Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 84 of 172
Found at i:28035173 original size:31 final size:30
Alignment explanation
Indices: 28035133--28035191 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
28035123 AAAAAATCAA
28035133 GTGAGTTAAATAAAAACTTCCAAATAGTTAT
1 GTGAGTTAAAT-AAAACTTCCAAATAGTTAT
* * *
28035164 GTGATTTAAATGAAACTTTCAAATAGTT
1 GTGAGTTAAATAAAACTTCCAAATAGTT
28035192 CAATGACCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (30 bp):
GTGAGTTAAATAAAACTTCCAAATAGTTAT
Found at i:28038049 original size:68 final size:69
Alignment explanation
Indices: 28037964--28038101 Score: 242
Period size: 68 Copynumber: 2.0 Consensus size: 69
28037954 GTTGAAGAAG
28037964 AAAGAAAAAAAGATGATATCTTTCTTTCACTTATTTTATTTTATGATATTTGATTAATTTACCAA
1 AAAGAAAAAAAGATGATATCTTTCTTTCACTTATTTTATTTTATGATATTTGATTAATTTACCAA
28038029 ATTA
66 ATTA
* * *
28038033 AAAG-AAAAAAGATGATATCTTTTTTTCACTTGTTTTATTTTATGATATTTTATTAATTTACCAA
1 AAAGAAAAAAAGATGATATCTTTCTTTCACTTATTTTATTTTATGATATTTGATTAATTTACCAA
28038097 ATTA
66 ATTA
28038101 A
1 A
28038102 CCTTAAGTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 62 0.94
69 4 0.06
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.46
Consensus pattern (69 bp):
AAAGAAAAAAAGATGATATCTTTCTTTCACTTATTTTATTTTATGATATTTGATTAATTTACCAA
ATTA
Found at i:28041377 original size:68 final size:69
Alignment explanation
Indices: 28041303--28041478 Score: 177
Period size: 68 Copynumber: 2.6 Consensus size: 69
28041293 CATCATGTGT
* ** * *
28041303 ACAAGAGAGCTACGAGATACTATGTAGTAGCTAGGTCACATGTGTGA-TAC-AG-GATGTATC-C
1 ACAAGAGAGCTACGAGAGA-TAAAT-GTAGCTAGGTCACATGTGTGATTACAAGTGAAGGA-CAC
28041364 CATGTAG
63 CATGTAG
* * *
28041371 ATAAGAGAGCTACGGGAGAGATAAATGTAGCTAGGTCGCATGTGTGATTCCAAGTGAAGGACACC
1 ACAAGAGAGCTAC--GAGAGATAAATGTAGCTAGGTCACATGTGTGATTACAAGTGAAGGACACC
28041436 ATGTAG
64 ATGTAG
*
28041442 ACAAGAGAGCTACGAGA-A-AAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGAGAGATAAATGTAGCTAGGTCACATG
28041479 GGTGGTACTA
Statistics
Matches: 91, Mismatches: 11, Indels: 14
0.78 0.09 0.12
Matches are distributed among these distances:
66 13 0.14
67 4 0.04
68 33 0.36
69 9 0.10
70 8 0.09
71 24 0.26
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (69 bp):
ACAAGAGAGCTACGAGAGATAAATGTAGCTAGGTCACATGTGTGATTACAAGTGAAGGACACCAT
GTAG
Found at i:28050564 original size:24 final size:24
Alignment explanation
Indices: 28050530--28050602 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
28050520 AGCCTGTCTA
*
28050530 GAGAAGATTTAGGAGCTGATAAGG
1 GAGAGGATTTAGGAGCTGATAAGG
* *
28050554 GAGAGGGTTTAGGAGCTGATCAGG
1 GAGAGGATTTAGGAGCTGATAAGG
*
28050578 GAGAGGATTTAGGAGCTGATTAGG
1 GAGAGGATTTAGGAGCTGATAAGG
28050602 G
1 G
28050603 TGAACTGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.30, C:0.05, G:0.42, T:0.22
Consensus pattern (24 bp):
GAGAGGATTTAGGAGCTGATAAGG
Found at i:28052081 original size:27 final size:27
Alignment explanation
Indices: 28052041--28052139 Score: 94
Period size: 27 Copynumber: 3.6 Consensus size: 27
28052031 AGGAAGCGTC
*
28052041 TTGGTGGCTATGCCACAATTATCTGAT
1 TTGGTGGCTCTGCCACAATTATCTGAT
28052068 TTGGTGGCTCTGCCAC-ATATATCTG-T
1 TTGGTGGCTCTGCCACAAT-TATCTGAT
* * *
28052094 TCCGGTGGTTCTGCCACGATTATCTGTAT
1 T-TGGTGGCTCTGCCACAATTATCTG-AT
* * *
28052123 CTGGTGACTCTGTCACA
1 TTGGTGGCTCTGCCACA
28052140 TGGGGTGTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
26 4 0.07
27 40 0.69
28 13 0.22
29 1 0.02
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
TTGGTGGCTCTGCCACAATTATCTGAT
Found at i:28054357 original size:72 final size:71
Alignment explanation
Indices: 28054233--28054478 Score: 289
Period size: 72 Copynumber: 3.4 Consensus size: 71
28054223 CCGGTTACTA
* * * ** * * **
28054233 ACTTTGTGTATAAACCCGTGAATAACTCGCTGAGCGAGCA-TATCATGTTAATGCTTTCTGGTCC
1 ACTTTGTGTATAAATCCGTGAGTAGCTCAATGAGCGGGCATTA-CATGATAATGCTTTGGGGTCC
28054297 GGGTATTG
65 GGGT-TTG
* *
28054305 ACTTTGTGTATAAA-CACGTGAGTAGCTCAATGAGTGGGCATTACATGATAATGTTTTGGGGTCC
1 ACTTTGTGTATAAATC-CGTGAGTAGCTCAATGAGCGGGCATTACATGATAATGCTTTGGGGTCC
* *
28054369 GAGTGCTG
65 GGGT-TTG
* *
28054377 ACTTTGTGTATAAATCCGTGAGTAGCTCAATGAGCAGGAATTACATGATAATGCTTTGGGGTCCG
1 ACTTTGTGTATAAATCCGTGAGTAGCTCAATGAGCGGGCATTACATGATAATGCTTTGGGGTCCG
28054442 GGTTCTG
66 GGTT-TG
*
28054449 ACTTTGTGTACAAATCCGTGAGTAGCTCAA
1 ACTTTGTGTATAAATCCGTGAGTAGCTCAA
28054479 ATGCGCGCAT
Statistics
Matches: 150, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
71 1 0.01
72 146 0.97
73 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (71 bp):
ACTTTGTGTATAAATCCGTGAGTAGCTCAATGAGCGGGCATTACATGATAATGCTTTGGGGTCCG
GGTTTG
Found at i:28056595 original size:48 final size:47
Alignment explanation
Indices: 28056526--28056736 Score: 205
Period size: 48 Copynumber: 4.5 Consensus size: 47
28056516 AAGCTGACGC
* *
28056526 CATGTCCCAGACAAGTCTTACACTAGCTTGTATATCGCGAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTT-TATATCTCGAGGCTGATG
* * ** * * *
28056574 CATGTCCCAGACATGTATTACACTAGCTCT-CGTCTCAATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTTATATCTCGAGGCTGATG
* * * *
28056620 CATGTCCTAGACATGTCGTACACTGGCTTAAATATCTCGAAGGC-GATG
1 CATGTCCCAGACATGTCTTACACTAGCTT-TATATCTCG-AGGCTGATG
* * *
28056668 CATGTCCCAGACATGTCTTACACTGGCTCTTTTA-CT-GTGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCT-TTATATCTCGAGGCTGATG
*
28056714 CATGTCCCAGACTTGTCTTACAC
1 CATGTCCCAGACATGTCTTACAC
28056737 AAATGAACCA
Statistics
Matches: 133, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
45 3 0.02
46 61 0.46
47 3 0.02
48 62 0.47
49 4 0.03
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCTTTATATCTCGAGGCTGATG
Found at i:28056642 original size:94 final size:94
Alignment explanation
Indices: 28056526--28056697 Score: 247
Period size: 94 Copynumber: 1.8 Consensus size: 94
28056516 AAGCTGACGC
* **
28056526 CATGTCCCAGACAAGTCTTACACTAGCTTGTATATCGCG-AGGCTGATGCATGTCCCAGACATGT
1 CATGTCCCAGACAAGTCGTACACTAGCTTAAATATCGCGAAGGC-GATGCATGTCCCAGACATGT
28056590 ATTACACTAGCTCTCGTCTCAATGCCGATG
65 ATTACACTAGCTCTCGTCTCAATGCCGATG
* * * * *
28056620 CATGTCCTAGACATGTCGTACACTGGCTTAAATATCTCGAAGGCGATGCATGTCCCAGACATGTC
1 CATGTCCCAGACAAGTCGTACACTAGCTTAAATATCGCGAAGGCGATGCATGTCCCAGACATGTA
*
28056685 TTACACTGGCTCT
66 TTACACTAGCTCT
28056698 TTTACTGTGG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
94 64 0.94
95 4 0.06
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (94 bp):
CATGTCCCAGACAAGTCGTACACTAGCTTAAATATCGCGAAGGCGATGCATGTCCCAGACATGTA
TTACACTAGCTCTCGTCTCAATGCCGATG
Found at i:28056714 original size:94 final size:93
Alignment explanation
Indices: 28056526--28056736 Score: 246
Period size: 94 Copynumber: 2.2 Consensus size: 93
28056516 AAGCTGACGC
* **
28056526 CATGTCCCAGACAAGTCTTACACTAGCTTGTATATCGCGAGGCTGATGCATGTCCCAGACATGTA
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCGCGAGGCTGATGCATGTCCCAGACATGTA
28056591 TTACACTAGCTCTCGTCTCAATGCCGATG
66 TTACACTAGCTCTC-TCTCAATGCCGATG
* * * *
28056620 CATGTCCTAGACATGTCGTACACTGGCTTAAATATCTCGAAGGC-GATGCATGTCCCAGACATGT
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCGCG-AGGCTGATGCATGTCCCAGACATGT
* * * ** *
28056684 CTTACACTGGCTCT-TTTACTGTGGCTGATG
65 ATTACACTAGCTCTCTCT-CAAT-GCCGATG
*
28056714 CATGTCCCAGACTTGTCTTACAC
1 CATGTCCCAGACATGTCTTACAC
28056737 AAATGAACCA
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
92 2 0.02
93 2 0.02
94 90 0.92
95 4 0.04
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (93 bp):
CATGTCCCAGACATGTCTTACACTAGCTTAAATATCGCGAGGCTGATGCATGTCCCAGACATGTA
TTACACTAGCTCTCTCTCAATGCCGATG
Found at i:28058701 original size:13 final size:13
Alignment explanation
Indices: 28058670--28058715 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
28058660 ATACTTAAGT
28058670 ATATAATAATAT-
1 ATATAATAATATA
28058682 A-ATAAT-ATATTA
1 ATATAATAATA-TA
28058694 ATATAATAATATA
1 ATATAATAATATA
28058707 ATATAATAA
1 ATATAATAA
28058716 AACATAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.10
11 6 0.20
12 2 0.07
13 16 0.53
14 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATAATAATATA
Found at i:28058715 original size:8 final size:8
Alignment explanation
Indices: 28058670--28058709 Score: 71
Period size: 8 Copynumber: 5.0 Consensus size: 8
28058660 ATACTTAAGT
28058670 ATATAATA
1 ATATAATA
28058678 ATATAATA
1 ATATAATA
*
28058686 ATATATTA
1 ATATAATA
28058694 ATATAATA
1 ATATAATA
28058702 ATATAATA
1 ATATAATA
28058710 TAATAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAATA
Found at i:28058715 original size:16 final size:15
Alignment explanation
Indices: 28058670--28058715 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
28058660 ATACTTAAGT
28058670 ATATAATAATATAATA
1 ATAT-ATAATATAATA
28058686 ATATATTAATATAAT-
1 ATATA-TAATATAATA
28058701 A-ATATAATATAATA
1 ATATATAATATAATA
28058715 A
1 A
28058716 AACATAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.32
14 4 0.14
15 2 0.07
16 13 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATATAATATAATA
Found at i:28059530 original size:27 final size:28
Alignment explanation
Indices: 28059481--28059538 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
28059471 TATATGTGTA
*
28059481 TGATTGAAAAGTGTATTGAATTGG-AAT
1 TGATTGAAAAGTATATTGAATTGGAAAT
*
28059508 TGATTGAAATTGTATATTG-ATTGGAAAT
1 TGATTGAAA-AGTATATTGAATTGGAAAT
28059536 TGA
1 TGA
28059539 ATTATGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (28 bp):
TGATTGAAAAGTATATTGAATTGGAAAT
Found at i:28059552 original size:18 final size:17
Alignment explanation
Indices: 28059506--28059553 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
