Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 92 of 332
Found at i:29475397 original size:25 final size:24
Alignment explanation
Indices: 29475357--29475412 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
29475347 CTAGTTTCTC
29475357 TTAATTTTTAATTTTATTCAATTA
1 TTAATTTTTAATTTTATTCAATTA
*
29475381 GTTAATTTTTCAA-TTTATTGAATTA
1 -TTAATTTTT-AATTTTATTCAATTA
29475406 TTAATTT
1 TTAATTT
29475413 CAATAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 7 0.24
25 20 0.69
26 2 0.07
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (24 bp):
TTAATTTTTAATTTTATTCAATTA
Found at i:29478860 original size:11 final size:11
Alignment explanation
Indices: 29478844--29478876 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
29478834 ATCATTCAAG
29478844 CCATCCCTCAT
1 CCATCCCTCAT
29478855 CCATCCC-CTAT
1 CCATCCCTC-AT
29478866 CCATCCCTCAT
1 CCATCCCTCAT
29478877 TCCACAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.05
11 18 0.90
12 1 0.05
ACGTcount: A:0.18, C:0.55, G:0.00, T:0.27
Consensus pattern (11 bp):
CCATCCCTCAT
Found at i:29482865 original size:33 final size:33
Alignment explanation
Indices: 29482828--29482894 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
29482818 GATTGGACTT
*
29482828 TATAAGTGTGACTATTCCATGACTTGTGTCCAA
1 TATAAGTGTGACTATTCAATGACTTGTGTCCAA
29482861 TATAAGTGTGACTATTCAATGACTTGTGTCCAA
1 TATAAGTGTGACTATTCAATGACTTGTGTCCAA
29482894 T
1 T
29482895 CTAGATATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (33 bp):
TATAAGTGTGACTATTCAATGACTTGTGTCCAA
Found at i:29488743 original size:22 final size:22
Alignment explanation
Indices: 29488718--29488773 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
29488708 TCCAAGCTAA
**
29488718 TGAACAGTAAGTTCTATTGAGC
1 TGAACAGTAAGTTCTATCAAGC
*
29488740 TGAAACGGTAAGTTCTATCAAGC
1 TG-AACAGTAAGTTCTATCAAGC
29488763 TGAACAGTAAG
1 TGAACAGTAAG
29488774 CTCATACGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (22 bp):
TGAACAGTAAGTTCTATCAAGC
Found at i:29488855 original size:73 final size:73
Alignment explanation
Indices: 29488768--29488929 Score: 306
Period size: 73 Copynumber: 2.2 Consensus size: 73
29488758 CAAGCTGAAC
*
29488768 AGTAAGCTCATACGAGTTGGAACGGTAAGCTCCAATGATCTGATAACAGTAAGCTCTTACGAGAT
1 AGTAAGCTCATACGAGTTGGAACGGTAAGCTCCAATGATCTGATAACAGTAAACTCTTACGAGAT
29488833 GATATATT
66 GATATATT
*
29488841 AGTAAGCTCATACGAGTTGGAACGGTAGGCTCCAATGATCTGATAACAGTAAACTCTTACGAGAT
1 AGTAAGCTCATACGAGTTGGAACGGTAAGCTCCAATGATCTGATAACAGTAAACTCTTACGAGAT
29488906 GATATATT
66 GATATATT
29488914 AGTAAGCTCATACGAG
1 AGTAAGCTCATACGAG
29488930 CTGTGGTGAG
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 87 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (73 bp):
AGTAAGCTCATACGAGTTGGAACGGTAAGCTCCAATGATCTGATAACAGTAAACTCTTACGAGAT
GATATATT
Found at i:29489268 original size:23 final size:23
Alignment explanation
Indices: 29489228--29489304 Score: 102
Period size: 24 Copynumber: 3.3 Consensus size: 23
29489218 TACATTCTAT
*
29489228 CGAGCTG-AACAGTGAGCTCATA
1 CGAGCTGAAACAGTAAGCTCATA
* *
29489250 CGAGCTGAAACAATAAGCTCTTA
1 CGAGCTGAAACAGTAAGCTCATA
*
29489273 CGAGCTGTTAACAGTAAGCTCATA
1 CGAGCTG-AAACAGTAAGCTCATA
29489297 CGAGCTGA
1 CGAGCTGA
29489305 TATATCACCT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
22 7 0.15
23 19 0.41
24 20 0.43
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (23 bp):
CGAGCTGAAACAGTAAGCTCATA
Found at i:29497050 original size:30 final size:30
Alignment explanation
Indices: 29496996--29497053 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29496986 GGGCTGGCAT
* *
29496996 ATGGGCGTGTGGCCTGCCCGTGTGGATCAC
1 ATGGGCGTGTGCCCAGCCCGTGTGGATCAC
* *
29497026 ATGGGCGTGTGCCCAGTCCTTGTGGATC
1 ATGGGCGTGTGCCCAGCCCGTGTGGATC
29497054 CTGAAAACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.10, C:0.26, G:0.38, T:0.26
Consensus pattern (30 bp):
ATGGGCGTGTGCCCAGCCCGTGTGGATCAC
Found at i:29497853 original size:9 final size:9
Alignment explanation
Indices: 29497839--29497872 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
29497829 ATATATGTAT
29497839 TTTTTTGAC
1 TTTTTTGAC
*
29497848 TTTTTTTAC
1 TTTTTTGAC
29497857 TTATTTTGAC
1 TT-TTTTGAC
29497867 TTTTTT
1 TTTTTT
29497873 TAGAACAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.74
Consensus pattern (9 bp):
TTTTTTGAC
Found at i:29497853 original size:10 final size:10
Alignment explanation
Indices: 29497838--29497873 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
29497828 CATATATGTA
29497838 TTTTTTTGAC
1 TTTTTTTGAC
29497848 TTTTTTT-AC
1 TTTTTTTGAC
*
29497857 TTATTTTGAC
1 TTTTTTTGAC
29497867 TTTTTTT
1 TTTTTTT
29497874 AGAACAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.11, C:0.08, G:0.06, T:0.75
Consensus pattern (10 bp):
TTTTTTTGAC
Found at i:29498975 original size:19 final size:19
Alignment explanation
Indices: 29498959--29498996 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
29498949 AAAAAAAACC
29498959 AAAGAGAAA-AG-AAAAAA
1 AAAGAGAAATAGCAAAAAA
29498976 AAAGAGAAATAGCAAAAAA
1 AAAGAGAAATAGCAAAAAA
29498995 AA
1 AA
29498997 TTAAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 2 0.11
19 8 0.42
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (19 bp):
AAAGAGAAATAGCAAAAAA
Found at i:29499103 original size:22 final size:20
Alignment explanation
Indices: 29499059--29499110 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
29499049 AATTAATTAG
*
29499059 TAAAATAAGAATAAATAATA
1 TAAAATAAAAATAAATAATA
29499079 TAACAATTAAAAATAAATCAA-A
1 TAA-AA-TAAAAATAAAT-AATA
29499101 TAAAATAAAA
1 TAAAATAAAA
29499111 TTGGGGAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.29
21 4 0.14
22 14 0.50
23 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (20 bp):
TAAAATAAAAATAAATAATA
Found at i:29499263 original size:30 final size:30
Alignment explanation
Indices: 29499228--29499310 Score: 139
Period size: 30 Copynumber: 2.7 Consensus size: 30
29499218 TGCCACGCCC
*
29499228 GTGTGGCCAGGCCGTGTACTCCACACACCG
1 GTGTGGCTAGGCCGTGTACTCCACACACCG
29499258 GTGTGGCTAGGCCGTGTACTCCACACACCG
1 GTGTGGCTAGGCCGTGTACTCCACACACCG
*
29499288 GTGTGGCTAAGCCGTGTAACTCC
1 GTGTGGCTAGGCCGTGT-ACTCC
29499311 CTAACTTTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 45 0.90
31 5 0.10
ACGTcount: A:0.17, C:0.33, G:0.30, T:0.20
Consensus pattern (30 bp):
GTGTGGCTAGGCCGTGTACTCCACACACCG
Found at i:29508594 original size:27 final size:27
Alignment explanation
Indices: 29508564--29508631 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 27
29508554 CAAATTACCA
* *
29508564 TTTTACCCTTGATTTGTAGAATTA-TCG
1 TTTTACCCTCGATTTATAGAATTACT-G
29508591 TTTTACCCTCGATTTATAGAATTACTG
1 TTTTACCCTCGATTTATAGAATTACTG
29508618 TTTTACCCTCGATT
1 TTTTACCCTCGATT
29508632 GTGAAATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (27 bp):
TTTTACCCTCGATTTATAGAATTACTG
Found at i:29508693 original size:27 final size:27
Alignment explanation
Indices: 29508663--29508788 Score: 173
Period size: 27 Copynumber: 4.7 Consensus size: 27
29508653 TATAGGATAG
29508663 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
*
29508690 AATTACCAAAATACCTCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
** * * *
29508717 AATTACTGAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
*
29508744 AATTACCAAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
29508771 AATTACCAAAATACCCCT
1 AATTACCAAAATACCCCT
29508789 GATTTACAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
26 3 0.04
27 78 0.92
28 4 0.05
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:29508793 original size:27 final size:27
Alignment explanation
Indices: 29508663--29508896 Score: 152
Period size: 27 Copynumber: 8.6 Consensus size: 27
29508653 TATAGGATAG
29508663 AATTACCAAAATACCCCT-AGTTTGTAA
1 AATTACCAAAATACCCCTGA-TTTGTAA
*
29508690 AATTACCAAAATACCTCT-AGTTTGTAA
1 AATTACCAAAATACCCCTGA-TTTGTAA
** * * *
29508717 AATTACTGAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTGATTTGTAA
*
29508744 AATTACCAAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-GATTTGTAA
**
29508771 AATTACCAAAATACCCCTGATTTACAA
1 AATTACCAAAATACCCCTGATTTGTAA
* * *
29508798 AATTA-TAGAAATACCCTTGACTTTCTAAA
1 AATTACCA-AAATACCCCTGA-TTTGT-AA
** ** * **
29508827 AATTATAAAAATACCATTGGTTTACAA
1 AATTACCAAAATACCCCTGATTTGTAA
** * * *
29508854 AATTACTGAAATACCCTTGGTTTGTAG
1 AATTACCAAAATACCCCTGATTTGTAA
* *
29508881 ATTTACCAAAACACCC
1 AATTACCAAAATACCC
29508897 TTGTAGGATG
Statistics
Matches: 165, Mismatches: 35, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
26 4 0.02
27 133 0.81
28 10 0.06
29 17 0.10
30 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGATTTGTAA
Found at i:29508800 original size:81 final size:81
Alignment explanation
Indices: 29508663--29508812 Score: 216
Period size: 81 Copynumber: 1.9 Consensus size: 81
29508653 TATAGGATAG
* * **
29508663 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCTCTAGTTTGTAAAATTACT-GAA
1 AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTA-TAGAA
29508727 ATACCACTGGTTTGTGA
65 ATACCACTGGTTTGTGA
29508744 AATTACCAAAATA-CCCTCAATTTGTAAAATTACCAAAATACCCCT-GATTTACAAAATTATAGA
1 AATTACCAAAATACCCCT-AATTTGTAAAATTACCAAAATACCCCTAG-TTTACAAAATTATAGA
29508807 AATACC
64 AATACC
29508813 CTTGACTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
80 6 0.10
81 56 0.90
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (81 bp):
AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTATAGAAA
TACCACTGGTTTGTGA
Found at i:29509842 original size:25 final size:24
Alignment explanation
Indices: 29509804--29509867 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 24
29509794 AGGAAGTGCT
*
29509804 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
