Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 101 of 120
Found at i:29784528 original size:217 final size:217
Alignment explanation
Indices: 29784259--29784681 Score: 720
Period size: 217 Copynumber: 1.9 Consensus size: 217
29784249 TGTATAATCA
* * *
29784259 TATACAAATTAAATTCAGCAATGTATAACCATATACAAATCAATTTGGCAACTTATATCCATATA
1 TATACAAATTAAATTCAGCAATATATAACAATATACAAATCAATTCGGCAACTTATATCCATATA
* *
29784324 CAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATATAATAATATACAA
66 CAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATACAACAATATACAA
*
29784389 ATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTA
131 ATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAATGTATAACCATATACAAATTA
*
29784454 ATTTTAGCAATACACAACAATG
196 ATTTCAGCAATACACAACAATG
* * * *
29784476 TATACAAATTAATTTCAGCAATATATAATAATATACGAATCAATTCGGCAACTTATATTCATATA
1 TATACAAATTAAATTCAGCAATATATAACAATATACAAATCAATTCGGCAACTTATATCCATATA
* * *
29784541 CAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATGTACAACCATATACGA
66 CAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATACAACAATATACAA
29784606 ATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAATGTATAACCATATACAAATTA
131 ATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAATGTATAACCATATACAAATTA
29784671 ATTTCAGCAAT
196 ATTTCAGCAAT
29784682 GTACAATCAT
Statistics
Matches: 192, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
217 192 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (217 bp):
TATACAAATTAAATTCAGCAATATATAACAATATACAAATCAATTCGGCAACTTATATCCATATA
CAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATACAACAATATACAA
ATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAATGTATAACCATATACAAATTA
ATTTCAGCAATACACAACAATG
Found at i:29784706 original size:92 final size:93
Alignment explanation
Indices: 29784141--29784758 Score: 491
Period size: 92 Copynumber: 6.7 Consensus size: 93
29784131 ATCCAATGCT
* * * * * * *
29784141 CAAATCAATTCAGCAATATATATTCATATACGAA--CAAAATTCGGCAATGTATATCTATATACA
1 CAAATCAATTCGGCAATGTATATTCATATACAAATTC-AATTTCAGCAATGTATAACCATATACA
* *
29784204 AATCAA-TTCGGCAATGTACAACCATATA
65 AATCAATTTCAGCAATGTACAATCATATA
* *
29784232 -AGAATCAAGTTCGGCAATGTATAATCATATACAAATT-AAATTCAGCAATGTATAACCATATAC
1 CA-AATCAA-TTCGGCAATGTATATTCATATACAAATTCAATTTCAGCAATGTATAACCATATAC
* *
29784295 AAATCAATTT-GGCAACT-TA-TATCCATATA
64 AAATCAATTTCAGCAA-TGTACAAT-CATATA
* ** ** * * **
29784324 CAATTCAATTTCAACAATGTATAACCATGTACAAATT-AATTTCAGCAATATATAATAATATACA
1 CAAATCAA-TTCGGCAATGTATATTCATATACAAATTCAATTTCAGCAATGTATAACCATATACA
* * *
29784388 AATCAA-TTCGGCAACT-TATATTCATATA
65 AATCAATTTCAGCAA-TGTACAATCATATA
* ** ** * * ** * *
29784416 CAATTCAATTTCAACAATGTATAACCATGTACAAATT-AATTTTAGCAATACACAACAATGTATA
1 CAAATCAA-TTCGGCAATGTATATTCATATACAAATTCAATTTCAGCAATGTATAACCA--TATA
* * * *
29784480 CAAATTAATTTCAGCAATATATAATAATATA
63 CAAATCAATTTCAGCAATGTACAATCATATA
* * *
29784511 CGAATCAATTCGGCAACT-TATATTCATATAC-AATTCAATTTCAACAATGTATAACCATGTACA
1 CAAATCAATTCGGCAA-TGTATATTCATATACAAATTCAATTTCAGCAATGTATAACCATATACA
* *
29784574 AATTAATTTCAGCAATGTACAACCATATA
65 AATCAATTTCAGCAATGTACAATCATATA
* *
29784603 CGAATCAATTCGGCAACT-TATATTCATATAC-AATTCAATTTCAACAATGTATAACCATATACA
1 CAAATCAATTCGGCAA-TGTATATTCATATACAAATTCAATTTCAGCAATGTATAACCATATACA
*
29784666 AATTAATTTCAGCAATGTACAATCATATA
65 AATCAATTTCAGCAATGTACAATCATATA
* * * * * *
29784695 CAAATCAATTCGGGAACT-TATATCCATATGCAAA-TCAATTTC-GACAACGTATAACTATAAAC
1 CAAATCAATTCGGCAA-TGTATATTCATATACAAATTCAATTTCAG-CAATGTATAACCATATAC
29784757 AA
64 AA
29784759 TTCGAATTCT
Statistics
Matches: 452, Mismatches: 57, Indels: 35
0.83 0.10 0.06
Matches are distributed among these distances:
90 1 0.00
91 9 0.02
92 364 0.81
93 11 0.02
94 43 0.10
95 24 0.05
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (93 bp):
CAAATCAATTCGGCAATGTATATTCATATACAAATTCAATTTCAGCAATGTATAACCATATACAA
ATCAATTTCAGCAATGTACAATCATATA
Found at i:29787319 original size:14 final size:15
Alignment explanation
Indices: 29787282--29787323 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
29787272 TGTGGCCGGT
*
29787282 TAAAATTTAGTATTA
1 TAAATTTTAGTATTA
29787297 TATATATTTTA-TATTA
1 TA-A-ATTTTAGTATTA
29787313 TAAATTTTAGT
1 TAAATTTTAGT
29787324 TAAATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 6 0.26
15 4 0.17
16 8 0.35
17 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (15 bp):
TAAATTTTAGTATTA
Found at i:29792927 original size:124 final size:124
Alignment explanation
Indices: 29792626--29793001 Score: 603
Period size: 124 Copynumber: 3.0 Consensus size: 124
29792616 TTAGGGTTTT
* *** * *
29792626 TAGGTCTTGGAAGAAATAATTTCGAGTTGACGTTTCTGATCAAATAGTATAAAATCACTTCTAGC
1 TAGGTCATGGAAGAAATAATTT-TTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
*
29792691 AGGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGAC-CGCTTTTGCTATAG
65 AGGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
29792750 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
1 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
*
29792815 GGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTAGACGCGCTTTTGCTACAG
66 GGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* *
29792874 TCGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGCATAAAATCGCTTCTAGCA
1 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
* *
29792939 GGATGATATTTGAGAAGAATTTGTGAAAATCGTGCCCTCGTGGACGCG-TTCTTGCTACAG
66 GGATGCTATTTGAGAAGAATTTGT-AAAATCGCGCCCTCGTGGACGCGCTT-TTGCTACAG
29792999 TAG
1 TAG
29793002 CATGTTTGGG
Statistics
Matches: 235, Mismatches: 14, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
123 81 0.34
124 122 0.52
125 32 0.14
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (124 bp):
TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
GGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:29796185 original size:17 final size:17
Alignment explanation
Indices: 29796118--29796185 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
29796108 TGTGTGAATG
*
29796118 TAAAATTATTAATT-GA
1 TAAAATTATTAATTATA
* *
29796134 TAAATTGTATTAATGATTA
1 TAAAAT-TATTAATTA-TA
*
29796153 GTAAAATTATCAAATTATA
1 -TAAAATTAT-TAATTATA
29796172 TAAAATTATTAATT
1 TAAAATTATTAATT
29796186 GTTAGTAGCA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 11 0.28
18 9 0.22
19 6 0.15
20 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:29796208 original size:116 final size:116
Alignment explanation
Indices: 29796004--29796247 Score: 418
Period size: 116 Copynumber: 2.1 Consensus size: 116
29795994 TAAGTTTGTG
*
29796004 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
** * *
29796069 TTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTGTGTGAATGTA
66 TTGTTAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
29796120 AAATTATTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
*
29796184 TTGTTAGTAGCAGGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
66 TTGTTAGTACCA-GAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
29796236 AAATTATTAATT
1 AAATTATTAATT
29796248 TAGTTTAGGG
Statistics
Matches: 121, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
115 40 0.33
116 81 0.67
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (116 bp):
AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
TTGTTAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
Found at i:29796273 original size:23 final size:23
Alignment explanation
Indices: 29796241--29796516 Score: 288
Period size: 23 Copynumber: 12.1 Consensus size: 23
29796231 AAGTAAAATT
* *
29796241 ATTAATTTAGTTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
29796264 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
*
29796287 ATTTAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
29796310 AGTT-AATTAGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
***
29796333 AGTT-AAGGGGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
29796356 AGTT-AATTAGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
*
29796379 AGTT---TAAGGTTTAGGGTTTTTA
1 A-TTAAATTAGG-TTAGGGTTTTTA
29796401 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
*
29796424 AGTT---TAAGGTTTAGGGTTTTTA
1 A-TTAAATTAGG-TTAGGGTTTTTA
29796446 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
*
29796469 AGT---TTAGGATTTAGGGTTTTTA
1 ATTAAATTAGG--TTAGGGTTTTTA
* *
29796491 ATTAAATTAGATTAGAGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
29796514 ATT
1 ATT
29796517 TAAGGGTATT
Statistics
Matches: 221, Mismatches: 17, Indels: 30
0.82 0.06 0.11
Matches are distributed among these distances:
20 5 0.02
21 12 0.05
22 40 0.18
23 148 0.67
24 12 0.05
25 4 0.02
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (23 bp):
ATTAAATTAGGTTAGGGTTTTTA
Found at i:29796409 original size:45 final size:45
Alignment explanation
Indices: 29796250--29796521 Score: 396
Period size: 45 Copynumber: 6.0 Consensus size: 45
29796240 TATTAATTTA
29796250 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTTAATTAG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTT-A--AG
29796297 G-TTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAG-TTAAGGG
1 GTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTTAA--G
*
29796342 GGTTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGTTTAAG
1 GTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTTAAG
29796387 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAAG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAAG
29796432 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTT-AG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAAG
* *
29796476 GATTTAGGGTTTTTAATTAAATTAGATTAGAGTTTTTAA-TTTAAG
1 G-TTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAAG
