Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1301
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1559340
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.30
Warning! 165545 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:454 original size:14 final size:14
Alignment explanation
Indices: 435--463 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
425 CGATCGGTGA
435 TGACCAGGCGCTGC
1 TGACCAGGCGCTGC
449 TGACCAGGCGCTGC
1 TGACCAGGCGCTGC
463 T
1 T
464 AGATTGCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.34, G:0.34, T:0.17
Consensus pattern (14 bp):
TGACCAGGCGCTGC
Found at i:4200 original size:12 final size:12
Alignment explanation
Indices: 4183--4216 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4173 GAACTACTGG
*
4183 CTCTTCCTCTTC
1 CTCTTCCTCCTC
4195 CTCTTCCTCCTC
1 CTCTTCCTCCTC
*
4207 CTCCTCCTCC
1 CTCTTCCTCC
4217 CGGTTAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (12 bp):
CTCTTCCTCCTC
Found at i:6353 original size:124 final size:121
Alignment explanation
Indices: 6132--6380 Score: 471
Period size: 124 Copynumber: 2.0 Consensus size: 121
6122 AAATGAAGAA
6132 TTTCCCACAATGATGTTCCAGTAAACAATATATATATATATATATGCGTTCCCCATTAAATCCGG
1 TTTCCCACAATGATGTTCCAGTAAACAATATATATATATATATATGCGTTCCCCATTAAATCCGG
6197 TATATAATGTAATAATAACTTTTTTCCTAACGAAACTTTTTGATAACACGGTTGAT
66 TATATAATGTAATAATAACTTTTTTCCTAACGAAACTTTTTGATAACACGGTTGAT
6253 TTTNCCCACAATGATGTTCCAGTAAACAATATATATATATATATATATGCGTTCCCCATTAAATC
1 TTT-CCCACAATGATGTTCCAGTAAAC-A-ATATATATATATATATATGCGTTCCCCATTAAATC
6318 CGGTATATAATGTAATAATAACTTTTTTCCTAACGAAACTTTTTGATAACACGGTTGAT
63 CGGTATATAATGTAATAATAACTTTTTTCCTAACGAAACTTTTTGATAACACGGTTGAT
6377 TTTC
1 TTTC
6381 TTTATTAAAG
Statistics
Matches: 125, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
121 3 0.02
122 23 0.18
123 2 0.02
124 97 0.78
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.38
Consensus pattern (121 bp):
TTTCCCACAATGATGTTCCAGTAAACAATATATATATATATATATGCGTTCCCCATTAAATCCGG
TATATAATGTAATAATAACTTTTTTCCTAACGAAACTTTTTGATAACACGGTTGAT
Found at i:11745 original size:59 final size:59
Alignment explanation
Indices: 11669--11816 Score: 235
Period size: 59 Copynumber: 2.5 Consensus size: 59
11659 CCCTCCCTTG
* * *
11669 ACTGTTGCTATGTGAACTTAGGTGACCCTGACAGTTGATATTTATGGTATCATC-CTTCA
1 ACTGTTGCTATGAGAACTAAGGTGACCCTGACAGTAGATATTTATGGTATCATCGC-TCA
* *
11728 ACTGTTGCTCTGAGAACTAAGGTGACCCTGTCAGTAGATATTTATGGTATCATCGCTCA
1 ACTGTTGCTATGAGAACTAAGGTGACCCTGACAGTAGATATTTATGGTATCATCGCTCA
11787 ACTGTTGCTATGAGAACTAAGGTGACCCTG
1 ACTGTTGCTATGAGAACTAAGGTGACCCTG
11817 GAGTCCTTAA
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
59 81 0.99
60 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (59 bp):
ACTGTTGCTATGAGAACTAAGGTGACCCTGACAGTAGATATTTATGGTATCATCGCTCA
Found at i:11944 original size:27 final size:27
Alignment explanation
Indices: 11914--11996 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 27
11904 GTCATTAATG
11914 TACCCCCTGACGTCATTGACTGTGAAC
1 TACCCCCTGACGTCATTGACTGTGAAC
*
11941 TACCCCCTGA---C--TG--T-AG-AC
1 TACCCCCTGACGTCATTGACTGTGAAC
*
11959 TACCCCTTGACGTCATTGACTGTGAAC
1 TACCCCCTGACGTCATTGACTGTGAAC
11986 TACCCCCTGAC
1 TACCCCCTGAC
11997 TGTAGACTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
18 11 0.26
19 1 0.02
20 1 0.02
21 1 0.02
22 2 0.05
23 2 0.05
24 1 0.02
25 1 0.02
26 1 0.02
27 22 0.51
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (27 bp):
TACCCCCTGACGTCATTGACTGTGAAC
Found at i:11953 original size:18 final size:18
Alignment explanation
Indices: 11930--12063 Score: 114
Period size: 18 Copynumber: 7.1 Consensus size: 18
11920 CTGACGTCAT
11930 TGACTGT-GAACTACCCCC
1 TGACTGTAG-ACTACCCCC
*
11948 TGACTGTAGACTACCCCT
1 TGACTGTAGACTACCCCC
11966 TGAC-GTCATTGACTGTGAACTACCCCC
1 TGACTGT-A--GAC--T--AC--CCC-C
11993 TGACTGTAGACT-CCCCC
1 TGACTGTAGACTACCCCC
*
12010 TGACTGTAGACTACCCCT
1 TGACTGTAGACTACCCCC
12028 TGACTGTAGACT-CCCCC
1 TGACTGTAGACTACCCCC
*
12045 TGACTGTAGACTCCCCCC
1 TGACTGTAGACTACCCCC
12063 T
1 T
12064 TGACCTAGTT
Statistics
Matches: 98, Mismatches: 4, Indels: 28
0.75 0.03 0.22
Matches are distributed among these distances:
17 31 0.32
18 45 0.46
19 1 0.01
20 4 0.04
22 1 0.01
23 1 0.01
24 2 0.02
25 3 0.03
26 3 0.03
27 5 0.05
28 2 0.02
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.25
Consensus pattern (18 bp):
TGACTGTAGACTACCCCC
Found at i:11970 original size:45 final size:45
Alignment explanation
Indices: 11914--12010 Score: 176
Period size: 45 Copynumber: 2.2 Consensus size: 45
11904 GTCATTAATG
*
11914 TACCCCCTGACGTCATTGACTGTGAACTACCCCCTGACTGTAGAC
1 TACCCCTTGACGTCATTGACTGTGAACTACCCCCTGACTGTAGAC
11959 TACCCCTTGACGTCATTGACTGTGAACTACCCCCTGACTGTAGAC
1 TACCCCTTGACGTCATTGACTGTGAACTACCCCCTGACTGTAGAC
*
12004 TCCCCCT
1 TACCCCT
12011 GACTGTAGAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.21, C:0.37, G:0.16, T:0.26
Consensus pattern (45 bp):
TACCCCTTGACGTCATTGACTGTGAACTACCCCCTGACTGTAGAC
Found at i:12010 original size:17 final size:17
Alignment explanation
Indices: 11975--12061 Score: 131
Period size: 17 Copynumber: 5.0 Consensus size: 17
11965 TTGACGTCAT
11975 TGACTGT-GAACTACCCCC
1 TGACTGTAG-ACT-CCCCC
11993 TGACTGTAGACTCCCCC
1 TGACTGTAGACTCCCCC
*
12010 TGACTGTAGACTACCCCT
1 TGACTGTAGACT-CCCCC
12028 TGACTGTAGACTCCCCC
1 TGACTGTAGACTCCCCC
12045 TGACTGTAGACTCCCCC
1 TGACTGTAGACTCCCCC
12062 CTTGACCTAG
Statistics
Matches: 65, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
17 38 0.58
18 26 0.40
19 1 0.02
ACGTcount: A:0.20, C:0.39, G:0.17, T:0.24
Consensus pattern (17 bp):
TGACTGTAGACTCCCCC
Found at i:12023 original size:35 final size:35
Alignment explanation
Indices: 11975--12063 Score: 144
Period size: 35 Copynumber: 2.5 Consensus size: 35
11965 TTGACGTCAT
11975 TGACTGT-GAACTACCCCCTGACTGTAGACTCCCCC
1 TGACTGTAG-ACTACCCCCTGACTGTAGACTCCCCC
*
12010 TGACTGTAGACTACCCCTTGACTGTAGACTCCCCC
1 TGACTGTAGACTACCCCCTGACTGTAGACTCCCCC
*
12045 TGACTGTAGACTCCCCCCT
1 TGACTGTAGACTACCCCCT
12064 TGACCTAGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
35 49 0.98
36 1 0.02
ACGTcount: A:0.19, C:0.39, G:0.17, T:0.25
Consensus pattern (35 bp):
TGACTGTAGACTACCCCCTGACTGTAGACTCCCCC
Found at i:13341 original size:2 final size:2
Alignment explanation
Indices: 13336--13367 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13326 GAAAGAAAAA
13336 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13368 TTGAGTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16838 original size:2 final size:2
Alignment explanation
Indices: 16831--16881 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
16821 ATCATATTTC
16831 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16873 AG AG AG AG A
1 AG AG AG AG A
16882 ATGTGAGTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18301 original size:10 final size:10
Alignment explanation
Indices: 18286--18318 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
18276 TATTAAAATT
18286 TTCATTAAAA
1 TTCATTAAAA
18296 TTCATTAAAAA
1 TTCATT-AAAA
18307 TTCATTAAAA
1 TTCATTAAAA
18317 TT
1 TT
18319 TTGTAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (10 bp):
TTCATTAAAA
Found at i:18308 original size:11 final size:11
Alignment explanation
Indices: 18286--18316 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
18276 TATTAAAATT
18286 TTCATT-AAAA
1 TTCATTAAAAA
18296 TTCATTAAAAA
1 TTCATTAAAAA
18307 TTCATTAAAA
1 TTCATTAAAA
18317 TTTTGTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (11 bp):
TTCATTAAAAA
Found at i:18895 original size:21 final size:21
Alignment explanation
Indices: 18868--18936 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
18858 ACGCTTTGCC
18868 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
* ** ** *
18889 TGAAACGCTTCAC-AATCACA
1 CGAAACGCTAAACGGTTTACA
18909 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
18930 CGAAACG
1 CGAAACG
18937 TTTCTTGCAC
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.17
Consensus pattern (21 bp):
CGAAACGCTAAACGGTTTACA
Found at i:26219 original size:135 final size:130
Alignment explanation
Indices: 25976--26371 Score: 493
Period size: 134 Copynumber: 3.0 Consensus size: 130
25966 GAATCCTGAC
* *
25976 CCCTAAACCATATATATTGTTGTTCC-TGTGTTAAGGAGCATCAAATGGTATGTAGGTCAT-G--
1 CCCTAAACCATGTATATT-TTGTTCCTTGTGTCAAGG-GCATCAAATGGTATGTAGGTCATGGCC
* *
26037 -GGGGGTGGTCCTGACCCCCCTCAAACAGGAAGTGCCCAAATAGCTTGAAAATGGTTAAGATCCC
64 TGGGGGTGGTCCTGACCCCCCTCAAACAGAAAGTGCCCAAATAACTTGAAAATGGTTAAGATCCC
26101 CA
129 CA
26103 CCCTTAAACCATGTATATTCTTGTTCCTTGTGTCAAGTGGCATCAAATGGTATGTAGGTCATGGA
1 CCC-TAAACCATGTATATT-TTGTTCCTTGTGTCAAG-GGCATCAAATGGTATGTAGGTCATGG-
*** **
26168 CCCTGGGGGTGGTCCTGACTTTCCTCAAACAGAAAGTGCCCACGTAACTTGAAAATGGTTAAGAT
62 -CCTGGGGGTGGTCCTGACCCCCCTCAAACAGAAAGTGCCCAAATAACTTGAAAATGGTTAAGAT
26233 CCCCA
126 CCCCA
26238 CCCTAAACCATGTATATTTCTGTTCCTTGTGTCAAGAGGCATCAAATGGTATGTAGGTCATGGGT
1 CCCTAAACCATGTATATTT-TGTTCCTTGTGTCAAG-GGCATCAAATGGTATGTAGGTCAT-GG-
* * * * * **
26303 CCTGGGGGTGGTCGTGACCCCCCTGAAAC---AAGTGCACGAATATCTTGAAAACAGTTAAGATC
62 CCTGGGGGTGGTCCTGACCCCCCTCAAACAGAAAGTGCCCAAATAACTTGAAAATGGTTAAGATC
26365 CCCA
127 CCCA
26369 CCC
1 CCC
26372 CTTCACAATA
Statistics
Matches: 234, Mismatches: 24, Indels: 18
0.85 0.09 0.07
Matches are distributed among these distances:
127 3 0.01
128 21 0.09
129 31 0.13
130 2 0.01
131 33 0.14
133 1 0.00
134 79 0.34
135 64 0.27
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (130 bp):
CCCTAAACCATGTATATTTTGTTCCTTGTGTCAAGGGCATCAAATGGTATGTAGGTCATGGCCTG
GGGGTGGTCCTGACCCCCCTCAAACAGAAAGTGCCCAAATAACTTGAAAATGGTTAAGATCCCCA
Found at i:32791 original size:350 final size:350
Alignment explanation
Indices: 32150--32849 Score: 1357
Period size: 350 Copynumber: 2.0 Consensus size: 350
32140 ACGGTAAACA
32150 AACCGAGAAATAGCACCTACGGAAAACAGAAAACACACAAAACACCGTTTAAACCTGTGATGCAG
1 AACCGAGAAATAGCACCTACGGAAAACAGAAAACACACAAAACACCGTTTAAACCTGTGATGCAG
*
32215 GGGAAGTGCTACCGTTGTGGTGGAAACCACAAGGCAAAGACTTGTAAACATCTGAACACTAAATG
66 GGGAAGTGCTACCGTTGTGGTGGAAACCACAAAGCAAAGACTTGTAAACATCTGAACACTAAATG
32280 CAGATATTGTGACAACCCTGGACACTTAGAAAAAGTTTGTTTTAAGAAACAACGTGACAGTAATG
131 CAGATATTGTGACAACCCTGGACACTTAGAAAAAGTTTGTTTTAAGAAACAACGTGACAGTAATG
32345 GTGGAAAAGTCCATTATGTTGATGAAGAAACAAGTGACGACAGTGACGAGTATGAACATAGCAGT
196 GTGGAAAAGTCCATTATGTTGATGAAGAAACAAGTGACGACAGTGACGAGTATGAACATAGCAGT
32410 TACCTGCTGCATTTCGGCGTGAACAAAGTATCCGTGGAGCCTA-TATGGTGACACCGAGGATCGA
261 TACCTGCTGCATTTCGGCGTGAACAAAGTATCCGTGGAGCCTATTATGGTGACACCGAGGATCGA
32474 GGGTGTGGAAATCCCTATGGAACTG
326 GGGTGTGGAAATCCCTATGGAACTG
32499 NAACCGAGAAATAGCACCTACGGAAAACAGAAAACACACAAAACACCGTTTAAACCTGTGATGCA
