Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold136
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: 1085849
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.31
Warning! 50585 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:327129 original size:27 final size:27
Alignment explanation
Indices: 327084--327364 Score: 274
Period size: 27 Copynumber: 10.4 Consensus size: 27
327074 CCTAGCAGTC
* * *
327084 ATTTTACCCTAACGGGGGTATTACAGTA
1 ATTTTACCC-ATCGGGGGTATTTCGGTA
* *
327112 ATTTTACCTATCGGGGGTATTTTGGTA
1 ATTTTACCCATCGGGGGTATTTCGGTA
* ** * *
327139 ATTTTACCTATTAGAGGTATTTCAGTA
1 ATTTTACCCATCGGGGGTATTTCGGTA
** *
327166 ATTTTACCCATCAAGGTTATTTCGGTA
1 ATTTTACCCATCGGGGGTATTTCGGTA
** * *
327193 ATTTTACCCATTAGAGGTATTTCGATA
1 ATTTTACCCATCGGGGGTATTTCGGTA
* ** *
327220 ATTTTACCTATTAGGGGTATTTTGGTA
1 ATTTTACCCATCGGGGGTATTTCGGTA
* *
327247 ATTTTACCCATTGGGGGTATTTTGGTA
1 ATTTTACCCATCGGGGGTATTTCGGTA
* *
327274 ATATTACCCATCGAGGGTATTTCGGTA
1 ATTTTACCCATCGGGGGTATTTCGGTA
* *
327301 ATTTTACCCATTGGGGGTATTTCGATA
1 ATTTTACCCATCGGGGGTATTTCGGTA
* * *
327328 ATTTTATCCATCGAGGGTATTTCGATA
1 ATTTTACCCATCGGGGGTATTTCGGTA
*
327355 ATTATACCCA
1 ATTTTACCCA
327365 CGAATCGCAC
Statistics
Matches: 213, Mismatches: 40, Indels: 1
0.84 0.16 0.00
Matches are distributed among these distances:
27 205 0.96
28 8 0.04
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.41
Consensus pattern (27 bp):
ATTTTACCCATCGGGGGTATTTCGGTA
Found at i:330929 original size:233 final size:233
Alignment explanation
Indices: 330522--330978 Score: 842
Period size: 233 Copynumber: 2.0 Consensus size: 233
330512 CATACCCGTG
*
330522 TCTTAGGCCACGTGGGCATTCGAAGTAGAGCACACGGCCGTGTCCCAGCCTGTGTCCAAATTTGG
1 TCTTAGGCCACGTAGGCATTCGAAGTAGAGCACACGGCCGTGTCCCAGCCTGTGTCCAAATTTGG
*
330587 GAGCATTCTTACTTAGGTCACACGGCCAAGCCACACGCCCGTGTGCTAGGCTATGTGAGAAATTC
66 GAGCATTCTTACTTAGGTCACACGGCCAAGCCACACGCCCGTATGCTAGGCTATGTGAGAAATTC
330652 TGAGCATTCTGTTTTGAATTTTAAAGATGCAGGGGACACACGGCCAAACCACACACCTATGTGCT
131 TGAGCATTCTGTTTTGAATTTTAAAGATGCAGGGGACACACGGCCAAACCACACACCTATGTGCT
330717 AGGCTGTGTGTCACACACAGCTGAGACACATGCTCGTA
196 AGGCTGTGTGTCACACACAGCTGAGACACATGCTCGTA
**
330755 TCTTAGGCCGTGTAGGCATTCGAAGTAGAGCACACGGCCGTGTCCCAGCCTGTGTCCAAATTTGG
1 TCTTAGGCCACGTAGGCATTCGAAGTAGAGCACACGGCCGTGTCCCAGCCTGTGTCCAAATTTGG
* *
330820 GAGCATTCTTACTTAGGTCACACGGCCAAGCCACATGCCCGTATGCTAGGCTGTGTGAGAAATTC
66 GAGCATTCTTACTTAGGTCACACGGCCAAGCCACACGCCCGTATGCTAGGCTATGTGAGAAATTC
*
330885 TGAGCATTCTGTTTTGAATTTTAAAGATGCAGGGGACACACGGCCAAACCACACATCTATGTGCT
131 TGAGCATTCTGTTTTGAATTTTAAAGATGCAGGGGACACACGGCCAAACCACACACCTATGTGCT
*
330950 AGGCTGTGTGTCACACACGGCTGAGACAC
196 AGGCTGTGTGTCACACACAGCTGAGACAC
330979 GCGCCCGTGT
Statistics
Matches: 216, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
233 216 1.00
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.24
Consensus pattern (233 bp):
TCTTAGGCCACGTAGGCATTCGAAGTAGAGCACACGGCCGTGTCCCAGCCTGTGTCCAAATTTGG
GAGCATTCTTACTTAGGTCACACGGCCAAGCCACACGCCCGTATGCTAGGCTATGTGAGAAATTC
TGAGCATTCTGTTTTGAATTTTAAAGATGCAGGGGACACACGGCCAAACCACACACCTATGTGCT
AGGCTGTGTGTCACACACAGCTGAGACACATGCTCGTA
Found at i:333256 original size:32 final size:32
Alignment explanation
Indices: 333195--333412 Score: 199
Period size: 32 Copynumber: 6.8 Consensus size: 32
333185 GCCATAAATA
* * *
333195 CAGTAATATGATTGGCACAAAGCCATCAGTAG
1 CAGTGATATGATCGACACAAAGCCATCAGTAG
* * *
333227 CAGTGATGTGATCGACACACAGCCATCAGTAA
1 CAGTGATATGATCGACACAAAGCCATCAGTAG
* *
333259 CGGTAATATGATCGAC-CTAAAGCCATCAGTAG
1 CAGTGATATGATCGACAC-AAAGCCATCAGTAG
* * *
333291 AAGTGATATGATCGGCACACAA-CCATCAGTAA
1 CAGTGATATGATCGACACA-AAGCCATCAGTAG
* * *
333323 CAGTAATATGACCAACACAAAGCCATCAGTAG
1 CAGTGATATGATCGACACAAAGCCATCAGTAG
* * * *
333355 CAGTGGTATGACCTG-TACAAAGCCATCAGTAA
1 CAGTGATATGATC-GACACAAAGCCATCAGTAG
* * *
333387 CGGTAATATGATCTACACAAAGCCAT
1 CAGTGATATGATCGACACAAAGCCAT
333413 TAGCAACATC
Statistics
Matches: 147, Mismatches: 33, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
31 3 0.02
32 141 0.96
33 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (32 bp):
CAGTGATATGATCGACACAAAGCCATCAGTAG
Found at i:333284 original size:64 final size:64
Alignment explanation
Indices: 333210--333412 Score: 268
Period size: 64 Copynumber: 3.2 Consensus size: 64
333200 ATATGATTGG
* *
333210 CACAAAGCCATCAGTAGCAGTGATGTGATCGACACACAGCCATCAGTAACGGTAATATGATCGA
1 CACAAAGCCATCAGTAGCAGTGATATGATCGACACACAGCCATCAGTAACGGTAATATGATCAA
* * * * *
333274 C-CTAAAGCCATCAGTAGAAGTGATATGATCGGCACACAACCATCAGTAACAGTAATATGACCAA
1 CAC-AAAGCCATCAGTAGCAGTGATATGATCGACACACAGCCATCAGTAACGGTAATATGATCAA
* * *
333338 CACAAAGCCATCAGTAGCAGTGGTATGACCTGTACA-A-AGCCATCAGTAACGGTAATATGATCT
1 CACAAAGCCATCAGTAGCAGTGATATGATC-G-ACACACAGCCATCAGTAACGGTAATATGATCA
333401 A
64 A
333402 CACAAAGCCAT
1 CACAAAGCCAT
333413 TAGCAACATC
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
63 1 0.01
64 114 0.95
65 3 0.03
66 2 0.02
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (64 bp):
CACAAAGCCATCAGTAGCAGTGATATGATCGACACACAGCCATCAGTAACGGTAATATGATCAA
Found at i:333396 original size:96 final size:96
Alignment explanation
Indices: 333196--333412 Score: 226
Period size: 96 Copynumber: 2.3 Consensus size: 96
333186 CCATAAATAC
* * * * * * * *
333196 AGTAATATGATTGGCACAAAGCCATCAGTAGCAGTGATGTGATCGACACACAGCCATCAGTAACG
1 AGTAATATGATCGGCACAAAGCCATCAGTAACAGTAATATGACCAACACAAAGCCATCAGTAACA
*
333261 GTAATATGATCGACCTAAAGCCATCAGTAGA
66 GTAATATGACCGACCTAAAGCCATCAGTAGA
* *
333292 AGTGATATGATCGGCACACAA-CCATCAGTAACAGTAATATGACCAACACAAAGCCATCAGTAGC
1 AGTAATATGATCGGCACA-AAGCCATCAGTAACAGTAATATGACCAACACAAAGCCATCAGTAAC
**
333356 AGTGGTATGACCTGTA-C-AAAGCCATCAGTA-A
65 AGTAATATGACC-G-ACCTAAAGCCATCAGTAGA
* **
333387 CGGTAATATGATCTACACAAAGCCAT
1 -AGTAATATGATCGGCACAAAGCCAT
333413 TAGCAACATC
Statistics
Matches: 99, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
95 3 0.03
96 91 0.92
97 4 0.04
98 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (96 bp):
AGTAATATGATCGGCACAAAGCCATCAGTAACAGTAATATGACCAACACAAAGCCATCAGTAACA
GTAATATGACCGACCTAAAGCCATCAGTAGA
Found at i:333733 original size:27 final size:27
Alignment explanation
Indices: 333703--333807 Score: 88
Period size: 27 Copynumber: 3.9 Consensus size: 27
333693 TTACCCTCTG
* *
333703 GGGGCATTATT-GTCATTTTACCTTATA
1 GGGGCATT-TTGGTCATTTTACCCTAGA
*
333730 GGGGTATTTTGGTCATTTTACCCTAGA
1 GGGGCATTTTGGTCATTTTACCCTAGA
* * * *
333757 GGGGTATCTCGGTCATTTTACCCTTCGA
1 GGGGCATTTTGGTCATTTTACCC-TAGA
* * *
333785 -GGGTAATTCGGTCATTTTACCCT
1 GGGGCATTTTGGTCATTTTACCCT
333808 TCGAGGGTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 3 0.04
27 62 0.91
28 3 0.04
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTTACCCTAGA
Found at i:333808 original size:27 final size:27
Alignment explanation
Indices: 333731--333990 Score: 272
Period size: 27 Copynumber: 9.6 Consensus size: 27
333721 TACCTTATAG
* * *
333731 GGGTATTTTGGTCATTTTACCC-TAGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
* *
333757 GGGGTATCTCGGTCATTTTACCCTTCGA
1 -GGGTATTTCGGTAATTTTACCCTTCGA
* *
333785 GGGTAATTCGGTCATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
*** *
333812 GGGTATTTTAATAATTTTACCTTTCG-
1 GGGTATTTCGGTAATTTTACCCTTCGA
* * *
333838 GGGATATTTCGATAATTTTACTCTTTGA
1 GGG-TATTTCGGTAATTTTACCCTTCGA
*
333866 GGGTATTTCGATAATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
* *
333893 AGGTATTTCGGTAATTTTACCCTTTGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
** *
333920 GGGTATTTCAATAATTGTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
** *
333947 GGGTATTTTAGTAATTTTACCCTTTGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
*
333974 GGGTATTTCAGTAATTT
1 GGGTATTTCGGTAATTT
333991 GCCCACGAAT
Statistics
Matches: 199, Mismatches: 31, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
26 3 0.02
27 190 0.95
28 6 0.03
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACCCTTCGA
Found at i:333816 original size:54 final size:54
Alignment explanation
Indices: 333731--333990 Score: 308
Period size: 54 Copynumber: 4.8 Consensus size: 54
333721 TACCTTATAG
* * * * ** *
333731 GGGTATTTTGGTCATTTTACCC-TAGAGGGGTATCTCGGTCATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTTGA-GGGTATTTCAATAATTTTACCCTTCGA
* * * * *
333785 GGGTAATTCGGTCATTTTACCCTTCGAGGGTATTTTAATAATTTTACCTTTCG-
1 GGGTATTTCGGTAATTTTACCCTTTGAGGGTATTTCAATAATTTTACCCTTCGA
* * *
333838 GGGATATTTCGATAATTTTACTCTTTGAGGGTATTTCGATAATTTTACCCTTCGA
1 GGG-TATTTCGGTAATTTTACCCTTTGAGGGTATTTCAATAATTTTACCCTTCGA
* *
333893 AGGTATTTCGGTAATTTTACCCTTTGAGGGTATTTCAATAATTGTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTTGAGGGTATTTCAATAATTTTACCCTTCGA
** *
333947 GGGTATTTTAGTAATTTTACCCTTTGAGGGTATTTCAGTAATTT
1 GGGTATTTCGGTAATTTTACCCTTTGAGGGTATTTCAATAATTT
333991 GCCCACGAAT
Statistics
Matches: 176, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
53 3 0.02
54 168 0.95
55 5 0.03
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (54 bp):
GGGTATTTCGGTAATTTTACCCTTTGAGGGTATTTCAATAATTTTACCCTTCGA
Found at i:337007 original size:21 final size:21
Alignment explanation
Indices: 336982--337035 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
336972 TGTGGGGTAA
* *
336982 ACATGCCCATGTGGAGGAGGC
1 ACATGCCCGTGTGGAGGAAGC
* *
337003 ACATGCTCGTGT-GAGTAAGC
1 ACATGCCCGTGTGGAGGAAGC
337023 ACATGCCCGTGTG
1 ACATGCCCGTGTG
337036 AGAGAACGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.20
Consensus pattern (21 bp):
ACATGCCCGTGTGGAGGAAGC
Found at i:337099 original size:21 final size:20
Alignment explanation
Indices: 337050--337101 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
337040 AACGTACACG
*
337050 GGCCGTGTGACTAAGGCGCA
1 GGCCGTGTGACTAAGGCACA
*
337070 CGCCTGTGTGACCTAAGG-ACA
1 GGCC-GTGTGA-CTAAGGCACA
337091 TGGCCGTGTGA
1 -GGCCGTGTGA
337102 ACAGGCCGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.12
21 14 0.54
22 9 0.35
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.19
Consensus pattern (20 bp):
GGCCGTGTGACTAAGGCACA
Found at i:345748 original size:15 final size:15
Alignment explanation
Indices: 345730--345767 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
345720 AGACTCTATT
*
345730 TTAATTATATTAGGA
1 TTAATTATATTAAGA
345745 TTAATTAATATTAAGA
1 TTAATT-ATATTAAGA
345761 -TAATTAT
1 TTAATTAT
345768 TAATGATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 11 0.52
16 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (15 bp):
TTAATTATATTAAGA
Found at i:353009 original size:42 final size:42
Alignment explanation
Indices: 352950--353035 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
352940 TATGGAGCAT
352950 TACCGGAAGTTAACAACATTCAACGAACATTTATTCAACCAA
1 TACCGGAAGTTAACAACATTCAACGAACATTTATTCAACCAA
352992 TACCGGAAGTTAACAACATTCAACGAACATTTATTCAACCAA
1 TACCGGAAGTTAACAACATTCAACGAACATTTATTCAACCAA
353034 TA
1 TA
353036 TGAAACATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.24
Consensus pattern (42 bp):
TACCGGAAGTTAACAACATTCAACGAACATTTATTCAACCAA
Found at i:365911 original size:27 final size:27
Alignment explanation
Indices: 365871--365926 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
365861 ACCCTCTAAA
** *
365871 GGGTCAAGTACTAAGTTTTTTTCCAAT