29796521 G
1 G
29796522 GTATTAATGG
Statistics
Matches: 213, Mismatches: 3, Indels: 20
0.90 0.01 0.08
Matches are distributed among these distances:
43 1 0.00
44 8 0.04
45 125 0.59
46 72 0.34
47 7 0.03
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (45 bp):
GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAAG
Found at i:29797065 original size:18 final size:18
Alignment explanation
Indices: 29797042--29797077 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29797032 CGAAAATGGG
*
29797042 TACATATAAGGGTTAGGA
1 TACATATAAGGGCTAGGA
29797060 TACATATAAGGGCTAGGA
1 TACATATAAGGGCTAGGA
29797078 AATGCACCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (18 bp):
TACATATAAGGGCTAGGA
Found at i:29797733 original size:7 final size:7
Alignment explanation
Indices: 29797723--29797747 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29797713 TTATATACAT
29797723 AATACTA
1 AATACTA
29797730 AATACTA
1 AATACTA
29797737 AATACTA
1 AATACTA
29797744 AATA
1 AATA
29797748 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:29798915 original size:11 final size:11
Alignment explanation
Indices: 29798899--29798940 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
29798889 GAAAAGGGAG
29798899 TTAAGAGAAAC
1 TTAAGAGAAAC
*
29798910 TTAAGAGGAAC
1 TTAAGAGAAAC
*
29798921 TTAAGAGGAAC
1 TTAAGAGAAAC
29798932 TTAAGAGAA
1 TTAAGAGAA
29798941 TTTTTGAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.50, C:0.07, G:0.24, T:0.19
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:29799779 original size:18 final size:18
Alignment explanation
Indices: 29799746--29799798 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
29799736 AGTTCAAAAA
* *
29799746 ATAAATTTATTAAAAATT
1 ATAAAATTATAAAAAATT
*
29799764 ATAAAATTATAAAAAAAT
1 ATAAAATTATAAAAAATT
*
29799782 -TGAAATT-TAAAAAATT
1 ATAAAATTATAAAAAATT
29799798 A
1 A
29799799 ATTAAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 8 0.28
17 6 0.21
18 15 0.52
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAAAATTATAAAAAATT
Found at i:29800292 original size:52 final size:52
Alignment explanation
Indices: 29800214--29800317 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
29800204 AGCTCATTAA
29800214 CCTGCTCTGGCAGTTGTTCTTGAACAAAGTGATTCCCTTCTGACATAAAAAT
1 CCTGCTCTGGCAGTTGTTCTTGAACAAAGTGATTCCCTTCTGACATAAAAAT
29800266 CCTGCTCTGGCAGTTGTTCTTGAACAAAGTGATTCCCTTCTGACATAAAAAT
1 CCTGCTCTGGCAGTTGTTCTTGAACAAAGTGATTCCCTTCTGACATAAAAAT
29800318 GATGTCCATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (52 bp):
CCTGCTCTGGCAGTTGTTCTTGAACAAAGTGATTCCCTTCTGACATAAAAAT
Found at i:29801250 original size:2 final size:2
Alignment explanation
Indices: 29801243--29801270 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29801233 TTTCCTATTA
29801243 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29801271 TTTGAGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29805605 original size:15 final size:15
Alignment explanation
Indices: 29805570--29805598 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29805560 AAATAAAAGC
29805570 AATAATGATAATAAT
1 AATAATGATAATAAT
29805585 AATAATGATAATAA
1 AATAATGATAATAA
29805599 AACTAATTAA
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:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
AATAATGATAATAAT
Found at i:29806974 original size:48 final size:48
Alignment explanation
Indices: 29806801--29807077 Score: 216
Period size: 50 Copynumber: 5.7 Consensus size: 48
29806791 GTCTTGCCAA
* * *
29806801 GGAAATAAGATTCGCCGTTGCGGCTTCAATCTGTTCTGCTGCATCGCC
1 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCAGCTGCATCGCC
* * * ** **
29806849 TGGAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-GTTGG
1 -GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCAGCTGC-ATCG--CC
* * * *
29806900 GGAAGTAAGATTCGCCATTGTAGCTTCAATCTGCTCCGCTGCATCGCC
1 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCAGCTGCATCGCC
* * * * ** *
29806948 AGAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-GTCGG
1 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCAGCTGC-ATCG-C-C
* * * * * *
29806998 GGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCT
1 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCAGCTGCATCGCC
* *
29807046 AGAAGTAAGATTCGCCGTTGTGGCTTCGATCT
1 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
29807078 TTTAAATTGC
Statistics
Matches: 171, Mismatches: 49, Indels: 17
0.72 0.21 0.07
Matches are distributed among these distances:
48 60 0.35
49 43 0.25
50 68 0.40
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.32
Consensus pattern (48 bp):
GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCAGCTGCATCGCC
Found at i:29806981 original size:98 final size:98
Alignment explanation
Indices: 29806801--29807089 Score: 470
Period size: 98 Copynumber: 2.9 Consensus size: 98
29806791 GTCTTGCCAA
* ** * * *
29806801 GGAAATAAGATTCGCCGTTGCGGCTTCAATCTGTTCTGCTGCATCGCCTGGAAGTAAGATTCGCC
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTCCGCTGCATCGCC-AGAAGTAAGATTCGCC
*
29806866 GTTGTGGCTTCGATCTTTTAAATTGCAATGTTGG
65 GTTGTGGCTTCGATCTTTTAAATTGCAATGTCGG
*
29806900 GGAAGTAAGATTCGCCATTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCG
29806965 TTGTGGCTTCGATCTTTTAAATTGCAATGTCGG
66 TTGTGGCTTCGATCTTTTAAATTGCAATGTCGG
* * *
29806998 GGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCTAGAAGTAAGATTCGCCG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCG
29807063 TTGTGGCTTCGATCTTTTAAATTGCAA
66 TTGTGGCTTCGATCTTTTAAATTGCAA
29807090 ACTATGATTT
Statistics
Matches: 178, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 136 0.76
99 42 0.24
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.32
Consensus pattern (98 bp):
GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCG
TTGTGGCTTCGATCTTTTAAATTGCAATGTCGG
Found at i:29816089 original size:22 final size:22
Alignment explanation
Indices: 29816061--29816113 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
29816051 TCTTTCATCT
29816061 CTTCAATTCTATTTAGGCTTGC
1 CTTCAATTCTATTTAGGCTTGC
29816083 CTTCAATTCTATTTAGGCTTGC
1 CTTCAATTCTATTTAGGCTTGC
29816105 CTTCAATTC
1 CTTCAATTC
29816114 CATCACAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.11, T:0.45
Consensus pattern (22 bp):
CTTCAATTCTATTTAGGCTTGC
Found at i:29820044 original size:15 final size:15
Alignment explanation
Indices: 29820009--29820037 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29819999 AAATAAAAGC
29820009 AATAATGATAATAAT
1 AATAATGATAATAAT
29820024 AATAATGATAATAA
1 AATAATGATAATAA
29820038 AACTAATTAA
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:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
AATAATGATAATAAT
Found at i:29822689 original size:60 final size:62
Alignment explanation
Indices: 29822594--29822723 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 62
29822584 CTTTATTCAT
* *
29822594 AAAACAAGCCAAAAAAACAAGCAAAAAGTTAAACAAAAGT-AA-AAAAAACACTACAACCT-AA
1 AAAACAAGCCAAAAAAACAAGCAAAAAGTGAAACAAAAGTCAAGAAAAAA-A-AACAACCTAAA
* *
29822655 AAAACAAGCC-CAAAAACAAGTAGAAAA-TGAAACAAAAGTCAAGAAAAAAAAACAACCTAAA
1 AAAACAAGCCAAAAAAACAAGCA-AAAAGTGAAACAAAAGTCAAGAAAAAAAAACAACCTAAA
29822716 AAAACAAG
1 AAAACAAG
29822724 GATCCTGTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
60 28 0.46
61 27 0.44
62 6 0.10
ACGTcount: A:0.68, C:0.17, G:0.08, T:0.07
Consensus pattern (62 bp):
AAAACAAGCCAAAAAAACAAGCAAAAAGTGAAACAAAAGTCAAGAAAAAAAAACAACCTAAA
Found at i:29831682 original size:12 final size:11
Alignment explanation
Indices: 29831665--29831721 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
29831655 AACAAATCCT
29831665 CTCTCATATTTC
1 CTCTCA-ATTTC
29831677 CTCTCAA-TTC
1 CTCTCAATTTC
29831687 CTCTCAATTTC
1 CTCTCAATTTC
*
29831698 CT-TCCAAAATT-
1 CTCT-C-AATTTC
29831709 CTCTCAATTTC
1 CTCTCAATTTC
29831720 CT
1 CT
29831722 TCCAAAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 15 0.39
11 12 0.32
12 11 0.29
ACGTcount: A:0.21, C:0.35, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:29831712 original size:22 final size:22
Alignment explanation
Indices: 29831682--29831734 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
29831672 ATTTCCTCTC
29831682 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
29831705 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
29831727 AATTCTCT
1 AATTCTCT
29831735 TAAATCCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:29831758 original size:40 final size:40
Alignment explanation
Indices: 29831712--29831801 Score: 162
Period size: 40 Copynumber: 2.2 Consensus size: 40
29831702 CAAAATTCTC
* *
29831712 TCAATTTCCTTCCAAAATTCTCTTAAATCCATATTTAATT
1 TCAATTTCCTTCCAAAAGTCTCTCAAATCCATATTTAATT
29831752 TCAATTTCCTTCCAAAAGTCTCTCAAATCCATATTTAATT
1 TCAATTTCCTTCCAAAAGTCTCTCAAATCCATATTTAATT
29831792 TCAATTTCCT
1 TCAATTTCCT
29831802 CTCAATTTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.31, C:0.24, G:0.01, T:0.43
Consensus pattern (40 bp):
TCAATTTCCTTCCAAAAGTCTCTCAAATCCATATTTAATT
Found at i:29832981 original size:7 final size:7
Alignment explanation
Indices: 29832971--29833008 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
29832961 ATTCGATTGA
29832971 TATTTAG
1 TATTTAG
29832978 TATTTAG
1 TATTTAG
29832985 TATTTAG
1 TATTTAG
29832992 TATTTAG
1 TATTTAG
29832999 T-TTTATG
1 TATTTA-G
29833006 TAT
1 TAT
29833009 ATAACTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 4 0.14
7 24 0.83
8 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (7 bp):
TATTTAG
Found at i:29834161 original size:29 final size:29
Alignment explanation
Indices: 29834122--29834368 Score: 428
Period size: 29 Copynumber: 8.6 Consensus size: 29
29834112 AAAACAGAAA