*
29509828 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
29509853 AGAAAGGGCTTTGCC
1 A-AAAGGGCTTTGCC
29509868 TTAGTTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 1 0.03
25 35 0.97
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:29510080 original size:42 final size:42
Alignment explanation
Indices: 29510021--29510112 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
29510011 TAGTCTCCCC
29510021 AAATGGGCTTGCATACAT-TCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCT-ATTGACATTACATGTGATATTG
*
29510063 AAATGGGCTTGCATACATCTATTGCCATTACATGTGATATTG
1 AAATGGGCTTGCATACATCTATTGACATTACATGTGATATTG
29510105 AAATGGGC
1 AAATGGGC
29510113 CTAAGGGCTA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 47 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCTATTGACATTACATGTGATATTG
Found at i:29510174 original size:31 final size:31
Alignment explanation
Indices: 29510136--29510281 Score: 240
Period size: 31 Copynumber: 4.7 Consensus size: 31
29510126 CGTTTACAGT
**
29510136 AAAGGCTTCGGCATAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
29510167 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
29510198 AAAGGTTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
29510229 AAAGGCTTCAGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
29510260 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
29510282 TCAAGACTAA
Statistics
Matches: 108, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 5 0.05
31 103 0.95
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:29517595 original size:23 final size:22
Alignment explanation
Indices: 29517520--29517606 Score: 77
Period size: 23 Copynumber: 3.8 Consensus size: 22
29517510 CTGATGAACA
*
29517520 GTAAGCTCTACTGAGCTGAAATG
1 GTAAGCTCTA-TGAGCTGAAACG
* * * *
29517543 ATAAGCTCTATCAAGC-GGAACA
1 GTAAGCTCTAT-GAGCTGAAACG
29517565 GTAAGCTCATATGAGCTGAAACG
1 GTAAGCTC-TATGAGCTGAAACG
*
29517588 GTAAGCTCCAATGAGCTGA
1 GTAAGCT-CTATGAGCTGA
29517607 TAATAGTAAG
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
22 14 0.28
23 35 0.70
24 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (22 bp):
GTAAGCTCTATGAGCTGAAACG
Found at i:29518296 original size:32 final size:32
Alignment explanation
Indices: 29518260--29518330 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
29518250 ATCTATCCTT
*
29518260 AAACATTTAACTACTCAATCATTCAATAATGG
1 AAACATTTAACTACTCAATCATTCAACAATGG
29518292 AAACATTTAACTACTCAATCATTCAACAATGG
1 AAACATTTAACTACTCAATCATTCAACAATGG
*
29518324 AATCATT
1 AAACATT
29518331 CAAAATCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.31
Consensus pattern (32 bp):
AAACATTTAACTACTCAATCATTCAACAATGG
Found at i:29518314 original size:16 final size:16
Alignment explanation
Indices: 29518263--29518314 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
29518253 TATCCTTAAA
29518263 CATTTAACTACTCAAT
1 CATTTAACTACTCAAT
* * * *
29518279 CATTCAA-TAATGGAAA
1 CATTTAACTACT-CAAT
29518295 CATTTAACTACTCAAT
1 CATTTAACTACTCAAT
29518311 CATT
1 CATT
29518315 CAACAATGGA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (16 bp):
CATTTAACTACTCAAT
Found at i:29518327 original size:16 final size:16
Alignment explanation
Indices: 29518276--29518333 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
29518266 TTAACTACTC
*
29518276 AATCATTCAATAATGG
1 AATCATTCAACAATGG
* * * *
29518292 AAACATTTAACTACT-C
1 AATCATTCAAC-AATGG
29518308 AATCATTCAACAATGG
1 AATCATTCAACAATGG
29518324 AATCATTCAA
1 AATCATTCAA
29518334 AATCTATAAC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
15 2 0.06
16 27 0.87
17 2 0.06
ACGTcount: A:0.45, C:0.19, G:0.07, T:0.29
Consensus pattern (16 bp):
AATCATTCAACAATGG
Found at i:29526388 original size:6 final size:6
Alignment explanation
Indices: 29526379--29526438 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
29526369 ATGGGGTGGT
* * ** * *
29526379 GATGAA GATGAA GATGAA GGTTG-A GATGAA GATGAA CATGGG GGTCAA
1 GATGAA GATGAA GATGAA -GATGAA GATGAA GATGAA GATGAA GATGAA
29526427 GATGAA GATGAA
1 GATGAA GATGAA
29526439 TATGGGGGTT
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
5 3 0.08
6 34 0.85
7 3 0.08
ACGTcount: A:0.42, C:0.03, G:0.37, T:0.18
Consensus pattern (6 bp):
GATGAA
Found at i:29526411 original size:24 final size:23
Alignment explanation
Indices: 29526354--29526445 Score: 94
Period size: 24 Copynumber: 3.9 Consensus size: 23
29526344 ACCATGGAAG
* *
29526354 GAGATAAAGATGAAGATGGGGTG
1 GAGATGAAGATGAAGATGGGGTC
* * *
29526377 GTGATGAAGATGAAGATGAAGGTT
1 GAGATGAAGATGAAGATG-GGGTC
*
29526401 GAGATGAAGATGAACATGGGGGTC
1 GAGATGAAGATGAAGAT-GGGGTC
* *
29526425 AAGATGAAGATGAATATGGGG
1 GAGATGAAGATGAAGATGGGG
29526446 GTTAAGGTGA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 20 0.35
24 36 0.63
25 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.40, T:0.20
Consensus pattern (23 bp):
GAGATGAAGATGAAGATGGGGTC
Found at i:29526446 original size:24 final size:24
Alignment explanation
Indices: 29526379--29526462 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
29526369 ATGGGGTGGT
* ** *
29526379 GATGAAGATGAAGATGAAGGTTGA
1 GATGAAGATGAACATGGGGGTTAA
*
29526403 GATGAAGATGAACATGGGGGTCAA
1 GATGAAGATGAACATGGGGGTTAA
*
29526427 GATGAAGATGAATATGGGGGTTAA
1 GATGAAGATGAACATGGGGGTTAA
* *
29526451 GGTGAAGGTGAA
1 GATGAAGATGAA
29526463 GACGATGAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.38, C:0.02, G:0.39, T:0.20
Consensus pattern (24 bp):
GATGAAGATGAACATGGGGGTTAA
Found at i:29531140 original size:40 final size:39
Alignment explanation
Indices: 29530950--29531133 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
29530940 CGAATGATGT
* * * *
29530950 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* *
29530990 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
*
29531030 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29531068 TTCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
29531109 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
29531134 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29531155 original size:79 final size:79
Alignment explanation
Indices: 29531002--29531166 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
29530992 GGACTAAGAT
* **
29531002 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
* *
29531067 ATTCGGGTTAAGTC
66 ATTCCGGTTAAATC
* *
29531081 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
29531144 TATA-TCCGGTTAAATT
63 TAAATTCCGGTTAAATC
29531160 CCGAAGG
1 CCGAAGG
29531167 TACGTGATTC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 51 0.69
80 21 0.28
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATTCCGGTTAAATC
Found at i:29533455 original size:17 final size:18
Alignment explanation
Indices: 29533433--29533466 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29533423 CATATTGAAG
29533433 TGTTTT-AGTGAAAACCT
1 TGTTTTCAGTGAAAACCT
*
29533450 TGTTTTCATTGAAAACC
1 TGTTTTCAGTGAAAACC
29533467 CTTCCACAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (18 bp):
TGTTTTCAGTGAAAACCT
Found at i:29534593 original size:28 final size:27
Alignment explanation
Indices: 29534539--29534597 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
29534529 ACATACATGC
* *
29534539 ATATGGCCCACTAGGCCTAATCTCATTT
1 ATATGGCCCACTAGCCCAAATCTCA-TT
*
29534567 ATATGGCCCATTCAGCCCAAATC-CATT
1 ATATGGCCCACT-AGCCCAAATCTCATT
29534594 ATAT
1 ATAT
29534598 CCATGCTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.22
28 13 0.48
29 8 0.30
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (27 bp):
ATATGGCCCACTAGCCCAAATCTCATT
Found at i:29534849 original size:16 final size:16
Alignment explanation
Indices: 29534809--29534851 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
29534799 GTAGCCAAAC
*
29534809 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGACA
**
29534825 TTTTGGCTTTTCGACA
1 TTTCAGCTTTTCGACA
29534841 TTTCAGCTTTT
1 TTTCAGCTTTT
29534852 GCCGATCTAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.21, G:0.16, T:0.51
Consensus pattern (16 bp):
TTTCAGCTTTTCGACA
Found at i:29537041 original size:40 final size:40
Alignment explanation
Indices: 29536979--29537154 Score: 241
Period size: 40 Copynumber: 4.5 Consensus size: 40
29536969 TATTCGGATG
* *
29536979 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACT
*
29537019 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACT
* * *
29537059 ATATCCGGGCT-AGTCACGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACT
* *
29537098 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACT
*
29537138 ATATCC-GGCTAAATCCC
1 ATATCCGGGCTAAGTCCC
29537155 AAAGATACTT
Statistics
Matches: 121, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
39 45 0.37
40 74 0.61
41 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACT
Found at i:29537111 original size:79 final size:80
Alignment explanation
Indices: 29536979--29537149 Score: 240
Period size: 79 Copynumber: 2.2 Consensus size: 80
29536969 TATTCGGATG
* * * * *
29536979 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATACCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCACGAAGGCATTTATGCAAGTGACTATACCCGGGCTAAGACCCGAAGGCA
29537044 TTTGTGCAAG-TGACT
66 TTTGTGCAAGTTG-CT
* *
29537059 ATATCCGGGCT-AGTCACGAAGGCATTTATGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGTCACGAAGGCATTTATGCAAGTGACTATACCCGGGCTAAGACCCGAAGGCA
*
29537123 TTTGTGCGAGTTGCT
66 TTTGTGCAAGTTGCT
29537138 ATATCC-GGCTAA
1 ATATCCGGGCTAA
29537150 ATCCCAAAGA
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
78 4 0.05
79 65 0.80
80 12 0.15
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCACGAAGGCATTTATGCAAGTGACTATACCCGGGCTAAGACCCGAAGGCA