1 GGGTCAAGTACTAAGGCTTTCTCCAAT
*
365898 GGGTCAAGTTCTAAGGCTTTCTCCAAT
1 GGGTCAAGTACTAAGGCTTTCTCCAAT
365925 GG
1 GG
365927 CTCTTCTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (27 bp):
GGGTCAAGTACTAAGGCTTTCTCCAAT
Found at i:371665 original size:20 final size:22
Alignment explanation
Indices: 371620--371676 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
371610 GTGAAGGTGG
*
371620 CACACGCCCGTGTGAATAGGAA
1 CACACTCCCGTGTGAATAGGAA
*
371642 CACA-T-CCGTGTGAA-AGGCAG
1 CACACTCCCGTGTGAATAGG-AA
371662 CACACTCCCGTGTGA
1 CACACTCCCGTGTGA
371677 CCCAAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 3 0.10
20 14 0.47
21 1 0.03
22 12 0.40
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (22 bp):
CACACTCCCGTGTGAATAGGAA
Found at i:374074 original size:30 final size:30
Alignment explanation
Indices: 373970--374079 Score: 98
Period size: 30 Copynumber: 3.7 Consensus size: 30
373960 TGTCGACGAT
* **
373970 CATCG-ACTAATGAAAAGGGATAGTTTCAAC
1 CATCGAACT-ATGAAAAGGGATGGTGACAAC
* * * *
374000 TATCGAACTATGAAAATGAATGGTGACAAA
1 CATCGAACTATGAAAAGGGATGGTGACAAC
* * *
374030 CAT-TAACAATGAAAAGGGATGGTGACGAC
1 CATCGAACTATGAAAAGGGATGGTGACAAC
*
374059 CATCGAACTATGAAAACGGAT
1 CATCGAACTATGAAAAGGGAT
374080 AGCTTCGGCT
Statistics
Matches: 61, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
29 23 0.38
30 35 0.57
31 3 0.05
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.21
Consensus pattern (30 bp):
CATCGAACTATGAAAAGGGATGGTGACAAC
Found at i:376763 original size:18 final size:18
Alignment explanation
Indices: 376727--376764 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
376717 CCCAAAACCC
*
376727 ACATGCCCATGTGGACCT
1 ACATGCCCATATGGACCT
376745 ACATGCCCAATATGG-CCT
1 ACATGCCC-ATATGGACCT
376763 AC
1 AC
376765 CGCTTGTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.21
Consensus pattern (18 bp):
ACATGCCCATATGGACCT
Found at i:380821 original size:43 final size:43
Alignment explanation
Indices: 380731--380835 Score: 106
Period size: 43 Copynumber: 2.4 Consensus size: 43
380721 TGTGTTTTCG
* * * * * *
380731 TGTAAGACTACATCTGGGATATTGGCATCGAATTATGTTTTCG
1 TGTAAGACCACGTCTGGGATAGTGGCATCGAATTATGATTACA
* *
380774 TGTAAGTCC-CTGTCTGGGATAGTGGCATCG-ATCTGTGATTACA
1 TGTAAGACCAC-GTCTGGGATAGTGGCATCGAAT-TATGATTACA
380817 TGTAAGACCACGTCTGGGA
1 TGTAAGACCACGTCTGGGA
380836 CGTTGGCATT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
42 3 0.06
43 46 0.92
44 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGATAGTGGCATCGAATTATGATTACA
Found at i:383536 original size:27 final size:27
Alignment explanation
Indices: 383506--383562 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
383496 AACAAAGTTG
*
383506 CCAGTAATAGT-ATATGTGGCCA-AGCCA
1 CCAGTAACAGTGAT-TGTGG-CAGAGCCA
383533 CCAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGTGATTGTGGCAGAGCCA
383560 CCA
1 CCA
383563 ATACAATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 23 0.85
28 2 0.07
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCAGAGCCA
Found at i:383676 original size:24 final size:24
Alignment explanation
Indices: 383637--383738 Score: 98
Period size: 24 Copynumber: 4.3 Consensus size: 24
383627 TGCTTAGAAC
383637 CAGTCATACAAATCACAGACAAAT
1 CAGTCATACAAATCACAGACAAAT
* * *
383661 CCGTCATACCATTCACAGACAAAT
1 CAGTCATACAAATCACAGACAAAT
**
383685 CAGTCATTTAAATCACAGAC-AAT
1 CAGTCATACAAATCACAGACAAAT
* ** * *
383708 GAGTCATTTACATCACGGACAAAT
1 CAGTCATACAAATCACAGACAAAT
*
383732 CAATCAT
1 CAGTCAT
383739 TTACACTCGA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 20 0.31
24 44 0.69
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (24 bp):
CAGTCATACAAATCACAGACAAAT
Found at i:383743 original size:24 final size:24
Alignment explanation
Indices: 383648--383743 Score: 108
Period size: 24 Copynumber: 4.0 Consensus size: 24
383638 AGTCATACAA
*
383648 ATCACAGACAAATCCGTCA--TACC
1 ATCACAGACAAATCAGTCATTTA-C
*
383671 ATTCACAGACAAATCAGTCATTTAA
1 A-TCACAGACAAATCAGTCATTTAC
*
383696 ATCACAGAC-AATGAGTCATTTAC
1 ATCACAGACAAATCAGTCATTTAC
* *
383719 ATCACGGACAAATCAATCATTTAC
1 ATCACAGACAAATCAGTCATTTAC
383743 A
1 A
383744 CTCGATGGGC
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
23 21 0.34
24 38 0.61
25 1 0.02
26 2 0.03
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.24
Consensus pattern (24 bp):
ATCACAGACAAATCAGTCATTTAC
Found at i:383817 original size:27 final size:26
Alignment explanation
Indices: 383784--383959 Score: 140
Period size: 27 Copynumber: 6.6 Consensus size: 26
383774 AGGGGCATTA
383784 CGGTCATTTTACCTTATAGAGGTATTT
1 CGGTCATTTTACCTTAT-GAGGTATTT
** * * *
383811 CTTTCATTTAACCCTATGGGGGTATTAT
1 CGGTCATTTTACCTTAT-GAGGTATT-T
* *
383839 -AGTCATTTTTTCC-TATGAGAGTATTT
1 CGGTCA-TTTTACCTTATGAG-GTATTT
*
383865 CGGTCATTTTACCTTATGGGGTATTT
1 CGGTCATTTTACCTTATGAGGTATTT
* * * *
383891 TGCTCATTCTACCCTATGAGGGTATTT
1 CGGTCATTTTACCTTATGA-GGTATTT
*
383918 CGGTCATTCTACCTTATGAGGGTATTT
1 CGGTCATTTTACCTTATGA-GGTATTT
* *
383945 CGATAATTTTACCTT
1 CGGTCATTTTACCTT
383960 TCAAGGGTAT
Statistics
Matches: 118, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
26 29 0.25
27 83 0.70
28 6 0.05
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.44
Consensus pattern (26 bp):
CGGTCATTTTACCTTATGAGGTATTT
Found at i:383924 original size:80 final size:81
Alignment explanation
Indices: 383784--383959 Score: 200
Period size: 80 Copynumber: 2.2 Consensus size: 81
383774 AGGGGCATTA
* * *
383784 CGGTCATTTTACCTTATAGAGGTATTTCTTTCATTTAACCCTATGGGGGTATTATAGTCATTTTT
1 CGGTCATTTTACCTTATAGAGGTATTTCTCTCATTTAACCCTATGAGGGTATTATAGTCA-TTCT
*
383849 TCC-TATGAGAGTATTT
65 ACCTTATGAGAGTATTT
* *
383865 CGGTCATTTTACCTTAT-GGGGTATTT-TGCTCATTCT-ACCCTATGAGGGTATT-TCGGTCATT
1 CGGTCATTTTACCTTATAGAGGTATTTCT-CTCATT-TAACCCTATGAGGGTATTAT-AGTCATT
*
383926 CTACCTTATGAGGGTATTT
63 CTACCTTATGAGAGTATTT
* *
383945 CGATAATTTTACCTT
1 CGGTCATTTTACCTT
383960 TCAAGGGTAT
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
79 7 0.09
80 57 0.70
81 18 0.22
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.44
Consensus pattern (81 bp):
CGGTCATTTTACCTTATAGAGGTATTTCTCTCATTTAACCCTATGAGGGTATTATAGTCATTCTA
CCTTATGAGAGTATTT
Found at i:383975 original size:54 final size:53
Alignment explanation
Indices: 383850--383979 Score: 145
Period size: 53 Copynumber: 2.4 Consensus size: 53
383840 GTCATTTTTT
* * * * * *
383850 CCTATGAGAGTATTTCGGTCATTTTACCTTATGGGGTATTTTGCTCATTCTAC
1 CCTATAAGGGTATTTCGGTCATTCTACCTTATGGGGTATTTCGATAATTCTAC
* *
383903 CCTATGAGGGTATTTCGGTCATTCTACCTTATGAGGGTATTTCGATAATTTTA-
1 CCTATAAGGGTATTTCGGTCATTCTACCTTATG-GGGTATTTCGATAATTCTAC
* *
383956 CCTTTCAAGGGTATATCGGTCATT
1 CCTAT-AAGGGTATTTCGGTCATT
383980 TAACAGCCTT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
53 35 0.53
54 31 0.47
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (53 bp):
CCTATAAGGGTATTTCGGTCATTCTACCTTATGGGGTATTTCGATAATTCTAC
Found at i:383980 original size:27 final size:27
Alignment explanation
Indices: 383784--383980 Score: 134
Period size: 27 Copynumber: 7.3 Consensus size: 27
383774 AGGGGCATTA
383784 CGGTCATTTTACCTTAT-AGAGGTATTT
1 CGGTCATTTTACCTTATAAG-GGTATTT
** * * **
383811 CTTTCATTTAACCCTATGGGGGTATTAT
1 CGGTCATTTTACCTTATAAGGGTATT-T
* * * *
383839 -AGTCATTTTTTCC-TATGAGAGTATTT
1 CGGTCA-TTTTACCTTATAAGGGTATTT
*
383865 CGGTCATTTTACCTTAT-GGGGTATTT
1 CGGTCATTTTACCTTATAAGGGTATTT
* * * * *
383891 TGCTCATTCTACCCTATGAGGGTATTT
1 CGGTCATTTTACCTTATAAGGGTATTT
* *
383918 CGGTCATTCTACCTTATGAGGGTATTT
1 CGGTCATTTTACCTTATAAGGGTATTT
* * *
383945 CGATAATTTTACCTT-TCAAGGGTATAT
1 CGGTCATTTTACCTTAT-AAGGGTATTT
383972 CGGTCATTT
1 CGGTCATTT
383981 AACAGCCTTT
Statistics
Matches: 133, Mismatches: 30, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
26 28 0.21
27 98 0.74
28 7 0.05
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.44
Consensus pattern (27 bp):
CGGTCATTTTACCTTATAAGGGTATTT
Found at i:392769 original size:44 final size:44
Alignment explanation
Indices: 392718--392894 Score: 354
Period size: 44 Copynumber: 4.0 Consensus size: 44
392708 ATAGATTTTT
392718 ACGAAGAAGGAGAACTTCTAGATTATTATCCCCATTAGAAGACA
1 ACGAAGAAGGAGAACTTCTAGATTATTATCCCCATTAGAAGACA
392762 ACGAAGAAGGAGAACTTCTAGATTATTATCCCCATTAGAAGACA
1 ACGAAGAAGGAGAACTTCTAGATTATTATCCCCATTAGAAGACA
392806 ACGAAGAAGGAGAACTTCTAGATTATTATCCCCATTAGAAGACA
1 ACGAAGAAGGAGAACTTCTAGATTATTATCCCCATTAGAAGACA
392850 ACGAAGAAGGAGAACTTCTAGATTATTATCCCCATTAGAAGACA
1 ACGAAGAAGGAGAACTTCTAGATTATTATCCCCATTAGAAGACA
392894 A
1 A
392895 AAGAATATTT
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 133 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (44 bp):
ACGAAGAAGGAGAACTTCTAGATTATTATCCCCATTAGAAGACA
Found at i:393989 original size:42 final size:42
Alignment explanation
Indices: 393934--394020 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
393924 CAATGTCATT
* * * * *
393934 TGTGTTAGGGAATAAATTTTGTTTCAAATTTG-TATTAGTGTG
1 TGTGTCAGGGAATAAATTCTCTTACAAATTTGCTA-TAATGTG
393976 TGTGTCAGGGAATAAATTCTCTTACAAATTTGCTATAATGTG
1 TGTGTCAGGGAATAAATTCTCTTACAAATTTGCTATAATGTG
394018 TGT
1 TGT
394021 CAAGGAATAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 37 0.95
43 2 0.05
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.44
Consensus pattern (42 bp):
TGTGTCAGGGAATAAATTCTCTTACAAATTTGCTATAATGTG
Found at i:413692 original size:29 final size:29
Alignment explanation
Indices: 413650--413838 Score: 170
Period size: 29 Copynumber: 6.4 Consensus size: 29
413640 TCATTGACAA
413650 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
*
413679 ATGAAAAGGGATAGC-TCTGGCTATCGATT
1 ATGAAAAGGGATAGCTTC-GGCTATCGAAT
* * *
413708 ATGAAAAGGGATAGTTTCGACTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
* * *
413737 ATGAAAAGGGAT-GGTGAT-GACCATCGAACT
1 ATGAAAAGGGATAGCT--TCGGCTATCGAA-T
* *
413767 ATGAAAAGGGATGGCTTCGGCTATCAAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
** **
413796 CATGAAAACAGATAGC-TCTGGCTATAAAATT
1 -ATGAAAAGGGATAGCTTC-GGCTATCGAA-T
413827 ATGAAAAGGGAT
1 ATGAAAAGGGAT
413839 GGTGACGACC
Statistics
Matches: 134, Mismatches: 16, Indels: 19
0.79 0.09 0.11
Matches are distributed among these distances:
28 4 0.03
29 73 0.54
30 54 0.40
31 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.25
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAAT
Found at i:413720 original size:58 final size:58
Alignment explanation
Indices: 413650--413838 Score: 209
Period size: 58 Copynumber: 3.2 Consensus size: 58
413640 TCATTGACAA
413650 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTCTGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTCTGGCTATCGATT
* * * * * * * *
413708 ATGAAAAGGGATAGTTTCGACTATCGATTATGAAAAGGGAT-GGTGATGACCATCGAACT
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCT-CTGGCTATCG-ATT
* * ** **
413767 ATGAAAAGGGATGGCTTCGGCTATCAAATCATGAAAACAGATAGCTCTGGCTATAAAATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT-ATGAAAAGGGATAGCTCTGGCTAT-CGATT
413827 ATGAAAAGGGAT
1 ATGAAAAGGGAT
413839 GGTGACGACC
Statistics
Matches: 104, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
57 2 0.02
58 45 0.43
59 26 0.25
60 29 0.28
61 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.25