*
29834122 TTAATTAAAAACCCTAACCCTAACTTAAT
1 TTAATTAAAAACCCTAACCCTAACCTAAT
29834151 TTAATTAAAAACCCTAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCCTAACCTAAT
29834180 TTAATT---AACCCTAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCCTAACCTAAT
*
29834206 TTAATTAAAAACCCTAACCCTAACCTAAA
1 TTAATTAAAAACCCTAACCCTAACCTAAT
*
29834235 TTAATTAAAAACCCTAACCCTAACCAAAAT
1 TTAATTAAAAACCCTAACCCTAACC-TAAT
*
29834265 TTAATTAAAAACCCTACCCCTAACCTAAT
1 TTAATTAAAAACCCTAACCCTAACCTAAT
29834294 TTAATTAAAAACCCTAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCCTAACCTAAT
29834323 TTAATTAAAAACCCTAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCCTAACCTAAT
29834352 TTAATTAAAAACCCTAA
1 TTAATTAAAAACCCTAA
29834369 ACTAAGTTAA
Statistics
Matches: 207, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
26 26 0.13
29 155 0.75
30 26 0.13
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (29 bp):
TTAATTAAAAACCCTAACCCTAACCTAAT
Found at i:29834313 original size:88 final size:87
Alignment explanation
Indices: 29834122--29834368 Score: 428
Period size: 88 Copynumber: 2.9 Consensus size: 87
29834112 AAAACAGAAA
*
29834122 TTAATTAAAAACCCTAACCCTAACTTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATT-
1 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTA
29834186 --AACCCTAACCCTAACCTAAT
66 AAAACCCTAACCCTAACCTAAT
* *
29834206 TTAATTAAAAACCCTAACCCTAACCTAAATTAATTAAAAACCCTAACCCTAACCAAAATTTAATT
1 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACC-TAATTTAATT
*
29834271 AAAAACCCTACCCCTAACCTAAT
65 AAAAACCCTAACCCTAACCTAAT
29834294 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTA
1 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTA
29834359 AAAACCCTAA
66 AAAACCCTAA
29834369 ACTAAGTTAA
Statistics
Matches: 152, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
84 52 0.34
85 9 0.06
87 19 0.12
88 72 0.47
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (87 bp):
TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTA
AAAACCCTAACCCTAACCTAAT
Found at i:29834531 original size:116 final size:116
Alignment explanation
Indices: 29834375--29834612 Score: 413
Period size: 116 Copynumber: 2.1 Consensus size: 116
29834365 CTAAACTAAG
* * *
29834375 TTAACAATGTTACATTCACGTAATGTTAGATTTGGAAAAATGTTTTGACTGGTACCAACAAATAA
1 TTAATAATGTTACATTCACATAATATTAGATTTGGAAAAATGTTTTGACTGGTACCAACAAATAA
29834440 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
* * *
29834491 TTAATAATTTTACATTCACATAATATTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAATAATGTTACATTCACATAATATTAGATTTGGAAAAATGTTTTGACTGGTACCAACAAATAA
*
29834556 TAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
29834607 TTAATA
1 TTAATA
29834613 CAATTTATCA
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 115 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.42
Consensus pattern (116 bp):
TTAATAATGTTACATTCACATAATATTAGATTTGGAAAAATGTTTTGACTGGTACCAACAAATAA
TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
Found at i:29834629 original size:17 final size:18
Alignment explanation
Indices: 29834588--29834629 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
29834578 TTTACTAACC
* *
29834588 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
29834606 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
29834623 ATTAATA
1 ATTAATA
29834630 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:29838283 original size:6 final size:6
Alignment explanation
Indices: 29838236--29838376 Score: 61
Period size: 6 Copynumber: 22.8 Consensus size: 6
29838226 AATATTGAAA
* * * * *
29838236 TAAAAT TAAACT TCAAAT CAAATAT AAAAAT TAAGCAT TAAAAT TAAAAT
1 TAAAAT TAAAAT TAAAAT TAAA-AT TAAAAT TAA-AAT TAAAAT TAAAAT
* * * * * * *
29838286 T-ACAT ATAAGAT ATATAAT TAAAA- TAAAAT TATAAAC TACATT TAATAT
1 TAAAAT -TAAAAT -TAAAAT TAAAAT TAAAAT TA-AAAT TAAAAT TAAAAT
* * * * *
29838335 ATAAAAG TAAAAG TAAAAT TAAAAC TATATT TAAAAT TAAAA
1 -TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAA
29838377 AGAATTACAT
Statistics
Matches: 98, Mismatches: 30, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
5 8 0.08
6 63 0.64
7 27 0.28
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.32
Consensus pattern (6 bp):
TAAAAT
Found at i:29838337 original size:37 final size:37
Alignment explanation
Indices: 29838274--29838376 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
29838264 AATTAAGCAT
* * * *
29838274 TAAAATTAAAATTACATATAAGATATATAATTAAAA-
1 TAAAATTAAAACTACATTTAAGATATAAAAGTAAAAG
*
29838310 TAAAATTATAAACTACATTTAATATATAAAAGTAAAAG
1 TAAAATTA-AAACTACATTTAAGATATAAAAGTAAAAG
* *
29838348 TAAAATTAAAACTATATTTAAAAT-TAAAA
1 TAAAATTAAAACTACATTTAAGATATAAAA
29838377 AGAATTACAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 13 0.22
37 37 0.64
38 8 0.14
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (37 bp):
TAAAATTAAAACTACATTTAAGATATAAAAGTAAAAG
Found at i:29838509 original size:14 final size:13
Alignment explanation
Indices: 29838490--29838528 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
29838480 TTGTTTCATT
29838490 GAAAATGACTTTA
1 GAAAATGACTTTA
*
29838503 GGAAAATGATTTTTA
1 -GAAAATGA-CTTTA
29838518 GAAAATGACTT
1 GAAAATGACTT
29838529 ACTTTCCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 16 0.73
15 4 0.18
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (13 bp):
GAAAATGACTTTA
Found at i:29839108 original size:16 final size:16
Alignment explanation
Indices: 29839077--29839111 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29839067 ATGTGAAGAA
29839077 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
29839093 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
29839109 TAT
1 TAT
29839112 CAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:29839152 original size:16 final size:19
Alignment explanation
Indices: 29839121--29839182 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
29839111 TCAAAATAAA
*
29839121 ATTAAAATATTAAATAATTT
1 ATTAATATATT-AATAATTT
29839141 ATTAA-A-A-TAATAAATTAT
1 ATTAATATATTAAT-AATT-T
29839159 ATTAATTATATTAATAATTT
1 ATTAA-TATATTAATAATTT
29839179 ATTA
1 ATTA
29839183 TATGGCTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.08
17 5 0.14
18 7 0.19
19 1 0.03
20 11 0.31
21 5 0.14
22 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAATATATTAATAATTT
Found at i:29839800 original size:22 final size:23
Alignment explanation
Indices: 29839747--29839802 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
29839737 CCCGTTTTTA
* * *
29839747 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
29839770 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
29839792 ATTAAAATTAA
1 ATTAAAATTAA
29839803 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:29839815 original size:16 final size:16
Alignment explanation
Indices: 29839778--29839817 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
29839768 TTAATAAAAT
* *
29839778 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
29839794 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
29839810 TAAAATTA
1 TAAAATTA
29839818 TCAAAGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:29839902 original size:9 final size:9
Alignment explanation
Indices: 29839890--29839917 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29839880 TTTATCAAAT
29839890 TATTAATTG
1 TATTAATTG
29839899 TATTAATTG
1 TATTAATTG
29839908 TATTAATTG
1 TATTAATTG
29839917 T
1 T
29839918 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:29839928 original size:68 final size:66
Alignment explanation
Indices: 29839806--29839948 Score: 241
Period size: 68 Copynumber: 2.1 Consensus size: 66
29839796 AAATTAATTG
*
29839806 TTAGTAAAATTATCAAAGTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTG
1 TTAGTAAAATTATCAAAGTATTAATTGTTAATTGTATTAATTGTTGTAACAAAATCTAACATTTG
29839871 A
66 A
* *
29839872 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAAGTATTAATTG--TTAATTGTATTAATTGTTGTAACAAAATCTAACATT
29839937 TGA
64 TGA
29839940 TTAGTAAAA
1 TTAGTAAAA
29839949 CAAATTTGAT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 25 0.35
68 46 0.65
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (66 bp):
TTAGTAAAATTATCAAAGTATTAATTGTTAATTGTATTAATTGTTGTAACAAAATCTAACATTTG
A
Found at i:29840041 original size:24 final size:22
Alignment explanation
Indices: 29840014--29840057 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 22
29840004 AAATAAACTT
29840014 AAAATAAAAAAATATTATATTTTA
1 AAAAT-AAAAAATA-TATATTTTA
29840038 AAAATAAAAAATATATATTT
1 AAAATAAAAAATATATATTT
29840058 AATATTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATAAAAAATATATATTTTA
Found at i:29843725 original size:24 final size:25
Alignment explanation
Indices: 29843681--29843739 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
29843671 TTTTAATATA
29843681 ATTTAATATAAAAAATATTAAATTG
1 ATTTAATATAAAAAATATTAAATTG
* *
29843706 ATTT-ATATAAAATATGTTAAA-T-
1 ATTTAATATAAAAAATATTAAATTG
29843728 ATTCTAATATAA
1 ATT-TAATATAA
29843740 TTTATTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 3 0.10
23 2 0.07
24 21 0.70
25 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (25 bp):
ATTTAATATAAAAAATATTAAATTG
Found at i:29843778 original size:56 final size:58
Alignment explanation
Indices: 29843667--29843791 Score: 191
Period size: 56 Copynumber: 2.2 Consensus size: 58
29843657 TCGTAAAAAC
*
29843667 AATATTTTAATATAATTTAATATAAAAAATATTAAATTGATTTATATAAAATATGTTA
1 AATATTTTAATATAATTTAATATAAAAAATATTAAATTAATTTATATAAAATATGTTA
* * * *
29843725 AATATTCTAATATAATTT-AT-TATAAAATATTAAATTAATTTATGTAAACTATGTTA
1 AATATTTTAATATAATTTAATATAAAAAATATTAAATTAATTTATATAAAATATGTTA
29843781 AATATTTTAAT
1 AATATTTTAAT