TTTGTGCAAGTTGCT
Found at i:29543315 original size:40 final size:40
Alignment explanation
Indices: 29543259--29543394 Score: 218
Period size: 40 Copynumber: 3.4 Consensus size: 40
29543249 ATATGTGCAT
29543259 AGCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAA
1 AGCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAA
*
29543299 AGCATTCGTGCAGGTTATTATAACCGGGTTAAGTCCCGAA
1 AGCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAA
* **
29543339 GGCATTCGTGCGGGTTATTATAATTGGGTTAAGTCCCGAA
1 AGCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAA
* *
29543379 GGCATTCGTGCTGGTT
1 AGCATTCGTGCGGGTT
29543395 GTTACATCCG
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 90 1.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (40 bp):
AGCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAA
Found at i:29543418 original size:80 final size:80
Alignment explanation
Indices: 29543260--29543418 Score: 210
Period size: 80 Copynumber: 2.0 Consensus size: 80
29543250 TATGTGCATA
*
29543260 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAAGCATTCGTGCAGGTTATTATAACCG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAAGCATTCGTGCAGGTTATTACAACCG
* ** *
29543325 GGTTAAGTCCCGAAG
66 AGCCAAATCCCGAAG
** * * * *
29543340 GCATTCGTGCGGGTTATTATAATTGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTACATCCG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAAGCATTCGTGCAGGTTATTACAACCG
*
29543405 AGCCAAATTCCGAA
66 AGCCAAATCCCGAA
29543419 AGTATTTATG
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (80 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAAGCATTCGTGCAGGTTATTACAACCG
AGCCAAATCCCGAAG
Found at i:29546853 original size:50 final size:50
Alignment explanation
Indices: 29546778--29546962 Score: 193
Period size: 50 Copynumber: 3.8 Consensus size: 50
29546768 TGATACTAGG
*
29546778 GAGATATGAGAGTTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
* *
29546828 GAGATATGAGAGCTAGCGTAAGACCATGTTTGGGACATGGCATCGG-CT-
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
* * * * * *
29546876 -TGATATGTG-TC-AGTGTAAGACCATGTCTAGGACATGGTATCGACAC-C
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTC
* * * * *
29546923 GATAGATAAGAGCCAGTGTAAGACCATGTCTGAGACATGG
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGG
29546963 AATCTGTAAC
Statistics
Matches: 110, Mismatches: 19, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
45 27 0.25
46 1 0.01
47 8 0.07
48 4 0.04
49 3 0.03
50 67 0.61
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (50 bp):
GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
Found at i:29552931 original size:23 final size:23
Alignment explanation
Indices: 29552905--29552978 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
29552895 GTCCTTCGGG
29552905 ACTTATCACAGTTATACACTTCC
1 ACTTATCACAGTTATACACTTCC
* *
29552928 ACTTCCATCCCA-TT-GAC-CATTCGGC
1 ACTT--ATCACAGTTATACAC-TTC--C
29552953 -CTTATCACAGTTATACACTTCC
1 ACTTATCACAGTTATACACTTCC
29552975 ACTT
1 ACTT
29552979 CCATCCCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 18
0.63 0.07 0.30
Matches are distributed among these distances:
22 7 0.18
23 14 0.37
24 10 0.26
25 7 0.18
ACGTcount: A:0.26, C:0.34, G:0.07, T:0.34
Consensus pattern (23 bp):
ACTTATCACAGTTATACACTTCC
Found at i:29552969 original size:47 final size:47
Alignment explanation
Indices: 29552918--29553365 Score: 704
Period size: 47 Copynumber: 9.4 Consensus size: 47
29552908 TATCACAGTT
* * * *
29552918 ATACACTTCCAC-TTCCATCCCATTGACCATTCGGCCTTATCACAGT-T
1 ATACACTTTCACATT-CATCACATTGGCCATTCGGCCTTATCACA-TAC
* *
29552965 ATACACTTCCAC-TTCCATCCCATTGGCCATTCGGCCTTATCACATAC
1 ATACACTTTCACATT-CATCACATTGGCCATTCGGCCTTATCACATAC
29553012 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
*
29553059 ATACACTTTCACATTCATCACATTGGCCATTTGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATAC
*
29553108 ATACACTTTCACATTCATCACATTGGTCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATAC
*
29553157 ATACACTTTCAAATTCATCACATTGGCCATTCGGCCTTATCACATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
*
29553204 ATACACTTTCACATTCATCAGATTGGCCATTCGGCCTTATCACATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
29553251 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
29553298 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATAC
29553347 ATACACTTTCACATTCATC
1 ATACACTTTCACATTCATC
29553366 GTAACAAAAT
Statistics
Matches: 383, Mismatches: 12, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
46 1 0.00
47 265 0.69
48 2 0.01
49 115 0.30
ACGTcount: A:0.27, C:0.32, G:0.08, T:0.33
Consensus pattern (47 bp):
ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
Found at i:29553127 original size:27 final size:27
Alignment explanation
Indices: 29553097--29553179 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 27
29553087 ATTTGGCCTT
29553097 ATCACATATACATACACTTTCACATTC
1 ATCACATATACATACACTTTCACATTC
** * *
29553124 ATCACAT-T-GGT-CA--TTCGGCCTT-
1 ATCACATATACATACACTTTC-ACATTC
*
29553146 ATCACATATACATACACTTTCAAATTC
1 ATCACATATACATACACTTTCACATTC
29553173 ATCACAT
1 ATCACAT
29553180 TGGCCATTCG
Statistics
Matches: 40, Mismatches: 9, Indels: 14
0.63 0.14 0.22
Matches are distributed among these distances:
22 10 0.25
23 4 0.10
24 3 0.08
25 3 0.08
26 3 0.08
27 17 0.43
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.34
Consensus pattern (27 bp):
ATCACATATACATACACTTTCACATTC
Found at i:29553337 original size:239 final size:239
Alignment explanation
Indices: 29552933--29553365 Score: 771
Period size: 239 Copynumber: 1.8 Consensus size: 239
29552923 CTTCCACTTC
* * *
29552933 CATCCCATTGACCATTCGGCCTTATCACAGTTATACACTTCCACTTCCATCCCATTGGCCATTCG
1 CATCACATTGACCATTCGGCCTTATCACAGTCATACACTTCCACTTCCATCACATTGGCCATTCG
29552998 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACATAC
66 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACATAC
*
29553063 ACTTTCACATTCATCACATTGGCCATTTGGCCTTATCACATATACATACACTTTCACATTCATCA
131 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCA
29553128 CATTGGTCATTCGGCCTTATCACATATACATACACTTTCAAATT
196 CATTGGTCATTCGGCCTTATCACATATACATACACTTTCAAATT
* * *
29553172 CATCACATTGGCCATTCGGCCTTATCACA-TACATACACTTTCACATT-CATCAGATTGGCCATT
1 CATCACATTGACCATTCGGCCTTATCACAGT-CATACACTTCCAC-TTCCATCACATTGGCCATT
29553235 CGGCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACAT
64 CGGCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACAT
29553300 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCAT
129 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCAT
29553365 C
194 C
29553366 GTAACAAAAT
Statistics
Matches: 185, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
238 1 0.01
239 182 0.98
240 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (239 bp):
CATCACATTGACCATTCGGCCTTATCACAGTCATACACTTCCACTTCCATCACATTGGCCATTCG
GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACATAC
ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCA
CATTGGTCATTCGGCCTTATCACATATACATACACTTTCAAATT
Found at i:29556719 original size:113 final size:110
Alignment explanation
Indices: 29556530--29556741 Score: 289
Period size: 113 Copynumber: 1.9 Consensus size: 110
29556520 TGAAAAAATG
* * * *
29556530 TTTCAAAATAGGCATTTTCATCGAATAATAATAAAAGCTTTAGAGGTGTGCAAAAACATGTTTTA
1 TTTCAAAAGAGGCATTTTCATCGAATAAAAATAAAAGCTTTAGAGGTGCGCAAAAACATGTTTCA
* *
29556595 GTAGACACATTTTCATCGAATAGTAATAATGAAATTGAAAACTCA
66 GCAGACACATTTTCATCGAATACTAATAATGAAATTGAAAACTCA
* * * **
29556640 TTTCAGAAGAGGCGTTTTCATCGAATAACAAAAATGAAAGCTTTAGAGGTGCGTGAAAACATGTT
1 TTTCAAAAGAGGCATTTTCATCGAAT---AAAAATAAAAGCTTTAGAGGTGCGCAAAAACATGTT
*
29556705 TCAGCAGACGCATTTTCATCGAATACTAATAATGAAA
63 TCAGCAGACACATTTTCATCGAATACTAATAATGAAA
29556742 AGGTCTTATG
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
110 23 0.26
113 64 0.74
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (110 bp):
TTTCAAAAGAGGCATTTTCATCGAATAAAAATAAAAGCTTTAGAGGTGCGCAAAAACATGTTTCA
GCAGACACATTTTCATCGAATACTAATAATGAAATTGAAAACTCA
Found at i:29563130 original size:43 final size:43
Alignment explanation
Indices: 29563041--29563196 Score: 163
Period size: 43 Copynumber: 3.6 Consensus size: 43
29563031 AATACCATAC
* * * * * * *
29563041 CCTAGATATCGTCTTACATGTTATCAC-ATATCGAGGCCACTAT
1 CCTAGACATGGTCTTACATGTAATCACAATA-CAATGCCAATGT
*
29563084 CCTAGACAGGGTCTTACATGTAATCACAATACAATGCCAAAT-T
1 CCTAGACATGGTCTTACATGTAATCACAATACAATGCC-AATGT
* *
29563127 CCTAGATATGGTCTTACACGTAATCACAATACAATGCCAATGT
1 CCTAGACATGGTCTTACATGTAATCACAATACAATGCCAATGT
* * *
29563170 CCCAAACATGGTCTTACATGCAATCAC
1 CCTAGACATGGTCTTACATGTAATCAC
29563197 TGTAACACCC
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 3 0.03
43 87 0.92
44 5 0.05
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (43 bp):
CCTAGACATGGTCTTACATGTAATCACAATACAATGCCAATGT
Found at i:29590975 original size:29 final size:28
Alignment explanation
Indices: 29590925--29591058 Score: 153
Period size: 29 Copynumber: 4.7 Consensus size: 28
29590915 TGGCCTACTA
* *
29590925 GGCCCAATCTCATTTATATGGCCCATCC
1 GGCCCAATCACATTCATATGGCCCATCC
* *
29590953 GACCCAATTCACATTCATATGGCCCATCA
1 GGCCCAA-TCACATTCATATGGCCCATCC
**
29590982 GGCCCAATTCACATTCATATGGCCCATTA
1 GGCCCAA-TCACATTCATATGGCCCATCC
* *
29591011 GGCCCCAATCTCATTTATATGGCCCATCC
1 GG-CCCAATCACATTCATATGGCCCATCC
29591040 GGCCCAAATCACATT-ATAT
1 GGCCC-AATCACATTCATAT
29591059 TCATGCTCAC
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
28 13 0.14
29 74 0.80
30 5 0.05
ACGTcount: A:0.27, C:0.34, G:0.13, T:0.27
Consensus pattern (28 bp):
GGCCCAATCACATTCATATGGCCCATCC
Found at i:29591033 original size:58 final size:56
Alignment explanation