Consensus pattern (58 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTCTGGCTATCGATT
Found at i:413772 original size:30 final size:29
Alignment explanation
Indices: 413707--413911 Score: 128
Period size: 29 Copynumber: 7.0 Consensus size: 29
413697 GGCTATCGAT
* ** * * *
413707 TATGAAAAGGGATAGTTTCGACTATCGAT
1 TATGAAAAGGGATGGTGACGACCATCAAC
*
413736 TATGAAAAGGGATGGTGATGACCATCGAAC
1 TATGAAAAGGGATGGTGACGACCATC-AAC
* * * *
413766 TATGAAAAGGGATGGCT-TCGGCTATCAAA
1 TATGAAAAGGGATGG-TGACGACCATCAAC
** * * * * *
413795 TCATGAAAACAGATAGCT--CTGGCTATAAAAT
1 T-ATGAAAAGGGAT-GGTGAC-GACCAT-CAAC
413826 TATGAAAAGGGATGGTGACGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
* * *
413855 AATGAAAAGGGTTGGTGACGATCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
* *
413884 AATGAAAAGGGTTGGTGACGACCATCAA
1 TATGAAAAGGGATGGTGACGACCATCAA
413912 AACGTGAAAA
Statistics
Matches: 140, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
29 82 0.59
30 52 0.37
31 6 0.04
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (29 bp):
TATGAAAAGGGATGGTGACGACCATCAAC
Found at i:413911 original size:118 final size:118
Alignment explanation
Indices: 413679--413960 Score: 291
Period size: 118 Copynumber: 2.4 Consensus size: 118
413669 GCTATCGAAT
** * ** * * **
413679 ATGAAAAGGGATAGCTCTGGCTATCGATTATGAAAAGGGATAGTTTCGACTATCGATTATGAAAA
1 ATGAAAAGGGATAGCTCTGGCTATAAATTATGAAAAGGGATGGTGACGACCATCAACAATGAAAA
* * * * * *
413744 GGGATGGTGATGACCATCGAACTATGAAAAGGGATGGCTTCGGCTATCAAATC
66 GGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCTACGACCATCAAAAC
**
413797 ATGAAAACAGATAGCTCTGGCTATAAAATTATGAAAAGGGATGGTGACGACCATCAACAATGAAA
1 ATGAAAAGGGATAGCTCTGGCTAT-AAATTATGAAAAGGGATGGTGACGACCATCAACAATGAAA
* * *
413862 AGGGTTGGTGACGATCATC-AACAATGAAAAGGGTTGG-TGACGACCATCAAAAC
65 AGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCT-ACGACCATCAAAAC
* * * *
413915 GTGAAAAGGGGTTGCT-TCGGCTATCGAATTATGAAAAGGGATGGTG
1 ATGAAAAGGGATAGCTCT-GGCTAT-AAATTATGAAAAGGGATGGTG
413961 TCAACCATTG
Statistics
Matches: 134, Mismatches: 27, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
117 2 0.01
118 85 0.63
119 47 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (118 bp):
ATGAAAAGGGATAGCTCTGGCTATAAATTATGAAAAGGGATGGTGACGACCATCAACAATGAAAA
GGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCTACGACCATCAAAAC
Found at i:413922 original size:30 final size:29
Alignment explanation
Indices: 413827--413924 Score: 153
Period size: 29 Copynumber: 3.3 Consensus size: 29
413817 CTATAAAATT
*
413827 ATGAAAAGGGATGGTGACGACCATCAACA
1 ATGAAAAGGGTTGGTGACGACCATCAACA
*
413856 ATGAAAAGGGTTGGTGACGATCATCAACA
1 ATGAAAAGGGTTGGTGACGACCATCAACA
413885 ATGAAAAGGGTTGGTGACGACCATCAA-A
1 ATGAAAAGGGTTGGTGACGACCATCAACA
413913 ACGTGAAAAGGG
1 A--TGAAAAGGG
413925 GTTGCTTCGG
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
28 2 0.03
29 53 0.83
30 9 0.14
ACGTcount: A:0.40, C:0.14, G:0.30, T:0.16
Consensus pattern (29 bp):
ATGAAAAGGGTTGGTGACGACCATCAACA
Found at i:416065 original size:52 final size:52
Alignment explanation
Indices: 415988--416184 Score: 385
Period size: 52 Copynumber: 3.8 Consensus size: 52
415978 CCACATAAGC
*
415988 AATGAATGCTTAGTAAGCTCGTATAACCATAAGCATAATATTACATTTCCAT
1 AATGAATGCTTAGTAAGCTCATATAACCATAAGCATAATATTACATTTCCAT
416040 AATGAATGCTTAGTAAGCTCATATAACCATAAGCATAATATTACATTTCCAT
1 AATGAATGCTTAGTAAGCTCATATAACCATAAGCATAATATTACATTTCCAT
416092 AATGAATGCTTAGTAAGCTCATATAACCATAAGCATAATATTACATTTCCAT
1 AATGAATGCTTAGTAAGCTCATATAACCATAAGCATAATATTACATTTCCAT
416144 AATGAATGCTTAGTAAGCTCATATAACCATAAGCATAATAT
1 AATGAATGCTTAGTAAGCTCATATAACCATAAGCATAATAT
416185 AAACCTATAT
Statistics
Matches: 144, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 144 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.32
Consensus pattern (52 bp):
AATGAATGCTTAGTAAGCTCATATAACCATAAGCATAATATTACATTTCCAT
Found at i:430772 original size:17 final size:16
Alignment explanation
Indices: 430750--430781 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
430740 TCATATATTA
430750 TTGGAAGCTCGATCAGT
1 TTGGAAGCTC-ATCAGT
430767 TTGGAAGCTCATCAG
1 TTGGAAGCTCATCAG
430782 AGATCTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (16 bp):
TTGGAAGCTCATCAGT
Found at i:434164 original size:2 final size:2
Alignment explanation
Indices: 434157--434186 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
434147 CTCATATTTA
434157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
434187 CACAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:442152 original size:40 final size:40
Alignment explanation
Indices: 442097--442348 Score: 253
Period size: 40 Copynumber: 6.3 Consensus size: 40
442087 TGAAAAAATC
*
442097 CCCCTGTTTACACATCAGTGCCCCTGATTGTACTTTGGTA
1 CCCCTGTTTGCACATCAGTGCCCCTGATTGTACTTTGGTA
* *
442137 CCCCTGTTTGCACATCAGT-ACCCT-ATTTCTACTTTGGTA
1 CCCCTGTTTGCACATCAGTGCCCCTGA-TTGTACTTTGGTA
* * *
442176 CCCCTATTTGCACATCAATGCCCCTAATTGTACTTTGGTA
1 CCCCTGTTTGCACATCAGTGCCCCTGATTGTACTTTGGTA
* * *
442216 CACATGTTTGCACATCAGTGCCCCTGCTTGTACTTTGGTA
1 CCCCTGTTTGCACATCAGTGCCCCTGATTGTACTTTGGTA
** * *
442256 CCCCTGAATGCACATCTA-TGCCCCT-ATTTGCACTTTGGTG
1 CCCCTGTTTGCACATC-AGTGCCCCTGA-TTGTACTTTGGTA
* ** * * *
442296 CCCCTGATCACACATTC-GTGCTCCTGATTGCACTTTGGTT
1 CCCCTGTTTGCACA-TCAGTGCCCCTGATTGTACTTTGGTA
442336 CCCCTGTTATGCA
1 CCCCTGTT-TGCA
442349 TATATGATGC
Statistics
Matches: 175, Mismatches: 28, Indels: 17
0.80 0.13 0.08
Matches are distributed among these distances:
38 1 0.01
39 33 0.19
40 134 0.77
41 7 0.04
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (40 bp):
CCCCTGTTTGCACATCAGTGCCCCTGATTGTACTTTGGTA
Found at i:442228 original size:79 final size:80
Alignment explanation
Indices: 442097--442294 Score: 247
Period size: 79 Copynumber: 2.5 Consensus size: 80
442087 TGAAAAAATC
* * * * * *
442097 CCCCTGTTTACACATCAGTGCCCCTGATTGTACTTTGGTACCCCTGTTTGCACATCAGT-ACCCT
1 CCCCTATTTGCACATCAATGCCCCTAATTGTACTTTGGTACACATGTTTGCACATCAGTGACCCT
*
442161 ATTTCTACTTTGGTA
66 ACTTCTACTTTGGTA
*
442176 CCCCTATTTGCACATCAATGCCCCTAATTGTACTTTGGTACACATGTTTGCACATCAGTGCCCCT
1 CCCCTATTTGCACATCAATGCCCCTAATTGTACTTTGGTACACATGTTTGCACATCAGTGACCCT
* *
442241 GCTTGTACTTTGGTA
66 ACTTCTACTTTGGTA
* * * *
442256 CCCCTGA-ATGCACATCTATGCCCCTATTTGCACTTTGGT
1 CCCCT-ATTTGCACATCAATGCCCCTAATTGTACTTTGGT
442295 GCCCCTGATC
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
79 53 0.51
80 49 0.48
81 1 0.01
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (80 bp):
CCCCTATTTGCACATCAATGCCCCTAATTGTACTTTGGTACACATGTTTGCACATCAGTGACCCT
ACTTCTACTTTGGTA
Found at i:442341 original size:20 final size:20
Alignment explanation
Indices: 442114--442341 Score: 79
Period size: 20 Copynumber: 11.4 Consensus size: 20
442104 TTACACATCA
*
442114 GTGCCCCTGATTGTACTTTG
1 GTGCCCCTGATTGCACTTTG
* * * **
442134 GTACCCCTGTTTGCACATCA
1 GTGCCCCTGATTGCACTTTG
* *
442154 GT-ACCCT-ATTTCTACTTTG
1 GTGCCCCTGATTGC-ACTTTG
* * **
442173 GTACCCCT-ATTTGCACATCA
1 GTGCCCCTGA-TTGCACTTTG
* * *
442193 ATGCCCCTAATTGTACTTTG
1 GTGCCCCTGATTGCACTTTG
* * * * * **
442213 GTACACATGTTTGCACATCA
1 GTGCCCCTGATTGCACTTTG
* *
442233 GTGCCCCTGCTTGTACTTTG
1 GTGCCCCTGATTGCACTTTG
* * *
442253 GTACCCCTGAATGCACATCT-
1 GTGCCCCTGATTGCAC-TTTG
*
442273 ATGCCCCT-ATTTGCACTTTG
1 GTGCCCCTGA-TTGCACTTTG
** * *
442293 GTGCCCCTGATCACACATTC
1 GTGCCCCTGATTGCACTTTG
*
442313 GTGCTCCTGATTGCACTTTG
1 GTGCCCCTGATTGCACTTTG
*
442333 GTTCCCCTG
1 GTGCCCCTG
442342 TTATGCATAT
Statistics
Matches: 138, Mismatches: 62, Indels: 16
0.64 0.29 0.07
Matches are distributed among these distances:
18 3 0.02
19 12 0.09
20 116 0.84
21 7 0.05
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.35
Consensus pattern (20 bp):
GTGCCCCTGATTGCACTTTG
Found at i:443859 original size:7 final size:7
Alignment explanation
Indices: 443843--443876 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
443833 CATGCTACAC
443843 TAATTCCA
1 TAATT-CA
443851 TAATTCA
1 TAATTCA
443858 TAATTCA
1 TAATTCA
443865 TAATTCA
1 TAATTCA
443872 TAATT
1 TAATT
443877 TAGAACCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.81
8 5 0.19
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATTCA
Found at i:447241 original size:39 final size:39
Alignment explanation
Indices: 447182--447331 Score: 228
Period size: 39 Copynumber: 3.8 Consensus size: 39
447172 ACCAATACAA
* * * *
447182 AGCCTGCTGGGCACAGAGCCCGAATAAACATCGGCACAC
1 AGCCTGCTAGGCACATAGCCCGAATAATCACCGGCACAC
* *
447221 AGCCTGCTAGGCACATAGCCCGAAGAATCACCGACACAC
1 AGCCTGCTAGGCACATAGCCCGAATAATCACCGGCACAC
*
447260 AGCCTGCTAGGCACATAGCCCGAATAATCACCGGCACAT
1 AGCCTGCTAGGCACATAGCCCGAATAATCACCGGCACAC
*
447299 AGCCTGCTAGGCACATAGCCTGAATAATCACCG
1 AGCCTGCTAGGCACATAGCCCGAATAATCACCG
447332 CATTTCTACG
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 101 1.00
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.13
Consensus pattern (39 bp):
AGCCTGCTAGGCACATAGCCCGAATAATCACCGGCACAC
Found at i:447817 original size:29 final size:29
Alignment explanation
Indices: 447774--447912 Score: 140
Period size: 29 Copynumber: 4.8 Consensus size: 29
447764 TATAAGTGAG
447774 CCTTTGTGGCGATCTCTGTTAAATGGAAA
1 CCTTTGTGGCGATCTCTGTTAAATGGAAA
* * * *
447803 TCTTTGTAGTGATCTCTGTTAAATGGAAG
1 CCTTTGTGGCGATCTCTGTTAAATGGAAA
* *
447832 CCTTTGTGGCGATCTCTAGTTTAA-GGAAG
1 CCTTTGTGGCGATCTCT-GTTAAATGGAAA
* *
447861 CCTTTGTGGCGGTCCCTGTT--ATGGGAAA
1 CCTTTGTGGCGATCTCTGTTAAAT-GGAAA
* *
447889 GCCTTTGTGGTGATTTCTGTTAAA
1 -CCTTTGTGGCGATCTCTGTTAAA
447913 AGGATGTGTT
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
26 1 0.01
28 7 0.08
29 75 0.84
30 5 0.06
31 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (29 bp):
CCTTTGTGGCGATCTCTGTTAAATGGAAA
Found at i:447925 original size:87 final size:85
Alignment explanation
Indices: 447772--447938 Score: 201
Period size: 87 Copynumber: 1.9 Consensus size: 85
447762 TATATAAGTG
* * *
447772 AGCCTTTGTGGCGATCTCTGTTAAATGGAAATCTTTGTAGTGATCTCTGTTAAATGGAAGCCTTT
1 AGCCTTTGTGGCGATCCCTGTT-AATGGAAACCTTTGTAGTGATCTCTGTTAAAAGGAAGCCTTT
447837 GTGGCGATCTCTAGTTTAAGGA
65 GTGGCGATCT-TAGTTTAAGGA
* * * * **
447859 AGCCTTTGTGGCGGTCCCTGTT-ATGGGAAAGCCTTTGTGGTGATTTCTGTTAAAAGGATGTGTT
1 AGCCTTTGTGGCGATCCCTGTTAAT-GGAAA-CCTTTGTAGTGATCTCTGTTAAAAGGAAGCCTT
*
447923 TGTGGCTATCTTAGTT
64 TGTGGCGATCTTAGTT
447939 AAATGAATGT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
85 2 0.03
86 10 0.15
87 56 0.82
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.38
Consensus pattern (85 bp):
AGCCTTTGTGGCGATCCCTGTTAATGGAAACCTTTGTAGTGATCTCTGTTAAAAGGAAGCCTTTG
TGGCGATCTTAGTTTAAGGA
Found at i:447939 original size:29 final size:29
Alignment explanation
Indices: 447907--448072 Score: 160
Period size: 29 Copynumber: 5.8 Consensus size: 29
447897 GGTGATTTCT
* * *
447907 GTTAAAAGGATGTGTTTGTGGCTATCTTA
1 GTTAAATGAATGTCTTTGTGGCTATCTTA
*
447936 GTTAAATGAATGTCTTTGTCGCTATCTTA
1 GTTAAATGAATGTCTTTGTGGCTATCTTA
* *
447965 GTTAAATGAATGTCTTTGTCGCTATCTTT
1 GTTAAATGAATGTCTTTGTGGCTATCTTA
*
447994 GTTAAATGAATGCCTTTGTGG-TCATCTCT-
1 GTTAAATGAATGTCTTTGTGGCT-ATCT-TA
* * * *
448023 GTTAAAAGGATGTCTTTGTGCCCATCTCTA
1 GTTAAATGAATGTCTTTGTGGCTATCT-TA
* *
448053 -TTAAAGGAATG-CCTTGTGGC
1 GTTAAATGAATGTCTTTGTGGC
448073 AAACTTTGTT