28059496 TTGAATTGGA
*
28059506 ATTGATTGAAATTGTAT
1 ATTGATTGAAATTGAAT
28059523 ATTGATTGGAAATTGAAT
1 ATTGATT-GAAATTGAAT
28059541 -TATGAATTGAAAT
1 AT-TG-ATTGAAAT
28059554 ACCCTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 8 0.30
18 16 0.59
19 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.42
Consensus pattern (17 bp):
ATTGATTGAAATTGAAT
Found at i:28068832 original size:27 final size:28
Alignment explanation
Indices: 28068800--28068857 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
28068790 CATATCTGTA
28068800 TGATTGAAAATT-T-TATTGAATTGG-AAT
1 TGATTG-AAATTGTATATTG-ATTGGAAAT
28068827 TGATTGAAATTGTATATTGATTGGAAAT
1 TGATTGAAATTGTATATTGATTGGAAAT
28068855 TGA
1 TGA
28068858 ATTATGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 5 0.18
27 12 0.43
28 11 0.39
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (28 bp):
TGATTGAAATTGTATATTGATTGGAAAT
Found at i:28068871 original size:18 final size:17
Alignment explanation
Indices: 28068825--28068872 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
28068815 TTGAATTGGA
*
28068825 ATTGATTGAAATTGTAT
1 ATTGATTGAAATTGAAT
28068842 ATTGATTGGAAATTGAAT
1 ATTGATT-GAAATTGAAT
28068860 -TATGAATTGAAAT
1 AT-TG-ATTGAAAT
28068873 ACCCTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 8 0.30
18 16 0.59
19 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.42
Consensus pattern (17 bp):
ATTGATTGAAATTGAAT
Found at i:28069178 original size:40 final size:40
Alignment explanation
Indices: 28069123--28069206 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
28069113 AAAATCGAAT
* *
28069123 AGATCGAGTACTAGCGGCGTTTCT-AGAAAAGCACCGCTAA
1 AGATCGAGAACTAGCGGCATTTCTAAG-AAAGCACCGCTAA
* * * *
28069163 AGATCGAGAATTAGCGGCATTTTTAAGGAAGCGCCGCTAA
1 AGATCGAGAACTAGCGGCATTTCTAAGAAAGCACCGCTAA
28069203 AGAT
1 AGAT
28069207 TGACCTATAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
40 35 0.95
41 2 0.05
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.21
Consensus pattern (40 bp):
AGATCGAGAACTAGCGGCATTTCTAAGAAAGCACCGCTAA
Found at i:28069798 original size:7 final size:7
Alignment explanation
Indices: 28069783--28069830 Score: 69
Period size: 7 Copynumber: 6.9 Consensus size: 7
28069773 TTTTGATCAT
28069783 CCCTAAA
1 CCCTAAA
*
28069790 CCTTAAA
1 CCCTAAA
*
28069797 CCTTAAA
1 CCCTAAA
28069804 CCCTAAA
1 CCCTAAA
*
28069811 TCCTAAA
1 CCCTAAA
28069818 CCCTAAA
1 CCCTAAA
28069825 CCCTAA
1 CCCTAA
28069831 CCCATTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCTAAA
Found at i:28069809 original size:21 final size:21
Alignment explanation
Indices: 28069783--28069839 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
28069773 TTTTGATCAT
*
28069783 CCCTAAACCTTAAACCTTAAA
1 CCCTAAACCTTAAACCCTAAA
28069804 CCCTAAATCC-TAAACCCTAAA
1 CCCTAAA-CCTTAAACCCTAAA
*
28069825 CCCTAACCCATTAAA
1 CCCTAAACC-TTAAA
28069840 TCAGTAACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 2 0.06
21 23 0.74
22 6 0.19
ACGTcount: A:0.42, C:0.37, G:0.00, T:0.21
Consensus pattern (21 bp):
CCCTAAACCTTAAACCCTAAA
Found at i:28069904 original size:21 final size:21
Alignment explanation
Indices: 28069880--28069922 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
28069870 TCTATAGTCG
*
28069880 TAAATCATAAACTA-TAAACCT
1 TAAACCATAAA-TATTAAACCT
*
28069901 TAAACCCTAAATATTAAACCT
1 TAAACCATAAATATTAAACCT
28069922 T
1 T
28069923 GGATCCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAACCATAAATATTAAACCT
Found at i:28070078 original size:21 final size:21
Alignment explanation
Indices: 28070044--28070100 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
28070034 TTATAAAACG
*
28070044 TCTTAAAACTATAAACCCTAAA
1 TCTT-AAACCATAAACCCTAAA
28070066 TCTTAAACCATAAACCCTAAA
1 TCTTAAACCATAAACCCTAAA
**
28070087 TCCAAAACCATAAA
1 TCTTAAACCATAAA
28070101 ACCTTAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (21 bp):
TCTTAAACCATAAACCCTAAA
Found at i:28070441 original size:3 final size:3
Alignment explanation
Indices: 28070433--28070482 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
28070423 TTAAATAGTA
28070433 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28070481 AA
1 AA
28070483 AAGAGAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28070950 original size:189 final size:187
Alignment explanation
Indices: 28070582--28070950 Score: 415
Period size: 189 Copynumber: 2.0 Consensus size: 187
28070572 TTGAAGCTTT
*
28070582 GTTATTAGTGGCGCTTCTAAAAACACCACAAAACATCTATTAAGAGAATGTAAAACGGCATCGTT
1 GTTATTAGTGGCGCTTCTAAAAACACCACAAAACATCTA-TAAGAGAATGTAAAACGGCAACGTT
* * ** *
28070647 TGCATCCTTATTATTAGTGGCGCTTCTATAAATGCCGCAAAAGATGTGATTTACCGGCATTTTTG
65 TGCATCCTTATTATTAGTGGCGCTTCTATAAACGCCACAAAAGATGTGAAATACCGGCATTTTCG
* * ** *
28070712 CTAAAAAACGCCACAAACATCCATTTGTATAATGCAAAACGGCGTCGTTTGTTACCAA
130 CTAAAAAACACCACAAAAATCCATTAATAGAATGCAAAACGGCGTCGTTTGTTACCAA
* * * *
28070770 GTTATTAGTGGCGCTTCTTGGAAAAACGCCACAAAACATGTA-AAGAG-ATTTCAAAACGTCAAC
1 GTTATTAGTGGCGCTTC-T--AAAAACACCACAAAACATCTATAAGAGAATGT-AAAACGGCAAC
* * * *
28070833 GTTT-TATAGCCTT-TTATTAGTGGCGCTTTTATAAACGCCACAAAAGATGTGAAATGCCGGCGT
62 GTTTGCAT--CCTTATTATTAGTGGCGCTTCTATAAACGCCACAAAAGATGTGAAATACCGGCAT
* * * * *
28070896 TTTCGCT-AGAAACACCACAAAAATCTATTAATAGAGTGCAGAAACTGTGTCGTTT
125 TTTCGCTAAAAAACACCACAAAAATCCATTAATAGAATGCA-AAACGGCGTCGTTT
28070951 TATAGCCTTT
Statistics
Matches: 150, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
188 47 0.31
189 80 0.53
190 4 0.03
191 19 0.13
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (187 bp):
GTTATTAGTGGCGCTTCTAAAAACACCACAAAACATCTATAAGAGAATGTAAAACGGCAACGTTT
GCATCCTTATTATTAGTGGCGCTTCTATAAACGCCACAAAAGATGTGAAATACCGGCATTTTCGC
TAAAAAACACCACAAAAATCCATTAATAGAATGCAAAACGGCGTCGTTTGTTACCAA
Found at i:28075248 original size:23 final size:23
Alignment explanation
Indices: 28075218--28075267 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
28075208 AACATTAATC
*
28075218 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATAAATTGCAGCCCTTT
28075241 AAATGTATAAATTGCAGCCCTTT
1 AAATGTATAAATTGCAGCCCTTT
28075264 AAAT
1 AAAT
28075268 AAACTTGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (23 bp):
AAATGTATAAATTGCAGCCCTTT
Found at i:28075823 original size:241 final size:239
Alignment explanation
Indices: 28075400--28075884 Score: 925
Period size: 241 Copynumber: 2.0 Consensus size: 239
28075390 ATGAATTAAT
28075400 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
28075465 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
*
28075530 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAATGCCACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
28075595 ATAAAGACTTGGAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 --AAAGACTTGGAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
28075641 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
28075706 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
* *
28075771 CTGTAAGATATAATGGATCCTCTCTATGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
28075836 AAAGACTTGGAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 AAAGACTTGGAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
28075880 TTTAT
1 TTTAT
28075885 ATAACATTAA
Statistics
Matches: 241, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
239 49 0.20
241 192 0.80
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (239 bp):
TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
AAAGACTTGGAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
Found at i:28076087 original size:9 final size:9
Alignment explanation
Indices: 28076064--28076191 Score: 121
Period size: 9 Copynumber: 13.6 Consensus size: 9
28076054 ATTGATTATT
*
28076064 ACTTAAATA
1 ACTTACATA
*
28076073 AATTACATA
1 ACTTACATA
28076082 ACTTACATA
1 ACTTACATA
* *
28076091 ACTCATATA
1 ACTTACATA
28076100 ACTTACATA
1 ACTTACATA
*
28076109 ATTTACATAACA
1 ACTTACAT---A
28076121 ACTTACATA
1 ACTTACATA
*
28076130 ACTCACATA
1 ACTTACATA
28076139 ACTTACATA
1 ACTTACATA
*
28076148 ATTTACATA
1 ACTTACATA
*
28076157 ACTCACATA
1 ACTTACATA
*
28076166 ACGTACATAACA
1 ACTTACAT---A
28076178 ACTTACATA
1 ACTTACATA
28076187 ACTTA
1 ACTTA
28076192 ACTAATACAT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 80 0.83
12 16 0.17
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:28076133 original size:39 final size:39
Alignment explanation
Indices: 28076081--28076158 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
28076071 TAAATTACAT
*
28076081 AACTTACATAACTCATATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
28076120 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
28076159 TCACATAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:28076158 original size:57 final size:57
Alignment explanation
Indices: 28076077--28076189 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 57
28076067 TAAATAAATT
* * **
28076077 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
* *
28076134 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACT
28076190 TAACTAATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
Found at i:28076277 original size:18 final size:17
Alignment explanation
Indices: 28076249--28076285 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
28076239 TTAAAGTTCA
28076249 AATCTCATAACTTACAT
1 AATCTCATAACTTACAT
28076266 AATCTACATAACTTACAT
1 AATCT-CATAACTTACAT
28076284 AA
1 AA
28076286 AACATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (17 bp):
AATCTCATAACTTACAT
Found at i:28081758 original size:21 final size:21
Alignment explanation
