCTCAAAC
65462867 GAGCTCAA
1 GAGCTCAA
65462875 GTGAGCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:65462881 original size:20 final size:21
Alignment explanation
Indices: 65462826--65462874 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
65462816 AAAAAGGAAT
* *
65462826 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATAC
65462847 GAGCTCAAACGAGCTAAA-AC
1 GAGCTCAAACGAGCTAAATAC
65462867 GAGCTCAA
1 GAGCTCAA
65462875 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATAC
Found at i:65464156 original size:30 final size:29
Alignment explanation
Indices: 65464071--65464157 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 29
65464061 CTAGCTTATA
**
65464071 TTCAGCTCACAAGCTAAACTTAGCTCAAC
1 TTCAGCTCAGGAGCTAAACTTAGCTCAAC
* *
65464100 TTCAGCTTAGGAG-TATAATCTCAGCTCAAC
1 TTCAGCTCAGGAGCTA-AA-CTTAGCTCAAC
* *
65464130 TTTAGCTCATGAGCTAAAGCTTAGCTCA
1 TTCAGCTCAGGAGCTAAA-CTTAGCTCA
65464158 TTTTAGTTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 2 0.04
29 12 0.26
30 30 0.65
31 2 0.04
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (29 bp):
TTCAGCTCAGGAGCTAAACTTAGCTCAAC
Found at i:65464813 original size:19 final size:19
Alignment explanation
Indices: 65464789--65464828 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
65464779 AGCTCCCATG
65464789 TAGCTC-CACACCAGCTCAT
1 TAGCTCGCA-ACCAGCTCAT
*
65464808 TAGCTCGGAACCAGCTCAT
1 TAGCTCGCAACCAGCTCAT
65464827 TA
1 TA
65464829 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCGCAACCAGCTCAT
Found at i:65466090 original size:14 final size:14
Alignment explanation
Indices: 65466068--65466115 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
65466058 ACCTAAACCG
* *
65466068 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
65466082 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
65466096 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
65466110 ACCATT
1 ACCATT
65466116 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:65466329 original size:16 final size:16
Alignment explanation
Indices: 65466308--65466347 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
65466298 TAGGTTCAGA
65466308 AAAAAAAAGAGTATAG
1 AAAAAAAAGAGTATAG
65466324 AAAAAAAAGAGTATAG
1 AAAAAAAAGAGTATAG
65466340 AAAAAAAA
1 AAAAAAAA
65466348 TTTTGTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (16 bp):
AAAAAAAAGAGTATAG
Found at i:65466519 original size:10 final size:10
Alignment explanation
Indices: 65466504--65466542 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
65466494 ATACAAGTTA
65466504 AAAAAAAATC
1 AAAAAAAATC
*
65466514 AAAAAAATTC
1 AAAAAAAATC
65466524 GAAAAAAAATC
1 -AAAAAAAATC
65466535 AAAAAAAA
1 AAAAAAAA
65466543 AGAAAGAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.79, C:0.08, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:65466519 original size:11 final size:11
Alignment explanation
Indices: 65466503--65466543 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
65466493 TATACAAGTT
65466503 AAAAAAAAATC
1 AAAAAAAAATC
*
65466514 -AAAAAAATTC
1 AAAAAAAAATC
*
65466524 GAAAAAAAATC
1 AAAAAAAAATC
65466535 AAAAAAAAA
1 AAAAAAAAA
65466544 GAAAGAGTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.10
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:65471787 original size:19 final size:19
Alignment explanation
Indices: 65471763--65471802 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
65471753 AGCTCCCATG
65471763 TAGCTC-CACACCAGCTCAT
1 TAGCTCGCA-ACCAGCTCAT
*
65471782 TAGCTCGGAACCAGCTCAT
1 TAGCTCGCAACCAGCTCAT
65471801 TA
1 TA
65471803 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCGCAACCAGCTCAT
Found at i:65473064 original size:14 final size:14
Alignment explanation
Indices: 65473042--65473089 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
65473032 ACCTAAACCG
* *
65473042 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
65473056 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
65473070 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
65473084 ACCATT
1 ACCATT
65473090 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:65473731 original size:30 final size:30
Alignment explanation
Indices: 65473707--65473805 Score: 101
Period size: 30 Copynumber: 3.3 Consensus size: 30
65473697 CGAGCTCACT
65473707 CTTAGCTCATA-TTCAGCTCACGAGCTAAAC
1 CTTAGCTCA-ACTTCAGCTCACGAGCTAAAC
* * * * *
65473737 CTTAGCTCAACTTCAGCTTAGGAGTTTAAT
1 CTTAGCTCAACTTCAGCTCACGAGCTAAAC
* * * *
65473767 CTCAGCTCAACTTTAGCTCACAAGCTAAAG
1 CTTAGCTCAACTTCAGCTCACGAGCTAAAC
65473797 CTTAGCTCA
1 CTTAGCTCA
65473806 TTTTAGTTTA
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
29 1 0.02
30 53 0.98
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.29