1 -AACCGAGAAATAGCACCTACGGAAAACAGAAAACACACAAAACACCGTTTAAACCTGTGATGCA
*
32564 GGGGAAGTGCTACCGTTGTGGTGGAGACCACAAAGCAAAGACTTGTAAACATCTGAACACTAAAT
65 GGGGAAGTGCTACCGTTGTGGTGGAAACCACAAAGCAAAGACTTGTAAACATCTGAACACTAAAT
*
32629 GCAGATATTGTGACAACCCTGGACACTTAGAAAAGGTTTGTTTTAAGAAACAACGTGACAGTAAT
130 GCAGATATTGTGACAACCCTGGACACTTAGAAAAAGTTTGTTTTAAGAAACAACGTGACAGTAAT
32694 GGTGGAAAAGTCCATTATGTTGATGAAGAAACAAGTGACGACAGTGACGAGTATGAACATAGCAG
195 GGTGGAAAAGTCCATTATGTTGATGAAGAAACAAGTGACGACAGTGACGAGTATGAACATAGCAG
32759 TTACCTGCTGCATTTCGGCGTGAACAAAGTATCCGTGGAGCCTATTATGGTGACACCGAGGATCG
260 TTACCTGCTGCATTTCGGCGTGAACAAAGTATCCGTGGAGCCTATTATGGTGACACCGAGGATCG
32824 AGGGTGTGGAAATCCCTATGGAACTG
325 AGGGTGTGGAAATCCCTATGGAACTG
32850 GACACCGGTG
Statistics
Matches: 346, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
350 300 0.87
351 46 0.13
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (350 bp):
AACCGAGAAATAGCACCTACGGAAAACAGAAAACACACAAAACACCGTTTAAACCTGTGATGCAG
GGGAAGTGCTACCGTTGTGGTGGAAACCACAAAGCAAAGACTTGTAAACATCTGAACACTAAATG
CAGATATTGTGACAACCCTGGACACTTAGAAAAAGTTTGTTTTAAGAAACAACGTGACAGTAATG
GTGGAAAAGTCCATTATGTTGATGAAGAAACAAGTGACGACAGTGACGAGTATGAACATAGCAGT
TACCTGCTGCATTTCGGCGTGAACAAAGTATCCGTGGAGCCTATTATGGTGACACCGAGGATCGA
GGGTGTGGAAATCCCTATGGAACTG
Found at i:41756 original size:2 final size:2
Alignment explanation
Indices: 41751--41789 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
41741 AGAGAAATGC
**
41751 AG AG AG AG AG AG AG AG AG AG AG AG AG AG TC AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
41790 AATCCCATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.46, T:0.03
Consensus pattern (2 bp):
AG
Found at i:42001 original size:117 final size:115
Alignment explanation
Indices: 41796--42028 Score: 394
Period size: 117 Copynumber: 2.0 Consensus size: 115
41786 GAGAAATCCC
*
41796 ATACATCATCAGACAATATGCTATTGTTTCTTTAAAAAAAAAATTACATCGAGATTTTCAAAGCT
1 ATACATCATCAGACAATATGCTATTGTTTCTTGAAAAAAAAAATTACATCGAGATTTTCAAAGCT
*
41861 GATCATAATTCTAGTACATACTTCGTTATGAACTAAGTGTTAAAATTTAA
66 GAACATAATTCTAGTACATACTTCGTTATGAACTAAGTGTTAAAATTTAA
* * *
41911 NATACATCATTAGACAATATGCTATTGTTTCTTGAAAAAAAAATTTTACATCGAGATTTTCGAAG
1 -ATACATCATCAGACAATATGCTATTGTTTCTTGAAAAAAAAA-ATTACATCGAGATTTTCAAAG
*
41976 CTGAACATAATTCTATTACATACTTCGTTATGAACTAAGTGTTAAAATTTAA
64 CTGAACATAATTCTAGTACATACTTCGTTATGAACTAAGTGTTAAAATTTAA
42028 A
1 A
42029 GAATCAAAGG
Statistics
Matches: 110, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
116 41 0.37
117 69 0.63
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.36
Consensus pattern (115 bp):
ATACATCATCAGACAATATGCTATTGTTTCTTGAAAAAAAAAATTACATCGAGATTTTCAAAGCT
GAACATAATTCTAGTACATACTTCGTTATGAACTAAGTGTTAAAATTTAA
Found at i:42739 original size:180 final size:179
Alignment explanation
Indices: 42133--42738 Score: 799
Period size: 180 Copynumber: 3.4 Consensus size: 179
42123 GTAAAATAAA
* ** **
42133 GTACCCCATATGCAATATTTTGTTAAAAAA-GACTTAGTTC-AAAGCTGGTA-TTTTTTCATAAA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACCAAGTTCAAAAGCTGGTATTTTTTTCATAAA
* * * * * * *
42195 -TAACTAGAAATAAAAATCCTAGAAATATGCACACCTCTGATACATGTACAATTAATCTGCAAAA
66 TTATC-AGTAATCAAAATCCTAGCAATATGCACACCTCTGATAAATGTATAATTGATCTGCAAAA
* * **
42259 GAACAACTTTTTATCTAT-AAAACTGTAGAATAGTTATCCGTACAATGAGG
130 GAACAACTTCTTAT-TTTGAAAACTGTAGAGGAGTTATCCGTACAATGAGG
* * * * * * *
42309 TTACCCTATATGCAATATTTTGCTAAAAATTGACCAACTTCAAAAGCTGGTATTTTTTCCACAAT
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACCAAGTTCAAAAGCTGGTATTTTTTTCATAAA
* *
42374 TTATAAGTAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTATAATTGATCTGCAAAAG
66 TTATCAGTAATCAAAATCCTAGCAATATGCACACCTCTGATAAATGTATAATTGATCTGCAAAAG
42439 AACAACTTCTTATTTTGAAAACTGTAAGAGGAGTTATCCGTACAATGAGG
131 AACAACTTCTTATTTTGAAAACTGT-AGAGGAGTTATCCGTACAATGAGG
* * * *
42489 GTACGCTATATGCAATATTTTGCCAAAACATGACTAAATTCAAAAGCTGGTATTTTTTTCATAAA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACCAAGTTCAAAAGCTGGTATTTTTTTCATAAA
* * * * * *
42554 TTATCGGTAACCACAATCCTATCATTAAGCACACCTCTGATAAATGTATAATTGATCTGCAAAAG
66 TTATCAGTAATCAAAATCCTAGCAATATGCACACCTCTGATAAATGTATAATTGATCTGCAAAAG
* *
42619 AACAACTTCCTATTTTGAAAACTGTAGGAGGACTTATCCGTACAATGAGG
131 AACAACTTCTTATTTTGAAAACTGTA-GAGGAGTTATCCGTACAATGAGG
*
42669 GTACCCTATATGCAATATTTTGCCAAAAAATGACCAAGTTCATAAGCTGGTATTTTTTTCATAAA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACCAAGTTCAAAAGCTGGTATTTTTTTCATAAA
42734 TTATC
66 TTATC
42739 GAAAATAAAA
Statistics
Matches: 376, Mismatches: 47, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
176 26 0.07
177 7 0.02
178 12 0.03
179 84 0.22
180 247 0.66
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.32
Consensus pattern (179 bp):
GTACCCTATATGCAATATTTTGCCAAAAAATGACCAAGTTCAAAAGCTGGTATTTTTTTCATAAA
TTATCAGTAATCAAAATCCTAGCAATATGCACACCTCTGATAAATGTATAATTGATCTGCAAAAG
AACAACTTCTTATTTTGAAAACTGTAGAGGAGTTATCCGTACAATGAGG
Found at i:42762 original size:12 final size:11
Alignment explanation
Indices: 42740--42767 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
42730 TAAATTATCG
42740 AAAATAAAAAA
1 AAAATAAAAAA
42751 AAAATAAAAAA
1 AAAATAAAAAA
42762 AAAATA
1 AAAATA
42768 CATTAGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (11 bp):
AAAATAAAAAA
Found at i:52791 original size:1 final size:1
Alignment explanation
Indices: 52787--52814 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
52777 AAAATGGGAT
52787 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
52815 CGCGGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:54519 original size:15 final size:15
Alignment explanation
Indices: 54499--54527 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54489 AATTTCAGAT
54499 CCCAAAAGAAGACAC
1 CCCAAAAGAAGACAC
54514 CCCAAAAGAAGACA
1 CCCAAAAGAAGACA
54528 ATGTCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.31, G:0.14, T:0.00
Consensus pattern (15 bp):
CCCAAAAGAAGACAC
Found at i:56331 original size:57 final size:59
Alignment explanation
Indices: 56262--56373 Score: 176
Period size: 61 Copynumber: 1.9 Consensus size: 59
56252 GCAGTATGTG
56262 TACTAGCCTGAGTAG-T-GAGGG-GGGGGTAGTGTGTATACTAGACTATGTAGTTTNGTC
1 TACTAGCCTGAGTAGTTGGAGGGAGGGGGTAGTGTGTATACTAGACTATGTAGTTT-GTC
*
56319 TACTAGCCTGAGTAGTTGGGGGGAAGGGGGTAGTGTGTATACTAGACTATGTAGT
1 TACTAGCCTGAGTAGTTGGAGGG-AGGGGGTAGTGTGTATACTAGACTATGTAGT
56374 CTTAAGGGTG
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
57 15 0.30
58 1 0.02
59 4 0.08
61 30 0.60
ACGTcount: A:0.22, C:0.10, G:0.37, T:0.30
Consensus pattern (59 bp):
TACTAGCCTGAGTAGTTGGAGGGAGGGGGTAGTGTGTATACTAGACTATGTAGTTTGTC
Found at i:56680 original size:12 final size:12
Alignment explanation
Indices: 56663--56691 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
56653 TAATGAAAAT
56663 AACAAGAAAACA
1 AACAAGAAAACA
56675 AACAAGAAAACA
1 AACAAGAAAACA
56687 AACAA
1 AACAA
56692 AACGAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.76, C:0.17, G:0.07, T:0.00
Consensus pattern (12 bp):
AACAAGAAAACA
Found at i:56706 original size:16 final size:17
Alignment explanation
Indices: 56687--56726 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
56677 CAAGAAAACA
56687 AACAAA-ACGAATAAAT
1 AACAAACACGAATAAAT
56703 AACAAGAACACGAATAAAT
1 AAC-A-AACACGAATAAAT
56722 AACAA
1 AACAA
56727 TGTCAATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 2 0.10
18 3 0.14
19 13 0.62
ACGTcount: A:0.68, C:0.15, G:0.07, T:0.10
Consensus pattern (17 bp):
AACAAACACGAATAAAT
Found at i:58292 original size:16 final size:16
Alignment explanation
Indices: 58271--58302 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
58261 AAATTCTTAA
58271 AAATATGAAAAAAAAT
1 AAATATGAAAAAAAAT
*
58287 AAATATGAAAATAAAT
1 AAATATGAAAAAAAAT
58303 TTCTAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (16 bp):
AAATATGAAAAAAAAT
Found at i:58314 original size:22 final size:21
Alignment explanation
Indices: 58234--58322 Score: 80
Period size: 22 Copynumber: 4.3 Consensus size: 21
58224 AAATATTCTC
* *
58234 AAAATAAAGTACTAGAAATATA
1 AAAATAAA-TTCTAGAAATATG
*
58256 AAAATAAATTCTTAAAAATATG
1 AAAATAAATTC-TAGAAATATG
*
58278 AAAA-AAA----ATAAATATG
1 AAAATAAATTCTAGAAATATG
58294 AAAATAAATTTCTAGAAATATG
1 AAAATAAA-TTCTAGAAATATG
58316 AAAATAA
1 AAAATAA
58323 TTTATATTGC
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
16 12 0.22
17 3 0.05
21 5 0.09
22 35 0.64
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (21 bp):
AAAATAAATTCTAGAAATATG
Found at i:58541 original size:2 final size:2
Alignment explanation
Indices: 58534--58573 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
58524 AGACTGAAAA
* *
58534 TC TC TC TC TC TC TC TC TC TC TC TC TG TC TG TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
58574 ATGCTTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.45, G:0.05, T:0.50
Consensus pattern (2 bp):
TC
Found at i:59106 original size:39 final size:39
Alignment explanation
Indices: 59052--59129 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
59042 CGTACTGACC
*
59052 TATACGACAGACAACATTGGATTAGATTATCTATATGTA
1 TATACGACAGACAACATTGGATCAGATTATCTATATGTA
59091 TATACGACAGACAACATTGGATCAGATTATCTATATGTA
1 TATACGACAGACAACATTGGATCAGATTATCTATATGTA
59130 AGGGGTATCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (39 bp):
TATACGACAGACAACATTGGATCAGATTATCTATATGTA
Found at i:60091 original size:19 final size:19
Alignment explanation
Indices: 60067--60103 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
60057 TTCACGTCTA
60067 ATTTTCAAGAATATGAACC
1 ATTTTCAAGAATATGAACC
60086 ATTTTCAAGAATATGAAC
1 ATTTTCAAGAATATGAAC
60104 TTTAAAACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (19 bp):
ATTTTCAAGAATATGAACC
Found at i:65609 original size:14 final size:14
Alignment explanation
Indices: 65587--65616 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
65577 GCAAGAATTC
*
65587 TATTTTTGCAATAA
1 TATTATTGCAATAA
65601 TATTATTGCAATAA
1 TATTATTGCAATAA
65615 TA
1 TA
65617 ACCTTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
TATTATTGCAATAA
Found at i:71279 original size:2 final size:2
Alignment explanation
Indices: 71272--71305 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
71262 AGAGTTGAAC
71272 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
71306 AAGCCGCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:76472 original size:1 final size:1
Alignment explanation
Indices: 76466--76527 Score: 97
Period size: 1 Copynumber: 62.0 Consensus size: 1
76456 CCGTACTTCA
* * *
76466 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCTCCCCCCCCCCCCCCCCACCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