Indices: 28081732--28081775 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
28081722 ACTTAGAGCG
*
28081732 GAGGCAGCAGTGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCA
28081753 GAGGCAGCAGCGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCA
28081774 GA
1 GA
28081776 CCAGAACAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.16, G:0.52, T:0.02
Consensus pattern (21 bp):
GAGGCAGCAGCGAGGGAGGCA
Found at i:28082135 original size:43 final size:43
Alignment explanation
Indices: 28082069--28082203 Score: 162
Period size: 43 Copynumber: 3.1 Consensus size: 43
28082059 ACTGGGCAAA
*** * * *
28082069 TTAGCGGCGTTTTTTAAAAAAGCGCCGTTATAAGTCCTGGTTT
1 TTAGCGGCGTTTTTTATGTAAGCGCCGCTAAAAGTCCTGGTCT
* *
28082112 TTAGCGGCATTTTTTATGTAAGCGCTGCTAAAAGTCCTGGTCT
1 TTAGCGGCGTTTTTTATGTAAGCGCCGCTAAAAGTCCTGGTCT
* * * *
28082155 TTAGTGGCGCTTTTTATGTAAGCACCGCTAAAAGTCCTAGTCT
1 TTAGCGGCGTTTTTTATGTAAGCGCCGCTAAAAGTCCTGGTCT
28082198 TTAGCG
1 TTAGCG
28082204 TCGCTTACCT
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 77 1.00
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTATGTAAGCGCCGCTAAAAGTCCTGGTCT
Found at i:28082308 original size:106 final size:107
Alignment explanation
Indices: 28082111--28082309 Score: 233
Period size: 106 Copynumber: 1.9 Consensus size: 107
28082101 AGTCCTGGTT
* * * * ***
28082111 TTTAGCGGCATTTTTTATGTAAGCGCTGCTAAAAGTCCTGGTCTTTAGTGGCGCTTTTTATGTAA
1 TTTAGCGGCATTTTTTATATAAGCGCCGCTAAAAGTCCTAGTCTTTAGCGGCGCTTTTTAAAAAA
* *
28082176 GCACCGCTAAAAGTCCTAGTCTTTAGCGTCGCTTACCTGATC
66 CCACCGCTAAAAGTCATAGTCTTTAGCGTCGCTTACCTGATC
** * *
28082218 TTTAGCGGTGTTTTTTTTATAAGCGCCGCTAAAAGTCCTAG-CTTTAGCGGCGTTTTTTAAAAAA
1 TTTAGCGGCATTTTTTATATAAGCGCCGCTAAAAGTCCTAGTCTTTAGCGGCGCTTTTTAAAAAA
*
28082282 CCGCCGCT-AAAGATCAT-GATCTTTAGCG
66 CCACCGCTAAAAG-TCATAG-TCTTTAGCG
28082310 GCATTACATA
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
105 5 0.07
106 36 0.47
107 35 0.46
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (107 bp):
TTTAGCGGCATTTTTTATATAAGCGCCGCTAAAAGTCCTAGTCTTTAGCGGCGCTTTTTAAAAAA
CCACCGCTAAAAGTCATAGTCTTTAGCGTCGCTTACCTGATC
Found at i:28085460 original size:25 final size:25
Alignment explanation
Indices: 28085411--28085466 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
28085401 CTGTTTTTAG
**
28085411 AAAGAAAAGAACCAAGAACCTCAAA
1 AAAGAAAAGAACCAAGAACAACAAA
28085436 AAAGAAAAGAAACCAAGAA-AACAAA
1 AAAGAAAAG-AACCAAGAACAACAAA
*
28085461 GAAGAA
1 AAAGAA
28085467 GAAAACATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.70, C:0.14, G:0.14, T:0.02
Consensus pattern (25 bp):
AAAGAAAAGAACCAAGAACAACAAA
Found at i:28085534 original size:5 final size:6
Alignment explanation
Indices: 28085482--28085533 Score: 61
Period size: 6 Copynumber: 8.7 Consensus size: 6
28085472 CATCCAGCCA
* * *
28085482 AAAAAG AAAAAG AAAAAT AAAAAT AAGTAA- AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT AAAAAT AAAAAT AAAAAT
28085530 AAAA
1 AAAA
28085534 TGTTAAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
5 2 0.05
6 37 0.90
7 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:28086502 original size:14 final size:14
Alignment explanation
Indices: 28086481--28086521 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28086471 TTGAAACTTG
28086481 CACAACTTGCACAT
1 CACAACTTGCACAT
** *
28086495 TGCAACTTGCAAAT
1 CACAACTTGCACAT
28086509 CACAACTTGCACA
1 CACAACTTGCACA
28086522 ATTAGGTAAG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.22
Consensus pattern (14 bp):
CACAACTTGCACAT
Found at i:28089167 original size:14 final size:14
Alignment explanation
Indices: 28089146--28089186 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28089136 TTGCAACTTG
28089146 CACAACTTGCACAT
1 CACAACTTGCACAT
** *
28089160 TGCAACTTGCAAAT
1 CACAACTTGCACAT
28089174 CACAACTTGCACA
1 CACAACTTGCACA
28089187 ATTAGGTAAG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.22
Consensus pattern (14 bp):
CACAACTTGCACAT
Found at i:28090024 original size:28 final size:28
Alignment explanation
Indices: 28089984--28090040 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
28089974 TTAATAAATA
28089984 TGTGCATCTTTTAATAAGGGGAATTTTC
1 TGTGCATCTTTTAATAAGGGGAATTTTC
28090012 TGTGCATCTTTTAATAAGGGGAATTTTC
1 TGTGCATCTTTTAATAAGGGGAATTTTC
28090040 T
1 T
28090041 CTAGAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.44
Consensus pattern (28 bp):
TGTGCATCTTTTAATAAGGGGAATTTTC
Found at i:28094079 original size:28 final size:28
Alignment explanation
Indices: 28094047--28094111 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
28094037 ATTTACTAGA
*
28094047 ATACCCCTATGTATGCAAAATTACCA-TT
1 ATACCCCTATGTATGCAAAATGA-CATTT
28094075 ATACCCCTATGTATGCAAAATGACATTT
1 ATACCCCTATGTATGCAAAATGACATTT
28094103 ATACCCCTA
1 ATACCCCTA
28094112 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 2 0.06
28 33 0.94
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACATTT
Found at i:28094275 original size:27 final size:28
Alignment explanation
Indices: 28094217--28094306 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
28094207 AGGAAGCGTC
*
28094217 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
28094245 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
28094272 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
28094301 CTGGTG
1 CTGGTG
28094307 ACTATGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:28094794 original size:19 final size:19
Alignment explanation
Indices: 28094770--28094808 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28094760 TTTTAATTAT
* *
28094770 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
28094789 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
28094808 T
1 T
28094809 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:28095405 original size:10 final size:10
Alignment explanation
Indices: 28095388--28095421 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
28095378 AGCCTGTTTA
28095388 TATTCTGAAT
1 TATTCTGAAT
*
28095398 TTTTCTGAAT
1 TATTCTGAAT
28095408 ATATTCTGAAT
1 -TATTCTGAAT
28095419 TAT
1 TAT
28095422 CTGTCTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:28095416 original size:11 final size:11
Alignment explanation
Indices: 28095386--28095418 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
28095376 CAAGCCTGTT
28095386 TATATTCTGAA
1 TATATTCTGAA
*
28095397 T-TTTTCTGAA
1 TATATTCTGAA
28095407 TATATTCTGAA
1 TATATTCTGAA
28095418 T
1 T
28095419 TATCTGTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (11 bp):
TATATTCTGAA
Found at i:28101957 original size:28 final size:28
Alignment explanation
Indices: 28101925--28101989 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
28101915 ATTTACTAGA
*
28101925 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
28101953 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
28101981 ATACCCCTA
1 ATACCCCTA
28101990 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:28102150 original size:27 final size:28
Alignment explanation
Indices: 28102105--28102184 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 28
28102095 CTTGTGGCTA
* * *
28102105 TGCCCCAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGGCAC
**
28102133 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGGCAC
28102160 TGCCACAAAATATCTGTATCTGGTG
1 TGCCACAAAATATCTGT-TCTGGTG
28102185 ACTATGTCAC
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 23 0.53
28 13 0.30
29 7 0.16
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.33
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGGCAC
Found at i:28102672 original size:19 final size:19
Alignment explanation
Indices: 28102648--28102686 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28102638 TTTTAATTAT
* *
28102648 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
28102667 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
28102686 T
1 T
28102687 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:28108270 original size:14 final size:14
Alignment explanation
Indices: 28108235--28108285 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
28108225 TAACAGTTAA
28108235 CTAACTA-TAACTG
1 CTAACTACTAACTG
28108248 CAATAACTACTAAGCT-
1 C--TAACTACTAA-CTG
28108264 CTAACTACTAACTG
1 CTAACTACTAACTG
28108278 CTAACTAC
1 CTAACTAC
28108286 CATAACCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.09
14 18 0.55
15 6 0.18
16 4 0.12
17 2 0.06
ACGTcount: A:0.39, C:0.27, G:0.06, T:0.27
Consensus pattern (14 bp):
CTAACTACTAACTG
Found at i:28108614 original size:17 final size:17
Alignment explanation
Indices: 28108594--28108631 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
28108584 ATGAGTTCTA
*
28108594 CAAAACTGTAAGTTCAT
1 CAAAACTGTAAGCTCAT
*
28108611 CAAAACTGTGAGCTCAT
1 CAAAACTGTAAGCTCAT
28108628 CAAA
1 CAAA
28108632 GGTGCGAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (17 bp):
CAAAACTGTAAGCTCAT
Found at i:28109553 original size:13 final size:13
Alignment explanation
Indices: 28109517--28109545 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
28109507 TTTTAAAACT
28109517 ATTTCTGAAAAGC
1 ATTTCTGAAAAGC
28109530 ATTTCTGAAAAGC
1 ATTTCTGAAAAGC
28109543 ATT
1 ATT
28109546 CTTGAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (13 bp):
ATTTCTGAAAAGC
Found at i:28111031 original size:31 final size:31
Alignment explanation
Indices: 28110993--28111052 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
28110983 AAATAACCAA
* * *
28110993 GTGACTTAAATGAATACTTCCGAATAGTTAG
1 GTGACTTAAATAAAAACTTCCAAATAGTTAG
*
28111024 GTGACTTAAATAAAAACTTTCAAATAGTT
1 GTGACTTAAATAAAAACTTCCAAATAGTT