Indices: 29590906--29591058 Score: 157
Period size: 58 Copynumber: 2.7 Consensus size: 56
29590896 ACCCCTACAT
* * * *
29590906 ACATGCATATGGCCTA-CTAGGCCCAATCTCATTTATATGGCCCATCCGACCCAATTC
1 ACATTCATATGGCCCATC-AGGCCCAATCACA-TTATATGGCCCATACGACCCAATTC
* *
29590963 ACATTCATATGGCCCATCAGGCCCAATTCACATTCATATGGCCCATTAGGCCCCAA-TC
1 ACATTCATATGGCCCATCAGGCCCAA-TCACATT-ATATGGCCCA-TACGACCCAATTC
* * *
29591021 TCATTTATATGGCCCATCCGGCCCAAATCACATTATAT
1 ACATTCATATGGCCCATCAGGCCC-AATCACATTATAT
29591059 TCATGCTCAC
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
57 28 0.34
58 45 0.55
59 9 0.11
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27
Consensus pattern (56 bp):
ACATTCATATGGCCCATCAGGCCCAATCACATTATATGGCCCATACGACCCAATTC
Found at i:29591311 original size:16 final size:16
Alignment explanation
Indices: 29591274--29591312 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
29591264 CCAAACTTTT
29591274 GGCTTTTCGGCATTTC
1 GGCTTTTCGGCATTTC
** *
29591290 AACTTTTTGGCATTTC
1 GGCTTTTCGGCATTTC
29591306 GGCTTTT
1 GGCTTTT
29591313 GCAGATCTAC
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.49
Consensus pattern (16 bp):
GGCTTTTCGGCATTTC
Found at i:29596743 original size:14 final size:15
Alignment explanation
Indices: 29596724--29596756 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
29596714 CAAGAAAATT
*
29596724 ATGATACATGAAAA-
1 ATGATAAATGAAAAC
29596738 ATGATAAATGAAAAC
1 ATGATAAATGAAAAC
29596753 ATGA
1 ATGA
29596757 GATGATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.58, C:0.06, G:0.15, T:0.21
Consensus pattern (15 bp):
ATGATAAATGAAAAC
Found at i:29597978 original size:26 final size:25
Alignment explanation
Indices: 29597949--29598023 Score: 96
Period size: 26 Copynumber: 2.9 Consensus size: 25
29597939 CAACACACCA
*
29597949 ATATCGCAGCAAAGCTGCCAGTAATT
1 ATATCGCAGCAAAGCTGCCAGTAA-C
* *
29597975 ATATCGCAGCAGAGCTGTCAGTAAC
1 ATATCGCAGCAAAGCTGCCAGTAAC
*
29598000 AGTAACGCAGCAAAGCTGCCAGTA
1 A-TATCGCAGCAAAGCTGCCAGTA
29598024 TTAGTATATG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 1 0.02
26 41 0.98
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.19
Consensus pattern (25 bp):
ATATCGCAGCAAAGCTGCCAGTAAC
Found at i:29604579 original size:68 final size:67
Alignment explanation
Indices: 29604502--29604651 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
29604492 CATCATCTAT
* * * *
29604502 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
29604564 ATGTAG
62 ATGTAG
** * *
29604570 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
29604635 AG
66 AG
29604637 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
29604652 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:29604607 original size:64 final size:64
Alignment explanation
Indices: 29604526--29604709 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
29604516 AGACATTATG
* *
29604526 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
29604590 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
29604655 AA
63 AA
* * * *
29604657 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
29604710 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:29609023 original size:68 final size:67
Alignment explanation
Indices: 29608951--29609100 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
29608941 CATCATGTGT
* * * *
29608951 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
29609013 ATGTAG
62 ATGTAG
** * *
29609019 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
29609084 AG
66 AG
29609086 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
29609101 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:29609056 original size:64 final size:64
Alignment explanation
Indices: 29608975--29609158 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
29608965 AGACATTATG
* *
29608975 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
29609039 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
29609104 AA
63 AA
* * * *
29609106 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
29609159 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:29611791 original size:29 final size:30
Alignment explanation
Indices: 29611749--29611814 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
29611739 GCACCTGTGT
29611749 TAGTTTAGCCTGAATCAGGTAAGGAA-TTA
1 TAGTTTAGCCTGAATCAGGTAAGGAATTTA
*
29611778 TAGTTTAGCCTGAATCGGGTAAGGAATTTA
1 TAGTTTAGCCTGAATCAGGTAAGGAATTTA
*
29611808 TAATTTA
1 TAGTTTA
29611815 CAGTGATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 25 0.74
30 9 0.26
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (30 bp):
TAGTTTAGCCTGAATCAGGTAAGGAATTTA
Found at i:29616131 original size:21 final size:21
Alignment explanation
Indices: 29616107--29616156 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
29616097 CGGCCTATAG
*
29616107 CACGGGCATGT-TATAGGACCA
1 CACGGGCATGTCCAT-GGACCA
29616128 CACGGGCATGTCCCATGGACCA
1 CACGGGCATGT-CCATGGACCA
29616150 CACGGGC
1 CACGGGC
29616157 GTGTGAGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.42
22 13 0.50
23 2 0.08
ACGTcount: A:0.24, C:0.32, G:0.30, T:0.14
Consensus pattern (21 bp):
CACGGGCATGTCCATGGACCA
Found at i:29620465 original size:15 final size:15
Alignment explanation
Indices: 29620445--29620474 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29620435 ATTATGAAAG
29620445 ATATGTTTTGGATTA
1 ATATGTTTTGGATTA
*
29620460 ATATGTTTTGTATTA
1 ATATGTTTTGGATTA
29620475 GAATTTTTGA
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:0.27, C:0.00, G:0.17, T:0.57
Consensus pattern (15 bp):
ATATGTTTTGGATTA
Found at i:29621130 original size:43 final size:43
Alignment explanation
Indices: 29621081--29621221 Score: 137
Period size: 43 Copynumber: 3.3 Consensus size: 43
29621071 AGAAAACATT
*
29621081 TGGGACATTGGCATCAATATGTGATTGCGCGTAAGACCATGTC
1 TGGGACATTGGCATCAATATGTGATTGCGTGTAAGACCATGTC
* * * *
29621124 TAGGACATCGACATCACAT-T-TGATT-TGTGTAAGACTC-TGTC
1 TGGGACATTGGCATCA-ATATGTGATTGCGTGTAAGAC-CATGTC
* * * * *
29621165 TGGGACAGTGGCATCGATATGTGATAGCATGTAAGACCACGTC
1 TGGGACATTGGCATCAATATGTGATTGCGTGTAAGACCATGTC
*
29621208 TGGGACGTTGGCAT
1 TGGGACATTGGCAT
29621222 TGTACGATAC
Statistics
Matches: 76, Mismatches: 16, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
40 2 0.03
41 24 0.32
42 11 0.14
43 37 0.49
44 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (43 bp):
TGGGACATTGGCATCAATATGTGATTGCGTGTAAGACCATGTC
Found at i:29625383 original size:37 final size:37
Alignment explanation
Indices: 29625324--29625432 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
29625314 AGCTCAGACG
* *
29625324 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
29625361 AAATCTCCACACGTGGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
29625398 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
29625433 ATATATTTCC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:29625635 original size:50 final size:48
Alignment explanation
Indices: 29625582--29625763 Score: 294
Period size: 48 Copynumber: 3.8 Consensus size: 48
29625572 CATCGCCTAT
* *
29625582 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATAT
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--ATAC
*
29625632 ATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCATAC
1 ATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCATAC
*
29625680 ATATTTCACATTAACCATTCGGCTTTACCACATATACATATCTCATAC
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAC
29625728 ATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATA
29625764 TGCATGTTCA
Statistics
Matches: 124, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
48 83 0.67
49 1 0.01
50 40 0.32
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (48 bp):
ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAC
Found at i:29625768 original size:98 final size:97
Alignment explanation
Indices: 29625582--29625762 Score: 303
Period size: 98 Copynumber: 1.9 Consensus size: 97
29625572 CATCGCCTAT
* *
29625582 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATTGAC
1 ATATTTCACACTAACCATTCGGCTTTACCACATATACATATCTCA-ATACATATTTCACATTGAC
29625647 CATTCGGCTTTACCACATATGCATATCTCATAC
65 CATTCGGCTTTACCACATATGCATATCTCATAC
*
29625680 ATATTTCACATTAACCATTCGGCTTTACCACATATACATATCTC-ATACATATTTCACATT-AGC
1 ATATTTCACACTAACCATTCGGCTTTACCACATATACATATCTCAATACATATTTCACATTGA-C
29625743 CATTCGGCTTTACCACATAT
65 CATTCGGCTTTACCACATAT
29625763 ATGCATGTTC
Statistics
Matches: 79, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
95 1 0.01
96 36 0.46
98 42 0.53
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.36
Consensus pattern (97 bp):
ATATTTCACACTAACCATTCGGCTTTACCACATATACATATCTCAATACATATTTCACATTGACC
ATTCGGCTTTACCACATATGCATATCTCATAC
Found at i:29625812 original size:47 final size:47
Alignment explanation
Indices: 29625733--29625973 Score: 365
Period size: 47 Copynumber: 5.1 Consensus size: 47
29625723 CATACATATT
* * * *
29625733 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * *
29625780 CCACATTGGCCATTCGGCCTTATCGCACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
29625827 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
29625874 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * **
29625921 TCACATTGGTCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
29625968 TCACAT
1 TCACAT
29625974 AAAATCCTAA
Statistics
Matches: 177, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 177 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:29625852 original size:22 final size:22
Alignment explanation
Indices: 29625826--29625901 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
29625816 GCTCACATTC