Consensus pattern (30 bp):
CTTAGCTCAACTTCAGCTCACGAGCTAAAC
Found at i:65476416 original size:10 final size:10
Alignment explanation
Indices: 65476401--65476427 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
65476391 TACTCCTTCA
65476401 AGCTCAAATC
1 AGCTCAAATC
65476411 AGCTCAAATC
1 AGCTCAAATC
65476421 AGCTCAA
1 AGCTCAA
65476428 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:65483226 original size:10 final size:10
Alignment explanation
Indices: 65483211--65483237 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
65483201 TACTCCTTCA
65483211 AGCTCAAATC
1 AGCTCAAATC
65483221 AGCTCAAATC
1 AGCTCAAATC
65483231 AGCTCAA
1 AGCTCAA
65483238 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:65488045 original size:10 final size:10
Alignment explanation
Indices: 65488030--65488056 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
65488020 TACTCCTTCA
65488030 AGCTCAAATC
1 AGCTCAAATC
65488040 AGCTCAAATC
1 AGCTCAAATC
65488050 AGCTCAA
1 AGCTCAA
65488057 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:65488214 original size:26 final size:26
Alignment explanation
Indices: 65488185--65488237 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
65488175 ATTTGTCATA
65488185 ATCTGGACATGTTTTAATTATGTTCT
1 ATCTGGACATGTTTTAATTATGTTCT
65488211 ATCTGGACATGTTTTAATTATGTTCT
1 ATCTGGACATGTTTTAATTATGTTCT
65488237 A
1 A
65488238 AATTAAGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (26 bp):
ATCTGGACATGTTTTAATTATGTTCT
Found at i:65490228 original size:93 final size:93
Alignment explanation
Indices: 65490116--65490286 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
65490106 ACCCCTAAGT
65490116 GAACTCGGACTCAACTCAACGAGCTCAAG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAG-TCAAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
65490180 ACGAGTTCGGATGCCTAGTTACATTTGAC
65 ACGAGTTCGGATGCCTAGTTACATTTGAC
***
65490209 GAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTCAAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
65490274 CGAGTTCGGATGC
66 CGAGTTCGGATGC
65490287 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTCAAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTGAC
Found at i:65490279 original size:46 final size:46
Alignment explanation
Indices: 65490111--65490279 Score: 184
Period size: 46 Copynumber: 3.7 Consensus size: 46
65490101 AACCCACCCC
* **
65490111 TAAGTGAACTCGGACTCAACTCAACGAG-CTCAAGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTTGGA-CATTCGCATCCA
* * *
65490157 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTTGGACATTCGC-A--TCCA
** *
65490203 TTTGACGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCA
1 TAAG-TGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCA
65490250 TAAGTGAACTCGGACTCAACTCAACGAGTT
1 TAAGTGAACTCGGACTCAACTCAACGAGTT
65490280 CGGATGCTCA
Statistics
Matches: 100, Mismatches: 15, Indels: 16
0.76 0.11 0.12
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
46 58 0.58
47 32 0.32
49 4 0.04
50 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCA
Found at i:65503548 original size:71 final size:71
Alignment explanation
Indices: 65503462--65503625 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
65503452 CGATTTGTCT
65503462 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
65503527 CTTTCA
66 CTTTCA
65503533 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
65503598 CTTTCA
66 CTTTCA
65503604 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
65503626 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:65503663 original size:71 final size:70
Alignment explanation
Indices: 65503462--65503659 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
65503452 CGATTTGTCT
* * * *
65503462 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
65503527 CTTTCA
65 CTTTCA
* * * *
65503533 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
65503598 CTTTCA
65 CTTTCA
* *
65503604 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
65503660 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:65510334 original size:9 final size:9
Alignment explanation
Indices: 65510319--65510353 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
65510309 TAAATCACTT
65510319 TTTTTTTCGA
1 TTTTTTT-GA
65510329 TTTTTTTGA
1 TTTTTTTGA
65510338 TTTTTTTGA
1 TTTTTTTGA
65510347 TTTTTTT
1 TTTTTTT
65510354 AACTTGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.72
10 7 0.28
ACGTcount: A:0.09, C:0.03, G:0.09, T:0.80
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:65512532 original size:13 final size:13
Alignment explanation
Indices: 65512514--65512538 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65512504 GTATTAATCA
65512514 TGTGTTCACACCT
1 TGTGTTCACACCT