29843792 CTAAAATATT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
56 42 0.69
57 2 0.03
58 17 0.28
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (58 bp):
AATATTTTAATATAATTTAATATAAAAAATATTAAATTAATTTATATAAAATATGTTA
Found at i:29843802 original size:56 final size:56
Alignment explanation
Indices: 29843692--29843803 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
29843682 TTTAATATAA
* **
29843692 AAAATATTAAATTGATTTATATAAAATATGTTAAATATTCTAATATAATTTATTAT
1 AAAATATTAAATTAATTTATATAAAATATGTTAAATATTCTAATATAAAATATTAT
* * * *
29843748 AAAATATTAAATTAATTTATGTAAACTATGTTAAATATTTTAATCTAAAATATTAT
1 AAAATATTAAATTAATTTATATAAAATATGTTAAATATTCTAATATAAAATATTAT
29843804 TTCCAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.46
Consensus pattern (56 bp):
AAAATATTAAATTAATTTATATAAAATATGTTAAATATTCTAATATAAAATATTAT
Found at i:29850199 original size:4 final size:4
Alignment explanation
Indices: 29850190--29850218 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
29850180 TCAATTGATT
29850190 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
29850219 CCTTCACCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:29851010 original size:13 final size:13
Alignment explanation
Indices: 29850992--29851016 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29850982 ATATACTACA
29850992 GTCAGCTTGATCG
1 GTCAGCTTGATCG
29851005 GTCAGCTTGATC
1 GTCAGCTTGATC
29851017 AAACTTCTTG
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:0.24, G:0.28, T:0.32
Consensus pattern (13 bp):
GTCAGCTTGATCG
Found at i:29862278 original size:13 final size:13
Alignment explanation
Indices: 29862260--29862285 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29862250 TTGTTTTATA
29862260 ATATTTTAAATGT
1 ATATTTTAAATGT
29862273 ATATTTTAAATGT
1 ATATTTTAAATGT
29862286 TTTATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATATTTTAAATGT
Found at i:29874266 original size:70 final size:69
Alignment explanation
Indices: 29874153--29874509 Score: 471
Period size: 70 Copynumber: 5.1 Consensus size: 69
29874143 TGATATTATA
* *
29874153 AAGGCTCGTATGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGTGTACGCTCCCAACTAGA
1 AAGGCTCGTAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGT-TACGCTCCCAACTGGA
29874218 ATCTT
65 ATCTT
* * *
29874223 AAGGCTCGTAGGTTCAATACCACAGCCTCCAAAACAGCTAGCGCGAGCGTACGCTCCCAACTGGA
1 AAGGCTCGTAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAG-TTACGCTCCCAACTGGA
*
29874288 ATCTC
65 ATCTT
* * *
29874293 AAGGCTCGTAGGTTCAATACCGCAGCCTCCAAAATAGTTAGTGCGAGCTTACGCTCCCAACTAGA
1 AAGGCTCGTAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAG-TTACGCTCCCAACTGGA
29874358 ATCTT
65 ATCTT
* * * * * * * *
29874363 AAGGCTCGCAGGTTCAATACCACAGCCTTCAAAATAGTTAGCTCGAGCCTATGCTCCCAGCTGGA
1 AAGGCTCGTAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAG-TTACGCTCCCAACTGGA
29874428 ATCTT
65 ATCTT
* * * **
29874433 AAGGCTCGCAGGTTCAATATCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACACTCCCAGTTGGA
1 AAGGCTCGTAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAG-TTACGCTCCCAACTGGA
29874498 ATCTT
65 ATCTT
29874503 AAGGCTC
1 AAGGCTC
29874510 ACTGGTTTAA
Statistics
Matches: 255, Mismatches: 31, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
70 255 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (69 bp):
AAGGCTCGTAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGTTACGCTCCCAACTGGAA
TCTT
Found at i:29874410 original size:140 final size:140
Alignment explanation
Indices: 29874153--29874509 Score: 536
Period size: 140 Copynumber: 2.5 Consensus size: 140
29874143 TGATATTATA
*
29874153 AAGGCTCGTATGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAG-TGTACGCTCCCAACTAG
1 AAGGCTCGTAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCT-TACGCTCCCAACTAG
* *
29874217 AATCTTAAGGCTCGTAGGTTCAATACCACAGCCTCCAAAACAGCTAGCGCGAGCGTACGCTCCCA
65 AATCTTAAGGCTCGCAGGTTCAATACCACAGCCTCCAAAACAGCTAGCGCGAGCCTACGCTCCCA
29874282 ACTGGAATCTC
130 ACTGGAATCTC
* *
29874293 AAGGCTCGTAGGTTCAATACCGCAGCCTCCAAAATAGTTAGTGCGAGCTTACGCTCCCAACTAGA
1 AAGGCTCGTAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCCAACTAGA
* * * * * *
29874358 ATCTTAAGGCTCGCAGGTTCAATACCACAGCCTTCAAAATAGTTAGCTCGAGCCTATGCTCCCAG
66 ATCTTAAGGCTCGCAGGTTCAATACCACAGCCTCCAAAACAGCTAGCGCGAGCCTACGCTCCCAA
*
29874423 CTGGAATCTT
131 CTGGAATCTC
* * * ** *
29874433 AAGGCTCGCAGGTTCAATATCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACACTCCCAGTTGGA
1 AAGGCTCGTAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCCAACTAGA
29874498 ATCTTAAGGCTC
66 ATCTTAAGGCTC
29874510 ACTGGTTTAA
Statistics
Matches: 196, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
140 195 0.99
141 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (140 bp):
AAGGCTCGTAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCCAACTAGA
ATCTTAAGGCTCGCAGGTTCAATACCACAGCCTCCAAAACAGCTAGCGCGAGCCTACGCTCCCAA
CTGGAATCTC
Found at i:29874539 original size:210 final size:210
Alignment explanation
Indices: 29874153--29874539 Score: 526
Period size: 210 Copynumber: 1.8 Consensus size: 210
29874143 TGATATTATA
* * * **
29874153 AAGGCTCGTATGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGTGTACGCTCCCAACTAGA
1 AAGGCTCGCAGGTTCAATACCACAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAACTAGA
* *
29874218 ATCTTAAGGCTCGTAGGTTCAATACCACAGCCTCCAAAACAGCTAGCGCGAGCGTACGCTCCCAA
66 ATCTTAAGGCTCGCAGGTTCAATACCACAGCCTCCAAAACAGCTAGCGCGAGCGTACACTCCCAA
* *
29874283 CTGGAATCTCAAGGCTCGTAGGTTCAATACCGCAGCCTCCAAAATAGTTAGTGCGAGCTTACGCT
131 CTGGAATCTCAAGGCTCCTAGGTTCAATACCGCAGCCTCAAAAATAGTTAGTGCGAGCTTACGCT
29874348 CCCAACTAGAATCTT
196 CCCAACTAGAATCTT
* * * * * *
29874363 AAGGCTCGCAGGTTCAATACCACAGCCTTCAAAATAGTTAGCTCGAGCCTATGCTCCCAGCTGGA
1 AAGGCTCGCAGGTTCAATACCACAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAACTAGA
* * * * *
29874428 ATCTTAAGGCTCGCAGGTTCAATATCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACACTCCCAG
66 ATCTTAAGGCTCGCAGGTTCAATACCACAGCCTCCAAAACAGCTAGCGCGAGCGTACACTCCCAA
* * * *
29874493 TTGGAATCTTAAGGCTCACT-GGTTTAATATCGC-GACCTCAAAAATAG
131 CTGGAATCTCAAGGCTC-CTAGGTTCAATACCGCAG-CCTCAAAAATAG
29874540 CTGGCGAACC
Statistics
Matches: 151, Mismatches: 24, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
209 1 0.01
210 149 0.99
211 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (210 bp):
AAGGCTCGCAGGTTCAATACCACAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCCCAACTAGA
ATCTTAAGGCTCGCAGGTTCAATACCACAGCCTCCAAAACAGCTAGCGCGAGCGTACACTCCCAA
CTGGAATCTCAAGGCTCCTAGGTTCAATACCGCAGCCTCAAAAATAGTTAGTGCGAGCTTACGCT
CCCAACTAGAATCTT
Found at i:29875008 original size:14 final size:15
Alignment explanation
Indices: 29874989--29875020 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29874979 TTTGTAATAA
29874989 AAATTTT-AAAACTT
1 AAATTTTGAAAACTT
29875003 AAATTTTGAAAACTT
1 AAATTTTGAAAACTT
29875018 AAA
1 AAA
29875021 AATTTGGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (15 bp):
AAATTTTGAAAACTT
Found at i:29882350 original size:41 final size:39
Alignment explanation
Indices: 29882305--29882450 Score: 143
Period size: 41 Copynumber: 3.6 Consensus size: 39
29882295 GGTTCTGTAC
29882305 CTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAA-TAATTCAGACTTTA-GT
*
29882346 CTAGCAGGCTTAATGCCGGTG-ATACATTTCAGACTATATGT
1 CTAGCAGGCTTAATGCCGGTGAATA-A-TTCAGACTTTA-GT
* * * * * *
29882387 CTAGCAGGC-TAAGCGCCGGTGTACTAAATCAGGCTTGAGC
1 CTAGCAGGCTTAA-TGCCGGTG-AATAATTCAGACTTTAGT
*
29882427 CTAGCAGGCTAAATGCCGGTGAAT
1 CTAGCAGGCTTAATGCCGGTGAAT
29882451 TTGTTTAAAT
Statistics
Matches: 87, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
39 4 0.05
40 22 0.25
41 58 0.67
42 1 0.01
43 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (39 bp):
CTAGCAGGCTTAATGCCGGTGAATAATTCAGACTTTAGT
Found at i:29882609 original size:2 final size:2
Alignment explanation
Indices: 29882602--29882662 Score: 79
Period size: 2 Copynumber: 30.0 Consensus size: 2
29882592 TATGCATTTG
* *
29882602 AT AT AT AT AT AT AT AT AT AT AC AT GT ACT CAT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT
29882645 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
29882663 TCGAATGTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
1 1 0.02
2 48 0.92
3 2 0.04
4 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29883575 original size:37 final size:37
Alignment explanation
Indices: 29883525--29883595 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
29883515 CTTGAAGAAT
*
29883525 GCTTTCTTTTTTATCATTATAATTTTTAAAGTAAAAC
1 GCTTTCTTTTTTATCATTATAATTATTAAAGTAAAAC
29883562 GCTTTCTTTTTTATCATTATAATTATTAAAGTAA
1 GCTTTCTTTTTTATCATTATAATTATTAAAGTAA
29883596 TCTTCACTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (37 bp):
GCTTTCTTTTTTATCATTATAATTATTAAAGTAAAAC
Found at i:29884528 original size:16 final size:16
Alignment explanation
Indices: 29884507--29884549 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
29884497 TCAAAGTTTC
29884507 TCCAAATTTTTAAGTT
1 TCCAAATTTTTAAGTT
*
29884523 TCCAAA-ATTTAAGTT
1 TCCAAATTTTTAAGTT
**
29884538 TTAAAATTTTTA
1 TCCAAATTTTTA
29884550 TTACAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (16 bp):
TCCAAATTTTTAAGTT
Found at i:29884679 original size:19 final size:17
Alignment explanation
Indices: 29884624--29884682 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 17
29884614 GCTTAATAAA
*
29884624 TTTTAAATTTTATATTT
1 TTTTAAAATTTATATTT
*
29884641 TATTAAAATTTAATAATTT
1 TTTTAAAATTT-AT-ATTT
*
29884660 TTCTAAAATTTATTATTT
1 TTTTAAAATTTA-TATTT
29884678 TTTTA
1 TTTTA
29884683 TATTTTTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 9 0.26
18 11 0.32
19 14 0.41
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTAAAATTTATATTT
Found at i:29885627 original size:13 final size:13
Alignment explanation
Indices: 29885591--29885629 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
29885581 GATATATTTG
*
29885591 TAATTTGAAAGCT
1 TAATTTGAAAACT
29885604 TAAGTTTTGAAAACT
1 TAA--TTTGAAAACT
29885619 TAATTTGAAAA
1 TAATTTGAAAA
29885630 TTTGAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 11 0.48
15 12 0.52
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:29885947 original size:35 final size:35
Alignment explanation
Indices: 29885908--29886086 Score: 195
Period size: 34 Copynumber: 5.2 Consensus size: 35
29885898 GAATATTTCA
*
29885908 TGTTCATGCATTATTTTGTTGCAAGGAATCTCTCC
1 TGTTCACGCATTATTTTGTTGCAAGGAATCTCTCC
* * * *
29885943 TGTTCACACA-TCTTTTCTTGCAGGGAATCTCTCC
1 TGTTCACGCATTATTTTGTTGCAAGGAATCTCTCC
29885977 TGTTCACGCATTATTTTGTTGC-AGGAAATCTCTCC
1 TGTTCACGCATTATTTTGTTGCAAGG-AATCTCTCC
* * * * *
29886012 TGTTCACACATCA-TTTCTTGCAGGGAATATCTCC
1 TGTTCACGCATTATTTTGTTGCAAGGAATCTCTCC
* *
29886046 TGTTCACGCATTATGTTGTTGC-AGAGAATCGCTCC
1 TGTTCACGCATTATTTTGTTGCAAG-GAATCTCTCC
*
29886081 TATTCA
1 TGTTCA
29886087 TGTATCAGTT
Statistics
Matches: 117, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
34 59 0.50
35 58 0.50
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.39
Consensus pattern (35 bp):
TGTTCACGCATTATTTTGTTGCAAGGAATCTCTCC
Found at i:29885970 original size:34 final size:35
Alignment explanation
Indices: 29885884--29886086 Score: 194
Period size: 35 Copynumber: 5.9 Consensus size: 35
29885874 TATTCACTTG
* * * * **
29885884 TCTTTACTTGCAGGGAATATTTCATGTTCATGCAT
1 TCTTTTCTTGCAGGGAATCTCTCCTGTTCACACAT
* * *
29885919 TATTTTGTTGCAAGGAATCTCTCCTGTTCACACA-
1 TCTTTTCTTGCAGGGAATCTCTCCTGTTCACACAT
*
29885953 TCTTTTCTTGCAGGGAATCTCTCCTGTTCACGCAT
1 TCTTTTCTTGCAGGGAATCTCTCCTGTTCACACAT
* * *
29885988 TATTTTGTTGCAGGAAATCTCTCCTGTTCACACA-
1 TCTTTTCTTGCAGGGAATCTCTCCTGTTCACACAT
* * *
29886022 TCATTTCTTGCAGGGAATATCTCCTGTTCACGCAT
1 TCTTTTCTTGCAGGGAATCTCTCCTGTTCACACAT
* * * * * *
29886057 TATGTTGTTGCAGAGAATCGCTCCTATTCA
1 TCTTTTCTTGCAGGGAATCTCTCCTGTTCA
29886087 TGTATCAGTT
Statistics
Matches: 135, Mismatches: 31, Indels: 4
0.79 0.18 0.02
Matches are distributed among these distances:
34 58 0.43
35 77 0.57
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (35 bp):
TCTTTTCTTGCAGGGAATCTCTCCTGTTCACACAT
Found at i:29885988 original size:69 final size:68
Alignment explanation
Indices: 29885884--29886086 Score: 298
Period size: 69 Copynumber: 2.9 Consensus size: 68
29885874 TATTCACTTG
* * * *
29885884 TCTTTACTTGCAGGGAATATTTCATGTTCATGCATTATTTTGTTGCAAGGAATCTCTCCTGTTCA
1 TCTTTTCTTGCAGGGAATATCTCCTGTTCACGCATTATTTTGTTGC-AGGAATCTCTCCTGTTCA
29885949 CACA
65 CACA
*
29885953 TCTTTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGAAATCTCTCCTGTTCA
1 TCTTTTCTTGCAGGGAATATCTCCTGTTCACGCATTATTTTGTTGCAGG-AATCTCTCCTGTTCA
29886018 CACA
65 CACA
* * * *
29886022 TCATTTCTTGCAGGGAATATCTCCTGTTCACGCATTATGTTGTTGCAGAGAATCGCTCCTATTCA
1 TCTTTTCTTGCAGGGAATATCTCCTGTTCACGCATTATTTTGTTGCAG-GAATCTCTCCTGTTCA
29886087 TGTATCAGTT
Statistics
Matches: 122, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
68 3 0.02
69 118 0.97
70 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (68 bp):
TCTTTTCTTGCAGGGAATATCTCCTGTTCACGCATTATTTTGTTGCAGGAATCTCTCCTGTTCAC
ACA
Found at i:29888828 original size:21 final size:22
Alignment explanation
Indices: 29888798--29888842 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
29888788 GAACAAATTG
29888798 TTGATTCTATTTCTTTCTTG-AT
1 TTGATTCTA-TTCTTTCTTGTAT
*
29888820 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCTTTCTTGTAT
29888841 TT
1 TT
29888843 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCTTTCTTGTAT
Found at i:29893457 original size:3 final size:3
Alignment explanation
Indices: 29893449--29893494 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
29893439 GAGCAAAGAA
*
29893449 AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29893495 GTTCAGATCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:29894891 original size:58 final size:58
Alignment explanation
Indices: 29894796--29894914 Score: 193
Period size: 58 Copynumber: 2.1 Consensus size: 58
29894786 GATTAGGGTC
*
29894796 ATATCTAAGAGGAAAGGAAAAAAGGACATCCTCATCCATTGGAGCATACATTGAGGAA
1 ATATCTAAGAGGAAAGGAAAAAAGGACATCCTCATCCATTGGAGCATACATTAAGGAA
* * * *
29894854 ATATCTAAGAGGAAAGGAAGAAATGACATCCTTATCCATTGGAGCATCCATTAAGGAA
1 ATATCTAAGAGGAAAGGAAAAAAGGACATCCTCATCCATTGGAGCATACATTAAGGAA
29894912 ATA
1 ATA
29894915 GTTGCAATCT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (58 bp):
ATATCTAAGAGGAAAGGAAAAAAGGACATCCTCATCCATTGGAGCATACATTAAGGAA
Found at i:29898956 original size:17 final size:15
Alignment explanation
Indices: 29898934--29899007 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 15
29898924 GCAACCAAAT
29898934 TTTTATTTTTATTTAA
1 TTTTATTTTTATTT-A
29898950 TTATTA-TTTTATTTA
1 TT-TTATTTTTATTTA
* *
29898965 TTATTTTATTTTCTTTA
1 TT-TTAT-TTTTATTTA
*
29898982 CTTTATTTATTATTTTA
1 TTTTATTT-TTA-TTTA
29898999 TTTTATTTT
1 TTTTATTTT
29899008 ATTAGTTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
15 8 0.17
16 16 0.34
17 23 0.49
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTTTTATTTA
Found at i:29898961 original size:5 final size:5
Alignment explanation
Indices: 29898934--29899010 Score: 66
Period size: 5 Copynumber: 14.4 Consensus size: 5
29898924 GCAACCAAAT
* *
29898934 TTTTA TTTTTA TTTAA TTATTA TTTTA TTTATTA TTTTA TTTT- CTTTA
1 TTTTA -TTTTA TTTTA TT-TTA TTTTA -TT-TTA TTTTA TTTTA TTTTA
*
29898982 CTTTA TTTATTA TTTTA TTTTA TTTTA TT
1 TTTTA -TT-TTA TTTTA TTTTA TTTTA TT
29899011 AGTTATTAGT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
4 3 0.05
5 36 0.59
6 16 0.26
7 6 0.10
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:29899008 original size:22 final size:22
Alignment explanation
Indices: 29898934--29899010 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 22
29898924 GCAACCAAAT
*
29898934 TTTTATTT-TTATTTAATTATTA
1 TTTTATTTATTATTTTATT-TTA
29898956 TTTTATTTATTATTTTATTTTCTTTA
1 TTTTATTTATTATTTTA---T-TTTA
*
29898982 CTTTATTTATTATTTTATTTTA
1 TTTTATTTATTATTTTATTTTA
29899004 TTTTATT
1 TTTTATT
29899011 AGTTATTAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
22 18 0.38
23 8 0.17
26 20 0.43
27 1 0.02
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTATTTATTATTTTATTTTA
Found at i:29899016 original size:22 final size:21
Alignment explanation
Indices: 29898934--29899017 Score: 79
Period size: 22 Copynumber: 4.1 Consensus size: 21
29898924 GCAACCAAAT
*
29898934 TTTTATTTTTATTTAATTATTA
1 TTTTA-TTTTATTTTATTATTA
29898956 TTTTA-TTTA--TTATT-TTA
1 TTTTATTTTATTTTATTATTA
* *
29898973 TTTT-CTTTACTTTATTTATTA
1 TTTTATTTTATTTTA-TTATTA
29898994 TTTTATTTTATTTTATTAGTTA
1 TTTTATTTTATTTTATTA-TTA
29899016 TT
1 TT
29899018 AGTTATTTGG
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
17 11 0.21
18 4 0.08
19 3 0.06
20 6 0.12
21 10 0.19
22 18 0.35
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.74
Consensus pattern (21 bp):
TTTTATTTTATTTTATTATTA
Found at i:29900100 original size:20 final size:20
Alignment explanation
Indices: 29900062--29900100 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29900052 TATAAATAAA
* *
29900062 AAATAAATATAAATCAAAAT
1 AAATAAATAAAAAACAAAAT
*
29900082 AAATAAATAAAAAAGAAAA
1 AAATAAATAAAAAACAAAA
29900101 AATATAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (20 bp):
AAATAAATAAAAAACAAAAT
Found at i:29900678 original size:15 final size:15
Alignment explanation
Indices: 29900653--29900687 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
29900643 GACTCTATTT
*
29900653 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
29900667 TAATTAATATTAAGA
1 TAATTAATATTAAGA
29900682 TAATTA
1 TAATTA
29900688 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:29903579 original size:94 final size:96
Alignment explanation
Indices: 29903454--29903755 Score: 326
Period size: 95 Copynumber: 3.2 Consensus size: 96
29903444 TAAATAATGG
* ** * * * *
29903454 ATTAAGGTTTAGGGTTTGTTAATTAAATTAATTATAAATTTTTCAAAATTGGATTA-GGTTTCGT
1 ATTAGGGTTTAGGGTTACTTGATTAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGT
** * *
29903518 GTTTATTATTTTTTA-AGAAAAATCAATTAA
66 GTTTAAGAGTTTTTATAGAAAAATCAAATAA
* * * ** *
29903548 ATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAATTTAAAAATTAGATTAGGGTTTAGA
1 ATTAGGGTTTAGGGTTACTTGATTAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGT
* *
29903613 G-TTAAGGGTTTTTATGGAAAAATCAAATAA
66 GTTTAAGAGTTTTTATAGAAAAATCAAATAA
* *
29903643 ATTAGGGTTAAGGATTACTTGATTAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAG
1 ATTAGGGTTTAGGGTTACTTGATTAAATTAATTATAAATTTTT-AAAAATTAGATTAGGGTTTAG
* *
29903708 TGTTTAAG-GTTTTTA-AGTACAAACTAAAATAA
65 TGTTTAAGAGTTTTTATAG-A-AAAATCAAATAA
*
29903740 ATTAGGGTTTGGGGTT
1 ATTAGGGTTTAGGGTT
29903756 TAGGGTTACT
Statistics
Matches: 169, Mismatches: 33, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
94 54 0.32
95 57 0.34
96 30 0.18
97 28 0.17
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (96 bp):
ATTAGGGTTTAGGGTTACTTGATTAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGT
GTTTAAGAGTTTTTATAGAAAAATCAAATAA
Found at i:29904017 original size:126 final size:126
Alignment explanation
Indices: 29903788--29904078 Score: 467
Period size: 126 Copynumber: 2.3 Consensus size: 126
29903778 TTATTAATTT
* *
29903788 AAAGAAGCTCTCACGTGGACGCGCTTTTACTACAGTAGCTCCTGAAAAAATAATTTTGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTAGAC
* *
29903853 GTTTCTGAGCAAATAGTGTTAAAAACGCTTTAAGCAGGATGCTTTGTTAACA-ATAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAACAGGATGCTTTGTTAACAGA-AGTACTG
* * *