29625826 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
29625848 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
29625872 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
29625895 ATCACAT
1 ATCACAT
29625902 ATATGCATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 17 0.41
23 7 0.17
24 7 0.17
25 10 0.24
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:29632045 original size:56 final size:56
Alignment explanation
Indices: 29631959--29632078 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
29631949 ACAAGGGATG
29631959 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
29632015 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
29632071 ATGGGCAA
1 ATGGGCAA
29632079 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:29633353 original size:38 final size:39
Alignment explanation
Indices: 29633207--29633429 Score: 263
Period size: 40 Copynumber: 5.6 Consensus size: 39
29633197 TCGAATGATG
* * * *
29633207 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
29633247 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29633287 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
29633326 T-CGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
29633364 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
29633405 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
29633430 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
38 35 0.22
39 35 0.22
40 81 0.50
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29639978 original size:56 final size:56
Alignment explanation
Indices: 29639892--29640065 Score: 325
Period size: 55 Copynumber: 3.1 Consensus size: 56
29639882 ACAAGGGATG
29639892 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
29639948 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGG-AAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
29640003 ATGGGCAAAACATGTCATGAAACAT-TTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
29640058 ATGGGCAA
1 ATGGGCAA
29640066 TAAACTAATA
Statistics
Matches: 116, Mismatches: 1, Indels: 3
0.97 0.01 0.03
Matches are distributed among these distances:
54 12 0.10
55 66 0.57
56 38 0.33
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:29641431 original size:40 final size:40
Alignment explanation
Indices: 29641193--29641417 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
29641183 TCGAATGATG
* * * *
29641193 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
29641233 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29641273 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29641312 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29641352 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
29641393 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29641418 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29641439 original size:119 final size:119
Alignment explanation
Indices: 29641193--29641450 Score: 292
Period size: 119 Copynumber: 2.2 Consensus size: 119
29641183 TCGAATGATG
* *
29641193 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
29641258 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * **
29641312 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
29641375 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
* *
29641432 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
29641451 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
118 3 0.03
119 84 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Found at i:29644626 original size:29 final size:29
Alignment explanation
Indices: 29644560--29644670 Score: 120
Period size: 29 Copynumber: 3.9 Consensus size: 29
29644550 AATTTCACAT
* * *
29644560 ACCTGTATCTGGCCCATTAAGCCC-AATC
1 ACCTATATATGGCCCATTAGGCCCAAATC
29644588 A--TATTCATATGGCCCATTAGGCCCAAATC
1 ACCTA-T-ATATGGCCCATTAGGCCCAAATC
*
29644617 ACCTATATATGGCCCATTAGGACCAAATC
1 ACCTATATATGGCCCATTAGGCCCAAATC
* * *
29644646 ACATTTATATGGCCCGTTAGGCCCA
1 ACCTATATATGGCCCATTAGGCCCA
29644671 GACACATTCA
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 17 0.24
29 48 0.69
30 1 0.01
31 2 0.03
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (29 bp):
ACCTATATATGGCCCATTAGGCCCAAATC
Found at i:29644658 original size:58 final size:57
Alignment explanation
Indices: 29644560--29644670 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 57
29644550 AATTTCACAT
* * * *
29644560 ACCTGTATCTGGCCCATTAAGCCCAATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAAGCCAAATCACATTCATATGGCCCATTAGGCCCAAATC
* * *
29644617 ACCTATATATGGCCCATTAGGACCAAATCACATTTATATGGCCCGTTAGGCCCA
1 ACCTATATATGGCCCATTAAG-CCAAATCACATTCATATGGCCCATTAGGCCCA
29644671 GACACATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 18 0.39
58 28 0.61
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (57 bp):
ACCTATATATGGCCCATTAAGCCAAATCACATTCATATGGCCCATTAGGCCCAAATC
Found at i:29644980 original size:21 final size:21
Alignment explanation
Indices: 29644956--29645021 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
29644946 CCAAACCTAC
29644956 AATCGATATCACTCAAAGATT
1 AATCGATATCACTCAAAGATT
* * **
29644977 AATC-TTA-CA-TACTAACCTAT
1 AATCGATATCACT-CAAAGAT-T
29644997 AATCGATATCACTCAAAGATT
1 AATCGATATCACTCAAAGATT
29645018 AATC
1 AATC
29645022 TTACATACTC
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
18 1 0.03
19 6 0.19
20 7 0.22
21 11 0.34
22 6 0.19
23 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (21 bp):
AATCGATATCACTCAAAGATT
Found at i:29645006 original size:41 final size:41
Alignment explanation
Indices: 29644949--29645030 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
29644939 CTTTACCCCA
29644949 AACCTACAATCGATATCACTCAAAGATTAATCTTACATACT
1 AACCTACAATCGATATCACTCAAAGATTAATCTTACATACT
*
29644990 AACCTATAATCGATATCACTCAAAGATTAATCTTACATACT
1 AACCTACAATCGATATCACTCAAAGATTAATCTTACATACT
29645031 CATCGAATAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.30
Consensus pattern (41 bp):
AACCTACAATCGATATCACTCAAAGATTAATCTTACATACT
Found at i:29645031 original size:21 final size:21
Alignment explanation
Indices: 29644966--29645032 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
29644956 AATCGATATC
29644966 ACTCAAAGATTAATCTTACAT
1 ACTCAAAGATTAATCTTACAT
** * *
29644987 ACT--AACCTATAATC-GATAT
1 ACTCAAAGAT-TAATCTTACAT
29645006 CACTCAAAGATTAATCTTACAT
1 -ACTCAAAGATTAATCTTACAT
29645028 ACTCA
1 ACTCA
29645033 TCGAATACTT
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
19 6 0.18
20 8 0.24
21 13 0.39
22 6 0.18
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.31
Consensus pattern (21 bp):
ACTCAAAGATTAATCTTACAT
Found at i:29657097 original size:21 final size:20
Alignment explanation
Indices: 29657068--29657120 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
29657058 AATAATAAAA
*
29657068 TAAATAAATAATTCATGAAGT
1 TAAAAAAATAATTC-TGAAGT
* *
29657089 TAAAAAAATAATTCTTAATT
1 TAAAAAAATAATTCTGAAGT
29657109 TAAAGAAAATAA
1 TAAA-AAAATAA
29657121 AGTAATTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (20 bp):
TAAAAAAATAATTCTGAAGT
Found at i:29668273 original size:74 final size:74
Alignment explanation
Indices: 29668152--29668303 Score: 268
Period size: 74 Copynumber: 2.1 Consensus size: 74
29668142 AATGCAAGAA
* * *
29668152 GGCAAAGTGATAGCTTATTCCTTGAGACAGTTAAAGCCTCATGAAAAGAACTATCTGCCACACGA
1 GGCAAAGTGATAGCTTATTCCTCGAGACAGTTAAAGCCTCATGAAAAGAACTATCCGACACACGA
29668217 CCTAGAGTT
66 CCTAGAGTT
*
29668226 GGCAAAGTGATAGCTTATTCCTCGAGACAGTTAAAGCCTCATGAAAAGAACTATCCGACACATGA
1 GGCAAAGTGATAGCTTATTCCTCGAGACAGTTAAAGCCTCATGAAAAGAACTATCCGACACACGA
29668291 CCTAGAGTT
66 CCTAGAGTT
29668300 GGCA
1 GGCA
29668304 GCCATTGTGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (74 bp):
GGCAAAGTGATAGCTTATTCCTCGAGACAGTTAAAGCCTCATGAAAAGAACTATCCGACACACGA
CCTAGAGTT
Found at i:29679328 original size:18 final size:18
Alignment explanation
Indices: 29679305--29679343 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
29679295 CACCTTGTTT
29679305 AAAACTTCTAGAAGGGGA
1 AAAACTTCTAGAAGGGGA
29679323 AAAACTTCTAGAAGGGGA
1 AAAACTTCTAGAAGGGGA
29679341 AAA
1 AAA
29679344 GTATTGACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.10, G:0.26, T:0.15
Consensus pattern (18 bp):
AAAACTTCTAGAAGGGGA
Found at i:29679358 original size:19 final size:19
Alignment explanation
Indices: 29679334--29679372 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
29679324 AAACTTCTAG
29679334 AAGGGGAAAAGTATTGACC
1 AAGGGGAAAAGTATTGACC
29679353 AAGGGGAAAAGTATTGACC
1 AAGGGGAAAAGTATTGACC
29679372 A
1 A
29679373 GTAAAACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.31, T:0.15
Consensus pattern (19 bp):
AAGGGGAAAAGTATTGACC
Found at i:29684128 original size:25 final size:25
Alignment explanation
Indices: 29684100--29684153 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
29684090 AGCTCTTCCA
*
29684100 AGCTAAATAGCAGGAAGCTCATGCG
1 AGCTAAATAACAGGAAGCTCATGCG
* * * *
29684125 AGCTGAATAACGGGAAGCTTATGTG
1 AGCTAAATAACAGGAAGCTCATGCG
29684150 AGCT
1 AGCT
29684154 GAGTATCGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (25 bp):
AGCTAAATAACAGGAAGCTCATGCG
Found at i:29684154 original size:25 final size:25
Alignment explanation
Indices: 29684112--29684170 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
29684102 CTAAATAGCA
29684112 GGAAGCTCATGCGAGCTGAATAACG
1 GGAAGCTCATGCGAGCTGAATAACG
* * * *
29684137 GGAAGCTTATGTGAGCTGAGTATCG
1 GGAAGCTCATGCGAGCTGAATAACG
29684162 GGAAGCTCA
1 GGAAGCTCA
29684171 GAAGAGCAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.34, T:0.20
Consensus pattern (25 bp):
GGAAGCTCATGCGAGCTGAATAACG
Found at i:29687189 original size:44 final size:44
Alignment explanation