28111053 GAGTAATCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (31 bp):
GTGACTTAAATAAAAACTTCCAAATAGTTAG
Found at i:28111389 original size:43 final size:43
Alignment explanation
Indices: 28111326--28111424 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
28111316 AGAATAGTTT
* * * *
28111326 TTTAGTGGCGCTTCTCATAAAAACGCTGCTAAAGAACATGACC
1 TTTAGCGGCGTTTCCCATAAAAACGCCGCTAAAGAACATGACC
* * **
28111369 TTTAGCGGCGTTTCCCATAAAAATGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTCCCATAAAAACGCCGCTAAAGAACATGACC
*
28111412 TTTACCGGCGTTT
1 TTTAGCGGCGTTT
28111425 GTGGGAGAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTCCCATAAAAACGCCGCTAAAGAACATGACC
Found at i:28111444 original size:43 final size:43
Alignment explanation
Indices: 28111397--28111478 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
28111387 AAAAATGCCG
*
28111397 CTAAAGACCATGTTCTTTACCGGCGTTTGTGGGAGAAACGACA
1 CTAAAGACCATGTTCTTTACCGGCGTTTGTGGGAAAAACGACA
** ** *
28111440 CTAAAGGTCATGTTCTTTAGTGGTGTTTGTGGGAAAAAC
1 CTAAAGACCATGTTCTTTACCGGCGTTTGTGGGAAAAAC
28111479 ACCACAAACT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (43 bp):
CTAAAGACCATGTTCTTTACCGGCGTTTGTGGGAAAAACGACA
Found at i:28122080 original size:12 final size:12
Alignment explanation
Indices: 28122039--28122117 Score: 54
Period size: 12 Copynumber: 6.3 Consensus size: 12
28122029 TAAATATTAG
28122039 TTAT-ATATATT
1 TTATCATATATT
*
28122050 ATTATCCATTATTTT
1 -TTAT-CA-TATATT
28122065 TTATCATATATT
1 TTATCATATATT
*
28122077 TTATCTATAAATT
1 TTATC-ATATATT
* *
28122090 ATATTATATATT
1 TTATCATATATT
*
28122102 ATT-TTATATATT
1 -TTATCATATATT
28122114 TTAT
1 TTAT
28122118 TTATATATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
11 2 0.04
12 30 0.56
13 12 0.22
14 5 0.09
15 5 0.09
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATCATATATT
Found at i:28122126 original size:15 final size:15
Alignment explanation
Indices: 28122088--28122130 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
28122078 TATCTATAAA
*
28122088 TTATATTATATATTAT
1 TTATA-TATATTTTAT
28122104 TT-TATATATTTTAT
1 TTATATATATTTTAT
28122118 TTATATATATTTT
1 TTATATATATTTT
28122131 TTAAAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 11 0.44
15 12 0.48
16 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATATATTTTAT
Found at i:28122133 original size:13 final size:13
Alignment explanation
Indices: 28122018--28122133 Score: 73
Period size: 13 Copynumber: 9.0 Consensus size: 13
28122008 TTAAATACTT
28122018 TATATATTTTTTA
1 TATATATTTTTTA
**
28122031 -A-ATATTAGTTA
1 TATATATTTTTTA
*
28122042 TATATA-TTATTA
1 TATATATTTTTTA
28122054 TCCAT-TATTTTTTA
1 T--ATATATTTTTTA
* *
28122068 TCATATATTTTATC
1 T-ATATATTTTTTA
* *
28122082 TATAAATTATATTA
1 TATATATT-TTTTA
*
28122096 TATAT-TATTTTA
1 TATATATTTTTTA
28122108 TATAT-TTTATTTA
1 TATATATTT-TTTA
28122121 TATATATTTTTTA
1 TATATATTTTTTA
28122134 AAAATTGTAT
Statistics
Matches: 79, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
11 8 0.10
12 18 0.23
13 28 0.35
14 25 0.32
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (13 bp):
TATATATTTTTTA
Found at i:28134336 original size:206 final size:207
Alignment explanation
Indices: 28133593--28134564 Score: 1457
Period size: 208 Copynumber: 4.7 Consensus size: 207
28133583 GCAGATCTGG
* *
28133593 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATACCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
*
28133658 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTAAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * * *
28133723 AGAACAAATCAAAGTTTTGTGTCTCCATATTCGAAGGAGGGTAGACACATAGCAGATCTGGCCTT
131 AGAACAAATCGAAGTTTGGGGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTGGCCTT
*
28133788 TAGATGTTTTATA
196 CAGATG-TTTATA
*
28133801 CTGAAGCAAGATCCAAGATGATTTGGCTTCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
*
28133866 GATTTGGCTTTCACGTGCTTACGATGAAGAAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* *
28133931 AGAACAAATCGAAGTTTGGGGTCTCCATATTCGATGGAGGGCAGACACATAGTAGATCTGGCCTT
131 AGAACAAATCGAAGTTTGGGGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTGGCCTT
*
28133996 CAGATATTTTATA
196 CAGAT-GTTTATA
28134009 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
* *
28134074 AATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * *
28134139 AGAACAAATCGAAGTTTGGCGTCTCCATATTTGACGGAGAGCAGACACATAGCAGATCTGGCCTT
131 AGAACAAATCGAAGTTTGGGGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTGGCCTT
*
28134204 CATATGTTTATA
196 CAGATGTTTATA
* *
28134216 CTGAAGC-AGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAA-ATCATAGT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGA-CATAGC
* * * *
28134279 TGATTTGGCTTTCACGTGCTTACGCTGAAGCAAGTTTAAGATGATTTGGCGTCTCTGTATTGTCA
65 TGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA
* ** * **
28134344 GGGAACAAATCGAAGTTTGGGGTCTCCATATTCGACAAAGGGCAGACACATAGCAAATCTAACCT
130 GAGAACAAATCGAAGTTTGGGGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTGGCCT
* *
28134409 TCAGATGATTAGA
195 TCAGATGTTTATA
* * * ** *
28134422 CTGAAGC-AGATCCAAGATGGTTTGGTATCTTTGTGCTTACAAGGCGCAAATCAAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
* * ** * *
28134486 GATTTGGTTTTCGCGTGCTTAC-ACTGAAGCAGGTCTAAGATGATTTGCCATCTTTGTATTGTCA
66 GATTTGGCTTTCACGTGCTTACGA-TGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA
*
28134550 GGGAACAAATCGAAG
130 GAGAACAAATCGAAG
28134565 AAGCAGATCT
Statistics
Matches: 700, Mismatches: 60, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
205 1 0.00
206 301 0.43
207 14 0.02
208 384 0.55
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (207 bp):
CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
AGAACAAATCGAAGTTTGGGGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTGGCCTT
CAGATGTTTATA
Found at i:28134814 original size:13 final size:13
Alignment explanation
Indices: 28134796--28134826 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28134786 GTATTTATTT
28134796 ATTTAAAATGTCC
1 ATTTAAAATGTCC
28134809 ATTTAAAATGTCC
1 ATTTAAAATGTCC
*
28134822 TTTTA
1 ATTTA
28134827 CAGAACCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (13 bp):
ATTTAAAATGTCC
Found at i:28139798 original size:163 final size:163
Alignment explanation
Indices: 28139528--28139858 Score: 583
Period size: 163 Copynumber: 2.0 Consensus size: 163
28139518 TCTTCTAGGC
28139528 TTATATTTTTCTTAAAATATTCCTTCTTTAAAGTACTTTTATGGTCTCTCCATTTCTTTCCTAAT
1 TTATATTTTTCTTAAAATATTCCTTCTTTAAAGTACTTTTATGGTCTCTCCATTTCTTTCCTAAT
* * * *
28139593 GCCTTCTTCACATAATTATCTAATACCTTTAAAGCAAATCTCTCCTGCAAATAACACAAGTTTAG
66 GCCTTCTTCACATAATTATCCAAGACCTCTAAAGCAAATCTCTCCTGCAAATAACACAAGTTTAA
28139658 AAAGTAAATATAAATGAAACTTAAACCAAAGTA
131 AAAGTAAATATAAATGAAACTTAAACCAAAGTA
28139691 TTATATTTTTCTTAAAATATTCCTTCTTTAAAGTACTTTTATGGTCTCTCCATTTCTTTCCTAAT
1 TTATATTTTTCTTAAAATATTCCTTCTTTAAAGTACTTTTATGGTCTCTCCATTTCTTTCCTAAT
* **
28139756 GCCTTCTTCACATAATTATCCGAGACCTCT-AAGACAAATCTCTTTTGCAAATAACACAAGTTTA
66 GCCTTCTTCACATAATTATCCAAGACCTCTAAAG-CAAATCTCTCCTGCAAATAACACAAGTTTA
28139820 AAAAGTAAATATAAATGAAACTTAAACCAAAGTA
130 AAAAGTAAATATAAATGAAACTTAAACCAAAGTA
28139854 TTATA
1 TTATA
28139859 AATTACATTC
Statistics
Matches: 160, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
162 3 0.02
163 157 0.98
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.39
Consensus pattern (163 bp):
TTATATTTTTCTTAAAATATTCCTTCTTTAAAGTACTTTTATGGTCTCTCCATTTCTTTCCTAAT
GCCTTCTTCACATAATTATCCAAGACCTCTAAAGCAAATCTCTCCTGCAAATAACACAAGTTTAA
AAAGTAAATATAAATGAAACTTAAACCAAAGTA
Found at i:28145026 original size:25 final size:26
Alignment explanation
Indices: 28144990--28145040 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
28144980 AATATATAGA
28144990 TAAATAATATTTATCTTTATGATAAT
1 TAAATAATATTTATCTTTATGATAAT
*
28145016 TAAAT-ATATTTATTTTTATGATAAT
1 TAAATAATATTTATCTTTATGATAAT
28145041 ATTTATGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (26 bp):
TAAATAATATTTATCTTTATGATAAT
Found at i:28154059 original size:11 final size:11
Alignment explanation
Indices: 28154043--28154067 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28154033 TTGAAGATGA
28154043 ATAAGCAAAAT
1 ATAAGCAAAAT
28154054 ATAAGCAAAAT
1 ATAAGCAAAAT
28154065 ATA
1 ATA
28154068 CAAACATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (11 bp):
ATAAGCAAAAT
Found at i:28154248 original size:24 final size:23
Alignment explanation
Indices: 28154201--28154244 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
28154191 TATATCAAAC
*
28154201 AAACAACACTTAATAATATTATG
1 AAACAACACTTAATAATATAATG
28154224 AAACTAACACTTAAT-ATATAA
1 AAAC-AACACTTAATAATATAA
28154245 ATGATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.30
Consensus pattern (23 bp):
AAACAACACTTAATAATATAATG
Found at i:28154350 original size:18 final size:19
Alignment explanation
Indices: 28154315--28154350 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28154305 GAGTAATTAA
28154315 AAAATATACATATATAATT
1 AAAATATACATATATAATT
*
28154334 AAAATATA-ATATTTAAT
1 AAAATATACATATATAAT
28154351 AATGCATGAT
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:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATATACATATATAATT
Found at i:28154557 original size:49 final size:49
Alignment explanation
Indices: 28154452--28154576 Score: 120
Period size: 48 Copynumber: 2.6 Consensus size: 49
28154442 AATATTTTAC
*
28154452 ATATAA-AAATATAATAAAAT-AAATAATATAATAAAAAAACATAAAAAA
1 ATATAATAAATAT-ATATAATGAAATAATATAATAAAAAAACATAAAAAA
* * * *
28154500 ACAGAATAAATATATATAATGAAAT-GTATAATAAAAGAAA-TTAAAAAA