Statistics
Matches: 117, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
28 8 0.07
29 108 0.92
30 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (29 bp):
GTTAAATGAATGTCTTTGTGGCTATCTTA
Found at i:447953 original size:58 final size:57
Alignment explanation
Indices: 447889--448071 Score: 192
Period size: 58 Copynumber: 3.2 Consensus size: 57
447879 TTATGGGAAA
*
447889 GCCTTTGTGGTGATTTCTGTTAAAAGGATGTGTTTGTGGCTATCTTAGTTAAATGAAT
1 GCCTTTGTGGT-ATTTCTGTTAAAAGGATGTCTTTGTGGCTATCTTAGTTAAATGAAT
* * * * * * *
447947 GTCTTTGTCGCTATCTT-AGTTAAATGAATGTCTTTGTCGCTATCTTTGTTAAATGAAT
1 GCCTTTGT-GGTAT-TTCTGTTAAAAGGATGTCTTTGTGGCTATCTTAGTTAAATGAAT
* * * *
448005 GCCTTTGTGGTCATCTCTGTTAAAAGGATGTCTTTGTGCCCATCTCTA-TTAAAGGAAT
1 GCCTTTGTGGT-ATTTCTGTTAAAAGGATGTCTTTGTGGCTATCT-TAGTTAAATGAAT
448063 GCC-TTGTGG
1 GCCTTTGTGG
448072 CAAACTTTGT
Statistics
Matches: 101, Mismatches: 19, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
57 9 0.09
58 87 0.86
59 5 0.05
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.42
Consensus pattern (57 bp):
GCCTTTGTGGTATTTCTGTTAAAAGGATGTCTTTGTGGCTATCTTAGTTAAATGAAT
Found at i:448057 original size:87 final size:86
Alignment explanation
Indices: 447936--448095 Score: 189
Period size: 87 Copynumber: 1.8 Consensus size: 86
447926 GGCTATCTTA
* * * * * * *
447936 GTTAAATGAATGTCTTTGTCGCTATCTTAGTTAAATGAATGTCTTTGTCGCTATCTTTGTTAAAT
1 GTTAAAAGAATGTCTTTGTCGCCATCTTAGTTAAAGGAATG-CCTTGTCGCAAACTTTGTTAAAA
*
448001 GAATGCCTTTGTGGTCATCTCT
65 GAACGCCTTTGTGGTCATCTCT
* *
448023 GTTAAAAGGATGTCTTTGT-GCCCATCTCTA-TTAAAGGAATGCCTTGTGGCAAACTTTGTTAAA
1 GTTAAAAGAATGTCTTTGTCG-CCATCT-TAGTTAAAGGAATGCCTTGTCGCAAACTTTGTTAAA
448086 AGAACGCCTT
64 AGAACGCCTT
448096 CATGGAAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
86 27 0.44
87 32 0.52
88 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.39
Consensus pattern (86 bp):
GTTAAAAGAATGTCTTTGTCGCCATCTTAGTTAAAGGAATGCCTTGTCGCAAACTTTGTTAAAAG
AACGCCTTTGTGGTCATCTCT
Found at i:451194 original size:13 final size:13
Alignment explanation
Indices: 451176--451203 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
451166 TATAATTTTA
451176 TTATTTTTATAAT
1 TTATTTTTATAAT
451189 TTATTTTTATAAT
1 TTATTTTTATAAT
451202 TT
1 TT
451204 TTAAACGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTTTATAAT
Found at i:453388 original size:18 final size:18
Alignment explanation
Indices: 453341--453389 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
453331 GTAGTGATTC
*
453341 AATTCGATTAATTCGGTT
1 AATTCGGTTAATTCGGTT
* *
453359 AATTAGGATAATTCGGTT
1 AATTCGGTTAATTCGGTT
453377 AATTCGGTTAATT
1 AATTCGGTTAATT
453390 TTTAACCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (18 bp):
AATTCGGTTAATTCGGTT
Found at i:454213 original size:16 final size:16
Alignment explanation
Indices: 454188--454235 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 16
454178 GGTGTTCTTC
454188 TTTC-CTCTTTTTCAT
1 TTTCTCTCTTTTTCAT
*
454203 TTTGTCTCTTTTT--T
1 TTTCTCTCTTTTTCAT
*
454217 TTTCTTTCTTTTTCAT
1 TTTCTCTCTTTTTCAT
454233 TTT
1 TTT
454236 TTAGCATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 12 0.44
15 3 0.11
16 12 0.44
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTCTCTCTTTTTCAT
Found at i:455287 original size:28 final size:27
Alignment explanation
Indices: 455256--455326 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
455246 AAAATATACG
*
455256 TATACTTATATACATTTTATAATACATA
1 TATAC-TATATATATTTTATAATACATA
* **
455284 TATA-TACATATATTTTATAATTTATA
1 TATACTATATATATTTTATAATACATA
455310 TATACATATATATATTT
1 TATAC-TATATATATTT
455327 GTTATATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 22 0.61
28 14 0.39
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (27 bp):
TATACTATATATATTTTATAATACATA
Found at i:459199 original size:24 final size:24
Alignment explanation
Indices: 459157--459208 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
459147 TAATCAAATC
** *
459157 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
459181 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
459205 AAAT
1 AAAT
459209 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:460067 original size:196 final size:195
Alignment explanation
Indices: 459733--460318 Score: 958
Period size: 196 Copynumber: 3.0 Consensus size: 195
459723 CTCAATCTCA
* * *
459733 TCATCTGGTTGTGGAGACAAAGCCGATGAAAGTCTAAAATAGGCTGCTAAAGGAGTACTAACAGG
1 TCATCTGATTGTGGAGACAAAGCCGATGAAAGTCTGAAATGGGCTGCTAAAGGAGTACTAACAGG
* * *
459798 CTTAGCA-TCCTGCATATTGAACATGCAAAGAACTTTCTCAATGTACCCGTTCTGACTTGGGTAC
66 CTTAGCACT-CTGCATATTGAAC-TGCAAAGAACTTTCTCAATGTACCCCTTCTAACTTAGGTAC
* * *
459862 AATTTACTTGCTTTTCTATCTCTGAGAATCTTCATACCAAATATCTTCTTTACTGGTCCCAAATC
129 AATTTACTTGCTTTTCTATCTCTGAGAATCTCCATACCAAGTATCTTATTTACTGGTCCCAAATC
459927 TT
194 TT
*
459929 TCATCTGATTGTGGAGACAAAGCTGATGAAAGTCTGAAATGGGCTGCTAAAGGAGTACTAACAGG
1 TCATCTGATTGTGGAGACAAAGCCGATGAAAGTCTGAAATGGGCTGCTAAAGGAGTACTAACAGG
459994 CTTAGCACTCTGCATATTGAATCTGCAAAGAACTTTCTCAATGTACCCCTTCTAACTTAGGTACA
66 CTTAGCACTCTGCATATTGAA-CTGCAAAGAACTTTCTCAATGTACCCCTTCTAACTTAGGTACA
* * *
460059 ATTTACTTGCTTTTCTATCTCTAAGAATCTCCATACCAAGTATCTTAGTTGCTGGTCCCAAATCT
130 ATTTACTTGCTTTTCTATCTCTGAGAATCTCCATACCAAGTATCTTATTTACTGGTCCCAAATCT
460124 T
195 T
* * *
460125 TCATCTGATCGTGGAGACAAAGCCGATGAAAGTCTGAAATGGGCTGCTAAGGGAATACTAACAGG
1 TCATCTGATTGTGGAGACAAAGCCGATGAAAGTCTGAAATGGGCTGCTAAAGGAGTACTAACAGG
* *
460190 CTTAGCACTCTGCATATTGAACCTGTAAAGAACTTTCTCAATGTACCCCTTCTTACTTAGGTACA
66 CTTAGCACTCTGCATATTGAA-CTGCAAAGAACTTTCTCAATGTACCCCTTCTAACTTAGGTACA
*
460255 ATTTACTTGCTTTTGTATCTCTGAGAATCTCCATACCAAGTATCTTATTTACTGGTCCCAAATC
130 ATTTACTTGCTTTTCTATCTCTGAGAATCTCCATACCAAGTATCTTATTTACTGGTCCCAAATC
460319 ATGAAAAGTC
Statistics
Matches: 364, Mismatches: 24, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
196 362 0.99
197 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (195 bp):
TCATCTGATTGTGGAGACAAAGCCGATGAAAGTCTGAAATGGGCTGCTAAAGGAGTACTAACAGG
CTTAGCACTCTGCATATTGAACTGCAAAGAACTTTCTCAATGTACCCCTTCTAACTTAGGTACAA
TTTACTTGCTTTTCTATCTCTGAGAATCTCCATACCAAGTATCTTATTTACTGGTCCCAAATCTT
Found at i:463515 original size:24 final size:24
Alignment explanation
Indices: 463499--463550 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
463489 AATCAAAGTC
463499 AAATATATTATGTTAATAAATGCT
1 AAATATATTATGTTAATAAATGCT
** *
463523 AAATATATTATACTAATAAATACT
1 AAATATATTATGTTAATAAATGCT
463547 AAAT
1 AAAT
463551 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATGTTAATAAATGCT
Found at i:464255 original size:17 final size:17
Alignment explanation
Indices: 464235--464298 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
464225 TATTCAAATA
*
464235 ATATTACTTGAATAGTT
1 ATATTACTTTAATAGTT
*
464252 ATATCTA-TTTAAGAG--
1 ATAT-TACTTTAATAGTT
464267 ATATTACTTTAATAGTT
1 ATATTACTTTAATAGTT
464284 ATATCTA-TTTAATAG
1 ATAT-TACTTTAATAG
464299 ATTTAATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 2 0.05
15 11 0.28
17 22 0.56
18 4 0.10
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (17 bp):
ATATTACTTTAATAGTT
Found at i:464260 original size:32 final size:32
Alignment explanation
Indices: 464219--464292 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
464209 AACAAAGAAA
*
464219 TATAACTATTCAA-ATAATATTACTTGAATAGT
1 TATATCTATTCAAGA-AATATTACTTGAATAGT
* * *
464251 TATATCTATTTAAGAGATATTACTTTAATAGT
1 TATATCTATTCAAGAAATATTACTTGAATAGT
464283 TATATCTATT
1 TATATCTATT
464293 TAATAGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 36 0.97
33 1 0.03
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (32 bp):
TATATCTATTCAAGAAATATTACTTGAATAGT
Found at i:464293 original size:32 final size:32
Alignment explanation
Indices: 464235--464300 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
464225 TATTCAAATA
464235 ATATTACTTGAATAGTTATATCTATTTAAGAG
1 ATATTACTTGAATAGTTATATCTATTTAAGAG
* *
464267 ATATTACTTTAATAGTTATATCTATTTAATAG
1 ATATTACTTGAATAGTTATATCTATTTAAGAG
464299 AT
1 AT
464301 TTAATTATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (32 bp):
ATATTACTTGAATAGTTATATCTATTTAAGAG
Found at i:464483 original size:40 final size:41
Alignment explanation
Indices: 464407--464488 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 41
464397 TTCTACAAAG
* * *
464407 ATAAAGAATTATTGTAGAGCTTTTTTTTAAACAAAATTGATT
1 ATAAAGAATTATTATAGAGC-TTTTTTAAAAAAAAATTGATT
464449 ATAAAGAATTATTATAGAG-TTTTTTAAAAAAAAATTGATT
1 ATAAAGAATTATTATAGAGCTTTTTTAAAAAAAAATTGATT
464489 TTCTTGTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 19 0.51
42 18 0.49
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (41 bp):
ATAAAGAATTATTATAGAGCTTTTTTAAAAAAAAATTGATT
Found at i:471734 original size:21 final size:20
Alignment explanation
Indices: 471685--471734 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
471675 TAATTTGCAT
*
471685 ATTTTGGTAGTTTAACTACA
1 ATTTTGGTAGTATAACTACA
* *
471705 TTTTCTGGTAGTATATCTACAA
1 ATTT-TGGTAGTATAACTAC-A
471727 ATTTTGGT
1 ATTTTGGT
471735 GGCTTGACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (20 bp):
ATTTTGGTAGTATAACTACA
Found at i:476396 original size:97 final size:96
Alignment explanation
Indices: 476265--476529 Score: 458
Period size: 97 Copynumber: 2.7 Consensus size: 96
476255 AAATAAGGGT
* * *
476265 TTAGGGTTTAGGGTTTCTTAATTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
476330 TTTATGGTTTTTAAGGAAAAAAATCAAATAAA
66 TTTATGGTTTTTAAGG-AAAAAATCAAATAAA
476362 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAGT
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAA-TTTTAAAAAATTAGATTAGGGTTTAGT
*
476427 GTTTAAGGTTTTTAAGGAAAAAATCAAATAAA
65 GTTTATGGTTTTTAAGGAAAAAATCAAATAAA
* *
476459 TTAGGATTTAGGATTACTTGAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
476524 TTTATG
66 TTTATG
476530 AAATTTAATA
Statistics
Matches: 160, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
96 33 0.21
97 84 0.52
98 43 0.27
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.41
Consensus pattern (96 bp):
TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
TTTATGGTTTTTAAGGAAAAAATCAAATAAA
Found at i:476886 original size:40 final size:41
Alignment explanation
Indices: 476833--476910 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
476823 GCGCTTTGTC
476833 CACGTGGACACAAAGCGCGCCCTCAAGAAAGCGTTTTCTGTG
1 CACGTGGA-ACAAAGCGCGCCCTCAAGAAAGCGTTTTCTGTG
** **
476875 CACGTGG-ACAAAGCGCTTCCTTGAGAAAGCGTTTTC
1 CACGTGGAACAAAGCGCGCCCTCAAGAAAGCGTTTTC
476911 CTGCTTTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 25 0.78
42 7 0.22
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.22
Consensus pattern (41 bp):
CACGTGGAACAAAGCGCGCCCTCAAGAAAGCGTTTTCTGTG
Found at i:480938 original size:28 final size:28
Alignment explanation
Indices: 480906--480961 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
480896 TGCAATAAAA
* * *
480906 TGGATCGAAGCGACAAGAGGCAGTGGAG
1 TGGATCAAAGCAACAAGACGCAGTGGAG
*
480934 TGGATCAAAGCAACAAGACTCAGTGGAG
1 TGGATCAAAGCAACAAGACGCAGTGGAG
480962 GGGAAGGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.36, T:0.12
Consensus pattern (28 bp):
TGGATCAAAGCAACAAGACGCAGTGGAG
Found at i:486031 original size:12 final size:12