Indices: 29687141--29687227 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
29687131 TTGCTGGGGA
29687141 ACTGAAATATTAGGAACGCTCAATTTTTATTACTTTAGCCATTG
1 ACTGAAATATTAGGAACGCTCAATTTTTATTACTTTAGCCATTG
29687185 ACTGAAATATTAGGAACGCTCAATTTTTATTACTTTAGCCATT
1 ACTGAAATATTAGGAACGCTCAATTTTTATTACTTTAGCCATT
29687228 TATTTTTCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (44 bp):
ACTGAAATATTAGGAACGCTCAATTTTTATTACTTTAGCCATTG
Found at i:29697376 original size:22 final size:22
Alignment explanation
Indices: 29697349--29697407 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
29697339 TAACTCTTAT
*
29697349 GAGCTTACTCTTCAGCTCGATA
1 GAGCTTACTCTTCAGCTCAATA
29697371 GAGCTTAC-CATTTCAGCTCAATA
1 GAGCTTACTC--TTCAGCTCAATA
*
29697394 GAGCTTACTGTTCA
1 GAGCTTACTCTTCA
29697408 TCAGCTCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 1 0.03
22 12 0.38
23 19 0.59
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (22 bp):
GAGCTTACTCTTCAGCTCAATA
Found at i:29697434 original size:26 final size:25
Alignment explanation
Indices: 29697360--29697434 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 25
29697350 AGCTTACTCT
* * *
29697360 TCAGCTCGATAGAGCTTACC-AT-T
1 TCAGCTCAAGAGAGCTTACCGATCA
* * *
29697383 TCAGCTCAATAGAGCTTACTGTTCA
1 TCAGCTCAAGAGAGCTTACCGATCA
*
29697408 TCAGCTCAAGATGAGTTTACCGATCA
1 TCAGCTCAAGA-GAGCTTACCGATCA
29697434 T
1 T
29697435 GGCTCGAAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 18 0.44
24 1 0.02
25 10 0.24
26 12 0.29
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (25 bp):
TCAGCTCAAGAGAGCTTACCGATCA
Found at i:29699377 original size:29 final size:29
Alignment explanation
Indices: 29699335--29699460 Score: 155
Period size: 29 Copynumber: 4.4 Consensus size: 29
29699325 ACATGCAATG
*
29699335 CAATTCACGTTCATATGGCCCATCAGGCC
1 CAATTCACATTCATATGGCCCATCAGGCC
* ** *
29699364 CAATTCACGTTCATATCACACATCAGGCC
1 CAATTCACATTCATATGGCCCATCAGGCC
*
29699393 CAATTCACATTCATATGGCCCATTAGGCC
1 CAATTCACATTCATATGGCCCATCAGGCC
* * *
29699422 CAA-TCCCATTTATATGGCCCATCCGGCC
1 CAATTCACATTCATATGGCCCATCAGGCC
*
29699450 CAAATCACATT
1 CAATTCACATT
29699461 ATAATCATGC
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 24 0.29
29 59 0.71
ACGTcount: A:0.28, C:0.34, G:0.13, T:0.25
Consensus pattern (29 bp):
CAATTCACATTCATATGGCCCATCAGGCC
Found at i:29699700 original size:16 final size:16
Alignment explanation
Indices: 29699676--29699710 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29699666 GTAGCCAAAC
* *
29699676 TTTTGGCTTTTCGGCA
1 TTTTAGCTTTTCAGCA
29699692 TTTTAGCTTTTCAGCA
1 TTTTAGCTTTTCAGCA
29699708 TTT
1 TTT
29699711 CGGCTTTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.54
Consensus pattern (16 bp):
TTTTAGCTTTTCAGCA
Found at i:29699716 original size:16 final size:16
Alignment explanation
Indices: 29699680--29699718 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
29699670 CCAAACTTTT
* *
29699680 GGCTTTTCGGCATTTT
1 GGCTTTTCAGCATTTC
*
29699696 AGCTTTTCAGCATTTC
1 GGCTTTTCAGCATTTC
29699712 GGCTTTT
1 GGCTTTT
29699719 GCCGATCTAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.49
Consensus pattern (16 bp):
GGCTTTTCAGCATTTC
Found at i:29701267 original size:49 final size:49
Alignment explanation
Indices: 29701206--29701388 Score: 185
Period size: 50 Copynumber: 3.7 Consensus size: 49
29701196 CTGGTACGCA
29701206 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACATG
* * * ** *
29701255 TAGTAGCCTGCACTTAGTACTACACATGTGACCTCACCA-TTTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAACAGTCTGGTACATG
* * * *
29701305 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGT--ATG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG---TCTGGTACATG
29701354 CATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 --TAGTAGCCTGCACTTAGTACTACACATGCGACC
29701389 TCACAATAGA
Statistics
Matches: 109, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 32 0.29
50 38 0.35
51 36 0.33
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACATG
Found at i:29701381 original size:101 final size:98
Alignment explanation
Indices: 29701206--29701392 Score: 261
Period size: 101 Copynumber: 1.9 Consensus size: 98
29701196 CTGGTACGCA
* *
29701206 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACATGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACA-GTAGTAGCCTGCACTTA
*
29701271 GTACTACACATGTGACCTCACCATTTAATACACG
65 GTACTACACATGCGACCTCACCATTTAATACACG
* *
29701305 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTATGCA-TAGTAGCCTGCA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG---TCGGGTA--CAGTAGTAGCCTGCA
29701368 CTTAGTACTACACATGCGACCTCAC
61 CTTAGTACTACACATGCGACCTCAC
29701393 AATAGATCAT
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
98 4 0.05
99 30 0.38
101 42 0.54
103 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACAGTAGTAGCCTGCACTTAG
TACTACACATGCGACCTCACCATTTAATACACG
Found at i:29702028 original size:16 final size:16
Alignment explanation
Indices: 29702007--29702037 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29701997 TAATTAGTCA
29702007 CACTTTTGCATATTTG
1 CACTTTTGCATATTTG
29702023 CACTTTTGCATATTT
1 CACTTTTGCATATTT
29702038 TTAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (16 bp):
CACTTTTGCATATTTG
Found at i:29708460 original size:13 final size:13
Alignment explanation
Indices: 29708442--29708473 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
29708432 TCTTCTCCCT
29708442 CGGCCCGATCATA
1 CGGCCCGATCATA
29708455 CGGCCCGATCATA
1 CGGCCCGATCATA
29708468 CGGCCC
1 CGGCCC
29708474 AGTCCCAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.44, G:0.25, T:0.12
Consensus pattern (13 bp):
CGGCCCGATCATA
Found at i:29710243 original size:57 final size:58
Alignment explanation
Indices: 29710178--29710315 Score: 156
Period size: 57 Copynumber: 2.4 Consensus size: 58
29710168 CCACTACACA
* * ** *
29710178 CAAT-CTCATTAATATGGCCCATTCGGTCCGA-TTCACGTTCATATGGCCCATTAGGCC
1 CAATACTCATTAATATGGCCCATTCAG-CCCATTTCACGTTCATATAACCCATCAGGCC
* *
29710235 CAA-ACTCATTTATATGGCCCATCCAGCCCATTTCACGTTCATATAACCCATCAGGCC
1 CAATACTCATTAATATGGCCCATTCAGCCCATTTCACGTTCATATAACCCATCAGGCC
* * *
29710292 CAATTCACATTCATATGGCCCATT
1 CAATACTCATTAATATGGCCCATT
29710316 AGGCCCAATC
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
56 3 0.04
57 48 0.72
58 16 0.24
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29
Consensus pattern (58 bp):
CAATACTCATTAATATGGCCCATTCAGCCCATTTCACGTTCATATAACCCATCAGGCC
Found at i:29710263 original size:28 final size:28
Alignment explanation
Indices: 29710178--29710351 Score: 140
Period size: 29 Copynumber: 6.1 Consensus size: 28
29710168 CCACTACACA
* *
29710178 CAATCTCATTAATATGGCCCATTC-GGTC
1 CAATCTCATTCATATGGCCCA-TCAGGCC
* *
29710206 CGAT-TCACGTTCATATGGCCCATTAGGCC
1 CAATCTCA--TTCATATGGCCCATCAGGCC
* *
29710235 CAAACTCATTTATATGGCCCATCCA-GCC
1 CAATCTCATTCATATGGCCCAT-CAGGCC
* **
29710263 C-ATTTCACGTTCATATAACCCATCAGGCC
1 CAATCTCA--TTCATATGGCCCATCAGGCC
* *
29710292 CAATTCACATTCATATGGCCCATTAGGCC
1 CAA-TCTCATTCATATGGCCCATCAGGCC
* *
29710321 CAATCTCATTTATATGGCCCATCCGGCC
1 CAATCTCATTCATATGGCCCATCAGGCC
29710349 CAA
1 CAA
29710352 ATTATATTAT
Statistics
Matches: 114, Mismatches: 22, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
27 7 0.06
28 47 0.41
29 53 0.46
30 4 0.04
31 3 0.03
ACGTcount: A:0.26, C:0.33, G:0.14, T:0.28
Consensus pattern (28 bp):
CAATCTCATTCATATGGCCCATCAGGCC
Found at i:29714358 original size:56 final size:56
Alignment explanation
Indices: 29714272--29714399 Score: 204
Period size: 56 Copynumber: 2.3 Consensus size: 56
29714262 CATTTTTTAG
* * *
29714272 TTGGCATCAATATGTGATTTAGATATGTGTGTGTGAGTAAGACCACGTTTAATACA
1 TTGGCATCGATATGTGATTTAGATATGTGTGTGCGAGTAAGACCACATTTAATACA
*
29714328 TTGGCATCGATATGTGATTCT-GATATGTGTGTGCGAGTAAGACCACATTTAATACG
1 TTGGCATCGATATGTGATT-TAGATATGTGTGTGCGAGTAAGACCACATTTAATACA
29714384 TTGGCATCGATATGTG
1 TTGGCATCGATATGTG
29714400 TGTGCGAGTA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
56 66 0.99
57 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.35
Consensus pattern (56 bp):
TTGGCATCGATATGTGATTTAGATATGTGTGTGCGAGTAAGACCACATTTAATACA
Found at i:29714397 original size:43 final size:43
Alignment explanation
Indices: 29714349--29714442 Score: 188
Period size: 43 Copynumber: 2.2 Consensus size: 43
29714339 ATGTGATTCT
29714349 GATATGTGTGTGCGAGTAAGACCACATTTAATACGTTGGCATC
1 GATATGTGTGTGCGAGTAAGACCACATTTAATACGTTGGCATC
29714392 GATATGTGTGTGCGAGTAAGACCACATTTAATACGTTGGCATC
1 GATATGTGTGTGCGAGTAAGACCACATTTAATACGTTGGCATC
29714435 GATATGTG
1 GATATGTG
29714443 ATTTCGATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (43 bp):
GATATGTGTGTGCGAGTAAGACCACATTTAATACGTTGGCATC
Found at i:29714553 original size:155 final size:159
Alignment explanation
Indices: 29714271--29714680 Score: 596
Period size: 168 Copynumber: 2.5 Consensus size: 159
29714261 ACATTTTTTA
* *
29714271 GTTGGCATCAATATGTGATTTAGATATGTGTGTGTGAGTAAGACCACGTTTAATACATTGGCATC
1 GTTGGCATCAATATGTGATTTCGATATGTGTGTGTGAGTAAGACCACGTTTAATACGTTGGCATC
* * *
29714336 GATATGTGATTCTGATATGTGTGTGCGAGTAAGACCACATTTAATACGTTGG-C-A-TC-GATAT
66 GATATGTGATTTTGATATGTGTGTGCAAGTAAGACAACATTTAATACGTTGGACAATTCAGATAT
*
29714397 GTGTGTGCGAGTAAGACCACATTTAATAC
131 GTGTGTGAGAGTAAGACCACATTTAATAC
*
29714426 GTTGGCATCGATATGTGATTTCGATATGTGTGTGTGAGTAAGACCACGTTTAATACGTTGGCATC
1 GTTGGCATCAATATGTGATTTCGATATGTGTGTGTGAGTAAGACCACGTTTAATACGTTGGCATC
*
29714491 GATATGTGATTTTGATATGTGTGTGCAAGTAAGACAACGTTTAATACGTTGGCATCAATATGTGA
66 GATATGTGATTTTGATATGTGTGTGCAAGTAAGACAACATTTAATACGTTGG-A-C---A----A
* *
29714556 TTCAGATATGTGTGTGAGAGTAAGACCACGTTTAATAT
122 TTCAGATATGTGTGTGAGAGTAAGACCACATTTAATAC