65512527 TGTGTTCACACC
1 TGTGTTCACACC
65512539 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:65517089 original size:19 final size:18
Alignment explanation
Indices: 65517055--65517090 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
65517045 TATTTTTCCT
*
65517055 TTTTTTTGATTTTTTTGA
1 TTTTTTTGATTGTTTTGA
65517073 TTTTTTTGAATTGTTTTG
1 TTTTTTTG-ATTGTTTTG
65517091 CTAAAATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.11, C:0.00, G:0.14, T:0.75
Consensus pattern (18 bp):
TTTTTTTGATTGTTTTGA
Found at i:65517090 original size:10 final size:9
Alignment explanation
Indices: 65517055--65517081 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
65517045 TATTTTTCCT
65517055 TTTTTTTGA
1 TTTTTTTGA
65517064 TTTTTTTGA
1 TTTTTTTGA
65517073 TTTTTTTGA
1 TTTTTTTGA
65517082 ATTGTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:65519882 original size:11 final size:11
Alignment explanation
Indices: 65519866--65519917 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
65519856 ATACAAGTAA
65519866 AAAAAAATTCG
1 AAAAAAATTCG
65519877 AAAAAAATTC-
1 AAAAAAATTCG
65519887 AAAAAGAATTTCG
1 AAAAA-AA-TTCG
* *
65519900 AAAAAAAATCT
1 AAAAAAATTCG
65519911 AAAAAAA
1 AAAAAAA
65519918 AGTATTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 5 0.14
11 21 0.58
12 5 0.14
13 5 0.14
ACGTcount: A:0.69, C:0.08, G:0.06, T:0.17
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:65519890 original size:23 final size:23
Alignment explanation
Indices: 65519864--65519918 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
65519854 TTATACAAGT
*
65519864 AAAAAAAAATTCGAAAAAAATTC
1 AAAAAAAAATTCGAAAAAAAATC
* *
65519887 AAAAAGAATTTCGAAAAAAAATC
1 AAAAAAAAATTCGAAAAAAAATC
*
65519910 TAAAAAAAA
1 AAAAAAAAA
65519919 GTATTTAATG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.71, C:0.07, G:0.05, T:0.16
Consensus pattern (23 bp):
AAAAAAAAATTCGAAAAAAAATC
Found at i:65520832 original size:9 final size:10
Alignment explanation
Indices: 65520825--65520887 Score: 58
Period size: 11 Copynumber: 6.0 Consensus size: 10
65520815 AAGAGAAAAC
65520825 AAAGAAAAGA
1 AAAGAAAAGA
65520835 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
65520847 AAAGAAGA-A
1 AAAGAAAAGA
65520856 AAAGAAAAAGA
1 AAAG-AAAAGA
65520867 AAATGAAATA-A
1 AAA-GAAA-AGA
65520878 AAAGAAAAGA
1 AAAGAAAAGA
65520888 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
9 6 0.14
10 12 0.27
11 19 0.43
12 7 0.16
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:65520848 original size:21 final size:21
Alignment explanation
Indices: 65520814--65520885 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
65520804 ACATTTTTGT
65520814 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAAGAAAAGA
*
65520835 AAAGAAAAAGCAAA-AGAAGAA
1 AAAGAAAAAGCAAAGAAAAG-A
*
65520856 AAAGAAAAAGAAAATGAAATA-A
1 AAAGAAAAAGCAAA-GAAA-AGA
65520878 AAAGAAAA
1 AAAGAAAA
65520886 GAGAGGCAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
20 8 0.19
21 23 0.53
22 9 0.21
23 2 0.05
24 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (21 bp):
AAAGAAAAAGCAAAGAAAAGA
Found at i:65520849 original size:6 final size:5
Alignment explanation
Indices: 65520825--65520887 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
65520815 AAGAGAAAAC
*
65520825 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGAA AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAG-A AAAGA AAA-GA
65520873 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
65520888 GAGGCAAGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
4 4 0.08
5 25 0.51
6 19 0.39
7 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:65520964 original size:12 final size:12
Alignment explanation
Indices: 65520956--65520980 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
65520946 TTTGAAAAGC
65520956 AAAAAGAAAATG
1 AAAAAGAAAATG
65520968 AAAAAGAAAATG
1 AAAAAGAAAATG
65520980 A
1 A
65520981 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:65520977 original size:18 final size:18
Alignment explanation
Indices: 65520950--65520992 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
65520940 AAAGCCTTTG
65520950 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
65520969 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
65520987 AAAAGA
1 AAAAGA
65520993 GAACGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:65520990 original size:30 final size:31
Alignment explanation
Indices: 65520956--65521037 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
65520946 TTTGAAAAGC
*
65520956 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
65520986 AAAAAGAGAACGAAAAA-AAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
65521016 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