29903914 AAAGAAGCTCCCAGGTGGACGCGCTTTTGCTACAGTAGCTCTTGAACAAATAATTTTGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTAGAC
* *
29903979 GTTTCTGAGTAAATAGTGTCAAAAACGCTTTAAACAGGATGCTTTGTTAGCAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAACAGGATGCTTTGTTAACAGAAGTACTG
* *
29904040 AAAGAAGCTCCCACATGGACGCGTTTTTGCTACAGTAGC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGC
29904079 GCATGTTTGG
Statistics
Matches: 152, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
126 151 0.99
127 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTAGAC
GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAACAGGATGCTTTGTTAACAGAAGTACTG
Found at i:29906707 original size:21 final size:21
Alignment explanation
Indices: 29906683--29906723 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29906673 CCAGCTTTCG
* *
29906683 GCGGGGGTTGTGGTTACTCCA
1 GCGGGGATTCTGGTTACTCCA
*
29906704 GCGGGGATTCTGGTTCCTCC
1 GCGGGGATTCTGGTTACTCC
29906724 GGTAGGGGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.24, G:0.39, T:0.29
Consensus pattern (21 bp):
GCGGGGATTCTGGTTACTCCA
Found at i:29908868 original size:11 final size:11
Alignment explanation
Indices: 29908854--29908910 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
29908844 TTTTTTAAAT
29908854 AGGAATTTGAG
1 AGGAATTTGAG
29908865 AGGAATTTGAG
1 AGGAATTTGAG
*
29908876 GGGAATTTGAG
1 AGGAATTTGAG
29908887 A-GAATATT-AG
1 AGGAAT-TTGAG
*
29908897 AGAGAAATTGAG
1 AG-GAATTTGAG
29908909 AG
1 AG
29908911 AAATGATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 7 0.18
11 25 0.64
12 7 0.18
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.25
Consensus pattern (11 bp):
AGGAATTTGAG
Found at i:29917518 original size:32 final size:31
Alignment explanation
Indices: 29917482--29917580 Score: 95
Period size: 31 Copynumber: 3.3 Consensus size: 31
29917472 AAGAGATTAC
29917482 GTACCAAATTAGGAAAAAAGAATCAAGTTTAA
1 GTACCAAATTA-GAAAAAAGAATCAAGTTTAA
* *
29917514 GTACCAAATTAGACAAAA-AA--AA-TCTAA
1 GTACCAAATTAGAAAAAAGAATCAAGTTTAA
29917541 GTACCAAATTAAGAAAAAATG--TCAAGTTT-A
1 GTACCAAATT-AGAAAAAA-GAATCAAGTTTAA
29917571 GATACCAAAT
1 G-TACCAAAT
29917581 ATTACATTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
27 14 0.25
28 9 0.16
30 6 0.11
31 16 0.29
32 11 0.20
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22
Consensus pattern (31 bp):
GTACCAAATTAGAAAAAAGAATCAAGTTTAA
Found at i:29918032 original size:13 final size:11
Alignment explanation
Indices: 29918005--29918035 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
29917995 CCATCTTCAA
29918005 TCTCTCAAATT
1 TCTCTCAAATT
29918016 TCTCTCAAATT
1 TCTCTCAAATT
29918027 TCTCTCAAA
1 TCTCTCAAA
29918036 GCTCTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:29919207 original size:7 final size:7
Alignment explanation
Indices: 29919195--29919227 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
29919185 TAGTCGATTC
29919195 GTATTTA
1 GTATTTA
29919202 GTATTTA
1 GTATTTA
*
29919209 TTATTTA
1 GTATTTA
29919216 GTATTTA
1 GTATTTA
29919223 GTATT
1 GTATT
29919228 ATGTATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (7 bp):
GTATTTA
Found at i:29919838 original size:18 final size:18
Alignment explanation
Indices: 29919815--29919857 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29919805 TGCCAGGTGC
* *
29919815 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
29919833 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
29919851 GTTTCCT
1 GTATCCT
29919858 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:29920278 original size:21 final size:22
Alignment explanation
Indices: 29920243--29920283 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29920233 CATTGATTTT
29920243 TATTTTAATATATTTGTATAAA
1 TATTTTAATATATTTGTATAAA
29920265 TATTTTGAATAT-TTT-TATA
1 TATTTT-AATATATTTGTATA
29920284 TTATTTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (22 bp):
TATTTTAATATATTTGTATAAA
Found at i:29923649 original size:126 final size:126
Alignment explanation
Indices: 29923424--29923691 Score: 484
Period size: 126 Copynumber: 2.1 Consensus size: 126
29923414 GCCAAATAGG
* *
29923424 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCATCT
1 AACTACTGTAGCAAAACAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCATCC
29923489 TGCTTGAAGCATTTTTGACACTATTTGCTCAGAAAC-TTCTTCTCAAAATTATTTTTTCAGA
66 TGCTTGAAGCATTTTTGACACTATTTGCTCAGAAACATT-TTCTCAAAATTATTTTTTCAGA
29923550 AACTACTGTAGCAAAACAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCATCC
1 AACTACTGTAGCAAAACAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCATCC
*
29923615 TGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATTTTCTCAAAATTATTTTTTCAGA
66 TGCTTGAAGCATTTTTGACACTATTTGCTCAGAAACATTTTCTCAAAATTATTTTTTCAGA
*
29923676 AACTGCTGTAGCAAAA
1 AACTACTGTAGCAAAA
29923692 GAGAATTTTA
Statistics
Matches: 137, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
126 135 0.99
127 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (126 bp):
AACTACTGTAGCAAAACAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCATCC
TGCTTGAAGCATTTTTGACACTATTTGCTCAGAAACATTTTCTCAAAATTATTTTTTCAGA
Found at i:29924737 original size:13 final size:13
Alignment explanation
Indices: 29924719--29924743 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29924709 TAAATAGAAG
29924719 TTGATTATGTAAA
1 TTGATTATGTAAA
29924732 TTGATTATGTAA
1 TTGATTATGTAA
29924744 TCTTGTAAAT
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:29925303 original size:14 final size:14
Alignment explanation
Indices: 29925286--29925317 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
29925276 ATGTAAAAAG
29925286 TTTTACGAAAAATA
1 TTTTACGAAAAATA
29925300 TTTTACGAAAAATA
1 TTTTACGAAAAATA
29925314 TTTT
1 TTTT
29925318 CTGCATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (14 bp):
TTTTACGAAAAATA
Found at i:29925711 original size:16 final size:16
Alignment explanation
Indices: 29925689--29925727 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
29925679 AATTTTATTT
29925689 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
29925706 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
29925721 TAATAAT
1 TAATAAT
29925728 CTGAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:29925727 original size:13 final size:13
Alignment explanation
Indices: 29925685--29925727 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
29925675 TTTCAATTTT
29925685 ATTTT-AATAATAA
1 ATTTTAAATAAT-A
29925698 ATTTTAAAAATAATA
1 ATTTT--AAATAATA
29925713 ATTTTAAATAATA
1 ATTTTAAATAATA
29925726 AT
1 AT
29925728 CTGAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 15 0.56
15 6 0.22
16 6 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTTAAATAATA
Found at i:29925766 original size:15 final size:15
Alignment explanation
Indices: 29925746--29925802 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
29925736 ATTCATTATT
29925746 AATATTTTAATAATA
1 AATATTTTAATAATA
*
29925761 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
29925780 AATATATTAATAATA
1 AATATTTTAATAATA
29925795 AATATTTT
1 AATATTTT
29925803 GTAATATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:29927033 original size:38 final size:38
Alignment explanation
Indices: 29926982--29927059 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
29926972 ATTTACCAAT
* *
29926982 ATTTTGAGTAAAAGAGACAAAATACACTCTAACTTTTA
1 ATTTTGAGTAAAAGAAACAAAATACAATCTAACTTTTA
*
29927020 ATTTTGAGTAAAAGAAACAAAATACAATCTGACTTTTA
1 ATTTTGAGTAAAAGAAACAAAATACAATCTAACTTTTA
29927058 AT
1 AT
29927060 ACACCTTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (38 bp):
ATTTTGAGTAAAAGAAACAAAATACAATCTAACTTTTA
Found at i:29927127 original size:15 final size:16
Alignment explanation
Indices: 29927102--29927134 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
29927092 ATATTTTAAA
29927102 AATATTCCACAAGGGG
1 AATATTCCACAAGGGG
29927118 AATA-TCCACAAGGGG
1 AATATTCCACAAGGGG
29927133 AA
1 AA
29927135 GTACCAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.15
Consensus pattern (16 bp):
AATATTCCACAAGGGG
Found at i:29936800 original size:32 final size:30
Alignment explanation
Indices: 29936764--29936822 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
29936754 TTTTCAATTT
*
29936764 TAAAAAGTAAAAAACAATTTTTTAAAAAAAAG
1 TAAAAA-TAAAAAA-AATATTTTAAAAAAAAG
*
29936796 TAAAAATAAAAAAAATATTTTGAAAAA
1 TAAAAATAAAAAAAATATTTTAAAAAA
29936823 CTAAACGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 12 0.48
31 7 0.28
32 6 0.24
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (30 bp):
TAAAAATAAAAAAAATATTTTAAAAAAAAG
Found at i:29939038 original size:29 final size:29
Alignment explanation
Indices: 29939005--29939067 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
29938995 AATCTCTATT
29939005 TTTAAAT-TTTAAAAATATGTTAAT-TTTTA
1 TTTAAATATTTAAAAAT-T-TTAATATTTTA
*
29939034 TTT-AATATTTAAAAATTTTATTATTTTA
1 TTTAAATATTTAAAAATTTTAATATTTTA
29939062 TTTAAA
1 TTTAAA
29939068 GATTATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
27 4 0.13
28 12 0.40
29 14 0.47
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (29 bp):
TTTAAATATTTAAAAATTTTAATATTTTA
Found at i:29939061 original size:28 final size:29
Alignment explanation
Indices: 29939012--29939066 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
29939002 ATTTTTAAAT
29939012 TTTAAAAATATGTTAATTTTTATTTAATA
1 TTTAAAAATATGTTAATTTTTATTTAATA
*
29939041 TTTAAAAAT-T-TTATTATTTTATTTAA
1 TTTAAAAATATGTTAAT-TTTTATTTAA
29939067 AGATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 11 0.46
29 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (29 bp):
TTTAAAAATATGTTAATTTTTATTTAATA
Found at i:29940268 original size:3 final size:3
Alignment explanation