Alignment explanation
Indices: 486014--486039 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
486004 AGGTATCTAT
486014 GGATTAGTAAGG
1 GGATTAGTAAGG
486026 GGATTAGTAAGG
1 GGATTAGTAAGG
486038 GG
1 GG
486040 GTTACGCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.46, T:0.23
Consensus pattern (12 bp):
GGATTAGTAAGG
Found at i:487678 original size:12 final size:12
Alignment explanation
Indices: 487661--487702 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
487651 AAGTTGGAGC
487661 AATGCAAGATCA
1 AATGCAAGATCA
* **
487673 AATGCAAAAGGA
1 AATGCAAGATCA
487685 AATGCAAGATCA
1 AATGCAAGATCA
487697 AATGCA
1 AATGCA
487703 TGAACGACTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.52, C:0.14, G:0.19, T:0.14
Consensus pattern (12 bp):
AATGCAAGATCA
Found at i:505028 original size:132 final size:132
Alignment explanation
Indices: 504791--505553 Score: 1213
Period size: 132 Copynumber: 5.8 Consensus size: 132
504781 GATAACCAGT
* *
504791 GATCTTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAG
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAG
* *
504856 TGGGAAGCAGATTTGAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTG
66 TGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTG
504921 TA
131 TA
* *
504923 GATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCGAATCTTATCTTTCTAAGATAG
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAG
* * *
504988 TGGGAAGCAGATTTAAGCCATCAAGCCTTGTCTCCCTGAGCAGCTGCGGAGAAGGTTGAATATTG
66 TGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTG
505053 TA
131 TA
*
505055 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCTAAGATAG
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAG
* ** * * *
505120 TGGGAAGCAGATTTAAGCCACCAAGCCTTATCTTTCTGAGTAGCTGCGGAGAAGGTTGAAGATTA
66 TGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTG
505185 TA
131 TA
*
505187 GATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAG
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAG
* * * *
505252 TGGGAAGCATATTTAAGCCACCAAGCCTTGTCT-CCTGATCAGTAGCGGAGAAGGTTGAAGATTA
66 TGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTG
505316 TA
131 TA
*
505318 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAG
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAG
* * *
505383 TGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCTTGAGCAGCAGCGGAGTAGGTTGAAGATTG
66 TGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTG
505448 TA
131 TA
* * * * *
505450 GATCTTATCTCCTTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATTTTATCTTTCCAAGATGG
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAG
* ** *
505515 TGGGAAGCAAATTTAAGCCACCAAATCTTATCTCCCTGA
66 TGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGA
505554 AGTTGCAGTG
Statistics
Matches: 587, Mismatches: 43, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
131 122 0.21
132 465 0.79
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (132 bp):
GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAG
TGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTG
TA
Found at i:505367 original size:44 final size:44
Alignment explanation
Indices: 504792--505503 Score: 207
Period size: 44 Copynumber: 16.2 Consensus size: 44
504782 ATAACCAGTG
* * **
504792 ATCTTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGACGGTGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * **
504836 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTG-AGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGA-TTGAAGACGGCAA
** * * * * * ** * *
504880 GCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * *
504924 ATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
** * * **
504968 ATCTTATCTTTCTAAG-A-TAGTGGGAAGCAGATTTAAGCCATCAA
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * * ** * *
505012 GCCTTGTCTCCCTGAGCAGCT-GCGGAGAAGGTTGAATATTGTAG
1 ATCTTATCTCCCTAAGCAG-TAGTGGAGCAGATTGAAGACGGCAA
* *
505056 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
** * * **
505100 ATCTTATCTTTCTAAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** ** * * * * * **** *
505144 GCCTTATCTTTCTGAGTAGCT-GCGGAGAAGGTTGAAGATTATAG
1 ATCTTATCTCCCTAAGCAG-TAGTGGAGCAGATTGAAGACGGCAA
* * *
505188 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * * **
505232 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCATATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * * **** *
505276 GCCTTGTCT-CCTGATCAGTAGCGGAGAAGGTTGAAGATTATAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
*
505319 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * **
505363 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
* * * * * * * * ** * *
505407 ACCTTGTCTCCTTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * *
505451 ATCTTATCTCCTTAAGCAGTAGCGGAGCAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
*
505495 ATTTTATCT
1 ATCTTATCT
505504 TTCCAAGATG
Statistics
Matches: 449, Mismatches: 186, Indels: 66
0.64 0.27 0.09
Matches are distributed among these distances:
42 22 0.05
43 41 0.09
44 351 0.78
45 26 0.06
46 7 0.02
47 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
Found at i:505522 original size:395 final size:396
Alignment explanation
Indices: 504791--505547 Score: 1264
Period size: 395 Copynumber: 1.9 Consensus size: 396
504781 GATAACCAGT
* *
504791 GATCTTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAG
1 GATCTTATCTCCCTAAGCAATAGTGGAACAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAG
* * *
504856 TGGGAAGCAGATTTGAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTG
66 TGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTA
* *
504921 TAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCGAATCTTATCTTTCTAAGAT
131 TAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGAT
* * * *
504986 AGTGGGAAGCAGATTTAAGCCATCAAGCCTTGTCTCCCTGAGCAGCTGCGGAGAAGGTTGAATAT
196 AGTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGAT
* * *
505051 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCTAAG
261 TGTAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAG
* *
505116 ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTATCTTTCTGAGTAGCTGCGGAGAAGGTTGAAG
326 ATAGTGGGAAGCAAATTTAAGCCACCAAACCTTATCTTTCTGAGTAGCTGCGGAGAAGGTTGAAG
505181 ATTATA
391 ATTATA
*
505187 GATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAG
1 GATCTTATCTCCCTAAGCAATAGTGGAACAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAG
* * *
505252 TGGGAAGCATATTTAAGCCACCAAGCCTTGTCT-CCTGATCAGTAGCGGAGAAGGTTGAAGATTA
66 TGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTA
*
505316 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGAT
131 TAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGAT
* *
505381 AGTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCTTGAGCAGCAGCGGAGTAGGTTGAAGAT
196 AGTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGAT
* *
505446 TGTAGATCTTATCTCCTTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATTTTATCTTTCCAAG
261 TGTAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAG
* *
505511 ATGGTGGGAAGCAAATTTAAGCCACCAAATCTTATCT
326 ATAGTGGGAAGCAAATTTAAGCCACCAAACCTTATCT
505548 CCCTGAAGTT
Statistics
Matches: 334, Mismatches: 27, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
395 241 0.72
396 93 0.28
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (396 bp):
GATCTTATCTCCCTAAGCAATAGTGGAACAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAG
TGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTA
TAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGAT
AGTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGAT
TGTAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAG
ATAGTGGGAAGCAAATTTAAGCCACCAAACCTTATCTTTCTGAGTAGCTGCGGAGAAGGTTGAAG
ATTATA
Found at i:512495 original size:28 final size:28
Alignment explanation
Indices: 512463--512518 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
512453 TGCAATAAAA
* * *
512463 TGGATCGAAGCGACAAGAGGCAGTGGAG
1 TGGATCAAAGCAACAAGACGCAGTGGAG
*
512491 TGGATCAAAGCAACAAGACTCAGTGGAG
1 TGGATCAAAGCAACAAGACGCAGTGGAG
512519 GGGAAGGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.36, T:0.12
Consensus pattern (28 bp):
TGGATCAAAGCAACAAGACGCAGTGGAG
Found at i:514652 original size:21 final size:22
Alignment explanation
Indices: 514627--514671 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
514617 TATTTATTTA
514627 TTATTTCATATACTTGTTT-TT
1 TTATTTCATATACTTGTTTCTT
* * *
514648 TTATTTTATGTATTTGTTTCTT
1 TTATTTCATATACTTGTTTCTT
514670 TT
1 TT
514672 TGATTATTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.71
Consensus pattern (22 bp):
TTATTTCATATACTTGTTTCTT
Found at i:521328 original size:22 final size:24
Alignment explanation
Indices: 521303--521353 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
521293 CTATAAACCT
* *
521303 TAACCTAATAAAA-CAAAAA-TCC
1 TAACCTAAAAAAATAAAAAAGTCC
521325 TAACCCTAAAAAAATAAAAAAGTCC
1 TAA-CCTAAAAAAATAAAAAAGTCC
521350 TAAC
1 TAAC
521354 ATTGGAGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 3 0.12
23 9 0.38
24 6 0.25
25 6 0.25
ACGTcount: A:0.59, C:0.22, G:0.02, T:0.18
Consensus pattern (24 bp):
TAACCTAAAAAAATAAAAAAGTCC
Found at i:521881 original size:29 final size:30
Alignment explanation
Indices: 521838--521895 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
521828 AAATTGAATC
521838 AAATAAAAATTTCATGTATAAAATTGTACA
1 AAATAAAAATTTCATGTATAAAATTGTACA
* * * *
521868 AAATCAAAA-TTCATTTATGACATTGTAC
1 AAATAAAAATTTCATGTATAAAATTGTAC
521896 TACATTGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (30 bp):
AAATAAAAATTTCATGTATAAAATTGTACA
Found at i:529528 original size:19 final size:20
Alignment explanation
Indices: 529486--529537 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
529476 CCGCAGTTTA
* **
529486 AAAATTTTAATATATTTTTG
1 AAAATTTTAATATATTCTCC
529506 AAAATTTTAAT-TATTCTCC
1 AAAATTTTAATATATTCTCC
*
529525 AAAAATTTAATAT
1 AAAATTTTAATAT
529538 TAAGATTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (20 bp):
AAAATTTTAATATATTCTCC
Found at i:531475 original size:57 final size:57
Alignment explanation
Indices: 531384--531501 Score: 218
Period size: 57 Copynumber: 2.1 Consensus size: 57
531374 TTAAATCCTA
* *
531384 AGTAAACATTCATGTTTGTAGGTAAACTACGACATCTTTTTCATGCTTAATCAACCC
1 AGTAAACATTCATGTTTGTAGGTAAACTAAGACATCTTTTTCATGCATAATCAACCC
531441 AGTAAACATTCATGTTTGTAGGTAAACTAAGACATCTTTTTCATGCATAATCAACCC
1 AGTAAACATTCATGTTTGTAGGTAAACTAAGACATCTTTTTCATGCATAATCAACCC
531498 AGTA
1 AGTA
531502 CTATGCAGGG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (57 bp):
AGTAAACATTCATGTTTGTAGGTAAACTAAGACATCTTTTTCATGCATAATCAACCC
Found at i:540793 original size:3 final size:3
Alignment explanation
Indices: 540785--540816 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
540775 CAAGGGGCTT
540785 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
540817 GAATGCTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:545153 original size:24 final size:23
Alignment explanation
Indices: 545126--545195 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
545116 TTTTTTGAAC
545126 TATTTTATTATTTATTTATTATTA
1 TATTTTATT-TTTATTTATTATTA
*