76528 ATCATTNCTG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.03, C:0.95, G:0.00, T:0.02
Consensus pattern (1 bp):
C
Found at i:76502 original size:31 final size:32
Alignment explanation
Indices: 76464--76528 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
76454 GGCCGTACTT
*
76464 CACCCCCCCC-CCCCCCCCCCCCCCCCCCCCC
1 CACCCCCCCCTCCCCCCCCCCCCCCCCACCCC
76495 CACCCCCCCCTCCCCCCCCCCCCCCCCACCCC
1 CACCCCCCCCTCCCCCCCCCCCCCCCCACCCC
76527 CA
1 CA
76529 TCATTNCTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 10 0.31
32 22 0.69
ACGTcount: A:0.06, C:0.92, G:0.00, T:0.02
Consensus pattern (32 bp):
CACCCCCCCCTCCCCCCCCCCCCCCCCACCCC
Found at i:78342 original size:22 final size:22
Alignment explanation
Indices: 78317--78446 Score: 78
Period size: 22 Copynumber: 6.0 Consensus size: 22
78307 GGTCGAACAT
*
78317 GCGAGAGTGCGA-AGTTGCGAAG
1 GCGAAAGTGCGAGAG-TGCGAAG
*
78339 GCGAAAGTGCGAGAGTGCGACG
1 GCGAAAGTGCGAGAGTGCGAAG
* * *
78361 GCGAAGGAGCGAAAGTGCGAAG
1 GCGAAAGTGCGAGAGTGCGAAG
* *
78383 ATGCG-ACG-GCGA-AGCGCGAAG
1 --GCGAAAGTGCGAGAGTGCGAAG
*
78404 ATGCG-AAG-GCGAAAGTGCGAAG
1 --GCGAAAGTGCGAGAGTGCGAAG
*
78426 GCGAAGGTGCGA-AG-GCGAAG
1 GCGAAAGTGCGAGAGTGCGAAG
78446 G
1 G
78447 AGCGATACTA
Statistics
Matches: 91, Mismatches: 11, Indels: 14
0.78 0.09 0.12
Matches are distributed among these distances:
20 10 0.11
21 23 0.25
22 51 0.56
23 4 0.04
24 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.45, T:0.08
Consensus pattern (22 bp):
GCGAAAGTGCGAGAGTGCGAAG
Found at i:78349 original size:14 final size:15
Alignment explanation
Indices: 78332--78444 Score: 82
Period size: 14 Copynumber: 7.9 Consensus size: 15
78322 AGTGCGAAGT
78332 TGCGAAG-GCGAAAG
1 TGCGAAGAGCGAAAG
* *
78346 TGCGAGAGTGCG-ACG
1 TGCGA-AGAGCGAAAG
78361 -GCGAAGGAGCGAAAG
1 TGCGAA-GAGCGAAAG
*
78376 TGCGAAGATGCG-ACG
1 TGCGAAGA-GCGAAAG
*
78391 -GCGAAGCGCG-AAG
1 TGCGAAGAGCGAAAG
78404 ATGCGAAG-GCGAAAG
1 -TGCGAAGAGCGAAAG
*
78419 TGCGAAG-GCGAAGG
1 TGCGAAGAGCGAAAG
78433 TGCGAAG-GCGAA
1 TGCGAAGAGCGAA
78445 GGAGCGATAC
Statistics
Matches: 83, Mismatches: 7, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
13 6 0.07
14 47 0.57
15 19 0.23
16 11 0.13
ACGTcount: A:0.32, C:0.17, G:0.44, T:0.07
Consensus pattern (15 bp):
TGCGAAGAGCGAAAG
Found at i:78350 original size:8 final size:7
Alignment explanation
Indices: 78316--78445 Score: 92
Period size: 8 Copynumber: 18.0 Consensus size: 7
78306 AGGTCGAACA
78316 TGCGAGAG
1 TGCGA-AG
78324 TGCGAAG
1 TGCGAAG
78331 TTGCGAAG
1 -TGCGAAG
78339 -GCGAAAG
1 TGCG-AAG
78346 TGCGAGAG
1 TGCGA-AG
*
78354 TGCGACG
1 TGCGAAG
78361 -GCGAAGG
1 TGCGAA-G
*
78368 AGCGAAAG
1 TGCG-AAG
78376 TGCGAAG
1 TGCGAAG
*
78383 ATGCGACG
1 -TGCGAAG
78391 -GCGAAG
1 TGCGAAG
*
78397 CGCGAAG
1 TGCGAAG
78404 ATGCGAAG
1 -TGCGAAG
78412 -GCGAAAG
1 TGCG-AAG
78419 TGCGAAG
1 TGCGAAG
78426 -GCGAAGG
1 TGCGAA-G
78433 TGCGAAG
1 TGCGAAG
78440 -GCGAAG
1 TGCGAAG
78446 GAGCGATACT
Statistics
Matches: 102, Mismatches: 6, Indels: 30
0.74 0.04 0.22
Matches are distributed among these distances:
6 26 0.25
7 25 0.25
8 49 0.48
9 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.45, T:0.08
Consensus pattern (7 bp):
TGCGAAG
Found at i:78402 original size:21 final size:22
Alignment explanation
Indices: 78369--78432 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
78359 CGGCGAAGGA
* *
78369 GCGAAAGTGCGAAGATGCGACG
1 GCGAAAGCGCGAAGATGCGAAG
78391 GCG-AAGCGCGAAGATGCGAAG
1 GCGAAAGCGCGAAGATGCGAAG
*
78412 GCGAAAGTGCGAAG--GCGAAG
1 GCGAAAGCGCGAAGATGCGAAG
78432 G
1 G
78433 TGCGAAGGCG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 7 0.18
21 19 0.50
22 12 0.32
ACGTcount: A:0.33, C:0.17, G:0.44, T:0.06
Consensus pattern (22 bp):
GCGAAAGCGCGAAGATGCGAAG
Found at i:78445 original size:14 final size:15
Alignment explanation
Indices: 78325--78451 Score: 81
Period size: 14 Copynumber: 8.8 Consensus size: 15
78315 ATGCGAGAGT
*
78325 GCGAAGTTGCGAAG-
1 GCGAAGGTGCGAAGA
* *
78339 GCGAAAGTGCGAGAGT
1 GCGAAGGTGCGA-AGA
*
78355 GCG-ACG-GCGAAGGA
1 GCGAAGGTGCGAA-GA
*
78369 GCGAAAGTGCGAAGA
1 GCGAAGGTGCGAAGA
* *
78384 TGCG-ACG-GCGAAGC
1 -GCGAAGGTGCGAAGA
*
78398 GCGAAGATGCGAAG-
1 GCGAAGGTGCGAAGA
*
78412 GCGAAAGTGCGAAG-
1 GCGAAGGTGCGAAGA
78426 GCGAAGGTGCGAAG-
1 GCGAAGGTGCGAAGA
*
78440 GCGAAGGAGCGA
1 GCGAAGGTGCGA
78452 TACTACTATC
Statistics
Matches: 92, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
13 4 0.04
14 61 0.66
15 16 0.17
16 11 0.12
ACGTcount: A:0.31, C:0.17, G:0.45, T:0.07
Consensus pattern (15 bp):
GCGAAGGTGCGAAGA
Found at i:79207 original size:14 final size:15
Alignment explanation
Indices: 79184--79249 Score: 54
Period size: 14 Copynumber: 4.6 Consensus size: 15
79174 ACAATTATTA
79184 AAAG-GCGAAG-GCG
1 AAAGTGCGAAGTGCG
79197 AAAGTGCGAAGATGCG
1 AAAGTGCGAAG-TGCG
79213 -AAG-GCGAGAGTGCG
1 AAAGTGCGA-AGTGCG
79227 -AAGATGCGAAG-GCG
1 AAAG-TGCGAAGTGCG
*
79241 AGAGTGCGA
1 AAAGTGCGA
79250 TAGTAGTATC
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
13 4 0.09
14 25 0.56
15 9 0.20
16 7 0.16
ACGTcount: A:0.35, C:0.14, G:0.44, T:0.08
Consensus pattern (15 bp):
AAAGTGCGAAGTGCG
Found at i:79216 original size:22 final size:22
Alignment explanation
Indices: 79188--79249 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
79178 TTATTAAAAG
*
79188 GCGAAGGCGAAAGTGCGAAGAT
1 GCGAAGGCGAGAGTGCGAAGAT
79210 GCGAAGGCGAGAGTGCGAAGAT
1 GCGAAGGCGAGAGTGCGAAGAT
79232 GCGAAGGCGAGAGTGCGA
1 GCGAAGGCGAGAGTGCGA
79250 TAGTAGTATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.32, C:0.15, G:0.45, T:0.08
Consensus pattern (22 bp):
GCGAAGGCGAGAGTGCGAAGAT
Found at i:79249 original size:8 final size:7
Alignment explanation
Indices: 79188--79249 Score: 58
Period size: 8 Copynumber: 8.6 Consensus size: 7
79178 TTATTAAAAG
79188 GCGAAG-
1 GCGAAGT
79194 GCGAAAGT
1 GCG-AAGT
79202 GCGAAGAT
1 GCGAAG-T
79210 GCGAAG-
1 GCGAAGT
79216 GCGAGAGT
1 GCGA-AGT
79224 GCGAAGAT
1 GCGAAG-T
79232 GCGAAG-
1 GCGAAGT
79238 GCGAGAGT
1 GCGA-AGT
79246 GCGA
1 GCGA
79250 TAGTAGTATC
Statistics
Matches: 48, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
6 11 0.23
7 12 0.25
8 25 0.52
ACGTcount: A:0.32, C:0.15, G:0.45, T:0.08
Consensus pattern (7 bp):
GCGAAGT
Found at i:79282 original size:14 final size:14
Alignment explanation
Indices: 79265--79363 Score: 64
Period size: 14 Copynumber: 6.9 Consensus size: 14
79255 GTATCGCTCC
79265 TTCGCCTTCGCACT
1 TTCGCCTTCGCACT
79279 TTCGCCTTCGCA-T
1 TTCGCCTTCGCACT
79292 CTTCGCGCTTCGC-C-
1 -TTCGC-CTTCGCACT
*
79306 GTCGCATCTTCGCACT
1 TTCGC--CTTCGCACT
79322 TTCGCTCCTTCGC-C-
1 TTCG--CCTTCGCACT
*
79336 GTCGCACCTTCGCACT
1 TTCG--CCTTCGCACT
*
79352 TTCGCCGTCGCA
1 TTCGCCTTCGCA
79364 ACTTCGCACT
Statistics
Matches: 68, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
13 5 0.07
14 41 0.60
15 9 0.13
16 12 0.18
18 1 0.01
ACGTcount: A:0.07, C:0.43, G:0.18, T:0.31
Consensus pattern (14 bp):
TTCGCCTTCGCACT
Found at i:79305 original size:21 final size:21
Alignment explanation
Indices: 79279--79318 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
79269 CCTTCGCACT
*
79279 TTCGCCTTCGCATCTTCGCGC
1 TTCGCCGTCGCATCTTCGCGC
79300 TTCGCCGTCGCATCTTCGC
1 TTCGCCGTCGCATCTTCGC
79319 ACTTTCGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.42, G:0.20, T:0.33
Consensus pattern (21 bp):
TTCGCCGTCGCATCTTCGCGC
Found at i:79335 original size:30 final size:30
Alignment explanation
Indices: 79299--79356 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
79289 CATCTTCGCG
*
79299 CTTCGCCGTCGCATCTTCGCACTTTCGCTC
1 CTTCGCCGTCGCACCTTCGCACTTTCGCTC
79329 CTTCGCCGTCGCACCTTCGCACTTTCGC
1 CTTCGCCGTCGCACCTTCGCACTTTCGC
79357 CGTCGCAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.07, C:0.45, G:0.17, T:0.31
Consensus pattern (30 bp):
CTTCGCCGTCGCACCTTCGCACTTTCGCTC
Found at i:79340 original size:22 final size:22
Alignment explanation
Indices: 79315--79372 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
79305 CGTCGCATCT
* *
79315 TCGCACTTTCGCTCCTTCGCCG
1 TCGCACCTTCGCACCTTCGCCG
*
79337 TCGCACCTTCGCACTTTCGCCG
1 TCGCACCTTCGCACCTTCGCCG
*
79359 TCGCAACTTCGCAC
1 TCGCACCTTCGCAC
79373 TCTCGCACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.10, C:0.45, G:0.17, T:0.28
Consensus pattern (22 bp):
TCGCACCTTCGCACCTTCGCCG
Found at i:79371 original size:30 final size:28
Alignment explanation
Indices: 79280--79380 Score: 82
Period size: 30 Copynumber: 3.5 Consensus size: 28
79270 CTTCGCACTT
* *
79280 TCGC-CTTCGCA-TCTTCGCGCTTCGCCG
1 TCGCACTTCGCACT-TTCGCCCGTCGCCG
*
79307 TCGCATCTTCGCACTTTCGCTCCTTCGCCG
1 TCGCA-CTTCGCACTTTCGC-CCGTCGCCG
*
79337 TCGCACCTTCGCACTTTCG-CCGTCGCAACT
1 TCGCA-CTTCGCACTTTCGCCCGTCGC--CG
79367 TCGCACTCTCGCAC
1 TCGCACT-TCGCAC
79381 CTCGACCTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
27 4 0.06
28 6 0.10
29 14 0.22
30 39 0.62
ACGTcount: A:0.09, C:0.45, G:0.18, T:0.29
Consensus pattern (28 bp):
TCGCACTTCGCACTTTCGCCCGTCGCCG
Found at i:79373 original size:22 final size:22
Alignment explanation
Indices: 79330--79378 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
79320 CTTTCGCTCC
*
79330 TTCGCCGTCGCACCTTCGCACT
1 TTCGCCGTCGCAACTTCGCACT
79352 TTCGCCGTCGCAACTTCGCACT
1 TTCGCCGTCGCAACTTCGCACT
*
79374 CTCGC
1 TTCGC
79379 ACCTCGACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.10, C:0.45, G:0.18, T:0.27
Consensus pattern (22 bp):
TTCGCCGTCGCAACTTCGCACT
Found at i:82036 original size:15 final size:16
Alignment explanation
Indices: 82006--82036 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
81996 AGCTACTGTA
82006 TATCATTTTCTTTTTT
1 TATCATTTTCTTTTTT
82022 TATCATTTT-TTTTTT
1 TATCATTTTCTTTTTT
82037 GTGAATACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (16 bp):
TATCATTTTCTTTTTT
Found at i:84542 original size:14 final size:14
Alignment explanation
Indices: 84523--84554 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
84513 ATATTTATTT
84523 TTTTTGTAATTTTA
1 TTTTTGTAATTTTA
*
84537 TTTTTGTTATTTTA
1 TTTTTGTAATTTTA
84551 TTTT
1 TTTT
84555 ATTAGCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (14 bp):
TTTTTGTAATTTTA
Found at i:85746 original size:2 final size:2
Alignment explanation
Indices: 85739--85782 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
85729 AGGCAAATAA
85739 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
85781 TC
1 TC
85783 GTTATGTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:91763 original size:21 final size:21
Alignment explanation
Indices: 91737--92847 Score: 1072
Period size: 21 Copynumber: 53.4 Consensus size: 21
91727 TTTTATTTTC
** *
91737 TACACTTTAAAGTGTAAATTT
1 TACACTTTAATCTGTAAAATT
*
91758 TACACTTTAATCTGTAAATTT