Indices: 29940255--29940285 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
29940245 AATGACGGTA
*
29940255 AAG ATG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
29940286 GGGAGATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:29942031 original size:23 final size:22
Alignment explanation
Indices: 29941999--29942058 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
29941989 TCTTCTTTCT
*
29941999 TTTTTTTTTTTTGGTTTTT-TC
1 TTTTTTTTTTTTGGTTTTTGTA
*
29942020 TCTCTTTTTTTTTTTGTTTTTGTA
1 T-T-TTTTTTTTTTGGTTTTTGTA
29942044 TTTTTTTTTTTTGGT
1 TTTTTTTTTTTTGGT
29942059 AATTAGTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 1 0.03
22 13 0.39
23 17 0.52
24 2 0.06
ACGTcount: A:0.02, C:0.05, G:0.10, T:0.83
Consensus pattern (22 bp):
TTTTTTTTTTTTGGTTTTTGTA
Found at i:29942047 original size:29 final size:31
Alignment explanation
Indices: 29941985--29942047 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
29941975 CGCACTGAGG
*
29941985 TTTCTCTTCTTTCTTTTTTTTTTTTTGGTTT
1 TTTCTCTTCTTTCTTTTTTTTTTTTTGGTAT
29942016 TTTCTC-TCTTT-TTTTTTTTGTTTTT-GTAT
1 TTTCTCTTCTTTCTTTTTTTT-TTTTTGGTAT
29942045 TTT
1 TTT
29942048 TTTTTTTTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 14 0.47
30 10 0.33
31 6 0.20
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.81
Consensus pattern (31 bp):
TTTCTCTTCTTTCTTTTTTTTTTTTTGGTAT
Found at i:29942048 original size:31 final size:31
Alignment explanation
Indices: 29941985--29942049 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
29941975 CGCACTGAGG
*
29941985 TTTCTCTTCTTTCTTTTTTTTTTTTTGGTTT
1 TTTCTCTTCTTTCTTTTTTTTTTTTTGATTT
29942016 TTTCTC-TCTTT-TTTTTTTTGTTTTTGTATTT
1 TTTCTCTTCTTTCTTTTTTTT-TTTTTG-ATTT
29942047 TTT
1 TTT
29942050 TTTTTTGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 8 0.26
30 11 0.35
31 12 0.39
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.82
Consensus pattern (31 bp):
TTTCTCTTCTTTCTTTTTTTTTTTTTGATTT
Found at i:29945542 original size:19 final size:19
Alignment explanation
Indices: 29945518--29945560 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
29945508 AGTGTATTAT
* *
29945518 ATTATTTAGTATTTTTGTA
1 ATTATTTAGCACTTTTGTA
29945537 ATTATTTAGCACTTTTGTA
1 ATTATTTAGCACTTTTGTA
29945556 ATTAT
1 ATTAT
29945561 ATTATTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (19 bp):
ATTATTTAGCACTTTTGTA
Found at i:29945681 original size:29 final size:28
Alignment explanation
Indices: 29945627--29945687 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
29945617 TGAATTGAAC
*
29945627 TGATTTGGTACAATTCGATACATGAACTT
1 TGATTTGGTACAATTC-ATACATGAAATT
*
29945656 TGATTTGGTGCAATT-ATACATGTGAAATT
1 TGATTTGGTACAATTCATACA--TGAAATT
29945685 TGA
1 TGA
29945688 ATTGTGATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.18
29 23 0.82
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (28 bp):
TGATTTGGTACAATTCATACATGAAATT
Found at i:29949065 original size:34 final size:34
Alignment explanation
Indices: 29949022--29949099 Score: 120
Period size: 34 Copynumber: 2.3 Consensus size: 34
29949012 CTCAAACAAA
* *
29949022 AACCCTAAACCCTACTTTAAATAAACAAAACCCT
1 AACCTTAAACCCTAATTTAAATAAACAAAACCCT
29949056 AACCTTAAACCCTAATTTAAATAAACAAAACCCT
1 AACCTTAAACCCTAATTTAAATAAACAAAACCCT
*
29949090 ACCCCTTAAA
1 A-ACCTTAAA
29949100 AATGACGCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 33 0.82
35 7 0.17
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (34 bp):
AACCTTAAACCCTAATTTAAATAAACAAAACCCT
Found at i:29949963 original size:11 final size:11
Alignment explanation
Indices: 29949940--29949975 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
29949930 GGGTTTTAAC
*
29949940 TTTAAAATGTT
1 TTTAAAATTTT
*
29949951 TTTATAATTTT
1 TTTAAAATTTT
29949962 TTTAAAATTTT
1 TTTAAAATTTT
29949973 TTT
1 TTT
29949976 TAAAGAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (11 bp):
TTTAAAATTTT
Found at i:29953891 original size:6 final size:7
Alignment explanation
Indices: 29953874--29953900 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
29953864 TAAAATATTA
29953874 AAAAAGC
1 AAAAAGC
29953881 AAAAAGC
1 AAAAAGC
29953888 AAAAAGC
1 AAAAAGC
29953895 AAAAAG
1 AAAAAG
29953901 GGACCTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.11, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAGC
Found at i:29958095 original size:25 final size:25
Alignment explanation
Indices: 29958012--29958126 Score: 81
Period size: 25 Copynumber: 4.6 Consensus size: 25
29958002 CACAGCTTTT
* * *
29958012 ATGAGCATCCTGATATTTGGCTCTC
1 ATGAGCTTCCCGATAATTGGCTCTC
* * *
29958037 ACGAGCTTTCTGATTAA-TGGCTCTC
1 ATGAGCTTCCCGA-TAATTGGCTCTC
* * *
29958062 TTGAACTTCCCGATAATTGGCTCGC
1 ATGAGCTTCCCGATAATTGGCTCTC
* * *
29958087 ATGAGCTTCTCGAT-TTATGGCTCTT
1 ATGAGCTTCCCGATAAT-TGGCTCTC
*
29958112 ATGAGCTTCTCGATA
1 ATGAGCTTCCCGATA
29958127 TATAGCTTGA
Statistics
Matches: 70, Mismatches: 16, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
24 4 0.06
25 64 0.91
26 2 0.03
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (25 bp):
ATGAGCTTCCCGATAATTGGCTCTC
Found at i:29958126 original size:50 final size:49
Alignment explanation
Indices: 29958010--29958126 Score: 121
Period size: 50 Copynumber: 2.3 Consensus size: 49
29958000 ACCACAGCTT
* * *
29958010 TTATGAGCATCCTGATATTTGGCTCTCACGAGCTTTCTGATTAATGGCTC
1 TTATGAGCTTCC-GATAATTGGCTCGCACGAGCTTTCTGATTAATGGCTC
* * *
29958060 TCT-TGAACTTCCCGATAATTGGCTCGCATGAGC-TTCTCGATTTATGGCTC
1 T-TATGAGCTT-CCGATAATTGGCTCGCACGAGCTTTCT-GATTAATGGCTC
29958110 TTATGAGCTTCTCGATA
1 TTATGAGCTTC-CGATA
29958127 TATAGCTTGA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
49 6 0.11
50 46 0.84
51 3 0.05
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (49 bp):
TTATGAGCTTCCGATAATTGGCTCGCACGAGCTTTCTGATTAATGGCTC
Found at i:29958141 original size:25 final size:25
Alignment explanation
Indices: 29958087--29958145 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
29958077 ATTGGCTCGC
* * *
29958087 ATGAGCTTCTCGATTTATGGCTCTT
1 ATGAGCTTCTCGATATATAGCTCTG
29958112 ATGAGCTTCTCGATATATAGCT-TG
1 ATGAGCTTCTCGATATATAGCTCTG
29958136 ATTGAGCTTC
1 A-TGAGCTTC
29958146 CCATTATACA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 2 0.07
25 28 0.93
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (25 bp):
ATGAGCTTCTCGATATATAGCTCTG
Found at i:29958153 original size:25 final size:25
Alignment explanation
Indices: 29958112--29958196 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 25
29958102 TATGGCTCTT
*
29958112 ATGAGCTTCTCGA-TATATAGCTTGA
1 ATGAGCTTC-CCATTATATAGCTTGA
* * *
29958137 TTGAGCTTCCCATTATACA--TTTA
1 ATGAGCTTCCCATTATATAGCTTGA
* *
29958160 CATGAGCTTCCCATTATATGGCTCGA
1 -ATGAGCTTCCCATTATATAGCTTGA
*
29958186 AAGAGCTTCCC
1 ATGAGCTTCCC
29958197 GTTTACATAT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
23 3 0.07
24 18 0.39
25 23 0.50
26 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (25 bp):
ATGAGCTTCCCATTATATAGCTTGA
Found at i:29958178 original size:49 final size:48
Alignment explanation
Indices: 29958112--29958204 Score: 107
Period size: 49 Copynumber: 1.9 Consensus size: 48
29958102 TATGGCTCTT
* * **
29958112 ATGAGCTTCTCGATATATAGCTTGATTGAGCTTCCCATTATACATTTAC
1 ATGAGCTTCTCCATATATAGCTCGAAAGAGCTTCCCATT-TACATTTAC
* *
29958161 ATGAGCTTC-CCATTATATGGCTCGAAAGAGCTTCCCGTTTACAT
1 ATGAGCTTCTCCA-TATATAGCTCGAAAGAGCTTCCCATTTACAT
29958205 ATTTGTATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
48 7 0.19
49 30 0.81
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (48 bp):
ATGAGCTTCTCCATATATAGCTCGAAAGAGCTTCCCATTTACATTTAC
Found at i:29958832 original size:2 final size:2
Alignment explanation
Indices: 29958827--29958866 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29958817 ATATTTTTTG
29958827 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29958867 GGCCTTATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30000485 original size:17 final size:18
Alignment explanation
Indices: 30000463--30000497 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
30000453 TTTATGTGAG
30000463 TTTAATTTCTAT-TTTTT
1 TTTAATTTCTATATTTTT
*
30000480 TTTAATTTTTATATTTTT
1 TTTAATTTCTATATTTTT
30000498 GAGATTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTAATTTCTATATTTTT
Found at i:30001303 original size:21 final size:21
Alignment explanation
Indices: 30001271--30001378 Score: 116
Period size: 21 Copynumber: 5.3 Consensus size: 21
30001261 GTGTTTTACT
*
30001271 TTCTGTTTAGCTTTTATGAGC
1 TTCTGTTCAGCTTTTATGAGC
* * *
30001292 TTCTTTTCAGCTTTTACGAGT
1 TTCTGTTCAGCTTTTATGAGC
* *
30001313 TTCTGTTCAGCTCTTAT--GT
1 TTCTGTTCAGCTTTTATGAGC
* *
30001332 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTTTTATGAGC
30001353 TTCTGTTCAGC-TTT-TGAGC
1 TTCTGTTCAGCTTTTATGAGC
30001372 TTCTGTT
1 TTCTGTT
30001379 GGCTCATTTG
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 29 0.39
20 2 0.03
21 43 0.58
ACGTcount: A:0.12, C:0.20, G:0.18, T:0.50
Consensus pattern (21 bp):
TTCTGTTCAGCTTTTATGAGC
Found at i:30001335 original size:19 final size:19
Alignment explanation
Indices: 30001311--30001347 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
30001301 GCTTTTACGA
30001311 GTTTCTGTTCAGCTCTTAT
1 GTTTCTGTTCAGCTCTTAT
30001330 GTTTCTGTTCAGCTCTTA
1 GTTTCTGTTCAGCTCTTA
30001348 CGAGCTTCTG
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:0.11, C:0.22, G:0.16, T:0.51
Consensus pattern (19 bp):
GTTTCTGTTCAGCTCTTAT
Found at i:30001376 original size:40 final size:40
Alignment explanation
Indices: 30001271--30001378 Score: 128
Period size: 40 Copynumber: 2.6 Consensus size: 40
30001261 GTGTTTTACT
* * * *
30001271 TTCTGTTTAGCTTTTATGAGCTTCTTTTCAGCTTTTACGAGT
1 TTCTGTTCAGC-TTT-TGAGCTTCTGTTCAGCTCTTACGAGC