545150 TATTATACTTGTTT-TTTATTATTA
1 TATTTTA-TT-TTTATTTATTATTA
* *
545174 T-TTATTATTTTCAATTATTATT
1 TATT-TTATTTTTATTTATTATT
545196 TACGTGTACA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 2 0.05
23 12 0.32
24 19 0.50
25 5 0.13
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (23 bp):
TATTTTATTTTTATTTATTATTA
Found at i:554602 original size:349 final size:349
Alignment explanation
Indices: 553959--554654 Score: 1038
Period size: 349 Copynumber: 2.0 Consensus size: 349
553949 GTCATACCAG
*
553959 GATATGCCGGGGTTGAGTACCGACATGGTAGTCCATCGTCTCCCTATAAGAGAAGATTGCAAGCC
1 GATATGCCGGGGTTAAGTACCGACATGGTAGTCCATCGTCTCCCTATAAGAGAAGATTGCAAGCC
*
554024 AGTACAGCAAAAACTCAGAAGGATGAGGCCTGATATCGTGTTGAAGATAAAGGAGGAGGTCCAAA
66 AGTACAGCAAAAACTCAGAAGGATGAGGCCTGATATCGTGTTGAAGATAAAAGAGGAGGTCCAAA
* * * * *
554089 AGCAGTTTGATGCCAGGTTTCTGCAAGAAGTCAGGTATTCTGAGTGGGTGGCTAACATCGTACCA
131 AGCAATTTGATGCCAGGATTCTGCAAGAAGTCAAGTATTCTAAGTGGGTGGCCAACATCGTACCA
* *
554154 GTTCCAAAGAAAGATGGAAAAGTAAGAATGTGTGTGGATTATCAGGATTTGAACAAGGCTAGTCC
196 GTTCCAAAGAAAGATGGAAAAGTAAGAATGTGTGTGGATTACCAGGATTTGAACAAGGCTAGCCC
* * * * * * * * *
554219 AAAGGATAATTTCCCATTGCCTCACATTGACACATTGGTAGACAATACTGCGGGCTTTTCACTGT
261 AAAAGATAACTTCCCATTACCCCACATCGACACATTGGTAGACAATACGGCAGGCTATTCACTAT
554284 TTTCCTTCATGGATGGTTTTTCTA
326 TTTCCTTCATGGATGGTTTTTCTA
* * * * *
554308 GATATGCCTGGGTTAAGTACTGACATTGTAGTCCATCG-CTTTCCTATAAGAGAAGATTGCAAGG
1 GATATGCCGGGGTTAAGTACCGACATGGTAGTCCATCGTC-TCCCTATAAGAGAAGATTGCAAGC
* * * *
554372 CAGTGCAGCAAAAGCTCAGAATGATGAGGCCTGATATCGTGTTGAAGATAAAAGAGGAGGTCCAG
65 CAGTACAGCAAAAACTCAGAAGGATGAGGCCTGATATCGTGTTGAAGATAAAAGAGGAGGTCCAA
* *
554437 AAGTAATTTGATGTC-GGAATTCTGCAAGAAGTCAAGTATTCTAAGTGGGTGGCCAACATCGTAC
130 AAGCAATTTGATGCCAGG-ATTCTGCAAGAAGTCAAGTATTCTAAGTGGGTGGCCAACATCGTAC
* *
554501 CAGTTCCAAAGAAAGAT-GAGAAAGTATGAATGTGTGTGGATTACCAGGATTTGAATAAGGCTAG
194 CAGTTCCAAAGAAAGATGGA-AAAGTAAGAATGTGTGTGGATTACCAGGATTTGAACAAGGCTAG
* * *
554565 CCCAAAAGATAACTTCCCATTACCCCACATCGACACATTGGTAGATAATCCGGCAGGCTATTCAT
258 CCCAAAAGATAACTTCCCATTACCCCACATCGACACATTGGTAGACAATACGGCAGGCTATTCAC
554630 TATTTTCCTTCATGGATGGTTTTTC
323 TATTTTCCTTCATGGATGGTTTTTC
554655 GGGGTACAAT
Statistics
Matches: 310, Mismatches: 34, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
348 5 0.02
349 305 0.98
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (349 bp):
GATATGCCGGGGTTAAGTACCGACATGGTAGTCCATCGTCTCCCTATAAGAGAAGATTGCAAGCC
AGTACAGCAAAAACTCAGAAGGATGAGGCCTGATATCGTGTTGAAGATAAAAGAGGAGGTCCAAA
AGCAATTTGATGCCAGGATTCTGCAAGAAGTCAAGTATTCTAAGTGGGTGGCCAACATCGTACCA
GTTCCAAAGAAAGATGGAAAAGTAAGAATGTGTGTGGATTACCAGGATTTGAACAAGGCTAGCCC
AAAAGATAACTTCCCATTACCCCACATCGACACATTGGTAGACAATACGGCAGGCTATTCACTAT
TTTCCTTCATGGATGGTTTTTCTA
Found at i:558259 original size:45 final size:44
Alignment explanation
Indices: 558195--558390 Score: 212
Period size: 44 Copynumber: 4.4 Consensus size: 44
558185 AATACAAAAA
* * *
558195 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAG
1 ATCTTGTCTTCACATACTGG-CGCGAAGTAGATCAAAGAAAACAG
** * * *
558240 ATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAG
1 ATCTTGTCTTCACATACTGGCGCGAAGTAGATCAAAGAAAACAG
* * * *
558284 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACGG
1 ATCTTGTCTTCACATACTGG-CGCGAAGTAGATCAAAGAAAACAG
** * * *
558329 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAG
1 ATCTTGTCTTCACATACTGGCGCGAAGTAGATCAAAGAAAACAG
*
558373 ATCTTGTCTTCCCATACT
1 ATCTTGTCTTCACATACT
558391 AACAGTGAAG
Statistics
Matches: 120, Mismatches: 30, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
44 69 0.57
45 51 0.43
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (44 bp):
ATCTTGTCTTCACATACTGGCGCGAAGTAGATCAAAGAAAACAG
Found at i:558285 original size:44 final size:44
Alignment explanation
Indices: 558219--558383 Score: 213
Period size: 44 Copynumber: 3.7 Consensus size: 44
558209 TACTGGTGGC
*
558219 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * *** * *
558263 GAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
* * *
558308 GAAGTAGATCGAAGAAAACGGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
*
558352 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTC
558384 CCATACTAAC
Statistics
Matches: 99, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
44 65 0.66
45 34 0.34
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (44 bp):
GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
Found at i:558411 original size:89 final size:89
Alignment explanation
Indices: 558195--558390 Score: 365
Period size: 89 Copynumber: 2.2 Consensus size: 89
558185 AATACAAAAA
558195 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
1 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
*
558260 CGTGAAGTAGATCAAAGATAGCAG
66 CGTGAAGTAGATCAAAGAAAGCAG
* *
558284 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACGGATCTTGTCTTCATGTATTGG
1 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
558349 CGTGAAGTAGATCAAAGAAAGCAG
66 CGTGAAGTAGATCAAAGAAAGCAG
558373 ATCTTGTCTTCCCATACT
1 ATCTTGTCTTCCCATACT
558391 AACAGTGAAG
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 104 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (89 bp):
ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
CGTGAAGTAGATCAAAGAAAGCAG
Found at i:558709 original size:45 final size:44
Alignment explanation
Indices: 558628--558715 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
558618 AATCGATCAA
** *
558628 AAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGG
1 AAAAAGCAGATCTTGTCTTCACATACTGGCGTGAAGTAGATCGG
* *
558672 AAAAAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCG
1 AAAAAGCAGATCTTGTCTTCACATACTGG-CGTGAAGTAGATCG
558716 AAGATACAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
44 25 0.66
45 13 0.34
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (44 bp):
AAAAAGCAGATCTTGTCTTCACATACTGGCGTGAAGTAGATCGG
Found at i:560182 original size:24 final size:23
Alignment explanation
Indices: 560155--560224 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
560145 TTTTTTGAAC
560155 TATTTTATTATTTATTTATTATTA
1 TATTTTATT-TTTATTTATTATTA
*
560179 TATTATACTTGTTT-TTTATTATTA
1 TATTTTA-TT-TTTATTTATTATTA
* *
560203 T-TTATTATTTTCAATTATTATT
1 TATT-TTATTTTTATTTATTATT
560225 TACGTGTACA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 2 0.05
23 12 0.32
24 19 0.50
25 5 0.13
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (23 bp):
TATTTTATTTTTATTTATTATTA
Found at i:560628 original size:95 final size:95
Alignment explanation
Indices: 560529--560721 Score: 359
Period size: 95 Copynumber: 2.0 Consensus size: 95
560519 AGTTTTTTTT
*
560529 TGTTTTTAAAAAAAATATCTATGTACATATGTTTTTATTTTTATTTTGTTTTTTTACAATATACT
1 TGTTTTTAAAAAAAATATCTATGTACATATGTTTTTATTTTTATTTTGGTTTTTTACAATATACT
560594 TATACTTTTCTTTGTAAATATATATACATA
66 TATACTTTTCTTTGTAAATATATATACATA
* *
560624 TGTTTTTTAAAAAAATATCTATGTACATATGTTTTTATTTTTATTTTGGTTTTTTACGATATACT
1 TGTTTTTAAAAAAAATATCTATGTACATATGTTTTTATTTTTATTTTGGTTTTTTACAATATACT
560689 TATACTTTTCTTTGTAAATATATATACATA
66 TATACTTTTCTTTGTAAATATATATACATA
560719 TGT
1 TGT
560722 GTATTTTGAT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (95 bp):
TGTTTTTAAAAAAAATATCTATGTACATATGTTTTTATTTTTATTTTGGTTTTTTACAATATACT
TATACTTTTCTTTGTAAATATATATACATA
Found at i:567475 original size:22 final size:22
Alignment explanation
Indices: 567415--567472 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
567405 AATCTTCAAG
567415 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
567434 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
567456 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
567473 GATTTAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:569326 original size:11 final size:11
Alignment explanation
Indices: 569310--569371 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
569300 AAATATGGGC
569310 AATTTTTTTTA
1 AATTTTTTTTA
*
569321 AA---TTTTAA
1 AATTTTTTTTA
* *
569329 AATATTTTTAA
1 AATTTTTTTTA
569340 AATACTTTTTTTA
1 AAT--TTTTTTTA
569353 AA-TTTTTTTA
1 AATTTTTTTTA
569363 AATTTTTTT
1 AATTTTTTT
569372 AATTTTAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
8 7 0.17
10 10 0.24
11 17 0.40
13 8 0.19
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
AATTTTTTTTA
Found at i:569394 original size:11 final size:11
Alignment explanation
Indices: 569373--569410 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
569363 AATTTTTTTA
569373 ATTTT-AAAAT
1 ATTTTCAAAAT
569383 ATTTTCAAAAT
1 ATTTTCAAAAT
569394 ATTTTCAAAAT
1 ATTTTCAAAAT
569405 ACTTTT
1 A-TTTT
569411 TTTTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 5 0.19
11 17 0.65
12 4 0.15
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTTTCAAAAT
Found at i:569411 original size:51 final size:50
Alignment explanation
Indices: 569313--569436 Score: 133
Period size: 51 Copynumber: 2.4 Consensus size: 50
569303 TATGGGCAAT
* **
569313 TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAAATTTTTTTAAA
1 TTTTTTT-AATTTTAAAATATTTTCAAAATAC-TTTTCAAAATTTTTTTAAA
**
569365 TTTTTTTAATTTTAAAATATTTTCAAAATA-TTTTCAAAATACTTTTTTTTA
1 TTTTTTTAATTTTAAAATATTTTCAAAATACTTTTCAAAAT--TTTTTTAAA
*
569416 TTTTTTAAAATTTTTAAAATA
1 TTTTTT-TAA-TTTTAAAATA
569437 AAAATGGGCC
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
49 8 0.13
51 35 0.56
52 9 0.15
53 10 0.16
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (50 bp):
TTTTTTTAATTTTAAAATATTTTCAAAATACTTTTCAAAATTTTTTTAAA
Found at i:569428 original size:10 final size:10
Alignment explanation
Indices: 569323--569435 Score: 54
Period size: 11 Copynumber: 10.9 Consensus size: 10
569313 TTTTTTTAAA
569323 TTTTAAAATAT
1 TTTTAAAAT-T
569334 TTTTAAAATACTT
1 TTTT-AAA-A-TT
*
569347 TTTTTAAATT
1 TTTTAAAATT
*
569357 TTTTTAAATT
1 TTTTAAAATT
*
569367 TTTT-TAA--
1 TTTTAAAATT
569374 TTTTAAAATAT
1 TTTTAAAAT-T
*
569385 TTTCAAAATAT
1 TTTTAAAAT-T
*
569396 TTTCAAAATACT
1 TTTTAAAAT--T
***
569408 TTTTTTTATT
1 TTTTAAAATT
569418 TTTTAAAA-T
1 TTTTAAAATT
569427 TTTTAAAAT
1 TTTTAAAAT
569436 AAAAATGGGC
Statistics
Matches: 81, Mismatches: 12, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
7 4 0.05
8 2 0.02
9 11 0.14
10 22 0.27
11 24 0.30
12 11 0.14
13 6 0.07
14 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:569961 original size:17 final size:19
Alignment explanation
Indices: 569921--569962 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
569911 GTGTGGAAAT
*
569921 CATATATTTAGAATATAAG
1 CATACATTTAGAATATAAG
*
569940 TATACATTT-GAATATAA-
1 CATACATTTAGAATATAAG
569957 CATACA
1 CATACA
569963 ATAAATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 5 0.25
18 8 0.40
19 7 0.35
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.36
Consensus pattern (19 bp):
CATACATTTAGAATATAAG
Found at i:574051 original size:82 final size:78
Alignment explanation
Indices: 573914--574077 Score: 195
Period size: 82 Copynumber: 2.1 Consensus size: 78
573904 TTAATAAATA
* * * *
573914 TTTGTGGCATTTATGAAAAATGCCACTATTGCTTACCTTTTTCGGCGTTTGTGAGAAAACGCCGC
1 TTTGTGGCATTTATGAAAAACGCCACTATAGCTAACCTTTTTCGGCGTTTATGAGAAAACGCCGC
*
573979 TATAGTTTTAACCT
66 TATAGCTTT-ACCT
* *
573993 TTTGTGGCATTTATGAGAAAAACGCCGCTATAGTCTAACCTTTTGT-GGTGTTTATGAGAAAACG