65521038 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 3 0.07
30 36 0.84
31 4 0.09
ACGTcount: A:0.66, C:0.01, G:0.21, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:65523073 original size:19 final size:19
Alignment explanation
Indices: 65523028--65523073 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
65523018 ATTAACACAC
*
65523028 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
65523047 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
65523065 AATTAATAA
1 AATTAATAA
65523074 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:65524929 original size:18 final size:19
Alignment explanation
Indices: 65524906--65524944 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
65524896 TTTATCTCAA
*
65524906 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
65524924 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
65524943 TT
1 TT
65524945 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:65524960 original size:48 final size:49
Alignment explanation
Indices: 65524908--65525011 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 49
65524898 TATCTCAATT
* * *
65524908 TCTTTTTCCACTCT-TTTTTC-TTGTTCACATTCTTTTTCTCTCTCAAAC
1 TCTTTTTCCACTCTCTTTTTCAAT-CTCACATTCTTTTTCACTCTCAAAC
* ** *
65524956 TCTTTTT-CATTCTCTTTTTCAATCTCATTTTCTTTTTCACTCTCAATC
1 TCTTTTTCCACTCTCTTTTTCAATCTCACATTCTTTTTCACTCTCAAAC
65525004 TCTTTTTC
1 TCTTTTTC
65525012 TTTTTCTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
47 5 0.11
48 40 0.87
49 1 0.02
ACGTcount: A:0.12, C:0.28, G:0.01, T:0.59
Consensus pattern (49 bp):
TCTTTTTCCACTCTCTTTTTCAATCTCACATTCTTTTTCACTCTCAAAC
Found at i:65524983 original size:18 final size:18
Alignment explanation
Indices: 65524962--65525011 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
65524952 AAACTCTTTT
65524962 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
65524980 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
65524998 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
65525012 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:65525001 original size:24 final size:24
Alignment explanation
Indices: 65524937--65525018 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
65524927 CTTGTTCACA
*
65524937 TTCTTTTTCTCTCTCAAACTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
* * * * *
65524961 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTTTCTCTCTCAATCTCTTT
*
65524985 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
65525009 TTCTTTTTCT
1 TTCTTTTTCT
65525019 TTCATTTCTT
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (24 bp):
TTCTTTTTCTCTCTCAATCTCTTT
Found at i:65525070 original size:42 final size:42
Alignment explanation
Indices: 65525015--65525111 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
65525005 CTTTTTCTTT
* * *
65525015 TTCTTTCA-TTTCTTTGTTTCTTTTCTCGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
65525056 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
65525098 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
65525112 CTCATAATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 7 0.14
42 44 0.86
ACGTcount: A:0.14, C:0.24, G:0.05, T:0.57
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:65525089 original size:21 final size:21
Alignment explanation
Indices: 65525022--65525089 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
65525012 TTTTTCTTTC
*
65525022 ATTTCTTTGTTTCTTTTCTCG
1 ATTTCTTTGTTTCTTCTCTCG
* *****
65525043 ATTTCATTCAAGATTCTCTC-
1 ATTTCTTTGTTTCTTCTCTCG
65525063 ATTTTCTTTGTTTCTTCTCTCG
1 A-TTTCTTTGTTTCTTCTCTCG
65525085 ATTTC
1 ATTTC
65525090 ATTCAAAATC
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.07, T:0.59
Consensus pattern (21 bp):
ATTTCTTTGTTTCTTCTCTCG
Found at i:65527290 original size:19 final size:19
Alignment explanation
Indices: 65527245--65527290 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
65527235 ATTAACACAC
*
65527245 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
65527264 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
65527282 AATTAATAA
1 AATTAATAA
65527291 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:65527517 original size:10 final size:10
Alignment explanation
Indices: 65527504--65527558 Score: 74
Period size: 10 Copynumber: 5.5 Consensus size: 10
65527494 AAGCTCGGTT
65527504 GAGCTCAAAC
1 GAGCTCAAAC
*
65527514 GAGCTGAAAC
1 GAGCTCAAAC
*
65527524 GAGCTCAAAT
1 GAGCTCAAAC
*
65527534 GAGCTGAAAC
1 GAGCTCAAAC
*
65527544 GAGCTCAAAT
1 GAGCTCAAAC
65527554 GAGCT
1 GAGCT
65527559 GAGTTGAGCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:65527567 original size:30 final size:30
Alignment explanation