* *
30001313 TTCTGTTCAGCTCTT-ATGTTTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTTTTGA-GCTTCTGTTCAGCTCTTACGAGC
30001353 TTCTGTTCAGCTTTTGAGCTTCTGTT
1 TTCTGTTCAGCTTTTGAGCTTCTGTT
30001379 GGCTCATTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
39 1 0.02
40 42 0.75
41 3 0.05
42 10 0.18
ACGTcount: A:0.12, C:0.20, G:0.18, T:0.50
Consensus pattern (40 bp):
TTCTGTTCAGCTTTTGAGCTTCTGTTCAGCTCTTACGAGC
Found at i:30002988 original size:21 final size:21
Alignment explanation
Indices: 30002964--30003008 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
30002954 TAATTTTCAA
* *
30002964 AAATTCAAAAAATATTTTTTT
1 AAATCCAAAAAATATATTTTT
**
30002985 AAATCCAAAATTTATATTTTT
1 AAATCCAAAAAATATATTTTT
30003006 AAA
1 AAA
30003009 AAATTTATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATCCAAAAAATATATTTTT
Found at i:30003011 original size:17 final size:17
Alignment explanation
Indices: 30002991--30003036 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
30002981 TTTTAAATCC
**
30002991 AAAATTTATATTTTTAA
1 AAAATTTATAAATTTAA
30003008 AAAATTTATAAATTTAA
1 AAAATTTATAAATTTAA
*
30003025 AAAATTTCTAAA
1 AAAATTTATAAA
30003037 GAATATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATTTATAAATTTAA
Found at i:30003029 original size:9 final size:9
Alignment explanation
Indices: 30003003--30003068 Score: 53
Period size: 9 Copynumber: 6.8 Consensus size: 9
30002993 AATTTATATT
30003003 TTTAAAAAA
1 TTTAAAAAA
*
30003012 TTT-ATAAA
1 TTTAAAAAA
30003020 TTTAAAAAA
1 TTTAAAAAA
30003029 TTTCTAAAGAATA
1 -TT-TAAA-AA-A
30003042 TATTAAAAAA
1 T-TTAAAAAA
*
30003052 TTAAAAAAA
1 TTTAAAAAA
30003061 TTCTAAAA
1 TT-TAAAA
30003069 TAAAAATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
8 7 0.15
9 16 0.35
10 8 0.17
11 6 0.13
12 7 0.15
13 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:30004089 original size:22 final size:22
Alignment explanation
Indices: 30004059--30004101 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
30004049 ACACCATAAC
*
30004059 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
*
30004081 AGGCCTTTAGCGGTGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
30004102 AGCGCCGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:30004275 original size:43 final size:43
Alignment explanation
Indices: 30004228--30004370 Score: 155
Period size: 43 Copynumber: 3.3 Consensus size: 43
30004218 ACTAAGAGCT
* *
30004228 TTAGCGGCGTTTTTAATATAACCGCCGCTATAGAT-TGGTGTCG
1 TTAGCGGCGTTTTTAATATAAGCGCCGCTATAGATCAGG-GTCG
* ** *
30004271 TTAGCAGCGTTTTTGTTGA-AAGCGCCGCTATAGATCAGGGTCT
1 TTAGCGGCGTTTTTAAT-ATAAGCGCCGCTATAGATCAGGGTCG
* * * *
30004314 TTAGCGGCGTTTTTTATATAAGCGCCGCTATAGATCATGGCCT
1 TTAGCGGCGTTTTTAATATAAGCGCCGCTATAGATCAGGGTCG
*
30004357 TTAGCGGCGCTTTT
1 TTAGCGGCGTTTTT
30004371 CCTAAAAACG
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
42 1 0.01
43 81 0.95
44 3 0.04
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (43 bp):
TTAGCGGCGTTTTTAATATAAGCGCCGCTATAGATCAGGGTCG
Found at i:30004383 original size:43 final size:43
Alignment explanation
Indices: 30004293--30004429 Score: 141
Period size: 43 Copynumber: 3.2 Consensus size: 43
30004283 TTGTTGAAAG
* * ** * *
30004293 CGCCGCTATAGATCAGGGTCTTTAGCGGCGTTTTTTATATAAG
1 CGCCGCTATAGATCATGGTCTTTAGCGGCGCTTTTCCTAAAAA
*
30004336 CGCCGCTATAGATCATGGCCTTTAGCGGCGCTTTTCCTAAAAA
1 CGCCGCTATAGATCATGGTCTTTAGCGGCGCTTTTCCTAAAAA
* * * * * *
30004379 CGCCGCAATAGACCCTGATCTATAGCGGCGCTTATCC-AGAAAA
1 CGCCGCTATAGATCATGGTCTTTAGCGGCGCTTTTCCTA-AAAA
30004422 CGCCGCTA
1 CGCCGCTA
30004430 AATACCCTTT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 1 0.01
43 77 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (43 bp):
CGCCGCTATAGATCATGGTCTTTAGCGGCGCTTTTCCTAAAAA
Found at i:30004383 original size:86 final size:86
Alignment explanation
Indices: 30004226--30004390 Score: 199
Period size: 86 Copynumber: 1.9 Consensus size: 86
30004216 AGACTAAGAG
* * ** *
30004226 CTTTAGCGGCGTTTTTAATATAACCGCCGCTATAGATTGGTGTCGTTAGCAGCGTTTTTGTTGAA
1 CTTTAGCGGCGTTTTTAATATAACCGCCGCTATAGATTGGTGCCGTTAGCAGCGCTTTTCCTAAA
* *
30004291 AGCGCCGCTATAGATCAGGGT
66 AACGCCGCAATAGATCAGGGT
* * * *
30004312 CTTTAGCGGCGTTTTTTATATAAGCGCCGCTATAGATCAT-G-GCCTTTAGCGGCGCTTTTCCTA
1 CTTTAGCGGCGTTTTTAATATAACCGCCGCTATAGAT--TGGTGCCGTTAGCAGCGCTTTTCCTA
30004375 AAAACGCCGCAATAGA
64 AAAACGCCGCAATAGA
30004391 CCCTGATCTA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
86 64 0.97
87 1 0.02
88 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.32
Consensus pattern (86 bp):
CTTTAGCGGCGTTTTTAATATAACCGCCGCTATAGATTGGTGCCGTTAGCAGCGCTTTTCCTAAA
AACGCCGCAATAGATCAGGGT
Found at i:30004437 original size:43 final size:42
Alignment explanation
Indices: 30004358--30004521 Score: 170
Period size: 43 Copynumber: 3.7 Consensus size: 42
30004348 TCATGGCCTT
*
30004358 TAGCGGCGCTTTTCCTAAAAACGCCGC-AATAGACCCTGATCTA
1 TAGCGGCGCTTTTCC-AAAAACGCCGCTAA-ATACCCTGATCTA
*
30004401 TAGCGGCGCTTATCCAGAAAACGCCGCTAAATACCCTTTG-TCTATA
1 TAGCGGCGCTTTTCCA-AAAACGCCGCTAAATACCC--TGATC--TA
* * * * *
30004447 TAGCGGCGCTTCGTACAAAAACACCGCTAAAAACCCTAATCTA
1 TAGCGGCGCTT-TTCCAAAAACGCCGCTAAATACCCTGATCTA
30004490 TAGCGGCGCTTTTACCAAAAACGCCGCTAAAT
1 TAGCGGCGCTTTT-CCAAAAACGCCGCTAAAT
30004522 TTGACAGATT
Statistics
Matches: 101, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 57 0.56
44 5 0.05
45 4 0.04
46 30 0.30
47 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (42 bp):
TAGCGGCGCTTTTCCAAAAACGCCGCTAAATACCCTGATCTA
Found at i:30004851 original size:21 final size:21
Alignment explanation
Indices: 30004825--30004917 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
30004815 TTTGACGCTG
30004825 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* **
30004846 CTCTGCTTCCCTCACTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
30004867 CTCTGCTTCCCTTGCTGTAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * * *
30004888 CTGTTCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
30004909 CTATGCTTC
1 CTCTGCTTC
30004918 TCTTGTTGCC
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.05, C:0.41, G:0.16, T:0.38
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:30004918 original size:21 final size:21
Alignment explanation
Indices: 30004865--30004929 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
30004855 CCTCACTTTA
* * **
30004865 GCCTCTGCTTCCCTTGCTGTA
1 GCCTATGCTTCTCTTGCTGCC
* *
30004886 GCCTGTTCTTCTCTTGCTGCC
1 GCCTATGCTTCTCTTGCTGCC
*
30004907 GCCTATGCTTCTCTTGTTGCC
1 GCCTATGCTTCTCTTGCTGCC
30004928 GC
1 GC
30004930 ATCTGCTCTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.03, C:0.37, G:0.20, T:0.40
Consensus pattern (21 bp):
GCCTATGCTTCTCTTGCTGCC
Found at i:30004936 original size:21 final size:21
Alignment explanation
Indices: 30004893--30004936 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
30004883 GTAGCCTGTT
*
30004893 CTTCTCTTGCTGCCGCCTATG
1 CTTCTCTTGCTGCCGCATATG
* *
30004914 CTTCTCTTGTTGCCGCATCTG
1 CTTCTCTTGCTGCCGCATATG
30004935 CT
1 CT
30004937 CTAAGCTGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.36, G:0.18, T:0.41
Consensus pattern (21 bp):
CTTCTCTTGCTGCCGCATATG
Found at i:30004998 original size:66 final size:66
Alignment explanation
Indices: 30004913--30005054 Score: 189
Period size: 66 Copynumber: 2.2 Consensus size: 66
30004903 TGCCGCCTAT
* * *
30004913 GCTTCTCTTGTTGCCGCATCTGCTCTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTTGAACC
1 GCTTCTCTCGCTGCCGCATCTGCTCTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTTGAACA
30004976 TCA
64 TCA
* * * *
30004979 GCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACATC
1 GCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGAACATC
30005044 A
66 A
30005045 GCTTCTCTCG
1 GCTTCTCTCG
30005055 ATGTTGCCTC
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
65 1 0.01
66 62 0.93
67 4 0.06
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.40
Consensus pattern (66 bp):
GCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGAACATC
A
Found at i:30005070 original size:66 final size:66
Alignment explanation
Indices: 30004947--30005077 Score: 192
Period size: 66 Copynumber: 2.0 Consensus size: 66
30004937 CTAAGCTGCT
* * *
30004947 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGT
1 GCTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
30005012 A
66 A
* * *
30005013 GCTGGAGTTCTTCATATCTTT-TTTGAACATCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTG
1 GCTGGAGTTCTTCATA-CTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTG
30005077 T
65 T
30005078 GTAATTTGCT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 54 0.93
67 4 0.07
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.41
Consensus pattern (66 bp):
GCTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
A
Found at i:30008364 original size:18 final size:18
Alignment explanation
Indices: 30008341--30008376 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
30008331 ATAGTTACGC
30008341 TATGTAAGTTATGTATTA
1 TATGTAAGTTATGTATTA
*
30008359 TATGTAAGTTATTTATTA
1 TATGTAAGTTATGTATTA
30008377 CCCAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (18 bp):
TATGTAAGTTATGTATTA
Found at i:30008542 original size:16 final size:16
Alignment explanation
Indices: 30008521--30008569 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
30008511 ATTAAAAAAA
30008521 TGTAAGTTATGT-AGAT
1 TGTAAGTTATGTAAG-T
30008537 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
30008553 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
30008569 T
1 T
30008570 ATGTATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 30 0.94
17 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Done.