*
29714594 GTTGGCATCAATATGTGA-TTCTGATATGTGTGTGCGAGTAAGACCACGTTTAATACGTTGGCAT
1 GTTGGCATCAATATGTGATTTC-GATATGTGTGTGTGAGTAAGACCACGTTTAATACGTTGGCAT
29714658 CGATATGTGATTTTGATATGTGT
65 CGATATGTGATTTTGATATGTGT
29714681 TTACGAGTAA
Statistics
Matches: 229, Mismatches: 12, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
155 110 0.48
158 1 0.00
166 1 0.00
167 5 0.02
168 112 0.49
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.35
Consensus pattern (159 bp):
GTTGGCATCAATATGTGATTTCGATATGTGTGTGTGAGTAAGACCACGTTTAATACGTTGGCATC
GATATGTGATTTTGATATGTGTGTGCAAGTAAGACAACATTTAATACGTTGGACAATTCAGATAT
GTGTGTGAGAGTAAGACCACATTTAATAC
Found at i:29714713 original size:56 final size:56
Alignment explanation
Indices: 29714392--29714694 Score: 480
Period size: 56 Copynumber: 5.4 Consensus size: 56
29714382 CGTTGGCATC
* *
29714392 GATATGTGTGTGCGAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTTC
1 GATATGTGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTTT
*
29714448 GATATGTGTGTGTGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTTT
1 GATATGTGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTTT
* * * **
29714504 GATATGTGTGTGCAAGTAAGACAACGTTTAATACGTTGGCATCAATATGTGATTCA
1 GATATGTGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTTT
* * * *
29714560 GATATGTGTGTGAGAGTAAGACCACGTTTAATATGTTGGCATCAATATGTGATTCT
1 GATATGTGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTTT
29714616 GATATGTGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTTT
1 GATATGTGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTTT
* *
29714672 GATATGTGTTTACGAGTAAGACC
1 GATATGTGTGTGCGAGTAAGACC
29714695 CTGTTTGGGA
Statistics
Matches: 227, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 227 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (56 bp):
GATATGTGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTTT
Found at i:29719903 original size:31 final size:30
Alignment explanation
Indices: 29719846--29719928 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 30
29719836 TCTGTCTCAA
29719846 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACT-GGCCGAAGCCTTTTCATAAAT
* *
29719876 CATATCACTGAGCCAAAGCTTTTTCATAAAT
1 CATATCACTG-GCCGAAGCCTTTTCATAAAT
*
29719907 TATATCACTGGCCGAAGCCTTT
1 CATATCACTGGCCGAAGCCTTT
29719929 ACTATAAGCG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 16 0.35
31 30 0.65
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (30 bp):
CATATCACTGGCCGAAGCCTTTTCATAAAT
Found at i:29720176 original size:25 final size:25
Alignment explanation
Indices: 29720148--29720216 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
29720138 CTCTTTTAAT
29720148 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTTGATA
*
29720173 AACTGGGGCAAAGCCCTTTTTGGTA
1 AACTGGGGCAAAGCCCTTTTTGATA
*
29720198 AACTGGGGCATAGCCCTTT
1 AACTGGGGCAAAGCCCTTT
29720217 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.28
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTTGATA
Found at i:29721174 original size:27 final size:27
Alignment explanation
Indices: 29721144--29721229 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
29721134 GTAAATCTAC
29721144 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
* *
29721171 AAACCAATGATATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* *
29721197 AGAAAGTCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
29721227 AAA
1 AAA
29721230 TTAGGGGTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
26 1 0.02
27 21 0.45
28 7 0.15
29 17 0.36
30 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:29721247 original size:27 final size:27
Alignment explanation
Indices: 29721207--29721330 Score: 135
Period size: 27 Copynumber: 4.6 Consensus size: 27
29721197 AGAAAGTCAA
** *
29721207 GGGTATTTCT-GTAATTTTGTAAATTAG
1 GGGTATTT-TGGTAATTTTACAAACTAG
* *
29721234 GGGTATTATGGTAATTTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACTAG
* * *
29721260 AGGGTATTTAGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAACTAG
*
29721288 TGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
29721315 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
29721331 ATACCCTATA
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
26 3 0.04
27 76 0.95
28 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:29721345 original size:81 final size:81
Alignment explanation
Indices: 29721208--29721360 Score: 186
Period size: 81 Copynumber: 1.9 Consensus size: 81
29721198 GAAAGTCAAG
** * * *
29721208 GGTATTTCTGTAATTTTGTAAATTAGGGGTATTATGGTAATTTTACAAATTGAGGGTATTT-AGG
1 GGTATTTCTGTAATTTTACAAACTAGGGGTATTATGGTAATTATACAAATTAAGGGTATTTCA-G
29721272 TAATTTCACAAACCAGT
65 TAATTTCACAAACCAGT
* **
29721289 GGTATTT-TGGTAATTTTACAAACTAGGGGTATTTTGGTAATTATAC-CCTATAAGGGTATTTCA
1 GGTATTTCT-GTAATTTTACAAACTAGGGGTATTATGGTAATTATACAAAT-TAAGGGTATTTCA
29721352 GTAATTTCA
64 GTAATTTCA
29721361 TAATCGAGGG
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
80 2 0.03
81 58 0.95
82 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.41
Consensus pattern (81 bp):
GGTATTTCTGTAATTTTACAAACTAGGGGTATTATGGTAATTATACAAATTAAGGGTATTTCAGT
AATTTCACAAACCAGT
Found at i:29721379 original size:26 final size:26
Alignment explanation
Indices: 29721350--29721436 Score: 104
Period size: 26 Copynumber: 3.3 Consensus size: 26
29721340 AAGGGTATTT
29721350 CAGTAATTTCATAATCGAGGGTAAAA
1 CAGTAATTTCATAATCGAGGGTAAAA
* *
29721376 CAGTAATTTCACAATCGAAGGTAAAA
1 CAGTAATTTCATAATCGAGGGTAAAA
* *
29721402 CAGTAA-TTCTGTAAATCAAGGGTAAAA
1 CAGTAATTTC-AT-AATCGAGGGTAAAA
*
29721429 TAGTAATT
1 CAGTAATT
29721437 CTATAAATTG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
25 3 0.06
26 30 0.59
27 17 0.33
28 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (26 bp):
CAGTAATTTCATAATCGAGGGTAAAA
Found at i:29721426 original size:27 final size:26
Alignment explanation
Indices: 29721362--29721444 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 26
29721352 GTAATTTCAT
* *
29721362 AATCGAGGGTAAAACAGTAATT-TCA
1 AATCAAGGGTAAAACAGTAATTCTTA
29721387 CAATCGAA-GGTAAAACAGTAATTCTGTA
1 -AATC-AAGGGTAAAACAGTAATTCT-TA
*
29721415 AATCAAGGGTAAAATAGTAATTCTATA
1 AATCAAGGGTAAAACAGTAATTCT-TA
29721442 AAT
1 AAT
29721445 TGAGGGTACT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
26 21 0.43
27 27 0.55
28 1 0.02
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.27
Consensus pattern (26 bp):
AATCAAGGGTAAAACAGTAATTCTTA
Found at i:29723645 original size:23 final size:24
Alignment explanation
Indices: 29723590--29723645 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
29723580 AGCCATAAAA
* *
29723590 CGGGAAGCTCACATAGAGCCATTT
1 CGGGAAGCTCACAAAGAGCCATAT
* *
29723614 TGGGAAGCTCATAAAGAGCC-TAT
1 CGGGAAGCTCACAAAGAGCCATAT
29723637 CGGGAAGCT
1 CGGGAAGCT
29723646 TATCCAGGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.20
Consensus pattern (24 bp):
CGGGAAGCTCACAAAGAGCCATAT
Found at i:29723711 original size:24 final size:24
Alignment explanation
Indices: 29723679--29723740 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
29723669 TTCATAAGAG
* *
29723679 CCATAATCAGGAAGTTCACAAATAA
1 CCAT-ATCAAGAAGTTCACAAAAAA
*
29723704 CCTTATCAAGAAGTTCACAAAAAA
1 CCATATCAAGAAGTTCACAAAAAA
*
29723728 CCATATCGAGAAG
1 CCATATCAAGAAG
29723741 CTCCGGATAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.47, C:0.21, G:0.13, T:0.19
Consensus pattern (24 bp):
CCATATCAAGAAGTTCACAAAAAA
Found at i:29724719 original size:50 final size:50
Alignment explanation
Indices: 29724658--29724759 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 50
29724648 TAGATTTAAC
* *
29724658 TATCCCGATCTCAAAAATATAAAAATTACTAAAAACGGGACAAGAAAACA
1 TATCCCAATCTCAAAAATATAAAAATTACTAAAAACAGGACAAGAAAACA
*
29724708 TATCCCAATCTCAAAAATATAAAAATTACTAAAAACAGGACAAGAAATCA
1 TATCCCAATCTCAAAAATATAAAAATTACTAAAAACAGGACAAGAAAACA
29724758 TA
1 TA
29724760 CCTAATTAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.55, C:0.18, G:0.08, T:0.20
Consensus pattern (50 bp):
TATCCCAATCTCAAAAATATAAAAATTACTAAAAACAGGACAAGAAAACA
Found at i:29726579 original size:25 final size:25
Alignment explanation
Indices: 29726516--29726605 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
29726506 TGTAAATAGT
* * * * *
29726516 AAGCTCTTCCGAGATAACTAATGGA
1 AAGCTCATACGAGCTAAATAATGGG
*
29726541 AAGCTCATGCGAGCTAAATAATGGG
1 AAGCTCATACGAGCTAAATAATGGG
* *
29726566 AAGCTCATACGAGCTGAGT-ATCGGG
1 AAGCTCATACGAGCTAAATAAT-GGG
*
29726591 AAGCTCATAAGAGCT
1 AAGCTCATACGAGCT
29726606 GTGGTGTGTC
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 2 0.04
25 53 0.96
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (25 bp):
AAGCTCATACGAGCTAAATAATGGG
Found at i:29739505 original size:11 final size:11
Alignment explanation
Indices: 29739489--29739514 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29739479 CGTTACTTGT
29739489 GTTATAAAATG
1 GTTATAAAATG
29739500 GTTATAAAATG
1 GTTATAAAATG
29739511 GTTA
1 GTTA
29739515 ACTATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (11 bp):
GTTATAAAATG
Found at i:29741223 original size:26 final size:25
Alignment explanation
Indices: 29741188--29741252 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 25
29741178 CTCATATTCA
* * *
29741188 TCATATTTTCACTTCTTATTTCGAT
1 TCATAATTTCACTTCATATTTCAAT
* *
29741213 ATCTTAATTTCAATTCATATTTCAAT
1 -TCATAATTTCACTTCATATTTCAAT
29741239 TCATAATTTCACTT
1 TCATAATTTCACTT
29741253 TCTCATACTT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 12 0.38
26 20 0.62
ACGTcount: A:0.28, C:0.18, G:0.02, T:0.52
Consensus pattern (25 bp):
TCATAATTTCACTTCATATTTCAAT
Found at i:29741249 original size:13 final size:13
Alignment explanation