Indices: 65527495--65527569 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
65527485 GCTGAAAGTA
* * *
65527495 AGCTCGGTTGAGCTCAAACGAGCTGAAACG
1 AGCTCAGTTGAGCTGAAACGAGCTCAAACG
** *
65527525 AGCTCAAATGAGCTGAAACGAGCTCAAATG
1 AGCTCAGTTGAGCTGAAACGAGCTCAAACG
*
65527555 AGCTGAGTTGAGCTG
1 AGCTCAGTTGAGCTG
65527570 GACGGAGCTC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.19
Consensus pattern (30 bp):
AGCTCAGTTGAGCTGAAACGAGCTCAAACG
Found at i:65527568 original size:20 final size:20
Alignment explanation
Indices: 65527504--65527560 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
65527494 AAGCTCGGTT
*
65527504 GAGCTCAAACGAGCTGAAAC
1 GAGCTCAAATGAGCTGAAAC
65527524 GAGCTCAAATGAGCTGAAAC
1 GAGCTCAAATGAGCTGAAAC
65527544 GAGCTCAAATGAGCTGA
1 GAGCTCAAATGAGCTGA
65527561 GTTGAGCTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (20 bp):
GAGCTCAAATGAGCTGAAAC
Found at i:65528010 original size:20 final size:20
Alignment explanation
Indices: 65527987--65528034 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
65527977 AGCTCCGTCC
65527987 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
65528007 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
65528027 AGCTCAAC
1 AGCTCAAC
65528035 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:65528387 original size:17 final size:16
Alignment explanation
Indices: 65528345--65528387 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
65528335 TGAAGAGATG
*
65528345 CATGAACGGGAAAGTT
1 CATGAACGGGAAAATT
65528361 CAATGAACGGGAAGAATT
1 C-ATGAACGGGAA-AATT
*
65528379 CATGCACGG
1 CATGAACGG
65528388 CCTGGTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 1 0.04
17 18 0.78
18 4 0.17
ACGTcount: A:0.37, C:0.16, G:0.30, T:0.16
Consensus pattern (16 bp):
CATGAACGGGAAAATT
Found at i:65533979 original size:30 final size:30
Alignment explanation
Indices: 65533893--65533990 Score: 88
Period size: 30 Copynumber: 3.3 Consensus size: 30
65533883 TTAAACTAAA
* * *
65533893 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCATGAGCTGAAG
* * * * * *
65533923 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCATGAGCTGAAG
* * *
65533953 CTGAGCTAAGGTTTAGCTCATGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCATGAGCTGAAG
65533983 ATGAGCTA
1 ATGAGCTA
65533991 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCATGAGCTGAAG
Found at i:65535366 original size:11 final size:11
Alignment explanation
Indices: 65535344--65535381 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
65535334 TATACAAGTT
65535344 AAAAAAAT--A
1 AAAAAAATCGA
65535353 AAAAAAATCGA
1 AAAAAAATCGA
65535364 AAAAAAATTCGA
1 AAAAAAA-TCGA
65535376 AAAAAA
1 AAAAAA
65535382 TAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 8 0.31
11 8 0.31
12 10 0.38
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (11 bp):
AAAAAAATCGA
Found at i:65540620 original size:19 final size:19
Alignment explanation
Indices: 65540596--65540635 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
65540586 AGCTCCCATG
65540596 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
65540615 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
65540634 TA
1 TA
65540636 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:65541071 original size:30 final size:30
Alignment explanation
Indices: 65541037--65541133 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
65541027 AGCTCAGTCC
65541037 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
65541067 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * *
65541097 CAGCTCAACTTTAGCTCGCGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
65541127 TAGCTCA
1 TAGCTCA
65541134 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:65548836 original size:15 final size:15
Alignment explanation
Indices: 65548816--65548863 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
65548806 TCAAAGATGG
65548816 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
65548831 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
65548846 -TTTATGGATATAAA
1 GTTTATGGATATGAA
65548860 GTTT
1 GTTT
65548864 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:65548843 original size:29 final size:29
Alignment explanation
Indices: 65548810--65548869 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
65548800 AAGGATTCAA
* *
65548810 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
65548839 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
65548868 AG
1 AG
65548870 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:65549839 original size:14 final size:14
Alignment explanation
Indices: 65549817--65549859 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
65549807 AAAGAAGCAA
*
65549817 TCATTAAATTAAAT
1 TCATTAAATTAAAC
*