1 TACACTTTAATCTGTAAAATT
91779 TACACTTTAATCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
* *
91800 TACACTGTAATCTGTAAATTT
1 TACACTTTAATCTGTAAAATT
* *
91821 TACACTTAAAGCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
** *
91842 TACACTTTAAAGTGTAAATTT
1 TACACTTTAATCTGTAAAATT
*
91863 TTCACTTTAATCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
*
91884 CACACTTTAATCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
* *
91905 CACACTTTAAGCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
* *
91926 CACACTTTAA-CGTGTAAATTT
1 TACACTTTAATC-TGTAAAATT
* *
91947 TACACTTTCATCTGTAAATTT
1 TACACTTTAATCTGTAAAATT
91968 TACACTTTAATCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
* * *
91989 CACATTTTTATCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
92010 TACACTTTAATCTGT-AAATT
1 TACACTTTAATCTGTAAAATT
*
92030 GTACACGTTAATCTGT-AAATT
1 -TACACTTTAATCTGTAAAATT
* * *
92051 TCACACATT-ATC--CACAATT
1 T-ACACTTTAATCTGTAAAATT
*
92070 TA-A-----A-GTGTAAAATT
1 TACACTTTAATCTGTAAAATT
*
92084 CACACTTTAATCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
*
92105 CACACTTTAATCTGT-AAATT
1 TACACTTTAATCTGTAAAATT
*
92125 GTACACTTTAATCTGTAAATTT
1 -TACACTTTAATCTGTAAAATT
**
92147 TACACTTTAAAGTGTAAAATT
1 TACACTTTAATCTGTAAAATT
* ** *
92168 CACACTTTAAAGTGTAAAACT
1 TACACTTTAATCTGTAAAATT
* *
92189 CACACTTAAATCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
* **
92210 CACACTTTAAAGTGTAAAATT
1 TACACTTTAATCTGTAAAATT
* ** *
92231 CACACTTTAAAGTGTAAAATC
1 TACACTTTAATCTGTAAAATT
* **
92252 CACACTTTAAAGTGTAAAATT
1 TACACTTTAATCTGTAAAATT
* * * *
92273 CACACTTTTATCGGTAAATTT
1 TACACTTTAATCTGTAAAATT
*
92294 TACACTTTAATCTGTAAATTT
1 TACACTTTAATCTGTAAAATT
*
92315 TACACTTTAATCTGCAAAATT
1 TACACTTTAATCTGTAAAATT
*
92336 CACACTTTAATCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
* **
92357 CACACTTTAAAATGT-AAATT
1 TACACTTTAATCTGTAAAATT
92377 ATACACTTTAATCTGT-AAATCT
1 -TACACTTTAATCTGTAAAAT-T
*
92399 AACACTTTAATCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
* **
92420 CACACTTTAAAATGTAAAATT
1 TACACTTTAATCTGTAAAATT
* * ** *
92441 CACACTTAAAAATGAAAAATT
1 TACACTTTAATCTGTAAAATT
*
92462 CACACTTTAATCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
92483 TACACTTTAATCTGT-AAATAT
1 TACACTTTAATCTGTAAAAT-T
92504 TACACTTTAATCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
* ** *
92525 CACACTTTAAAGTGTGAAATT
1 TACACTTTAATCTGTAAAATT
* ** * * *
92546 CACAAGTAAATCTGTTAATTT
1 TACACTTTAATCTGTAAAATT
*
92567 TACACTTTAATCTAT-AAATAT
1 TACACTTTAATCTGTAAAAT-T
92588 TACACTTTAATCTGT-AAATT
1 TACACTTTAATCTGTAAAATT
*
92608 TCATACTTTAATCTGTAAAATT
1 T-ACACTTTAATCTGTAAAATT
* *
92630 CACACTTTAATGTGTAAAATT
1 TACACTTTAATCTGTAAAATT
* * *
92651 CACAGTTTAATCTGTAAATTT
1 TACACTTTAATCTGTAAAATT
*
92672 TACACTTTAATCTGTAAATTT
1 TACACTTTAATCTGTAAAATT
92693 TACACTTTAATCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
*
92714 CACACTTTAATCTGTAAAATT
1 TACACTTTAATCTGTAAAATT
* *
92735 CACACTTTAATCTGTAAATTT
1 TACACTTTAATCTGTAAAATT
*
92756 TACACTTTAATCTGTAAATTT
1 TACACTTTAATCTGTAAAATT
* ** * *
92777 TTCACTTTAAAGTGTGAATTT
1 TACACTTTAATCTGTAAAATT
** * **
92798 TACAGATCAAAGTGTAAAATT
1 TACACTTTAATCTGTAAAATT
** **
92819 TACAGATTAAAGTGTAAAATT
1 TACACTTTAATCTGTAAAATT
92840 TACACTTT
1 TACACTTT
92848 TAAGTGTAGA
Statistics
Matches: 938, Mismatches: 128, Indels: 48
0.84 0.11 0.04
Matches are distributed among these distances:
13 1 0.00
14 6 0.01
15 1 0.00
17 1 0.00
18 1 0.00
19 5 0.01
20 30 0.03
21 874 0.93
22 19 0.02
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (21 bp):
TACACTTTAATCTGTAAAATT
Found at i:97766 original size:2 final size:2
Alignment explanation
Indices: 97759--97794 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
97749 GAAGACAAAG
97759 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
97795 TTTGCAAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:130370 original size:17 final size:17
Alignment explanation
Indices: 130350--130382 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
130340 GATTTGTAAA
130350 TGTATCATATTTAGCTG
1 TGTATCATATTTAGCTG
*
130367 TGTATTATATTTAGCT
1 TGTATCATATTTAGCT
130383 TTTTTAGCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (17 bp):
TGTATCATATTTAGCTG
Found at i:132333 original size:16 final size:16
Alignment explanation
Indices: 132312--132342 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
132302 TTAATTTTAC
132312 TTCGTTATATCCATAA
1 TTCGTTATATCCATAA
132328 TTCGTTATATCCATA
1 TTCGTTATATCCATA
132343 TAACGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.45
Consensus pattern (16 bp):
TTCGTTATATCCATAA
Found at i:146505 original size:2 final size:2
Alignment explanation
Indices: 146500--146542 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
146490 CTGTTTTACG
146500 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
146542 T
1 T
146543 GCTAAACCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:147875 original size:165 final size:165
Alignment explanation
Indices: 147543--148051 Score: 734
Period size: 165 Copynumber: 3.0 Consensus size: 165
147533 AAAGAATTAT
* * *
147543 CTGGTTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGGTTCTGAGAAGAAGATTTTTAAAGATTTATTCTATATATTCCTATGTAAAAC-
* *
147608 TTAAC-ACCCCCCCCCCAATGTGGCCCCACTCTACCCCCGGGGATCATGATTTTCACAACTTTGA
65 TT--CGA-----CCCCCATTGTGGCCCCACCCTACCCCCGGGGATCATGATTTTCACAACTTTGA
*
147672 ATCTACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
123 ATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
147715 CTGGCTGATTAGGTTCTGAGAAGAAGATTTTTAAAGATTTATTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGGTTCTGAGAAGAAGATTTTTAAAGATTTATTCTATATATTCCTATGTAAAACT
* * ** *
147780 TCGACCCCCATTGTGACCCCACCCTACCGCTAGGGATCATGATTTTCACAATTTTGAATCTACAC
66 TCGACCCCCATTGTGGCCCCACCCTACCCCCGGGGATCATGATTTTCACAACTTTGAATCTACAC
*
147845 TACCTGAGAATGCTTCCACACAAGTTTCAGCTTTC
131 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* *
147880 CTGGCTGATTAGGTTTTGAGAAGAAGATTTTTAAAGATTT-TCTCTATACATTCCTATGTAAAAA
1 CTGGCTGATTAGGTTCTGAGAAGAAGATTTTTAAAGATTTAT-TCTATATATTCCTATGT-AAAA
* * * *
147944 CTTCGACCCCCATTGTGGCCCAACCCTACCCCCGGGGGTCATGATTATCACAACTTTCAATCTAC
64 CTTCGACCCCCATTGTGGCCCCACCCTACCCCCGGGGATCATGATTTTCACAACTTTGAATCTAC
* *
148009 ACTACTTGAGGAGGCTTCCACACAAGTTTCAGCTTTC
129 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
148046 CTGGCT
1 CTGGCT
148052 TTCTTGAGAA
Statistics
Matches: 308, Mismatches: 26, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
164 1 0.00
165 142 0.46
166 100 0.32
169 1 0.00
170 1 0.00
171 2 0.01
172 61 0.20
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (165 bp):
CTGGCTGATTAGGTTCTGAGAAGAAGATTTTTAAAGATTTATTCTATATATTCCTATGTAAAACT
TCGACCCCCATTGTGGCCCCACCCTACCCCCGGGGATCATGATTTTCACAACTTTGAATCTACAC
TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
Found at i:152257 original size:27 final size:27
Alignment explanation
Indices: 152226--152347 Score: 145
Period size: 27 Copynumber: 4.3 Consensus size: 27
152216 CTTACTTTTA
152226 GCTTTCATCATCCGCAACACATTCTTC
1 GCTTTCATCATCCGCAACACATTCTTC
*
152253 TCTTTAATCGTCATCATCCGCAACACATTCTTC
1 GC--T--T--TCATCATCCGCAACACATTCTTC
* *
152286 GTTTTCATCATCCGCTACACATTCTTC
1 GCTTTCATCATCCGCAACACATTCTTC
* *
152313 GCTTTCATCATCCACTACACATTCTTC
1 GCTTTCATCATCCGCAACACATTCTTC
152340 GCTTTCAT
1 GCTTTCAT
152348 TTTCATCAAC
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
27 56 0.67
29 2 0.02
31 2 0.02
33 23 0.28
ACGTcount: A:0.21, C:0.34, G:0.07, T:0.38
Consensus pattern (27 bp):
GCTTTCATCATCCGCAACACATTCTTC
Found at i:155254 original size:14 final size:14
Alignment explanation
Indices: 155235--155268 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
155225 CCGCATTTTG
155235 ACTGTTGGACTGGA
1 ACTGTTGGACTGGA
*
155249 ACTGTTGGATTGGA
1 ACTGTTGGACTGGA
155263 ACTGTT
1 ACTGTT
155269 AAAATCGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.32, T:0.35
Consensus pattern (14 bp):
ACTGTTGGACTGGA
Found at i:156881 original size:17 final size:17
Alignment explanation
Indices: 156843--156887 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
156833 TCTGGTAGGC
*
156843 CTCTTTCTTTGTGCTTCT
1 CTCTTTCTTT-TCCTTCT
*
156861 -TCTTTCTTTTCCTTTT
1 CTCTTTCTTTTCCTTCT
156877 CTCTTTCTTTT
1 CTCTTTCTTTT
156888 TTATTGGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.00, C:0.27, G:0.04, T:0.69
Consensus pattern (17 bp):
CTCTTTCTTTTCCTTCT
Found at i:162876 original size:35 final size:35
Alignment explanation
Indices: 162729--163118 Score: 227
Period size: 35 Copynumber: 10.3 Consensus size: 35
162719 ATGTTTGTAG
*
162729 GTAAGTACATGTTACA-TGTACATTTTAGTGTTGATGTAATT
1 GTAAGTACATGTTACACT-TACATTCTAGTG-T--TG--A-T
*
162770 GTAAGTACATGTTACATGACTGTACACTCTAGTGTTGAT
1 GTAAGTACATGTTAC---ACT-TACATTCTAGTGTTGAT
** * *
162809 GTAAGTATACAT-TATATGC-T-CAATCTATTGTTGAT
1 GTAAG--TACATGT-TACACTTACATTCTAGTGTTGAT
*
162844 GTAAGTAGATGTTACACTTACATTCTAGTGTTGAT
1 GTAAGTACATGTTACACTTACATTCTAGTGTTGAT
*
162879 GTAACATGTTAGAACATGTTACATTTACATTCTATAGTGTTGAT
1 GT-A-A-G-T---ACATGTTACACTTACATTC--TAGTGTTGAT
* * * *
162923 ATAAGTACATTTTACA-TGCACATTCTAGTATTGAT
1 GTAAGTACATGTTACACT-TACATTCTAGTGTTGAT
* * *
162958 GTAAGTACATATTACATTTACATTCTATATTGTTGAT
1 GTAAGTACATGTTACACTTACATTC--TAGTGTTGAT
*
162995 GTAAGTACATGTTACACATACATTCTAGTGTTGAT
1 GTAAGTACATGTTACACTTACATTCTAGTGTTGAT
* * *
163030 G-ATGTAACATGTAAGTACACATTTGCATTCTACATTGTTGAT
1 GTAAGT-ACATGT---TACAC--TTACATTCT--AGTGTTGAT
* *
163072 GTAAGTACAAGTTACA-TCTATATTCTAGTGTTGAT
1 GTAAGTACATGTTACACT-TACATTCTAGTGTTGAT
163107 GTAAGTACATGT
1 GTAAGTACATGT
163119 ATATGCTACA
Statistics
Matches: 280, Mismatches: 36, Indels: 72
0.72 0.09 0.19
Matches are distributed among these distances:
33 7 0.03
34 5 0.02
35 97 0.35
36 5 0.02
37 52 0.19
38 7 0.03
39 11 0.04
40 10 0.04
41 23 0.08
42 34 0.12
43 4 0.01
44 13 0.05
45 12 0.04
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (35 bp):
GTAAGTACATGTTACACTTACATTCTAGTGTTGAT
Found at i:162973 original size:114 final size:112
Alignment explanation
Indices: 162729--162998 Score: 283
Period size: 114 Copynumber: 2.3 Consensus size: 112
162719 ATGTTTGTAG
* * *
162729 GTAAGTACATGTTACATGTACATTTTAGTGTTGATGTAATTGTAAGTACATGTTACATGACTGTA
1 GTAAGTACATGTTACAT-TACATTCTAGTGTTGATGTAAATGTAAGAACATGTTACAT-A-TGTA
* * * * * * *
162794 CACTCTAGTGTTGATGTAAGTATACATTATATGCTCAATCTATTGTTGAT
63 CACTATAGTGTTGATATAAGTACACATTACATGCACAATCTAGTATTGAT
* *
162844 GTAAGTAGATGTTACACTTACATTCTAGTGTTGATGTAACATGTTAGAACATGTTACAT-T-TAC
1 GTAAGTACATGTTACA-TTACATTCTAGTGTTGATGTAA-ATGTAAGAACATGTTACATATGTAC
** *
162907 ATTCTATAGTGTTGATATAAGTACATTTTACATGCACATTCTAGTATTGAT