1 ATATAATAAATATATATAATGAAATAATATAATAAAA-AAACATAAAAAA
*
28154548 AGTATAAT-AATA-ATCTAATG-AATAATATA
1 A-TATAATAAATATATATAATGAAATAATATA
28154577 TACTATTTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
46 3 0.05
47 11 0.17
48 32 0.51
49 17 0.27
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.26
Consensus pattern (49 bp):
ATATAATAAATATATATAATGAAATAATATAATAAAAAAACATAAAAAA
Found at i:28157015 original size:25 final size:25
Alignment explanation
Indices: 28156987--28157037 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
28156977 CCCTTATAAT
*
28156987 GTGAAAATGACCT-TTTTACCCCTAG
1 GTGAAAATGA-CTATTATACCCCTAG
28157012 GTGAAAATGACTATTATACCCCTAG
1 GTGAAAATGACTATTATACCCCTAG
28157037 G
1 G
28157038 GTTATGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (25 bp):
GTGAAAATGACTATTATACCCCTAG
Found at i:28157217 original size:25 final size:25
Alignment explanation
Indices: 28157150--28157219 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
28157140 GAGGAAGTGC
* * *
28157150 AAAAGGGCTATGCCCCAATTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
28157175 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
28157200 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
28157220 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:28157232 original size:24 final size:24
Alignment explanation
Indices: 28157149--28157246 Score: 76
Period size: 25 Copynumber: 4.0 Consensus size: 24
28157139 GGAGGAAGTG
* * *
28157149 CAAAAG-GGCTATGCCCCAATTTAC
1 CAAAAGAGGCTTTGCCCC-AGTTAT
28157173 CGAAAAG-GGCTTTGCCCCAGTTTAT
1 C-AAAAGAGGCTTTGCCCCAG-TTAT
28157198 CAAAA-AGGGCTTTGCCCCAGTTAT
1 CAAAAGA-GGCTTTGCCCCAGTTAT
* **
28157222 TAAAAGAGGCTAGGCCTCCAGTTAT
1 CAAAAGAGGCTTTGCC-CCAGTTAT
28157247 ATGATAAAGC
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
24 21 0.34
25 41 0.66
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (24 bp):
CAAAAGAGGCTTTGCCCCAGTTAT
Found at i:28157501 original size:31 final size:30
Alignment explanation
Indices: 28157466--28157530 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 30
28157456 TGATATGAAT
*
28157466 TATGAATAATGAAAAGGCTTCGGCCTAGTGA
1 TATGAATAATGAAAAGGCTTCGGCCCAGT-A
*
28157497 TATGAATAATGTAAAGGCTTCGGCCCAGTA
1 TATGAATAATGAAAAGGCTTCGGCCCAGTA
28157527 TATG
1 TATG
28157531 CTGAGATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (30 bp):
TATGAATAATGAAAAGGCTTCGGCCCAGTA
Found at i:28158664 original size:9 final size:9
Alignment explanation
Indices: 28158650--28158677 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
28158640 CCATTAACAA
28158650 TTTGGGCCT
1 TTTGGGCCT
28158659 TTTGGGCCT
1 TTTGGGCCT
28158668 TTTGGGCCT
1 TTTGGGCCT
28158677 T
1 T
28158678 GTATGCTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.21, G:0.32, T:0.46
Consensus pattern (9 bp):
TTTGGGCCT
Found at i:28165410 original size:34 final size:34
Alignment explanation
Indices: 28165367--28165431 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
28165357 AAAAACGTTG
*
28165367 CTATTGCCTTACCTTTTGCGGTGTTTATGGGCTA
1 CTATTGCCTTACCTTTTGCGGCGTTTATGGGCTA
*
28165401 CTATTGCCTTACCTTTTGCTGCGTTTATGGG
1 CTATTGCCTTACCTTTTGCGGCGTTTATGGG
28165432 AAAAACACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.45
Consensus pattern (34 bp):
CTATTGCCTTACCTTTTGCGGCGTTTATGGGCTA
Found at i:28165939 original size:24 final size:24
Alignment explanation
Indices: 28165902--28165969 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
28165892 GTCTGGAAAA
28165902 GATTTAGGAA-CTGATAAGGGAGAG
1 GATTTA-GAAGCTGATAAGGGAGAG
*
28165926 GATTTAGAAGCTGATCAGGGAGAG
1 GATTTAGAAGCTGATAAGGGAGAG
* *
28165950 GATTTAGGAGCTGATTAGGG
1 GATTTAGAAGCTGATAAGGG
28165970 GGAACTGTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 3 0.08
24 37 0.93
ACGTcount: A:0.32, C:0.06, G:0.38, T:0.24
Consensus pattern (24 bp):
GATTTAGAAGCTGATAAGGGAGAG
Found at i:28167447 original size:27 final size:26
Alignment explanation
Indices: 28167406--28167517 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
28167396 AGGAAGCGTC
**
28167406 CTGGTGGCTAGGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
28167433 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
28167460 CTGGTGGTTCTACCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
28167488 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
28167514 CTGG
1 CTGG
28167518 AAGCCATGCT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 7 0.10
27 49 0.69
28 15 0.21
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:28167745 original size:78 final size:78
Alignment explanation
Indices: 28167631--28167782 Score: 277
Period size: 78 Copynumber: 1.9 Consensus size: 78
28167621 TTGGGTTTTA
* *
28167631 CATATACATGAAATATCTGATCTGATCTATTATGGGCCTATGGGCTTAATTCTGTATTCTGTTTT
1 CATATACATGAAATATCTGATCTGATCTATTATGGGCCTATAGGCTTAATTCTGTATTCTGTTCT
28167696 GGGCTAAGATTTG
66 GGGCTAAGATTTG
*
28167709 CATATACATGAAATATCTGATCTGATCTGTTATGGGCCTATAGGCTTAATTCTGTATTCTGTTCT
1 CATATACATGAAATATCTGATCTGATCTATTATGGGCCTATAGGCTTAATTCTGTATTCTGTTCT
28167774 GGGCTAAGA
66 GGGCTAAGA
28167783 CCAATTTATT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.39
Consensus pattern (78 bp):
CATATACATGAAATATCTGATCTGATCTATTATGGGCCTATAGGCTTAATTCTGTATTCTGTTCT
GGGCTAAGATTTG
Found at i:28170424 original size:46 final size:46
Alignment explanation
Indices: 28170357--28170523 Score: 169
Period size: 46 Copynumber: 3.6 Consensus size: 46
28170347 TGTAACCCGC
** *
28170357 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCGTTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACAAGCTCGGGCATTTGCAT
* * *
28170403 CCATAAGTGAACTCGGACTCAACTCAACAAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACAAGCTCGG--G-C-ATTTGCAT
* * * * *
28170453 -C-TCA-CGAACTTGGACTCAACTCAACAAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACAAGCTCGGGCATTTGCAT
*
28170496 CCATAAGTGAACTCGGACTCAACTCAAC
1 CCATAAGCGAACTCGGACTCAACTCAAC
28170524 GAGTTCGGAT
Statistics
Matches: 97, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
43 5 0.05
44 2 0.02
45 2 0.02
46 52 0.54
47 26 0.27
48 3 0.03
49 2 0.02
50 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACAAGCTCGGGCATTTGCAT
Found at i:28170471 original size:93 final size:93
Alignment explanation
Indices: 28170364--28170536 Score: 265
Period size: 93 Copynumber: 1.9 Consensus size: 93
28170354 CGCCCATAAG
** * * *
28170364 CGAACTCGGACTCAACTCAATGAGCTCGGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28170429 ACAAGCTCGGATGCCTAGTTACATCTCA
66 ACAAGCTCGGATGCCTAGTTACATCTCA
* *
28170457 CGAACTTGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
28170522 ACGAGTTCGGATGCC
66 ACAAGCTCGGATGCC
28170537 CAAATATCCC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACAAGCTCGGATGCCTAGTTACATCTCA
Found at i:28176579 original size:85 final size:85
Alignment explanation
Indices: 28176428--28176593 Score: 314
Period size: 85 Copynumber: 2.0 Consensus size: 85
28176418 CTGGGCTTTT
*
28176428 AAGTATTAACTGGGTAAAAGAGGACACAAGGAAGCCTGTGGTAAGTTGGCATGTGATGCCACTTA
1 AAGTATTAACTGGGTAAAAGAGGACACAAGGAAGCCTGTGGTAAGTTGGCATGTGACGCCACTTA
28176493 GGGGCTTAGAGGTGGCATGA
66 GGGGCTTAGAGGTGGCATGA
*
28176513 AAGTATTAACTGGGTAAAAGAGGACACAAGGAAGCCTGTGGTAAGTTGGCATGTGACGCCAGTTA
1 AAGTATTAACTGGGTAAAAGAGGACACAAGGAAGCCTGTGGTAAGTTGGCATGTGACGCCACTTA
28176578 GGGGCTTAGAGGTGGC
66 GGGGCTTAGAGGTGGC
28176594 GTGTGGATGA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.30, C:0.13, G:0.35, T:0.22
Consensus pattern (85 bp):
AAGTATTAACTGGGTAAAAGAGGACACAAGGAAGCCTGTGGTAAGTTGGCATGTGACGCCACTTA
GGGGCTTAGAGGTGGCATGA
Found at i:28176738 original size:24 final size:24
Alignment explanation
Indices: 28176705--28176778 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 24
28176695 AAGTCTGTCT
* *
28176705 GGAGAAGATTTAGGAACTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
28176729 GGAGAGGATTCAGGAGCTGATCAG
1 GGAGAGGATTTAGGAGCTGATAAG
* * *
28176753 GGAGAGAATTTAAGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
28176777 GG
1 GG
28176779 TGAACTGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.35, C:0.07, G:0.38, T:0.20
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:28178246 original size:27 final size:26
Alignment explanation
Indices: 28178216--28178327 Score: 98
Period size: 27 Copynumber: 4.2 Consensus size: 26
28178206 AGGAAGCGTC
*
28178216 CTGGTGGCTATACCACAATTATCTGAT
1 CTGGTGGCTATGCCAC-ATTATCTGAT
* * *
28178243 CTGGAGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAT-TATCTGAT
* *
28178270 CTGGTGGTTTTGCCACGATTATCTGTAT
1 CTGGTGGCTATGCCAC-ATTATCTG-AT
* * * *
28178298 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACATTATCTGAT
28178324 CTGG
1 CTGG
28178328 CAGCCATGCT
Statistics
Matches: 69, Mismatches: 13, Indels: 7
0.78 0.15 0.08
Matches are distributed among these distances:
26 7 0.10
27 47 0.68
28 15 0.22
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTATGCCACATTATCTGAT
Found at i:28184673 original size:18 final size:18
Alignment explanation
Indices: 28184650--28184686 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28184640 TCTACCTTAG
28184650 ATTAGAGTTTATTTTTCT
1 ATTAGAGTTTATTTTTCT
28184668 ATTAGAGTTTATTTTTCT
1 ATTAGAGTTTATTTTTCT
28184686 A
1 A
28184687 ATTTTACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.59
Consensus pattern (18 bp):
ATTAGAGTTTATTTTTCT
Found at i:28186709 original size:24 final size:24
Alignment explanation
Indices: 28186676--28186725 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
28186666 AAGTCTGTCT
28186676 GGAGAAGATTTAGAAGCTGATAAG
1 GGAGAAGATTTAGAAGCTGATAAG