65549831 TCATCAAA-TAAAC
1 TCATTAAATTAAAC
65549844 TCATTTAAATTAAAC
1 TCA-TTAAATTAAAC
65549859 T
1 T
65549860 AAGATGAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 7 0.29
14 11 0.46
15 6 0.25
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (14 bp):
TCATTAAATTAAAC
Found at i:65551397 original size:13 final size:13
Alignment explanation
Indices: 65551379--65551403 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65551369 GTATTGATCA
65551379 TGTGTTCACACCT
1 TGTGTTCACACCT
65551392 TGTGTTCACACC
1 TGTGTTCACACC
65551404 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:65558665 original size:68 final size:67
Alignment explanation
Indices: 65558593--65558742 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
65558583 CATCATGTGT
* * * *
65558593 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
65558655 ATGTAG
62 ATGTAG
** * *
65558661 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
65558726 AG
66 AG
65558728 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
65558743 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:65558698 original size:64 final size:64
Alignment explanation
Indices: 65558617--65558800 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
65558607 AGACATTATG
* *
65558617 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
65558681 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
65558746 AA
63 AA
* * * *
65558748 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
65558801 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:65559892 original size:2 final size:2
Alignment explanation
Indices: 65559885--65559909 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
65559875 TCATGACATG
65559885 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 T
65559910 GACTAGTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:65561878 original size:30 final size:30
Alignment explanation
Indices: 65561793--65561880 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
65561783 TAAGCTAAAA
* *
65561793 TGAGCTAAGCTTTAGC-CCTTAAGCTAAAGT
1 TGAGCTAAGATTTAGCTCC-TAAGCTGAAGT
*
65561823 TGAGCTGAGATTATA-CTCCTAAGCTGAAGT
1 TGAGCTAAGATT-TAGCTCCTAAGCTGAAGT
* * *
65561853 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
1 TGAGCTAAGATTTAGCTCCTAAGCTGAA
65561881 TATAAGCTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 2 0.04
30 42 0.88
31 4 0.08
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCCTAAGCTGAAGT
Found at i:65562997 original size:30 final size:31
Alignment explanation
Indices: 65562939--65562998 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
65562929 ATAGTAAAAG
* *
65562939 AAACGAGCTGGAAAGAAGCTAAATTGAGCTC
1 AAACGAGCTGGAAACAAGCTAAAGTGAGCTC
* *
65562970 AAACGAGCT-GACACAAGCTCAAGTGAGCT
1 AAACGAGCTGGAAACAAGCTAAAGTGAGCT
65562999 GATTGGAGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (31 bp):
AAACGAGCTGGAAACAAGCTAAAGTGAGCTC
Found at i:65563398 original size:62 final size:63
Alignment explanation
Indices: 65563301--65563427 Score: 193
Period size: 62 Copynumber: 2.0 Consensus size: 63
65563291 CAACACTAAA
* * *
65563301 AAGTGATACGAACTGTCTCGGGAAGAGTCGAGTCGTATG-TAGATTGCCCGATCGCCTACGAG
1 AAGTGATACGAACCGCCTCGGGAAGAGTCGAGTCGTATGCGAGATTGCCCGATCGCCTACGAG
* * *
65563363 AAGTGATACGAACCGCCTCGGGGAGAGTCGAGTCGTATGCGAGTTTGCCCGATCGTCTACGAG
1 AAGTGATACGAACCGCCTCGGGAAGAGTCGAGTCGTATGCGAGATTGCCCGATCGCCTACGAG
65563426 AA
1 AA
65563428 AGTATCGTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
62 36 0.62
63 22 0.38
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.21
Consensus pattern (63 bp):
AAGTGATACGAACCGCCTCGGGAAGAGTCGAGTCGTATGCGAGATTGCCCGATCGCCTACGAG
Found at i:65566601 original size:30 final size:30
Alignment explanation
Indices: 65566507--65566594 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
65566497 TAAACTAAAA
* *
65566507 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
65566537 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
65566567 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
65566595 TATGAGCAGT
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:65567880 original size:20 final size:20
Alignment explanation
Indices: 65567834--65567881 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
65567824 AGTAAGCTCG
65567834 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** * *
65567854 AACGAGCTTAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
65567874 GTTGAGCT
1 GTTGAGCT
65567882 GGACGAAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:65569509 original size:18 final size:18
Alignment explanation
Indices: 65569480--65569529 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
65569470 AAACTCTTTT
*