64 A--CTATAGTGTTGATATAAGTACACATTACATGCACAATCTAGTATTGAT
* *
162958 GTAAGTACATATTACATTTACATTCTATATTGTTGATGTAA
1 GTAAGTACATGTTACA-TTACATTC--TAGTGTTGATGTAA
162999 GTACATGTTA
Statistics
Matches: 130, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
112 4 0.03
113 1 0.01
114 60 0.46
115 35 0.27
116 30 0.23
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (112 bp):
GTAAGTACATGTTACATTACATTCTAGTGTTGATGTAAATGTAAGAACATGTTACATATGTACAC
TATAGTGTTGATATAAGTACACATTACATGCACAATCTAGTATTGAT
Found at i:162981 original size:72 final size:71
Alignment explanation
Indices: 162892--163116 Score: 247
Period size: 72 Copynumber: 3.1 Consensus size: 71
162882 ACATGTTAGA
* * * * *
162892 ACATGTTACATTTACATTCTATAGTGTTGATATAAGTACATTTTACATGCACATTCTAGTATTGA
1 ACATATTACATTTACATTCTATATTGTTGATGTAAGTACATGTTACAT-CACATTCTAGTGTTGA
162957 TGTAAGT
65 TGTAAGT
162964 ACATATTACATTTACATTCTATATTGTTGATGTAAGTACATGTTACA-CATACATTCTAGTGTTG
1 ACATATTACATTTACATTCTATATTGTTGATGTAAGTACATGTTACATC--ACATTCTAGTGTTG
*
163028 ATG-ATGT
64 ATGTAAGT
* * * * *
163035 AACATGTAAGTACACATTTGCATTCTACATTGTTGATGTAAGTACAAGTTACATCTATATTCTAG
1 -ACA--T-A-T-TACATTTACATTCTATATTGTTGATGTAAGTACATGTTACATC-ACATTCTAG
163100 TGTTGATGTAAGT
59 TGTTGATGTAAGT
163113 ACAT
1 ACAT
163117 GTATATGCTA
Statistics
Matches: 131, Mismatches: 12, Indels: 17
0.82 0.08 0.11
Matches are distributed among these distances:
70 1 0.01
71 3 0.02
72 62 0.47
74 1 0.01
75 2 0.02
76 1 0.01
77 57 0.44
78 4 0.03
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (71 bp):
ACATATTACATTTACATTCTATATTGTTGATGTAAGTACATGTTACATCACATTCTAGTGTTGAT
GTAAGT
Found at i:163117 original size:77 final size:75
Alignment explanation
Indices: 162899--163119 Score: 265
Period size: 77 Copynumber: 3.0 Consensus size: 75
162889 AGAACATGTT
* * * *
162899 ACATTTACATTCTATAGTGTTGATATAAGTACATTTTACATGC-ACATTCTAGTATTGATGTAAG
1 ACATTTACATTCTATATTGTTGATGTAAGTACATGTTACAT-CTACATTCTAGTGTTGATGTAAG
*
162963 TACA--T-ATT
65 TACATGTAATC
*
162971 ACATTTACATTCTATATTGTTGATGTAAGTACATGTTACA-CATACATTCTAGTGTTGATG-ATG
1 ACATTTACATTCTATATTGTTGATGTAAGTACATGTTACATC-TACATTCTAGTGTTGATGTAAG
163034 TAACATGTAAGTAC
65 T-ACATGTAA-T-C
* * * *
163048 ACATTTGCATTCTACATTGTTGATGTAAGTACAAGTTACATCTATATTCTAGTGTTGATGTAAGT
1 ACATTTACATTCTATATTGTTGATGTAAGTACATGTTACATCTACATTCTAGTGTTGATGTAAGT
163113 ACATGTA
66 ACATGTA
163120 TATGCTACAT
Statistics
Matches: 128, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
70 1 0.01
71 3 0.02
72 56 0.44
74 1 0.01
75 1 0.01
76 1 0.01
77 61 0.48
78 4 0.03
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (75 bp):
ACATTTACATTCTATATTGTTGATGTAAGTACATGTTACATCTACATTCTAGTGTTGATGTAAGT
ACATGTAATC
Found at i:163129 original size:149 final size:144
Alignment explanation
Indices: 162797--163131 Score: 372
Period size: 149 Copynumber: 2.2 Consensus size: 144
162787 GACTGTACAC
* *
162797 TCTAGTGTTGATGTAAGTATACATTATATGCT-CAATCTATTGTTGATGTAAGTAGATGTTACAC
1 TCTAGTGTTGATGTAAG--TACATTATATGCTACATTCTATTGTTGATGTAAGTACATGTTACAC
* * *
162861 TTACATTCTAGTGTTGATGTAACATGTTAGAACATGTTACATTTACATTCTATAGTGTTGATATA
64 ATACATTCTAGTGTTGATGTAACATGTAAGAAC----TACATTTACATTCTACAGTGTTGATATA
**
162926 AGTACATTTTACATGCACAT
125 AGTACAAGTTACATGCACAT
* * *
162946 TCTAGTATTGATGTAAGTACATATTACAT-TTACATTCTATATTGTTGATGTAAGTACATGTTAC
1 TCTAGTGTTGATGTAAGTAC--ATTATATGCTACATTC--TATTGTTGATGTAAGTACATGTTAC
* * * *
163010 ACATACATTCTAGTGTTGATGATGTAACATGTAAGTAC-ACATTTGCATTCTACATTGTTGATGT
62 ACATACATTCTAGTG-T--TGATGTAACATGTAAGAACTACATTTACATTCTACAGTGTTGATAT
*
163074 AAGTACAAGTTACAT-CTATAT
124 AAGTACAAGTTACATGC-ACAT
163095 TCTAGTGTTGATGTAAGTACATGTATATGCTACATTC
1 TCTAGTGTTGATGTAAGTACAT-TATATGCTACATTC
163132 AAGCTGAGCT
Statistics
Matches: 157, Mismatches: 18, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
147 5 0.03
148 6 0.04
149 90 0.57
151 38 0.24
152 1 0.01
154 17 0.11
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.41
Consensus pattern (144 bp):
TCTAGTGTTGATGTAAGTACATTATATGCTACATTCTATTGTTGATGTAAGTACATGTTACACAT
ACATTCTAGTGTTGATGTAACATGTAAGAACTACATTTACATTCTACAGTGTTGATATAAGTACA
AGTTACATGCACAT
Found at i:170484 original size:228 final size:227
Alignment explanation
Indices: 170085--170541 Score: 896
Period size: 228 Copynumber: 2.0 Consensus size: 227
170075 TCACTACCGG
170085 TATTTGAGGATGCTTCCATGCAAGTTTCAGCTTTTCTGGCCTAATGGGTTTTAGTAGAAGATTTT
1 TATTTGAGGATGCTTCCATGCAAGTTTCAGCTTTTCTGGCCTAATGGGTTTTAGTAGAAGATTTT
170150 CAAAGAATAACTCTATATACGTATTTCTATGTAAAACTTCGACCTCCCCATTGTGGCCCCATCTT
66 CAAAGAATAACTCTATATACGTATTTCTATGTAAAACTTCGACCTCCCCATTGTGGCCCCATCTT
170215 ACCCATTACCATAATTTGAACAAACTTGAATCTACACCATCTGATGATGCTTCCACACAAGGTGC
131 ACCCATTACCATAATTTGAACAAACTTGAATCTACACCATCTGATGATGCTTCCACACAAGGTGC
170280 AGCTTTTCTGTCCAATTGGTTGTTAAAAAGTT
196 AGCTTTTCTGTCCAATTGGTTGTTAAAAAGTT
*
170312 TANTTTGAGGATGCTTCCATGCAAGTTTCAGCTTTTCTGGCCTAATGGTTTTTAGTAGAAGATTT
1 TA-TTTGAGGATGCTTCCATGCAAGTTTCAGCTTTTCTGGCCTAATGGGTTTTAGTAGAAGATTT
170377 TCAAAGAATAACTCTATATACGTATTTCTATGTAAAACTTCGACCTCCCCATTGTGGCCCCATCT
65 TCAAAGAATAACTCTATATACGTATTTCTATGTAAAACTTCGACCTCCCCATTGTGGCCCCATCT
170442 TACCCATTACCATAATTTGAACAAACTTGAATCTACACCATCTGATGATGCTTCCACACAAGGTG
130 TACCCATTACCATAATTTGAACAAACTTGAATCTACACCATCTGATGATGCTTCCACACAAGGTG
170507 CAGCTTTTCTGTCCAATTGGTTGTTAAAAAGTT
195 CAGCTTTTCTGTCCAATTGGTTGTTAAAAAGTT
170540 TA
1 TA
170542 AAGCTGCTTG
Statistics
Matches: 228, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
227 2 0.01
228 226 0.99
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (227 bp):
TATTTGAGGATGCTTCCATGCAAGTTTCAGCTTTTCTGGCCTAATGGGTTTTAGTAGAAGATTTT
CAAAGAATAACTCTATATACGTATTTCTATGTAAAACTTCGACCTCCCCATTGTGGCCCCATCTT
ACCCATTACCATAATTTGAACAAACTTGAATCTACACCATCTGATGATGCTTCCACACAAGGTGC
AGCTTTTCTGTCCAATTGGTTGTTAAAAAGTT
Found at i:171429 original size:166 final size:167
Alignment explanation
Indices: 171154--171480 Score: 498
Period size: 166 Copynumber: 2.0 Consensus size: 167
171144 CCAAGCAGCT
*
171154 TTAACTCTATATACTCCTATGTAAAACTTCGACCTCCCCATTGTGGCCCCATCTTAACCCCGGAG
1 TTAACTCTATATACTCCTATGTAAAACTTCGACCTCCCCATTGTGGCCCCACCTTAACCCCGGAG
* ** **
171219 ACCATGATTTGCACAAACTTGAATCTATGTGATCTGAGGATGCTTCCACACAAGTTTCAGCTTTT
66 ACCATGATTTGAACAAACACGAATCTAACTGATCTGAGGATGCTTCCACACAAGTTTCAGCTTTT
* *
171284 CTGGCCAAATGGTTTTTGAGAAAAAGATTTTTAAAGA
131 CTCGCCAAATGGTTATTGAGAAAAAGATTTTTAAAGA
* *
171321 TTAACTCTATATACTCCTTTGTAAAACTTCGACC-CCCCATTGTGGCCCCACCTTACCCCCGG-G
1 TTAACTCTATATACTCCTATGTAAAACTTCGACCTCCCCATTGTGGCCCCACCTTAACCCCGGAG
*
171384 TACCATGATTTGAACAAACACGAATGTACACT-ATCTGAGGATGCTTCCACACAAGTTTCAGCTT
66 -ACCATGATTTGAACAAACACGAATCTA-ACTGATCTGAGGATGCTTCCACACAAGTTTCAGCTT
* *
171448 TTCTCGCCTAATGGTTATTGAGAAGAAGATTTT
129 TTCTCGCCAAATGGTTATTGAGAAAAAGATTTT
171481 AAAAAAATAT
Statistics
Matches: 145, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
165 1 0.01
166 110 0.76
167 34 0.23
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (167 bp):
TTAACTCTATATACTCCTATGTAAAACTTCGACCTCCCCATTGTGGCCCCACCTTAACCCCGGAG
ACCATGATTTGAACAAACACGAATCTAACTGATCTGAGGATGCTTCCACACAAGTTTCAGCTTTT
CTCGCCAAATGGTTATTGAGAAAAAGATTTTTAAAGA
Found at i:210118 original size:2 final size:2
Alignment explanation
Indices: 210113--210166 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
210103 GTGTGTGTGA
210113 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
210155 AG AG AG AG AG AG
1 AG AG AG AG AG AG
210167 NGTGTGCTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:211313 original size:200 final size:200
Alignment explanation
Indices: 210970--211369 Score: 800
Period size: 200 Copynumber: 2.0 Consensus size: 200
210960 AAGGGAAACA
210970 TTGGGTTGTGGAAATTGCCTGGTTTAGTGAAATTCATTCATTTTGTTACCTTTAGTATGTGCTGT
1 TTGGGTTGTGGAAATTGCCTGGTTTAGTGAAATTCATTCATTTTGTTACCTTTAGTATGTGCTGT
211035 TTATTTTCATGAATGCAGTATTTTTATTTGTCAAACCCTTTCTTTGTATTTTCTTTGCATGATTT
66 TTATTTTCATGAATGCAGTATTTTTATTTGTCAAACCCTTTCTTTGTATTTTCTTTGCATGATTT
211100 ATTTGATTAAACTAAAGTAATCTTGGAAAGAAATACTTCATTTAATTATCCATAATATTCCTGTA
131 ATTTGATTAAACTAAAGTAATCTTGGAAAGAAATACTTCATTTAATTATCCATAATATTCCTGTA
211165 TCCTT
196 TCCTT
211170 TTGGGTTGTGGAAATTGCCTGGTTTAGTGAAATTCATTCATTTTGTTACCTTTAGTATGTGCTGT
1 TTGGGTTGTGGAAATTGCCTGGTTTAGTGAAATTCATTCATTTTGTTACCTTTAGTATGTGCTGT
211235 TTATTTTCATGAATGCAGTATTTTTATTTGTCAAACCCTTTCTTTGTATTTTCTTTGCATGATTT
66 TTATTTTCATGAATGCAGTATTTTTATTTGTCAAACCCTTTCTTTGTATTTTCTTTGCATGATTT
211300 ATTTGATTAAACTAAAGTAATCTTGGAAAGAAATACTTCATTTAATTATCCATAATATTCCTGTA
131 ATTTGATTAAACTAAAGTAATCTTGGAAAGAAATACTTCATTTAATTATCCATAATATTCCTGTA
211365 TCCTT
196 TCCTT
211370 GCTTGATTTT
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 200 1.00
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (200 bp):
TTGGGTTGTGGAAATTGCCTGGTTTAGTGAAATTCATTCATTTTGTTACCTTTAGTATGTGCTGT
TTATTTTCATGAATGCAGTATTTTTATTTGTCAAACCCTTTCTTTGTATTTTCTTTGCATGATTT
ATTTGATTAAACTAAAGTAATCTTGGAAAGAAATACTTCATTTAATTATCCATAATATTCCTGTA
TCCTT
Found at i:217238 original size:11 final size:11
Alignment explanation
Indices: 217207--217250 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
217197 TAGAAATTTC
*
217207 TTTTCTTTTGT
1 TTTTTTTTTGT
217218 TTTTGTTTTTGT
1 TTTT-TTTTTGT
*
217230 TTTTTTTTTCT
1 TTTTTTTTTGT
217241 TCTTTTTTTT
1 T-TTTTTTTT
217251 TCCCCACGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 11 0.38
12 18 0.62
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:217238 original size:17 final size:16
Alignment explanation
Indices: 217203--217251 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
217193 TGTCTAGAAA
* *
217203 TTTCTTTTCTTTTGTT
1 TTTCTTTTTTTTTTTT
*
217219 TTTGTTTTTGTTTTTTT
1 TTTCTTTTT-TTTTTTT
217236 TTTCTTCTTTTTTTTT
1 TTTCTT-TTTTTTTTT
217252 CCCCACGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 7 0.26
17 17 0.63
18 3 0.11
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.86
Consensus pattern (16 bp):
TTTCTTTTTTTTTTTT
Found at i:224148 original size:17 final size:17
Alignment explanation
Indices: 224126--224161 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
224116 GTTTTAGTCA
* *
224126 ATTTCCGAGTGTTGAGC
1 ATTTCCAAGTATTGAGC
224143 ATTTCCAAGTATTGAGC
1 ATTTCCAAGTATTGAGC
224160 AT
1 AT
224162 ATTTATAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (17 bp):
ATTTCCAAGTATTGAGC
Found at i:233718 original size:25 final size:25
Alignment explanation
Indices: 233682--233743 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
233672 TATCATATCA
* *
233682 TGATCGGTTTATTGATCTCTTTGAT
1 TGATCGGTTTATTGATCTCTGTAAT
*
233707 TGATCGGCTTATTGATCTCTGTAAT
1 TGATCGGTTTATTGATCTCTGTAAT
233732 TGATCGGTTTAT
1 TGATCGGTTTAT
233744 AAATGACCGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.48