* * *
28186700 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAAGATTTAGAAGCTGATAAG
28186724 GG
1 GG
28186726 TGAACTGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.04, G:0.40, T:0.22
Consensus pattern (24 bp):
GGAGAAGATTTAGAAGCTGATAAG
Found at i:28188269 original size:27 final size:27
Alignment explanation
Indices: 28188163--28188269 Score: 128
Period size: 27 Copynumber: 3.9 Consensus size: 27
28188153 AGGAAGCGTC
*
28188163 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
28188190 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACAT-TATCTGTAT
* *
28188217 CTGGTGGTTCTACCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
* *
28188245 CTGGTGACTCTGTCACATTATCTGT
1 CTGGTGGCTCTGCCACATTATCTGT
28188270 TCTAGCAGCC
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
26 2 0.03
27 52 0.75
28 15 0.22
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTATCTGTAT
Found at i:28192676 original size:79 final size:81
Alignment explanation
Indices: 28192540--28192724 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
28192530 TTGAATGATG
* *
28192540 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
28192604 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
28192619 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
28192681 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
28192699 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28192725 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:28192738 original size:40 final size:40
Alignment explanation
Indices: 28192541--28192724 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
28192531 TGAATGATGT
* * * *
28192541 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
28192581 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
28192621 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
28192659 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28192700 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28192725 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:28192746 original size:79 final size:79
Alignment explanation
Indices: 28192593--28192757 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
28192583 GGACTAAGAT
* * **
28192593 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28192658 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
28192672 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28192735 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
28192751 CCGAAGG
1 CCGAAGG
28192758 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28194951 original size:17 final size:16
Alignment explanation
Indices: 28194913--28194971 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
28194903 TCTGAAAAAT
* *
28194913 AAAATAAAAACAACTA
1 AAAATAAAAAAAAGTA
28194929 ACAAATAAAAGAAAAGTA
1 A-AAATAAAA-AAAAGTA
28194947 AAAATAGAAAAAAAG-A
1 AAAATA-AAAAAAAGTA
*
28194963 AAAAGAAAA
1 AAAATAAAA
28194972 TTAAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 3 0.08
16 7 0.19
17 18 0.49
18 9 0.24
ACGTcount: A:0.78, C:0.05, G:0.08, T:0.08
Consensus pattern (16 bp):
AAAATAAAAAAAAGTA
Found at i:28194981 original size:22 final size:22
Alignment explanation
Indices: 28194931--28194981 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
28194921 AACAACTAAC
28194931 AAAT-AAAAGAAAAGTAAAAAT
1 AAATAAAAAGAAAAGTAAAAAT
*
28194952 AGAA-AAAAAGAAAAAG-AAAATT
1 A-AATAAAAAG-AAAAGTAAAAAT
28194974 AAATAAAA
1 AAATAAAA
28194982 CATAAAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 17 0.68
23 5 0.20
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (22 bp):
AAATAAAAAGAAAAGTAAAAAT
Found at i:28194993 original size:17 final size:17
Alignment explanation
Indices: 28194968--28195004 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
28194958 AAAGAAAAAG
*
28194968 AAAATTAAATAAAACAT
1 AAAACTAAATAAAACAT
*
28194985 AAAACTAAATAAAATAT
1 AAAACTAAATAAAACAT
28195002 AAA
1 AAA
28195005 TACTTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAACTAAATAAAACAT
Found at i:28196870 original size:30 final size:30
Alignment explanation
Indices: 28196812--28196873 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
28196802 TTTAAGAAAT
* *
28196812 TTACCATATTGTTCGTTCATGCGGTCTTTC
1 TTACCATATTGTTCGTTCATACGATCTTTC
*
28196842 TTACCATATTGTTCGTTCATATGATCTTTC
1 TTACCATATTGTTCGTTCATACGATCTTTC
28196872 TT
1 TT
28196874 CACTTTTTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.50
Consensus pattern (30 bp):
TTACCATATTGTTCGTTCATACGATCTTTC
Found at i:28199506 original size:40 final size:40
Alignment explanation
Indices: 28199458--28199725 Score: 473
Period size: 40 Copynumber: 6.7 Consensus size: 40
28199448 GCAAACACAT
* * *
28199458 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
28199498 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28199538 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
28199578 TTGCCTTCAGGTCTTAGCCCGGATATATCGACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28199618 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
28199658 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
28199698 TTGCCTTCGGGTTTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
28199726 TCCAATGCTC
Statistics
Matches: 218, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 218 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:28204207 original size:81 final size:81
Alignment explanation
Indices: 28204072--28204233 Score: 306
Period size: 81 Copynumber: 2.0 Consensus size: 81
28204062 GTAGCCAAGA
28204072 TACCATGTAACCCGCCCAAAAGTGAACTCGGACTCAACTCAACAAGCTCAGACGTTCGCATCCAT
1 TACCATGTAACCCGCCCAAAAGTGAACTCGGACTCAACTCAACAAGCTCAGACGTTCGCATCCAT
28204137 AAGTGAACTCGGACTC
66 AAGTGAACTCGGACTC
* *
28204153 TACCATGTAACCCGCCCATAAGTGAACTCGGACTCAACTCAACAAGCTCGGACGTTCGCATCCAT
1 TACCATGTAACCCGCCCAAAAGTGAACTCGGACTCAACTCAACAAGCTCAGACGTTCGCATCCAT
28204218 AAGTGAACTCGGACTC
66 AAGTGAACTCGGACTC
28204234 AACTCAACGA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.19
Consensus pattern (81 bp):
TACCATGTAACCCGCCCAAAAGTGAACTCGGACTCAACTCAACAAGCTCAGACGTTCGCATCCAT
AAGTGAACTCGGACTC
Found at i:28204333 original size:46 final size:46
Alignment explanation
Indices: 28204168--28204332 Score: 162
Period size: 46 Copynumber: 3.7 Consensus size: 46
28204158 TGTAACCCGC
* *
28204168 CCATAAGTGAACTCGGACTCAACTCAACAAGCTCGGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
28204214 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--A-T-GCCT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*** ** * * *
28204256 AGTTACA-T-CTCTCGAACTCGGACTCAACGAGTTCGGACATTCGCAT
1 CCATA-AGTGAACTCGGACTC-AACTCAACGAGCTCGGACATTCGCAT
*
28204302 CCATAAGTGAACTCAGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
28204333 TTTGGATGCT
Statistics
Matches: 91, Mismatches: 20, Indels: 16
0.72 0.16 0.13
Matches are distributed among these distances:
41 8 0.09
42 20 0.22
43 2 0.02
44 1 0.01
45 2 0.02
46 51 0.56
47 7 0.08
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:28208999 original size:6 final size:6
Alignment explanation
Indices: 28208986--28209047 Score: 69
Period size: 6 Copynumber: 11.0 Consensus size: 6
28208976 TTGAAATGAG
* * *
28208986 AATAAA AATCAA AAGAAA AATAAA AAT-AA AAT-AA AATAAA AATAAG
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
28209032 AAT--A AATAAA AATAAA
1 AATAAA AATAAA AATAAA
28209048 TGAGGATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 3 0.06
5 10 0.21
6 34 0.72
ACGTcount: A:0.79, C:0.02, G:0.03, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:28209021 original size:22 final size:22
Alignment explanation
Indices: 28208990--28209042 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
28208980 AATGAGAATA
28208990 AAAATCAAAAGAAAAATAAAAAT
1 AAAAT-AAAAGAAAAATAAAAAT
* *
28209013 AAAATAAAATAAAAATAAGAAT
1 AAAATAAAAGAAAAATAAAAAT
28209035 -AAATAAAA
1 AAAATAAAA
28209043 ATAAATGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 8 0.29
22 15 0.54
23 5 0.18
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (22 bp):
AAAATAAAAGAAAAATAAAAAT
Found at i:28209023 original size:16 final size:16
Alignment explanation
Indices: 28208986--28209047 Score: 81
Period size: 16 Copynumber: 3.8 Consensus size: 16
28208976 TTGAAATGAG
*
28208986 AATAAAAATCAAAAGAAA
1 AATAAAAAT-AAAA-TAA
28209004 AATAAAAATAAAATAA
1 AATAAAAATAAAATAA
28209020 AATAAAAATAAGAAT-A
1 AATAAAAATAA-AATAA
28209036 AATAAAAATAAA
1 AATAAAAATAAA
28209048 TGAGGATTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
15 1 0.02
16 25 0.60
17 7 0.17
18 9 0.21
ACGTcount: A:0.79, C:0.02, G:0.03, T:0.16
Consensus pattern (16 bp):
AATAAAAATAAAATAA
Found at i:28209035 original size:12 final size:11
Alignment explanation
Indices: 28208986--28209047 Score: 65
Period size: 11 Copynumber: 5.5 Consensus size: 11
28208976 TTGAAATGAG
28208986 AATAAAAATCAA
1 AATAAAAAT-AA
*
28208998 AAGAAAAATAA
1 AATAAAAATAA
28209009 AA-ATAAAATAA
1 AATA-AAAATAA
28209020 AATAAAAATAA
1 AATAAAAATAA
*
28209031 GAATAAATA-AA
1 -AATAAAAATAA
28209042 AATAAA
1 AATAAA
28209048 TGAGGATTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
10 7 0.16
11 22 0.49
12 16 0.36
ACGTcount: A:0.79, C:0.02, G:0.03, T:0.16
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:28212388 original size:16 final size:16
Alignment explanation
Indices: 28212369--28212399 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28212359 CTTCTTCACT
28212369 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
28212385 TACTTACTTACTTAA
1 TACTCACTTACTTAA