1 TTTGTGGCATTTAT--GAAAAACGCCACTATAG-CTAACCTTTT-TCGGCGTTTATGAGAAAACG
* *
574057 TCGCTATTGCTTTACCT
62 CCGCTATAGCTTTACCT
574074 TTTG
1 TTTG
574078 CAGTGTTTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
79 14 0.19
81 22 0.31
82 35 0.49
83 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (78 bp):
TTTGTGGCATTTATGAAAAACGCCACTATAGCTAACCTTTTTCGGCGTTTATGAGAAAACGCCGC
TATAGCTTTACCT
Found at i:574074 original size:40 final size:40
Alignment explanation
Indices: 573914--574077 Score: 165
Period size: 41 Copynumber: 4.1 Consensus size: 40
573904 TTAATAAATA
* * * *
573914 TTTGTGGCATTTATGA-AAAATGCCACTATTGC-TTACCT
1 TTTGTGGCGTTTATGAGAAAACGCCGCTATAGCTTTACCT
* *
573952 TTT-TCGGCGTTTGTGAGAAAACGCCGCTATAGTTTTAACCT
1 TTTGT-GGCGTTTATGAGAAAACGCCGCTATAGCTTT-ACCT
* *
573993 TTTGTGGCATTTATGAGAAAAACGCCGCTATAG-TCTAACCT
1 TTTGTGGCGTTTATGAG-AAAACGCCGCTATAGCT-TTACCT
* * *
574034 TTTGTGGTGTTTATGAGAAAACGTCGCTATTGCTTTACCT
1 TTTGTGGCGTTTATGAGAAAACGCCGCTATAGCTTTACCT
574074 TTTG
1 TTTG
574078 CAGTGTTTTT
Statistics
Matches: 104, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
37 1 0.01
38 12 0.12
39 12 0.12
40 24 0.23
41 38 0.37
42 17 0.16
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (40 bp):
TTTGTGGCGTTTATGAGAAAACGCCGCTATAGCTTTACCT
Found at i:582306 original size:41 final size:42
Alignment explanation
Indices: 582249--582366 Score: 152
Period size: 41 Copynumber: 2.9 Consensus size: 42
582239 NNNNNNNNTA
* *
582249 ATTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGA-A-ATT
1 ATTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACA-T
582290 ATTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACAT
1 ATTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACAT
* * * *
582332 -TTCGGACTATAAGTCTAGCAGGCTAAAAGCCGGTG
1 ATTCAGACTATATGTCTAGCAGGCTTAATGCCGGTG
582367 TACCGAATCA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
41 66 0.96
42 2 0.03
43 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (42 bp):
ATTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACAT
Found at i:584146 original size:82 final size:78
Alignment explanation
Indices: 584009--584172 Score: 195
Period size: 82 Copynumber: 2.1 Consensus size: 78
583999 TTAATAAATA
* * * *
584009 TTTGTGGCATTTATGAAAAATGCCACTATTGCTTACCTTTTTCGGCGTTTGTGAGAAAACGCCGC
1 TTTGTGGCATTTATGAAAAACGCCACTATAGCTAACCTTTTTCGGCGTTTATGAGAAAACGCCGC
*
584074 TATAGTTTTAACCT
66 TATAGCTTT-ACCT
* *
584088 TTTGTGGCATTTATGAGAAAAACGCCGCTATAGTCTAACCTTTTGT-GGTGTTTATGAGAAAACG
1 TTTGTGGCATTTAT--GAAAAACGCCACTATAG-CTAACCTTTT-TCGGCGTTTATGAGAAAACG
* *
584152 TCGCTATTGCTTTACCT
62 CCGCTATAGCTTTACCT
584169 TTTG
1 TTTG
584173 CAGTGTTTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
79 14 0.19
81 22 0.31
82 35 0.49
83 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (78 bp):
TTTGTGGCATTTATGAAAAACGCCACTATAGCTAACCTTTTTCGGCGTTTATGAGAAAACGCCGC
TATAGCTTTACCT
Found at i:584169 original size:40 final size:40
Alignment explanation
Indices: 584009--584172 Score: 165
Period size: 41 Copynumber: 4.1 Consensus size: 40
583999 TTAATAAATA
* * * *
584009 TTTGTGGCATTTATGA-AAAATGCCACTATTGC-TTACCT
1 TTTGTGGCGTTTATGAGAAAACGCCGCTATAGCTTTACCT
* *
584047 TTT-TCGGCGTTTGTGAGAAAACGCCGCTATAGTTTTAACCT
1 TTTGT-GGCGTTTATGAGAAAACGCCGCTATAGCTTT-ACCT
* *
584088 TTTGTGGCATTTATGAGAAAAACGCCGCTATAG-TCTAACCT
1 TTTGTGGCGTTTATGAG-AAAACGCCGCTATAGCT-TTACCT
* * *
584129 TTTGTGGTGTTTATGAGAAAACGTCGCTATTGCTTTACCT
1 TTTGTGGCGTTTATGAGAAAACGCCGCTATAGCTTTACCT
584169 TTTG
1 TTTG
584173 CAGTGTTTTT
Statistics
Matches: 104, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
37 1 0.01
38 12 0.12
39 12 0.12
40 24 0.23
41 38 0.37
42 17 0.16
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (40 bp):
TTTGTGGCGTTTATGAGAAAACGCCGCTATAGCTTTACCT
Found at i:587047 original size:124 final size:124
Alignment explanation
Indices: 586857--587201 Score: 548
Period size: 124 Copynumber: 2.8 Consensus size: 124
586847 TCGAGTTGAT
* *
586857 ATTTCTGATCAAATAGTATAAAATCGCTTCTAGCTAGATGCTATTTGAGAAGAATTTGTGAAATC
1 ATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAATC
*
586922 GCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGGAAGAAAT-AATTTTTTTGGAC
66 GCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGGAAGAAATAAATTTTTTT-AAC
* *
586981 ATTTCTGAGCAAATAGTATAAAATCACTTCTAGCTGGATGCTAATTGAGAAGAATTTGTGAAATC
1 ATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAATC
* * *
587046 GCGCCTTCGTGGACGCGTTTTTGCTATAGTAGGTCATGGAAGAAATAAATTTTTTTAAC
66 GCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGGAAGAAATAAATTTTTTTAAC
* * *
587105 GTTTCTGAGCAAATAGTATAAAATTGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATC
1 ATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAATC
* * *
587170 ACGCCCTCGTGAACGCGCTTTTGCTACAGTAG
66 GCGCCCTCGTGGACGCGATTTTGCTACAGTAG
587202 CATGTTGGGC
Statistics
Matches: 202, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
124 193 0.96
125 9 0.04
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (124 bp):
ATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAATC
GCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGGAAGAAATAAATTTTTTTAAC
Found at i:609008 original size:21 final size:21
Alignment explanation
Indices: 608982--609022 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
608972 ACCTTTTTTA
*
608982 AAGTTAAAAGTCAAAACCATT
1 AAGTTAAAAGGCAAAACCATT
609003 AAGTTAAAAGGCAAAACCAT
1 AAGTTAAAAGGCAAAACCAT
609023 GTTGTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.20
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACCATT
Found at i:614249 original size:58 final size:59
Alignment explanation
Indices: 614187--614302 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 59
614177 TTATAGGTCA
* * * *
614187 TTTTCATTTTGGAGAAAATCACATTCATTTTCAAATGGTTC-CATTTCTCCATTTTCAT
1 TTTTCATTTTGGAGAAAAGCACAATCATTTCCAAATAGTTCTCATTTCTCCATTTTCAT
* * *
614245 TTTTCATTTTGGATAAAAGCATAATCATTTCCAAATATTTCTCATTTCTCCATTTTCA
1 TTTTCATTTTGGAGAAAAGCACAATCATTTCCAAATAGTTCTCATTTCTCCATTTTCA
614303 CATTCCTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 34 0.68
59 16 0.32
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.47
Consensus pattern (59 bp):
TTTTCATTTTGGAGAAAAGCACAATCATTTCCAAATAGTTCTCATTTCTCCATTTTCAT
Found at i:615108 original size:56 final size:56
Alignment explanation
Indices: 615046--615152 Score: 169
Period size: 56 Copynumber: 1.9 Consensus size: 56
615036 AAACAAATGT
*
615046 TTTAGCTCTACTTTATGTGAGCTCTCTGTTTAGCTCTACTTTGTGCGAGCTCTCTG
1 TTTAGCTCTACTTTATGTGAGCTCTCTGTTTAGCTCTACTTCGTGCGAGCTCTCTG
* * * *
615102 TTTAGCTTTTCTTTGTGTGAGCTTTCTGTTTAGCTCTACTTCGTGCGAGCT
1 TTTAGCTCTACTTTATGTGAGCTCTCTGTTTAGCTCTACTTCGTGCGAGCT
615153 TTCTATTTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (56 bp):
TTTAGCTCTACTTTATGTGAGCTCTCTGTTTAGCTCTACTTCGTGCGAGCTCTCTG
Found at i:615156 original size:28 final size:28
Alignment explanation
Indices: 615046--615152 Score: 151
Period size: 28 Copynumber: 3.8 Consensus size: 28
615036 AAACAAATGT
* *
615046 TTTAGCTCTACTTTATGTGAGCTCTCTG
1 TTTAGCTCTACTTTGTGCGAGCTCTCTG
615074 TTTAGCTCTACTTTGTGCGAGCTCTCTG
1 TTTAGCTCTACTTTGTGCGAGCTCTCTG
* * * *
615102 TTTAGCTTTTCTTTGTGTGAGCTTTCTG
1 TTTAGCTCTACTTTGTGCGAGCTCTCTG
*
615130 TTTAGCTCTACTTCGTGCGAGCT
1 TTTAGCTCTACTTTGTGCGAGCT
615153 TTCTATTTTG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (28 bp):
TTTAGCTCTACTTTGTGCGAGCTCTCTG
Found at i:617995 original size:13 final size:13
Alignment explanation
Indices: 617977--618002 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
617967 ATGTTCAATT
617977 TTTACTAGAAAAC
1 TTTACTAGAAAAC
617990 TTTACTAGAAAAC
1 TTTACTAGAAAAC
618003 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:630948 original size:14 final size:14
Alignment explanation
Indices: 630914--630948 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
630904 ATCTTCCTTC
*
630914 TTAAAAATTTAAAA
1 TTAAAAATTCAAAA
*
630928 TTCAAAATTCAAAA
1 TTAAAAATTCAAAA
630942 TTAAAAA
1 TTAAAAA
630949 ATGAATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
TTAAAAATTCAAAA
Found at i:633232 original size:32 final size:31
Alignment explanation
Indices: 633187--633248 Score: 106
Period size: 32 Copynumber: 2.0 Consensus size: 31
633177 ATGCAACAAC
*
633187 TTTTTCCTTTGAAAACCAAAATGTTAACCTT
1 TTTTTCCCTTGAAAACCAAAATGTTAACCTT
633218 TTTTCTCCCTTGAAAACCAAAATGTTAACCT
1 TTTT-TCCCTTGAAAACCAAAATGTTAACCT
633249 CTCTATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 4 0.14
32 25 0.86
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (31 bp):
TTTTTCCCTTGAAAACCAAAATGTTAACCTT
Found at i:651550 original size:173 final size:173
Alignment explanation
Indices: 651243--651722 Score: 694
Period size: 173 Copynumber: 2.8 Consensus size: 173
651233 CAGATCGTTG
* * * * * *
651243 AGATCACACCAGGACTTATCTCTCTGAGGTTGCAGCAGAGTAGATCGAAGAAGCAGGTCTTATAT
1 AGATCACATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGTAGATCGAAGAATCAGGTCTTATCT
* *
651308 CCCTGAGGTTACAGTGGAGCAGATGGAAGCTGATAATCCTATCTCCCTGAAGTTACAGTGGAACG
66 CCCTGAGGTTGCAGTGGAGCAGATGGAAGCTGATAATCCTATCTCCCTGAAGTTACAGTGGAGCG
* *
651373 GATTGAAATAATAGATCTTATCTCTCTGAAATTACAGCAGAGT
131 GATTGAAATAATAGATCTTATCTCTCTCAAATTACAGCAGAGA
* * *
651416 AGATCATATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGTCGATCGAAGAATCAGGTATTATCT
1 AGATCACATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGTAGATCGAAGAATCAGGTCTTATCT
* * * *
651481 CTCTAAGGTTGCAGTGGAGCAAATGGAAGCTGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCG
66 CCCTGAGGTTGCAGTGGAGCAGATGGAAGCTGATAATCCTATCTCCCTGAAGTTACAGTGGAGCG
* ** *
651546 GATTGAAATAATAGATCTTATCTCTCTCAAGTTGTAGTAGAGA
131 GATTGAAATAATAGATCTTATCTCTCTCAAATTACAGCAGAGA
* *
651589 AGATCACATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGTAGGTCGAAGAAGT-AAGTCTTATC
1 AGATCACATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGTAGATCGAAGAA-TCAGGTCTTATC
* *
651653 TCCCTGAGGTTGCAGTGGAGCAGATTGAAGCAGATAATCCTATCTCCCT-AGAGTTACAGTGGAG
65 TCCCTGAGGTTGCAGTGGAGCAGATGGAAGCTGATAATCCTATCTCCCTGA-AGTTACAGTGGAG
*
651717 TGGATT
129 CGGATT
651723 AAAACAGTAG
Statistics
Matches: 272, Mismatches: 33, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
172 1 0.00
173 270 0.99
174 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (173 bp):
AGATCACATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGTAGATCGAAGAATCAGGTCTTATCT
CCCTGAGGTTGCAGTGGAGCAGATGGAAGCTGATAATCCTATCTCCCTGAAGTTACAGTGGAGCG
GATTGAAATAATAGATCTTATCTCTCTCAAATTACAGCAGAGA
Found at i:651568 original size:44 final size:44
Alignment explanation
Indices: 651300--651716 Score: 173
Period size: 44 Copynumber: 9.6 Consensus size: 44
651290 AAGAAGCAGG
* * * * * *
651300 TCTTATATCCCTGAGGTTACAGTGGAGCAGATGGAAGCTGATA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-ATAATAGA
* * * *
651344 TCCTATCTCCCTGAAGTTACAGTGGAACGGATTGAAATAATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATAATAGA
* * * ** * * *
651388 TCTTATCTCTCTGAAATTACAGCAGAGTAGA-T--CAT-ATCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATAAT-AGA
* * * * *
651429 TCTTATCTCCCTGAGGTTGCAGCGGAGTC-GATCG-AAGAATCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAATAAT-AGA