Indices: 29741217--29741249 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
29741207 TTCGATATCT
29741217 TAATTTCAATTCA
1 TAATTTCAATTCA
29741230 T-ATTTCAATTCA
1 TAATTTCAATTCA
29741242 TAATTTCA
1 TAATTTCA
29741250 CTTTCTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATTTCAATTCA
Found at i:29742159 original size:34 final size:34
Alignment explanation
Indices: 29742121--29742186 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
29742111 AGTAACAGTC
29742121 CAGTAACAGT-TAGGGCCTTAGCCCAATACAGTGT
1 CAGTAACAGTGT-GGGCCTTAGCCCAATACAGTGT
* * *
29742155 CAGTAGCAGTGTGGGCTTTAGCCCATTACAGT
1 CAGTAACAGTGTGGGCCTTAGCCCAATACAGT
29742187 AATAGTAGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (34 bp):
CAGTAACAGTGTGGGCCTTAGCCCAATACAGTGT
Found at i:29742194 original size:34 final size:34
Alignment explanation
Indices: 29742133--29742197 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
29742123 GTAACAGTTA
*
29742133 GGGCCTTAGCCCAATACAGTGTCAGTAGCAGTGT
1 GGGCCTTAGCCCAATACAGTATCAGTAGCAGTGT
* *
29742167 GGGCTTTAGCCCATTACAGTAAT-AGTAGCAG
1 GGGCCTTAGCCCAATACAGT-ATCAGTAGCAG
29742198 AAATACAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (34 bp):
GGGCCTTAGCCCAATACAGTATCAGTAGCAGTGT
Found at i:29743610 original size:27 final size:27
Alignment explanation
Indices: 29743580--29743783 Score: 250
Period size: 27 Copynumber: 7.6 Consensus size: 27
29743570 ATATTAAGTC
* * *
29743580 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
29743607 CGCACACTTAGTGC-ACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
29743634 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
29743661 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
29743688 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
29743715 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
*
29743742 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
29743769 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29743784 GTACAATTTA
Statistics
Matches: 158, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
26 7 0.04
27 143 0.91
28 8 0.05
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:29751533 original size:27 final size:27
Alignment explanation
Indices: 29751503--29751705 Score: 241
Period size: 27 Copynumber: 7.6 Consensus size: 27
29751493 ATATTAAGTC
* * *
29751503 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
29751530 CGCACACTTAGTGC-ACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
29751557 CGCACACTTAGT-CTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
29751583 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
29751610 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
29751637 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
*
29751664 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
29751691 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29751706 GTACAATTTA
Statistics
Matches: 156, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
26 24 0.15
27 131 0.84
28 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:29767226 original size:41 final size:37
Alignment explanation
Indices: 29767126--29767227 Score: 87
Period size: 41 Copynumber: 2.6 Consensus size: 37
29767116 AGTTCAAAGC
* * *
29767126 AAAGTTGACAGCCAGTGTCTCTTCGACCTAGCCGAAGT
1 AAAG-TGACACCCAGTGTCTCATCAACCTAGCCGAAGT
* * ** *
29767164 AAAGTGATACCCAATACCTCATCAAACCTATCCGAAGT
1 AAAGTGACACCCAGTGTCTCATC-AACCTAGCCGAAGT
29767202 AAAATAGTGACACCCAGTGTCTCATC
1 --AA-AGTGACACCCAGTGTCTCATC
29767228 GACTTAAGGT
Statistics
Matches: 48, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
37 13 0.27
38 16 0.33
40 2 0.04
41 17 0.35
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (37 bp):
AAAGTGACACCCAGTGTCTCATCAACCTAGCCGAAGT
Found at i:29768765 original size:18 final size:18
Alignment explanation
Indices: 29768739--29768773 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29768729 ATTGTAATTA
*
29768739 TTTAATTAATAATTATAT
1 TTTAATTAATAAATATAT
*
29768757 TTTACTTAATAAATATA
1 TTTAATTAATAAATATA
29768774 AATACTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAATTAATAAATATAT
Found at i:29775440 original size:16 final size:15
Alignment explanation
Indices: 29775419--29775448 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29775409 CAAAATATAC
29775419 TATATTAAAATAAATT
1 TATATTAAAA-AAATT
29775435 TATATTAAAAAAAT
1 TATATTAAAAAAAT
29775449 CCCATAGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TATATTAAAAAAATT
Found at i:29775549 original size:23 final size:25
Alignment explanation
Indices: 29775506--29775555 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
29775496 CACATGGTGC
*
29775506 ATTTTGAACAAAAAATTTACAGGGT
1 ATTTTGAACAAAAAATATACAGGGT
*
29775531 ATTTTGAA-AAAAAA-ATACATGGT
1 ATTTTGAACAAAAAATATACAGGGT
29775554 AT
1 AT
29775556 ATTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 9 0.39
24 6 0.26
25 8 0.35
ACGTcount: A:0.48, C:0.06, G:0.14, T:0.32
Consensus pattern (25 bp):
ATTTTGAACAAAAAATATACAGGGT
Found at i:29777671 original size:21 final size:21
Alignment explanation
Indices: 29777646--29777688 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
29777636 ACATTCATGA
29777646 AGTAAATTAATAAAGTTGTCT
1 AGTAAATTAATAAAGTTGTCT
29777667 AGTAAATTAATAAAGTTGTCT
1 AGTAAATTAATAAAGTTGTCT
29777688 A
1 A
29777689 TGCGCTGAAC
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:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (21 bp):
AGTAAATTAATAAAGTTGTCT
Found at i:29777752 original size:15 final size:15
Alignment explanation
Indices: 29777732--29777762 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29777722 CTGACTTGGA
29777732 CAAGATTTTTAATAT
1 CAAGATTTTTAATAT
29777747 CAAGATTTTTAATAT
1 CAAGATTTTTAATAT
29777762 C
1 C
29777763 CTAAGTCAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (15 bp):
CAAGATTTTTAATAT
Found at i:29778034 original size:19 final size:17
Alignment explanation
Indices: 29777982--29778042 Score: 50
Period size: 19 Copynumber: 3.3 Consensus size: 17
29777972 AATTCTTCGA
29777982 ATTTTTATATTTTTCAAAT
1 ATTTTTAT-TTTTT-AAAT
**
29778001 ATTTTTAATCATTTAAAGTT
1 ATTTTT-ATTTTTTAAA--T
*
29778021 ATTTTTATTTTTTAAAA
1 ATTTTTATTTTTTAAAT
29778038 ATTTT
1 ATTTT
29778043 AAAGAGTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
17 5 0.15
18 3 0.09
19 17 0.50
20 9 0.26
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTTTTATTTTTTAAAT
Found at i:29784484 original size:46 final size:48
Alignment explanation
Indices: 29784337--29784642 Score: 187
Period size: 47 Copynumber: 6.5 Consensus size: 48
29784327 TTTGTGTGCT
* * * * * *
29784337 AGTGTAAGA-CATGTTTGGGGCATGCATCGGCC-ACA-TTATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGCATC-GCCTAGAGATGTGAGAGCC
* * * * * *
29784383 AGCGTAAGACCATGTCTAGGACATGGCATCGACATTA-AGA--CGATAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCG-C-CTAGAGATGTGAGAGCC
* *
29784431 AGTGTAAGA-CATGTCTAGGACATGCATCAGCCTCGAGATGT-A-AGCC
1 AGTGTAAGACCATGTCTGGGACATGCATC-GCCTAGAGATGTGAGAGCC
* * *
29784477 AGTGTAAGA-CATGTCTGGGACATGCATCGGCTATATGATGT----GTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGCCTAGA-GATGTGAGAGCC
* * *
29784521 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-AGATATATGAGAGTC
1 AGTGTAAGACCATGTCTGGGACAT-GCATC-GC-CTAGAGATGTGAGAGCC
* * *
29784571 AGTGTAAGACCATGTCTGGGACATGGCATCGACT-TA-ACGTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGCCTAGAGATGTGAGAGCC
*
29784618 AGTGTAAGACCATGTCTAGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
29784643 GCATTGGCAT
Statistics
Matches: 212, Mismatches: 28, Indels: 40
0.76 0.10 0.14
Matches are distributed among these distances:
44 11 0.05
45 19 0.09
46 61 0.29
47 62 0.29
48 23 0.11
49 2 0.01
50 34 0.16
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGCCTAGAGATGTGAGAGCC
Found at i:29784632 original size:47 final size:46
Alignment explanation
Indices: 29784375--29784646 Score: 227
Period size: 47 Copynumber: 5.8 Consensus size: 46
29784365 GGCCACATTA
* *
29784375 TGAGAGCTAGCGTAAGACCATGTCTAGGACATGGCATCGACATTAAG
1 TGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGAC-TTAAG
* * * * **
29784422 ACGATAGCTAGTGTAAGA-CATGTCTAGGACAT-GCATCAGCCTCGAG
1 -TGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATC-GACTTAAG
* *
29784468 ATGTA-AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TATA-
1 -TG-AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACTTA-AG
* * * *
29784512 TGATGTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATA-
1 TGA-GAGCCAGTGTAAGACCATGTCTAGGACATGGCATC-G-AC--TTA-AG
* *
29784563 TGAGAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTAACG
1 TGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACTTAA-G
29784610 TGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCAT
1 TGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCAT
29784647 TGGCATTATA
Statistics
Matches: 191, Mismatches: 19, Indels: 29
0.80 0.08 0.12
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 11 0.06
45 18 0.09
46 47 0.25
47 53 0.28
48 17 0.09
49 1 0.01
50 34 0.18
51 7 0.04
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (46 bp):
TGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACTTAAG
Found at i:29785780 original size:30 final size:30
Alignment explanation
Indices: 29785746--29785808 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
29785736 TAATAACAAG
*
29785746 CAAATGCATCTAAAATAATAACAAAATTAA
1 CAAATACATCTAAAATAATAACAAAATTAA
* *
29785776 CAAATACCTTTAAAATAATAACAAAATTAA
1 CAAATACATCTAAAATAATAACAAAATTAA
29785806 CAA
1 CAA
29785809 TAAAATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (30 bp):
CAAATACATCTAAAATAATAACAAAATTAA
Done.