28212400 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:28212405 original size:20 final size:20
Alignment explanation
Indices: 28212366--28212405 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28212356 AAACTTCTTC
* *
28212366 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
28212386 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
28212406 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:28212516 original size:23 final size:24
Alignment explanation
Indices: 28212478--28212522 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
28212468 TTTGCTCTTC
*
28212478 TAGCATGAACTTGTCTTACCTTTT
1 TAGCATGAACTCGTCTTACCTTTT
28212502 TAGCAT-AACTCGTCTTACCTT
1 TAGCATGAACTCGTCTTACCTT
28212523 ACCTTACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.42
Consensus pattern (24 bp):
TAGCATGAACTCGTCTTACCTTTT
Found at i:28212781 original size:55 final size:53
Alignment explanation
Indices: 28212648--28212845 Score: 175
Period size: 55 Copynumber: 3.7 Consensus size: 53
28212638 AACTTGCCAT
*
28212648 TGCCATGTCTTAACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAA
1 TGCCATGTCTTAACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAA
* ** * *
28212701 TGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTTATCAA
1 TGCCATGTCTTAACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AACTCACCAA
* *** * *
28212756 TGCCATGTCTTAACACGGTCTTACATGATTTCCTTGCTTTA-GAAACCTTACCAA
1 TGCCATGTCTTAACATGGTCTTACATGGGATCCTTGCCTTATG-AA-CTCACCAA
* ** * *
28212810 TTGCCATGCCTTGGCATGGTCTTATATGGTATCCTT
1 -TGCCATGTCTTAACATGGTCTTACATGGGATCCTT
28212846 AAACCCTAAT
Statistics
Matches: 116, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
52 2 0.02
53 38 0.33
54 8 0.07
55 66 0.57
56 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (53 bp):
TGCCATGTCTTAACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAA
Found at i:28224598 original size:43 final size:43
Alignment explanation
Indices: 28224475--28224601 Score: 123
Period size: 43 Copynumber: 3.0 Consensus size: 43
28224465 TAAAACTCGT
* * *
28224475 ACAATGCC-ATATCCTAGATATGGTCTTACATGTTATCACATA
1 ACAATGCCAATGTCCCAGATATGGTCTTACATGTAATCACATA
* * * * * * * *
28224517 TCAATGCCATTGTCCCAAATAGGGTTTTGCACT-AAATCATATA
1 ACAATGCCAATGTCCCAGATATGGTCTTACA-TGTAATCACATA
*
28224560 ACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAT
1 ACAATGCCAATGTCCCAGATATGGTCTTACATGTAATCACAT
28224602 CTCGATAACC
Statistics
Matches: 62, Mismatches: 20, Indels: 5
0.71 0.23 0.06
Matches are distributed among these distances:
42 8 0.13
43 53 0.85
44 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (43 bp):
ACAATGCCAATGTCCCAGATATGGTCTTACATGTAATCACATA
Found at i:28230552 original size:12 final size:12
Alignment explanation
Indices: 28230535--28230567 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
28230525 AATTTCCAAC
28230535 ATTACCTATGTA
1 ATTACCTATGTA
28230547 ATTACCTATGTA
1 ATTACCTATGTA
28230559 ATTACCTAT
1 ATTACCTAT
28230568 AGGTTCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (12 bp):
ATTACCTATGTA
Found at i:28232012 original size:200 final size:200
Alignment explanation
Indices: 28231669--28232068 Score: 782
Period size: 200 Copynumber: 2.0 Consensus size: 200
28231659 CAACCTCCGA
28231669 TGGGCTAATTATGTGCGATGGATCAGATCGATAGCGTCGAAGCATCGAAACATGAAAGACGTCAT
1 TGGGCTAATTATGTGCGATGGATCAGATCGATAGCGTCGAAGCATCGAAACATGAAAGACGTCAT
28231734 GAATCTTTTCAAGCTCCGGGGGCAAAATCAATCTATACGCAACCGGGCCAACTCGTTCGGAGATC
66 GAATCTTTTCAAGCTCCGGGGGCAAAATCAATCTATACGCAACCGGGCCAACTCGTTCGGAGATC
28231799 TCGTACGGCCCAATGAATCTTGGGCTCAACTTGCCCTTACGGCCAAACCTGAGTATCTTTTTCCA
131 TCGTACGGCCCAATGAATCTTGGGCTCAACTTGCCCTTACGGCCAAACCTGAGTATCTTTTTCCA
28231864 AGGTG
196 AGGTG
28231869 TGGGCTAATTATGTGCGATGGATCAGATCGATAGCGTCGAAGCATCGAAACATGAAAGACGTCAT
1 TGGGCTAATTATGTGCGATGGATCAGATCGATAGCGTCGAAGCATCGAAACATGAAAGACGTCAT
*
28231934 GAATCTTTTCAAGCTCCGGGGGCAAAATCAATCTATACGCAACCGGGCCAACTCGTTCGGAGATT
66 GAATCTTTTCAAGCTCCGGGGGCAAAATCAATCTATACGCAACCGGGCCAACTCGTTCGGAGATC
*
28231999 TCGTACGGCCCAATGAATCTTGGGCTCAACTTGCCCTTACGGCCGAACCTGAGTATCTTTTTCCA
131 TCGTACGGCCCAATGAATCTTGGGCTCAACTTGCCCTTACGGCCAAACCTGAGTATCTTTTTCCA
28232064 AGGTG
196 AGGTG
28232069 AAACCTTAAG
Statistics
Matches: 198, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 198 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (200 bp):
TGGGCTAATTATGTGCGATGGATCAGATCGATAGCGTCGAAGCATCGAAACATGAAAGACGTCAT
GAATCTTTTCAAGCTCCGGGGGCAAAATCAATCTATACGCAACCGGGCCAACTCGTTCGGAGATC
TCGTACGGCCCAATGAATCTTGGGCTCAACTTGCCCTTACGGCCAAACCTGAGTATCTTTTTCCA
AGGTG
Found at i:28237335 original size:40 final size:40
Alignment explanation
Indices: 28237289--28238233 Score: 1863
Period size: 40 Copynumber: 23.6 Consensus size: 40
28237279 AAACACATTA
* * *
28237289 GCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237329 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237369 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237409 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237449 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237489 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237529 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237569 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237609 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237649 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237689 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237729 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237769 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237809 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237849 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237889 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237929 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28237969 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28238009 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28238049 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28238089 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28238129 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28238169 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
28238209 GCCTTCGGGTCTTAGCCCGGATATA
1 GCCTTCGGGTCTTAGCCCGGATATA
28238234 ATCCAATGCT
Statistics
Matches: 902, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 902 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATATCAACGCGCATAATT
Found at i:28241070 original size:16 final size:18
Alignment explanation
Indices: 28241049--28241081 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28241039 GGCATGCTAT
28241049 AATATA-GT-CATACATG
1 AATATAGGTCCATACATG
28241065 AATATAGGTCCATACAT
1 AATATAGGTCCATACAT
28241082 CACATAGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (18 bp):
AATATAGGTCCATACATG
Found at i:28246582 original size:49 final size:49
Alignment explanation
Indices: 28246521--28246651 Score: 156
Period size: 49 Copynumber: 2.7 Consensus size: 49
28246511 ACATCAAAGT
* * *
28246521 CAATGCTATGTCCCAGACAAGTCTTACACTGACTTTCATATTTCGAG-GC
1 CAATGCCATGTCCCAGACAAGTCTTACACTGACTCTCATATATCG-GTGC
* * * *
28246570 CAATGCCATGTCCTAGACAAGTCTTACACTGGCTCTCATCTATCGGTGT
1 CAATGCCATGTCCCAGACAAGTCTTACACTGACTCTCATATATCGGTGC
* * *
28246619 CGATGCCATGTCCCAGATAGGTCTTACACTGAC
1 CAATGCCATGTCCCAGACAAGTCTTACACTGAC
28246652 ACACAACAAG
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
48 1 0.01
49 68 0.99
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (49 bp):
CAATGCCATGTCCCAGACAAGTCTTACACTGACTCTCATATATCGGTGC
Found at i:28251572 original size:45 final size:45
Alignment explanation
Indices: 28251468--28251623 Score: 136
Period size: 45 Copynumber: 3.4 Consensus size: 45
28251458 TGAATCAGAC
* * * *
28251468 GAATAAGTCCATGGCT-GAAAGACACTATGGCAACACAA-CGTAAAAT
1 GAATAAGACCATGG-TAGAAAGACACCATGGCATCA-AATCG-AGAAT
* * *** * *
28251514 GATTAAGACCATGGTAGAGAGACATTGTGGCATCAAATTGGGAAT
1 GAATAAGACCATGGTAGAAAGACACCATGGCATCAAATCGAGAAT
* * *
28251559 GAATAAGACCATGGTTGAAAGACACCATGGCATCTAGTCGAGAAT
1 GAATAAGACCATGGTAGAAAGACACCATGGCATCAAATCGAGAAT
*
28251604 GAATAAGACCATGGTTGAAA
1 GAATAAGACCATGGTAGAAA
28251624 AATGCCACGG
Statistics
Matches: 89, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
45 61 0.69
46 28 0.31
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (45 bp):
GAATAAGACCATGGTAGAAAGACACCATGGCATCAAATCGAGAAT
Found at i:28252926 original size:27 final size:27
Alignment explanation
Indices: 28252896--28252998 Score: 107
Period size: 27 Copynumber: 3.8 Consensus size: 27
28252886 ATTACCAAAG
* **
28252896 TACCCCCAATTTACAAAATTACCGTCC
1 TACCCTCAATTTACAAAATTACCGTTT
* * * *
28252923 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCAATTTACAAAATTACCGTTT
* * * *
28252950 TACCTTCAATTTATAGAATTATCGTTT
1 TACCCTCAATTTACAAAATTACCGTTT
28252977 TACCCTCAATTTACAAAATTAC
1 TACCCTCAATTTACAAAATTAC
28252999 TAAAATACCC
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (27 bp):
TACCCTCAATTTACAAAATTACCGTTT
Found at i:28253007 original size:27 final size:27
Alignment explanation
Indices: 28252977--28253109 Score: 101
Period size: 28 Copynumber: 4.9 Consensus size: 27
28252967 ATTATCGTTT
28252977 TACCCTC-AATTTACAAAATTACTAAAA
1 TACCCTCTAATTTA-AAAATTACTAAAA
* *
28253004 TACCC-CTAGTTTGTAAAATTACTAAAA
1 TACCCTCTAATTT-AAAAATTACTAAAA
* * * *
28253031 TACCCCCTGATTTGTAAAATTACTGAAA
1 TACCCTCTAATTT-AAAAATTACTAAAA
* * * *
28253059 TACCCTCGACTTGTAAAAATTACCAAAG
1 TACCCTCTAATT-TAAAAATTACTAAAA
* *
28253087 TACCCTC-AATTTATAGATTACTA
1 TACCCTCTAATTTAAAAATTACTA
28253110 TTTTACCCTC
Statistics