Consensus pattern (25 bp):
TGATCGGTTTATTGATCTCTGTAAT
Found at i:242014 original size:2 final size:2
Alignment explanation
Indices: 242007--242088 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
241997 TAGTGTTCTC
242007 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
242049 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
242089 GCGATGAATG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:243439 original size:13 final size:13
Alignment explanation
Indices: 243421--243447 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
243411 TATGATTGAG
243421 TTAAAAACAAAAA
1 TTAAAAACAAAAA
243434 TTAAAAACAAAAA
1 TTAAAAACAAAAA
243447 T
1 T
243448 AGATGTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (13 bp):
TTAAAAACAAAAA
Found at i:252126 original size:39 final size:40
Alignment explanation
Indices: 252052--252146 Score: 138
Period size: 39 Copynumber: 2.4 Consensus size: 40
252042 TTTACGGATC
* * *
252052 GTAAACCATAGTTACCGACGTTAATCTATACTTCACATCT
1 GTAAACTATAGTTAACGACGATAATCTATACTTCACATCT
**
252092 GTAAACTATAGTTAACG-CGATAATCTATGTTTCACATCT
1 GTAAACTATAGTTAACGACGATAATCTATACTTCACATCT
252131 GTAAACTATAGTTAAC
1 GTAAACTATAGTTAAC
252147 ACTGAAAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 35 0.70
40 15 0.30
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.34
Consensus pattern (40 bp):
GTAAACTATAGTTAACGACGATAATCTATACTTCACATCT
Found at i:252353 original size:40 final size:40
Alignment explanation
Indices: 252294--252376 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
252284 ATAAACTAGG
* **
252294 GTTATCGACTGTTAACTATAGTTTCGGATC-CTAAACTATA
1 GTTACCGACTGTTAACTATA-TTTCACATCTCTAAACTATA
*
252334 GTTACCGAC-GTTAATCTATATTTCACATCTGTAAACTATA
1 GTTACCGACTGTTAA-CTATATTTCACATCTCTAAACTATA
252374 GTT
1 GTT
252377 TACGAATGCG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 12 0.32
40 25 0.68
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (40 bp):
GTTACCGACTGTTAACTATATTTCACATCTCTAAACTATA
Found at i:257420 original size:20 final size:18
Alignment explanation
Indices: 257395--257433 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
257385 AGAAGTTTTG
257395 TGATGTACTTATTCATATAT
1 TGATGTA-TT-TTCATATAT
*
257415 TGATGTATTTTCATGTAT
1 TGATGTATTTTCATATAT
257433 T
1 T
257434 TCTTAGTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.54
Consensus pattern (18 bp):
TGATGTATTTTCATATAT
Found at i:258436 original size:14 final size:14
Alignment explanation
Indices: 258417--258444 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
258407 CTTGAGGCTG
258417 TATAAAACAATCTC
1 TATAAAACAATCTC
258431 TATAAAACAATCTC
1 TATAAAACAATCTC
258445 GCAGTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
TATAAAACAATCTC
Found at i:258669 original size:15 final size:15
Alignment explanation
Indices: 258636--258694 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
258626 ATTAAGTTAA
* *
258636 AAAAAAAACAAACAT
1 AAAAAAAACAAAAAC
*
258651 AAAAACAACAAAAAC
1 AAAAAAAACAAAAAC
*
258666 AAAAAAAA-AATAACC
1 AAAAAAAACAA-AAAC
258681 AAACAAAAA-AAAAA
1 AAA-AAAAACAAAAA
258695 ATAAGTTGCC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 2 0.06
15 27 0.75
16 7 0.19
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.03
Consensus pattern (15 bp):
AAAAAAAACAAAAAC
Found at i:258674 original size:20 final size:20
Alignment explanation
Indices: 258639--258694 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
258629 AAGTTAAAAA
*
258639 AAAAACAAACATAAAAACAAC
1 AAAAACAAA-AAAAAAACAAC
*
258660 AAAAACAAAAAAAAAATAAC
1 AAAAACAAAAAAAAAACAAC
*
258680 -CAAACAAAAAAAAAA
1 AAAAACAAAAAAAAAA
258695 ATAAGTTGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 14 0.44
20 9 0.28
21 9 0.28
ACGTcount: A:0.82, C:0.14, G:0.00, T:0.04
Consensus pattern (20 bp):
AAAAACAAAAAAAAAACAAC
Found at i:258675 original size:21 final size:21
Alignment explanation
Indices: 258639--258695 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
258629 AAGTTAAAAA
* *
258639 AAAAACAAACATAAAAACAAC
1 AAAAACAAAAAAAAAAACAAC
*
258660 AAAAAC-AAAAAAAAAATAAC
1 AAAAACAAAAAAAAAAACAAC
*
258680 -CAAACAAAAAAAAAAA
1 AAAAACAAAAAAAAAAA
258696 TAAGTTGCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 4 0.13
20 21 0.68
21 6 0.19
ACGTcount: A:0.82, C:0.14, G:0.00, T:0.04
Consensus pattern (21 bp):
AAAAACAAAAAAAAAAACAAC
Found at i:258698 original size:20 final size:19
Alignment explanation
Indices: 258634--258694 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 19
258624 TCATTAAGTT
*
258634 AAAAAAAA-AA-CAAACAT
1 AAAAAAAATAACCAAACAA
* *
258651 AAAAACAACAA--AAACAA
1 AAAAAAAATAACCAAACAA
258668 AAAAAAAATAACCAAACAA
1 AAAAAAAATAACCAAACAA
258687 AAAAAAAA
1 AAAAAAAA
258695 ATAAGTTGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 21 0.57
18 2 0.05
19 14 0.38
ACGTcount: A:0.84, C:0.13, G:0.00, T:0.03
Consensus pattern (19 bp):
AAAAAAAATAACCAAACAA
Found at i:265777 original size:2 final size:2
Alignment explanation
Indices: 265772--265807 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
265762 TTCAGGACTA
265772 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
265808 ATTTATAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:267992 original size:167 final size:167
Alignment explanation
Indices: 267717--268370 Score: 946
Period size: 167 Copynumber: 3.9 Consensus size: 167
267707 TCATCNTATT
*
267717 CCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCTGGGGGTCATGATTTTCACAA
1 CCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAA
*
267782 CTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTA-GTTT
66 CTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCT-ATTATGGTT
* *
267846 C-TGAGAAGAAGATTGTTAAAGATTTACTCTATATATC
130 CATGAGAAGAAGATTTTTAAAGATTTACTCTATATATA
* * * * *
267883 CCTATGTAAAAGTTTGACCCCCCCATTGTGGCCCCATCCTACCCCCGGGGGTTATGAATTTCACA
1 CCTATGTAAAACTTCGA-CCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACA
* * *
267948 ACATTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCT-GATCTTATGGTT
65 ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTATTATGGTT
* * *
268012 CATGAGAAGAAGATTTTTAAACATTTACTCTGTATATT
130 CATGAGAAGAAGATTTTTAAAGATTTACTCTATATATA
* * * *
268050 CCTATGTAAAAGTTCGACCCCCCATTGTGGTCCCACCCTACTTCCGGGGGGTCATGATTTTCACA
1 CCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTAC-CCCCGGGGGTCATGATTTTCACA
* * * *
268115 ACTTTGAATCTACACTACCAGAGGATGCTTTCACACAAGTGTCAGCTTTCCTGGCTGATTA-GTT
65 ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCT-ATTATGGT
268179 TC-TGAGAAGAAGATTTTTAAAGATTTACTCTATATATA
129 TCATGAGAAGAAGATTTTTAAAGATTTACTCTATATATA
* *
268217 CCTATGTTAAACTTTGACCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAA
1 CCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAA
* * *
268282 CTTTGAAT-TAACACTACCTGAGGATGCTTTCACACAAGTTTCAGCTCTCCTGG-TCTTATGGTT
66 CTTTGAATCT-ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTATTATGGTT
268345 CATGAGAAGAAGATTTTTGAAA-ATTT
130 CATGAGAAGAAGATTTTT-AAAGATTT
268371 CTCGAAAATT
Statistics
Matches: 436, Mismatches: 42, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
164 3 0.01
165 9 0.02
166 133 0.31
167 282 0.65
168 6 0.01
169 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (167 bp):
CCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAA
CTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTATTATGGTTC
ATGAGAAGAAGATTTTTAAAGATTTACTCTATATATA
Found at i:268319 original size:333 final size:333
Alignment explanation
Indices: 267713--268370 Score: 1106
Period size: 333 Copynumber: 2.0 Consensus size: 333
267703 AGAATCATCN
*
267713 TATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCTGGGGGTCATGATTTTC
1 TATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCGGGGGGTCATGATTTTC
* *
267778 ACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAG
66 ACAACTTTGAATCTACACTACCAGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAG
* *
267843 TTTCTGAGAAGAAGATTGTTAAAGATTTACTCTATATATCCCTATGTAAAAGTTTGACCCCCCCA
131 TTTCTGAGAAGAAGATTGTTAAAGATTTACTCTATATATACCTATGTAAAACTTTGACCCCCCCA
* *
267908 TTGTGGCCCCATCCTACCCCCGGGGGTTATGAATTTCACAACATTGAATCTACACTACCTGAGGA
196 TTGTGGCCCCACCCTACCCCCGGGGGTCATGAATTTCACAACATTGAATCTACACTACCTGAGGA
*
267973 TGCTTCCACACAAGTTTCAGCTTTCCTGATCTTATGGTTCATGAGAAGAAGATTTTT-AAACATT
261 TGCTTCCACACAAGTTTCAGCTCTCCTGATCTTATGGTTCATGAGAAGAAGATTTTTGAAA-ATT
268037 TACTCTGTA
325 TACTCTGTA
* * *
268046 TATTCCTATGTAAAAGTTCGACCCCCCATTGTGGTCCCACCCTACTTCCGGGGGGTCATGATTTT
1 TATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTAC-CCCGGGGGGTCATGATTTT
*
268111 CACAACTTTGAATCTACACTACCAGAGGATGCTTTCACACAAGTGTCAGCTTTCCTGGCTGATTA
65 CACAACTTTGAATCTACACTACCAGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTA
* *
268176 GTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATACCTATGTTAAACTTTGA-CCCCCC
130 GTTTCTGAGAAGAAGATTGTTAAAGATTTACTCTATATATACCTATGTAAAACTTTGACCCCCCC
* *
268240 ATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAAT-TAACACTACCTGAG
195 ATTGTGGCCCCACCCTACCCCCGGGGGTCATGAATTTCACAACATTGAATCT-ACACTACCTGAG
* *
268304 GATGCTTTCACACAAGTTTCAGCTCTCCTGGTCTTATGGTTCATGAGAAGAAGATTTTTGAAAAT
259 GATGCTTCCACACAAGTTTCAGCTCTCCTGATCTTATGGTTCATGAGAAGAAGATTTTTGAAAAT
268369 TT
324 TT
268371 CTCGAAAATT
Statistics
Matches: 304, Mismatches: 18, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
332 1 0.00
333 167 0.55
334 136 0.45
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (333 bp):
TATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACCCCGGGGGGTCATGATTTTC
ACAACTTTGAATCTACACTACCAGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAG
TTTCTGAGAAGAAGATTGTTAAAGATTTACTCTATATATACCTATGTAAAACTTTGACCCCCCCA
TTGTGGCCCCACCCTACCCCCGGGGGTCATGAATTTCACAACATTGAATCTACACTACCTGAGGA
TGCTTCCACACAAGTTTCAGCTCTCCTGATCTTATGGTTCATGAGAAGAAGATTTTTGAAAATTT
ACTCTGTA
Found at i:275130 original size:40 final size:38
Alignment explanation
Indices: 275086--275164 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 38
275076 TTTTTTTTGT
* * **
275086 AGTTATAGGTTTTACCCCCCCCCCCCCCCACTGGATTAGG
1 AGTTATAGGTTTAACCCACCCCAACCCCC-C-GGATTAGG
275126 AGTTATAGGTTTAACCCACCCCAACCCCCCGGATTAGG
1 AGTTATAGGTTTAACCCACCCCAACCCCCCGGATTAGG
275164 A
1 A
275165 TTTTCAGGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 9 0.26
39 1 0.03
40 25 0.71
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (38 bp):
AGTTATAGGTTTAACCCACCCCAACCCCCCGGATTAGG
Found at i:279754 original size:22 final size:22
Alignment explanation
Indices: 279729--279778 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
279719 GAAGCGATGT
*
279729 TGCGATAGCGCGATGACAATGA