65569480 TCATTCTTTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
65569498 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
65569516 TCATTCTCTTTTTC
1 TCATTCTCTTTTTC
65569530 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:65569564 original size:21 final size:21
Alignment explanation
Indices: 65569540--65569607 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
65569530 TTTTTCTTTC
*
65569540 ATTTCTTTGTTTCTTTTCTCG
1 ATTTCTTTGTTTCTTCTCTCG
* *****
65569561 ATTTCATTCAAGATTCTCTCG
1 ATTTCTTTGTTTCTTCTCTCG
*
65569582 TTTTCTTTGTTTCTTCTCTCG
1 ATTTCTTTGTTTCTTCTCTCG
65569603 ATTTC
1 ATTTC
65569608 ATTCAAAATC
Statistics
Matches: 32, Mismatches: 15, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.10, C:0.22, G:0.09, T:0.59
Consensus pattern (21 bp):
ATTTCTTTGTTTCTTCTCTCG
Found at i:65569588 original size:42 final size:42
Alignment explanation
Indices: 65569541--65569629 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
65569531 TTTTCTTTCA
* * * *
65569541 TTTCTTTGTTTCTTTTCTCGATTTCATTCAAGATTCTCTCGT
1 TTTCTTTGTTTCTTCTCTCGATTTCATTCAAAATCCTCTCAT
65569583 TTTCTTTGTTTCTTCTCTCGATTTCATTCAAAATCCTCTCAT
1 TTTCTTTGTTTCTTCTCTCGATTTCATTCAAAATCCTCTCAT
65569625 TTTCT
1 TTTCT
65569630 CTCATAATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.13, C:0.24, G:0.07, T:0.56
Consensus pattern (42 bp):
TTTCTTTGTTTCTTCTCTCGATTTCATTCAAAATCCTCTCAT
Found at i:65574004 original size:20 final size:20
Alignment explanation
Indices: 65573958--65574005 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
65573948 AGTAAGCTCG
65573958 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** * *
65573978 AACGAGCTTAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
65573998 GTTGAGCT
1 GTTGAGCT
65574006 GGACGAGCTC
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:65575784 original size:20 final size:20
Alignment explanation
Indices: 65575738--65575785 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
65575728 AGTAAGCTCG
65575738 GTTGAGCTCAAACCAGCTGA
1 GTTGAGCTCAAACCAGCTGA
*** **
65575758 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACCAGCTGA
65575778 GTTGAGCT
1 GTTGAGCT
65575786 GGACGGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACCAGCTGA
Found at i:65576607 original size:22 final size:21
Alignment explanation
Indices: 65576574--65576615 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
65576564 TCAAACCTAC
65576574 ACAAGCATGCAAAATTTACACA
1 ACAAGCATGCAAAA-TTACACA
*
65576596 ACAAGGCA-GCAACATTACAC
1 ACAA-GCATGCAAAATTACAC
65576616 CACCATCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 9 0.50
23 3 0.17
ACGTcount: A:0.48, C:0.26, G:0.12, T:0.14
Consensus pattern (21 bp):
ACAAGCATGCAAAATTACACA
Found at i:65577177 original size:18 final size:18
Alignment explanation
Indices: 65577156--65577215 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
65577146 ATACTCACTC
65577156 TCTTTTTCAATTTTCTTT
1 TCTTTTTCAATTTTCTTT
**
65577174 TCTTGATCAA-TTTCTTTT
1 TCTTTTTCAATTTTC-TTT
* *
65577192 TCCTTTTC-ATTTTGTTT
1 TCTTTTTCAATTTTCTTT
65577209 T-TTTTTC
1 TCTTTTTC
65577216 TCATTCTCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
16 5 0.15
17 9 0.27
18 19 0.58
ACGTcount: A:0.10, C:0.17, G:0.03, T:0.70
Consensus pattern (18 bp):
TCTTTTTCAATTTTCTTT
Found at i:65580532 original size:29 final size:30
Alignment explanation
Indices: 65580431--65580526 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
65580421 AGCTCACTCC
65580431 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * *
65580461 TAGCTCAACTTCAGCTTA-GAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
65580490 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
65580520 TAGCTCA
1 TAGCTCA
65580527 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
29 24 0.45
30 29 0.55
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:65583097 original size:6 final size:5
Alignment explanation
Indices: 65583062--65583129 Score: 50
Period size: 5 Copynumber: 13.0 Consensus size: 5
65583052 ACATTCTTGT
* **
65583062 AAAGA AAAAA CAAAGA AAAGA AAAGAA AAAGCA AAAGA CGA-A AAAGA
1 AAAGA AAAGA -AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA
65583109 AAATGA AATA-A AAAGA AAAGA
1 AAA-GA AA-AGA AAAGA AAAGA
65583130 GAGGCAAGAG
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
4 3 0.06
5 28 0.56
6 18 0.36
7 1 0.02
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:65583173 original size:21 final size:21
Alignment explanation
Indices: 65583148--65583220 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
65583138 AGGCAAGTAA
65583148 GAGAGAAAATGAGCAAATCTT
1 GAGAGAAAATGAGCAAATCTT
** * *
65583169 GAGAGAACTTGA-AAAAGCCATT
1 GAGAGAAAATGAGCAAA-TC-TT
65583191 AAGAGAGAAAATGAGCAAATCTT
1 --GAGAGAAAATGAGCAAATCTT