Matches: 85, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
26 10 0.12
27 30 0.35
28 44 0.52
29 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.32
Consensus pattern (27 bp):
TACCCTCTAATTTAAAAATTACTAAAA
Found at i:28253046 original size:28 final size:28
Alignment explanation
Indices: 28252991--28253091 Score: 118
Period size: 28 Copynumber: 3.6 Consensus size: 28
28252981 CTCAATTTAC
28252991 AAAATTACTAAAATA-CCCCT-AGTTTGT
1 AAAATTACTAAAATACCCCCTGA-TTTGT
28253018 AAAATTACTAAAATACCCCCTGATTTGT
1 AAAATTACTAAAATACCCCCTGATTTGT
* * *
28253046 AAAATTACTGAAATACCCTC-GACTTGT
1 AAAATTACTAAAATACCCCCTGATTTGT
* *
28253073 AAAAATTACCAAAGTACCC
1 -AAAATTACTAAAATACCC
28253092 TCAATTTATA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
27 21 0.32
28 43 0.66
29 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.29
Consensus pattern (28 bp):
AAAATTACTAAAATACCCCCTGATTTGT
Found at i:28253167 original size:27 final size:28
Alignment explanation
Indices: 28253103--28253177 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
28253093 CAATTTATAG
28253103 ATTACTATTTTA-CCCTCGATTTACAAA
1 ATTACTATTTTACCCCTCGATTTACAAA
* *
28253130 ATTGCTGTTTTACCCCT-GATTTACAAA
1 ATTACTATTTTACCCCTCGATTTACAAA
*
28253157 ATTACCATTTTA-CCCTCGATT
1 ATTACTATTTTACCCCTCGATT
28253178 GTGAAATTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.10
27 33 0.80
28 4 0.10
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (28 bp):
ATTACTATTTTACCCCTCGATTTACAAA
Found at i:28253265 original size:27 final size:26
Alignment explanation
Indices: 28253209--28253359 Score: 108
Period size: 27 Copynumber: 5.7 Consensus size: 26
28253199 TATAGGGTAG
* *
28253209 AATTACCAAAACACCCTTGTTTGTAA
1 AATTACCAAAATACCCTAGTTTGTAA
* *
28253235 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACC-CTAGTTTGTAA
* * * *
28253262 AATTATCGAAATACCCTCAATTTATAA
1 AATTACCAAAATACCCT-AGTTTGTAA
**
28253289 AATTACCAAAATACCCCT-GATTTACAA
1 AATTACCAAAATA-CCCTAG-TTTGTAA
* *
28253316 AATTA-CAGAAATACCCTTAATTTGTAG
1 AATTACCA-AAATACCC-TAGTTTGTAA
* *
28253343 ATTTACCAAAACACCCT
1 AATTACCAAAATACCCT
28253360 TGTAGGATGA
Statistics
Matches: 98, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
26 22 0.22
27 70 0.71
28 6 0.06
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (26 bp):
AATTACCAAAATACCCTAGTTTGTAA
Found at i:28253302 original size:54 final size:54
Alignment explanation
Indices: 28253232--28253353 Score: 147
Period size: 54 Copynumber: 2.3 Consensus size: 54
28253222 CCCTTGTTTG
* ***
28253232 TAAAATTACCAAAATACCACTGGTTTGTGAAATTATC-GAAATACCCTCAATTTA
1 TAAAATTACCAAAATACCACTGATTTACAAAATTA-CAGAAATACCCTCAATTTA
* * *
28253286 TAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAAATACCCTTAATTTG
1 TAAAATTACCAAAATACCACTGATTTACAAAATTACAGAAATACCCTCAATTTA
* *
28253340 TAGATTTACCAAAA
1 TAAAATTACCAAAA
28253354 CACCCTTGTA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 1 0.02
54 57 0.98
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.30
Consensus pattern (54 bp):
TAAAATTACCAAAATACCACTGATTTACAAAATTACAGAAATACCCTCAATTTA
Found at i:28253422 original size:27 final size:27
Alignment explanation
Indices: 28253379--28253452 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
28253369 AAATGACTAA
*
28253379 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
28253406 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
28253433 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
28253453 TGATGAATAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:28254232 original size:19 final size:20
Alignment explanation
Indices: 28254163--28254248 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
28254153 GATATGATAT
*
28254163 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
*
28254183 ACATGATATGTATAAAATGC
1 ACATGATATGTATGAAATGC
28254203 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
28254223 ACAT-ATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
28254242 ACATGAT
1 ACATGAT
28254249 GTATTCATAA
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
19 19 0.31
20 40 0.66
21 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:28254242 original size:39 final size:40
Alignment explanation
Indices: 28254163--28254248 Score: 131
Period size: 39 Copynumber: 2.2 Consensus size: 40
28254153 GATATGATAT
*
28254163 ACATGATTGATATGATATGCACATGATATGTATAAAATGC
1 ACATGATTGATATGAAATGCACATGATATGTATAAAATGC
*
28254203 ACATGATATG-TATGAAATGCACAT-ATATGTATGAAATGC
1 ACATGAT-TGATATGAAATGCACATGATATGTATAAAATGC
28254242 ACATGAT
1 ACATGAT
28254249 GTATTCATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
39 21 0.49
40 20 0.47
41 2 0.05
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (40 bp):
ACATGATTGATATGAAATGCACATGATATGTATAAAATGC
Found at i:28254395 original size:25 final size:26
Alignment explanation
Indices: 28254298--28254445 Score: 257
Period size: 26 Copynumber: 5.8 Consensus size: 26
28254288 GAGGAAGTGC
28254298 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
28254324 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
28254350 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
28254376 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
28254401 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
28254426 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28254446 ATTAAAAGAG
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
25 58 0.49
26 60 0.51
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.25
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:28254650 original size:42 final size:42
Alignment explanation
Indices: 28254591--28254684 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 42
28254581 TAGTCTCCCC
* * *
28254591 AAATGGGCTTGCATACATTCATT-AGTATTTCATGTCATATTG
1 AAATGGGCTTGCATACATCCATTGA-CATTACATGTCATATTG
*
28254633 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTCATATTG
28254675 AAATGGGCTT
1 AAATGGGCTT
28254685 ATGGGCCATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
42 46 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTCATATTG
Found at i:28254741 original size:31 final size:31
Alignment explanation
Indices: 28254706--28254815 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
28254696 CGTTTACAGT
*
28254706 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
28254737 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
28254768 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
28254799 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
28254816 AACCGTTAGA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:28263577 original size:27 final size:27
Alignment explanation
Indices: 28263547--28263696 Score: 122
Period size: 27 Copynumber: 5.5 Consensus size: 27
28263537 ATATTGAGCC
* *
28263547 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCCATATAATCAACT
* ** *
28263574 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCCATATAATCAACT
* * * *
28263601 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCCATATAATCA-ACT
* ** *
28263629 CGCACACTTAGTGCCGTATGGTCAATT
1 CGCACACTTAGTGCCATATAATCAACT
* **
28263656 CGCACACTTAGTG-CATCATATTCATTT
1 CGCACACTTAGTGCCAT-ATAATCAACT
28263683 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28263697 AACAAAGTAG
Statistics
Matches: 98, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
26 2 0.02
27 75 0.77
28 21 0.21
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCCATATAATCAACT
Found at i:28263697 original size:27 final size:27
Alignment explanation
Indices: 28263568--28263723 Score: 108
Period size: 27 Copynumber: 5.7 Consensus size: 27
28263558 TGCTATATAA
* * * *
28263568 TCAACTCGCACATTTAGTGCCACGTA-A
1 TCAATTCGCACACTTAGTG-CACATATG
*
28263595 TCAAATCGCACACTTAGTGCTACATA-G
1 TCAATTCGCACACTTAGTGC-ACATATG
* * *
28263622 TTAGACTCGCACACTTAGTGC-CGTATGG
1 TCA-ATTCGCACACTTAGTGCACATAT-G
28263650 TCAATTCGCACACTTAGTGCATCATAT-
1 TCAATTCGCACACTTAGTGCA-CATATG
* *
28263677 TCATTTCGCACACTTAGTGCAACA-AAG
1 TCAATTCGCACACTTAGTGC-ACATATG
*
28263704 T-AGAATCGCACACTTAGTGC
1 TCA-ATTCGCACACTTAGTGC
28263724 TGTACAATTT
Statistics
Matches: 106, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
26 6 0.06
27 76 0.72
28 20 0.19
29 4 0.04
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (27 bp):
TCAATTCGCACACTTAGTGCACATATG
Found at i:28266752 original size:77 final size:77
Alignment explanation
Indices: 28266661--28266813 Score: 243
Period size: 77 Copynumber: 2.0 Consensus size: 77
28266651 ATTTACAGGG
* * * *
28266661 GAGAGATTTTGATGATGAAATTTTCTTAAAAAAGGGAGAGCTGTCATAGCCTATTTTTTAGTAGT
1 GAGAGATTTCGATGATGAAATTTTCTTAAAAAAGGGAGAGCTGTAATAACCCATTTTTTAGTAGT
28266726 GTCGAAAATGGA
66 GTCGAAAATGGA
* * *
28266738 GAGAGGTTTCGATGATGGAATTTTCTTAAAAATGGGAGAGCTGTAATAACCCATTTTTTAGTAGT
1 GAGAGATTTCGATGATGAAATTTTCTTAAAAAAGGGAGAGCTGTAATAACCCATTTTTTAGTAGT
28266803 GTCGAAAATGG
66 GTCGAAAATGG
28266814 TGGTTTCAGA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (77 bp):
GAGAGATTTCGATGATGAAATTTTCTTAAAAAAGGGAGAGCTGTAATAACCCATTTTTTAGTAGT
GTCGAAAATGGA
Found at i:28268134 original size:45 final size:45
Alignment explanation
Indices: 28268085--28268172 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
28268075 TCATATCGAA
* * * *
28268085 AATGAGTAAGACAATATCTGGAAGACGTTATGGCATCACGATTTC
1 AATGAATAAGACAAGAGCTGAAAGACGTTATGGCATCACGATTTC
* *
28268130 AATGAATAAGACTAGAGCTGAAAGATGTTATGGCATCACGATT
1 AATGAATAAGACAAGAGCTGAAAGACGTTATGGCATCACGATT
28268173 CTAACAAGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (45 bp):
AATGAATAAGACAAGAGCTGAAAGACGTTATGGCATCACGATTTC
Done.