1 TGCGATAACGCGATGACAATGA
* * * *
279751 TGCGACAATGCGATGACGATGG
1 TGCGATAACGCGATGACAATGA
279773 TGCGAT
1 TGCGAT
279779 GACACAATGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.20
Consensus pattern (22 bp):
TGCGATAACGCGATGACAATGA
Found at i:280560 original size:1 final size:1
Alignment explanation
Indices: 280554--280580 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
280544 TCTCTCTCTC
280554 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
280581 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:289936 original size:2 final size:2
Alignment explanation
Indices: 289929--289977 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
289919 AGAAAAGGTA
289929 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
289971 AG AG AG A
1 AG AG AG A
289978 ATATGTATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:293717 original size:10 final size:10
Alignment explanation
Indices: 293702--293729 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
293692 NNNNNNNNNA
293702 ATATATATTT
1 ATATATATTT
293712 ATATATATTT
1 ATATATATTT
293722 ATATATAT
1 ATATATAT
293730 AGATCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATATATATTT
Found at i:295169 original size:21 final size:21
Alignment explanation
Indices: 295144--295287 Score: 225
Period size: 21 Copynumber: 6.9 Consensus size: 21
295134 TCTTCATAAT
*
295144 ATGCTGATACTTCAACATTAC
1 ATGCTGATACTTTAACATTAC
295165 ATGCTGATACTTTAACATTAC
1 ATGCTGATACTTTAACATTAC
* *
295186 ATGATGGTACTTTAACATTAC
1 ATGCTGATACTTTAACATTAC
* *
295207 GTGCTGATACTTCAACATTAC
1 ATGCTGATACTTTAACATTAC
295228 ATGCTGATACTTTAACATTAC
1 ATGCTGATACTTTAACATTAC
* *
295249 ATGATGGTACTTTAACATTAC
1 ATGCTGATACTTTAACATTAC
295270 ATGCTGATACTTTAACAT
1 ATGCTGATACTTTAACAT
295288 CACCTAAAGT
Statistics
Matches: 110, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 110 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGCTGATACTTTAACATTAC
Found at i:295244 original size:63 final size:63
Alignment explanation
Indices: 295144--295287 Score: 270
Period size: 63 Copynumber: 2.3 Consensus size: 63
295134 TCTTCATAAT
295144 ATGCTGATACTTCAACATTACATGCTGATACTTTAACATTACATGATGGTACTTTAACATTAC
1 ATGCTGATACTTCAACATTACATGCTGATACTTTAACATTACATGATGGTACTTTAACATTAC
*
295207 GTGCTGATACTTCAACATTACATGCTGATACTTTAACATTACATGATGGTACTTTAACATTAC
1 ATGCTGATACTTCAACATTACATGCTGATACTTTAACATTACATGATGGTACTTTAACATTAC
*
295270 ATGCTGATACTTTAACAT
1 ATGCTGATACTTCAACAT
295288 CACCTAAAGT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 78 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (63 bp):
ATGCTGATACTTCAACATTACATGCTGATACTTTAACATTACATGATGGTACTTTAACATTAC
Found at i:297144 original size:20 final size:20
Alignment explanation
Indices: 297107--297143 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
297097 TATTATCCGT
297107 TTTTTTGTGTTTTATTTTTG
1 TTTTTTGTGTTTTATTTTTG
297127 TTTTTTGT-TTTT-TTTTT
1 TTTTTTGTGTTTTATTTTT
297144 TAGATTTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (20 bp):
TTTTTTGTGTTTTATTTTTG
Found at i:300163 original size:2 final size:2
Alignment explanation
Indices: 300156--300191 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
300146 AGGTACCGGG
300156 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
300192 GGGAAGTGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:304701 original size:45 final size:45
Alignment explanation
Indices: 304661--304939 Score: 409
Period size: 45 Copynumber: 6.2 Consensus size: 45
304651 CCCTATCCCA
* * * * * *
304661 ACAAAGTCTACTACTGCCACGCCATCACCTGGCAAAC-CTATC-CGA
1 ACAAAGGCTCCTACTGCCGCGCCATCACCTGAC-AACTCTAACAC-T
* * * * * * *
304706 ACAAAGTCTACTACTGCCACGCCTTCACCTGACAACCCTATCCCT
1 ACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACT
304751 ACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACT
1 ACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACT
304796 ACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACT
1 ACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACT
304841 ACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACT
1 ACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACT
304886 ACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACT
1 ACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACT
304931 ACAAAGGCT
1 ACAAAGGCT
304940 AAGACTACCA
Statistics
Matches: 222, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
44 3 0.01
45 218 0.98
46 1 0.00
ACGTcount: A:0.29, C:0.39, G:0.13, T:0.18
Consensus pattern (45 bp):
ACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACT
Found at i:304855 original size:135 final size:135
Alignment explanation
Indices: 304661--305002 Score: 436
Period size: 135 Copynumber: 2.5 Consensus size: 135
304651 CCCTATCCCA
* * * *
304661 ACAAAGTCTACTACTGCCACGCCATCACCTGGCAAACCTATCCGAACAAAGTCTACTACTGCCAC
1 ACAAAGGCTACTACTGCCACGCCATCACCTGACAAACCTAACCGAACAAAGGCTACTACTGCCAC
* * *
304726 GCCTTCACCTGACAACCCTATCCCTACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTA
66 GCCATCACCTGACAACCCTAACACTACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTA
304791 ACACT
131 ACACT
* * * *
304796 ACAAAGGCTCCTACTGCCGCGCCATCACCTGAC-AACTCTAACAC-TACAAAGGCTCCTACTGCC
1 ACAAAGGCTACTACTGCCACGCCATCACCTGACAAAC-CTAAC-CGAACAAAGGCTACTACTGCC
* *
304859 GCGCCATCACCTGACAACTCTAACACTACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTC
64 ACGCCATCACCTGACAACCCTAACACTACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTC
304924 TAACACT
129 TAACACT
** * * * * * * * *
304931 ACAAAGGCTAAGACTACCACACCATCACTTGACAACCCTAACCCAACAAAAGCTAGTACTACCAC
1 ACAAAGGCTACTACTGCCACGCCATCACCTGACAAACCTAACCGAACAAAGGCTACTACTGCCAC
*
304996 ACCATCA
66 GCCATCA
305003 AATGTCAAAT
Statistics
Matches: 175, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
134 4 0.02
135 168 0.96
136 3 0.02
ACGTcount: A:0.32, C:0.39, G:0.12, T:0.18
Consensus pattern (135 bp):
ACAAAGGCTACTACTGCCACGCCATCACCTGACAAACCTAACCGAACAAAGGCTACTACTGCCAC
GCCATCACCTGACAACCCTAACACTACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTA
ACACT
Found at i:304956 original size:45 final size:45
Alignment explanation
Indices: 304730--305093 Score: 311
Period size: 45 Copynumber: 8.1 Consensus size: 45
304720 TGCCACGCCT
* * * ** * * *
304730 TCACCTGACAACCCTATCCCTACAAAGGCTCCTACTGCCGCGCCA
1 TCACCTGACAACTCTAACACTACAAAGGCTCAGACTACCACACCA
** * * *
304775 TCACCTGACAACTCTAACACTACAAAGGCTCCTACTGCCGCGCCA
1 TCACCTGACAACTCTAACACTACAAAGGCTCAGACTACCACACCA
** * * *
304820 TCACCTGACAACTCTAACACTACAAAGGCTCCTACTGCCGCGCCA
1 TCACCTGACAACTCTAACACTACAAAGGCTCAGACTACCACACCA
** * * *
304865 TCACCTGACAACTCTAACACTACAAAGGCTCCTACTGCCGCGCCA
1 TCACCTGACAACTCTAACACTACAAAGGCTCAGACTACCACACCA
*
304910 TCACCTGACAACTCTAACACTACAAAGGCTAAGACTACCACACCA
1 TCACCTGACAACTCTAACACTACAAAGGCTCAGACTACCACACCA
* * * * *
304955 TCACTTGACAACCCTAACCCAACAAAAGCT-AGTACTACCACACCA
1 TCACCTGACAACTCTAACACTACAAAGGCTCAG-ACTACCACACCA
** * * * *
305000 TCAAATGTCAAATCTCAA-ACTCCAAAGGCTAAGACTACCACACCA
1 TCACCTGACAACTCT-AACACTACAAAGGCTCAGACTACCACACCA
** * * * *
305045 TCAAATGTCAAATCTCAA-ACTCCAAAGGCTAAGACTACCACACCA
1 TCACCTGACAACTCT-AACACTACAAAGGCTCAGACTACCACACCA
305090 TCAC
1 TCAC
305094 TTGTCACCCC
Statistics
Matches: 292, Mismatches: 24, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
44 2 0.01
45 286 0.98
46 4 0.01
ACGTcount: A:0.34, C:0.38, G:0.11, T:0.17
Consensus pattern (45 bp):
TCACCTGACAACTCTAACACTACAAAGGCTCAGACTACCACACCA
Found at i:304956 original size:90 final size:90
Alignment explanation
Indices: 304706--305047 Score: 362
Period size: 90 Copynumber: 3.8 Consensus size: 90
304696 ACCTATCCGA
* * * * * *** * *
304706 ACAAAGTCTACTACTGCCACGCCTTCACCTGACAACCCTATCCCTACAAAGGCTCCTACTGCCGC
1 ACAAAGGCTACTACTGCCACGCCATCACCTGACAACTCTAACACTACAAAGGCTAAGACTACCAC
*
304771 GCCATCACCTGACAACTCTAACACT
66 ACCATCACCTGACAACTCTAACACT
* * *** * *
304796 ACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACTACAAAGGCTCCTACTGCCGC
1 ACAAAGGCTACTACTGCCACGCCATCACCTGACAACTCTAACACTACAAAGGCTAAGACTACCAC
*
304861 GCCATCACCTGACAACTCTAACACT
66 ACCATCACCTGACAACTCTAACACT
* *
304886 ACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACTACAAAGGCTAAGACTACCAC
1 ACAAAGGCTACTACTGCCACGCCATCACCTGACAACTCTAACACTACAAAGGCTAAGACTACCAC
* * * *
304951 ACCATCACTTGACAACCCTAACCCA
66 ACCATCACCTGACAACTCTAACACT
* * * * ** * * *
304976 ACAAAAGCTAGTACTACCACACCATCAAATGTCAAATCTCAA-ACTCCAAAGGCTAAGACTACCA
1 ACAAAGGCTACTACTGCCACGCCATCACCTGACAACTCT-AACACTACAAAGGCTAAGACTACCA
305040 CACCATCA
65 CACCATCA
305048 AATGTCAAAT
Statistics
Matches: 223, Mismatches: 28, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
90 221 0.99
91 2 0.01
ACGTcount: A:0.33, C:0.38, G:0.11, T:0.18
Consensus pattern (90 bp):
ACAAAGGCTACTACTGCCACGCCATCACCTGACAACTCTAACACTACAAAGGCTAAGACTACCAC
ACCATCACCTGACAACTCTAACACT
Found at i:305026 original size:135 final size:135
Alignment explanation
Indices: 304749--305109 Score: 384
Period size: 135 Copynumber: 2.7 Consensus size: 135
304739 AACCCTATCC
*** *
304749 CTACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACTACAAAGGCTCCTACTGCC
1 CTACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACTACAAAGGCTAAGACTACC
* * * * * * * * * * * ** *
304814 GCGCCATCACCTGACAACTCTAACACTACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTC
66 ACACCATCACTTGACAACCCTAACCCAACAAAAGCTACTACTACCACACCATCAAATGACAAATC
304879 TAACA
131 TAACA
304884 CTACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACTACAAAGGCTAAGACTACC
1 CTACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACTACAAAGGCTAAGACTACC
* *
304949 ACACCATCACTTGACAACCCTAACCCAACAAAAGCTAGTACTACCACACCATCAAATGTCAAATC
66 ACACCATCACTTGACAACCCTAACCCAACAAAAGCTACTACTACCACACCATCAAATGACAAATC
305014 TCAA-A
131 T-AACA
* *** * * * ** * * *
305019 CTCCAAAGGCTAAGACTACCACACCATCAAATGTCAAATCTCAA-ACTCCAAAGGCTAAGACTAC
1 CTACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCT-AACACTACAAAGGCTAAGACTAC
* *
305083 CACACCATCACTTGTCACCCCTAACCC
65 CACACCATCACTTGACAACCCTAACCC
305110 TACGAAGACT
Statistics
Matches: 190, Mismatches: 34, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
135 186 0.98
136 4 0.02
ACGTcount: A:0.34, C:0.38, G:0.11, T:0.17
Consensus pattern (135 bp):
CTACAAAGGCTCCTACTGCCGCGCCATCACCTGACAACTCTAACACTACAAAGGCTAAGACTACC
ACACCATCACTTGACAACCCTAACCCAACAAAAGCTACTACTACCACACCATCAAATGACAAATC
TAACA
Found at i:315001 original size:163 final size:164
Alignment explanation
Indices: 314725--315040 Score: 474
Period size: 163 Copynumber: 1.9 Consensus size: 164
314715 AATTTATTGT
* * *
314725 TCAGTAAATATGAAAGGTAATATTTAAATACATTTTGGTAATGTAAAGGTCAACTTTGCATCTTT