65583214 GAGAGAA
1 GAGAGAA
65583221 CTTGAAAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
20 3 0.08
21 18 0.46
22 2 0.05
23 2 0.05
24 11 0.28
25 3 0.08
ACGTcount: A:0.49, C:0.10, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGAGAAAATGAGCAAATCTT
Found at i:65583194 original size:45 final size:45
Alignment explanation
Indices: 65583145--65583235 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
65583135 AAGAGGCAAG
65583145 TAAGAGAGAAAATGAGCAAATCTTGAGAGAACTTGAAAAAGCCAT
1 TAAGAGAGAAAATGAGCAAATCTTGAGAGAACTTGAAAAAGCCAT
65583190 TAAGAGAGAAAATGAGCAAATCTTGAGAGAACTTGAAAAAGCCAT
1 TAAGAGAGAAAATGAGCAAATCTTGAGAGAACTTGAAAAAGCCAT
65583235 T
1 T
65583236 GAAAAACAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.48, C:0.11, G:0.22, T:0.19
Consensus pattern (45 bp):
TAAGAGAGAAAATGAGCAAATCTTGAGAGAACTTGAAAAAGCCAT
Found at i:65583274 original size:12 final size:12
Alignment explanation
Indices: 65583247--65583291 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
65583237 AAAAACAAAA
* *
65583247 GAAAAAGAAAAA
1 GAAAAAGAGAAT
* *
65583259 GAAAATGAGATT
1 GAAAAAGAGAAT
65583271 GAAAAAGAGAAT
1 GAAAAAGAGAAT
65583283 GAAAAAGAG
1 GAAAAAGAG
65583292 TTTGAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (12 bp):
GAAAAAGAGAAT
Found at i:65583274 original size:24 final size:24
Alignment explanation
Indices: 65583247--65583309 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
65583237 AAAAACAAAA
*
65583247 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAAAGAGATT
* * *
65583271 GAAAAAGAGAATGAAAAAGAGTTT
1 GAAAAAGAAAAAGAAAAAGAGATT
* *
65583295 GAGAGAGAAAAAGAA
1 GAAAAAGAAAAAGAA
65583310 TGTGAACAAG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.25, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAAAGAGATT
Found at i:65584876 original size:286 final size:283
Alignment explanation
Indices: 65584361--65584929 Score: 1012
Period size: 286 Copynumber: 2.0 Consensus size: 283
65584351 TAAGCACTTT
* *
65584361 TGATGAGATCCGGCCCGGGTAGATGAGTCGAATTCACGTAGTTGCCGATCGTAGTTTGAGAGAGT
1 TGATGAGATCCGGCCCGGGTAGATGAATCGAATTCACGTAGTTGCCGATCGTAGTTCGAGAGAGT
*
65584426 CGTTCGTGCCTCGGATTTTAGTAATAAAAGTAAAATAATGGATGAATAAGTGAAAGATTTCAAGA
66 CGTTCGTGCCTCGGATTTTAGTAATAAAAGTAAAATAATGGATGAATAAGCGAAAGATTTCAAGA
*
65584491 AGGGTAAGTTTAGTAATAGGTTCGGTTATGTGTAGCAAAGATGGGTGATGGATAAATGGGTCGGT
131 AGGGTAAGTTTAGTAATAGGTTCGGTTATGTGTAGCAAAGATGGGTGATGGATAAATGGGTCGAT
*
65584556 TTGGTTACAAGAAGGAAAGTTGAAAGATGGGGGATAGAAAAATGAACTCAACATCAAGAATGATT
196 TTGGTTACAAGAAGGAAAGTTGAAAGATGGGGGATAGAAAAACGAACTCAACATCAAGAATGATT
65584621 CAACACTAAGAAGTGTCACCCCG
261 CAACACTAAGAAGTGTCACCCCG
*
65584644 TGATGTGATCCGGCCCGGGTAGATGAATCGAATTCACGTAGTTGCCCGATCGTAGTTCGAGAGAG
1 TGATGAGATCCGGCCCGGGTAGATGAATCGAATTCACGTAGTTG-CCGATCGTAGTTCGAGAGAG
* *
65584709 TCGTTCGTGCCTCGGATTTTAGTAATAAAAGTAAAATAATGGATTAGAATAAGCGGAAGGTTTCA
65 TCGTTCGTGCCTCGGATTTTAGTAATAAAAGTAAAATAATGGA-T-GAATAAGCGAAAGATTTCA
65584774 AGAAGGGTAAGTTTAGTAATAGGTTCGGTTATGTGTAGCAAAGATGGGTGATGGATAAATGGGTC
128 AGAAGGGTAAGTTTAGTAATAGGTTCGGTTATGTGTAGCAAAGATGGGTGATGGATAAATGGGTC
* * *
65584839 GATTTGGTTACAAGAAGGAAAGTTGAAAGATGGGGGATGGAAAAACGAACTCAACGTCAGGAATG
193 GATTTGGTTACAAGAAGGAAAGTTGAAAGATGGGGGATAGAAAAACGAACTCAACATCAAGAATG
65584904 ATTCAACACTAAGAAGTGTCACCCCG
258 ATTCAACACTAAGAAGTGTCACCCCG
65584930 GTTCCTATAT
Statistics
Matches: 272, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
283 42 0.15
284 62 0.23
285 1 0.00
286 167 0.61
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.25
Consensus pattern (283 bp):
TGATGAGATCCGGCCCGGGTAGATGAATCGAATTCACGTAGTTGCCGATCGTAGTTCGAGAGAGT
CGTTCGTGCCTCGGATTTTAGTAATAAAAGTAAAATAATGGATGAATAAGCGAAAGATTTCAAGA
AGGGTAAGTTTAGTAATAGGTTCGGTTATGTGTAGCAAAGATGGGTGATGGATAAATGGGTCGAT
TTGGTTACAAGAAGGAAAGTTGAAAGATGGGGGATAGAAAAACGAACTCAACATCAAGAATGATT
CAACACTAAGAAGTGTCACCCCG
Found at i:65586041 original size:20 final size:20
Alignment explanation
Indices: 65585995--65586042 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
65585985 AGTAAGCTCG
65585995 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** * *
65586015 AACGAGCTTAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
65586035 GTTGAGCT
1 GTTGAGCT
65586043 GGATGGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:65587500 original size:10 final size:10
Alignment explanation
Indices: 65587487--65587532 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
65587477 AAAAAGAAAT
65587487 GAGCTGAATC
1 GAGCTGAATC
65587497 GAGCTGAATTC
1 GAGCTGAA-TC
* * *
65587508 TAGCTCAAAC
1 GAGCTGAATC
65587518 GAGCTGAATC
1 GAGCTGAATC
65587528 GAGCT
1 GAGCT
65587533 CAAGTGAGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (10 bp):
GAGCTGAATC
Done.