* * * * * *
651473 TATTATCTCTCT-AAGGTTGCAGTGGAGCAAATGGAAGCTGATA-A
1 TCTTATCTCCCTGAA-GTTGCAGTGGAGCAGATTGAA-ATAATAGA
* *
651517 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAATAATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATAATAGA
* * * * * * * * *
651561 TCTTATCTCTCTCAAGTTGTAGTAGAGAAGA-TCACAT--CAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATAATAGA
* * * * * *
651602 TCTTATCTCCCTGAGGTTGCAGCGGAGTAGGTCGAAGA-AGTA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-ATAATAGA
* **
651645 GTCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCAGATA-A
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATA-ATAGA
* *
651690 TCCTATCTCCCT-AGAGTTACAGTGGAG
1 TCTTATCTCCCTGA-AGTTGCAGTGGAG
651717 TGGATTAAAA
Statistics
Matches: 275, Mismatches: 78, Indels: 40
0.70 0.20 0.10
Matches are distributed among these distances:
40 2 0.01
41 53 0.19
42 1 0.00
43 18 0.07
44 192 0.70
45 7 0.03
46 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATAATAGA
Found at i:652096 original size:28 final size:26
Alignment explanation
Indices: 652052--652103 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
652042 ATGTTATTAA
652052 TATAATATATATATGTTATAATAAGG
1 TATAATATATATATGTTATAATAAGG
652078 TATAATATATTATTATGTTATAATAA
1 TATAATATA-TA-TATGTTATAATAA
652104 ACATTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 9 0.38
27 2 0.08
28 13 0.54
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (26 bp):
TATAATATATATATGTTATAATAAGG
Found at i:653796 original size:41 final size:41
Alignment explanation
Indices: 653751--653883 Score: 205
Period size: 41 Copynumber: 3.2 Consensus size: 41
653741 GGCTCGGTGC
* * **
653751 CTAGCAGGCTTGATGCCAGTGATATGTTTCAGACTTTAAGT
1 CTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTAAGT
653792 CTAGCAGGCTTG-TCGCCGGTGAAACATTTCAGACTTTAAGT
1 CTAGCAGGCTTGAT-GCCGGTGAAACATTTCAGACTTTAAGT
*
653833 CTAGCAGGCTTGACGCCGGTGAAACATTTCAGACTTTAAGT
1 CTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTAAGT
653874 CTAGCAGGCT
1 CTAGCAGGCT
653884 AAGTGCCAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
40 1 0.01
41 84 0.99
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (41 bp):
CTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTAAGT
Found at i:662855 original size:14 final size:14
Alignment explanation
Indices: 662836--662865 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
662826 CTATTATTAT
662836 GGATAGAGATCCAC
1 GGATAGAGATCCAC
662850 GGATAGAGATCCAC
1 GGATAGAGATCCAC
662864 GG
1 GG
662866 TTTACATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.13
Consensus pattern (14 bp):
GGATAGAGATCCAC
Found at i:670848 original size:16 final size:18
Alignment explanation
Indices: 670829--670862 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
670819 TTAACCAATC
670829 AATTTA-AAA-AAATATA
1 AATTTACAAACAAATATA
670845 AATTTACAAACAAATATA
1 AATTTACAAACAAATATA
670863 CTATACTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AATTTACAAACAAATATA
Found at i:677428 original size:39 final size:40
Alignment explanation
Indices: 677293--677429 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 40
677283 CGTTTGGACA
* * * *
677293 AAAAACGCCAGTAAAAATTGAGCATTAGCAGCGCTTTAT-G
1 AAAAACGCCACTAAAAA-TGAGCATTAGCGGCGTTTTTTAG
* * * * *
677333 GAAATCGCCACTAAAGATTAAGCATTAGCGGCGTTTTTCA-
1 AAAAACGCCACTAAA-AATGAGCATTAGCGGCGTTTTTTAG
* * *
677373 AACAACACCGCTAAAAATGAGCATTAGCGGCGTTTTTTAG
1 AAAAACGCCACTAAAAATGAGCATTAGCGGCGTTTTTTAG
*
677413 AAAAACGCCACAAAAAA
1 AAAAACGCCACTAAAAA
677430 CCTAAGCCTA
Statistics
Matches: 73, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
39 21 0.29
40 51 0.70
41 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (40 bp):
AAAAACGCCACTAAAAATGAGCATTAGCGGCGTTTTTTAG
Found at i:677537 original size:42 final size:41
Alignment explanation
Indices: 677461--677581 Score: 179
Period size: 42 Copynumber: 2.9 Consensus size: 41
677451 TTTTGACCTT
*
677461 TCGGGGCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
677502 TCGGGGCTTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCG-TTTTTGAAAAAGCGCCGCTAATGC
** * * *
677544 TCAAGGTTTTAGCGGCGTTTTTGAAAAGGCGCCTCTAA
1 TCGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
677582 ATACATTTTA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
41 35 0.48
42 38 0.52
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (41 bp):
TCGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:677966 original size:14 final size:15
Alignment explanation
Indices: 677934--677976 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
677924 ATTTTAAGGT
* *
677934 TTAGGGAGTATGGTT
1 TTAGGGATTATGGTA
677949 TTAGGGATTATGG-A
1 TTAGGGATTATGGTA
677963 TTAGGGATTATGGT
1 TTAGGGATTATGGT
677977 TTAAGGGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (15 bp):
TTAGGGATTATGGTA
Found at i:678038 original size:22 final size:22
Alignment explanation
Indices: 677991--678055 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
677981 GGGTTGAGAT
* *
677991 TTAAGGTTTAGAAGTTAGGGGT
1 TTAAGGGTTAGAAGTTAGGGGA
*
678013 TTAAGGGTTAGACA-TTATGGGA
1 TTAAGGGTTAGA-AGTTAGGGGA
* *
678035 TTAAGAGTTAGGAATTTAGGG
1 TTAAGGGTTA-GAAGTTAGGG
678056 TTTAGAGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 27 0.77
23 8 0.23
ACGTcount: A:0.31, C:0.02, G:0.34, T:0.34
Consensus pattern (22 bp):
TTAAGGGTTAGAAGTTAGGGGA
Found at i:678208 original size:14 final size:14
Alignment explanation
Indices: 678186--678237 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
678176 TTAATTATGA
*
678186 TTATAGTTTAGGGT
1 TTATGGTTTAGGGT
678200 TTATGGTTTAGGGT
1 TTATGGTTTAGGGT
* *
678214 ATATGGTGTAGGGT
1 TTATGGTTTAGGGT
*
678228 TTAAGGTTTA
1 TTATGGTTTA
678238 AGAGTTACTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (14 bp):
TTATGGTTTAGGGT
Found at i:679973 original size:12 final size:13
Alignment explanation
Indices: 679942--679975 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
679932 GTTTTTTTTT
679942 CTTTGATTATTTA
1 CTTTGATTATTTA
*
679955 TTTTGATTA-TTA
1 CTTTGATTATTTA
679967 CTTTGATTA
1 CTTTGATTA
679976 ATGTCACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.62
Consensus pattern (13 bp):
CTTTGATTATTTA
Found at i:680543 original size:23 final size:23
Alignment explanation
Indices: 680475--680544 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
680465 GTCTTGAAAT
680475 GATCCTTGTATGGCAGTGTCTTA
1 GATCCTTGTATGGCAGTGTCTTA
* ***
680498 GATTCTTGTGATTATAGTGTCTTA
1 GATCCTTGT-ATGGCAGTGTCTTA
680522 GATCCTTGTATGGCAGTGTCTTA
1 GATCCTTGTATGGCAGTGTCTTA
680545 AATTGAAACT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (23 bp):
GATCCTTGTATGGCAGTGTCTTA
Found at i:680631 original size:14 final size:14
Alignment explanation
Indices: 680612--680654 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
680602 TCATTGTTTA
680612 TGATTTATACATAT
1 TGATTTATACATAT
680626 TGATTTATACATA-
1 TGATTTATACATAT
*
680639 -G-TGTATACATAT
1 TGATTTATACATAT
680651 TGAT
1 TGAT
680655 CAAATCAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 1 0.04
14 14 0.56
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.47
Consensus pattern (14 bp):
TGATTTATACATAT
Found at i:684613 original size:42 final size:43
Alignment explanation
Indices: 684557--684655 Score: 130
Period size: 43 Copynumber: 2.3 Consensus size: 43
684547 ATTTGTGATA
* *
684557 AAAGCGCCGCTAAAGATCATGT-TTTTAGCGGCGTATGT-GGG
1 AAAGCGTCGCTAAAGATCACGTCTTTTAGCGGCGTATGTAGGG
* * *
684598 TAAAGTGTCGTTAAAGATCACGTCTTTTAGCGGCGTTTGTAGGG
1 -AAAGCGTCGCTAAAGATCACGTCTTTTAGCGGCGTATGTAGGG
684642 AAAGCGTCGCTAAA
1 AAAGCGTCGCTAAA
684656 AGTCATGATC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 18 0.38
43 27 0.56
44 3 0.06
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.28
Consensus pattern (43 bp):
AAAGCGTCGCTAAAGATCACGTCTTTTAGCGGCGTATGTAGGG
Found at i:687569 original size:32 final size:32
Alignment explanation
Indices: 687506--687569 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
687496 TCGAGGCGTG
* *
687506 ACAAATATTATATATAATAATAAAAGATATAT
1 ACAAATATTAAATATAATAATAAAAAATATAT
* *
687538 ACAATTATTAAATATTA-AATAAAAAATTATAT
1 ACAAATATTAAATATAATAATAAAAAA-TATAT
687570 TTAAGAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (32 bp):
ACAAATATTAAATATAATAATAAAAAATATAT
Found at i:694887 original size:22 final size:23
Alignment explanation
Indices: 694859--694901 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
694849 GATGAGAGAT
694859 ATCATTT-TT-TTCACCCAAAACC
1 ATCATTTCTTCTTC-CCCAAAACC
694881 ATCATTTCTTCTTCCCCAAAA
1 ATCATTTCTTCTTCCCCAAAA
694902 ATTTCCATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 9 0.47
24 3 0.16
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (23 bp):
ATCATTTCTTCTTCCCCAAAACC
Found at i:698568 original size:43 final size:43
Alignment explanation
Indices: 698520--698607 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
698510 TGATCAGAGA
*
698520 CTGTTTAAAAGCAACTATAGATAGACAAAAGTCTTATGTCGAT
1 CTGTTTAAAAGCAACTATAGATAGACAAAAATCTTATGTCGAT
698563 CTGTTTAAAAGCAACTATAGATAGACAAAAATCTTATGTCGAT
1 CTGTTTAAAAGCAACTATAGATAGACAAAAATCTTATGTCGAT
698606 CT
1 CT
698608 TAAAAGAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (43 bp):
CTGTTTAAAAGCAACTATAGATAGACAAAAATCTTATGTCGAT
Found at i:699340 original size:37 final size:37
Alignment explanation
Indices: 699290--699366 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
699280 TTGTGGCCAA
699290 AGTAAGAAAAATAATAAGTTAGGAGATACATAGTAGT
1 AGTAAGAAAAATAATAAGTTAGGAGATACATAGTAGT
699327 AGTAAGAAAAATAATAAGTTAGGAGATACATAGTAGT
1 AGTAAGAAAAATAATAAGTTAGGAGATACATAGTAGT
699364 AGT
1 AGT
699367 GGAAAAGGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.51, C:0.03, G:0.22, T:0.25
Consensus pattern (37 bp):
AGTAAGAAAAATAATAAGTTAGGAGATACATAGTAGT
Found at i:700530 original size:22 final size:22
Alignment explanation
Indices: 700503--700571 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
700493 TCTTCGGTTA
*
700503 TTAGCACATTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTTTGT
*
700525 TTAGCACATTCA-TGCTCTTTAT
1 TTAGCACATT-AGTGCTCTTTGT
* *
700547 GTAGCACTTTAGTGCTCTTTGT
1 TTAGCACATTAGTGCTCTTTGT
700569 TTA
1 TTA
700572 ATAGTGCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 1 0.03
22 37 0.95
23 1 0.03
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTTTGT
Found at i:702923 original size:20 final size:19
Alignment explanation
Indices: 702883--702928 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
702873 TTTTATCCAA
702883 ATTTTAATTTAATTAATTT
1 ATTTTAATTTAATTAATTT
*
702902 ATATTTATTTTAATT-ATATT
1 AT-TTTAATTTAATTAAT-TT
702922 ATTTTAA
1 ATTTTAA
702929 AATTTTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTAATTTAATTAATTT
Found at i:702925 original size:14 final size:16
Alignment explanation
Indices: 702895--702928 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
702885 TTTAATTTAA
702895 TTAATTTATATTTATT
1 TTAATTTATATTTATT
702911 TTAA-TTATA-TTATT
1 TTAATTTATATTTATT
702925 TTAA
1 TTAA
702929 AATTTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 5 0.28
16 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAATTTATATTTATT
Done.