1 TCAGTAAACATGAAAGGTAATATTTAAATACATTTTGGTAAGGTAAAGATCAACTTTGCATCTTT
** * * *
314790 ACTTTGATTAAAGTTGATACAAAGGTATATCTAAAATTCTGGGCATCTTTATTTAAATTTACTG-
66 ACTTCAATTAAAGTTGATACAAAGGTATACCTAAAATTCCGGGCATCTTTAATTAAATTTACTGC
314854 TAAAGTAAATTTTTGTAAAGGTGTGAATTACTGC
131 TAAAGTAAATTTTTGTAAAGGTGTGAATTACTGC
* *
314888 TCAGTAAACATGAAAGGTAATATTTAAATACATTTTGGTACGGTAAAGATCAACTTTGTATCTTT
1 TCAGTAAACATGAAAGGTAATATTTAAATACATTTTGGTAAGGTAAAGATCAACTTTGCATCTTT
* * *
314953 ACTTCAATTAAAGTTGATACAAAGGTA-ACCTTGATATTCCGTGCATCTTTAATTAAATTTACTG
66 ACTTCAATTAAAGTTGATACAAAGGTATACC-TAAAATTCCGGGCATCTTTAATTAAATTTACTG
**
315017 CTGCAGTAAATTTTTGTAAAGGTG
130 CTAAAGTAAATTTTTGTAAAGGTG
315041 GTTTTTCAAG
Statistics
Matches: 136, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
162 2 0.01
163 113 0.83
164 21 0.15
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (164 bp):
TCAGTAAACATGAAAGGTAATATTTAAATACATTTTGGTAAGGTAAAGATCAACTTTGCATCTTT
ACTTCAATTAAAGTTGATACAAAGGTATACCTAAAATTCCGGGCATCTTTAATTAAATTTACTGC
TAAAGTAAATTTTTGTAAAGGTGTGAATTACTGC
Found at i:315291 original size:17 final size:17
Alignment explanation
Indices: 315269--315301 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
315259 TTTCATCTAA
315269 ATGAAATTCCAAAAAAT
1 ATGAAATTCCAAAAAAT
*
315286 ATGAAATTCTAAAAAA
1 ATGAAATTCCAAAAAA
315302 AAATATGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.09, G:0.06, T:0.24
Consensus pattern (17 bp):
ATGAAATTCCAAAAAAT
Found at i:320991 original size:4 final size:4
Alignment explanation
Indices: 320982--321060 Score: 63
Period size: 4 Copynumber: 19.0 Consensus size: 4
320972 TGATTTGCAT
* * *
320982 ATTG ATTG ATTG ATTG AAAT- ATTG TTTG AATT- ATTG ATTG ATTG ATTTT
1 ATTG ATTG ATTG ATTG -ATTG ATTG ATTG -ATTG ATTG ATTG ATTG A-TTG
*
321031 ATTG ATTG ATTC ATCTTG ATTG ATTG ATTG
1 ATTG ATTG ATTG A--TTG ATTG ATTG ATTG
321061 TTTGGTTCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
3 5 0.08
4 45 0.75
5 7 0.12
6 3 0.05
ACGTcount: A:0.27, C:0.03, G:0.19, T:0.52
Consensus pattern (4 bp):
ATTG
Found at i:321036 original size:13 final size:14
Alignment explanation
Indices: 321018--321055 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
321008 TGAATTATTG
*
321018 ATTGATTGATT-TT
1 ATTGATTGATTCAT
321031 ATTGATTGATTCAT
1 ATTGATTGATTCAT
*
321045 CTTGATTGATT
1 ATTGATTGATT
321056 GATTGTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.55
Consensus pattern (14 bp):
ATTGATTGATTCAT
Found at i:321051 original size:14 final size:13
Alignment explanation
Indices: 320990--321055 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 13
320980 ATATTGATTG
*
320990 ATTGATTGA-AAT
1 ATTGATTGATTAT
*
321002 ATTGTTTGAATTATT
1 ATTGATTG-ATTA-T
*
321017 GATTGATTGATTTT
1 -ATTGATTGATTAT
321031 ATTGATTGATTCAT
1 ATTGATTGATT-AT
*
321045 CTTGATTGATT
1 ATTGATTGATT
321056 GATTGTTTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
12 7 0.16
13 12 0.28
14 13 0.30
15 4 0.09
16 7 0.16
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.53
Consensus pattern (13 bp):
ATTGATTGATTAT
Found at i:321069 original size:26 final size:27
Alignment explanation
Indices: 321019--321070 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
321009 GAATTATTGA
*
321019 TTGATTGATTTTATTGATTGATTCATC
1 TTGATTGATTTGATTGATTGATTCATC
* *
321046 TTGATTGA-TTGATTGTTTGGTTCAT
1 TTGATTGATTTGATTGATTGATTCAT
321071 TGAAGATCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (27 bp):
TTGATTGATTTGATTGATTGATTCATC
Found at i:324530 original size:2 final size:2
Alignment explanation
Indices: 324523--324559 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
324513 NNNNNNNAGC
324523 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
324560 GCAAGTATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:328119 original size:2 final size:2
Alignment explanation
Indices: 328112--328152 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
328102 CATGTAGCAA
328112 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
328153 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:332653 original size:11 final size:11
Alignment explanation
Indices: 332639--332685 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
332629 ACTAGAGTGG
332639 ACCCAGAGTAA
1 ACCCAGAGTAA
332650 ACCCCA-AGTAA
1 A-CCCAGAGTAA
**
332661 ACCCAGAGTGG
1 ACCCAGAGTAA
*
332672 ACACAGAGTAA
1 ACCCAGAGTAA
332683 ACC
1 ACC
332686 TCGATCAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
10 4 0.14
11 20 0.71
12 4 0.14
ACGTcount: A:0.43, C:0.30, G:0.19, T:0.09
Consensus pattern (11 bp):
ACCCAGAGTAA
Found at i:333171 original size:30 final size:30
Alignment explanation
Indices: 333130--333188 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
333120 AATATATACC
*
333130 AATAGATATTTAATGTTAACTTCTACATGA
1 AATAAATATTTAATGTTAACTTCTACATGA
*
333160 AATAAATATTTAATGTTAACTTGTACATG
1 AATAAATATTTAATGTTAACTTCTACATG
333189 GACTAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (30 bp):
AATAAATATTTAATGTTAACTTCTACATGA
Found at i:338801 original size:16 final size:16
Alignment explanation
Indices: 338780--338811 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
338770 TCCTATGGGA
338780 ATGTATGTTACTATGT
1 ATGTATGTTACTATGT
338796 ATGTATGTTACTATGT
1 ATGTATGTTACTATGT
338812 TTAAACTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (16 bp):
ATGTATGTTACTATGT
Found at i:343370 original size:367 final size:366
Alignment explanation
Indices: 342697--343428 Score: 1446
Period size: 367 Copynumber: 2.0 Consensus size: 366
342687 AATTAAATTG
342697 TCAAATGATTTACAACGAACTACTCTATGGAATCATTTGCAAACGGAATTTGCACAGGAAGACAT
1 TCAAATGATTTACAACGAACTACTCTATGGAATCATTTGCAAACGGAATTTGCACAGGAAGACAT
342762 TGATATAATGTTGATTGAATCAAGCAATCTAAATGGATTTTCATTCAAAAATATGAATTACACAA
66 TGATATAATGTTGATTGAATCAAGCAATCTAAATGGATTTTCATTCAAAAATATGAATTACACAA
342827 GGTAAGAAGATACAGTGTACTTCTCATGAAATAAGTAGAAATTCCTTATATCAATGATACTTTAA
131 GGTAAGAAGATACAGTGTACTTCTCATGAAATAAGTAGAAATTCCTTATATCAATGATACTTTAA
342892 TTGATTGAAACTTGGTGACCATGTTTTCCATGCAACGTATACCAAGGAGGTAGAGCTTAAACCCC
196 TTGATTGAAACTTGGTGACCATGTTTTCCATGCAACGTATACCAAGGAGGTAGAGCTTAAACCCC
342957 ATCCACCCCCCACCCCCCACCCCTGCACGCCAACCAAAAAAATCCAATTTGCGTTGCAGTAGTTT
261 ATCCACCCCCCACCCCCCACCCCTGCACGCCAACCAAAAAAATCCAATTTGCGTTGCAGTAGTTT
343022 TGTGTTTGGTCTAAAAAGAACACTTGCTGTTTATCGGCTTT
326 TGTGTTTGGTCTAAAAAGAACACTTGCTGTTTATCGGCTTT
343063 NTCAAATGATTTACAACGAACTACTCTATGGAATCATTTGCAAACGGAATTTGCACAGGAAGACA
1 -TCAAATGATTTACAACGAACTACTCTATGGAATCATTTGCAAACGGAATTTGCACAGGAAGACA
343128 TTGATATAATGTTGATTGAATCAAGCAATCTAAATGGATTTTCATTCAAAAATATGAATTACACA
65 TTGATATAATGTTGATTGAATCAAGCAATCTAAATGGATTTTCATTCAAAAATATGAATTACACA
343193 AGGTAAGAAGATACAGTGTACTTCTCATGAAATAAGTAGAAATTCCTTATATCAATGATACTTTA
130 AGGTAAGAAGATACAGTGTACTTCTCATGAAATAAGTAGAAATTCCTTATATCAATGATACTTTA
343258 ATTGATTGAAACTTGGTGACCATGTTTTCCATGCAACGTATACCAAGGAGGTAGAGCTTAAACCC
195 ATTGATTGAAACTTGGTGACCATGTTTTCCATGCAACGTATACCAAGGAGGTAGAGCTTAAACCC
343323 CATCCACCCCCCACCCCCCACCCCTGCACGCCAACCAAAAAAATCCAATTTGCGTTGCAGTAGTT
260 CATCCACCCCCCACCCCCCACCCCTGCACGCCAACCAAAAAAATCCAATTTGCGTTGCAGTAGTT
*
343388 TTGTGTTTGGTCTAAAAAGAACACTTGCTGTTTATTGGCTT
325 TTGTGTTTGGTCTAAAAAGAACACTTGCTGTTTATCGGCTT
343429 GACCTGTTGT
Statistics
Matches: 364, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
367 364 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (366 bp):
TCAAATGATTTACAACGAACTACTCTATGGAATCATTTGCAAACGGAATTTGCACAGGAAGACAT
TGATATAATGTTGATTGAATCAAGCAATCTAAATGGATTTTCATTCAAAAATATGAATTACACAA
GGTAAGAAGATACAGTGTACTTCTCATGAAATAAGTAGAAATTCCTTATATCAATGATACTTTAA
TTGATTGAAACTTGGTGACCATGTTTTCCATGCAACGTATACCAAGGAGGTAGAGCTTAAACCCC
ATCCACCCCCCACCCCCCACCCCTGCACGCCAACCAAAAAAATCCAATTTGCGTTGCAGTAGTTT
TGTGTTTGGTCTAAAAAGAACACTTGCTGTTTATCGGCTTT
Found at i:343682 original size:13 final size:13
Alignment explanation
Indices: 343664--343688 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
343654 GTTTCTCTTC
343664 CAAGTCCCGCTTG
1 CAAGTCCCGCTTG
343677 CAAGTCCCGCTT
1 CAAGTCCCGCTT
343689 CAATGCAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.20, T:0.24
Consensus pattern (13 bp):
CAAGTCCCGCTTG
Found at i:351083 original size:4 final size:4
Alignment explanation
Indices: 351076--351102 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
351066 AATGGGAGGT
351076 AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAA
351103 AATCTACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:365632 original size:18 final size:18
Alignment explanation
Indices: 365609--365643 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
365599 TTATTACACC
*
365609 TGGTTTCACATATTCATT
1 TGGTTTAACATATTCATT
*
365627 TGGTTTAACATTTTCAT
1 TGGTTTAACATATTCAT
365644 ATTTGACACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.51
Consensus pattern (18 bp):
TGGTTTAACATATTCATT
Found at i:372272 original size:12 final size:12
Alignment explanation
Indices: 372253--372286 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
372243 TCTCAGTTCT
*
372253 TGTGGTGGTTGC
1 TGTGGTGGTAGC
*
372265 TTTGGTGGTAGC
1 TGTGGTGGTAGC
372277 TGTGGTGGTA
1 TGTGGTGGTA
372287 CTCACAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.06, G:0.47, T:0.41
Consensus pattern (12 bp):
TGTGGTGGTAGC
Found at i:376888 original size:23 final size:22
Alignment explanation
Indices: 376850--376893 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
376840 TACAAAGTGC
376850 CTGTTTTATTATCTATTGTTAAT
1 CTGTTTTATTATCTATT-TTAAT
376873 CTGTTTTATT-TGCTATTTTAA
1 CTGTTTTATTAT-CTATTTTAA
376894 AGTAACCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.61
Consensus pattern (22 bp):
CTGTTTTATTATCTATTTTAAT
Found at i:378765 original size:13 final size:13
Alignment explanation
Indices: 378747--378773 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
378737 TGATAAGTTC
378747 CATCAATACCAAT
1 CATCAATACCAAT
378760 CATCAATACCAAT
1 CATCAATACCAAT
378773 C
1 C
378774 GAAAAAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (13 bp):
CATCAATACCAAT
Found at i:393019 original size:2 final size:2
Alignment explanation
Indices: 393012--393048 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
393002 AGATGCCTTG
393012 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
393049 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:396431 original size:2 final size:2
Alignment explanation
Indices: 396426--396484 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
396416 CACACACACA
*
396426 CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
396468 CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
396485 AAAAGCGCAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Done.